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Module dcm2bids.dcm2niix_gen⚓︎

Dcm2niix class

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# -*- coding: utf-8 -*-

"""Dcm2niix class"""

import logging

import os

import shlex

import shutil

import tarfile

import zipfile

from glob import glob

from dcm2bids.utils.io import valid_path

from dcm2bids.utils.utils import DEFAULT, run_shell_command

class Dcm2niixGen(object):

    """ Object to handle dcm2niix execution

    Args:

        dicom_dirs (list): A list of folder with dicoms to convert

        bids_dir (str): A path to the root BIDS directory

        participant: Optional Participant object

        skip_dcm2niix: Optional if input only NIFTI and JSON files

        options (str): Optional arguments for dcm2niix

    Properties:

        sidecars (list): A list of sidecar path created by dcm2niix

    """

    def __init__(

        self,

        dicom_dirs,

        bids_dir,

        participant=None,

        skip_dcm2niix=DEFAULT.skip_dcm2niix,

        options=DEFAULT.dcm2niixOptions,

        helper=False

    ):

        self.logger = logging.getLogger(__name__)

        self.sidecarsFiles = []

        self.dicom_dirs = dicom_dirs

        self.bids_dir = bids_dir

        self.participant = participant

        self.skip_dcm2niix = skip_dcm2niix

        self.options = options

        self.helper = helper

        self.rm_tmp_dir = False

    @property

    def output_dir(self):

        """

        Returns:

            A directory to save all the output files of dcm2niix

        """

        tmpDir = self.participant.prefix if self.participant else DEFAULT.helper_dir

        tmpDir = self.bids_dir / DEFAULT.tmp_dir_name / tmpDir

        if self.helper:

            tmpDir = self.bids_dir

        return tmpDir

    def run(self, force=False):

        """ Run dcm2niix if necessary

        Args:

            force (boolean): Forces a cleaning of a previous execution of

                             dcm2niix

        Sets:

            sidecarsFiles (list): A list of sidecar path created by dcm2niix

        """

        try:

            oldOutput = os.listdir(self.output_dir) != []

        except Exception:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("'force' argument is set to True")

            self.logger.warning("Cleaning the previous directory and running dcm2bids")

            shutil.rmtree(self.output_dir, ignore_errors=True)

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("Use --force_dcm2bids to rerun dcm2bids\n")

        else:

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        self.sidecarFiles = glob(os.path.join(self.output_dir, "*.json"))

    def execute(self):

        """ Execute dcm2niix for each directory in dicom_dirs

        """

        if not self.skip_dcm2niix:

            for dicomDir in self.dicom_dirs:

                if os.path.isfile(dicomDir):

                    tmp_dcm_name = os.path.join(self.output_dir.parent,

                                                self.output_dir.name + '_tmp')

                    self.rm_tmp_dir = valid_path(tmp_dcm_name, type="folder")

                    if tarfile.is_tarfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with tarfile.open(dicomDir) as archive:

                            archive.extractall(self.rm_tmp_dir)

                    elif zipfile.is_zipfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with zipfile.ZipFile(dicomDir, 'r') as zip_ref:

                            zip_ref.extractall(self.rm_tmp_dir)

                    else:

                        self.logger.error(f"\n{dicomDir} is not a supported file" +

                                          " extension." +

                                          DEFAULT.arch_extensions + " are supported.")

                    dicomDir = self.rm_tmp_dir

                cmd = ['dcm2niix', *shlex.split(self.options),

                       '-o', self.output_dir, dicomDir]

                output = run_shell_command(cmd)

                try:

                    output = output.decode()

                except Exception:

                    pass

                if self.rm_tmp_dir:

                    shutil.rmtree(self.rm_tmp_dir)

                    self.logger.info("Temporary dicom directory removed.")

                if "Warning" in output or "Error" in output:

                    self.logger.info("Log from dcm2niix execution")

                    if "Warning" in output:

                        self.logger.warning(f"{output}")

                    else:

                        self.logger.error(f"{output}")

                else:

                    self.logger.debug(f"\n{output}")

                    self.logger.info("Check log file for dcm2niix output\n")

        else:

            for dicomDir in self.dicom_dirs:

                shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)

                cmd = ['cp', '-r', dicomDir, self.output_dir]

                self.logger.info("Running: %s", " ".join(str(item) for item in cmd))

            self.logger.info("Not running dcm2niix\n")

Classes⚓︎

Dcm2niixGen⚓︎

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class Dcm2niixGen(
    dicom_dirs,
    bids_dir,
    participant=None,
    skip_dcm2niix=False,
    options="-b y -ba y -z y -f '%3s_%f_%p_%t'",
    helper=False
)

Object to handle dcm2niix execution

Attributes⚓︎

Name Type Description Default
dicom_dirs list A list of folder with dicoms to convert None
bids_dir str A path to the root BIDS directory None
participant None Optional Participant object None
skip_dcm2niix None Optional if input only NIFTI and JSON files None
options str Optional arguments for dcm2niix None
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class Dcm2niixGen(object):

    """ Object to handle dcm2niix execution

    Args:

        dicom_dirs (list): A list of folder with dicoms to convert

        bids_dir (str): A path to the root BIDS directory

        participant: Optional Participant object

        skip_dcm2niix: Optional if input only NIFTI and JSON files

        options (str): Optional arguments for dcm2niix

    Properties:

        sidecars (list): A list of sidecar path created by dcm2niix

    """

    def __init__(

        self,

        dicom_dirs,

        bids_dir,

        participant=None,

        skip_dcm2niix=DEFAULT.skip_dcm2niix,

        options=DEFAULT.dcm2niixOptions,

        helper=False

    ):

        self.logger = logging.getLogger(__name__)

        self.sidecarsFiles = []

        self.dicom_dirs = dicom_dirs

        self.bids_dir = bids_dir

        self.participant = participant

        self.skip_dcm2niix = skip_dcm2niix

        self.options = options

        self.helper = helper

        self.rm_tmp_dir = False

    @property

    def output_dir(self):

        """

        Returns:

            A directory to save all the output files of dcm2niix

        """

        tmpDir = self.participant.prefix if self.participant else DEFAULT.helper_dir

        tmpDir = self.bids_dir / DEFAULT.tmp_dir_name / tmpDir

        if self.helper:

            tmpDir = self.bids_dir

        return tmpDir

    def run(self, force=False):

        """ Run dcm2niix if necessary

        Args:

            force (boolean): Forces a cleaning of a previous execution of

                             dcm2niix

        Sets:

            sidecarsFiles (list): A list of sidecar path created by dcm2niix

        """

        try:

            oldOutput = os.listdir(self.output_dir) != []

        except Exception:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("'force' argument is set to True")

            self.logger.warning("Cleaning the previous directory and running dcm2bids")

            shutil.rmtree(self.output_dir, ignore_errors=True)

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("Use --force_dcm2bids to rerun dcm2bids\n")

        else:

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        self.sidecarFiles = glob(os.path.join(self.output_dir, "*.json"))

    def execute(self):

        """ Execute dcm2niix for each directory in dicom_dirs

        """

        if not self.skip_dcm2niix:

            for dicomDir in self.dicom_dirs:

                if os.path.isfile(dicomDir):

                    tmp_dcm_name = os.path.join(self.output_dir.parent,

                                                self.output_dir.name + '_tmp')

                    self.rm_tmp_dir = valid_path(tmp_dcm_name, type="folder")

                    if tarfile.is_tarfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with tarfile.open(dicomDir) as archive:

                            archive.extractall(self.rm_tmp_dir)

                    elif zipfile.is_zipfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with zipfile.ZipFile(dicomDir, 'r') as zip_ref:

                            zip_ref.extractall(self.rm_tmp_dir)

                    else:

                        self.logger.error(f"\n{dicomDir} is not a supported file" +

                                          " extension." +

                                          DEFAULT.arch_extensions + " are supported.")

                    dicomDir = self.rm_tmp_dir

                cmd = ['dcm2niix', *shlex.split(self.options),

                       '-o', self.output_dir, dicomDir]

                output = run_shell_command(cmd)

                try:

                    output = output.decode()

                except Exception:

                    pass

                if self.rm_tmp_dir:

                    shutil.rmtree(self.rm_tmp_dir)

                    self.logger.info("Temporary dicom directory removed.")

                if "Warning" in output or "Error" in output:

                    self.logger.info("Log from dcm2niix execution")

                    if "Warning" in output:

                        self.logger.warning(f"{output}")

                    else:

                        self.logger.error(f"{output}")

                else:

                    self.logger.debug(f"\n{output}")

                    self.logger.info("Check log file for dcm2niix output\n")

        else:

            for dicomDir in self.dicom_dirs:

                shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)

                cmd = ['cp', '-r', dicomDir, self.output_dir]

                self.logger.info("Running: %s", " ".join(str(item) for item in cmd))

            self.logger.info("Not running dcm2niix\n")

Instance variables⚓︎

1
output_dir

Methods⚓︎

execute⚓︎

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def execute(
    self
)

Execute dcm2niix for each directory in dicom_dirs

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    def execute(self):

        """ Execute dcm2niix for each directory in dicom_dirs

        """

        if not self.skip_dcm2niix:

            for dicomDir in self.dicom_dirs:

                if os.path.isfile(dicomDir):

                    tmp_dcm_name = os.path.join(self.output_dir.parent,

                                                self.output_dir.name + '_tmp')

                    self.rm_tmp_dir = valid_path(tmp_dcm_name, type="folder")

                    if tarfile.is_tarfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with tarfile.open(dicomDir) as archive:

                            archive.extractall(self.rm_tmp_dir)

                    elif zipfile.is_zipfile(dicomDir):

                        self.logger.info(f"Extracting archive {dicomDir} to temporary "

                                         f"dicom directory {self.rm_tmp_dir}.")

                        with zipfile.ZipFile(dicomDir, 'r') as zip_ref:

                            zip_ref.extractall(self.rm_tmp_dir)

                    else:

                        self.logger.error(f"\n{dicomDir} is not a supported file" +

                                          " extension." +

                                          DEFAULT.arch_extensions + " are supported.")

                    dicomDir = self.rm_tmp_dir

                cmd = ['dcm2niix', *shlex.split(self.options),

                       '-o', self.output_dir, dicomDir]

                output = run_shell_command(cmd)

                try:

                    output = output.decode()

                except Exception:

                    pass

                if self.rm_tmp_dir:

                    shutil.rmtree(self.rm_tmp_dir)

                    self.logger.info("Temporary dicom directory removed.")

                if "Warning" in output or "Error" in output:

                    self.logger.info("Log from dcm2niix execution")

                    if "Warning" in output:

                        self.logger.warning(f"{output}")

                    else:

                        self.logger.error(f"{output}")

                else:

                    self.logger.debug(f"\n{output}")

                    self.logger.info("Check log file for dcm2niix output\n")

        else:

            for dicomDir in self.dicom_dirs:

                shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)

                cmd = ['cp', '-r', dicomDir, self.output_dir]

                self.logger.info("Running: %s", " ".join(str(item) for item in cmd))

            self.logger.info("Not running dcm2niix\n")

run⚓︎

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def run(
    self,
    force=False
)

Run dcm2niix if necessary

Parameters:

Name Type Description Default
force boolean Forces a cleaning of a previous execution of
dcm2niix		 None
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    def run(self, force=False):

        """ Run dcm2niix if necessary

        Args:

            force (boolean): Forces a cleaning of a previous execution of

                             dcm2niix

        Sets:

            sidecarsFiles (list): A list of sidecar path created by dcm2niix

        """

        try:

            oldOutput = os.listdir(self.output_dir) != []

        except Exception:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("'force' argument is set to True")

            self.logger.warning("Cleaning the previous directory and running dcm2bids")

            shutil.rmtree(self.output_dir, ignore_errors=True)

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2bids temporary directory output found:")

            self.logger.warning(self.output_dir)

            self.logger.warning("Use --force_dcm2bids to rerun dcm2bids\n")

        else:

            if not os.path.exists(self.output_dir):

                os.makedirs(self.output_dir)

            self.execute()

        self.sidecarFiles = glob(os.path.join(self.output_dir, "*.json"))
Last update: 2024-07-26
Created: 2024-07-26