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Module dcm2bids.dcm2bids⚓︎

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

None

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# -*- 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())

Functions⚓︎

main⚓︎

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def main(

)

Let's go

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def main():

    """Let's go"""

    parser = _build_arg_parser()

    args = parser.parse_args()

    app = Dcm2bids(**vars(args))

    return app.run()

Classes⚓︎

Dcm2bids⚓︎

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class Dcm2bids(
    dicom_dir,
    participant,
    config,
    output_dir=PosixPath('/home/runner/work/Dcm2Bids/Dcm2Bids'),
    session='',
    clobber=False,
    forceDcm2niix=False,
    log_level='WARNING',
    **_
)

Attributes⚓︎

Name Type Description Default
dicom_dir str or list A list of folder with dicoms to convert None
participant str Label of your participant None
config path Path to a dcm2bids configuration file None
output_dir path Path to the BIDS base folder None
session str Optional label of a session None
clobber boolean Overwrite file if already in BIDS folder None
forceDcm2niix boolean Forces a cleaning of a previous execution of
dcm2niix None
log_level str logging level None
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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

Instance variables⚓︎

1
dicomDirs

List of DICOMs directories

Methods⚓︎

move⚓︎

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def move(
    self,
    acquisition,
    intendedForList
)

Move an acquisition to BIDS format

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    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

run⚓︎

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def run(
    self
)

Run dcm2bids

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    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)

set_logger⚓︎

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def set_logger(
    self
)

Set a basic logger

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    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__)

Last update: 2022-06-17
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