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)