freesurfer-surface/freesurfer_surface/__main__.py

# freesurfer-surface - Read and Write Surface Files in Freesurfer’s TriangularSurface Format
#
# Copyright (C) 2020 Fabian Peter Hammerle <fabian@hammerle.me>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.

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)