Module dcm2bids.helper

helper module

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# -*- coding: utf-8 -*-

"""helper module"""

import argparse

import os

from pathlib import Path

import sys

from dcm2bids.dcm2niix import Dcm2niix

from dcm2bids.utils import DEFAULT, assert_dirs_empty

def _build_arg_parser():

    p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.EPILOG,

                                formatter_class=argparse.RawTextHelpFormatter)

    p.add_argument("-d", "--dicom_dir",

                   type=Path,

                   required=True, nargs="+",

                   help="DICOM files directory.")

    p.add_argument("-o", "--output_dir",

                   required=False, default=Path.cwd(),

                   type=Path,

                   help="Output BIDS directory. "

                        "(Default: %(default)s)")

    p.add_argument('--force',

                   dest='overwrite', action='store_true',

                   help='Force command to overwrite existing output files.')

    return p

def main():

    """Let's go"""

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_folder = args.output_dir / DEFAULT.tmpDirName / DEFAULT.helperDir

    assert_dirs_empty(parser, args, out_folder)

    app = Dcm2niix(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)

    rsl = app.run()

    print(f"Example in: {out_folder}")

    return rsl

if __name__ == "__main__":

    sys.exit(main())

Functions

main

def main(

)

Let's go

View Source

def main():

    """Let's go"""

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_folder = args.output_dir / DEFAULT.tmpDirName / DEFAULT.helperDir

    assert_dirs_empty(parser, args, out_folder)

    app = Dcm2niix(dicomDirs=args.dicom_dir, bidsDir=args.output_dir)

    rsl = app.run()

    print(f"Example in: {out_folder}")

    return rsl

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Last update: 2023-07-13
Created: 2023-07-13