search

talmolab / sleap

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

Fix IndexError for hdf5 file import for single instance analysis files #1695

Closed shrivaths16 closed 8 months ago

shrivaths16 commented 8 months ago

Description

While performing inference for single instances, there seems to be no track names generated. This is causing IndexError while trying to load a HDF5 file since, the number of tracks is 1 and the track_names is empty. So we add a condition to check this and create a single track accordingly.

Types of changes

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

coderabbitai[bot] commented 8 months ago

Walkthrough

A new test function was added to test_formats.py to test reading Sleap analysis files using SleapAnalysisAdaptor. This addition enhances the testing suite's coverage for reading Sleap analysis files.

Changes

File Path Change Summary
tests/fixtures/videos.py Added import for FileHandle.
Added constants and fixtures for single fly data.
tests/io/test_formats.py Added test function test_sleap_analysis_read.

🐇📝🧪
Tests and fixtures, a rabbit's delight,
New functions added, shining bright.
Code and data, hand in hand,
Ensuring Sleap files are grand.
🌟🐾🔍

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: - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `Generate unit-tests 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 tests 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 tests.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` 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 as PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger a review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai help` to get help. Additionally, you can add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. ### CodeRabbit Configration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - The JSON schema for the configuration file is available [here](https://coderabbit.ai/integrations/coderabbit-overrides.v2.json). - 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/coderabbit-overrides.v2.json` ### CodeRabbit Discord Community Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback.
codecov[bot] commented 8 months ago

Codecov Report

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

Project coverage is 73.38%. Comparing base (60a441f) to head (4d48a65). Report is 1 commits behind head on develop.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1695 +/- ## ======================================== Coverage 73.38% 73.38% ======================================== Files 134 134 Lines 24064 24064 ======================================== + Hits 17659 17660 +1 + Misses 6405 6404 -1 ```

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