outf = '/data/intradb/home/hileman/intradb_python_pipeline/log/%s_%s_%s.csv' % (idb.project, pipeline, timestamp)
print outf
if __name__ == "__main__":
sessions = idb.getSessions(idb.project)
session_labels = list()
for s in sessions:
#if 'Stroop' not in s.get('label'):
# continue
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
idb.session_label = s
sub = idb.getSessionSubject()
# fails sometimes, so check that this found something
#if not sub:
# sub = s.split('_')[0]
print sub
command = "python resources.py -u %s -p %s -H %s -s %s -S %s -P %s -f %s -i %s -I" % \
(idb.username, idb.password, idb.url, sub, s, idb.project, outf, pipeline)
print command
p = envoy.run(command)
if p.std_err:
print p.std_err
print "Here's your output:", outf
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:
