Added base excess as blood chemistry system data.

cdm/cpp/properties/SEScalarAmountPerVolume.cpp

@@ -7,6 +7,7 @@ PROTO_PUSH
 #include "bind/cdm/Properties.pb.h"
 PROTO_POP
 
+AmountPerVolumeUnit AmountPerVolumeUnit::meq_Per_L("meq/L");
 AmountPerVolumeUnit AmountPerVolumeUnit::mol_Per_L("mol/L");
 AmountPerVolumeUnit AmountPerVolumeUnit::mol_Per_mL("mol/mL");
 AmountPerVolumeUnit AmountPerVolumeUnit::mmol_Per_L("mmol/L");
@@ -16,6 +17,8 @@ AmountPerVolumeUnit AmountPerVolumeUnit::ct_Per_uL("ct/uL");
 
 bool AmountPerVolumeUnit::IsValidUnit(const std::string& unit)
 {
+  if (meq_Per_L.GetString().compare(unit) == 0)
+    return true;
   if (mol_Per_L.GetString().compare(unit) == 0)
     return true;
   if (mol_Per_mL.GetString().compare(unit) == 0)
@@ -33,6 +36,8 @@ bool AmountPerVolumeUnit::IsValidUnit(const std::string& unit)
 
 const AmountPerVolumeUnit& AmountPerVolumeUnit::GetCompoundUnit(const std::string& unit)
 {
+  if (meq_Per_L.GetString().compare(unit) == 0)
+    return meq_Per_L;
   if (mol_Per_L.GetString().compare(unit) == 0)
     return mol_Per_L;
   if (mol_Per_mL.GetString().compare(unit) == 0)

cdm/cpp/properties/SEScalarAmountPerVolume.h

@@ -14,6 +14,7 @@ public:
   static bool IsValidUnit(const std::string& unit);
   static const AmountPerVolumeUnit& GetCompoundUnit(const std::string& unit);
 
+  static AmountPerVolumeUnit meq_Per_L;
   static AmountPerVolumeUnit mol_Per_L;
   static AmountPerVolumeUnit mol_Per_mL;
   static AmountPerVolumeUnit mmol_Per_L;

cdm/cpp/system/physiology/SEBloodChemistrySystem.cpp

@@ -18,6 +18,7 @@ SEBloodChemistrySystem::SEBloodChemistrySystem(Logger* logger) : SESystem(logger
 {
   m_BloodDensity = nullptr;
   
+  m_BaseExcess = nullptr;
   m_BloodPH = nullptr;
   m_BloodSpecificHeat = nullptr;
   m_BloodUreaNitrogenConcentration = nullptr;
@@ -56,6 +57,7 @@ void SEBloodChemistrySystem::Clear()
 {
   SESystem::Clear();
 
+  SAFE_DELETE(m_BaseExcess);
   SAFE_DELETE(m_BloodDensity);
   SAFE_DELETE(m_BloodPH);
   SAFE_DELETE(m_BloodSpecificHeat);
@@ -88,6 +90,8 @@ void SEBloodChemistrySystem::Clear()
 
 const SEScalar* SEBloodChemistrySystem::GetScalar(const std::string& name)
 {
+  if (name.compare("BaseExcess") == 0)
+    return &GetBaseExcess();
   if (name.compare("BloodDensity") == 0)
     return &GetBloodDensity();
   if (name.compare("BloodPH") == 0)
@@ -153,6 +157,8 @@ void SEBloodChemistrySystem::Load(const cdm::BloodChemistrySystemData& src, SEBl
 void SEBloodChemistrySystem::Serialize(const cdm::BloodChemistrySystemData& src, SEBloodChemistrySystem& dst)
 {
   dst.Clear();
+  if (src.has_baseexcess())
+    SEScalarAmountPerVolume::Load(src.baseexcess(), dst.GetBaseExcess());
   if (src.has_blooddensity())
     SEScalarMassPerVolume::Load(src.blooddensity(), dst.GetBloodDensity());
   if (src.has_bloodph())
@@ -218,6 +224,8 @@ cdm::BloodChemistrySystemData* SEBloodChemistrySystem::Unload(const SEBloodChemi
 }
 void SEBloodChemistrySystem::Serialize(const SEBloodChemistrySystem& src, cdm::BloodChemistrySystemData& dst)
 {
+  if (src.HasBaseExcess())
+    dst.set_allocated_baseexcess(SEScalarAmountPerVolume::Unload(*src.m_BaseExcess));
   if (src.HasBloodDensity())
     dst.set_allocated_blooddensity(SEScalarMassPerVolume::Unload(*src.m_BloodDensity));
   if (src.HasBloodPH())
@@ -275,6 +283,23 @@ void SEBloodChemistrySystem::Serialize(const SEBloodChemistrySystem& src, cdm::B
     dst.set_allocated_venousoxygenpressure(SEScalarPressure::Unload(*src.m_VenousOxygenPressure));
 }
 
+bool SEBloodChemistrySystem::HasBaseExcess() const
+{
+  return m_BaseExcess == nullptr ? false : m_BaseExcess->IsValid();
+}
+SEScalarAmountPerVolume& SEBloodChemistrySystem::GetBaseExcess()
+{
+  if (m_BaseExcess == nullptr)
+    m_BaseExcess = new SEScalarAmountPerVolume();
+  return *m_BaseExcess;
+}
+double SEBloodChemistrySystem::GetBaseExcess(const AmountPerVolumeUnit& unit) const
+{
+  if (m_BaseExcess == nullptr)
+    return SEScalar::dNaN();
+  return m_BaseExcess->GetValue(unit);
+}
+
 bool SEBloodChemistrySystem::HasBloodDensity() const
 {
   return m_BloodDensity == nullptr ? false : m_BloodDensity->IsValid();

cdm/cpp/system/physiology/SEBloodChemistrySystem.h

@@ -26,6 +26,16 @@ protected:
   static void Serialize(const SEBloodChemistrySystem& src, cdm::BloodChemistrySystemData& dst);       /**< @copydoc DOXY_CDM_SERIALIZE_OUT *///@}
   
 public:
+  /** @name BaseExcess
+  *  @brief @copybrief Physiology_BloodChemistrySystemData_BaseExcess
+  *  @{*/
+  /// %Test if member has been allocated
+  virtual bool HasBaseExcess() const;
+  /// Get member class, allocate if nullptr
+  virtual SEScalarAmountPerVolume& GetBaseExcess();
+  virtual double GetBaseExcess(AmountPerVolumeUnit& unit) const;
+  //@}
+
   /**  @name BloodDensity *///@{ @copybrief Physiology_BloodChemistrySystemData_BloodDensity
   virtual bool HasBloodDensity() const;                                                               /**< @copydoc DOXY_CDM_HAS */
   virtual SEScalarMassPerVolume& GetBloodDensity();                                                   /**< @copydoc DOXY_CDM_GET */
@@ -293,6 +303,7 @@ public:
 
 protected:
 
+  SEScalarAmountPerVolume *         m_BaseExcess;
   SEScalarMassPerVolume*          m_BloodDensity;
   SEScalar*                       m_BloodPH;
   SEScalarHeatCapacitancePerMass* m_BloodSpecificHeat;

cdm/java/mil/tatrc/physiology/datamodel/system/physiology/SEBloodChemistrySystem.java

@@ -9,6 +9,7 @@ import mil.tatrc.physiology.datamodel.system.SESystem;
 
 public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESystem
 {
+  protected SEScalarAmountPerVolume        baseExcess;
   protected SEScalarMassPerVolume          bloodDensity;
   protected SEScalar                       bloodPH;
   protected SEScalarHeatCapacitancePerMass bloodSpecificHeat;
@@ -40,7 +41,8 @@ public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESyst
 
   public SEBloodChemistrySystem()
   {
-    bloodDensity = null;
+    baseExcess = null;
+	bloodDensity = null;
     bloodPH = null;
     bloodSpecificHeat = null;
     bloodUreaNitrogenConcentration = null;
@@ -72,6 +74,8 @@ public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESyst
 
   public void reset()
   {
+    if (baseExcess != null)
+      baseExcess.invalidate();
     if (bloodDensity != null)
       bloodDensity.invalidate();
     if (bloodPH != null)
@@ -131,6 +135,8 @@ public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESyst
 
   public static void load(BloodChemistrySystemData src, SEBloodChemistrySystem dst)
   {
+    if (src.hasBaseExcess())
+      SEScalarAmountPerVolume.load(src.getBaseExcess(),dst.getBaseExcess());
     if (src.hasBloodDensity())
       SEScalarMassPerVolume.load(src.getBloodDensity(),dst.getBloodDensity());
     if (src.hasBloodPH())
@@ -197,6 +203,8 @@ public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESyst
 
   protected static void unload(SEBloodChemistrySystem src, BloodChemistrySystemData.Builder dst)
   {
+    if (src.hasBaseExcess())
+      dst.setBaseExcess(SEScalarAmountPerVolume.unload(src.getBaseExcess()));
     if (src.hasBloodDensity())
       dst.setBloodDensity(SEScalarMassPerVolume.unload(src.getBloodDensity()));
     if (src.hasBloodPH())
@@ -254,6 +262,17 @@ public class SEBloodChemistrySystem extends SEPhysiologySystem implements SESyst
       dst.setVenousCarbonDioxidePressure(SEScalarPressure.unload(src.getVenousCarbonDioxidePressure()));
   }
 
+    public boolean hasBaseExcess()
+  {
+    return baseExcess == null ? false : baseExcess.isValid();
+  }
+  public SEScalarAmountPerVolume getBaseExcess()
+  {
+    if (baseExcess == null)
+      baseExcess = new SEScalarAmountPerVolume();
+    return baseExcess;
+  }
+  
   public boolean hasBloodDensity()
   {
     return bloodDensity == null ? false : bloodDensity.isValid();

engine/cpp/Systems/BloodChemistry.cpp

@@ -296,6 +296,10 @@ void BloodChemistry::Process()
   /// \todo Change system data so that we have ArterialBloodPH (from aorta) and VenousBloodPH (from vena cava)
   GetBloodPH().Set(m_aorta->GetPH());
 
+  // Calculate Base Excess
+  double HCO3_mEq_Per_L = m_aortaBicarbonate->GetMolarity(AmountPerVolumeUnit::mmol_Per_L);
+  GetBaseExcess().SetValue(0.93 * HCO3_mEq_Per_L + 13.77 * m_aorta->GetPH().GetValue() - 124.58, AmountPerVolumeUnit::meq_Per_L);
+
   // Pressures
   // arterial gas partial pressures -  
   GetArterialOxygenPressure().Set(m_aortaO2->GetPartialPressure());

schema/proto/cdm/Physiology.proto

@@ -22,6 +22,7 @@ message PupillaryResponseData
     and will be improved in future releases to include more substances that can provide clinician level details and assessments, such as a CBC and blood panel.*/
 message BloodChemistrySystemData
 {
+  ScalarAmountPerVolumeData           BaseExcess                                     = 28;/**<< @brief Excess or deficit, respectively, in the amount of base present in the blood. */
   ScalarMassPerVolumeData             BloodDensity                                   = 1; /**<< @brief Mass per unit volume of the blood. */
   ScalarData                          BloodPH                                        = 2; /**<< @brief Measure of acidity or basicity of the blood. */
   ScalarHeatCapacitancePerMassData    BloodSpecificHeat                              = 3; /**<< @brief The amount of energy required to raise one kilogram of blood by one degree Celsius. */