SEBloodChemistrySystem.h

/**************************************************************************************
Copyright 2015 Applied Research Associates, Inc.
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:
http://www.apache.org/licenses/LICENSE-2.0
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.
**************************************************************************************/

#pragma once

#include <biogears/cdm/system/SESystem.h>
#include <biogears/exports.h>
#include <biogears/schema/biogears/BioGearsPhysiology.hxx>

namespace biogears {
class SEScalar;
class SEScalar0To1;
class SEScalarMass;
class MassUnit;
class SEScalarTime;
class TimeUnit;
class SEScalarMassPerVolume;
class MassPerVolumeUnit;
class SEScalarHeatCapacitancePerMass;
class HeatCapacitancePerMassUnit;
class SEScalarFraction;
class SEScalarVolume;
class VolumeUnit;
class SEScalarAmountPerVolume;
class AmountPerVolumeUnit;
class SEScalarPressure;
class PressureUnit;
class SEInflammatoryResponse;

class BIOGEARS_API SEBloodChemistrySystem : public SESystem {
public:
  SEBloodChemistrySystem(Logger* logger);
  ~SEBloodChemistrySystem() override;

  static size_t TypeHash() { return reinterpret_cast<size_t>(&TypeHash); }
  static constexpr char const* const TypeTag() { return "SEBloodChemistrySystem"; }
  const char* classname() const override { return TypeTag(); }
  size_t hash_code() const override { return TypeHash(); }

  void Clear() override; 
  const SEScalar* GetScalar(const char* name) override;
  const SEScalar* GetScalar(const std::string& name) override;  //@{
  bool Load(const CDM::BloodChemistrySystemData& in); 
  CDM::BloodChemistrySystemData* Unload() const override; 
  Tree<const char*> GetPhysiologyRequestGraph() const override;

protected:
  void Unload(CDM::BloodChemistrySystemData& data) const;  //@}
public: //@{ @copybrief Physiology_BloodChemistrySystemData_BloodDensity
  bool HasBloodDensity() const; 
  SEScalarMassPerVolume& GetBloodDensity(); 
  double GetBloodDensity(const MassPerVolumeUnit& unit) const;  //@}

  bool HasArterialBloodPH() const;
  SEScalar& GetArterialBloodPH();
  double GetArterialBloodPH() const;

  bool HasArterialBloodPHBaseline() const;
  SEScalar& GetArterialBloodPHBaseline();
  double GetArterialBloodPHBaseline() const;

  bool HasVenousBloodPH() const;
  SEScalar& GetVenousBloodPH();
  double GetVenousBloodPH() const;

  bool HasBloodSpecificHeat() const;
  SEScalarHeatCapacitancePerMass& GetBloodSpecificHeat();
  double GetBloodSpecificHeat(const HeatCapacitancePerMassUnit& unit) const;

  bool HasBloodUreaNitrogenConcentration() const;
  SEScalarMassPerVolume& GetBloodUreaNitrogenConcentration();
  double GetBloodUreaNitrogenConcentration(const MassPerVolumeUnit& unit) const;

  bool HasCarbonDioxideSaturation() const;
  SEScalarFraction& GetCarbonDioxideSaturation();
  double GetCarbonDioxideSaturation() const;

  bool HasCarbonMonoxideSaturation() const;
  SEScalarFraction& GetCarbonMonoxideSaturation();
  double GetCarbonMonoxideSaturation() const;

  bool HasHematocrit() const;
  SEScalarFraction& GetHematocrit();
  double GetHematocrit() const;

  bool HasHemoglobinContent() const;
  SEScalarMass& GetHemoglobinContent();
  double GetHemoglobinContent(const MassUnit& unit) const;

  bool HasHemoglobinLostToUrine() const;
  SEScalarMass& GetHemoglobinLostToUrine();
  double GetHemoglobinLostToUrine(const MassUnit& unit) const;

  bool HasOxygenSaturation() const;
  SEScalarFraction& GetOxygenSaturation();
  double GetOxygenSaturation() const;

  bool HasOxygenVenousSaturation() const;
  SEScalarFraction& GetOxygenVenousSaturation();
  double GetOxygenVenousSaturation() const;

  bool HasPhosphate() const;
  SEScalarAmountPerVolume& GetPhosphate();
  double GetPhosphate(const AmountPerVolumeUnit& unit) const;

  bool HasPlasmaVolume() const;
  SEScalarVolume& GetPlasmaVolume();
  double GetPlasmaVolume(const VolumeUnit& unit) const;

  bool HasPulseOximetry() const;
  SEScalarFraction& GetPulseOximetry();
  double GetPulseOximetry() const;

  bool HasRedBloodCellAcetylcholinesterase() const;
  SEScalarAmountPerVolume& GetRedBloodCellAcetylcholinesterase();
  double GetRedBloodCellAcetylcholinesterase(const AmountPerVolumeUnit& unit) const;

  bool HasRedBloodCellCount() const;
  SEScalarAmountPerVolume& GetRedBloodCellCount();
  double GetRedBloodCellCount(const AmountPerVolumeUnit& unit) const;

  bool HasStrongIonDifference() const;
  SEScalarAmountPerVolume& GetStrongIonDifference();
  double GetStrongIonDifference(const AmountPerVolumeUnit& unit) const;

  bool HasShuntFraction() const;
  SEScalarFraction& GetShuntFraction();
  double GetShuntFraction() const;

  bool HasTotalBilirubin() const;
  SEScalarMassPerVolume& GetTotalBilirubin();
  double GetTotalBilirubin(const MassPerVolumeUnit& unit) const;

  bool HasTotalProteinConcentration() const;
  SEScalarMassPerVolume& GetTotalProteinConcentration();
  double GetTotalProteinConcentration(const MassPerVolumeUnit& unit) const;

  bool HasRhTransfusionReactionVolume() const;
  virtual SEScalarVolume& GetRhTransfusionReactionVolume();
  double GetRhTransfusionReactionVolume(const VolumeUnit& unit) const;

  bool HasVolumeFractionNeutralPhospholipidInPlasma() const;
  SEScalarFraction& GetVolumeFractionNeutralPhospholipidInPlasma();
  double GetVolumeFractionNeutralPhospholipidInPlasma() const;

  bool HasVolumeFractionNeutralLipidInPlasma() const;
  SEScalarFraction& GetVolumeFractionNeutralLipidInPlasma();
  double GetVolumeFractionNeutralLipidInPlasma() const;

  bool HasWhiteBloodCellCount() const;
  SEScalarAmountPerVolume& GetWhiteBloodCellCount();
  double GetWhiteBloodCellCount(const AmountPerVolumeUnit& unit) const;

  bool HasArterialCarbonDioxidePressure() const;
  SEScalarPressure& GetArterialCarbonDioxidePressure();
  double GetArterialCarbonDioxidePressure(const PressureUnit& unit) const;

  bool HasArterialOxygenPressure() const;
  SEScalarPressure& GetArterialOxygenPressure();
  double GetArterialOxygenPressure(const PressureUnit& unit) const;

  bool HasPulmonaryArterialCarbonDioxidePressure() const;
  SEScalarPressure& GetPulmonaryArterialCarbonDioxidePressure();
  double GetPulmonaryArterialCarbonDioxidePressure(const PressureUnit& unit) const;

  bool HasPulmonaryArterialOxygenPressure() const;
  SEScalarPressure& GetPulmonaryArterialOxygenPressure();
  double GetPulmonaryArterialOxygenPressure(const PressureUnit& unit) const;

  bool HasPulmonaryVenousCarbonDioxidePressure() const;
  SEScalarPressure& GetPulmonaryVenousCarbonDioxidePressure();
  double GetPulmonaryVenousCarbonDioxidePressure(const PressureUnit& unit) const;

  bool HasPulmonaryVenousOxygenPressure() const;
  SEScalarPressure& GetPulmonaryVenousOxygenPressure();
  double GetPulmonaryVenousOxygenPressure(const PressureUnit& unit) const;

  bool HasVenousCarbonDioxidePressure() const;
  SEScalarPressure& GetVenousCarbonDioxidePressure();
  double GetVenousCarbonDioxidePressure(const PressureUnit& unit) const;

  bool HasVenousOxygenPressure() const;
  SEScalarPressure& GetVenousOxygenPressure();
  double GetVenousOxygenPressure(const PressureUnit& unit) const;

  virtual bool HasInflammatoryResponse() const;
  virtual SEInflammatoryResponse& GetInflammatoryResponse();
  virtual SEInflammatoryResponse& GetInflammatoryResponse() const;

protected:
  SEScalarMassPerVolume* m_BloodDensity;
  SEScalar* m_ArterialBloodPH;
  SEScalar* m_ArterialBloodPHBaseline;
  SEScalar* m_VenousBloodPH;
  SEScalarHeatCapacitancePerMass* m_BloodSpecificHeat;
  SEScalarMassPerVolume* m_BloodUreaNitrogenConcentration;
  SEScalarFraction* m_CarbonDioxideSaturation;
  SEScalarFraction* m_CarbonMonoxideSaturation;
  SEScalarFraction* m_Hematocrit;
  SEScalarMass* m_HemoglobinContent;
  SEScalarMass* m_HemoglobinLostToUrine;
  SEScalarFraction* m_OxygenSaturation;
  SEScalarFraction* m_OxygenVenousSaturation;
  SEScalarAmountPerVolume* m_Phosphate;
  SEScalarVolume* m_PlasmaVolume;
  SEScalarFraction* m_PulseOximetry;
  SEScalarAmountPerVolume* m_RedBloodCellAcetylcholinesterase;
  SEScalarAmountPerVolume* m_RedBloodCellCount;
  SEScalarFraction* m_ShuntFraction;
  SEScalarAmountPerVolume* m_StrongIonDifference;
  SEScalarMassPerVolume* m_TotalBilirubin;
  SEScalarMassPerVolume* m_TotalProteinConcentration;
  SEScalarVolume* m_RhTransfusionReactionVolume;
  SEScalarFraction* m_VolumeFractionNeutralPhospholipidInPlasma;
  SEScalarFraction* m_VolumeFractionNeutralLipidInPlasma;
  SEScalarAmountPerVolume* m_WhiteBloodCellCount;


  SEScalarPressure* m_ArterialCarbonDioxidePressure;
  SEScalarPressure* m_ArterialOxygenPressure;
  SEScalarPressure* m_PulmonaryArterialCarbonDioxidePressure;
  SEScalarPressure* m_PulmonaryArterialOxygenPressure;
  SEScalarPressure* m_PulmonaryVenousCarbonDioxidePressure;
  SEScalarPressure* m_PulmonaryVenousOxygenPressure;
  SEScalarPressure* m_VenousCarbonDioxidePressure;
  SEScalarPressure* m_VenousOxygenPressure;
  SEInflammatoryResponse* m_InflammatoryResponse;
};

class BIOGEARS_API SEInflammatoryResponse {
public:
  SEInflammatoryResponse();
  ~SEInflammatoryResponse();

  static size_t TypeHash() { return reinterpret_cast<size_t>(&TypeHash); }
  static constexpr char const* const TypeTag() { return "SEInflammatoryResponse"; }
  const char* classname() const  { return TypeTag(); }
  size_t hash_code() const  { return TypeHash(); }

  void Clear();

  bool Load(const CDM::InflammatoryResponseData& in);
  CDM::InflammatoryResponseData* Unload() const;
  bool IsValid();

  void Initialize();
  const SEScalar* GetScalar(const char* name);
  const SEScalar* GetScalar(const std::string& name);

protected:
  void Unload(CDM::InflammatoryResponseData& data) const;

public:
  bool HasLocalPathogen() const;
  SEScalar& GetLocalPathogen();
  double GetLocalPathogen() const;

  bool HasLocalBarrier() const;
  SEScalar& GetLocalBarrier();
  double GetLocalBarrier() const;

  bool HasLocalMacrophage() const;
  SEScalar& GetLocalMacrophage();
  double GetLocalMacrophage() const;

  bool HasLocalNeutrophil() const;
  SEScalar& GetLocalNeutrophil();
  double GetLocalNeutrophil() const;

  bool HasActiveTLR() const {return m_ActiveTLR == CDM::enumOnOff::value(-1) ? false : true;};
  CDM::enumOnOff GetActiveTLR() { return m_ActiveTLR; };
  void SetActiveTLR(CDM::enumOnOff value) { m_ActiveTLR = value; };

  bool HasAutonomicResponseLevel() const;
  SEScalar& GetAutonomicResponseLevel();
  double GetAutonomicResponseLevel() const;

  bool HasCatecholamines() const;
  SEScalar& GetCatecholamines();
  double GetCatecholamines() const;

  bool HasConstitutiveNOS() const;
  SEScalar& GetConstitutiveNOS();
  double GetConstitutiveNOS() const;

  bool HasInducibleNOSPre() const;
  SEScalar& GetInducibleNOSPre();
  double GetInducibleNOSPre() const;

  bool HasInducibleNOS() const;
  SEScalar& GetInducibleNOS();
  double GetInducibleNOS() const;

  bool HasInterleukin6() const;
  SEScalar& GetInterleukin6();
  double GetInterleukin6() const;

  bool HasInterleukin10() const;
  SEScalar& GetInterleukin10();
  double GetInterleukin10() const;

  bool HasInterleukin12() const;
  SEScalar& GetInterleukin12();
  double GetInterleukin12() const;

  bool HasMacrophageResting() const;
  SEScalar& GetMacrophageResting();
  double GetMacrophageResting() const;

  bool HasMacrophageActive() const;
  SEScalar& GetMacrophageActive();
  double GetMacrophageActive() const;

  bool HasNeutrophilResting() const;
  SEScalar& GetNeutrophilResting();
  double GetNeutrophilResting() const;

  bool HasNeutrophilActive() const;
  SEScalar& GetNeutrophilActive();
  double GetNeutrophilActive() const;

  bool HasNitrate() const;
  SEScalar& GetNitrate();
  double GetNitrate() const;

  bool HasNitricOxide() const;
  SEScalar& GetNitricOxide();
  double GetNitricOxide() const;

  bool HasBloodPathogen() const;
  SEScalar& GetBloodPathogen();
  double GetBloodPathogen() const;

  bool HasTissueIntegrity() const;
  SEScalar0To1& GetTissueIntegrity();
  double GetTissueIntegrity() const;

  bool HasTrauma() const;
  SEScalar& GetTrauma();
  double GetTrauma() const;

  bool HasTumorNecrosisFactor() const;
  SEScalar& GetTumorNecrosisFactor();
  double GetTumorNecrosisFactor() const;

  bool HasInflammationTime() const;
  SEScalarTime& GetInflammationTime();
  double GetInflammationTime(const TimeUnit& unit) const;

  bool HasInflammationSources() const;
  std::vector<CDM::enumInflammationSource>& GetInflammationSources();
  bool HasInflammationSource(CDM::enumInflammationSource::value src);

  Tree<const char*> GetPhysiologyRequestGraph() const;

protected:
  SEScalar* m_LocalPathogen;
  SEScalar* m_LocalMacrophage;
  SEScalar* m_LocalNeutrophil;
  SEScalar* m_LocalBarrier;
  CDM::enumOnOff::value m_ActiveTLR;
  SEScalar* m_AutonomicResponseLevel;
  SEScalar* m_Catecholamines;
  SEScalar* m_ConstitutiveNOS;
  SEScalar* m_InducibleNOSPre;
  SEScalar* m_InducibleNOS;
  SEScalar* m_Interleukin6;
  SEScalar* m_Interleukin10;
  SEScalar* m_Interleukin12;
  SEScalar* m_MacrophageResting;
  SEScalar* m_MacrophageActive;
  SEScalar* m_NeutrophilResting;
  SEScalar* m_NeutrophilActive;
  SEScalar* m_Nitrate;
  SEScalar* m_NitricOxide;
  SEScalar* m_BloodPathogen;
  SEScalar0To1* m_TissueIntegrity;
  SEScalar* m_Trauma;
  SEScalar* m_TumorNecrosisFactor;
  SEScalarTime* m_InflammationTime;
  std::vector<CDM::enumInflammationSource> m_InflammationSources;
};
}