Hello!

Very sad to be entering into our last couple of weeks at MBARI, however, it is rewarding seeing the project come together. This week and the next will be spent cobbling together my final paper and presentation to be ready for August 8th, as I suspect most of us will be doing. More importantly, I am excited to see the new condos we will be moving into tomorrow morning, though it comes at the cost of moving out of our beloved Strawberry apartments and further away from the CSUMB beach...

Hope everything is going smoothly for everyone!

I've spent the past week reading papers and building up a literature list, cleaning up my data set a bit more, and looking at preliminary numbers and graphs with the goal of deciding how to represent the data. Over the next few days I plan to continue with data analysis and begin preparing my final paper and presentation; after I help the Barry lab sacrifice some poorly-fated abalone that is...

See you all at NASA!

Hi everyone!

I have been working through the feedback given to me by my mentors on my paper and should be finishing up soon. Yesterday I got to go out on the Paragon and launch a long range AUV which was awesome to see. Other than working on my paper I have been mentally preparing myself to pack everything up from the apartments and move tomorrow. Hope everyone has a great weekend!

Hi everyone!

This week has been very successful concerning my project. The scripts run great, and we finally settled on a BIC calculation that seems reliable (which we will most likely confirm later today). So now my focus is to compare the manually corrected data with our new autonomously corrected data, so we can assess how reliable and how much better our new method is. There is still so much that can be done to improve it, but it seems like we are finishing up the fundamentals for now. From there, we can always add or change things.

Once the comparison is done, I will start writing the paper and preparing my presentation, since we have less than two weeks left ( ). I definitely enjoy working here, and can't wait to see how my project will contribute to MBARI in the long run (hopefully positively).

Additionally, I got to go out on the paragon again on Wednesday, and we deployed a new AUV for the first time (It is still in its testing phase). That was really cool to see and experience, and if it is successful, MBARI will increase its fleet number to 7 I believe, which is awesome!

I hope everyone has a great time

MONDAY: Completed the v1.0 release of the CPF MCS GUI (available on my BitBucket). Began working with IS (Ticket 26142) to setup a virtual machine (VM) which will run the MCS system and host my website. Jumped over to my side CPF Depth Controller project. Reviewed Laughlin Barker's (2014 intern) paper again. Verified that my state space model matches his s-domain transfer function.
TUESDAY: Identified fundamental design limitations associated with the system's open loop transfer function (i.e. overshoot is unavoidable, ...). Experimented with several control strategies (dual lead compensation, dual + feedforward, dual + feedforward + pre-compensation) and the MATLAB optimizer. Satisfied the max overshoot requirement and the settling time for a 1 m step command, but the control signal exceeds the saturation limit (50 rev/s) for step inputs of 20 m. Also, the time it takes for the steady state error (E_ss) to reach zero is greater than 5 mins. This is (in my opinion) undesirable. These controllers also cannot protect against input disturbances (read: issues that cause the pump motor to perform sub-optimally like bio-fouling ).
WEDNESDAY: Took a step back to re-evaluate my control strategy. Spent much of the day reviewing Gene's "Feedback Control of Dynamic Systems" textbook (3rd Edition). Considered adding a lag compensator along with the dual lead compensator to provide integral control. Went out on the Paragon with Brian K. and Ben to deploy the WHOI VHS AUV for the first time! Worked for a couple hours at night trying to develop a better controller. Came to the following conclusion: the long settling time is unavoidable for this system (because it contains a double integrator) unless more overshoot is allowed AND/OR a stronger pump is acquired. Will chat with Gene about this.
THURSDAY: Planning on deploying my website.

This is my last week before giving my presentation so I have been very busy trying to finish analysis on all my various project tasks and making sure every last detail is figured out in preparation for the talk. So far I'm feeling confident about having all my Total Alkalinity analysis done on four datasets relating to respectively smaller geographic ranges: NOAA WCOA, BOG, Tiburon, Elkhorn Slough. I'm also done with figuring out the applicability of regression-based algorithms on basically predicting carbonate parameter measurements from easier-to-measure data like temperature, salinity, and oxygen. So the next couple of days will be spent on synthesizing all my work into a digestible and concise 12 minutes, as well as making all my figures look pretty/not just random screen shots on my desktop

Hope everyone enjoyed the BBQ yesterday!

I have begun writing my paper as we are entering the final weeks of the internship. I have also thought of additional results and observations to add for the labeled songs as they are just so dang complex! Tom has been working on the topic model (ROST) and we have been able to make some preliminary comparisons with my labeled data set. Hopefully it'll be able to distinguish units from non-units (noise).

Yesterday I got to go out on the Paragon for the first time with Brian K. and Ben to launch an AUV which was awesome!

My composition is slowly developing into something pleasant haha. So far I have 3 unit types incorporated into my piece and hopefully I can add some more, depending on how well I can mimic them on my instrument.

This week I have been applying my Matlab program to real larvacean tail kinematics. I hope to come up with a good comparison method this week so I can finalize the coding and focus on getting the most accurate tail movement I can get from my physical models on Monday/Tuesday. After finalizing that work I will focus on the presentation and potentially measure flow of the tail.

Hi all,

This past week has been awesome. On Monday, I worked mostly on perfecting the stereo camera calibration workflow, and I think I've worked it to a T. Now, it is able to automatically glob a file structure to extract matching pairs of images, detect chessboard patterns within them, and iteratively calibrate to reduce error while maintaining a steady calibration. From there, it can calculate stereo rectification transformations from provided flags, and can perform a range of image undistortions.

On Tuesday, I took off on the Rachel Carson with Ethan, Larissa, and Tom. We went over to sponge ridge (after repairing a fluid leak in the engine room) for a survey of the seafloor. Hanging out in the engine room and seeing everyone's work was fascinating.

Wednesday morning, I was invited to go on the Paragon for an LRAUV deployment with Brian Kieft and Ben Raanan. That experience, besides being an awesome break from my work, was very fun. The rest of the day consisted of a few operations regarding the FathomNet dataset (cleaning, reorganizing).

I'm currently working on making a few more tools for using the dataset in machine learning models, and it seems that there's finally a light at the end of the tunnel of all of this data organizing!

On Monday I made some modifications to the preprocessing (gaussian filtering and normalization) and re-ran it and the ROST topic model. This improved the results, and I am now seeing topic distributions that correspond to both song units and noise. Since then I have been tuning the ROST parameters to optimize the results, and experimenting with different visualizations.

Also got to go out on the Rachel Carson on Wednesday with Ethan and Mira to watch and listen and learn while engineers from MBARI and Stanford worked together to tune the control logic for a lidar sled mounted on ROV Ventana, and launch two short range AUVs. A big thanks to David Caress and everyone else on the Rachel Carson for the opportunity.

Hi all,
Final design for the release mechanism is complete. Today I am getting the opportunity to learn how to use the mill down at the machine shop. This is going to be helpful to get exact measurements/cuts for the base plates(while also being pretty cool). On the final stages of coming up with the overall design package!

Hi,

I can't believe it's Thursday already! This week for me has been evaluating how well the phytoplankton display went at open house and working out everything I have to/can do/need to change before we go. I had a great conversation with an educator at the phytoplankton lab in Santa Cruz who was really excited with what I'm doing, so that was good to hear. I'm planning meetings with as many sci comm experts in Monterey as possible next week, which started with Susan from the video lab about social media this afternoon.

It's Thursday. Surprisingly.

I've spent the week working bugs out of my eddy covariance analysis code and finishing off the last pieces of it all. Nina and I spent Tuesday afternoon and Wednesday morning working on the bbq, so that took a lot of time as well.
I've also spent some time starting to create my talk for Wednesday.

Hi everyone!

This week has been busy but exciting.
On Tuesday I got to go on the Rachel Carson with Kevin and Ethan. Bit of a rough start because there was a gas leak, but we eventually made it to sponge ridge where I got to see the ROV ventana do its work from the control room.
The trip was awesome!
Today we sacrificed 78 of the abalone from the upwelling experiment so I'm finally going to get some results!
We only sacrificed some because the entire experiment will run until after the internship is over.
Huge thanks to Erin who helped us out with weighing again!
We had a very productive day in the lab

This week was exciting and busy, with three trips out on the Rachel Carson to do low altitude surveys with the ROV and launch two overnight AUV missions. The ROV was being used to test out new control algorithms/code to run bottom scans not only horizontally but vertically on steep underwater surfaces using the articulating LiDAR platform.  On Tuesday the ROV was able to collect a full suite of data on a section of sponge ridge that I will be able to use my algorithm on, fusing together the LiDAR and multi-beam sonar data along with the stereo cameras.

 On the coding side, there is a bit of pain. I multi-threaded the code but that (predictably) caused some problems. So I am working to figure out why, and fix the problem so that I can process the sponge ridge data first thing next week. It is promising though, the multi-threaded version is faster as expected with my test data being processed in 2 minutes instead of 8.

Hello,

This week, I started out looking for the parts for my respirometry system for my main project. I went to building G for scraps and made the prototype for the chambers. I also got to go aboard the Rachel Carlson and got to see the process for the AUV collection. I also got to go to the control room to see an automated driving of the ROV. There were a lot of rattail fish on the bottom and me and some of the interns got some pressurized styrofoam cups that we made last night!

Last Thursday I missed my confluence update because I was on the Western Flyer...
Let's talk about the Western Flyer cruise for a sec:
In a parallel universe where the wind and waves were lazily flowing around the boat, I had a great time. I gathered the majority of my data, made new friends, was up for every ROV dive, it was just PEACHY. However, in the universe in which we live, there was a lot of banging into things, nausea (Can't spell nausea without SEA), and naps from being spaced out and groggy from all the motion sickness meds. In all seriousness, I really did have a great time when I wasn't questioning whether I needed to throw up or not. I mean the things we get to do and see are just AMAZING. It's such a great feeling to be sitting in the control room and seeing with your own eyes all of these fascinating animals whose pictures are pinned all over the lab. It's even more exciting to fish them out of the sample containers at the end of the dives, just taking a minute to marvel at them. It's an experience I will never forget, and I feel so lucky and undeserving that I got to experience this world that very few people are able to see in their lifetime.
On a side note, I also got to fly the ROV, and that was a humorous experience. I felt really powerful but also under-qualified. I think that's a feeling that will follow me through life haha.