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Module dcm2bids.cli.dcm2bids_scaffold⚓︎

Create basic BIDS files and directories.

Based on the material provided by https://github.com/bids-standard/bids-starter-kit

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#!/usr/bin/env python3

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

"""

    Create basic BIDS files and directories.

    Based on the material provided by

    https://github.com/bids-standard/bids-starter-kit

"""

import argparse

import datetime

import logging

import os

import sys

import platform

from os.path import join as opj

from dcm2bids.utils.io import write_txt

from pathlib import Path

from dcm2bids.utils.args import add_overwrite_arg, assert_dirs_empty

from dcm2bids.utils.utils import DEFAULT, run_shell_command, TreePrinter

from dcm2bids.utils.tools import check_latest

from dcm2bids.utils.scaffold import bids_starter_kit

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("-o", "--output_dir",

                   required=False,

                   default=DEFAULT.output_dir,

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

    add_overwrite_arg(p)

    return p

def main():

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_dir = Path(args.output_dir)

    log_file = (out_dir

                / DEFAULT.tmp_dir_name

                / "log"

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

    assert_dirs_empty(parser, args, args.output_dir)

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

    for _ in ["code", "derivatives", "sourcedata"]:

        os.makedirs(opj(args.output_dir, _), exist_ok=True)

    setup_logging("INFO", log_file)

    logger = logging.getLogger(__name__)

    logger.info("--- dcm2bids_scaffold 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("Checking for software update")

    check_latest("dcm2bids")

    logger.info("The files used to create your BIDS directory were taken from "

                "https://github.com/bids-standard/bids-starter-kit. \n")

    # CHANGES

    write_txt(opj(args.output_dir, "CHANGES"),

              bids_starter_kit.CHANGES.replace('DATE',

                                               datetime.date.today().strftime(

                                                 "%Y-%m-%d")

                                               )

              )

    # dataset_description

    write_txt(opj(args.output_dir, "dataset_description.json"),

              bids_starter_kit.dataset_description.replace("BIDS_VERSION",

                                                           DEFAULT.bids_version))

    # participants.json

    write_txt(opj(args.output_dir, "participants.json"),

              bids_starter_kit.participants_json)

    # participants.tsv

    write_txt(opj(args.output_dir, "participants.tsv"),

              bids_starter_kit.participants_tsv)

    # .bidsignore

    write_txt(opj(args.output_dir, ".bidsignore"),

              "tmp_dcm2bids")

    # README

    try:

        run_shell_command(['wget', '-q', '-O', opj(args.output_dir, "README"),

                           'https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD'],

                          log=False)

    except Exception:

        write_txt(opj(args.output_dir, "README"),

                  bids_starter_kit.README)

    # output tree representation of where the scaffold was built.

    TreePrinter(args.output_dir).print_tree()

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

    logger.info("--- dcm2bids_scaffold end ---")

if __name__ == "__main__":

    main()

Functions⚓︎

main⚓︎

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def main(

)
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def main():

    parser = _build_arg_parser()

    args = parser.parse_args()

    out_dir = Path(args.output_dir)

    log_file = (out_dir

                / DEFAULT.tmp_dir_name

                / "log"

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

    assert_dirs_empty(parser, args, args.output_dir)

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

    for _ in ["code", "derivatives", "sourcedata"]:

        os.makedirs(opj(args.output_dir, _), exist_ok=True)

    setup_logging("INFO", log_file)

    logger = logging.getLogger(__name__)

    logger.info("--- dcm2bids_scaffold 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("Checking for software update")

    check_latest("dcm2bids")

    logger.info("The files used to create your BIDS directory were taken from "

                "https://github.com/bids-standard/bids-starter-kit. \n")

    # CHANGES

    write_txt(opj(args.output_dir, "CHANGES"),

              bids_starter_kit.CHANGES.replace('DATE',

                                               datetime.date.today().strftime(

                                                 "%Y-%m-%d")

                                               )

              )

    # dataset_description

    write_txt(opj(args.output_dir, "dataset_description.json"),

              bids_starter_kit.dataset_description.replace("BIDS_VERSION",

                                                           DEFAULT.bids_version))

    # participants.json

    write_txt(opj(args.output_dir, "participants.json"),

              bids_starter_kit.participants_json)

    # participants.tsv

    write_txt(opj(args.output_dir, "participants.tsv"),

              bids_starter_kit.participants_tsv)

    # .bidsignore

    write_txt(opj(args.output_dir, ".bidsignore"),

              "tmp_dcm2bids")

    # README

    try:

        run_shell_command(['wget', '-q', '-O', opj(args.output_dir, "README"),

                           'https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD'],

                          log=False)

    except Exception:

        write_txt(opj(args.output_dir, "README"),

                  bids_starter_kit.README)

    # output tree representation of where the scaffold was built.

    TreePrinter(args.output_dir).print_tree()

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

    logger.info("--- dcm2bids_scaffold end ---")

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