if not opts.username:
parser.print_help()
sys.exit(-1)
if opts.csv:
try:
csv_file = open(opts.csv, 'a')
except:
print "Problem with file " + opts.csv
exit(-1)
else:
print "No CSV option"
idb = HcpInterface(opts.hostname, opts.username, opts.password, opts.project)
idb.subject_label = opts.subject
idb.session_label = opts.session
deface_types = ('Bias_Transmit', 'Bias_Receive', 'T1w', 'T2w', 'T1w_MEG', 'T2w_MEG')
deface_seriesdescs = ('BIAS_BC', 'BIAS_32CH', 'AFI', 'T1w_MPR1', 'T2w_SPC1', 'T1w_MPR2', 'T2w_SPC2')
def verifyValidation():
"""
Checks for ProtocolVal at the experiment level.
"""
print "--Verifying Validation"
uri = '/REST/experiments?xsiType=val:protocolData&project=%s&session_label=%s' % \
(idb.project, idb.session_label)
validation = idb.getJson(uri)
print msg
log.warning(msg)
continue
idb.scan_resource = 'NIFTI'
log.info("Putting NIFTI resource - " + abspath)
idb.putScanResource(abspath)
if __name__ == "__main__":
subjects = get_subjects_from(opts.source)
idb.project = opts.project
if opts.dicom:
msg = "== Applying anonymize script: " + opts.anon
print msg
log.info(msg)
for sub in subjects:
os.path.walk(sub, process_dicoms, sub)
upload_dicom()
elif opts.nifti:
for sub in subjects:
idb.subject_label = sub
idb.session_label = sub
msg = "\n== Uploading NIFTI for subject " + sub + "..."
print msg
log.info(msg)
upload_nifti()
else:
print "Either --dicom or --nifti must be specified."
parser.print_help()
sys.exit(-1)
for qc_ass in qc_assessments:
idb.deleteSessionAssessor(qc_ass['label'])
if __name__ == "__main__":
sessions = opts.sessions.split(',')
print "=" * 82
print "Launching %s pipeline for %s sessions on %s" % \
(opts.pipeline, sessions.__len__(), idb.url)
print "Build directory: " + builddir
print "Archive directory: " + archivedir
print "=" * 82
for s in sessions:
idb.session_label = s
idb.subject_label = idb.getSessionSubject()
# TODO - fails sometimes, so check that this found something
if not idb.subject_label:
idb.subject_label = s.split('_')[0] # Not general, but often works
print '\n** Subject: ' + idb.subject_label
print '** Session: ' + s + '\n'
if opts.pipeline == 'validation':
launchValidation()
elif opts.pipeline == 'facemask':
launchFacemask()
elif opts.pipeline == 'dcm2nii':
launchDicomToNifti()
elif opts.pipeline == 'level2qc':
# Set default delay for level2qc
if not opts.delay:
