ITK/Examples/WishList/Segmentation/kMeansClustering

KMeansClassification.cxx

<source lang="cpp">

1. include <itkImage.h>
2. include <itkImageFileReader.h>
3. include <itkImageFileWriter.h>
4. include <itkScalarImageKmeansImageFilter.h>

int main( int argc, char * argv [] ) {

 //sample usage
 //./KMeansClassification input.jpg output.jpg 1 3 0 100 200
 
 //verify command line arguments
 if( argc < 5 )
   {
   std::cerr << "Usage: " << std::endl;
   std::cerr << argv[0];
   std::cerr << " inputScalarImage outputLabeledImage contiguousLabels";
   std::cerr << " numberOfClasses mean1 mean2... meanN " << std::endl;
   return EXIT_FAILURE;
   }

 //parse command line arguments
 const char * inputImageFileName = argv[1];
 const char * outputImageFileName = argv[2];
 const unsigned int useNonContiguousLabels = atoi( argv[3] );
 const unsigned int numberOfInitialClasses = atoi( argv[4] );
 
 const unsigned int argoffset = 5;

 if( static_cast<unsigned int>(argc) <
     numberOfInitialClasses + argoffset )
   {
   std::cerr << "Error: " << std::endl;
   std::cerr << numberOfInitialClasses << " classes has been specified ";
   std::cerr << "but no enough means have been provided in the command ";
   std::cerr << "line arguments " << std::endl;
   return EXIT_FAILURE;
   }
   
 std::vector<double> userMeans;
 for( unsigned k = 0; k < numberOfInitialClasses; k++ )
   {
   const double userProvidedInitialMean = atof( argv[k+argoffset] );
   userMeans.push_back(userProvidedInitialMean);
   }
   
 // Define the pixel type and dimension of the image that we intend to
 // classify. 
 
 typedef signed short       PixelType;
 const unsigned int          Dimension = 2;

 typedef itk::Image<PixelType, Dimension > ImageType;

 // create a reader  
 typedef itk::ImageFileReader< ImageType > ReaderType;
 ReaderType::Pointer reader = ReaderType::New();
 reader->SetFileName( inputImageFileName );

 // Instantiate the ScalarImageKmeansImageFilter  
 typedef itk::ScalarImageKmeansImageFilter< ImageType > KMeansFilterType;

 KMeansFilterType::Pointer kmeansFilter = KMeansFilterType::New();

 kmeansFilter->SetInput( reader->GetOutput() );

 // Make the output image intellegable by expanding the range of output image values, if desired
 
 kmeansFilter->SetUseNonContiguousLabels( useNonContiguousLabels );

 // initialize using the user input means
 
   for( unsigned k = 0; k < numberOfInitialClasses; k++ )
   {
   kmeansFilter->AddClassWithInitialMean( userMeans[k] );
   }

 // Create and setup a writer
 
 typedef KMeansFilterType::OutputImageType  OutputImageType;

 typedef itk::ImageFileWriter< OutputImageType > WriterType;

 WriterType::Pointer writer = WriterType::New();
 
 writer->SetInput( kmeansFilter->GetOutput() );

 writer->SetFileName( outputImageFileName );

 // execut the pipeline
 try
   {
   writer->Update();
   }
 catch( itk::ExceptionObject & excp )
   {
   std::cerr << "Problem encountered while writing ";
   std::cerr << " image file : " << outputImageFileName << std::endl;
   std::cerr << excp << std::endl;
   return EXIT_FAILURE;
   }

 // inspect the means
 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;
   }

 return EXIT_SUCCESS;
 

}

</source>

CMakeLists.txt

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

PROJECT(KMeansClassification)

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

ADD_EXECUTABLE(KMeansClassification KMeansClassification.cxx) TARGET_LINK_LIBRARIES(KMeansClassification ITKNumerics ITKIO)

</source>