def CheckForVmtkLibrary(self):
try:
t = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter()
except Exception:
d = slicer.vtkKWMessageDialog()
d.SetParent(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetMasterWindow(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetStyleToMessage()
d.SetText("VmtkSlicerModule not found! Please install the VmtkSlicerModule extension to use this module!")
d.Create()
d.Invoke()
return 0
return 1
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 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 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
