def createTaskHtml(self, tags, htmlLink=None):
"""
Create html file for the task
Arg:
tags: dict with the following keys to parse the html template
subject, taskInfo, taskName, parseHtmlTables, parseVersionTables
Script fills missing keys
"""
versions = ''
if self.getName() == 'qa':
print self.logDir
print self.get('general', 'versions_file_name')
versions = minidom.parse(
os.path.join(self.logDir,
self.get('general', 'versions_file_name')))
versions = versions.toprettyxml()
if htmlLink == None:
htmlLink = self.qaHtml
# Fill missing keys
baseTags = {
'jqueryFile': self.config.get('qa', 'jquery'),
'subject': self.subject.getName(),
'taskName': self.getName(),
'taskInfo': '',
'parseHtmlTables': '',
'parseVersionTables': versions,
}
for key, value in baseTags.iteritems():
if not tags.has_key(key): tags[key] = value
# Parse template and create html file
htmlCode = self.parseTemplate(tags, self.qaHtmlTemplate)
util.createScript(htmlLink, htmlCode)
def createTaskHtml(self, tags, htmlLink=None):
"""
Create html file for the task
Arg:
tags: dict with the following keys to parse the html template
subject, taskInfo, taskName, parseHtmlTables, parseVersionTables
Script fills missing keys
"""
versions = minidom.parse(os.path.join(
self.logDir, self.get('general','versions_file_name')))
if htmlLink == None:
htmlLink = self.qaHtml
# Fill missing keys
baseTags = {
'jqueryFile': self.config.get('qa', 'jquery'),
'subject': self.subject.getName(),
'taskName': self.getName(),
'taskInfo': '',
'parseHtmlTables': '',
'parseVersionTables': versions.toprettyxml()
}
for key, value in baseTags.iteritems():
if not tags.has_key(key): tags[key] = value
# Parse template and create html file
htmlCode = self.parseTemplate(tags, self.qaHtmlTemplate)
util.createScript(htmlLink, htmlCode)
def __createSegmentationScript(self, source, options):
"""Create a file which contains all necessary instruction to launch a segmentation with spm
Args:
source: the input image file name
options: an array of nine integer elements representing Boolean. See config.cfg for the meaning of the elements
Returns:
The resulting script file name
"""
scriptName = os.path.join(
self.workingDir,
os.path.basename(source).replace(".nii", ".m"))
self.info("Creating spm segmentation script {}".format(scriptName))
tags = {
'source': source,
'gm1': options[0],
'gm2': options[1],
'gm3': options[2],
'csf1': options[3],
'csf2': options[4],
'csf3': options[5],
'wm1': options[6],
'wm2': options[7],
'wm3': options[8]
}
template = self.parseTemplate(
tags, os.path.join(self.toadDir, "templates/files/segment.tpl"))
util.createScript(scriptName, template)
return scriptName
def createQaReport(self, images):
"""create html report for a task with qaSupplier implemented
Args:
images : an Images object
"""
mainTemplate = os.path.join(self.qaDir, self.get('qa', 'subject_template'))
tableTemplate = os.path.join(self.toadDir, 'templates', 'files', 'qa.table.tpl')
taskInfo = images.getInformation()
imagesDir = os.path.join(self.qaDir, self.config.get('qa', 'images_dir'))
tablesCode = ''
print "createQaReport images =", images
for imageLink, legend in images:
if imageLink:
path, filename = os.path.split(imageLink)
classType = 'large_view'
if any(_ in filename for _ in ['_translations', '_rotations', '_vectors', '_sigma']):
classType = 'small_view'
shutil.copyfile(imageLink, os.path.join(imagesDir, filename))
relativeLink = os.path.join(self.config.get('qa', 'images_dir'), filename)
tags = {
'imageLink':relativeLink,
'legend':legend,
'class':classType,
}
tablesCode += self.parseTemplate(tags, tableTemplate)
else:
tags = {'imageLink':'', 'legend':legend}
tablesCode += self.parseTemplate(tags, tableTemplate)
tags = {'taskInfo':taskInfo,'parseHtmlTables':tablesCode}
htmlCode = self.parseTemplate(tags, mainTemplate)
htmlFile = os.path.join(self.qaDir,'{}.html'.format(self.getName()))
util.createScript(htmlFile, htmlCode)
def __createLpcaScript(self, source, target):
scriptName = os.path.join(self.workingDir,
"{}.m".format(self.get("script_name")))
self.info("Creating denoising script {}".format(scriptName))
tags = {
'source': source,
'target': target,
'workingDir': self.workingDir,
'beta': self.get('beta'),
'rician': self.get('rician'),
'nbthreads': self.getNTreads()
}
if self.get("algorithm") == "aonlm":
template = self.parseTemplate(
tags,
os.path.join(self.toadDir,
"templates/files/denoise_aonlm.tpl"))
else:
template = self.parseTemplate(
tags,
os.path.join(self.toadDir, "templates/files/denoise_lpca.tpl"))
util.createScript(scriptName, template)
return scriptName
def createMethoHtml(self):
templateDir = os.path.join(self.toadDir, 'templates', 'files')
jinja2Env = Environment(loader=FileSystemLoader(templateDir),
trim_blocks=True)
tpl = jinja2Env.get_template('metho.tpl')
tags_softwares = self.__getVersions()
tags_metho = self.__getTags(tags_softwares)
# print tags_metho
htmlCode = tpl.render(**tags_metho)
util.createScript(os.path.join(self.qaDir, 'metho.html'), htmlCode)
def createMethoHtml(self):
templateDir = os.path.join(self.toadDir, 'templates', 'files')
jinja2Env = Environment(
loader=FileSystemLoader(templateDir), trim_blocks=True)
tpl = jinja2Env.get_template('metho.tpl')
tags_softwares = self.__getVersions()
tags_metho = self.__getTags(tags_softwares)
# print tags_metho
htmlCode = tpl.render(**tags_metho)
util.createScript(os.path.join(self.qaDir,'metho.html'), htmlCode)
def __createIndexFile(self, dimensions):
"""Create the file that will contain the index
Args:
dimensions: the number of direction into the B0 images
Returns:
The resulting file name
"""
target = os.path.join(self.workingDir, self.get('index_filename'))
self.info("Creating index file {}".format(target))
text = ""
for i in range(0, dimensions):
text += "1 "
util.createScript(target, text)
return target
def __createIndexFile(self, dimensions):
"""Create the file that will contain the index
Args:
dimensions: the number of direction into the B0 images
Returns:
The resulting file name
"""
target = os.path.join(self.workingDir, self.get('index_filename'))
self.info("Creating index file {}".format(target))
text = ""
for i in range(0, dimensions):
text += "1 "
util.createScript(target, text)
return target
def __createLpcaScript(self, source, target):
scriptName = os.path.join(self.workingDir, "{}.m".format(self.get("script_name")))
self.info("Creating denoising script {}".format(scriptName))
tags={ 'source': source, 'target':target,
'workingDir': self.workingDir,
'beta': self.get('beta'),
'rician': self.get('rician'),
'nbthreads': self.getNTreads()}
if self.get("algorithm") == "aonlm":
template = self.parseTemplate(tags, os.path.join(self.toadDir, "templates/files/denoise_aonlm.tpl"))
else:
template = self.parseTemplate(tags, os.path.join(self.toadDir, "templates/files/denoise_lpca.tpl"))
util.createScript(scriptName, template)
return scriptName
def __createAcquisitionParameterFile(self, type):
"""Create the acquire parameter (--acqp) file for topup or eddy
For topup, the image will concatenate b0AP first then b0PA
#A>>P, 0 -1 0
#P>>A, 0 1 0
#R>>L, 1 0 0
#L>>R, -1 0 0
Args:
type: algorithm this file is create for. Valid value are: topup, eddy
Returns:
the acquisition parameter file name
"""
try:
phaseEncDir = int(self.get('phase_enc_dir'))
except ValueError:
self.error("Cannot determine the phase encoding direction")
try:
echoSpacing = float(self.get('echo_spacing'))
epiFactor = float(self.get('epi_factor'))
factor = (epiFactor - 1) * (echoSpacing / 1000)
except ValueError:
self.warning("Cannot find suitable Echo Spacing value, will use a factor of 0.1")
factor = "0.1"
if type == 'topup':
parameter = 'acqp_topup'
text = ""
for nDim in range(self.dimB0s[0]):
text += "0 1 0 {}\n".format(factor)
for nDim in range(self.dimB0s[1]):
text += "0 -1 0 {}\n".format(factor)
elif type == 'eddy':
parameter = 'acqp_eddy'
text = "0 1 0 {}\n".format(factor)
else:
self.error("Type must be of value: topup or eddy")
return False
target = os.path.join(self.workingDir, self.get(parameter))
if not util.createScript(target, text):
self.error("Unable to create script {}".format(target))
return target
def __createSegmentationScript(self, source, options):
"""Create a file which contains all necessary instruction to launch a segmentation with spm
Args:
source: the input image file name
options: an array of nine integer elements representing Boolean. See config.cfg for the meaning of the elements
Returns:
The resulting script file name
"""
scriptName = os.path.join(self.workingDir, os.path.basename(source).replace(".nii",".m"))
self.info("Creating spm segmentation script {}".format(scriptName))
tags={ 'source': source,
'gm1': options[0], 'gm2': options[1], 'gm3': options[2],
'csf1': options[3], 'csf2': options[4], 'csf3': options[5],
'wm1': options[6], 'wm2': options[7], 'wm3': options[8]}
template = self.parseTemplate(tags, os.path.join(self.toadDir, "templates/files/segment.tpl"))
util.createScript(scriptName, template)
return scriptName
def __createAcquisitionParameterFile(self, type):
"""Create the acquire parameter (--acqp) file for topup or eddy
For topup, the image is always concatenate b0AP first then b0PA
#A>>P, 0 -1 0
#P>>A, 0 1 0
#R>>L, 1 0 0
#L>>R, -1 0 0
Args:
type: algorithm this file is create for. Valid value are: topup, eddy
Returns:
the acquisition parameter file name
"""
try:
phaseEncDir = int(self.get('phase_enc_dir'))
except ValueError:
self.error("Cannot determine the phase encoding direction")
try:
echoSpacing = float(self.get('echo_spacing'))
epiFactor = int(self.get('epi_factor'))
factor = (epiFactor-1) * (echoSpacing/1000)
except ValueError:
self.warning("Cannot find suitable Echo Spacing value, will use a factor of 0.1")
factor = "0.1"
if type=='topup':
parameter='acqp_topup'
text = "0 -1 0 {}\n0 1 0 {}\n".format(factor, factor)
elif type=='eddy':
parameter='acqp_eddy'
if phaseEncDir==0: #P>>A
text = "0 1 0 {}\n".format(factor)
elif phaseEncDir==1: #A>>P
text = "0 -1 0 {}\n".format(factor)
else:
self.error("Cannot determine the phase encoding direction, got value of: {}".format(phaseEncDir))
else:
self.error("Type must be of value: topup or eddy")
return False
target = os.path.join(self.workingDir, self.get(parameter))
if not util.createScript(target, text):
self.error("Unable to create script {}".format(target))
return target
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 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)
#Create menu links only for tasks with implemented QA
menuHtml = ""
menuLinkTemplate = "\n<li><a id=\"{0}\" href=\"{0}.html\">{0}</a></li>"
qaTasksList = []
for task in sorted(self.tasksAsReferences):
if "qaSupplier" in dir(task):
qaTasksList.append(task.getName())
for taskName in qaTasksList:
menuHtml += menuLinkTemplate.format(taskName)
#Create temporary html for each task
message = "Task is being processed. Refresh to check completion."
for taskName in qaTasksList:
htmlTaskFileName = "{}.html".format(taskName)
if not os.path.exists(htmlTaskFileName):
tags = {
'subject':self.__subject.getName(),
'menuHtml':menuHtml,
'taskInfo':'',
'parseHtmlTables':message,
}
htmlCode = self.parseTemplate(tags, mainTemplate)
util.createScript(htmlTaskFileName, htmlCode)
#Create template specific to the subject
tags = {
'subject':self.__subject.getName(),
'menuHtml':menuHtml,
}
htmlCode = self.parseTemplate(tags, mainTemplate)
util.createScript(self.get('qa', 'subject_template'), htmlCode)
#Create index.html
tags = {
'subject':self.__subject.getName(),
'menuHtml':menuHtml,
'taskInfo':'',
'parseHtmlTables':'',
}
htmlCode = self.parseTemplate(tags, mainTemplate)
util.createScript('index.html', htmlCode)