class ADNI_V1_FMRI:
def __init__(self):
self.DBClient = DbUtils()
self.niak = Niak()
# This is called upon by Pipelines/PipelineHandler.py
def process(self, processingItem):
processingItemObj = ProcessingItemObj(processingItem)
self.runNiak(processingItemObj)
def runNiak(self, processingItemObj):
# Run Niak
if not processingItemObj.skip:
self.niak.process(processingItemObj)
elif processingItemObj.skip:
pass
else:
PipelineLogger.log('manager', 'error', 'Error handling obj for processing - {0}'.format(processingItemObj))
return 0
def runSmoothing(self, processingItemObj):
if not processingItemObj.skip and processingItemObj.finished:
smoothing.execute(processingItemObj)
__author__ = 'wang'
# Testing Pipelines.ADNI_Fmri.Niak.replaceString function
from Pipelines.ADNI_Fmri.Niak import Niak
if __name__ == "__main__":
niakTemplateFile = '/home/wang/Documents/bin/PyCharmProjects/Processing_Pipeline/Pipelines/ADNI_Fmri/MatlabScripts/niakPreprocessingTemplate.m'
with open(niakTemplateFile, 'r') as templateFile:
templateFileWithInformation = templateFile.read()
templateFile.close()
replacing_dict = {'%{patient_information}': '2453',
'%{opt.folder_out}': '/data/data03/wang/NiakFolder',
'%{niak_location}': '/data/data01/wang/references/niak-0.7.1-ammo/',
'%{nu_correct}': '6'
}
new_text = Niak.replaceString(templateFileWithInformation, replacing_dict)
print(new_text)
def __init__(self):
self.DBClient = DbUtils()
self.niak = Niak()
