def process_experiment(xnat, project, ident):
experiment_label = ident.get_xnat_experiment_id()
logger.info("Processing experiment: {}".format(experiment_label))
try:
xnat_experiment = xnat.get_experiment(project,
ident.get_xnat_subject_id(),
experiment_label)
except Exception as e:
logger.error("Unable to retrieve experiment {} from XNAT server. "
"{}: {}".format(experiment_label,
type(e).__name__, e))
return
if not db_ignore:
logger.debug("Adding session {} to dashboard".format(experiment_label))
try:
db_session = dashboard.get_session(ident, create=True)
except dashboard.DashboardException as e:
logger.error("Failed adding session {}. Reason: {}".format(
experiment_label, e))
else:
set_alt_ids(db_session, ident)
set_date(db_session, xnat_experiment)
if xnat_experiment.resource_files:
process_resources(xnat, ident, xnat_experiment)
if xnat_experiment.scans:
process_scans(xnat, ident, xnat_experiment)
def xnat_to_bids(xnat, project, ident, dcm2bids_opt):
bids_sub = ident.get_bids_name()
bids_ses = ident.timepoint
experiment_label = ident.get_xnat_experiment_id()
try:
xnat_experiment = xnat.get_experiment(project,
ident.get_xnat_subject_id(),
experiment_label)
except datman.exceptions.XnatException as e:
logger.error("Unable to retrieve experiment {} from XNAT server. "
"{}: {}".format(experiment_label,
type(e).__name__, e))
return
with datman.utils.make_temp_directory(prefix='xnat_to_bids_') as tempdir:
for scan in xnat_experiment.scans:
scan_temp = get_dicom_archive_from_xnat(xnat, scan, tempdir)
if not scan_temp:
logger.error("Failed getting series {} for experiment {} "
"from XNAT".format(scan.series, scan.experiment))
return
sub_dcm_dir = os.path.join(tempdir, experiment_label, "scans")
try:
dcm2bids_app = Dcm2bids(sub_dcm_dir,
bids_sub,
dcm2bids_opt.dcm2bids_config,
output_dir=dcm2bids_opt.bids_out,
session=bids_ses,
clobber=dcm2bids_opt.clobber,
forceDcm2niix=dcm2bids_opt.force_dcm2niix,
log_level="INFO")
dcm2bids_app.run()
except Exception as e:
logger.error("Dcm2Bids failed to run for experiment {}. {}:"
" {}".format(experiment_label,
type(e).__name__, e))
return
def process_session(session):
xnat_project = session[0]
session_label = session[1]
logger.info('Processing session:{}'.format(session[1]))
# check the session is valid on xnat
try:
xnat.get_session(xnat_project, session_label)
except Exception as e:
return
try:
experiments = xnat.get_experiments(xnat_project, session_label)
except Exception as e:
logger.warning('Failed getting experiments for:{} in project:{}'
' with reason:{}'.format(session_label, xnat_project,
e))
return
if len(experiments) > 1:
logger.error('Found more than one experiment for session:{}'
'in study:{} Skipping'.format(session_label,
xnat_project))
return
if not experiments:
logger.error('Session:{} in study:{} has no experiments'.format(
session_label, xnat_project))
return
experiment_label = experiments[0]['label']
# sesssion_label should be a valid datman scanid
try:
ident = datman.scanid.parse(session_label)
except datman.scanid.ParseException:
logger.error('Invalid session:{}, skipping'.format(session_label))
return
# experiment_label should be the same as the session_label
if not experiment_label == session_label:
logger.warning(
'Experiment label:{} doesnt match session_label:{}'.format(
experiment_label, session_label))
try:
experiment = xnat.get_experiment(xnat_project, session_label,
experiment_label)
except Exception as e:
logger.error(
'Failed getting experiment for session:{} with reason'.format(
session_label, e))
return
if not experiment:
logger.warning(
'No experiments found for session:{}'.format(session_label))
return
if dashboard:
logger.debug('Adding session:{} to db'.format(session_label))
try:
db_session_name = ident.get_full_subjectid_with_timepoint()
db_session = dashboard.get_add_session(
db_session_name,
date=experiment['data_fields']['date'],
create=True)
if ident.session and int(ident.session) > 1:
db_session.is_repeated = True
db_session.repeat_count = int(ident.session)
except datman.dashboard.DashboardException as e:
logger.error(
'Failed adding session:{} to dashboard'.format(session_label))
for data in experiment['children']:
if data['field'] == 'resources/resource':
process_resources(xnat_project, session_label, experiment_label,
data)
elif data['field'] == 'scans/scan':
process_scans(xnat_project, session_label, experiment_label, data)
else:
logger.warning('Unrecognised field type:{} for experiment:{}'
'in session:{} from study:{}'.format(
data['field'], experiment_label, session_label,
xnat_project))
def process_session(session):
xnat_project = session[0]
session_label = session[1]
logger.info("Processing session: {}".format(session_label))
# session_label should be a valid datman scanid
try:
ident = datman.scanid.parse(session_label)
except datman.scanid.ParseException:
logger.error("Invalid session: {}. Skipping".format(session_label))
return
# check that the session is valid on XNAT
try:
xnat.get_session(xnat_project, session_label)
except Exception as e:
logger.error("Error while getting session {} from XNAT. "
"Message: {}".format(session_label, e.message))
return
# look into XNAT project and get list of experiments
try:
experiments = xnat.get_experiments(xnat_project, session_label)
except Exception as e:
logger.warning("Failed getting experiments for: {} in project: {} "
"with reason: {}".format(session_label, xnat_project,
e))
return
# we expect exactly 1 experiment per session
if len(experiments) > 1:
logger.error("Found more than one experiment for session: {} "
"in study: {}. Skipping".format(session_label,
xnat_project))
return
if not experiments:
logger.error("Session: {} in study: {} has no experiments".format(
session_label, xnat_project))
return
experiment_label = experiments[0]['label']
# experiment_label should be the same as the session_label
if not experiment_label == session_label:
logger.warning(
"Experiment label: {} doesn't match session label: {}".format(
experiment_label, session_label))
# retrieve json table from project --> session --> experiment
try:
experiment = xnat.get_experiment(xnat_project, session_label,
experiment_label)
except Exception as e:
logger.error(
"Failed getting experiment for session: {} with reason".format(
session_label, e))
return
if not experiment:
logger.warning(
"No experiments found for session: {}".format(session_label))
return
if not db_ignore:
logger.debug("Adding session {} to dashboard".format(session_label))
try:
db_session = dashboard.get_session(ident, create=True)
except dashboard.DashboardException as e:
logger.error("Failed adding session {}. Reason: {}".format(
session_label, e))
else:
set_date(db_session, experiment)
# experiment['children'] is a list of top level folders in XNAT
# project --> session --> experiments
for data in experiment['children']:
if data['field'] == 'resources/resource':
process_resources(xnat_project, session_label, experiment_label,
data)
elif data['field'] == 'scans/scan':
process_scans(ident, xnat_project, session_label, experiment_label,
data)
else:
logger.warning("Unrecognised field type: {} for experiment: {} "
"in session: {} from study: {}".format(
data['field'], experiment_label, session_label,
xnat_project))