Activate new conditions, Add Multiply Scalar support, and other bug fixes

cdm/cpp/compartment/substances/SEGasSubstanceQuantity.cpp

@@ -48,13 +48,13 @@ void SEGasSubstanceQuantity::Clear()
 
 void SEGasSubstanceQuantity::SetToZero()
 {
-  auto pp = GetPartialPressure();
+  auto& pp = GetPartialPressure();
   if (pp.HasUnit())
     pp.SetValue(0, *pp.GetUnit());
   else
     pp.SetValue(0, PressureUnit::mmHg);
 
-  auto vol = GetVolume();
+  auto& vol = GetVolume();
   if (vol.HasUnit())
     vol.SetValue(0, *vol.GetUnit());
   else

cdm/cpp/compartment/substances/SELiquidSubstanceQuantity.cpp

@@ -85,19 +85,19 @@ void SELiquidSubstanceQuantity::Clear()
 
 void SELiquidSubstanceQuantity::SetToZero()
 {
-  auto c = GetConcentration();
+  auto& c = GetConcentration();
   if (c.HasUnit())
     c.SetValue(0, *c.GetUnit());
   else
     c.SetValue(0, MassPerVolumeUnit::mg_Per_mL);
 
-  auto m = GetMass();
+  auto& m = GetMass();
   if (m.HasUnit())
     m.SetValue(0, *m.GetUnit());
   else
     m.SetValue(0, MassUnit::mg);
 
-  auto mol = GetMolarity();
+  auto& mol = GetMolarity();
   if (mol.HasUnit())
     mol.SetValue(0, *mol.GetUnit());
   else
@@ -105,7 +105,7 @@ void SELiquidSubstanceQuantity::SetToZero()
 
   if (m_Substance.GetState() == eSubstance_State::Gas)
   {
-    auto pp = GetPartialPressure();
+    auto& pp = GetPartialPressure();
     if (pp.HasUnit())
       pp.SetValue(0, *pp.GetUnit());
     else
@@ -115,19 +115,19 @@ void SELiquidSubstanceQuantity::SetToZero()
   if (m_isO2 || m_isCO || m_isCO2)
     GetSaturation().SetValue(0);
 
-  auto mc = GetMassCleared();
+  auto& mc = GetMassCleared();
   if (mc.HasUnit())
     mc.SetValue(0, *mc.GetUnit());
   else
     mc.SetValue(0, MassUnit::mg);
 
-  auto md = GetMassDeposited();
+  auto& md = GetMassDeposited();
   if (md.HasUnit())
     md.SetValue(0, *md.GetUnit());
   else
     md.SetValue(0, MassUnit::mg);
 
-  auto me = GetMassExcreted();
+  auto& me = GetMassExcreted();
   if (me.HasUnit())
     me.SetValue(0, *me.GetUnit());
   else
@@ -379,7 +379,7 @@ SEScalarAmountPerVolume& SELiquidSubstanceQuantity::GetMolarity()
       m_Molarity->Invalidate();
     else
     {
-      double molarity_mmol_Per_mL = GetMass(MassUnit::mg) / m_Substance.GetMolarMass(MassPerAmountUnit::mg_Per_mmol) / m_Compartment.GetVolume(VolumeUnit::mL);      
+      double molarity_mmol_Per_mL = GetMass(MassUnit::mg) / m_Substance.GetMolarMass(MassPerAmountUnit::mg_Per_mmol) / m_Compartment.GetVolume(VolumeUnit::mL);
       m_Molarity->SetValue(molarity_mmol_Per_mL, AmountPerVolumeUnit::mmol_Per_mL);
     }
     m_Molarity->SetReadOnly(true);

cdm/cpp/engine/SEConditionManager.cpp

@@ -408,6 +408,8 @@ const SEInitialEnvironmentConditions* SEConditionManager::GetInitialEnvironmentC
 
 void SEConditionManager::GetAllConditions(std::vector<const SECondition*>& conditions) const
 {
+  if (HasAcuteRespiratoryDistressSyndrome())
+    conditions.push_back(GetAcuteRespiratoryDistressSyndrome());
   if (HasChronicAnemia())
     conditions.push_back(GetChronicAnemia());
   if (HasChronicObstructivePulmonaryDisease())
@@ -424,12 +426,17 @@ void SEConditionManager::GetAllConditions(std::vector<const SECondition*>& condi
     conditions.push_back(GetImpairedAlveolarExchange());
   if (HasLobarPneumonia())
     conditions.push_back(GetLobarPneumonia());
+  if (HasSepsis())
+    conditions.push_back(GetSepsis());
+
   if (HasInitialEnvironmentConditions())
     conditions.push_back(GetInitialEnvironmentConditions());
 }
 
 bool SEConditionManager::IsEmpty() const
 {
+  if (HasAcuteRespiratoryDistressSyndrome())
+    return false;
   if (HasChronicAnemia())
     return false;
   if (HasChronicObstructivePulmonaryDisease())
@@ -446,6 +453,9 @@ bool SEConditionManager::IsEmpty() const
     return false;
   if (HasLobarPneumonia())
     return false;
+  if (HasSepsis())
+    return false;
+
   if (HasInitialEnvironmentConditions())
     return false;
   return true;

cdm/cpp/properties/SEScalar.cpp

@@ -36,7 +36,7 @@ SEScalar::~SEScalar()
 
 void SEScalar::Clear()
 {
-  SEProperty::Clear();  
+  SEProperty::Clear();
   m_readOnly = false;
   Invalidate();
 }
@@ -51,7 +51,7 @@ bool SEScalar::Set(const SEScalar& s)
     throw CommonDataModelException("Scalar is marked read-only");
   m_value = s.m_value;
   m_isnan = (std::isnan(m_value)) ? true : false;
-  m_isinf = (std::isinf(m_value)) ? true : false;  
+  m_isinf = (std::isinf(m_value)) ? true : false;
   return true;
 }
 
@@ -154,6 +154,27 @@ double SEScalar::IncrementValue(double d)
   return m_value;
 }
 
+
+double SEScalar::Multiply(const SEScalar& s)
+{
+  if (!s.IsValid())
+    Invalidate();
+  else
+    MultiplyValue(s.GetValue());
+  return m_value;
+}
+
+double SEScalar::MultiplyValue(double d)
+{
+  if (!IsValid())
+  {
+    SetValue(d);
+    return d;
+  }
+  SetValue(m_value * d);
+  return m_value;
+}
+
 void SEScalar::Average(int cnt)
 {
   if (!IsValid() || cnt == 0)

cdm/cpp/properties/SEScalar.h

@@ -66,6 +66,9 @@ public:
   double Increment(const SEScalar& s);
   double IncrementValue(double d);
 
+  double Multiply(const SEScalar& s);
+  double MultiplyValue(double d);
+
   void Average(int cnt);
 
   bool Equals(const SEScalar& to) const;
@@ -117,6 +120,7 @@ public:
   virtual void   SetValue(double d, const CCompoundUnit& unit) = 0;
   virtual void   ForceValue(double d, const CCompoundUnit& unit) = 0;
   virtual double IncrementValue(double d, const CCompoundUnit& unit) = 0;
+  virtual double MultiplyValue(double d, const CCompoundUnit& unit) = 0;
 
 protected:
   virtual const CCompoundUnit* GetCompoundUnit(const std::string& unit) const = 0;
@@ -145,6 +149,7 @@ protected:
   virtual void   SetValue(double d, const CCompoundUnit& unit);
   virtual void   ForceValue(double d, const CCompoundUnit& unit);
   virtual double IncrementValue(double d, const CCompoundUnit& unit);
+  virtual double MultiplyValue(double d, const CCompoundUnit& unit);
 
   virtual const CCompoundUnit* GetCompoundUnit(const std::string& unit) const;
 
@@ -171,6 +176,12 @@ public:
   double Increment(const SEScalar& s) = delete;// Must provide a unit
   virtual double Increment(const SEScalarQuantity& s);
 
+  double MultiplyValue(double d) = delete;// Must provide a unit
+  virtual double MultiplyValue(double d, const Unit& unit);
+
+  double Multiply(const SEScalar& s) = delete;// Must provide a unit
+  virtual double Multiply(const SEScalarQuantity& s);
+
   bool Equals(const SEScalar& to) const = delete;// Must provide a unit
   virtual bool Equals(const SEScalarQuantity<Unit>& to) const;
 

cdm/cpp/properties/SEScalar.inl

@@ -181,6 +181,38 @@ double SEScalarQuantity<Unit>::IncrementValue(double d, const CCompoundUnit& uni
   return this->IncrementValue(d, *u);
 }
 
+
+template<typename Unit>
+double SEScalarQuantity<Unit>::Multiply(const SEScalarQuantity<Unit>& s)
+{
+  if (!s.IsValid())
+    this->Invalidate();
+  else
+    return this->MultiplyValue(s.m_value, *s.m_unit);
+  return m_value;
+}
+
+template<typename Unit>
+double SEScalarQuantity<Unit>::MultiplyValue(double d, const Unit& unit)
+{
+  if (!IsValid())
+  {
+    this->SetValue(d, unit);
+    return d;
+  }
+  this->SetValue(m_value * Convert(d, unit, *m_unit), *m_unit);
+  return Convert(m_value, *m_unit, unit);
+}
+
+template<typename Unit>
+double SEScalarQuantity<Unit>::MultiplyValue(double d, const CCompoundUnit& unit)
+{
+  const Unit* u = dynamic_cast<const Unit*>(&unit);
+  if (u == nullptr)
+    throw CommonDataModelException("Provided unit is not of proper quantity type");
+  return this->MultiplyValue(d, *u);
+}
+
 template<typename Unit>
 bool SEScalarQuantity<Unit>::Equals(const SEScalarQuantity<Unit>& to) const
 {

cdm/cpp/system/physiology/SERespiratorySystem.cpp

@@ -36,6 +36,7 @@ SERespiratorySystem::SERespiratorySystem(Logger* logger) : SESystem(logger)
   m_InspiratoryFlow = nullptr;
   m_InspiratoryPulmonaryResistance = nullptr;
   m_IntrapleuralPressure = nullptr;
+  m_IntrapulmonaryPressure = nullptr;
   m_LungCompliance = nullptr;
   m_MaximalInspiratoryPressure = nullptr;
   m_PatientPowerOfBreathing = nullptr;
@@ -61,6 +62,7 @@ SERespiratorySystem::SERespiratorySystem(Logger* logger) : SESystem(logger)
   m_TransairwayPressure = nullptr;
   m_TransalveolarPressure = nullptr;
   m_TransChestWallPressure = nullptr;
+  m_TransMusclePressure = nullptr;
   m_TranspulmonaryPressure = nullptr;
   m_TransrespiratoryPressure = nullptr;
   m_TransthoracicPressure = nullptr;
@@ -93,6 +95,7 @@ void SERespiratorySystem::Clear()
   SAFE_DELETE(m_InspiratoryFlow);
   SAFE_DELETE(m_InspiratoryPulmonaryResistance);
   SAFE_DELETE(m_IntrapleuralPressure);
+  SAFE_DELETE(m_IntrapulmonaryPressure);
   SAFE_DELETE(m_LungCompliance);
   SAFE_DELETE(m_MaximalInspiratoryPressure);
   SAFE_DELETE(m_PatientPowerOfBreathing);
@@ -118,6 +121,7 @@ void SERespiratorySystem::Clear()
   SAFE_DELETE(m_TransairwayPressure);
   SAFE_DELETE(m_TransalveolarPressure);
   SAFE_DELETE(m_TransChestWallPressure);
+  SAFE_DELETE(m_TransMusclePressure);
   SAFE_DELETE(m_TranspulmonaryPressure);
   SAFE_DELETE(m_TransrespiratoryPressure);
   SAFE_DELETE(m_TransthoracicPressure);

engine/cpp/controller/Engine.cpp

@@ -175,8 +175,6 @@ bool PulseEngine::InitializeEngine(const SEPatientConfiguration& patient_configu
   if(patient_configuration.HasConditions())
     m_Conditions->Copy(*patient_configuration.GetConditions());
   AtSteadyState(EngineState::AtInitialStableState);// This will peek at conditions
-  // Copy any changes to the current patient to the initial patient
-  m_InitialPatient->Copy(*m_CurrentPatient);
 
   m_State = EngineState::SecondaryStabilization;
   // Apply conditions and anything else to the physiology
@@ -193,6 +191,8 @@ bool PulseEngine::InitializeEngine(const SEPatientConfiguration& patient_configu
       return false;
   }
   AtSteadyState(EngineState::AtSecondaryStableState);
+  // Copy any changes to the current patient to the initial patient
+  m_InitialPatient->Copy(*m_CurrentPatient);
 
   m_State = EngineState::Active;
   // Hook up the handlers (Note events will still be in the log)

test/config/DebugRun.config

@@ -31,6 +31,6 @@ Macro EngineUnitTest=EngineUnitTestDriver FastPlot Baseline=unit_tests/pulse/ Co
 Macro EngineUnitTestFull=EngineUnitTestDriver FullPlot Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse
 Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
 
-#patient/BasicStandard.json = ScenarioTest
+patient/ARDSExacerbation.json = ScenarioTest
+#patient/ARDSModerateBothLungs.json = ScenarioTest
 
-RespiratoryDriver = EngineUnitTest Results=RespiratoryDriverOutput