def _path_to_running_marker_file(self, subject_info):
file_name = self.PIPELINE_NAME
file_name += '.' + subject_info.subject_id
file_name += '_' + subject_info.classifier
file_name += '.' + 'RUNNING'
archive = ccf_archive.CcfArchive()
self.running_status_dir = archive.running_status_dir_full_path(subject_info)
path = self.running_status_dir + os.sep + file_name
#print("path: " + path)
return path
'--check-all',
dest='check_all',
action='store_true',
required=False,
default=False)
parser.add_argument('-m',
'--marked',
dest='marked',
action='store_true',
required=False,
default=False)
# parse the command line arguments
args = parser.parse_args()
# check the specified subject for structural preprocessing completion
archive = ccf_archive.CcfArchive()
subject_info = ccf_subject.SubjectInfo(args.project, args.subject,
args.classifier)
completion_checker = OneSubjectCompletionXnatChecker()
if args.output:
processing_output = open(args.output, 'w')
else:
processing_output = sys.stdout
if args.marked:
if completion_checker.is_processing_marked_complete(
archive=archive, subject_info=subject_info):
print("Exiting with 0 code - Marked Completion Check Successful")
exit(0)
else:
def main():
# create a parser object for getting the command line arguments
parser = my_argparse.MyArgumentParser()
# mandatory arguments
parser.add_argument('-p',
'--project',
dest='project',
required=True,
type=str)
parser.add_argument('-s',
'--subject',
dest='subject',
required=True,
type=str)
parser.add_argument('-d',
'--study-dir',
dest='output_study_dir',
required=True,
type=str)
# optional arguments
parser.add_argument('-a',
'--scan',
dest='scan',
required=False,
type=str,
default=None)
parser.add_argument('-c',
'--copy',
dest='copy',
action='store_true',
required=False,
default=False)
parser.add_argument('-l',
'--log',
dest='log',
action='store_true',
required=False,
default=False)
parser.add_argument('-r',
'--remove-non-subdirs',
dest='remove_non_subdirs',
action='store_true',
required=False,
default=False)
phase_choices = [
"STRUCT_PREPROC_PREREQS", "struct_preproc_prereqs",
"STRUCT_PREPROC_HAND_EDIT_PREREQS", "struct_preproc_hand_edit_prereqs",
"DIFF_PREPROC_PREREQS", "diff_preproc_prereqs", "FUNC_PREPROC_PREREQS",
"func_preproc_prereqs", "MULTIRUNICAFIX_PREREQS",
"multirunicafix_prereqs", "MSMALL_PREREQS", "msmall_prereqs",
"DEDRIFTANDRESAMPLE_PREREQS", "dedriftandresample_prereqs",
"REAPPLYFIX_PREREQS", "reapplyfix_prereqs"
]
default_phase_choice = phase_choices[0]
parser.add_argument('-ph',
'--phase',
dest='phase',
required=False,
choices=phase_choices,
default=default_phase_choice)
parser.add_argument('-cl',
'--classifier',
dest='session_classifier',
required=False,
type=str,
default='3T')
# parse the command line arguments
args = parser.parse_args()
# convert phase argument to uppercase
args.phase = args.phase.upper()
# show arguments
module_logger.info("Arguments:")
module_logger.info(" Project: " + args.project)
module_logger.info(" Subject: " + args.subject)
module_logger.info(" Session Classifier: " + args.session_classifier)
module_logger.info(" Output Dir: " + args.output_study_dir)
module_logger.info(" Phase: " + args.phase)
if args.copy:
module_logger.info(" Copy: " + str(args.copy))
if args.log:
module_logger.info(" Log: " + str(args.log))
if args.remove_non_subdirs:
module_logger.info(" Remove Non-Subdirs: " +
str(args.remove_non_subdirs))
subject_info = ccf_subject.SubjectInfo(args.project, args.subject,
args.session_classifier, args.scan)
archive = ccf_archive.CcfArchive()
data_retriever = DataRetriever(archive)
data_retriever.copy = args.copy
data_retriever.show_log = args.log
# retrieve data based on phase requested
if args.phase == "STRUCT_PREPROC_PREREQS":
data_retriever.get_struct_preproc_prereqs(subject_info,
args.output_study_dir)
elif args.phase == "STRUCT_PREPROC_HAND_EDIT_PREREQS":
data_retriever.get_struct_preproc_hand_edit_prereqs(
subject_info, args.output_study_dir)
elif args.phase == "DIFF_PREPROC_PREREQS":
data_retriever.get_diffusion_preproc_prereqs(subject_info,
args.output_study_dir)
elif args.phase == "FUNC_PREPROC_PREREQS":
data_retriever.get_functional_preproc_prereqs(subject_info,
args.output_study_dir)
elif args.phase == "MULTIRUNICAFIX_PREREQS":
data_retriever.get_multirunicafix_prereqs(subject_info,
args.output_study_dir)
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)
def __init__(self):
super().__init__(ccf_archive.CcfArchive())
print("reg_name: " + args.reg_name)
# get list of subjects to check
subject_file_name = 'subjectfiles' + os.sep + file_utils.get_subjects_file_name(
__file__)
module_logger.info("Retrieving subject list from: " + subject_file_name)
subject_list = ccf_subject.read_subject_info_list(subject_file_name,
separator=":")
# open output file
output_file = open('ReApplyFix.status', 'w')
_write_header()
# create archive
archive = ccf_archive.CcfArchive('3T')
# create one subject completion checker
completion_checker = one_subject_completion_checker.OneSubjectCompletionChecker(
)
if args.reg_name != "":
module_logger.info("setting completion checker reg_name to " +
args.reg_name)
completion_checker.reg_name = args.reg_name
for subject in subject_list:
subject_id = subject.subject_id
project = subject.project
scan = subject.extra
module_logger.debug(" id: " + subject_id)
