Add `InstancesList` class to handle backref to `LabeledFrame`

roomrys commented 5 months ago

Description

This PR proposes a custom data structure (sub-classed from list) to handle the back reference attribute Instance.frame namely for LabeledFrame.instances.

This also solves the error we were getting of when trying to double click a PredictedInstance that was predicted on an already existing LabeledFrame. During the merge process, the PredictedInstance.frame is set to None, https://github.com/talmolab/sleap/blob/bbe124666781ef6f72931cfe17df5f1d5a96ba54/sleap/instance.py#L1703-L1704

but then when extending the LabeledFrame.instances list, no care is taken to handle updating the PredictedInstance.frame attribute. https://github.com/talmolab/sleap/blob/bbe124666781ef6f72931cfe17df5f1d5a96ba54/sleap/instance.py#L1733-L1734

Hence, the error:

Traceback (most recent call last):
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\app.py", line 1592, in _handle_instance_double_click
    copy_instance=instance, mark_complete=mark_complete
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 522, in newInstance
    mark_complete=mark_complete,
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 241, in execute
    command().execute(context=self, params=kwargs)
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 137, in execute
    self.do_with_signal(context, params)
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 161, in do_with_signal
    cls.do_action(context, params)
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 2879, in do_action
    from_prev_frame=from_prev_frame,
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 2911, in create_new_instance
    mark_complete=mark_complete,
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 3002, in set_visible_nodes
    cls.do_action(context, params)
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 2879, in do_action
    from_prev_frame=from_prev_frame,
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 2911, in create_new_instance
    mark_complete=mark_complete,
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\gui\commands.py", line 3002, in set_visible_nodes
    old_size_width = copy_instance.frame.video.shape[2]
AttributeError: 'NoneType' object has no attribute 'video

This issue is only noticeable after merging in:

1568

Types of changes

[ ] Bugfix
[ ] 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!

:heart:

Summary by CodeRabbit

New Features
- Introduced InstancesList class for managing lists of instances within a labeled frame.
Bug Fixes
- Improved handling and setting of frames for instances to ensure data integrity.
Tests
- Enhanced test coverage for InstancesList and updated relevant test functions to ensure robustness.
Refactor
- Modified Instance and LabeledFrame classes to improve internal handling of instances.

coderabbitai[bot] commented 5 months ago

Walkthrough

The recent changes in the codebase primarily focus on enhancing the management of instance annotations within labeled frames. The key update is the introduction of the InstancesList class, which encapsulates handling lists of instances, ensuring each instance's frame is set correctly. Additionally, the Instance class modifications, including making the frame attribute private, and updates to LabeledFrame, streamline instance-frame interactions.

Changes

Files	Change Summary
`sleap/instance.py`	Modified `Instance` class to make `frame` attribute private; introduced `InstancesList` class to manage instance lists.
`tests/test_instance.py`	Added import statements, including `from typing import List`, and updated test functions for `InstancesList` functionality.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant LabeledFrame
    participant InstancesList
    participant Instance

    User->>LabeledFrame: Add Instance
    LabeledFrame->>InstancesList: Add Instance to List
    InstancesList->>Instance: Set Instance Frame
    Instance-->>InstancesList: Instance Frame Set
    InstancesList-->>LabeledFrame: Instance Added
    LabeledFrame-->>User: Instance Added Successfully

Poem

In the world of frames and instance ties, A rabbit smiles, swift and wise. With lists of instances in tow, The code now takes a smoother flow. Tests are ready, the stage is set, For sleeker sleap, you can bet! 🐰✨

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codecov[bot] commented 5 months ago

Codecov Report

Attention: Patch coverage is 96.77419% with 2 lines in your changes missing coverage. Please review.

Project coverage is 74.17%. Comparing base (7ed1229) to head (5b3ef99). Report is 15 commits behind head on develop.

Files	Patch %	Lines
sleap/instance.py	96.77%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #1807 +/- ## =========================================== + Coverage 73.30% 74.17% +0.86% =========================================== Files 134 135 +1 Lines 24087 24557 +470 =========================================== + Hits 17658 18214 +556 + Misses 6429 6343 -86 ```

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

talmolab / sleap