def groups(self):
subject_info = ccf_subject.SubjectInfo(self.project, self.subject, self.classifier)
preproc_dirs = self.archive.available_functional_preproc_dir_full_paths(subject_info)
groupsA = []
for preproc_dir in preproc_dirs:
groupsA.append(preproc_dir[preproc_dir.rindex(os.sep)+1:preproc_dir.index("_preproc")])
groupsA.sort()
return groupsA
def create_process_data_job_script(self):
module_logger.debug(debug_utils.get_name())
xnat_pbs_jobs_control_folder = os_utils.getenv_required(
'XNAT_PBS_JOBS_CONTROL')
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier, self.scan)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
mem_limit_str = str(self.mem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN) + ':gpus=1:K20x'
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + mem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
load_cuda = "module load cuda-9.1"
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version(
)
xnat_pbs_setup_singularity_process = 'singularity exec --nv -B ' + xnat_pbs_jobs_control_folder + ':/opt/xnat_pbs_jobs_control,' \
+ self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' + self._get_xnat_pbs_setup_script_singularity_qunexrun_path()
parameter_line = ' --parameterfolder=' + self._get_xnat_pbs_setup_script_singularity_qunexparameter_path(
)
studyfolder_line = ' --studyfolder=' + self.working_directory_name + '/' + self.subject + '_' + self.classifier
subject_line = ' --subjects=' + self.subject + '_' + self.classifier
overwrite_line = ' --overwrite=yes'
hcppipelineprocess_line = ' --hcppipelineprocess=DiffusionPreprocessing'
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(load_cuda + os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process + ' \\' +
os.linesep)
script.write(parameter_line + ' \\' + os.linesep)
script.write(studyfolder_line + ' \\' + os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(overwrite_line + ' \\' + os.linesep)
self._group_list = []
script.write(' --boldlist="' + self._expand(self.groups) +
'" \\' + os.linesep)
script.write(hcppipelineprocess_line + os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
def groups(self):
subject_info = ccf_subject.SubjectInfo(self.project, self.subject, self.classifier)
preproc_dirs = self.archive.available_functional_preproc_dir_full_paths(subject_info)
groupsA = []
for preproc_dir in preproc_dirs:
groupsA.append(preproc_dir[preproc_dir.rindex(os.sep)+1:preproc_dir.index("_preproc")])
def fmrisort(x):
priority = [ "rfMRI_REST1_AP","rfMRI_REST1_PA","rfMRI_REST1a_PA","rfMRI_REST1a_AP","rfMRI_REST1b_PA","rfMRI_REST1b_AP",
"tfMRI_GUESSING_PA","tfMRI_GUESSING_AP","tfMRI_VISMOTOR_PA","tfMRI_CARIT_PA","tfMRI_CARIT_AP","tfMRI_EMOTION_PA","tfMRI_FACENAME_PA",
"rfMRI_REST2_AP","rfMRI_REST2_PA","rfMRI_REST2a_AP","rfMRI_REST2a_PA","rfMRI_REST2b_AP","rfMRI_REST2b_PA" ]
return priority.index(x);
groupsA = sorted(groupsA, key=fmrisort)
return groupsA
def groups(self):
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier)
# diffusion not working, commenting it out and using functional
#preproc_dirs = self.archive.available_diffusion_preproc_dir_full_paths(subject_info)
preproc_dirs = self.archive.available_functional_preproc_dir_full_paths(
subject_info)
groupsA = []
for preproc_dir in preproc_dirs:
groupsA.append(preproc_dir[preproc_dir.rindex(os.sep) +
1:preproc_dir.index("_preproc")])
#groupsA.sort()
return groupsA
dest='output',
required=False,
type=str)
parser.add_argument('-a',
'--check-all',
dest='check_all',
action='store_true',
required=False,
default=False)
# parse the command line arguments
args = parser.parse_args()
# check the specified subject for structural preprocessing completion
subject_info = ccf_subject.SubjectInfo(project='irrelevant',
subject_id=args.subject,
classifier=args.classifier)
completion_checker = OneSubjectCompletionChecker()
if args.output:
processing_output = open(args.output, 'w')
else:
processing_output = sys.stdout
if completion_checker.is_processing_complete(
working_dir=args.working_dir,
fieldmap=args.fieldmap,
subject_info=subject_info,
verbose=args.verbose,
output=processing_output,
short_circuit=not args.check_all):
dest='output',
required=False,
type=str)
parser.add_argument('-a',
'--check-all',
dest='check_all',
action='store_true',
required=False,
default=False)
# parse the command line arguments
args = parser.parse_args()
# check the specified subject and scan for functional preprocessing completion
#subject_info = ccf_subject.SubjectInfo(project=args.project,subject_id=args.subject,classifier=args.classifier,extra=args.scan)
subject_info = ccf_subject.SubjectInfo('irrelevant', args.subject,
args.classifier, args.scan)
completion_checker = OneSubjectCompletionChecker()
if args.output:
processing_output = open(args.output, 'w')
else:
processing_output = sys.stdout
if completion_checker.is_processing_complete(
working_dir=args.working_dir,
subject_info=subject_info,
verbose=args.verbose,
output=processing_output,
short_circuit=not args.check_all):
print("Exiting with 0 code - Completion Check Successful")
exit(0)
qstat_queued_cmd = 'qstat -u ' + USER
qstat_queued_cmd += ' | grep ' + subject_info.subject_id + '.Struc'
qstat_queued_cmd += ' | grep " Q "'
qstat_stream = platform.popen(qstat_queued_cmd, "r")
qstat_results = qstat_stream.readline()
qstat_stream.close()
if qstat_results:
return 'Q'
return None
if __name__ == "__main__":
subject = ccf_subject.SubjectInfo(sys.argv[1], sys.argv[2], sys.argv[3])
status_checker = OneSubjectRunStatusChecker()
if status_checker.get_queued_or_running(subject):
print("-----")
print("project: " + subject.project)
print("subject: " + subject.subject_id)
print("session classifier: " + subject.classifier)
print("JOB IS ALREADY QUEUED OR RUNNING")
else:
print ("-----")
print("project: " + subject.project)
print("subject: " + subject.subject_id)
print("session classifier: " + subject.classifier)
print("JOB IS NOT RUNNING")
if __name__ == '__main__':
logging.config.fileConfig(
file_utils.get_logging_config_file_name(__file__),
disable_existing_loggers=False)
# get Database credentials
xnat_server = os_utils.getenv_required('XNAT_PBS_JOBS_XNAT_SERVER')
userid, password = user_utils.get_credentials(xnat_server)
# get list of subjects to process
subjectArg = sys.argv[1] if len(
sys.argv) > 1 and sys.argv[1].count(":") > 1 else None
if (subjectArg):
# Pull from first argument if passed
print("Retrieving subject list passed argument: " + subjectArg)
subject_list = []
subjectArg = subjectArg.strip()
(project, subject_id, classifier, extra) = subjectArg.split(":")
subject_info = ccf_subject.SubjectInfo(project, subject_id, classifier,
extra)
subject_list.append(subject_info)
else:
# Otherwise, pull from file
subject_file_name = file_utils.get_subjects_file_name(__file__)
print("Retrieving subject list from: " + subject_file_name)
subject_list = ccf_subject.read_subject_info_list(subject_file_name,
separator=":")
do_submissions(userid, password, subject_list)
def create_process_data_job_script(self):
project_build_dir = self.build_home + os.sep + self.project
pipeline_processing_dir = self.working_directory_name.replace(
project_build_dir + os.sep, '')
scratch_processing_dir = self._SCRATCH_PROCESSING_DIR + os.sep + self.project
if not os.path.exists(scratch_processing_dir):
os.mkdir(scratch_processing_dir)
module_logger.debug(debug_utils.get_name())
xnat_pbs_jobs_control_folder = os_utils.getenv_required(
'XNAT_PBS_JOBS_CONTROL')
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN) + ':haswell'
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + vmem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version(
)
xnat_pbs_setup_singularity_process = 'singularity exec -B ' \
+ self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' + self._get_xnat_pbs_setup_script_singularity_qunexrun_path()
parameter_line = ' --parameterfolder=' + self._get_xnat_pbs_setup_script_singularity_qunexparameter_path(
)
#studyfolder_line = ' --studyfolder=' + self.working_directory_name + '/' + self.subject + '_' + self.classifier
studyfolder_line = ' --studyfolder=' + scratch_processing_dir + os.sep + pipeline_processing_dir + os.sep + self.subject + '_' + self.classifier
subject_line = ' --subjects=' + self.subject + '_' + self.classifier
overwrite_line = ' --overwrite=yes'
hcppipelineprocess_line = ' --hcppipelineprocess=StructuralPreprocessing'
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(os.linesep)
script.write(
'# TEMPORARILY MOVE PROCESSING DIRECTORY TO SCRATCH SPACE DUE TO "Cannot allocate memory" ERRORS IN BUILD SPACE'
+ os.linesep)
script.write('mv ' + self.working_directory_name + " " +
scratch_processing_dir + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process + ' \\' +
os.linesep)
script.write(parameter_line + ' \\' + os.linesep)
script.write(studyfolder_line + ' \\' + os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(overwrite_line + ' \\' + os.linesep)
script.write(hcppipelineprocess_line + os.linesep)
script.write(os.linesep)
script.write('# MOVE PROCESSING BACK' + os.linesep)
script.write('mv ' + scratch_processing_dir + os.sep +
pipeline_processing_dir + ' ' + project_build_dir +
os.linesep)
script.write(os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
def create_process_data_job_script(self):
module_logger.debug(debug_utils.get_name())
# copy the .XNAT_PROCESS script to the working directory
processing_script_source_path = self.xnat_pbs_jobs_home
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += '.XNAT_PROCESS'
processing_script_dest_path = self.working_directory_name
processing_script_dest_path += os.sep + self.PIPELINE_NAME
processing_script_dest_path += '.XNAT_PROCESS'
shutil.copy(processing_script_source_path, processing_script_dest_path)
os.chmod(processing_script_dest_path, stat.S_IRWXU | stat.S_IRWXG)
# write the process data job script (that calls the .XNAT_PROCESS script)
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier, self.scan)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN)
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + vmem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
xnat_pbs_setup_line = 'source ' + self._get_xnat_pbs_setup_script_path(
) + ' ' + self._get_db_name()
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version(
)
xnat_pbs_setup_singularity_process = 'singularity exec -B ' + self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ',' + self._get_xnat_pbs_setup_script_freesurfer_license_path() + ':/export/freesurfer_license' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' + processing_script_source_path
subject_line = ' --subject=' + self.subject
scan_line = ' --scan=' + self.scan
session_classifier_line = ' --classifier=' + self.classifier
dcmethod_line = ' --dcmethod=TOPUP'
topupconfig_line = ' --topupconfig=b02b0.cnf'
gdcoeffs_line = ' --gdcoeffs=Prisma_3T_coeff_AS82.grad'
wdir_line = ' --working-dir=' + self.working_directory_name
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_line + os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process + ' \\' +
os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(scan_line + ' \\' + os.linesep)
script.write(session_classifier_line + ' \\' + os.linesep)
script.write(dcmethod_line + ' \\' + os.linesep)
script.write(topupconfig_line + ' \\' + os.linesep)
script.write(gdcoeffs_line + ' \\' + os.linesep)
script.write(wdir_line + os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
def create_process_data_job_script(self):
module_logger.debug(debug_utils.get_name())
xnat_pbs_jobs_control_folder = os_utils.getenv_required('XNAT_PBS_JOBS_CONTROL')
subject_info = ccf_subject.SubjectInfo(self.project, self.subject, self.classifier)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
## Using mem option instead of vmem for IcaFix
#vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
mem_limit_str = str(self.mem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN)
## FIX shouldn't be limited to haswell cores
#resources_line += ':haswell'
resources_line += ',walltime=' + walltime_limit_str
#resources_line += ',vmem=' + vmem_limit_str
resources_line += ',mem=' + mem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
scratch_tmpdir = '/scratch/' + os.getenv('USER') + '/singularity/tmp/' + self.subject + "_" + self.classifier;
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version()
make_scratch_tmpdir = 'mkdir -p ' + scratch_tmpdir
xnat_pbs_setup_singularity_process = 'singularity exec -B ' + xnat_pbs_jobs_control_folder + ':/opt/xnat_pbs_jobs_control' \
+ ',' + scratch_tmpdir + ':/tmp' \
+ ',' + self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' + self._get_xnat_pbs_setup_script_singularity_qunexrun_path()
#xnat_pbs_setup_singularity_process = '/opt/xnat_pbs_jobs_control/run_qunexContainer.sh'
#xnat_pbs_setup_singularity_process = self._get_xnat_pbs_setup_script_singularity_qunexrun_path()
#container_line = ' --containerpath=' + self._get_xnat_pbs_setup_script_singularity_container_path()
## Per MH, parameterfolder is irrelevant to MR-FIX
#parameter_line = ' --parameterfolder=' + self._get_xnat_pbs_setup_script_singularity_qunexparameter_path()
studyfolder_line = ' --studyfolder=' + self.working_directory_name + '/' + self.subject + '_' + self.classifier
subject_line = ' --subjects=' + self.subject+ '_' + self.classifier
overwrite_line = ' --overwrite=yes'
hcppipelineprocess_line = ' --hcppipelineprocess=MultiRunIcaFixProcessing'
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(make_scratch_tmpdir + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process+ ' \\' + os.linesep)
## Per MH, parameterfolder is irrelevant to MR-FIX
#script.write(parameter_line + ' \\' + os.linesep)
script.write(studyfolder_line + ' \\' + os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(overwrite_line + ' \\' + os.linesep)
#script.write(container_line + ' \\' + os.linesep)
self._group_list = []
script.write(' --boldlist="' + self._expand(self.groups) + '" \\' + os.linesep)
script.write(hcppipelineprocess_line + os.linesep)
script.close()
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
def create_process_data_job_script(self):
module_logger.debug(debug_utils.get_name())
# copy the .XNAT_PROCESS script to the working directory
processing_script_source_path = self.xnat_pbs_jobs_home
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += '.XNAT_PROCESS'
processing_script_dest_path = self.working_directory_name
processing_script_dest_path += os.sep + self.PIPELINE_NAME
processing_script_dest_path += '.XNAT_PROCESS'
shutil.copy(processing_script_source_path, processing_script_dest_path)
os.chmod(processing_script_dest_path, stat.S_IRWXU | stat.S_IRWXG)
# write the process data job script (that calls the .XNAT_PROCESS script)
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN)
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + vmem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
xnat_pbs_setup_line = 'source ' + self._get_xnat_pbs_setup_script_path(
) + ' ' + self._get_db_name()
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version(
)
xnat_pbs_setup_singularity_process = 'singularity exec -B ' + self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ',' + self._get_xnat_pbs_setup_script_freesurfer_license_path() + ':/export/freesurfer_license' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' + processing_script_source_path
subject_line = ' --subject=' + self.subject
session_classifier_line = ' --classifier=' + self.classifier
if self._has_spin_echo_field_maps(subject_info):
fieldmap_type_line = ' --fieldmap-type=' + 'SpinEcho'
else:
fieldmap_type_line = ' --fieldmap-type=' + 'SiemensGradientEcho'
first_t1w_directory_name_line = ' --first-t1w-directory-name=' + self._get_first_t1w_directory_name(
subject_info)
first_t1w_file_name_line = ' --first-t1w-file-name=' + self._get_first_t1w_file_name(
subject_info)
first_t2w_directory_name_line = ' --first-t2w-directory-name=' + self._get_first_t2w_directory_name(
subject_info)
first_t2w_file_name_line = ' --first-t2w-file-name=' + self._get_first_t2w_file_name(
subject_info)
brain_size_line = ' --brainsize=' + str(self.brain_size)
t1template_line = ' --t1template=' + self.T1W_TEMPLATE_NAME
t1templatebrain_line = ' --t1templatebrain=' + self.T1W_TEMPLATE_BRAIN_NAME
t1template2mm_line = ' --t1template2mm=' + self.T1W_TEMPLATE_2MM_NAME
t2template_line = ' --t2template=' + self.T2W_TEMPLATE_NAME
t2templatebrain_line = ' --t2templatebrain=' + self.T2W_TEMPLATE_BRAIN_NAME
t2template2mm_line = ' --t2template2mm=' + self.T2W_TEMPLATE_2MM_NAME
templatemask_line = ' --templatemask=' + self.TEMPLATE_MASK_NAME
template2mmmask_line = ' --template2mmmask=' + self.TEMPLATE_2MM_MASK_NAME
fnirtconfig_line = ' --fnirtconfig=' + self.FNIRT_CONFIG_FILE_NAME
if subject_info.project in OneSubjectJobSubmitter._CONNECTOME_SKYRA_SCANNER_PROJECTS:
gdcoeffs_line = ' --gdcoeffs=' + self.CONNECTOME_GDCOEFFS_FILE_NAME
elif subject_info.project in OneSubjectJobSubmitter._PRISMA_3T_PROJECTS:
gdcoeffs_line = ' --gdcoeffs=' + self.PRISMA_3T_GDCOEFFS_FILE_NAME
else:
raise ValueError(
"Unrecognized project for setting gradient distortion coefficients file: "
+ subject_info.project)
topupconfig_line = ' --topupconfig=' + self.TOPUP_CONFIG_FILE_NAME
if self._has_spin_echo_field_maps(subject_info):
se_phase_pos_line = ' --se-phase-pos=' + self._get_positive_spin_echo_file_name(
subject_info)
se_phase_neg_line = ' --se-phase-neg=' + self._get_negative_spin_echo_file_name(
subject_info)
# mag_line = None
# phase_line = None
else:
se_phase_pos_line = None
se_phase_neg_line = None
# mag_line = ' --fmapmag=' + self._get_fmap_mag_file_name(subject_info)
# phase_line = ' --fmapphase=' + self._get_fmap_phase_file_name(subject_info)
wdir_line = ' --working-dir=' + self.working_directory_name
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_line + os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process + ' \\' +
os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(session_classifier_line + ' \\' + os.linesep)
script.write(fieldmap_type_line + ' \\' + os.linesep)
script.write(first_t1w_directory_name_line + ' \\' + os.linesep)
script.write(first_t1w_file_name_line + ' \\' + os.linesep)
script.write(first_t2w_directory_name_line + ' \\' + os.linesep)
script.write(first_t2w_file_name_line + ' \\' + os.linesep)
script.write(brain_size_line + ' \\' + os.linesep)
script.write(t1template_line + ' \\' + os.linesep)
script.write(t1templatebrain_line + ' \\' + os.linesep)
script.write(t1template2mm_line + ' \\' + os.linesep)
script.write(t2template_line + ' \\' + os.linesep)
script.write(t2templatebrain_line + ' \\' + os.linesep)
script.write(t2template2mm_line + ' \\' + os.linesep)
script.write(templatemask_line + ' \\' + os.linesep)
script.write(template2mmmask_line + ' \\' + os.linesep)
script.write(fnirtconfig_line + ' \\' + os.linesep)
script.write(gdcoeffs_line + ' \\' + os.linesep)
script.write(topupconfig_line + ' \\' + os.linesep)
if (se_phase_pos_line):
script.write(se_phase_pos_line + ' \\' + os.linesep)
if (se_phase_neg_line):
script.write(se_phase_neg_line + ' \\' + os.linesep)
# if (mag_line): script.write(mag_line + ' \\' + os.linesep)
# if (phase_line): script.write(phase_line + ' \\' + os.linesep)
script.write(wdir_line + os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
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 create_process_data_job_script(self):
project_build_dir = self.build_home + os.sep + self.project
pipeline_processing_dir = self.working_directory_name.replace(project_build_dir + os.sep, '');
hand_edit_processing_dir = self._HAND_EDIT_PROCESSING_DIR + os.sep + self.project
if not os.path.exists(hand_edit_processing_dir):
os.mkdir(hand_edit_processing_dir)
module_logger.debug(debug_utils.get_name())
xnat_pbs_jobs_control_folder = os_utils.getenv_required('XNAT_PBS_JOBS_CONTROL')
subject_info = ccf_subject.SubjectInfo(self.project, self.subject, self.classifier)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN) + ':haswell'
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + vmem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
xnat_pbs_setup_line = 'source ' + self._get_xnat_pbs_setup_script_path() + ' ' + self._get_db_name()
xnat_pbs_setup_singularity_load = 'module load ' + self._get_xnat_pbs_setup_script_singularity_version()
## PREVIOUS LINE IS TEMPORARY ##
## TEMPORARY ##
##+ '/opt/xnat_pbs_jobs_control/run_qunex.sh'
xnat_pbs_setup_singularity_process = 'singularity exec -B ' \
+ xnat_pbs_jobs_control_folder + ':/opt/xnat_pbs_jobs_control' \
+ ',' + self._get_xnat_pbs_setup_script_archive_root() + ',' + self._get_xnat_pbs_setup_script_singularity_bind_path() \
+ ',' + self._get_xnat_pbs_setup_script_gradient_coefficient_path() + ':/export/HCP/gradient_coefficient_files' \
+ ' ' + self._get_xnat_pbs_setup_script_singularity_container_path() + ' ' \
+ os_utils.getenv_required('SINGULARITY_QUNEXRUN_PATH')
parameter_line = ' --parameterfolder=' + self._get_xnat_pbs_setup_script_singularity_qunexparameter_path()
#studyfolder_line = ' --studyfolder=' + self.working_directory_name + '/' + self.subject + '_' + self.classifier
studyfolder_line = ' --studyfolder=' + hand_edit_processing_dir + os.sep + pipeline_processing_dir + os.sep + self.subject + '_' + self.classifier
subject_line = ' --subjects=' + self.subject+ '_' + self.classifier
#hcpdatapath_line = ' --hcpdatapath=' + self.working_directory_name
#parameterfile_line = ' --parameterfile=' + xnat_pbs_jobs_control_folder + '/batch_parameters.txt'
#mapfile_line = ' --mapfile=' + xnat_pbs_jobs_control_folder + '/hcp_mapping.txt'
overwrite_line = ' --overwrite=yes'
hcppipelineprocess_line = ' --hcppipelineprocess=StructuralPreprocessingHandEdit'
fsextrareconall_line = ' --fs-extra-reconall=\'' + os_utils.getenv_required('FS_EXTRA_RECONALL') + '\''
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_line + os.linesep)
script.write(xnat_pbs_setup_singularity_load + os.linesep)
script.write(os.linesep)
script.write('# TEMPORARILY MOVE PROCESSING DIRECTORY TO SCRATCH SPACE DUE TO "Cannot allocate memory" ERRORS IN BUILD SPACE' + os.linesep)
script.write('mv ' + self.working_directory_name + " " + hand_edit_processing_dir + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_singularity_process+ ' \\' + os.linesep)
script.write(parameter_line + ' \\' + os.linesep)
script.write(studyfolder_line + ' \\' + os.linesep)
script.write(subject_line + ' \\' + os.linesep)
#script.write(hcpdatapath_line + ' \\' + os.linesep)
#script.write(parameterfile_line + ' \\' + os.linesep)
#script.write(mapfile_line + ' \\' + os.linesep)
script.write(overwrite_line + ' \\' + os.linesep)
script.write(hcppipelineprocess_line + ' \\' + os.linesep)
script.write(fsextrareconall_line + os.linesep)
script.write(os.linesep)
script.write('# MOVE PROCESSING BACK' + os.linesep)
script.write('mv ' + hand_edit_processing_dir + os.sep + pipeline_processing_dir + ' ' + project_build_dir + os.linesep)
script.write(os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
# optional arguments
parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',
required=False, default=False)
parser.add_argument('-o', '--output', dest='output', required=False, type=str)
parser.add_argument('-a', '--check-all', dest='check_all', action='store_true',
required=False, default=False)
# parse the command line arguments
args = parser.parse_args()
# check the specified subject and scan for functional preprocessing completion
archive = ccf_archive.CcfArchive()
subject_info = ccf_subject.SubjectInfo(
project=args.project,
subject_id=args.subject,
classifier=args.classifier,
extra=args.scan)
completion_checker = OneSubjectCompletionChecker()
if args.output:
processing_output = open(args.output, 'w')
else:
processing_output = sys.stdout
if completion_checker.is_processing_complete(
archive=archive,
subject_info=subject_info,
verbose=args.verbose,
output=processing_output,
short_circuit=not args.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:
print("Exiting with 1 code - Marked Completion Check Unsuccessful")
exit(1)
def create_process_data_job_script(self):
module_logger.debug(debug_utils.get_name())
# copy the .XNAT_PROCESS script to the working directory
processing_script_source_path = self.xnat_pbs_jobs_home
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += os.sep + self.PIPELINE_NAME
processing_script_source_path += '.XNAT_PROCESS'
processing_script_dest_path = self.working_directory_name
processing_script_dest_path += os.sep + self.PIPELINE_NAME
processing_script_dest_path += '.XNAT_PROCESS'
shutil.copy(processing_script_source_path, processing_script_dest_path)
os.chmod(processing_script_dest_path, stat.S_IRWXU | stat.S_IRWXG)
# write the process data job script (that calls the .XNAT_PROCESS script)
subject_info = ccf_subject.SubjectInfo(self.project, self.subject,
self.classifier, self.scan)
script_name = self.process_data_job_script_name
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit_str = str(self.walltime_limit_hours) + ':00:00'
vmem_limit_str = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=' + str(self.WORK_NODE_COUNT)
resources_line += ':ppn=' + str(self.WORK_PPN)
resources_line += ',walltime=' + walltime_limit_str
resources_line += ',mem=' + vmem_limit_str
stdout_line = '#PBS -o ' + self.working_directory_name
stderr_line = '#PBS -e ' + self.working_directory_name
xnat_pbs_setup_line = 'source ' + self._get_xnat_pbs_setup_script_path(
) + ' ' + self._get_db_name()
script_line = processing_script_dest_path
user_line = ' --user='******' --password='******' --server=' + str_utils.get_server_name(self.server)
project_line = ' --project=' + self.project
subject_line = ' --subject=' + self.subject
session_line = ' --session=' + self.session
scan_line = ' --scan=' + self.scan
session_classifier_line = ' --session-classifier=' + self.classifier
dcmethod_line = ' --dcmethod=TOPUP'
topupconfig_line = ' --topupconfig=b02b0.cnf'
gdcoeffs_line = ' --gdcoeffs=Prisma_3T_coeff_AS82.grad'
wdir_line = ' --working-dir=' + self.working_directory_name
setup_line = ' --setup-script=' + self.setup_file_name
with open(script_name, 'w') as script:
script.write(resources_line + os.linesep)
script.write(stdout_line + os.linesep)
script.write(stderr_line + os.linesep)
script.write(os.linesep)
script.write(xnat_pbs_setup_line + os.linesep)
script.write(os.linesep)
script.write(script_line + ' \\' + os.linesep)
script.write(user_line + ' \\' + os.linesep)
script.write(password_line + ' \\' + os.linesep)
script.write(server_line + ' \\' + os.linesep)
script.write(project_line + ' \\' + os.linesep)
script.write(subject_line + ' \\' + os.linesep)
script.write(session_line + ' \\' + os.linesep)
script.write(scan_line + ' \\' + os.linesep)
script.write(session_classifier_line + ' \\' + os.linesep)
script.write(dcmethod_line + ' \\' + os.linesep)
script.write(topupconfig_line + ' \\' + os.linesep)
script.write(gdcoeffs_line + ' \\' + os.linesep)
script.write(wdir_line + ' \\' + os.linesep)
script.write(setup_line + os.linesep)
os.chmod(script_name, stat.S_IRWXU | stat.S_IRWXG)
