#!/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
#!/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")
# Check resources for which pipeline?
pipeline = "dcm2nii"
# For which project
idb.project = "Mamah_CPC"
timestamp = datetime.now().strftime("%Y%m%d")
outf = "/data/intradb/home/hileman/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:
session_labels.append(s.get("label"))
session_labels = sorted(session_labels, key=lambda s: s.split("_")[0])
for s in session_labels:
sub = s.split("_")[0]
command = "python intradbPipelineResources.py -u %s -p %s -H %s -s %s -S %s -P %s -f %s -i %s -I" % (
idb.username,
idb.password,
idb.url,
#!/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')
# Check resources for which pipeline?
pipeline = 'level2qc'
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:
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
sub = s.split('_')[0]
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
#!/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 = 'LS_Phase1a'
pipeline = 'all'
timestamp = datetime.now().strftime("%Y%m%d")
outf = '/data/intradb/home/hileman/pipeline/log/%s_%s_%s.csv' % (idb.project, pipeline, timestamp)
if __name__ == "__main__":
sessions = idb.getSessions(idb.project)
session_labels = list()
for s in sessions:
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
sub = s.split('_')[0]
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
fh.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
fh.setFormatter(formatter)
log.addHandler(fh)
#################
### LOAD SCAN MAP ###
if opts.map:
with open(opts.map) as data:
scan_file_map = json.load(data)
#####################
SCRIPTDIR = os.path.abspath(os.path.curdir) + '/'
DCMADDRESS = 'dicom://' + opts.host + ':8104/HCP'
#idb = HcpInterface(config='/home/NRG/mhilem01/.hcpxnat_intradb_dev.cfg')
idb = HcpInterface(config='/data/intradb/home/hileman/.hcpxnat_intradb.cfg')
idb.url = 'https://' + opts.host
def get_subjects_from(directory):
"""
Assumes the source directory contains subject labels
"""
os.chdir(directory)
dirs = [d for d in os.listdir(os.curdir)
if os.path.isdir(os.path.join(os.curdir, d))]
subs = []
for d in dirs:
if d.isdigit():
subs.append(d)
return subs
# Currently assume overwrite for facemask and dcm2nii
parser.add_option("-U", "--unusable", action="store_true", dest="unusable", default=False,
help='Try defacing unusable scans (skipped by default)')
parser.add_option("-d", "--delay", action="store", type="string", dest="delay",
help='Delay between pipeline launches in minutes')
parser.add_option("-D", "--dryRun", action="store_true", dest="dryRun", default=False)
# For existing resources, we currently assume Overwrite
(opts, args) = parser.parse_args()
if not opts.username:
parser.print_help()
sys.exit(-1)
idb = HcpInterface(opts.hostname, opts.username, opts.password, opts.project)
timestamp = datetime.datetime.now().strftime("%Y%m%d%M%s")
builddir = '/data/intradb/build/' + opts.project + '/' + timestamp
archivedir = '/data/intradb/archive/' + opts.project + '/arc001'
if not os.path.exists(builddir):
os.makedirs(builddir)
runOtherParam = 'Y' if opts.runOther else 'N'
#######################################################
# Pipline versions
facemask_versions = {
'HCP_Phase2': 'FaceMasking/FaceMasking.xml',
#!/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
#!/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_7T'
# Check resources for which pipeline?
pipeline = 'level2qc'
timestamp = datetime.now().strftime("%Y%m%d")
outf = '/data/intradb/home/hileman/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:
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
sub = s.split('_')[0]
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:
import sys
import os
import argparse
from hcpxnat.interface import HcpInterface
"""
Takes a CSV submitted to NDA by CCF contributor and uploads
"""
# hcpxnat module config
config_file = os.path.join(os.path.expanduser('~'), '.xnat_dev.cfg')
idb = HcpInterface(config=config_file)
# argument parser
parser = argparse.ArgumentParser(prog='genxsd.py')
parser.add_argument('-p', dest='project', required=True,
help='Project to upload to')
parser.add_argument('-f', dest='filename', required=True,
help='CSV filename to upload')
parser.add_argument('--create-subject', dest='create_subject', required=False,
action='store_true', help='Create the subject')
args = parser.parse_args()
idb.project = args.project
if not idb.projectExists():
print "++ Project {} does not exists. Exiting...".format(args.project)
sys.exit(1)
def createSubject():
print "-- Creating subject {sub}".format(sub=idb.subject_label)
#!/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')
mapping = {
#'REST_645': 'rfMRI',
#'MPRAGE_SIEMENS': 'T1w',
#'REST_1400': 'rfMRI',
#'REST_CAP': 'rfMRI',
#'CHECKERBOARD_645': 'tfMRI',
#'CHECKERBOARD_1400': 'tfMRI',
#'BREATH_HOLD_1400': 'tfMRI',
#'DIFF_137_AP': 'dMRI'
#'MPRAGE_SIEMENS_DEFACED': 'T1w',
#'MPRAGE_SIEMENS_MUSIC ONLY': 'T1w',
#'FLAIR - ch32 iPAT2 -CLINICAL': 'T2w',
'MPRAGE': 'T1w'
}
for s in sessions:
idb.subject_label = idb.session_label = s.get('label')
scans = idb.getSessionScans()
print "\nModifying series_desc for session " + idb.session_label
for s in scans:
idb.scan_id = s.get('ID')
sd = s.get('series_description')
#!/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')
# Check resources for which pipeline?
pipeline = 'level2qc'
# For which project
idb.project = 'Mamah_CPC'
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:
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
sub = s.split('_')[0]
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)
(opts, args) = parser.parse_args()
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)
#!/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')
# Check resources for which pipeline?
pipeline = 'level2qc'
idb.project = 'LS_3T7T_1B'
timestamp = datetime.now().strftime("%Y%m%d")
outf = '/data/intradb/home/hileman/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:
session_labels.append(s.get('label'))
session_labels = sorted(session_labels, key=lambda s: s.split('_')[0])
for s in session_labels:
sub = s.split('_')[0]
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)
#!/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 = "LS_Phase1b"
pipeline = "level2qc"
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__":
sessions = idb.getSessions(idb.project)
session_labels = list()
for s in sessions:
session_labels.append(s.get("label"))
session_labels = sorted(session_labels, key=lambda s: s.split("_")[0])
for s in session_labels:
sub = s.split("_")[0]
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,
#!/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')
# 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
import os
parser = OptionParser()
parser.add_option("-s", "--sessions", action="store", type="string", dest="sessions")
parser.add_option("-p", "--project", action="store", type="string", dest="project",
help="Not yet implemented")
parser.add_option("-u", "--sge-user", action="store", type="string", dest="user",
help="Not yet implemented")
(opts, args) = parser.parse_args()
if not (opts.sessions or opts.project or opts.user):
#print('Monitoring all pipeline processes for hcpinternal ...')
#time.sleep(3)
parser.print_help()
sys.exit(-1)
idb = HcpInterface(config='/data/intradb/home/hileman/.hcpxnat_intradb.cfg')
idb.project = opts.project
sessions_list = []
def get_sessions_list():
sessions = idb.getSessions(project=idb.project)
for s in sessions:
sessions_list.append(s['label'])
if opts.sessions:
sessions_list = opts.sessions.split(',')
sessions_str = opts.sessions.replace(',', '|')
def monitor_sessions():
"""
Assumes hcpinternal user
#!/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')
# Check resources for which pipeline?
pipeline = 'facemask'
# For which project
idb.project = 'PDSIII'
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:
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:
print "getSessionSubject() failed. Assuming a naming convention."
