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Add LightningPoseDataInterface and LightningPoseConverter #633

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merged 33 commits into from
Dec 7, 2023

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weiglszonja
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@weiglszonja weiglszonja commented Nov 8, 2023

Add converter for LightningPose, uses ndx-pose==0.1.0 to add PoseEstimation with the PoseEstimationSeries from the predictions CSV file. The original video is added as ImageSeries to nwbfile.acquisition, while the optional labeled video is added to nwbfile.processing["behavior"] both in external mode.

Resolve #628

https://github.com/danbider/lightning-pose/blob/main/docs/directory_structures.md#model-directory-structure

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@weiglszonja weiglszonja self-assigned this Nov 8, 2023
@weiglszonja weiglszonja marked this pull request as draft November 8, 2023 14:19
@weiglszonja weiglszonja marked this pull request as ready for review December 3, 2023 15:19
@weiglszonja weiglszonja changed the title Add LightningPoseDataInterface Add LightningPoseDataInterface and LightningPoseConverter Dec 3, 2023
@CodyCBakerPhD
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@weiglszonja Do you happen to have an example file from a full conversion to examine alongside this PR?

@CodyCBakerPhD
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Looks great to me, thanks a bunch @weiglszonja

The only small detail that I'm OK with since this isn't required for a full publication ready conversion using main (unlike a similar consideration given to FicTrac recently) is the lack of H5DataIO wrappers around the pose series data, but now that #557 is merged you could technically just add that call to configure_backend in the Pinto conversion script to achieve the same effect (this will soon be integrated into the core Interface/Converter classes to be seamless and not require a manual call, ideally prior to next offical release)

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Retriggering CI docs...

auto-merge was automatically disabled December 7, 2023 20:03

Pull request was closed

@CodyCBakerPhD CodyCBakerPhD reopened this Dec 7, 2023
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codecov bot commented Dec 7, 2023

Codecov Report

Merging #633 (7058c65) into main (7796a69) will increase coverage by 0.10%.
Report is 1 commits behind head on main.
The diff coverage is 95.73%.

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@@            Coverage Diff             @@
##             main     #633      +/-   ##
==========================================
+ Coverage   91.90%   92.00%   +0.10%     
==========================================
  Files         113      115       +2     
  Lines        5792     5956     +164     
==========================================
+ Hits         5323     5480     +157     
- Misses        469      476       +7     
Flag Coverage Δ
unittests 92.00% <95.73%> (+0.10%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
src/neuroconv/converters/__init__.py 100.00% <100.00%> (ø)
src/neuroconv/datainterfaces/__init__.py 100.00% <100.00%> (ø)
...s/behavior/lightningpose/lightningposeconverter.py 96.66% <96.66%> (ø)
...havior/lightningpose/lightningposedatainterface.py 95.09% <95.09%> (ø)

@CodyCBakerPhD CodyCBakerPhD merged commit 4adb093 into main Dec 7, 2023
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@CodyCBakerPhD CodyCBakerPhD deleted the add_lightning_pose branch December 7, 2023 20:33
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[New Format]: Lightning Pose
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