import argparse import csv import sys from freesurfer_surface import Annotation, Surface def annotation_labels(): """ List Labels Stored in Freesurfer's Annotation File (i.e., label/lh.aparc.annot) """ argparser = argparse.ArgumentParser( description=annotation_labels.__doc__.strip()) argparser.add_argument('--delimiter', default='\t', help='default: %(default)r') argparser.add_argument('annotation_file_path') args = argparser.parse_args() annotation = Annotation.read(args.annotation_file_path) csv_writer = csv.writer(sys.stdout, delimiter=args.delimiter) csv_writer.writerow(('index', 'color', 'name')) labels = sorted(annotation.labels.values(), key=lambda l: l.index) csv_writer.writerows((l.index, l.hex_color_code, l.name,) for l in labels) def unite_surfaces(): """ Unite Multiple Surfaces in Freesurfer's TriangularSurface Format Into a Single TriangularSurface File (i.e., lh.pial, lh.white) """ argparser = argparse.ArgumentParser( description=unite_surfaces.__doc__.strip()) argparser.add_argument('--output', metavar='OUTPUT_PATH', dest='output_path', required=True) argparser.add_argument('input_paths', metavar='INPUT_PATH', nargs='+') args = argparser.parse_args() union = Surface.unite(Surface.read_triangular(p) for p in args.input_paths) union.write_triangular(args.output_path)