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 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 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