def Execute(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
self.vmtkRenderer.AddKeyBinding('u', 'Undo.', self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Add points.',
self.PickCallback)
self.InputInfo(
'Please position the mouse and press space to add target points, \'u\' to undo\n'
)
# this is necessary to set up the async watch loop.
any = 0
while any == 0:
self.vmtkRenderer.Render()
try:
any = self.CurrentPickedPolyData
except AttributeError:
any = None
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self._Surface == None):
self.PrintError(
'vmtkPickPointSeedSelector Error: Surface not set.')
return
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
##self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('u', 'Undo.', self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Add points.',
self.PickCallback)
self.InputInfo(
'Please position the mouse and press space to add target points, \'u\' to undo\n'
)
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
try:
any = self.PickedScalarData.GetValue(0)
except AttributeError:
any = None
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.vmtkRenderer.AddKeyBinding('i','Interact.', self.InteractCallback)
self.Display()
while (self.BoxActive == 1):
self.PaintVOI()
self.Display()
else:
self.PaintVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
contourScalars = vtk.vtkDoubleArray()
contourScalars.SetNumberOfComponents(1)
contourScalars.SetNumberOfTuples(self.Surface.GetNumberOfPoints())
contourScalars.SetName(self.ContourScalarsArrayName)
contourScalars.FillComponent(0,self.OutsideValue)
self.Surface.GetPointData().AddArray(contourScalars)
self.Surface.GetPointData().SetActiveScalars(self.ContourScalarsArrayName)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.Surface)
mapper.ScalarVisibilityOn()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetMapper().SetScalarRange(-1.0,0.0)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.ContourWidget = vtk.vtkContourWidget()
self.ContourWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(self.ContourWidget.GetRepresentation())
rep.GetLinesProperty().SetColor(1, 0.2, 0)
rep.GetLinesProperty().SetLineWidth(3.0)
pointPlacer = vtk.vtkPolygonalSurfacePointPlacer()
pointPlacer.AddProp(self.Actor)
pointPlacer.GetPolys().AddItem(self.Surface)
rep.SetPointPlacer(pointPlacer)
self.Interpolator = vtk.vtkPolygonalSurfaceContourLineInterpolator()
self.Interpolator.GetPolys().AddItem(self.Surface)
rep.SetLineInterpolator(self.Interpolator)
self.vmtkRenderer.AddKeyBinding('space','Generate scalars',self.ScalarsCallback)
self.vmtkRenderer.AddKeyBinding('d','Delete contour',self.DeleteContourCallback)
self.vmtkRenderer.AddKeyBinding('i','Start interaction',self.InteractCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
contourScalars = vtk.vtkDoubleArray()
contourScalars.SetNumberOfComponents(1)
contourScalars.SetNumberOfTuples(self.Surface.GetNumberOfPoints())
contourScalars.SetName(self.ContourScalarsArrayName)
contourScalars.FillComponent(0,self.OutsideValue)
self.Surface.GetPointData().AddArray(contourScalars)
self.Surface.GetPointData().SetActiveScalars(self.ContourScalarsArrayName)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.Surface)
mapper.ScalarVisibilityOn()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetMapper().SetScalarRange(-1.0,0.0)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.ContourWidget = vtk.vtkContourWidget()
self.ContourWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(self.ContourWidget.GetRepresentation())
rep.GetLinesProperty().SetColor(1, 0.2, 0)
rep.GetLinesProperty().SetLineWidth(3.0)
pointPlacer = vtk.vtkPolygonalSurfacePointPlacer()
pointPlacer.AddProp(self.Actor)
pointPlacer.GetPolys().AddItem(self.Surface)
rep.SetPointPlacer(pointPlacer)
self.Interpolator = vtk.vtkPolygonalSurfaceContourLineInterpolator()
self.Interpolator.GetPolys().AddItem(self.Surface)
rep.SetLineInterpolator(self.Interpolator)
self.vmtkRenderer.AddKeyBinding('space','Generate scalars',self.ScalarsCallback)
self.vmtkRenderer.AddKeyBinding('d','Delete contour',self.DeleteContourCallback)
self.vmtkRenderer.AddKeyBinding('i','Start interaction',self.InteractCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
from vmtk import vmtkscripts
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
self.tagviewer = vmtkscripts.vmtkSurfaceViewer()
self.tagviewer.Surface = self.Surface
self.tagviewer.vmtkRenderer = self.vmtkRenderer
self.tagviewer.Representation = 'edges'
self.tagviewer.Opacity = self.Opacity
self.tagviewer.Execute()
self.ContourWidget = vtk.vtkContourWidget()
self.ContourWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(
self.ContourWidget.GetRepresentation())
rep.GetLinesProperty().SetColor(1, 0, 0)
rep.GetLinesProperty().SetLineWidth(4.0)
pointPlacer = vtk.vtkPolygonalSurfacePointPlacer()
pointPlacer.AddProp(self.tagviewer.Actor)
pointPlacer.GetPolys().AddItem(self.Surface)
rep.SetPointPlacer(pointPlacer)
self.Interpolator = vtk.vtkPolygonalSurfaceContourLineInterpolator()
self.Interpolator.GetPolys().AddItem(self.Surface)
rep.SetLineInterpolator(self.Interpolator)
self.InputInfo("Building loop ...\n")
self.vmtkRenderer.AddKeyBinding('space', 'Generate loop',
self.LoopCallback)
self.vmtkRenderer.AddKeyBinding('d', 'Delete contour',
self.DeleteContourCallback)
self.vmtkRenderer.AddKeyBinding('i', 'Start/stop contour drawing',
self.InteractCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self._Surface is None:
self.PrintError(
'vmtkPickPointSeedSelector Error: Surface not set.')
return
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphs.SetInputData(self.PickedSeeds)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToDataScalingOff()
glyphs.SetScaleFactor(self._Surface.GetLength() * 0.01)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputData(glyphs.GetOutput())
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
self.SeedActor = vtk.vtkActor()
self.SeedActor.SetMapper(glyphMapper)
self.SeedActor.GetProperty().SetColor(1.0, 0.0, 0.0)
self.SeedActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SeedActor)
self.vmtkRenderer.AddKeyBinding('u', 'Undo.', self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Add points.',
self.PickCallback)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self._Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(1.0)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
guiText = VtkText(self.text)
self.vmtkRenderer.Renderer.AddActor(guiText.text)
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._TargetSeedIds.DeepCopy(self.PickedSeedIds)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
self._SourceSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphs.SetInputData(self.PickedSeeds)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToDataScalingOff()
glyphs.SetScaleFactor(self._Surface.GetLength()*0.01)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
self.SeedActor = vtk.vtkActor()
self.SeedActor.SetMapper(glyphMapper)
self.SeedActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SeedActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SeedActor)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space','Add points.',self.PickCallback)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self._Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(1)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
# create a text actor
txt = vtk.vtkTextActor()
info = "Position mouse and press space. "
info += "Select seeds in this order: RSpv, RIpv, LIpv, LSpv. "
info += "Fifth seed requires --use_laa_seed command."
txt.SetInput(info)
txtprop=txt.GetTextProperty()
txtprop.SetFontFamilyToArial()
txtprop.SetFontSize(13)
txtprop.SetColor(1, 1, 1)
txt.SetDisplayPosition(0, 10)
self.vmtkRenderer.Renderer.AddActor(txt)
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._SourceSeedIds.DeepCopy(self.PickedSeedIds)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
from vmtk import vmtkscripts
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
self.tagviewer = vmtkscripts.vmtkSurfaceViewer()
self.tagviewer.Surface = self.Surface
self.tagviewer.vmtkRenderer = self.vmtkRenderer
self.tagviewer.Representation = 'edges'
self.tagviewer.Opacity = self.Opacity
self.tagviewer.Execute()
self.ContourWidget = vtk.vtkContourWidget()
self.ContourWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(self.ContourWidget.GetRepresentation())
rep.GetLinesProperty().SetColor(1, 0, 0)
rep.GetLinesProperty().SetLineWidth(4.0)
pointPlacer = vtk.vtkPolygonalSurfacePointPlacer()
pointPlacer.AddProp(self.tagviewer.Actor)
pointPlacer.GetPolys().AddItem(self.Surface)
rep.SetPointPlacer(pointPlacer)
self.Interpolator = vtk.vtkPolygonalSurfaceContourLineInterpolator()
self.Interpolator.GetPolys().AddItem(self.Surface)
rep.SetLineInterpolator(self.Interpolator)
self.InputInfo("Building loop ...\n")
self.vmtkRenderer.AddKeyBinding('space','Generate loop',self.LoopCallback)
self.vmtkRenderer.AddKeyBinding('d','Delete contour',self.DeleteContourCallback)
self.vmtkRenderer.AddKeyBinding('i','Start/stop contour drawing',self.InteractCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidget = vtk.vtkImplicitPlaneWidget()
if self.Actor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.Mesh != None:
self.MeshCutFilter = vtk.vtkCutter()
self.MeshCutFilter.SetInputData(self.Mesh)
cutPlane = vtk.vtkPlane()
self.PlaneWidget.GetPlane(cutPlane)
self.MeshCutFilter.SetCutFunction(cutPlane)
self.MeshCutFilter.Update()
self.Surface = self.MeshCutFilter.GetOutput()
self.PlaneWidget.AddObserver("StartInteractionEvent",
self.StartPlaneCallback)
self.PlaneWidget.AddObserver("EndInteractionEvent",
self.EndPlaneCallback)
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.Mesh)
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.PlaneWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidget.SetPlaceFactor(1.25)
self.PlaneWidget.DrawPlaneOn()
self.PlaneWidget.GetPlaneProperty().SetOpacity(0.1)
self.PlaneWidget.SetProp3D(self.Actor)
self.PlaneWidget.PlaceWidget()
self.PlaneWidget.SetOrigin(self.Actor.GetCenter())
self.PlaneWidget.On()
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidget = vtk.vtkImplicitPlaneWidget()
if self.Actor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.Mesh != None:
self.MeshCutFilter = vtk.vtkCutter()
self.MeshCutFilter.SetInputData(self.Mesh)
cutPlane = vtk.vtkPlane()
self.PlaneWidget.GetPlane(cutPlane)
self.MeshCutFilter.SetCutFunction(cutPlane)
self.MeshCutFilter.Update()
self.Surface = self.MeshCutFilter.GetOutput()
self.PlaneWidget.AddObserver("StartInteractionEvent",self.StartPlaneCallback)
self.PlaneWidget.AddObserver("EndInteractionEvent",self.EndPlaneCallback)
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.Mesh)
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.PlaneWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidget.SetPlaceFactor(1.25)
self.PlaneWidget.DrawPlaneOn()
self.PlaneWidget.GetPlaneProperty().SetOpacity(0.1)
self.PlaneWidget.SetProp3D(self.Actor)
self.PlaneWidget.PlaceWidget()
self.PlaneWidget.SetOrigin(self.Actor.GetCenter())
self.PlaneWidget.On()
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def surface_smooth():
'''
网格表面的平滑
'''
input_file = 'id2_model.vtp'
output_file = 'id2_mode_sm_laplace.vtp'
surfacereader = sr.vmtkSurfaceReader()
surfacereader.InputFileName = input_file
surfacereader.Execute()
# 没有平滑的网格表面
originsurface_mapper = vtk.vtkPolyDataMapper()
originsurface_mapper.SetInputData(surfacereader.Surface)
originsurface_actor = vtk.vtkActor()
originsurface_actor.SetMapper(originsurface_mapper)
color = [0, 1, 0]
originsurface_actor.GetProperty().SetColor(color)
originsurface_actor.GetProperty().SetOpacity(0.8)
surfacesmooth = ss.vmtkSurfaceSmoothing()
surfacesmooth.Surface = surfacereader.Surface
surfacesmooth.NumberOfIterations = 30
surfacesmooth.PassBand = 1.0
surfacesmooth.RelaxationFactor = 0.01
surfacesmooth.BoundarySmoothing = 1
surfacesmooth.NormalizeCoordinates = 1
surfacesmooth.Method = "laplace" # ["taubin","laplace"]
surfacesmooth.Execute()
renderer = rd.vmtkRenderer()
renderer.Initialize()
renderer.Renderer.AddActor(originsurface_actor)
surface_viewer = sv.vmtkSurfaceViewer()
surface_viewer.vmtkRenderer = renderer
surface_viewer.Surface = surfacesmooth.Surface
surface_viewer.Display = 1
surface_viewer.Color = [1.0, 0, 0]
surface_viewer.ColorMap = "cooltowarm"
surface_viewer.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.OutputFileName = output_file
surface_writer.Surface = surfacesmooth.Surface
surface_writer.Execute()
def Execute(self):
if (self.Image == None) & (self.Display == 1):
self.PrintError('Error: no Image.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
##self.PrintLog('Ctrl + left click to add seed.')
self.Picker = vtk.vtkCellPicker()
self.Picker.SetTolerance(0.005)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetX.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetX.SetPicker(self.Picker)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetY.SetPicker(self.Picker)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetZ.SetPicker(self.Picker)
self.Seeds = vtk.vtkPolyData()
self.InitializeSeeds()
self.BuildView()
self.WidgetsOff()
if not self.KeepSeeds:
self.vmtkRenderer.Renderer.RemoveActor(self.SeedActor)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
self.CroppedImage.DeepCopy(self.Image)
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
#self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.InputInfo("Press 'i' to activate interactor")
self.Display()
while (self.BoxActive == 1):
self.ExtractVOI()
self.Image = self.CroppedImage
self.Display()
else:
self.ExtractVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
self.Image = self.CroppedImage
def centerlines():
'''
显示中心线
'''
input_file = "data\\levelSet\\vessellevelset_0.vtp"
surfacereader = sr.vmtkSurfaceReader()
surfacereader.InputFileName = input_file
surfacereader.Execute()
centerline = cl.vmtkCenterlines()
centerline.Surface = surfacereader.Surface
centerline.Execute()
''' centerline_mapper = vtk.vtkPolyDataMapper()
centerline_mapper.SetInputData(centerline.Centerlines)
centerline_actor = vtk.vtkActor()
centerline_actor.SetMapper(centerline_mapper)
centerline.vmtkRenderer.Renderer.AddActor(centerline_actor)
surface_actor = centerline.vmtkRenderer.Renderer.GetActors().GetLastActor()
surface_actor.GetProperty().SetOpacity(0)
surface_actor.GetProperty().SetColor([0.1, 0.2, 0.5])
centerline.vmtkRenderer.Render()'''
surface_mapper = vtk.vtkPolyDataMapper()
surface_mapper.SetInputData(surfacereader.Surface)
surface_actor = vtk.vtkActor()
surface_actor.SetMapper(surface_mapper)
surface_actor.GetProperty().SetOpacity(0.3)
color = [0.5, 0.6, 0.7]
surface_actor.GetProperty().SetColor(color)
renderer = rd.vmtkRenderer()
renderer.Initialize()
renderer.Renderer.AddActor(surface_actor)
surfaceviewer = sv.vmtkSurfaceViewer()
surfaceviewer.Surface = centerline.Centerlines
# surfaceviwer.Surface = centerline.VoronoiDiagram
surfaceviewer.Color = [0.5, 0.6, 0.7]
surfaceviewer.ColorMap = "rainbow" # "rainbow","blackbody","cooltowarm","grayscale"
surfaceviewer.vmtkRenderer = renderer # centerline中vmtkrenderer在调用结束后，就回收内存了
surfaceviewer.ArrayName = "MaximumInscribedSphereRadius"
surfaceviewer.Execute()
def Execute(self):
if (self.Image == None) & (self.Display == 1):
self.PrintError('Error: no Image.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
##self.PrintLog('Ctrl + left click to add seed.')
self.Picker = vtk.vtkCellPicker()
self.Picker.SetTolerance(0.005)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetX.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetX.SetPicker(self.Picker)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetY.SetPicker(self.Picker)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ.AddObserver("StartInteractionEvent", self.AddSeed)
self.PlaneWidgetZ.SetPicker(self.Picker)
self.Seeds = vtk.vtkPolyData()
self.InitializeSeeds()
self.BuildView()
self.WidgetsOff()
if not self.KeepSeeds:
self.vmtkRenderer.Renderer.RemoveActor(self.SeedActor)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space','Add points.',self.PickCallback)
self.InputInfo('Please position the mouse and press space to add target points, \'u\' to undo\n')
# this is necessary to set up the async watch loop.
any = 0
while any == 0:
self.vmtkRenderer.Render()
try:
any = self.CurrentPickedPolyData
except AttributeError:
any = None
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if self.Actor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.ScalarBarActor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.ScalarBarActor)
if self.Mesh != None:
self.InitialMesh = self.Mesh
self.DisplayMesh = self.Mesh
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.DisplayMesh)
array = None
if (self.ArrayName != ''):
if self.DisplayCellData == 0:
self.Mesh.GetPointData().SetActiveScalars(self.ArrayName)
array = self.Mesh.GetPointData().GetScalars()
else:
self.Mesh.GetCellData().SetActiveScalars(self.ArrayName)
array = self.Mesh.GetCellData().GetScalars()
mapper.SetScalarModeToUseCellData()
if (array != None):
if (self.ScalarRange[1] > self.ScalarRange[0]):
mapper.SetScalarRange(self.ScalarRange)
else:
mapper.SetScalarRange(array.GetRange(0))
if (self.Grayscale == 1):
lut = vtk.vtkLookupTable()
lut.SetValueRange(0.0,1.0)
lut.SetSaturationRange(0.0,0.0)
mapper.SetLookupTable(lut)
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
if (self.Color[0] >= 0.0):
self.Actor.GetProperty().SetColor(self.Color)
if (self.FlatInterpolation == 1):
self.Actor.GetProperty().SetInterpolationToFlat()
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if (self.Legend == 1) & (self.Actor != None):
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
## self.ScalarBarActor.GetLabelTextProperty().SetColor(0.0,0.0,0.0)
self.ScalarBarActor.SetLabelFormat('%.2f')
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
#self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.vmtkRenderer.AddKeyBinding('c','Clip.',self.ClipCallback)
self.vmtkRenderer.AddKeyBinding('e','Extract.',self.ExtractCallback)
self.vmtkRenderer.AddKeyBinding('n','Show clipped area.',self.NCallback)
self.vmtkRenderer.AddKeyBinding('d','Switch clipped/unclipped area.',self.DCallback)
self.vmtkRenderer.AddKeyBinding('t','Redo.',self.TCallback)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.PlaneWidget = vtk.vtkImplicitPlaneWidget()
self.PlaneWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidget.SetPlaceFactor(1.25)
self.PlaneWidget.DrawPlaneOff()
self.PlaneWidget.SetProp3D(self.Actor)
self.PlaneWidget.PlaceWidget()
#Work around bug/strange behaviour in vtk
self.PlaneWidget.SetOrigin(self.Actor.GetCenter())
if (self.Display == 1):
self.vmtkRenderer.Render()
self.Mesh = self.InitialMesh
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1)
glyphs.SetInputData(self.Spheres)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToScaleByScalar()
glyphs.SetScaleFactor(1.)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
glyphMapper.ScalarVisibilityOff()
self.SpheresActor = vtk.vtkActor()
self.SpheresActor.SetMapper(glyphMapper)
self.SpheresActor.GetProperty().SetColor(1.0, 0.0, 0.0)
self.SpheresActor.GetProperty().SetOpacity(self.Opacity)
self.SpheresActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SpheresActor)
examineGlyphs = vtk.vtkGlyph3D()
examineGlyphSource = vtk.vtkSphereSource()
examineGlyphSource.SetRadius(1)
examineGlyphs.SetInputData(self.ExamineSpheres)
examineGlyphs.SetSourceConnection(examineGlyphSource.GetOutputPort())
examineGlyphs.SetScaleModeToScaleByScalar()
examineGlyphs.SetScaleFactor(1.)
examineGlyphMapper = vtk.vtkPolyDataMapper()
examineGlyphMapper.SetInputConnection(examineGlyphs.GetOutputPort())
examineGlyphMapper.ScalarVisibilityOff()
self.ExamineSpheresActor = vtk.vtkActor()
self.ExamineSpheresActor.SetMapper(examineGlyphMapper)
self.ExamineSpheresActor.GetProperty().SetColor(0.0, 1.0, 0.0)
self.ExamineSpheresActor.GetProperty().SetOpacity(self.Opacity)
self.ExamineSpheresActor.PickableOff()
self.ExamineSpheresActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ExamineSpheresActor)
#self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('u', 'undo', self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('plus', 'Increase sphere radius',
self.PlusCallback)
self.vmtkRenderer.AddKeyBinding('minus', 'Decrease sphere radius',
self.MinusCallback)
self.vmtkRenderer.AddKeyBinding('n', 'Show next sphere',
self.NextSphereCallback)
self.vmtkRenderer.AddKeyBinding('v', 'Show previous sphere',
self.PreviousSphereCallback)
self.vmtkRenderer.AddKeyBinding('d', 'Display ', self.DisplayCallback)
self.vmtkRenderer.AddKeyBinding(
'w', 'Switch beetween examien and interact mode ',
self.ExmienModeCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Pick sphere',
self.PickCallback)
self.SurfaceMapper = vtk.vtkPolyDataMapper()
self.SurfaceMapper.SetInputData(self.Surface)
self.SurfaceMapper.SetScalarVisibility(self.DisplayArray)
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(self.SurfaceMapper)
surfaceActor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.SurfaceMapper.GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
self.ScalarBarActor.SetLabelFormat('%.2f')
self.ScalarBarActor.SetTitle('distances')
self.ScalarBarActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
self.SphereWidget = vtk.vtkSphereWidget()
self.SphereWidget.TranslationOff()
self.SphereWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.SphereWidget.AddObserver("InteractionEvent", self.SphereCallback)
self.ExamineText = vtk.vtkTextActor()
self.ExamineText.SetInput("Examine Mode")
self.ExamineText.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedViewport()
self.ExamineText.SetPosition(0.05, 0.95)
self.ExamineText.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor2D(self.ExamineText)
self.InputInfo(
'Please position the mouse and press space to add spheres, \'u\' to undo\n'
)
any = 0
while any == 0:
self.InitializeSpheres()
self.vmtkRenderer.Render()
any = (self.Spheres.GetNumberOfPoints() > 1)
self.Surface = self.ComputeArray()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self._Surface == None):
self.PrintError(
'vmtkOpenProfilesSeedSelector Error: Surface not set.')
return
if (self._SeedIds == None):
self.PrintError(
'vmtkOpenProfilesSeedSelector Error: SeedIds not set.')
return
self._SourceSeedIds.Initialize()
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
seedPoints = vtk.vtkPoints()
for i in range(self._SeedIds.GetNumberOfIds()):
seedPoints.InsertNextPoint(
self._Surface.GetPoint(self._SeedIds.GetId(i)))
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()
seedIdString = self.InputText(
"Please input list of inlet profile ids: ")
separator = ' '
if seedIdString.find(',') != -1:
separator = ','
seedIdList = seedIdString.split(separator)
for seedIdString in seedIdList:
self._SourceSeedIds.InsertNextId(int(seedIdString.strip()))
seedIdString = self.InputText(
"Please input list of outlet profile ids (leave empty for all available profiles): "
)
if seedIdString.strip() == '':
self.InputInfo("Selected outlets: ")
for i in range(seedPoints.GetNumberOfPoints()):
if self._SourceSeedIds.IsId(i) == -1:
self._TargetSeedIds.InsertNextId(i)
self.InputInfo("%d " % i)
self.InputInfo("\n")
else:
seedIdList = seedIdString.split(separator)
for seedIdString in seedIdList:
self._TargetSeedIds.InsertNextId(int(seedIdString.strip()))
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self.InputTraces == None):
self.PrintError('Error: no Traces.')
if (self.TimeStep == None):
self.PrintError('Error: no TimeStep.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
surfaceViewer = vmtksurfaceviewer.vmtkSurfaceViewer()
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.Surface = self.InputTraces
surfaceViewer.ArrayName = self.ArrayName
surfaceViewer.ColorMap = self.ColorMap
surfaceViewer.NumberOfColors = self.NumberOfColors
surfaceViewer.Execute()
if self.ColorMap == 'grayscale':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
lut.SetValueRange(0.0,1.0)
lut.SetSaturationRange(0.0,0.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'rainbow':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetHueRange(0.666667,0.0)
lut.SetSaturationRange(0.75,0.75)
lut.SetValueRange(1.0,1.0)
lut.SetAlphaRange(1.0,1.0)
lut.SetNumberOfColors(self.NumberOfColors)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'blackbody':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToRGB()
colorTransferFunction.AddRGBPoint(0,0.0,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.4,0.901961,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.8,0.901961,0.901961,0.0)
colorTransferFunction.AddRGBPoint(1.0,1.0,1.0,1.0)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'cooltowarm':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToDiverging()
colorTransferFunction.AddRGBPoint(0,0.231373,0.298039,0.752941)
colorTransferFunction.AddRGBPoint(0.5,0.865003,0.865003,0.865003)
colorTransferFunction.AddRGBPoint(1.0,0.705882,0.0156863,0.14902)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if (self.Legend == 1):
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(surfaceViewer.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
self.ScalarBarActor.SetWidth(0.1)
self.ScalarBarActor.SetHeight(0.6)
self.ScalarBarActor.SetNumberOfLabels(4)
self.ScalarBarActor.SetTitle(self.ArrayName+" ["+self.ArrayUnit+"]")
self.ScalarBarActor.SetLabelFormat('%.2f')
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
self.Traces = vtk.vtkPolyData()
self.Traces.DeepCopy(self.InputTraces)
self.Traces.GetPointData().SetActiveScalars("IntegrationTime")
timeRange = self.Traces.GetPointData().GetScalars().GetRange(0)
currentCycle = 0
minTime = self.MinTime
currentTime = self.TimeStep
maxTime = self.MaxTime
if (self.ArrayMax == None and self.ArrayName == "Velocity"):
self.ArrayMax = round(self.Traces.GetPointData().GetArray('Speed').GetRange()[1],0)
if self.Method is 'particles':
particleTime = minTime
imageNumber = 0
while particleTime <= maxTime:
contour = vtk.vtkContourFilter()
contour.SetInputData(self.Traces)
i = 0
while i <= currentCycle:
time = minTime + currentTime + (maxTime - minTime) * i
if time < timeRange[0] or time > timeRange[1]:
pass
else:
contour.SetValue(i,time)
i+=1
contour.Update()
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.Actor.GetProperty().SetPointSize(self.PointSize)
vtk.vtkPolyDataMapper.SafeDownCast(surfaceViewer.Actor.GetMapper()).SetInputConnection(contour.GetOutputPort())
surfaceViewer.Actor.GetMapper().GetLookupTable().SetVectorModeToMagnitude()
surfaceViewer.Actor.GetMapper().SetScalarModeToUsePointFieldData()
surfaceViewer.Actor.GetMapper().SelectColorArray(self.ArrayName)
surfaceViewer.Actor.GetMapper().SetScalarRange([0.0,self.ArrayMax])
surfaceViewer.vmtkRenderer.RenderWindow.Render()
if self.WithScreenshots:
self.Screenshot(surfaceViewer,imageNumber)
particleTime+=self.TimeStep
currentTime+=self.TimeStep
imageNumber+=1
elif self.Method is 'streaklines':
particleTime = minTime
imageNumber = 0
while particleTime <= maxTime:
clip1 = vtk.vtkClipPolyData()
clip1.SetInputData(self.Traces)
clip1.GenerateClipScalarsOff()
clip1.InsideOutOn()
clip2 = vtk.vtkClipPolyData()
clip2.SetInputConnection(clip1.GetOutputPort())
clip2.GenerateClipScalarsOff()
clip2.InsideOutOff()
cyclesPerRange = (int((timeRange[1]-timeRange[0])/(maxTime-minTime))) + 1
cycle = currentCycle % cyclesPerRange
time = minTime + currentTime + (maxTime - minTime) * cycle
streakLineTimeLength = self.StreakLineTimeLength
clip1.SetValue(time)
clip2.SetValue(time - streakLineTimeLength)
clip2.Update()
surfaceViewer.Actor.GetProperty().SetLineWidth(self.LineWidth)
vtk.vtkPolyDataMapper.SafeDownCast(surfaceViewer.Actor.GetMapper()).SetInputConnection(clip2.GetOutputPort())
surfaceViewer.Actor.GetMapper().GetLookupTable().SetVectorModeToMagnitude()
surfaceViewer.Actor.GetMapper().SetScalarModeToUsePointFieldData()
surfaceViewer.Actor.GetMapper().SelectColorArray(self.ArrayName)
surfaceViewer.Actor.GetMapper().SetScalarRange([0.0,self.ArrayMax])
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.vmtkRenderer.RenderWindow.Render()
if self.WithScreenshots:
self.Screenshot(surfaceViewer,imageNumber)
particleTime+=self.TimeStep
currentTime+=self.TimeStep
imageNumber+=1
else:
self.PrintError('Error: pathlineanimator method not supported.')
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1)
glyphs.SetInputData(self.Spheres)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToScaleByScalar()
glyphs.SetScaleFactor(1.)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
glyphMapper.ScalarVisibilityOff()
self.SpheresActor = vtk.vtkActor()
self.SpheresActor.SetMapper(glyphMapper)
self.SpheresActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SpheresActor.GetProperty().SetOpacity(self.Opacity)
self.SpheresActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SpheresActor)
examineGlyphs = vtk.vtkGlyph3D()
examineGlyphSource = vtk.vtkSphereSource()
examineGlyphSource.SetRadius(1)
examineGlyphs.SetInputData(self.ExamineSpheres)
examineGlyphs.SetSourceConnection(examineGlyphSource.GetOutputPort())
examineGlyphs.SetScaleModeToScaleByScalar()
examineGlyphs.SetScaleFactor(1.)
examineGlyphMapper = vtk.vtkPolyDataMapper()
examineGlyphMapper.SetInputConnection(examineGlyphs.GetOutputPort())
examineGlyphMapper.ScalarVisibilityOff()
self.ExamineSpheresActor = vtk.vtkActor()
self.ExamineSpheresActor.SetMapper(examineGlyphMapper)
self.ExamineSpheresActor.GetProperty().SetColor(0.0,1.0,0.0)
self.ExamineSpheresActor.GetProperty().SetOpacity(self.Opacity)
self.ExamineSpheresActor.PickableOff()
self.ExamineSpheresActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ExamineSpheresActor)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space','Place picks.',self.PickCallback)
self.vmtkRenderer.AddKeyBinding('+','Increase sphere radius.',self.IncreaseSphereRadiusCallback)
self.vmtkRenderer.AddKeyBinding('-','Decrease sphere radius.',self.DecreaseSphereRadiusCallback)
self.vmtkRenderer.AddKeyBinding('n','Skip to next sphere.',self.NextCallback)
self.vmtkRenderer.AddKeyBinding('v','Skip to previous sphere.',self.PreviousCallback)
self.vmtkRenderer.AddKeyBinding('d','Show distances graph.',self.DistancesCallback)
self.vmtkRenderer.AddKeyBinding('x','Examine mode.',self.ExamineCallback)
#self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.SurfaceMapper = vtk.vtkPolyDataMapper()
self.SurfaceMapper.SetInputData(self.Surface)
self.SurfaceMapper.SetScalarVisibility(self.DisplayArray)
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(self.SurfaceMapper)
surfaceActor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.SurfaceMapper.GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
self.ScalarBarActor.SetLabelFormat('%.2f')
self.ScalarBarActor.SetTitle('distances')
self.ScalarBarActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
self.SphereWidget = vtk.vtkSphereWidget()
self.SphereWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.SphereWidget.AddObserver("InteractionEvent", self.SphereCallback)
self.ExamineText = vtk.vtkTextActor()
self.ExamineText.SetInput("Examine Mode")
self.ExamineText.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
self.ExamineText.SetPosition(0.05,0.95)
self.ExamineText.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor2D(self.ExamineText)
self.InputInfo('Please position the mouse and press space to add spheres, \'u\' to undo\n')
any = 0
while any == 0:
self.InitializeSpheres()
self.vmtkRenderer.Render()
any = (self.Spheres.GetNumberOfPoints()>1)
self.InputInfo('Please position the mouse and press space to add spheres, \'u\' to undo\nInsert at least 2 spheres.')
self.Surface = self.ComputeArray()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildViewWithTag(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Actor:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.ScalarBarActor:
self.vmtkRenderer.Renderer.RemoveActor(self.ScalarBarActor)
if self.Surface.GetPointData().GetArray(self.RegionTagArrayName) == None and self.Surface.GetCellData().GetArray(self.RegionTagArrayName) == None:
self.PrintError('Error: no regiontagarray with name specified')
elif self.Surface.GetPointData().GetArray(self.RegionTagArrayName) != None:
regionTagArray = self.Surface.GetPointData().GetArray(self.RegionTagArrayName)
for j in range (self.Surface.GetNumberOfPoints()):
if regionTagArray.GetTuple1(j) not in self.TagSet:
self.TagSet.append(regionTagArray.GetTuple1(j))
self.TagSet.sort()
self.NumberOfRegions = len(self.TagSet)
tagSetCopy = list(self.TagSet)
labelPoints = vtk.vtkPoints()
labelPoints.SetNumberOfPoints(len(self.TagSet))
point = [0.0,0.0,0.0]
for j in range (self.Surface.GetNumberOfPoints()):
item = regionTagArray.GetTuple1(j)
if item in tagSetCopy:
self.Surface.GetPoint(j, point)
labelPoints.SetPoint(self.TagSet.index(item), point)
tagSetCopy.remove(item)
self.Surface.GetPointData().SetActiveScalars(self.RegionTagArrayName)
elif self.Surface.GetCellData().GetArray(self.RegionTagArrayName) != None:
regionTagArray = self.Surface.GetCellData().GetArray(self.RegionTagArrayName)
for j in range (self.Surface.GetNumberOfCells()):
if regionTagArray.GetTuple1(j) not in self.TagSet:
self.TagSet.append(regionTagArray.GetTuple1(j))
self.TagSet.sort()
self.NumberOfRegions = len(self.TagSet)
tagSetCopy = list(self.TagSet)
labelPoints = vtk.vtkPoints()
labelPoints.SetNumberOfPoints(len(self.TagSet))
point = [0.0,0.0,0.0]
cellCenters = vtk.vtkCellCenters()
cellCenters.SetInputData(self.Surface)
cellCenters.Update()
regionTagArrayCenters = cellCenters.GetOutput().GetPointData().GetArray(self.RegionTagArrayName)
for j in range (cellCenters.GetOutput().GetNumberOfPoints()):
item = regionTagArrayCenters.GetTuple1(j)
if item in tagSetCopy:
cellCenters.GetOutput().GetPoint(j, point)
labelPoints.SetPoint(self.TagSet.index(item), point)
tagSetCopy.remove(item)
self.Surface.GetCellData().SetActiveScalars(self.RegionTagArrayName)
labelPolyData = vtk.vtkPolyData()
labelPolyData.SetPoints(labelPoints)
labelArray = vtk.vtkIntArray()
labelArray.SetNumberOfComponents(1)
labelArray.SetNumberOfTuples(self.NumberOfRegions)
labelArray.SetName('label')
labelArray.FillComponent(0,0)
labelPolyData.GetPointData().AddArray(labelArray)
for item in self.TagSet:
labelArray.SetTuple1(self.TagSet.index(item), item)
labelPolyData.GetPointData().SetActiveScalars('label')
labelsMapper = vtk.vtkLabeledDataMapper()
labelsMapper.SetInputData(labelPolyData)
labelsMapper.SetLabelModeToLabelScalars()
labelsMapper.GetLabelTextProperty().SetColor(1, 1, 1)
labelsMapper.GetLabelTextProperty().SetFontSize(14)
self.labelsActor = vtk.vtkActor2D()
self.labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(self.labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOn()
surfaceMapper.SetScalarRange(self.TagSet[0], self.TagSet[self.NumberOfRegions-1])
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(surfaceMapper)
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.Actor.GetProperty().SetLineWidth(self.LineWidth)
if self.FlatInterpolation:
self.Actor.GetProperty().SetInterpolationToFlat()
self.SetSurfaceRepresentation(self.Representation)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.vmtkRenderer.AddKeyBinding('w','Change surface representation.',self.RepresentationCallback)
if self.Legend and self.Actor:
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
## self.ScalarBarActor.GetLabelTextProperty().SetColor(0.0,0.0,0.0)
self.ScalarBarActor.SetLabelFormat('%.2f')
self.ScalarBarActor.SetTitle(self.LegendTitle)
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
if self.Display:
self.vmtkRenderer.Render()
## self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
## self.vmtkRenderer.Renderer.RemoveActor(self.ScalarBarActor)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Actor:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.ScalarBarActor:
self.vmtkRenderer.Renderer.RemoveActor(self.ScalarBarActor)
if self.Mesh:
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.Mesh)
if self.ArrayName:
self.Mesh.GetPointData().SetActiveScalars(self.ArrayName)
array = self.Mesh.GetPointData().GetScalars()
if self.ScalarRange[1] > self.ScalarRange[0]:
mapper.SetScalarRange(self.ScalarRange)
else:
mapper.SetScalarRange(array.GetRange(0))
if self.ColorMap == 'grayscale':
lut = mapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
lut.SetValueRange(0.0,1.0)
lut.SetSaturationRange(0.0,0.0)
lut.Build()
mapper.SetLookupTable(lut)
if self.ColorMap == 'rainbow':
lut = mapper.GetLookupTable()
lut.SetHueRange(0.666667,0.0)
lut.SetSaturationRange(0.75,0.75)
lut.SetValueRange(1.0,1.0)
lut.SetAlphaRange(1.0,1.0)
lut.SetNumberOfColors(self.NumberOfColors)
lut.Build()
mapper.SetLookupTable(lut)
if self.ColorMap == 'blackbody':
lut = mapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToRGB()
colorTransferFunction.AddRGBPoint(0,0.0,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.4,0.901961,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.8,0.901961,0.901961,0.0)
colorTransferFunction.AddRGBPoint(1.0,1.0,1.0,1.0)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
mapper.SetLookupTable(lut)
if self.ColorMap == 'cooltowarm':
lut = mapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToDiverging()
colorTransferFunction.AddRGBPoint(0,0.231373,0.298039,0.752941)
colorTransferFunction.AddRGBPoint(0.5,0.865003,0.865003,0.865003)
colorTransferFunction.AddRGBPoint(1.0,0.705882,0.0156863,0.14902)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
mapper.SetLookupTable(lut)
else:
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
if (self.Color[0] >= 0.0):
self.Actor.GetProperty().SetColor(self.Color)
if self.FlatInterpolation:
self.Actor.GetProperty().SetInterpolationToFlat()
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.vmtkRenderer.AddKeyBinding('w','Change surface representation.',self.RepresentationCallback)
if self.Legend and self.Actor:
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
## self.ScalarBarActor.GetLabelTextProperty().SetColor(0.0,0.0,0.0)
self.ScalarBarActor.SetLabelFormat('%.2f')
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
if self.Display:
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if (self.CenterlineNormals) and (self.Centerlines == None):
self.PrintError('Error: No input centerlines.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
if (self.CenterlineNormals):
self.SeedSelector.SetOutlets = 1
self.SeedSelector.SetSurface(self.Surface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
mainBodySeedIds = self.SeedSelector.GetMainBodySeedIds()
mainBodySeedId = mainBodySeedIds.GetId(0)
mainBodyPoint = self.Surface.GetPoint(mainBodySeedId)
clipSeedIds = self.SeedSelector.GetSourceSeedIds()
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
clippedSurface = surfaceTriangulator.GetOutput()
n_seeds = clipSeedIds.GetNumberOfIds() # get the number of inlets
if (self.CenterlineNormals):
targetSeedIds = self.SeedSelector.GetTargetSeedIds()
for i in range(targetSeedIds.GetNumberOfIds()):
clipSeedIds.InsertNextId(targetSeedIds.GetId(i))
locator_ctr = vtk.vtkPointLocator()
locator_ctr.SetDataSet(self.Centerlines)
locator_ctr.BuildLocator()
for i in range(clipSeedIds.GetNumberOfIds()):
seedId = clipSeedIds.GetId(i)
seedPoint = self.Surface.GetPoint(seedId)
# the frenet tangent must be inverted as it is directed outwards
# the seam filter requires an inward facing normal
if (self.CenterlineNormals):
centerlinePointId = locator_ctr.FindClosestPoint(seedPoint)
origin = self.Centerlines.GetPoint(centerlinePointId)
normal = self.Centerlines.GetPointData().GetArray(
self.FrenetTangentArrayName).GetTuple(centerlinePointId)
if (i >= n_seeds):
# invert outward facing normals
normal = tuple(-p for p in normal)
else:
locator = vtk.vtkPointLocator()
locator.SetDataSet(clippedSurface)
locator.BuildLocator()
seedPointId = locator.FindClosestPoint(seedPoint)
planeEstimator = vtkvmtk.vtkvmtkPolyDataNormalPlaneEstimator()
planeEstimator.SetInputData(clippedSurface)
planeEstimator.SetOriginPointId(seedPointId)
planeEstimator.Update()
origin = planeEstimator.GetOrigin()
normal = planeEstimator.GetNormal()
plane = vtk.vtkPlane()
plane.SetOrigin(origin)
plane.SetNormal(normal)
seamFilter = vtkvmtk.vtkvmtkTopologicalSeamFilter()
seamFilter.SetInputData(clippedSurface)
seamFilter.SetClosestPoint(seedPoint)
seamFilter.SetSeamScalarsArrayName("SeamScalars")
seamFilter.SetSeamFunction(plane)
clipper = vtk.vtkClipPolyData()
clipper.SetInputConnection(seamFilter.GetOutputPort())
clipper.GenerateClipScalarsOff()
clipper.GenerateClippedOutputOn()
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInputConnection(clipper.GetOutputPort())
connectivity.SetExtractionModeToClosestPointRegion()
connectivity.SetClosestPoint(mainBodyPoint)
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputConnection(connectivity.GetOutputPort())
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(
surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
#clippedSurface = vtk.vtkPolyData()
#clippedSurface.DeepCopy(surfaceTriangulator.GetOutput())
clippedSurface = surfaceTriangulator.GetOutput()
self.Surface = clippedSurface
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Volume:
self.vmtkRenderer.Renderer.RemoveVolume(self.Volume)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
scalarRange = [0.0, 0.0]
if self.WindowLevel[0] > 0.0:
scalarRange = [self.WindowLevel[1] - self.WindowLevel[0] / 2.0,
self.WindowLevel[1] + self.WindowLevel[0] / 2.0]
else:
scalarRange = self.Image.GetScalarRange()
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(scalarRange[0], 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(scalarRange[1], 1.0, 1.0, 1.0)
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToMaximumIntensity()
if self.AutoSampleDistance:
volumeMapper.AutoAdjustSampleDistancesOn()
else:
volumeMapper.SetSampleDistance(self.SampleDistance)
opacityFunction = vtk.vtkPiecewiseFunction()
imageRange = self.Image.GetScalarRange()
if self.Opacity is not None:
opacityFunction.AddPoint(imageRange[0], 0)
opacityFunction.AddPoint(scalarRange[0], self.Opacity[0])
opacityFunction.AddPoint(scalarRange[0], self.Opacity[1])
opacityFunction.AddPoint(imageRange[1], 1)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetColor(colorTransferFunction)
if self.Opacity is not None:
volumeProperty.SetScalarOpacity(opacityFunction)
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface to for Execute().')
self.Clipper = vtk.vtkClipPolyData()
self.Clipper.SetInputData(self.Surface)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.SetInsideOut(self.InsideOut)
if self.Interactive:
if self.WidgetType == "box":
self.ClipFunction = vtk.vtkPlanes()
elif self.WidgetType == "sphere":
self.ClipFunction = vtk.vtkSphere()
self.Clipper.SetClipFunction(self.ClipFunction)
self.Cutter = vtk.vtkCutter()
self.Cutter.SetInputData(self.Surface)
self.Cutter.SetCutFunction(self.ClipFunction)
self.ClippedSurface = vtk.vtkPolyData()
self.CutLines = vtk.vtkPolyData()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.Surface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.WidgetType == "box":
self.ClipWidget = vtk.vtkBoxWidget()
self.ClipWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetFaceProperty().SetOpacity(0.25)
elif self.WidgetType == "sphere":
self.ClipWidget = vtk.vtkSphereWidget()
self.ClipWidget.GetSphereProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetSphereProperty().SetOpacity(0.25)
self.ClipWidget.GetSelectedSphereProperty().SetColor(0.6,0.0,0.0)
self.ClipWidget.GetSelectedSphereProperty().SetOpacity(0.75)
self.ClipWidget.SetRepresentationToSurface()
self.ClipWidget.SetPhiResolution(20)
self.ClipWidget.SetThetaResolution(20)
self.ClipWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
# Try AutoClip here
if not self.ClipsIn == None:
self.AutoClip()
self.vmtkRenderer.AddKeyBinding('space','Clip.',self.ClipCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Transform = vtk.vtkTransform()
if self.WidgetType == "box":
self.ClipWidget.GetTransform(self.Transform)
# Add items from ClipCollection to MultiBlockDataSet
self.ClipsOut = vtk.vtkMultiBlockDataSet()
ClipTotal = self.ClipCollection.GetNumberOfItems()
BlockNum = 0
self.ClipCollection.InitTraversal()
while BlockNum < ClipTotal:
blockin = vtk.vtkPolyData()
blockin.DeepCopy(self.ClipCollection.GetNextItem())
self.PrintLog('The bounds of blockin are: ' + str(blockin.GetBounds()))
self.ClipsOut.SetBlock(BlockNum, blockin)
BlockNum += 1
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
else:
self.Surface.GetPointData().SetActiveScalars(self.ClipArrayName)
self.Clipper.GenerateClipScalarsOff()
self.Clipper.SetValue(self.ClipValue)
self.Clipper.Update()
self.Cutter = vtk.vtkContourFilter()
self.Cutter.SetInputData(self.Surface)
self.Cutter.SetValue(0,self.ClipValue)
self.Cutter.Update()
self.Surface = self.Clipper.GetOutput()
self.ClippedSurface = self.Clipper.GetClippedOutput()
self.CutLines = self.Cutter.GetOutput()
if self.CleanOutput == 1:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.Surface)
cleaner.Update()
self.Surface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.ClippedSurface)
cleaner.Update()
self.ClippedSurface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.CutLines)
cleaner.Update()
stripper = vtk.vtkStripper()
stripper.SetInputConnection(cleaner.GetOutputPort())
stripper.Update()
self.CutLines = stripper.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 BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Volume:
self.vmtkRenderer.Renderer.RemoveVolume(self.Volume)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
scalarRange = [0.0, 0.0]
if self.WindowLevel[0] > 0.0:
scalarRange = [
self.WindowLevel[1] - self.WindowLevel[0] / 2.0,
self.WindowLevel[1] + self.WindowLevel[0] / 2.0
]
else:
scalarRange = self.Image.GetScalarRange()
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(scalarRange[0], 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(scalarRange[1], 1.0, 1.0, 1.0)
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToMaximumIntensity()
if self.AutoSampleDistance:
volumeMapper.AutoAdjustSampleDistancesOn()
else:
volumeMapper.SetSampleDistance(self.SampleDistance)
opacityFunction = vtk.vtkPiecewiseFunction()
imageRange = self.Image.GetScalarRange()
if self.Opacity is not None:
opacityFunction.AddPoint(imageRange[0], 0)
opacityFunction.AddPoint(scalarRange[0], self.Opacity[0])
opacityFunction.AddPoint(scalarRange[0], self.Opacity[1])
opacityFunction.AddPoint(imageRange[1], 1)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetColor(colorTransferFunction)
if self.Opacity is not None:
volumeProperty.SetScalarOpacity(opacityFunction)
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1)
glyphs.SetInputData(self.SeedPoints)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToDataScalingOff()
glyphs.SetScaleFactor(self.Surface.GetLength()*0.01)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
glyphMapper.ScalarVisibilityOff()
self.PointActor = vtk.vtkActor()
self.PointActor.SetMapper(glyphMapper)
self.PointActor.GetProperty().SetColor(1.0,0.0,0.0)
self.PointActor.GetProperty().SetOpacity(self.Opacity)
self.PointActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.PointActor)
examineGlyphs = vtk.vtkGlyph3D()
examineGlyphSource = vtk.vtkSphereSource()
examineGlyphSource.SetRadius(1)
examineGlyphs.SetInputData(self.ExamineSpheres)
examineGlyphs.SetSourceConnection(examineGlyphSource.GetOutputPort())
examineGlyphs.SetScaleModeToScaleByScalar()
examineGlyphs.SetScaleFactor(1.)
examineGlyphMapper = vtk.vtkPolyDataMapper()
examineGlyphMapper.SetInputConnection(examineGlyphs.GetOutputPort())
examineGlyphMapper.ScalarVisibilityOff()
self.ExamineSpheresActor = vtk.vtkActor()
self.ExamineSpheresActor.SetMapper(examineGlyphMapper)
self.ExamineSpheresActor.GetProperty().SetColor(0.0,1.0,0.0)
self.ExamineSpheresActor.GetProperty().SetOpacity(self.Opacity)
self.ExamineSpheresActor.PickableOff()
self.ExamineSpheresActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ExamineSpheresActor)
#self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space','Pick points.',self.SpaceCallback)
self.vmtkRenderer.AddKeyBinding('w','Examine mode.',self.ExamineCallback)
self.vmtkRenderer.AddKeyBinding('d','Display Distance.',self.DisplayDistanceCallback)
self.vmtkRenderer.AddKeyBinding('a','Add.',self.AddCallback)
self.SurfaceMapper = vtk.vtkPolyDataMapper()
self.SurfaceMapper.SetInputData(self.Surface)
self.SurfaceMapper.SetScalarVisibility(self.DisplayArray)
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(self.SurfaceMapper)
surfaceActor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(self.SurfaceMapper.GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
self.ScalarBarActor.SetLabelFormat('%.2f')
self.ScalarBarActor.SetTitle('distances')
self.ScalarBarActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
self.ExamineText = vtk.vtkTextActor()
self.ExamineText.SetInput("Examine Mode")
self.ExamineText.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
self.ExamineText.SetPosition(0.05,0.95)
self.ExamineText.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor2D(self.ExamineText)
self.InputInfo('Please position the mouse and press space to add points, \'u\' to undo\n')
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.SeedIds.GetNumberOfIds()
self.Surface = self.ComputeDistances()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Centerlines:
self.PrintError('Error: No input centerlines.')
return
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.CellDataArrayName:
cellCenters = vtk.vtkCellCenters()
cellCenters.SetInputData(self.Centerlines)
cellCenters.Update()
cellCenters.GetOutput().GetPointData().SetActiveScalars(self.CellDataArrayName)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputConnection(cellCenters.GetOutputPort())
labelsMapper.SetLabelModeToLabelScalars()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
centerlineMapper = vtk.vtkPolyDataMapper()
centerlineMapper.SetInputData(self.Centerlines)
if self.CellDataArrayName and not self.PointDataArrayName:
centerlineMapper.ScalarVisibilityOn()
centerlineMapper.SetScalarModeToUseCellData()
self.Centerlines.GetCellData().SetActiveScalars(self.CellDataArrayName)
centerlineMapper.SetScalarRange(self.Centerlines.GetCellData().GetScalars().GetRange(0))
elif self.PointDataArrayName:
centerlineMapper.ScalarVisibilityOn()
centerlineMapper.SetScalarModeToUsePointData()
self.Centerlines.GetPointData().SetActiveScalars(self.PointDataArrayName)
centerlineMapper.SetScalarRange(self.Centerlines.GetPointData().GetScalars().GetRange(0))
else:
centerlineMapper.ScalarVisibilityOff()
if self.ColorMap == 'grayscale':
lut = centerlineMapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
lut.SetValueRange(0.0,1.0)
lut.SetSaturationRange(0.0,0.0)
lut.Build()
centerlineMapper.SetLookupTable(lut)
if self.ColorMap == 'rainbow':
lut = centerlineMapper.GetLookupTable()
lut.SetHueRange(0.666667,0.0)
lut.SetSaturationRange(0.75,0.75)
lut.SetValueRange(1.0,1.0)
lut.SetAlphaRange(1.0,1.0)
lut.SetNumberOfColors(self.NumberOfColors)
lut.Build()
centerlineMapper.SetLookupTable(lut)
if self.ColorMap == 'blackbody':
lut = centerlineMapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToRGB()
colorTransferFunction.AddRGBPoint(0,0.0,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.4,0.901961,0.0,0.0)
colorTransferFunction.AddRGBPoint(0.8,0.901961,0.901961,0.0)
colorTransferFunction.AddRGBPoint(1.0,1.0,1.0,1.0)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
centerlineMapper.SetLookupTable(lut)
if self.ColorMap == 'cooltowarm':
lut = centerlineMapper.GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToDiverging()
colorTransferFunction.AddRGBPoint(0,0.231373,0.298039,0.752941)
colorTransferFunction.AddRGBPoint(0.5,0.865003,0.865003,0.865003)
colorTransferFunction.AddRGBPoint(1.0,0.705882,0.0156863,0.14902)
for ii,ss in enumerate([float(xx)/float(self.NumberOfColors) for xx in range(self.NumberOfColors)]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.Build()
centerlineMapper.SetLookupTable(lut)
centerlineActor = vtk.vtkActor()
centerlineActor.SetMapper(centerlineMapper)
self.vmtkRenderer.Renderer.AddActor(centerlineActor)
scalarBarActor = None
if self.Legend and centerlineActor and self.PointDataArrayName:
scalarBarActor = vtk.vtkScalarBarActor()
scalarBarActor.SetLookupTable(centerlineActor.GetMapper().GetLookupTable())
scalarBarActor.GetLabelTextProperty().ItalicOff()
scalarBarActor.GetLabelTextProperty().BoldOff()
scalarBarActor.GetLabelTextProperty().ShadowOff()
scalarBarActor.SetLabelFormat('%.2f')
scalarBarActor.SetTitle(self.PointDataArrayName)
self.vmtkRenderer.Renderer.AddActor(scalarBarActor)
if self.Display:
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSurface(self.Surface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
mainBodySeedIds = self.SeedSelector.GetSourceSeedIds()
mainBodySeedId = mainBodySeedIds.GetId(0)
mainBodyPoint = self.Surface.GetPoint(mainBodySeedId)
clipSeedIds = self.SeedSelector.GetTargetSeedIds()
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
clippedSurface = surfaceTriangulator.GetOutput()
for i in range(clipSeedIds.GetNumberOfIds()):
seedId = clipSeedIds.GetId(i)
locator = vtk.vtkPointLocator()
locator.SetDataSet(clippedSurface)
locator.BuildLocator()
seedPoint = self.Surface.GetPoint(seedId)
seedPointId = locator.FindClosestPoint(seedPoint)
planeEstimator = vtkvmtk.vtkvmtkPolyDataNormalPlaneEstimator()
planeEstimator.SetInputData(clippedSurface)
planeEstimator.SetOriginPointId(seedPointId)
planeEstimator.Update()
plane = vtk.vtkPlane()
plane.SetOrigin(planeEstimator.GetOrigin())
plane.SetNormal(planeEstimator.GetNormal())
seamFilter = vtkvmtk.vtkvmtkTopologicalSeamFilter()
seamFilter.SetInputData(clippedSurface)
seamFilter.SetClosestPoint(seedPoint)
seamFilter.SetSeamScalarsArrayName("SeamScalars")
seamFilter.SetSeamFunction(plane)
clipper = vtk.vtkClipPolyData()
clipper.SetInputConnection(seamFilter.GetOutputPort())
clipper.GenerateClipScalarsOff()
clipper.GenerateClippedOutputOn()
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInputConnection(clipper.GetOutputPort())
connectivity.SetExtractionModeToClosestPointRegion()
connectivity.SetClosestPoint(mainBodyPoint)
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputConnection(connectivity.GetOutputPort())
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
#clippedSurface = vtk.vtkPolyData()
#clippedSurface.DeepCopy(surfaceTriangulator.GetOutput())
clippedSurface = surfaceTriangulator.GetOutput()
self.Surface = clippedSurface
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
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.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if (nonManifoldChecker.NumberOfNonManifoldEdges > 0):
self.PrintLog(nonManifoldChecker.Report)
return
if not self.vmtkRenderer and self.SeedSelectorName in ['pickpoint','openprofiles']:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
centerlineInputSurface = surfaceTriangulator.GetOutput()
capCenterIds = None
if self.SeedSelectorName in ['openprofiles', 'carotidprofiles', 'pickpoint', 'profileidlist']:
self.PrintLog('Capping surface.')
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
centerlineInputSurface = surfaceCapper.GetOutput()
capCenterIds = surfaceCapper.GetCapCenterIds()
if self.SeedSelector:
pass
elif self.SeedSelectorName:
if self.SeedSelectorName == 'pickpoint':
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
elif self.SeedSelectorName == 'openprofiles':
self.SeedSelector = vmtkOpenProfilesSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'carotidprofiles':
self.SeedSelector = vmtkCarotidProfilesSeedSelector()
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'idlist':
self.SeedSelector = vmtkIdListSeedSelector()
self.SeedSelector.SourceIds = self.SourceIds
self.SeedSelector.TargetIds = self.TargetIds
elif self.SeedSelectorName == 'pointlist':
self.SeedSelector = vmtkPointListSeedSelector()
self.SeedSelector.SourcePoints = self.SourcePoints
self.SeedSelector.TargetPoints = self.TargetPoints
elif self.SeedSelectorName != 'profileidlist':
self.PrintError("SeedSelectorName unknown (available: pickpoint, openprofiles, carotidprofiles, profileidlist, idlist, pointlist)")
return
else:
self.PrintError('vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified')
return
if self.SeedSelector:
self.SeedSelector.SetSurface(centerlineInputSurface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
inletSeedIds = self.SeedSelector.GetSourceSeedIds()
outletSeedIds = self.SeedSelector.GetTargetSeedIds()
else:
inletSeedIds = vtk.vtkIdList()
outletSeedIds = vtk.vtkIdList()
for id in self.SourceIds:
inletSeedIds.InsertNextId(id)
if self.TargetIds:
for id in self.TargetIds:
outletSeedIds.InsertNextId(id)
else:
for i in range(capCenterIds.GetNumberOfIds()):
if i not in self.SourceIds:
outletSeedIds.InsertNextId(i)
self.PrintLog('Computing centerlines.')
self.InputInfo('Computing centerlines...')
centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInputData(centerlineInputSurface)
if self.SeedSelectorName in ['openprofiles','carotidprofiles','profileidlist']:
centerlineFilter.SetCapCenterIds(capCenterIds)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self.RadiusArrayName)
centerlineFilter.SetCostFunction(self.CostFunction)
centerlineFilter.SetFlipNormals(self.FlipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi)
if self.DelaunayTessellation != None:
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation)
centerlineFilter.SetDelaunayTolerance(self.DelaunayTolerance)
if self.UseTetGen==1:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = centerlineInputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter == 1:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(tetgen.Mesh)
centerlineFilter.SetCenterlineResampling(self.Resampling)
centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength)
centerlineFilter.Update()
self.Centerlines = centerlineFilter.GetOutput()
self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram()
self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation()
self.PoleIds = centerlineFilter.GetPoleIds()
self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName()
self.EdgeArrayName = centerlineFilter.GetEdgeArrayName()
self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName()
self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Network:
self.Network = vtk.vtkPolyData()
networkPoints = vtk.vtkPoints()
networkLines = vtk.vtkCellArray()
radiusArray = vtk.vtkDoubleArray()
radiusArray.SetName(self.RadiusArrayName)
self.Network.SetPoints(networkPoints)
self.Network.SetLines(networkLines)
self.Network.GetPointData().AddArray(radiusArray)
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.ExitAfterTextInputMode = False
self.vmtkRenderer.RegisterScript(self)
if self.Image and (not self.PlaneWidgetX or not self.PlaneWidgetY or not self.PlaneWidgetZ):
imageViewer = vmtkimageviewer.vmtkImageViewer()
imageViewer.Image = self.Image
imageViewer.vmtkRenderer = self.vmtkRenderer
imageViewer.Display = 0
imageViewer.Execute()
self.PlaneWidgetX = imageViewer.PlaneWidgetX
self.PlaneWidgetY = imageViewer.PlaneWidgetY
self.PlaneWidgetZ = imageViewer.PlaneWidgetZ
if self.Image:
spacing = self.Image.GetSpacing()
self.CurrentRadius = min(spacing)
if self.UseActiveTubes and not self.FeatureImage:
imageFeatures = vmtkimagefeatures.vmtkImageFeatures()
imageFeatures.Image = self.Image
imageFeatures.FeatureImageType = 'vtkgradient'
imageFeatures.Execute()
self.FeatureImage = imageFeatures.FeatureImage
self.NetworkRadiusArray = self.Network.GetPointData().GetArray(self.RadiusArrayName)
self.Network.GetPointData().SetActiveScalars(self.RadiusArrayName)
networkMapper = vtk.vtkPolyDataMapper()
networkMapper.SetInputData(self.Network)
networkMapper.SetScalarModeToUseCellData()
self.NetworkActor = vtk.vtkActor()
self.NetworkActor.SetMapper(networkMapper)
self.vmtkRenderer.Renderer.AddActor(self.NetworkActor)
self.NetworkTube = vtk.vtkTubeFilter()
self.NetworkTube.SetInputData(self.Network)
self.NetworkTube.SetVaryRadiusToVaryRadiusByAbsoluteScalar()
self.NetworkTube.SetNumberOfSides(20)
networkTubeMapper = vtk.vtkPolyDataMapper()
networkTubeMapper.SetInputConnection(self.NetworkTube.GetOutputPort())
networkTubeMapper.ScalarVisibilityOff()
networkTubeActor = vtk.vtkActor()
networkTubeActor.SetMapper(networkTubeMapper)
networkTubeActor.PickableOff()
networkTubeActor.GetProperty().SetOpacity(0.2)
self.vmtkRenderer.Renderer.AddActor(networkTubeActor)
self.Selection = vtk.vtkPolyData()
self.SelectionPoints = vtk.vtkPoints()
self.SelectionRadiusArray = vtk.vtkDoubleArray()
self.SelectionRadiusArray.SetName(self.RadiusArrayName)
self.Selection.SetPoints(self.SelectionPoints)
self.Selection.GetPointData().AddArray(self.SelectionRadiusArray)
self.Selection.GetPointData().SetActiveScalars(self.RadiusArrayName)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1.0)
glyphSource.SetThetaResolution(20)
glyphSource.SetPhiResolution(20)
glyphs.SetInputData(self.Selection)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToScaleByScalar()
glyphs.SetScaleFactor(1.0)
selectionMapper = vtk.vtkPolyDataMapper()
selectionMapper.SetInputConnection(glyphs.GetOutputPort())
self.SelectionActor = vtk.vtkActor()
self.SelectionActor.SetMapper(selectionMapper)
self.SelectionActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SelectionActor.GetProperty().SetOpacity(0.5)
self.SelectionActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SelectionActor)
self.ActiveSegmentSeeds = vtk.vtkPolyData()
self.ActiveSegmentSeedsPoints = vtk.vtkPoints()
self.ActiveSegmentSeedsRadiusArray = vtk.vtkDoubleArray()
self.ActiveSegmentSeedsRadiusArray.SetName(self.RadiusArrayName)
self.ActiveSegmentSeeds.SetPoints(self.ActiveSegmentSeedsPoints)
self.ActiveSegmentSeeds.GetPointData().AddArray(self.ActiveSegmentSeedsRadiusArray)
self.ActiveSegmentSeeds.GetPointData().SetActiveScalars(self.RadiusArrayName)
activeSegmentSeedsGlyphs = vtk.vtkGlyph3D()
activeSegmentSeedsGlyphSource = vtk.vtkSphereSource()
activeSegmentSeedsGlyphSource.SetRadius(1.0)
activeSegmentSeedsGlyphSource.SetThetaResolution(20)
activeSegmentSeedsGlyphSource.SetPhiResolution(20)
activeSegmentSeedsGlyphs.SetInputData(self.ActiveSegmentSeeds)
activeSegmentSeedsGlyphs.SetSourceConnection(activeSegmentSeedsGlyphSource.GetOutputPort())
activeSegmentSeedsGlyphs.SetScaleModeToScaleByScalar()
activeSegmentSeedsGlyphs.SetScaleFactor(1.0)
activeSegmentSeedsMapper = vtk.vtkPolyDataMapper()
activeSegmentSeedsMapper.SetInputConnection(activeSegmentSeedsGlyphs.GetOutputPort())
activeSegmentSeedsMapper.ScalarVisibilityOff()
self.ActiveSegmentSeedsActor = vtk.vtkActor()
self.ActiveSegmentSeedsActor.SetMapper(activeSegmentSeedsMapper)
self.ActiveSegmentSeedsActor.GetProperty().SetColor(1.0,0.0,0.0)
self.ActiveSegmentSeedsActor.GetProperty().SetOpacity(0.5)
self.ActiveSegmentSeedsActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.ActiveSegmentSeedsActor)
self.ActiveSegment = vtk.vtkPolyData()
self.ActiveSegmentPoints = vtk.vtkPoints()
self.ActiveSegmentCellArray = vtk.vtkCellArray()
self.ActiveSegmentRadiusArray = vtk.vtkDoubleArray()
self.ActiveSegmentRadiusArray.SetName(self.RadiusArrayName)
self.ActiveSegment.SetPoints(self.ActiveSegmentPoints)
self.ActiveSegment.SetLines(self.ActiveSegmentCellArray)
self.ActiveSegment.GetPointData().AddArray(self.ActiveSegmentRadiusArray)
self.ActiveSegment.GetPointData().SetActiveScalars(self.RadiusArrayName)
activeSegmentMapper = vtk.vtkPolyDataMapper()
activeSegmentMapper.ScalarVisibilityOff()
if self.SplineInterpolation and self.Image != None:
splineFilter = vtk.vtkSplineFilter()
splineFilter.SetInputData(self.ActiveSegment)
splineFilter.SetSubdivideToLength()
splineFilter.SetLength(2.0*min(self.Image.GetSpacing()))
activeSegmentMapper.SetInputConnection(splineFilter.GetOutputPort())
else:
activeSegmentMapper.SetInputData(self.ActiveSegment)
self.ActiveSegmentActor = vtk.vtkActor()
self.ActiveSegmentActor.SetMapper(activeSegmentMapper)
self.ActiveSegmentActor.GetProperty().SetColor(1.0,1.0,1.0)
self.ActiveSegmentActor.GetProperty().SetLineWidth(3.0)
self.ActiveSegmentActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.ActiveSegmentActor)
activeTube = vtk.vtkTubeFilter()
activeTube.SetInputConnection(activeSegmentMapper.GetInputPort())
activeTube.SetVaryRadiusToVaryRadiusByAbsoluteScalar()
activeTube.SetNumberOfSides(20)
activeTubeMapper = vtk.vtkPolyDataMapper()
activeTubeMapper.SetInputConnection(activeTube.GetOutputPort())
activeTubeMapper.ScalarVisibilityOff()
activeTubeActor = vtk.vtkActor()
activeTubeActor.SetMapper(activeTubeMapper)
activeTubeActor.PickableOff()
activeTubeActor.GetProperty().SetOpacity(0.6)
self.vmtkRenderer.Renderer.AddActor(activeTubeActor)
self.NetworkLabelsArray = vtk.vtkStringArray.SafeDownCast(self.Network.GetCellData().GetAbstractArray(self.LabelsArrayName))
if not self.NetworkLabelsArray:
self.NetworkLabelsArray = vtk.vtkStringArray()
self.NetworkLabelsArray.SetName(self.LabelsArrayName)
self.NetworkLabelsArray.SetNumberOfValues(self.Network.GetNumberOfCells())
for i in range(self.Network.GetNumberOfCells()):
self.NetworkLabelsArray.SetValue(i,'')
self.Network.GetCellData().AddArray(self.NetworkLabelsArray)
self.CellCenters = vtk.vtkCellCenters()
self.CellCenters.SetInputData(self.Network)
self.CellCenters.VertexCellsOff()
self.CellCenters.Update()
labeledMapper = vtk.vtkLabeledDataMapper()
labeledMapper.SetInputConnection(self.CellCenters.GetOutputPort())
labeledMapper.SetLabelModeToLabelFieldData()
labeledMapper.SetFieldDataName(self.LabelsArrayName)
labeledMapper.GetLabelTextProperty().SetFontFamilyToArial()
labeledMapper.GetLabelTextProperty().BoldOff()
labeledMapper.GetLabelTextProperty().ItalicOff()
labeledMapper.GetLabelTextProperty().ShadowOff()
self.LabelsActor = vtk.vtkActor2D()
self.LabelsActor.SetMapper(labeledMapper)
self.LabelsActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.LabelsActor)
self.CellPicker = vtk.vtkCellPicker()
self.CellPicker.SetTolerance(1E-2)
self.CellPicker.InitializePickList()
self.CellPicker.AddPickList(self.NetworkActor)
self.CellPicker.PickFromListOn()
self.vmtkRenderer.AddKeyBinding('a','Add mode.',self.AddCallback)
self.vmtkRenderer.AddKeyBinding('d','Delete mode.',self.DeleteCallback)
self.vmtkRenderer.AddKeyBinding('m','Merge mode.',self.MergeCallback)
self.vmtkRenderer.AddKeyBinding('s','Split mode.',self.SplitCallback)
self.vmtkRenderer.AddKeyBinding('l','Label mode.',self.LabelCallback)
self.vmtkRenderer.AddKeyBinding('Tab','Show labels.',self.ShowLabelCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyReleaseEvent", self.KeyReleaseCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("LeftButtonPressEvent", self.LeftButtonPressCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("MouseMoveEvent", self.MouseMoveCallback)
if self.PlaneWidgetX:
self.PlaneWidgetX.UseContinuousCursorOn()
self.PlaneWidgetX.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
if self.PlaneWidgetY:
self.PlaneWidgetY.UseContinuousCursorOn()
self.PlaneWidgetY.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
if self.PlaneWidgetZ:
self.PlaneWidgetZ.UseContinuousCursorOn()
self.PlaneWidgetZ.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
self.FirstRender()
self.Surface = self.NetworkTube.GetOutput()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Centerlines:
self.PrintError('Error: No input centerlines.')
if not self.GroupIdsArrayName:
self.PrintError('Error: GroupIdsArrayName not specified.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
groupIdsArray = self.Centerlines.GetCellData().GetArray(
self.GroupIdsArrayName)
groupIds = []
for i in range(groupIdsArray.GetNumberOfTuples()):
groupIds.append(int(groupIdsArray.GetComponent(i, 0)))
groupIds.sort()
uniqueGroupIds = []
for groupId in groupIds:
if groupId not in uniqueGroupIds:
uniqueGroupIds.append(groupId)
labelMap = {}
if not self.Labeling:
viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
viewer.Centerlines = self.Centerlines
viewer.CellDataArrayName = self.GroupIdsArrayName
viewer.vmtkRenderer = self.vmtkRenderer
viewer.InputStream = self.InputStream
viewer.OutputStream = self.OutputStream
#viewer.InputText = self.InputText
#viewer.OutputText = self.OutputText
#viewer.PrintError = self.PrintError
#viewer.PringLog = self.PrintLog
viewer.Execute()
ok = False
while not ok:
labelString = self.InputText(
"Please input labels for the following groupIds:\n%s\n" %
" ".join([str(groupId) for groupId in uniqueGroupIds]),
self.LabelValidator)
labels = [int(label) for label in labelString.split()]
if len(labels) == len(uniqueGroupIds):
ok = True
for groupId in uniqueGroupIds:
labelMap[groupId] = labels[uniqueGroupIds.index(groupId)]
else:
if len(self.Labeling) != 2 * len(uniqueGroupIds):
self.PrintError('Error: incorrect labeling specified')
for i in range(len(self.Labeling) / 2):
groupId = self.Labeling[2 * i]
labelId = self.Labeling[2 * i + 1]
if not groupId in uniqueGroupIds:
self.PrintError('Error: groupId %d does not exist' %
groupId)
labelMap[groupId] = labelId
labelIdsArray = vtk.vtkIntArray()
labelIdsArray.SetName(self.LabelIdsArrayName)
labelIdsArray.SetNumberOfComponents(1)
labelIdsArray.SetNumberOfTuples(self.Centerlines.GetNumberOfCells())
groupIdsArray = self.Centerlines.GetCellData().GetArray(
self.GroupIdsArrayName)
for i in range(groupIdsArray.GetNumberOfTuples()):
groupId = int(groupIdsArray.GetComponent(i, 0))
labelIdsArray.SetComponent(i, 0, labelMap[groupId])
self.Centerlines.GetCellData().AddArray(labelIdsArray)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Mesh:
self.PrintError('Error: No input mesh.')
return
if not self.CellEntityIdsArrayName:
self.PrintError('Error: No input CellEntityIdsArrayName.')
return
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
threshold = vtk.vtkThreshold()
threshold.SetInputData(self.Mesh)
threshold.ThresholdByUpper(self.VolumeCellEntityId+0.5)
threshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
threshold.Update()
boundaryMesh = threshold.GetOutput()
boundaryMesh.GetCellData().SetActiveScalars(self.CellEntityIdsArrayName)
boundaryMapper = vtk.vtkDataSetMapper()
boundaryMapper.SetInputData(boundaryMesh)
boundaryMapper.ScalarVisibilityOn()
boundaryMapper.SetScalarModeToUseCellData()
boundaryMapper.SetScalarRange(boundaryMesh.GetCellData().GetScalars().GetRange())
boundaryActor = vtk.vtkActor()
boundaryActor.SetMapper(boundaryMapper)
self.vmtkRenderer.Renderer.AddActor(boundaryActor)
wallThreshold = vtk.vtkThreshold()
wallThreshold.SetInputData(boundaryMesh)
wallThreshold.ThresholdByLower(self.WallCellEntityId+0.5)
wallThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
wallThreshold.Update()
wallMeshToSurface = vtk.vtkGeometryFilter()
wallMeshToSurface.SetInputConnection(wallThreshold.GetOutputPort())
wallMeshToSurface.Update()
boundaryReferenceSystems = vtkvmtk.vtkvmtkBoundaryReferenceSystems()
boundaryReferenceSystems.SetInputConnection(wallMeshToSurface.GetOutputPort())
boundaryReferenceSystems.SetBoundaryRadiusArrayName("BoundaryRadius")
boundaryReferenceSystems.SetBoundaryNormalsArrayName("BoundaryNormals")
boundaryReferenceSystems.SetPoint1ArrayName("Point1Array")
boundaryReferenceSystems.SetPoint2ArrayName("Point2Array")
boundaryReferenceSystems.Update()
self.ReferenceSystems = boundaryReferenceSystems.GetOutput()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(self.ReferenceSystems.GetNumberOfPoints())
self.ReferenceSystems.GetPointData().AddArray(cellEntityIdsArray)
boundaryThreshold = vtk.vtkThreshold()
boundaryThreshold.SetInputData(boundaryMesh)
boundaryThreshold.ThresholdByUpper(self.WallCellEntityId+0.5)
boundaryThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
boundaryThreshold.Update()
boundaryMeshToSurface = vtk.vtkGeometryFilter()
boundaryMeshToSurface.SetInputConnection(boundaryThreshold.GetOutputPort())
boundaryMeshToSurface.Update()
boundarySurface = boundaryMeshToSurface.GetOutput()
pointCells = vtk.vtkIdList()
surfaceCellEntityIdsArray = vtk.vtkIntArray()
surfaceCellEntityIdsArray.DeepCopy(boundarySurface.GetCellData().GetArray(self.CellEntityIdsArrayName))
self.PrintLog('')
for i in range(self.ReferenceSystems.GetNumberOfPoints()):
pointId = boundarySurface.FindPoint(self.ReferenceSystems.GetPoint(i))
boundarySurface.GetPointCells(pointId,pointCells)
cellId = pointCells.GetId(0)
cellEntityId = surfaceCellEntityIdsArray.GetValue(cellId)
cellEntityIdsArray.SetValue(i,cellEntityId)
origin = self.ReferenceSystems.GetPoint(i)
normal = self.ReferenceSystems.GetPointData().GetArray("BoundaryNormals").GetTuple3(i)
radius = self.ReferenceSystems.GetPointData().GetArray("BoundaryRadius").GetTuple1(i)
logLine = 'CellEntityId: %d\n' % cellEntityId
logLine += ' Origin: %f, %f, %f\n' % (origin[0],origin[1],origin[2])
logLine += ' Normal: %f, %f, %f\n' % (normal[0],normal[1],normal[2])
logLine += ' Radius: %f\n' % radius
self.PrintLog(logLine)
self.ReferenceSystems.GetPointData().SetActiveScalars(self.CellEntityIdsArrayName)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(self.ReferenceSystems)
labelsMapper.SetLabelModeToLabelScalars()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self.Surface == None):
self.PrintError('Error: no Surface.')
#if (self.ReferenceSurface == None):
# self.PrintError('Error: no Reference Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Transform == None:
self.Transform = vtk.vtkTransform()
if self.TransformFilter == None:
self.TransformFilter= vtk.vtkTransformPolyDataFilter()
self.TransformFilter.SetInputData(self.Surface)
self.TransformFilter.SetTransform(self.Transform)
self.TransformFilter.Update()
self.TransformedSurface.ShallowCopy(self.TransformFilter.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.TransformedSurface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetProperty().SetColor(1.0, 0.1, 0.1)
#self.Actor.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.ReferenceSurface:
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputData(self.ReferenceSurface)
mapper2.ScalarVisibilityOff()
self.Actor2 = vtk.vtkActor()
self.Actor2.SetMapper(mapper2)
self.Actor2.GetProperty().SetColor(1.0, 1.0, 1.0)
self.Actor2.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor2)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetPlaceFactor(1.0)
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.BoxWidget.ScalingEnabledOff()
self.BoxWidget.HandlesOff()
if self.Scaling:
self.BoxWidget.ScalingEnabledOn()
self.BoxWidget.HandlesOn()
self.vmtkRenderer.RegisterScript(self)
self.InputInfo('Use the left-mousebutton to rotate the box \nUse the middle-mouse-button to move the box \nPress space to move the surface to its new postion')
#self.OutputText('Press \'i\' to activate the box widget interactor \n')
#self.OutputText('Use the left-mousebutton to rotate the box \n')
#self.OutputText('Use the middle-mouse-button to move the box \n')
#self.OutputText('Press space to move the surface to its new postion \n')
#self.OutputText('Press \'q\' to quit and apply the transform \n')
self.vmtkRenderer.AddKeyBinding('space','Move the surface.',self.MoveCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Surface = self.TransformedSurface
self.Matrix4x4 = self.Transform.GetMatrix()
matrix = self.Matrix4x4
self.MatrixCoefficients = [
matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Surface:
self.PrintError('Error: No input surface.')
if not self.Centerlines:
self.PrintError('Error: No input centerlines.')
if self.Interactive and not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if self.Interactive:
self.vmtkRenderer.RegisterScript(self)
viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
viewer.Centerlines = self.Centerlines
viewer.CellDataArrayName = self.GroupIdsArrayName
viewer.vmtkRenderer = self.vmtkRenderer
viewer.InputText = self.InputText
viewer.OutputText = self.OutputText
viewer.PrintError = self.PrintError
viewer.PringLog = self.PrintLog
viewer.Display = 0
viewer.Execute()
groupIdsString = self.InputText("Please input groupIds to clip:\n",self.GroupIdsValidator)
self.GroupIds = [int(groupId) for groupId in groupIdsString.split()]
clipper = vtkvmtk.vtkvmtkPolyDataCenterlineGroupsClipper()
clipper.SetInputData(self.Surface)
clipper.SetCenterlines(self.Centerlines)
clipper.SetCenterlineGroupIdsArrayName(self.GroupIdsArrayName)
clipper.SetGroupIdsArrayName(self.GroupIdsArrayName)
clipper.SetCenterlineRadiusArrayName(self.RadiusArrayName)
clipper.SetBlankingArrayName(self.BlankingArrayName)
clipper.SetCutoffRadiusFactor(self.CutoffRadiusFactor)
clipper.SetClipValue(self.ClipValue)
clipper.SetUseRadiusInformation(self.UseRadiusInformation)
if self.GroupIds:
groupIds = vtk.vtkIdList()
for groupId in self.GroupIds:
groupIds.InsertNextId(groupId)
clipper.SetCenterlineGroupIds(groupIds)
clipper.ClipAllCenterlineGroupIdsOff()
else:
clipper.ClipAllCenterlineGroupIdsOn()
if not self.InsideOut:
clipper.GenerateClippedOutputOff()
else:
clipper.GenerateClippedOutputOn()
clipper.Update()
if not self.InsideOut:
self.Surface = clipper.GetOutput()
else:
self.Surface = clipper.GetClippedOutputData()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self.Surface == None):
self.PrintError('Error: no Surface.')
#if (self.ReferenceSurface == None):
# self.PrintError('Error: no Reference Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Transform == None:
self.Transform = vtk.vtkTransform()
if self.TransformFilter == None:
self.TransformFilter= vtk.vtkTransformPolyDataFilter()
self.TransformFilter.SetInputData(self.Surface)
self.TransformFilter.SetTransform(self.Transform)
self.TransformFilter.Update()
self.TransformedSurface.ShallowCopy(self.TransformFilter.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.TransformedSurface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetProperty().SetColor(1.0, 0.1, 0.1)
#self.Actor.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.ReferenceSurface:
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputData(self.ReferenceSurface)
mapper2.ScalarVisibilityOff()
self.Actor2 = vtk.vtkActor()
self.Actor2.SetMapper(mapper2)
self.Actor2.GetProperty().SetColor(1.0, 1.0, 1.0)
self.Actor2.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor2)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetPlaceFactor(1.0)
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.BoxWidget.ScalingEnabledOff()
self.BoxWidget.HandlesOff()
if self.Scaling:
self.BoxWidget.ScalingEnabledOn()
self.BoxWidget.HandlesOn()
self.vmtkRenderer.RegisterScript(self)
self.InputInfo('Use the left-mousebutton to rotate the box \nUse the middle-mouse-button to move the box \nPress space to move the surface to its new postion')
#self.OutputText('Press \'i\' to activate the box widget interactor \n')
#self.OutputText('Use the left-mousebutton to rotate the box \n')
#self.OutputText('Use the middle-mouse-button to move the box \n')
#self.OutputText('Press space to move the surface to its new postion \n')
#self.OutputText('Press \'q\' to quit and apply the transform \n')
self.vmtkRenderer.AddKeyBinding('space','Move the surface.',self.MoveCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Surface = self.TransformedSurface
self.Matrix4x4 = self.Transform.GetMatrix()
matrix = self.Matrix4x4
self.MatrixCoefficients = [
matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
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 BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if self.Actor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.Actor)
if self.ScalarBarActor != None:
self.vmtkRenderer.Renderer.RemoveActor(self.ScalarBarActor)
if self.Mesh != None:
self.InitialMesh = self.Mesh
self.DisplayMesh = self.Mesh
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.DisplayMesh)
array = None
if (self.ArrayName != ''):
if self.DisplayCellData == 0:
self.Mesh.GetPointData().SetActiveScalars(self.ArrayName)
array = self.Mesh.GetPointData().GetScalars()
else:
self.Mesh.GetCellData().SetActiveScalars(self.ArrayName)
array = self.Mesh.GetCellData().GetScalars()
mapper.SetScalarModeToUseCellData()
if (array != None):
if (self.ScalarRange[1] > self.ScalarRange[0]):
mapper.SetScalarRange(self.ScalarRange)
else:
mapper.SetScalarRange(array.GetRange(0))
if (self.Grayscale == 1):
lut = vtk.vtkLookupTable()
lut.SetValueRange(0.0, 1.0)
lut.SetSaturationRange(0.0, 0.0)
mapper.SetLookupTable(lut)
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
if (self.Color[0] >= 0.0):
self.Actor.GetProperty().SetColor(self.Color)
if (self.FlatInterpolation == 1):
self.Actor.GetProperty().SetInterpolationToFlat()
self.Actor.GetProperty().SetOpacity(self.Opacity)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if (self.Legend == 1) & (self.Actor != None):
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(
self.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
## self.ScalarBarActor.GetLabelTextProperty().SetColor(0.0,0.0,0.0)
self.ScalarBarActor.SetLabelFormat('%.2f')
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
#self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('i', 'Interact.',
self.InteractCallback)
self.vmtkRenderer.AddKeyBinding('c', 'Clip.', self.ClipCallback)
self.vmtkRenderer.AddKeyBinding('e', 'Extract.', self.ExtractCallback)
self.vmtkRenderer.AddKeyBinding('n', 'Show clipped area.',
self.NCallback)
self.vmtkRenderer.AddKeyBinding('d', 'Switch clipped/unclipped area.',
self.DCallback)
self.vmtkRenderer.AddKeyBinding('t', 'Redo.', self.TCallback)
self.vmtkRenderer.AddKeyBinding('u', 'Undo.', self.UndoCallback)
self.PlaneWidget = vtk.vtkImplicitPlaneWidget()
self.PlaneWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidget.SetPlaceFactor(1.25)
self.PlaneWidget.DrawPlaneOff()
self.PlaneWidget.SetProp3D(self.Actor)
self.PlaneWidget.PlaceWidget()
#Work around bug/strange behaviour in vtk
self.PlaneWidget.SetOrigin(self.Actor.GetCenter())
if (self.Display == 1):
self.vmtkRenderer.Render()
self.Mesh = self.InitialMesh
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
# a check to make sure nothing has ran out of order.
if self.SeedSelector:
pass
else:
# initialize the seed selection method
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
# label all non-connected regions in an input surface.
allRegionConnectivity = vtk.vtkPolyDataConnectivityFilter()
allRegionConnectivity.SetInputData(self.Surface)
allRegionConnectivity.SetExtractionModeToAllRegions()
allRegionConnectivity.ColorRegionsOn()
allRegionConnectivity.Update()
# create the actor/mapper which renders the labeled input surface
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(allRegionConnectivity.GetOutput())
mapper.ScalarVisibilityOff()
mapper.Update()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(0.7, 0.7, 0.7) # standard gray color
actor.GetProperty().SetDiffuse(0.9)
actor.GetProperty().SetSpecular(0.2)
actor.GetProperty().SetRepresentationToSurface()
actor.GetProperty().EdgeVisibilityOff()
# add this as the main actor to the scene (the first think you see)
self.vmtkRenderer.Renderer.AddActor(actor)
if self.SeedSelector:
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
# until SeedSelector releases control of execution, the program will not
# proceed past the next line. SeedSelector handles all user interaction and
# modification/logging of actor properties & region Ids
self.SeedSelector.Execute()
# we store each extracted region as individual vtkPolyData objects within a list.
# They are combined into one dataset below.
polyDataAppender = vtk.vtkAppendPolyData()
for outputSurfacePolyData in self.SeedSelector._OutputPolyDataList:
polyDataAppender.AddInputData(outputSurfacePolyData)
# Even though we clean the selection in the SeedSelection, this is necessary because it
# may be possible for a user to select the same polydata object twice. If this is not cleaned,
# a double selection may mess with further post processing scripts.
polyDataCleaner = vtk.vtkCleanPolyData()
polyDataCleaner.SetInputConnection(polyDataAppender.GetOutputPort())
polyDataCleaner.Update()
self.Surface = polyDataAppender.GetOutput()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self._Surface == None):
self.PrintError(
'vmtkPickPointSeedSelector Error: Surface not set.')
return
self._SourceSeedIds.Initialize()
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphs.SetInputData(self.PickedSeeds)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToDataScalingOff()
glyphs.SetScaleFactor(self._Surface.GetLength() * 0.01)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
self.SeedActor = vtk.vtkActor()
self.SeedActor.SetMapper(glyphMapper)
self.SeedActor.GetProperty().SetColor(1.0, 0.0, 0.0)
self.SeedActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SeedActor)
##self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('u', 'Undo.', self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Add points.',
self.PickCallback)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self._Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(1.0)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
self.InputInfo(
'Please position the mouse and press space to add source points, \'u\' to undo\n'
)
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._SourceSeedIds.DeepCopy(self.PickedSeedIds)
self.InputInfo(
'Please position the mouse and press space to add target points, \'u\' to undo\n'
)
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._TargetSeedIds.DeepCopy(self.PickedSeedIds)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def visualize_landmarks(landmarks, centerline, algorithm, surface_path):
"""
Visualize the interfaces between the resulting landmarks (points)
Args:
landmarks (ndarray): Points defining landmarks / interfaces between segments
centerline (vtkPolyData): Centerline which has been landmarked
algorithm (str): Name of landmarking algorithm
surface_path (str): Location of surface model
"""
vtkPoints = vtk.vtkPoints()
landmarkSpheres = []
for key, point in landmarks.items():
sphere = vtk.vtkSphereSource()
sphere.SetRadius(1)
sphere.SetCenter(point[0], point[1], point[2])
sphere.Update()
landmarkSpheres.append(sphere.GetOutput())
vtkPoints.InsertNextPoint(point)
landmarkData = vtk_merge_polydata(landmarkSpheres)
surface = None
if path.exists(surface_path):
surface = read_polydata(surface_path)
vtkNameArray = vtk.vtkStringArray()
vtkNameArray.SetNumberOfValues(7)
if algorithm == "piccinelli":
start = len(landmarks) - 1
stop = -1
interfaces = ["Bend %s-%s" % (i, i + 1) for i in range(len(landmarks))]
elif algorithm == "bogunovic":
start = 3
stop = -1
interfaces = [
"Anterior-Posterior",
"Posterior-Inferior",
"Inferior (Start)",
"Superior-Anterior",
]
for i in range(start, stop, -1):
if i == 0:
if algorithm == "piccinelli":
vtkNameArray.SetValue(i, 'Bend 1 (Start)')
elif algorithm == "bogunovic":
vtkNameArray.SetValue(i, interfaces[i])
else:
vtkNameArray.SetValue(i, interfaces[i])
# Create the dataset with landmarking points
labeledPolydata = vtk.vtkPolyData()
labeledPolydata.SetPoints(vtkPoints)
labeledPolydata.GetPointData().AddArray(vtkNameArray)
centerlineMapper = vtk.vtkPolyDataMapper()
centerlineMapper.SetInputData(centerline)
centerlineActor = vtk.vtkActor()
centerlineActor.SetMapper(centerlineMapper)
centerlineActor.GetProperty().SetLineWidth(10)
centerlineActor.GetProperty().SetColor(1, 0, 0)
landmarkMapper = vtk.vtkPolyDataMapper()
landmarkMapper.SetInputData(landmarkData)
landmarkActor = vtk.vtkActor()
landmarkActor.SetMapper(landmarkMapper)
labelsMapper = vtk.vtkLabeledDataMapper()
labelsMapper.SetInputData(labeledPolydata)
labelsMapper.SetLabelModeToLabelFieldData()
labelsMapper.GetLabelTextProperty().SetColor(1, 1, 1)
labelsMapper.GetLabelTextProperty().SetFontSize(35)
labelsMapper.GetLabelTextProperty().ItalicOff()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
vmtkRenderer = vmtkrenderer.vmtkRenderer()
vmtkRenderer.Initialize()
vmtkRenderer.Renderer.AddActor(centerlineActor)
vmtkRenderer.Renderer.AddActor(labelsActor)
vmtkRenderer.Renderer.AddActor(landmarkActor)
if surface is not None:
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(surface)
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.3)
vmtkRenderer.Renderer.AddActor(surfaceActor)
vmtkRenderer.Render()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if (nonManifoldChecker.NumberOfNonManifoldEdges > 0):
self.PrintLog(nonManifoldChecker.Report)
return
if not self.vmtkRenderer and self.SeedSelectorName in [
'pickpoint', 'openprofiles'
]:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
centerlineInputSurface = surfaceTriangulator.GetOutput()
capCenterIds = None
if self.SeedSelectorName in [
'openprofiles', 'carotidprofiles', 'pickpoint', 'profileidlist'
]:
self.PrintLog('Capping surface.')
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(
surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
centerlineInputSurface = surfaceCapper.GetOutput()
capCenterIds = surfaceCapper.GetCapCenterIds()
if self.SeedSelector:
pass
elif self.SeedSelectorName:
if self.SeedSelectorName == 'pickpoint':
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
elif self.SeedSelectorName == 'openprofiles':
self.SeedSelector = vmtkOpenProfilesSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'carotidprofiles':
self.SeedSelector = vmtkCarotidProfilesSeedSelector()
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'idlist':
self.SeedSelector = vmtkIdListSeedSelector()
self.SeedSelector.SourceIds = self.SourceIds
self.SeedSelector.TargetIds = self.TargetIds
elif self.SeedSelectorName == 'pointlist':
self.SeedSelector = vmtkPointListSeedSelector()
self.SeedSelector.SourcePoints = self.SourcePoints
self.SeedSelector.TargetPoints = self.TargetPoints
elif self.SeedSelectorName != 'profileidlist':
self.PrintError(
"SeedSelectorName unknown (available: pickpoint, openprofiles, carotidprofiles, profileidlist, idlist, pointlist)"
)
return
else:
self.PrintError(
'vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified'
)
return
if self.SeedSelector:
self.SeedSelector.SetSurface(centerlineInputSurface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
inletSeedIds = self.SeedSelector.GetSourceSeedIds()
outletSeedIds = self.SeedSelector.GetTargetSeedIds()
else:
inletSeedIds = vtk.vtkIdList()
outletSeedIds = vtk.vtkIdList()
for id in self.SourceIds:
inletSeedIds.InsertNextId(id)
if self.TargetIds:
for id in self.TargetIds:
outletSeedIds.InsertNextId(id)
else:
for i in range(capCenterIds.GetNumberOfIds()):
if i not in self.SourceIds:
outletSeedIds.InsertNextId(i)
self.PrintLog('Computing centerlines.')
self.InputInfo('Computing centerlines...')
centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInputData(centerlineInputSurface)
if self.SeedSelectorName in [
'openprofiles', 'carotidprofiles', 'profileidlist'
]:
centerlineFilter.SetCapCenterIds(capCenterIds)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self.RadiusArrayName)
centerlineFilter.SetCostFunction(self.CostFunction)
centerlineFilter.SetFlipNormals(self.FlipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi)
if self.DelaunayTessellation != None:
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation)
centerlineFilter.SetDelaunayTolerance(self.DelaunayTolerance)
if self.UseTetGen == 1:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = centerlineInputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter == 1:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(tetgen.Mesh)
centerlineFilter.SetCenterlineResampling(self.Resampling)
centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength)
centerlineFilter.Update()
self.Centerlines = centerlineFilter.GetOutput()
self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram()
self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation()
self.PoleIds = centerlineFilter.GetPoleIds()
self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName(
)
self.EdgeArrayName = centerlineFilter.GetEdgeArrayName()
self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName()
self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName(
)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
wholeExtent = self.Image.GetExtent()
if self.Picker == None:
self.Picker = vtk.vtkCellPicker()
if self.PlaneWidgetX == None:
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
if self.PlaneWidgetY == None:
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
if self.PlaneWidgetZ == None:
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.Picker.SetTolerance(0.005)
self.PlaneWidgetX.SetResliceInterpolateToLinear()
self.PlaneWidgetX.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetX.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetX.SetInputData(self.Image)
self.PlaneWidgetX.SetPlaneOrientationToXAxes()
self.PlaneWidgetX.SetSliceIndex(wholeExtent[0])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetX.DisplayTextOn()
else:
self.PlaneWidgetX.DisplayTextOff()
self.PlaneWidgetX.SetPicker(self.Picker)
self.PlaneWidgetX.KeyPressActivationOff()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetX.SetMarginSizeX(0.05)
self.PlaneWidgetX.SetMarginSizeY(0.05)
else:
self.PlaneWidgetX.SetMarginSizeX(0.0)
self.PlaneWidgetX.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetX.SetWindowLevel(self.WindowLevel[0],self.WindowLevel[1])
self.PlaneWidgetX.On()
self.PlaneWidgetY.SetResliceInterpolateToLinear()
self.PlaneWidgetY.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetY.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetY.SetInputData(self.Image)
self.PlaneWidgetY.SetPlaneOrientationToYAxes()
self.PlaneWidgetY.SetSliceIndex(wholeExtent[2])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetY.DisplayTextOn()
else:
self.PlaneWidgetY.DisplayTextOff()
self.PlaneWidgetY.SetPicker(self.Picker)
self.PlaneWidgetY.KeyPressActivationOff()
self.PlaneWidgetY.SetLookupTable(self.PlaneWidgetX.GetLookupTable())
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetY.SetMarginSizeX(0.05)
self.PlaneWidgetY.SetMarginSizeY(0.05)
else:
self.PlaneWidgetY.SetMarginSizeX(0.0)
self.PlaneWidgetY.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetY.SetWindowLevel(self.WindowLevel[0],self.WindowLevel[1])
self.PlaneWidgetY.On()
self.PlaneWidgetZ.SetResliceInterpolateToLinear()
self.PlaneWidgetZ.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetZ.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetZ.SetInputData(self.Image)
self.PlaneWidgetZ.SetPlaneOrientationToZAxes()
self.PlaneWidgetZ.SetSliceIndex(wholeExtent[4])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetZ.DisplayTextOn()
else:
self.PlaneWidgetZ.DisplayTextOff()
self.PlaneWidgetZ.SetPicker(self.Picker)
self.PlaneWidgetZ.KeyPressActivationOff()
self.PlaneWidgetZ.SetLookupTable(self.PlaneWidgetX.GetLookupTable())
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetZ.SetMarginSizeX(0.05)
self.PlaneWidgetZ.SetMarginSizeY(0.05)
else:
self.PlaneWidgetZ.SetMarginSizeX(0.0)
self.PlaneWidgetZ.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetZ.SetWindowLevel(self.WindowLevel[0],self.WindowLevel[1])
self.PlaneWidgetZ.On()
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self._Surface == None):
self.PrintError('vmtkPickPointSeedSelector Error: Surface not set.')
return
self._SourceSeedIds.Initialize()
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphs.SetInputData(self.PickedSeeds)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToDataScalingOff()
glyphs.SetScaleFactor(self._Surface.GetLength()*0.01)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
self.SeedActor = vtk.vtkActor()
self.SeedActor.SetMapper(glyphMapper)
self.SeedActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SeedActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SeedActor)
##self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyPressEvent", self.KeyPressed)
self.vmtkRenderer.AddKeyBinding('u','Undo.',self.UndoCallback)
self.vmtkRenderer.AddKeyBinding('space','Add points.',self.PickCallback)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self._Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(1.0)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
self.InputInfo('Please position the mouse and press space to add a point on the main body of the model, \'u\' to undo\n')
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._SourceSeedIds.DeepCopy(self.PickedSeedIds)
self.InputInfo('Please position the mouse and press space to add points at clip locations, \'u\' to undo\n')
any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._TargetSeedIds.DeepCopy(self.PickedSeedIds)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Mesh:
self.PrintError('Error: No input mesh.')
if not self.Centerlines:
self.PrintError('Error: No input centerlines.')
if self.Interactive and not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if self.Interactive:
self.vmtkRenderer.RegisterScript(self)
viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
viewer.Centerlines = self.Centerlines
viewer.CellDataArrayName = self.GroupIdsArrayName
viewer.vmtkRenderer = self.vmtkRenderer
viewer.InputText = self.InputText
viewer.OutputText = self.OutputText
viewer.PrintError = self.PrintError
viewer.PringLog = self.PrintLog
viewer.Display = 0
viewer.Execute()
groupIdsString = self.InputText("Please input groupIds to clip:\n",
self.GroupIdsValidator)
self.GroupIds = [
int(groupId) for groupId in groupIdsString.split()
]
clipper = vtkvmtk.vtkvmtkUnstructuredGridCenterlineGroupsClipper()
clipper.SetInputData(self.Mesh)
clipper.SetCenterlines(self.Centerlines)
clipper.SetCenterlineGroupIdsArrayName(self.GroupIdsArrayName)
clipper.SetGroupIdsArrayName(self.GroupIdsArrayName)
clipper.SetCenterlineRadiusArrayName(self.RadiusArrayName)
clipper.SetBlankingArrayName(self.BlankingArrayName)
clipper.SetCutoffRadiusFactor(self.CutoffRadiusFactor)
clipper.SetClipValue(self.ClipValue)
clipper.SetUseRadiusInformation(self.UseRadiusInformation)
if self.GroupIds:
groupIds = vtk.vtkIdList()
for groupId in self.GroupIds:
groupIds.InsertNextId(groupId)
clipper.SetCenterlineGroupIds(groupIds)
clipper.ClipAllCenterlineGroupIdsOff()
else:
clipper.ClipAllCenterlineGroupIdsOn()
if not self.InsideOut:
clipper.GenerateClippedOutputOff()
else:
clipper.GenerateClippedOutputOn()
clipper.Update()
if not self.InsideOut:
self.Mesh = clipper.GetOutput()
else:
self.Mesh = clipper.GetClippedOutputData()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if not self.Centerlines:
self.PrintError('Error: No input centerlines.')
if not self.GroupIdsArrayName:
self.PrintError('Error: GroupIdsArrayName not specified.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
groupIdsArray = self.Centerlines.GetCellData().GetArray(self.GroupIdsArrayName)
groupIds = []
for i in range(groupIdsArray.GetNumberOfTuples()):
groupIds.append(int(groupIdsArray.GetComponent(i,0)))
groupIds.sort()
uniqueGroupIds = []
for groupId in groupIds:
if groupId not in uniqueGroupIds:
uniqueGroupIds.append(groupId)
labelMap = {}
if not self.Labeling:
viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
viewer.Centerlines = self.Centerlines
viewer.CellDataArrayName = self.GroupIdsArrayName
viewer.vmtkRenderer = self.vmtkRenderer
viewer.InputStream = self.InputStream
viewer.OutputStream = self.OutputStream
#viewer.InputText = self.InputText
#viewer.OutputText = self.OutputText
#viewer.PrintError = self.PrintError
#viewer.PringLog = self.PrintLog
viewer.Execute()
ok = False
while not ok:
labelString = self.InputText("Please input labels for the following groupIds:\n%s\n" % " ".join([str(groupId) for groupId in uniqueGroupIds]),self.LabelValidator)
labels = [int(label) for label in labelString.split()]
if len(labels) == len(uniqueGroupIds):
ok = True
for groupId in uniqueGroupIds:
labelMap[groupId] = labels[uniqueGroupIds.index(groupId)]
else:
if len(self.Labeling) != 2 * len(uniqueGroupIds):
self.PrintError('Error: incorrect labeling specified')
for i in range(len(self.Labeling)/2):
groupId = self.Labeling[2*i]
labelId = self.Labeling[2*i+1]
if not groupId in uniqueGroupIds:
self.PrintError('Error: groupId %d does not exist' % groupId)
labelMap[groupId] = labelId
labelIdsArray = vtk.vtkIntArray()
labelIdsArray.SetName(self.LabelIdsArrayName)
labelIdsArray.SetNumberOfComponents(1)
labelIdsArray.SetNumberOfTuples(self.Centerlines.GetNumberOfCells())
groupIdsArray = self.Centerlines.GetCellData().GetArray(self.GroupIdsArrayName)
for i in range(groupIdsArray.GetNumberOfTuples()):
groupId = int(groupIdsArray.GetComponent(i,0))
labelIdsArray.SetComponent(i,0,labelMap[groupId])
self.Centerlines.GetCellData().AddArray(labelIdsArray)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self._Surface == None):
self.PrintError('vmtkOpenProfilesSeedSelector Error: Surface not set.')
return
if (self._SeedIds == None):
self.PrintError('vmtkOpenProfilesSeedSelector Error: SeedIds not set.')
return
self._SourceSeedIds.Initialize()
self._TargetSeedIds.Initialize()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self.Script)
seedPoints = vtk.vtkPoints()
for i in range(self._SeedIds.GetNumberOfIds()):
seedPoints.InsertNextPoint(self._Surface.GetPoint(self._SeedIds.GetId(i)))
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()
seedIdString = self.InputText("Please input list of inlet profile ids: ")
separator = ' '
if seedIdString.find(',') != -1:
separator = ','
seedIdList = seedIdString.split(separator)
for seedIdString in seedIdList:
self._SourceSeedIds.InsertNextId(int(seedIdString.strip()))
seedIdString = self.InputText("Please input list of outlet profile ids (leave empty for all available profiles): ")
if seedIdString.strip() == '':
self.InputInfo("Selected outlets: ")
for i in range(seedPoints.GetNumberOfPoints()):
if self._SourceSeedIds.IsId(i) == -1:
self._TargetSeedIds.InsertNextId(i)
self.InputInfo("%d " % i)
self.InputInfo("\n")
else:
seedIdList = seedIdString.split(separator)
for seedIdString in seedIdList:
self._TargetSeedIds.InsertNextId(int(seedIdString.strip()))
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
wholeExtent = self.Image.GetExtent()
if self.Picker == None:
self.Picker = vtk.vtkCellPicker()
if self.PlaneWidgetX == None:
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
if self.PlaneWidgetY == None:
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
if self.PlaneWidgetZ == None:
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.Picker.SetTolerance(0.005)
self.PlaneWidgetX.SetResliceInterpolateToLinear()
self.PlaneWidgetX.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetX.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetX.SetInputData(self.Image)
self.PlaneWidgetX.SetPlaneOrientationToXAxes()
self.PlaneWidgetX.SetSliceIndex(wholeExtent[0])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetX.DisplayTextOn()
else:
self.PlaneWidgetX.DisplayTextOff()
self.PlaneWidgetX.SetPicker(self.Picker)
self.PlaneWidgetX.KeyPressActivationOff()
self.PlaneWidgetX.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetX.SetMarginSizeX(0.05)
self.PlaneWidgetX.SetMarginSizeY(0.05)
else:
self.PlaneWidgetX.SetMarginSizeX(0.0)
self.PlaneWidgetX.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetX.SetWindowLevel(self.WindowLevel[0],
self.WindowLevel[1])
self.PlaneWidgetX.On()
self.PlaneWidgetY.SetResliceInterpolateToLinear()
self.PlaneWidgetY.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetY.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetY.SetInputData(self.Image)
self.PlaneWidgetY.SetPlaneOrientationToYAxes()
self.PlaneWidgetY.SetSliceIndex(wholeExtent[2])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetY.DisplayTextOn()
else:
self.PlaneWidgetY.DisplayTextOff()
self.PlaneWidgetY.SetPicker(self.Picker)
self.PlaneWidgetY.KeyPressActivationOff()
self.PlaneWidgetY.SetLookupTable(self.PlaneWidgetX.GetLookupTable())
self.PlaneWidgetY.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetY.SetMarginSizeX(0.05)
self.PlaneWidgetY.SetMarginSizeY(0.05)
else:
self.PlaneWidgetY.SetMarginSizeX(0.0)
self.PlaneWidgetY.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetY.SetWindowLevel(self.WindowLevel[0],
self.WindowLevel[1])
self.PlaneWidgetY.On()
self.PlaneWidgetZ.SetResliceInterpolateToLinear()
self.PlaneWidgetZ.SetTextureInterpolate(self.TextureInterpolation)
self.PlaneWidgetZ.SetUseContinuousCursor(self.ContinuousCursor)
self.PlaneWidgetZ.SetInputData(self.Image)
self.PlaneWidgetZ.SetPlaneOrientationToZAxes()
self.PlaneWidgetZ.SetSliceIndex(wholeExtent[4])
if self.vmtkRenderer.Annotations:
self.PlaneWidgetZ.DisplayTextOn()
else:
self.PlaneWidgetZ.DisplayTextOff()
self.PlaneWidgetZ.SetPicker(self.Picker)
self.PlaneWidgetZ.KeyPressActivationOff()
self.PlaneWidgetZ.SetLookupTable(self.PlaneWidgetX.GetLookupTable())
self.PlaneWidgetZ.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
if self.Margins:
self.PlaneWidgetZ.SetMarginSizeX(0.05)
self.PlaneWidgetZ.SetMarginSizeY(0.05)
else:
self.PlaneWidgetZ.SetMarginSizeX(0.0)
self.PlaneWidgetZ.SetMarginSizeY(0.0)
if self.WindowLevel[0] != 0.0:
self.PlaneWidgetZ.SetWindowLevel(self.WindowLevel[0],
self.WindowLevel[1])
self.PlaneWidgetZ.On()
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
# Error handling
if self.Surface == None:
self.PrintError(
'Error: no input surface was supplied, ensure file exists, ensure correct environment'
)
# Allocate a renderer and label own renderer in use to prevent multiple renderers from being used
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
# Render and build view of the input surface
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
# Test question in render window
#queryStr = 'Is this the question you wanted to see? '
#inputStr = self.YesNoInput(queryStr, self.YesNoValidator)
# Surface smoothing, try defaults first then take user input if not adequate
acceptableResult = 0
response = 0
while acceptableResult == 0:
if response == 0:
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
self.SurfaceSmoothing.NumberOfIterations = 100
self.PassBand = 0.001
elif response == 1:
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
#Take passband from user
queryStr = 'Please enter value for pass band (0.001 - 0.1): '
self.SurfaceSmoothing.PassBand = float(
self.InputText(queryStr, self.PassBandValidator))
#Take number of iterations from user
queryStr = 'Please enter number of iterations (1-999): '
self.SurfaceSmoothing.NumberOfIterations = int(
self.InputText(queryStr, self.IterationValidator))
self.SurfaceSmoothing.Surface = self.Surface
self.SurfaceSmoothing.Execute()
self.SurfaceViewer.Surface = self.SurfaceSmoothing.Surface
self.SurfaceViewer.BuildView()
# Accept or reject result of smoothing surface
queryStr = 'Accept result of smoothing?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.SurfaceSmoothing.Surface
else:
acceptableResult = 0
response = 1
# Surface clipping
# The only issue here is that 2 renderers get built 2/2 the structure of vmtkSurfaceClipper
# Issue to be revisited later
acceptableResult = 0
while acceptableResult == 0:
self.SurfaceClipper = vmtkscripts.vmtkSurfaceClipper()
self.SurfaceClipper.Surface = self.Surface
self.SurfaceClipper.Execute()
self.SurfaceViewer.Surface = self.SurfaceClipper.Surface
self.SurfaceViewer.BuildView()
queryStr = 'Accept result of clipping?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.SurfaceClipper.Surface
else:
acceptableResult = 0
self.SurfaceViewer.Surface = self.SurfaceClipper.Surface
self.SurfaceViewer.BuildView()
# Create centerlines based off the acceptable clipped surface
centerliner = vmtkscripts.vmtkCenterlines()
centerliner.Surface = self.Surface
centerliner.SeedSelectorName = 'openprofiles'
centerliner.Execute()
self.Centerlines = centerliner.Centerlines
# Add flow extensions until user has acceptable result
acceptableResult = 0
response = 0
while (acceptableResult == 0):
self.FlowExtensions = vmtkscripts.vmtkFlowExtensions()
self.FlowExtensions.Surface = self.Surface
self.FlowExtensions.Centerlines = self.Centerlines
self.FlowExtensions.AdaptiveExtensionLength = 1
#self.FlowExtensions.CenterlineNormalEstimationDistanceRatio = 1
self.FlowExtensions.Interactive = 0
# Take user extension ratio if response to acceptable outcome question
# Default extension ratio is 10
if (response == 0):
self.FlowExtensions.ExtensionRatio = 10
elif (response == 1):
#Take extension ratio from user
queryStr = 'Please enter value for pass band; default is 20 (min/max 1-50): '
self.FlowExtensions.ExtensionRatio = float(
self.InputText(queryStr, self.ExtensionRatioValidator))
self.FlowExtensions.Execute()
self.SurfaceViewer.Surface = self.FlowExtensions.Surface
self.SurfaceViewer.BuildView()
queryStr = 'Accept flow extensions?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.FlowExtensions.Surface
else:
acceptableResult = 0
response = 1
# self.SurfaceViewer.BuildView()
# Deallocate renderer
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self.InputTraces == None):
self.PrintError('Error: no Traces.')
if (self.TimeStep == None):
self.PrintError('Error: no TimeStep.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
surfaceViewer = vmtksurfaceviewer.vmtkSurfaceViewer()
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.Surface = self.InputTraces
surfaceViewer.ArrayName = self.ArrayName
surfaceViewer.ColorMap = self.ColorMap
surfaceViewer.NumberOfColors = self.NumberOfColors
surfaceViewer.Execute()
if self.ColorMap == 'grayscale':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
lut.SetValueRange(0.0, 1.0)
lut.SetSaturationRange(0.0, 0.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'rainbow':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetHueRange(0.666667, 0.0)
lut.SetSaturationRange(0.75, 0.75)
lut.SetValueRange(1.0, 1.0)
lut.SetAlphaRange(1.0, 1.0)
lut.SetNumberOfColors(self.NumberOfColors)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'blackbody':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToRGB()
colorTransferFunction.AddRGBPoint(0, 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(0.4, 0.901961, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(0.8, 0.901961, 0.901961, 0.0)
colorTransferFunction.AddRGBPoint(1.0, 1.0, 1.0, 1.0)
for ii, ss in enumerate([
float(xx) / float(self.NumberOfColors)
for xx in range(self.NumberOfColors)
]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii, cc[0], cc[1], cc[2], 1.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if self.ColorMap == 'cooltowarm':
lut = surfaceViewer.Actor.GetMapper().GetLookupTable()
lut.SetNumberOfTableValues(self.NumberOfColors)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.SetColorSpaceToDiverging()
colorTransferFunction.AddRGBPoint(0, 0.231373, 0.298039, 0.752941)
colorTransferFunction.AddRGBPoint(0.5, 0.865003, 0.865003,
0.865003)
colorTransferFunction.AddRGBPoint(1.0, 0.705882, 0.0156863,
0.14902)
for ii, ss in enumerate([
float(xx) / float(self.NumberOfColors)
for xx in range(self.NumberOfColors)
]):
cc = colorTransferFunction.GetColor(ss)
lut.SetTableValue(ii, cc[0], cc[1], cc[2], 1.0)
lut.Build()
surfaceViewer.Actor.GetMapper().SetLookupTable(lut)
if (self.Legend == 1):
self.ScalarBarActor = vtk.vtkScalarBarActor()
self.ScalarBarActor.SetLookupTable(
surfaceViewer.Actor.GetMapper().GetLookupTable())
self.ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.ScalarBarActor.GetLabelTextProperty().BoldOff()
self.ScalarBarActor.GetLabelTextProperty().ShadowOff()
self.ScalarBarActor.SetWidth(0.1)
self.ScalarBarActor.SetHeight(0.6)
self.ScalarBarActor.SetNumberOfLabels(4)
self.ScalarBarActor.SetTitle(self.ArrayName + " [" +
self.ArrayUnit + "]")
self.ScalarBarActor.SetLabelFormat('%.2f')
self.vmtkRenderer.Renderer.AddActor(self.ScalarBarActor)
self.Traces = vtk.vtkPolyData()
self.Traces.DeepCopy(self.InputTraces)
self.Traces.GetPointData().SetActiveScalars("IntegrationTime")
timeRange = self.Traces.GetPointData().GetScalars().GetRange(0)
currentCycle = 0
minTime = self.MinTime
currentTime = self.TimeStep
maxTime = self.MaxTime
if (self.ArrayMax == None and self.ArrayName == "Velocity"):
self.ArrayMax = round(
self.Traces.GetPointData().GetArray('Speed').GetRange()[1], 0)
if self.Method is 'particles':
particleTime = minTime
imageNumber = 0
while particleTime <= maxTime:
contour = vtk.vtkContourFilter()
contour.SetInputData(self.Traces)
i = 0
while i <= currentCycle:
time = minTime + currentTime + (maxTime - minTime) * i
if time < timeRange[0] or time > timeRange[1]:
pass
else:
contour.SetValue(i, time)
i += 1
contour.Update()
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.Actor.GetProperty().SetPointSize(self.PointSize)
vtk.vtkPolyDataMapper.SafeDownCast(
surfaceViewer.Actor.GetMapper()).SetInputConnection(
contour.GetOutputPort())
surfaceViewer.Actor.GetMapper().GetLookupTable(
).SetVectorModeToMagnitude()
surfaceViewer.Actor.GetMapper(
).SetScalarModeToUsePointFieldData()
surfaceViewer.Actor.GetMapper().SelectColorArray(
self.ArrayName)
surfaceViewer.Actor.GetMapper().SetScalarRange(
[0.0, self.ArrayMax])
surfaceViewer.vmtkRenderer.RenderWindow.Render()
if self.WithScreenshots:
self.Screenshot(surfaceViewer, imageNumber)
particleTime += self.TimeStep
currentTime += self.TimeStep
imageNumber += 1
elif self.Method is 'streaklines':
particleTime = minTime
imageNumber = 0
while particleTime <= maxTime:
clip1 = vtk.vtkClipPolyData()
clip1.SetInputData(self.Traces)
clip1.GenerateClipScalarsOff()
clip1.InsideOutOn()
clip2 = vtk.vtkClipPolyData()
clip2.SetInputConnection(clip1.GetOutputPort())
clip2.GenerateClipScalarsOff()
clip2.InsideOutOff()
cyclesPerRange = (int(
(timeRange[1] - timeRange[0]) / (maxTime - minTime))) + 1
cycle = currentCycle % cyclesPerRange
time = minTime + currentTime + (maxTime - minTime) * cycle
streakLineTimeLength = self.StreakLineTimeLength
clip1.SetValue(time)
clip2.SetValue(time - streakLineTimeLength)
clip2.Update()
surfaceViewer.Actor.GetProperty().SetLineWidth(self.LineWidth)
vtk.vtkPolyDataMapper.SafeDownCast(
surfaceViewer.Actor.GetMapper()).SetInputConnection(
clip2.GetOutputPort())
surfaceViewer.Actor.GetMapper().GetLookupTable(
).SetVectorModeToMagnitude()
surfaceViewer.Actor.GetMapper(
).SetScalarModeToUsePointFieldData()
surfaceViewer.Actor.GetMapper().SelectColorArray(
self.ArrayName)
surfaceViewer.Actor.GetMapper().SetScalarRange(
[0.0, self.ArrayMax])
surfaceViewer.vmtkRenderer = self.vmtkRenderer
surfaceViewer.vmtkRenderer.RenderWindow.Render()
if self.WithScreenshots:
self.Screenshot(surfaceViewer, imageNumber)
particleTime += self.TimeStep
currentTime += self.TimeStep
imageNumber += 1
else:
self.PrintError('Error: pathlineanimator method not supported.')
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
self.Clipper = vtk.vtkClipPolyData()
self.Clipper.SetInputData(self.Surface)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.SetInsideOut(self.InsideOut)
if self.Interactive:
if self.WidgetType == "box":
self.ClipFunction = vtk.vtkPlanes()
elif self.WidgetType == "sphere":
self.ClipFunction = vtk.vtkSphere()
self.Clipper.SetClipFunction(self.ClipFunction)
self.Cutter = vtk.vtkCutter()
self.Cutter.SetInputData(self.Surface)
self.Cutter.SetCutFunction(self.ClipFunction)
self.ClippedSurface = vtk.vtkPolyData()
self.CutLines = vtk.vtkPolyData()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.Surface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.WidgetType == "box":
self.ClipWidget = vtk.vtkBoxWidget()
self.ClipWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetFaceProperty().SetOpacity(0.25)
elif self.WidgetType == "sphere":
self.ClipWidget = vtk.vtkSphereWidget()
self.ClipWidget.GetSphereProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetSphereProperty().SetOpacity(0.25)
self.ClipWidget.GetSelectedSphereProperty().SetColor(0.6,0.0,0.0)
self.ClipWidget.GetSelectedSphereProperty().SetOpacity(0.75)
self.ClipWidget.SetRepresentationToSurface()
self.ClipWidget.SetPhiResolution(20)
self.ClipWidget.SetThetaResolution(20)
self.ClipWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.vmtkRenderer.AddKeyBinding('space','Clip.',self.ClipCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Transform = vtk.vtkTransform()
if self.WidgetType == "box":
self.ClipWidget.GetTransform(self.Transform)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
else:
self.Surface.GetPointData().SetActiveScalars(self.ClipArrayName)
self.Clipper.GenerateClipScalarsOff()
self.Clipper.SetValue(self.ClipValue)
self.Clipper.Update()
self.Cutter = vtk.vtkContourFilter()
self.Cutter.SetInputData(self.Surface)
self.Cutter.SetValue(0,self.ClipValue)
self.Cutter.Update()
self.Surface = self.Clipper.GetOutput()
self.ClippedSurface = self.Clipper.GetClippedOutput()
self.CutLines = self.Cutter.GetOutput()
if self.CleanOutput == 1:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.Surface)
cleaner.Update()
self.Surface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.ClippedSurface)
cleaner.Update()
self.ClippedSurface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.CutLines)
cleaner.Update()
stripper = vtk.vtkStripper()
stripper.SetInputConnection(cleaner.GetOutputPort())
stripper.Update()
self.CutLines = stripper.GetOutput()
def Execute(self):
if self.Centerlines == None:
self.PrintError('Error: No input centerlines.')
if self.ReferenceSystems == None:
self.PrintError('Error: No input reference systems.')
if self.Interactive and not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if self.Interactive:
self.vmtkRenderer.RegisterScript(self)
viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
viewer.Centerlines = self.Centerlines
viewer.CellDataArrayName = self.GroupIdsArrayName
viewer.vmtkRenderer = self.vmtkRenderer
viewer.InputText = self.InputText
viewer.OutputText = self.OutputText
viewer.PrintError = self.PrintError
viewer.PringLog = self.PrintLog
viewer.Display = 0
viewer.Execute()
groupIdString = self.InputText(
"Please input the reference groupId:\n", self.GroupIdValidator)
self.ReferenceGroupId = int(groupIdString)
offsetFilter = vtkvmtk.vtkvmtkCenterlineReferenceSystemAttributesOffset(
)
offsetFilter.SetInputData(self.Centerlines)
offsetFilter.SetReferenceSystems(self.ReferenceSystems)
offsetFilter.SetAbscissasArrayName(self.AbscissasArrayName)
offsetFilter.SetNormalsArrayName(self.NormalsArrayName)
if not self.ReplaceAttributes:
offsetFilter.SetOffsetAbscissasArrayName(
self.OffsetAbscissasArrayName)
offsetFilter.SetOffsetNormalsArrayName(self.OffsetNormalsArrayName)
else:
offsetFilter.SetOffsetAbscissasArrayName(self.AbscissasArrayName)
offsetFilter.SetOffsetNormalsArrayName(self.NormalsArrayName)
offsetFilter.SetGroupIdsArrayName(self.GroupIdsArrayName)
offsetFilter.SetCenterlineIdsArrayName(self.CenterlineIdsArrayName)
offsetFilter.SetReferenceSystemsNormalArrayName(
self.ReferenceSystemsNormalArrayName)
offsetFilter.SetReferenceSystemsGroupIdsArrayName(
self.GroupIdsArrayName)
offsetFilter.SetReferenceGroupId(self.ReferenceGroupId)
offsetFilter.Update()
self.Centerlines = offsetFilter.GetOutput()
if self.ReferenceGroupId == -1:
self.ReferenceGroupId = offsetFilter.GetReferenceGroupId()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSurface(self.Surface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
mainBodySeedIds = self.SeedSelector.GetSourceSeedIds()
mainBodySeedId = mainBodySeedIds.GetId(0)
mainBodyPoint = self.Surface.GetPoint(mainBodySeedId)
clipSeedIds = self.SeedSelector.GetTargetSeedIds()
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
clippedSurface = surfaceTriangulator.GetOutput()
for i in range(clipSeedIds.GetNumberOfIds()):
seedId = clipSeedIds.GetId(i)
locator = vtk.vtkPointLocator()
locator.SetDataSet(clippedSurface)
locator.BuildLocator()
seedPoint = self.Surface.GetPoint(seedId)
seedPointId = locator.FindClosestPoint(seedPoint)
planeEstimator = vtkvmtk.vtkvmtkPolyDataNormalPlaneEstimator()
planeEstimator.SetInputData(clippedSurface)
planeEstimator.SetOriginPointId(seedPointId)
planeEstimator.Update()
plane = vtk.vtkPlane()
plane.SetOrigin(planeEstimator.GetOrigin())
plane.SetNormal(planeEstimator.GetNormal())
seamFilter = vtkvmtk.vtkvmtkTopologicalSeamFilter()
seamFilter.SetInputData(clippedSurface)
seamFilter.SetClosestPoint(seedPoint)
seamFilter.SetSeamScalarsArrayName("SeamScalars")
seamFilter.SetSeamFunction(plane)
clipper = vtk.vtkClipPolyData()
clipper.SetInputConnection(seamFilter.GetOutputPort())
clipper.GenerateClipScalarsOff()
clipper.GenerateClippedOutputOn()
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInputConnection(clipper.GetOutputPort())
connectivity.SetExtractionModeToClosestPointRegion()
connectivity.SetClosestPoint(mainBodyPoint)
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputConnection(connectivity.GetOutputPort())
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(
surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
#clippedSurface = vtk.vtkPolyData()
#clippedSurface.DeepCopy(surfaceTriangulator.GetOutput())
clippedSurface = surfaceTriangulator.GetOutput()
self.Surface = clippedSurface
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def BuildView(self):
# ensure python 2-3 compatibility for checking string type (difference with unicode str handeling)
PY3 = sys.version_info[0] == 3
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
if PY3:
string_types = str,
else:
string_types = basestring,
if not isinstance(self.VolumeRenderingMethod, string_types):
self.PrintError(
'Specified Rendering Method is not of required "string" type')
# create volume mapper and apply requested volume rendering method
volumeMapper = vtk.vtkSmartVolumeMapper()
if self.VolumeRenderingMethod.lower() == 'default':
volumeMapper.SetRequestedRenderModeToDefault()
elif self.VolumeRenderingMethod.lower() == 'gpu':
volumeMapper.SetRequestedRenderModeToGPU()
elif self.VolumeRenderingMethod.lower() == 'ospray':
volumeMapper.SetRequestedRenderModeToOSPRay()
elif self.VolumeRenderingMethod.lower() == 'raycast':
volumeMapper.SetRequestedRenderModeToRayCast()
else:
self.PrintError(
'Specified Rendering Method: ' + self.VolumeRenderingMethod +
' not supported. Please choose from ["default", "gpu", "ospray", "raycast"]'
)
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToComposite()
# parse the xml file which is loaded in the same path as the vmtkimagevolumeviewer.py file at runtime
presetElementTree = ET.parse(
os.path.join(os.path.dirname(__file__), 'share',
'vmtkimagevolumeviewerpresets.xml'))
presetRoot = presetElementTree.getroot()
volProperties = presetRoot.findall(
'VolumeProperty[@name="' + self.Preset +
'"]') # should return a list with only one element
volPropertiesDict = volProperties[0].attrib
def chunks(l, n):
"""Yield successive n-sized chunks from l."""
if PY3:
range_func = range
else:
range_func = xrange
for i in range_func(0, len(l), n):
yield l[i:i + n]
# need to convert the space seperated string displaying values into a list of floats
colorList = [
float(i) for i in volPropertiesDict['colorTransfer'].split()
]
gradientOpacityList = [
float(i) for i in volPropertiesDict['gradientOpacity'].split()
]
opacityList = [
float(i) for i in volPropertiesDict['scalarOpacity'].split()
]
# create an array of arrays with each list split into subarrays of desired size
colorMapList = chunks(colorList, 4)
gradientOpacityMapList = chunks(gradientOpacityList, 2)
opacityMapList = chunks(opacityList, 2)
# create vtk objects from the mapped lists (now arrays of arrays)
self.ColorTransferFunction = self.BuildVTKColorTransferFunction(
colorMapList)
self.GradientOpacityTransferFunction = self.BuildVTKPiecewiseFunction(
gradientOpacityMapList)
self.OpacityTransferFunction = self.BuildVTKPiecewiseFunction(
opacityMapList)
# assign other properties from the element tree to variables with the appropriate type
self.InterpolationType = int(volPropertiesDict['interpolation'])
self.Shade = int(volPropertiesDict['shade'])
self.SpecularPower = float(volPropertiesDict['specularPower'])
self.Specular = float(volPropertiesDict['specular'])
self.Diffuse = float(volPropertiesDict['diffuse'])
self.Ambient = float(volPropertiesDict['ambient'])
# set transfer function and lighting properties of the vtk volume object
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetScalarOpacity(self.OpacityTransferFunction)
volumeProperty.SetGradientOpacity(self.GradientOpacityTransferFunction)
volumeProperty.SetColor(self.ColorTransferFunction)
volumeProperty.SetInterpolationType(self.InterpolationType)
volumeProperty.SetShade(self.Shade)
volumeProperty.SetSpecularPower(self.SpecularPower)
volumeProperty.SetSpecular(self.Specular)
volumeProperty.SetDiffuse(self.Diffuse)
volumeProperty.SetAmbient(self.Ambient)
# create the volume from the mapper (defining image data and render mode) with the defined properties
# this is the last pipeline step applied. self.Volume just needs to now be added to the Renderer
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
# add the actors to the renderer
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
# This next section is responsible for creating the box outline around the volume's data extent.
if self.BoxOutline:
outline = vtk.vtkOutlineFilter()
outline.SetInputData(self.Image)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
boxWidget.SetPlaceFactor(1.0)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputData(self.Image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
# Add the actors to the renderer
self.vmtkRenderer.Renderer.AddActor(outlineActor)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if (self.Mesh == None):
self.PrintError('Error: no Mesh.')
if (self.Centerlines == None):
self.PrintError('Error: no Centerlines')
#Save the centerlines
previousCenterlines = self.Centerlines
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(self.Centerlines)
cleaner.Update()
self.Centerlines = cleaner.GetOutput()
if self.Tolerance == -1:
self.Tolerance = 0.000001*self.Mesh.GetLength()
if self.RadiusArrayName != '':
self.RadiusArray = self.Centerlines.GetPointData().GetArray(self.RadiusArrayName)
if self.RadiusArray == None:
self.PrintError('Error : could not find radius array')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
meshMapper = vtk.vtkDataSetMapper()
meshMapper.SetInputData(self.Mesh)
meshMapper.ScalarVisibilityOff()
self.MeshActor = vtk.vtkActor()
self.MeshActor.SetMapper(meshMapper)
self.MeshActor.GetProperty().SetOpacity(0.25)
self.MeshActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.MeshActor)
centerlinesMapper = vtk.vtkDataSetMapper()
centerlinesMapper.SetInputData(self.Centerlines)
centerlinesMapper.ScalarVisibilityOff()
self.CenterlinesActor = vtk.vtkActor()
self.CenterlinesActor.SetMapper(centerlinesMapper)
self.vmtkRenderer.Renderer.AddActor(self.CenterlinesActor)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1)
glyphs.SetInputData(self.Spheres)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToScaleByScalar()
glyphs.SetScaleFactor(1.)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutput())
glyphMapper.ScalarVisibilityOff()
self.SpheresActor = vtk.vtkActor()
self.SpheresActor.SetMapper(glyphMapper)
self.SpheresActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SpheresActor.GetProperty().SetOpacity(0.25)
self.SpheresActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SpheresActor)
self.InterpolatedGlyphs = vtk.vtkGlyph3D()
interpolatedGlyphSource = vtk.vtkSphereSource()
interpolatedGlyphSource.SetRadius(1)
self.InterpolatedGlyphs.SetInputData(self.Centerlines)
self.InterpolatedGlyphs.SetSourceConnection(interpolatedGlyphSource.GetOutputPort())
#scaling is off for now
self.InterpolatedGlyphs.SetScaleModeToDataScalingOff()
self.InterpolatedGlyphs.SetScaleFactor(0.)
interpolatedGlyphMapper = vtk.vtkPolyDataMapper()
interpolatedGlyphMapper.SetInputConnection(self.InterpolatedGlyphs.GetOutputPort())
interpolatedGlyphMapper.ScalarVisibilityOff()
self.InterpolatedSpheresActor = vtk.vtkActor()
self.InterpolatedSpheresActor.SetMapper(interpolatedGlyphMapper)
self.InterpolatedSpheresActor.GetProperty().SetColor(0.0,1.0,0.0)
self.InterpolatedSpheresActor.GetProperty().SetOpacity(0.25)
self.InterpolatedSpheresActor.PickableOff()
self.InterpolatedSpheresActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.InterpolatedSpheresActor)
polyBallMapper = vtk.vtkPolyDataMapper()
polyBallMapper.ScalarVisibilityOff()
self.PolyBallActor = vtk.vtkActor()
self.PolyBallActor.SetMapper(polyBallMapper)
self.PolyBallActor.GetProperty().SetColor(0.0,1.0,0.0)
self.PolyBallActor.GetProperty().SetOpacity(0.25)
self.PolyBallActor.PickableOff()
self.PolyBallActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.PolyBallActor)
self.SphereWidget = vtk.vtkSphereWidget()
self.SphereWidget.TranslationOff()
self.SphereWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.SphereWidget.AddObserver("InteractionEvent", self.SphereCallback)
self.Clipper = vtk.vtkClipDataSet()
self.Clipper.SetInputData(self.Mesh)
self.Clipper.SetInsideOut(self.InsideOut)
self.Clipper.GenerateClippedOutputOn()
#self.LineClipper = vtkvmtk.vtkvmtkClipDataSetLine()
#self.LineClipper.SetInputData(self.Mesh)
#self.LineClipper.SetInsideOut(self.InsideOut)
#self.LineClipper.GenerateClippedOutputOn()
self.InitializeSpheres()
self.PreviewMesh = self.Mesh
self.Display()
self.PolyBallActor.VisibilityOff()
self.ClipMesh()
if self.ClippedMesh == None:
#return an empty mesh
self.ClippedMesh = vtk.vtkUnstructuredGrid()
elif self.IncludeSurfaceCells:
#Create the surface cells
self.PreviewMesh = self.CreateSurfaceCells(self.PreviewMesh)
self.ClippedMesh = self.CreateSurfaceCells(self.ClippedMesh)
self.Mesh = self.PreviewMesh
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
#Restore the centerlines
self.Centerlines = previousCenterlines
