Module dcm2bids.dcm2niix
Dcm2niix class
View Source
# -*- 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
class Dcm2niix(
dicomDirs,
bidsDir,
participant=None,
options="-b y -ba y -z y -f '%3s_%f_%p_%t'"
)
Object to handle dcm2niix execution
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 | None |
View Source
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
outputDir
Methods
execute
def execute(
self
)
Execute dcm2niix for each directory in dicomDirs
View Source
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
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 |
View Source
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:
2023-07-13
Created: 2023-07-13
Created: 2023-07-13