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Remove bounding box warning test
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tests/tasks/test_workflows_cellpose_segmentation.py

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Original file line numberDiff line numberDiff line change
@@ -602,49 +602,6 @@ def test_workflow_bounding_box(
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assert "encoding-version" in table_group.attrs.asdict().keys()
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def test_workflow_bounding_box_with_overlap(
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tmp_path: Path,
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zenodo_zarr: list[str],
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caplog: pytest.LogCaptureFixture,
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monkeypatch: MonkeyPatch,
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):
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monkeypatch.setattr(
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"fractal_tasks_core.tasks.cellpose_segmentation.cellpose.core.use_gpu",
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patched_cellpose_core_use_gpu,
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)
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monkeypatch.setattr(
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"fractal_tasks_core.tasks.cellpose_segmentation.segment_ROI",
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patched_segment_ROI_overlapping_organoids,
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)
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# Setup caplog fixture, see
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# https://docs.pytest.org/en/stable/how-to/logging.html#caplog-fixture
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caplog.set_level(logging.WARNING)
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# Use pre-made 3D zarr
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zarr_dir = tmp_path / "tmp_out/"
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zarr_urls = prepare_3D_zarr(str(zarr_dir), zenodo_zarr)
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debug(zarr_dir)
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debug(zarr_urls)
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# Per-FOV labeling
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channel = CellposeChannel1InputModel(
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wavelength_id="A01_C01", normalize=CellposeCustomNormalizer()
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)
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for zarr_url in zarr_urls:
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cellpose_segmentation(
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zarr_url=zarr_url,
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channel=channel,
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level=3,
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relabeling=True,
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diameter_level0=80.0,
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output_ROI_table="bbox_table",
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)
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debug(caplog.text)
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assert "bounding-box pairs overlap" in caplog.text
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def test_cellpose_within_masked_bb_with_overlap(
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tmp_path: Path,
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zenodo_zarr: list[str],

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