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PolyDataContourToImageData

vtk-examples/Python/PolyData/PolyDataContourToImageData

Description

  • Contributed by: Lars Friedrich, Peter Gruber

This example generates a sphere, cuts it with a plane and, therefore, generates a circlular contour (vtkPolyData). Subsequently a binary image representation (vtkImageData) is extracted from it. Internally vtkPolyDataToImageStencil and vtkLinearExtrusionFilter are utilized. Both the circular poly data (circle.vtp) and the resultant image (labelImage.mhd) are saved to disk.

Note

Similarily to example PolyDataToImageStencil, I am not really sure whether or not the image origin needs to be adjusted as the sphere-image-overlay shows some offset in paraview visualization (at least I think ...). Maybe someone could verify that. Thanks!

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Question

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Code

PolyDataContourToImageData.py

#!/usr/bin/env python

import math

# noinspection PyUnresolvedReferences
import vtkmodules.vtkInteractionStyle
# noinspection PyUnresolvedReferences
import vtkmodules.vtkRenderingOpenGL2
from vtkmodules.vtkCommonCore import VTK_UNSIGNED_CHAR
from vtkmodules.vtkCommonDataModel import (
    vtkImageData,
    vtkPlane
)
from vtkmodules.vtkFiltersCore import (
    vtkCutter,
    vtkStripper
)
from vtkmodules.vtkFiltersModeling import vtkLinearExtrusionFilter
from vtkmodules.vtkFiltersSources import vtkSphereSource
from vtkmodules.vtkIOImage import (
    vtkMetaImageWriter,
    vtkPNGWriter
)
from vtkmodules.vtkIOXML import vtkXMLPolyDataWriter
from vtkmodules.vtkImagingStencil import (
    vtkImageStencil,
    vtkPolyDataToImageStencil
)


def main():
    # 3D source sphere
    sphereSource = vtkSphereSource()
    sphereSource.SetPhiResolution(30)
    sphereSource.SetThetaResolution(30)
    sphereSource.SetCenter(40, 40, 0)
    sphereSource.SetRadius(20)

    # generate circle by cutting the sphere with an implicit plane
    # (through its center, axis-aligned)
    circleCutter = vtkCutter()
    circleCutter.SetInputConnection(sphereSource.GetOutputPort())
    cutPlane = vtkPlane()
    cutPlane.SetOrigin(sphereSource.GetCenter())
    cutPlane.SetNormal(0, 0, 1)
    circleCutter.SetCutFunction(cutPlane)

    stripper = vtkStripper()
    stripper.SetInputConnection(circleCutter.GetOutputPort())  # valid circle
    stripper.Update()

    # that's our circle
    circle = stripper.GetOutput()

    # write circle out
    polyDataWriter = vtkXMLPolyDataWriter()
    polyDataWriter.SetInputData(circle)

    polyDataWriter.SetFileName('circle.vtp')
    polyDataWriter.SetCompressorTypeToNone()
    polyDataWriter.SetDataModeToAscii()
    polyDataWriter.Write()

    # prepare the binary image's voxel grid
    whiteImage = vtkImageData()
    bounds = [0] * 6
    circle.GetBounds(bounds)
    spacing = [0] * 3  # desired volume spacing
    spacing[0] = 0.5
    spacing[1] = 0.5
    spacing[2] = 0.5
    whiteImage.SetSpacing(spacing)

    # compute dimensions
    dim = [0] * 3
    for i in range(3):
        dim[i] = int(math.ceil((bounds[i * 2 + 1] - bounds[i * 2]) / spacing[i])) + 1
        if dim[i] < 1:
            dim[i] = 1
    whiteImage.SetDimensions(dim)
    whiteImage.SetExtent(0, dim[0] - 1, 0, dim[1] - 1, 0, dim[2] - 1)
    origin = [0] * 3
    # NOTE: I am not sure whether or not we had to add some offset!
    origin[0] = bounds[0]  # + spacing[0] / 2
    origin[1] = bounds[2]  # + spacing[1] / 2
    origin[2] = bounds[4]  # + spacing[2] / 2
    whiteImage.SetOrigin(origin)
    whiteImage.AllocateScalars(VTK_UNSIGNED_CHAR, 1)

    # fill the image with foreground voxels:
    inval = 255
    outval = 0
    count = whiteImage.GetNumberOfPoints()
    # for (vtkIdType i = 0 i < count ++i)
    for i in range(count):
        whiteImage.GetPointData().GetScalars().SetTuple1(i, inval)

    # sweep polygonal data (this is the important thing with contours!)
    extruder = vtkLinearExtrusionFilter()
    extruder.SetInputData(circle)
    extruder.SetScaleFactor(1.0)
    # extruder.SetExtrusionTypeToNormalExtrusion()
    extruder.SetExtrusionTypeToVectorExtrusion()
    extruder.SetVector(0, 0, 1)
    extruder.Update()

    # polygonal data -. image stencil:
    pol2stenc = vtkPolyDataToImageStencil()
    pol2stenc.SetTolerance(0)  # important if extruder.SetVector(0, 0, 1) !!!
    pol2stenc.SetInputConnection(extruder.GetOutputPort())
    pol2stenc.SetOutputOrigin(origin)
    pol2stenc.SetOutputSpacing(spacing)
    pol2stenc.SetOutputWholeExtent(whiteImage.GetExtent())
    pol2stenc.Update()

    # cut the corresponding white image and set the background:
    imgstenc = vtkImageStencil()
    imgstenc.SetInputData(whiteImage)
    imgstenc.SetStencilConnection(pol2stenc.GetOutputPort())
    imgstenc.ReverseStencilOff()
    imgstenc.SetBackgroundValue(outval)
    imgstenc.Update()

    imageWriter = vtkMetaImageWriter()
    imageWriter.SetFileName('labelImage.mhd')
    imageWriter.SetInputConnection(imgstenc.GetOutputPort())
    imageWriter.Write()

    imageWriter = vtkPNGWriter()
    imageWriter.SetFileName('labelImage.png')
    imageWriter.SetInputConnection(imgstenc.GetOutputPort())
    imageWriter.Write()


if __name__ == '__main__':
    main()