def DisplayPoints(self, polyDataLine,name): """ Will display all of the points of a given Polydata Line """ sphere= vtk.vtkSphereSource() sphere.SetRadius(0.3) sphere.Update() glyphFilter=vtk.vtkGlyph3D() glyphFilter.ScalingOff() glyphFilter.SetSourceData(sphere.GetOutput()) #object at eachPoint glyphFilter.SetInputData(polyDataLine) glyphFilter.Update() node=self.DisplayPolyData(name, glyphFilter.GetOutput()) node.SetColor(0.3,0.4,1) #Max 1 for each column node.SetAmbient(1) return node
def DisplayPoints(self, polyDataLine, name):
""" Will display all of the points of a given Polydata Line
"""
sphere = vtk.vtkSphereSource()
sphere.SetRadius(0.3)
sphere.Update()
glyphFilter = vtk.vtkGlyph3D()
glyphFilter.ScalingOff()
glyphFilter.SetSourceData(sphere.GetOutput()) #object at eachPoint
glyphFilter.SetInputData(polyDataLine)
glyphFilter.Update()
node = self.DisplayPolyData(name, glyphFilter.GetOutput())
node.SetColor(0.3, 0.4, 1) #Max 1 for each column
node.SetAmbient(1)
return node
def startTransformMapping(self, groundTruthTransformNode, mappedTransformNode, outputVisitedPointsModelNode, positionErrorTransformNode, orientationErrorTransformNode):
self.removeObservers()
self.groundTruthTransformNode = groundTruthTransformNode
self.mappedTransformNode = mappedTransformNode
self.outputVisitedPointsModelNode = outputVisitedPointsModelNode
self.positionErrorTransformNode = positionErrorTransformNode
self.orientationErrorTransformNode = orientationErrorTransformNode
self.positionErrorMagnitudeList = []
self.orientationErrorMagnitudeList = []
if self.outputVisitedPointsModelNode:
if not self.outputVisitedPointsModelNode.GetDisplayNode():
modelDisplay = slicer.vtkMRMLModelDisplayNode()
#modelDisplay.SetSliceIntersectionVisibility(False) # Show in slice view
#modelDisplay.SetEdgeVisibility(True) # Hide in 3D view
modelDisplay.SetEdgeVisibility(True)
slicer.mrmlScene.AddNode(modelDisplay)
self.outputVisitedPointsModelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
self.visitedPoints = vtk.vtkPoints()
self.visitedPointsPolydata = vtk.vtkPolyData()
self.visitedPointsPolydata.SetPoints(self.visitedPoints)
glyph = vtk.vtkPolyData()
cubeSource = vtk.vtkCubeSource()
cubeSource.SetXLength(self.minimumSamplingDistance)
cubeSource.SetYLength(self.minimumSamplingDistance)
cubeSource.SetZLength(self.minimumSamplingDistance)
self.visitedPointsGlyph3d = vtk.vtkGlyph3D()
self.visitedPointsGlyph3d.SetSourceConnection(cubeSource.GetOutputPort())
self.visitedPointsGlyph3d.SetInputData(self.visitedPointsPolydata)
self.visitedPointsGlyph3d.Update()
self.outputVisitedPointsModelNode.SetPolyDataConnection(self.visitedPointsGlyph3d.GetOutputPort())
self.initializeErrorTransform(self.positionErrorTransformNode)
self.initializeErrorTransform(self.orientationErrorTransformNode)
# Start the updates
self.addObservers()
self.onGroundTruthTransformNodeModified(0,0)
def startTransformMapping(self, groundTruthTransformNode, mappedTransformNode, outputVisitedPointsModelNode, positionErrorTransformNode, orientationErrorTransformNode):
self.removeObservers()
self.groundTruthTransformNode = groundTruthTransformNode
self.mappedTransformNode = mappedTransformNode
self.outputVisitedPointsModelNode = outputVisitedPointsModelNode
self.positionErrorTransformNode = positionErrorTransformNode
self.orientationErrorTransformNode = orientationErrorTransformNode
self.positionErrorMagnitudeList = []
self.orientationErrorMagnitudeList = []
if self.outputVisitedPointsModelNode:
if not self.outputVisitedPointsModelNode.GetDisplayNode():
modelDisplay = slicer.vtkMRMLModelDisplayNode()
#modelDisplay.SetSliceIntersectionVisibility(False) # Show in slice view
#modelDisplay.SetEdgeVisibility(True) # Hide in 3D view
modelDisplay.SetEdgeVisibility(True)
slicer.mrmlScene.AddNode(modelDisplay)
self.outputVisitedPointsModelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
self.visitedPoints = vtk.vtkPoints()
self.visitedPointsPolydata = vtk.vtkPolyData()
self.visitedPointsPolydata.SetPoints(self.visitedPoints)
glyph = vtk.vtkPolyData()
cubeSource = vtk.vtkCubeSource()
cubeSource.SetXLength(self.minimumSamplingDistance)
cubeSource.SetYLength(self.minimumSamplingDistance)
cubeSource.SetZLength(self.minimumSamplingDistance)
self.visitedPointsGlyph3d = vtk.vtkGlyph3D()
self.visitedPointsGlyph3d.SetSourceConnection(cubeSource.GetOutputPort())
self.visitedPointsGlyph3d.SetInputData(self.visitedPointsPolydata)
self.visitedPointsGlyph3d.Update()
self.outputVisitedPointsModelNode.SetPolyDataConnection(self.visitedPointsGlyph3d.GetOutputPort())
self.initializeErrorTransform(self.positionErrorTransformNode)
self.initializeErrorTransform(self.orientationErrorTransformNode)
# Start the updates
self.addObservers()
self.onGroundTruthTransformNodeModified(0,0)
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()
