MeshLabelImageColor

VTKExamples/Python/DataManipulation/MeshLabelImageColor


Description

This example takes a label image in Meta format and meshes a single label of it. It then smooths 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 labels.tgz.

Code

MeshLabelImageColor.py

from __future__ import print_function

import vtk


def main():
    colors = vtk.vtkNamedColors()
    ifn, index = get_program_parameters()

    # Prepare to read the file.
    readerVolume = vtk.vtkMetaImageReader()
    readerVolume.SetFileName(ifn)
    readerVolume.Update()

    # Extract the region of interest.
    voi = vtk.vtkExtractVOI()
    if vtk.VTK_MAJOR_VERSION <= 5:
        voi.SetInput(readerVolume.GetOutput())
    else:
        voi.SetInputConnection(readerVolume.GetOutputPort())
    voi.SetVOI(0, 517, 0, 228, 0, 392)
    voi.SetSampleRate(1, 1, 1)
    voi.Update()  # Necessary for GetScalarRange().
    srange = voi.GetOutput().GetScalarRange()  # Needs Update() before!
    print("Range", srange)

    # Prepare surface generation.
    contour = vtk.vtkDiscreteMarchingCubes()  # For label images.
    if vtk.VTK_MAJOR_VERSION <= 5:
        contour.SetInput(voi.GetOutput())
    else:
        contour.SetInputConnection(voi.GetOutputPort())
    # contour.ComputeNormalsOn()

    print("Doing label", index)

    contour.SetValue(0, index)
    contour.Update()  # Needed for GetNumberOfPolys()!!!

    smoother = vtk.vtkWindowedSincPolyDataFilter()
    if vtk.VTK_MAJOR_VERSION <= 5:
        smoother.SetInput(contour.GetOutput())
    else:
        smoother.SetInputConnection(contour.GetOutputPort())
    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("Smoother error range:", 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 = 0.3  # This way colours of different particles are comparable.
    # maxz = 1
    minz = 0.3
    maxz = 0.6

    # 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()

    # Calculate cell normals.
    triangleCellNormals = vtk.vtkPolyDataNormals()
    if vtk.VTK_MAJOR_VERSION <= 5:
        triangleCellNormals.SetInput(smoothed_polys)
    else:
        triangleCellNormals.SetInputData(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.
    if vtk.VTK_MAJOR_VERSION <= 5:
        mapper.SetInput(triangleCellNormals.GetOutput())  # This is better for vis;-)
    else:
        mapper.SetInputConnection(triangleCellNormals.GetOutputPort())  # 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 the renderer.
    ren = vtk.vtkRenderer()
    ren.SetBackground(colors.GetColor3d("DimGray"))
    ren.AddActor(actor)

    # Create a window for the renderer of size 600X600
    renWin = vtk.vtkRenderWindow()
    renWin.AddRenderer(ren)
    renWin.SetSize(600, 600)

    # Set a user interface interactor for the render window.
    iren = vtk.vtkRenderWindowInteractor()
    iren.SetRenderWindow(renWin)

    # Start the initialization and rendering.
    iren.Initialize()
    renWin.Render()
    ren.GetActiveCamera().SetPosition(268.628410, 128.452157, 24.517175)
    ren.GetActiveCamera().SetFocalPoint(256.006912, 175.949646, 24.175843)
    ren.GetActiveCamera().SetViewUp(0.844464, 0.227883, 0.484716)
    ren.ResetCameraClippingRange()
    renWin.Render()

    iren.Start()


def get_program_parameters():
    import argparse
    description = 'MeshLabelImageColor.'
    epilogue = '''
        Takes a label image in Meta format and meshes a single label of it.

   '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue)
    parser.add_argument('filename', help='labels.mhd')
    parser.add_argument('label', nargs='?', const=1, type=int, default=31, help='The label to use e.g 31')
    args = parser.parse_args()
    return args.filename, args.label


if __name__ == '__main__':
    main()