ScalarImageKmeansImageFilter.cxx

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkScalarImageKmeansImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkImageRegionIterator.h"
 
#include <itkImageToVTKImageFilter.h>
 
#include "vtkVersion.h"
#include "vtkImageViewer.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkSmartPointer.h"
#include "vtkImageActor.h"
#include "vtkImageMapper3D.h"
#include "vtkInteractorStyleImage.h"
#include "vtkRenderer.h"
 
typedef itk::Image<unsigned char, 2 > ImageType;
 
static void CreateImage(ImageType::Pointer image);
 
int main(int, char*[])
{
  ImageType::Pointer image = ImageType::New();
  CreateImage(image);
 
  typedef itk::ScalarImageKmeansImageFilter< ImageType > KMeansFilterType;
 
  KMeansFilterType::Pointer kmeansFilter = KMeansFilterType::New();
 
  kmeansFilter->SetInput(image);
  kmeansFilter->SetUseNonContiguousLabels(true);
  kmeansFilter->AddClassWithInitialMean(8);
  kmeansFilter->AddClassWithInitialMean(110);
  kmeansFilter->AddClassWithInitialMean(210);
  kmeansFilter->Update();
 
  KMeansFilterType::ParametersType estimatedMeans = kmeansFilter->GetFinalMeans();
 
  const unsigned int numberOfClasses = estimatedMeans.Size();
 
  for(unsigned int i = 0 ; i < numberOfClasses ; ++i)
    {
    std::cout << "cluster[" << i << "] ";
    std::cout << "    estimated mean : " << estimatedMeans[i] << std::endl;
    }
 
  typedef KMeansFilterType::OutputImageType  OutputImageType;
 
  typedef itk::RelabelComponentImageFilter<
                                OutputImageType,
                                OutputImageType > RelabelFilterType;
 
  RelabelFilterType::Pointer relabeler = RelabelFilterType::New();
 
  relabeler->SetInput( kmeansFilter->GetOutput() );
 
  typedef itk::RescaleIntensityImageFilter< ImageType, ImageType > RescaleFilterType;
  RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
  rescaleFilter->SetInput(relabeler->GetOutput());
  rescaleFilter->SetOutputMinimum(0);
  rescaleFilter->SetOutputMaximum(255);
 
  typedef std::vector< unsigned long > SizesType;
 
  const SizesType &  sizes = relabeler->GetSizeOfObjectsInPixels();
 
  SizesType::const_iterator sizeItr = sizes.begin();
  SizesType::const_iterator sizeEnd = sizes.end();
 
  std::cout << "Number of pixels per class " << std::endl;
  unsigned int kclass = 0;
  while( sizeItr != sizeEnd )
    {
    std::cout << "Class " << kclass << " = " << *sizeItr << std::endl;
    ++kclass;
    ++sizeItr;
    }
 
  // Visualize
  typedef itk::ImageToVTKImageFilter<ImageType> ConnectorType;
  ConnectorType::Pointer originalConnector = ConnectorType::New();
  originalConnector->SetInput(image);
  vtkSmartPointer<vtkImageActor> originalActor =
    vtkSmartPointer<vtkImageActor>::New();
#if VTK_MAJOR_VERSION <= 5
  originalActor->SetInput(originalConnector->GetOutput());
#else
  originalConnector->Update();
  originalActor->SetInputData(originalConnector->GetOutput());
#endif
 
  ConnectorType::Pointer outputConnector = ConnectorType::New();
  outputConnector->SetInput(rescaleFilter->GetOutput());
 
  vtkSmartPointer<vtkImageActor> outputActor =
    vtkSmartPointer<vtkImageActor>::New();
#if VTK_MAJOR_VERSION <= 5
  outputActor->SetInput(outputConnector->GetOutput());
#else
  outputConnector->Update();
  outputActor->SetInputData(outputConnector->GetOutput());
#endif
 
  // There will be one render window
  vtkSmartPointer<vtkRenderWindow> renderWindow =
    vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->SetSize(600, 300);
 
  vtkSmartPointer<vtkRenderWindowInteractor> interactor =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  interactor->SetRenderWindow(renderWindow);
 
  // Define viewport ranges
  // (xmin, ymin, xmax, ymax)
  double leftViewport[4] = {0.0, 0.0, 0.5, 1.0};
  double rightViewport[4] = {0.5, 0.0, 1.0, 1.0};
 
  // Setup both renderers
  vtkSmartPointer<vtkRenderer> leftRenderer =
    vtkSmartPointer<vtkRenderer>::New();
  renderWindow->AddRenderer(leftRenderer);
  leftRenderer->SetViewport(leftViewport);
  leftRenderer->SetBackground(.6, .5, .4);
 
  vtkSmartPointer<vtkRenderer> rightRenderer =
    vtkSmartPointer<vtkRenderer>::New();
  renderWindow->AddRenderer(rightRenderer);
  rightRenderer->SetViewport(rightViewport);
  rightRenderer->SetBackground(.4, .5, .6);
 
 
  // Add the sphere to the left and the cube to the right
  leftRenderer->AddActor(originalActor);
  rightRenderer->AddActor(outputActor);
 
  leftRenderer->ResetCamera();
  rightRenderer->ResetCamera();
 
  renderWindow->Render();
 
  vtkSmartPointer<vtkInteractorStyleImage> style =
    vtkSmartPointer<vtkInteractorStyleImage>::New();
 
  interactor->SetInteractorStyle(style);
 
  interactor->Start();
 
  return EXIT_SUCCESS;
}
 
void CreateImage(ImageType::Pointer image)
{
  // Create an image with 2 connected components
  ImageType::RegionType region;
  ImageType::IndexType start;
  start[0] = 0;
  start[1] = 0;
 
  ImageType::SizeType size;
  size[0] = 200;
  size[1] = 300;
 
  region.SetSize(size);
  region.SetIndex(start);
 
  image->SetRegions(region);
  image->Allocate();
 
  itk::ImageRegionIterator<ImageType> imageIterator(image,region);
 
  while(!imageIterator.IsAtEnd())
    {
    if(imageIterator.GetIndex()[0] > 100 &&
      imageIterator.GetIndex()[0] < 150 &&
      imageIterator.GetIndex()[1] > 100 &&
      imageIterator.GetIndex()[1] < 150)
      {
      imageIterator.Set(100);
      }
    else if(imageIterator.GetIndex()[0] > 50 &&
      imageIterator.GetIndex()[0] < 70 &&
      imageIterator.GetIndex()[1] > 50 &&
      imageIterator.GetIndex()[1] < 70)
      {
      imageIterator.Set(200);
      }
    else
      {
      imageIterator.Set(10);
      }
 
    ++imageIterator;
  }
}

CMakeLists.txt

cmake_minimum_required(VERSION 2.8)
 
project(ScalarImageKmeansImageFilter)
 
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
if (ITKVtkGlue_LOADED)
  find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
else()
  find_package(ItkVtkGlue REQUIRED)
  include(${ItkVtkGlue_USE_FILE})
  set(Glue ItkVtkGlue)
endif()
 
add_executable(ScalarImageKmeansImageFilter MACOSX_BUNDLE ScalarImageKmeansImageFilter.cxx)
target_link_libraries(ScalarImageKmeansImageFilter
  ${Glue}  ${VTK_LIBRARIES} ${ITK_LIBRARIES})

Download and Build ScalarImageKmeansImageFilter

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

cd ScalarImageKmeansImageFilter/build 

• If ITK is installed:

cmake ..

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

cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project,

make

and run it:

./ScalarImageKmeansImageFilter

WINDOWS USERS PLEASE NOTE: Be sure to add the VTK and ITK bin directories to your path. This will resolve the VTK and ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.