Update experiment creation to use prepare_sd_card

[mbreiser]

Description:

Refactor create_experiment_folder_g41 to use the new prepare_sd_card() function instead of handling pattern renaming/copying internally.

Changes needed

• replace current pattern copying logic from create_experiment_folder_g41
• Call prepare_sd_card() with extracted pattern paths
• Store returned mapping in experiment record
• SD drive letter will need to be handled, passed in somehow (see Add rig configuration file for IP addresses and hardware-specific settings #6)

New workflow

YAML → extract patterns → prepare_sd_card() → SD card ready

Related (on the g41-controller-update branch)

• utils/prepare_sd_card.m
• docs/sd_card_deployment_notes.md (integration sketch)

[mbreiser]

@taylorlm88 -- should we close this issue now? anything else you plan to add or want to test ?

[mbreiser]

some updates from testing @taylorlm88 new code. Learned some things:

1. we need to first install the yaml add-on for Matlab, created by Martin Koch.
2. even on windows, file paths in the YAML files must use '/' and not ''

some issues:

1. I was surprised to see the original YAML file get overwritten. This was disorienting! The document I had modified and would want to keep as a record of the experiment got updated, and the format changed, a lot! there must be a better way to do this, or at least create a new version with the SD copying timestamp.

2. the edits tot he YAML file appear to make many of the fields into floats, when they should be kept (or cast) as integers.

3. it was also surprising to see that 6 pattern IDs updated, when there are only 4 patterns, but I understand what this means now.

4. I ran in to trouble with the staging directory -- but I will test this some more -- I think this is an issue with prepare_sd_card being too aggressive -- for more typical use case, should have option to automatically make a new dir with the SD cards timestamp appended to the name.

5. When running "run_protocol," nothing was displayed on the arena, and the arena threw connection errors "WSA error: WSAECONNRESET," but the experiment kept going. This event was not logged!

• right before this command, confirmed that arena reponded to allOn/allOff, after confirmed it was locked up.

6. All the run-time validation seems unnecessary. We should validate before/after files are copied to the SD card before an experiment, not during an experiment.

7. log file should have a more descriptive and unique name. Not 'experiment' - maybe 'experimentLog_TIMESTAMP'

...only a partial list, not able to test everything today

[taylorlm88]

Regarding the issues so far:

1. Yes, I have noticed this problem too. Unlike a .mat file where you can edit a single variable from it and just save that back into the file, with yaml it gets the struct which contains all the information from the yaml, edits it, and then re-saves the whole thing, and this does really mess up the formatting. The empty lines are gone and its much harder to read. It doesn't affect execution but if you want to go back later and look at the experiment again, it's harder to read. I'm looking for a solution. I have downloaded a different yaml library that says it's designed for both reading and writing yamls, which the current add-on does not actually say it is for writing yaml files. I am going to see if this new library can write them with better formatting. If it's not better, I'll look into writing a function that can perhaps reformat the yaml file as if it were a text file after the new data is saved? Not sure, but looking for a solution.

2. I will fix this.

3. I'm not sure what you're referring to but if you understand it and it makes sense, great! Do you mean that if a pattern is re-used in the yaml file, the ID is updated in more places than there are patterns?

4. I'm not sure what you mean on this one - do you mean automatically make a new directory to be the staging directory? I thought the staging directory would want to be cleaned up and removed after everything's been moved to the sd card anyway. Or are you talking about the output directory?

5. I asked Peter what this error meant when I got it during testing and he said he has a Watchdog timer on the firmware that resets the connection if it locks up for any reason for more than a second or two, and that's matlab's way to tell you the connection was reset. When testing with Laura we got rid of this error by making sure the patterns on the sd card were formatted correctly, the right size, and we were using the right sd card (because there was an issue where some sd cards work but others don't). I definitely need to make sure the error is always logged and I will update so that it stops the experiment. Can you share what you were trying to run so I can debug and figure out why it was locking up the firmware?

6. I can move validation to file copying stage. What about validating they are the same size as the arena? When you load patterns onto an sd card, do you already know for sure which arena it will be used on? Is there any case in which an sd card might contain patterns for multiple differently sized arenas so multiple people can use it? Or does one sd card always stick with one arena?

7. Can do.

[mbreiser]

Did some troubleshooting + updating with Claude, and now things seem to be working (further testing required with more interpretable patterns and trials, but that will come later). PR just put through PR #10

related to issues of files and names, with the fix in the PR, output files now go to indicated directory, but the summary.txt name is too generic

[taylorlm88]

Issues 1 and 2 you listed (saving separate yamls and ensuring integers are preserved as integers) are now fixed in commit 155810c

[mbreiser]

great. I'll do some more testing this week and hopefully we can close the issue soon

[taylorlm88]

I've implemented fixes for 5, 6, and 7 that you listed above on the branch errorHandling on the maDisplayTools repo.

I added error handling to catch controller errors, so errors from the arena should be logged and cause the experiment to abort appropriately now. This is not tested because I haven't gotten on an arena with it yet.

I took out a lot of the runtime validation and moved the yaml and pattern validation step to the sd deployment process. Now, before patterns are actually sent to the sd card, a function runs to validate that all the yamls provided are sound and that all the patterns in the yamls match the arena dimensions given in the yamls. Can easily add other validations to this function (like checking pattern headers or anything) later if we decide to. This has been tested and works on my machine.

I updated the log/summary files to have more descriptive, timestamped names.

This needs real world testing, particularly the experiment execution. Once we know it's working, I think we can close this issue.

[mbreiser]

thank you @taylorlm88 ! I will do some testing tomorrow (Wednesday). If all goes well, it could be fast, but if I encounter problems, we'll see how far I can get. On my other branch, I've implemented a new, cleaner way to handle arena configs. It's not complicated, so you don't need to worry about it now, but I wanted to let you know that these updates should be pushed sometime next week, once everything has been further tested and integrated.

[taylorlm88]

Sounds good, if we have a new config file with arena info, it can be used in the validation step I just created to make sure the experiments/patterns being deployed are on the correct arena. Right now it knows what arena size the yaml files think they are for and it knows the pattern size but doesn't know the actual arena size.