talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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Use `Video.from_filename` when structuring videos #1905

Closed roomrys closed 3 months ago

roomrys commented 3 months ago

Description

When upgrading dependencies in a downstream branch, we are running into problems with cattrs inferring the Video.backend type. This PR fixes this issue by using the Video.from_filename function to determine the Video backend.


Prior to this, just the attributes in the serialized "backend" dictionary were used by cattrs to automatically infer which Video.backend type to use. Thus, we had a test fixture with the Video.filename == "test" which would fail with our new way of structuring (since there are no extensions on the filename). I don't foresee this being a problem as all videos should have correct filenames (even pkg.slp format converts the . filename: https://github.com/talmolab/sleap/blob/076f3dda2036c5833dec35ff4479d3ae1c7f7f55/sleap/io/format/hdf5.py#L100-L101 to the extension expected by the HDF5Video backend: https://github.com/talmolab/sleap/blob/efdf3faa87019b070438eddbde1f917433aeff9a/sleap/io/video.py#L47-L66 https://github.com/talmolab/sleap/blob/efdf3faa87019b070438eddbde1f917433aeff9a/sleap/io/video.py#L1265-L1266 ), but please double check me.

Types of changes

Does this address any currently open issues?

Outside contributors checklist

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

coderabbitai[bot] commented 3 months ago

Walkthrough

Recent changes enhance the sleap/io/video.py functionality by refactoring the fixup_video function to streamline the handling of video file paths and backend configurations. The test suite in tests/io/test_dataset.py was also updated to better align with expected video formats. These modifications improve clarity, maintainability, and the overall efficiency of the codebase.

Changes

Files Change Summary
sleap/io/video.py Refactored fixup_video function to improve path handling and backend registration; updated type annotations.
tests/io/test_dataset.py Updated filename parameter in removal_test_labels fixture to "test.mp4" for better test accuracy.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant VideoHandler
    participant MediaBackend

    User->>VideoHandler: Request video processing
    VideoHandler->>MediaBackend: Retrieve backend info
    MediaBackend-->>VideoHandler: Provide backend configuration
    VideoHandler->>VideoHandler: Fix video paths
    VideoHandler-->>User: Return processed video

🐰 "In the code where bunnies hop,
A path was fixed, not a single flop!
With video flows so neat and fine,
Our tests now dance, oh how they shine!
Hooray for changes, clear and bright,
Let’s code and play, from day to night!" 🐇


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codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 74.49%. Comparing base (7ed1229) to head (ae341cc). Report is 31 commits behind head on develop.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1905 +/- ## =========================================== + Coverage 73.30% 74.49% +1.18% =========================================== Files 134 135 +1 Lines 24087 24788 +701 =========================================== + Hits 17658 18466 +808 + Misses 6429 6322 -107 ```

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