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375 | # -*- coding: utf-8 -*-
"""
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
"""
import logging
import os
from pathlib import Path
from glob import glob
import shutil
from dcm2bids.dcm2niix_gen import Dcm2niixGen
from dcm2bids.sidecar import Sidecar, SidecarPairing
from dcm2bids.participant import Participant
from dcm2bids.utils.utils import DEFAULT, run_shell_command
from dcm2bids.utils.io import load_json, save_json, valid_path
class Dcm2BidsGen(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
force_dcm2bids (boolean): Forces a cleaning of a previous execution of
dcm2bids
log_level (str): logging level
"""
def __init__(
self,
dicom_dir,
participant,
config,
output_dir=DEFAULT.output_dir,
bids_validate=DEFAULT.bids_validate,
auto_extract_entities=DEFAULT.auto_extract_entities,
do_not_reorder_entities = DEFAULT.do_not_reorder_entities,
session=DEFAULT.session,
clobber=DEFAULT.clobber,
force_dcm2bids=DEFAULT.force_dcm2bids,
skip_dcm2niix=DEFAULT.skip_dcm2niix,
log_level=DEFAULT.logLevel,
**_
):
self._dicom_dirs = []
self.dicom_dirs = dicom_dir
self.bids_dir = valid_path(output_dir, type="folder")
self.config = load_json(valid_path(config, type="file"))
self.participant = Participant(participant, session)
self.clobber = clobber
self.bids_validate = bids_validate
self.auto_extract_entities = auto_extract_entities
self.do_not_reorder_entities = do_not_reorder_entities
self.force_dcm2bids = force_dcm2bids
self.skip_dcm2niix = skip_dcm2niix
self.logLevel = log_level
self.logger = logging.getLogger(__name__)
if self.auto_extract_entities and self.do_not_reorder_entities:
raise ValueError("Auto extract entities is set to True and "
"do not reorder entities is set to True. "
"Please choose only one option.")
@property
def dicom_dirs(self):
"""List of DICOMs directories"""
return self._dicom_dirs
@dicom_dirs.setter
def dicom_dirs(self, value):
dicom_dirs = value if isinstance(value, list) else [value]
valid_dirs = [valid_path(_dir, "folder") for _dir in dicom_dirs]
self._dicom_dirs = valid_dirs
def run(self):
"""Run dcm2bids"""
dcm2niix = Dcm2niixGen(
self.dicom_dirs,
self.bids_dir,
self.participant,
self.skip_dcm2niix,
self.config.get("dcm2niixOptions", DEFAULT.dcm2niixOptions),
)
dcm2niix.run(self.force_dcm2bids)
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("extractors", {}),
self.auto_extract_entities,
self.do_not_reorder_entities,
self.config.get("search_method", DEFAULT.search_method),
self.config.get("case_sensitive", DEFAULT.case_sensitive),
self.config.get("dup_method", DEFAULT.dup_method),
self.config.get("post_op", DEFAULT.post_op),
self.config.get("bids_uri", DEFAULT.bids_uri)
)
parser.build_graph()
parser.build_acquisitions(self.participant)
parser.find_runs()
output_dir = os.path.join(self.bids_dir, self.participant.directory)
if parser.acquisitions:
self.logger.info("Moving acquisitions into BIDS "
f"folder \"{output_dir}\".\n")
else:
self.logger.warning("No pairing was found. "
f"BIDS folder \"{output_dir}\" won't be created. "
"Check your config file.\n".upper())
idList = {}
for acq in parser.acquisitions:
idList = self.move(acq, idList, parser.post_op)
if self.bids_validate:
try:
self.logger.info("BIDS VALIDATION")
bids_version = run_shell_command(['bids-validator', '-v'], False)
self.logger.info(f"Use bids-validator version: {bids_version.decode()[:-1]}")
bids_report = run_shell_command(['bids-validator', self.bids_dir])
self.logger.info("Report from bids-validator")
self.logger.info(bids_report.decode())
except Exception:
self.logger.error("The bids-validator does not seem to work properly. "
"The bids-validator may not be installed on your "
"computer. Please check: "
"https://github.com/bids-standard/bids-validator.")
def move(self, acq, idList, post_op):
"""Move an acquisition to BIDS format"""
for srcFile in sorted(glob(f"{acq.srcRoot}.*"), reverse=True):
ext = Path(srcFile).suffixes
ext = [curr_ext for curr_ext in ext if curr_ext in ['.nii', '.gz',
'.json',
'.bval', '.bvec']]
dstFile = (self.bids_dir / acq.dstRoot).with_suffix("".join(ext))
dstFile.parent.mkdir(parents=True, exist_ok=True)
# checking if destination file exists
if dstFile.exists():
self.logger.info(f"'{dstFile}' already exists")
if self.clobber:
self.logger.info("Overwriting because of --clobber option")
else:
self.logger.info("Use --clobber option to overwrite")
continue
# Populate idList
if '.nii' in ext:
if acq.id in idList:
idList[acq.id].append(os.path.join(acq.participant.name,
acq.dstId + "".join(ext)))
else:
idList[acq.id] = [os.path.join(acq.participant.name,
acq.dstId + "".join(ext))]
for curr_post_op in post_op:
if acq.datatype in curr_post_op['datatype'] or 'any' in curr_post_op['datatype']:
if acq.suffix in curr_post_op['suffix'] or '_any' in curr_post_op['suffix']:
cmd = curr_post_op['cmd'].replace('src_file', str(srcFile))
# If custom entities it means that the user
# wants to have both versions
# before and after post_op
if 'custom_entities' in curr_post_op:
acq.setExtraDstFile(curr_post_op["custom_entities"])
extraDstFile = self.bids_dir / acq.extraDstFile
# Copy json file with this new set of custom entities.
shutil.copy(
str(srcFile).replace("".join(ext), ".json"),
f"{str(extraDstFile)}.json",
)
cmd = cmd.replace('dst_file',
str(extraDstFile) + ''.join(ext))
else:
cmd = cmd.replace('dst_file', str(dstFile))
try:
std_out = run_shell_command(cmd.split())
self.logger.debug(f"Log from: {cmd}")
self.logger.debug(std_out.decode())
self.logger.info("")
continue
except Exception:
self.logger.error(
f"The command post_op: \"{cmd}\" "
"does not seem to work properly. "
"Check if it is installed on your "
"computer.\n")
if ".json" in ext:
data = acq.dstSidecarData(idList)
save_json(dstFile, data)
os.remove(srcFile)
# just move
elif not os.path.exists(dstFile):
os.rename(srcFile, dstFile)
return idList
|