print pixel_array2.min()
ds.PixelData = pixel_array2.tostring()
# Save the image
ds.save_as(filename)
if __name__ == '__main__':
args = parse_args()
# Scans on XNAT:
try:
xnat = XnatUtils.get_interface()
li_scans = XnatUtils.list_project_scans(xnat, args.project)
# Filter:
if args.sessions:
li_scans = XnatUtils.filter_list_dicts_regex(
li_scans, 'session_label', args.sessions.split(','))
if args.subjects:
li_scans = XnatUtils.filter_list_dicts_regex(
li_scans, 'subject_label', args.subjects.split(','))
li_scans = sorted(li_scans, key=lambda k: k['session_label'])
for scan_d in li_scans:
if scan_d['ID'] == 'n004':
print (' -> converting session: %s /scan: %s'
% (scan_d['session_label'], scan_d['ID']))
if 'IMG' in scan_d['resources']:
if 'NIFTI' not in scan_d['resources'] or args.force:
tmp_dir = os.path.join(args.directory,
scan_d['session_label'],
scan_d['ID'])
if not os.path.isdir(tmp_dir):
os.makedirs(tmp_dir)
from dax import XnatUtils
import os
if __name__ == "__main__":
# Variables:
project = 'DIAN'
types = {'': 'PhoenixZIPReport'}
with XnatUtils.get_interface(host=os.environ['DPUK']) as xnat:
scans = XnatUtils.list_project_scans(xnat, project)
scans = XnatUtils.filter_list_dicts_regex(scans, 'type', types.keys())
for scan in sorted(scans, key=lambda k: k['session_label']):
print "%s - %s - %s - %s" % (scan["session_label"],
scan["ID"],
scan["type"],
scan["series_description"])
scan_obj = XnatUtils.get_full_object(xnat, scan)
scan_obj.attrs.set('type', types[scan['type']])
print(' new type: {}'.format(types[scan['type']]))
HOST = os.environ['XNAT_HOST']
if ARGS.username:
MSG = ("Please provide the password for user <%s> on xnat(%s):"
% (ARGS.username, HOST))
PWD = getpass.getpass(prompt=MSG)
else:
PWD = None
if not os.path.isdir(ARGS.tmpdir):
os.makedirs(ARGS.tmpdir)
print 'INFO: connection to xnat <%s>:' % (HOST)
XNAT = XnatUtils.get_interface(host=ARGS.host, user=ARGS.username,
pwd=PWD)
li_assessors = XnatUtils.list_project_assessors(XNAT, ARGS.project)
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'proctype',
['GIF_Parcellation_v2'])
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'procstatus',
['COMPLETE'])
li_assessors = filter(lambda x: 'WHOLEBRAIN' not in x['resources'],
li_assessors)
li_assessors = sorted(li_assessors, key=lambda k: k['session_label'])
start = False
for assessor in li_assessors:
if ARGS.session:
if assessor['session_label'] == ARGS.session:
start = True
else:
start = True
if start:
def get_sessions_list():
"""Extract sessions list from XNAT to be deleted."""
li_sessions = XnatUtils.list_sessions(XNAT, OPTIONS.project)
li_sessions = XnatUtils.filter_list_dicts_regex(
li_sessions, 'session_label', OPTIONS.sessions.split(','))
return li_sessions
if ARGS.host:
HOST = ARGS.host
else:
HOST = os.environ['XNAT_HOST']
if ARGS.username:
MSG = ("Please provide the password for user <%s> on xnat(%s):"
% (ARGS.username, HOST))
PWD = getpass.getpass(prompt=MSG)
else:
PWD = None
print 'INFO: connection to xnat <%s>:' % (HOST)
XNAT = XnatUtils.get_interface(host=ARGS.host, user=ARGS.username,
pwd=PWD)
li_assessors = XnatUtils.list_project_assessors(XNAT, ARGS.project)
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'proctype',
ARGS.proctype.split(','))
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'procstatus',
['COMPLETE'])
li_assessors = sorted(li_assessors, key=lambda k: k['session_label'])
for assessor in li_assessors:
assessor_obj = XnatUtils.get_full_object(XNAT, assessor)
if not assessor_obj.resource('PBS').exists():
assessor_obj.resource('PBS').create()
print 'Resource PBS added to %s.' % assessor['label']
finally:
XNAT.disconnect()
import sys
from dax import XnatUtils
SCAN = 'T2 Axial'
HOST = 'https://prostate-xnat.cs.ucl.ac.uk'
PROJECT = 'PICTURE'
RESOURCE = 'OsiriX'
OLD_FILE = 'mantonelli_Unnamed.rois_series'
NEW_FILE = 'Mrishta_Unnamed.rois_series'
TMP_DIR = '/Users/byvernault/data/temp_roi_upgrade/'
with XnatUtils.get_interface(host=HOST) as xnat:
li_scans = XnatUtils.list_project_scans(xnat, PROJECT)
li_scans = XnatUtils.filter_list_dicts_regex(li_scans, 'type', SCAN)
li_scans = filter(lambda x: RESOURCE in x['resources'], li_scans)
sys.stdout.write('Renaming file %s to %s for scan type %s\n'
% (OLD_FILE, NEW_FILE, SCAN))
for scan in li_scans:
sys.stdout.write(' - scan: %s / %s ...\n'
% (scan['session_label'], scan['ID']))
scan_obj = XnatUtils.get_full_object(xnat, scan)
res_obj = scan_obj.resource(RESOURCE)
files = None
if res_obj.exists() and OLD_FILE in res_obj.files().get()[:]:
# fpath = XnatUtils.download_file_from_obj(TMP_DIR, res_obj,
# fname=OLD_FILE)
# if fpath:
