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')
