More fixes due to keeping around the actions in the managers

Also fixed auto serialization testing, and some bugs there...

bin/EngineState.json

-{
+{"Scenario": {
   "Name":"BasicStandard",
   "Description":"Basic scenario measuring patient vitals with no insults or interventions",
   "EngineStateFile":"./states/StandardMale@0s.pbb",
@@ -93,4 +93,21 @@
     {"DecimalFormat":{"Precision":2}, "Category":"LiquidCompartment","CompartmentName":"Pericardium","PropertyName":"Pressure","Unit":"mmHg"}
   ]},
 
-  "AnyAction":[{"AdvanceTime":{"Time":{"ScalarTime":{"Value":2.0,"Unit":"min"}}}}]}
\ No newline at end of file
+  "AnyAction":[{"AdvanceTime":{"Time":{"ScalarTime":{"Value":2.0,"Unit":"min"}}}}]},
+  
+  "Configuration": {
+    "AutoSerialization": {
+      "Directory": "./states/testing/",
+      "Filename": "patient/HemorrhageVaryingSeverity",
+      "AfterActions": "On",
+      "Period": {
+        "ScalarTime": {
+          "Value": 5.0,
+          "Unit": "s"
+        }
+      },
+      "PeriodTimeStamps": "On",
+      "ReloadState": "On"
+    }
+  }
+}

data/config/DebugRun.config

@@ -20,7 +20,7 @@ Threads=-1
 #UseStates=true
 # AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
 # Time stamp periods is creating a file per save and using the time stamp as naming convention
-#AutoSerialization=./states/testing/,5,On,On,On
+#AutoSerialization=./states/testing/,0,On,On,On
 
 Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
 Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver

data/human/adult/scenarios/showcase/EnvironmentExposure.json

 {
   "Name": "EnvironmentExposure",
   "Description": "Showcase scenario: Patient is exposed to sub-zero temperatures and develops hypothermia.",
-    "PatientConfiguration": { "PatientFile": "Jane.json" },
+  "PatientConfiguration": { "PatientFile": "Jane.json" },
   "DataRequestManager": {
     "DataRequest": [{
       "DecimalFormat": {

src/cpp/cdm/engine/SEAutoSerialization.cpp

@@ -20,7 +20,7 @@ SEAutoSerialization::~SEAutoSerialization()
   SAFE_DELETE(m_Period);
   m_PeriodTimeStamps = eSwitch::Off;
   m_AfterActions = eSwitch::Off;
-  m_AfterActions = eSwitch::Off;
+  m_ReloadState = eSwitch::Off;
   m_Directory = "";
   m_FileName = "";
 }
@@ -30,16 +30,16 @@ void SEAutoSerialization::Clear()
   INVALIDATE_PROPERTY(m_Period);
   m_PeriodTimeStamps = eSwitch::Off;
   m_AfterActions = eSwitch::Off;
-  m_AfterActions = eSwitch::Off;
+  m_ReloadState = eSwitch::Off;
   m_Directory = "";
   m_FileName = "";
 }
 
 bool SEAutoSerialization::IsValid() const
 {
-  if (!HasPeriod())
+  if (HasPeriod() && m_Period->IsNegative())
     return false;
-  if (m_Period->IsNegative())
+  else if (m_AfterActions == eSwitch::Off)
     return false;
   if (!HasDirectory())
     return false;

src/cpp/cdm/engine/SEEngineTracker.cpp

@@ -163,6 +163,7 @@ void SEEngineTracker::SetupRequests()
     bool isOpen = m_ResultsStream.is_open();
     if (!isOpen || m_ForceConnection)
     {// Process/Hook up all requests with their associated scalers
+      DELETE_MAP_SECOND(m_Request2Scalar);// Get our scalars again
       for (SEDataRequest* dr : m_DataRequestMgr->GetDataRequests())
       {
         if (!TrackRequest(*dr))

src/cpp/cdm/io/protobuf/PBEquipmentActions.cpp

@@ -261,7 +261,7 @@ CDM_BIND::AnesthesiaMachineOxygenTankPressureLossData* PBEquipmentAction::Unload
 void PBEquipmentAction::Serialize(const SEAnesthesiaMachineOxygenTankPressureLoss& src, CDM_BIND::AnesthesiaMachineOxygenTankPressureLossData& dst)
 {
   PBEquipmentAction::Serialize(src, *dst.mutable_anesthesiamachineaction());
-  dst.set_state(src.IsActive() ? CDM_BIND::eSwitch::On : CDM_BIND::eSwitch::Off);
+  dst.set_state(src.GetState()==eSwitch::On ? CDM_BIND::eSwitch::On : CDM_BIND::eSwitch::Off);
 }
 void PBEquipmentAction::Copy(const SEAnesthesiaMachineOxygenTankPressureLoss& src, SEAnesthesiaMachineOxygenTankPressureLoss& dst)
 {
@@ -290,7 +290,7 @@ CDM_BIND::AnesthesiaMachineOxygenWallPortPressureLossData* PBEquipmentAction::Un
 void PBEquipmentAction::Serialize(const SEAnesthesiaMachineOxygenWallPortPressureLoss& src, CDM_BIND::AnesthesiaMachineOxygenWallPortPressureLossData& dst)
 {
   PBEquipmentAction::Serialize(src, *dst.mutable_anesthesiamachineaction());
-  dst.set_state(src.IsActive() ? CDM_BIND::eSwitch::On : CDM_BIND::eSwitch::Off);
+  dst.set_state(src.GetState()==eSwitch::On ? CDM_BIND::eSwitch::On : CDM_BIND::eSwitch::Off);
 }
 void PBEquipmentAction::Copy(const SEAnesthesiaMachineOxygenWallPortPressureLoss& src, SEAnesthesiaMachineOxygenWallPortPressureLoss& dst)
 {

src/cpp/cdm/io/protobuf/PBSubstance.cpp

@@ -328,7 +328,6 @@ void PBSubstance::Serialize(const CDM_BIND::SubstanceCompoundData& src, SESubsta
   std::string err;
 
   const SESubstance* substance = nullptr;
-  SESubstanceConcentration* cc;
   for (int i = 0; i < src.component_size(); i++)
   {
     const CDM_BIND::SubstanceConcentrationData& cData = src.component(i);
@@ -339,10 +338,8 @@ void PBSubstance::Serialize(const CDM_BIND::SubstanceCompoundData& src, SESubsta
       dst.Fatal("Could not load find substance compound component : " + cData.name(), "SESubstanceCompound::Load");
       continue;
     }
-    cc = new SESubstanceConcentration(*substance);
-    PBSubstance::Load(cData, *cc);
-    dst.m_Components.push_back(cc);
-    dst.m_cComponents.push_back(cc);
+    SESubstanceConcentration& sc = dst.GetComponent(*substance);
+    PBSubstance::Load(cData, sc);
   }
 }
 

src/cpp/cdm/patient/actions/SESupplementalOxygen.cpp

@@ -43,10 +43,7 @@ bool SESupplementalOxygen::IsValid() const
 
 bool SESupplementalOxygen::IsActive() const
 {
-  if (!SEPatientAction::IsActive())
-    return false;
-  return m_Device != eSupplementalOxygen_Device::None;
-  // Defaults will be used if no flow/volume supplied
+  return SEPatientAction::IsActive();
 }
 void SESupplementalOxygen::Deactivate()
 {

src/cpp/cdm/substance/SESubstanceCompound.cpp

@@ -68,7 +68,7 @@ const std::vector<const SESubstanceConcentration*>& SESubstanceCompound::GetComp
 {
   return m_cComponents;
 }
-const SESubstanceConcentration& SESubstanceCompound::GetComponent(SESubstance& substance)
+SESubstanceConcentration& SESubstanceCompound::GetComponent(const SESubstance& substance)
 {
   for (SESubstanceConcentration* sq : m_Components)
   {
@@ -81,7 +81,7 @@ const SESubstanceConcentration& SESubstanceCompound::GetComponent(SESubstance& s
   m_cComponents.push_back(sq);
   return *sq;
 }
-const SESubstanceConcentration* SESubstanceCompound::GetComponent(SESubstance& substance) const
+const SESubstanceConcentration* SESubstanceCompound::GetComponent(const SESubstance& substance) const
 {
   for (SESubstanceConcentration* sq : m_Components)
   {
@@ -100,6 +100,7 @@ void SESubstanceCompound::RemoveComponent(const SESubstance& substance)
       m_Components.erase(m_Components.begin() + i);
       m_cComponents.erase(m_cComponents.begin() + i);
       delete sq;
+      break;
     }
     i++;
   }

src/cpp/cdm/substance/SESubstanceCompound.h

@@ -26,10 +26,10 @@ public:
 
   bool HasComponent() const;
   bool HasComponent(const SESubstance& substance) const;
-  const std::vector<SESubstanceConcentration*>& GetComponents();  
+  const std::vector<SESubstanceConcentration*>& GetComponents();
   const std::vector<const SESubstanceConcentration*>& GetComponents() const;
-  const SESubstanceConcentration& GetComponent(SESubstance& substance);
-  const SESubstanceConcentration* GetComponent(SESubstance& substance) const;
+  SESubstanceConcentration& GetComponent(const SESubstance& substance);
+  const SESubstanceConcentration* GetComponent(const SESubstance& substance) const;
   void RemoveComponent(const SESubstance& substance);
 
 protected: 

src/cpp/cdm/system/environment/SEEnvironment.cpp

@@ -134,9 +134,7 @@ bool SEEnvironment::ProcessChange(SEChangeEnvironmentalConditions& change, SESub
 {
   // If we have data then we merge it, if a file was provided
   // we reset and set the environment to the file, so we only have the file data
-  if (change.HasEnvironmentalConditions())
-    GetEnvironmentalConditions().Merge(change.GetEnvironmentalConditions(), subMgr);
-  else if (change.HasEnvironmentalConditionsFile())
+  if (change.HasEnvironmentalConditionsFile())
   {
     // Update the action with the file contents
     std::string cfg_file = change.GetEnvironmentalConditionsFile();
@@ -148,6 +146,8 @@ bool SEEnvironment::ProcessChange(SEChangeEnvironmentalConditions& change, SESub
     }
     GetEnvironmentalConditions().Merge(change.GetEnvironmentalConditions(), subMgr);
   }
+  else if (change.HasEnvironmentalConditions())
+    GetEnvironmentalConditions().Merge(change.GetEnvironmentalConditions(), subMgr);
   StateChange();
   return true;
 }

src/cpp/cdm/system/environment/SEEnvironmentalConditions.cpp

@@ -329,14 +329,19 @@ double SEEnvironmentalConditions::GetRespirationAmbientTemperature(const Tempera
 
 bool SEEnvironmentalConditions::HasAmbientGas() const
 {
-  return m_AmbientGases.size() == 0 ? false : true;
+  if (m_AmbientGases.empty())
+    return false;
+  for (auto g : m_AmbientGases)
+    if (g->HasFractionAmount() && g->GetFractionAmount().IsPositive())
+      return true;
+  return false;
 }
 bool SEEnvironmentalConditions::HasAmbientGas(const SESubstance& s) const
 {
   for (const SESubstanceFraction* sf : m_AmbientGases)
   {
     if (&s == &sf->GetSubstance())
-      return sf->GetFractionAmount() > 0;
+      return sf->HasFractionAmount() && sf->GetFractionAmount() > 0;
   }
   return false;
 }
@@ -385,14 +390,19 @@ void SEEnvironmentalConditions::RemoveAmbientGases()
 
 bool SEEnvironmentalConditions::HasAmbientAerosol() const
 {
-  return m_AmbientAerosols.size() == 0 ? false : true;
+  if (m_AmbientAerosols.empty())
+    return false;
+  for (auto a : m_AmbientAerosols)
+    if (a->HasConcentration() && a->GetConcentration().IsPositive())
+      return true;
+  return false;
 }
 bool SEEnvironmentalConditions::HasAmbientAerosol(const SESubstance& substance) const
 {
   for (SESubstanceConcentration* sc : m_AmbientAerosols)
   {
     if (&substance == &sc->GetSubstance())
-      return sc->GetConcentration().IsPositive();
+      return sc->HasConcentration() && sc->GetConcentration().IsPositive();
   }
   return false;
 }

src/cpp/cdm/system/equipment/anesthesia_machine/actions/SEAnesthesiaMachineOxygenTankPressureLoss.cpp

@@ -49,6 +49,10 @@ const SEScalar* SEAnesthesiaMachineOxygenTankPressureLoss::GetScalar(const std::
   return nullptr;
 }
 
+eSwitch SEAnesthesiaMachineOxygenTankPressureLoss::GetState() const
+{
+  return m_State.GetEnum();
+}
 void SEAnesthesiaMachineOxygenTankPressureLoss::SetState(eSwitch state)
 {
   m_State.SetEnum(state);

src/cpp/cdm/system/equipment/anesthesia_machine/actions/SEAnesthesiaMachineOxygenTankPressureLoss.h

@@ -18,6 +18,7 @@ public:
   virtual bool IsActive() const;
   virtual void Deactivate();
 
+  virtual eSwitch GetState() const;
   virtual void SetState(eSwitch state);
 
   virtual void ToString(std::ostream &str) const;

src/cpp/cdm/system/equipment/anesthesia_machine/actions/SEAnesthesiaMachineOxygenWallPortPressureLoss.cpp

@@ -49,6 +49,11 @@ const SEScalar* SEAnesthesiaMachineOxygenWallPortPressureLoss::GetScalar(const s
   return nullptr;
 }
 
+
+eSwitch SEAnesthesiaMachineOxygenWallPortPressureLoss::GetState() const
+{
+  return m_State.GetEnum();
+}
 void SEAnesthesiaMachineOxygenWallPortPressureLoss::SetState(eSwitch state)
 {
   m_State.SetEnum(state);

src/cpp/cdm/system/equipment/anesthesia_machine/actions/SEAnesthesiaMachineOxygenWallPortPressureLoss.h

@@ -18,6 +18,7 @@ public:
   virtual bool IsActive() const;
   virtual void Deactivate();
 
+  virtual eSwitch GetState() const;
   virtual void SetState(eSwitch state);
 
   virtual void ToString(std::ostream &str) const;

src/cpp/cdm/system/equipment/mechanical_ventilator/SEMechanicalVentilator.cpp

@@ -692,7 +692,12 @@ eMechanicalVentilator_DriverWaveform SEMechanicalVentilator::GetInspirationWavef
 
 bool SEMechanicalVentilator::HasFractionInspiredGas() const
 {
-  return m_FractionInspiredGases.size() == 0 ? false : true;
+  if (m_FractionInspiredGases.empty())
+    return false;
+  for (auto a : m_FractionInspiredGases)
+    if (a->HasFractionAmount() && a->GetFractionAmount().IsPositive())
+      return true;
+  return false;
 }
 bool SEMechanicalVentilator::HasFractionInspiredGas(const SESubstance& s) const
 {
@@ -748,7 +753,12 @@ void SEMechanicalVentilator::RemoveFractionInspiredGases()
 
 bool SEMechanicalVentilator::HasConcentrationInspiredAerosol() const
 {
-  return m_ConcentrationInspiredAerosols.size() == 0 ? false : true;
+  if (m_ConcentrationInspiredAerosols.empty())
+    return false;
+  for (auto a : m_ConcentrationInspiredAerosols)
+    if (a->HasConcentration() && a->GetConcentration().IsPositive())
+      return true;
+  return false;
 }
 bool SEMechanicalVentilator::HasConcentrationInspiredAerosol(const SESubstance& substance) const
 {

src/cpp/cpm/PulseScenarioExec.cpp

@@ -167,37 +167,33 @@ bool PulseScenarioExec::Execute(PhysiologyEngine& engine, const PulseScenario& s
   return success;
 }
 
-bool PulseScenarioExec::ProcessActions(PulseEngine& engine, const SEScenario& scenario)
+bool PulseScenarioExec::ProcessActions(PhysiologyEngine& engine, const SEScenario& scenario)
 {
   return SEScenarioExec::ProcessActions(engine, scenario);
 }
-bool PulseScenarioExec::ProcessAction(PulseEngine& engine, const SEAction& action)
+bool PulseScenarioExec::ProcessAction(PhysiologyEngine& engine, const SEAction& action)
 {
-  if (m_AutoSerializationAfterActions == eSwitch::On)
+  if (m_AutoSerializationAfterActions == eSwitch::On && m_AutoSerializationActions.str().empty())
   {
-     m_ss << action;
-     size_t start = m_ss.str().find(": ") + 2;
-     size_t end = m_ss.str().find('\n');
-     m_AutoSerializationActions << "-" << m_ss.str().substr(start, end - start);
-     m_ss.str("");
+     m_AutoSerializationActions << "/AfterActions";
   }
   return SEScenarioExec::ProcessAction(engine, action);
 }
 
-void PulseScenarioExec::AdvanceEngine(PulseEngine& engine)
+void PulseScenarioExec::AdvanceEngine(PhysiologyEngine& engine)
 {
   if (m_AutoSerializationPeriod_s > 0)
   {
     m_AutoSerializationTime_s += engine.GetTimeStep(TimeUnit::s);
     if (m_AutoSerializationTime_s >= m_AutoSerializationPeriod_s)
     {
-      Info("Serializing state after requested period : " + m_AutoSerializationActions.str());
       m_AutoSerializationTime_s = 0;
       m_AutoSerializationOutput.str("");
       m_AutoSerializationOutput << m_AutoSerializationDirectory <<"/"<< m_AutoSerializationFileName;
       if (m_AutoSerializationTimeStamps == eSwitch::On)
-        m_AutoSerializationOutput << "@" << engine.GetSimulationTime(TimeUnit::s);
+        m_AutoSerializationOutput << "/" << m_AutoSerializationFileName<< "@" << engine.GetSimulationTime(TimeUnit::s);
       engine.SerializeToFile(m_AutoSerializationOutput.str() + ".json");
+      Info("Serializing state after requested period : " + m_AutoSerializationOutput.str() + ".json");
       if (m_AutoSerializationReload == eSwitch::On)
       {
         engine.SerializeFromFile(m_AutoSerializationOutput.str() + ".json");
@@ -208,14 +204,15 @@ void PulseScenarioExec::AdvanceEngine(PulseEngine& engine)
   engine.AdvanceModelTime();
   if (m_AutoSerializationActions.str().length() > 0)
   {
-    Info("Serializing state after actions : " + m_AutoSerializationActions.str());
     m_AutoSerializationOutput.str("");
     m_AutoSerializationOutput << m_AutoSerializationDirectory <<"/"<< m_AutoSerializationFileName<<m_AutoSerializationActions.str();
     if (m_AutoSerializationTimeStamps == eSwitch::On)
       m_AutoSerializationOutput << "@" << engine.GetSimulationTime(TimeUnit::s);
     engine.SerializeToFile(m_AutoSerializationOutput.str() + ".json");
+    Info("Serializing state after actions : " + m_AutoSerializationOutput.str()+".json");
     if (m_AutoSerializationReload == eSwitch::On)
     {
+      Info("Reloading and saving reloaded state to : " + m_AutoSerializationOutput.str() + ".Reload.json");
       engine.SerializeFromFile(m_AutoSerializationOutput.str() + ".json");
       engine.SerializeToFile(m_AutoSerializationOutput.str() + ".Reloaded.json");
     }

src/cpp/cpm/PulseScenarioExec.h

@@ -35,7 +35,7 @@ protected:
   std::stringstream          m_AutoSerializationOutput;
   std::stringstream          m_AutoSerializationActions;
 
-  virtual bool ProcessActions(PulseEngine& engine, const SEScenario& scenario);
-  virtual bool ProcessAction(PulseEngine& engine, const SEAction& action);
-  virtual void AdvanceEngine(PulseEngine& engine);
+  virtual bool ProcessActions(PhysiologyEngine& engine, const SEScenario& scenario) override;
+  virtual bool ProcessAction(PhysiologyEngine& engine, const SEAction& action) override;
+  virtual void AdvanceEngine(PhysiologyEngine& engine) override;
 };
\ No newline at end of file

src/cpp/cpm/environment/Environment.cpp

@@ -153,7 +153,7 @@ void Environment::StateChange()
   if (m_AmbientGases == nullptr ||m_AmbientAerosols == nullptr)
     return;
 
-  if (GetEnvironmentalConditions().GetAmbientGases().size() > 0)
+  if (GetEnvironmentalConditions().HasAmbientGas())
   {
     // Add Gases to the environment
     //Check to make sure fractions sum to 1.0