Copying raw navigation files to a temporary directory and opening the MBnavedit program

*NOTE:  items in red are for example purposes.  You must use the appropriate year, dive number, and ROV (vnta, tibr, docr, minirov) when naming and navigating in the directories.
 

Nav files are stored on atlas/RovNavEdit in folders by years.

1. Currently using XQuartz for connecting to systems for nav file editing.

2. Mount a temporary directory (ex: smb://atlas.shore.mbari.org/yourshare). Files must be copied to a temporary directory before working on them to avoid overwriting original files; you will delete these copies when you are done with a session. Also mount smb://atlas.shore.mbari.org/RovNavEdit.

3. XQuartz: type in the following commands:
       a. cd /volumes/yourshare
       b. cp /volumes/ROVNavEdit/2016/vnta/nav2016326vnta.txt . (this copies the file to the temp location for editing). For some reason, you will get an error saying that permission is denied, but note that the file IS copied and all is well. MiniROV files take the form of NAV_090517000000.mb165, but open the same as the .txt files.
c. ssh -Y menard (Sign in using your password; you may to ask for permissions (Dave Caress) the first time. Wait until you get the new prompt -bash-4.2$ (this currently takes a minute)
       d. mbnavedit -X -N

Configuring the MBnavedit program window
 
When the mbnavedit program opens, you need to configure it properly.

1. Uncheck the boxes for "time interval plot" and "heading plot"
2. Uncheck all the "show original data" check boxes
3. Click the CONTROLS button and choose "Nav Modeling" from the pull down menu
4. Click on "Gaussian Mean" or "inversion"
   1. When using Gaussian mean, use the slider titled Gaussian Mean Time Window to adjust the mean value. ~47 is a good starting point. When using Inversion, set the Speed Deviation and Acceleration fields to 5.   You can adjust how tight the blue line fits between raw data points by adjusting the mean value with the slider.  The lower the value the tighter the line and vice versa.
   2. Click "Apply"

Move the Nav Model panel somewhere on your screen where it is not completely overlapping the main MBnavedit window 
Click the "File" button in the upper left corner of the main MBnavedit window.  Choose the file you want to edit, then click O.K.  

If you get an error dialog box that says "Duplicate or reverse order time stamps", Click "Control" and select Time interpolation and click 'Apply'.

           
Editing a dive
 
Start with Sonar Depth panel at bottom.

Use "Pick" or "Select" radio button to identify depth points outside of reasonable range.  When outlying points are selected, click "Interpolate" button. 
Now zoom in to look at a smaller region of the track.

Click "Pick Zoom" button, then left click (for left boundary) and middle click (for right boundary) of area to zoom in....then right click in the middle of the area.

Right mouse button will move the graph to the right, middle button will move to the left.  Pick out outlying point and interpolate those. 
Click "Show All" button to zoom out and see the whole track again.

Now, move up to the Latitude and Longitude panels.

The Navigation Model was applied when the file opened, so the blue line shows the estimated navigation path. 

Use "Pick Zoom" to zoom in on the beginning edge case.  Select points in the pre-dive area and a few after the dive began, "Flag" and "Apply" the navigation model.  Move right along the data page, select outlying points, then "Flag", and "Apply" within each window as you go.  By applying at each window, you can see the effect of your actions; if something didn't work out as expected, you can fix it now.  The goal is to have no spikes in the Speed plot over 10 km/hour.  If you do, zoom in to these spikes on the Latitude and Longitude plots and see if you can make further corrections.

To Finish the dive, first click 'Show All' then click "Select All", click in the longitude window and then "Use Solution" 

* If two dives occurred on one day (this typically happens with Tiburon and Doc Ricketts), you will see two distinct entities in the sonar depth plot.  Work on each dive individually by selecting, and flagging points as described above. Once both dives have been smoothed, "Select All" dives and "Use Solution" .

Copying the edited file back to the atlas/RovNavEdit directory
 
After quitting MBnavedit go back to the terminal window and type in the following command:

cp (space)nav2009221vntaedited.txt (space)/mbari/RovNavEdit/2009/vnta      

** Once you've completed editing files, delete the files from the tmp folder you used

If there are severe navigation scatter problems, or long drop-outs of data on a particular dives (or set of dives), document this in the Expedition Database. Go to the cruise and "Edit Postcruise". In the data comments box, put in a note (ex: Navigation for this dive is scattered and somewhat unreliable, Drop off of navigation data between 20:25 and 20:34, etc.