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 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 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 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 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 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
