PolyDataContourToImageData

VTKExamples/Python/PolyData/PolyDataContourToImageData

Description

• Contributed by: Lars Friedrich, Peter Gruber

== Brief Description ==

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 , 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 vtk
import math

# 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()