Use oks score for reprojections #1836

roomrys · 2024-06-27T23:22:22Z

Description

This PR does 3 main things (described in more detail further down):

Use same OKS score for all PredictedInstance.scores
Add InstanceGroup.score attribute
Display InstanceGroup.score in table

Additionally, to use the sleap.nn.evals.compute_oks function inside a sleap.io file, we needed to move the compute_oks function to sleap.util to avoid a circular import between sleap.nn and sleap.io files.

Use same OKS score for all `PredictedInstance.score`s

Previously, all the PredictedInstances created and updated through (re)projection had a default nan score. This PR uses an average oks (calculated from ground truth Instances and their reprojections) as the score for all (re)projected PredictedInstances.

Add `InstanceGroup.score` attribute

To be most correct, even the Instances which have reprojected nodes should have a score associated with them. There is currently no Instance.score attribute, and since this score really applies to the entire InstanceGroup (not just the PredictedInstances in the InstanceGroup), this PR also adds an InstanceGroup.score attribute that is updated each time we call InstanceGroup.update_points.

Display `InstanceGroup.score` in table

This InstanceGroup.score is likely the most useful information for users to see, so this PR also adds a score column to the table displaying InstanceGroup information.

Types of changes

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

Review the guidelines for contributing to this repository
Read and sign the CLA and add yourself to the authors list
Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
Add tests that prove your fix is effective or that your feature works
Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

❤️

coderabbitai · 2024-06-27T23:22:32Z

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codecov · 2024-06-27T23:44:36Z

Codecov Report

Attention: Patch coverage is 93.42105% with 5 lines in your changes missing coverage. Please review.

Project coverage is 74.16%. Comparing base (475283d) to head (c6cd295).

Files	Patch %	Lines
sleap/util.py	92.85%	3 Missing ⚠️
sleap/gui/dataviews.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@                           Coverage Diff                           @@
##           liezl/add-gui-elements-for-sessions    #1836      +/-   ##
=======================================================================
+ Coverage                                74.10%   74.16%   +0.05%     
=======================================================================
  Files                                      135      135              
  Lines                                    25345    25368      +23     
=======================================================================
+ Hits                                     18782    18813      +31     
+ Misses                                    6563     6555       -8

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

…-score-to-reprojections

eberrigan

Looks good! Just made some comments about a print statement and cleaning up a comment

sleap/io/cameras.py

eberrigan · 2024-07-08T20:48:07Z

tests/io/test_cameras.py

+    # The score of instances will NOT be updated on initialization.
+    for instance in instance_group_from_dict.instances:
+        if isinstance(instance, PredictedInstance):
+            assert instance.score != instance_group_from_dict.score

    # Test `__repr__`
    print(instance_group)


did you mean to leave this?

Yes, the __repr__ method is used when calling print

…-score-to-reprojections

roomrys added 5 commits June 27, 2024 15:29

Move compute_oks function to utils (avoid circular import)

de49fac

Update InstanceGroup score when update_points

14579b5

Add score to InstanceGroup repr

c86fcde

Add score to InstanceGroup table

f865365

(De)Serialize new score attribute

b3bb92b

roomrys added the MultiView Stack This PR is part of the MultView stacked PRs. label Jun 27, 2024

roomrys added 3 commits July 2, 2024 10:37

Add more docs on score attribute

006e8f9

Test score attribute

5d3e046

Merge branch 'liezl/add-gui-elements-for-sessions' into liezl/add-oks…

9dcc671

…-score-to-reprojections

roomrys marked this pull request as ready for review July 2, 2024 17:38

roomrys requested a review from eberrigan July 8, 2024 18:26

eberrigan approved these changes Jul 8, 2024

View reviewed changes

eberrigan and others added 2 commits July 8, 2024 13:50

Merge branch 'liezl/add-gui-elements-for-sessions' into liezl/add-oks…

c6cd295

…-score-to-reprojections

Merge branch 'liezl/add-gui-elements-for-sessions' into liezl/add-oks…

edb4b15

…-score-to-reprojections

roomrys merged commit 16e775d into liezl/add-gui-elements-for-sessions Jul 9, 2024
4 of 5 checks passed

roomrys deleted the liezl/add-oks-score-to-reprojections branch July 9, 2024 17:15

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Use oks score for reprojections #1836

Use oks score for reprojections #1836

roomrys commented Jun 27, 2024 •

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roomrys Jul 8, 2024

Use oks score for reprojections #1836

Use oks score for reprojections #1836

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roomrys commented Jun 27, 2024 • edited Loading

Description

Use same OKS score for all PredictedInstance.scores

Add InstanceGroup.score attribute

Display InstanceGroup.score in table

Types of changes

Does this address any currently open issues?

Outside contributors checklist

Thank you for contributing to SLEAP!

coderabbitai bot commented Jun 27, 2024 • edited Loading

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CodeRabbit Commands (invoked as PR comments)

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roomrys commented Jun 27, 2024 •

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Use same OKS score for all `PredictedInstance.score`s

Add `InstanceGroup.score` attribute

Display `InstanceGroup.score` in table

coderabbitai bot commented Jun 27, 2024 •

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CodeRabbit Configration File (`.coderabbit.yaml`)

codecov bot commented Jun 27, 2024 •

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