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
def Centerlines(self):
inModel = self._outModelPrepSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
vModel = self._outVSelector.GetSelected()
seeds = self._seedsSelector.GetSelected()
targetSeeds = self._targetSeedsSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if inModel and outModel and seeds and targetSeeds and vModel and vmtkFound:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
pointLocator = slicer.vtkPointLocator()
pointLocator.SetDataSet(inModel.GetPolyData())
pointLocator.BuildLocator()
for i in range(seeds.GetNumberOfFiducials()):
rasPt = seeds.GetNthFiducialXYZ(i)
id = pointLocator.FindClosestPoint(int(rasPt[0]),int(rasPt[1]),int(rasPt[2]))
sourceSeedIds.InsertNextId(id)
for i in range(targetSeeds.GetNumberOfFiducials()):
rasPt = targetSeeds.GetNthFiducialXYZ(i)
id = pointLocator.FindClosestPoint(int(rasPt[0]),int(rasPt[1]),int(rasPt[2]))
targetSeedIds.InsertNextId(id)
result = slicer.vtkPolyData()
result.DeepCopy(self._logic.computeCenterlines(inModel.GetPolyData(),sourceSeedIds,targetSeedIds))
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0, 0, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
vd = slicer.vtkPolyData()
vd.DeepCopy(self._logic.GetVoronoiDiagram())
vd.Update()
vModel.SetAndObservePolyData(vd)
vModel.SetModifiedSinceRead(1)
dNode = vModel.GetModelDisplayNode()
if not dNode:
dNode = slicer.vtkMRMLModelDisplayNode()
dNode.SetPolyData(vModel.GetPolyData())
dNode.SetScalarVisibility(1)
dNode.SetBackfaceCulling(0)
dNode.SetActiveScalarName("MaximumInscribedSphereRadius")
dNode.SetAndObserveColorNodeID(self.GetLogic().GetMRMLScene().GetNodesByName("Labels").GetItemAsObject(0).GetID())
dNode.SetVisibility(1)
dNode.SetOpacity(0.5)
self.GetLogic().GetMRMLScene().AddNode(dNode)
vModel.SetAndObserveDisplayNodeID(dNode.GetID())
def Centerlines(self):
inModel = self._outModelPrepSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
vModel = self._outVSelector.GetSelected()
seeds = self._seedsSelector.GetSelected()
targetSeeds = self._targetSeedsSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if inModel and outModel and seeds and targetSeeds and vModel and vmtkFound:
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
pointLocator = slicer.vtkPointLocator()
pointLocator.SetDataSet(inModel.GetPolyData())
pointLocator.BuildLocator()
for i in range(seeds.GetNumberOfFiducials()):
rasPt = seeds.GetNthFiducialXYZ(i)
id = pointLocator.FindClosestPoint(int(rasPt[0]),
int(rasPt[1]),
int(rasPt[2]))
sourceSeedIds.InsertNextId(id)
for i in range(targetSeeds.GetNumberOfFiducials()):
rasPt = targetSeeds.GetNthFiducialXYZ(i)
id = pointLocator.FindClosestPoint(int(rasPt[0]),
int(rasPt[1]),
int(rasPt[2]))
targetSeedIds.InsertNextId(id)
result = slicer.vtkPolyData()
result.DeepCopy(
self._logic.computeCenterlines(inModel.GetPolyData(),
sourceSeedIds, targetSeedIds))
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0, 0, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
vd = slicer.vtkPolyData()
vd.DeepCopy(self._logic.GetVoronoiDiagram())
vd.Update()
vModel.SetAndObservePolyData(vd)
vModel.SetModifiedSinceRead(1)
dNode = vModel.GetModelDisplayNode()
if not dNode:
dNode = slicer.vtkMRMLModelDisplayNode()
dNode.SetPolyData(vModel.GetPolyData())
dNode.SetScalarVisibility(1)
dNode.SetBackfaceCulling(0)
dNode.SetActiveScalarName("MaximumInscribedSphereRadius")
dNode.SetAndObserveColorNodeID(
self.GetLogic().GetMRMLScene().GetNodesByName(
"Labels").GetItemAsObject(0).GetID())
dNode.SetVisibility(1)
dNode.SetOpacity(0.5)
self.GetLogic().GetMRMLScene().AddNode(dNode)
vModel.SetAndObserveDisplayNodeID(dNode.GetID())
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