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talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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Handle skeleton decoding internally #1961

Closed roomrys closed 3 days ago

roomrys commented 2 weeks ago

Description

It has become apparent that it will be safer for us to handle (de)serialization of our data structures internally rather than relying on external libraries such as cattr and jsonpickle to do this for us. Without constraining these (de)serialization dependencies (which may also cause other upgrade/dependency constraints elsewhere), we cannot expect that the format of (de)serialization will be backwards compatible within (even the same!) version of SLEAP (albeit installed at different times).

Keeping with the theme above, this PR is the first of many that starts migrating (de)serialization to internal SLEAP code. In this PR, we add a function to replace jsonpickle.decode which is intended to be used on jsonpickle.encoded Skeletons.

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 2 weeks ago

Walkthrough

The changes encompass the introduction of a new SkeletonDecoder class for improved decoding of skeleton data, including nodes and edges, while replacing previous decoding methods. The DockWidget class in the GUI has been updated to utilize this new decoder for handling preview images. Additionally, a new JSON file representing a fly's skeletal structure has been added, along with corresponding test fixtures and modifications to existing tests to validate the new functionality.

Changes

Files Change Summary
sleap/gui/widgets/docks.py Updated DockWidget to use SkeletonDecoder.decode_preview_image for decoding preview images.
sleap/skeleton.py Introduced SkeletonDecoder class, which replaces jsonpickle.decode with custom methods for decoding skeleton data, including nodes, edges, and preview images.
sleap/util.py Removed unused imports and the decode_preview_image function, streamlining the codebase.
tests/data/skeleton/fly_skeleton_legs_pystate_dict.json Added a JSON file defining a directed multigraph for a fly's skeletal structure, including nodes and links.
tests/fixtures/skeletons.py Added new fixture fly_legs_skeleton_dict_json for testing, providing a path to the new JSON file.
tests/test_skeleton.py Modified tests to use SkeletonDecoder, added tests for decoding preview images and validating the SkeletonDecoder functionality.
tests/test_util.py Removed the test_decode_preview_image function, which was redundant following the refactor.

Assessment against linked issues

Objective Addressed Explanation
Validate new decoding mechanism ✅
Ensure proper handling of preview images ✅

Possibly related issues

Possibly related PRs

Suggested labels

MultiView Stack

Poem

In the garden where the data flows,
A rabbit hops where the skeleton grows.
With a decoder bright, it shows the way,
To images and nodes, we cheer and play!
Hopping high, our code's a delight,
With every change, we take flight! 🐇✨

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codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 98.07692% with 2 lines in your changes missing coverage. Please review.

Project coverage is 75.40%. Comparing base (7ed1229) to head (6a4647d). Report is 52 commits behind head on develop.

Files with missing lines Patch % Lines
sleap/skeleton.py 98.01% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1961 +/- ## =========================================== + Coverage 73.30% 75.40% +2.09% =========================================== Files 134 133 -1 Lines 24087 24552 +465 =========================================== + Hits 17658 18514 +856 + Misses 6429 6038 -391 ```

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