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PolyDataContourToImageData

vtk-examples/Cxx/PolyData/PolyDataContourToImageData

Description

  • Contributed by: Lars Friedrich

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 [vtkPolyData](https://www.vtk.org/doc/nightly/html/classvtkPolyData.html#details)ToImageStencil and vtkLinearExtrusionFilter are utilized. Both the circular poly data (circle.vtp) and the resultant image (labelImage.mhd) are saved to disk.

Note

Similar to example PolyDataToImageData, 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!

Other languages

See (Python)

Question

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Code

PolyDataContourToImageData.cxx

#include <vtkCutter.h>
#include <vtkImageData.h>
#include <vtkImageStencil.h>
#include <vtkLinearExtrusionFilter.h>
#include <vtkMetaImageWriter.h>
#include <vtkNew.h>
#include <vtkPlane.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkPolyDataToImageStencil.h>
#include <vtkSphereSource.h>
#include <vtkStripper.h>
#include <vtkXMLPolyDataWriter.h>

// 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.

int main(int, char*[])
{
  // 3D source sphere
  vtkNew<vtkSphereSource> sphereSource;
  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)
  vtkNew<vtkCutter> circleCutter;
  circleCutter->SetInputConnection(sphereSource->GetOutputPort());
  vtkNew<vtkPlane> cutPlane;
  cutPlane->SetOrigin(sphereSource->GetCenter());
  cutPlane->SetNormal(0, 0, 1);
  circleCutter->SetCutFunction(cutPlane);

  vtkNew<vtkStripper> stripper;
  stripper->SetInputConnection(circleCutter->GetOutputPort()); // valid circle
  stripper->Update();

  // that's our circle
  auto circle = stripper->GetOutput();

  // write circle out
  vtkNew<vtkXMLPolyDataWriter> polyDataWriter;
  polyDataWriter->SetInputData(circle);
  polyDataWriter->SetFileName("circle.vtp");
  polyDataWriter->SetCompressorTypeToNone();
  polyDataWriter->SetDataModeToAscii();
  polyDataWriter->Write();

  // prepare the binary image's voxel grid
  vtkNew<vtkImageData> whiteImage;
  double bounds[6];
  circle->GetBounds(bounds);
  double spacing[3]; // desired volume spacing
  spacing[0] = 0.5;
  spacing[1] = 0.5;
  spacing[2] = 0.5;
  whiteImage->SetSpacing(spacing);

  // compute dimensions
  int dim[3];
  for (int i = 0; i < 3; i++)
  {
    dim[i] = static_cast<int>(
                 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);
  double origin[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:
  unsigned char inval = 255;
  unsigned char outval = 0;
  vtkIdType count = whiteImage->GetNumberOfPoints();
  for (vtkIdType i = 0; i < count; ++i)
  {
    whiteImage->GetPointData()->GetScalars()->SetTuple1(i, inval);
  }

  // sweep polygonal data (this is the important thing with contours!)
  vtkNew<vtkLinearExtrusionFilter> extruder;
  extruder->SetInputData(circle);
  extruder->SetScaleFactor(1.);
  extruder->SetExtrusionTypeToVectorExtrusion();
  extruder->SetVector(0, 0, 1);
  extruder->Update();

  // polygonal data --> image stencil:
  vtkNew<vtkPolyDataToImageStencil> pol2stenc;
  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:
  vtkNew<vtkImageStencil> imgstenc;
  imgstenc->SetInputData(whiteImage);
  imgstenc->SetStencilConnection(pol2stenc->GetOutputPort());
  imgstenc->ReverseStencilOff();
  imgstenc->SetBackgroundValue(outval);
  imgstenc->Update();
  imgstenc->GetOutput()->Print(std::cout);

  vtkNew<vtkMetaImageWriter> imageWriter;
  imageWriter->SetFileName("labelImage.mhd");
  imageWriter->SetInputConnection(imgstenc->GetOutputPort());
  imageWriter->Write();

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(PolyDataContourToImageData)

find_package(VTK COMPONENTS 
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersCore
  vtkFiltersModeling
  vtkFiltersSources
  vtkIOImage
  vtkIOXML
  vtkImagingStencil
  QUIET
)

if (NOT VTK_FOUND)
  message("Skipping PolyDataContourToImageData: ${VTK_NOT_FOUND_MESSAGE}")
  return()
endif()
message (STATUS "VTK_VERSION: ${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
  # old system
  include(${VTK_USE_FILE})
  add_executable(PolyDataContourToImageData MACOSX_BUNDLE PolyDataContourToImageData.cxx )
  target_link_libraries(PolyDataContourToImageData PRIVATE ${VTK_LIBRARIES})
else()
  # Prevent a "command line is too long" failure in Windows.
  set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
  add_executable(PolyDataContourToImageData MACOSX_BUNDLE PolyDataContourToImageData.cxx )
  target_link_libraries(PolyDataContourToImageData PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS PolyDataContourToImageData
    MODULES ${VTK_LIBRARIES}
    )
endif()

Download and Build PolyDataContourToImageData

Click here to download PolyDataContourToImageData and its CMakeLists.txt file. Once the tarball PolyDataContourToImageData.tar has been downloaded and extracted,

cd PolyDataContourToImageData/build

If VTK is installed:

cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

make

and run it:

./PolyDataContourToImageData

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.