#!/usr/bin/env python from hcpxnat.interface import HcpInterface idb = HcpInterface(config='/home/NRG/mhilem01/.hcpxnat_intradb.cfg') idb.project = 'NKI' sessions = idb.getSessions(project='NKI') for s in sessions: idb.subject_label = idb.session_label = s.get('label') idb.setExperimentElement('xnat:mrSessionData', 'scanner', 'MRC35390') idb.setExperimentElement('xnat:mrSessionData', 'acquisition_site', 'Nathan Kline Institute for Psychiatric Research')
#!/usr/bin/env python from hcpxnat.interface import HcpInterface from datetime import datetime import envoy # Use hcpxnat config file or assign each instance variable, e.g., # xnat = HcpInterface(url='http://intradb..', username='******', password='******', project='Proj') idb = HcpInterface(config='/data/intradb/home/hileman/.hcpxnat_intradb.cfg') idb.project = 'Phase2_Retest' pipeline = 'facemask' timestamp = datetime.now().strftime("%Y%m%d") outf = '/data/intradb/home/hileman/intradb_python_pipeline/log/%s_%s_%s.csv' % (idb.project, pipeline, timestamp) if __name__ == "__main__": session_labels = [s['label'] for s in idb.getSessions(idb.project)] session_labels = sorted(session_labels, key=lambda s: s.split('_')[0]) for s in session_labels: sub = s.split('_')[0] #if sub != '122317': # continue command = "python intradbPipelineResources.py -u %s -p %s -H %s -s %s -S %s -P %s -f %s -i %s" % \ (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 "\nHere's your csv:\n", outf
from datetime import datetime import envoy # Use hcpxnat config file or assign each instance variable, e.g., # xnat = HcpInterface(url='http://intradb..', username='******', password='******', project='Proj') idb = HcpInterface(config='/data/intradb/home/hileman/.hcpxnat_intradb.cfg') # Check resources for which pipeline? pipeline = 'dcm2nii' # For which project idb.project = 'DMC_Phase1a' timestamp = datetime.now().strftime("%Y%m%d") 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]
#!/usr/bin/env python from hcpxnat.interface import HcpInterface idb = HcpInterface(config="/home/NRG/mhilem01/.hcpxnat_intradb.cfg") idb.project = "NKI" sessions = idb.getSessions(project="NKI") for s in sessions: idb.subject_label = idb.session_label = s.get("label") scans = idb.getSessionScans() for s in scans: idb.scan_id = s.get("ID") sd = s.get("series_description") if "MUSIC" in sd: print s