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393 | # -*- coding: utf-8 -*-
"""
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
"""
import argparse
import logging
import os
from pathlib import Path
import platform
import sys
from datetime import datetime
from glob import glob
from dcm2bids.dcm2niix import Dcm2niix
from dcm2bids.logger import setup_logging
from dcm2bids.sidecar import Sidecar, SidecarPairing
from dcm2bids.structure import Participant
from dcm2bids.utils import (DEFAULT, load_json, save_json,
splitext_, run_shell_command, valid_path)
from dcm2bids.version import __version__, check_latest, dcm2niix_version
class Dcm2bids(object):
""" Object to handle dcm2bids execution steps
Args:
dicom_dir (str or list): A list of folder with dicoms to convert
participant (str): Label of your participant
config (path): Path to a dcm2bids configuration file
output_dir (path): Path to the BIDS base folder
session (str): Optional label of a session
clobber (boolean): Overwrite file if already in BIDS folder
forceDcm2niix (boolean): Forces a cleaning of a previous execution of
dcm2niix
log_level (str): logging level
"""
def __init__(
self,
dicom_dir,
participant,
config,
output_dir=DEFAULT.outputDir,
session=DEFAULT.session,
clobber=DEFAULT.clobber,
forceDcm2niix=DEFAULT.forceDcm2niix,
log_level=DEFAULT.logLevel,
**_
):
self._dicomDirs = []
self.dicomDirs = dicom_dir
self.bidsDir = valid_path(output_dir, type="folder")
self.config = load_json(valid_path(config, type="file"))
self.participant = Participant(participant, session)
self.clobber = clobber
self.forceDcm2niix = forceDcm2niix
self.logLevel = log_level
# logging setup
self.set_logger()
self.logger.info("--- dcm2bids start ---")
self.logger.info("OS:version: %s", platform.platform())
self.logger.info("python:version: %s", sys.version.replace("\n", ""))
self.logger.info("dcm2bids:version: %s", __version__)
self.logger.info("dcm2niix:version: %s", dcm2niix_version())
self.logger.info("participant: %s", self.participant.name)
self.logger.info("session: %s", self.participant.session)
self.logger.info("config: %s", os.path.realpath(config))
self.logger.info("BIDS directory: %s", os.path.realpath(output_dir))
@property
def dicomDirs(self):
"""List of DICOMs directories"""
return self._dicomDirs
@dicomDirs.setter
def dicomDirs(self, value):
dicom_dirs = value if isinstance(value, list) else [value]
valid_dirs = [valid_path(_dir, "folder") for _dir in dicom_dirs]
self._dicomDirs = valid_dirs
def set_logger(self):
""" Set a basic logger"""
logDir = self.bidsDir / DEFAULT.tmpDirName / "log"
logFile = logDir / f"{self.participant.prefix}_{datetime.now().isoformat().replace(':', '')}.log"
logDir.mkdir(parents=True, exist_ok=True)
setup_logging(self.logLevel, logFile)
self.logger = logging.getLogger(__name__)
def run(self):
"""Run dcm2bids"""
dcm2niix = Dcm2niix(
self.dicomDirs,
self.bidsDir,
self.participant,
self.config.get("dcm2niixOptions", DEFAULT.dcm2niixOptions),
)
check_latest()
check_latest("dcm2niix")
dcm2niix.run(self.forceDcm2niix)
sidecars = []
for filename in dcm2niix.sidecarFiles:
sidecars.append(
Sidecar(filename, self.config.get("compKeys", DEFAULT.compKeys))
)
sidecars = sorted(sidecars)
parser = SidecarPairing(
sidecars,
self.config["descriptions"],
self.config.get("searchMethod", DEFAULT.searchMethod),
self.config.get("caseSensitive", DEFAULT.caseSensitive)
)
parser.build_graph()
parser.build_acquisitions(self.participant)
parser.find_runs()
self.logger.info("moving acquisitions into BIDS folder")
intendedForList = [[] for i in range(len(parser.descriptions))]
for acq in parser.acquisitions:
acq.setDstFile()
intendedForList = self.move(acq, intendedForList)
def move(self, acquisition, intendedForList):
"""Move an acquisition to BIDS format"""
for srcFile in glob(acquisition.srcRoot + ".*"):
ext = Path(srcFile).suffixes
ext = [curr_ext for curr_ext in ext if curr_ext in ['.nii','.gz',
'.json',
'.bval','.bvec']]
dstFile = (self.bidsDir / acquisition.dstRoot).with_suffix("".join(ext))
dstFile.parent.mkdir(parents = True, exist_ok = True)
# checking if destination file exists
if dstFile.exists():
self.logger.info("'%s' already exists", dstFile)
if self.clobber:
self.logger.info("Overwriting because of --clobber option")
else:
self.logger.info("Use --clobber option to overwrite")
continue
# it's an anat nifti file and the user using a deface script
if (
self.config.get("defaceTpl")
and acquisition.dataType == "func"
and ".nii" in ext
):
try:
os.remove(dstFile)
except FileNotFoundError:
pass
defaceTpl = self.config.get("defaceTpl")
cmd = [w.replace('srcFile', srcFile) for w in defaceTpl]
cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
run_shell_command(cmd)
intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + "".join(ext))
elif ".json" in ext:
data = acquisition.dstSidecarData(self.config["descriptions"],
intendedForList)
save_json(dstFile, data)
os.remove(srcFile)
# just move
else:
os.rename(srcFile, dstFile)
intendedFile = acquisition.dstIntendedFor + ".nii.gz"
if intendedFile not in intendedForList[acquisition.indexSidecar]:
intendedForList[acquisition.indexSidecar].append(intendedFile)
return intendedForList
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument("-d", "--dicom_dir",
type=Path, required=True, nargs="+",
help="DICOM directory(ies).")
p.add_argument("-p", "--participant",
required=True,
help="Participant ID.")
p.add_argument("-s", "--session",
required=False,
default="",
help="Session ID.")
p.add_argument("-c", "--config",
type=Path,
required=True,
help="JSON configuration file (see example/config.json).")
p.add_argument("-o", "--output_dir",
required=False,
type=Path,
default=Path.cwd(),
help="Output BIDS directory. (Default: %(default)s)")
p.add_argument("--forceDcm2niix",
action="store_true",
help="Overwrite previous temporary dcm2niix "
"output if it exists.")
p.add_argument("--clobber",
action="store_true",
help="Overwrite output if it exists.")
p.add_argument("-l", "--log_level",
required=False,
default=DEFAULT.cliLogLevel,
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="Set logging level. [%(default)s]")
return p
def main():
"""Let's go"""
parser = _build_arg_parser()
args = parser.parse_args()
app = Dcm2bids(**vars(args))
return app.run()
if __name__ == "__main__":
sys.exit(main())
|