gandlf_constructCSV

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

import os, argparse, sys
from datetime import date
from GANDLF.utils import writeTrainingCSV


def main():
    copyrightMessage = (
        "Contact: software@cbica.upenn.edu\n\n"
        + "This program is NOT FDA/CE approved and NOT intended for clinical use.\nCopyright (c) "
        + str(date.today().year)
        + " University of Pennsylvania. All rights reserved."
    )

    parser = argparse.ArgumentParser(
        prog="GANDLF_ConstructCSV",
        formatter_class=argparse.RawTextHelpFormatter,
        description="Generate training/inference CSV from data directory.\n\n"
        + copyrightMessage,
    )
    parser.add_argument(
        "-i",
        "--inputDir",
        metavar="",
        type=str,
        help="Input data directory which contains images in specified format",
    )
    parser.add_argument(
        "-c",
        "--channelsID",
        metavar="",
        type=str,
        help="Channels/modalities identifier string to check for in all files in 'input_dir'; for example: --channelsID _t1.nii.gz,_t2.nii.gz",
    )
    parser.add_argument(
        "-l",
        "--labelID",
        default=None,
        type=str,
        help="Label/mask identifier string to check for in all files in 'input_dir'; for example: --labelID _seg.nii.gz",
    )
    parser.add_argument(
        "-o",
        "--outputFile",
        metavar="",
        type=str,
        help="Output CSV file",
    )

    args = parser.parse_args()

    # check for required parameters - this is needed here to keep the cli clean
    for param_none_check in [
        args.inputDir,
        args.channelsID,
        args.outputFile,
    ]:
        if param_none_check is None:
            sys.exit("ERROR: Missing required parameter:", param_none_check)

    inputDir = os.path.normpath(args.inputDir)
    outputFile = os.path.normpath(args.outputFile)

    writeTrainingCSV(inputDir, args.channelsID, args.labelID, outputFile)


# main function
if __name__ == "__main__":
    main()