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 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 ClipData(self, ROI, noisySurfacePolyData):
""" Returns the clipped polydata from the region defined by the ROI
Turn on the Debug to make the clipped object appear,
For specific filter functionality see DataFlow doc: ClipData.pdf
"""
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
self.utility.PolyDataWriter(
noisySurfacePolyData, "C:\\MakeHDRApplicatorMask\\doc\\" + "DebugPolyData\\PreClipped.vtk"
)
connectivityFilter.SetInputData(noisySurfacePolyData)
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
self.skinSurface = connectivityFilter.GetOutput() # skinSurface Set
if self.DEBUG_CONNECTIVITYFACE:
self.utility.DisplayPolyData("ConnectedFace", self.skinSurface)
# Expansion of ROI is explained in vtkImplicitModeller limitations
ROIExtents = self.utility.GetROIExtents(ROI)
BiggerROI = self.utility.ExpandExtents(ROIExtents, 0.5)
# See vtkImplicitModdeler limitations.pdf for explanation
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(BiggerROI)
clipper = vtk.vtkClipPolyData()
clipper.InsideOutOn() # Clip the regions outside of implicit function
clipper.SetInputConnection(connectivityFilter.GetOutputPort())
clipper.SetClipFunction(implicitBoxRegion)
clipper.Update()
self.clippedSurface = clipper.GetOutput()
return clipper
def ClipData(self, ROI, noisySurfacePolyData):
""" Returns the clipped polydata from the region defined by the ROI
Turn on the Debug to make the clipped object appear,
For specific filter functionality see DataFlow doc: ClipData.pdf
"""
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
self.utility.PolyDataWriter(noisySurfacePolyData,
"C:\\MakeHDRApplicatorMask\\doc\\"+\
"DebugPolyData\\PreClipped.vtk")
connectivityFilter.SetInputData(noisySurfacePolyData)
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
self.skinSurface = connectivityFilter.GetOutput() #skinSurface Set
if self.DEBUG_CONNECTIVITYFACE:
self.utility.DisplayPolyData("ConnectedFace", self.skinSurface)
# Expansion of ROI is explained in vtkImplicitModeller limitations
ROIExtents = self.utility.GetROIExtents(ROI)
BiggerROI = self.utility.ExpandExtents(ROIExtents, .5)
#See vtkImplicitModdeler limitations.pdf for explanation
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(BiggerROI)
clipper = vtk.vtkClipPolyData()
clipper.InsideOutOn() # Clip the regions outside of implicit function
clipper.SetInputConnection(connectivityFilter.GetOutputPort())
clipper.SetClipFunction(implicitBoxRegion)
clipper.Update()
self.clippedSurface = clipper.GetOutput()
return clipper
def getAverageNormalFromModelPoint(model, point):
normalsOfModel = slicer.util.arrayFromModelPointData(model, 'Normals')
modelMesh = model.GetMesh()
pointID = modelMesh.FindPoint(point)
normalAtPointID = normalsOfModel[pointID]
cylinder = vtk.vtkCylinder()
cylinder.SetRadius(3)
cylinder.SetCenter(point)
cylinder.SetAxis(normalAtPointID)
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(model.GetPolyData())
clipper.InsideOutOn()
clipper.SetClipFunction(cylinder)
clipper.Update()
connectivityFilter = vtk.vtkConnectivityFilter()
connectivityFilter.SetInputData(clipper.GetOutput())
connectivityFilter.SetClosestPoint(point)
connectivityFilter.SetExtractionModeToClosestPointRegion()
connectivityFilter.Update()
cylinderIntersectionModel = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLModelNode', 'cylinderIntersection')
cylinderIntersectionModel.CreateDefaultDisplayNodes()
cylinderIntersectionModel.SetAndObservePolyData(
connectivityFilter.GetOutput())
averageNormal = getAverageNormalFromModel(cylinderIntersectionModel)
slicer.mrmlScene.RemoveNode(cylinderIntersectionModel)
return averageNormal
def MinimumDistanceMask(self,
vtkAlgorythmObject,
distanceFromMask,
ROI,
ruler,
isBubble=False):
""" Takes an algorythm object which is will send through a pipeline to
create a mask defining the minimum distance value from the skin surface
returns an algorythm object as well to preform GetOutput() -> polydata
or GetOutputPort() -> algorythm
see MinimumDistanceMask.pdf
"""
if distanceFromMask < 2:
print "WARNING: MouldLogic: MinimumDistanceMask implicit",
"modeling is very unstable below 1.5 , mask may degrade",
"and lines will become discontinuous."
Extents = self.utility.GetROIExtents(ROI)
if (isBubble):
Extents = self.utility.ExpandExtents(Extents, 100)
implicitModeller = vtk.vtkImplicitModeller()
implicitModeller.SetInputConnection(vtkAlgorythmObject.GetOutputPort())
implicitModeller.SetMaximumDistance(distanceFromMask)
implicitModeller.SetModelBounds(Extents)
implicitModeller.AdjustBoundsOn()
implicitModeller.SetAdjustBounds(10) # Removes the boundary effects
implicitModeller.CappingOff(
) # Important to create disjoint inner and outer masks
implicitModeller.SetProcessModeToPerVoxel()
implicitModeller.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, distanceFromMask)
contourFilter.SetInputConnection(implicitModeller.GetOutputPort())
contourFilter.Update()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.FlipNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
normalsFunction.Update()
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(Extents)
clipper2 = vtk.vtkClipPolyData()
clipper2.InsideOutOn() # Clip the regions outside of implicit function
clipper2.SetInputConnection(normalsFunction.GetOutputPort())
clipper2.SetClipFunction(implicitBoxRegion)
clipper2.Update()
closestPoint = [0, 0, 0]
ruler.GetPosition1(closestPoint)
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputConnection(clipper2.GetOutputPort())
connectivityFilter.SetExtractionModeToClosestPointRegion()
connectivityFilter.SetClosestPoint(closestPoint)
connectivityFilter.Update()
return connectivityFilter.GetOutput()
def getIntersectionBetweenModelAnd1PlaneWithNormalAndOrigin(
modelNode, normal, origin, intersectionModel):
plane = vtk.vtkPlane()
plane.SetOrigin(origin)
plane.SetNormal(normal)
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(modelNode.GetPolyData())
clipper.SetClipFunction(plane)
clipper.Update()
intersectionModel.SetAndObservePolyData(clipper.GetOutput())
def MinimumDistanceMask(self, vtkAlgorythmObject, distanceFromMask, ROI, ruler, isBubble=False):
""" Takes an algorythm object which is will send through a pipeline to
create a mask defining the minimum distance value from the skin surface
returns an algorythm object as well to preform GetOutput() -> polydata
or GetOutputPort() -> algorythm
see MinimumDistanceMask.pdf
"""
if distanceFromMask < 2:
print "WARNING: MouldLogic: MinimumDistanceMask implicit",
"modeling is very unstable below 1.5 , mask may degrade",
"and lines will become discontinuous."
Extents = self.utility.GetROIExtents(ROI)
if isBubble:
Extents = self.utility.ExpandExtents(Extents, 100)
implicitModeller = vtk.vtkImplicitModeller()
implicitModeller.SetInputConnection(vtkAlgorythmObject.GetOutputPort())
implicitModeller.SetMaximumDistance(distanceFromMask)
implicitModeller.SetModelBounds(Extents)
implicitModeller.AdjustBoundsOn()
implicitModeller.SetAdjustBounds(10) # Removes the boundary effects
implicitModeller.CappingOff() # Important to create disjoint inner and outer masks
implicitModeller.SetProcessModeToPerVoxel()
implicitModeller.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, distanceFromMask)
contourFilter.SetInputConnection(implicitModeller.GetOutputPort())
contourFilter.Update()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.FlipNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
normalsFunction.Update()
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(Extents)
clipper2 = vtk.vtkClipPolyData()
clipper2.InsideOutOn() # Clip the regions outside of implicit function
clipper2.SetInputConnection(normalsFunction.GetOutputPort())
clipper2.SetClipFunction(implicitBoxRegion)
clipper2.Update()
closestPoint = [0, 0, 0]
ruler.GetPosition1(closestPoint)
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputConnection(clipper2.GetOutputPort())
connectivityFilter.SetExtractionModeToClosestPointRegion()
connectivityFilter.SetClosestPoint(closestPoint)
connectivityFilter.Update()
return connectivityFilter.GetOutput()
def clipSurfaceAtEndPoints(self, networkPolyData, surfacePolyData):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
from libvtkvmtkComputationalGeometryPython import *
from libvtkvmtkMiscPython import *
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk4 libraries!"
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(networkPolyData)
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks(0)
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray('Radius')
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName('Radius')
endpoints.SetPoints(endpointsPoints)
endpoints.GetPointData().AddArray(endpointsRadius)
radiusFactor = 1.2
minRadius = 0.01
for i in range(network.GetNumberOfCells()):
numberOfCellPoints = network.GetCell(i).GetNumberOfPoints()
pointId0 = network.GetCell(i).GetPointId(0)
pointId1 = network.GetCell(i).GetPointId(numberOfCellPoints - 1)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId0, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId0)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId0)
radius = radiusArray.GetValue(pointId0)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId1, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId1)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId1)
radius = radiusArray.GetValue(pointId1)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
polyBall = vtkvmtkPolyBall()
polyBall.SetInput(endpoints)
polyBall.SetPolyBallRadiusArrayName('Radius')
clipper = vtk.vtkClipPolyData()
clipper.SetInput(surfacePolyData)
clipper.SetClipFunction(polyBall)
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInput(clipper.GetOutput())
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy(clippedSurface)
outPolyData.Update()
return [outPolyData, endpointsPoints]
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 clipSurfaceAtEndPoints( self, networkPolyData, surfacePolyData ):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
import vtkvmtkComputationalGeometryPython as vtkvmtkComputationalGeometry
import vtkvmtkMiscPython as vtkvmtkMisc
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData( networkPolyData )
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks( 0 )
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray( 'Radius' )
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName( 'Radius' )
endpoints.SetPoints( endpointsPoints )
endpoints.GetPointData().AddArray( endpointsRadius )
radiusFactor = 1.2
minRadius = 0.01
for i in range( network.GetNumberOfCells() ):
numberOfCellPoints = network.GetCell( i ).GetNumberOfPoints()
pointId0 = network.GetCell( i ).GetPointId( 0 )
pointId1 = network.GetCell( i ).GetPointId( numberOfCellPoints - 1 )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId0, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId0 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId0 )
radius = radiusArray.GetValue( pointId0 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId1, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId1 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId1 )
radius = radiusArray.GetValue( pointId1 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
polyBall = vtkvmtkComputationalGeometry.vtkvmtkPolyBall()
#polyBall.SetInputData( endpoints )
polyBall.SetInput( endpoints )
polyBall.SetPolyBallRadiusArrayName( 'Radius' )
clipper = vtk.vtkClipPolyData()
clipper.SetInputData( surfacePolyData )
clipper.SetClipFunction( polyBall )
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputData( clipper.GetOutput() )
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy( clippedSurface )
return [outPolyData, endpointsPoints]
def run(self, inputModel, spherePosition, sphereRadius, outputTransform):
"""
Run the actual algorithm
"""
if not self.isValidInputOutputData(inputModel, outputTransform):
slicer.util.errorDisplay(
'Input model is the same as sphere model. Choose a different input model.'
)
return False
logging.info('Processing started')
# Convert sphere model to an implicit dataset to clip input model with it
sphere = vtk.vtkSphere()
sphere.SetCenter(spherePosition)
sphere.SetRadius(sphereRadius)
# Clip and clean input model
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(triangle.GetOutput())
clip.SetClipFunction(sphere)
clip.InsideOutOn()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(clip.GetOutputPort())
clean.Update()
# Compute average normal
clippedModel = clip.GetOutput()
cellsNormal = clippedModel.GetPointData().GetNormals()
averageNormal = [0.0, 0.0, 0.0]
nOfNormals = 0
for cellIndex in range(0, cellsNormal.GetNumberOfTuples()):
cellNormal = [0.0, 0.0, 0.0]
cellsNormal.GetTuple(cellIndex, cellNormal)
if not (math.isnan(cellNormal[0]) or math.isnan(cellNormal[1])
or math.isnan(cellNormal[2])):
averageNormal[0] = averageNormal[0] + cellNormal[0]
averageNormal[1] = averageNormal[1] + cellNormal[1]
averageNormal[2] = averageNormal[2] + cellNormal[2]
nOfNormals = nOfNormals + 1
# Compute perpendicular vectors
v1 = [0.0, 0.0, 0.0]
v2 = [0.0, 0.0, 0.0]
vtkmath = vtk.vtkMath()
#vtkmath.Perpendiculars(averageNormal, v2, v1, 0)
self.calculatePerpendicularVectors(averageNormal, v2, v1)
# Normalize vectors
vtkmath.Normalize(averageNormal)
vtkmath.Normalize(v1)
vtkmath.Normalize(v2)
# Create Matrix4x4
outputMatrix = vtk.vtkMatrix4x4()
outputMatrix.SetElement(0, 0, v1[0])
outputMatrix.SetElement(1, 0, v1[1])
outputMatrix.SetElement(2, 0, v1[2])
outputMatrix.SetElement(3, 0, 0.0)
outputMatrix.SetElement(0, 1, averageNormal[0])
outputMatrix.SetElement(1, 1, averageNormal[1])
outputMatrix.SetElement(2, 1, averageNormal[2])
outputMatrix.SetElement(3, 1, 0.0)
outputMatrix.SetElement(0, 2, v2[0])
outputMatrix.SetElement(1, 2, v2[1])
outputMatrix.SetElement(2, 2, v2[2])
outputMatrix.SetElement(3, 2, 0.0)
outputMatrix.SetElement(0, 3, spherePosition[0])
outputMatrix.SetElement(1, 3, spherePosition[1])
outputMatrix.SetElement(2, 3, spherePosition[2])
outputMatrix.SetElement(3, 3, 1.0)
outputTransform.SetMatrixTransformToParent(outputMatrix)
logging.info('Processing completed')
return True
def run(self, inputModel, spherePosition, sphereRadius, outputTransform):
"""
Run the actual algorithm
"""
if not self.isValidInputOutputData(inputModel, outputTransform):
slicer.util.errorDisplay('Input model is the same as sphere model. Choose a different input model.')
return False
logging.info('Processing started')
# Convert sphere model to an implicit dataset to clip input model with it
sphere = vtk.vtkSphere()
sphere.SetCenter(spherePosition)
sphere.SetRadius(sphereRadius)
# Clip and clean input model
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(triangle.GetOutput())
clip.SetClipFunction(sphere)
clip.InsideOutOn()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(clip.GetOutputPort())
clean.Update()
# Compute average normal
clippedModel = clip.GetOutput()
cellsNormal = clippedModel.GetPointData().GetNormals()
averageNormal = [0.0, 0.0, 0.0]
nOfNormals = 0;
for cellIndex in range(0, cellsNormal.GetNumberOfTuples()):
cellNormal = [0.0, 0.0, 0.0]
cellsNormal.GetTuple(cellIndex, cellNormal)
if not(math.isnan(cellNormal[0]) or math.isnan(cellNormal[1]) or math.isnan(cellNormal[2])):
averageNormal[0] = averageNormal[0] + cellNormal[0]
averageNormal[1] = averageNormal[1] + cellNormal[1]
averageNormal[2] = averageNormal[2] + cellNormal[2]
nOfNormals = nOfNormals + 1
# Compute perpendicular vectors
v1 = [0.0, 0.0, 0.0]
v2 = [0.0, 0.0, 0.0]
vtkmath = vtk.vtkMath()
#vtkmath.Perpendiculars(averageNormal, v2, v1, 0)
self.calculatePerpendicularVectors(averageNormal, v2, v1)
# Normalize vectors
vtkmath.Normalize(averageNormal)
vtkmath.Normalize(v1)
vtkmath.Normalize(v2)
# Create Matrix4x4
outputMatrix = vtk.vtkMatrix4x4()
outputMatrix.SetElement(0,0,v1[0])
outputMatrix.SetElement(1,0,v1[1])
outputMatrix.SetElement(2,0,v1[2])
outputMatrix.SetElement(3,0,0.0)
outputMatrix.SetElement(0,1,averageNormal[0])
outputMatrix.SetElement(1,1,averageNormal[1])
outputMatrix.SetElement(2,1,averageNormal[2])
outputMatrix.SetElement(3,1,0.0)
outputMatrix.SetElement(0,2,v2[0])
outputMatrix.SetElement(1,2,v2[1])
outputMatrix.SetElement(2,2,v2[2])
outputMatrix.SetElement(3,2,0.0)
outputMatrix.SetElement(0,3,spherePosition[0])
outputMatrix.SetElement(1,3,spherePosition[1])
outputMatrix.SetElement(2,3,spherePosition[2])
outputMatrix.SetElement(3,3,1.0)
outputTransform.SetMatrixTransformToParent(outputMatrix)
logging.info('Processing completed')
return True
