Filter OOB points while training

[gitttt-1234]

Description

This PR converts all out-of-boundary and negative points to nans while generating the dataset and while computing the crop size to avoid errors while training.

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?

#1901

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• [ ] 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!

:heart:

Summary by CodeRabbit

Summary by CodeRabbit

• New Features

  • Enhanced dataset creation by filtering out-of-bounds points, ensuring only valid instance coordinates are included.
  • Improved cropping functionality with robust calculations for crop size based on valid instance points.
  • New utility function to handle out-of-bounds points in datasets.

• Bug Fixes

  • Adjusted expected output in model predictions for better accuracy.

• Documentation

  • Minor formatting updates in the configuration file for documentation settings.

• Tests

  • Added new tests to validate filtering of out-of-bounds points and crop size calculations.
  • Introduced tests for model training with out-of-bounds points.

[coderabbitai[bot]]

Walkthrough

The pull request introduces a minor formatting adjustment in the Sphinx documentation configuration file docs/conf.py, along with significant enhancements to the LabelsReader class in sleap/nn/data/providers.py. The modifications in the data providers file focus on improving data integrity by implementing a filtering mechanism for instance coordinates, removing out-of-bounds points and ensuring only valid data is processed. Additionally, new tests have been added to validate the filtering functionality and the cropping size calculations.

Changes

File	Change Summary
docs/conf.py	Minor formatting change from single to double quotes for html_css_files path
sleap/nn/data/providers.py	- Added import for Instance from sleap.instance - Enhanced make_dataset method to filter out-of-bounds points - Replaced invalid coordinates with NaN - Removed instances with NaN coordinates
tests/nn/data/test_providers.py	Added test_labels_filter_oob_points to verify filtering of OOB points in LabelsReader
sleap/nn/data/instance_cropping.py	- Updated find_instance_crop_size to handle image dimensions and validate points - Adjusted transform_dataset in InstanceCropper and PredictedInstanceCropper for new cropping logic
tests/nn/test_inference.py	Modified assertion in test_topdown_model for expected output of n_valid key
tests/nn/data/test_instance_cropping.py	Added test_find_instance_crop_size to validate crop size calculations based on instance points
tests/nn/test_training.py	Added test_train_topdown_with_oob_pts to evaluate training with out-of-bounds points
sleap/nn/data/utils.py	Added new function filter_oob_points to filter out-of-bounds points

Poem

🐰 In the realm of data's wild terrain,
Where pixels dance and numbers reign,
Our rabbit filters with keen delight,
Casting out points that just aren't right!
Clean data hops, no bounds too tight! 🌟

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[codecov[bot]]

Codecov Report

:x: Patch coverage is 44.73684% with 21 lines in your changes missing coverage. Please review. :white_check_mark: Project coverage is 76.11%. Comparing base (7ed1229) to head (768ca90). :warning: Report is 161 commits behind head on develop.

Files with missing lines	Patch %	Lines
sleap/nn/data/providers.py	9.09%	20 Missing :warning:
sleap/nn/data/instance_cropping.py	90.00%	1 Missing :warning:

:x: Your patch status has failed because the patch coverage (44.73%) 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    #2061      +/-   ##
===========================================
+ Coverage    73.30%   76.11%   +2.80%     
===========================================
  Files          134      134              
  Lines        24087    24786     +699     
===========================================
+ Hits         17658    18865    +1207     
+ Misses        6429     5921     -508     

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[gitttt-1234]

Looks good! Code rabbits suggestions of parameterizing could be implemented.

Sure, added those in the latest commit!