def main():
parser = _buildArgsParser()
args = parser.parse_args()
# Check if the files exist
if not os.path.isfile(args.transformation):
parser.error('"{0}" must be a file!'.format(args.transformation))
if not os.path.isfile(args.ref_file):
parser.error('"{0}" must be a file!'.format(args.ref_file))
if not os.path.isfile(args.in_file):
parser.error('"{0}" must be a file!'.format(args.in_file))
if os.path.isfile(args.out_name) and not args.force_overwrite:
parser.error('"{0}" already exists! Use -f to overwrite it.'.format(
args.out_name))
transfo = np.loadtxt(args.transformation)
if args.inverse:
transfo = np.linalg.inv(transfo)
ref_name, ref_extension = split_name_with_nii(args.ref_file)
in_name, in_extension = split_name_with_nii(args.in_file)
if ref_extension not in ['.nii', '.nii.gz']:
parser.error('"{0}" is in an unsupported format.'.format(
args.ref_file))
if in_extension not in ['.nii', '.nii.gz']:
parser.error('"{0}" is in an unsupported format.'.format(args.in_file))
transform_anatomy(transfo, args.ref_file, args.in_file, args.out_name)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_file, args.ref_file])
assert_outputs_exist(parser, args, args.out_file)
transform_anatomy(np.eye(4), args.ref_file, args.in_file,
args.out_file, interp=args.interpolation)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser,
[args.in_file, args.ref_file, args.transformation])
assert_outputs_exists(parser, args, [args.out_name])
transfo = np.loadtxt(args.transformation)
if args.inverse:
transfo = np.linalg.inv(transfo)
_, ref_extension = split_name_with_nii(args.ref_file)
_, in_extension = split_name_with_nii(args.in_file)
if ref_extension not in ['.nii', '.nii.gz']:
parser.error('{} is an unsupported format.'.format(args.in_file))
if in_extension not in ['.nii', '.nii.gz']:
parser.error('{} is an unsupported format.'.format(args.ref_file))
transform_anatomy(transfo, args.ref_file, args.in_file, args.out_name)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_file, args.in_target_file,
args.in_transfo])
assert_outputs_exist(parser, args, args.out_name)
transfo = load_matrix_in_any_format(args.in_transfo)
if args.inverse:
transfo = np.linalg.inv(transfo)
_, ref_extension = split_name_with_nii(args.in_target_file)
_, in_extension = split_name_with_nii(args.in_file)
if ref_extension not in ['.nii', '.nii.gz']:
parser.error('{} is an unsupported format.'.format(args.in_target_file))
if in_extension not in ['.nii', '.nii.gz']:
parser.error('{} is an unsupported format.'.format(args.in_file))
transform_anatomy(transfo, args.in_target_file, args.in_file,
args.out_name, keep_dtype=args.keep_dtype)