ITK/Examples/Statistics/ScalarImageKmeansImageFilter

ScalarImageKmeansImageFilter.cxx

<source lang="cpp">

1. include "itkImageFileReader.h"
2. include "itkImageFileWriter.h"
3. include "itkScalarImageKmeansImageFilter.h"
4. include "itkRelabelComponentImageFilter.h"
5. include "itkRescaleIntensityImageFilter.h"
6. include "itkImageRegionIterator.h"

1. include <itkImageToVTKImageFilter.h>

1. include "vtkImageViewer.h"
2. include "vtkRenderWindowInteractor.h"
3. include "vtkSmartPointer.h"
4. include "vtkImageActor.h"
5. include "vtkInteractorStyleImage.h"
6. include "vtkRenderer.h"

typedef itk::Image<unsigned char, 2 > ImageType;

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();
 originalActor->SetInput(originalConnector->GetOutput());

 ConnectorType::Pointer outputConnector = ConnectorType::New();
 outputConnector->SetInput(rescaleFilter->GetOutput());

 vtkSmartPointer<vtkImageActor> outputActor =
   vtkSmartPointer<vtkImageActor>::New();
 outputActor->SetInput(outputConnector->GetOutput());

 // 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;
 }

} </source>

CMakeLists.txt

<source lang="cmake"> cmake_minimum_required(VERSION 2.6)

PROJECT(ScalarImageKmeansImageFilter)

include_directories(/home/doriad/src/ITK/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/src/)

FIND_PACKAGE(VTK REQUIRED) INCLUDE(${VTK_USE_FILE})

FIND_PACKAGE(ITK REQUIRED) INCLUDE(${ITK_USE_FILE})

ADD_EXECUTABLE(ScalarImageKmeansImageFilter ScalarImageKmeansImageFilter.cxx) TARGET_LINK_LIBRARIES(ScalarImageKmeansImageFilter vtkHybrid ITKBasicFilters ITKCommon ITKIO ITKStatistics) </source>