BloodChemistry.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/CommonDataModel.h>
#include <biogears/exports.h>

#include <biogears/cdm/patient/SEPatient.h>
#include <biogears/cdm/system/physiology/SEBloodChemistrySystem.h>
#include <biogears/cdm/utils/RunningAverage.h>
#include <biogears/engine/Controller/BioGearsSystem.h>
#include <biogears/schema/biogears/BioGearsPhysiology.hxx>

namespace biogears {
class SECompleteBloodCount;
class SEComprehensiveMetabolicPanel;
class SELiquidCompartment;
class SELiquidSubstanceQuantity;
class SEPatientActionCollection;
class BioGears;
class BIOGEARS_API BloodChemistry : public SEBloodChemistrySystem, public BioGearsSystem {
  friend BioGears;
  friend class BioGearsEngineTest;

protected:
  static auto make_unique(BioGears& bg) -> std::unique_ptr<BloodChemistry>;
  BloodChemistry(BioGears& bg);
  BioGears& m_data;

public:
  virtual ~BloodChemistry() override;

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

  void Clear() override;

  // Set members to a stable homeostatic state
  void Initialize() override;

  // Load a state
  bool Load(const CDM::BioGearsBloodChemistrySystemData& in);
  CDM::BioGearsBloodChemistrySystemData* Unload() const override;

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

  // Set pointers and other member variables common to both homeostatic initialization and loading a state
  void SetUp() override;

public:
  void AtSteadyState() override;
  void PreProcess() override;
  void Process() override;
  void PostProcess() override;

  bool CalculateCompleteBloodCount(SECompleteBloodCount& cbc);
  bool CalculateComprehensiveMetabolicPanel(SEComprehensiveMetabolicPanel& cmp);
  SEScalar& CalculateCoagulationSOFA();
  void CalculateHemolyticTransfusionReaction(bool rhMismatch = false);

protected:
  void CheckBloodSubstanceLevels();
  void InflammatoryResponse();
  void ManageSIRS();        //SIRS = Systemic Inflammatory Response Syndrome

  //Override
  void ProcessOverride();
  void OverrideControlLoop();

  // Serializable member variables (Set in Initialize and in schema)
  RunningAverage m_ArterialOxygen_mmHg;
  RunningAverage m_ArterialCarbonDioxide_mmHg;

  // Patient
  SEPatient* m_Patient;
  SEPatientActionCollection* m_PatientActions;

  // Stateless member variable (Set in SetUp())
  double m_redBloodCellVolume_mL;
  double m_HbLostToUrine_g;
  double m_RhTransfusionReactionVolume_mL;
  double m_HbPerRedBloodCell_ug_Per_ct;
  SEInflammatoryResponse* m_InflammatoryResponse;
  double m_RhFactorMismatch_ct;
  SELiquidCompartment* m_aorta;
  SELiquidSubstanceQuantity* m_aortaO2;
  SELiquidSubstanceQuantity* m_aortaCO2;
  SELiquidSubstanceQuantity* m_aortaCO;
  SELiquidSubstanceQuantity* m_aortaBicarbonate;
  SELiquidSubstanceQuantity* m_brainO2;
  SELiquidSubstanceQuantity* m_myocardiumO2;
  SELiquidSubstanceQuantity* m_pulmonaryArteriesO2;
  SELiquidSubstanceQuantity* m_pulmonaryArteriesCO2;
  SELiquidSubstanceQuantity* m_pulmonaryVeinsO2;
  SELiquidSubstanceQuantity* m_pulmonaryVeinsCO2;
  SELiquidCompartment* m_venaCava;
  SELiquidSubstanceQuantity* m_venaCavaO2;
  SELiquidSubstanceQuantity* m_venaCavaCO2;
  SELiquidSubstanceQuantity* m_venaCavaAlbumin;
  SELiquidSubstanceQuantity* m_venaCavaAminoAcids;
  SELiquidSubstanceQuantity* m_venaCavaBicarbonate;
  SELiquidSubstanceQuantity* m_venaCavaCalcium;
  SELiquidSubstanceQuantity* m_venaCavaChloride;
  SELiquidSubstanceQuantity* m_venaCavaCreatinine;
  SELiquidSubstanceQuantity* m_venaCavaEpinephrine;
  SELiquidSubstanceQuantity* m_venaCavaGlucagon;
  SELiquidSubstanceQuantity* m_venaCavaGlucose;
  SELiquidSubstanceQuantity* m_venaCavaInsulin;
  SELiquidSubstanceQuantity* m_venaCavaKetones;
  SELiquidSubstanceQuantity* m_venaCavaLactate;
  SELiquidSubstanceQuantity* m_venaCavaPotassium;
  SELiquidSubstanceQuantity* m_venaCavaRBC;
  SELiquidSubstanceQuantity* m_venaCavaSodium;
  SELiquidSubstanceQuantity* m_venaCavaTriacylglycerol;
  SELiquidSubstanceQuantity* m_venaCavaUrea;

  //Initialize HTR concentrations
  double m_donorRBC_ct;
  double m_patientRBC_ct;
  double m_2Agglutinate_ct;
  double m_p3Agglutinate_ct;
  double m_d3Agglutinate_ct;
  double m_4Agglutinate_ct;
  double m_RemovedRBC_ct;
};
}