def put_dicoms(self, project, session, experiment, filename, retries=3):
"""Upload an archive of dicoms to XNAT
filename: archive to upload"""
headers = {'Content-Type': 'application/zip'}
upload_url = "{server}/data/services/import?project={project}" \
"&subject={subject}&session={session}&overwrite=delete" \
"&prearchive=false&inbody=true"
upload_url = upload_url.format(server=self.server,
project=project,
subject=session,
session=experiment)
try:
with open(filename) as data:
self._make_xnat_post(upload_url, data, retries, headers)
except XnatException as e:
e.study = project
e.session = session
raise e
except IOError as e:
logger.error('Failed to open file:{} with excuse:'
.format(filename, e.strerror))
err = XnatException("Error in file:{}".
format(filename))
err.study = project
err.session = session
raise err
except requests.exceptions.RequestException as e:
err = XnatException("Error uploading data with url:{}"
.format(upload_url))
err.study = project
err.session = session
raise err
def get_dicom(self, project, session, experiment, scan,
filename=None, retries=3):
"""Downloads a dicom file from xnat to filename
If filename is not specified creates a temporary file
and returns the path to that, user needs to be responsible
for cleaning up any created tempfiles"""
url = '{}/data/archive/projects/{}/' \
'subjects/{}/experiments/{}/' \
'scans/{}/resources/DICOM/files?format=zip' \
.format(self.server, project, session, experiment, scan)
if not filename:
filename = tempfile.mkstemp(prefix="dm2_xnat_extract_")
# mkstemp returns a filename and a file object
# dealing with the filename in future so close the file object
os.close(filename[0])
try:
self._get_xnat_stream(url, filename, retries)
return(filename)
except:
try:
os.remove(filename[1])
except OSError as e:
logger.warning('Failed to delete tempfile:{} with excuse:{}'
.format(filename, str(e)))
err = XnatException("Failed getting dicom with url:{}".format(url))
err.study = project
err.session = session
raise err
def get_scan_list(self, study, session, experiment):
"""The list of dicom scans in an experiment"""
url = '{}/data/archive/projects/{}' \
'/subjects/{}/experiments/{}' \
'/scans/?format=json'.format(self.server,
study,
session,
experiment)
try:
result = self._make_xnat_query(url)
except:
return XnatException('Failed getting scans with url:{}'
.format(url))
if result is None:
e = XnatException('Scan not found for experiment:{}'
.format(experiment))
e.study = study
e.session = session
raise e
return(result['ResultSet']['Result'])
def put_resource(self, project, session, experiment, filename, data, folder,
retries=3):
"""POST a resource file to the xnat server
filename: string to store filename as
data: string containing data
(such as produced by zipfile.ZipFile.read())"""
resource_id = self.get_resource_ids(project,
session,
experiment,
folderName=folder)
attach_url = "{server}/data/archive/projects/{project}/" \
"subjects/{subject}/experiments/{experiment}/" \
"resources/{resource_id}/" \
"files/{filename}?inbody=true"
uploadname = urllib.quote(filename)
url = attach_url.format(server=self.server,
project=project,
subject=session,
experiment=experiment,
resource_id=resource_id,
filename=uploadname)
try:
self._make_xnat_post(url, data)
except XnatException as err:
err.study = project
err.session = session
raise err
except:
logger.warning("Failed adding resource to xnat with url:{}"
.format(url))
err = XnatException("Failed adding resource to xnat")
err.study = project
err.session = session
def get_scan_info(self, study, session, experiment, scanid):
"""Returns info about an xnat scan"""
url = '{}/data/archive/projects/{}' \
'/subjects/{}/experiments/{}' \
'/scans/{}/?format=json'.format(self.server,
study,
session,
experiment,
scanid)
try:
result = self._make_xnat_query(url)
except:
return XnatException('Failed getting scan with url:{}'
.format(url))
if result is None:
e = XnatException('Scan:{} not found for experiment:{}'
.format(scanid, experiment))
e.study = study
e.session = session
raise e
return(result['items'][0])