Added PhysiolgyEngine& to non public processAction calls to allow Actions and Conditions to record initnalization conditions from patientdata

StevenAWhite · StevenAWhite · commit 90ea5994252b · 2024-01-16T10:02:57.000-05:00
(cherry picked from commit 757df66)
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/engine/PhysiologyEngine.h b/projects/biogears/libBiogears/include/biogears/cdm/engine/PhysiologyEngine.h
@@ -158,7 +158,7 @@ class BIOGEARS_API PhysiologyEngine {
   //! \brief
   //! returns the current time of the simulation.
   //!-------------------------------------------------------------------------------------------------
-  virtual double GetSimulationTime(const TimeUnit& unit) = 0;
+  virtual double GetSimulationTime(const TimeUnit& unit) const = 0;
 
   //!-------------------------------------------------------------------------------------------------
   //! \brief
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEActionManager.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEActionManager.h
@@ -19,6 +19,7 @@ specific language governing permissions and limitations under the License.
 namespace biogears {
 class SESubstanceManager;
 class SEAction;
+class PhysiologyEngine;
 
 class BIOGEARS_API SEActionManager : public Loggable {
 public:
@@ -29,8 +30,8 @@ class BIOGEARS_API SEActionManager : public Loggable {
 
   void Unload(std::vector<CDM::ActionData*>& to);
 
-  bool ProcessAction(const SEAction& action);
-  bool ProcessAction(const CDM::ActionData& in);
+  bool ProcessAction(const SEAction& action, const PhysiologyEngine& engine);
+  bool ProcessAction(const CDM::ActionData& in, const PhysiologyEngine& engine);
 
   SEEnvironmentActionCollection& GetEnvironmentActions() { return m_EnvironmentActions; }
   SEPatientActionCollection& GetPatientActions() { return m_PatientActions; }
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEAnesthesiaMachineActionCollection.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEAnesthesiaMachineActionCollection.h
@@ -29,6 +29,8 @@ specific language governing permissions and limitations under the License.
 #include <biogears/cdm/system/equipment/Anesthesia/actions/SEYPieceDisconnect.h>
 
 namespace biogears {
+class PhysiologyEngine;
+
 class BIOGEARS_API SEAnesthesiaMachineActionCollection : public Loggable {
 public:
   SEAnesthesiaMachineActionCollection(SESubstanceManager&);
@@ -38,8 +40,8 @@ class BIOGEARS_API SEAnesthesiaMachineActionCollection : public Loggable {
 
   void Unload(std::vector<CDM::ActionData*>& to);
 
-  bool ProcessAction(const SEAnesthesiaMachineAction& action);
-  bool ProcessAction(const CDM::AnesthesiaMachineActionData& action);
+  bool ProcessAction(const SEAnesthesiaMachineAction& action, const PhysiologyEngine& engine);
+  bool ProcessAction(const CDM::AnesthesiaMachineActionData& action, const PhysiologyEngine& engine);
 
   // STATE ACTION
   bool HasConfiguration() const;
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEConditionManager.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEConditionManager.h
@@ -32,6 +32,7 @@ specific language governing permissions and limitations under the License.
 CDM_BIND_DECL(ConditionData);
 
 namespace biogears {
+class PhysiologyEngine;
 
 class BIOGEARS_API SEConditionManager : public Loggable {
 public:
@@ -42,8 +43,8 @@ class BIOGEARS_API SEConditionManager : public Loggable {
 
   void Unload(std::vector<CDM::ConditionData*>& to);
 
-  bool ProcessCondition(const SECondition& condition);
-  bool ProcessCondition(const CDM::ConditionData& condition);
+  bool ProcessCondition(const SECondition& condition, const PhysiologyEngine& engine);
+  bool ProcessCondition(const CDM::ConditionData& condition, const PhysiologyEngine& engine);
 
   // Not too many conditions, so just have one manager
   // If we start getting alot, I will make patient/environment/equipment condition managers, like the action managers
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEEnvironmentActionCollection.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEEnvironmentActionCollection.h
@@ -17,6 +17,8 @@ specific language governing permissions and limitations under the License.
 #include <biogears/schema/cdm/EnvironmentActions.hxx>
 
 namespace biogears {
+class PhysiologyEngine;
+
 class BIOGEARS_API SEEnvironmentActionCollection : public Loggable {
 public:
   SEEnvironmentActionCollection(SESubstanceManager&);
@@ -26,8 +28,8 @@ class BIOGEARS_API SEEnvironmentActionCollection : public Loggable {
 
   void Unload(std::vector<CDM::ActionData*>& to);
 
-  bool ProcessAction(const SEEnvironmentAction& action);
-  bool ProcessAction(const CDM::EnvironmentActionData& action);
+  bool ProcessAction(const SEEnvironmentAction& action, const PhysiologyEngine& engine);
+  bool ProcessAction(const CDM::EnvironmentActionData& action, const PhysiologyEngine& engine);
 
   // STATE ACTION
   bool HasChange() const;
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEInhalerActionCollection.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEInhalerActionCollection.h
@@ -17,6 +17,8 @@ specific language governing permissions and limitations under the License.
 #include <biogears/cdm/system/equipment/Inhaler/actions/SEInhalerConfiguration.h>
 
 namespace biogears {
+class PhysiologyEngine;
+
 class BIOGEARS_API SEInhalerActionCollection : public Loggable {
 public:
   SEInhalerActionCollection(SESubstanceManager&);
@@ -26,8 +28,8 @@ class BIOGEARS_API SEInhalerActionCollection : public Loggable {
 
   void Unload(std::vector<CDM::ActionData*>& to);
 
-  bool ProcessAction(const SEInhalerAction& action);
-  bool ProcessAction(const CDM::InhalerActionData& action);
+  bool ProcessAction(const SEInhalerAction& action, const PhysiologyEngine& engine);
+  bool ProcessAction(const CDM::InhalerActionData& action, const PhysiologyEngine& engine);
 
   // STATE ACTION
   bool HasConfiguration() const;
diff --git a/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEPatientActionCollection.h b/projects/biogears/libBiogears/include/biogears/cdm/scenario/SEPatientActionCollection.h
@@ -207,8 +207,8 @@ class BIOGEARS_API SEPatientActionCollection : public Loggable {
 
   void Unload(std::vector<CDM::ActionData*>& to);
 
-  bool ProcessAction(const SEPatientAction& action);
-  bool ProcessAction(const CDM::PatientActionData& action);
+  bool ProcessAction(const SEPatientAction& action, const PhysiologyEngine& engine);
+  bool ProcessAction(const CDM::PatientActionData& action, const PhysiologyEngine& engine);
 
   bool HasAcuteRespiratoryDistress() const;
   SEAcuteRespiratoryDistress* GetAcuteRespiratoryDistress() const;
@@ -434,6 +434,8 @@ class BIOGEARS_API SEPatientActionCollection : public Loggable {
   SEUrinate* m_Urinate;
   SEOverride* m_OverrideAction;
 
+  double m_BurnIntroductionTimeStamp;
+
   std::map<std::string, SEHemorrhage*> m_Hemorrhages;
   mutable std::map<std::string, SEHemorrhage*>::const_iterator m_HemorrhageItr;
 
diff --git a/projects/biogears/libBiogears/include/biogears/engine/Controller/BioGearsEngine.h b/projects/biogears/libBiogears/include/biogears/engine/Controller/BioGearsEngine.h
@@ -69,7 +69,7 @@ class BIOGEARS_API BioGearsEngine : public PhysiologyEngine, public BioGears {
   virtual const PhysiologyEngineConfiguration* GetConfiguration() override;
 
   virtual double GetTimeStep(const TimeUnit& unit) override;
-  virtual double GetSimulationTime(const TimeUnit& unit) override;
+  virtual double GetSimulationTime(const TimeUnit& unit) const override;
 
   //!-------------------------------------------------------------------------------------------------
   //! \brief
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEActionManager.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEActionManager.cpp
@@ -11,6 +11,7 @@ specific language governing permissions and limitations under the License.
 **************************************************************************************/
 
 #include <biogears/cdm/scenario/SEActionManager.h>
+#include <biogears/cdm/engine/PhysiologyEngine.h>
 
 namespace biogears {
 SEActionManager::SEActionManager(SESubstanceManager& substances)
@@ -37,20 +38,20 @@ void SEActionManager::Clear()
   m_ProcessedActions.clear();
 }
 //-------------------------------------------------------------------------------
-bool SEActionManager::ProcessAction(const CDM::ActionData& in)
+bool SEActionManager::ProcessAction(const CDM::ActionData& in, const PhysiologyEngine& engine)
 {
   const CDM::PatientActionData* pAction = dynamic_cast<const CDM::PatientActionData*>(&in);
   if (pAction != nullptr)
-    return m_PatientActions.ProcessAction(*pAction);
+    return m_PatientActions.ProcessAction(*pAction, engine);
   const CDM::EnvironmentActionData* eAction = dynamic_cast<const CDM::EnvironmentActionData*>(&in);
   if (eAction != nullptr)
-    return m_EnvironmentActions.ProcessAction(*eAction);
+    return m_EnvironmentActions.ProcessAction(*eAction, engine);
   const CDM::AnesthesiaMachineActionData* aAction = dynamic_cast<const CDM::AnesthesiaMachineActionData*>(&in);
   if (aAction != nullptr)
-    return m_AnesthesiaMachineActions.ProcessAction(*aAction);
+    return m_AnesthesiaMachineActions.ProcessAction(*aAction, engine);
   const CDM::InhalerActionData* iAction = dynamic_cast<const CDM::InhalerActionData*>(&in);
   if (iAction != nullptr)
-    return m_InhalerActions.ProcessAction(*iAction);
+    return m_InhalerActions.ProcessAction(*iAction, engine);
   Error("Unknown Action Type");
   return false;
 }
@@ -63,24 +64,24 @@ void SEActionManager::Unload(std::vector<CDM::ActionData*>& to)
   m_InhalerActions.Unload(to);
 }
 //-------------------------------------------------------------------------------
-bool SEActionManager::ProcessAction(const SEAction& action)
+bool SEActionManager::ProcessAction(const SEAction& action, const PhysiologyEngine& engine)
 {
   // Store the action data. This is intended to be able to
   // Serialize out all the actions that the engine was asked to perform
   CDM::ActionData* aData = action.Unload();
   m_ProcessedActions.push_back(action.Unload());
 
   if (dynamic_cast<const SEPatientAction*>(&action) != nullptr)
-    return m_PatientActions.ProcessAction(dynamic_cast<const CDM::PatientActionData&>(*aData));
+    return m_PatientActions.ProcessAction(dynamic_cast<const CDM::PatientActionData&>(*aData, engine));
 
   if (dynamic_cast<const SEAnesthesiaMachineAction*>(&action) != nullptr)
-    return m_AnesthesiaMachineActions.ProcessAction(dynamic_cast<const CDM::AnesthesiaMachineActionData&>(*aData));
+    return m_AnesthesiaMachineActions.ProcessAction(dynamic_cast<const CDM::AnesthesiaMachineActionData&>(*aData, engine));
 
   if (dynamic_cast<const SEEnvironmentAction*>(&action) != nullptr)
-    return m_EnvironmentActions.ProcessAction(dynamic_cast<const CDM::EnvironmentActionData&>(*aData));
+    return m_EnvironmentActions.ProcessAction(dynamic_cast<const CDM::EnvironmentActionData&>(*aData, engine));
 
   if (dynamic_cast<const SEInhalerAction*>(&action) != nullptr)
-    return m_InhalerActions.ProcessAction(dynamic_cast<const CDM::InhalerActionData&>(*aData));
+    return m_InhalerActions.ProcessAction(dynamic_cast<const CDM::InhalerActionData&>(*aData, engine));
 
   /// \error Unsupported Action
   Error("Unsupported Action");
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEAnesthesiaMachineActionCollection.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEAnesthesiaMachineActionCollection.cpp
@@ -97,17 +97,17 @@ void SEAnesthesiaMachineActionCollection::Unload(std::vector<CDM::ActionData*>&
     to.push_back(GetYPieceDisconnect()->Unload());
 }
 //-------------------------------------------------------------------------------
-bool SEAnesthesiaMachineActionCollection::ProcessAction(const SEAnesthesiaMachineAction& action)
+bool SEAnesthesiaMachineActionCollection::ProcessAction(const SEAnesthesiaMachineAction& action, const PhysiologyEngine& engine)
 {
   if (!IsValid(action))
     return false;
   CDM::AnesthesiaMachineActionData* bind = action.Unload();
-  bool b = ProcessAction(*bind);
+  bool b = ProcessAction(*bind, engine);
   delete bind;
   return b;
 }
 //-------------------------------------------------------------------------------
-bool SEAnesthesiaMachineActionCollection::ProcessAction(const CDM::AnesthesiaMachineActionData& action)
+bool SEAnesthesiaMachineActionCollection::ProcessAction(const CDM::AnesthesiaMachineActionData& action, const PhysiologyEngine& engine)
 {
   const CDM::AnesthesiaMachineConfigurationData* config = dynamic_cast<const CDM::AnesthesiaMachineConfigurationData*>(&action);
   if (config != nullptr) {
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEConditionManager.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEConditionManager.cpp
@@ -74,17 +74,17 @@ void SEConditionManager::Unload(std::vector<CDM::ConditionData*>& to)
     to.push_back(c->Unload());
 }
 
-bool SEConditionManager::ProcessCondition(const SECondition& condition)
+bool SEConditionManager::ProcessCondition(const SECondition& condition, const PhysiologyEngine& engine)
 {
   //if (!IsValid(action))
   //  return false;
   CDM::ConditionData* bind = condition.Unload();
-  bool b = ProcessCondition(*bind);
+  bool b = ProcessCondition(*bind, engine);
   delete bind;
   return b;
 }
 
-bool SEConditionManager::ProcessCondition(const CDM::ConditionData& condition)
+bool SEConditionManager::ProcessCondition(const CDM::ConditionData& condition, const PhysiologyEngine& engine)
 {
   const CDM::ChronicAnemiaData* anemiaData = dynamic_cast<const CDM::ChronicAnemiaData*>(&condition);
   if (anemiaData != nullptr) {
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEEnvironmentActionCollection.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEEnvironmentActionCollection.cpp
@@ -43,17 +43,17 @@ void SEEnvironmentActionCollection::Unload(std::vector<CDM::ActionData*>& to)
     to.push_back(GetThermalApplication()->Unload());
 }
 
-bool SEEnvironmentActionCollection::ProcessAction(const SEEnvironmentAction& action)
+bool SEEnvironmentActionCollection::ProcessAction(const SEEnvironmentAction& action, const PhysiologyEngine& engine)
 {
   if (!IsValid(action))
     return false;
   CDM::EnvironmentActionData* bind = action.Unload();
-  bool b = ProcessAction(*bind);
+  bool b = ProcessAction(*bind, engine);
   delete bind;
   return b;
 }
 
-bool SEEnvironmentActionCollection::ProcessAction(const CDM::EnvironmentActionData& action)
+bool SEEnvironmentActionCollection::ProcessAction(const CDM::EnvironmentActionData& action, const PhysiologyEngine& engine)
 {
   const CDM::EnvironmentChangeData* change = dynamic_cast<const CDM::EnvironmentChangeData*>(&action);
   if (change != nullptr) {
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEInhalerActionCollection.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEInhalerActionCollection.cpp
@@ -37,17 +37,17 @@ void SEInhalerActionCollection::Unload(std::vector<CDM::ActionData*>& to)
     to.push_back(GetConfiguration()->Unload());
 }
 
-bool SEInhalerActionCollection::ProcessAction(const SEInhalerAction& action)
+bool SEInhalerActionCollection::ProcessAction(const SEInhalerAction& action, const PhysiologyEngine& engine)
 {
   if (!IsValid(action))
     return false;
   CDM::InhalerActionData* bind = action.Unload();
-  bool b = ProcessAction(*bind);
+  bool b = ProcessAction(*bind, engine);
   delete bind;
   return b;
 }
 
-bool SEInhalerActionCollection::ProcessAction(const CDM::InhalerActionData& action)
+bool SEInhalerActionCollection::ProcessAction(const CDM::InhalerActionData& action, const PhysiologyEngine& engine)
 {
   const CDM::InhalerConfigurationData* config = dynamic_cast<const CDM::InhalerConfigurationData*>(&action);
   if (config != nullptr) {
diff --git a/projects/biogears/libBiogears/src/cdm/scenario/SEPatientActionCollection.cpp b/projects/biogears/libBiogears/src/cdm/scenario/SEPatientActionCollection.cpp
@@ -14,6 +14,7 @@ specific language governing permissions and limitations under the License.
 #include <biogears/cdm/properties/SEScalarVolumePerTime.h>
 #include <biogears/cdm/substance/SESubstanceCompound.h>
 #include <biogears/cdm/substance/SESubstanceConcentration.h>
+#include <biogears/cdm/engine/PhysiologyEngine.h>
 
 #include <map>
 #include <vector>
@@ -487,18 +488,18 @@ void SEPatientActionCollection::Unload(std::vector<CDM::ActionData*>& to)
   }
 }
 //-------------------------------------------------------------------------------
-bool SEPatientActionCollection::ProcessAction(const SEPatientAction& action)
+bool SEPatientActionCollection::ProcessAction(const SEPatientAction& action, const PhysiologyEngine& engine)
 {
   if (!IsValid(action)) {
     return false;
   }
   CDM::PatientActionData* bind = action.Unload();
-  bool b = ProcessAction(*bind);
+  bool b = ProcessAction(*bind, engine);
   delete bind;
   return b;
 }
 //-------------------------------------------------------------------------------
-bool SEPatientActionCollection::ProcessAction(const CDM::PatientActionData& action)
+bool SEPatientActionCollection::ProcessAction(const CDM::PatientActionData& action, const PhysiologyEngine& engine)
 {
   const CDM::PatientAssessmentRequestData* patientAssessment = dynamic_cast<const CDM::PatientAssessmentRequestData*>(&action);
   if (patientAssessment != nullptr) {
@@ -630,7 +631,10 @@ bool SEPatientActionCollection::ProcessAction(const CDM::PatientActionData& acti
     if (m_BurnWound == nullptr) {
       m_BurnWound = new SEBurnWound();
     }
+
+
     m_BurnWound->Load(*burn);
+    m_BurnIntroductionTimeStamp = engine.GetSimulationTime(TimeUnit::s);
     if (!m_BurnWound->IsActive()) {
       RemoveBurnWound();
       return true;
diff --git a/projects/biogears/libBiogears/src/engine/Controller/BioGearsEngine.cpp b/projects/biogears/libBiogears/src/engine/Controller/BioGearsEngine.cpp
@@ -238,14 +238,14 @@ bool BioGearsEngine::LoadState(const CDM::PhysiologyEngineStateData& state, cons
   // Conditions //
   m_Conditions->Clear();
   for (const CDM::ConditionData& cData : bgState->Condition()) {
-    if (!m_Conditions->ProcessCondition(cData)) {
+    if (!m_Conditions->ProcessCondition(cData, *this)) {
       m_ss << "Unable to load condition" << std::endl;
     }
   }
   // Actions //
   m_Actions->Clear();
   for (const CDM::ActionData& cData : bgState->ActiveAction()) {
-    if (!m_Actions->ProcessAction(cData)) {
+    if (!m_Actions->ProcessAction(cData, *this)) {
       m_ss << "Unable to load action" << std::endl;
     }
   }
@@ -646,7 +646,7 @@ bool BioGearsEngine::InitializeEngine(const std::vector<const SECondition*>* con
     for (const SECondition* c : *conditions) {
       m_ss << "[Condition] " << *c;
       m_Logger->Info(m_ss.str(), "BioGearsEngine");
-      if (!m_Conditions->ProcessCondition(*c)) {
+      if (!m_Conditions->ProcessCondition(*c, *this)) {
         return false;
       }
     }
@@ -696,7 +696,7 @@ double BioGearsEngine::GetTimeStep(const TimeUnit& unit)
   return m_Config->GetTimeStep(unit);
 }
 //-------------------------------------------------------------------------------
-double BioGearsEngine::GetSimulationTime(const TimeUnit& unit)
+double BioGearsEngine::GetSimulationTime(const TimeUnit& unit) const
 {
   return m_SimulationTime->GetValue(unit);
 }

Original file line number	Diff line number	Diff line change
`@@ -97,17 +97,17 @@ void SEAnesthesiaMachineActionCollection::Unload(std::vector<CDM::ActionData*>&`
`97`	`97`	`to.push_back(GetYPieceDisconnect()->Unload());`
`98`	`98`	`}`
`99`	`99`	`//-------------------------------------------------------------------------------`
`100`		`-bool SEAnesthesiaMachineActionCollection::ProcessAction(const SEAnesthesiaMachineAction& action)`
	`100`	`+bool SEAnesthesiaMachineActionCollection::ProcessAction(const SEAnesthesiaMachineAction& action, const PhysiologyEngine& engine)`
`101`	`101`	`{`
`102`	`102`	`if (!IsValid(action))`
`103`	`103`	`return false;`
`104`	`104`	`CDM::AnesthesiaMachineActionData* bind = action.Unload();`
`105`		`- bool b = ProcessAction(*bind);`
	`105`	`+ bool b = ProcessAction(*bind, engine);`
`106`	`106`	`delete bind;`
`107`	`107`	`return b;`
`108`	`108`	`}`
`109`	`109`	`//-------------------------------------------------------------------------------`
`110`		`-bool SEAnesthesiaMachineActionCollection::ProcessAction(const CDM::AnesthesiaMachineActionData& action)`
	`110`	`+bool SEAnesthesiaMachineActionCollection::ProcessAction(const CDM::AnesthesiaMachineActionData& action, const PhysiologyEngine& engine)`
`111`	`111`	`{`
`112`	`112`	`const CDM::AnesthesiaMachineConfigurationData* config = dynamic_cast<const CDM::AnesthesiaMachineConfigurationData*>(&action);`
`113`	`113`	`if (config != nullptr) {`