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173 | # -*- 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.utils.args import assert_dirs_empty
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)
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")
assert_dirs_empty(parser, args, out_dir)
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()
|