def openSurfaceAtPoint( self, polyData, seed ):
'''
Returns a new surface with an opening at the given seed.
'''
someradius = 1.0
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet( polyData )
pointLocator.BuildLocator()
# find the closest point next to the seed on the surface
# id = pointLocator.FindClosestPoint(int(seed[0]),int(seed[1]),int(seed[2]))
id = pointLocator.FindClosestPoint( seed )
# the seed is now guaranteed on the surface
seed = polyData.GetPoint( id )
sphere = vtk.vtkSphere()
sphere.SetCenter( seed[0], seed[1], seed[2] )
sphere.SetRadius( someradius )
clip = vtk.vtkClipPolyData()
clip.SetInputData( polyData )
clip.SetClipFunction( sphere )
clip.Update()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy( clip.GetOutput() )
return outPolyData
def openSurfaceAtPoint(self, polyData, seed):
'''
Returns a new surface with an opening at the given seed.
'''
someradius = 1.0
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(polyData)
pointLocator.BuildLocator()
# find the closest point next to the seed on the surface
#id = pointLocator.FindClosestPoint(int(seed[0]),int(seed[1]),int(seed[2]))
id = pointLocator.FindClosestPoint(seed)
# the seed is now guaranteed on the surface
seed = polyData.GetPoint(id)
sphere = vtk.vtkSphere()
sphere.SetCenter(seed[0], seed[1], seed[2])
sphere.SetRadius(someradius)
clip = vtk.vtkClipPolyData()
clip.SetInput(polyData)
clip.SetClipFunction(sphere)
clip.Update()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy(clip.GetOutput())
outPolyData.Update()
return outPolyData
def addModelPointLocator(self, name, polydata):
if not name in self.pointLocatorDictionary:
print "Adding point locator: {0}".format(name)
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(polydata)
pointLocator.AutomaticOn()
pointLocator.BuildLocator()
self.pointLocatorDictionary[name] = pointLocator
def addModelPointLocator(self, name, polydata):
if not name in self.pointLocatorDictionary:
print "Adding point locator: {0}".format(name)
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(polydata)
pointLocator.AutomaticOn()
pointLocator.BuildLocator()
self.pointLocatorDictionary[name] = pointLocator
def __init__(self):
self.controlPointsMarkupNode = None
self.curveModelNode = None
self.tubeRadius = 5.0
self.tubeResolution = 20
self.numberOfIntermediatePoints = 20
self.curvePoly = vtk.vtkPolyData()
self.curvePoints = vtk.vtkPoints()
self.curvePoly.SetPoints(self.curvePoints)
self.curvePointsLocator = vtk.vtkPointLocator()
self.curvePointsLocator.SetDataSet(self.curvePoly)
self.interpolationMethod = InterpolationLinear
self.pointInterpolationFunction = self.getInterpolatedPointsLinear
self.closed = False
def start( self, preview=False ):
'''
'''
SlicerVmtk4CommonLib.Helper.Debug( "Starting Centerline Computation.." )
# first we need the nodes
currentModelNode = self.__inputModelNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentOutputModelNode = self.__outputModelNodeSelector.currentNode()
currentVoronoiModelNode = self.__voronoiModelNodeSelector.currentNode()
if not currentModelNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentOutputModelNode or currentOutputModelNode.GetID() == currentModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentOutputModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode( currentOutputModelNode )
if not currentVoronoiModelNode or currentVoronoiModelNode.GetID() == currentModelNode.GetID() or currentVoronoiModelNode.GetID() == currentOutputModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__voronoiModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentVoronoiModelNode = newModelNode
self.__voronoiModelNodeSelector.setCurrentNode( currentVoronoiModelNode )
# the output models
preparedModel = vtk.vtkPolyData()
model = vtk.vtkPolyData()
network = vtk.vtkPolyData()
voronoi = vtk.vtkPolyData()
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates( currentCoordinatesRAS )
# prepare the model
preparedModel.DeepCopy( self.GetLogic().prepareModel( currentModelNode.GetPolyData() ) )
preparedModel.Update()
# decimate the model (only for network extraction)
model.DeepCopy( self.GetLogic().decimateSurface( preparedModel ) )
model.Update()
# open the model at the seed (only for network extraction)
model.DeepCopy( self.GetLogic().openSurfaceAtPoint( model, currentCoordinatesRAS ) )
model.Update()
# extract Network
network.DeepCopy( self.GetLogic().extractNetwork( model ) )
network.Update()
#
#
# not preview mode: real computation!
if not preview:
# here we start the actual centerline computation which is mathematically more robust and accurate but takes longer than the network extraction
# clip surface at endpoints identified by the network extraction
tupel = self.GetLogic().clipSurfaceAtEndPoints( network, currentModelNode.GetPolyData() )
clippedSurface = tupel[0]
endpoints = tupel[1]
# now find the one endpoint which is closest to the seed and use it as the source point for centerline computation
# all other endpoints are the target points
sourcePoint = [0, 0, 0]
# the following arrays have the same indexes and are synchronized at all times
distancesToSeed = []
targetPoints = []
# we now need to loop through the endpoints two times
# first loop is to detect the endpoint resulting in the tiny hole we poked in the surface
# this is very close to our seed but not the correct sourcePoint
for i in range( endpoints.GetNumberOfPoints() ):
currentPoint = endpoints.GetPoint( i )
# get the euclidean distance
currentDistanceToSeed = math.sqrt( math.pow( ( currentPoint[0] - currentCoordinatesRAS[0] ), 2 ) +
math.pow( ( currentPoint[1] - currentCoordinatesRAS[1] ), 2 ) +
math.pow( ( currentPoint[2] - currentCoordinatesRAS[2] ), 2 ) )
targetPoints.append( currentPoint )
distancesToSeed.append( currentDistanceToSeed )
# now we have a list of distances with the corresponding points
# the index with the most minimal distance is the holePoint, we want to ignore it
# the index with the second minimal distance is the point closest to the seed, we want to set it as sourcepoint
# all other points are the targetpoints
# get the index of the holePoint, which we want to remove from our endPoints
holePointIndex = distancesToSeed.index( min( distancesToSeed ) )
# .. and remove it
distancesToSeed.pop( holePointIndex )
targetPoints.pop( holePointIndex )
# now find the sourcepoint
sourcePointIndex = distancesToSeed.index( min( distancesToSeed ) )
# .. and remove it after saving it as the sourcePoint
sourcePoint = targetPoints[sourcePointIndex]
distancesToSeed.pop( sourcePointIndex )
targetPoints.pop( sourcePointIndex )
# again, at this point we have a) the sourcePoint and b) a list of real targetPoints
# now create the sourceIdList and targetIdList for the actual centerline computation
sourceIdList = vtk.vtkIdList()
targetIdList = vtk.vtkIdList()
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet( preparedModel )
pointLocator.BuildLocator()
# locate the source on the surface
sourceId = pointLocator.FindClosestPoint( sourcePoint )
sourceIdList.InsertNextId( sourceId )
f = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLAnnotationFiducialNode" )
f.SetFiducialCoordinates( sourcePoint )
f.Initialize( slicer.mrmlScene )
f.SelectedOn()
# locate the endpoints on the surface
for p in targetPoints:
f = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLAnnotationFiducialNode" )
f.SetFiducialCoordinates( p )
f.Initialize( slicer.mrmlScene )
id = pointLocator.FindClosestPoint( p )
targetIdList.InsertNextId( id )
tupel = self.GetLogic().computeCenterlines( preparedModel, sourceIdList, targetIdList )
network.DeepCopy( tupel[0] )
voronoi.DeepCopy( tupel[1] )
#
#
# update the display of the original model in terms of opacity
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentModelDisplayNode )
currentModelDisplayNode.SetOpacity( 0.4 )
currentModelDisplayNode.Modified()
currentModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID( currentModelDisplayNode.GetID() )
currentModelNode.Modified()
currentModelNode.SetModifiedSinceRead( 1 )
#
# finally:
# propagate output model to nodes
currentOutputModelNode.SetAndObservePolyData( network )
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead( 1 )
currentOutputModelDisplayNode = currentOutputModelNode.GetDisplayNode()
if not currentOutputModelDisplayNode:
# create new displayNode
currentOutputModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentOutputModelDisplayNode )
# always configure the displayNode to show the model
currentOutputModelDisplayNode.SetPolyData( currentOutputModelNode.GetPolyData() )
currentOutputModelDisplayNode.SetColor( 0.0, 0.0, 0.4 ) # red
currentOutputModelDisplayNode.SetBackfaceCulling( 0 )
currentOutputModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentOutputModelDisplayNode.SetVisibility( 1 )
currentOutputModelDisplayNode.SetOpacity( 1.0 )
currentOutputModelDisplayNode.Modified()
currentOutputModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentOutputModelNode.SetAndObserveDisplayNodeID( currentOutputModelDisplayNode.GetID() )
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead( 1 )
# only update the voronoi node if we are not in preview mode
if not preview:
currentVoronoiModelNode.SetAndObservePolyData( voronoi )
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead( 1 )
currentVoronoiModelDisplayNode = currentVoronoiModelNode.GetDisplayNode()
if not currentVoronoiModelDisplayNode:
# create new displayNode
currentVoronoiModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentVoronoiModelDisplayNode )
# always configure the displayNode to show the model
currentVoronoiModelDisplayNode.SetPolyData( currentVoronoiModelNode.GetPolyData() )
currentVoronoiModelDisplayNode.SetScalarVisibility( 1 )
currentVoronoiModelDisplayNode.SetBackfaceCulling( 0 )
currentVoronoiModelDisplayNode.SetActiveScalarName( "Radius" )
currentVoronoiModelDisplayNode.SetAndObserveColorNodeID( slicer.mrmlScene.GetNodesByName( "Labels" ).GetItemAsObject( 0 ).GetID() )
currentVoronoiModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentVoronoiModelDisplayNode.SetVisibility( 1 )
currentVoronoiModelDisplayNode.SetOpacity( 0.5 )
currentVoronoiModelDisplayNode.Modified()
currentVoronoiModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentVoronoiModelNode.SetAndObserveDisplayNodeID( currentVoronoiModelDisplayNode.GetID() )
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead( 1 )
SlicerVmtk4CommonLib.Helper.Debug( "End of Centerline Computation.." )
def start(self, preview=False):
'''
'''
SlicerVmtk4CommonLib.Helper.Debug("Starting Centerline Computation..")
# first we need the nodes
currentModelNode = self.__inputModelNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentOutputModelNode = self.__outputModelNodeSelector.currentNode()
currentVoronoiModelNode = self.__voronoiModelNodeSelector.currentNode()
if not currentModelNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentOutputModelNode or currentOutputModelNode.GetID(
) == currentModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentOutputModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode(
currentOutputModelNode)
if not currentVoronoiModelNode or currentVoronoiModelNode.GetID(
) == currentModelNode.GetID() or currentVoronoiModelNode.GetID(
) == currentOutputModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__voronoiModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentVoronoiModelNode = newModelNode
self.__voronoiModelNodeSelector.setCurrentNode(
currentVoronoiModelNode)
# the output models
preparedModel = vtk.vtkPolyData()
model = vtk.vtkPolyData()
network = vtk.vtkPolyData()
voronoi = vtk.vtkPolyData()
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates(currentCoordinatesRAS)
# prepare the model
preparedModel.DeepCopy(self.GetLogic().prepareModel(
currentModelNode.GetPolyData()))
preparedModel.Update()
# decimate the model (only for network extraction)
model.DeepCopy(self.GetLogic().decimateSurface(preparedModel))
model.Update()
# open the model at the seed (only for network extraction)
model.DeepCopy(self.GetLogic().openSurfaceAtPoint(
model, currentCoordinatesRAS))
model.Update()
# extract Network
network.DeepCopy(self.GetLogic().extractNetwork(model))
network.Update()
#
#
# not preview mode: real computation!
if not preview:
# here we start the actual centerline computation which is mathematically more robust and accurate but takes longer than the network extraction
# clip surface at endpoints identified by the network extraction
tupel = self.GetLogic().clipSurfaceAtEndPoints(
network, currentModelNode.GetPolyData())
clippedSurface = tupel[0]
endpoints = tupel[1]
# now find the one endpoint which is closest to the seed and use it as the source point for centerline computation
# all other endpoints are the target points
sourcePoint = [0, 0, 0]
# the following arrays have the same indexes and are synchronized at all times
distancesToSeed = []
targetPoints = []
# we now need to loop through the endpoints two times
# first loop is to detect the endpoint resulting in the tiny hole we poked in the surface
# this is very close to our seed but not the correct sourcePoint
for i in range(endpoints.GetNumberOfPoints()):
currentPoint = endpoints.GetPoint(i)
# get the euclidean distance
currentDistanceToSeed = math.sqrt(
math.pow((currentPoint[0] - currentCoordinatesRAS[0]), 2) +
math.pow((currentPoint[1] - currentCoordinatesRAS[1]), 2) +
math.pow((currentPoint[2] - currentCoordinatesRAS[2]), 2))
targetPoints.append(currentPoint)
distancesToSeed.append(currentDistanceToSeed)
# now we have a list of distances with the corresponding points
# the index with the most minimal distance is the holePoint, we want to ignore it
# the index with the second minimal distance is the point closest to the seed, we want to set it as sourcepoint
# all other points are the targetpoints
# get the index of the holePoint, which we want to remove from our endPoints
holePointIndex = distancesToSeed.index(min(distancesToSeed))
# .. and remove it
distancesToSeed.pop(holePointIndex)
targetPoints.pop(holePointIndex)
# now find the sourcepoint
sourcePointIndex = distancesToSeed.index(min(distancesToSeed))
# .. and remove it after saving it as the sourcePoint
sourcePoint = targetPoints[sourcePointIndex]
distancesToSeed.pop(sourcePointIndex)
targetPoints.pop(sourcePointIndex)
# again, at this point we have a) the sourcePoint and b) a list of real targetPoints
# now create the sourceIdList and targetIdList for the actual centerline computation
sourceIdList = vtk.vtkIdList()
targetIdList = vtk.vtkIdList()
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(preparedModel)
pointLocator.BuildLocator()
# locate the source on the surface
sourceId = pointLocator.FindClosestPoint(sourcePoint)
sourceIdList.InsertNextId(sourceId)
f = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLAnnotationFiducialNode")
f.SetFiducialCoordinates(sourcePoint)
f.Initialize(slicer.mrmlScene)
f.SelectedOn()
# locate the endpoints on the surface
for p in targetPoints:
f = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLAnnotationFiducialNode")
f.SetFiducialCoordinates(p)
f.Initialize(slicer.mrmlScene)
id = pointLocator.FindClosestPoint(p)
targetIdList.InsertNextId(id)
tupel = self.GetLogic().computeCenterlines(preparedModel,
sourceIdList,
targetIdList)
network.DeepCopy(tupel[0])
voronoi.DeepCopy(tupel[1])
#
#
# update the display of the original model in terms of opacity
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentModelDisplayNode)
currentModelDisplayNode.SetOpacity(0.4)
currentModelDisplayNode.Modified()
currentModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID(
currentModelDisplayNode.GetID())
currentModelNode.Modified()
currentModelNode.SetModifiedSinceRead(1)
#
# finally:
# propagate output model to nodes
currentOutputModelNode.SetAndObservePolyData(network)
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead(1)
currentOutputModelDisplayNode = currentOutputModelNode.GetDisplayNode()
if not currentOutputModelDisplayNode:
# create new displayNode
currentOutputModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentOutputModelDisplayNode)
# always configure the displayNode to show the model
currentOutputModelDisplayNode.SetPolyData(
currentOutputModelNode.GetPolyData())
currentOutputModelDisplayNode.SetColor(0.0, 0.0, 0.4) # red
currentOutputModelDisplayNode.SetBackfaceCulling(0)
currentOutputModelDisplayNode.SetSliceIntersectionVisibility(0)
currentOutputModelDisplayNode.SetVisibility(1)
currentOutputModelDisplayNode.SetOpacity(1.0)
currentOutputModelDisplayNode.Modified()
currentOutputModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentOutputModelNode.SetAndObserveDisplayNodeID(
currentOutputModelDisplayNode.GetID())
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead(1)
# only update the voronoi node if we are not in preview mode
if not preview:
currentVoronoiModelNode.SetAndObservePolyData(voronoi)
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead(1)
currentVoronoiModelDisplayNode = currentVoronoiModelNode.GetDisplayNode(
)
if not currentVoronoiModelDisplayNode:
# create new displayNode
currentVoronoiModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentVoronoiModelDisplayNode)
# always configure the displayNode to show the model
currentVoronoiModelDisplayNode.SetPolyData(
currentVoronoiModelNode.GetPolyData())
currentVoronoiModelDisplayNode.SetScalarVisibility(1)
currentVoronoiModelDisplayNode.SetBackfaceCulling(0)
currentVoronoiModelDisplayNode.SetActiveScalarName("Radius")
currentVoronoiModelDisplayNode.SetAndObserveColorNodeID(
slicer.mrmlScene.GetNodesByName("Labels").GetItemAsObject(
0).GetID())
currentVoronoiModelDisplayNode.SetSliceIntersectionVisibility(0)
currentVoronoiModelDisplayNode.SetVisibility(1)
currentVoronoiModelDisplayNode.SetOpacity(0.5)
currentVoronoiModelDisplayNode.Modified()
currentVoronoiModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentVoronoiModelNode.SetAndObserveDisplayNodeID(
currentVoronoiModelDisplayNode.GetID())
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead(1)
SlicerVmtk4CommonLib.Helper.Debug("End of Centerline Computation..")
