def main():
archive = hcp3t_archive.Hcp3T_Archive()
project_names = ['HCP_500', 'HCP_900']
for project_name in project_names:
subject_ids = archive.available_subject_ids(project_name)
for subject_id in subject_ids:
subject_info = hcp3t_subject.Hcp3TSubjectInfo(
project_name, subject_id)
available_diffusion_scan_names = archive.available_diffusion_scan_names(
subject_info)
dir95_scan_LR_scan_name = subject_info.subject_id + '_3T_DWI_dir95_LR.nii.gz'
dir95_scan_RL_scan_name = subject_info.subject_id + '_3T_DWI_dir95_RL.nii.gz'
dir96_scan_LR_scan_name = subject_info.subject_id + '_3T_DWI_dir96_LR.nii.gz'
dir96_scan_RL_scan_name = subject_info.subject_id + '_3T_DWI_dir96_RL.nii.gz'
dir97_scan_LR_scan_name = subject_info.subject_id + '_3T_DWI_dir97_LR.nii.gz'
dir97_scan_RL_scan_name = subject_info.subject_id + '_3T_DWI_dir97_RL.nii.gz'
if ((dir96_scan_LR_scan_name in available_diffusion_scan_names) and
(dir96_scan_RL_scan_name in available_diffusion_scan_names) and
(dir97_scan_LR_scan_name in available_diffusion_scan_names) and
(dir97_scan_RL_scan_name in available_diffusion_scan_names)):
if ((dir95_scan_LR_scan_name in available_diffusion_scan_names)
and (dir95_scan_RL_scan_name
not in available_diffusion_scan_names)):
_inform(
"Subject: " + str(subject_info) +
" has all dir96 and dir97 scans and only dir95_LR.")
elif ((dir95_scan_LR_scan_name
not in available_diffusion_scan_names)
and (dir95_scan_RL_scan_name
in available_diffusion_scan_names)):
_inform(
"Subject: " + str(subject_info) +
" has all dir96 and dir97 scans and only dir95_RL.")
def main():
# create a parser object for getting the command line options
parser = my_argparse.MyArgumentParser(description="Program to check Diffusion Preprocessing Output size")
# mandatory arguments
parser.add_argument('-p', '--project', dest='project', required=True, type=str)
# optional arguments
parser.add_argument('-s', '--subject', dest='subject', required=False, default='all', type=str)
# parse the command line arguments
args = parser.parse_args()
# show parsed arguments
log.debug("Project: " + args.project)
log.debug("Subject: " + args.subject)
# create archive
archive = hcp3t_archive.Hcp3T_Archive()
# Create a list of subjects to process
subject_list = _build_subject_list(archive, args.project, args.subject)
all_succeeded = True
# Create a DiffusionOutputSizeChecker
size_checker = DiffusionOutputSizeChecker()
print("Subject\tExpected Volumes\tCheck Success")
for subject in subject_list:
subject_info = hcp3t_subject.Hcp3TSubjectInfo(args.project, subject)
try:
# check the diffusion preprocessing size for the specified subject
(success, expected_size, msg) = size_checker.check_diffusion_preproc_size(archive, subject_info)
print(subject_info.subject_id + "\t" + str(expected_size) + "\t" + str(success) + "\t" + msg)
all_succeeded = all_succeeded and success
except NoDiffusionPreprocResource as e:
print(subject_info.subject_id + "\t" + "N/A" + "\t" + "N/A" + "\t" + "No Diff Preproc Resource")
all_succeeded = False
except FileNotFoundError as e:
print(subject_info.subject_id + "\t" + "N/A" + "\t" + "N/A" + "\t" + "A necessary output file was not found")
all_succeeded = False
return all_succeeded
def _simple_interactive_demo():
archive = hcp3t_archive.Hcp3T_Archive()
completion_checker = OneSubjectCompletionChecker()
# 100307
subject_id_list = [
100307, 100408, 101006, 101107, 101309, 101410, 101915, 102008, 102311,
102816, 103111, 103414, 103515, 103818, 104012, 104820, 105014, 105115,
105216, 105923, 106016, 106319, 106521, 107321, 107422, 108121, 108323,
108525, 108828, 109123, 109325, 110411, 111312, 901442, 904044, 907656,
910241, 912447, 917255, 922854, 930449, 932554, 937160, 951457, 957974,
958976, 959574, 965367, 965771, 978578, 979984, 983773, 984472, 987983,
991267, 992774, 994273
]
for subject_id in subject_id_list:
hcp3t_subject_info = hcp3t_subject.Hcp3TSubjectInfo(
'HCP_500', str(subject_id))
log.info("Checking subject: " + hcp3t_subject_info.subject_id)
resource_exists = completion_checker.does_processed_resource_exist(
archive, hcp3t_subject_info)
log.info("resource_exists: " + str(resource_exists))
processing_complete = completion_checker.is_processing_complete(
archive, hcp3t_subject_info, False)
log.info("processing_complete: " + str(processing_complete))
try:
(success, expected_size,
msg) = output_size_checker.check_diffusion_preproc_size(
archive, hcp3t_subject_info)
log.info("expected_size: " + str(expected_size) + "\tsuccess: " +
str(success) + "\t" + msg)
except output_size_checker.NoDiffusionPreprocResource as e:
log.info("expected_size: " + "N/A" + "tsuccess: " + "N/A" + "\t" +
"No Diff Preproc Resource")
except FileNotFoundError as e:
log.info("expected_size: " + "N/A" + "tsuccess: " + "N/A" + "\t" +
"A necessary output file was not found")
def main():
archive = hcp3t_archive.Hcp3T_Archive()
project_names = ['HCP_500', 'HCP_900']
for project_name in project_names:
subject_ids = archive.available_subject_ids(project_name)
for subject_id in subject_ids:
subject_info = hcp3t_subject.Hcp3TSubjectInfo(project_name, subject_id)
available_diffusion_scan_fullpaths = archive.available_diffusion_scan_fullpaths(subject_info)
for diffusion_scan in available_diffusion_scan_fullpaths:
#_inform("")
volume_count = get_volume_count(diffusion_scan)
#_inform("diffusion_scan: " + diffusion_scan + " volume_count: " + str(volume_count))
expected_volume_count = get_expected_volume_count(diffusion_scan)
#_inform("diffusion_scan: " + diffusion_scan + " expected_volume_count: " + str(expected_volume_count))
if volume_count != expected_volume_count:
_inform("diffusion_scan: " + os.path.basename(diffusion_scan) +
" has expected volume count: " + str(expected_volume_count) +
" and actual volume count: " + str(volume_count))
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')
# open complete and incomplete files for writing
complete_file = open('complete.status', 'w')
incomplete_file = open('incomplete.status', 'w')
# create archive access object
archive = hcp3t_archive.Hcp3T_Archive()
# create on subject completion checker
completion_checker = one_subject_completion_checker.OneSubjectCompletionChecker(
)
# create and output the header line
header_line = "\t".join([
"Project", "Subject ID", "Output Resource Exists",
"Output Resource Date", "Files Exist"
])
print(header_line)
for subject in subject_list:
logger.debug("subject: " + str(subject))
def __init__(self):
super().__init__(hcp3t_archive.Hcp3T_Archive())
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)
parser.add_argument('-t',
'--structural-reference-project',
dest='structural_reference_project',
required=True,
type=str)
# optional arguments
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)
parser.add_argument('-j',
'--remove-job-and-catalog-files',
dest='remove_job_and_catalog_files',
action='store_true',
required=False,
default=False)
phase_choices = [
"FULL", "full", "DIFFUSION_PREPROC_VETTING",
"diffusion_preproc_vetting", "MULTIRUNICAFIX_PREREQS",
"multirunicafix_prereqs", "ICAFIX", "icafix", "MULTIRUNICAFIX",
"multirunicafix", "POSTFIX", "postfix"
]
parser.add_argument('-ph',
'--phase',
dest='phase',
required=False,
choices=phase_choices,
default="full")
# parse the command line arguments
args = parser.parse_args()
# show arguments
log.info("Arguments:")
log.info(" Project: " + args.project)
log.info(" Structural Ref Project: " + args.structural_reference_project)
log.info(" Subject: " + args.subject)
log.info(" Output Study Dir: " + args.output_study_dir)
log.info(" Copy: " + str(args.copy))
log.info(" Phase: " + args.phase)
log.info(" Log: " + str(args.log))
log.info(" Remove Non-Subdirs: " + str(args.remove_non_subdirs))
subject_info = hcp7t_subject.Hcp7TSubjectInfo(
project=args.project,
structural_reference_project=args.structural_reference_project,
subject_id=args.subject)
archive = hcp7t_archive.Hcp7T_Archive()
reference_archive = hcp3t_archive.Hcp3T_Archive()
# create and configure CinabStyleDataRetriever
data_retriever = CinabStyleDataRetriever(archive, reference_archive)
data_retriever.copy = args.copy
data_retriever.show_log = args.log
# retrieve data based on phase requested
args.phase = args.phase.upper()
if args.phase == "FULL":
data_retriever.get_full_data(subject_info, args.output_study_dir)
elif args.phase == "DIFFUSION_PREPROC_VETTING":
data_retriever.get_diffusion_preproc_vetting_data(
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 == "ICAFIX":
data_retriever.get_data_through_ICAFIX(subject_info,
args.output_study_dir)
elif args.phase == "MULTIRUNICAFIX":
data_retriever.get_data_through_multirun_ICAFIX(
subject_info, args.output_study_dir)
elif args.phase == "POSTFIX":
data_retriever.get_data_through_PostFix(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)
data_retriever.remove_non_subdirs(args.output_study_dir + os.sep +
subject_info.subject_id)
if args.remove_job_and_catalog_files:
# remove any PBS job files and XNAT catalog files
data_retriever.remove_pbs_job_files(args.output_study_dir)
data_retriever.remove_xnat_catalog_files(args.output_study_dir)
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('-c',
'--copy',
dest='copy',
action='store_true',
required=False,
default=False)
phase_choices = [
"FULL", "full", "DIFFUSION_PREPROC_VETTING",
"diffusion_preproc_vetting", "STRUCT_PREPROC", "struct_preproc",
"DIFFUSION_PREPROC", "diffusion_preproc", "DIFFUSION_BEDPOSTX",
"diffusion_bedpostx", "APPLY_HAND_RECLASSIFICATION_PREREQS",
"apply_hand_reclassification_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)
# parse the command line arguments
args = parser.parse_args()
# show arguments
module_logger.info("Arguments:")
module_logger.info(" Project: " + args.project)
module_logger.info(" Subject: " + args.subject)
module_logger.info(" Output Study Dir: " + args.output_study_dir)
module_logger.info(" Copy: " + str(args.copy))
module_logger.info(" Phase: " + args.phase)
subject_info = hcp3t_subject.Hcp3TSubjectInfo(args.project, args.subject)
archive = hcp3t_archive.Hcp3T_Archive()
# create and configure CinabStyleDataRetriever
data_retriever = CinabStyleDataRetriever(archive)
data_retriever.copy = args.copy
data_retriever.show_log = True
# retrieve data based on phase requested
if (args.phase.upper() == "FULL"):
module_logger.debug("phase = FULL")
data_retriever.get_full_data(subject_info, args.output_study_dir)
elif (args.phase.upper() == "DIFFUSION_PREPROC_VETTING"):
data_retriever.get_diffusion_preproc_vetting_data(
subject_info, args.output_study_dir)
elif (args.phase.upper() == "STRUCT_PREPROC"):
data_retriever.get_data_through_STRUCT_PREPROC(subject_info,
args.output_study_dir)
elif (args.phase.upper() == "DIFFUSION_PREPROC"):
data_retriever.get_data_through_DIFFUSION_PREPROC(
subject_info, args.output_study_dir)
elif (args.phase.upper() == "DIFFUSION_BEDPOSTX"):
data_retriever.get_diffusion_bedpostx_data(subject_info,
args.output_study_dir)
elif (args.phase.upper() == "APPLY_HAND_RECLASSIFICATION_PREREQS"):
data_retriever.get_apply_hand_reclassification_prereqs(
subject_info, args.output_study_dir)
elif (args.phase.upper() == "REAPPLYFIX_PREREQS"):
data_retriever.get_reapplyfix_prereqs(subject_info,
args.output_study_dir)
data_retriever.remove_symlinks(args.output_study_dir)
