def __convertDwi(self, sequence, session, target):
""" Convert a dwi dicomparser images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
dwi = util.buildName(self.__configParser, target,
sequence.getPrefix().getValue(),
session.getName(), 'nii.gz')
bEnc = util.buildName(self.__configParser, target, dwi, None, "b")
bvals = util.buildName(self.__configParser, target, dwi, None, "bvals")
bvecs = util.buildName(self.__configParser, target, dwi, None, "bvecs")
cmd = "mrconvert {} {} -force -export_grad_mrtrix {} -export_grad_fsl {} {}"\
.format(sequence.getEscapedDirectory(), dwi, bEnc, bvecs, bvals)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3,4 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)
def __convertDwi(self, sequence, session, target):
""" Convert a dwi dicom images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
dwi = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(),'nii.gz')
bEnc = util.buildName(self.__configParser, target, dwi, None, "b")
bvals = util.buildName(self.__configParser, target, dwi, None, "bvals")
bvecs = util.buildName(self.__configParser, target, dwi, None, "bvecs")
cmd = "mrconvert {} {} -force -export_grad_mrtrix {} -export_grad_fsl {} {}"\
.format(sequence.getEscapedDirectory(), dwi, bEnc, bvecs, bvals)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3,4 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig( self.__configFilename)
util.launchCommand(cmd)
def __convert(self, sequence, session, target):
filename = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
if sequence.getPrefix().getName() == 'phase':
cmd += " -datatype float32 "
print cmd
util.launchCommand(cmd)
def __convertMagnitude(self, sequence, session, target):
""" Convert a magnitude fieldmap dicomparser images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
def __setMagnitudeFieldmapInConfigFiles(echo1, echo2):
""" write magnitude image properties into a config file
Args:
configFile: a config file
echo1: the echo time of the first magnitude map
echo2: the echo time of the secong magnitude map
"""
if os.path.exists(self.__configFilename):
self.__configParser.read(self.__configFilename)
if not self.__configParser.has_section("correction"):
self.__configParser.add_section('correction')
self.__configParser.set('correction', "echo_time_mag1", echo1)
self.__configParser.set('correction', "echo_time_mag2", echo2)
with open(self.__configFilename, 'w') as w:
self.__configParser.write(w)
values = []
pattern = os.path.join(session.getDirectory(),
os.path.dirname(sequence.getName()), 'echo_*')
for directory in glob.glob(pattern):
values.append(
(os.path.basename(directory).strip('echo_'), directory))
try:
echo1 = float(values[0][0])
echo2 = float(values[1][0])
if not self.__arguments.noConfig:
if echo1 > echo2:
__setMagnitudeFieldmapInConfigFiles(echo2, echo1)
else:
__setMagnitudeFieldmapInConfigFiles(echo1, echo2)
except IndexError:
return
filename = util.buildName(self.__configParser, target,
sequence.getPrefix().getValue(),
session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(
sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
print cmd
util.launchCommand(cmd)
def __convertMagnitude(self, sequence, session, target):
""" Convert a magnitude fieldmap dicom images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
def __setMagnitudeFieldmapInConfigFiles(echo1, echo2):
""" write magnitude image properties into a config file
Args:
configFile: a config file
echo1: the echo time of the first magnitude map
echo2: the echo time of the secong magnitude map
"""
if os.path.exists(self.__configFilename):
self.__configParser.read(self.__configFilename)
if not self.__configParser.has_section("correction"):
self.__configParser.add_section('correction')
self.__configParser.set('correction', "echo_time_mag1", echo1)
self.__configParser.set('correction', "echo_time_mag2", echo2)
with open(self.__configFilename,'w') as w:
self.__configParser.write(w)
values = []
pattern = os.path.join(session.getDirectory(), os.path.dirname(sequence.getName()),'echo_*')
for directory in glob.glob(pattern):
values.append((os.path.basename(directory).strip('echo_'), directory))
try:
echo1 = float(values[0][0])
echo2 = float(values[1][0])
if not self.__arguments.noConfig:
if echo1 > echo2:
__setMagnitudeFieldmapInConfigFiles(echo2, echo1)
else:
__setMagnitudeFieldmapInConfigFiles(echo1, echo2)
except IndexError:
return
filename = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
print cmd
util.launchCommand(cmd)
def buildName(self, source, postfix, ext=None, absolute = True):
"""A simple utility function that return a file name that contain the postfix and the current working directory
The filename is always into the current working directory
The extension name will be the same as source unless specify as argument
Args:
source: the input file name
postfix: single element or array of elements which option item specified in config at the postfix section
ext: the extension of the new target
Returns:
a file name that contain the postfix and the current working directory
"""
absoluteBuildName = util.buildName(self.config, self.workingDir, source, postfix, ext, absolute)
return os.path.basename(absoluteBuildName.replace("'",""))
def buildName(self, source, postfix, ext=None, absolute=True):
"""A simple utility function that return a file name that contain the postfix and the current working directory
The path of the filename contain the current working directory
The extension name will be the same as source unless specify as argument
Args:
source: the input file name
postfix: single element or array of elements which option item specified in config at the postfix section
ext: the extension of the new target
Returns:
a file name that contain the postfix and the current working directory
"""
return util.buildName(self.config, self.workingDir, source, postfix,
ext, absolute)
def __convert(self, sequence, session, target):
filename = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
if sequence.getPrefix().getName() == 'phase':
cmd += " -datatype float32 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)
def __convert(self, sequence, session, target):
filename = util.buildName(self.__configParser, target,
sequence.getPrefix().getValue(),
session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(
sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
if sequence.getPrefix().getName() == 'phase':
cmd += " -datatype float32 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)