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175 | #!/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"),
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()
|