# import of third party modules
# import of local modules
import hcp.hcp3t.archive as hcp3t_archive
import hcp.hcp3t.bedpostx.one_subject_completion_checker as one_subject_completion_checker
import hcp.hcp3t.subject as hcp3t_subject
import utils.file_utils as file_utils
# authorship information
__author__ = "Timothy B. Brown"
__copyright__ = "Copyright 2016, The Human Connectome Project"
__maintainer__ = "Timothy B. Brown"
# configure logging and create module logger
logging.config.fileConfig(file_utils.get_logging_config_file_name(__file__))
logger = logging.getLogger(file_utils.get_logger_name(__file__))
# module constants
DNM = "---" # Does Not Matter
NA = "N/A" # Not Available
DATE_FORMAT = '%Y-%m-%d %H:%M:%S'
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 = hcp3t_subject.read_subject_info_list(subject_file_name,
separator='\t')
# import of third party modules
# None
# import of local modules
import hcp.hcp7t.archive as hcp7t_archive
import hcp.hcp7t.resting_state_stats.one_subject_completion_checker as one_subject_completion_checker
import hcp.hcp7t.subject as hcp7t_subject
import utils.file_utils as file_utils
# authorship information
__author__ = "Timothy B. Brown"
__copyright__ = "Copyright 2016, The Human Connectome Project"
__maintainer__ = "Timothy B. Brown"
# configure logging and create module logger
logging.config.fileConfig(file_utils.get_logging_config_file_name(__file__))
logger = logging.getLogger(file_utils.get_logger_name(__file__))
DNM = "---" # Does Not Matter
NA = "N/A" # Not Available
DATE_FORMAT = '%Y-%m-%d %H:%M:%S'
def get_resource_name(scan_name):
return scan_name + '_RSS'
def _is_subject_complete(subject_results_dict):
for scan, scan_results_dict in subject_results_dict.items():
if scan_results_dict['files_exist'] == 'FALSE':
return False
# read the configuration file
config_file_name = file_utils.get_config_file_name(__file__)
print("Reading configuration from file: " + config_file_name)
config = my_configparser.MyConfigParser()
config.read(config_file_name)
# process subjects in the list
batch_submitter = BatchSubmitter()
batch_submitter.submit_jobs(userid, password, subject_list, config,
force_submission)
if __name__ == '__main__':
logging_config_file_name = file_utils.get_logging_config_file_name(
__file__)
print("Reading logging configuration from file: " +
logging_config_file_name)
logging.config.fileConfig(logging_config_file_name,
disable_existing_loggers=False)
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',
elif args.phase == "MSMALL_PREREQS":
data_retriever.get_msmall_prereqs(subject_info, args.output_study_dir)
elif args.phase == "DEDRIFTANDRESAMPLE_PREREQS":
data_retriever.get_dedriftandresample_prereqs(subject_info,
args.output_study_dir)
# Get the group average drift data
# As of February 2017, the group average drift data has been moved from HCP_Staging to
# HCP_1200
data_retriever.get_msm_group_average_drift_data(
"HCP_1200", args.output_study_dir)
elif args.phase == "REAPPLYFIX_PREREQS":
data_retriever.get_reapplyfix_prereqs(subject_info,
args.output_study_dir)
if args.remove_non_subdirs:
# remove any non-subdirectory data at the output study directory level
data_retriever.remove_non_subdirs(args.output_study_dir)
if __name__ == '__main__':
logging_config_file_name = file_utils.get_logging_config_file_name(
__file__, use_env_variable=False)
print("logging_config_file_name:", logging_config_file_name)
logging.config.fileConfig(logging_config_file_name,
disable_existing_loggers=False)
main()
