def ExecuteSeeds(self, inVolumeNode, sourceSeedsNode):
self._helper.debug("Starting execution of seeds...")
if not inVolumeNode or not sourceSeedsNode:
slicer.Application.ErrorMessage(
"Not enough information. Aborting Seeds..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
seeds = sourceSeedsNode
initialLevelSets = slicer.vtkImageData()
initialLevelSets.DeepCopy(image)
initialLevelSets.Update()
levelSetsInputScalars = initialLevelSets.GetPointData().GetScalars(
)
levelSetsInputScalars.FillComponent(0, 1.0)
for i in range(seeds.GetNumberOfFiducials()):
rasPt = seeds.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
id = image.ComputePointId(int(ijkPt[0]), int(ijkPt[1]),
int(ijkPt[2]))
levelSetsInputScalars.SetComponent(id, 0, -1.0)
dilateErode = slicer.vtkImageDilateErode3D()
dilateErode.SetInput(initialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3, 3, 3)
dilateErode.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(dilateErode.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 0.0)
self._helper.debug("Seeds done...")
return outputContainer
def ExecuteSeeds(self,inVolumeNode,sourceSeedsNode):
self._helper.debug("Starting execution of seeds...")
if not inVolumeNode or not sourceSeedsNode:
slicer.Application.ErrorMessage("Not enough information. Aborting Seeds..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
seeds = sourceSeedsNode
initialLevelSets = slicer.vtkImageData()
initialLevelSets.DeepCopy(image)
initialLevelSets.Update()
levelSetsInputScalars = initialLevelSets.GetPointData().GetScalars()
levelSetsInputScalars.FillComponent(0,1.0)
for i in range(seeds.GetNumberOfFiducials()):
rasPt = seeds.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
id = image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2]))
levelSetsInputScalars.SetComponent(id,0,-1.0)
dilateErode = slicer.vtkImageDilateErode3D()
dilateErode.SetInput(initialLevelSets)
dilateErode.SetDilateValue(-1.0)
dilateErode.SetErodeValue(1.0)
dilateErode.SetKernelSize(3,3,3)
dilateErode.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(dilateErode.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,0.0)
self._helper.debug("Seeds done...")
return outputContainer
def SetAndMergeEvolVolume(self,resultContainer):
scene = self._mainGUIClass.GetLogic().GetMRMLScene()
volumeNode = resultContainer.GetNode()
threshold = resultContainer.GetThreshold()
if self._mainGUIClass._outEvolVolume == None:
# no node so far
self._mainGUIClass._outEvolVolume = slicer.vtkMRMLScalarVolumeNode()
self._mainGUIClass._outEvolVolume.SetName("VMTK Level-Set Evolution Output Volume")
self._mainGUIClass._outEvolVolume.SetScene(scene)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(slicer.vtkImageData())
scene.AddNode(self._mainGUIClass._outEvolVolume)
self._mainGUIClass._outEvolVolumeLast = slicer.vtkMRMLScalarVolumeNode()
self._mainGUIClass._outEvolVolumeLast.SetName("VMTK Level-Set Evolution Output Volume (Last Step)")
self._mainGUIClass._outEvolVolumeLast.SetScene(scene)
self._mainGUIClass._outEvolVolumeLast.SetAndObserveImageData(slicer.vtkImageData())
scene.AddNode(self._mainGUIClass._outEvolVolumeLast)
matrix = slicer.vtkMatrix4x4()
# copy current outEvolVolume to outEvolVolumeLast
self._mainGUIClass._outEvolVolumeLast.SetAndObserveImageData(self._mainGUIClass._outEvolVolume.GetImageData())
self._mainGUIClass._outEvolVolume.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolumeLast.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolumeLast.SetModifiedSinceRead(1)
volumeNodeData = volumeNode.GetImageData()
# merge the oldVolume with volumeNode if oldVolume has already content
if self._mainGUIClass._outEvolVolume.GetImageData().GetPointData().GetScalars():
# evolVolumeLast has already content
minFilter = slicer.vtkImageMathematics()
minFilter.SetOperationToMin()
minFilter.SetInput1(self._mainGUIClass._outEvolVolume.GetImageData()) #the old one
minFilter.SetInput2(volumeNode.GetImageData()) #the new one
minFilter.Update()
volumeNodeData.DeepCopy(minFilter.GetOutput())
# copy new volume to outEvolVolume
volumeNode.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(volumeNodeData)
self._mainGUIClass._outEvolVolume.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetModifiedSinceRead(1)
outputContainer = SlicerVMTKLevelSetContainer(self._mainGUIClass._outEvolVolume,threshold)
return outputContainer
def Apply(self):
if not self.GetScriptedModuleNode():
slicer.Application.ErrorMessage("No input ScriptedModuleNode found")
return
scriptedModuleNode = self.GetScriptedModuleNode()
inVolume = scriptedModuleNode.GetParameter('InputVolumeRef')
if not inVolume:
slicer.Application.ErrorMessage("No input volume found")
return
outVolume = scriptedModuleNode.GetParameter('OutputVolumeRef')
if not outVolume:
slicer.Application.ErrorMessage("No output volume found")
return
outVolume.CopyOrientation(inVolume)
outVolume.SetAndObserveTransformNodeID(inVolume.GetTransformNodeID())
gradientAnisotropicDiffusionImageFilter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter()
gradientAnisotropicDiffusionImageFilter.SetInput(inVolume.GetImageData())
gradientAnisotropicDiffusionImageFilter.SetConductanceParameter(scriptedModuleNode.GetParameter('Conductance'))
gradientAnisotropicDiffusionImageFilter.SetNumberOfIterations(scriptedModuleNode.GetParameter('NumberOfIterations'))
gradientAnisotropicDiffusionImageFilter.SetTimeStep(scriptedModuleNode.GetParameter('TimeStep'))
gradientAnisotropicDiffusionImageFilter.Update()
image = slicer.vtkImageData()
image.DeepCopy(gradientAnisotropicDiffusionImageFilter.GetOutput())
outVolume.SetAndObserveImageData(image)
outVolume.ModifiedSinceReadOn()
slicer.Application.InformationMessage("Done applying GradientAnisotropicDiffusion.")
def dispV0(dataD, inputVolume, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ApplyVED(self,image,sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,beta,gamma,c,timestep,epsilon,wstrength,sensitivity,numberOfIterations,numberOfDiffusionSubIterations):
self._helper.debug("Starting execution of VED...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkVesselEnhancingDiffusionImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha(alpha)
v.SetBeta(beta)
v.SetGamma(gamma)
v.SetC(c)
v.SetTimeStep(timestep)
v.SetEpsilon(epsilon)
v.SetWStrength(wstrength)
v.SetSensitivity(sensitivity)
v.SetNumberOfIterations(numberOfIterations)
v.SetNumberOfDiffusionSubIterations(numberOfDiffusionSubIterations)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def ApplySatoVesselness(self,image,sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,alpha2):
self._helper.debug(image.GetSpacing())
self._helper.debug("Starting execution of Sato...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkSatoVesselnessMeasureImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha1(alpha)
v.SetAlpha2(alpha2)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def dispUV(dataD, org, spa, mat, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToUnsignedShort()
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ApplyFrangiVesselness(self,image,sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,beta,gamma):
self._helper.debug("Starting execution of Frangi...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkVesselnessMeasureImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha(alpha)
v.SetBeta(beta)
v.SetGamma(gamma)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def BinarizeImageByLabel(self, imageData, labelValue):
'''
Binarize an image to 0 and 1, while just keeping the voxels with the labelValue
imageData
vtkImageData
labelValue
the value of the voxels to keep
Returns
vtkImageData after binarizing
'''
threshold = slicer.vtkImageThreshold()
threshold.SetInput(imageData)
threshold.ThresholdBetween(labelValue, labelValue)
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.Update()
output = slicer.vtkImageData()
output.DeepCopy(threshold.GetOutput())
return output
def dispW1(dataD, G, b, org, spa, mat, mu, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
r1.SetAndObserveImageData(imgD)
r1.SetNumberOfGradients(shpV[3])
r1.SetIJKToRASMatrix(mat)
r1.SetMeasurementFrameMatrix(mu)
r1.SetDiffusionGradients(G)
r1.SetBValues(b)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ApplySatoVesselness(self, image, sigmaMin, sigmaMax,
numberOfSigmaSteps, alpha, alpha2):
self._helper.debug(image.GetSpacing())
self._helper.debug("Starting execution of Sato...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkSatoVesselnessMeasureImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha1(alpha)
v.SetAlpha2(alpha2)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def dispUV(dataD, org, spa, mat, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToUnsignedShort()
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ApplyVED(self, image, sigmaMin, sigmaMax, numberOfSigmaSteps, alpha,
beta, gamma, c, timestep, epsilon, wstrength, sensitivity,
numberOfIterations, numberOfDiffusionSubIterations):
self._helper.debug("Starting execution of VED...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkVesselEnhancingDiffusionImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha(alpha)
v.SetBeta(beta)
v.SetGamma(gamma)
v.SetC(c)
v.SetTimeStep(timestep)
v.SetEpsilon(epsilon)
v.SetWStrength(wstrength)
v.SetSensitivity(sensitivity)
v.SetNumberOfIterations(numberOfIterations)
v.SetNumberOfDiffusionSubIterations(numberOfDiffusionSubIterations)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def ApplyFrangiVesselness(self, image, sigmaMin, sigmaMax,
numberOfSigmaSteps, alpha, beta, gamma):
self._helper.debug("Starting execution of Frangi...")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = slicer.vtkvmtkVesselnessMeasureImageFilter()
v.SetInput(image)
v.SetSigmaMin(sigmaMin)
v.SetSigmaMax(sigmaMax)
v.SetNumberOfSigmaSteps(numberOfSigmaSteps)
v.SetAlpha(alpha)
v.SetBeta(beta)
v.SetGamma(gamma)
v.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(v.GetOutput())
outVolumeData.Update()
outVolumeData.GetPointData().GetScalars().Modified()
return outVolumeData
def dispW1(dataD, G, b, org, spa, mat, mu, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
r1.SetAndObserveImageData(imgD)
r1.SetNumberOfGradients(shpV[3])
r1.SetIJKToRASMatrix(mat)
r1.SetMeasurementFrameMatrix(mu)
r1.SetDiffusionGradients(G)
r1.SetBValues(b)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def dispW0(dataD, inputVolume, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def dispV0(dataD, inputVolume, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ExecuteCurves(self, origInVolumeNode, inVolumeNode, numberOfIterations,
propagationScaling, curvatureScaling, advectionScaling,
calculateFeatureImage):
self._helper.debug("Starting execution of Curves..")
if not inVolumeNode or not origInVolumeNode:
slicer.Application.ErrorMessage(
"Not enough information!!! Aborting Geodesic..\n")
return
else:
cast = slicer.vtkImageCast()
cast.SetInput(origInVolumeNode.GetImageData())
cast.SetOutputScalarTypeToFloat()
cast.Update()
origImage = cast.GetOutput()
image = inVolumeNode.GetImageData()
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
self._helper.debug("FeatureImageCalc: " +
str(calculateFeatureImage))
if calculateFeatureImage == 1:
levelSets.SetFeatureImage(
self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self.FeatureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(image)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self.IsoSurfaceValue)
levelSets.SetMaximumRMSError(self.MaximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 0.0)
return outputContainer
def ExecuteCurves(self,origInVolumeNode,inVolumeNode,numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,calculateFeatureImage):
self._helper.debug("Starting execution of Curves..")
if not inVolumeNode or not origInVolumeNode:
slicer.Application.ErrorMessage("Not enough information!!! Aborting Geodesic..\n")
return
else:
cast = slicer.vtkImageCast()
cast.SetInput(origInVolumeNode.GetImageData())
cast.SetOutputScalarTypeToFloat()
cast.Update()
origImage = cast.GetOutput()
image = inVolumeNode.GetImageData()
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
self._helper.debug("FeatureImageCalc: " + str(calculateFeatureImage))
if calculateFeatureImage==1:
levelSets.SetFeatureImage(self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self.FeatureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(image)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self.IsoSurfaceValue)
levelSets.SetMaximumRMSError(self.MaximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,0.0)
return outputContainer
def Execute(self):
SlicerVMTKAdvancedPageSkeleton.Execute(self)
inVolume = self._parentClass._inVolumeSelector.GetSelected()
outVolume = self._parentClass._outVolumeSelector.GetSelected()
if not inVolume or not outVolume or not self.CheckForVmtkLibrary():
slicer.Application.ErrorMessage("No input volume or no output volume found. Aborting Frangi..\n")
return
else:
sigmaMin = float(self._sigmaMin.GetWidget().GetValue())
sigmaMax = float(self._sigmaMax.GetWidget().GetValue())
numberOfSigmaSteps = int(self._numberOfSigmaSteps.GetValue())
alpha = float(self._alpha.GetWidget().GetValue())
beta = float(self._beta.GetWidget().GetValue())
gamma = float(self._gamma.GetWidget().GetValue())
imageData = slicer.vtkImageData()
imageData.DeepCopy(inVolume.GetImageData())
imageData.Update()
if (self._sigmaUnit.GetWidget().GetWidget(0).GetSelectedState()==1):
self._parentClass.debug("use mm!")
imageData.SetSpacing(inVolume.GetSpacing()[0], inVolume.GetSpacing()[1], inVolume.GetSpacing()[2])
outVolumeImage = self._parentClass._logic.ApplyFrangiVesselness(imageData,sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,beta,gamma)
outVolumeImage.SetSpacing(1,1,1)
matrix = slicer.vtkMatrix4x4()
inVolume.GetIJKToRASMatrix(matrix)
outVolume.SetAndObserveImageData(outVolumeImage)
outVolume.SetIJKToRASMatrix(matrix)
displayNode = inVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode);
outVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
newDisplayNode.AutoWindowLevelOff()
newDisplayNode.AutoWindowLevelOn() # renew auto windowlevel
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inVolume.GetLabelMap():
outVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(outVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outVolume.GetID())
appLogic.PropagateVolumeSelection()
def ExecuteThreshold(self,inVolumeNode,lowerThreshold,higherThreshold):
self._helper.debug("Starting execution of Threshold...")
if not inVolumeNode:
slicer.Application.ErrorMessage("No input volume found. Aborting Threshold..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold,higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetInValue(-1.0)
threshold.SetOutValue(1.0)
threshold.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(threshold.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,0.0)
self._helper.debug("Threshold done...")
return outputContainer
def ExecuteIsosurface(self, inVolumeNode, value):
self._helper.debug("Starting execution of Isosurface...")
if not inVolumeNode:
slicer.Application.ErrorMessage(
"No input volume found. Aborting Isosurface..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
imageMathematics = slicer.vtkImageMathematics()
imageMathematics.SetInput(image)
imageMathematics.SetConstantK(-1.0)
imageMathematics.SetOperationToMultiplyByK()
imageMathematics.Update()
subtract = slicer.vtkImageMathematics()
subtract.SetInput(imageMathematics.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(value)
subtract.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 10)
self._helper.debug("Isosurface done...")
return outputContainer
def ExecuteThreshold(self, inVolumeNode, lowerThreshold, higherThreshold):
self._helper.debug("Starting execution of Threshold...")
if not inVolumeNode:
slicer.Application.ErrorMessage(
"No input volume found. Aborting Threshold..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold, higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetInValue(-1.0)
threshold.SetOutValue(1.0)
threshold.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(threshold.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 0.0)
self._helper.debug("Threshold done...")
return outputContainer
def ExecuteIsosurface(self,inVolumeNode,value):
self._helper.debug("Starting execution of Isosurface...")
if not inVolumeNode:
slicer.Application.ErrorMessage("No input volume found. Aborting Isosurface..\n")
return
else:
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
imageMathematics = slicer.vtkImageMathematics()
imageMathematics.SetInput(image)
imageMathematics.SetConstantK(-1.0)
imageMathematics.SetOperationToMultiplyByK()
imageMathematics.Update()
subtract = slicer.vtkImageMathematics()
subtract.SetInput(imageMathematics.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(value)
subtract.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,10)
self._helper.debug("Isosurface done...")
return outputContainer
def BuildSimpleLabelMap(self, image, inValue, outValue):
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdByLower(0)
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetOutValue(outValue)
threshold.SetInValue(inValue)
threshold.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(threshold.GetOutput())
outVolumeData.Update()
return outVolumeData
def BuildSimpleLabelMap(self,image,inValue,outValue):
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdByLower(0)
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetOutValue(outValue)
threshold.SetInValue(inValue)
threshold.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(threshold.GetOutput())
outVolumeData.Update()
return outVolumeData
def BuildGradientBasedFeatureImage(self, imageData):
cast = slicer.vtkImageCast()
cast.SetInput(imageData)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if (self._derivativeSigma > 0.0):
gradientMagnitude = slicer.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter(
)
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.SetSigma(self._derivativeSigma)
gradientMagnitude.SetNormalizeAcrossScale(0)
gradientMagnitude.Update()
else:
gradientMagnitude = slicer.vtkvmtkGradientMagnitudeImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.Update()
featureImage = None
if self._sigmoidRemapping == 1:
scalarRange = gradientMagnitude.GetOutput().GetPointData(
).GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = -(inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = slicer.vtkvmtkSigmoidImageFilter()
sigmoid.SetInput(gradientMagnitude.GetOutput())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = slicer.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInput(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
featureImageOutput = slicer.vtkImageData()
featureImageOutput.DeepCopy(featureImage)
featureImageOutput.Update()
return featureImageOutput
def ExecuteGAC(self, origImage, segmentationImage, numberOfIterations,
propagationScaling, curvatureScaling, advectionScaling,
method):
self._parentClass.GetHelper().debug("Starting GAC..")
calculateFeatureImage = 1
cast = slicer.vtkImageCast()
cast.SetInput(origImage)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if method == 'curves':
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
else:
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter(
)
if calculateFeatureImage == 1:
levelSets.SetFeatureImage(
self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self._featureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(segmentationImage)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self._isoSurfaceValue)
levelSets.SetMaximumRMSError(self._maximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of GAC..")
return outVolumeData
def BuildGradientBasedFeatureImage(self,imageData):
cast = slicer.vtkImageCast()
cast.SetInput(imageData)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if (self.DerivativeSigma > 0.0):
gradientMagnitude = slicer.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.SetSigma(self.DerivativeSigma)
gradientMagnitude.SetNormalizeAcrossScale(0)
gradientMagnitude.Update()
else:
gradientMagnitude = slicer.vtkvmtkGradientMagnitudeImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.Update()
featureImage = None
if self.SigmoidRemapping==1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = - (inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = slicer.vtkvmtkSigmoidImageFilter()
sigmoid.SetInput(gradientMagnitude.GetOutput())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = slicer.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInput(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
featureImageOutput = slicer.vtkImageData()
featureImageOutput.DeepCopy(featureImage)
featureImageOutput.Update()
return featureImageOutput
def dispS(dataD, inputVolume, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
r11.ScalarVisibilityOn()
r11.SetScalarRange(dataD.min(), dataD.max())
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetNumberOfScalarComponents(1)
imgD.SetScalarTypeToDouble()
imgD.AllocateScalars()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().GetPointData().GetScalars().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
dataD = reshape(dataD, (shpV[0]*shpV[1]*shpV[2], 1))
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def ExecuteGAC(self,origImage,segmentationImage,numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,method):
self._parentClass.GetHelper().debug("Starting GAC..")
calculateFeatureImage = 1
cast = slicer.vtkImageCast()
cast.SetInput(origImage)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if method=='curves':
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
else:
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter()
if calculateFeatureImage==1:
levelSets.SetFeatureImage(self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self._featureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(segmentationImage)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self._isoSurfaceValue)
levelSets.SetMaximumRMSError(self._maximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of GAC..")
return outVolumeData
def dispS(dataD, inputVolume, shpV):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLScalarVolumeNode()
r11 = slicer.vtkMRMLScalarVolumeDisplayNode()
r11.ScalarVisibilityOn()
r11.SetScalarRange(dataD.min(), dataD.max())
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetNumberOfScalarComponents(1)
imgD.SetScalarTypeToDouble()
imgD.AllocateScalars()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().GetPointData().GetScalars().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
dataD = reshape(dataD, (shpV[0] * shpV[1] * shpV[2], 1))
tmp[:] = dataD[:]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def AddImages(self, imageData1, imageData2):
'''
Adds two images
imageData1
vtkImageData
imageData2
vtkImageData
Returns
vtkImageData after addition
'''
add = slicer.vtkImageMathematics()
add.SetInput1(imageData1)
add.SetInput2(imageData2)
add.SetOperationToAdd()
add.Update()
output = slicer.vtkImageData()
output.DeepCopy(add.GetOutput())
return output
def dispW0(dataD, inputVolume, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
scene.AddNode(r11)
r1.AddAndObserveDisplayNodeID(r11.GetName())
imgD = slicer.vtkImageData()
imgD.SetDimensions(shpV[0], shpV[1], shpV[2])
imgD.SetScalarTypeToShort()
org = inputVolume.GetOrigin()
spa = inputVolume.GetSpacing()
mat = slicer.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(mat)
r1.SetAndObserveImageData(imgD)
r1.SetIJKToRASMatrix(mat)
r1.SetOrigin(org[0], org[1], org[2])
r1.SetSpacing(spa[0], spa[1], spa[2])
scene.AddNode(r1)
tmp = r1.GetImageData().ToArray()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def MultiplyImage(self, imageData, factor):
'''
Multiply an image
This includes automatic Re-Cast to Float
imageData
vtkImageData
dividend
the number to divide with, will be casted to float
Returns
vtkImageData after multiplication
'''
imageData.DeepCopy(self.ReCastImage(imageData, "Float"))
mul = slicer.vtkImageMathematics()
mul.SetInput(imageData)
mul.SetOperationToMultiplyByK()
mul.SetConstantK(factor)
mul.Update()
output = slicer.vtkImageData()
output.DeepCopy(mul.GetOutput())
return output
def ExecuteFM(self, image, lowerThreshold, higherThreshold, sourceSeedIds,
targetSeedIds, sideBranches):
self._parentClass.GetHelper().debug("Starting FM..")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max(imageDimensions)
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold, higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1 / (scalarRange[1] - scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if sideBranches:
# ignore sidebranches, use colliding fronts
self._parentClass.GetHelper().debug("COLLIDINGFRONTS")
fastMarching = slicer.vtkvmtkCollidingFrontsImageFilter()
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds1(sourceSeedIds)
fastMarching.SetSeeds2(targetSeedIds)
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10 * fastMarching.GetNegativeEpsilon())
subtract.Update()
else:
fastMarching = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter(
)
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset(0.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
#self._parentClass.GetHelper().debug("No target mode "+str(fastMarching.GetTargetValue()))
subtract = slicer.vtkImageThreshold()
subtract.SetInput(fastMarching.GetOutput())
subtract.ThresholdByLower(2000) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of FM..")
return outVolumeData
def SetAndMergeEvolVolume(self, resultContainer):
scene = self._mainGUIClass.GetLogic().GetMRMLScene()
volumeNode = resultContainer.GetNode()
threshold = resultContainer.GetThreshold()
if self._mainGUIClass._outEvolVolume == None:
# no node so far
self._mainGUIClass._outEvolVolume = slicer.vtkMRMLScalarVolumeNode(
)
self._mainGUIClass._outEvolVolume.SetName(
"VMTK Level-Set Evolution Output Volume")
self._mainGUIClass._outEvolVolume.SetScene(scene)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(
slicer.vtkImageData())
scene.AddNode(self._mainGUIClass._outEvolVolume)
self._mainGUIClass._outEvolVolumeLast = slicer.vtkMRMLScalarVolumeNode(
)
self._mainGUIClass._outEvolVolumeLast.SetName(
"VMTK Level-Set Evolution Output Volume (Last Step)")
self._mainGUIClass._outEvolVolumeLast.SetScene(scene)
self._mainGUIClass._outEvolVolumeLast.SetAndObserveImageData(
slicer.vtkImageData())
scene.AddNode(self._mainGUIClass._outEvolVolumeLast)
matrix = slicer.vtkMatrix4x4()
# copy current outEvolVolume to outEvolVolumeLast
self._mainGUIClass._outEvolVolumeLast.SetAndObserveImageData(
self._mainGUIClass._outEvolVolume.GetImageData())
self._mainGUIClass._outEvolVolume.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolumeLast.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolumeLast.SetModifiedSinceRead(1)
volumeNodeData = volumeNode.GetImageData()
# merge the oldVolume with volumeNode if oldVolume has already content
if self._mainGUIClass._outEvolVolume.GetImageData().GetPointData(
).GetScalars():
# evolVolumeLast has already content
minFilter = slicer.vtkImageMathematics()
minFilter.SetOperationToMin()
minFilter.SetInput1(
self._mainGUIClass._outEvolVolume.GetImageData()) #the old one
minFilter.SetInput2(volumeNode.GetImageData()) #the new one
minFilter.Update()
volumeNodeData.DeepCopy(minFilter.GetOutput())
# copy new volume to outEvolVolume
volumeNode.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(
volumeNodeData)
self._mainGUIClass._outEvolVolume.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetModifiedSinceRead(1)
outputContainer = SlicerVMTKLevelSetContainer(
self._mainGUIClass._outEvolVolume, threshold)
return outputContainer
def ExecuteCollidingFronts(self,inVolumeNode,lowerThreshold,higherThreshold,sourceSeedsNode,targetSeedsNode):
self._helper.debug("Starting execution of Colliding Fronts..")
if not inVolumeNode or not sourceSeedsNode or not targetSeedsNode:
self._helper.debug(inVolumeNode)
self._helper.debug(lowerThreshold)
self._helper.debug(higherThreshold)
self._helper.debug(sourceSeedsNode)
self._helper.debug(targetSeedsNode)
slicer.Application.ErrorMessage("Not enough information!!! Aborting Colliding Fronts..\n")
return
else:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
rasPt = sourceSeedsNode.GetNthFiducialXYZ(0)
self._helper.debug(rasPt)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
self._helper.debug(ijkPt)
sourceSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
rasPt = targetSeedsNode.GetNthFiducialXYZ(0)
self._helper.debug(rasPt)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
self._helper.debug(ijkPt)
targetSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
scalarRange = image.GetScalarRange()
self._helper.debug("CF: after converting seeds")
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold, higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
self._helper.debug("CF: after thresholding")
scalarRange = threshold.GetOutput().GetScalarRange()
thresholdedImage = threshold.GetOutput()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1/(scalarRange[1]-scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
self._helper.debug("CF: after shiftScale")
collidingFronts = slicer.vtkvmtkCollidingFrontsImageFilter()
collidingFronts.SetInput(speedImage)
collidingFronts.SetSeeds1(sourceSeedIds)
collidingFronts.SetSeeds2(targetSeedIds)
collidingFronts.ApplyConnectivityOn()
collidingFronts.StopOnTargetsOn()
collidingFronts.Update()
self._helper.debug("CF: after CF")
subtract = slicer.vtkImageMathematics()
subtract.SetInput(collidingFronts.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10.0 * collidingFronts.GetNegativeEpsilon())
subtract.Update()
self._helper.debug("CF: after substract")
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,collidingFronts.GetNegativeEpsilon())
self._helper.debug("Colliding Fronts done...")
return outputContainer
def ExecuteFastMarching(self,inVolumeNode,lowerThreshold,higherThreshold,sourceSeedsNode,targetSeedsNode):
self._helper.debug("Starting execution of Fast Marching...")
if not inVolumeNode or not sourceSeedsNode:
self._helper.debug(inVolumeNode)
self._helper.debug(lowerThreshold)
self._helper.debug(higherThreshold)
self._helper.debug(sourceSeedsNode)
self._helper.debug(targetSeedsNode)
slicer.Application.ErrorMessage("Not enough information!!! Aborting Fast Marching..\n")
return
else:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
for i in range(sourceSeedsNode.GetNumberOfFiducials()):
rasPt = sourceSeedsNode.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
sourceSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
if targetSeedsNode:
for i in range(targetSeedsNode.GetNumberOfFiducials()):
rasPt = targetSeedsNode.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
targetSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
scalarRange = image.GetScalarRange()
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold,higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
scalarRange = threshold.GetOutput().GetScalarRange()
thresholdedImage = threshold.GetOutput()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1/(scalarRange[1]-scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
fastMarching = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter()
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOff()
fastMarching.SetTargetOffset(100.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
subtract = slicer.vtkImageThreshold()
subtract.SetInput(fastMarching.GetOutput())
subtract.ThresholdByLower(1000)#better value soon
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,0.0)
self._helper.debug("Fast Marching done...")
return outputContainer
def ReCastImage(self, imageData, castString):
'''
Re-Cast an image to a different type
imageData
vtkImageData
castString
New type as a String, possible values are
"Char"
"Unsigned Char"
"Double"
"Float"
"Int"
"Unsigned Int"
"Long"
"Unsigned Long"
"Short"
"Unsigned Short"
other values will result in "Short"
Returns
vtkImageData after Re-Cast
'''
# get the current type
currentType = imageData.GetScalarType()
cast = slicer.vtkImageCast()
cast.SetInput(imageData)
cast.ClampOverflowOn()
needToCast = False
if (castString == "Char" and (currentType != 2 or currentType != 15)):
cast.SetOutputScalarTypeToChar()
needToCast = True
elif (castString == "Unsigned Char" and currentType != 3):
cast.SetOutputScalarTypeToUnsignedChar()
needToCast = True
elif (castString == "Double" and currentType != 11):
cast.SetOutputScalarTypeToUnsignedChar()
needToCast = True
elif (castString == "Float" and currentType != 10):
cast.SetOutputScalarTypeToFloat()
needToCast = True
elif (castString == "Int" and currentType != 6):
cast.SetOutputScalarTypeToInt()
needToCast = True
elif (castString == "Unsigned Int" and currentType != 7):
cast.SetOutputScalarTypeToUnsignedInt()
needToCast = True
elif (castString == "Long" and currentType != 8):
cast.SetOutputScalarTypeToLong()
needToCast = True
elif (castString == "Unsigned Long" and currentType != 9):
cast.SetOutputScalarTypeToUnsignedLong()
needToCast = True
elif (castString == "Short" and currentType != 4):
cast.SetOutputScalarTypeToShort()
needToCast = True
elif (castString == "Unsigned Short" and currentType != 5):
cast.SetOutputScalarTypeToUnsignedShort()
needToCast = True
else:
cast.SetOutputScalarTypeToShort()
needToCast = True
# check if we really need to cast,
# else exit here and return the input imageData
if not needToCast:
return imageData
cast.Update()
output = slicer.vtkImageData()
output.DeepCopy(cast.GetOutput())
return output
def ExecuteCollidingFronts(self, inVolumeNode, lowerThreshold,
higherThreshold, sourceSeedsNode,
targetSeedsNode):
self._helper.debug("Starting execution of Colliding Fronts..")
if not inVolumeNode or not sourceSeedsNode or not targetSeedsNode:
self._helper.debug(inVolumeNode)
self._helper.debug(lowerThreshold)
self._helper.debug(higherThreshold)
self._helper.debug(sourceSeedsNode)
self._helper.debug(targetSeedsNode)
slicer.Application.ErrorMessage(
"Not enough information!!! Aborting Colliding Fronts..\n")
return
else:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
rasPt = sourceSeedsNode.GetNthFiducialXYZ(0)
self._helper.debug(rasPt)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
self._helper.debug(ijkPt)
sourceSeedIds.InsertNextId(
image.ComputePointId(int(ijkPt[0]), int(ijkPt[1]),
int(ijkPt[2])))
rasPt = targetSeedsNode.GetNthFiducialXYZ(0)
self._helper.debug(rasPt)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
self._helper.debug(ijkPt)
targetSeedIds.InsertNextId(
image.ComputePointId(int(ijkPt[0]), int(ijkPt[1]),
int(ijkPt[2])))
scalarRange = image.GetScalarRange()
self._helper.debug("CF: after converting seeds")
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold, higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
self._helper.debug("CF: after thresholding")
scalarRange = threshold.GetOutput().GetScalarRange()
thresholdedImage = threshold.GetOutput()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1 / (scalarRange[1] - scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
self._helper.debug("CF: after shiftScale")
collidingFronts = slicer.vtkvmtkCollidingFrontsImageFilter()
collidingFronts.SetInput(speedImage)
collidingFronts.SetSeeds1(sourceSeedIds)
collidingFronts.SetSeeds2(targetSeedIds)
collidingFronts.ApplyConnectivityOn()
collidingFronts.StopOnTargetsOn()
collidingFronts.Update()
self._helper.debug("CF: after CF")
subtract = slicer.vtkImageMathematics()
subtract.SetInput(collidingFronts.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10.0 * collidingFronts.GetNegativeEpsilon())
subtract.Update()
self._helper.debug("CF: after substract")
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(
outVolumeNode, collidingFronts.GetNegativeEpsilon())
self._helper.debug("Colliding Fronts done...")
return outputContainer
def ExecuteFM(self,image,lowerThreshold,higherThreshold,sourceSeedIds,targetSeedIds,sideBranches):
self._parentClass.GetHelper().debug("Starting FM..")
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max(imageDimensions)
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold,higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1/(scalarRange[1]-scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if sideBranches:
# ignore sidebranches, use colliding fronts
self._parentClass.GetHelper().debug("COLLIDINGFRONTS")
fastMarching = slicer.vtkvmtkCollidingFrontsImageFilter()
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds1(sourceSeedIds)
fastMarching.SetSeeds2(targetSeedIds)
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10*fastMarching.GetNegativeEpsilon())
subtract.Update()
else:
fastMarching = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter()
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset(0.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
#self._parentClass.GetHelper().debug("No target mode "+str(fastMarching.GetTargetValue()))
subtract = slicer.vtkImageThreshold()
subtract.SetInput(fastMarching.GetOutput())
subtract.ThresholdByLower(2000) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of FM..")
return outVolumeData
def Apply(self):
inputVolume = self.VolumeSelector.GetSelected()
if not inputVolume:
self.ErrorDialog("No input volume found")
return
outputVolume = self.OutVolumeSelector.GetSelected()
if not outputVolume:
self.ErrorDialog("No output volume found")
return
inputSeeds = self.FiducialsNodeSelector.GetSelected()
if not inputSeeds:
self.ErrorDialog("No fiducials found")
return
if inputSeeds.GetNumberOfFiducials() < 2:
self.ErrorDialog("Need at least 2 fiducials in the list")
return
self.Status("Applying Subvolume...")
# get the seed points (RAS)
p0 = inputSeeds.GetNthFiducialXYZ(0)
p1 = inputSeeds.GetNthFiducialXYZ(1)
lower = map(min, p0, p1)
# convert seed points to input volume IJK
rasToIJK = slicer.vtkMatrix4x4()
inputVolume.GetRASToIJKMatrix(rasToIJK)
p0IJK = rasToIJK.MultiplyPoint(p0[0], p0[1], p0[2], 1.0)
p1IJK = rasToIJK.MultiplyPoint(p1[0], p1[1], p1[2], 1.0)
# find the bounding box of the seeds
lowerIJK = map(int, map(min, p0IJK, p1IJK))
upperIJK = map(int, map(max, p0IJK, p1IJK))
# get an array of the input volume, extract the sub
a = inputVolume.GetImageData().ToArray()
sub = a[lowerIJK[2] : upperIJK[2], lowerIJK[1] : upperIJK[1], lowerIJK[0] : upperIJK[0]]
# set up output node
outImage = slicer.vtkImageData()
outImage.SetDimensions(sub.shape[2], sub.shape[1], sub.shape[0])
outImage.AllocateScalars()
outImage.ToArray()[:] = sub[:]
outputVolume.SetAndObserveImageData(outImage)
rasToIJK.Invert()
ijkToRAS = rasToIJK
outputVolume.SetIJKToRASMatrix(rasToIJK)
origin = ijkToRAS.MultiplyPoint(lowerIJK[0], lowerIJK[1], lowerIJK[2], 1.0)
outputVolume.SetOrigin(origin[0], origin[1], origin[2])
outputVolume.ModifiedSinceReadOn()
displayNode = inputVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode)
outputVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inputVolume.GetLabelMap():
outputVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(outputVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
appLogic.PropagateVolumeSelection()
self.Status("Done applying Subvolume.")
def ExecuteFastMarching(self, inVolumeNode, lowerThreshold,
higherThreshold, sourceSeedsNode, targetSeedsNode):
self._helper.debug("Starting execution of Fast Marching...")
if not inVolumeNode or not sourceSeedsNode:
self._helper.debug(inVolumeNode)
self._helper.debug(lowerThreshold)
self._helper.debug(higherThreshold)
self._helper.debug(sourceSeedsNode)
self._helper.debug(targetSeedsNode)
slicer.Application.ErrorMessage(
"Not enough information!!! Aborting Fast Marching..\n")
return
else:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
image = inVolumeNode.GetImageData()
cast = slicer.vtkImageCast()
cast.SetInput(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
for i in range(sourceSeedsNode.GetNumberOfFiducials()):
rasPt = sourceSeedsNode.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
sourceSeedIds.InsertNextId(
image.ComputePointId(int(ijkPt[0]), int(ijkPt[1]),
int(ijkPt[2])))
if targetSeedsNode:
for i in range(targetSeedsNode.GetNumberOfFiducials()):
rasPt = targetSeedsNode.GetNthFiducialXYZ(i)
ijkPt = self._helper.ConvertRAS2IJK(rasPt)
targetSeedIds.InsertNextId(
image.ComputePointId(int(ijkPt[0]), int(ijkPt[1]),
int(ijkPt[2])))
scalarRange = image.GetScalarRange()
threshold = slicer.vtkImageThreshold()
threshold.SetInput(image)
threshold.ThresholdBetween(lowerThreshold, higherThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
scalarRange = threshold.GetOutput().GetScalarRange()
thresholdedImage = threshold.GetOutput()
shiftScale = slicer.vtkImageShiftScale()
shiftScale.SetInput(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1 / (scalarRange[1] - scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
fastMarching = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter(
)
fastMarching.SetInput(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOff()
fastMarching.SetTargetOffset(100.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = slicer.vtkImageMathematics()
subtract.SetInput(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
subtract = slicer.vtkImageThreshold()
subtract.SetInput(fastMarching.GetOutput())
subtract.ThresholdByLower(1000) #better value soon
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(subtract.GetOutput())
outVolumeData.Update()
# volume calculated...
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 0.0)
self._helper.debug("Fast Marching done...")
return outputContainer
