Small improvements to tracking

[getzze]

Description

Several things were buggy when running tracking-only from GUI or sleap-track from CLI with only tracking:

• improve the ETA in the GUI progress bar by computing the list of frames before starting the timer.
• show a progress bar when tracking, like for inference(+tracking)
• correctly pass default options for tracking to CLI. It seems all tracking options that were not defined were given the None value, which is boolean-False, so it could give the opposite for True-by-default options (there are none so far, fortunately).
• small bug in GUI video that makes it crash when clicking.
• switch the default value of save_shifted_instances to True and give back access to setting it from the GUI (removed in #1447, I don't know why)
• allow running tracking only on defined frames. It always run on the full video now.
• [EDIT] fix a bug introduced by #1875, where the data_path variable was overwritten.

Types of changes

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

Does this address any currently open issues?

None

Outside contributors checklist

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

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

Summary by CodeRabbit

• New Features

  • Enhanced tracking capabilities with improved reporting options, allowing for more user control over output.
  • Reintroduced and refined configuration options for saving shifted instances during tracking.
  • Introduced new inference pipeline options, including movenet-lightning, movenet-thunder, and tracking-only.
  • Added a custom progress rate display for better user feedback during tasks.

• Bug Fixes

  • Improved error handling in mouse event detection to prevent negative values.
  • Adjusted calculations to ensure non-negative counts during tracking.

• Refactor

  • Integrated tracking logic directly into the Tracker class, removing standalone functions for better encapsulation.
  • Updated the data processing flow for batch predictions to enhance modularity and clarity.
  • Simplified tracking test logic by removing intermediary functions.

• Tests

  • Updated tracking tests to incorporate image scaling and parameterized testing for improved coverage.
  • Adjusted expected outcomes in tracking integration tests for accuracy.

[coderabbitai[bot]]

Walkthrough

The recent updates to the Sleap framework enhance tracking and inference capabilities. Key modifications include refined configuration options, improved error handling, and better user experience. Changes optimize performance, introduce new reporting features, and streamline object-oriented design, making the system more maintainable and extendable.

Changes

Files	Change Summary
sleap/config/pipeline_form.yaml	Removed tracking.max_tracking; added tracking.save_shifted_instances with default false; updated default for tracking.match to greedy.
sleap/gui/learning/dialog.py	Adjusted no_result_count calculation to prevent negative values, enhancing reliability.
sleap/gui/widgets/video.py	Introduced _down_pos for mouse tracking; improved logic in mouseReleaseEvent to ensure error-free click detection.
sleap/nn/inference.py	Replaced report_period with a cached property; added _process_batch, _run_batch_json, and _run_batch_rich methods; improved error handling.
sleap/nn/tracking.py	Added verbosity and report_rate attributes; introduced run_step, _run_tracker_json, and _run_tracker_rich methods; improved tracking feedback mechanisms.
sleap/util.py	Introduced RateColumn for custom progress rendering; reorganized imports for clarity.
tests/nn/test_tracker_components.py	Renamed tracker_by_name to run_tracker_by_name; included img_scale parameter for enhanced testing capabilities.
tests/nn/test_tracking_integration.py	Updated assertions in test_simple_tracker; refactored tests to utilize instance methods for tracking.

Possibly related PRs

• #1986: The changes in the main PR, which focus on modifying tracking parameters in the configuration file, are related to the retrieved PR that introduces a max_tracking feature in the Tracker class, as both involve enhancements to tracking capabilities and parameters in the tracking module.

Suggested labels

Re-tracking Spread, MultiView Stack

Suggested reviewers

• talmo
• gitttt-1234

🐰 In a world of code so bright,
Each change brings a new delight!
With tracking swift and errors few,
Our framework hops to something new.
Here’s to progress, let’s all cheer,
For every byte, we hold so dear! 🌟

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[getzze]

Also fixes a bug introduced by #1875, where the data_path variable was overwritten.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 71.42857% with 58 lines in your changes missing coverage. Please review.

Project coverage is 76.29%. Comparing base (7991f14) to head (d2249c8). Report is 109 commits behind head on develop.

Files with missing lines	Patch %	Lines
sleap/nn/tracking.py	67.77%	29 Missing :warning:
sleap/nn/inference.py	72.91%	26 Missing :warning:
sleap/gui/learning/dialog.py	0.00%	1 Missing :warning:
sleap/gui/widgets/video.py	50.00%	1 Missing :warning:
sleap/util.py	92.85%	1 Missing :warning:

:x: Your patch status has failed because the patch coverage (72.00%) is below the target coverage (100.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1894      +/-   ##
===========================================
+ Coverage    75.43%   76.29%   +0.85%     
===========================================
  Files          134      133       -1     
  Lines        24749    24995     +246     
===========================================
+ Hits         18670    19069     +399     
+ Misses        6079     5926     -153     

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

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[getzze]

It's ready for review!

[talmo]

Thanks for the updates @getzze! Just keep us posted on when it's ready for review again.

[getzze]

It's ready to review!

[gitttt-1234]

Hi @getzze ,

I rebased you branch off of our updated develop branch and I noticed there are few errors in the tests because of the new features added. (One of the main addition is having a new parameter img_hw to the Tracker.track() method) Since I don't have access to your branch, could you please resolve the issues so that we could merge this PR to develop?

Thanks,

Divya

[getzze]

Hi @gitttt-1234, I just pushed the changes.

Thanks

[getzze]

Hi @gitttt-1234, I rebased to develop and tests are passing.

[getzze]

@gitttt-1234 thanks for reviewing! I modified the code to address your points (I hope :) ).

[getzze]

@gitttt-1234 I made all the corrections, thanks!

[gitttt-1234]

Thanks @getzze ! Could you also resolve the errors caught in our CI tests?

[getzze]

@gitttt-1234 the tests should pass now

[getzze]

@gitttt-1234 Tests are passing and PR is rebased

[getzze]

@gitttt-1234 Everything good!

[getzze]

sorry to bug you @gitttt-1234 but is there anything else to do?

[gitttt-1234]

Hi @getzze !

Apologies for the delay! Sorry I missed your previous comments, I'll do a quick pass today and merge it if everything looks good!

Thanks,

Divya

[getzze]

CI is failing because the conda-incubator/setup-miniconda action used in CI.yml is now pulling conda 25.3.0 and mamba 2.x. Before it pulled conda 24.x and mamba 1.x.

[getzze]

Hey @gitttt-1234 , maybe this can be merged now?