def loadTestData(self):
#download data and add to dicom database
zipFileUrl = 'http://slicer.kitware.com/midas3/download/item/257234/QIN-HEADNECK-01-0139-PET.zip'
zipFilePath = self.tempDataDir + '/dicom.zip'
zipFileData = self.tempDataDir + '/dicom'
expectedNumOfFiles = 545
if not os.access(self.tempDataDir, os.F_OK):
os.mkdir(self.tempDataDir)
if not os.access(zipFileData, os.F_OK):
os.mkdir(zipFileData)
slicer.util.downloadAndExtractArchive(zipFileUrl, zipFilePath,
zipFileData,
expectedNumOfFiles)
DICOMUtils.importDicom(zipFileData)
# load dataset
dicomFiles = slicer.util.getFilesInDirectory(zipFileData)
loadablesByPlugin, loadEnabled = DICOMUtils.getLoadablesFromFileLists(
[dicomFiles], ['DICOMScalarVolumePlugin'])
loadedNodeIDs = DICOMUtils.loadLoadables(loadablesByPlugin)
imageNode = slicer.mrmlScene.GetNodeByID(loadedNodeIDs[0])
imageNode.SetSpacing(
3.3940266832237, 3.3940266832237, 2.02490234375
) # mimic spacing as produced by Slicer 4.10 for which the test was originally developed
imageNode.SetOrigin(
285.367523193359375, 494.58682250976556816, -1873.3819580078125
) # mimic origin as produced by Slicer 4.10 for which the test was originally developed
# apply the SUVbw conversion factor and set units and quantity
suvNormalizationFactor = 0.00040166400000000007
quantity = slicer.vtkCodedEntry()
quantity.SetFromString(
'CodeValue:126400|CodingSchemeDesignator:DCM|CodeMeaning:Standardized Uptake Value'
)
units = slicer.vtkCodedEntry()
units.SetFromString(
'CodeValue:{SUVbw}g/ml|CodingSchemeDesignator:UCUM|CodeMeaning:Standardized Uptake Value body weight'
)
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(suvNormalizationFactor)
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
imageNode.GetVolumeDisplayNode().SetWindowLevel(6, 3)
imageNode.GetVolumeDisplayNode().SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeInvertedGrey')
imageNode.SetVoxelValueQuantity(quantity)
imageNode.SetVoxelValueUnits(units)
return imageNode
def loadTestData(self):
self.patienName = 'UNIFORMITY^Bio-mCT'
#download data and add to dicom database
zipFileUrl = 'https://github.com/QIICR/SlicerPETPhantomAnalysis/releases/download/test-data/PETCylinderPhantom.zip'
zipFilePath = self.tempDataDir + '/dicom.zip'
zipFileData = self.tempDataDir + '/dicom'
expectedNumOfFiles = 171
if not os.access(self.tempDataDir, os.F_OK):
os.mkdir(self.tempDataDir)
if not os.access(zipFileData, os.F_OK): # download DICOM test dataset
os.mkdir(zipFileData)
slicer.util.downloadAndExtractArchive(zipFileUrl, zipFilePath,
zipFileData,
expectedNumOfFiles)
DICOMUtils.importDicom(zipFileData)
# load dataset
dicomFiles = slicer.util.getFilesInDirectory(zipFileData)
loadablesByPlugin, loadEnabled = DICOMUtils.getLoadablesFromFileLists(
[dicomFiles], ['DICOMScalarVolumePlugin'])
loadedNodeIDs = DICOMUtils.loadLoadables(loadablesByPlugin)
imageNode = slicer.mrmlScene.GetNodeByID(loadedNodeIDs[0])
# apply the SUVbw conversion factor and set units and quantity
suvNormalizationFactor = 0.00012595161151
quantity = slicer.vtkCodedEntry()
quantity.SetFromString(
'CodeValue:126400|CodingSchemeDesignator:DCM|CodeMeaning:Standardized Uptake Value'
)
units = slicer.vtkCodedEntry()
units.SetFromString(
'CodeValue:{SUVbw}g/ml|CodingSchemeDesignator:UCUM|CodeMeaning:Standardized Uptake Value body weight'
)
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(suvNormalizationFactor)
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
imageNode.GetVolumeDisplayNode().SetWindowLevel(6, 3)
imageNode.GetVolumeDisplayNode().SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeInvertedGrey')
imageNode.SetVoxelValueQuantity(quantity)
imageNode.SetVoxelValueUnits(units)
return imageNode
def accessDICOMwebStudy(self, request, requestBody):
"""
Access DICOMweb server to download requested study, add it to
Slicer's dicom database, and load it into the scene.
:param requestBody: is a json string
:param requestBody['dicomWEBPrefix']: is the start of the url
:param requestBody['dicomWEBStore']: is the middle of the url
:param requestBody['studyUID']: is the end of the url
:param requestBody['accessToken']: is the authorization bearer token for the DICOMweb server
"""
p = urllib.parse.urlparse(request.decode())
q = urllib.parse.parse_qs(p.query)
request = json.loads(requestBody), b'application/json'
dicomWebEndpoint = request['dicomWEBPrefix'] + '/' + request[
'dicomWEBStore']
print(f"Loading from {dicomWebEndpoint}")
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(
dicomWebEndpoint=request['dicomWEBPrefix'] + '/' +
request['dicomWEBStore'],
studyInstanceUID=request['studyUID'],
accessToken=request['accessToken'])
files = []
for studyUID in loadedUIDs:
for seriesUID in slicer.dicomDatabase.seriesForStudy(studyUID):
for instance in slicer.dicomDatabase.instancesForSeries(
seriesUID):
files.append(
slicer.dicomDatabase.fileForInstance(instance))
loadables = DICOMUtils.getLoadablesFromFileLists([files])
loadedNodes = DICOMUtils.loadLoadables(loadLoadables)
print(f"Loaded {loadedUIDs}, and {loadedNodes}")
return b'{"result": "ok"}'
