def main():
"""main function of this Python program"""
from pyHCP import pyHCP, getHCP
command_line_options = parse_command_line()
show_options(command_line_options)
Username = command_line_options.get_user_name()
Password = command_line_options.get_password()
Server = command_line_options.get_server_name()
Pipeline = command_line_options.get_pipeline()
Project = command_line_options.get_project()
FunctionalTaskNames = command_line_options.get_functional_task_names()
IcaTaskNames = command_line_options.get_ica_task_names()
DiffusionVoxelSize = command_line_options.get_diffusion_voxel_size()
Subjects = command_line_options.get_subjects()
OutputPath = command_line_options.get_output_path()
Verbose = command_line_options.get_verbose()
pyHCP = pyHCP(Username, Password, Server)
getHCP = getHCP(pyHCP)
getHCP.Project = Project
if (Subjects is not "All"):
subjects_to_check = ((Subjects.split(',')))
else:
subjects_to_check = getHCP.getSubjects()
processing_status_list = list()
# Cycle through specified subjects to check
for i in xrange(0, len(subjects_to_check)):
if ('struct' in Pipeline.lower()):
structural_processing_status = check_structural_status(Verbose, getHCP, subjects_to_check[i])
processing_status_list.append(structural_processing_status)
if ('funct' in Pipeline.lower()):
functional_processing_status_list = check_functional_status(Verbose, getHCP, subjects_to_check[i], FunctionalTaskNames)
for functional_processing_status in functional_processing_status_list:
processing_status_list.append(functional_processing_status)
if ('diff' in Pipeline.lower()):
diffusion_processing_status = check_diffusion_status(Verbose, getHCP, subjects_to_check[i], DiffusionVoxelSize)
processing_status_list.append(diffusion_processing_status)
if ('fix' in Pipeline.lower()):
fix_processing_status_list = check_fix_status(Verbose, getHCP, subjects_to_check[i], IcaTaskNames)
for fix_processing_status in fix_processing_status_list:
processing_status_list.append(fix_processing_status)
if ('task' in Pipeline.lower()):
task_processing_status_list = check_task_analysis_status(Verbose, getHCP, subjects_to_check[i])
for task_processing_status in task_processing_status_list:
processing_status_list.append(task_processing_status)
# Output Results
create_output_file(OutputPath, processing_status_list)
def getSubjects(self):
global getHCP
# self.subjectsComboBox.clear()
# print self.projectListWidget.currentItem().text()
getHCP.Project = str(self.projectListWidget.currentItem().text())
# getHCP.Project = str(self.projectsComboBox.currentText())
Subjects = sorted(getHCP.getSubjects())
# self.subjectsTextEdit.setText('\n'.join(Subjects))
# self.subjectsComboBox.addItems(Subjects)
self.subjectsListWidget.clear()
for i in xrange(0, len(Subjects)):
self.subjectsListWidget.addItem(Subjects[i])
def getSubjects(self):
global getHCP
# self.subjectsComboBox.clear()
# print self.projectListWidget.currentItem().text()
getHCP.Project = str(self.projectListWidget.currentItem().text())
# getHCP.Project = str(self.projectsComboBox.currentText())
Subjects = sorted(getHCP.getSubjects())
# self.subjectsTextEdit.setText('\n'.join(Subjects))
# self.subjectsComboBox.addItems(Subjects)
self.subjectsListWidget.clear()
for i in xrange(0, len(Subjects)):
self.subjectsListWidget.addItem(Subjects[i])
print "Running %s on %s" % (os.path.split(sys.argv[0])[1], socket.gethostname())
pyHCP = pyHCP(User, Password, Server)
getHCP = getHCP(pyHCP)
writeHCP = writeHCP(getHCP, OutputDir)
getHCP.Verbose = True
getHCP.Project = 'HCP_Phase2'
#===============================================================================
# Setup output...
#===============================================================================
if (inputSubjects == None):
inputSubjectsList = getHCP.getSubjects()
elif (inputSubjects != None):
inputSubjectsList = inputSubjects.split(',')
if (len(inputSubjectsList) == 1):
outputFileAppend = inputSubjectsList[0]
else:
outputFileAppend = inputProject
outputFileExt = '.txt'
#===============================================================================
# grab output files...
# NOTES: need to deal with xtr QC...
#===============================================================================
#===============================================================================
print "Running %s on %s" % (os.path.split(
sys.argv[0])[1], socket.gethostname())
pyHCP = pyHCP(User, Password, Server)
getHCP = getHCP(pyHCP)
writeHCP = writeHCP(getHCP, OutputDir)
getHCP.Verbose = True
getHCP.Project = 'HCP_Phase2'
#===============================================================================
# Setup output...
#===============================================================================
if (inputSubjects == None):
inputSubjectsList = getHCP.getSubjects()
elif (inputSubjects != None):
inputSubjectsList = inputSubjects.split(',')
if (len(inputSubjectsList) == 1):
outputFileAppend = inputSubjectsList[0]
else:
outputFileAppend = inputProject
outputFileExt = '.txt'
#===============================================================================
# grab output files...
# NOTES: need to deal with xtr QC...
#===============================================================================
getHCP.Verbose = True
if (getHCP.Server.find('intradb') != -1):
getHCP.Scan = '2'
getHCP.Project = 'HCP_Phase2'
else:
getHCP.Scan = '105'
getHCP.Project = 'HCP_Q1'
DestinationDir = outputDir + os.sep
writeHCP = writeHCP(getHCP, DestinationDir)
#===============================================================================
# Setup subjects...
#===============================================================================
if (Subjects == None):
getHCP.Subjects = getHCP.getSubjects()
elif (Subjects != None):
getHCP.Subjects = Subjects.split(',')
#outputFileExt = '.txt'
#outputDirFile = '%s\\%s%s%s' % (outputDir, outputFileBase, outputFileAppend, outputFileExt)
#===============================================================================
# show usage of class...
#===============================================================================
if (showClassUsage):
#==============================================================================
# getAssessorIDs
# getAssessorOutputFile
# getFileInfo
getHCP.Verbose = True
if getHCP.Server.find("intradb") != -1:
getHCP.Scan = "2"
getHCP.Project = "HCP_Phase2"
else:
getHCP.Scan = "105"
getHCP.Project = "HCP_Q1"
DestinationDir = outputDir + os.sep
writeHCP = writeHCP(getHCP, DestinationDir)
# ===============================================================================
# Setup subjects...
# ===============================================================================
if Subjects == None:
getHCP.Subjects = getHCP.getSubjects()
elif Subjects != None:
getHCP.Subjects = Subjects.split(",")
# outputFileExt = '.txt'
# outputDirFile = '%s\\%s%s%s' % (outputDir, outputFileBase, outputFileAppend, outputFileExt)
# ===============================================================================
# show usage of class...
# ===============================================================================
if showClassUsage:
# ==============================================================================
# getAssessorIDs
# getAssessorOutputFile
# getFileInfo
