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Module dcm2bids.dcm2niix⚓︎

Dcm2niix class

None

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

"""Dcm2niix class"""

import logging

import os

from pathlib import Path

import shlex

import shutil

from glob import glob

from .utils import DEFAULT, run_shell_command

class Dcm2niix(object):

    """ Object to handle dcm2niix execution

    Args:

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

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

        participant: Optional Participant object

        options (str): Optional arguments for dcm2niix

    Properties:

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

    """

    def __init__(

        self, dicomDirs, bidsDir, participant=None, options=DEFAULT.dcm2niixOptions

    ):

        self.logger = logging.getLogger(__name__)

        self.sidecarsFiles = []

        self.dicomDirs = dicomDirs

        self.bidsDir = bidsDir

        self.participant = participant

        self.options = options

    @property

    def outputDir(self):

        """

        Returns:

            A directory to save all the output files of dcm2niix

        """

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

        return self.bidsDir / DEFAULT.tmpDirName / 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.outputDir) != []

        except:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

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

            self.logger.warning("Cleaning the previous directory and running dcm2niix")

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

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

            self.logger.warning("Use --forceDcm2niix to rerun dcm2niix")

        else:

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

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

    def execute(self):

        """ Execute dcm2niix for each directory in dicomDirs

        """

        for dicomDir in self.dicomDirs:

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

                   '-o', self.outputDir, dicomDir]

            output = run_shell_command(cmd)

            try:

                output = output.decode()

            except:

                pass

            self.logger.debug("\n%s", output)

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

Classes⚓︎

Dcm2niix⚓︎

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class Dcm2niix(
    dicomDirs,
    bidsDir,
    participant=None,
    options="-b y -ba y -z y -f '%3s_%f_%p_%t'"
)

Attributes⚓︎

Name Type Description Default
dicomDirs list A list of folder with dicoms to convert None
bidsDir str A path to the root BIDS directory None
participant None Optional Participant object None
options str Optional arguments for dcm2niix
Properties: None
sidecars list A list of sidecar path created by dcm2niix None
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class Dcm2niix(object):

    """ Object to handle dcm2niix execution

    Args:

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

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

        participant: Optional Participant object

        options (str): Optional arguments for dcm2niix

    Properties:

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

    """

    def __init__(

        self, dicomDirs, bidsDir, participant=None, options=DEFAULT.dcm2niixOptions

    ):

        self.logger = logging.getLogger(__name__)

        self.sidecarsFiles = []

        self.dicomDirs = dicomDirs

        self.bidsDir = bidsDir

        self.participant = participant

        self.options = options

    @property

    def outputDir(self):

        """

        Returns:

            A directory to save all the output files of dcm2niix

        """

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

        return self.bidsDir / DEFAULT.tmpDirName / 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.outputDir) != []

        except:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

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

            self.logger.warning("Cleaning the previous directory and running dcm2niix")

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

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

            self.logger.warning("Use --forceDcm2niix to rerun dcm2niix")

        else:

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

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

    def execute(self):

        """ Execute dcm2niix for each directory in dicomDirs

        """

        for dicomDir in self.dicomDirs:

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

                   '-o', self.outputDir, dicomDir]

            output = run_shell_command(cmd)

            try:

                output = output.decode()

            except:

                pass

            self.logger.debug("\n%s", output)

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

Instance variables⚓︎

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outputDir

Returns:

A directory to save all the output files of dcm2niix

Methods⚓︎

execute⚓︎

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def execute(
    self
)

Execute dcm2niix for each directory in dicomDirs

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    def execute(self):

        """ Execute dcm2niix for each directory in dicomDirs

        """

        for dicomDir in self.dicomDirs:

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

                   '-o', self.outputDir, dicomDir]

            output = run_shell_command(cmd)

            try:

                output = output.decode()

            except:

                pass

            self.logger.debug("\n%s", output)

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

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

Sets: | None | | sidecarsFiles | list | A list of sidecar path created by 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.outputDir) != []

        except:

            oldOutput = False

        if oldOutput and force:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

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

            self.logger.warning("Cleaning the previous directory and running dcm2niix")

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

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

        elif oldOutput:

            self.logger.warning("Previous dcm2niix directory output found:")

            self.logger.warning(self.outputDir)

            self.logger.warning("Use --forceDcm2niix to rerun dcm2niix")

        else:

            # os.makedirs(self.outputDir, exist_ok=True)

            # python2 compatibility

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

                os.makedirs(self.outputDir)

            self.execute()

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

Last update: 2022-06-17
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