Updates for new 6.2 engine release, see README for modeling details

Author: ajbaird

src/cdm/cpp/engine/PhysiologyEngineDynamicStabilization.cpp

@@ -365,7 +365,7 @@ bool PhysiologyEngineDynamicStabilization::Merge()
 	return true;
 }
 
-// This basically tests the current property with the target proptry and if they are in a window of acceptance
+// This basically tests the current property with the target property and if they are in a window of acceptance
 bool PropertyConvergence::Test(double time_s)
 {
   double v = !m_DataRequestScalar.HasUnit() ?

src/cdm/cpp/patient/SEPatient.cpp

@@ -420,6 +420,12 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 			case CDM::enumPatientEvent::Hypoglycemia:
 				m_ss << " Patient has Hypoglycemia";
 				break;
+      case CDM::enumPatientEvent::HypoglycemicShock:
+        m_ss << " Patient is in Hypoglycemic Shock";
+        break;
+      case CDM::enumPatientEvent::HypoglycemicComa:
+        m_ss << " Patient has fallen into Hypoglycemic Coma";
+        break;
 			case CDM::enumPatientEvent::Hypothermia:
 				m_ss << " Patient is Hypothermic";
 				break;
@@ -442,8 +448,11 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 				m_ss << " Patient has Ketoacidosis";
 				break;
 			case CDM::enumPatientEvent::LacticAcidosis:
-				m_ss << " Patient has LacticAcidosis";
+				m_ss << " Patient has Lactic Acidosis";
 				break;
+      case CDM::enumPatientEvent::LiverGlycogenDepleted:
+        m_ss << " Patient's liver glycogen is depleted";
+        break;
       case CDM::enumPatientEvent::MaximumPulmonaryVentilationRate:
 				m_ss << " Patient's Respiratory Driver has exceeded the maximum target pulmonary ventilation rate, setting value to the maximum allowable rate";
 				break;
@@ -459,6 +468,9 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
       case CDM::enumPatientEvent::ModerateAcuteRespiratoryDistress:
         m_ss << " The patient has Moderate Acute Respiratory Distress";
         break;
+      case CDM::enumPatientEvent::MuscleGlycogenDepleted:
+        m_ss << " Patient's muscle glycogen is depleted";
+        break;
       case CDM::enumPatientEvent::MyocardiumOxygenDeficit:
         m_ss << " The patient's heart is not receiving enough oxygen";
         break;
@@ -547,6 +559,12 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 			case CDM::enumPatientEvent::Hypoglycemia:
 				m_ss << " Patient no longer has Hypoglycemia";
 				break;
+      case CDM::enumPatientEvent::HypoglycemicShock:
+        m_ss << " Patient is no longer in Hypoglycemic Shock";
+        break;
+      case CDM::enumPatientEvent::HypoglycemicComa:
+        m_ss << " Patient is no longer in a Hypoglycemic Coma";
+        break;
 			case CDM::enumPatientEvent::Hypothermia:
 				m_ss << " Patient is no longer has Hypothermic";
 				break;
@@ -569,8 +587,11 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 				m_ss << " Patient no longer has Ketoacidosis";
 				break;
 			case CDM::enumPatientEvent::LacticAcidosis:
-				m_ss << " Patient no longer has LacticAcidosis";
+				m_ss << " Patient no longer has Lactic Acidosis";
 				break;
+      case CDM::enumPatientEvent::LiverGlycogenDepleted:
+        m_ss << " Patient's liver glycogen is no longer depleted";
+        break;
 			case CDM::enumPatientEvent::MaximumPulmonaryVentilationRate:
 				m_ss << " Patient's Respiratory Driver is no longer exceeding the maximum target pulmonary ventilation rate";
 				break;
@@ -586,6 +607,9 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
       case CDM::enumPatientEvent::ModerateAcuteRespiratoryDistress:
         m_ss << " Patient no longer has a Moderate Acute Respiratory Distress";
         break;
+      case CDM::enumPatientEvent::MuscleGlycogenDepleted:
+        m_ss << " Patient's muscle glycogen is no longer depleted";
+        break;
       case CDM::enumPatientEvent::MyocardiumOxygenDeficit:
         m_ss << " Patient no longer has a Myocardium Oxygen Deficit";
         break;

src/cdm/cpp/patient/actions/SEHemorrhage.cpp

@@ -15,11 +15,27 @@ specific language governing permissions and limitations under the License.
 #include "bind/HemorrhageData.hxx"
 #include "properties/SEScalarVolumePerTime.h"
 #include "bind/ScalarVolumePerTimeData.hxx"
+#include "bind/IntegerArray.hxx"
+#include "bind/IntegerList.hxx"
 
 SEHemorrhage::SEHemorrhage() : SEPatientAction()
 {
-  m_Compartment = "";
-	m_Rate=nullptr;
+  m_Compartment = ""; //This is the compartment we use to store information about hemorrhage
+  m_MCIS;
+  m_BleedName = "";	  //This is the name of the pathway in circuit that will have its resistance changed
+
+  //Place organs in a map so that we don't get too messy with nested conditionals.  Each vector is digits 2-4 of the MCIS code
+  organMap[{6, 4}] = std::make_pair("AortaBleed", "Major Artery");
+  organMap[{6, 6}] = std::make_pair("VenaCavaBleed", "Vena Cava");
+  organMap[{6, 5}] = std::make_pair("AortaBleed", "Major Artery");
+  organMap[{7, 1}] = std::make_pair("LungBleed", "Lungs");
+  organMap[{7, 2}] = std::make_pair("HeartBleed", "Heart");
+  organMap[{8, 1}] = std::make_pair("LiverBleed", "Liver");
+  organMap[{8, 2}] = std::make_pair("SpleenBleed", "Spleen");
+  organMap[{8, 3}] = std::make_pair("SplanchnicBleed", "Splanchnic");
+  organMap[{8, 4}] = std::make_pair("KidneyBleed", "Kidney");
+  organMap[{8, 5}] = std::make_pair("SmallIntestineBleed", "Small Intestine");
+  organMap[{8, 6}] = std::make_pair("LargeIntestineBleed", "Large Intestine");
 }
 
 SEHemorrhage::~SEHemorrhage()
@@ -30,25 +46,43 @@ SEHemorrhage::~SEHemorrhage()
 void SEHemorrhage::Clear()
 {
 	SEPatientAction::Clear();
-  m_Compartment = "";
-	SAFE_DELETE(m_Rate);
+    m_Compartment = "";
+	m_MCIS.clear();
+	m_BleedName = "";
 }
 
 bool SEHemorrhage::IsValid() const
 {
-	return SEPatientAction::IsValid() && HasCompartment() && HasRate();
+	return SEPatientAction::IsValid() && HasCompartment() && HasMCIS() && HasBleedName();
 }
 
 bool SEHemorrhage::IsActive() const
 {
-	return IsValid() ? !m_Rate->IsZero() : false;
+	return IsValid() ? !m_MCIS[0]==0 : false;
 }
 
 bool SEHemorrhage::Load(const CDM::HemorrhageData& in)
 {
 	SEPatientAction::Load(in);
-	GetRate().Load(in.Rate());
-	m_Compartment=in.Compartment();
+	if (in.MCIS().present())
+	{
+		for (size_t i = 0; i < in.MCIS().get().IntegerList().size(); i++)
+		{
+			m_MCIS.push_back(in.MCIS().get().IntegerList()[i]);
+		}
+		if ((m_MCIS[0] < 0) || (m_MCIS[0] > 5)) //check to make sure no one puts in a severity of a million
+		{
+			SetComment("Invalid MCIS Code: Severity out of bounds (0-5).  Defaulting to 3");
+			m_MCIS[0] = 3;
+		}
+		if (m_MCIS.size() != 5)	//make sure mcis code is proper length
+		{
+			SetComment("Invalid MCIS Code:  Code must be 5 digits.  Defaulting to aorta with bleeding severity = 3");
+			m_MCIS = { 3,2,6,3,0 };
+		}
+	}
+	ProcessMCIS();
+
 	return true;
 }
 
@@ -62,10 +96,72 @@ CDM::HemorrhageData* SEHemorrhage::Unload() const
 void SEHemorrhage::Unload(CDM::HemorrhageData& data) const
 {
 	SEPatientAction::Unload(data);
-	if(m_Rate!=nullptr)
-		data.Rate(std::unique_ptr<CDM::ScalarVolumePerTimeData>(m_Rate->Unload()));
-	if(HasCompartment())
-		data.Compartment(m_Compartment);
+	//Create Integer Array that stores Integer List and pass m_MCIS values to it (modeled after GetActiveIndices in electrocardiogram-
+	//interpolatorWaveform.cpp)
+	data.MCIS(std::unique_ptr<CDM::IntegerArray>(new CDM::IntegerArray()));
+	data.MCIS().get().IntegerList(std::unique_ptr<CDM::IntegerList>(new CDM::IntegerList()));
+	for (int i : m_MCIS)
+		data.MCIS().get().IntegerList().push_back(i);
+}
+
+void SEHemorrhage::ProcessMCIS()
+{
+	switch (m_MCIS[1]) {
+	case Head:
+		//Note that this assumes that the third digit is 6 (for vessels).
+		if (m_MCIS[3] == 1) //If bleeding is intracranial 
+		{
+			SetBleedName("BrainBleed");
+			SetCompartment("Head");
+		}
+		else
+		{	//If the bleeding is from the carotid artery/jugular vein			
+			SetBleedName("AortaBleed");
+			SetCompartment("Major Artery");
+		}
+		break;
+	case Torso:
+		if (organMap.find({ m_MCIS.begin() + 2, m_MCIS.end()-1}) != organMap.end()) //extract the two digits that map to an organ
+		{
+			SetBleedName(organMap[{m_MCIS.begin() + 2, m_MCIS.end()-1}].first);
+			SetCompartment(organMap[{m_MCIS.begin() + 2, m_MCIS.end()-1}].second);
+		}
+		else
+		{
+			SetComment("Invalid MCIS Code: Does not map to BioGears compartment.  Defaulting to Aorta");
+			SetBleedName("AortaBleed");
+			SetCompartment("Major Artery");
+		}
+		break;
+	case Arms:
+		SetBleedName("ArmBleed");
+		SetCompartment("Arm");
+		break;
+	case Legs:
+		SetBleedName("LegBleed");
+		SetCompartment("Leg");
+		break;
+	default:
+		SetComment("Invalid MCIS Code: Does not map to BioGears compartment.  Defaulting to Aorta");
+		SetBleedName("AortaBleed");
+		SetCompartment("Major Artery");
+		break;
+	}
+}
+
+
+
+std::string SEHemorrhage::GetBleedName() const
+{
+	return m_BleedName;
+}
+void SEHemorrhage::SetBleedName(const std::string& name)
+{
+	m_BleedName = name;
+}
+bool SEHemorrhage::HasBleedName() const
+{
+	return !m_BleedName.empty();
 }
 
 std::string SEHemorrhage::GetCompartment() const
@@ -88,24 +184,29 @@ void SEHemorrhage::InvalidateCompartment()
   m_Compartment = "";
 }
 
-bool SEHemorrhage::HasRate() const
+bool SEHemorrhage::HasMCIS() const
 {
-	return m_Rate==nullptr?false:m_Rate->IsValid();
+	return !m_MCIS.empty();
 }
 
-SEScalarVolumePerTime& SEHemorrhage::GetRate()
+void SEHemorrhage::SetMCIS(const std::vector<unsigned int>& mcisIn)
 {
-	if(m_Rate==nullptr)
-		m_Rate=new SEScalarVolumePerTime();
-	return *m_Rate;
+	if (mcisIn.size() != 5)
+		Error("MCIS code must be five digits");
+	else
+		m_MCIS = mcisIn;
 }
 
 void SEHemorrhage::ToString(std::ostream &str) const
 {
-	str << "Patient Action : Hemorrhage"; 
-	if(HasComment())
-		str<<"\n\tComment: "<<m_Comment;
-	str << "\n\tRate: "; HasRate() ? str << *m_Rate : str << "NaN";
-	str << "\n\tFor Compartment: "; HasCompartment()? str << GetCompartment() : str << "No Compartment Set"; 
+	str << "Patient Action : Hemorrhage";
+	if (HasComment())
+		str << "\n\tComment: " << m_Comment;
+	str << "\n\tInjury Code: ";
+	for (int i : m_MCIS)
+		str << i;
+	str << "\n\tCompartment: "; HasCompartment() ? str << GetCompartment() : str << "No Compartment Set";
+	str << "\n\tSeverity:  ";  str << m_MCIS[0];
 	str << std::flush;
+	
 }

src/cdm/cpp/patient/actions/SEHemorrhage.h

@@ -14,6 +14,12 @@ specific language governing permissions and limitations under the License.
 #include "patient/actions/SEPatientAction.h"
 #include "bind/HemorrhageData.hxx"
 
+
+
+
+
+
+
 class DLL_DECL SEHemorrhage : public SEPatientAction
 {
 public:
@@ -37,14 +43,24 @@ class DLL_DECL SEHemorrhage : public SEPatientAction
 	virtual void SetCompartment(const std::string& name);
 	virtual bool HasCompartment() const;
 	virtual void InvalidateCompartment();
+	virtual void ProcessMCIS();
+	
+	virtual bool HasMCIS() const;
+	virtual std::vector<unsigned int>& GetMCIS() { return m_MCIS; }
+	virtual void SetMCIS(const std::vector<unsigned int>& mcisIn);
 
-	virtual bool HasRate() const;
-	virtual SEScalarVolumePerTime& GetRate();	
+	virtual bool HasBleedName() const;
+	virtual std::string GetBleedName() const;
+	virtual void SetBleedName(const std::string& name);
 
+	
 	virtual void ToString(std::ostream &str) const;
 
 protected:
-  std::string             m_Compartment;
-	SEScalarVolumePerTime*  m_Rate;
-	
+	std::string             m_Compartment;
+	std::vector<unsigned int>		m_MCIS;
+	std::string				m_BleedName;
+	std::map<std::vector<int>, std::pair<std::string, std::string>> organMap;
+
+	enum region { Head = 1, Torso = 2, Arms = 3, Legs = 4 }; //mcis digit 2
 };    

src/cdm/cpp/scenario/SEPatientActionCollection.cpp

@@ -387,18 +387,29 @@ bool SEPatientActionCollection::ProcessAction(const CDM::PatientActionData& acti
 	const CDM::HemorrhageData* hem = dynamic_cast<const CDM::HemorrhageData*>(&action);
 	if(hem!=nullptr)
 	{
-		SEHemorrhage* myHem = m_Hemorrhages[hem->Compartment()];		
-		if (myHem == nullptr)
+		//We only store the MCIS on the CDM (so that our input is just one code and nothing else).  But we need the compartment information to 
+		//check if hemorrhage already exists in m_Hemorrhages map.  Thus we use a temporary variable to check.
+		SEHemorrhage* myHem;
+		SEHemorrhage* temp = new SEHemorrhage;
+		temp->Load(*hem);
+		if (m_Hemorrhages.find(temp->GetCompartment()) == m_Hemorrhages.end())
 		{
-			myHem = new SEHemorrhage();
-			m_Hemorrhages[hem->Compartment()] = myHem;
+			myHem = new SEHemorrhage;
+			m_Hemorrhages[temp->GetCompartment()] = myHem;
+			myHem->Load(*hem);
 		}
-    myHem->Load(*hem);
+		else
+		{
+			myHem = m_Hemorrhages[temp->GetCompartment()];
+			myHem->Load(*hem);
+		} 
     if (!myHem->IsActive())
     {
-      RemoveHemorrhage(hem->Compartment());
+      RemoveHemorrhage(myHem->GetCompartment());
+	  SAFE_DELETE(temp);
       return true;
     }
+	SAFE_DELETE(temp);
     return IsValid(*myHem);
 	}