def generate_deformation_field(args, reg_params):
logging.info("Generating deformation field")
try:
safe_execute_command(
prepare_deformation_field_cmd(args, reg_params),
args.paths.tmp__deformation_log_file_path,
args.paths.tmp__deformation_error_path,
)
except SafeExecuteCommandError as err:
raise TransformationError(
"Generation of deformation field failed ; {}".format(err))
def generate_deformation_field(self, deformation_field_path):
logging.info("Generating deformation field")
try:
safe_execute_command(
self._prepare_deformation_field_cmd(deformation_field_path),
self.paths.deformation_log_file_path,
self.paths.deformation_error_file_path,
)
except SafeExecuteCommandError as err:
raise TransformationError(
"Generation of deformation field failed ; {}".format(err)
)
def safe_transform(transformation_command, log_file_path, error_file_path):
"""
Using a specified niftyreg command, transforms an image, and catches
any logs or errors.
:param str transformation_command: Full niftyreg command
:param log_file_path: Path to save the log file to
:param error_file_path: Path to save the error file to
"""
try:
safe_execute_command(
transformation_command, log_file_path, error_file_path
)
except SafeExecuteCommandError as err:
raise TransformationError("Transformation failed; {}".format(err))
def transform_to_standard_space(self, image_path, destination_path):
"""
Transform an image in sample space to standard space
"""
try:
safe_execute_command(
self._prepare_inverse_registration_cmd(
image_path, destination_path,
),
self.paths.inverse_transform_log_file,
self.paths.inverse_transform_error_file,
)
except SafeExecuteCommandError as err:
raise TransformationError(
"Reverse transformation failed; {}".format(err)
)
def safely_execute_amap_registration(error_file_path, log_file_path, reg_cmd):
print("Running registration")
try:
safe_execute_command(reg_cmd, log_file_path, error_file_path)
except SafeExecuteCommandError as err:
raise TransformationError("ROI registration failed; {}".format(err))