def __init__(self):
ScriptedModuleGUI.__init__(self)
self.vtkScriptedModuleGUI.SetCategory("IGT")
self.TransformNodeSelector = slicer.vtkSlicerNodeSelectorWidget()
self.StartStopButton = slicer.vtkKWPushButton()
self.LabelMapSelector = slicer.vtkSlicerNodeSelectorWidget()
self.LabelMapIJKToRAS = slicer.vtkMatrix4x4()
self.LabelMapTransform = slicer.vtkMatrix4x4()
self.ObservedTransform = 0
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 fiberGPFieldToMRMLScalarVN(fib, vn):
from Slicer import slicer
matrix = slicer.vtkMatrix4x4()
matrix.SetElement(0, 0, 0)
matrix.SetElement(1, 1, 0)
matrix.SetElement(2, 2, 0)
matrix.SetElement(0, 2, 2)
matrix.SetElement(1, 1, 2)
matrix.SetElement(2, 0, 2)
matrix.SetElement(0, 3, fib[0][0, 0])
matrix.SetElement(1, 3, fib[0][0, 1])
matrix.SetElement(2, 3, fib[0][0, 2])
matrix.Invert()
vn.SetRASToIJKMatrix(matrix)
id = vn.GetImageData()
fb = fib[1]
shape = fb.shape
id.SetDimensions(shape[-1], shape[-2], shape[-3])
id.SetNumberOfScalarComponents(1)
id.AllocateScalars()
id.ToArray()[:] = fb
id.Modified()
vn.Modified()
def fiberGPFieldToMRMLScalarVN( fib, vn ): from Slicer import slicer matrix = slicer.vtkMatrix4x4() matrix.SetElement(0,0,0) matrix.SetElement(1,1,0) matrix.SetElement(2,2,0) matrix.SetElement(0,2,2) matrix.SetElement(1,1,2) matrix.SetElement(2,0,2) matrix.SetElement(0,3,fib[0][0,0]) matrix.SetElement(1,3,fib[0][0,1]) matrix.SetElement(2,3,fib[0][0,2]) matrix.Invert() vn.SetRASToIJKMatrix(matrix) id = vn.GetImageData() fb = fib[1] shape = fb.shape id.SetDimensions( shape[-1], shape[-2], shape[-3] ) id.SetNumberOfScalarComponents(1) id.AllocateScalars() id.ToArray()[:] = fb id.Modified() vn.Modified()
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 dispW0(dataD, inputVolume, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
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()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
def VolumeRendering(self, volumeNode, color, flipImage=0, cf=0):
matrix = slicer.vtkMatrix4x4()
image = volumeNode.GetImageData()
volumeNode.GetIJKToRASMatrix(matrix)
scalarRange = image.GetPointData().GetScalars().GetRange()
if color == "red": # initialization mode
r = 0.8
g = 0.0
b = 0.0
if flipImage:
minV = 0
maxV = scalarRange[1]
else:
minV = scalarRange[0]
maxV = 0
if cf:
minV = scalarRange[0]
maxV = -0.1
elif color == "blue": # evolution mode
r = 1.0
g = 1.0
b = 0.0
minV = -0.4
maxV = 0.4
self._parentClass.GetMyLogic().VolumeRendering(image, matrix, minV, maxV, [r, g, b])
def VolumeRendering(self, volumeNode, color, flipImage=0, cf=0):
matrix = slicer.vtkMatrix4x4()
image = volumeNode.GetImageData()
volumeNode.GetIJKToRASMatrix(matrix)
scalarRange = image.GetPointData().GetScalars().GetRange()
if color == 'red': # initialization mode
r = 0.8
g = 0.0
b = 0.0
if flipImage:
minV = 0
maxV = scalarRange[1]
else:
minV = scalarRange[0]
maxV = 0
if cf:
minV = scalarRange[0]
maxV = -0.1
elif color == 'blue': # evolution mode
r = 1.0
g = 1.0
b = 0.0
minV = -0.4
maxV = 0.4
self._parentClass.GetMyLogic().VolumeRendering(image, matrix, minV,
maxV, [r, g, b])
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 Execute(self):
SlicerVMTKAdvancedPageSkeleton.Execute(self)
inVolume = self._parentClass._inVolumeSelector.GetSelected()
outVolume = self._parentClass._outVolumeSelector.GetSelected()
if not inVolume or not outVolume or not self.CheckForVmtkLibrary():
slicer.Application.ErrorMessage(
"No input volume or no output volume found. Aborting VED..\n")
return
else:
sigmaMin = float(self._sigmaMin.GetWidget().GetValue())
sigmaMax = float(self._sigmaMax.GetWidget().GetValue())
numberOfSigmaSteps = int(self._numberOfSigmaSteps.GetValue())
numberOfIterations = int(self._numberOfIterations.GetValue())
numberOfDiffusionSubIterations = int(
self._numberOfDiffusionSubIterations.GetValue())
alpha = float(self._alpha.GetWidget().GetValue())
beta = float(self._beta.GetWidget().GetValue())
gamma = float(self._gamma.GetWidget().GetValue())
c = float(self._c.GetWidget().GetValue())
timestep = float(self._timestep.GetWidget().GetValue())
epsilon = float(self._epsilon.GetWidget().GetValue())
wstrength = float(self._wstrength.GetWidget().GetValue())
sensitivity = float(self._sensitivity.GetWidget().GetValue())
outVolumeImage = self._parentClass._logic.ApplyVED(
inVolume.GetImageData(), sigmaMin, sigmaMax,
numberOfSigmaSteps, alpha, beta, gamma, c, timestep, epsilon,
wstrength, sensitivity, numberOfIterations,
numberOfDiffusionSubIterations)
matrix = slicer.vtkMatrix4x4()
inVolume.GetIJKToRASMatrix(matrix)
outVolume.SetAndObserveImageData(outVolumeImage)
outVolume.SetIJKToRASMatrix(matrix)
displayNode = inVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode)
outVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
newDisplayNode.AutoWindowLevelOff()
newDisplayNode.AutoWindowLevelOn() # renew auto windowlevel
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inVolume.GetLabelMap():
outVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(
outVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outVolume.GetID())
appLogic.PropagateVolumeSelection()
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 GenerateEvolutionModel(self, resultContainer):
matrix = slicer.vtkMatrix4x4()
image = resultContainer.GetNode().GetImageData()
resultContainer.GetNode().GetIJKToRASMatrix(matrix)
threshold = 0.0
polyData = slicer.vtkPolyData()
if image.GetPointData().GetScalars():
# marching Cubes, only if image has content
polyData.DeepCopy(self._mainGUIClass.GetMyLogic().MarchingCubes(
image, matrix, threshold))
scene = self._mainGUIClass.GetLogic().GetMRMLScene()
if self._mainGUIClass._outEvolModel == None:
# no node so far
self._mainGUIClass._outEvolModel = slicer.vtkMRMLModelNode()
self._mainGUIClass._outEvolModel.SetName(
"VMTK Level-Set Evolution Output Model")
self._mainGUIClass._outEvolModel.SetAndObservePolyData(
slicer.vtkPolyData())
self._mainGUIClass._outEvolModel.SetScene(scene)
scene.AddNode(self._mainGUIClass._outEvolModel)
self._mainGUIClass._outEvolModelDisplay = slicer.vtkMRMLModelDisplayNode(
)
self._mainGUIClass._outEvolModelDisplay.SetColor(0.0, 0.0, 0.8)
self._mainGUIClass._outEvolModelDisplay.SetPolyData(
slicer.vtkPolyData())
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(
1)
self._mainGUIClass._outEvolModel.SetAndObservePolyData(polyData)
self._mainGUIClass._outEvolModel.SetModifiedSinceRead(1)
self._mainGUIClass._outEvolModelDisplay.SetPolyData(
self._mainGUIClass._outEvolModel.GetPolyData())
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(
1)
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
scene.AddNode(self._mainGUIClass._outEvolModelDisplay)
self._mainGUIClass._outEvolModel.SetAndObserveDisplayNodeID(
self._mainGUIClass._outEvolModelDisplay.GetID())
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(
1)
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
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 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 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 Execute(self):
SlicerVMTKAdvancedPageSkeleton.Execute(self)
inVolume = self._parentClass._inVolumeSelector.GetSelected()
outVolume = self._parentClass._outVolumeSelector.GetSelected()
if not inVolume or not outVolume or not self.CheckForVmtkLibrary():
slicer.Application.ErrorMessage("No input volume or no output volume found. Aborting Frangi..\n")
return
else:
sigmaMin = float(self._sigmaMin.GetWidget().GetValue())
sigmaMax = float(self._sigmaMax.GetWidget().GetValue())
numberOfSigmaSteps = int(self._numberOfSigmaSteps.GetValue())
alpha = float(self._alpha.GetWidget().GetValue())
beta = float(self._beta.GetWidget().GetValue())
gamma = float(self._gamma.GetWidget().GetValue())
imageData = slicer.vtkImageData()
imageData.DeepCopy(inVolume.GetImageData())
imageData.Update()
if (self._sigmaUnit.GetWidget().GetWidget(0).GetSelectedState()==1):
self._parentClass.debug("use mm!")
imageData.SetSpacing(inVolume.GetSpacing()[0], inVolume.GetSpacing()[1], inVolume.GetSpacing()[2])
outVolumeImage = self._parentClass._logic.ApplyFrangiVesselness(imageData,sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,beta,gamma)
outVolumeImage.SetSpacing(1,1,1)
matrix = slicer.vtkMatrix4x4()
inVolume.GetIJKToRASMatrix(matrix)
outVolume.SetAndObserveImageData(outVolumeImage)
outVolume.SetIJKToRASMatrix(matrix)
displayNode = inVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode);
outVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
newDisplayNode.AutoWindowLevelOff()
newDisplayNode.AutoWindowLevelOn() # renew auto windowlevel
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inVolume.GetLabelMap():
outVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(outVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outVolume.GetID())
appLogic.PropagateVolumeSelection()
def slicerMRMLVolumeNode2Image_ras2ijk(volumeNode):
from Slicer import slicer
from numpy import eye, ndindex
vtk_ras2ijk = slicer.vtkMatrix4x4()
volumeNode.GetRASToIJKMatrix(vtk_ras2ijk)
image = volumeNode.GetImageData().ToArray().T
ras2ijk = eye(4)
for c in ndindex(ras2ijk.shape):
ras2ijk[c] = vtk_ras2ijk.GetElement(c[0], c[1])
return image, ras2ijk
def slicerMRMLVolumeNode2Image_ras2ijk( volumeNode ):
from Slicer import slicer
from numpy import eye, ndindex
vtk_ras2ijk = slicer.vtkMatrix4x4()
volumeNode.GetRASToIJKMatrix( vtk_ras2ijk )
image = volumeNode.GetImageData().ToArray().T
ras2ijk = eye(4)
for c in ndindex( ras2ijk.shape ):
ras2ijk[c] = vtk_ras2ijk.GetElement( c[0], c[1] )
return image, ras2ijk
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 Execute(self):
SlicerVMTKAdvancedPageSkeleton.Execute(self)
inVolume = self._parentClass._inVolumeSelector.GetSelected()
outVolume = self._parentClass._outVolumeSelector.GetSelected()
if not inVolume or not outVolume or not self.CheckForVmtkLibrary():
slicer.Application.ErrorMessage("No input volume or no output volume found. Aborting VED..\n")
return
else:
sigmaMin = float(self._sigmaMin.GetWidget().GetValue())
sigmaMax = float(self._sigmaMax.GetWidget().GetValue())
numberOfSigmaSteps = int(self._numberOfSigmaSteps.GetValue())
numberOfIterations = int(self._numberOfIterations.GetValue())
numberOfDiffusionSubIterations = int(self._numberOfDiffusionSubIterations.GetValue())
alpha = float(self._alpha.GetWidget().GetValue())
beta = float(self._beta.GetWidget().GetValue())
gamma = float(self._gamma.GetWidget().GetValue())
c = float(self._c.GetWidget().GetValue())
timestep = float(self._timestep.GetWidget().GetValue())
epsilon = float(self._epsilon.GetWidget().GetValue())
wstrength = float(self._wstrength.GetWidget().GetValue())
sensitivity = float(self._sensitivity.GetWidget().GetValue())
outVolumeImage = self._parentClass._logic.ApplyVED(inVolume.GetImageData(),sigmaMin,sigmaMax,numberOfSigmaSteps,alpha,beta,gamma,c,timestep,epsilon,wstrength,sensitivity,numberOfIterations,numberOfDiffusionSubIterations)
matrix = slicer.vtkMatrix4x4()
inVolume.GetIJKToRASMatrix(matrix)
outVolume.SetAndObserveImageData(outVolumeImage)
outVolume.SetIJKToRASMatrix(matrix)
displayNode = inVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode);
outVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
newDisplayNode.AutoWindowLevelOff()
newDisplayNode.AutoWindowLevelOn() # renew auto windowlevel
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inVolume.GetLabelMap():
outVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(outVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outVolume.GetID())
appLogic.PropagateVolumeSelection()
def UndoEvol(self):
# copy outEvolVolumeLast to outEvolVolume
matrix = slicer.vtkMatrix4x4()
self._mainGUIClass._outEvolVolumeLast.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(self._mainGUIClass._outEvolVolumeLast.GetImageData())
self._mainGUIClass._outEvolVolume.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetModifiedSinceRead(1)
outputContainer = SlicerVMTKLevelSetContainer(self._mainGUIClass._outEvolVolume,0.0)
return outputContainer
def UndoEvol(self):
# copy outEvolVolumeLast to outEvolVolume
matrix = slicer.vtkMatrix4x4()
self._mainGUIClass._outEvolVolumeLast.GetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetAndObserveImageData(
self._mainGUIClass._outEvolVolumeLast.GetImageData())
self._mainGUIClass._outEvolVolume.SetIJKToRASMatrix(matrix)
self._mainGUIClass._outEvolVolume.SetModifiedSinceRead(1)
outputContainer = SlicerVMTKLevelSetContainer(
self._mainGUIClass._outEvolVolume, 0.0)
return outputContainer
def ConvertCoordinates2IJK(self, which, coordinates):
#need RAS
rasPt = self.ConvertCoordinates2RAS(which, coordinates)
#convert to IJK
node = self._mainGUIClass.GetScriptedModuleNode()
if node:
inVolume = node.GetParameter('InputVolumeRef')
if not inVolume:
slicer.Application.ErrorMessage("No input volume found\n")
return
else:
matrixIJK = slicer.vtkMatrix4x4()
inVolume.GetRASToIJKMatrix(matrixIJK)
ijkPt = matrixIJK.MultiplyPoint(*rasPt)
return ijkPt
def ConvertCoordinates2IJK(self,which,coordinates):
#need RAS
rasPt = self.ConvertCoordinates2RAS(which,coordinates)
#convert to IJK
node = self._mainGUIClass.GetScriptedModuleNode()
if node:
inVolume = node.GetParameter('InputVolumeRef')
if not inVolume:
slicer.Application.ErrorMessage("No input volume found\n")
return
else:
matrixIJK = slicer.vtkMatrix4x4()
inVolume.GetRASToIJKMatrix(matrixIJK)
ijkPt = matrixIJK.MultiplyPoint(*rasPt)
return ijkPt
def GenerateModel(self, volumeNode, color):
if color == 'red':
r = 0.8
g = 0.0
b = 0.0
name = "VMTK Initialization Model"
registerModel = 1
elif color == 'blue':
r = 1.0
g = 1.0
b = 0.0
name = "VMTK Evolution Model"
registerModel = 0
matrix = slicer.vtkMatrix4x4()
image = volumeNode.GetImageData()
volumeNode.GetIJKToRASMatrix(matrix)
polyData = slicer.vtkPolyData()
if image.GetPointData().GetScalars():
# marching Cubes, only if image has content
polyData.DeepCopy(self._parentClass.GetMyLogic().MarchingCubes(
image, matrix, 0.0))
scene = self._parentClass.GetLogic().GetMRMLScene()
newModel = slicer.vtkMRMLModelNode()
newModel.SetName(name)
newModel.SetScene(scene)
newModel.SetAndObservePolyData(polyData)
scene.AddNode(newModel)
newModelDisplay = slicer.vtkMRMLModelDisplayNode()
newModelDisplay.SetPolyData(newModel.GetPolyData())
newModelDisplay.SetColor(r, g, b)
newModelDisplay.SetBackfaceCulling(0)
newModelDisplay.SetSliceIntersectionVisibility(1)
newModelDisplay.SetVisibility(1)
newModelDisplay.SetOpacity(1.0)
scene.AddNode(newModelDisplay)
newModel.SetAndObserveDisplayNodeID(newModelDisplay.GetID())
if registerModel:
self._parentClass.SetOutInitModelDisplay(newModelDisplay)
def GenerateModel(self, volumeNode, color):
if color == "red":
r = 0.8
g = 0.0
b = 0.0
name = "VMTK Initialization Model"
registerModel = 1
elif color == "blue":
r = 1.0
g = 1.0
b = 0.0
name = "VMTK Evolution Model"
registerModel = 0
matrix = slicer.vtkMatrix4x4()
image = volumeNode.GetImageData()
volumeNode.GetIJKToRASMatrix(matrix)
polyData = slicer.vtkPolyData()
if image.GetPointData().GetScalars():
# marching Cubes, only if image has content
polyData.DeepCopy(self._parentClass.GetMyLogic().MarchingCubes(image, matrix, 0.0))
scene = self._parentClass.GetLogic().GetMRMLScene()
newModel = slicer.vtkMRMLModelNode()
newModel.SetName(name)
newModel.SetScene(scene)
newModel.SetAndObservePolyData(polyData)
scene.AddNode(newModel)
newModelDisplay = slicer.vtkMRMLModelDisplayNode()
newModelDisplay.SetPolyData(newModel.GetPolyData())
newModelDisplay.SetColor(r, g, b)
newModelDisplay.SetBackfaceCulling(0)
newModelDisplay.SetSliceIntersectionVisibility(1)
newModelDisplay.SetVisibility(1)
newModelDisplay.SetOpacity(1.0)
scene.AddNode(newModelDisplay)
newModel.SetAndObserveDisplayNodeID(newModelDisplay.GetID())
if registerModel:
self._parentClass.SetOutInitModelDisplay(newModelDisplay)
def GenerateEvolutionModel(self,resultContainer):
matrix = slicer.vtkMatrix4x4()
image = resultContainer.GetNode().GetImageData()
resultContainer.GetNode().GetIJKToRASMatrix(matrix)
threshold = 0.0
polyData = slicer.vtkPolyData()
if image.GetPointData().GetScalars():
# marching Cubes, only if image has content
polyData.DeepCopy(self._mainGUIClass.GetMyLogic().MarchingCubes(image,matrix,threshold))
scene = self._mainGUIClass.GetLogic().GetMRMLScene()
if self._mainGUIClass._outEvolModel == None:
# no node so far
self._mainGUIClass._outEvolModel = slicer.vtkMRMLModelNode()
self._mainGUIClass._outEvolModel.SetName("VMTK Level-Set Evolution Output Model")
self._mainGUIClass._outEvolModel.SetAndObservePolyData(slicer.vtkPolyData())
self._mainGUIClass._outEvolModel.SetScene(scene)
scene.AddNode(self._mainGUIClass._outEvolModel)
self._mainGUIClass._outEvolModelDisplay = slicer.vtkMRMLModelDisplayNode()
self._mainGUIClass._outEvolModelDisplay.SetColor(0.0, 0.0, 0.8)
self._mainGUIClass._outEvolModelDisplay.SetPolyData(slicer.vtkPolyData())
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(1)
self._mainGUIClass._outEvolModel.SetAndObservePolyData(polyData)
self._mainGUIClass._outEvolModel.SetModifiedSinceRead(1)
self._mainGUIClass._outEvolModelDisplay.SetPolyData(self._mainGUIClass._outEvolModel.GetPolyData())
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
scene.AddNode(self._mainGUIClass._outEvolModelDisplay)
self._mainGUIClass._outEvolModel.SetAndObserveDisplayNodeID(self._mainGUIClass._outEvolModelDisplay.GetID())
self._mainGUIClass._outEvolModelDisplay.SetSliceIntersectionVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetVisibility(1)
self._mainGUIClass._outEvolModelDisplay.SetOpacity(0.5)
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 dispW0(dataD, inputVolume, shpV, nvol):
scene = slicer.MRMLScene
r1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
r11 = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
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()
print 'tmp : ', tmp.shape
print 'dataD : ', dataD.shape
tmp[...] = dataD[..., nvol]
r1.GetDisplayNode().SetDefaultColorMap()
r1.Modified()
return
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 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 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 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 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 Apply(self):
inputVolume = self.VolumeSelector.GetSelected()
if not inputVolume:
self.ErrorDialog("No input volume found")
return
outputVolume = self.OutVolumeSelector.GetSelected()
if not outputVolume:
self.ErrorDialog("No output volume found")
return
inputSeeds = self.FiducialsNodeSelector.GetSelected()
if not inputSeeds:
self.ErrorDialog("No fiducials found")
return
if inputSeeds.GetNumberOfFiducials() < 2:
self.ErrorDialog("Need at least 2 fiducials in the list")
return
self.Status("Applying Subvolume...")
# get the seed points (RAS)
p0 = inputSeeds.GetNthFiducialXYZ(0)
p1 = inputSeeds.GetNthFiducialXYZ(1)
lower = map(min, p0, p1)
# convert seed points to input volume IJK
rasToIJK = slicer.vtkMatrix4x4()
inputVolume.GetRASToIJKMatrix(rasToIJK)
p0IJK = rasToIJK.MultiplyPoint(p0[0], p0[1], p0[2], 1.0)
p1IJK = rasToIJK.MultiplyPoint(p1[0], p1[1], p1[2], 1.0)
# find the bounding box of the seeds
lowerIJK = map(int, map(min, p0IJK, p1IJK))
upperIJK = map(int, map(max, p0IJK, p1IJK))
# get an array of the input volume, extract the sub
a = inputVolume.GetImageData().ToArray()
sub = a[lowerIJK[2] : upperIJK[2], lowerIJK[1] : upperIJK[1], lowerIJK[0] : upperIJK[0]]
# set up output node
outImage = slicer.vtkImageData()
outImage.SetDimensions(sub.shape[2], sub.shape[1], sub.shape[0])
outImage.AllocateScalars()
outImage.ToArray()[:] = sub[:]
outputVolume.SetAndObserveImageData(outImage)
rasToIJK.Invert()
ijkToRAS = rasToIJK
outputVolume.SetIJKToRASMatrix(rasToIJK)
origin = ijkToRAS.MultiplyPoint(lowerIJK[0], lowerIJK[1], lowerIJK[2], 1.0)
outputVolume.SetOrigin(origin[0], origin[1], origin[2])
outputVolume.ModifiedSinceReadOn()
displayNode = inputVolume.GetDisplayNode()
if displayNode != None:
newDisplayNode = displayNode.NewInstance()
newDisplayNode.Copy(displayNode)
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode)
outputVolume.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
appLogic = slicer.ApplicationLogic
selectionNode = appLogic.GetSelectionNode()
if inputVolume.GetLabelMap():
outputVolume.SetLabelMap(1)
selectionNode.SetReferenceActiveLabelVolumeID(outputVolume.GetID())
else:
selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
appLogic.PropagateVolumeSelection()
self.Status("Done applying Subvolume.")
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
