def test_load_dicom_image_random(test_output_dirs: OutputFolderForTests,
is_signed: bool, is_monochrome2: bool, bits_stored: int) -> None:
"""
Test loading of 2D Dicom images of type (uint16) and (int16).
"""
array_size = (20, 30)
if not is_signed:
array = np.random.randint(0, 200, size=array_size, dtype='uint16')
else:
array = np.random.randint(-200, 200, size=array_size, dtype='int16')
assert array.shape == array_size
if is_monochrome2:
to_write = array
else:
if not is_signed:
to_write = 2 ** bits_stored - 1 - array
else:
to_write = -1 * array - 1
dcm_file = test_output_dirs.root_dir / "file.dcm"
assert is_dicom_file_path(dcm_file)
write_test_dicom(array=to_write, path=dcm_file)
with mock.patch.object(sitk.ImageFileReader, 'GetMetaData',
new=get_mock_function(is_monochrome2=is_monochrome2, bits_stored=bits_stored)):
image = load_dicom_image(dcm_file)
assert image.ndim == 3 and image.shape == (1,) + array_size
assert np.array_equal(image, array[None, ...])
image_and_segmentation = load_image_in_known_formats(dcm_file, load_segmentation=False)
assert image_and_segmentation.images.ndim == 3 and image_and_segmentation.images.shape == (1,) + array_size
assert np.array_equal(image_and_segmentation.images, array[None, ...])
def test_load_dicom_image_ones(test_output_dirs: TestOutputDirectories,
is_signed: bool, is_monochrome2: bool) -> None:
"""
Test loading of 2D Dicom images filled with binary array of type (uint16) and (int16).
"""
array_size = (20, 30)
if not is_signed:
array = np.ones(array_size, dtype='uint16')
array[::2] = 0
else:
array = -1 * np.ones(array_size, dtype='int16')
array[::2] = 0
assert array.shape == array_size
if is_monochrome2:
to_write = array
else:
if not is_signed:
to_write = np.zeros(array_size, dtype='uint16')
to_write[::2] = 1
else:
to_write = np.zeros(array_size, dtype='int16')
to_write[::2] = -1
dcm_file = Path(test_output_dirs.root_dir) / "file.dcm"
assert is_dicom_file_path(dcm_file)
write_test_dicom(array=to_write, path=dcm_file)
with mock.patch.object(sitk.ImageFileReader,
'GetMetaData',
new=get_mock_function(is_monochrome2=is_monochrome2,
bits_stored=1)):
image = load_dicom_image(dcm_file)
assert image.ndim == 3 and image.shape == (1, ) + array_size
assert np.array_equal(image, array[None, ...])
image_and_segmentation = load_image_in_known_formats(
dcm_file, load_segmentation=False)
assert image_and_segmentation.images.ndim == 3 and image_and_segmentation.images.shape == (
1, ) + array_size
assert np.array_equal(image_and_segmentation.images, array[None, ...])
def __getitem__(self, index: int) -> OptionalIndexInputAndLabel:
"""
:param index: The index of the sample to be fetched
:return: The image and (fake) label tensors
"""
filename = self.filenames[index]
target = self.targets[index] if self.targets is not None else 0
if is_dicom_file_path(str(filename)):
scan_image = load_dicom_image(filename)
# Dicom files have arbitrary pixel intensities, convert to [0,255] range so that PIL can
# read the array into an Image object.
scan_image = (scan_image - scan_image.min()) * 255. / (scan_image.max() - scan_image.min())
# Load as PIL Image in grey-scale (convert("L") step), yields a 1-channel image.
scan_image = Image.fromarray(scan_image).convert("L")
else:
# Load as PIL Image in grey-scale (convert("L") step), yields a 1-channel image with pixel values in range
# [0,1] (float).
scan_image = Image.open(filename).convert("L")
if self.transforms is not None:
scan_image = self.transforms(scan_image)
return scan_image, target
def test_load_dicom_image_ones(test_output_dirs: OutputFolderForTests,
is_signed: bool, is_monochrome2: bool) -> None:
"""
Test loading of 2D Dicom images filled with binary array of type (uint16) and (int16).
"""
array_size = (20, 30)
if not is_signed:
array = np.ones(array_size, dtype='uint16')
array[::2] = 0
else:
array = -1 * np.ones(array_size, dtype='int16')
array[::2] = 0
assert array.shape == array_size
if is_monochrome2:
to_write = array
else:
if not is_signed:
to_write = np.zeros(array_size, dtype='uint16')
to_write[::2] = 1
else:
to_write = np.zeros(array_size, dtype='int16')
to_write[::2] = -1
dcm_file = test_output_dirs.root_dir / "file.dcm"
assert is_dicom_file_path(dcm_file)
write_test_dicom(array=to_write,
path=dcm_file,
is_monochrome2=is_monochrome2,
bits_stored=1)
image = load_dicom_image(dcm_file)
assert image.ndim == 2 and image.shape == array_size
assert np.array_equal(image, array)
image_and_segmentation = load_image_in_known_formats(
dcm_file, load_segmentation=False)
assert image_and_segmentation.images.ndim == 2 and image_and_segmentation.images.shape == array_size
assert np.array_equal(image_and_segmentation.images, array)
def test_load_dicom_image_random_signed(
test_output_dirs: TestOutputDirectories) -> None:
"""
Test loading of 2D Dicom images of type (int16).
"""
array_size = (20, 30)
array = np.random.randint(-200, 200, size=array_size, dtype='int16')
assert array.shape == array_size
dcm_file = Path(test_output_dirs.root_dir) / "file.dcm"
assert is_dicom_file_path(dcm_file)
write_test_dicom(array, dcm_file)
image = load_dicom_image(dcm_file)
assert image.ndim == 3 and image.shape == (1, ) + array_size
assert np.array_equal(image, array[None, ...])
image_and_segmentation = load_image_in_known_formats(
dcm_file, load_segmentation=False)
assert image_and_segmentation.images.ndim == 3 and image_and_segmentation.images.shape == (
1, ) + array_size
assert np.array_equal(image_and_segmentation.images, array[None, ...])
def test_is_dicom_file(input: Tuple[str, bool]) -> None:
file, expected = input
assert is_dicom_file_path(file) == expected
assert is_dicom_file_path(Path(file)) == expected
