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fix: add function to handle out of bounds coordinates for a RegionBox…
… in an image (#221) This works the same way as `_adjust_negative_coordinates`, but requires the image as an addition input and modifies the RegionBox object directly. A message is logged in the debugger if a dimension is adjusted. I also updated the `crop_image` function to call this before applying the crop.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,200 +1,139 @@ | ||
| import pytest | ||
| import SimpleITK as sitk | ||
| from rich import print as rprint | ||
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| from imgtools.coretypes import BoxPadMethod, Coordinate3D, RegionBox, Size3D | ||
| import SimpleITK as sitk | ||
| from imgtools.coretypes import RegionBox, Coordinate3D, Size3D, BoxPadMethod | ||
| from imgtools.coretypes.box import BoundingBoxOutsideImageError | ||
| from imgtools.datasets import example_data | ||
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| # Simple tests | ||
| def test_regionbox_initialization() -> None: | ||
| def test_regionbox_initialization(): | ||
| min_coord = Coordinate3D(0, 0, 0) | ||
| max_coord = Coordinate3D(10, 10, 10) | ||
| box = RegionBox(min_coord, max_coord) | ||
| assert box.min == min_coord | ||
| assert box.max == max_coord | ||
| assert box.size == Size3D(10, 10, 10) | ||
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| def test_regionbox_invalid_initialization() -> None: | ||
| def test_regionbox_invalid_initialization(): | ||
| min_coord = Coordinate3D(10, 10, 10) | ||
| max_coord = Coordinate3D(0, 0, 0) | ||
| with pytest.raises(ValueError): | ||
| RegionBox(min_coord, max_coord) | ||
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| def test_regionbox_from_tuple() -> None: | ||
| def test_regionbox_from_tuple(): | ||
| box = RegionBox.from_tuple((0, 0, 0), (10, 10, 10)) | ||
| assert box.min == Coordinate3D(0, 0, 0) | ||
| assert box.max == Coordinate3D(10, 10, 10) | ||
| assert box.size == Size3D(10, 10, 10) | ||
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| def test_regionbox_pad_symmetric() -> None: | ||
| def test_regionbox_pad_symmetric(): | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| padded_box = box.pad(5) | ||
| assert padded_box.min == Coordinate3D(0, 0, 0) | ||
| assert padded_box.max == Coordinate3D(15, 15, 15) | ||
| assert padded_box.size == Size3D(15, 15, 15) | ||
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| def test_regionbox_pad_end() -> None: | ||
| def test_regionbox_pad_end(): | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| padded_box = box.pad(5, method=BoxPadMethod.END) | ||
| assert padded_box.min == Coordinate3D(5, 5, 5) | ||
| assert padded_box.max == Coordinate3D(15, 15, 15) | ||
| assert padded_box.size == Size3D(10, 10, 10) | ||
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| def test_regionbox_expand_to_cube() -> None: | ||
| def test_regionbox_expand_to_cube(): | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| cube_box = box.expand_to_cube(15) | ||
| assert cube_box.size == Size3D(15, 15, 15) | ||
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| def test_regionbox_expand_to_min_size() -> None: | ||
| def test_regionbox_expand_to_min_size(): | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(15, 15, 15)) | ||
| min_size_box = box.expand_to_min_size(20) | ||
| assert min_size_box.size == Size3D(20, 20, 20) | ||
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| def test_regionbox_crop_image() -> None: | ||
| def test_regionbox_crop_image(): | ||
| image = sitk.Image(100, 100, 100, sitk.sitkInt16) | ||
| box = RegionBox(Coordinate3D(10, 10, 10), Coordinate3D(20, 20, 20)) | ||
| cropped_image = box.crop_image(image) | ||
| assert cropped_image.GetSize() == (10, 10, 10) | ||
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| def test_regionbox_crop_image_outside() -> None: | ||
| def test_regionbox_crop_image_outside(): | ||
| image = sitk.Image(100, 100, 100, sitk.sitkInt16) | ||
| box = RegionBox(Coordinate3D(90, 90, 90), Coordinate3D(110, 110, 110)) | ||
| cropped = box.crop_image(image) | ||
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| assert cropped.GetSize() == (20, 20, 20) | ||
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| def test_regionbox_crop_image_and_mask() -> None: | ||
| def test_regionbox_crop_image_and_mask(): | ||
| image = sitk.Image(100, 100, 100, sitk.sitkInt16) | ||
| mask = sitk.Image(100, 100, 100, sitk.sitkUInt8) | ||
| box = RegionBox(Coordinate3D(10, 10, 10), Coordinate3D(20, 20, 20)) | ||
| cropped_image, cropped_mask = box.crop_image_and_mask(image, mask) | ||
| assert cropped_image.GetSize() == (10, 10, 10) | ||
| assert cropped_mask.GetSize() == (10, 10, 10) | ||
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| # Edge cases | ||
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| def test_regionbox_from_centroid_odd_cube(): | ||
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| def test_regionbox_from_centroid_odd_cube() -> None: | ||
| mask = example_data()["mask"] | ||
| mask = example_data()['mask'] | ||
| bbox = RegionBox.from_mask_centroid(mask, 1, 5) | ||
| expected = RegionBox(Coordinate3D(47, 26, 73), Coordinate3D(52, 31, 78)) | ||
| expected = RegionBox( | ||
| Coordinate3D(47, 26, 73), | ||
| Coordinate3D(52, 31, 78) | ||
| ) | ||
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| assert bbox.min == expected.min | ||
| assert bbox.max == expected.max | ||
| assert bbox.size == expected.size | ||
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| def test_bbox_cubed() -> None: | ||
| region = RegionBox(Coordinate3D(12, 13, 14), Coordinate3D(21, 23, 25)) | ||
| def test_bbox_cubed()->None: | ||
| mask = example_data()['mask'] | ||
| region = RegionBox( | ||
| Coordinate3D(12, 13, 14), | ||
| Coordinate3D(21, 23, 25) | ||
| ) | ||
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| expanded_region = region.expand_to_cube(13) | ||
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| expected = RegionBox(Coordinate3D(10, 11, 13), Coordinate3D(23, 24, 26)) | ||
| expected = RegionBox( | ||
| Coordinate3D(10, 11, 13), | ||
| Coordinate3D(23, 24, 26) | ||
| ) | ||
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| assert expanded_region.min == expected.min | ||
| assert expanded_region.max == expected.max | ||
| assert expanded_region.size == expected.size | ||
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| def test_adjust_max() -> None: | ||
| region = RegionBox(Coordinate3D(12, 13, 14), Coordinate3D(21, 23, 25)) | ||
| def test_adjust_max()->None: | ||
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| # save a copy to compare size after | ||
| region = RegionBox( | ||
| Coordinate3D(12, 13, 14), | ||
| Coordinate3D(21, 23, 25) | ||
| ) | ||
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| #save a copy to compare size after | ||
| region_copy = region.copy() | ||
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| image = sitk.Image(20, 20, 20, sitk.sitkInt16) | ||
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| region.check_out_of_bounds_coordinates(image=image) | ||
| region.check_out_of_bounds_coordinates( | ||
| image=image | ||
| ) | ||
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| assert region.size == region_copy.size | ||
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| expected_min = Coordinate3D(11, 10, 9) | ||
| expected_max = Coordinate3D(20, 20, 20) | ||
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| assert region.min == expected_min | ||
| assert region.max == expected_max | ||
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| def test_expand_cube_smaller_size() -> None: | ||
| region = RegionBox(Coordinate3D(12, 13, 14), Coordinate3D(200, 23, 25)) | ||
| with pytest.raises(ValueError): | ||
| _ = region.expand_to_cube(10) | ||
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| def test_regionbox_from_mask_bbox() -> None: | ||
| mask = example_data()["mask"] | ||
| bbox = RegionBox.from_mask_bbox(mask) | ||
| expected = RegionBox(Coordinate3D(45, 21, 67), Coordinate3D(55, 38, 84)) | ||
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| assert bbox.min == expected.min | ||
| assert bbox.max == expected.max | ||
| assert bbox.size == expected.size | ||
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| def test_regionbox_expand_to_min_size_no_change() -> None: | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(15, 15, 15)) | ||
| min_size_box = box.expand_to_min_size(5) | ||
| assert min_size_box.size == Size3D(10, 10, 10) | ||
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| def test_regionbox_expand_to_cube_no_change() -> None: | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(15, 15, 15)) | ||
| cube_box = box.expand_to_cube(10) | ||
| assert cube_box.size == Size3D(10, 10, 10) | ||
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| def test_regionbox_pad_no_change() -> None: | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| padded_box = box.pad(0) | ||
| assert padded_box.min == Coordinate3D(5, 5, 5) | ||
| assert padded_box.max == Coordinate3D(10, 10, 10) | ||
| assert padded_box.size == Size3D(5, 5, 5) | ||
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| def test_regionbox_repr() -> None: | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| repr_str = repr(box) | ||
| expected_str = ( | ||
| "RegionBox(\n" | ||
| "\tmin=Coordinate3D(x=5, y=5, z=5),\n" | ||
| "\tmax=Coordinate3D(x=10, y=10, z=10)\n" | ||
| "\tsize=Size3D(w=5, h=5, d=5)\n" | ||
| ")" | ||
| def test_expand_cube_smaller_size()->None: | ||
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| region = RegionBox( | ||
| Coordinate3D(12, 13, 14), | ||
| Coordinate3D(200, 23, 25) | ||
| ) | ||
| assert repr_str == expected_str | ||
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| def test_regionbox_copy() -> None: | ||
| box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10)) | ||
| box_copy = box.copy() | ||
| assert box_copy.min == box.min | ||
| assert box_copy.max == box.max | ||
| assert box_copy.size == box.size | ||
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| def test_regionbox_adjust_negative_coordinates() -> None: | ||
| min_coord = Coordinate3D(-5, -5, -5) | ||
| max_coord = Coordinate3D(10, 10, 10) | ||
| RegionBox._adjust_negative_coordinates(min_coord, max_coord) | ||
| assert min_coord == Coordinate3D(0, 0, 0) | ||
| assert max_coord == Coordinate3D(15, 15, 15) | ||
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| def test_regionbox_check_out_of_bounds_coordinates() -> None: | ||
| image = sitk.Image(20, 20, 20, sitk.sitkInt16) | ||
| region = RegionBox(Coordinate3D(12, 13, 14), Coordinate3D(21, 23, 25)) | ||
| region.check_out_of_bounds_coordinates(image) | ||
| assert region.min == Coordinate3D(11, 10, 9) | ||
| assert region.max == Coordinate3D(20, 20, 20) | ||
| with pytest.raises(ValueError): | ||
| expanded_region = region.expand_to_cube(10) |