mitkCorrelationCalculator.h

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
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 or http://www.mitk.org for details.

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

#ifndef _MITK_CORRELATIONCALCULATOR_H
#define _MITK_CORRELATIONCALCULATOR_H

#include "mitkCommon.h"
#include <itkObject.h>
#include <mitkImage.h>
#include <vnl/vnl_matrix.h>
#include <mitkConnectomicsNetwork.h>

namespace mitk {

  template< class T >
  class CorrelationCalculator : public itk::Object
  {

  public:

    // Standard macros
    mitkClassMacroItkParent(CorrelationCalculator, itk::Object);
    itkFactorylessNewMacro(Self)
    itkCloneMacro(Self)

    
    enum ParcelMode
    {
      UseAverageTimeSeries,
      UseMaximumCorrelation,
      UseAverageCorrelation
    };

    static double CalculatePearsonCorrelationCoefficient( const std::vector<T>& one, const std::vector<T>& two );

    static double CalculateCovariance( const std::vector<T>& one, const std::vector<T>& two );

    std::vector< double > ExtractAverageTimeSeriesOfParcel( int parcelValue );

    void DoWholeCorrelation();

    void DoParcelCorrelation( ParcelMode mode = UseAverageTimeSeries );

    virtual void Modified();

    const vnl_matrix< double >* GetCorrelationMatrix() const;
    const std::map< unsigned int, int >* GetLabelOrderMap() const;
    mitk::ConnectomicsNetwork::Pointer GetConnectomicsNetwork();

    // Get/Set macros
    itkSetMacro(ParcellationImage, mitk::Image::Pointer)
    itkSetMacro(TimeSeriesImage, mitk::Image::Pointer)

  protected:

    // intentionally not accessible, use our non-const Modified function instead
    virtual void Modified() const override;

    CorrelationCalculator();
    virtual ~CorrelationCalculator();

    template< typename TPixel, unsigned int VImageDimension >
    void ExtractAllAverageTimeSeries( itk::Image< TPixel, VImageDimension>* itkTimeSeriesImage );

    void ExtractCenterOfMassForParcels();


    double GetParcelCorrelation(const int& parcelA,const int& parcelB, ParcelMode& mode) const;

    // Member variables
    bool m_InvalidTimeSeries;

    mitk::Image::Pointer m_ParcellationImage;
    mitk::Image::Pointer m_TimeSeriesImage;

    std::map< int, std::vector<double> > m_AverageTimeSeries;
    std::map< int, std::vector<std::vector< T > > > m_ParcelTimeSeries;

    std::map< int, mitk::Point3D > m_ParcelCenterOfMass;

    vnl_matrix< double > m_CorrelationMatrix;

    std::map< unsigned int, int > m_LabelOrderMap;
  };

}

#include <mitkCorrelationCalculator.txx>

#endif /* _MITK_CORRELATIONCALCULATOR_H */