def ExtractMesh(outputModelNode, modelNode, colorRgb, colorTolerance):
fullPolyData = modelNode.GetPolyData()
pointData = fullPolyData.GetPointData()
redValues = pointData.GetArray('ColorRed')
greenValues = pointData.GetArray('ColorGreen')
blueValues = pointData.GetArray('ColorBlue')
redMaxTolerance = colorRgb[0] + colorTolerance
redMinTolerance = colorRgb[0] - colorTolerance
greenMaxTolerance = colorRgb[1] + colorTolerance
greenMinTolerance = colorRgb[1] - colorTolerance
blueMaxTolerance = colorRgb[2] + colorTolerance
blueMinTolerance = colorRgb[2] - colorTolerance
lengthTuples = int(redValues.GetNumberOfTuples())
selectedPointIds = vtk.vtkIdTypeArray()
for pointId in range(lengthTuples):
if redValues.GetValue(
pointId) >= redMinTolerance and redValues.GetValue(
pointId) <= redMaxTolerance and greenValues.GetValue(
pointId) >= greenMinTolerance and greenValues.GetValue(
pointId
) <= greenMaxTolerance and blueValues.GetValue(
pointId
) >= blueMinTolerance and blueValues.GetValue(
pointId) <= blueMaxTolerance:
selectedPointIds.InsertNextValue(pointId)
selectedPointIds.InsertNextValue(pointId)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(selectedPointIds)
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.CONTAINING_CELLS(),
1)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0, fullPolyData)
extractSelection.SetInputData(1, selection)
extractSelection.Update()
convertToPolydata = vtk.vtkDataSetSurfaceFilter()
convertToPolydata.SetInputConnection(extractSelection.GetOutputPort())
convertToPolydata.Update()
outputModelNode.SetAndObservePolyData(convertToPolydata.GetOutput())
if not outputModelNode.GetDisplayNode():
md2 = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(md2)
outputModelNode.SetAndObserveDisplayNodeID(md2.GetID())
def ExtractMesh(outputModelNode, modelNode, colorRgb, colorTolerance):
fullPolyData = modelNode.GetPolyData()
pointData=fullPolyData.GetPointData()
redValues = pointData.GetArray('ColorRed')
greenValues = pointData.GetArray('ColorGreen')
blueValues = pointData.GetArray('ColorBlue')
redMaxTolerance = colorRgb[0] + colorTolerance
redMinTolerance = colorRgb[0] - colorTolerance
greenMaxTolerance = colorRgb[1] + colorTolerance
greenMinTolerance = colorRgb[1] - colorTolerance
blueMaxTolerance = colorRgb[2] + colorTolerance
blueMinTolerance = colorRgb[2] - colorTolerance
lengthTuples = int(redValues.GetNumberOfTuples())
selectedPointIds = vtk.vtkIdTypeArray()
for pointId in range(lengthTuples):
if redValues.GetValue(pointId) >= redMinTolerance and redValues.GetValue(pointId) <= redMaxTolerance and greenValues.GetValue(pointId) >= greenMinTolerance and greenValues.GetValue(pointId) <= greenMaxTolerance and blueValues.GetValue(pointId) >= blueMinTolerance and blueValues.GetValue(pointId) <= blueMaxTolerance:
selectedPointIds.InsertNextValue(pointId)
selectedPointIds.InsertNextValue(pointId)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(selectedPointIds)
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.CONTAINING_CELLS(), 1);
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0,fullPolyData)
extractSelection.SetInputData(1,selection);
extractSelection.Update();
convertToPolydata = vtk.vtkDataSetSurfaceFilter()
convertToPolydata.SetInputConnection(extractSelection.GetOutputPort())
convertToPolydata.Update()
outputModelNode.SetAndObservePolyData(convertToPolydata.GetOutput())
if not outputModelNode.GetDisplayNode():
md2 = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(md2)
outputModelNode.SetAndObserveDisplayNodeID(md2.GetID())
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 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()
