PolyDataContourToImageData

VTKExamples/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!

Code

PolyDataContourToImageData.py

import math

import vtk

# 3D source sphere
sphereSource = vtk.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 = vtk.vtkCutter()
circleCutter.SetInputConnection(sphereSource.GetOutputPort())
cutPlane = vtk.vtkPlane()
cutPlane.SetOrigin(sphereSource.GetCenter())
cutPlane.SetNormal(0, 0, 1)
circleCutter.SetCutFunction(cutPlane)
stripper = vtk.vtkStripper()
stripper.SetInputConnection(circleCutter.GetOutputPort())  # valid circle
stripper.Update()
# that's our circle
circle = stripper.GetOutput()

# write circle out
polyDataWriter = vtk.vtkXMLPolyDataWriter()
if vtk.VTK_MAJOR_VERSION <= 5:
    polyDataWriter.SetInput(circle)
else:
    polyDataWriter.SetInputData(circle)

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

# prepare the binary image's voxel grid
whiteImage = vtk.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)
if vtk.VTK_MAJOR_VERSION <= 5:
    whiteImage.SetScalarTypeToUnsignedChar()
    whiteImage.AllocateScalars()
else:
    whiteImage.AllocateScalars(vtk.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 = vtk.vtkLinearExtrusionFilter()
if vtk.VTK_MAJOR_VERSION <= 5:
    extruder.SetInput(circle)
else:
    extruder.SetInputData(circle)

extruder.SetScaleFactor(1.)
extruder.SetExtrusionTypeToNormalExtrusion()
extruder.SetVector(0, 0, 1)
extruder.Update()

# polygonal data -. image stencil:
pol2stenc = vtk.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 = vtk.vtkImageStencil()
if vtk.VTK_MAJOR_VERSION <= 5:
    imgstenc.SetInput(whiteImage)
    imgstenc.SetStencil(pol2stenc.GetOutput())
else:
    imgstenc.SetInputData(whiteImage)
    imgstenc.SetStencilConnection(pol2stenc.GetOutputPort())

imgstenc.ReverseStencilOff()
imgstenc.SetBackgroundValue(outval)
imgstenc.Update()

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

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