def test_raises_on_empty_segmentation_after_skipped_missing_segment_declarations(
self, ) -> None:
data = np.full((1, 1, 1), fill_value=4, dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template, skip_missing_segment=True)
with pytest.raises(ValueError, match="No segments found.*"):
writer.write(segmentation, [])
def test_raises_on_invalid_rank(self) -> None:
data = np.zeros((1, 1), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
with pytest.raises(ValueError, match=".*3D.*"):
writer = MultiClassWriter(self.template)
writer.write(segmentation, [])
def test_full_slice_encoding(self) -> None:
data = np.ones((1, 512, 512), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 1
assert ds.Rows == 512
assert ds.Columns == 512
def test_slice_encoding_without_cropping(self) -> None:
data = np.zeros((1, 512, 512), dtype=np.uint8)
data[0, 128:-128, 64:-64] = 1
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template, inplane_cropping=False)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 1
assert ds.Rows == 512
assert ds.Columns == 512
def test_missing_segment(self) -> None:
data = np.zeros((3, 512, 512), dtype=np.uint8)
data[0, 64:128, 64:128] = 1
data[2, -128:-64, -128:-64] = 4
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template, skip_missing_segment=True)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 1
assert len(ds.SegmentSequence) == 1
def test_multi_class_slice_encoding_with_cropping(self) -> None:
data = np.zeros((1, 512, 512), dtype=np.uint8)
data[0, 64:128, 64:128] = 1
data[0, -128:-64, -128:-64] = 2
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template, inplane_cropping=True)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 2
assert ds.Rows == 384
assert ds.Columns == 384
def test_multi_class_encoding(self):
data = np.ones((1, 512, 512), dtype=np.uint8)
data[0, 128:-128, 128:-128] = 2
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
ds = writer.write(segmentation, [])
assert ds.Rows == 512
assert ds.Columns == 512
assert ds.NumberOfFrames == 2
assert ds.PerFrameFunctionalGroupsSequence[0].SegmentIdentificationSequence[0].ReferencedSegmentNumber == 1
assert ds.PerFrameFunctionalGroupsSequence[1].SegmentIdentificationSequence[0].ReferencedSegmentNumber == 2
def test_skip_empty_slices_between_filled_slices(self) -> None:
data = np.zeros((3, 512, 512), dtype=np.uint8)
data[0, 64:128, 64:128] = 1
data[2, -128:-64, -128:-64] = 1
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template,
inplane_cropping=True,
skip_empty_slices=True)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 2
assert ds.Rows == 384
assert ds.Columns == 384
def test_noskip_empty_slices_multi_class(self) -> None:
data = np.zeros((2, 512, 512), dtype=np.uint8)
data[0, 64:128, 64:128] = 1
data[1, -128:-64, -128:-64] = 2
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template,
inplane_cropping=True,
skip_empty_slices=False)
ds = writer.write(segmentation, [])
assert ds.NumberOfFrames == 4
assert ds.Rows == 384
assert ds.Columns == 384
assert ds.pixel_array[0].any() # slice=0, segment=1
assert not ds.pixel_array[1].any() # slice=1, segment=1, only zeros
assert not ds.pixel_array[2].any() # slice=0, segment=2, only zeros
assert ds.pixel_array[3].any() # slice=1, segment=2
def test_frame_of_reference_copied_from_reference_image(self):
data = np.ones((1, 512, 512), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
dummy_dcm = pydicom.dcmread(os.path.join(
os.path.dirname(os.path.dirname(__file__)),
'pydicom_seg',
'externals',
'dcmqi',
'data',
'segmentations',
'ct-3slice',
'01.dcm'
))
ds = writer.write(segmentation, [dummy_dcm])
assert ds.FrameOfReferenceUID == dummy_dcm.FrameOfReferenceUID
def test_frame_of_reference_copied_from_reference_image(self) -> None:
data = np.ones((1, 512, 512), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
dummy_dcm = pydicom.dcmread(
os.path.join(
os.path.dirname(os.path.dirname(__file__)),
"pydicom_seg",
"externals",
"dcmqi",
"data",
"segmentations",
"ct-3slice",
"01.dcm",
))
ds = writer.write(segmentation, [dummy_dcm])
assert ds.FrameOfReferenceUID == dummy_dcm.FrameOfReferenceUID
def test_shared_functional_groups_encoding(self) -> None:
data = np.ones((1, 512, 512), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
segmentation.SetSpacing((0.8, 0.8, 5.0))
segmentation.SetDirection(
(1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0))
writer = MultiClassWriter(self.template)
ds = writer.write(segmentation, [])
sfg = ds.SharedFunctionalGroupsSequence[0]
print(sfg)
assert sfg.PixelMeasuresSequence[0].PixelSpacing[0] == 0.8
assert sfg.PixelMeasuresSequence[0].PixelSpacing[1] == 0.8
assert sfg.PixelMeasuresSequence[0].SliceThickness == 5.0
assert sfg.PixelMeasuresSequence[0].SpacingBetweenSlices == 5.0
assert all([
x == y for x, y in zip(
sfg.PlaneOrientationSequence[0].ImageOrientationPatient,
[1.0, 0.0, 0.0, 0.0, -1.0, 0.0],
)
])
def test_raises_on_missing_segment_declaration(self) -> None:
data = np.full((1, 1, 1), fill_value=4, dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template, skip_missing_segment=False)
with pytest.raises(ValueError, match=".*declaration is missing.*"):
writer.write(segmentation, [])
def test_raises_on_empty_segmentation(self) -> None:
data = np.zeros((1, 1, 1), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
with pytest.raises(ValueError, match=".*not contain any labels"):
writer.write(segmentation, [])
def test_raises_on_invalid_component_count(self) -> None:
data = np.zeros((1, 1, 1, 2), dtype=np.uint8)
segmentation = sitk.GetImageFromArray(data, isVector=True)
writer = MultiClassWriter(self.template)
with pytest.raises(ValueError, match=".*single component per voxel"):
writer.write(segmentation, [])
def test_raises_on_invalid_data_type(self, dtype: np.dtype) -> None:
data = np.zeros((1, 1, 1), dtype=dtype)
segmentation = sitk.GetImageFromArray(data)
writer = MultiClassWriter(self.template)
with pytest.raises(ValueError, match="Unsigned integer data type.*"):
writer.write(segmentation, [])