def read_data(self):
vector_image_sitk = sitkh.read_sitk_vector_image(self._path_to_image,
dtype=np.float64)
if self._path_to_image_mask is not None:
vector_image_sitk_mask = sitkh.read_sitk_vector_image(
self._path_to_image_mask,
dtype=np.uint8,
)
N_components = vector_image_sitk.GetNumberOfComponentsPerPixel()
self._stacks = [None] * N_components
filename_base = os.path.basename(self._path_to_image).split(".")[0]
for i in range(N_components):
image_sitk = sitk.VectorIndexSelectionCast(vector_image_sitk, i)
if self._path_to_image_mask is not None:
image_sitk_mask = sitk.VectorIndexSelectionCast(
vector_image_sitk_mask, i)
else:
image_sitk_mask = None
if self._slice_thickness is None:
slice_thickness = image_sitk.GetSpacing()[-1]
else:
slice_thickness = self._slice_thickness
filename = filename_base + "_" + str(i)
self._stacks[i] = st.Stack.from_sitk_image(
image_sitk=image_sitk,
filename=filename,
image_sitk_mask=image_sitk_mask,
slice_thickness=float(slice_thickness),
)
if self._dir_motion_correction is not None:
motion_updater = mu.MotionUpdater(
stacks=self._stacks,
dir_motion_correction=self._dir_motion_correction,
volume_motion_only=self._volume_motion_only,
)
motion_updater.run()
self._stacks = motion_updater.get_data()
def read_data(self):
self._check_input()
self._stacks = [None] * len(self._file_paths)
for i, file_path in enumerate(self._file_paths):
if self._file_paths_masks is None:
file_path_mask = self._get_path_to_potential_mask(file_path)
else:
if i < len(self._file_paths_masks):
file_path_mask = self._file_paths_masks[i]
else:
file_path_mask = None
self._stacks[i] = st.Stack.from_filename(
file_path,
file_path_mask,
slice_thickness=self._stacks_slice_thicknesses[i],
extract_slices=self._extract_slices,
)
# if given image is actually a mask, update the filename so that
# subsequent MotionUpdater can associate the slice transformation
# files
if file_path == file_path_mask:
filename = self._stacks[i].get_filename()
filename = re.sub(self._suffix_mask, "", filename)
self._stacks[i].set_filename(filename)
if self._dir_motion_correction is not None:
motion_updater = mu.MotionUpdater(
stacks=self._stacks,
dir_motion_correction=self._dir_motion_correction)
motion_updater.run()
self._stacks = motion_updater.get_data()