/* Distributed under the Apache License, Version 2.0.
   See accompanying NOTICE file for details.*/

#include "stdafx.h"
#include "physiology/Drugs.h"
#include "controller/Compartments.h"
#include "controller/Circuits.h"
#include "controller/Substances.h"
#include "PulseConfiguration.h"
// Dependent Systems
#include "system/physiology/SEBloodChemistrySystem.h"
#include "system/physiology/SECardiovascularSystem.h"
#include "system/physiology/SETissueSystem.h"
#include "system/physiology/SEPupillaryResponse.h"
// Actions
#include "engine/SEActionManager.h"
#include "engine/SEPatientActionCollection.h"
#include "patient/actions/SESubstanceBolus.h"
#include "patient/actions/SESubstanceInfusion.h"
#include "patient/actions/SESubstanceCompoundInfusion.h"
// CDM
#include "patient/SEPatient.h"
#include "substance/SESubstance.h"
#include "substance/SESubstanceCompound.h"
#include "substance/SESubstanceConcentration.h"
#include "substance/SESubstanceClearance.h"
#include "substance/SESubstancePhysicochemicals.h"
#include "substance/SESubstancePharmacodynamics.h"
#include "substance/SESubstancePharmacokinetics.h"
#include "substance/SESubstanceTissuePharmacokinetics.h"
#include "circuit/fluid/SEFluidCircuit.h"
#include "compartment/tissue/SETissueCompartment.h"
#include "compartment/fluid/SELiquidCompartmentGraph.h"
#include "compartment/substances/SELiquidSubstanceQuantity.h"
#include "properties/SEScalarPressure.h"
#include "properties/SEScalarMassPerVolume.h"
#include "properties/SEScalarVolumePerTime.h"
#include "properties/SEScalar0To1.h"
#include "properties/SEScalarInversePressure.h"
#include "properties/SEScalarFrequency.h"
#include "properties/SEScalarVolume.h"
#include "properties/SEScalarMass.h"
#include "properties/SEScalarMassPerMass.h"
#include "properties/SEScalarArea.h"
#include "properties/SEScalarAreaPerTimePressure.h"
#include "properties/SEScalarTemperature.h"
#include "properties/SEScalarMassPerTime.h"
#include "properties/SEScalarTime.h"
#include "properties/SEScalarLength.h"
#include "properties/SEScalarMassPerAmount.h"
#include "properties/SEScalarAmountPerMass.h"
#include "properties/SEScalarVolumePerTimeMass.h"
#include "properties/SEScalarVolumePerTimePressure.h"
#include "properties/SEScalarNegative1To1.h"

Drugs::Drugs(PulseController& data) : SEDrugSystem(data.GetLogger()), m_data(data)
{
  Clear();
}

Drugs::~Drugs()
{
  Clear();
}

void Drugs::Clear()
{
  SEDrugSystem::Clear();
  m_aortaVascular    = nullptr;
  m_venaCavaVascular = nullptr;
  m_muscleIntracellular = nullptr;
  m_liverVascular    = nullptr;
  m_liverTissue      = nullptr;
  m_IVToVenaCava     = nullptr;
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Initializes system properties to valid homeostatic values.
//--------------------------------------------------------------------------------------------------
void Drugs::Initialize()
{
  PulseSystem::Initialize();

  GetBronchodilationLevel().SetValue(0.0);
  GetHeartRateChange().SetValue(0.0, FrequencyUnit::Per_min);
  GetMeanBloodPressureChange().SetValue(0.0, PressureUnit::mmHg);
  GetNeuromuscularBlockLevel().SetValue(0.0);
  GetPulsePressureChange().SetValue(0.0, PressureUnit::mmHg);
  GetPupillaryResponse().GetSizeModifier().SetValue(0);
  GetPupillaryResponse().GetReactivityModifier().SetValue(0);
  GetRespirationRateChange().SetValue(0.0, FrequencyUnit::Per_min);
  GetSedationLevel().SetValue(0.0);
  GetTidalVolumeChange().SetValue(0.0, VolumeUnit::mL);
  GetTubularPermeabilityChange().SetValue(0);
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Initializes parameters for the Drugs Class
///
///  \details
///   Initializes member variables and system level values on the common data model.
//--------------------------------------------------------------------------------------------------
void Drugs::SetUp()
{
  m_dt_s = m_data.GetTimeStep().GetValue(TimeUnit::s);
  m_muscleIntracellular = m_data.GetCompartments().GetLiquidCompartment(pulse::ExtravascularCompartment::MuscleIntracellular);
  m_aortaVascular = m_data.GetCompartments().GetLiquidCompartment(pulse::VascularCompartment::Aorta);
  m_venaCavaVascular = m_data.GetCompartments().GetLiquidCompartment(pulse::VascularCompartment::VenaCava);
  m_fatTissue = m_data.GetCompartments().GetTissueCompartment(pulse::TissueCompartment::Fat);
  m_liverVascular = m_data.GetCompartments().GetLiquidCompartment(pulse::VascularCompartment::Liver);
  m_liverTissue = m_data.GetCompartments().GetTissueCompartment(pulse::TissueCompartment::Liver);
  m_IVToVenaCava = m_data.GetCircuits().GetCardiovascularCircuit().GetPath(pulse::CardiovascularPath::IVToVenaCava);
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Determines if the engine is stable.
///
/// \details
/// When the engine is stable, the CDM makes this call to update the member variable.
//--------------------------------------------------------------------------------------------------
void Drugs::AtSteadyState()
{

}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Substance Preprocess function
///
/// \details
/// The AdminsterSubstances, AdministerIVSubstances, and Hemorrhage actions are processed in this step. The masses
/// of the substances associated with these actions are updated as the actions are processed.
//--------------------------------------------------------------------------------------------------
void Drugs::PreProcess()
{
  AdministerSubstanceBolus();
  AdministerSubstanceInfusion();
  AdministerSubstanceCompoundInfusion();
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Substances process function
///
/// \details
/// For any drugs circulating in the system the renal and hepatic clearance factors and metabolic factors
/// are assigned to the appropriate compartments.
/// The drug effects categories and system level drug effects are calculated and the values are set on the common data
/// model for use in other systems. Drug effects are only calculated if the PD is enabled.
//--------------------------------------------------------------------------------------------------
void Drugs::Process()
{  
  CalculatePartitionCoefficients();

  CalculateSubstanceClearance();

  CalculatePlasmaSubstanceConcentration();

  if (m_data.GetConfiguration().IsPDEnabled())  
    CalculateDrugEffects();  
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Increments the mass of a substance to represent drug injection
///
/// \details
/// The mass of a substance is increased based on the administration of a substance. For a bolus administration,
/// the user specifies a dose (amount), a concentration, and a substance. The calculated mass is then incrementally
/// added to the vena cava over two seconds. 
//--------------------------------------------------------------------------------------------------
void Drugs::AdministerSubstanceBolus()
{
  //Need to loop over Bolus Dose Objects
  const std::map<const SESubstance*, SESubstanceBolus*>& boluses = m_data.GetActions().GetPatientActions().GetSubstanceBoluses();
  if (boluses.empty())
    return;

  std::vector<const SESubstance*> completedBolus;
  SESubstanceBolus*               bolus;
  const SESubstance*              sub;
  SELiquidSubstanceQuantity*      subQ;
  SESubstanceBolusState*          bolusState;
  double dose_mL;
  double concentration_ugPermL;
  double massIncrement_ug = 0;
  double administrationTime_s = 2; //administer dose over 2 seconds for a bolus dose

  for (auto b : boluses)
  {    
    sub = b.first;
    bolus = b.second;
    bolusState = &bolus->GetState();
    dose_mL = bolus->GetDose().GetValue(VolumeUnit::mL);
    if (bolusState->GetAdministeredDose().GetValue(VolumeUnit::mL)>=dose_mL)
    {
      // Finished, remove it
      completedBolus.push_back(&bolus->GetSubstance());
      continue;
    }

    switch (bolus->GetAdminRoute())
    {
    case eSubstanceAdministration_Route::Intraarterial:
      subQ = m_aortaVascular->GetSubstanceQuantity(*sub);
      break;
    case eSubstanceAdministration_Route::Intravenous:
      subQ = m_venaCavaVascular->GetSubstanceQuantity(*sub);
      break;
    case eSubstanceAdministration_Route::Intramuscular:
      subQ = m_muscleIntracellular->GetSubstanceQuantity(*sub);            
      break;
    default:
      /// \error Error: Unavailable Administration Route
      Error("Unavailable Bolus Administration Route for substance "+b.first->GetName(), "Drugs::AdministerSubstanceBolus");
      completedBolus.push_back(b.first);// Remove it 
      continue;
    }
    
    concentration_ugPermL = bolus->GetConcentration().GetValue(MassPerVolumeUnit::ug_Per_mL);
    massIncrement_ug = dose_mL*concentration_ugPermL*m_dt_s / administrationTime_s;
    bolusState->GetElapsedTime().IncrementValue(m_dt_s, TimeUnit::s);
    bolusState->GetAdministeredDose().IncrementValue(massIncrement_ug / concentration_ugPermL,VolumeUnit::mL);

    subQ->GetMass().IncrementValue(massIncrement_ug, MassUnit::ug);
    subQ->Balance(BalanceLiquidBy::Mass);
    /// \todo Add fluid amount to fluid system
  }
  // Remove any bolus that are complete
  for (const SESubstance* s : completedBolus)
    m_data.GetActions().GetPatientActions().RemoveSubstanceBolus(*s);
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Increments the mass of a substance to represent drug infusion
///
/// \details
/// The mass of a substance is increased based on the administration of a substance. 
/// For an infusion, the user specifies a concentration and a rate. The calculated mass
/// is then added to the vena cava every time step until the infusion is stopped.
//--------------------------------------------------------------------------------------------------
void Drugs::AdministerSubstanceInfusion()
{
  const std::map<const SESubstance*, SESubstanceInfusion*>& infusions = m_data.GetActions().GetPatientActions().GetSubstanceInfusions();
  if (infusions.empty())
    return;

  SESubstanceInfusion*            infusion;
  SESubstance*                    sub;
  SELiquidSubstanceQuantity*      subQ;
  double concentration_ug_Per_mL;
  double rate_mL_Per_s;
  double massIncrement_ug = 0;

  for (auto i : infusions)
  {
    sub = (SESubstance*)i.first; /// \todo sub needs to be const
    infusion = i.second;
    concentration_ug_Per_mL = infusion->GetConcentration().GetValue(MassPerVolumeUnit::ug_Per_mL);
    rate_mL_Per_s = infusion->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s);
    massIncrement_ug = rate_mL_Per_s*concentration_ug_Per_mL*m_dt_s;
    subQ = m_venaCavaVascular->GetSubstanceQuantity(*sub);
    subQ->GetMass().IncrementValue(massIncrement_ug, MassUnit::ug);
    /// \todo Enforce limits and remove the fatal error
    /// \error Fatal: Titration administration cannot be negative
    if (massIncrement_ug<0)
    {
      std::stringstream AdministeredTitrationDoseError;
      AdministeredTitrationDoseError << "Cannot specify a dose of less than 0. Current dose is: " << massIncrement_ug << " ug";
      Fatal(AdministeredTitrationDoseError);
      return;
    }

    /// \todo Need to add fluid amount to fluid system

    /// \todo Support state, and how would a user remove this action?
  }
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Increases the substance masses for compounds
///
/// \details
/// The masses of all substances associated with the compound substance are increased.
/// The mass of each substance is incremented in the vena cava based on the rate specified by the user 
/// and a concentration specified in the compound substance file.
//--------------------------------------------------------------------------------------------------
void Drugs::AdministerSubstanceCompoundInfusion()
{
  const std::map<const SESubstanceCompound*, SESubstanceCompoundInfusion*>& infusions = m_data.GetActions().GetPatientActions().GetSubstanceCompoundInfusions();
  if (infusions.empty())
    return;

  SESubstanceCompoundInfusion*        infusion;
  const SESubstanceCompound*          compound;
  SELiquidSubstanceQuantity*          subQ;
  double concentration_ug_Per_mL=0;
  double rate_mL_Per_s = 0;
  double totalRate_mL_Per_s = 0;
  double massIncrement_ug=0;
  double patientMass_kg = m_data.GetPatient().GetWeight(MassUnit::kg);
  double densityFluid_kg_Per_mL = 0.0;

  std::vector<const SESubstanceCompound*> emptyBags;

  for(auto i : infusions)
  {
    compound = i.first;
    infusion = i.second;

    rate_mL_Per_s = infusion->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s);
    totalRate_mL_Per_s += rate_mL_Per_s;
    /// \todo Enforce limits and remove the fatal error
    /// \error Fatal: rate cannot exceed 285 mL/min
    if (rate_mL_Per_s>285) // from http://emedsa.org.au/EDHandbook/resuscitation/IVCannula.htm... 1000mL/3.5 min ~= 285 mL/min
    {  
      m_ss<<"Cannot specify an Infusion rate greater than 285 mL/min. Current administration rate is: "<< infusion->GetRate();
      Fatal(m_ss);
      return;
    }    

    infusion->GetBagVolume().IncrementValue(-rate_mL_Per_s*m_dt_s, VolumeUnit::mL);
    double total_mL = infusion->GetBagVolume().GetValue(VolumeUnit::mL);
    if (total_mL <= 0)
    { /// \todo correct the mass based on what we have left in the bag
      emptyBags.push_back(compound);
      continue;
    }
      
    for (const SESubstanceConcentration* component : compound->GetComponents())
    {      
      subQ = m_venaCavaVascular->GetSubstanceQuantity(component->GetSubstance());
      double massIncrement_ug = rate_mL_Per_s*component->GetConcentration(MassPerVolumeUnit::ug_Per_mL)*m_dt_s;
      subQ->GetMass().IncrementValue(massIncrement_ug, MassUnit::ug);
      subQ->Balance(BalanceLiquidBy::Mass);
    }    

    if (compound->GetName().compare("Saline") == 0)
      densityFluid_kg_Per_mL = m_data.GetConfiguration().GetWaterDensity(MassPerVolumeUnit::kg_Per_mL);
    else if (compound->GetName().compare("Blood") == 0)
      densityFluid_kg_Per_mL = m_data.GetBloodChemistry().GetBloodDensity(MassPerVolumeUnit::kg_Per_mL);
    patientMass_kg -= rate_mL_Per_s*densityFluid_kg_Per_mL*m_dt_s;
  }

  for (const SESubstanceCompound* c : emptyBags)
    m_data.GetActions().GetPatientActions().RemoveSubstanceCompoundInfusion(*c);

  m_data.GetPatient().GetWeight().SetValue(patientMass_kg, MassUnit::kg);
  m_IVToVenaCava->GetNextFlowSource().SetValue(totalRate_mL_Per_s, VolumePerTimeUnit::mL_Per_s);
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Calculate partition coefficients for the PK Model
///
/// \param  vSubstances
/// Coefficients are calculated for the substances in the vector with IonicState. 
/// 
/// \details
/// The partition coefficients are calculated for each substance in the input vector (active substances). 
/// To ensure the diffusion is modeled with PK for the substance, a check is performed for Ionic State. If 
/// the property is present the coefficients are calculated. They are calculated for all tissue compartments.
/// coefficients are set on the substance compartment effects for use during the diffusion calculation.
//--------------------------------------------------------------------------------------------------
void Drugs::CalculatePartitionCoefficients()
{
  SEBloodChemistrySystem& BloodChemistry = m_data.GetBloodChemistry();
  double IntracellularPH = m_data.GetTissue().GetIntracellularFluidPH().GetValue();
  double PlasmaPH = BloodChemistry.GetBloodPH().GetValue();
  double NeutralLipidInPlasmaVolumeFraction = BloodChemistry.GetVolumeFractionNeutralLipidInPlasma().GetValue();
  double NeutralPhosphoLipidInPlasmaVolumeFraction = BloodChemistry.GetVolumeFractionNeutralPhospholipidInPlasma().GetValue();
  double IntracellularPHEffects = 0;
  double PlasmaPHEffects = 0;
  double PHEffectPower = 0;
  double PHEffects = 0;
  double EquationPartA = 0;
  double EquationPartB = 0;
  double EquationPartC = 0;
  double PartitionCoefficient = 0;
  double TissueToPlasmaProteinRatio = 0;

  //Loop over tissue nodes
  for (SETissueCompartment* tissue : m_data.GetCompartments().GetTissueLeafCompartments())
  {
    if (!tissue->HasMatrixVolume())
    {
      continue;
    }
    SELiquidCompartment& ExtracellularFluid = m_data.GetCompartments().GetExtracellularFluid(*tissue);
    SELiquidCompartment& IntracellularFluid = m_data.GetCompartments().GetIntracellularFluid(*tissue);

    //Loop over substances
    for (SESubstance* sub : m_data.GetCompartments().GetLiquidCompartmentSubstances())
    {
      if (!sub->HasPK())
        continue;        
      if(!sub->GetPK().HasPhysicochemicals())
        continue;
      
      SESubstancePhysicochemicals& pk = sub->GetPK().GetPhysicochemicals();
      eSubstance_IonicState IonicState = pk.GetIonicState();
      double AcidDissociationConstant = pk.GetAcidDissociationConstant().GetValue();
      double P = exp(log(10) * pk.GetLogP().GetValue()); //Getting P from logP value
      if (tissue == m_fatTissue)
      {
        P = 1.115 * pk.GetLogP().GetValue() - 1.35;
        P = exp(log(10) * P);
      }
      if (pk.GetBindingProtein() == eSubstance_BindingProtein::AAG)
      {
        TissueToPlasmaProteinRatio = tissue->GetTissueToPlasmaAlphaAcidGlycoproteinRatio().GetValue();
      }
      else if (pk.GetBindingProtein() == eSubstance_BindingProtein::Albumin)
      {
        TissueToPlasmaProteinRatio = tissue->GetTissueToPlasmaAlbuminRatio().GetValue();
      }
      else if (pk.GetBindingProtein() == eSubstance_BindingProtein::Lipoprotein)
      {
        TissueToPlasmaProteinRatio = tissue->GetTissueToPlasmaLipoproteinRatio().GetValue();
      }
      else
      {
        /// \error Fatal: Binding Protein not supported
        std::stringstream ss;
        ss << "The binding protein is not supported. Unable to compute partition coefficient for: ";
        ss << sub->GetName();
        ss << " in compartment: ";
        ss << tissue->GetName();
        Fatal(ss);
      }
      //Based on the ionic state, the partition coefficient equation and/or pH effect equations are varied.
      if (IonicState == eSubstance_IonicState::Base)
      {
        IntracellularPHEffects = pow(10.0, (AcidDissociationConstant - IntracellularPH));
        PHEffectPower = PlasmaPH - AcidDissociationConstant;
        PlasmaPHEffects = 1.0 + pow(10.0, PHEffectPower);
        EquationPartA = 1.0 + IntracellularPHEffects * IntracellularFluid.GetWaterVolumeFraction().GetValue() / PlasmaPHEffects;
        /// \todo How to support oral absorption - should I check if oral administration then use Oral absorption rate otherwise assume 1?
        EquationPartB = tissue->GetAcidicPhospohlipidConcentration().GetValue(MassPerMassUnit::mg_Per_g) * IntracellularPHEffects / PlasmaPHEffects;
        EquationPartC = P * tissue->GetNeutralLipidsVolumeFraction().GetValue() + (0.3 * P + 0.7) * tissue->GetNeutralPhospholipidsVolumeFraction().GetValue() / PlasmaPHEffects;
      }
      else
      {
        if (IonicState == eSubstance_IonicState::Acid)
        {
          PHEffectPower = IntracellularPH - AcidDissociationConstant;
          IntracellularPHEffects = 1.0 + pow(10.0, PHEffectPower);
          PHEffectPower = PlasmaPH - AcidDissociationConstant;
          PlasmaPHEffects = 1.0 + pow(10.0, PHEffectPower);
        }
        else if (IonicState == eSubstance_IonicState::WeakBase)
        {
          PHEffectPower = AcidDissociationConstant - IntracellularPH;
          IntracellularPHEffects = 1.0 + pow(10.0, PHEffectPower);
          PHEffectPower = AcidDissociationConstant - PlasmaPH;
          PlasmaPHEffects = 1.0 + pow(10.0, PHEffectPower);
        }
        else
        {
          IntracellularPHEffects = 1.0;
          PlasmaPHEffects = 1.0;
        }
        EquationPartA = IntracellularPHEffects * IntracellularFluid.GetWaterVolumeFraction().GetValue() / PlasmaPHEffects;
        EquationPartB = (P * tissue->GetNeutralLipidsVolumeFraction().GetValue() + (0.3 * P + 0.7) * tissue->GetNeutralPhospholipidsVolumeFraction().GetValue())
          / PlasmaPHEffects;
        EquationPartC = ((1 / pk.GetFractionUnboundInPlasma().GetValue()) - 1.0 - ((P * NeutralLipidInPlasmaVolumeFraction + (0.3 * P + 0.7) * NeutralPhosphoLipidInPlasmaVolumeFraction)
          / PlasmaPHEffects)) * TissueToPlasmaProteinRatio;

      }
      //Calculate the partition coefficient and set it on the substance compartment effects
      PartitionCoefficient = EquationPartA + ExtracellularFluid.GetWaterVolumeFraction().GetValue() + EquationPartB + EquationPartC;
      PartitionCoefficient = PartitionCoefficient * pk.GetFractionUnboundInPlasma().GetValue() / pk.GetBloodPlasmaRatio().GetValue();
      sub->GetPK().GetTissueKinetics(tissue->GetName()).GetPartitionCoefficient().SetValue(PartitionCoefficient);
    }
    
  }
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Calculates the drug effects on other system parameters
///
/// \details
/// If the substance is a drug with an EC50 value, the effects on heart rate, blood pressure, respiration rate,
/// tidal volume, neuromuscular block level, sedation level, bronchodilation level, and pupillary state are 
/// calculated using the current plasma concentration, the EC50, and the maximum drug response. 
//--------------------------------------------------------------------------------------------------
void Drugs::CalculateDrugEffects()
{
  double deltaHeartRate_Per_min = 0;
  double deltaDiastolicBP_mmHg = 0;
  double deltaSystolicBP_mmHg = 0;
  double deltaRespirationRate_Per_min = 0;
  double deltaTidalVolume_mL = 0;
  double neuromuscularBlockLevel = 0;
  double sedationLevel = 0;
  double bronchodilationLevel = 0;
  double plasmaConcentration_ug_Per_mL = 0;
  double concentrationEffects_unitless = 0;
  double deltaTubularPermeability = 0.0;
  double pupilSizeResponseLevel = 0;
  double pupilReactivityResponseLevel = 0;
  double shapeParameter = 1.;
  SEPatient& patient = m_data.GetPatient();
  double HRBaseline_per_min = patient.GetHeartRateBaseline(FrequencyUnit::Per_min);
  
  //Loop over substances
  for (SESubstance* sub : m_data.GetCompartments().GetLiquidCompartmentSubstances())
  {
    if (!sub->HasPD())
      continue;

    const SESubstancePharmacodynamics& pd = sub->GetPD();
    plasmaConcentration_ug_Per_mL = sub->GetPlasmaConcentration(MassPerVolumeUnit::ug_Per_mL);
    shapeParameter = pd.GetEMaxShapeParameter();
    if(shapeParameter == 1) // Avoiding using pow if we don't have to. I don't know if this is good practice or not, but seems legit.
      concentrationEffects_unitless = plasmaConcentration_ug_Per_mL / (pd.GetEC50(MassPerVolumeUnit::ug_Per_mL) + plasmaConcentration_ug_Per_mL);
    else
      concentrationEffects_unitless = pow(plasmaConcentration_ug_Per_mL, shapeParameter) / (pow(pd.GetEC50(MassPerVolumeUnit::ug_Per_mL), shapeParameter) + pow(plasmaConcentration_ug_Per_mL, shapeParameter));
    /// \todo The drug effect is being applied to the baseline, so if the baseline changes the delta heart rate changes.
    // This would be a problem for something like a continuous infusion of a drug or an environmental drug
    // where we need to establish a new homeostatic point. Once the patient stabilizes with the drug effect included, a new baseline is
    // set, and suddenly the drug effect is being computed using the new baseline. We may need to add another layer of 
    // stabilization and restrict drugs to post-feedback stabilization. Alternatively, we could base the drug effect on a baseline
    // concentration which is normally zero but which gets set to a new baseline concentration at the end of feedback (see chemoreceptor
    // and the blood gas setpoint reset for example).
    deltaHeartRate_Per_min += HRBaseline_per_min * pd.GetHeartRateModifier() * concentrationEffects_unitless;

    deltaDiastolicBP_mmHg += patient.GetDiastolicArterialPressureBaseline(PressureUnit::mmHg) * pd.GetDiastolicPressureModifier() * concentrationEffects_unitless;

    deltaSystolicBP_mmHg += patient.GetSystolicArterialPressureBaseline(PressureUnit::mmHg) * pd.GetSystolicPressureModifier() * concentrationEffects_unitless;

    sedationLevel += pd.GetSedation() * concentrationEffects_unitless;

    deltaTubularPermeability += (pd.GetTubularPermeabilityModifier())*concentrationEffects_unitless;

    if (sedationLevel > 0.15)
    {
      deltaRespirationRate_Per_min += patient.GetRespirationRateBaseline(FrequencyUnit::Per_min) * pd.GetRespirationRateModifier();
      deltaTidalVolume_mL += patient.GetTidalVolumeBaseline(VolumeUnit::mL) * pd.GetTidalVolumeModifier();
    }
    else
    {
      deltaRespirationRate_Per_min += patient.GetRespirationRateBaseline(FrequencyUnit::Per_min) * pd.GetRespirationRateModifier() * concentrationEffects_unitless;
      deltaTidalVolume_mL += patient.GetTidalVolumeBaseline(VolumeUnit::mL) * pd.GetTidalVolumeModifier() * concentrationEffects_unitless;
    }
      
    neuromuscularBlockLevel += pd.GetNeuromuscularBlock() * concentrationEffects_unitless;
    bronchodilationLevel += pd.GetBronchodilation() * concentrationEffects_unitless;

    const SEPupillaryResponse* pr = pd.GetPupillaryResponse();
    pupilSizeResponseLevel += pr->GetSizeModifier() * concentrationEffects_unitless;
    pupilReactivityResponseLevel += pr->GetReactivityModifier() * concentrationEffects_unitless;
  }

  //Translate Diastolic and Systolic Pressure to pulse pressure and mean pressure
  double deltaMeanPressure_mmHg = (2 * deltaDiastolicBP_mmHg + deltaSystolicBP_mmHg) / 3;

  double deltaPulsePressure_mmHg = (deltaSystolicBP_mmHg - deltaDiastolicBP_mmHg);

  //Bound things that are fractions
  sedationLevel = LIMIT(sedationLevel, 0.0, 1.0);
  bronchodilationLevel = LIMIT(bronchodilationLevel, -1.0, 1.0);
  neuromuscularBlockLevel = LIMIT(neuromuscularBlockLevel, 0.0, 1.0);
  deltaTubularPermeability = LIMIT(deltaTubularPermeability, -1.0, 1.0);

  //Set values on the CDM System Values
  GetHeartRateChange().SetValue(deltaHeartRate_Per_min, FrequencyUnit::Per_min);
  GetMeanBloodPressureChange().SetValue(deltaMeanPressure_mmHg, PressureUnit::mmHg);
  GetPulsePressureChange().SetValue(deltaPulsePressure_mmHg, PressureUnit::mmHg);
  GetRespirationRateChange().SetValue(deltaRespirationRate_Per_min, FrequencyUnit::Per_min);
  GetTidalVolumeChange().SetValue(deltaTidalVolume_mL, VolumeUnit::mL);
  GetNeuromuscularBlockLevel().SetValue(neuromuscularBlockLevel);
  GetSedationLevel().SetValue(sedationLevel);
  GetBronchodilationLevel().SetValue(bronchodilationLevel);
  GetTubularPermeabilityChange().SetValue(deltaTubularPermeability);
  

  // Bound the pupil modifiers
  BLIM(pupilSizeResponseLevel, -1, 1);
  BLIM(pupilReactivityResponseLevel, -1, 1);
  GetPupillaryResponse().GetSizeModifier().SetValue(pupilSizeResponseLevel);
  GetPupillaryResponse().GetReactivityModifier().SetValue(pupilReactivityResponseLevel);
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Calculates the concentration of a substance in the plasma
///
/// \details
/// If the substance has PK properties, the concentration of the substance in the plasma is calculated. 
/// PlasmaConcentration = TotalMassInTheBlood / PlasmaVolume.
/// The plasma concentration is then set on the substance.
/// The concentration computation is obviously erroneous. This is a known issue. See @ref pharmacokinetics
//--------------------------------------------------------------------------------------------------
void Drugs::CalculatePlasmaSubstanceConcentration()
{
  double PlasmaMass_ug = 0;
  double PlasmaVolume_mL = m_data.GetBloodChemistry().GetPlasmaVolume(VolumeUnit::mL);

  for (SESubstance* sub : m_data.GetCompartments().GetLiquidCompartmentSubstances())
  {
    PlasmaMass_ug = m_data.GetSubstances().GetSubstanceMass(*sub, m_data.GetCompartments().GetVascularLeafCompartments(), MassUnit::ug);
    sub->GetPlasmaConcentration().SetValue(PlasmaMass_ug / PlasmaVolume_mL, MassPerVolumeUnit::ug_Per_mL);
  }
}

//--------------------------------------------------------------------------------------------------
/// \brief
/// Calculates the substance mass cleared
///
/// \details
/// If the substance has PK properties, the substance clearance is calculated. The renal, liver, and systemic 
/// clearance terms are applied to each anatomy compartment per substance. The amount of mass is then removed from the
/// tissue node each time step. The tissue node mass and concentration are then updated. Sets the amount of substance
/// cleared as a compartment effect for each substance.
//--------------------------------------------------------------------------------------------------
void Drugs::CalculateSubstanceClearance()
{
  double PatientWeight_kg = m_data.GetPatient().GetWeight(MassUnit::kg);
  double HepaticClearance_mLPers = 0;
  double FractionUnboundInPlasma = 0;
  double IntrinsicClearance_mLPersPerkg = 0;
  double TotalVolumeCleared_mL = 0;
  double RenalVolumeCleared_mL = 0;
  double HepaticVolumeCleared_mL = 0;
  double OtherSystemicVolumeCleared_mL = 0;

  for (SESubstance* sub : m_data.GetCompartments().GetLiquidCompartmentSubstances())
  {
    if (!sub->HasClearance() || !sub->GetClearance().HasSystemic())
      continue;
    SESubstanceClearance& clearance = sub->GetClearance();

    //Renal Volume Cleared - Clearance happens through the renal system
    RenalVolumeCleared_mL = (clearance.GetRenalClearance().GetValue(VolumePerTimeMassUnit::mL_Per_s_kg) * PatientWeight_kg * m_dt_s);

    //Intrinsic Clearance
    IntrinsicClearance_mLPersPerkg = clearance.GetIntrinsicClearance().GetValue(VolumePerTimeMassUnit::mL_Per_s_kg);
    FractionUnboundInPlasma = clearance.GetFractionUnboundInPlasma().GetValue();
    //Hepatic Clearance
    double LiverVascularFlow_mL_Per_s = m_liverVascular->GetInFlow().GetValue(VolumePerTimeUnit::mL_Per_s);
    HepaticClearance_mLPers = (LiverVascularFlow_mL_Per_s * FractionUnboundInPlasma * IntrinsicClearance_mLPersPerkg * PatientWeight_kg) / (LiverVascularFlow_mL_Per_s + (FractionUnboundInPlasma * IntrinsicClearance_mLPersPerkg * PatientWeight_kg));
    HepaticVolumeCleared_mL = HepaticClearance_mLPers * m_dt_s;

    //Systemic Clearance
    TotalVolumeCleared_mL = clearance.GetSystemicClearance().GetValue(VolumePerTimeMassUnit::mL_Per_s_kg) * PatientWeight_kg * m_dt_s;
    OtherSystemicVolumeCleared_mL = TotalVolumeCleared_mL - RenalVolumeCleared_mL - HepaticVolumeCleared_mL;
    // The following makes it so that you cannot have more than the total systemic clearance for the substance.
    LLIM(OtherSystemicVolumeCleared_mL, 0.);

    //Hepatic Clearance    
    m_data.GetSubstances().CalculateGenericClearance(HepaticVolumeCleared_mL, *m_liverTissue, *sub);

    //Systemic Clearance
    m_data.GetSubstances().CalculateGenericClearance(OtherSystemicVolumeCleared_mL, *m_venaCavaVascular, *sub);

    //Hepatic Excretion
    m_data.GetSubstances().CalculateGenericExcretion(LiverVascularFlow_mL_Per_s, *m_liverTissue, *sub, clearance.GetFractionExcretedInFeces().GetValue(), m_dt_s);
  }

}