search

talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
Other
435 stars 97 forks source link

Handle skeleton decoding internally #1961

Closed roomrys closed 1 month ago

roomrys commented 2 months 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 months 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! 🐇✨

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share - [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)
Tips ### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai generate interesting stats about this repository and render them as a table.` - `@coderabbitai show all the console.log statements in this repository.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (Invoked using PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. ### Other keywords and placeholders - Add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. - Add `@coderabbitai summary` to generate the high-level summary at a specific location in the PR description. - Add `@coderabbitai` anywhere in the PR title to generate the title automatically. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.
codecov[bot] commented 2 months 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 ```

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