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Repo info
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    Eviatar
    @Eviatar
    Trying this using GitHub desktop for Mac. For some reason I can't see my branch nor my commits on the GitHub website. I'm trying to Publish but received an error that one of the files is too big (I had a test.avi at ~250MB). I removed the file, committed the revision but still receive the error when trying to Publish. What should I do? Thanks.
    Also, apparently I forked SegWorm. How do I unfork so I can just use branches of the main?
    Eviatar
    @Eviatar
    Pull request created.
    Chee Wai Lee
    @cheelee
    @Eviatar I've merged the pull request, thanks!
    Michael Currie
    @MichaelCurrie
    @eviatar if you want to save test.avi somewhere, please feel free to add it to our Google Drive example folder: https://drive.google.com/drive/u/0/folders/0B7to9gBdZEyGNWtWUElWVzVxc0E
    @Eviatar on your question about unforking, I would just delete your account's copy of SegWorm as it is now behind openworm:master
    You can go to settings and in the "danger zone" delete the repo.
    Thanks again for the updates! Feel free to use github to push more updates to segworm if it's being actively worked on. Next step is probably to identify areas where the Open Worm Analysis Toolbox needs to be brought into sync with your ~3 years of changes...
    Michael Currie
    @MichaelCurrie
    I've put an issue up on the OWAT repository for this: openworm/open-worm-analysis-toolbox#189
    @Eviatar I'd appreciate any help you can offer here in identifying what needs to be ported.
    thanks!
    ido77778
    @ido77778
    Hello, I am new to the open Worm project and I want to help around here as I will have some free time in the coming months. I know Python and C++, so I believe I have the nessasry
    Necessary* Skillset. I have been told to go he in the main Chat... So how can I be of help, do you have any beginner project/tasks?
    Michael Currie
    @MichaelCurrie
    Hi @ido77778 ! There is a project-wide effort to flag certain issues as "well-specified" so they can be handled by someone not familiar with any context about the project. For now the best candidates are openworm/tracker-commons#100 and openworm/tracker-commons#113
    For #113, I agree with your suggestion that converting from WCON to BDML will be easier than the reverse, so if you start with that it would be awesome!
    You'll probably still have questions - if you do please feel free to set up a quick meeting by google hangouts with me using http://www.meetme.so/MichaelCurrie
    Or just chat away on here if you prefer
    Cheers! Thanks for your interest!
    ido77778
    @ido77778
    @MichaelCurrie Well, I don't have any questions right now so I'll start working right away. Anyway, thanks for the help and if I'll have any question I will probably ask it in this chat.
    ido77778
    @ido77778
    @MichaelCurrie I have a question about outputing the data as an ordered dictionary... From what I understand the dic cotains subdics, each representing a worm, my question is how those subdictionarys arranged, are the Indexed by timestep (Like BDML)? Or is there some other arrangement? Any way the way to convert the data to BDML is probably by two nested loops, the outer loop loops over the worms and the inner loop loops over the data and generates the XML file.
    ido77778
    @ido77778
    The biggest issue is the fact that BDML requires a sort of graphical representaition for each object, which means we must create one for each worm, proceduraly. Cronin, Et al. create such a thing by patching together a bunch of lines, I hope Dr. Ken Ho can help us with such a thing.
    Michael Currie
    @MichaelCurrie
    Hi @ido77778! The format is discussed in detail here https://github.com/openworm/tracker-commons/blob/master/WCON_format.md and the schema is here. The part of the schema relevant to your question is the "data" part.
    However, rather than writing a tool to parse WCON files yourself, I highly recommend you use https://github.com/openworm/tracker-commons/tree/master/src/Python or one of the other languages available here: https://github.com/openworm/tracker-commons/tree/master/src.
    I wrote the Python version and I can say that you would do something like import wcon; w = wcon.WCONWorms.load_from_file('test_file.wcon')
    then, you can access the worm's data as a pandas dataframe.
    just play with the w object in your python shell to see what's possible
    Your task to complete the issue openworm/tracker-commons#113 would be to write a function that can take such a w object and output a valid BDML object.
    So by doing this, I've saved you half the effort (loading WCON).
    So you won't have to puzzle over the nested format of WCON at all.
    Hope this helps! Let me know if you need anything else.
    Michael Currie
    @MichaelCurrie

    Hey @aexbrown @ichoran @ver228 @Eviatar here is OpenWorm senior contributor Balázs Szigeti's omega turns survey: ​http://groups.inf.ed.ac.uk/worms/index.html

    Please consider participating!

    Eviatar
    @Eviatar
    Hi, I took the survey and have some strong thoughts on omega turns. So here we go:
    1. Worm literature is notoriously poor in defining behavior. We have a strong definition for pirouettes at http://www.wormbook.org/chapters/www_behavior/behavior.html#sec7_6
    But it's a weird and forced definition.
    Worse yet
    From Wormbook "Some researchers include omega turns as reversals. And, some researchers count increased backward locomotion as a reversal or response; most do not. A precise definition of the behavior to be scored is critical for analysis."
    Generally, behavior has been a fudge and we need stronger definitions.
    Stephen Larson
    @slarson
    (cc: @balazs1987)
    Eviatar
    @Eviatar
    1. Andre defined upsilon turns to differentiate less sharp turns that are not omega turns but we really should just quantify omega-like turns with a histogram to see what the distribution is. If it's clearly unimodal, we need a new definition. Otherwise, we can strike a threshold using the histo.
    Should've been labeled #2. Is Gitter autocorrecting me?
    Sorry Stephen, should I move the convo elsewhere?
    Stephen Larson
    @slarson
    I think it thinks that is markdown, Ev
    No no, this is good!
    Eviatar
    @Eviatar
    Great!
    Continung.
    Stephen Larson
    @slarson
    I just want Balazs to see it
    Eviatar
    @Eviatar
    1. The list of videos is quite interesting. Sometimes the worm touches itself & sometimes it doesn't but comes close. For me, an omega turn is a ~180 degree reorienting event that uses proprioception to determine the opposing direction. Do we need touch to do this? How about just the wave of food/media motion that can be felt as the worm approaches its tail compressing the media between its 2 extremities? And, maybe my definition isn't teh popular one?
    Arggghhh. That was #3.