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 "itkImageRegionIteratorWithIndex.h"
6. include "itkImageToListSampleAdaptor.h"
7. include "itkDistanceToCentroidMembershipFunction.h"
8. include "itkSampleClassifierFilter.h"
9. 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); void CreateBlankImage(GrayscaleImageType::Pointer image, ColorImageType::Pointer inputImage);

int main(int, char* [] ) {

 // Create a demo image
 ColorImageType::Pointer image = ColorImageType::New();
 CreateImage(image);

 // Compute pixel clusters using KMeans
 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();

 // Classify each pixel
 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;

 // Setup membership functions
 MembershipFunctionPointerVector kmeansMembershipFunctions =
   kmeansEstimator->GetMembershipFunctions();

 MembershipFunctionVectorObjectType::Pointer  membershipFunctionsVectorObject = MembershipFunctionVectorObjectType::New();
 classifier->SetMembershipFunctions(membershipFunctionsVectorObject);

 MembershipFunctionVectorType &  membershipFunctionsVector = membershipFunctionsVectorObject->Get();

 for(unsigned int i = 0; i < kmeansMembershipFunctions.size(); i++)
   {
   membershipFunctionsVector.push_back(kmeansMembershipFunctions[i].GetPointer());
   }

 // Setup class labels
 ClassLabelVectorObjectType::Pointer  classLabelsObject = ClassLabelVectorObjectType::New();
 classifier->SetClassLabels( classLabelsObject );

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

 // Perform the classification
 typedef itk::Statistics::ImageToListSampleAdaptor< ColorImageType > SampleAdaptorType;
 SampleAdaptorType::Pointer sample = SampleAdaptorType::New();
 sample->SetImage(image);

 classifier->SetInput(sample);
 classifier->Update();
 
 // Prepare the output image
 GrayscaleImageType::Pointer outputImage = GrayscaleImageType::New();
 CreateBlankImage(outputImage, image);

 // Setup the membership iterator
 const ClassifierType::MembershipSampleType* membershipSample = classifier->GetOutput();
 ClassifierType::MembershipSampleType::ConstIterator membershipIterator = membershipSample->Begin();

 // Setup the output image iterator - this is automatically synchronized with the membership iterator since the sample is an adaptor
 itk::ImageRegionIteratorWithIndex<GrayscaleImageType> outputIterator(outputImage,outputImage->GetLargestPossibleRegion());
 outputIterator.GoToBegin();
 
 while(membershipIterator != membershipSample->End())
   {
   int classLabel = membershipIterator.GetClassLabel();
   std::cout << "Class label: " << classLabel << std::endl;
   outputIterator.Set(static_cast<unsigned char>(classLabel));
   ++membershipIterator;
   ++outputIterator;
   }

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

 vtkSmartPointer<vtkImageActor> originalActor =
   vtkSmartPointer<vtkImageActor>::New();
 originalActor->SetInput(originalVTKImage);

 // Kmeans image
 vtkSmartPointer<vtkImageData> kmeansVTKImage =
   vtkSmartPointer<vtkImageData>::New();
 ITKImagetoVTKImageGrayscale(outputImage, kmeansVTKImage);

 vtkSmartPointer<vtkImageActor> kmeansActor =
   vtkSmartPointer<vtkImageActor>::New();
 kmeansActor->SetInput(kmeansVTKImage);
 
 // There will be one render window
 vtkSmartPointer<vtkRenderWindow> renderWindow =
   vtkSmartPointer<vtkRenderWindow>::New();
 renderWindow->SetSize(600, 300);

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

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

 leftRenderer->AddActor(originalActor);
 leftRenderer->ResetCamera();

 vtkSmartPointer<vtkRenderer> rightRenderer =
   vtkSmartPointer<vtkRenderer>::New();
 renderWindow->AddRenderer(rightRenderer);
 rightRenderer->SetViewport(rightViewport);
 rightRenderer->SetBackground(.7, .4, .4);

 rightRenderer->AddActor(kmeansActor);
 rightRenderer->ResetCamera();

 renderWindow->Render();

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

 interactor->Start();

 return EXIT_SUCCESS;

}

void CreateImage(ColorImageType::Pointer image) {

 // Create a black image with a red square and a green square
 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);
     }
   }

}

void CreateBlankImage(GrayscaleImageType::Pointer image, ColorImageType::Pointer inputImage) {

 image->SetRegions(inputImage->GetLargestPossibleRegion());
 image->Allocate();

 itk::ImageRegionIterator<GrayscaleImageType> imageIterator(image,image->GetLargestPossibleRegion());

 while(!imageIterator.IsAtEnd())
   {

   imageIterator.Set(0);

   ++imageIterator;
   }

} </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>