itkMahalanobisDistanceMetric.h

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 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
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 *         http://www.apache.org/licenses/LICENSE-2.0.txt
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 *  See the License for the specific language governing permissions and
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#ifndef itkMahalanobisDistanceMetric_h
#define itkMahalanobisDistanceMetric_h

#include "vnl/vnl_vector.h"
#include "vnl/vnl_vector_ref.h"
#include "vnl/vnl_transpose.h"
#include "vnl/vnl_matrix.h"
#include "vnl/algo/vnl_matrix_inverse.h"
#include "vnl/algo/vnl_determinant.h"
#include "itkArray.h"

#include "itkDistanceMetric.h"

namespace itk
{
namespace Statistics
{
template< typename TVector >
class MahalanobisDistanceMetric:
  public DistanceMetric< TVector >
{
public:
  typedef MahalanobisDistanceMetric  Self;
  typedef DistanceMetric< TVector >  Superclass;
  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  itkTypeMacro(MahalanobisDistanceMetric, DistanceMetric);
  itkNewMacro(Self);

  typedef typename Superclass::MeasurementVectorType MeasurementVectorType;

  typedef typename Superclass::MeasurementVectorSizeType MeasurementVectorSizeType;

  typedef typename Superclass::OriginType MeanVectorType;

  typedef vnl_matrix< double > CovarianceMatrixType;

  virtual void SetMeasurementVectorSize(MeasurementVectorSizeType) ITK_OVERRIDE;

  void SetMean(const MeanVectorType & mean);

  const MeanVectorType & GetMean() const;

  void SetCovariance(const CovarianceMatrixType & cov);

  itkGetConstReferenceMacro(Covariance, CovarianceMatrixType);

  void SetInverseCovariance(const CovarianceMatrixType & invcov);

  itkGetConstReferenceMacro(InverseCovariance, CovarianceMatrixType);

  double Evaluate(const MeasurementVectorType & measurement) const ITK_OVERRIDE;

  double Evaluate(const MeasurementVectorType & x1, const MeasurementVectorType & x2) const ITK_OVERRIDE;

  itkSetMacro(Epsilon, double);
  itkGetConstMacro(Epsilon, double);

  itkSetMacro(DoubleMax, double);
  itkGetConstMacro(DoubleMax, double);

protected:
  MahalanobisDistanceMetric();
  virtual ~MahalanobisDistanceMetric(void) {}
  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

private:
  MeanVectorType       m_Mean;               // mean
  CovarianceMatrixType m_Covariance;         // covariance matrix

  // inverse covariance matrix which is automatically calculated
  // when covariace matirx is set.  This speed up the GetProbability()
  CovarianceMatrixType m_InverseCovariance;

  double m_Epsilon;
  double m_DoubleMax;

  void CalculateInverseCovariance();
};
} // end of namespace Statistics
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMahalanobisDistanceMetric.hxx"
#endif

#endif