PseudoEcgCalculator.hpp

/*

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*/

#ifndef _PSEUDOECGALCALCULATOR_HPP_
#define _PSEUDOECGALCALCULATOR_HPP_

#include "AbstractFunctionalCalculator.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "ChastePoint.hpp"
#include "UblasCustomFunctions.hpp"
#include "Hdf5DataReader.hpp"

/*
 * NB I don't think that this class needs to be templated over PROBLEM_DIM,
 *  since even when working with Bidomain we only integrate one thing at once,
 *  and hence still need to call AbstractFunctionalCalculator<ELEMENT_DIM, SPACE_DIM, 1>.
 *  See PostProcessingWriter.cpp line ~141. The fact that it is only explicitly
 *  instantiated (at the bottom of the cpp) for cases with 1, would agree with this.
 *
 *  But at the same time it probably isn't worth breaking users' code by changing it.
 *  Might also make it easier to copy and paste for any new class that does a
 *  fancier integral with more quantities.
 */
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class PseudoEcgCalculator : public AbstractFunctionalCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>
{
private:

    friend class TestPseudoEcgCalculator;//for testing

    Hdf5DataReader* mpDataReader; 
    unsigned mNumberOfNodes; 
    unsigned mNumTimeSteps;
    AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& mrMesh;
    ChastePoint<SPACE_DIM> mProbeElectrode; 
    double mDiffusionCoefficient;
    std::string mVariableName;
    double GetIntegrand(ChastePoint<SPACE_DIM>& rX,
                        c_vector<double,PROBLEM_DIM>& rU,
                        c_matrix<double,PROBLEM_DIM,SPACE_DIM>& rGradU);


    double ComputePseudoEcgAtOneTimeStep(unsigned timeStep);

    bool ShouldSkipThisElement(Element<ELEMENT_DIM,SPACE_DIM>& rElement);

public:

    PseudoEcgCalculator(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
                        const ChastePoint<SPACE_DIM>& rProbeElectrode,
                        std::string directory,
                        std::string hdf5File,
                        std::string variableName = "V",
                        bool makeAbsolute = true);

    ~PseudoEcgCalculator();


    void SetDiffusionCoefficient(double diffusionCoefficient);

    void WritePseudoEcg();

};

#endif //_PSEUDOECGALCALCULATOR_HPP_