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Add multi-animal pose functionality #3

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talmo
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@talmo talmo commented Dec 15, 2021

Adds PoseGroupingSeries, AnimalIdentitySeries to enable storage of metadata for multi-animal pose tracking, such as part grouping and tracking scores.

@bendichter
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bendichter commented Dec 16, 2021

@talmo We were scoping this for 1-subject for now, but I suppose it doesn't hurt to think about how to extend this to multi-subject. I think we already go some way to handling this use-case.

In the example code, we show the PoseEstimation object holding only a single PoseEstimationSeries, but it is designed to store 1+ such objects, and can be used to group together joint trackings associated with a specific animal. Then we could put multiple PoseEstimation objects in the behavior module to handle multiple animals. So I don't think we need the PoseGroupingSeries but I may be missing something. I had originally thought of this as a hard assignment where we could have multiple Subject objects and hard assign a PoseEstimation to a subject, but it looks here like this should be a soft assignment over time that handles uncertainty in the assignment. Is that right?

@rly rly mentioned this pull request Dec 16, 2021
@AlexEMG
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AlexEMG commented Dec 21, 2021

I thought we had discussed that for NWB each animal has its own file (e.g. to store neural data) and thus also only one PoseEstimationSeries. So, our plan was to export a DLC output into multiple PoseEstimationSeries.

@calebweinreb calebweinreb mentioned this pull request Jul 28, 2023
rly added a commit that referenced this pull request Mar 14, 2024
* Add tests for using Image in TrainingFrame.source_image

* Add SkeletonInstances in TrainingFrame (#3)

* Add `SkeletonInstances` class for multiple instances

* Merge changes from main

* Start changing tests

* Add `SkeletonInstances` to `TrainingFrame`

* Add name to distinguish instances

* Add `SkeletonInstances` to tests

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Co-authored-by: eberrigan <berri104@gmail.com>

* Update authors

* Update requirements to get latest bug fixes

* Store Skeletons in behavior processing module, update docs&tests

* MInor fixes to spec and mock functions

---------

Co-authored-by: eberrigan <berri104@gmail.com>
Co-authored-by: rly <rly@lbl.gov>
@talmo talmo closed this Jul 19, 2024
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3 participants