def _retrieve_series_metadata(args):
'''Retrieves metadata for all Instances of a given Series and either
writes it to standard output or to files on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
metadata = client.retrieve_series_metadata(args.study_instance_uid,
args.series_instance_uid)
if args.save:
for md in metadata:
tag = client.lookup_tag('SOPInstanceUID')
sop_instance_uid = md[tag]['Value'][0]
_save_metadata(md, args.output_dir, sop_instance_uid,
args.prettify, args.dicomize)
else:
_print_metadata(metadata, args.prettify, args.dicomize)
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Progress is displayed and if errors occur then they are displayed in a popup window in the end.
If all the instances in a series are already imported then the series will not be retrieved and imported again.
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
Example: calling from PythonSlicer console
.. code-block:: python
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
"""
from dicomweb_client.api import DICOMwebClient
seriesImported = []
errors = []
clientLogger = logging.getLogger('dicomweb_client')
originalClientLogLevel = clientLogger.level
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
try:
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(
study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if seriesInstanceUID is not None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
# Turn off detailed logging, because it would slow down the file transfer
clientLogger.setLevel(logging.WARNING)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(
seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
try:
seriesInfo = client.retrieve_series_metadata(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
numberOfInstances = len(seriesInfo)
# Skip retrieve and import of this series if it is already imported
alreadyImportedInstances = slicer.dicomDatabase.instancesForSeries(
currentSeriesInstanceUID)
seriesAlreadyImported = True
for serieInfo in seriesInfo:
sopInstanceUID = serieInfo['00080018']['Value'][0]
if sopInstanceUID not in alreadyImportedInstances:
seriesAlreadyImported = False
break
if seriesAlreadyImported:
seriesImported.append(currentSeriesInstanceUID)
continue
instances = client.iter_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime(
).toString("yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(
outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instanceIndex, instance in enumerate(instances):
progressDialog.setValue(
int(100 * instanceIndex / numberOfInstances))
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
filename = outputDirectoryPath + "/" + str(
fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
if cancelled:
# cancel was requested in instance retrieve loop,
# stop the entire import process
break
importDicom(outputDirectoryPath)
seriesImported.append(currentSeriesInstanceUID)
except Exception as e:
import traceback
errors.append(
f"Error importing series {currentSeriesInstanceUID}: {str(e)} ({traceback.format_exc()})"
)
except Exception as e:
import traceback
errors.append(f"{str(e)} ({traceback.format_exc()})")
finally:
progressDialog.close()
clientLogger.setLevel(originalClientLogLevel)
if errors:
slicer.util.errorDisplay(
f"Errors occurred during DICOMweb import of {len(errors)} series.",
detailedText="\n\n".join(errors))
elif cancelled and (len(seriesImported) < len(seriesInstanceUIDs)):
slicer.util.infoDisplay(
f"DICOMweb import has been interrupted after completing {len(seriesImported)} out of {len(seriesInstanceUIDs)} series."
)
return seriesImported
