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Module dcm2bids.dcm2bids_gen⚓︎

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

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# -*- 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=False,

        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.force_dcm2bids = force_dcm2bids

        self.skip_dcm2niix = skip_dcm2niix

        self.logLevel = log_level

        self.logger = logging.getLogger(__name__)

    @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.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)

        )

        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(f"Validate if {self.output_dir} is BIDS valid.")

                self.logger.info("Use bids-validator version: ")

                run_shell_command(['bids-validator', '-v'])

                run_shell_command(['bids-validator', self.bids_dir])

            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))

                            run_shell_command(cmd.split())

                            continue

            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

Classes⚓︎

Dcm2BidsGen⚓︎

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class Dcm2BidsGen(
    dicom_dir,
    participant,
    config,
    output_dir=PosixPath('/home/runner/work/Dcm2Bids/Dcm2Bids'),
    bids_validate=False,
    auto_extract_entities=False,
    session='',
    clobber=False,
    force_dcm2bids=False,
    skip_dcm2niix=False,
    log_level='WARNING',
    **_
)

Object to handle dcm2bids execution steps

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
force_dcm2bids boolean Forces a cleaning of a previous execution of
dcm2bids
None
log_level str logging level None
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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=False,

        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.force_dcm2bids = force_dcm2bids

        self.skip_dcm2niix = skip_dcm2niix

        self.logLevel = log_level

        self.logger = logging.getLogger(__name__)

    @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.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)

        )

        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(f"Validate if {self.output_dir} is BIDS valid.")

                self.logger.info("Use bids-validator version: ")

                run_shell_command(['bids-validator', '-v'])

                run_shell_command(['bids-validator', self.bids_dir])

            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))

                            run_shell_command(cmd.split())

                            continue

            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

Instance variables⚓︎

1
dicom_dirs

List of DICOMs directories

Methods⚓︎

move⚓︎

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def move(
    self,
    acq,
    idList,
    post_op
)

Move an acquisition to BIDS format

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    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))

                            run_shell_command(cmd.split())

                            continue

            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

run⚓︎

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def run(
    self
)

Run dcm2bids

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    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.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)

        )

        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(f"Validate if {self.output_dir} is BIDS valid.")

                self.logger.info("Use bids-validator version: ")

                run_shell_command(['bids-validator', '-v'])

                run_shell_command(['bids-validator', self.bids_dir])

            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.")

Last update: 2023-10-11
Created: 2023-10-11