gandlf_constructCSV

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

import os, argparse
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(
        "-inputDir",
        type=str,
        help="Input data directory which contains images in specified format",
        required=True,
    )
    parser.add_argument(
        "-channelsID",
        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",
        required=True,
    )
    parser.add_argument(
        "-labelID",
        type=str,
        help="Label/mask identifier string to check for in all files in 'input_dir'; for example: -labelID _seg.nii.gz",
        required=False,
    )
    parser.add_argument("-outputFile", type=str, help="Output CSV file", required=True)

    args = parser.parse_args()

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

    if not args.labelID:
        args.labelID = ""

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


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