VerticalAbioticEnvironment.h

#ifndef VERTICAL_ABIOTIC_ENVIRONMENT_H
#define VERTICAL_ABIOTIC_ENVIRONMENT_H
 
#include <algorithm>
#include <iostream>
#include <string>
#ifdef WIN32
#include <io.h>
#define access _access
#endif
 
#include <Eigen/Eigen>
#include <unordered_map>
#include <CPrintDuringExec.h>
//#include <SimObject.h>
#include <CIntegratorOptions.h>
#include "fish/eigen_matrix_defs.h" //Consider fixing this with includes in cmakelists file
#include <CFhSimMgr.h>
#include <string>
#include "CEnvironment.h"
#ifdef FH_VISUALIZATION
    //#include "sfh/ogre/C3DLine.h"
#endif
 
    class VerticalAbioticEnvironment : public SimObject
    {
    public:
    VerticalAbioticEnvironment(std::string simObjectName, ISimObjectCreator *creator);
    virtual ~VerticalAbioticEnvironment();
    std::vector<std::string>    SplitString(std::string sData,std::string separator);
    void                        GetLightDatasetFromSlagstadModel(double latitude, double attenuationCoeff, double backgroundRadiation, int startDayOfYear,int endDayOfYear, double** dataSet,std::string lightIntFileLocationFolder);
    virtual void                OdeFcn(const double T, const double *const X, double *const XDot, const bool isMajorTimeStep);
    virtual void                getValueAndGradient(std::string dataType,Fish::vec3 position, double* valueAndGradient);
    //virtual void InitialConditionSetup(const double T, const double *const currentIC, double *const updatedIC, ISimObjectCreator *const creator);
    //void FinalSetup(const double T, const double *const X, ISimObjectCreator *const creator);
 
#ifdef FH_VISUALIZATION
    virtual void RenderInit(Ogre::Root *const ogreRoot, ISimObjectCreator *const creator);
    virtual void RenderUpdate(const double T, const double *const X);
#endif
 
 
    protected:
        // Functions
        virtual double ArtificialLightEffect(Fish::vec3 position);
 
        // Parameters
        double                              m_verticalResolution;
        double                              m_timeResolution;
        int                                 m_verticalDimension;
        int                                 m_timeDimension;
        double*                             m_times;
        double*                             m_depths;
        std::unordered_map<std::string,int> m_dataTypes;
        std::vector<double**>               m_fullDatasets;                     
        std::vector<double*>                m_presentStates;                    
        double                              m_timeOfLastUpdate;
 
        // Artificial light parameters
        int                                 m_artificialLightNumber;            
        Fish::vec3*                         m_artificialLightPositions;         
        double                              m_artificialLightAttenuationFactor; 
        double                              m_artificialLightSourceRadius;      
        double                              m_artificialLightBaseIntensity;     
 
        ISimObjectCreator*                  m_creator;
 
#ifdef FH_VISUALIZATION
 
#endif
 
    };
#endif