def open_subjects_file(self): control_location = os.getenv('XNAT_PBS_JOBS_CONTROL', default="") options = QFileDialog.Options() #options |= QFileDialog.DontUseNativeDialog #subject_file_name, other_stuff = QFileDialog.getOpenFileName(self, "Open Subject File", "", "Subject Files (*.subjects);;All Files (*)", options=options) subject_file_name, other_stuff = QFileDialog.getOpenFileName( self, "Open Subject File", control_location, "Subject Files (*.subjects);;All Files (*)", options=options) if subject_file_name: new_subject_list = hcp7t_subject.read_subject_info_list( subject_file_name, separator=":") self.controlPanel.subject_list = new_subject_list
def main(): # create a parser object for getting the command line arguments parser = my_argparse.MyArgumentParser() parser.add_argument('-a', '--all-subjects=', dest='all_subjects', required=True, type=str) parser.add_argument('-t', '--todo-subjects=', dest='todo_subjects', required=True, type=str) args = parser.parse_args() # print("Retrieving all subjects from: " + args.all_subjects) all_subjects_list = hcp7t_subject.read_subject_info_list(args.all_subjects, separator=":") # print("Retrieving subject ids in TODO list from: " + args.todo_subjects) to_do_subjects_list = [] to_do_ids_file = open(args.todo_subjects, "r") for line in to_do_ids_file: subject_id = line[:-1] for subject in all_subjects_list: if subject_id == subject.subject_id: print(str(subject)) break
"""Outputs a message that is prefixed by the module file name.""" print(os.path.basename(__file__) + ": " + msg) if __name__ == "__main__": # Get environment variables subject_files_dir = os.getenv('SUBJECT_FILES_DIR') if subject_files_dir is None: _inform("Environment variable SUBJECT_FILES_DIR must be set!") sys.exit(1) # Get list of all HCP7T subjects all_subjects_file_name = subject_files_dir + os.sep + 'FunctionalPreprocessingHCP7T.subjects.everybody' _inform("Retrieveing all subjects from: " + all_subjects_file_name) all_subjects_list = hcp7t_subject.read_subject_info_list(all_subjects_file_name) # _inform("all_subjects_list: " + str(all_subjects_list)) # Get list of subject IDs that need to be packaged subjects_to_use_file_name = subject_files_dir + os.sep + 'CreateAllPackages.subjects' _inform("Retrieving subjects to use from: " + subjects_to_use_file_name) subject_ids_to_use_list = hcp7t_subject.read_subject_id_list(subjects_to_use_file_name) _inform("subject_ids_to_use_list: " + str(subject_ids_to_use_list)) # get full subject information for all subjects that are in the subject_ids_to_use_list subjects_to_use_list = [subj_info for subj_info in all_subjects_list if subj_info.subject_id in subject_ids_to_use_list] # write out the subjects_to_use_list hcp7t_subject.write_subject_info_list('newlist', subjects_to_use_list)
self.increment_shadow_number() time.sleep(60) if __name__ == "__main__": # Get environment variables scripts_home = os.getenv('SCRIPTS_HOME') if scripts_home is None: _inform("Environment variable SCRIPTS_HOME must be set!") sys.exit(1) home = os.getenv('HOME') if home is None: _inform("Environment variable HOME must be set!") sys.exit(1) # Get Connectome DB credentials userid = input("Connectome DB Username: "******"Connectome DB Password: ") # Get list of subjects to process subject_file_name = file_utils.get_subjects_file_name(__file__) _inform('Retrieving subject list from: ' + subject_file_name) subject_list = hcp7t_subject.read_subject_info_list(subject_file_name) # Process subjects in list batch_submitter = DeDriftAndResampleHcp7T_HighResBatchSubmitter() batch_submitter.submit_jobs(subject_list)
parser = my_argparse.MyArgumentParser( description="Submit a batch of HCP 7T MultiRunIcaFix Jobs") # option arguments # The -f or --force option tells this program to ignore the fact that a job may # already be running for a specified subject/scan and submit jobs anyhow. # Keep in mind that this will very likely royally screw up the mechanism for # keeping track of whether jobs are queued or running for that subject/scan. # But sometimes, particularly during testing, it is useful and necessary. parser.add_argument('-f', '--force', dest='force', action='store_true', required=False, default=False) # parse the command line arguments args = parser.parse_args() # get Database credentials userid = input("DB Username: "******"DB Password: "******"Retrieving subject list from: " + subject_file_name) subject_list = hcp7t_subject.read_subject_info_list(subject_file_name, separator=":") do_submissions(userid, password, subject_list, args.force)
submitter.put_server = put_server submitter.submit_jobs() if __name__ == "__main__": # Get Environment varialbles xnat_pbs_jobs_home = os.getenv('XNAT_PBS_JOBS') if not xnat_pbs_jobs_home: _inform("Environment variable XNAT_PBS_JOBS must be set!") sys.exit(1) # home = os.getenv('HOME') # if home == None: # _inform("Environment variable HOME must be set!") # sys.exit(1) # Get Connectome DB credentials userid = input("Connectome DB Username: "******"Connectome DB Password: ") # Get list of subjects to process subject_file_name = 'SubmitDiffusionPreprocessingHCP7TBatch.subjects' _inform('Retrieving subject list from: ' + subject_file_name) subject_list = hcp7t_subject.read_subject_info_list(subject_file_name) # Process the subjects in the list batch_submitter = BatchSubmitter() batch_submitter.submit_jobs(subject_list)
scan_results_dict['resource_exists'], scan_results_dict['resource_date'], scan_results_dict['files_exist']]) afile.write(output_str + os.linesep) print(output_str) print("") if __name__ == "__main__": # get list of subjects to check subject_file_name = file_utils.get_subjects_file_name(__file__) logger.info("Retrieving subject list from: " + subject_file_name) subject_list = hcp7t_subject.read_subject_info_list(subject_file_name, separator="\t") # create list of scans to check scans_to_check_list = [] scans_to_check_list.append('rfMRI_REST1_PA') scans_to_check_list.append('rfMRI_REST2_AP') scans_to_check_list.append('rfMRI_REST3_PA') scans_to_check_list.append('rfMRI_REST4_AP') scans_to_check_list.append('tfMRI_MOVIE1_AP') scans_to_check_list.append('tfMRI_MOVIE2_PA') scans_to_check_list.append('tfMRI_MOVIE3_PA') scans_to_check_list.append('tfMRI_MOVIE4_AP') # open complete and incomplete files for writing complete_file = open('complete.status', 'w') incomplete_file = open('incomplete.status', 'w')