def from_filename(cls,
file_path,
slice_number,
slice_thickness,
file_path_mask=None,
verbose=False,
):
slice = cls()
if not ph.file_exists(file_path):
raise exceptions.FileNotExistent(file_path)
slice._dir_input = os.path.dirname(file_path)
slice._filename = os.path.basename(file_path).split(".")[0]
slice._slice_number = slice_number
slice._slice_thickness = slice_thickness
# Append stacks as SimpleITK and ITK Image objects
slice.sitk = sitkh.read_nifti_image_sitk(file_path, sitk.sitkFloat64)
slice.itk = sitkh.get_itk_from_sitk_image(slice.sitk)
# Append masks (if provided)
if file_path_mask is None:
slice.sitk_mask = slice._generate_identity_mask()
if verbose:
ph.print_info(
"Identity mask created for '%s'." % (file_path))
else:
if not ph.file_exists(file_path_mask):
raise exceptions.FileNotExistent(file_path_mask)
slice.sitk_mask = sitkh.read_nifti_image_sitk(
file_path_mask, sitk.sitkUInt8)
try:
# ensure mask occupies the same physical space
slice.sitk_mask.CopyInformation(slice.sitk)
except RuntimeError as e:
raise IOError(
"Given image and its mask do not occupy the same space: %s" %
e.message)
slice.itk_mask = sitkh.get_itk_from_sitk_image(slice.sitk_mask)
# Store current affine transform of image
slice._affine_transform_sitk = sitkh.get_sitk_affine_transform_from_sitk_image(
slice.sitk)
# Prepare history of affine transforms, i.e. encoded spatial
# position+orientation of slice, and motion estimates of slice
# obtained in the course of the registration/reconstruction process
slice._history_affine_transforms = []
slice._history_affine_transforms.append(slice._affine_transform_sitk)
slice._history_motion_corrections = []
slice._history_motion_corrections.append(sitk.Euler3DTransform())
return slice
def from_filename(cls,
file_path,
slice_number,
file_path_mask=None,
verbose=False):
slice = cls()
if not ph.file_exists(file_path):
raise exceptions.FileNotExistent(file_path)
slice._dir_input = os.path.dirname(file_path)
slice._filename = os.path.basename(file_path).split(".")[0]
slice._slice_number = slice_number
# Append stacks as SimpleITK and ITK Image objects
slice.sitk = sitk.ReadImage(file_path, sitk.sitkFloat64)
slice.itk = sitkh.get_itk_from_sitk_image(slice.sitk)
# Append masks (if provided)
if file_path_mask is None:
slice.sitk_mask = slice._generate_identity_mask()
if verbose:
ph.print_info("Identity mask created for '%s'." % (file_path))
else:
if not ph.file_exists(file_path_mask):
raise exceptions.FileNotExistent(file_path_mask)
slice.sitk_mask = sitk.ReadImage(file_path_mask, sitk.sitkUInt8)
slice.itk_mask = sitkh.get_itk_from_sitk_image(slice.sitk_mask)
# Store current affine transform of image
slice._affine_transform_sitk = sitkh.get_sitk_affine_transform_from_sitk_image(
slice.sitk)
# Prepare history of affine transforms, i.e. encoded spatial
# position+orientation of slice, and motion estimates of slice
# obtained in the course of the registration/reconstruction process
slice._history_affine_transforms = []
slice._history_affine_transforms.append(slice._affine_transform_sitk)
slice._history_motion_corrections = []
slice._history_motion_corrections.append(sitk.Euler3DTransform())
return slice
def from_filename(
cls,
file_path,
file_path_mask=None,
extract_slices=True,
verbose=False,
slice_thickness=None,
):
stack = cls()
if not ph.file_exists(file_path):
raise exceptions.FileNotExistent(file_path)
path_to_directory = os.path.dirname(file_path)
# Strip extension from filename and remove potentially included "."
filename = [
re.sub("." + ext, "", os.path.basename(file_path))
for ext in ALLOWED_EXTENSIONS if file_path.endswith(ext)
][0]
# filename = filename.replace(".", "p")
stack._dir = os.path.dirname(file_path)
stack._filename = filename
# Append stacks as SimpleITK and ITK Image objects
stack.sitk = sitkh.read_nifti_image_sitk(file_path, sitk.sitkFloat64)
stack.itk = sitkh.get_itk_from_sitk_image(stack.sitk)
# Set slice thickness of acquisition
if slice_thickness is None:
stack._slice_thickness = stack.sitk.GetSpacing()[-1]
else:
stack._slice_thickness = slice_thickness
# Append masks (either provided or binary mask)
if file_path_mask is None:
stack.sitk_mask = stack._generate_identity_mask()
if verbose:
ph.print_info("Identity mask created for '%s'." % (file_path))
else:
if not ph.file_exists(file_path_mask):
raise exceptions.FileNotExistent(file_path_mask)
stack.sitk_mask = sitkh.read_nifti_image_sitk(
file_path_mask, sitk.sitkUInt8)
try:
# ensure masks occupy same physical space
stack.sitk_mask.CopyInformation(stack.sitk)
except RuntimeError as e:
raise IOError(
"Given image and its mask do not occupy the same space: %s"
% e.message)
stack._is_unity_mask = False
# Append itk object
stack.itk_mask = sitkh.get_itk_from_sitk_image(stack.sitk_mask)
# Store current affine transform of image
stack._affine_transform_sitk = sitkh.get_sitk_affine_transform_from_sitk_image(
stack.sitk)
# Prepare history of affine transforms, i.e. encoded spatial
# position+orientation of stack, and motion estimates of stack
# obtained in the course of the registration/reconstruction process
stack._history_affine_transforms = []
stack._history_affine_transforms.append(stack._affine_transform_sitk)
stack._history_motion_corrections = []
stack._history_motion_corrections.append(sitk.Euler3DTransform())
# Extract all slices and their masks from the stack and store them
if extract_slices:
dimenson = stack.sitk.GetDimension()
if dimenson == 3:
stack._N_slices = stack.sitk.GetSize()[-1]
stack._slices = stack._extract_slices(
slice_thickness=stack.get_slice_thickness())
elif dimenson == 2:
stack._N_slices = 1
stack._slices = [stack.sitk[:, :]]
else:
stack._N_slices = 0
stack._slices = None
if verbose:
ph.print_info(
"Stack (image + mask) associated to '%s' successfully read." %
(file_path))
return stack
def from_filename(cls,
file_path,
file_path_mask=None,
extract_slices=True,
verbose=False):
stack = cls()
if not ph.file_exists(file_path):
raise exceptions.FileNotExistent(file_path)
path_to_directory = os.path.dirname(file_path)
# Strip extension from filename and remove potentially included "."
filename = [re.sub("." + ext, "", os.path.basename(file_path))
for ext in ALLOWED_EXTENSIONS
if file_path.endswith(ext)][0]
# filename = filename.replace(".", "p")
stack._dir = os.path.dirname(file_path)
stack._filename = filename
# Append stacks as SimpleITK and ITK Image objects
stack.sitk = sitk.ReadImage(file_path, sitk.sitkFloat64)
stack.itk = sitkh.get_itk_from_sitk_image(stack.sitk)
# Append masks (either provided or binary mask)
if file_path_mask is None:
stack.sitk_mask = stack._generate_identity_mask()
if verbose:
ph.print_info(
"Identity mask created for '%s'." % (file_path))
else:
if not ph.file_exists(file_path_mask):
raise exceptions.FileNotExistent(file_path_mask)
stack.sitk_mask = sitk.ReadImage(file_path_mask, sitk.sitkUInt8)
stack._is_unity_mask = False
# Append itk object
stack.itk_mask = sitkh.get_itk_from_sitk_image(stack.sitk_mask)
# Extract all slices and their masks from the stack and store them
if extract_slices:
dimenson = stack.sitk.GetDimension()
if dimenson == 3:
stack._N_slices = stack.sitk.GetSize()[-1]
stack._slices = stack._extract_slices()
elif dimenson == 2:
stack._N_slices = 1
stack._slices = [stack.sitk[:, :]]
else:
stack._N_slices = 0
stack._slices = None
if verbose:
ph.print_info(
"Stack (image + mask) associated to '%s' successfully read." %
(file_path))
return stack