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Integrate retracking into sleap-track #898

Merged
merged 8 commits into from
Aug 9, 2022
Merged

Integrate retracking into sleap-track #898

merged 8 commits into from
Aug 9, 2022

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roomrys
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@roomrys roomrys commented Aug 8, 2022

Description

Allow pre-existing predictions to be tracked using sleap-track CLI without generating new predictions. This feature was added in #260 and then accidentally removed in Revert to 28a0031.


Side note: Also changed the CI yaml to only run when:

  1. push to develop/master or
  2. open/reopen/synchronize all PRs

Types of changes

  • Bugfix
  • New feature
  • Refactor / Code style update (no logical changes)
  • Build / CI changes
  • Documentation Update
  • Other (explain)

Does this address any currently open issues?

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!

❤️

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codecov bot commented Aug 8, 2022

Codecov Report

Merging #898 (b4bd5bc) into develop (44e4661) will increase coverage by 1.45%.
The diff coverage is 93.10%.

@@             Coverage Diff             @@
##           develop     #898      +/-   ##
===========================================
+ Coverage    66.85%   68.30%   +1.45%     
===========================================
  Files          129      129              
  Lines        21742    21754      +12     
===========================================
+ Hits         14535    14859     +324     
+ Misses        7207     6895     -312     
Impacted Files Coverage Δ
sleap/io/convert.py 83.67% <ø> (ø)
sleap/nn/inference.py 75.20% <93.10%> (+9.35%) ⬆️
sleap/nn/system.py 49.18% <0.00%> (+9.83%) ⬆️
sleap/nn/tracker/components.py 70.98% <0.00%> (+11.39%) ⬆️
sleap/nn/tracking.py 71.18% <0.00%> (+34.83%) ⬆️
sleap/version.py 100.00% <0.00%> (+84.61%) ⬆️

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@roomrys roomrys marked this pull request as ready for review August 8, 2022 23:27
@roomrys roomrys requested a review from talmo August 8, 2022 23:27
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@talmo talmo left a comment

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Lgtm

args = f"{slp_path} --model {min_centered_instance_model_path}".split()

# Run inference
sleap_track(args=args)
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Maybe only run for a couple of frames so tests aren't slower?

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@roomrys roomrys Aug 9, 2022

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Ah, good catch. Only predict/track on frames 1-3 now.

@roomrys roomrys merged commit 219a60f into develop Aug 9, 2022
@roomrys roomrys deleted the liezl/retracking branch August 9, 2022 16:34
@roomrys roomrys restored the liezl/retracking branch August 17, 2022 17:56
@roomrys roomrys deleted the liezl/retracking branch August 17, 2022 18:12
@roomrys roomrys mentioned this pull request Sep 11, 2022
@getzze getzze mentioned this pull request Sep 30, 2022
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2 participants