def warp_surface(args):
print("warp the surface ")
reader = vmtkscripts.vmtkSurfaceReader()
reader.InputFileName = args.surface
reader.Execute()
Surface = reader.Surface
boundaries = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaries.SetInputData(Surface)
boundaries.Update()
boundaryReferenceSystems = vtkvmtk.vtkvmtkBoundaryReferenceSystems()
boundaryReferenceSystems.SetInputData(Surface)
boundaryReferenceSystems.SetBoundaryRadiusArrayName('BoundaryRadius')
boundaryReferenceSystems.SetBoundaryNormalsArrayName('BoundaryNormals')
boundaryReferenceSystems.SetPoint1ArrayName('Point1')
boundaryReferenceSystems.SetPoint2ArrayName('Point2')
boundaryReferenceSystems.Update()
ReferenceSystems = boundaryReferenceSystems.GetOutput()
writer = vmtkscripts.vmtkSurfaceWriter()
writer.OutputFileName = args.file_out
writer.Input = warp.GetOutput()
writer.Execute()
def _Execute(self, *args):
assert isinstance(self.Value, int)
assert isinstance(self.Iolet, Iolet)
input = self.GetPolyDataInput()
clipped = self._Clip(input)
clipped.BuildLinks(0)
newPoints = vtkPoints()
newPoints.DeepCopy(clipped.GetPoints())
newPolys = vtkCellArray()
newPolys.DeepCopy(clipped.GetPolys())
newData = vtkIntArray()
newData.DeepCopy(clipped.GetCellData().GetScalars())
boundaryExtractor = vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(clipped)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
boundariesPointIdMap = boundaries.GetPointData().GetScalars()
for i in xrange(boundaries.GetNumberOfCells()):
boundary = vtkPolyLine.SafeDownCast(boundaries.GetCell(i))
barycentre = [0., 0., 0.]
vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(
boundary.GetPoints(),
barycentre)
barycentreId = newPoints.InsertNextPoint(barycentre)
numberOfBoundaryPoints = boundary.GetNumberOfPoints()
trianglePoints = vtkIdList()
trianglePoints.SetNumberOfIds(3)
for j in xrange(numberOfBoundaryPoints):
trianglePoints.SetId(0,
boundariesPointIdMap.GetValue(boundary.GetPointId(j)))
trianglePoints.SetId(1, barycentreId)
trianglePoints.SetId(2,
boundariesPointIdMap.GetValue(boundary.GetPointId((j + 1) % numberOfBoundaryPoints))
)
newPolys.InsertNextCell(trianglePoints)
newData.InsertNextValue(self.Value)
continue
continue
output = self.GetPolyDataOutput()
output.SetPoints(newPoints)
output.SetPolys(newPolys)
output.GetCellData().SetScalars(newData)
return
def _Execute(self, *args):
assert isinstance(self.Value, int)
assert isinstance(self.Iolet, Iolet)
input = self.GetPolyDataInput()
clipped = self._Clip(input)
clipped.BuildLinks(0)
newPoints = vtkPoints()
newPoints.DeepCopy(clipped.GetPoints())
newPolys = vtkCellArray()
newPolys.DeepCopy(clipped.GetPolys())
newData = vtkIntArray()
newData.DeepCopy(clipped.GetCellData().GetScalars())
boundaryExtractor = vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(clipped)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
boundariesPointIdMap = boundaries.GetPointData().GetScalars()
for i in xrange(boundaries.GetNumberOfCells()):
boundary = vtkPolyLine.SafeDownCast(boundaries.GetCell(i))
barycentre = [0., 0., 0.]
vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(
boundary.GetPoints(), barycentre)
barycentreId = newPoints.InsertNextPoint(barycentre)
numberOfBoundaryPoints = boundary.GetNumberOfPoints()
trianglePoints = vtkIdList()
trianglePoints.SetNumberOfIds(3)
for j in xrange(numberOfBoundaryPoints):
trianglePoints.SetId(
0, boundariesPointIdMap.GetValue(boundary.GetPointId(j)))
trianglePoints.SetId(1, barycentreId)
trianglePoints.SetId(
2,
boundariesPointIdMap.GetValue(
boundary.GetPointId((j + 1) % numberOfBoundaryPoints)))
newPolys.InsertNextCell(trianglePoints)
newData.InsertNextValue(self.Value)
continue
continue
output = self.GetPolyDataOutput()
output.SetPoints(newPoints)
output.SetPolys(newPolys)
output.GetCellData().SetScalars(newData)
return
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
# cleaner = vtk.vtkCleanPolyData()
# cleaner.SetInput(self.Surface)
# cleaner.Update()
#
# triangleFilter = vtk.vtkTriangleFilter()
# triangleFilter.SetInput(cleaner.GetOutput())
# triangleFilter.Update()
#
# self.Surface = triangleFilter.GetOutput()
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
from vmtk import vmtkrenderer
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(boundaries.GetCell(i).GetPoints(),barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
labelString = self.InputText("Please input boundary ids: ",self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
for label in labels:
boundaryIds.InsertNextId(label)
if self.Method == 'simple':
capper = vtkvmtk.vtkvmtkSimpleCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'centerpoint':
capper = vtkvmtk.vtkvmtkCapPolyData()
capper.SetInputData(self.Surface)
capper.SetDisplacement(0.0)
capper.SetInPlaneDisplacement(0.0)
elif self.Method == 'smooth':
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
capper = vtkvmtk.vtkvmtkSmoothCapPolyData()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetConstraintFactor(self.ConstraintFactor)
capper.SetNumberOfRings(self.NumberOfRings)
elif self.Method == 'annular':
capper = vtkvmtk.vtkvmtkAnnularCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'concaveannular':
from vmtk import vtkvmtkcontrib
capper = vtkvmtkcontrib.vtkvmtkConcaveAnnularCapPolyData()
capper.SetInputData(self.Surface)
if self.Interactive:
capper.SetBoundaryIds(boundaryIds)
capper.SetCellEntityIdsArrayName(self.CellEntityIdsArrayName)
capper.SetCellEntityIdOffset(self.CellEntityIdOffset)
capper.Update()
self.Surface = capper.GetOutput()
if self.TriangleOutput == 1:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
self.Surface = triangle.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(self.Surface)
normals.AutoOrientNormalsOn()
normals.SplittingOff()
normals.ConsistencyOn()
normals.Update()
self.Surface = normals.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.ExtensionMode == "centerlinedirection" and self.Centerlines == None:
self.PrintError('Error: No input centerlines.')
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(
boundaries.GetCell(i).GetPoints(), barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper()
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
if (self.Exclude):
labelString = self.InputText(
"Please input boundary ids to exclude: ",
self.LabelValidator)
else:
labelString = self.InputText("Please input boundary ids: ",
self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
if (self.Exclude):
for label in list(range(numberOfBoundaries)):
if label not in labels:
boundaryIds.InsertNextId(label)
else:
for label in labels:
boundaryIds.InsertNextId(label)
flowExtensionsFilter = vtkvmtk.vtkvmtkPolyDataFlowExtensionsFilter()
flowExtensionsFilter.SetInputData(self.Surface)
flowExtensionsFilter.SetCenterlines(self.Centerlines)
flowExtensionsFilter.SetSigma(self.Sigma)
flowExtensionsFilter.SetAdaptiveExtensionLength(
self.AdaptiveExtensionLength)
flowExtensionsFilter.SetAdaptiveExtensionRadius(
self.AdaptiveExtensionRadius)
flowExtensionsFilter.SetAdaptiveNumberOfBoundaryPoints(
self.AdaptiveNumberOfBoundaryPoints)
flowExtensionsFilter.SetExtensionLength(self.ExtensionLength)
flowExtensionsFilter.SetExtensionRatio(self.ExtensionRatio)
flowExtensionsFilter.SetExtensionRadius(self.ExtensionRadius)
flowExtensionsFilter.SetTransitionRatio(self.TransitionRatio)
flowExtensionsFilter.SetCenterlineNormalEstimationDistanceRatio(
self.CenterlineNormalEstimationDistanceRatio)
flowExtensionsFilter.SetNumberOfBoundaryPoints(
self.TargetNumberOfBoundaryPoints)
if self.ExtensionMode == "centerlinedirection":
flowExtensionsFilter.SetExtensionModeToUseCenterlineDirection()
elif self.ExtensionMode == "boundarynormal":
flowExtensionsFilter.SetExtensionModeToUseNormalToBoundary()
if self.InterpolationMode == "linear":
flowExtensionsFilter.SetInterpolationModeToLinear()
elif self.InterpolationMode == "thinplatespline":
flowExtensionsFilter.SetInterpolationModeToThinPlateSpline()
if self.Interactive:
flowExtensionsFilter.SetBoundaryIds(boundaryIds)
flowExtensionsFilter.Update()
self.Surface = flowExtensionsFilter.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.ExtensionMode == "centerlinedirection" and self.Centerlines == None:
self.PrintError('Error: No input centerlines.')
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(boundaries.GetCell(i).GetPoints(),barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
if(self.Exclude):
labelString = self.InputText("Please input boundary ids to exclude: ",self.LabelValidator)
else:
labelString = self.InputText("Please input boundary ids: ",self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
if(self.Exclude):
for label in list(range(numberOfBoundaries)):
if label not in labels:
boundaryIds.InsertNextId(label)
else:
for label in labels:
boundaryIds.InsertNextId(label)
flowExtensionsFilter = vtkvmtk.vtkvmtkPolyDataFlowExtensionsFilter()
flowExtensionsFilter.SetInputData(self.Surface)
flowExtensionsFilter.SetCenterlines(self.Centerlines)
flowExtensionsFilter.SetSigma(self.Sigma)
flowExtensionsFilter.SetAdaptiveExtensionLength(self.AdaptiveExtensionLength)
flowExtensionsFilter.SetAdaptiveExtensionRadius(self.AdaptiveExtensionRadius)
flowExtensionsFilter.SetAdaptiveNumberOfBoundaryPoints(self.AdaptiveNumberOfBoundaryPoints)
flowExtensionsFilter.SetExtensionLength(self.ExtensionLength)
flowExtensionsFilter.SetExtensionRatio(self.ExtensionRatio)
flowExtensionsFilter.SetExtensionRadius(self.ExtensionRadius)
flowExtensionsFilter.SetTransitionRatio(self.TransitionRatio)
flowExtensionsFilter.SetCenterlineNormalEstimationDistanceRatio(self.CenterlineNormalEstimationDistanceRatio)
flowExtensionsFilter.SetNumberOfBoundaryPoints(self.TargetNumberOfBoundaryPoints)
if self.ExtensionMode == "centerlinedirection":
flowExtensionsFilter.SetExtensionModeToUseCenterlineDirection()
elif self.ExtensionMode == "boundarynormal":
flowExtensionsFilter.SetExtensionModeToUseNormalToBoundary()
if self.InterpolationMode == "linear":
flowExtensionsFilter.SetInterpolationModeToLinear()
elif self.InterpolationMode == "thinplatespline":
flowExtensionsFilter.SetInterpolationModeToThinPlateSpline()
if self.Interactive:
flowExtensionsFilter.SetBoundaryIds(boundaryIds)
flowExtensionsFilter.Update()
self.Surface = flowExtensionsFilter.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
curvatureFilter = vtk.vtkCurvatures()
curvatureFilter.SetInputData(self.Surface)
if self.CurvatureType == 'mean':
curvatureFilter.SetCurvatureTypeToMean()
elif self.CurvatureType == 'gaussian':
curvatureFilter.SetCurvatureTypeToGaussian()
elif self.CurvatureType == 'maximum':
curvatureFilter.SetCurvatureTypeToMaximum()
elif self.CurvatureType == 'minimum':
curvatureFilter.SetCurvatureTypeToMinimum()
curvatureFilter.Update()
activeScalars = curvatureFilter.GetOutput().GetPointData().GetScalars()
activeScalars.SetName('Curvature')
if self.AbsoluteCurvature:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i,abs(value))
neighborhoods = None
if not self.CurvatureOnBoundaries or self.MedianFiltering:
neighborhoods = vtkvmtk.vtkvmtkNeighborhoods()
neighborhoods.SetNeighborhoodTypeToPolyDataManifoldNeighborhood()
neighborhoods.SetDataSet(self.Surface)
neighborhoods.Build()
if not self.CurvatureOnBoundaries:
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaryIdsArray = vtk.vtkIdTypeArray.SafeDownCast(boundaryExtractor.GetOutput().GetPointData().GetScalars())
boundaryIds = vtk.vtkIdList()
boundaryIds.SetNumberOfIds(boundaryIdsArray.GetNumberOfTuples())
for i in range(boundaryIdsArray.GetNumberOfTuples()):
boundaryIds.SetId(i,boundaryIdsArray.GetValue(i))
self.Surface.BuildLinks()
for i in range(boundaryIds.GetNumberOfIds()):
pointId = boundaryIds.GetId(i)
neighborhood = neighborhoods.GetNeighborhood(pointId)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
if boundaryIds.IsId(neighborId) != -1:
continue
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1)/2]
activeScalars.SetTuple1(pointId,medianValue)
if self.MedianFiltering:
for i in range(neighborhoods.GetNumberOfNeighborhoods()):
neighborhood = neighborhoods.GetNeighborhood(i)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1)/2]
activeScalars.SetTuple1(i,medianValue)
if self.BoundedReciprocal:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
reciprocalValue = 1.0 / (self.Epsilon + value)
activeScalars.SetTuple1(i,reciprocalValue)
if self.Offset:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i,value + self.Offset)
if self.ReferenceSurface == None:
self.Surface.GetPointData().AddArray(activeScalars)
else:
self.ReferenceSurface.GetPointData().AddArray(activeScalars)
self.Surface = self.ReferenceSurface
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
# cleaner = vtk.vtkCleanPolyData()
# cleaner.SetInput(self.Surface)
# cleaner.Update()
#
# triangleFilter = vtk.vtkTriangleFilter()
# triangleFilter.SetInput(cleaner.GetOutput())
# triangleFilter.Update()
#
# self.Surface = triangleFilter.GetOutput()
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
from vmtk import vmtkrenderer
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(boundaries.GetCell(i).GetPoints(),barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
labelString = self.InputText("Please input boundary ids: ",self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
for label in labels:
boundaryIds.InsertNextId(label)
if self.Method == 'simple':
capper = vtkvmtk.vtkvmtkSimpleCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'centerpoint':
capper = vtkvmtk.vtkvmtkCapPolyData()
capper.SetInputData(self.Surface)
capper.SetDisplacement(0.0)
capper.SetInPlaneDisplacement(0.0)
elif self.Method == 'smooth':
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
capper = vtkvmtk.vtkvmtkSmoothCapPolyData()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetConstraintFactor(self.ConstraintFactor)
capper.SetNumberOfRings(self.NumberOfRings)
elif self.Method == 'annular':
capper = vtkvmtk.vtkvmtkAnnularCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'concaveannular':
from vmtk import vtkvmtkcontrib
capper = vtkvmtkcontrib.vtkvmtkConcaveAnnularCapPolyData()
capper.SetInputData(self.Surface)
if self.Interactive:
capper.SetBoundaryIds(boundaryIds)
capper.SetCellEntityIdsArrayName(self.CellEntityIdsArrayName)
capper.SetCellEntityIdOffset(self.CellEntityIdOffset)
capper.Update()
self.Surface = capper.GetOutput()
if self.TriangleOutput == 1:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
self.Surface = triangle.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(self.Surface)
normals.AutoOrientNormalsOn()
normals.SplittingOff()
normals.ConsistencyOn()
normals.Update()
self.Surface = normals.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
curvatureFilter = vtk.vtkCurvatures()
curvatureFilter.SetInputData(self.Surface)
if self.CurvatureType == 'mean':
curvatureFilter.SetCurvatureTypeToMean()
elif self.CurvatureType == 'gaussian':
curvatureFilter.SetCurvatureTypeToGaussian()
elif self.CurvatureType == 'maximum':
curvatureFilter.SetCurvatureTypeToMaximum()
elif self.CurvatureType == 'minimum':
curvatureFilter.SetCurvatureTypeToMinimum()
curvatureFilter.Update()
activeScalars = curvatureFilter.GetOutput().GetPointData().GetScalars()
activeScalars.SetName('Curvature')
if self.AbsoluteCurvature:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i, abs(value))
neighborhoods = None
if not self.CurvatureOnBoundaries or self.MedianFiltering:
neighborhoods = vtkvmtk.vtkvmtkNeighborhoods()
neighborhoods.SetNeighborhoodTypeToPolyDataManifoldNeighborhood()
neighborhoods.SetDataSet(self.Surface)
neighborhoods.Build()
if not self.CurvatureOnBoundaries:
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaryIdsArray = vtk.vtkIdTypeArray.SafeDownCast(
boundaryExtractor.GetOutput().GetPointData().GetScalars())
boundaryIds = vtk.vtkIdList()
boundaryIds.SetNumberOfIds(boundaryIdsArray.GetNumberOfTuples())
for i in range(boundaryIdsArray.GetNumberOfTuples()):
boundaryIds.SetId(i, boundaryIdsArray.GetValue(i))
self.Surface.BuildLinks()
for i in range(boundaryIds.GetNumberOfIds()):
pointId = boundaryIds.GetId(i)
neighborhood = neighborhoods.GetNeighborhood(pointId)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
if boundaryIds.IsId(neighborId) != -1:
continue
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1) / 2]
activeScalars.SetTuple1(pointId, medianValue)
if self.MedianFiltering:
for i in range(neighborhoods.GetNumberOfNeighborhoods()):
neighborhood = neighborhoods.GetNeighborhood(i)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1) / 2]
activeScalars.SetTuple1(i, medianValue)
if self.BoundedReciprocal:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
reciprocalValue = 1.0 / (self.Epsilon + value)
activeScalars.SetTuple1(i, reciprocalValue)
if self.Offset:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i, value + self.Offset)
if self.ReferenceSurface == None:
self.Surface.GetPointData().AddArray(activeScalars)
else:
self.ReferenceSurface.GetPointData().AddArray(activeScalars)
self.Surface = self.ReferenceSurface
