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 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 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 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 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