[vtkusers] isosurface of labeled blobs: all contours just red

[Bill Lorensen]

There have been a number of questions regarding how to generate
surfaces from labeled volumes. I just added an example to the vtk wiki
that shows how to do this.

http://www.vtk.org/Wiki/Create_models_from_labeled_volume_data_(Discrete_MarchingCubes)

I hope this helps,

Bill


On Sat, Aug 8, 2009 at 12:41 PM, Bill Lorensen<bill.lorensen at gmail.com> wrote:
> If your data is labelled with integer values and not continuous
> values, you should use discrete marching cubes. Discrete marching
> cubes will label each cell (not point) with the label value. You must
> tell the mapper to SetScalarModeToUseCellData().
>
> Bill
>
> On Sat, Aug 8, 2009 at 4:57 AM, <lynx.abraxas at freenet.de> wrote:
>> Hello!
>>
>>
>> I'm new to VTK. I want to generate a surface of labeld blobs (3D-TIF from ITK)
>> that I'd like to import into blender but I'm stuck in VTK:
>> I used http://www.evl.uic.edu/aspale/cs526/final/3-5-2-0.htm as  a  start  and
>> modified                   it                   according                   to
>> http://public.kitware.com/pipermail/vtkusers/2004-November/077288.html.    But
>> Tracy's problem is now also my problem: How do I get the surfaces of my labels
>> colored differently?
>> From the docs I'd understand that GenerateValues(10,1,11) should  generate  10
>> sufaces of my first 10 labels but I always see all 955 labels in red.
>> When only dots are shown during rotation I can see some different colors.
>> If I use GenerateValues(10 ,1,955) I can see multiple colored layers in the blobs that
>> are cut through by the border.
>>
>> So how do I get my blobs colored differently with just one layer?
>> What is GenerateValues() doing exactly?
>>
>> Many thanks for any hints or help
>> Lynx
>>
>>
>> import Tkinter
>>
>> import vtk
>>
>> from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
>>
>>
>>
>> # Prepare to read the file
>>
>> readerVolume = vtk.vtkImageReader()
>> #readerVolume = vtk.vtkTIFFReader()
>> readerVolume.SetDataScalarType( vtk.VTK_UNSIGNED_SHORT )
>> readerVolume.SetFileDimensionality( 3 )
>> readerVolume.SetDataExtent ( 0,517, 0,228, 0,392)
>> readerVolume.SetDataSpacing( 1,1,1 )
>> readerVolume.SetNumberOfScalarComponents( 1 )
>> readerVolume.SetDataByteOrderToBigEndian()
>> #readerVolume.SetFileName( "./Female.raw" )
>> readerVolume.SetFileName( "../stack_ws01.raw" )
>>
>>
>>
>> # Extract the region of interest
>>
>> voiHead = vtk.vtkExtractVOI()
>>
>> voiHead.SetInput( readerVolume.GetOutput() )
>>
>> #voiHead.SetVOI( 0,255, 60,255, 0,100 )
>> voiHead.SetVOI(0,517, 0,228, 0,392)
>> #voiHead.SetSampleRate(1,1,1)
>> voiHead.SetSampleRate(3,3,3)
>> voiHead.Update()#necessary for GetScalarRange()
>> srange= voiHead.GetOutput().GetScalarRange()#needs Update() before!
>> print "Range", srange
>>
>> # Generate an isosurface
>>
>> # UNCOMMENT THE FOLLOWING LINE FOR CONTOUR FILTER
>>
>> #contourBoneHead = vtk.vtkContourFilter()
>> contourBoneHead = vtk.vtkMarchingCubes()
>>
>> contourBoneHead.SetInput( voiHead.GetOutput() )
>>
>> contourBoneHead.ComputeNormalsOn()
>> #contourBoneHead.GenerateValues(10,1,11)
>> #contourBoneHead.GenerateValues(955,1,955)
>> contourBoneHead.GenerateValues(10 ,1,955)
>> #contourBoneHead.SetValue( 0, 100. )  #second value has no effect!?!
>> print "# Values:", contourBoneHead.GetNumberOfContours()
>> contourBoneHead.Update() #needed for GetNumberOfPolys() !!!
>> print "Creating ", contourBoneHead.GetOutput().GetNumberOfPolys(), " polygons."
>>
>> # define lookuptable
>> lut = vtk.vtkLookupTable()
>> lut.SetHueRange (0.0,0.667)
>> lut.SetNumberOfColors (256)
>> lut.Build()
>> for i in range(0, 53):
>>    lut.SetTableValue(i, (i+1)/255.0, (i+2)/255.0, (i+3)/255.0, 1.0)
>>
>> # Take the isosurface data and create geometry
>>
>> geoBoneMapper = vtk.vtkPolyDataMapper()
>>
>> geoBoneMapper.SetInput( contourBoneHead.GetOutput() )
>>
>> #geoBoneMapper.ScalarVisibilityOff()#show no colour
>> geoBoneMapper.ScalarVisibilityOn()#show colour
>> geoBoneMapper.SetScalarRange(srange)
>> #geoBoneMapper.SetLookupTable(lut)
>>
>>
>> # Take the isosurface data and create geometry
>>
>> actorBone = vtk.vtkLODActor()
>>
>> actorBone.SetNumberOfCloudPoints( 100000 )
>> actorBone.SetMapper( geoBoneMapper )
>> #actorBone.GetProperty().SetColor( 1, 1, 1 ) #for ScalarVisibilityOff()
>>
>>
>>
>> # Create renderer
>>
>> ren = vtk.vtkRenderer()
>> ren.SetBackground( 0.329412, 0.34902, 0.427451 ) #Paraview blue
>> ren.AddActor(actorBone)
>>
>>
>>
>> # 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()
>>
>> #   vtkPolyDataWriter *volwriter1 = vtkPolyDataWriter::New();
>> #    volwriter1->SetInput( iso->GetOutput() );
>> #   volwriter1->SetFileName("braintstem6740.vtk");
>> #   volwriter1->Write();
>>
>>
>>
>>
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