Module dcm2bids.scaffold

scaffold module

View Source

"""scaffold module"""

import sys

import argparse

import datetime

import os

import shutil

import importlib.resources as resources

from typing import Optional

from ..utils import write_txt

def _get_arguments():

    """Load arguments for main"""

    parser = argparse.ArgumentParser(

        formatter_class=argparse.RawDescriptionHelpFormatter,

        description="""

            Create basic BIDS files and directories

            """,

        epilog="""

            Documentation at https://github.com/unfmontreal/Dcm2Bids

            """,

    )

    parser.add_argument(

        "-o",

        "--output_dir",

        required=False,

        default=os.getcwd(),

        help="Output BIDS directory, Default: current directory",

    )

    args = parser.parse_args()

    return args

def scaffold(output_dir_override: Optional[str] = None):

    """scaffold entry point"""

    args = _get_arguments()

    output_dir_ = output_dir_override if output_dir_override is not None else args.output_dir

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

        os.makedirs(os.path.join(output_dir_, _), exist_ok=True)

    for _ in [

        "dataset_description.json",

        "participants.json",

        "participants.tsv",

        "README",

    ]:

        dest = os.path.join(output_dir_, _)

        with resources.path(__name__, _) as src:

            shutil.copyfile(src, dest)

    with resources.path(__name__, "CHANGES") as changes_template:

        with open(changes_template) as _:

            data = _.read().format(datetime.date.today().strftime("%Y-%m-%d"))

        write_txt(

            os.path.join(output_dir_, "CHANGES"),

            data.split("\n")[:-1],

    )

Functions

scaffold

def scaffold(
    output_dir_override: Optional[str] = None
)

scaffold entry point

View Source

def scaffold(output_dir_override: Optional[str] = None):

    """scaffold entry point"""

    args = _get_arguments()

    output_dir_ = output_dir_override if output_dir_override is not None else args.output_dir

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

        os.makedirs(os.path.join(output_dir_, _), exist_ok=True)

    for _ in [

        "dataset_description.json",

        "participants.json",

        "participants.tsv",

        "README",

    ]:

        dest = os.path.join(output_dir_, _)

        with resources.path(__name__, _) as src:

            shutil.copyfile(src, dest)

    with resources.path(__name__, "CHANGES") as changes_template:

        with open(changes_template) as _:

            data = _.read().format(datetime.date.today().strftime("%Y-%m-%d"))

        write_txt(

            os.path.join(output_dir_, "CHANGES"),

            data.split("\n")[:-1],

    )

---

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