#!/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
