scil_filter_streamlines_by_length.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
Script to filter streamlines based on their lengths.
"""

import argparse
import json
import logging

from dipy.io.streamline import save_tractogram
import numpy as np

from scilpy.tracking.tools import filter_streamlines_by_length
from scilpy.io.streamlines import load_tractogram_with_reference
from scilpy.io.utils import (add_json_args,
                             add_overwrite_arg,
                             add_reference_arg,
                             add_verbose_arg,
                             assert_inputs_exist,
                             assert_outputs_exist)


def _build_arg_parser():
    p = argparse.ArgumentParser(
        formatter_class=argparse.RawTextHelpFormatter, description=__doc__)

    p.add_argument('in_tractogram',
                   help='Streamlines input file name.')
    p.add_argument('out_tractogram',
                   help='Streamlines output file name.')
    p.add_argument('--minL', default=0., type=float,
                   help='Minimum length of streamlines, in mm. [%(default)s]')
    p.add_argument('--maxL', default=np.inf, type=float,
                   help='Maximum length of streamlines, in mm. [%(default)s]')
    p.add_argument('--no_empty', action='store_true',
                   help='Do not write file if there is no streamline.')
    p.add_argument('--display_counts', action='store_true',
                   help='Print streamline count before and after filtering')

    add_reference_arg(p)
    add_overwrite_arg(p)
    add_verbose_arg(p)
    add_json_args(p)

    return p


def main():

    parser = _build_arg_parser()
    args = parser.parse_args()

    assert_inputs_exist(parser, args.in_tractogram)
    assert_outputs_exist(parser, args, args.out_tractogram)

    if args.verbose:
        logging.basicConfig(level=logging.DEBUG)

    if args.minL == 0 and np.isinf(args.maxL):
        logging.debug("You have not specified minL nor maxL. Output will "
                      "simply be a copy of your input!")

    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)

    new_sft = filter_streamlines_by_length(sft, args.minL, args.maxL)

    if args.display_counts:
        sc_bf = len(sft.streamlines)
        sc_af = len(new_sft.streamlines)
        print(json.dumps({'streamline_count_before_filtering': int(sc_bf),
                         'streamline_count_after_filtering': int(sc_af)},
                         indent=args.indent))

    if len(new_sft.streamlines) == 0:
        if args.no_empty:
            logging.debug("The file {} won't be written "
                          "(0 streamline).".format(args.out_tractogram))

            return

        logging.debug('The file {} contains 0 streamline'.format(
            args.out_tractogram))

    save_tractogram(new_sft, args.out_tractogram)


if __name__ == "__main__":
    main()