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 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()