VTK/Examples/Python/MeshLabelImageColor
From KitwarePublic
This example takes a label image in Meta format and meshes a single label of it. It then smoothes the mesh and colours the vertices according to the displacement error introduced by the smoothing. The whole thing is then displayed. An example data can be found here Media:labels.tgz
MeshLabelImageColor.py
import vtk input='labels.mhd' # Prepare to read the file readerVolume = vtk.vtkMetaImageReader() readerVolume.SetFileName(input) readerVolume.Update() # Extract the region of interest voi = vtk.vtkExtractVOI() voi.SetInput(readerVolume.GetOutput()) #voi.SetVOI(0,517, 0,228, 0,392) voi.SetSampleRate(1,1,1) #voi.SetSampleRate(3,3,3) voi.Update()#necessary for GetScalarRange() srange= voi.GetOutput().GetScalarRange()#needs Update() before! print "Range", srange ##Prepare surface generation contour = vtk.vtkDiscreteMarchingCubes() #for label images contour.SetInput( voi.GetOutput() ) #contour.ComputeNormalsOn() #choose one lable index= 31 print "Doing label", index contour.SetValue(0, index) contour.Update() #needed for GetNumberOfPolys() !!! smoother= vtk.vtkWindowedSincPolyDataFilter() smoother.SetInput(contour.GetOutput()) smoother.SetNumberOfIterations(30) #this has little effect on the error! #smoother.BoundarySmoothingOff() #smoother.FeatureEdgeSmoothingOff() #smoother.SetFeatureAngle(120.0) #smoother.SetPassBand(.001) #this increases the error a lot! smoother.NonManifoldSmoothingOn() smoother.NormalizeCoordinatesOn() smoother.GenerateErrorScalarsOn() #smoother.GenerateErrorVectorsOn() smoother.Update() smoothed_polys= smoother.GetOutput() smoother_error= smoothed_polys.GetPointData().GetScalars() ##Find min and max z se_range= smoother_error.GetRange() print se_range minz= se_range[0] #min(smoother_error) maxz= se_range[1] #max(smoother_error) if (maxz > 1): print "Big smoother error: min/max:", minz, maxz minz= .3 #this way colours of different particles are comparable maxz= 1 ## Create the color map colorLookupTable= vtk.vtkLookupTable() colorLookupTable.SetTableRange(minz, maxz) #this does nothing, use mapper.SetScalarRange(minz, maxz) colorLookupTable.SetHueRange(2/3.0, 1) #colorLookupTable.SetSaturationRange(0, 0) #colorLookupTable.SetValueRange(1, 0) #colorLookupTable.SetNumberOfColors(256) #256 default colorLookupTable.Build() ##calc cell normal triangleCellNormals= vtk.vtkPolyDataNormals() triangleCellNormals.SetInput(smoothed_polys) triangleCellNormals.ComputeCellNormalsOn() triangleCellNormals.ComputePointNormalsOff() triangleCellNormals.ConsistencyOn() triangleCellNormals.AutoOrientNormalsOn() triangleCellNormals.Update() #creates vtkPolyData mapper= vtk.vtkPolyDataMapper() #mapper.SetInput(smoothed_polys) #this has no normals mapper.SetInput(triangleCellNormals.GetOutput()) #this is better for vis;-) mapper.ScalarVisibilityOn()#show colour mapper.SetScalarRange(minz, maxz) #mapper.SetScalarModeToUseCellData() # contains the label eg. 31 mapper.SetScalarModeToUsePointData() #the smoother error relates to the verts mapper.SetLookupTable(colorLookupTable) # Take the isosurface data and create geometry actor = vtk.vtkLODActor() actor.SetNumberOfCloudPoints( 100000 ) actor.SetMapper(mapper) # Create renderer ren = vtk.vtkRenderer() ren.SetBackground( 0, 0, 0 ) ren.AddActor(actor) # Create a window for the renderer of size 250x250 renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren) renWin.SetSize(250, 250) # Set an user interface interactor for the render window iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) # Start the initialization and rendering iren.Initialize() renWin.Render() iren.Start()
