def get_dicom_archive_from_xnat(xnat_project, session_label, experiment_label,
series):
"""Downloads and extracts a dicom archive from xnat to a local temp folder
Returns the path to the tempdir (for later cleanup) as well as the
path to the .dcm files inside the tempdir
"""
# going to create a local directory and make a copy of the
# dicom files there
tempdir = tempfile.mkdtemp(prefix='dm2_xnat_extract_')
logger.debug('Downloading dicoms for:{}, series:{}.'.format(
session_label, series))
try:
dicom_archive = xnat.get_dicom(xnat_project, session_label,
experiment_label, series)
except Exception as e:
logger.error(
'Failed to download dicom archive for:{}, series:{}'.format(
session_label, series))
return None, None
logger.debug('Unpacking archive')
try:
with zipfile.ZipFile(dicom_archive[1], 'r') as myzip:
myzip.extractall(tempdir)
except:
logger.error('An error occurred unpacking dicom archive for:{}'
' skipping'.format(session_label))
os.remove(dicom_archive[1])
return None, None
logger.debug('Deleting archive file')
os.remove(dicom_archive[1])
# get the root dir for the extracted files
archive_files = []
for root, dirname, filenames in os.walk(tempdir):
for filename in filenames:
f = os.path.join(root, filename)
if is_valid_dicom(f):
archive_files.append(f)
try:
base_dir = os.path.dirname(archive_files[0])
except IndexError:
logger.warning(
'There were no valid dicom files in xnat session:{}, series:{}'.
format(session_label, series))
shutil.rmtree(tempdir)
return None, None
return (tempdir, base_dir)
def get_dicom_archive_from_xnat(xnat_project, session_label, experiment_label,
series, tempdir):
"""
Downloads and extracts a dicom archive from XNAT to a local temp folder
Returns the path to the tempdir (for later cleanup) as well as the
path to the .dcm files inside the tempdir
"""
# make a copy of the dicom files in a local directory
logger.info("Downloading dicoms for: {}, series: {}".format(
session_label, series))
try:
dicom_archive = xnat.get_dicom(xnat_project, session_label,
experiment_label, series)
except Exception as e:
logger.error(
"Failed to download dicom archive for: {}, series: {}".format(
session_label, series))
return None
logger.info("Unpacking archive")
try:
with zipfile.ZipFile(dicom_archive, 'r') as myzip:
myzip.extractall(tempdir)
except:
logger.error(
"An error occurred unpacking dicom archive for: {}. Skipping".
format(session_label))
os.remove(dicom_archive)
return None
logger.info("Deleting archive file")
os.remove(dicom_archive)
# get the root dir for the extracted files
archive_files = []
for root, dirname, filenames in os.walk(tempdir):
for filename in filenames:
f = os.path.join(root, filename)
if is_valid_dicom(f):
archive_files.append(f)
try:
base_dir = os.path.dirname(archive_files[0])
except IndexError:
logger.warning(
"There were no valid dicom files in XNAT session: {}, series: {}".
format(session_label, series))
return None
return base_dir