def computeCenterlines(self,polydata,inletSeedIds,outletSeedIds):
centerlineFilter = slicer.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInput(polydata)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self._radiusArrayName)
centerlineFilter.SetCostFunction(self._costFunction)
centerlineFilter.SetFlipNormals(self._flipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self._appendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self._simplifyVoronoi)
centerlineFilter.SetCenterlineResampling(self._resampling)
centerlineFilter.SetResamplingStepLength(self._resamplingStepLength)
centerlineFilter.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(centerlineFilter.GetOutput())
polyDataNew.Update()
self._vd = slicer.vtkPolyData()
self._vd.DeepCopy(centerlineFilter.GetVoronoiDiagram())
self._vd.Update()
return polyDataNew
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 Extract(self):
inModel = self._inModelSelector.GetSelected()
seeds = self._seedsSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
vmtkFound=self.CheckForVmtkLibrary()
if inModel and outModel and seeds and vmtkFound:
result = slicer.vtkPolyData()
result.DeepCopy(self._logic.extractNetwork(inModel.GetPolyData(),seeds.GetNthFiducialXYZ(0)))
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.SetScalarVisibility(1)
displayNode.SetActiveScalarName("Topology")
displayNode.SetAndObserveColorNodeID(self.GetLogic().GetMRMLScene().GetNodesByName("Labels").GetItemAsObject(0).GetID())
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
dNode = inModel.GetModelDisplayNode()
dNode.SetOpacity(0.5)
inModel.SetAndObserveDisplayNodeID(dNode.GetID())
def PrepCenterlines(self):
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelPrepSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if inModel and outModel and vmtkFound:
displayNodeIn = inModel.GetModelDisplayNode()
if displayNodeIn:
displayNodeIn.SetVisibility(0)
result = slicer.vtkPolyData()
result.DeepCopy(self._logic.prepareModel(inModel.GetPolyData()))
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0, 0.8, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(0.7)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
def PrepCenterlines(self):
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelPrepSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if inModel and outModel and vmtkFound:
displayNodeIn = inModel.GetModelDisplayNode()
if displayNodeIn:
displayNodeIn.SetVisibility(0)
result = slicer.vtkPolyData()
result.DeepCopy(self._logic.prepareModel(inModel.GetPolyData()))
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0, 0.8, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(0.7)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
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 MarchingCubes(self, image, matrix, threshold):
self._parentClass.GetHelper().debug("Starting MarchingCubes..")
transformIJKtoRAS = slicer.vtkTransform()
transformIJKtoRAS.SetMatrix(matrix)
marchingCubes = slicer.vtkMarchingCubes()
marchingCubes.SetInput(image)
marchingCubes.SetValue(0, threshold)
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
self.debug("Determinant smaller than 0")
reverser = slicer.vtkReverseSense()
reverser.SetInput(marchingCubes.GetOutput())
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = slicer.vtkTransformPolyDataFilter()
transformer.SetInput(correctedOutput)
transformer.SetTransform(transformIJKtoRAS)
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = slicer.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput(transformer.GetOutput())
normals.SetFeatureAngle(60)
normals.SetSplitting(1)
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = slicer.vtkStripper()
stripper.SetInput(normals.GetOutput())
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = slicer.vtkPolyData()
result.DeepCopy(stripper.GetOutput())
result.Update()
self._parentClass.GetHelper().debug("End MarchingCubes..")
return result
def MarchingCubes(self,image,matrix,threshold):
self._parentClass.GetHelper().debug("Starting MarchingCubes..")
transformIJKtoRAS = slicer.vtkTransform()
transformIJKtoRAS.SetMatrix(matrix)
marchingCubes = slicer.vtkMarchingCubes()
marchingCubes.SetInput(image)
marchingCubes.SetValue(0,threshold)
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
self.debug("Determinant smaller than 0")
reverser = slicer.vtkReverseSense()
reverser.SetInput(marchingCubes.GetOutput())
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = slicer.vtkTransformPolyDataFilter()
transformer.SetInput(correctedOutput)
transformer.SetTransform(transformIJKtoRAS)
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = slicer.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput(transformer.GetOutput())
normals.SetFeatureAngle(60)
normals.SetSplitting(1)
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = slicer.vtkStripper()
stripper.SetInput(normals.GetOutput())
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = slicer.vtkPolyData()
result.DeepCopy(stripper.GetOutput())
result.Update()
self._parentClass.GetHelper().debug("End MarchingCubes..")
return result
def splitModels(self, Surface):
dataArray = Surface.GetPointData().GetScalars("GroupIds")
scalarRange = dataArray.GetRange()
newPdList = []
newCaList = []
self._parentClass._helper.debug("started splitter")
# generate containers CellArray & PolyData + copy points
for i in range(1, int(scalarRange[1]) + 2):
newCellArray = slicer.vtkCellArray()
newPolyData = slicer.vtkPolyData()
points = slicer.vtkPoints()
points.DeepCopy(Surface.GetPoints())
newPolyData.SetPoints(points)
newPolyData.SetPolys(newCellArray)
newPolyData.Update()
newPdList.append(newPolyData)
newCaList.append(newCellArray)
#Fill containers with Polys
for i in range(0, Surface.GetPolys().GetNumberOfCells()):
poi = Surface.GetCell(i).GetPointIds()
if (poi.GetNumberOfIds() == 0):
continue
scalarsOfPoints = []
for pid in range(0, poi.GetNumberOfIds()):
p = poi.GetId(pid)
scalarsOfPoints.append(dataArray.GetValue(p))
max = 0
largestIndex = 0
for j in range(1, int(scalarRange[1]) + 2):
c = scalarsOfPoints.count(j)
if c >= max:
max = c
largestIndex = j
newCaList[largestIndex].InsertNextCell(Surface.GetCell(i))
# clean PolyData
for pd in newPdList:
cleanPolyData = slicer.vtkCleanPolyData()
cleanPolyData.SetInput(pd)
cleanPolyData.Update()
pd.DeepCopy(cleanPolyData.GetOutput())
self._parentClass._helper.debug("finished splitter")
return newPdList
def splitModels(self,Surface):
dataArray=Surface.GetPointData().GetScalars("GroupIds")
scalarRange=dataArray.GetRange()
newPdList=[]
newCaList=[]
self._parentClass._helper.debug("started splitter")
# generate containers CellArray & PolyData + copy points
for i in range(1,int(scalarRange[1])+2):
newCellArray=slicer.vtkCellArray()
newPolyData=slicer.vtkPolyData()
points=slicer.vtkPoints()
points.DeepCopy(Surface.GetPoints())
newPolyData.SetPoints(points)
newPolyData.SetPolys(newCellArray)
newPolyData.Update()
newPdList.append(newPolyData)
newCaList.append(newCellArray)
#Fill containers with Polys
for i in range (0,Surface.GetPolys().GetNumberOfCells()):
poi=Surface.GetCell(i).GetPointIds()
if(poi.GetNumberOfIds()==0):
continue
scalarsOfPoints =[]
for pid in range(0,poi.GetNumberOfIds()):
p=poi.GetId(pid)
scalarsOfPoints.append(dataArray.GetValue(p))
max=0
largestIndex=0
for j in range(1,int(scalarRange[1])+2):
c=scalarsOfPoints.count(j)
if c >= max:
max=c
largestIndex=j
newCaList[largestIndex].InsertNextCell(Surface.GetCell(i))
# clean PolyData
for pd in newPdList:
cleanPolyData = slicer.vtkCleanPolyData();
cleanPolyData.SetInput(pd);
cleanPolyData.Update();
pd.DeepCopy(cleanPolyData.GetOutput())
self._parentClass._helper.debug("finished splitter")
return newPdList
def branchSplitting(self,centerlines,model):
self.Centerlines = centerlines
self._parentClass._helper.debug("started branchExtractor")
branchExtractor = slicer.vtkvmtkCenterlineBranchExtractor()
branchExtractor.SetInput(centerlines)
branchExtractor.SetBlankingArrayName(self._BlankingArrayName)
branchExtractor.SetRadiusArrayName(self._RadiusArrayName)
branchExtractor.SetGroupIdsArrayName(self._GroupIdsArrayName)
branchExtractor.SetCenterlineIdsArrayName(self._CenterlineIdsArrayName)
branchExtractor.SetTractIdsArrayName(self._TractIdsArrayName)
branchExtractor.Update()
self._parentClass._helper.debug("finished branchExtractor")
self._parentClass._helper.debug("started clipper")
clipper = slicer.vtkvmtkPolyDataCenterlineGroupsClipper()
clipper.SetInput(model)
clipper.SetCenterlines(branchExtractor.GetOutput())
clipper.SetCenterlineGroupIdsArrayName(self._GroupIdsArrayName)
clipper.SetGroupIdsArrayName(self._GroupIdsArrayName)
clipper.SetCenterlineRadiusArrayName(self._RadiusArrayName)
clipper.SetBlankingArrayName(self._BlankingArrayName)
clipper.SetCutoffRadiusFactor(self._CutoffRadiusFactor)
clipper.SetClipValue(self._ClipValue)
clipper.SetUseRadiusInformation(self._UseRadiusInformation)
clipper.ClipAllCenterlineGroupIdsOn()
clipper.Update()
self._parentClass._helper.debug("finished clipper")
if not self._InsideOut:
clipper.GenerateClippedOutputOff()
else:
clipper.GenerateClippedOutputOn()
clipper.Update()
if not self._InsideOut:
Surface = clipper.GetOutput()
else:
Surface = clipper.GetClippedOutput()
# shift values because first value is invisible in default LabelMap
dataArray=Surface.GetPointData().GetScalars("GroupIds")
newDa=slicer.vtkIntArray()
newDa.SetName("GroupIds")
newDa.InsertTuple1(0, 0)
for i in range (1,dataArray.GetSize()):
newDa.InsertTuple1(i, dataArray.GetValue(i)+1)
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(Surface)
polyDataNew.GetPointData().SetScalars(newDa)
polyDataNew.Update()
return polyDataNew
def branchSplitting(self, centerlines, model):
self.Centerlines = centerlines
self._parentClass._helper.debug("started branchExtractor")
branchExtractor = slicer.vtkvmtkCenterlineBranchExtractor()
branchExtractor.SetInput(centerlines)
branchExtractor.SetBlankingArrayName(self._BlankingArrayName)
branchExtractor.SetRadiusArrayName(self._RadiusArrayName)
branchExtractor.SetGroupIdsArrayName(self._GroupIdsArrayName)
branchExtractor.SetCenterlineIdsArrayName(self._CenterlineIdsArrayName)
branchExtractor.SetTractIdsArrayName(self._TractIdsArrayName)
branchExtractor.Update()
self._parentClass._helper.debug("finished branchExtractor")
self._parentClass._helper.debug("started clipper")
clipper = slicer.vtkvmtkPolyDataCenterlineGroupsClipper()
clipper.SetInput(model)
clipper.SetCenterlines(branchExtractor.GetOutput())
clipper.SetCenterlineGroupIdsArrayName(self._GroupIdsArrayName)
clipper.SetGroupIdsArrayName(self._GroupIdsArrayName)
clipper.SetCenterlineRadiusArrayName(self._RadiusArrayName)
clipper.SetBlankingArrayName(self._BlankingArrayName)
clipper.SetCutoffRadiusFactor(self._CutoffRadiusFactor)
clipper.SetClipValue(self._ClipValue)
clipper.SetUseRadiusInformation(self._UseRadiusInformation)
clipper.ClipAllCenterlineGroupIdsOn()
clipper.Update()
self._parentClass._helper.debug("finished clipper")
if not self._InsideOut:
clipper.GenerateClippedOutputOff()
else:
clipper.GenerateClippedOutputOn()
clipper.Update()
if not self._InsideOut:
Surface = clipper.GetOutput()
else:
Surface = clipper.GetClippedOutput()
# shift values because first value is invisible in default LabelMap
dataArray = Surface.GetPointData().GetScalars("GroupIds")
newDa = slicer.vtkIntArray()
newDa.SetName("GroupIds")
newDa.InsertTuple1(0, 0)
for i in range(1, dataArray.GetSize()):
newDa.InsertTuple1(i, dataArray.GetValue(i) + 1)
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(Surface)
polyDataNew.GetPointData().SetScalars(newDa)
polyDataNew.Update()
return polyDataNew
def prepareModel(self,polydata):
if polydata == None:
return -1
# skip nonmanifold
surfaceCleaner = slicer.vtkCleanPolyData()
surfaceCleaner.SetInput(polydata)
surfaceCleaner.Update()
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(surfaceCleaner.GetOutput())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
smooth = slicer.vtkWindowedSincPolyDataFilter()
smooth.SetInput(subdiv.GetOutput())
smooth.SetNumberOfIterations(20)
smooth.SetPassBand(0.1)
smooth.SetBoundarySmoothing(1)
smooth.NormalizeCoordinatesOn()
smooth.Update()
normals = slicer.vtkPolyDataNormals()
normals.SetInput(smooth.GetOutput())
normals.SetAutoOrientNormals(1)
normals.SetFlipNormals(0)
normals.SetConsistency(1)
normals.SplittingOff()
normals.Update()
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(normals.GetOutput())
surfaceCapper.SetDisplacement(self._capDisplacement)
surfaceCapper.SetInPlaneDisplacement(self._capDisplacement)
surfaceCapper.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(surfaceCapper.GetOutput())
polyDataNew.Update()
return polyDataNew
def prepareModel(self, polydata):
if polydata == None:
return -1
# skip nonmanifold
surfaceCleaner = slicer.vtkCleanPolyData()
surfaceCleaner.SetInput(polydata)
surfaceCleaner.Update()
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(surfaceCleaner.GetOutput())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
smooth = slicer.vtkWindowedSincPolyDataFilter()
smooth.SetInput(subdiv.GetOutput())
smooth.SetNumberOfIterations(20)
smooth.SetPassBand(0.1)
smooth.SetBoundarySmoothing(1)
smooth.NormalizeCoordinatesOn()
smooth.Update()
normals = slicer.vtkPolyDataNormals()
normals.SetInput(smooth.GetOutput())
normals.SetAutoOrientNormals(1)
normals.SetFlipNormals(0)
normals.SetConsistency(1)
normals.SplittingOff()
normals.Update()
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(normals.GetOutput())
surfaceCapper.SetDisplacement(self._capDisplacement)
surfaceCapper.SetInPlaneDisplacement(self._capDisplacement)
surfaceCapper.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(surfaceCapper.GetOutput())
polyDataNew.Update()
return polyDataNew
def computeCenterlines(self, polydata, inletSeedIds, outletSeedIds):
centerlineFilter = slicer.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInput(polydata)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self._radiusArrayName)
centerlineFilter.SetCostFunction(self._costFunction)
centerlineFilter.SetFlipNormals(self._flipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self._appendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self._simplifyVoronoi)
centerlineFilter.SetCenterlineResampling(self._resampling)
centerlineFilter.SetResamplingStepLength(self._resamplingStepLength)
centerlineFilter.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(centerlineFilter.GetOutput())
polyDataNew.Update()
self._vd = slicer.vtkPolyData()
self._vd.DeepCopy(centerlineFilter.GetVoronoiDiagram())
self._vd.Update()
return polyDataNew
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 Splitting(self):
inCeLine = self._inCenterLineSelector.GetSelected()
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
split = self._checkButton.GetSelectedState()
vmtkFound = self.CheckForVmtkLibrary()
if inCeLine and inModel and outModel and vmtkFound:
result = slicer.vtkPolyData()
r = self._logic.branchSplitting(inCeLine.GetPolyData(),
inModel.GetPolyData())
result.DeepCopy(r)
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(1, 0, 0)
displayNode.SetScalarVisibility(1)
displayNode.SetActiveScalarName(self._logic._GroupIdsArrayName)
displayNode.SetAndObserveColorNodeID(
self.GetLogic().GetMRMLScene().GetNodesByName(
"Labels").GetItemAsObject(0).GetID())
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
dNode = inModel.GetModelDisplayNode()
dNode.SetOpacity(0.0)
inModel.SetAndObserveDisplayNodeID(dNode.GetID())
if split == 1:
ctr = 0
newPdList = self._logic.splitModels(result)
for i in newPdList:
if i.GetNumberOfCells() == 0:
continue
self._helper.debug("Number of Cells are: " +
str(i.GetNumberOfCells()))
ctr += 1
scene = self.GetLogic().GetMRMLScene()
newNode = slicer.vtkMRMLModelNode()
newNode.SetName("VMTKBranchSplittingOut_Branch" + str(ctr))
newNode.SetScene(scene)
newNode.SetAndObservePolyData(i)
scene.AddNode(newNode)
dn = slicer.vtkMRMLModelDisplayNode()
dn.SetPolyData(newNode.GetPolyData())
dn.SetColor(random.random(), random.random(),
random.random())
dn.SetBackfaceCulling(0)
dn.SetSliceIntersectionVisibility(1)
dn.SetVisibility(1)
dn.SetOpacity(1.0)
scene.AddNode(dn)
newNode.SetAndObserveDisplayNodeID(dn.GetName())
def Import(self):
outModel = self._importModelSelector.GetSelected()
outputFileName = self._loadButton.GetFileName()
if outModel and outputFileName:
self._helper.debug("Start import..")
points = slicer.vtkPoints()
conn = slicer.vtkCellArray()
polyData = slicer.vtkPolyData()
f=open(outputFileName)
lines = f.readlines()
i = 0
lastId = None
for line in lines:
if self._importHeaders.GetSelectedState()==1 and i==0:
self._helper.debug("Ignore first line..")
else:
# now parse the rest
splitted = line.split()
x = float(splitted[0])
y = float(splitted[1])
z = float(splitted[2])
if self._importNifti.GetSelectedState()==1:
x = x*(-1)
y = y*(-1)
#self._helper.debug("Found point: "+str(x)+","+str(y)+","+str(z))
id = points.InsertNextPoint(x,y,z)
#self._helper.debug(id)
if lastId:
curLine = slicer.vtkLine()
curLine.GetPointIds().SetId(0,lastId)
curLine.GetPointIds().SetId(1,id)
conn.InsertNextCell(curLine)
#conn.InsertCellPoint(id)
lastId = id
i = i+1
f.close()
result = slicer.vtkPolyData()
result.SetPoints(points)
result.SetLines(conn)
result.Update()
self._helper.debug(result)
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0.8, 0, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.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 Execute(dwi_node, seeds_node, mask_node, ff_node, \
record_fa = False, record_state = False, record_cov = False, \
model="two-tensor", FA_min=.15, GA_min=.10,
seeds=1, labels=[1],
Qm=.0030, Ql=100, Rs=.015, theta_max=45):
for i in xrange(10):
print ''
is_2t = (model == "two-tensor")
print 'HACK hardcode 2T'
is_2t = True
follow = iff(is_2t, follow2t, follow1t)
state_dim = iff(is_2t, 10, 5) # dimension of state space
theta_min = 5 # angle which triggers branch
param = dict({
'FA_min': FA_min, # fractional anisotropy stopping threshold
'GA_min': GA_min, # generalized anisotropy stopping threshold
'dt': .2, # forward Euler step size (path integration)
'max_len': 250, # stop if fiber gets this long
'min_radius': .87, # stop if fiber curves this much
'seeds': seeds, # number of seeds in each voxel
'theta_min':
np.cos(theta_min * np.pi / 180), # angle which triggers branch
'theta_max':
np.cos(theta_max * np.pi / 180), # angle which triggers branch
'min_radius': .87, # stop if fiber curves this much
'record_fa': record_fa,
'record_st': record_state,
'record_co': record_cov,
# Kalman filter parameters
'Qm': Qm, # injected angular noise
'Ql': Ql, # injected eigenvalue noise
'Rs': Rs, # dependent on latent noise in your data
'P0': 0.01 * np.eye(state_dim)
}) # initial covariance
from Slicer import slicer
# foo = slicer.vtkFloatArray()
# foo.SetNumberOfComponents(1)
# foo.SetName('foo')
# foo.InsertNextValue(234) # Success
# foo.InsertNextValue(23.4) # Success
# foo.InsertNextValue(255 * np.random.rand()) # Success
# foo.InsertNextValue(np.empty(1,dtype='float32')) # FAIL
# foo.InsertNextValue(np.empty(1,dtype='float64')) # FAIL
# asdf
scene = slicer.MRMLScene
dwi_node = scene.GetNodeByID(dwi_node)
seeds_node = scene.GetNodeByID(seeds_node)
mask_node = scene.GetNodeByID(mask_node)
ff_node = scene.GetNodeByID(ff_node)
# ensure normalized signal
bb = dwi_node.GetBValues().ToArray()
if np.any(bb.sum(1) == 0):
import Slicer
Slicer.tk.eval(
'tk_messageBox -message "Use the \'Normalize Signal\' module to prepare the DWI data"'
)
return
b = bb.mean()
S = dwi_node.GetImageData().ToArray()
u = dwi_node.GetDiffusionGradients().ToArray()
i2r = vtk2mat(dwi_node.GetIJKToRASMatrix, slicer)
r2i = vtk2mat(dwi_node.GetRASToIJKMatrix, slicer)
mf = vtk2mat(dwi_node.GetMeasurementFrameMatrix, slicer)
voxel = np.mat(dwi_node.GetSpacing()).reshape(3, 1)
voxel = voxel[::-1] # HACK Numpy has [z y x]
# generalized loading...
R = r2i[0:3, 0:3] / voxel.T # normalize each column
M = mf[0:3, 0:3]
# transform gradients
u = dwi_node.GetDiffusionGradients().ToArray()
u = u * (np.linalg.inv(R) * M).T
u = u / np.sqrt(np.power(u, 2).sum(1))
u = np.vstack((u, -u)) # duplicate signal
param['voxel'] = voxel
mask = mask_node.GetImageData().ToArray().astype('uint16')
# pull all seeds
seeds_ = seeds_node.GetImageData().ToArray()
seeds = np.zeros(seeds_.shape, dtype='bool')
for lbl in labels:
seeds |= (seeds_ == lbl)
seeds = zip(*seeds.nonzero())
# ensure seeds
if len(seeds) == 0:
import Slicer
Slicer.tk.eval(
'tk_messageBox -message "No seeds found for this label"')
return
# double check branching
if 0 < theta_max and theta_max < 5:
import Slicer
Slicer.tk.eval(
'tk_messageBox -message "Nonzero branching angle must be greater than 5 degrees"'
)
return
is_branching = is_2t and param['theta_max'] < 1
# tractography...
ff1 = init(S, seeds, u, b, param, is_2t)
ff2, ff_fa, ff_st, ff_co = [], [], [], []
t1 = time.time()
for i in xrange(0, len(ff1)):
print '[%3.0f%%] (%7d - %7d)' % (100.0 * i / len(ff1), i, len(ff1))
ff1[i], next, extra = follow(S, u, b, mask, ff1[i], param,
is_branching)
ff2.extend(next)
# store extras
if record_fa: ff_fa.append(extra[0])
if record_state: ff_st.append(extra[1])
if record_cov: ff_co.append(extra[2])
t2 = time.time()
print 'Time: ', t2 - t1, 'sec'
if is_branching:
for i in xrange(0, len(ff2)):
print '[%3.0f%%] (%7d - %7d)' % (100.0 * i / len(ff2), i, len(ff2))
f, _ = follow(S, u, b, mask, ff2[i], param, False)
ff1.append(f)
print 'Time: ', time.time() - t2, 'sec'
# build polydata
ss_x = slicer.vtkPoints()
lines = slicer.vtkCellArray()
if record_fa:
ss_fa = slicer.vtkFloatArray()
ss_fa.SetNumberOfComponents(1)
ss_fa.SetName('FA')
if record_state:
ss_st = slicer.vtkFloatArray()
ss_st.SetNumberOfComponents(state_dim)
ss_st.SetName('state')
if record_cov:
ss_co = slicer.vtkFloatArray()
ss_co.SetNumberOfComponents(state_dim**2)
ss_co.SetName('covariance')
cell_id = 0
for i in xrange(0, len(ff1)):
f = ff1[i]
lines.InsertNextCell(len(f))
if record_fa: f_fa = ff_fa[i]
if record_state: f_st = ff_st[i]
if record_cov: f_co = ff_co[i]
for j in xrange(0, len(f)):
lines.InsertCellPoint(cell_id)
cell_id += 1
x = f[j]
x = x[::-1] # HACK
x_ = np.array(transform(i2r, x)).ravel() # HACK
ss_x.InsertNextPoint(x_[0], x_[1], x_[2])
if record_fa:
ss_fa.InsertNextValue(255 * f_fa[j]) # FIXME numpy type
if record_state: ss_st.InsertNextValue(f_fa[j]) # FIXME tuples?
if record_cov: ss_co.InsertNextValue(f_fa[j]) # FIXME tuples?
# setup output fibers
dnode = ff_node.GetDisplayNode()
if not dnode:
dnode = slicer.vtkMRMLModelDisplayNode()
ff_node.GetScene().AddNodeNoNotify(dnode)
ff_node.SetAndObserveDisplayNodeID(dnode.GetID())
pd = ff_node.GetPolyData()
if not pd:
pd = slicer.vtkPolyData() # create if necessary
ff_node.SetAndObservePolyData(pd)
pd.SetPoints(ss_x)
if record_fa: pd.GetPointData().SetScalars(ss_fa)
pd.SetLines(lines)
pd.Update()
ff_node.Modified()
asdf # HACK flush stdio
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 Execute(dwi_node, seeds_node, mask_node, ff_node, \
record_fa = False, record_state = False, record_cov = False, \
model="two-tensor", FA_min=.15, GA_min=.10,
seeds=1, labels=[1],
Qm=.0030, Ql=100, Rs=.015, theta_max=45):
for i in xrange(10) : print ''
is_2t = (model == "two-tensor")
print 'HACK hardcode 2T'; is_2t = True
follow = iff(is_2t, follow2t, follow1t)
state_dim = iff(is_2t, 10, 5) # dimension of state space
theta_min = 5 # angle which triggers branch
param = dict({'FA_min': FA_min, # fractional anisotropy stopping threshold
'GA_min': GA_min, # generalized anisotropy stopping threshold
'dt': .2, # forward Euler step size (path integration)
'max_len': 250, # stop if fiber gets this long
'min_radius': .87, # stop if fiber curves this much
'seeds' : seeds, # number of seeds in each voxel
'theta_min': np.cos(theta_min * np.pi/180), # angle which triggers branch
'theta_max': np.cos(theta_max * np.pi/180), # angle which triggers branch
'min_radius': .87, # stop if fiber curves this much
'record_fa' : record_fa,
'record_st' : record_state,
'record_co' : record_cov,
# Kalman filter parameters
'Qm': Qm, # injected angular noise
'Ql': Ql, # injected eigenvalue noise
'Rs': Rs, # dependent on latent noise in your data
'P0': 0.01 * np.eye(state_dim)}) # initial covariance
from Slicer import slicer
# foo = slicer.vtkFloatArray()
# foo.SetNumberOfComponents(1)
# foo.SetName('foo')
# foo.InsertNextValue(234) # Success
# foo.InsertNextValue(23.4) # Success
# foo.InsertNextValue(255 * np.random.rand()) # Success
# foo.InsertNextValue(np.empty(1,dtype='float32')) # FAIL
# foo.InsertNextValue(np.empty(1,dtype='float64')) # FAIL
# asdf
scene = slicer.MRMLScene
dwi_node = scene.GetNodeByID(dwi_node)
seeds_node = scene.GetNodeByID(seeds_node)
mask_node = scene.GetNodeByID(mask_node)
ff_node = scene.GetNodeByID(ff_node)
# ensure normalized signal
bb = dwi_node.GetBValues().ToArray()
if np.any(bb.sum(1) == 0):
import Slicer
Slicer.tk.eval('tk_messageBox -message "Use the \'Normalize Signal\' module to prepare the DWI data"')
return
b = bb.mean()
S = dwi_node.GetImageData().ToArray()
u = dwi_node.GetDiffusionGradients().ToArray()
i2r = vtk2mat(dwi_node.GetIJKToRASMatrix, slicer)
r2i = vtk2mat(dwi_node.GetRASToIJKMatrix, slicer)
mf = vtk2mat(dwi_node.GetMeasurementFrameMatrix, slicer)
voxel = np.mat(dwi_node.GetSpacing()).reshape(3,1)
voxel = voxel[::-1] # HACK Numpy has [z y x]
# generalized loading...
R = r2i[0:3,0:3] / voxel.T # normalize each column
M = mf[0:3,0:3]
# transform gradients
u = dwi_node.GetDiffusionGradients().ToArray()
u = u * (np.linalg.inv(R) * M).T
u = u / np.sqrt(np.power(u,2).sum(1))
u = np.vstack((u,-u)) # duplicate signal
param['voxel'] = voxel
mask = mask_node.GetImageData().ToArray().astype('uint16')
# pull all seeds
seeds_ = seeds_node.GetImageData().ToArray()
seeds = np.zeros(seeds_.shape, dtype='bool')
for lbl in labels:
seeds |= (seeds_ == lbl)
seeds = zip(*seeds.nonzero())
# ensure seeds
if len(seeds) == 0:
import Slicer
Slicer.tk.eval('tk_messageBox -message "No seeds found for this label"')
return
# double check branching
if 0 < theta_max and theta_max < 5:
import Slicer
Slicer.tk.eval('tk_messageBox -message "Nonzero branching angle must be greater than 5 degrees"')
return
is_branching = is_2t and param['theta_max'] < 1
# tractography...
ff1 = init(S, seeds, u, b, param, is_2t)
ff2,ff_fa,ff_st,ff_co = [],[],[],[]
t1 = time.time()
for i in xrange(0,len(ff1)):
print '[%3.0f%%] (%7d - %7d)' % (100.0*i/len(ff1), i, len(ff1))
ff1[i],next,extra = follow(S,u,b,mask,ff1[i],param,is_branching)
ff2.extend(next)
# store extras
if record_fa: ff_fa.append(extra[0])
if record_state: ff_st.append(extra[1])
if record_cov: ff_co.append(extra[2])
t2 = time.time()
print 'Time: ', t2 - t1, 'sec'
if is_branching:
for i in xrange(0,len(ff2)):
print '[%3.0f%%] (%7d - %7d)' % (100.0*i/len(ff2), i, len(ff2))
f,_ = follow(S,u,b,mask,ff2[i],param,False)
ff1.append(f)
print 'Time: ', time.time() - t2, 'sec'
# build polydata
ss_x = slicer.vtkPoints()
lines = slicer.vtkCellArray()
if record_fa: ss_fa = slicer.vtkFloatArray(); ss_fa.SetNumberOfComponents(1); ss_fa.SetName('FA');
if record_state: ss_st = slicer.vtkFloatArray(); ss_st.SetNumberOfComponents(state_dim); ss_st.SetName('state');
if record_cov: ss_co = slicer.vtkFloatArray(); ss_co.SetNumberOfComponents(state_dim**2); ss_co.SetName('covariance');
cell_id = 0
for i in xrange(0,len(ff1)):
f = ff1[i]
lines.InsertNextCell(len(f))
if record_fa: f_fa = ff_fa[i]
if record_state: f_st = ff_st[i]
if record_cov: f_co = ff_co[i]
for j in xrange(0,len(f)):
lines.InsertCellPoint(cell_id)
cell_id += 1
x = f[j]
x = x[::-1] # HACK
x_ = np.array(transform(i2r, x)).ravel() # HACK
ss_x.InsertNextPoint(x_[0],x_[1],x_[2])
if record_fa : ss_fa.InsertNextValue(255 * f_fa[j]) # FIXME numpy type
if record_state : ss_st.InsertNextValue(f_fa[j]) # FIXME tuples?
if record_cov : ss_co.InsertNextValue(f_fa[j]) # FIXME tuples?
# setup output fibers
dnode = ff_node.GetDisplayNode()
if not dnode:
dnode = slicer.vtkMRMLModelDisplayNode()
ff_node.GetScene().AddNodeNoNotify(dnode)
ff_node.SetAndObserveDisplayNodeID(dnode.GetID())
pd = ff_node.GetPolyData()
if not pd:
pd = slicer.vtkPolyData() # create if necessary
ff_node.SetAndObservePolyData(pd)
pd.SetPoints(ss_x)
if record_fa : pd.GetPointData().SetScalars(ss_fa)
pd.SetLines(lines)
pd.Update()
ff_node.Modified()
asdf # HACK flush stdio
def Splitting(self):
inCeLine = self._inCenterLineSelector.GetSelected()
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
split = self._checkButton.GetSelectedState()
vmtkFound=self.CheckForVmtkLibrary()
if inCeLine and inModel and outModel and vmtkFound:
result = slicer.vtkPolyData()
r=self._logic.branchSplitting(inCeLine.GetPolyData(),inModel.GetPolyData())
result.DeepCopy(r)
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(1, 0, 0)
displayNode.SetScalarVisibility(1)
displayNode.SetActiveScalarName(self._logic._GroupIdsArrayName)
displayNode.SetAndObserveColorNodeID(self.GetLogic().GetMRMLScene().GetNodesByName("Labels").GetItemAsObject(0).GetID())
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
dNode = inModel.GetModelDisplayNode()
dNode.SetOpacity(0.0)
inModel.SetAndObserveDisplayNodeID(dNode.GetID())
if split == 1:
ctr=0
newPdList=self._logic.splitModels(result)
for i in newPdList:
if i.GetNumberOfCells() == 0:
continue
self._helper.debug("Number of Cells are: "+str(i.GetNumberOfCells()))
ctr+=1
scene=self.GetLogic().GetMRMLScene()
newNode=slicer.vtkMRMLModelNode()
newNode.SetName("VMTKBranchSplittingOut_Branch"+str(ctr))
newNode.SetScene(scene)
newNode.SetAndObservePolyData(i)
scene.AddNode(newNode)
dn=slicer.vtkMRMLModelDisplayNode()
dn.SetPolyData(newNode.GetPolyData())
dn.SetColor(random.random() ,random.random() ,random.random() )
dn.SetBackfaceCulling(0)
dn.SetSliceIntersectionVisibility(1)
dn.SetVisibility(1)
dn.SetOpacity(1.0)
scene.AddNode(dn)
newNode.SetAndObserveDisplayNodeID(dn.GetName())
def Import(self):
outModel = self._importModelSelector.GetSelected()
outputFileName = self._loadButton.GetFileName()
if outModel and outputFileName:
self._helper.debug("Start import..")
points = slicer.vtkPoints()
conn = slicer.vtkCellArray()
polyData = slicer.vtkPolyData()
f = open(outputFileName)
lines = f.readlines()
i = 0
lastId = None
for line in lines:
if self._importHeaders.GetSelectedState() == 1 and i == 0:
self._helper.debug("Ignore first line..")
else:
# now parse the rest
splitted = line.split()
x = float(splitted[0])
y = float(splitted[1])
z = float(splitted[2])
if self._importNifti.GetSelectedState() == 1:
x = x * (-1)
y = y * (-1)
#self._helper.debug("Found point: "+str(x)+","+str(y)+","+str(z))
id = points.InsertNextPoint(x, y, z)
#self._helper.debug(id)
if lastId:
curLine = slicer.vtkLine()
curLine.GetPointIds().SetId(0, lastId)
curLine.GetPointIds().SetId(1, id)
conn.InsertNextCell(curLine)
#conn.InsertCellPoint(id)
lastId = id
i = i + 1
f.close()
result = slicer.vtkPolyData()
result.SetPoints(points)
result.SetLines(conn)
result.Update()
self._helper.debug(result)
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(0.8, 0, 0)
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
def extractNetwork(self,polydata,seed):
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(polydata)
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
# now close the surface
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(subdiv.GetOutput())
surfaceCapper.SetDisplacement(0.0)
surfaceCapper.SetInPlaneDisplacement(0.0)
surfaceCapper.Update()
# re-open it where the seed is placed
someradius = 1.0
surface=surfaceCapper.GetOutput()
pointLocator = slicer.vtkPointLocator()
pointLocator.SetDataSet(surface)
pointLocator.BuildLocator()
id=pointLocator.FindClosestPoint(int(seed[0]),int(seed[1]),int(seed[2]))
seed = surface.GetPoint(id)
sphere = slicer.vtkSphere()
sphere.SetCenter(seed[0],seed[1],seed[2])
sphere.SetRadius(someradius)
clip = slicer.vtkClipPolyData()
clip.SetInput(surface)
clip.SetClipFunction(sphere)
clip.Update()
opensurface = clip.GetOutput()
networkExtraction = slicer.vtkvmtkPolyDataNetworkExtraction()
networkExtraction.SetInput(opensurface)
networkExtraction.SetAdvancementRatio(self._advancementRatio)
networkExtraction.SetRadiusArrayName(self._radiusArrayName)
networkExtraction.SetTopologyArrayName(self._topologyArrayName)
networkExtraction.SetMarksArrayName(self._marksArrayName)
networkExtraction.Update()
self._parentClass._helper.debug(self._topologyArrayName)
network=networkExtraction.GetOutput()
arrayNames = []
celldata = network.GetCellData()
for i in range(celldata.GetNumberOfArrays()):
array = celldata.GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if (arrayName[-1]=='_'):
continue
arrayNames.append(arrayName)
numberOfPoints = network.GetNumberOfPoints()
for i in range(numberOfPoints):
point = network.GetPoint(numberOfPoints - i - 1)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = celldata.GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + arrayName + ": " + str(array.GetComponent(numberOfPoints - i,j))
self._parentClass._helper.debug(line)
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(network)
polyDataNew.Update()
return polyDataNew