def importFromDICOMWeb(dicomWebEndpoint, studyInstanceUID, seriesInstanceUID=None, accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
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")
: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
"""
from dicomweb_client.api import DICOMwebClient
import random
if accessToken is None:
client = DICOMwebClient(url = dicomWebEndpoint)
else:
client = DICOMwebClient(
url = dicomWebEndpoint,
headers = { "Authorization": "Bearer {}".format(accessToken) },
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
for currentSeriesInstanceUID in seriesInstanceUIDs:
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
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 instance in instances:
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
slicer.app.processEvents()
importDicom(outputDirectoryPath)
return seriesInstanceUIDs
def _retrieve_series(args):
'''Retrieves all Instances of a given Series and either writes them 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)
instances = client.retrieve_series(
args.study_instance_uid,
args.series_instance_uid,
media_types=args.media_types,
)
for inst in instances:
sop_instance_uid = inst.SOPInstanceUID
if args.save:
_save_instance(inst, args.output_dir, sop_instance_uid)
else:
_print_instance(inst)
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
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")
: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
"""
from dicomweb_client.api import DICOMwebClient
import random
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint,
callback=progressCallback)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
progressDialog.setValue(
int(100 * seriesIndex / len(seriesInstanceUIDs)))
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):
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
importDicom(outputDirectoryPath)
if cancelled:
break
progressDialog.close()
return seriesInstanceUIDs
