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])
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