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Module dcm2bids.cli.dcm2bids_helper⚓︎

Converts DICOM files to NIfTI files including their JSON sidecars in a

temporary directory which can be inspected to make a dc2mbids config file.

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

"""

Converts DICOM files to NIfTI files including their JSON sidecars in a

temporary directory which can be inspected to make a dc2mbids config file.

"""

import argparse

import logging

import platform

import sys

import os

from pathlib import Path

from datetime import datetime

from dcm2bids.dcm2niix_gen import Dcm2niixGen

from dcm2bids.utils.utils import DEFAULT

from dcm2bids.utils.tools import dcm2niix_version, check_latest

from dcm2bids.utils.logger import setup_logging

from dcm2bids.version import __version__

def _build_arg_parser():

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

                                formatter_class=argparse.RawTextHelpFormatter)

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

                   required=True, nargs="+",

                   help="DICOM directory(ies) or archive(s) (" +

                        DEFAULT.arch_extensions + ").")

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

                   required=False,

                   default=Path(DEFAULT.output_dir) / DEFAULT.tmp_dir_name /

                   DEFAULT.helper_dir,

                   help="Output directory. (Default: [%(default)s]")

    p.add_argument("-n", "--nest",

                   nargs="?", const=True, default=False, required=False,

                   help="Nest a directory in <output_dir>. Useful if many helper "

                        "runs are needed\nto make a config file due to slight "

                        "variations in MRI acquisitions.\n"

                        "Defaults to DICOM_DIR if no name is provided.\n"

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

    p.add_argument('--force', '--force_dcm2bids',

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

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

    p.add_argument("-l", "--log_level",

                   required=False,

                   default=DEFAULT.cli_log_level,

                   choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],

                   help="Set logging level to the console. [%(default)s]")

    return p

def main():

    """Let's go"""

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_dir = Path(args.output_dir)

    if args.output_dir != parser.get_default('output_dir'):

        out_dir = (Path(args.output_dir)

                   / DEFAULT.tmp_dir_name

                   / DEFAULT.helper_dir)

        log_file = (Path(args.output_dir)

                    / DEFAULT.tmp_dir_name

                    / "log"

                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")

    else:

        log_file = (Path(DEFAULT.output_dir)

                    / DEFAULT.tmp_dir_name

                    / "log"

                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")

    if args.nest:

        if isinstance(args.nest, str):

            log_file = Path(

              str(log_file).replace("helper_",

                                    f"helper_{args.nest.replace(os.path.sep, '-')}_"))

            out_dir = out_dir / args.nest

        else:

            log_file = Path(str(log_file).replace(

              "helper_", f"helper_{args.dicom_dir[0].replace(os.path.sep, '-')}_")

                            )

            out_dir = out_dir / args.dicom_dir[0]

    log_file.parent.mkdir(parents=True, exist_ok=True)

    setup_logging(args.log_level, log_file)

    logger = logging.getLogger(__name__)

    logger.info("--- dcm2bids_helper start ---")

    logger.info("Running the following command: " + " ".join(sys.argv))

    logger.info("OS version: %s", platform.platform())

    logger.info("Python version: %s", sys.version.replace("\n", ""))

    logger.info(f"dcm2bids version: { __version__}")

    logger.info(f"dcm2niix version: {dcm2niix_version()}")

    logger.info("Checking for software update")

    check_latest("dcm2bids")

    check_latest("dcm2niix")

    app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)

    rsl = app.run(force=args.overwrite)

    logger.info(f"Helper files in: {out_dir}\n")

    logger.info(f"Log file saved at {log_file}")

    logger.info("--- dcm2bids_helper end ---")

    return rsl

if __name__ == "__main__":

    main()

Functions⚓︎

main⚓︎

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def main(

)

Let's go

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def main():

    """Let's go"""

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_dir = Path(args.output_dir)

    if args.output_dir != parser.get_default('output_dir'):

        out_dir = (Path(args.output_dir)

                   / DEFAULT.tmp_dir_name

                   / DEFAULT.helper_dir)

        log_file = (Path(args.output_dir)

                    / DEFAULT.tmp_dir_name

                    / "log"

                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")

    else:

        log_file = (Path(DEFAULT.output_dir)

                    / DEFAULT.tmp_dir_name

                    / "log"

                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")

    if args.nest:

        if isinstance(args.nest, str):

            log_file = Path(

              str(log_file).replace("helper_",

                                    f"helper_{args.nest.replace(os.path.sep, '-')}_"))

            out_dir = out_dir / args.nest

        else:

            log_file = Path(str(log_file).replace(

              "helper_", f"helper_{args.dicom_dir[0].replace(os.path.sep, '-')}_")

                            )

            out_dir = out_dir / args.dicom_dir[0]

    log_file.parent.mkdir(parents=True, exist_ok=True)

    setup_logging(args.log_level, log_file)

    logger = logging.getLogger(__name__)

    logger.info("--- dcm2bids_helper start ---")

    logger.info("Running the following command: " + " ".join(sys.argv))

    logger.info("OS version: %s", platform.platform())

    logger.info("Python version: %s", sys.version.replace("\n", ""))

    logger.info(f"dcm2bids version: { __version__}")

    logger.info(f"dcm2niix version: {dcm2niix_version()}")

    logger.info("Checking for software update")

    check_latest("dcm2bids")

    check_latest("dcm2niix")

    app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)

    rsl = app.run(force=args.overwrite)

    logger.info(f"Helper files in: {out_dir}\n")

    logger.info(f"Log file saved at {log_file}")

    logger.info("--- dcm2bids_helper end ---")

    return rsl

Last update: 2024-07-26
Created: 2024-07-26