itkSimpleKMeansClusteringImageFilter.h

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/*=============================================================================

  NifTK: A software platform for medical image computing.

  Copyright (c) University College London (UCL). All rights reserved.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.

  See LICENSE.txt in the top level directory for details.

=============================================================================*/

#ifndef itkSimpleKMeansClusteringImageFilter_h
#define itkSimpleKMeansClusteringImageFilter_h

#include <itkImageToImageFilter.h>
#include <itkMacro.h>
#include <itkWeightedCentroidKdTreeGenerator.h>
#include <itkKdTreeBasedKmeansEstimator.h>
#include <itkListSample.h>


namespace itk
{

template <class TInputImage, class TInputMask, class TOutputImage>
class ITK_EXPORT SimpleKMeansClusteringImageFilter: 
  public ImageToImageFilter<TInputImage, TOutputImage>
{
public:
  typedef SimpleKMeansClusteringImageFilter Self;
  typedef ImageToImageFilter<TInputImage,TOutputImage> Superclass;
  typedef SmartPointer<Self> Pointer;
  typedef SmartPointer<const Self> ConstPointer;
  itkNewMacro(Self);  
  itkTypeMacro(SimpleKMeansClusteringImageFilter, ImageToImageFilter);
  typedef typename TInputImage::Pointer TInputImagePointer;
  typedef typename TInputMask::Pointer TInputMaskPointer;
  typedef itk::Vector< double, 1 > MeasurementVectorType ;
  typedef typename itk::Statistics::ListSample< MeasurementVectorType > SampleType ;
  typedef itk::Statistics::WeightedCentroidKdTreeGenerator<SampleType> TreeGeneratorType;
  typedef typename TreeGeneratorType::KdTreeType TreeType;
  typedef itk::Statistics::KdTreeBasedKmeansEstimator<TreeType> EstimatorType;
  typedef typename EstimatorType::ParametersType ParametersType;
  itkSetMacro(InputMask, TInputMaskPointer);
  itkGetMacro(InputMask, TInputMaskPointer);
  itkSetMacro(NumberOfClasses, unsigned int);
  itkGetMacro(NumberOfClasses, unsigned int);
  itkSetMacro(InitialMeans, ParametersType);
  itkGetMacro(InitialMeans, ParametersType);
  itkGetMacro(FinalMeans, ParametersType);
  itkGetMacro(FinalStds, ParametersType);
  itkGetMacro(RSS, double);
  itkGetMacro(NumberOfSamples, double);
  itkGetMacro(FinalClassSizes, ParametersType);
  itkSetMacro(IsEstimateInitValuesUsingMask, bool);
  
protected:
  SimpleKMeansClusteringImageFilter()
  {
      this->m_NumberOfClasses = 3;
      this->m_RSS = 0.0;
      this->m_NumberOfSamples = 0.0;
      this->m_IsEstimateInitValuesUsingMask = false;
  }
  virtual ~SimpleKMeansClusteringImageFilter() {}
  void GenerateData();
  void EstimateIntensityFromDilatedMask(double& csfMean, double& csfSd, double& gmMean, double& wmMean);
  
private:
  TInputMaskPointer m_InputMask; 
  unsigned int m_NumberOfClasses; 
  ParametersType m_InitialMeans;
  ParametersType m_FinalMeans;
  ParametersType m_FinalStds;
  ParametersType m_FinalClassSizes;
  double m_RSS; 
  double m_NumberOfSamples; 
  bool m_IsEstimateInitValuesUsingMask;
  

};

}

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkSimpleKMeansClusteringImageFilter.txx"
#endif

#endif