search

talmolab / sleap

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

Allowing inference on multiple videos via `sleap-track` #1784

Closed emdavis02 closed 4 months ago

emdavis02 commented 5 months ago

Description

Adding an option to add a directory to sleap-track to allow the command to iterate through the files in the directory and run inferences on all of them.

Types of changes

Does this address any currently open issues?

1777

Outside contributors checklist

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

coderabbitai[bot] commented 5 months ago

Walkthrough

The recent updates to the sleap/nn/inference.py and corresponding test files enhance the software to handle multiple video inputs. The changes refactor the code to iterate over a list of file paths, create providers for each file, run the inference, and save the results. Enhancements include better error handling, improved metadata management, and robust testing for various scenarios.

Changes

File Change Summary
sleap/nn/inference.py Refactored logic to handle multiple video inputs, created a provider list, managed output paths, and added provenance metadata.
tests/nn/test_inference.py Added fixtures and test functions for multiple inference scenarios, including parameterized tests and handling invalid inputs.

Poem

In the land of code where videos roam,
A rabbit worked to bring them home.
With paths aplenty and providers in tow,
Each file's secrets would soon show.
Tests were written, robust and clear,
Ensuring the code ran without fear.
🎥✨🐇 The rabbit's joy was quick to grow!

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 as 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. Additionally, you can add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. ### 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 4 months ago

Codecov Report

Attention: Patch coverage is 89.16667% with 13 lines in your changes missing coverage. Please review.

Project coverage is 74.19%. Comparing base (7ed1229) to head (fb587e5). Report is 21 commits behind head on develop.

Files Patch % Lines
sleap/nn/inference.py 89.16% 13 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1784 +/- ## =========================================== + Coverage 73.30% 74.19% +0.88% =========================================== Files 134 135 +1 Lines 24087 24639 +552 =========================================== + Hits 17658 18280 +622 + Misses 6429 6359 -70 ```

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

talmo commented 4 months ago

Review notes from subgroup:

talmo commented 4 months ago

In addition to the changes above, another comment re: supporting inputs that are multiple SLP files:

@roomrys am I missing any other dangerzone cases?

talmo commented 4 months ago

In addition to the changes above, another comment re: supporting inputs that are multiple SLP files:

  • We do want to support having multiple SLP files that have predicted poses on all frames and that the user wants to retrack only.
  • We do want to support having multiple SLP files that have suggestion frames and that the user wants to generate predicted poses for, but not track.
  • We do not want to overwrite SLP files in any case.
  • We really do not want to mess around with .pkg.slp files, particularly not overwrite them. When re-saving labels that had embedded images, they'll get saved without the embedded images and will restore the source videos. If the user had embedded images, it'd be a serious data loss event to have that file get re-saved without the images. In this case, saving to a separate SLP file is the best compromise.

@roomrys am I missing any other dangerzone cases?

On further assessment during subgroup: let's actually just not do multiple SLP file support.