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303 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
"""
import argparse
import logging
import platform
import sys
import os
from pathlib import Path
from datetime import datetime
from dcm2bids.dcm2bids_gen import Dcm2BidsGen
from dcm2bids.utils.utils import DEFAULT
from dcm2bids.utils.tools import dcm2niix_version, check_latest
from dcm2bids.utils.schema import load_schema
from dcm2bids.participant import Participant
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="Path to one or more directories or archives"
f" ({DEFAULT.arch_extensions}) containing the DICOM files for a"
" single participant and session to be converted to BIDS."
)
p.add_argument("-p", "--participant",
required=True,
help="Participant ID to be used in the BIDS dataset filenames"
" (e.g. sub-<PARTICIPANT>)."
)
p.add_argument("-s", "--session",
required=False,
default=DEFAULT.cli_session,
help="Session ID to be used in the BIDS dataset filenames"
" (e.g. ses-<SESSION>). If not provided, no session"
" entity will be added to the BIDS filenames."
)
p.add_argument("-c", "--config",
required=True,
help="JSON configuration that specifies additional parameters for"
" BIDS conversion. See the documentation for more information:"
f" \nhttps://unfmontreal.github.io/Dcm2Bids/{__version__}/how-to/create-config-file/" # noqa: E501
)
p.add_argument("-o", "--output_dir",
required=False,
default=DEFAULT.output_dir,
help="Output BIDS directory. Defaults to the current working directory."
)
g = p.add_mutually_exclusive_group()
g.add_argument("--auto_extract_entities",
action='store_true',
help="If set, it will automatically try to extract entity "
"information [task, dir, echo] based on the suffix and datatype."
" Default is [%(default)s]")
g.add_argument("--do_not_reorder_entities",
action='store_true',
help="If set, it will not reorder entities according to the relative "
"ordering indicated in the BIDS specification and use the "
"order defined in custom_entities by the user.\n"
"Cannot be used with --auto_extract_entities. "
" Default is [%(default)s]")
p.add_argument("-b", "--bids_version",
default=None,
help=(
"Set the BIDS specification version to follow (e.g. 'v1.11.1', 'stable', 'latest' or 'default')."
"\nThis controls which BIDS schema and rules dcm2bids uses for automatic entity extraction and ordering."
"\nIf not provided, dcm2bids uses the 'default' BIDS spec for reproducible, offline-friendly behavior."
"\nFor long-running or shared pipelines, consider pinning a specific tag (e.g. 'v1.11.1')."
"\nWhen internet is available, it will check once whether the remote 'stable' is newer and, if so, \n"
"suggest updating to that specific version tag."
),
)
p.add_argument("--bids_validate",
action='store_true',
help="If set, once your conversion is done it "
"will check if your output folder is BIDS valid. [%(default)s]"
"\nbids-validator needs to be installed check: "
f"{DEFAULT.link_bids_validator}")
p.add_argument("--force_dcm2bids",
action="store_true",
help="Overwrite previous temporary dcm2bids "
"output if it exists.")
p.add_argument("--skip_dcm2niix",
action="store_true",
help="Skip dcm2niix conversion. "
"Option -d should contains NIFTI and json files.")
p.add_argument("--clobber",
action="store_true",
help="Overwrite output if it exists.")
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."
" The default level is [%(default)s]"
)
p.add_argument("-v", "--version",
action="version",
# This uses version.__BIDSversion__, which reflects the bundled schema version.
version=(
f"dcm2bids version:\t{__version__}\n"
f"default BIDS version:\t{DEFAULT.bids_version} "
"unless overridden by --bids_version."
),
help="Report dcm2bids version and the default BIDS specification version it follows by default."
)
return p
def main():
parser = _build_arg_parser()
args = parser.parse_args()
participant = Participant(args.participant, args.session)
log_dir = Path(args.output_dir) / DEFAULT.tmp_dir_name / "log"
log_file = (log_dir /
f"{participant.prefix}_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
log_dir.mkdir(parents=True, exist_ok=True)
setup_logging(args.log_level, log_file)
logger = logging.getLogger(__name__)
logger.info("--- dcm2bids 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", log_dir=log_dir)
if not args.skip_dcm2niix:
check_latest("dcm2niix", log_dir=log_dir)
schema, derived_entities = load_schema(args.bids_version, log_dir=log_dir)
# Update the DEFAULT based on the requested version directly, otherwise uses default values
if args.bids_version is not None:
DEFAULT.bids_version = schema["bids_version"]
DEFAULT.entityTableKeys = derived_entities.get("entity_table_keys",
DEFAULT.entityTableKeys)
DEFAULT.auto_entities = derived_entities.get("auto_entities",
DEFAULT.auto_entities)
logger.info(f"participant: {participant.name}")
if participant.session:
logger.info(f"session: {participant.session}")
logger.info(f"config: {os.path.realpath(args.config)}")
logger.info(f"BIDS directory: {os.path.realpath(args.output_dir)}")
logger.info(f"Auto extract entities: {args.auto_extract_entities}")
logger.info(f"Reorder entities: {not args.do_not_reorder_entities}")
logger.info(f"Validate BIDS: {args.bids_validate}\n")
app = Dcm2BidsGen(**vars(args)).run()
logger.info(f"Logs saved in {log_file}")
logger.info("--- dcm2bids end ---")
return app
if __name__ == "__main__":
main()
|