(3e -> 3a) Add `InstanceGroup` class

roomrys commented 11 months ago

Description

This PR adds and implements the InstanceGroup datastructure and should be used to update InstanceGroup.

Types of changes

[ ] 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?

[list open issues here]

Outside contributors checklist

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

Thank you for contributing to SLEAP!

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Summary by CodeRabbit

Refactor
- Updated imports to streamline camera-related functionalities and types.
Tests
- Adjusted test imports to align with the refactored camera module.
- Added new test functions for testing InstanceGroup and FrameGroup data structures.

coderabbitai[bot] commented 11 months ago

Walkthrough

The changes encompass a comprehensive overhaul of the camera-related functionalities in SLEAP. This includes refactoring imports, updating logic for handling instances and points, introducing new data structures, and refining the test suite to align with the enhanced codebase.

Changes

File Path	Change Summary
`sleap/io/cameras.py`	Updated imports, added `triangulate` import, included new types from `sleap.types`.
`sleap/gui/commands.py` `sleap/instance.py`	Enhanced logic for handling instances and points, respectively.
`tests/io/test_cameras.py`	Added new imports, modified function signatures, introduced `InstanceGroup` and `FrameGroup` testing functions.
`tests/fixtures/datasets.py`	Added `multiview_min_session_user_labels` fixture for minimal session user-labeled data.
`tests/gui/test_commands.py`	Removed various test functions related to multi-view triangulation scenarios.

🐇✨ In the code where cameras lie, A rabbit hopped, refactoring high. With types anew, the tests align, A sleeker codebase, by design. 🌟 🐾📸

Recent Review Details

**Configuration used: CodeRabbit UI**

Commits

Files that changed from the base of the PR and between ad5fb9e6a9db4cb84831c1b107a7a3b800e37be9 and 0c057c1284605d3eaf7854125c57b4e7af121ccd.

Files selected for processing (6)

* sleap/gui/commands.py (2 hunks) * sleap/instance.py (2 hunks) * sleap/io/cameras.py (7 hunks) * tests/fixtures/datasets.py (1 hunks) * tests/gui/test_commands.py (1 hunks) * tests/io/test_cameras.py (2 hunks)

Files not summarized due to errors (1)

* sleap/io/cameras.py: Error: Message exceeds token limit

Additional comments not posted (15)

tests/fixtures/datasets.py (1)
`283-288`: The new fixture `multiview_min_session_user_labels` correctly loads user-labeled data for a minimal session. This aligns with the PR's objective to enhance data handling capabilities.

tests/io/test_cameras.py (3)
`8-14`: The updated imports correctly include `InstanceGroup` and `FrameGroup`, which are necessary for the new functionalities being tested. --- `292-339`: The function `create_instance_group` has been updated to optionally include a dummy instance in the returned data. This is useful for testing scenarios where not all data points are valid or present. The implementation handles the conditional logic and data structure manipulation correctly. --- `342-416`: The test `test_instance_group` effectively checks the functionality of the `InstanceGroup` data structure, including edge cases with the dummy instance. The assertions cover various properties and methods, ensuring the structure behaves as expected.

sleap/instance.py (8)
Line range hint `34-63`: LGTM! The `Point` class implementation is clear and well-defined. --- Line range hint `75-110`: LGTM! The `PredictedPoint` class correctly extends the `Point` class with additional functionality for handling prediction scores. --- Line range hint `118-183`: LGTM! The `PointArray` class provides necessary functionality for handling arrays of `Point` objects efficiently. --- Line range hint `185-209`: LGTM! The `PredictedPointArray` class correctly extends `PointArray` to handle `PredictedPoint` objects, maintaining consistency in the API. --- Line range hint `211-235`: LGTM! The `Track` class implementation is straightforward and provides essential functionality for tracking objects across frames. --- `500-505`: > :memo: **NOTE** > This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [237-729] The methods in the `Instance` class are well-implemented and cover a wide range of functionalities required for managing instances in SLEAP. --- Line range hint `1654-1791`: LGTM! The `PredictedInstance` class correctly extends the `Instance` class to handle additional attributes and functionalities specific to predicted instances. --- Line range hint `1793-2428`: LGTM! The `LabeledFrame` class provides comprehensive functionality for managing labeled data within a single frame, including methods for merging frames and handling instances.

sleap/gui/commands.py (3)
`3421-3425`: Consider handling the case where `instance_group` is `None` more explicitly. It might be beneficial to add a specific error message or handling logic when `instance_group` is `None`, as this could indicate a deeper issue with the data or assumptions being made. --- `3444-3449`: Ensure that the `triangulate` function handles exceptions or errors gracefully. --- `3458-3465`: Validate the dimensions and data integrity of `points_reprojected` before updating. Consider adding checks to ensure that the dimensions and data integrity of `points_reprojected` are as expected before calling `upsert_points`. This can prevent potential runtime errors or data corruption.

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roomrys commented 11 months ago

@coderabbitai review

codecov[bot] commented 11 months ago

Codecov Report

Attention: Patch coverage is 76.88172% with 43 lines in your changes are missing coverage. Please review.

Project coverage is 73.85%. Comparing base (443d410) to head (95071c1).

:exclamation: Current head 95071c1 differs from pull request most recent head 0c057c1. Consider uploading reports for the commit 0c057c1 to get more accurate results

Files	Patch %	Lines
sleap/io/cameras.py	71.42%	42 Missing :warning:
sleap/gui/commands.py	96.77%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## liezl/add-method-to-match-instances-across-views #1618 +/- ## ==================================================================================== + Coverage 73.81% 73.85% +0.03% ==================================================================================== Files 135 135 Lines 24636 24807 +171 ==================================================================================== + Hits 18186 18322 +136 - Misses 6450 6485 +35 ```

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

roomrys commented 11 months ago

   Ordered by: cumulative time
   List reduced from 5387 to 100 due to restriction <100>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000   11.447   11.447 runner.py:111(pytest_runtest_protocol)
    17/11    0.000    0.000   11.447    1.041 _hooks.py:427(__call__)
    17/11    0.000    0.000   11.447    1.041 _manager.py:103(_hookexec)
    17/11    0.000    0.000   11.447    1.041 _callers.py:30(_multicall)
        1    0.000    0.000   11.446   11.446 runner.py:119(runtestprotocol)
        3    0.000    0.000   11.446    3.815 runner.py:219(call_and_report)
        3    0.000    0.000   11.446    3.815 runner.py:247(call_runtest_hook)
        3    0.000    0.000   11.446    3.815 runner.py:318(from_call)
        3    0.000    0.000   11.446    3.815 runner.py:262(<lambda>)
        1    0.000    0.000   11.427   11.427 runner.py:160(pytest_runtest_call)
        1    0.000    0.000   11.427   11.427 python.py:1790(runtest)
        1    0.000    0.000   11.427   11.427 python.py:187(pytest_pyfunc_call)
        1    0.000    0.000   11.427   11.427 test_commands.py:1304(test_triangulate_session)
        2    0.000    0.000   11.427    5.714 commands.py:617(triangulateSession)
        2    0.000    0.000   11.427    5.714 commands.py:242(execute)
        2    0.000    0.000   11.427    5.714 commands.py:109(execute)
        2    0.000    0.000   11.416    5.708 commands.py:158(do_with_signal)
        2    0.000    0.000   11.416    5.708 commands.py:3393(do_action)
        2    0.000    0.000   11.416    5.708 commands.py:3766(get_instance_grouping_and_reprojected_coords)
        2    0.000    0.000   11.416    5.708 commands.py:3998(calculate_error_per_frame)
        2    0.023    0.012   11.416    5.708 commands.py:3858(_calculate_reprojection_error)
        2    0.000    0.000   10.871    5.435 commands.py:4391(calculate_reprojected_points)
        2    0.000    0.000   10.833    5.417 commands.py:4271(_calculate_reprojected_points)
        2    0.000    0.000   10.509    5.255 triangulation.py:72(triangulate)
        2    0.000    0.000   10.509    5.254 triangulation.py:177(<listcomp>)
        4    0.012    0.003   10.509    2.627 cameras.py:1161(triangulate_optim)
        6    0.000    0.000    8.176    1.363 dispatcher.py:388(_compile_for_args)
     33/9    0.000    0.000    7.983    0.887 compiler.py:469(_compile_core)

talmolab / sleap