lochhh commented 1 month ago

Description

What is this PR

[ ] Bug fix
[x] Addition of a new feature
[ ] Other

Why is this PR needed? Closes #277

What does this PR do?

Adds functions to compute pairwise distances between elements (e.g. individuals, keypoints)
- between a single pair of elements (cdist - open to rename suggestions!)
- between multiple or all pairs of elements (compute_interindividual_distances, compute_interkeypoint_distances)
Includes example usage in docstrings
Adds tests for the new functions
- with poses dataset (with single and multiple individuals/keypoints) or da.sel data with coord_val.ndim == 0
- with bboxes dataset (with single and multiple individuals, but missing keypoints dim)

TO-DO:

[x] Handle poses dataset
- [x] with single individual/keypoint coord_val.ndim == 1
- [x] from da.sel with coord_val.ndim == 0
- [x] with multiple individuals/keypoints
[x] Handle datasets without "individuals" or "keypoints" dim, e.g. bboxes dataset doesn't have "keypoints" dim
[x] Revert de4a96b5792cfac32923a579c69a265b2b673e51 that works around failing tests due to sleap-io's incompatibility with NumPy 2.0.

References

277

How has this PR been tested?

Tests passing locally and on CI

Does this PR require an update to the documentation?

Docstrings with examples are provided alongside the new functions.

Checklist:

[x] The code has been tested locally
[x] Tests have been added to cover all new functionality
[x] The documentation has been updated to reflect any changes
[x] The code has been formatted with pre-commit

codecov[bot] commented 1 month ago

Codecov Report

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

Project coverage is 99.78%. Comparing base (9c80786) to head (98d2388).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #278 +/- ## ======================================= Coverage 99.77% 99.78% ======================================= Files 15 15 Lines 887 923 +36 ======================================= + Hits 885 921 +36 Misses 2 2 ```

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