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rly / ndx-pose

NWB extension to store pose estimation data
BSD 3-Clause "New" or "Revised" License
13 stars 11 forks source link

Enhance training dataset format support #24

Closed talmo closed 6 months ago

talmo commented 6 months ago

Overview

Goal: Be able to store SLEAP package files (example) in PoseTraining objects so we can embed images used for training models together with the ground truth poses.

Data model equivalences

sleap-io ndx-pose
Labels PoseTraining
LabeledFrame TrainingFrame
Skeleton Skeleton
Instance SkeletonInstance
Video ImageSeries
Labels.skeletons Skeletons
Labels.labeled_frames TrainingFrames
Labels.videos SourceVideos

TODO

MVP

Nice to have

rly commented 6 months ago

Hi @talmo and @eberrigan, thank you for all your work on this PR and for looking through the recent changes in the main branch at brainhack! I am happy to take on updating the README example and test, but I think you all would be better suited to do Integrate into sleap_io.io.nwb and Update docs/readme. Let me know if you'd like me to jump in to update the README example and test.

eberrigan commented 6 months ago

Feel free to update the readme. Thanks so much!

On Fri, Mar 8, 2024, 3:05 PM Ryan Ly @.***> wrote:

Hi @talmo https://github.com/talmo and @eberrigan https://github.com/eberrigan, thank you for all your work on this PR and for looking through the recent changes in the main branch at brainhack! I am happy to take on updating the README example and test, but I think you all would be better suited to do Integrate into sleap_io.io.nwb and Update docs/readme. Let me know if you'd like me to jump in to update the README example and test.

— Reply to this email directly, view it on GitHub https://github.com/rly/ndx-pose/pull/24#issuecomment-1986544886, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZOPO6WZEICIYKAD36M2HXTYXI723AVCNFSM6AAAAABD6CULCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGU2DIOBYGY . You are receiving this because you were mentioned.Message ID: @.***>

rly commented 6 months ago

@talmo Can you give me write access to your fork? It will be easier than me creating a fork of your fork and us having to merge each fork in one by one...

talmo commented 6 months ago

@talmo Can you give me write access to your fork? It will be easier than me creating a fork of your fork and us having to merge each fork in one by one...

Done! https://github.com/talmolab/ndx-pose/invitations

rly commented 6 months ago

Thanks! I made a few changes - I moved the Skeletons type out of the PoseTraining container type because the PoseEstimation type now requires a Skeleton object and, for people who don't have (or want to include) training data with their pose estimates, it feels weird in my opinion, to require them to make a PoseTraining container just to put Skeletons into it.

I also updated the readme and tests and made some other minor adjustments.

@talmo I would like to merge this PR soon so that it will be easier for me to refactor the repo to use the latest ndx-template. Then you could start a new PR with any necessary adjustments for integration with SLEAP and any other changes you want to make (or you can make those changes here if you have time). Would that be all right?

talmo commented 6 months ago

Yes that works for me @rly!