def generateResectionVolume(self, fiducialNode, modelNode):
if (fiducialNode != None):
self.FiducialNode = fiducialNode
self.PolyData = vtk.vtkPolyData()
self.updatePoints()
self.Delaunay = vtk.vtkDelaunay3D()
if (vtk.VTK_MAJOR_VERSION <= 5):
self.Delaunay.SetInput(self.PolyData)
else:
self.Delaunay.SetInputData(self.PolyData)
self.Delaunay.Update()
self.SurfaceFilter = vtk.vtkDataSetSurfaceFilter()
self.SurfaceFilter.SetInputConnection(
self.Delaunay.GetOutputPort())
self.SurfaceFilter.Update()
self.Smoother = vtk.vtkButterflySubdivisionFilter()
self.Smoother.SetInputConnection(
self.SurfaceFilter.GetOutputPort())
self.Smoother.SetNumberOfSubdivisions(3)
self.Smoother.Update()
if modelNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
modelDisplayNode.SetColor(0, 0, 1) # Blue
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
if (vtk.VTK_MAJOR_VERSION <= 5):
modelNode.SetAndObservePolyData(self.Smoother.GetOutput())
else:
modelNode.SetPolyDataConnection(self.Smoother.GetOutputPort())
modelNode.Modified()
self.tag = self.FiducialNode.AddObserver(
'ModifiedEvent', self.updateResectionVolume)
def generateResectionVolume(self, fiducialNode, modelNode):
if (fiducialNode != None):
self.FiducialNode = fiducialNode
self.PolyData = vtk.vtkPolyData()
self.updatePoints()
self.Delaunay = vtk.vtkDelaunay3D()
if (vtk.VTK_MAJOR_VERSION <= 5):
self.Delaunay.SetInput(self.PolyData)
else:
self.Delaunay.SetInputData(self.PolyData)
self.Delaunay.Update()
self.SurfaceFilter = vtk.vtkDataSetSurfaceFilter()
self.SurfaceFilter.SetInputConnection(self.Delaunay.GetOutputPort())
self.SurfaceFilter.Update()
self.Smoother = vtk.vtkButterflySubdivisionFilter()
self.Smoother.SetInputConnection(self.SurfaceFilter.GetOutputPort())
self.Smoother.SetNumberOfSubdivisions(3)
self.Smoother.Update()
if modelNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLModelDisplayNode")
modelDisplayNode.SetColor(0,0,1) # Blue
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
if (vtk.VTK_MAJOR_VERSION <= 5):
modelNode.SetAndObservePolyData(self.Smoother.GetOutput())
else:
modelNode.SetPolyDataConnection(self.Smoother.GetOutputPort())
modelNode.Modified()
self.tag = self.FiducialNode.AddObserver('ModifiedEvent', self.updateResectionVolume)
def run(self, inputModel, sModel, seedList):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
tri = vtk.vtkDelaunay3D()
tri.SetInputData(sModel.GetPolyData())
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(tri.GetOutput())
implicitDataSet = vtk.vtkImplicitDataSet()
implicitDataSet.SetDataSet(elev.GetOutput())
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
computeNormals = vtk.vtkPolyDataNormals()
computeNormals.SetInputData(triangle.GetOutput())
computeNormals.ComputeCellNormalsOn()
computeNormals.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(computeNormals.GetOutput())
clip.SetClipFunction(implicitDataSet)
clip.InsideOutOff()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputData(clip.GetOutput())
clean.Update()
polydata = clean.GetOutput()
cellData = polydata.GetCellData()
normals = cellData.GetNormals()
meanNormal = [0, 0, 0]
nOfTuples = normals.GetNumberOfTuples()
for cellIndex in range(0, nOfTuples):
cellNormal = [0, 0, 0]
cell = polydata.GetCell(cellIndex)
normals.GetTuple(cellIndex, cellNormal)
meanNormal[0] = meanNormal[0] + cellNormal[0]
meanNormal[1] = meanNormal[1] + cellNormal[1]
meanNormal[2] = meanNormal[2] + cellNormal[2]
meanNormal[0] = meanNormal[0] / nOfTuples
meanNormal[1] = meanNormal[1] / nOfTuples
meanNormal[2] = meanNormal[2] / nOfTuples
print("Normal: " + str(meanNormal))
seed1 = [0, 0, 0]
seedList.GetNthFiducialPosition(0, seed1)
vector = [
seed1[0] + 50 * meanNormal[0], seed1[1] + 50 * meanNormal[1],
seed1[2] + 50 * meanNormal[2]
]
seedList.AddFiducialFromArray(vector)
# Calculate perpendicular vectors
v1 = [0, 0, 0]
v2 = [0, 0, 0]
math = vtk.vtkMath()
math.Perpendiculars(meanNormal, v2, v1, 0)
# Normalize vectors
math.Normalize(meanNormal)
math.Normalize(v1)
math.Normalize(v2)
# create matrix4x4
transform = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLLinearTransformNode')
slicer.mrmlScene.AddNode(transform)
matrix = transform.GetMatrixTransformToParent()
matrix.SetElement(0, 0, v1[0])
matrix.SetElement(1, 0, v1[1])
matrix.SetElement(2, 0, v1[2])
matrix.SetElement(3, 0, 0.0)
matrix.SetElement(0, 1, meanNormal[0])
matrix.SetElement(1, 1, meanNormal[1])
matrix.SetElement(2, 1, meanNormal[2])
matrix.SetElement(3, 1, 0.0)
matrix.SetElement(0, 2, v2[0])
matrix.SetElement(1, 2, v2[1])
matrix.SetElement(2, 2, v2[2])
matrix.SetElement(3, 2, 0.0)
matrix.SetElement(0, 3, seed1[0])
matrix.SetElement(1, 3, seed1[1])
matrix.SetElement(2, 3, seed1[2])
matrix.SetElement(3, 3, 1.0)
return True
def run(self,inputModel,sModel,seedList):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
tri = vtk.vtkDelaunay3D()
tri.SetInputData(sModel.GetPolyData())
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(tri.GetOutput())
implicitDataSet = vtk.vtkImplicitDataSet()
implicitDataSet.SetDataSet(elev.GetOutput())
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
computeNormals = vtk.vtkPolyDataNormals()
computeNormals.SetInputData(triangle.GetOutput())
computeNormals.ComputeCellNormalsOn()
computeNormals.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(computeNormals.GetOutput())
clip.SetClipFunction(implicitDataSet)
clip.InsideOutOff()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputData(clip.GetOutput())
clean.Update()
polydata = clean.GetOutput()
cellData = polydata.GetCellData()
normals = cellData.GetNormals()
meanNormal = [0,0,0]
nOfTuples = normals.GetNumberOfTuples()
for cellIndex in range(0, nOfTuples):
cellNormal = [0,0,0]
cell = polydata.GetCell(cellIndex)
normals.GetTuple(cellIndex, cellNormal)
meanNormal[0] = meanNormal[0] + cellNormal[0]
meanNormal[1] = meanNormal[1] + cellNormal[1]
meanNormal[2] = meanNormal[2] + cellNormal[2]
meanNormal[0] = meanNormal[0] / nOfTuples
meanNormal[1] = meanNormal[1] / nOfTuples
meanNormal[2] = meanNormal[2] / nOfTuples
print("Normal: " + str(meanNormal))
seed1 = [0,0,0]
seedList.GetNthFiducialPosition(0,seed1)
vector = [seed1[0]+50*meanNormal[0],
seed1[1]+50*meanNormal[1],
seed1[2]+50*meanNormal[2]]
seedList.AddFiducialFromArray(vector)
# Calculate perpendicular vectors
v1 = [0,0,0]
v2 = [0,0,0]
math = vtk.vtkMath()
math.Perpendiculars(meanNormal, v2, v1, 0)
# Normalize vectors
math.Normalize(meanNormal)
math.Normalize(v1)
math.Normalize(v2)
# create matrix4x4
transform = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLinearTransformNode')
slicer.mrmlScene.AddNode(transform)
matrix = transform.GetMatrixTransformToParent()
matrix.SetElement(0,0,v1[0])
matrix.SetElement(1,0,v1[1])
matrix.SetElement(2,0,v1[2])
matrix.SetElement(3,0,0.0)
matrix.SetElement(0,1,meanNormal[0])
matrix.SetElement(1,1,meanNormal[1])
matrix.SetElement(2,1,meanNormal[2])
matrix.SetElement(3,1,0.0)
matrix.SetElement(0,2,v2[0])
matrix.SetElement(1,2,v2[1])
matrix.SetElement(2,2,v2[2])
matrix.SetElement(3,2,0.0)
matrix.SetElement(0,3,seed1[0])
matrix.SetElement(1,3,seed1[1])
matrix.SetElement(2,3,seed1[2])
matrix.SetElement(3,3,1.0)
return True
def updateModelFromMarkup(self, inputMarkup, outputModel):
"""
Update model to enclose all points in the input markup list
"""
# Delaunay triangulation is robust and creates nice smooth surfaces from a small number of points,
# however it can only generate convex surfaces robustly.
useDelaunay = True
# Create polydata point set from markup points
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
numberOfPoints = inputMarkup.GetNumberOfFiducials()
# Surface generation algorithms behave unpredictably when there are not enough points
# return if there are very few points
if useDelaunay:
if numberOfPoints < 3:
return
else:
if numberOfPoints < 10:
return
points.SetNumberOfPoints(numberOfPoints)
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
inputMarkup.GetNthFiducialPosition(i, new_coord)
points.SetPoint(i, new_coord)
cellArray.InsertNextCell(numberOfPoints)
for i in range(numberOfPoints):
cellArray.InsertCellPoint(i)
pointPolyData = vtk.vtkPolyData()
pointPolyData.SetLines(cellArray)
pointPolyData.SetPoints(points)
# Create surface from point set
if useDelaunay:
delaunay = vtk.vtkDelaunay3D()
delaunay.SetInputData(pointPolyData)
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
smoother = vtk.vtkButterflySubdivisionFilter()
smoother.SetInputConnection(surfaceFilter.GetOutputPort())
smoother.SetNumberOfSubdivisions(3)
smoother.Update()
outputModel.SetPolyDataConnection(smoother.GetOutputPort())
else:
surf = vtk.vtkSurfaceReconstructionFilter()
surf.SetInputData(pointPolyData)
surf.SetNeighborhoodSize(20)
surf.SetSampleSpacing(
80
) # lower value follows the small details more closely but more dense pointset is needed as input
cf = vtk.vtkContourFilter()
cf.SetInputConnection(surf.GetOutputPort())
cf.SetValue(0, 0.0)
# Sometimes the contouring algorithm can create a volume whose gradient
# vector and ordering of polygon (using the right hand rule) are
# inconsistent. vtkReverseSense cures this problem.
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(cf.GetOutputPort())
reverse.ReverseCellsOff()
reverse.ReverseNormalsOff()
outputModel.SetPolyDataConnection(reverse.GetOutputPort())
# Create default model display node if does not exist yet
if not outputModel.GetDisplayNode():
modelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
modelDisplayNode.SetColor(0, 0, 1) # Blue
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
outputModel.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
outputModel.GetDisplayNode().SliceIntersectionVisibilityOn()
outputModel.Modified()
def createTumorFromMarkups(self):
logging.debug('createTumorFromMarkups')
#self.tumorMarkups_Needle.SetDisplayVisibility(0)
# Create polydata point set from markup points
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
numberOfPoints = self.tumorMarkups_Needle.GetNumberOfFiducials()
if numberOfPoints > 0:
self.deleteLastFiducialButton.setEnabled(True)
self.deleteAllFiducialsButton.setEnabled(True)
self.deleteLastFiducialDuringNavigationButton.setEnabled(True)
# Surface generation algorithms behave unpredictably when there are not enough points
# return if there are very few points
if numberOfPoints < 1:
return
points.SetNumberOfPoints(numberOfPoints)
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
self.tumorMarkups_Needle.GetNthFiducialPosition(i, new_coord)
points.SetPoint(i, new_coord)
cellArray.InsertNextCell(numberOfPoints)
for i in range(numberOfPoints):
cellArray.InsertCellPoint(i)
pointPolyData = vtk.vtkPolyData()
pointPolyData.SetLines(cellArray)
pointPolyData.SetPoints(points)
delaunay = vtk.vtkDelaunay3D()
if numberOfPoints < 10:
logging.debug("use glyphs")
sphere = vtk.vtkCubeSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputData(pointPolyData)
glyph.SetSourceConnection(sphere.GetOutputPort())
#glyph.SetVectorModeToUseNormal()
#glyph.SetScaleModeToScaleByVector()
#glyph.SetScaleFactor(0.25)
delaunay.SetInputConnection(glyph.GetOutputPort())
else:
delaunay.SetInputData(pointPolyData)
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
smoother = vtk.vtkButterflySubdivisionFilter()
smoother.SetInputConnection(surfaceFilter.GetOutputPort())
smoother.SetNumberOfSubdivisions(3)
smoother.Update()
forceConvexShape = True
if (forceConvexShape == True):
delaunaySmooth = vtk.vtkDelaunay3D()
delaunaySmooth.SetInputData(smoother.GetOutput())
delaunaySmooth.Update()
smoothSurfaceFilter = vtk.vtkDataSetSurfaceFilter()
smoothSurfaceFilter.SetInputConnection(
delaunaySmooth.GetOutputPort())
self.tumorModel_Needle.SetPolyDataConnection(
smoothSurfaceFilter.GetOutputPort())
else:
self.tumorModel_Needle.SetPolyDataConnection(
smoother.GetOutputPort())
self.tumorModel_Needle.Modified()
def createTumorFromMarkups(self):
logging.debug("createTumorFromMarkups")
# self.tumorMarkups_Needle.SetDisplayVisibility(0)
# Create polydata point set from markup points
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
numberOfPoints = self.tumorMarkups_Needle.GetNumberOfFiducials()
if numberOfPoints > 0:
self.deleteLastFiducialButton.setEnabled(True)
self.deleteAllFiducialsButton.setEnabled(True)
self.deleteLastFiducialDuringNavigationButton.setEnabled(True)
# Surface generation algorithms behave unpredictably when there are not enough points
# return if there are very few points
if numberOfPoints < 1:
return
points.SetNumberOfPoints(numberOfPoints)
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
self.tumorMarkups_Needle.GetNthFiducialPosition(i, new_coord)
points.SetPoint(i, new_coord)
cellArray.InsertNextCell(numberOfPoints)
for i in range(numberOfPoints):
cellArray.InsertCellPoint(i)
pointPolyData = vtk.vtkPolyData()
pointPolyData.SetLines(cellArray)
pointPolyData.SetPoints(points)
delaunay = vtk.vtkDelaunay3D()
if numberOfPoints < 10:
logging.debug("use glyphs")
sphere = vtk.vtkCubeSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputData(pointPolyData)
glyph.SetSourceConnection(sphere.GetOutputPort())
# glyph.SetVectorModeToUseNormal()
# glyph.SetScaleModeToScaleByVector()
# glyph.SetScaleFactor(0.25)
delaunay.SetInputConnection(glyph.GetOutputPort())
else:
delaunay.SetInputData(pointPolyData)
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
smoother = vtk.vtkButterflySubdivisionFilter()
smoother.SetInputConnection(surfaceFilter.GetOutputPort())
smoother.SetNumberOfSubdivisions(3)
smoother.Update()
forceConvexShape = True
if forceConvexShape == True:
delaunaySmooth = vtk.vtkDelaunay3D()
delaunaySmooth.SetInputData(smoother.GetOutput())
delaunaySmooth.Update()
smoothSurfaceFilter = vtk.vtkDataSetSurfaceFilter()
smoothSurfaceFilter.SetInputConnection(delaunaySmooth.GetOutputPort())
self.tumorModel_Needle.SetPolyDataConnection(smoothSurfaceFilter.GetOutputPort())
else:
self.tumorModel_Needle.SetPolyDataConnection(smoother.GetOutputPort())
self.tumorModel_Needle.Modified()