ITK/Examples/Broken/Statistics/ImageKmeansModelEstimator

KmeansModelEstimator.cxx

<source lang="cpp">

1. include "itkImage.h"
2. include "itkListSample.h"
3. include "itkVector.h"
4. include "itkImageKmeansModelEstimator.h"
5. include "itkImageToListSampleAdaptor.h"
6. include "itkDistanceToCentroidMembershipFunction.h"
7. include "itkSampleClassifierFilter.h"
8. include "itkMinimumDecisionRule2.h"

1. include "vtkSmartPointer.h"
2. include "vtkImageActor.h"
3. include "vtkImageData.h"
4. include "vtkInteractorStyleImage.h"
5. include "vtkRenderer.h"
6. include "vtkRenderWindow.h"
7. include "vtkRenderWindowInteractor.h"

typedef itk::Vector<unsigned char,3> MeasurementVectorType; typedef itk::Image<MeasurementVectorType,2> ColorImageType; typedef itk::Image<unsigned char,2> GrayscaleImageType;

void CreateImage(ColorImageType::Pointer image); void ITKImagetoVTKImageColor(ColorImageType::Pointer image, vtkImageData* outputImage); void ITKImagetoVTKImageGrayscale(GrayscaleImageType::Pointer image, vtkImageData* outputImage);

int main(int, char* [] ) {

 ColorImageType::Pointer image = ColorImageType::New();
 CreateImage(image);
 
 typedef itk::Statistics::DistanceToCentroidMembershipFunction< itk::Vector<unsigned char,3> >
   MembershipFunctionType ;
 typedef MembershipFunctionType::Pointer MembershipFunctionPointer ;

 typedef std::vector< MembershipFunctionPointer >
   MembershipFunctionPointerVector;

 typedef itk::ImageKmeansModelEstimator<ColorImageType, MembershipFunctionType>
   ImageKmeansModelEstimatorType;

 ImageKmeansModelEstimatorType::Pointer
   kmeansEstimator = ImageKmeansModelEstimatorType::New();
 kmeansEstimator->SetInputImage(image);
 kmeansEstimator->SetNumberOfModels(3);
 kmeansEstimator->SetThreshold(0.01 );
 kmeansEstimator->SetOffsetAdd( 0.01 );
 kmeansEstimator->SetOffsetMultiply( 0.01 );
 kmeansEstimator->SetMaxSplitAttempts( 10 );
 kmeansEstimator->Update();
 typedef itk::Statistics::ListSample< MeasurementVectorType > SampleType ;
 typedef itk::Statistics::SampleClassifierFilter< SampleType > ClassifierType;
 ClassifierType::Pointer classifier = ClassifierType::New();

 typedef itk::Statistics::MinimumDecisionRule2 DecisionRuleType;
 DecisionRuleType::Pointer decisionRule = DecisionRuleType::New();
 
 classifier->SetDecisionRule(decisionRule);
 
 classifier->SetNumberOfClasses(3);

 typedef ClassifierType::ClassLabelVectorObjectType               ClassLabelVectorObjectType;
 typedef ClassifierType::ClassLabelVectorType                     ClassLabelVectorType;
 typedef ClassifierType::MembershipFunctionVectorObjectType       MembershipFunctionVectorObjectType;
 typedef ClassifierType::MembershipFunctionVectorType             MembershipFunctionVectorType;

 MembershipFunctionPointerVector membershipFunctions =
 kmeansEstimator->GetMembershipFunctions();
   
 ClassLabelVectorObjectType::Pointer  classLabelsObject = ClassLabelVectorObjectType::New();
 classifier->SetClassLabels( classLabelsObject );

 ClassLabelVectorType &  classLabelsVector = classLabelsObject->Get();
 classLabelsVector.push_back( 50 );
 classLabelsVector.push_back( 150 );
 classLabelsVector.push_back( 250 );

 GrayscaleImageType::Pointer outputImage = GrayscaleImageType::New();
 outputImage->SetRegions(image->GetLargestPossibleRegion());

 itk::ImageRegionIterator<ColorImageType> imageIterator(image,image->GetLargestPossibleRegion());
 itk::ImageRegionIterator<GrayscaleImageType> outputIterator(outputImage,outputImage->GetLargestPossibleRegion());
 
 while(!imageIterator.IsAtEnd())
   {
   SampleType::Pointer sample = SampleType::New();
   sample->PushBack(imageIterator.Get());
   //sample->Get
   classifier->SetInput(sample);
   unsigned char label = static_cast<unsigned char>(classifier->GetOutput()->GetClassLabel(0));
   outputIterator.Set(label);

   ++imageIterator;

   }

 // Visualize
 vtkSmartPointer<vtkImageData> VTKImage =
   vtkSmartPointer<vtkImageData>::New();
   
 ITKImagetoVTKImageColor(image, VTKImage);

 vtkSmartPointer<vtkImageActor> actor =
   vtkSmartPointer<vtkImageActor>::New();
 actor->SetInput(VTKImage);

 // There will be one render window
 vtkSmartPointer<vtkRenderWindow> renderWindow =
   vtkSmartPointer<vtkRenderWindow>::New();
 renderWindow->SetSize(300, 300);

 vtkSmartPointer<vtkRenderWindowInteractor> interactor =
   vtkSmartPointer<vtkRenderWindowInteractor>::New();
 interactor->SetRenderWindow(renderWindow);

 vtkSmartPointer<vtkRenderer> renderer =
   vtkSmartPointer<vtkRenderer>::New();
 renderWindow->AddRenderer(renderer);
 renderer->SetBackground(.6, .5, .4);

 renderer->AddActor(actor);

 renderer->ResetCamera();

 renderWindow->Render();

 vtkSmartPointer<vtkInteractorStyleImage> style =
   vtkSmartPointer<vtkInteractorStyleImage>::New();
 interactor->SetInteractorStyle(style);

 interactor->Start();
 
 //classdist = membershipFunctions[idx]->Evaluate( outIt.Get() );
 //std::cout << "Distance of first pixel to class " << idx << " is: " << classdist << std::endl;

 return EXIT_SUCCESS;

}

void CreateImage(ColorImageType::Pointer image) {

 // Create an image with 2 connected components
 ColorImageType::RegionType region;
 ColorImageType::IndexType start;
 start[0] = 0;
 start[1] = 0;

 ColorImageType::SizeType size;
 size[0] = 200;
 size[1] = 300;

 region.SetSize(size);
 region.SetIndex(start);

 image->SetRegions(region);
 image->Allocate();

 itk::ImageRegionIterator<ColorImageType> imageIterator(image,region);

 itk::Vector<unsigned char, 3> redPixel;
 redPixel[0] = 255;
 redPixel[1] = 0;
 redPixel[2] = 0;

 itk::Vector<unsigned char, 3> greenPixel;
 greenPixel[0] = 0;
 greenPixel[1] = 255;
 greenPixel[2] = 0;
 
 itk::Vector<unsigned char, 3> blackPixel;
 blackPixel[0] = 0;
 blackPixel[1] = 0;
 blackPixel[2] = 0;
 
 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 100 &&
     imageIterator.GetIndex()[0] < 150 &&
     imageIterator.GetIndex()[1] > 100 &&
     imageIterator.GetIndex()[1] < 150)
     {
     imageIterator.Set(redPixel);
     }
   else if(imageIterator.GetIndex()[0] > 50 &&
     imageIterator.GetIndex()[0] < 70 &&
     imageIterator.GetIndex()[1] > 50 &&
     imageIterator.GetIndex()[1] < 70)
     {
     imageIterator.Set(greenPixel);
     }
   else
     {
     imageIterator.Set(blackPixel);
     }

   ++imageIterator;
 }

}

void ITKImagetoVTKImageColor(ColorImageType::Pointer image, vtkImageData* outputImage) {

 outputImage->SetNumberOfScalarComponents(3);
 outputImage->SetScalarTypeToUnsignedChar();

 outputImage->SetDimensions(image->GetLargestPossibleRegion().GetSize()[0],
                            image->GetLargestPossibleRegion().GetSize()[1],
                            1);

 outputImage->AllocateScalars();

 int* dims = outputImage->GetDimensions();

 for (int y = 0; y < dims[1]; y++)
   {
   for (int x = 0; x < dims[0]; x++)
     {
     unsigned char* pixel = static_cast<unsigned char*>(outputImage->GetScalarPointer(x,y,0));
     ColorImageType::IndexType index;

     index[0] = x;
     index[1] = y;
     pixel[0] = image->GetPixel(index)[0];
     pixel[1] = image->GetPixel(index)[1];
     pixel[2] = image->GetPixel(index)[2];
     }
   }

}

void ITKImagetoVTKImageGrayscale(GrayscaleImageType::Pointer image, vtkImageData* outputImage) {

 outputImage->SetNumberOfScalarComponents(1);
 outputImage->SetScalarTypeToUnsignedChar();

 outputImage->SetDimensions(image->GetLargestPossibleRegion().GetSize()[0],
                            image->GetLargestPossibleRegion().GetSize()[1],
                            1);

 outputImage->AllocateScalars();

 int* dims = outputImage->GetDimensions();

 for (int y = 0; y < dims[1]; y++)
   {
   for (int x = 0; x < dims[0]; x++)
     {
     unsigned char* pixel = static_cast<unsigned char*>(outputImage->GetScalarPointer(x,y,0));
     GrayscaleImageType::IndexType index;

     index[0] = x;
     index[1] = y;
     pixel[0] = image->GetPixel(index);
     }
   }

} </source>

CMakeLists.txt

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

PROJECT(ImageKmeansModelEstimator)

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

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

ADD_EXECUTABLE(ImageKmeansModelEstimator ImageKmeansModelEstimator.cxx) TARGET_LINK_LIBRARIES(ImageKmeansModelEstimator ITKIO ITKStatistics vtkHybrid)

</source>