def __dilate_mask__(
self,
mask_path: str,
temp_path: str,
dil_rate: float = preferences.mask_dilation_rate,
dil_threshold: float = preferences.mask_dilation_threshold,
):
"""Dilate mask using gaussian blur and write to disk to use with Elastix.
Args:
mask_path (str | MedicalVolume): File path for mask or mask to use to use as
focus points for registration. Mask must be binary.
temp_path (str): Directory path to store temporary data.
dil_rate (`float`, optional): Dilation rate (sigma).
Defaults to ``preferences.mask_dilation_rate``.
dil_threshold (`float`, optional): Threshold to binarize dilated mask.
Must be between [0, 1]. Defaults to ``preferences.mask_dilation_threshold``.
Returns:
str: File path of dilated mask.
Raises:
FileNotFoundError: If `mask_path` not valid file.
ValueError: If `dil_threshold` not in range [0, 1].
"""
if dil_threshold < 0 or dil_threshold > 1:
raise ValueError("'dil_threshold' must be in range [0, 1]")
if isinstance(mask_path, MedicalVolume):
mask = mask_path
elif os.path.isfile(mask_path):
mask = fio_utils.generic_load(mask_path, expected_num_volumes=1)
else:
raise FileNotFoundError("File {} not found".format(mask_path))
dilated_mask = (sni.gaussian_filter(np.asarray(mask.volume,
dtype=np.float32),
sigma=dil_rate) > dil_threshold)
fixed_mask = np.asarray(dilated_mask, dtype=np.int8)
fixed_mask_filepath = os.path.join(io_utils.mkdirs(temp_path),
"dilated-mask.nii.gz")
dilated_mask_volume = MedicalVolume(fixed_mask, affine=mask.affine)
dilated_mask_volume.save_volume(fixed_mask_filepath)
return fixed_mask_filepath
def test_4d(self):
vol = np.stack([np.ones((10, 20, 30)), 2 * np.ones((10, 20, 30))],
axis=-1)
mv = MedicalVolume(vol, self._AFFINE)
assert mv.orientation == ("SI", "AP", "LR")
assert mv.shape == (10, 20, 30, 2)
assert np.all(mv[..., 0].volume == 1)
assert np.all(mv[..., 1].volume == 2)
ornt = ("AP", "IS", "RL")
mv2 = mv.reformat(ornt)
assert mv2.orientation == ornt
assert mv2.shape == (20, 10, 30, 2)
mv2 = mv.reformat(ornt).reformat(mv.orientation)
assert mv2.is_identical(mv)
fp = os.path.join(self._TEMP_PATH, "test_4d.nii.gz")
mv.save_volume(fp)
mv2 = NiftiReader().load(fp)
assert mv2.is_identical(mv)