Small improvements to tracking

getzze commented 1 month ago

Description

Several things were buggy when running tracking-only from GUI or sleap-track from CLI with only tracking:

improve the ETA in the GUI progress bar by computing the list of frames before starting the timer.
show a progress bar when tracking, like for inference(+tracking)
correctly pass default options for tracking to CLI. It seems all tracking options that were not defined were given the None value, which is boolean-False, so it could give the opposite for True-by-default options (there are none so far, fortunately).
small bug in GUI video that makes it crash when clicking.
switch the default value of save_shifted_instances to True and give back access to setting it from the GUI (removed in #1447, I don't know why)
allow running tracking only on defined frames. It always run on the full video now.
[EDIT] fix a bug introduced by #1875, where the data_path variable was overwritten.

Types of changes

[x] Bugfix
[x] New feature
[ ] Refactor / Code style update (no logical changes)
[ ] Build / CI changes
[ ] Documentation Update
[ ] Other (explain)

Does this address any currently open issues?

None

Outside contributors checklist

[x] Review the guidelines for contributing to this repository
[x] Read and sign the CLA and add yourself to the authors list
[x] Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
[x] Add tests that prove your fix is effective or that your feature works
[x] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

New Features
- Enhanced tracking capabilities with improved reporting options, allowing for more user control over output.
- Reintroduced and refined configuration options for saving shifted instances during tracking.
- Introduced a custom progress rate display for better user feedback during tasks.
Bug Fixes
- Improved error handling in mouse event detection to prevent negative values.
- Adjusted calculations to ensure non-negative counts during tracking.
Refactor
- Integrated tracking logic directly into the Tracker class, removing standalone functions for better encapsulation.
- Updated the data processing flow for batch predictions to enhance modularity and clarity.
- Simplified tracking test logic by removing intermediary functions.
Tests
- Updated tracking tests to incorporate image scaling and parameterized testing for improved coverage.
- Adjusted expected outcomes in tracking integration tests for accuracy.

coderabbitai[bot] commented 1 month ago

Walkthrough

The recent updates to the Sleap framework enhance tracking and inference capabilities. Key modifications include refined configuration options, improved error handling, and better user experience. Changes optimize performance, introduce new reporting features, and streamline object-oriented design, making the system more maintainable and extendable.

Changes

Files	Change Summary
`sleap/config/pipeline_form.yaml`	Removed `tracking.max_tracking`; reintroduced `tracking.save_shifted_instances` with updated defaults and help description.
`sleap/gui/learning/dialog.py`	Adjusted `no_result_count` calculation to prevent negative values, enhancing reliability.
`sleap/gui/widgets/video.py`	Introduced `_down_pos` for mouse tracking; improved logic in `mouseReleaseEvent` to ensure error-free click detection.
`sleap/nn/inference.py`	Added methods for batch processing and improved progress reporting; refactored existing logic for clarity and efficiency.
`sleap/nn/tracking.py`	Added `verbosity` and `report_rate` attributes; expanded `run_tracker` method; improved tracking feedback mechanisms.
`sleap/util.py`	Introduced `RateColumn` for custom progress rendering; reorganized imports for clarity.
`tests/nn/test_tracker_components.py`	Renamed `tracker_by_name` to `run_tracker_by_name`; included `img_scale` parameter for enhanced testing capabilities.
`tests/nn/test_tracking_integration.py`	Updated assertions in `test_simple_tracker`; refactored tests to utilize instance methods for tracking.

Possibly related PRs

#1824: The changes in the main PR regarding the configuration option tracking.save_shifted_instances and the removal of tracking.max_tracking relate to the modifications in the training GUI that introduce a checkbox for retaining prediction visualization images after training, indicating a focus on tracking functionalities.
#1875: The enhancements to the tracking functionality in the main PR align with the introduction of CSV and text file support in the sleap track tool, as both involve improvements to how tracking data is managed and processed.
#1939: The addition of the normalized_instance_similarity method in the main PR complements the changes in the tracking system, as both aim to improve the accuracy and reliability of instance matching in tracking processes.

Suggested labels

MultiView Stack

Suggested reviewers

talmo

🐰 In a world of code so bright,
Each change brings a new delight!
With tracking swift and errors few,
Our framework hops to something new.
Here’s to progress, let’s all cheer,
For every byte, we hold so dear! 🌟

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 , please review it.` - `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 gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.` - `@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.

getzze commented 1 month ago

Also fixes a bug introduced by #1875, where the data_path variable was overwritten.

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 67.06587% with 55 lines in your changes missing coverage. Please review.

Project coverage is 75.29%. Comparing base (7ed1229) to head (10799b9). Report is 47 commits behind head on develop.

Files with missing lines	Patch %	Lines
sleap/nn/tracking.py	64.19%	29 Missing :warning:
sleap/nn/inference.py	66.17%	23 Missing :warning:
sleap/gui/learning/dialog.py	0.00%	1 Missing :warning:
sleap/gui/widgets/video.py	50.00%	1 Missing :warning:
sleap/util.py	93.33%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #1894 +/- ## =========================================== + Coverage 73.30% 75.29% +1.98% =========================================== Files 134 133 -1 Lines 24087 24553 +466 =========================================== + Hits 17658 18486 +828 + Misses 6429 6067 -362 ```

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

getzze commented 3 weeks ago

It's ready for review!

talmo commented 2 weeks ago

Thanks for the updates @getzze! Just keep us posted on when it's ready for review again.

getzze commented 2 weeks ago

It's ready to review!

gitttt-1234 commented 1 day ago

Hi @getzze ,

I rebased you branch off of our updated develop branch and I noticed there are few errors in the tests because of the new features added. (One of the main addition is having a new parameter img_hw to the Tracker.track() method) Since I don't have access to your branch, could you please resolve the issues so that we could merge this PR to develop?

Thanks,

Divya

talmolab / sleap