Extend napari dimension slider tests to bboxes data (closes #591) by Tushar7012 · Pull Request #864 · neuroinformatics-unit/movement

Tushar7012 · 2026-03-03T07:01:07Z

Description

What is this PR?

Addition of a new feature

Why is this PR needed?

The dimension slider tests (test_dimension_slider_with_nans and test_dimension_slider_multiple_files) introduced in PR #503 only run on poses data. As noted in issue #591, these should also cover bounding box data now that VIA-tracks export (PR #580) is merged.

What does this PR do?

Adds bboxes equivalents of the existing poses-based dimension slider tests:

test_dimension_slider_with_nans_bboxes — parametrized over NaN time locations (start, middle, end) and individual combinations, verifies the frame slider covers the full range when bboxes layers have NaNs
test_dimension_slider_multiple_files_bboxes — verifies the frame slider uses the maximum frame count when loading multiple bboxes files in different orders

New test fixtures in tests/fixtures/napari.py:

valid_bboxes_path_and_ds — saves a bboxes dataset as VIA-tracks CSV and returns (path, dataset)
valid_bboxes_path_and_ds_short — same but truncated to 5 frames
valid_bboxes_path_and_ds_with_localised_nans — factory fixture for bboxes datasets with NaNs at specific time/individual locations
valid_bboxes_path_and_ds_nan_start / valid_bboxes_path_and_ds_nan_end — convenience fixtures with NaNs at first/last frame

References

Closes #591

How has this PR been tested?

New test functions added in test_data_loader_widget.py. The existing poses tests are unchanged. The full non-napari test suite (1031 tests) passes locally with no regressions. The napari tests require napari to be installed and should be verified in CI.

Is this a breaking change?

No. This is purely additive — no existing tests or code were modified.

Does this PR require an update to the documentation?

No. These are test-only changes.

Checklist

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

Copilot

Pull request overview

Extends the existing napari DataLoader dimension slider regression tests (previously covering only poses) to also cover bounding-box (VIA-tracks) datasets, aligning test coverage with the recently added bboxes export/import path.

Changes:

Add bboxes equivalents of the “dimension slider with NaNs” and “multiple files” tests in the napari plugin test suite.
Add new napari test fixtures for exporting valid bboxes datasets (including shortened and NaN-localized variants) as VIA-tracks CSV.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
`tests/test_unit/test_napari_plugin/test_data_loader_widget.py`	Adds two new bboxes-focused dimension slider tests mirroring the existing poses tests.
`tests/fixtures/napari.py`	Adds VIA-tracks bboxes export fixtures used by the new tests and updates imports to include `save_bboxes`.

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Copilot · 2026-03-03T07:06:17Z

tests/fixtures/napari.py

+
+    The fixture is derived from the ``valid_bboxes_dataset`` fixture.
+    """
+    valid_bboxes_dataset = valid_bboxes_dataset.sel(time=slice(0, 5))


This fixture claims to truncate to 5 frames, but sel(time=slice(0, 5)) is label-based and (with the current valid_bboxes_dataset time coords 0..9) will include both endpoints, yielding 6 frames (0..5). Use isel(time=slice(0, 5)) (first 5 indices) or sel(time=slice(0, 4)) to match the docstring and produce a true 5-frame dataset.

Suggested change

valid_bboxes_dataset = valid_bboxes_dataset.sel(time=slice(0, 5))

valid_bboxes_dataset = valid_bboxes_dataset.isel(time=slice(0, 5))

Copilot · 2026-03-03T07:06:17Z

tests/fixtures/napari.py

+        if nan_location["time"] == "start":
+            time_point = 0
+        elif nan_location["time"] == "middle":
+            time_point = ds.coords["time"][ds.coords["time"].shape[0] // 2]
+        elif nan_location["time"] == "end":
+            time_point = ds.coords["time"][-1]
+
+        ds.position.loc[
+            {
+                "individuals": nan_location["individuals"],
+                "time": time_point,
+            }
+        ] = np.nan
+
+        out_path = tmp_path / filename
+        save_bboxes.to_via_tracks_file(ds, out_path)
+        return (out_path, ds)
+


save_bboxes.to_via_tracks_file skips writing any row for bboxes that contain NaNs, and the VIA-tracks loader only builds its frame index from frame numbers present in the file. If nan_location['individuals'] includes all individuals at a given timepoint, that frame will have zero rows and will disappear entirely on reload, making it impossible for downstream napari slider logic to cover the original full frame range. To keep the fixture usable for the slider tests, ensure at least one bbox is written for every frame (e.g., only null a subset of individuals), or adjust the export/import to explicitly encode empty frames.

Copilot · 2026-03-03T07:06:17Z

tests/test_unit/test_napari_plugin/test_data_loader_widget.py

+    [["id_0"], ["id_0", "id_1"]],
+    ids=["one_individual", "all_individuals"],


nan_individuals includes the all_individuals case, which can make an entire frame have no bboxes. In VIA-tracks, frames with zero regions are omitted from the CSV, so the loader cannot infer those frames and the viewer cannot be expected to keep the original full frame range. This parametrization will make the test fail (notably for nan_time_location='start'/'end' with all individuals). Consider restricting this test to cases where at least one bbox exists in every frame (e.g., only set NaNs for a subset of individuals), or update the VIA-tracks export/import to explicitly encode empty frames and preserve frame numbers.

Suggested change

[["id_0"], ["id_0", "id_1"]],

ids=["one_individual", "all_individuals"],

[["id_0"]],

ids=["one_individual"],

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codecov · 2026-03-03T07:22:13Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (8d49d6a) to head (14c458f).

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #864   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           38        38           
  Lines         2284      2284           
=========================================
  Hits          2284      2284

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sonarqubecloud · 2026-03-03T09:04:58Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

Copilot AI review requested due to automatic review settings March 3, 2026 07:01

Copilot started reviewing on behalf of Tushar7012 March 3, 2026 07:01 View session

Copilot AI reviewed Mar 3, 2026

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Extend napari dimension slider tests to bboxes data

92cde26

Tushar7012 force-pushed the fix/extend-napari-tests-bboxes-591 branch from 7433ba3 to 92cde26 Compare March 3, 2026 07:11

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Tushar7012 added 2 commits March 3, 2026 13:26

ci: trigger re-run of flaky Windows py3.13 checks

ae4b1a9

fix: use isel instead of sel for 5-frame bboxes short fixture

14c458f

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Extend napari dimension slider tests to bboxes data (closes #591)#864

Extend napari dimension slider tests to bboxes data (closes #591)#864
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	valid_bboxes_dataset = valid_bboxes_dataset.sel(time=slice(0, 5))
	valid_bboxes_dataset = valid_bboxes_dataset.isel(time=slice(0, 5))

		[["id_0"], ["id_0", "id_1"]],
		ids=["one_individual", "all_individuals"],

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Tushar7012 commented Mar 3, 2026

Description

References

How has this PR been tested?

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist

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