CurvatureBandsWithGlyphs

VTKExamples/Python/Visualization/CurvatureBandsWithGlyphs


Description

In this example we are coloring the surface by partitioning the gaussian curvature into bands and using arrows to display the normals on the surface.

Rather beautiful surfaces are generated.

The banded contour filter and an indexed lookup table are used along with the gaussian curvature filter to generate the banding on the surface. To further enhance the surface the surface normals are glyphed and colored by elevation using the default lookup table.

The example also demonstrates partitioning the pipelines into functions and how to generate a custom lookup table to handle irregular distributions of data.

For generating surfaces, the trick here is to return vtkPolydata for surfaces thereby hiding the particular surface properties in the implementation of the function. This allows us to specify multiple surface types and, in this code, to use an enum to pick the one we want.

The surface selected is the parametric random hills surface. The problem with the random hills surface is that most of the gaussian curvatures will lie in the range -1 to 0.2 (say) with a few large values say 20 to 40 at the peaks of the hills. Thus we need to manually allocate the color banding, this is done in the function MakeCustomBands(). The ranges selected in this function were determined by generating a frequency table for 20 bands and seeing where the values lie in the table. Then from this the distribution of the bands was made to best show the nature of the surface. The edges of the random hills surface have large irregular values so these are clipped.

The process is as follows:

  1. Use an enum to select your surface generating elevations and curvatures and clipping is needed.

  2. Use vtkColorSeries to make an indexed lookup table.

  3. Then we use the number of colors in the lookup table and the scalar range of the surface to create a list/vector of bands. If need be we generate manual bands.

  4. This list is then used to define the labels for the scalar bar using the midpoints of the ranges in the bands as the labels.

  5. Once this is done, we annotate the lookup table and then create a reversed lookup table. This will be used by the scalar bar actor.

  6. The maximum values in the ranges in the bands are used to set the bands in the banded contour filter.

  7. Glyphs are then created for the normals.

  8. Then everything is put together for the rendering in the usual actor/mapper pipeline. The reversed lookup table is used by the scalar bar actor so that the maximum value is at the top if the actor is placed in its default orientation/position.

  9. The function Display() pulls together all the components and returns a vtkRenderWindowInteractor so that you can interact with the image.

Feel free to experiment with different color schemes and/or the other sources from the parametric function group or the torus etc.

or versions of VTK older than VTK 8.0:

In the function MakeParametricHills() you may have to set ClockwiseOrderingOff() when using vtkParametricRandomHills as a source, this ensures that the normals face in the expected direction, the default is ClockwiseOrderingOn(). As an alternative, in MakeGlyphs(), you can set reverseNormals to True thereby invoking vtkReverseSense to achieve the same effect.

You will usually need to adjust the parameters for maskPts, arrow and glyph for a nice appearance. Do this in the function MakeGlyphs().

PrintBands() and PrintFrequencies() allow you to inspect the bands and the number of scalars in each band. These are useful if you want to get an idea of the distribution of the scalars in each band.

Code

CurvatureBandsWithGlyphs.py

#!/usr/bin/env python

from __future__ import print_function

import math

import vtk

# Available surfaces are:
SURFACE_TYPE = {"TORUS", "PARAMETRIC_HILLS", "PARAMETRIC_TORUS"}


def WritePNG(ren, fn, magnification=1):
    """
    Save the image as a PNG
    :param: ren - the renderer.
    :param: fn - the file name.
    :param: magnification - the magnification, usually 1.
    """
    renLgeIm = vtk.vtkRenderLargeImage()
    imgWriter = vtk.vtkPNGWriter()
    renLgeIm.SetInput(ren)
    renLgeIm.SetMagnification(magnification)
    imgWriter.SetInputConnection(renLgeIm.GetOutputPort())
    imgWriter.SetFileName(fn)
    imgWriter.Write()


def MakeBands(dR, numberOfBands, nearestInteger):
    """
    Divide a range into bands
    :param: dR - [min, max] the range that is to be covered by the bands.
    :param: numberOfBands - the number of bands, a positive integer.
    :param: nearestInteger - if True then [floor(min), ceil(max)] is used.
    :return: A List consisting of [min, midpoint, max] for each band.
    """
    bands = list()
    if (dR[1] < dR[0]) or (numberOfBands <= 0):
        return bands
    x = list(dR)
    if nearestInteger:
        x[0] = math.floor(x[0])
        x[1] = math.ceil(x[1])
    dx = (x[1] - x[0]) / float(numberOfBands)
    b = [x[0], x[0] + dx / 2.0, x[0] + dx]
    i = 0
    while i < numberOfBands:
        bands.append(b)
        b = [b[0] + dx, b[1] + dx, b[2] + dx]
        i += 1
    return bands


def MakeCustomBands(dR, numberOfBands):
    """
    Divide a range into custom bands.

    You need to specify each band as a list [r1, r2] where r1 < r2 and
    append these to a list (called x in the implementation).
    The list should ultimately look
    like this: x = [[r1, r2], [r2, r3], [r3, r4]...]

    :param: dR - [min, max] the range that is to be covered by the bands.
    :param: numberOfBands - the number of bands, a positive integer.
    :return: A List consisting of [min, midpoint, max] for each band.
    """
    bands = list()
    if (dR[1] < dR[0]) or (numberOfBands <= 0):
        return bands
    x = list()
    x.append([-0.7, -0.05])
    x.append([-0.05, 0])
    x.append([0, 0.13])
    x.append([0.13, 1.07])
    x.append([1.07, 35.4])
    x.append([35.4, 37.1])
    # Set the minimum to match the range minimum.
    x[0][0] = dR[0]
    if len(x) >= numberOfBands:
        x = x[:numberOfBands]
    # Adjust the last band.
    t = (x[len(x) - 1])
    if t[0] > dR[1]:
        t[0] = dR[1]
    t[1] = dR[1]
    x[len(x) - 1] = t
    for e in x:
        bands.append([e[0], e[0] + (e[1] - e[0]) / 2, e[1]])
    return bands


def Frequencies(bands, src):
    """
    Count the number of scalars in each band.
    :param: bands - the bands.
    :param: src - the vtkPolyData source.
    :return: The frequencies of the scalars in each band.
    """
    freq = dict()
    for i in range(len(bands)):
        freq[i] = 0
    tuples = src.GetPointData().GetScalars().GetNumberOfTuples()
    for i in range(tuples):
        x = src.GetPointData().GetScalars().GetTuple1(i)
        for j in range(len(bands)):
            if x <= bands[j][2]:
                freq[j] = freq[j] + 1
                break
    return freq


def MakeElevations(src):
    """
    Generate elevations over the surface.
    :param: src - the vtkPolyData source.
    :return: - vtkPolyData source with elevations.
    """
    bounds = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
    src.GetBounds(bounds)
    elevFilter = vtk.vtkElevationFilter()
    elevFilter.SetInputData(src)
    elevFilter.SetLowPoint(0, bounds[2], 0)
    elevFilter.SetHighPoint(0, bounds[3], 0)
    elevFilter.SetScalarRange(bounds[2], bounds[3])
    elevFilter.Update()
    return elevFilter.GetPolyDataOutput()


def MakeTorus():
    """
    Make a torus as the source.
    :return: vtkPolyData with normal and scalar data.
    """
    source = vtk.vtkSuperquadricSource()
    source.SetCenter(0.0, 0.0, 0.0)
    source.SetScale(1.0, 1.0, 1.0)
    source.SetPhiResolution(64)
    source.SetThetaResolution(64)
    source.SetThetaRoundness(1)
    source.SetThickness(0.5)
    source.SetSize(10)
    source.SetToroidal(1)

    # The quadric is made of strips, so pass it through a triangle filter as
    # the curvature filter only operates on polys
    tri = vtk.vtkTriangleFilter()
    tri.SetInputConnection(source.GetOutputPort())

    # The quadric has nasty discontinuities from the way the edges are generated
    # so let's pass it though a CleanPolyDataFilter and merge any points which
    # are coincident, or very close
    cleaner = vtk.vtkCleanPolyData()
    cleaner.SetInputConnection(tri.GetOutputPort())
    cleaner.SetTolerance(0.005)
    cleaner.Update()
    return CalculateCurvatures(MakeElevations(cleaner.GetOutput()))


def MakeParametricTorus():
    """
    Make a parametric torus as the source.
    :return: vtkPolyData with normal and scalar data.
    """
    fn = vtk.vtkParametricTorus()
    fn.SetRingRadius(5)
    fn.SetCrossSectionRadius(2)

    source = vtk.vtkParametricFunctionSource()
    source.SetParametricFunction(fn)
    source.SetUResolution(50)
    source.SetVResolution(50)
    source.SetScalarModeToZ()
    source.Update()
    # Name the arrays (not needed in VTK 6.2+ for vtkParametricFunctionSource)
    source.GetOutput().GetPointData().GetNormals().SetName('Normals')
    # We have calculated the elevation, just rename the scalars.
    source.GetOutput().GetPointData().GetScalars().SetName('Elevation')
    return CalculateCurvatures(source.GetOutput())


def MakeParametricHills():
    """
    Make a parametric hills surface as the source.
    :return: vtkPolyData with normal and scalar data.
    """
    fn = vtk.vtkParametricRandomHills()
    fn.AllowRandomGenerationOn()
    fn.SetRandomSeed(1)
    fn.SetNumberOfHills(30)
    # Make the normals face out of the surface.
    # Not needed with VTK 8.0 or later.
    # if fn.GetClassName() == 'vtkParametricRandomHills':
    #    fn.ClockwiseOrderingOff()

    source = vtk.vtkParametricFunctionSource()
    source.SetParametricFunction(fn)
    source.SetUResolution(50)
    source.SetVResolution(50)
    source.SetScalarModeToZ()
    source.Update()
    # Name the arrays (not needed in VTK 6.2+ for vtkParametricFunctionSource)
    source.GetOutput().GetPointData().GetNormals().SetName('Normals')
    # We have calculated the elevation, just rename the scalars.
    source.GetOutput().GetPointData().GetScalars().SetName('Elevation')
    return CalculateCurvatures(source.GetOutput())


def Clipper(src, dx, dy, dz):
    """
    Clip a vtkPolyData source.
    A cube is made whose size corresponds the the bounds of the source.
    Then each side is shrunk by the appropriate dx, dy or dz. After
    this operation the source is clipped by the cube.
    :param: src - the vtkPolyData source
    :param: dx - the amount to clip in the x-direction
    :param: dy - the amount to clip in the y-direction
    :param: dz - the amount to clip in the z-direction
    :return: vtkPolyData.
    """
    bounds = [0, 0, 0, 0, 0, 0]
    src.GetBounds(bounds)

    plane1 = vtk.vtkPlane()
    plane1.SetOrigin(bounds[0] + dx, 0, 0)
    plane1.SetNormal(1, 0, 0)

    plane2 = vtk.vtkPlane()
    plane2.SetOrigin(bounds[1] - dx, 0, 0)
    plane2.SetNormal(-1, 0, 0)

    plane3 = vtk.vtkPlane()
    plane3.SetOrigin(0, bounds[2] + dy, 0)
    plane3.SetNormal(0, 1, 0)

    plane4 = vtk.vtkPlane()
    plane4.SetOrigin(0, bounds[3] - dy, 0)
    plane4.SetNormal(0, -1, 0)

    plane5 = vtk.vtkPlane()
    plane5.SetOrigin(0, 0, bounds[4] + dz)
    plane5.SetNormal(0, 0, 1)

    plane6 = vtk.vtkPlane()
    plane6.SetOrigin(0, 0, bounds[5] - dz)
    plane6.SetNormal(0, 0, -1)

    clipFunction = vtk.vtkImplicitBoolean()
    clipFunction.SetOperationTypeToUnion()
    clipFunction.AddFunction(plane1)
    clipFunction.AddFunction(plane2)
    clipFunction.AddFunction(plane3)
    clipFunction.AddFunction(plane4)
    clipFunction.AddFunction(plane5)
    clipFunction.AddFunction(plane6)

    # Clip it.
    clipper = vtk.vtkClipPolyData()
    clipper.SetClipFunction(clipFunction)
    clipper.SetInputData(src)
    clipper.GenerateClipScalarsOff()
    clipper.GenerateClippedOutputOff()
    # clipper.GenerateClippedOutputOn()
    clipper.Update()
    return clipper.GetOutput()


def CalculateCurvatures(src):
    """
    The source must be triangulated.
    :param: src - the source.
    :return: vtkPolyData with normal and scalar data representing curvatures.
    """
    curvature = vtk.vtkCurvatures()
    curvature.SetCurvatureTypeToGaussian()
    curvature.SetInputData(src)
    curvature.Update()
    return curvature.GetOutput()


def MakeEnneper():
    """
    Make a parametric surface as the source.
    :return: vtkPolyData with normal and scalar data.
    """
    fn = vtk.vtkParametricEnneper()

    source = vtk.vtkParametricFunctionSource()
    source.SetParametricFunction(fn)
    source.SetUResolution(50)
    source.SetVResolution(50)
    source.SetScalarModeToZ()
    source.Update()
    # Name the arrays (not needed in VTK 6.2+ for vtkParametricFunctionSource)
    source.GetOutput().GetPointData().GetNormals().SetName('Normals')
    # We have calculated the elevation, just rename the scalars.
    source.GetOutput().GetPointData().GetScalars().SetName('Elevation')
    return CalculateCurvatures(source.GetOutput())


def MakeBoys():
    """
    Make a parametric surface as the source.
    :return: vtkPolyData with normal and scalar data.
    """
    fn = vtk.vtkParametricBoy()

    source = vtk.vtkParametricFunctionSource()
    source.SetParametricFunction(fn)
    source.SetUResolution(50)
    source.SetVResolution(50)
    source.SetScalarModeToZ()
    source.Update()
    # Name the arrays (not needed in VTK 6.2+ for vtkParametricFunctionSource)
    source.GetOutput().GetPointData().GetNormals().SetName('Normals')
    # We have calculated the elevation, just rename the scalars.
    source.GetOutput().GetPointData().GetScalars().SetName('Elevation')
    return CalculateCurvatures(source.GetOutput())


def MakeLUT():
    """
    Make a lookup table using vtkColorSeries.
    :return: An indexed lookup table.
    """
    # Make the lookup table.
    colorSeries = vtk.vtkColorSeries()
    # Select a color scheme.
    # colorSeriesEnum = colorSeries.BREWER_DIVERGING_BROWN_BLUE_GREEN_9
    # colorSeriesEnum = colorSeries.BREWER_DIVERGING_SPECTRAL_10
    # colorSeriesEnum = colorSeries.BREWER_DIVERGING_SPECTRAL_3
    # colorSeriesEnum = colorSeries.BREWER_DIVERGING_PURPLE_ORANGE_9
    # colorSeriesEnum = colorSeries.BREWER_SEQUENTIAL_BLUE_PURPLE_9
    # colorSeriesEnum = colorSeries.BREWER_SEQUENTIAL_BLUE_GREEN_9
    colorSeriesEnum = colorSeries.BREWER_QUALITATIVE_SET3
    # colorSeriesEnum = colorSeries.CITRUS
    colorSeries.SetColorScheme(colorSeriesEnum)
    lut = vtk.vtkLookupTable()
    colorSeries.BuildLookupTable(lut)
    lut.SetNanColor(0, 0, 0, 1)
    return lut


def ReverseLUT(lut):
    """
    Create a lookup table with the colors reversed.
    :param: lut - An indexed lookup table.
    :return: The reversed indexed lookup table.
    """
    lutr = vtk.vtkLookupTable()
    lutr.DeepCopy(lut)
    t = lut.GetNumberOfTableValues() - 1
    revRange = reversed(list(range(t + 1)))
    for i in revRange:
        rgba = [0.0] * 3
        v = float(i)
        lut.GetColor(v, rgba)
        rgba.append(lut.GetOpacity(v))
        lutr.SetTableValue(t - i, rgba)
    t = lut.GetNumberOfAnnotatedValues() - 1
    revRange = reversed(list(range(t + 1)))
    for i in revRange:
        lutr.SetAnnotation(t - i, lut.GetAnnotation(i))
    return lutr


def MakeGlyphs(src, reverseNormals):
    """
    Glyph the normals on the surface.

    You may need to adjust the parameters for maskPts, arrow and glyph for a
    nice appearance.

    :param: src - the surface to glyph.
    :param: reverseNormals - if True the normals on the surface are reversed.
    :return: The glyph object.

    """
    # Sometimes the contouring algorithm can create a volume whose gradient
    # vector and ordering of polygon (using the right hand rule) are
    # inconsistent. vtkReverseSense cures this problem.
    reverse = vtk.vtkReverseSense()

    # Choose a random subset of points.
    maskPts = vtk.vtkMaskPoints()
    maskPts.SetOnRatio(5)
    maskPts.RandomModeOn()
    if reverseNormals:
        reverse.SetInputData(src)
        reverse.ReverseCellsOn()
        reverse.ReverseNormalsOn()
        maskPts.SetInputConnection(reverse.GetOutputPort())
    else:
        maskPts.SetInputData(src)

    # Source for the glyph filter
    arrow = vtk.vtkArrowSource()
    arrow.SetTipResolution(16)
    arrow.SetTipLength(0.3)
    arrow.SetTipRadius(0.1)

    glyph = vtk.vtkGlyph3D()
    glyph.SetSourceConnection(arrow.GetOutputPort())
    glyph.SetInputConnection(maskPts.GetOutputPort())
    glyph.SetVectorModeToUseNormal()
    glyph.SetScaleFactor(1)
    glyph.SetColorModeToColorByVector()
    glyph.SetScaleModeToScaleByVector()
    glyph.OrientOn()
    glyph.Update()
    return glyph


def DisplaySurface(st):
    """
    Make and display the surface.
    :param: st - the surface to display.
    :return The vtkRenderWindowInteractor.
    """
    surface = st.upper()
    if not (surface in SURFACE_TYPE):
        print(st, "is not a surface.")
        iren = vtk.vtkRenderWindowInteractor()
        return iren

    colors = vtk.vtkNamedColors()

    # Set the background color.
    colors.SetColor("BkgColor", [179, 204, 255, 255])

    # ------------------------------------------------------------
    # Create the surface, lookup tables, contour filter etc.
    # ------------------------------------------------------------
    src = vtk.vtkPolyData()
    if surface == "TORUS":
        src = MakeTorus()
    elif surface == "PARAMETRIC_TORUS":
        src = MakeParametricTorus()
    elif surface == "PARAMETRIC_HILLS":
        src = Clipper(MakeParametricHills(), 0.5, 0.5, 0.0)
    # Here we are assuming that the active scalars are the curvatures.
    curvatureName = src.GetPointData().GetScalars().GetName()
    # Use this range to color the glyphs for the normals by elevation.
    src.GetPointData().SetActiveScalars('Elevation')
    scalarRangeElevation = src.GetScalarRange()
    src.GetPointData().SetActiveScalars(curvatureName)
    scalarRangeCurvatures = src.GetScalarRange()
    scalarRange = scalarRangeCurvatures

    lut = MakeLUT()
    numberOfBands = lut.GetNumberOfTableValues()
    bands = MakeBands(scalarRange, numberOfBands, False)
    if surface == "PARAMETRIC_HILLS":
        # Comment this out if you want to see how allocating
        # equally spaced bands works.
        bands = MakeCustomBands(scalarRange, numberOfBands)
        # Adjust the number of table values
        numberOfBands = len(bands)
        lut.SetNumberOfTableValues(numberOfBands)

    lut.SetTableRange(scalarRange)

    # We will use the midpoint of the band as the label.
    labels = []
    for i in range(numberOfBands):
        labels.append('{:4.2f}'.format(bands[i][1]))

    # Annotate
    values = vtk.vtkVariantArray()
    for i in range(len(labels)):
        values.InsertNextValue(vtk.vtkVariant(labels[i]))
    for i in range(values.GetNumberOfTuples()):
        lut.SetAnnotation(i, values.GetValue(i).ToString())

    # Create a lookup table with the colors reversed.
    lutr = ReverseLUT(lut)

    # Create the contour bands.
    bcf = vtk.vtkBandedPolyDataContourFilter()
    bcf.SetInputData(src)
    # Use either the minimum or maximum value for each band.
    for i in range(0, numberOfBands):
        bcf.SetValue(i, bands[i][2])
    # We will use an indexed lookup table.
    bcf.SetScalarModeToIndex()
    bcf.GenerateContourEdgesOn()

    # Generate the glyphs on the original surface.
    glyph = MakeGlyphs(src, False)

    # ------------------------------------------------------------
    # Create the mappers and actors
    # ------------------------------------------------------------
    srcMapper = vtk.vtkPolyDataMapper()
    srcMapper.SetInputConnection(bcf.GetOutputPort())
    srcMapper.SetScalarRange(scalarRange)
    srcMapper.SetLookupTable(lut)
    srcMapper.SetScalarModeToUseCellData()

    srcActor = vtk.vtkActor()
    srcActor.SetMapper(srcMapper)
    srcActor.RotateX(-45)
    srcActor.RotateZ(45)

    # Create contour edges
    edgeMapper = vtk.vtkPolyDataMapper()
    edgeMapper.SetInputData(bcf.GetContourEdgesOutput())
    edgeMapper.SetResolveCoincidentTopologyToPolygonOffset()

    edgeActor = vtk.vtkActor()
    edgeActor.SetMapper(edgeMapper)
    edgeActor.GetProperty().SetColor(colors.GetColor3d("Black"))
    edgeActor.RotateX(-45)
    edgeActor.RotateZ(45)

    glyphMapper = vtk.vtkPolyDataMapper()
    glyphMapper.SetInputConnection(glyph.GetOutputPort())
    glyphMapper.SetScalarModeToUsePointFieldData()
    glyphMapper.SetColorModeToMapScalars()
    glyphMapper.ScalarVisibilityOn()
    glyphMapper.SelectColorArray('Elevation')
    # Colour by scalars.
    glyphMapper.SetScalarRange(scalarRangeElevation)

    glyphActor = vtk.vtkActor()
    glyphActor.SetMapper(glyphMapper)
    glyphActor.RotateX(-45)
    glyphActor.RotateZ(45)

    # Add a scalar bar.
    scalarBar = vtk.vtkScalarBarActor()
    # This LUT puts the lowest value at the top of the scalar bar.
    # scalarBar->SetLookupTable(lut);
    # Use this LUT if you want the highest value at the top.
    scalarBar.SetLookupTable(lutr)
    scalarBar.SetTitle('Gaussian\nCurvature')

    # ------------------------------------------------------------
    # Create the RenderWindow, Renderer and Interactor
    # ------------------------------------------------------------
    ren = vtk.vtkRenderer()
    renWin = vtk.vtkRenderWindow()
    iren = vtk.vtkRenderWindowInteractor()

    renWin.AddRenderer(ren)
    iren.SetRenderWindow(renWin)

    # add actors
    ren.AddViewProp(srcActor)
    ren.AddViewProp(edgeActor)
    ren.AddViewProp(glyphActor)
    ren.AddActor2D(scalarBar)

    ren.SetBackground(colors.GetColor3d("BkgColor"))
    renWin.SetSize(800, 800)
    renWin.Render()

    ren.GetActiveCamera().Zoom(1.5)

    return iren


if __name__ == '__main__':
    # interactor = vtk.vtkRenderWindowInteractor()
    # interactor = DisplaySurface("TORUS")
    # interactor = DisplaySurface("PARAMETRIC_TORUS")
    interactor = DisplaySurface("PARAMETRIC_HILLS")
    interactor.Render()
    interactor.Start()
    # WritePNG(interactor.GetRenderWindow().GetRenderers().GetFirstRenderer(),
    #               "CurvatureBandsWithGlyphs.png")