getzze commented 1 year ago

Description

Importing Deeplabcut project with multiple animals failed because:

the video has a ".avi" extension and current code assumes .mp4 extenstion.
the DLC config file has a non-empty uniquebodyparts list. Unique body parts do not belong to any individual, so parsing the .csv file containing the labeled frames leads to key error of the type: Cannot find key ("animal", "unique_body_part"). Unique body parts belong to the "single" individual.

In addition, this PR creates Tracks with the animal names (and "single" for the unique body parts), which is a new feature.

I added tests for importing Multiple animal DLC with uniquebodyparts.

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?

734

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!

:heart:

Summary by CodeRabbit

New Feature: Enhanced the software's ability to handle different video file extensions, improving the flexibility of video file input.
Improvement: Updated the system to store individual animal tracks in a dictionary, enhancing the organization and accessibility of data.
Bug Fix: Corrected a spelling error in the summary() function, improving the readability of the code.
Test: Added a new test case test_maudlc to ensure the correct parsing and organization of data from CSV files.
Test: Updated existing test cases to align with new data structures and functionalities, ensuring the reliability of the software.
Refactor: Replaced the animal_names list with a tracks dictionary for better data management.

coderabbitai[bot] commented 1 year ago

Walkthrough

This pull request introduces significant changes to the sleap/io/format/deeplabcut.py file, enhancing the handling of tracks and instances, and improving video file detection. It also updates the corresponding tests in tests/io/test_formats.py to reflect these changes, and corrects a minor spelling error in sleap/nn/system.py.

Changes

File	Summary
`sleap/io/format/deeplabcut.py`	Introduced a `tracks` dictionary for better track handling, improved video file detection, and updated the `read()` function to add nodes from the "uniquebodyparts" field.
`sleap/nn/system.py`	Corrected a spelling error in the `summary()` function.
`tests/io/test_formats.py`	Updated test cases to reflect changes in `sleap/io/format/deeplabcut.py`, added a new test case `test_maudlc`, and removed the `test_matching_adaptor` function.
`tests/gui/test_commands.py`	Updated the assertion in `test_import_labels_from_dlc_folder()` to expect three tracks instead of none.

🐇

In the land of code, changes are afoot,

With tracks and instances given a new look.

Video files found with greater ease,

And tests updated to put minds at peace.

A spelling error, small but keen,

In the system's summary, now pristine.

So here's to the coder, with vision so bright,

Making the codebase a sheer delight! 🎉

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talmo commented 1 year ago

Thanks for the contribution @getzze! Looks like there's still a failing test related to the tracks, but just ping us when you're ready for review :)

codecov[bot] commented 1 year ago

Codecov Report

Merging #1562 (bfae2dc) into develop (1e0627a) will decrease coverage by 0.01%. Report is 1 commits behind head on develop. The diff coverage is 66.66%.

@@             Coverage Diff             @@
##           develop    #1562      +/-   ##
===========================================
- Coverage    73.37%   73.36%   -0.01%     
===========================================
  Files          134      134              
  Lines        23976    24009      +33     
===========================================
+ Hits         17592    17614      +22     
- Misses        6384     6395      +11

Files	Coverage Δ
sleap/nn/system.py	`42.85% <0.00%> (ø)`
sleap/io/format/deeplabcut.py	`81.65% <69.23%> (-3.22%)`	:arrow_down:

... and 3 files with indirect coverage changes

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