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/*=========================================================================
*
* Copyright NumFOCUS
*
* 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
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#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
{
/**
* \class MahalanobisDistanceMetric
* \brief MahalanobisDistanceMetric class computes a Mahalanobis
* distance given a mean and covariance.
*
* \sa DistanceMetric
* \sa EuclideanDistanceMetric
* \sa EuclideanSquareDistanceMetric
* \ingroup ITKStatistics
*/
template <typename TVector>
class ITK_TEMPLATE_EXPORT MahalanobisDistanceMetric : public DistanceMetric<TVector>
{
public:
/** Standard class type aliases */
using Self = MahalanobisDistanceMetric;
using Superclass = DistanceMetric<TVector>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(MahalanobisDistanceMetric);
itkNewMacro(Self);
/** Typedef to represent the measurement vector type */
using typename Superclass::MeasurementVectorType;
/** Typedef to represent the length of measurement vectors */
using typename Superclass::MeasurementVectorSizeType;
/** Type used for representing the mean vector */
using MeanVectorType = typename Superclass::OriginType;
/** Type used for representing the covariance matrix */
using CovarianceMatrixType = vnl_matrix<double>;
/** Set the length of each measurement vector. */
void SetMeasurementVectorSize(MeasurementVectorSizeType) override;
/** Method to set mean */
void
SetMean(const MeanVectorType & mean);
/** Method to get mean */
const MeanVectorType &
GetMean() const;
/**
* Method to set covariance matrix
* Also, this function calculates inverse covariance and pre factor of
* MahalanobisDistance Distribution to speed up GetProbability */
void
SetCovariance(const CovarianceMatrixType & cov);
/** Method to get covariance matrix */
itkGetConstReferenceMacro(Covariance, CovarianceMatrixType);
/**
* Method to set inverse covariance matrix */
void
SetInverseCovariance(const CovarianceMatrixType & invcov);
/** Method to get covariance matrix */
itkGetConstReferenceMacro(InverseCovariance, CovarianceMatrixType);
/**
* Method to get probability of an instance. The return value is the
* value of the density function, not probability. */
double
Evaluate(const MeasurementVectorType & measurement) const override;
/** Gets the distance between x1 and x2. */
double
Evaluate(const MeasurementVectorType & x1, const MeasurementVectorType & x2) const override;
/** Set/Get tolerance values */
itkSetMacro(Epsilon, double);
itkGetConstMacro(Epsilon, double);
itkSetMacro(DoubleMax, double);
itkGetConstMacro(DoubleMax, double);
protected:
MahalanobisDistanceMetric();
~MahalanobisDistanceMetric() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
private:
MeanVectorType m_Mean{}; // mean
CovarianceMatrixType m_Covariance{}; // covariance matrix
// inverse covariance matrix which is automatically calculated
// when covariance matrix is set. This speeds up the GetProbability()
CovarianceMatrixType m_InverseCovariance{};
double m_Epsilon{ 1e-100 };
double m_DoubleMax{ 1e+20 };
void
CalculateInverseCovariance();
};
} // end of namespace Statistics
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkMahalanobisDistanceMetric.hxx"
#endif
#endif
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