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 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 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 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 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 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 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 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 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 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 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 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 GAC(self): origVolume = self._inVolumeSelector.GetSelected() segmentationVolume = self._outVolumeSelector.GetSelected() outVolume = self._outEvolVolumeSelector.GetSelected() seeds = self._seedsSelector.GetSelected() targetSeeds = self._targetSeedsSelector.GetSelected() vmtkFound = self.CheckForVmtkLibrary() if origVolume and segmentationVolume and outVolume and vmtkFound: numberOfIterations = int(self._iterationsSpinbox.GetWidget().GetValue()) propagationScaling = self._propagationScale.GetValue() curvatureScaling = self._curvatureScale.GetValue() advectionScaling = self._advectionScale.GetValue() if (self._evolMethod.GetWidget().GetWidget(0).GetSelectedState()==1): result = self._logic.ExecuteGAC(origVolume.GetImageData(),segmentationVolume.GetImageData(),numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,'geodesic') else: result = self._logic.ExecuteGAC(origVolume.GetImageData(),segmentationVolume.GetImageData(),numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,'curves') ijkToRasMatrix = slicer.vtkMatrix4x4() origVolume.GetIJKToRASMatrix(ijkToRasMatrix) #outVolume.LabelMapOn() outVolume.SetAndObserveImageData(result) outVolume.SetIJKToRASMatrix(ijkToRasMatrix) outVolume.SetModifiedSinceRead(1) inValue = 0 outValue = 5 if seeds and targetSeeds: if targetSeeds.GetID()!=seeds.GetID(): # switch thresholds for labelmap when using target points inValue = 5 outValue = 0 scene = self.GetLogic().GetMRMLScene() newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode() newDisplayNode.SetScene(scene) newDisplayNode.SetDefaultColorMap() slicer.MRMLScene.AddNodeNoNotify(newDisplayNode) labelMap = slicer.vtkMRMLScalarVolumeNode() labelMap.SetName("VMTKEvolutionLabelMap") labelMap.SetAndObserveImageData(self._logic.BuildSimpleLabelMap(result,inValue,outValue)) labelMap.SetIJKToRASMatrix(ijkToRasMatrix) labelMap.LabelMapOn() labelMap.SetAndObserveDisplayNodeID(newDisplayNode.GetID()) scene.AddNode(labelMap) slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(labelMap.GetID()) slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveVolumeID(origVolume.GetID()) slicer.ApplicationLogic.PropagateVolumeSelection() #slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(outVolume.GetID()) #slicer.ApplicationLogic.PropagateVolumeSelection() if self._outInitModelDisplay != None: # deactivate old init model if it exists #nodeId = self.GetLogic().GetMRMLScene().GetNodeByID(self._outInitModelDisplay.GetID()) #if nodeId: #if self.GetLogic().GetMRMLScene().IsNodePresent(nodeId): self._helper.debug("hiding old model..") self._outInitModelDisplay.SetVisibility(0) self._outInitModelDisplay.SetModifiedSinceRead(1) if self._vrCheckButton.GetSelectedState(): self._helper.HideVR() if targetSeeds: self._helper.VolumeRendering(outVolume,'blue',targetSeeds.GetID()==seeds.GetID()) else: self._helper.VolumeRendering(outVolume,'blue',1) #self._helper.VolumeRendering(outVolume,'blue') self._helper.ShowVR() else: self._helper.HideVR() self._helper.GenerateModel(outVolume,'blue')
def FM(self): inVolume = self._inVolumeSelector.GetSelected() outVolume = self._outVolumeSelector.GetSelected() seeds = self._seedsSelector.GetSelected() targetSeeds = self._targetSeedsSelector.GetSelected() vmtkFound = self.CheckForVmtkLibrary() if inVolume and outVolume and seeds and vmtkFound: extentValues = self._thresholdExtent.GetExtent() sourceSeedIds = slicer.vtkIdList() targetSeedIds = slicer.vtkIdList() image = inVolume.GetImageData() rasToIjkMatrix = slicer.vtkMatrix4x4() inVolume.GetRASToIJKMatrix(rasToIjkMatrix) for i in range(seeds.GetNumberOfFiducials()): rasPt = seeds.GetNthFiducialXYZ(i) rasPt.append(1) ijkPt = rasToIjkMatrix.MultiplyPoint(*rasPt) sourceSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2]))) inValue = 0 outValue = 5 sideBranchSwitch=0 if targetSeeds: if targetSeeds.GetID()!=seeds.GetID(): #only run if different fiducial lists self._helper.debug("Using target points..") for i in range(targetSeeds.GetNumberOfFiducials()): rasPt = targetSeeds.GetNthFiducialXYZ(i) rasPt.append(1) ijkPt = rasToIjkMatrix.MultiplyPoint(*rasPt) targetSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2]))) if self._sbCheckButton.GetSelectedState(): sideBranchSwitch=1 # allow side branches only if targetseeds are available # switch thresholds for labelmap when using target points inValue = 5 outValue = 0 result = self._logic.ExecuteFM(inVolume.GetImageData(),extentValues[0],extentValues[1],sourceSeedIds,targetSeedIds,sideBranchSwitch) #self._helper.debug(result) ijkToRasMatrix = slicer.vtkMatrix4x4() inVolume.GetIJKToRASMatrix(ijkToRasMatrix) self.CreateOutVolumeNode() #outVolume.LabelMapOn() outVolume.SetAndObserveImageData(result) outVolume.SetIJKToRASMatrix(ijkToRasMatrix) outVolume.SetModifiedSinceRead(1) scene = self.GetLogic().GetMRMLScene() newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode() newDisplayNode.SetScene(scene) newDisplayNode.SetDefaultColorMap() slicer.MRMLScene.AddNodeNoNotify(newDisplayNode) labelMap = slicer.vtkMRMLScalarVolumeNode() labelMap.SetName("VMTKInitializationLabelMap") labelMap.SetAndObserveImageData(self._logic.BuildSimpleLabelMap(result,inValue,outValue)) labelMap.SetIJKToRASMatrix(ijkToRasMatrix) labelMap.LabelMapOn() labelMap.SetAndObserveDisplayNodeID(newDisplayNode.GetID()) labelMap.SetModifiedSinceRead(1) scene.AddNode(labelMap) slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(labelMap.GetID()) slicer.ApplicationLogic.PropagateVolumeSelection() displayNode = inVolume.GetDisplayNode() # reset threshold for visualization extentValues = self._thresholdExtent.GetExtentRange() displayNode.SetLowerThreshold(extentValues[0]) displayNode.SetUpperThreshold(extentValues[1]) displayNode.SetApplyThreshold(1) if self._vrCheckButton.GetSelectedState(): self._helper.HideVR() if targetSeeds: self._helper.VolumeRendering(outVolume,'red',targetSeeds.GetID()==seeds.GetID(),sideBranchSwitch) else: self._helper.VolumeRendering(outVolume,'red',1) self._helper.ShowVR() else: self._helper.HideVR() self._helper.GenerateModel(outVolume,'red')
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 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