def implement(self):
structs = {
'dwi': self.getUpsamplingImage('dwi'),
'anat': self.getRegistrationImage('anat',
['freesurfer', 'resample']),
'mask': self.getRegistrationImage('mask', 'resample')
}
for postfix, image in structs.iteritems():
util.copy(
image, self.workingDir,
self.buildName(self.subject.getName(), postfix, 'nii.gz'))
for extension in ['bvals', 'bvecs', 'benc']:
util.copy(self.getUpsamplingImage('grad', None, extension),
self.workingDir,
self.buildName(self.subject.getName(), None, extension))
self.__copyMetrics(['mrtrix', 'dipy', 'fsl'], ['fa', 'ad', 'rd', 'md'],
'tensor')
self.__copyMetrics(['mrtrix', 'dipy'], ['nufo', 'csd', 'gfa'], 'hardi')
self.createMethoHtml()
self.__finished = True
def __copyMetrics(self, softwares, postfixs, method):
for software in softwares:
for postfix in postfixs:
source = getattr(self,
"get{}{}Image".format(method,
software))("dwi",
postfix)
target = self.buildName(self.subject.getName(),
[software, postfix], 'nii.gz')
util.copy(source, self.workingDir, target)
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 __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 implement(self):
structs = {'dwi': self.getUpsamplingImage('dwi'),
'anat': self.getRegistrationImage('anat', ['freesurfer', 'resample']),
'mask': self.getRegistrationImage('mask', 'resample'),
'brodmann': self.getRegistrationImage('brodmann', 'resample')}
for postfix, image in structs.iteritems():
util.copy(image, self.workingDir, self.buildName(self.subject.getName(), postfix, 'nii.gz'))
for extension in ['bvals', 'bvecs', 'benc']:
util.copy(self.getUpsamplingImage('grad', None, extension), self.workingDir, self.buildName(self.subject.getName(), None, extension))
self.__copyMetrics(['mrtrix', 'dipy', 'fsl'], ['fa','ad','rd','md'], 'tensor')
self.__copyMetrics(['mrtrix', 'dipy'], ['nufo','csd','gfa'], 'hardi')
self.__finished = True
def implement(self):
if not os.path.exists(self.qaImagesDir):
os.makedirs(self.qaImagesDir)
#Copy logo
logoName = self.config.get('qa', 'logo')
logoLink = os.path.join(
self.toadDir, 'templates', 'files', logoName)
util.copy(logoLink, self.qaImagesDir, logoName)
#Copy menu, css & js
styleFiles = ('menu', 'css', 'jquery', 'js')
for tag in styleFiles:
fileName = self.config.get('qa', tag)
fileLink = os.path.join(
self.toadDir, 'templates', 'files', fileName)
util.copy(fileLink, self.workingDir, fileName)
#Create index.html
self.createTaskHtml({}, 'index.html')
def implement(self):
if not os.path.exists(self.qaImagesDir):
os.makedirs(self.qaImagesDir)
#Copy logo
logoName = self.config.get('qa', 'logo')
logoLink = os.path.join(
self.toadDir, 'templates', 'files', logoName)
util.copy(logoLink, self.qaImagesDir, logoName)
#Copy menu, css & js
styleFiles = ('menu', 'css', 'jquery', 'js')
for tag in styleFiles:
fileName = self.config.get('qa', tag)
fileLink = os.path.join(
self.toadDir, 'templates', 'files', fileName)
util.copy(fileLink, self.workingDir, fileName)
#Create index.html
self.createTaskHtml(
{'parseHtmlTables':'<div id="metho">Methodology when pipeline is finished</div>'}, 'index.html')
def implement(self):
mainTemplate = os.path.join(self.toadDir, 'templates', 'files', 'qa.main.tpl')
imagesDir = os.path.join(self.workingDir, self.get('qa', 'images_dir'))
if not os.path.exists(imagesDir):
os.makedirs(imagesDir)
#Copy style.css
styleTemplate = os.path.join(self.toadDir, 'templates', 'files', 'qa.style.tpl')
util.copy(styleTemplate, self.workingDir, 'style.css')
#Create menu.html only for tasks with implemented QA
menuTemplate = os.path.join(self.toadDir, 'templates', 'files', 'qa.menu.tpl')
util.copy(menuTemplate, self.workingDir, 'menu.html')
#Create index.html
tags = {
'subject':self.__subject.getName(),
'taskInfo':'',
'parseHtmlTables':'',
}
htmlCode = self.parseTemplate(tags, mainTemplate)
util.createScript('index.html', htmlCode)
def __copyMetrics(self, softwares, postfixs, method):
for software in softwares:
for postfix in postfixs:
source = getattr(self, "get{}{}Image".format(method, software))("dwi", postfix)
target = self.buildName(self.subject.getName(), [software, postfix], 'nii.gz')
util.copy(source, self.workingDir, target)