def put(project,
subject,
sessions,
sub_folder,
config=None,
url=None,
pwd=None,
user=None,
processed=False):
if config is not None:
interface = Interface(config)
else:
interface = Interface(server=url,
user=user,
password=pwd,
proxy='www-int2:80')
uri = '/data/projects/%s/subjects/%s' % (project, subject)
response = interface.put(uri)
subject_uid = response.content
print('New subject %s created!' % subject_uid)
xnat_subs = interface.select.project(project).subjects()
xnat_sub = [x for x in xnat_subs if x.label() == subject][0]
sub_id = interface.select.project(project).subject(xnat_sub.id())
for session in sessions:
print('Processing session {}'.format(session))
session_folder = os.path.join(sub_folder, session)
scans = [
x for x in sorted(glob.glob(session_folder + '/*'))
if os.path.isfile(x)
]
match = session_modality_re.match(session)
proc = ''
if match is None and processed:
experiment_type = 'xnat:mrSessionData'
scan_type = 'xnat:mrScanData'
proc = '_processed'
elif match.group(1) == 'MR':
experiment_type = 'xnat:mrSessionData'
scan_type = 'xnat:mrScanData'
elif match.group(1) == 'CT' or match.group(1) == 'CTREF':
experiment_type = 'xnat:ctSessionData'
scan_type = 'xnat:ctScanData'
elif match.group(1) == 'RT':
experiment_type = 'xnat:rtSessionData'
scan_type = 'xnat:rtScanData'
experiment = sub_id.experiment('%s_%s%s' %
(xnat_sub.label(), session, proc))
if not experiment.exists():
try:
experiment.create(experiments=experiment_type)
except DatabaseError:
experiment.create(experiments=experiment_type)
print('New experiment %s created!' % experiment.id())
for scan in scans:
_, scan_name, extention = split_filename(scan)
res_format = get_resource_name(scan)
# scan_name = scan.split('/')[-1].split('.')[0]
print('Uploading {}...'.format(scan_name))
xnat_scan = experiment.scan(scan_name)
if not xnat_scan.exists():
done = False
z = 1
while not done:
try:
xnat_scan.create(scans=scan_type)
done = True
except DatabaseError:
print('Same Database error: {} times'.format(z))
z = z + 1
# xnat_scan.create(scans=scan_type)
print('New scan %s created!' % xnat_scan.id())
resource = xnat_scan.resource(res_format)
if not resource.exists():
try:
resource.create()
except DatabaseError:
resource.create()
print('New resource %s created!' % resource.id())
else:
print('Resource %s already in the repository!' %
resource.id())
xnat_resource = resource.file(scan_name + extention)
response = xnat_resource.put(src=scan,
format=res_format,
content=res_format,
extract=False,
overwrite=True)
else:
print('Scan %s already in the repository!' % xnat_scan.id())
