SubstanceManager.h

/* Distributed under the Apache License, Version 2.0.
   See accompanying NOTICE file for details.*/
 
#pragma once
 
#include "engine/CommonDefs.h"
#include "cdm/substance/SESubstanceManager.h"
class SELiquidCompartment;
class SETissueCompartment;
 
namespace pulse
{
  class Data;
  class PULSE_DECL SizeIndependentDepositionEfficencyCoefficient
  {
    friend class SubstanceManager;
  public:
    SizeIndependentDepositionEfficencyCoefficient() {};
    ~SizeIndependentDepositionEfficencyCoefficient() {}
 
    double GetAirway() const { return m_airway; }
    double GetCarina() const { return m_carina; }
    double GetDeadSpace() const { return m_deadSpace; }
    double GetAlveoli() const { return m_alveoli; }
 
  protected:
    double m_airway = 0;
    double m_carina = 0;
    double m_deadSpace = 0;
    double m_alveoli = 0;
  };
 
  class PULSE_DECL SubstanceManager : public SESubstanceManager
  {
    friend class EngineTest;
  public:
    SubstanceManager(Data& data);
    virtual ~SubstanceManager() = default;
 
    void Clear() override;
    bool LoadSubstanceDirectory(const std::string& data_dir = ".") override;
 
    virtual bool Setup();
    virtual void InitializeSubstances();
 
    virtual void AddActiveSubstance(const SESubstance& substance) override;
    virtual bool IsActive(const SESubstance& sub) const override;
 
    inline SESubstance& GetO2() { return *m_O2; }
    inline SESubstance& GetCO() { return *m_CO; }
    inline SESubstance& GetCO2() { return *m_CO2; }
    inline SESubstance& GetN2() { return *m_N2; }
    inline SESubstance& GetHb() { return *m_Hb; }
    inline SESubstance& GetHbO2() { return *m_HbO2; }
    inline SESubstance& GetHbCO2() { return *m_HbCO2; }
    inline SESubstance& GetHbCO() { return *m_HbCO; }
    inline SESubstance& GetHbO2CO2() { return *m_HbO2CO2; }
    inline SESubstance& GetHCO3() { return *m_HCO3; }
    inline SESubstance& GetEpi() { return *m_epi; }
    inline SESubstance& GetNorepi() { return *m_norepi; }
 
    inline SESubstance& GetAcetoacetate() { return *m_acetoacetate; }
    inline SESubstance& GetAlbumin() { return *m_albumin; }
    inline SESubstance& GetBicarbonate() { return *m_HCO3; }
    inline SESubstance& GetCalcium() { return *m_calcium; }
    inline SESubstance& GetChloride() { return *m_chloride; }
    inline SESubstance& GetCreatinine() { return *m_creatinine; }
    inline SESubstance& GetGlobulin() { return *m_globulin; }
    inline SESubstance& GetGlucose() { return *m_glucose; }
    inline SESubstance& GetInsulin() { return *m_insulin; }
    inline SESubstance& GetLactate() { return *m_lactate; }
    inline SESubstance& GetPotassium() { return *m_potassium; }
    inline SESubstance& GetTristearin() { return *m_tristearin; }
    inline SESubstance& GetSodium() { return *m_sodium; }
    inline SESubstance& GetUrea() { return *m_urea; }
 
    void CalculateGenericClearance(double volumeCleared_mL, SELiquidCompartment& cmpt, SESubstance& sub, SEScalarMass* cleared = nullptr);
    void CalculateGenericClearance(double volumeCleared_mL, SETissueCompartment& cmpt, SESubstance& sub, SEScalarMass* cleared = nullptr);
    void CalculateGenericExcretion(double VascularFlow_mL_Per_s, SETissueCompartment& cmpt, SESubstance& sub, double FractionExcreted, double timestep_s, SEScalarMass* excreted = nullptr);
 
    const SizeIndependentDepositionEfficencyCoefficient& GetSizeIndependentDepositionEfficencyCoefficient(const SESubstance& substance);
 
    double GetSubstanceMass(SESubstance&, const std::vector<SELiquidCompartment*>&, const MassUnit& unit);
    double GetSubstanceMass(SESubstance&, const std::vector<SETissueCompartment*>&, const MassUnit& unit);
 
    void WriteBloodGases();
    void WritePulmonaryGases();
    void ProbeBloodGases(SELiquidCompartment& cmpt, const std::string& prefix = "");
 
    virtual void InitializeGasCompartments();
    virtual void InitializeLiquidCompartmentGases();
    virtual void InitializeLiquidCompartmentNonGases();
 
  protected:
    virtual void CopyConcentrations(SELiquidCompartment& src, SELiquidCompartment& tgt);
    virtual void InitializeBloodGases(SETissueCompartment& tissue, SELiquidCompartment& vascular);
    virtual void InitializeBloodGases(SELiquidCompartment& cmpt, double Hb_total_mM, double O2_sat, double O2_mmol_Per_L, double CO2_sat, double CO2_mmol_Per_L, double HCO3_mmol_Per_L, double pH, bool distribute = true);
 
    void   SetSubstanceMolarity(SESubstance&, const std::vector<SELiquidCompartment*>&, const SEScalarAmountPerVolume& molarity);
    void   SetSubstanceMolarity(SESubstance&, const std::vector<SETissueCompartment*>&, const SEScalarAmountPerVolume& molarity);
    void   SetSubstanceMolarity(SESubstance&, const std::vector<SETissueCompartment*>&, const SEScalarAmountPerVolume& extracellular, const SEScalarAmountPerVolume& intracellular);
 
    void   SetSubstanceConcentration(SESubstance&, const std::vector<SELiquidCompartment*>&, const SEScalarMassPerVolume& concentration);
    void   SetSubstanceConcentration(SESubstance&, const std::vector<SETissueCompartment*>&, const SEScalarMassPerVolume& concentration);
    void   SetSubstanceConcentration(SESubstance&, const std::vector<SETissueCompartment*>&, const SEScalarMassPerVolume& extracellular, const SEScalarMassPerVolume& intracellular);
 
    // Common Substances
    //Substances
    SESubstance* m_O2;
    SESubstance* m_CO;
    SESubstance* m_CO2;
    SESubstance* m_N2;
    SESubstance* m_Hb;
    SESubstance* m_HbO2;
    SESubstance* m_HbCO2;
    SESubstance* m_HbCO;
    SESubstance* m_HbO2CO2;
    SESubstance* m_HCO3;
    SESubstance* m_epi;
    SESubstance* m_norepi;
 
    SESubstance* m_acetoacetate;
    SESubstance* m_albumin;
    SESubstance* m_calcium;
    SESubstance* m_chloride;
    SESubstance* m_creatinine;
    SESubstance* m_globulin;
    SESubstance* m_glucose;
    SESubstance* m_insulin;
    SESubstance* m_lactate;
    SESubstance* m_tristearin;
    SESubstance* m_potassium;
    SESubstance* m_sodium;
    SESubstance* m_urea;
 
    bool          m_isCOActive;
 
    std::map<const SESubstance*, SizeIndependentDepositionEfficencyCoefficient*> m_SIDECoefficients;
 
    Data& m_data;
  };
END_NAMESPACE