def __implement(self):
"""Generic implementation of a tasks
-A task should create and move into is own working space
"""
self.info("Launching implementation of {} task".format(self.getName()))
if not os.path.exists(self.workingDir):
self.info("Creating {} directory".format(self.workingDir))
os.mkdir(self.workingDir)
if self.config.has_option("arguments", "stop_before_task"):
if (self.config.get("arguments", "stop_before_task") == self.__name or
self.config.get("arguments", "stop_before_task") == self.__moduleName.lower()):
self.quit("Reach {} which is the value set by stop_before_task. Stopping the pipeline as user request"
.format(self.config.get("arguments", "stop_before_task")))
os.chdir(self.workingDir)
util.symlink(self.getLogFileName(), self.workingDir)
if "qaSupplier" in dir(self):
self.updateQaMenu()
self.implement()
self.info("Create and supply images to the qa report ")
if "qaSupplier" in dir(self):
self.createQaReport(self.qaSupplier())
else:
self.info("task {} does not implement qaSupplier method".format(self.getName()))
os.chdir(self.subjectDir)
def implement(self):
images = {'aparc_aseg':self.getImage(self.dependDir,'aparc_aseg'),
'anat_freesurfer':self.getImage(self.dependDir,'anat_freesurfer'),
'brodmann':self.getImage(self.dependDir,'brodmann')}
for key, value in images.iteritems():
if value:
self.info("Found {} area image, create link from {} to {}".format(key, value, self.workingDir))
util.symlink(value, self.workingDir)
if not (images['aparc_aseg'] and images['anat_freesurfer'] and images['brodmann']):
self.info("Set SUBJECTS_DIR to {}".format(self.workingDir))
os.environ["SUBJECTS_DIR"] = self.workingDir
anat = self.getImage(self.dependDir, 'anat')
self.__reconAll(anat)
self.__createBrodmannArea()
dicts = {'anat_freesurfer': "{}/{}/mri/T1.mgz",
'aparc_aseg': "{}/{}/mri/aparc+aseg.mgz",
'brodmann': "{}/{}/mri/brodmann.mgz"}
for key, value in dicts.iteritems():
images = glob.glob(value.format(self.workingDir, self.id))
if len(images) > 0:
self.__mgz2nii(images.pop(), os.path.join(self.workingDir, self.get(key)))
def implement(self):
dwi = self.__linkDwiImage()
bVals= self.getCorrectionImage('grad', None, 'bvals')
bVecs= self.getCorrectionImage('grad', None, 'bvecs')
bEnc = self.getCorrectionImage('grad', None, 'benc')
if not bVals or not bVecs:
bVals= self.getPreparationImage('grad', None, 'bvals')
bVecs= self.getPreparationImage('grad', None, 'bvecs')
bEnc= self.getPreparationImage('grad', None, 'benc')
bVals = util.symlink(bVals, self.workingDir)
bVecs = util.symlink(bVecs, self.workingDir)
bEnc = util.symlink(bEnc, self.workingDir)
if self.get('skipUpsampling'):
dwiUpsample = self.rename(os.path.join(self.workingDir, os.path.basename(dwi)), self.buildName(dwi, "upsample"))
else:
interp = self.get('interp')
template = self.getParcellationImage('anat','freesurfer','nii.gz')
voxelSize = mriutil.getMriVoxelSize(template) # Get t1 voxel size to upsample
voxelSize = str(voxelSize).translate(None, '[],') # Remove specific caracteres
dwiUpsample= self.__upsampling(dwi, voxelSize, interp, self.buildName(dwi, "upsample"))
b0Upsample = os.path.join(self.workingDir, os.path.basename(dwiUpsample).replace(self.get("prefix", 'dwi'), self.get("prefix", 'b0')))
self.info(mriutil.extractFirstB0FromDwi(dwiUpsample, b0Upsample, bVals))
def __implement(self):
"""Generic implementation of a tasks
-A task should create and move into is own working space
"""
self.info("Launching implementation of {} task".format(self.getName()))
if not os.path.exists(self.workingDir):
self.info("Creating {} directory".format(self.workingDir))
os.mkdir(self.workingDir)
os.chdir(self.workingDir)
util.symlink(self.getLogFileName(), self.workingDir)
if "qaSupplier" in dir(self):
self.updateQaMenu()
self.implement()
# Save ConfigRunning File
configRunningPath = os.path.join(self.subjectDir, '00-backup',
'configRunning.cfg')
self.subject.writeConfigRunning(configRunningPath)
self.info("Create and supply images to the qa report ")
if "qaSupplier" in dir(self):
self.createQaReport(self.qaSupplier())
else:
self.info("task {} does not implement qaSupplier method".format(
self.getName()))
os.chdir(self.subjectDir)
def __produceEncodingFiles(self, bEncs, bVecs, bVals, dwi):
self.info("Produce .b .bvals and .bvecs gradient file if not existing")
if not bEncs:
bEncs = self.buildName(dwi, None, "b")
self.info(mriutil.fslToMrtrixEncoding(dwi, bVecs, bVals, bEncs))
else:
self.info("Linking {} to {}".format(
bEncs, util.symlink(bEncs, self.workingDir)))
if not bVecs or not bVals:
self.info(
mriutil.mrtrixToFslEncoding(dwi, bEncs,
self.buildName(dwi, None, "bvecs"),
self.buildName(dwi, None,
"bvals")))
else:
self.info("Linking {} to {}".format(
bVecs, util.symlink(bVecs, self.workingDir)))
self.info("Linking {} to {}".format(
bVals, util.symlink(bVals, self.workingDir)))
return (self.getImage('grad', None,
'b'), self.getImage('grad', None, 'bvecs'),
self.getImage('grad', None, 'bvals'))
def implement(self):
dwi = self.getBackupImage('dwi')
bEncs = self.getBackupImage('grad', None, 'b')
bVals = self.getBackupImage('grad', None, 'bvals')
bVecs = self.getBackupImage('grad', None, 'bvecs')
(bEncs, bVecs,
bVals) = self.__produceEncodingFiles(bEncs, bVecs, bVals,
dwi) # Convert bvecs bval
expectedLayout = self.get('stride_orientation')
if not mriutil.isDataStridesOrientationExpected(dwi, expectedLayout) \
and self.get("force_realign_strides"):
self.warning("Reorienting strides for image {}".format(dwi))
self.__stride4DImage(dwi, bEncs, bVecs, bVals, expectedLayout)
else:
self.info("Linking {} to {}".format(
dwi, util.symlink(dwi, self.workingDir)))
images = Images(
(self.getBackupImage('anat'), 'high resolution'),
(self.getBackupImage('b0_pa'), 'B0 posterior to anterior'),
(self.getBackupImage('b0_ap'), 'B0 anterior to posterior'),
(self.getBackupImage('mag'), 'MR magnitude'),
(self.getBackupImage('phase'), 'MR phase '),
(self.getBackupImage('aparc_aseg'), 'parcellation'),
(self.getBackupImage('anat',
'freesurfer'), 'freesurfer anatomical'),
(self.getBackupImage('lh_ribbon'), 'left hemisphere ribbon'),
(self.getBackupImage('rh_ribbon'), 'right hemisphere ribbon'),
(self.getBackupImage('brodmann'), 'brodmann'),
)
for image, description in images.getData():
if image:
if not mriutil.isDataStridesOrientationExpected(image, expectedLayout) \
and self.get("force_realign_strides"):
self.info(
mriutil.stride3DImage(image,
self.buildName(image, "stride"),
expectedLayout))
else:
self.info("Found {} image, linking {} to {}".format(
description, image,
util.symlink(image, self.workingDir)))
for directory in [
os.path.join(self.backupDir, directory)
for directory in os.listdir(self.backupDir)
if os.path.isdir(os.path.join(self.backupDir, directory))
]:
if mriutil.isAfreesurferStructure(directory):
self.info(
"{} seem\'s a valid freesurfer structure: linking to {} directory"
.format(directory, self.workingDir))
util.symlink(directory, self.workingDir,
self.get("parcellation", "id"))
def __implement(self):
"""Generic implementation of a tasks
-A task should create and move into is own working space
"""
self.info("Launching implementation of {} task".format(self.getName()))
if not os.path.exists(self.workingDir):
self.info("Creating {} directory".format(self.workingDir))
os.mkdir(self.workingDir)
os.chdir(self.workingDir)
util.symlink(self.getLogFileName(), self.workingDir)
if "qaSupplier" in dir(self):
self.updateQaMenu()
self.implement()
# Save ConfigRunning File
configRunningPath = os.path.join(
self.subjectDir, '00-backup', 'configRunning.cfg')
self.subject.writeConfigRunning(configRunningPath)
self.info("Create and supply images to the qa report ")
if "qaSupplier" in dir(self):
self.createQaReport(self.qaSupplier())
else:
self.info("task {} does not implement qaSupplier method".format(self.getName()))
os.chdir(self.subjectDir)
def __getConfigFile(self, prefix, defaultFile):
target = self.getPreparationImage(prefix, None, "json")
if target:
util.symlink(target, self.buildName(target, None, "json"))
else:
defaultFileName = "{}.json".format(defaultFile)
defaultFileLink = os.path.join(self.toadDir, "templates", "tractometry", defaultFileName)
target = defaultFileLink
util.copy(defaultFileLink, self.workingDir, defaultFileName)
return target
def __findAndLinkFreesurferStructure(self):
"""Look if a freesurfer structure already exists in the backup.
freesurfer structure will be link and id will be update
Returns:
Return the linked directory name if a freesurfer structure is found, False otherwise
"""
freesurferStructure = os.path.join(self.preparationDir, self.id)
if mriutil.isAfreesurferStructure(freesurferStructure):
self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(freesurferStructure, self.workingDir))
util.symlink(freesurferStructure, self.id)
return True
return False
def __implement(self):
"""Generic implementation of a tasks
-A task should create and move into is own working space
"""
if not os.path.exists(self.workingDir):
self.info("Creating {} directory".format(self.workingDir))
os.mkdir(self.workingDir)
currentDir = os.getcwd()
os.chdir(self.workingDir)
util.symlink(self.getLogFileName(), self.workingDir)
self.implement()
os.chdir(currentDir)
def __linkDwiImage(self):
dwi = self.getCorrectionImage('dwi', 'corrected')
if not dwi:
dwi = self.getDenoisingImage('dwi', 'denoise')
if not dwi:
dwi = self.getPreparationImage('dwi')
return util.symlink(dwi, self.workingDir)
def __getConfigFile(self, prefix, defaultFile):
target = self.getPreparationImage(prefix, None, 'json')
if target:
util.symlink(target, self.buildName(target, None, 'json'))
else:
defaultFileName = '{}.json'.format(defaultFile)
defaultFileLink = os.path.join(
self.toadDir,
"templates",
"tractometry",
defaultFileName,
)
target = defaultFileLink
util.copy(defaultFileLink, self.workingDir, defaultFileName)
return target
def __findAndLinkFreesurferStructure(self):
"""Look if a freesurfer structure already exists in the backup.
freesurfer structure will be link and id will be update
Returns:
Return the linked directory name if a freesurfer structure is found, False otherwise
"""
freesurferStructure = os.path.join(self.preparationDir, self.id)
if mriutil.isAfreesurferStructure(freesurferStructure):
self.info(
"{} seem\'s a valid freesurfer structure: moving it to {} directory"
.format(freesurferStructure, self.workingDir))
util.symlink(freesurferStructure, self.workingDir, self.id)
return True
return False
def implement(self):
dwi = self.getBackupImage('dwi')
bEncs = self.getBackupImage('grad', None, 'b')
bVals = self.getBackupImage('grad', None, 'bvals')
bVecs = self.getBackupImage('grad', None, 'bvecs')
(bEncs, bVecs, bVals) = self.__produceEncodingFiles(bEncs, bVecs, bVals, dwi) # Convert bvecs bval
expectedLayout = self.get('stride_orientation')
if not mriutil.isDataStridesOrientationExpected(dwi, expectedLayout) \
and self.get("force_realign_strides"):
self.warning("Reorienting strides for image {}".format(dwi))
self.__stride4DImage(dwi, bEncs, bVecs, bVals, expectedLayout)
else:
self.info("Linking {} to {}".format(dwi, util.symlink(dwi, self.workingDir)))
images = Images(
(self.getBackupImage('anat'),'high resolution'),
(self.getBackupImage('b0_pa'),'B0 posterior to anterior'),
(self.getBackupImage('b0_ap'),'B0 anterior to posterior'),
(self.getBackupImage('mag'),'MR magnitude'),
(self.getBackupImage('phase'),'MR phase '),
(self.getBackupImage('aparc_aseg'),'parcellation'),
(self.getBackupImage('anat', 'freesurfer'),'freesurfer anatomical'),
(self.getBackupImage('lh_ribbon'),'left hemisphere ribbon'),
(self.getBackupImage('rh_ribbon'),'right hemisphere ribbon'),
(self.getBackupImage('brodmann'),'brodmann'),
)
for image, description in images.getData():
if image:
if not mriutil.isDataStridesOrientationExpected(image, expectedLayout) \
and self.get("force_realign_strides"):
self.info(mriutil.stride3DImage(image, self.buildName(image, "stride"), expectedLayout))
else:
self.info("Found {} image, linking {} to {}".format(description, image, util.symlink(image, self.workingDir)))
for directory in [os.path.join(self.backupDir, directory) for directory in os.listdir(self.backupDir) if os.path.isdir(os.path.join(self.backupDir, directory))]:
if mriutil.isAfreesurferStructure(directory):
self.info("{} seem\'s a valid freesurfer structure: linking to {} directory".format(directory, self.workingDir))
util.symlink(directory, self.workingDir, self.get("parcellation", "id"))
def implement(self):
dwi = self.__linkDwiImage()
bVals= self.getCorrectionImage('grad', None, 'bvals')
bVecs= self.getCorrectionImage('grad', None, 'bvecs')
bEnc = self.getCorrectionImage('grad', None, 'benc')
if not bVals or not bVecs:
bVals= self.getPreparationImage('grad', None, 'bvals')
bVecs= self.getPreparationImage('grad', None, 'bvecs')
bEnc= self.getPreparationImage('grad', None, 'benc')
bVals = util.symlink(bVals, self.workingDir)
bVecs = util.symlink(bVecs, self.workingDir)
bEnc = util.symlink(bEnc, self.workingDir)
dwiUpsample= self.__upsampling(dwi, self.get('voxel_size'), self.buildName(dwi, "upsample"))
b0Upsample = os.path.join(self.workingDir, os.path.basename(dwiUpsample).replace(self.get("prefix", 'dwi'), self.get("prefix", 'b0')))
self.info(mriutil.extractFirstB0FromDwi(dwiUpsample, b0Upsample, bVals))
def __linkExistingImage(self, images):
"""
Create symbolic link for each existing input images into the current working directory.
Args:
images: A list of image
Returns:
A list of invalid images
"""
unlinkedImages = {}
# look for existing map store into preparation and link it so they are not created
for key, value in images.iteritems():
if value:
self.info("Found {} area image, create link from {} to {}".format(key, value, self.workingDir))
util.symlink(value, self.workingDir)
else:
unlinkedImages[key] = value
return unlinkedImages
def __produceEncodingFiles(self, bEncs, bVecs, bVals, dwi):
self.info("Produce .b .bvals and .bvecs gradient file if not existing")
if not bEncs:
bEncs = self.buildName(dwi, None, "b")
self.info(mriutil.fslToMrtrixEncoding(dwi, bVecs, bVals, bEncs))
else:
self.info("Linking {} to {}".format(bEncs, util.symlink(bEncs, self.workingDir)))
if not bVecs or not bVals:
self.info(mriutil.mrtrixToFslEncoding(dwi,
bEncs,
self.buildName(dwi, None, "bvecs"),
self.buildName(dwi, None, "bvals")))
else:
self.info("Linking {} to {}".format(bVecs, util.symlink(bVecs, self.workingDir)))
self.info("Linking {} to {}".format(bVals, util.symlink(bVals, self.workingDir)))
return (self.getImage('grad', None, 'b'),
self.getImage('grad', None, 'bvecs'),
self.getImage('grad', None, 'bvals'))
def __linkExistingImage(self, images):
"""
Create symbolic link for each existing input images into the current working directory.
Args:
images: A list of image
Returns:
A list of invalid images
"""
unlinkedImages = {}
# look for existing map store into preparation and link it so they are not created
for key, value in images.iteritems():
if value:
self.info(
"Found {} area image, create link from {} to {}".format(
key, value, self.workingDir))
util.symlink(value, self.workingDir)
else:
unlinkedImages[key] = value
return unlinkedImages
def implement(self):
images = {
'aparc_aseg': self.getImage(self.dependDir, 'aparc_aseg'),
'anat_freesurfer': self.getImage(self.dependDir,
'anat_freesurfer'),
'brodmann': self.getImage(self.dependDir, 'brodmann')
}
for key, value in images.iteritems():
if value:
self.info(
"Found {} area image, create link from {} to {}".format(
key, value, self.workingDir))
util.symlink(value, self.workingDir)
if not (images['aparc_aseg'] and images['anat_freesurfer']
and images['brodmann']):
self.info("Set SUBJECTS_DIR to {}".format(self.workingDir))
os.environ["SUBJECTS_DIR"] = self.workingDir
anat = self.getImage(self.dependDir, 'anat')
self.__reconAll(anat)
self.__createBrodmannArea()
dicts = {
'anat_freesurfer': "{}/{}/mri/T1.mgz",
'aparc_aseg': "{}/{}/mri/aparc+aseg.mgz",
'brodmann': "{}/{}/mri/brodmann.mgz"
}
for key, value in dicts.iteritems():
images = glob.glob(value.format(self.workingDir, self.id))
if len(images) > 0:
self.__mgz2nii(
images.pop(),
os.path.join(self.workingDir, self.get(key)))
def implement(self):
self.info("Produce .b .bval and .bvec gradient file if not existing")
self.__produceEncodingFiles()
dwi = self.getImage(self.dependDir, 'dwi')
b0PA = self.getImage(self.dependDir, 'b0PA')
b0AP = self.getImage(self.dependDir, 'b0AP')
if b0PA:
self.info(
"Found B0 posterior to anterior image, linking file {} to {}".
format(b0AP, self.workingDir))
util.symlink(b0PA, self.workingDir)
if b0AP:
self.info(
"Found B0 anterior to posterior image, linking file {} to {}".
format(b0AP, self.workingDir))
util.symlink(b0AP, self.workingDir)
if b0PA and (b0AP is False):
#Produire la carte AP si elle n'existe pas
self.info(
"No anterior posterior image found, I will try to produce one")
b0AP = self.__extractB0APSubVolumeFromDWI(dwi)
images = {
'high resolution': self.getImage(self.dependDir, 'anat'),
'diffusion weighted': dwi,
'MR magnitude ': self.getImage(self.dependDir, 'mag'),
'MR phase ': self.getImage(self.dependDir, 'phase'),
'parcellation': self.getImage(self.dependDir, 'aparc_aseg'),
'anatomical': self.getImage(self.dependDir, 'anat_freesurfer'),
'brodmann': self.getImage(self.dependDir, 'brodmann')
}
for key, value in images.iteritems():
if value:
self.info("Found {} image, linking file {} to {}".format(
key, value, self.workingDir))
util.symlink(value, self.workingDir)
def __produceEncodingFiles(self):
#produire les fichiers gradient encoding pour dipy ainsi que mrtrix
bEnc = self.getImage(self.dependDir, 'grad', None, 'b')
bVal = self.getImage(self.dependDir, 'grad', None, 'bval')
bVec = self.getImage(self.dependDir, 'grad', None, 'bvec')
if not bEnc:
mriutil.bValBVec2BEnc(bVal, bVec, self.workingDir)
else:
util.symlink(bEnc, self.workingDir)
if not bVal:
mriutil.bEnc2BVal(bEnc, self.workingDir)
else:
util.symlink(bVal, self.workingDir)
if not bVec:
mriutil.bEnc2BVec(bEnc, self.workingDir)
else:
util.symlink(bVec, self.workingDir)