Update Java with new respiratory properties

Fix testing for new patient setup

cdm/java/com/kitware/physiology/datamodel/system/physiology/SERespiratorySystem.java

@@ -21,11 +21,14 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
   protected SEScalar0To1                  endTidalOxygenFraction;
   protected SEScalarPressure              endTidalOxygenPressure;
   protected SEScalarVolumePerTime         expiratoryFlow;
+  protected SEScalarPressureTimePerVolume expiratoryPulmonaryResistance;
   protected SEScalarPower                 imposedPowerOfBreathing;
   protected SEScalarEnergy                imposedWorkOfBreathing;
   protected SEScalar                      inspiratoryExpiratoryRatio;
   protected SEScalarVolumePerTime         inspiratoryFlow;
+  protected SEScalarPressureTimePerVolume inspiratoryPulmonaryResistance;
   protected SEScalarPressure              intrapleuralPressure;
+  protected SEScalarPressure              intrapulmonaryPressure;
   protected SEScalarVolumePerPressure     lungCompliance;
   protected SEScalarPressure              maximalInspiratoryPressure;
   protected SEScalarPower                 patientPowerOfBreathing;
@@ -35,7 +38,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
   protected SEScalarPressure              positiveEndExpiratoryPressure;
   protected SEScalarVolumePerPressure     pulmonaryCompliance;
   protected SEScalarPressurePerVolume     pulmonaryElastance;
-  protected SEScalarPressureTimePerVolume pulmonaryResistance;
   protected SEScalarEnergy                resistiveExpiratoryWorkOfBreathing;
   protected SEScalarEnergy                resistiveInspiratoryWorkOfBreathing;
   protected SEScalarFrequency             respirationRate;
@@ -52,6 +54,7 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
   protected SEScalarPressure              transairwayPressure;
   protected SEScalarPressure              transalveolarPressure;
   protected SEScalarPressure              transChestWallPressure;
+  protected SEScalarPressure              transMusclePressure;
   protected SEScalarPressure              transpulmonaryPressure;
   protected SEScalarPressure              transrespiratoryPressure;
   protected SEScalarPressure              transthoracicPressure;
@@ -70,11 +73,14 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     endTidalOxygenFraction = null;
     endTidalOxygenPressure = null;
     expiratoryFlow = null;
+    expiratoryPulmonaryResistance = null;
     imposedPowerOfBreathing = null;
     imposedWorkOfBreathing = null;
     inspiratoryExpiratoryRatio = null;
     inspiratoryFlow = null;
+    inspiratoryPulmonaryResistance = null;
     intrapleuralPressure = null;
+    intrapulmonaryPressure = null;
     lungCompliance = null;
     maximalInspiratoryPressure = null;
     patientPowerOfBreathing = null;
@@ -84,7 +90,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     positiveEndExpiratoryPressure = null;
     pulmonaryCompliance = null;
     pulmonaryElastance = null;
-    pulmonaryResistance = null;
     resistiveExpiratoryWorkOfBreathing = null;
     resistiveInspiratoryWorkOfBreathing = null;
     respirationRate = null;
@@ -101,6 +106,7 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     transairwayPressure = null;
     transalveolarPressure = null;
     transChestWallPressure = null;
+    transMusclePressure = null;
     transpulmonaryPressure = null;
     transrespiratoryPressure = null;
     transthoracicPressure = null;
@@ -130,6 +136,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       endTidalOxygenPressure.invalidate();
     if (expiratoryFlow != null)
       expiratoryFlow.invalidate();
+    if (expiratoryPulmonaryResistance != null)
+      expiratoryPulmonaryResistance.invalidate();
     if (imposedPowerOfBreathing != null)
       imposedPowerOfBreathing.invalidate();
     if (imposedWorkOfBreathing != null)
@@ -138,8 +146,12 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       inspiratoryExpiratoryRatio.invalidate();
     if (inspiratoryFlow != null)
       inspiratoryFlow.invalidate();
+    if (inspiratoryPulmonaryResistance != null)
+      inspiratoryPulmonaryResistance.invalidate();
     if (intrapleuralPressure != null)
       intrapleuralPressure.invalidate();
+    if (intrapulmonaryPressure != null)
+      intrapulmonaryPressure.invalidate();
     if (lungCompliance != null)
       lungCompliance.invalidate();
     if (maximalInspiratoryPressure != null)
@@ -158,8 +170,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       pulmonaryCompliance.invalidate();
     if (pulmonaryElastance != null)
       pulmonaryElastance.invalidate();
-    if (pulmonaryResistance != null)
-      pulmonaryResistance.invalidate();
     if (resistiveExpiratoryWorkOfBreathing != null)
       resistiveExpiratoryWorkOfBreathing.invalidate();
     if (resistiveInspiratoryWorkOfBreathing != null)
@@ -192,6 +202,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       transalveolarPressure.invalidate();
     if (transChestWallPressure != null)
       transChestWallPressure.invalidate();
+    if (transMusclePressure != null)
+      transMusclePressure.invalidate();
     if (transpulmonaryPressure != null)
       transpulmonaryPressure.invalidate();
     if (transrespiratoryPressure != null)
@@ -224,6 +236,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       SEScalarPressure.load(src.getEndTidalOxygenPressure(),dst.getEndTidalOxygenPressure());
     if (src.hasExpiratoryFlow())
       SEScalarVolumePerTime.load(src.getExpiratoryFlow(),dst.getExpiratoryFlow());
+    if (src.hasExpiratoryPulmonaryResistance())
+      SEScalarPressureTimePerVolume.load(src.getExpiratoryPulmonaryResistance(),dst.getExpiratoryPulmonaryResistance()); 
     if (src.hasImposedPowerOfBreathing())
       SEScalarPower.load(src.getImposedPowerOfBreathing(),dst.getImposedPowerOfBreathing()); 
     if (src.hasImposedWorkOfBreathing())
@@ -232,8 +246,12 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       SEScalar.load(src.getInspiratoryExpiratoryRatio(),dst.getInspiratoryExpiratoryRatio()); 
     if (src.hasInspiratoryFlow())
       SEScalarVolumePerTime.load(src.getInspiratoryFlow(),dst.getInspiratoryFlow()); 
+    if (src.hasInspiratoryPulmonaryResistance())
+      SEScalarPressureTimePerVolume.load(src.getInspiratoryPulmonaryResistance(),dst.getInspiratoryPulmonaryResistance()); 
     if (src.hasIntrapleuralPressure())
-      SEScalarPressure.load(src.getIntrapleuralPressure(),dst.getIntrapleuralPressure()); 
+      SEScalarPressure.load(src.getIntrapleuralPressure(),dst.getIntrapleuralPressure());
+    if (src.hasIntrapulmonaryPressure())
+      SEScalarPressure.load(src.getIntrapulmonaryPressure(),dst.getIntrapulmonaryPressure()); 
     if (src.hasLungCompliance())
       SEScalarVolumePerPressure.load(src.getLungCompliance(),dst.getLungCompliance()); 
     if (src.hasMaximalInspiratoryPressure())
@@ -252,8 +270,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       SEScalarVolumePerPressure.load(src.getPulmonaryCompliance(),dst.getPulmonaryCompliance()); 
     if (src.hasPulmonaryElastance())
       SEScalarPressurePerVolume.load(src.getPulmonaryElastance(),dst.getPulmonaryElastance()); 
-    if (src.hasPulmonaryResistance())
-      SEScalarPressureTimePerVolume.load(src.getPulmonaryResistance(),dst.getPulmonaryResistance()); 
     if (src.hasResistiveExpiratoryWorkOfBreathing())
       SEScalarEnergy.load(src.getResistiveExpiratoryWorkOfBreathing(),dst.getResistiveExpiratoryWorkOfBreathing()); 
     if (src.hasResistiveInspiratoryWorkOfBreathing())
@@ -286,6 +302,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       SEScalarPressure.load(src.getTransalveolarPressure(),dst.getTransalveolarPressure());
     if (src.hasTransChestWallPressure())
       SEScalarPressure.load(src.getTransChestWallPressure(),dst.getTransChestWallPressure());
+    if (src.hasTransMusclePressure())
+      SEScalarPressure.load(src.getTransMusclePressure(),dst.getTransMusclePressure());
     if (src.hasTranspulmonaryPressure())
       SEScalarPressure.load(src.getTranspulmonaryPressure(),dst.getTranspulmonaryPressure());
     if (src.hasTransrespiratoryPressure())
@@ -325,6 +343,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       dst.setEndTidalOxygenPressure(SEScalarPressure.unload(src.getEndTidalOxygenPressure())); 
     if (src.hasExpiratoryFlow())
       dst.setExpiratoryFlow(SEScalarVolumePerTime.unload(src.getExpiratoryFlow()));
+    if (src.hasExpiratoryPulmonaryResistance())
+      dst.setExpiratoryPulmonaryResistance(SEScalarPressureTimePerVolume.unload(src.getExpiratoryPulmonaryResistance()));
     if (src.hasImposedPowerOfBreathing())
       dst.setImposedPowerOfBreathing(SEScalarPower.unload(src.getImposedPowerOfBreathing()));
     if (src.hasImposedWorkOfBreathing())
@@ -333,8 +353,12 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       dst.setInspiratoryExpiratoryRatio(SEScalar.unload(src.getInspiratoryExpiratoryRatio()));
     if (src.hasInspiratoryFlow())
       dst.setInspiratoryFlow(SEScalarVolumePerTime.unload(src.getInspiratoryFlow()));
+    if (src.hasInspiratoryPulmonaryResistance())
+      dst.setInspiratoryPulmonaryResistance(SEScalarPressureTimePerVolume.unload(src.getInspiratoryPulmonaryResistance()));
     if (src.hasIntrapleuralPressure())
       dst.setIntrapleuralPressure(SEScalarPressure.unload(src.getIntrapleuralPressure()));
+    if (src.hasIntrapulmonaryPressure())
+      dst.setIntrapulmonaryPressure(SEScalarPressure.unload(src.getIntrapulmonaryPressure()));
     if (src.hasLungCompliance())
       dst.setLungCompliance(SEScalarVolumePerPressure.unload(src.getLungCompliance()));
     if (src.hasMaximalInspiratoryPressure())
@@ -353,8 +377,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       dst.setPulmonaryCompliance(SEScalarVolumePerPressure.unload(src.getPulmonaryCompliance()));
     if (src.hasPulmonaryElastance())
         dst.setPulmonaryElastance(SEScalarPressurePerVolume.unload(src.getPulmonaryElastance()));
-    if (src.hasPulmonaryResistance())
-      dst.setPulmonaryResistance(SEScalarPressureTimePerVolume.unload(src.getPulmonaryResistance()));
     if (src.hasResistiveExpiratoryWorkOfBreathing())
       dst.setResistiveExpiratoryWorkOfBreathing(SEScalarEnergy.unload(src.getResistiveExpiratoryWorkOfBreathing()));
     if (src.hasResistiveInspiratoryWorkOfBreathing())
@@ -387,6 +409,8 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       dst.setTransalveolarPressure(SEScalarPressure.unload(src.getTransalveolarPressure()));
     if (src.hasTransChestWallPressure())
       dst.setTransChestWallPressure(SEScalarPressure.unload(src.getTransChestWallPressure()));
+    if (src.hasTransMusclePressure())
+      dst.setTransMusclePressure(SEScalarPressure.unload(src.getTransMusclePressure()));
     if (src.hasTranspulmonaryPressure())
       dst.setTranspulmonaryPressure(SEScalarPressure.unload(src.getTranspulmonaryPressure()));
     if (src.hasTransrespiratoryPressure())
@@ -516,6 +540,18 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     return expiratoryFlow;
   }
 
+  public boolean hasExpiratoryPulmonaryResistance()
+  {
+    return expiratoryPulmonaryResistance == null ? false : expiratoryPulmonaryResistance.isValid();
+  }
+  public SEScalarPressureTimePerVolume getExpiratoryPulmonaryResistance()
+  {
+    if (expiratoryPulmonaryResistance == null)
+      expiratoryPulmonaryResistance = new SEScalarPressureTimePerVolume();
+    return expiratoryPulmonaryResistance;
+  }
+  
+
   public boolean hasImposedPowerOfBreathing()
   {
     return imposedPowerOfBreathing == null ? false : imposedPowerOfBreathing.isValid();
@@ -560,6 +596,17 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     return inspiratoryFlow;
   }
   
+  public boolean hasInspiratoryPulmonaryResistance()
+  {
+    return inspiratoryPulmonaryResistance == null ? false : inspiratoryPulmonaryResistance.isValid();
+  }
+  public SEScalarPressureTimePerVolume getInspiratoryPulmonaryResistance()
+  {
+    if (inspiratoryPulmonaryResistance == null)
+      inspiratoryPulmonaryResistance = new SEScalarPressureTimePerVolume();
+    return inspiratoryPulmonaryResistance;
+  }
+  
   public boolean hasIntrapleuralPressure()
   {
     return intrapleuralPressure == null ? false : intrapleuralPressure.isValid();
@@ -571,6 +618,17 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     return intrapleuralPressure;
   }
   
+  public boolean hasIntrapulmonaryPressure()
+  {
+    return intrapulmonaryPressure == null ? false : intrapulmonaryPressure.isValid();
+  }
+  public SEScalarPressure getIntrapulmonaryPressure()
+  {
+    if (intrapulmonaryPressure == null)
+      intrapulmonaryPressure = new SEScalarPressure();
+    return intrapulmonaryPressure;
+  }
+  
   public boolean hasLungCompliance()
   {
     return lungCompliance == null ? false : lungCompliance.isValid();
@@ -661,7 +719,7 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
 
   public boolean hasPulmonaryElastance()
   {
-    return pulmonaryElastance == null ? false : pulmonaryResistance.isValid();
+    return pulmonaryElastance == null ? false : pulmonaryElastance.isValid();
   }
   public SEScalarPressurePerVolume getPulmonaryElastance()
   {
@@ -669,17 +727,6 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
       pulmonaryElastance = new SEScalarPressurePerVolume();
     return pulmonaryElastance;
   }
-
-  public boolean hasPulmonaryResistance()
-  {
-    return pulmonaryResistance == null ? false : pulmonaryResistance.isValid();
-  }
-  public SEScalarPressureTimePerVolume getPulmonaryResistance()
-  {
-    if (pulmonaryResistance == null)
-      pulmonaryResistance = new SEScalarPressureTimePerVolume();
-    return pulmonaryResistance;
-  }
   
   public boolean hasResistiveExpiratoryWorkOfBreathing()
   {
@@ -857,6 +904,17 @@ public class SERespiratorySystem extends SEPhysiologySystem implements SESystem
     return transChestWallPressure;
   }
 
+  public boolean hasTransMusclePressure()
+  {
+    return transMusclePressure == null ? false : transMusclePressure.isValid();
+  }
+  public SEScalarPressure getTransMusclePressure()
+  {
+    if (transMusclePressure == null)
+      transMusclePressure = new SEScalarPressure();
+    return transMusclePressure;
+  }
+
   public boolean hasTranspulmonaryPressure()
   {
     return transpulmonaryPressure == null ? false : transpulmonaryPressure.isValid();

engine/cpp/controller/Controller.cpp

@@ -148,11 +148,11 @@ DataTrack& PulseController::GetDataTrack()
   return *m_DataTrack;
 }
 
-bool PulseController::Initialize(const PulseConfiguration* config)
+bool PulseController::Initialize(const PulseConfiguration* config, SEPatient const& patient)
 {
   m_State = EngineState::NotReady;
   Info("Configuring patient");
-  if (!SetupPatient())
+  if (!SetupPatient(patient))
     return false;
 
   Info("Resetting Substances");
@@ -286,10 +286,12 @@ void PulseController::SetIntubation(eSwitch s)
 }
 eSwitch PulseController::GetIntubation() { return m_Intubation; }
 
-bool PulseController::SetupPatient()
+
+bool PulseController::SetupPatient(SEPatient const& patient)
 {
   bool err = false;
   std::stringstream ss;
+  m_InitialPatient->Copy(patient);
 
   //Sex is the only thing we absolutely need to be defined, the CDM assumes male if not provided
 

engine/cpp/controller/Controller.h

@@ -131,8 +131,8 @@ protected:
   void SetupExternalTemperature();
   void SetupInternalTemperature();
 
-  bool Initialize(const PulseConfiguration* config);
-  bool SetupPatient();
+  bool Initialize(const PulseConfiguration* config, const SEPatient& patient);
+  bool SetupPatient(const SEPatient& patient);
 
   // Notify systems that steady state has been achieved
   virtual void AtSteadyState(EngineState state);

engine/cpp/controller/Engine.cpp

@@ -122,22 +122,6 @@ bool PulseEngine::InitializeEngine(const std::string& patient_configuration, Ser
 
 bool PulseEngine::InitializeEngine(const SEPatientConfiguration& patient_configuration, const SEEngineConfiguration* config)
 {
-  if (patient_configuration.HasPatient())
-    m_InitialPatient->Copy(*patient_configuration.GetPatient());
-  else if (patient_configuration.HasPatientFile())
-  {
-    std::string pFile = patient_configuration.GetPatientFile();
-    if (pFile.find("/patients") == std::string::npos)
-    {// Prepend the patient directory if it's not there
-      pFile = "./patients/";
-      pFile += patient_configuration.GetPatientFile();
-    }
-    if (!m_InitialPatient->SerializeFromFile(pFile, JSON))// TODO Support all serialization formats
-      return false;
-  }
-  else
-    return false;
-
   const PulseConfiguration* pConfig = nullptr;
   if (config != nullptr)
   {
@@ -150,7 +134,26 @@ bool PulseEngine::InitializeEngine(const SEPatientConfiguration& patient_configu
   }
   m_EngineTrack->ResetFile();
   m_State = EngineState::Initialization;
-  if (!PulseController::Initialize(pConfig))
+  if (patient_configuration.HasPatient())
+  {
+    if (!PulseController::Initialize(pConfig, *patient_configuration.GetPatient()))
+      return false;
+  }
+  else if (patient_configuration.HasPatientFile())
+  {
+    SEPatient patient(m_Logger);
+    std::string pFile = patient_configuration.GetPatientFile();
+    if (pFile.find("/patients") == std::string::npos)
+    {// Prepend the patient directory if it's not there
+      pFile = "./patients/";
+      pFile += patient_configuration.GetPatientFile();
+    }
+    if (!patient.SerializeFromFile(pFile, JSON))// TODO Support all serialization formats
+      return false;
+    if (!PulseController::Initialize(pConfig, patient))
+      return false;
+  }
+  else
     return false;
 
   // We don't capture events during initialization

test/engine/cpp/AerosolTest.cpp

@@ -260,8 +260,9 @@ void PulseEngineTest::DepositionFractionTest(SETestSuite& suite, SESubstance& su
   tc.SetName(substance.GetName()+"DepositionFraction");
 
   PulseController pc(m_Logger);
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();

test/engine/cpp/AnesthesiaCircuit.cpp

@@ -50,8 +50,9 @@ void PulseEngineTest::AnesthesiaMachineCircuitAndTransportTest(RespiratoryConfig
   std::ofstream fileGraph;
   
   PulseController pc(sTestDirectory + "/AnesthesiaMachineCircuitAndTransportTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();

test/engine/cpp/CardiovascularCircuit.cpp

@@ -131,10 +131,9 @@ void PulseEngineTest::TuneCardiovascularCircuitTest(SETestSuite& testSuite, cons
   timer.Start("TestCase");
   PulseController pc(testSuite.GetLogger());
   testSuite.GetLogger()->Info("Running " + sTestName);
-  pc.GetPatient().Copy(patient);
   pc.m_Config->EnableRenal(eSwitch::On);
   pc.m_Config->EnableTissue(eSwitch::On);
-  pc.SetupPatient();
+  pc.SetupPatient(patient);
   pc.CreateCircuitsAndCompartments();
 
   SETestCase& testCase = testSuite.CreateTestCase();
@@ -195,13 +194,14 @@ void PulseEngineTest::CardiovascularCircuitAndTransportTest(CardiovascularDriver
   double binding_s = 0;
   PulseController pc(sTestDirectory + "/" + tName.str() + "CircuitAndTransportTest.log");
   pc.GetLogger()->Info("Running " + tName.str());
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   if (heartRate_bpm <= 0)
-    heartRate_bpm = pc.GetPatient().GetHeartRateBaseline().GetValue(FrequencyUnit::Per_min);
+    heartRate_bpm = pc.GetCurrentPatient().GetHeartRateBaseline(FrequencyUnit::Per_min);
   else
   {
-    pc.GetPatient().GetHeartRateBaseline().SetValue(heartRate_bpm, FrequencyUnit::Per_min);
+    pc.GetCurrentPatient().GetHeartRateBaseline().SetValue(heartRate_bpm, FrequencyUnit::Per_min);
   }
 
   pc.m_Config->EnableRenal(connectRenal ? eSwitch::On : eSwitch::Off);

test/engine/cpp/FourCompartmentTest.cpp

@@ -85,8 +85,9 @@ void PulseEngineTest::FourCompartmentTest(bool usingAcidBase, bool usingProducti
   SEFluidCircuitCalculator calc(VolumePerPressureUnit::mL_Per_mmHg, VolumePerTimeUnit::mL_Per_s, PressureTimeSquaredPerVolumeUnit::mmHg_s2_Per_mL, PressureUnit::mmHg, VolumeUnit::mL, PressureTimePerVolumeUnit::mmHg_s_Per_mL, m_Logger);
   PulseController pc(m_Logger);
   Tissue& tsu = (Tissue&)pc.GetTissue();
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();

test/engine/cpp/NervousTests.cpp

@@ -66,8 +66,9 @@ void PulseEngineTest::BrainInjuryTest(const std::string& sTestDirectory)
 
   PulseController pc(sTestDirectory + "/" + tName + ".log");
   pc.GetLogger()->Info("Running " + tName);
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
 
   //Renal and Tissue are on
   pc.m_Config->EnableRenal(eSwitch::On);

test/engine/cpp/RenalCircuit.cpp

@@ -48,8 +48,9 @@ void PulseEngineTest::RenalCircuitAndTransportTest(const std::string& sTestDirec
   std::ofstream graphFile;
 
   PulseController pc(sTestDirectory + "/RenalCircuitAndTransportTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json",JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::On);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -174,8 +175,9 @@ void PulseEngineTest::RenalFeedbackTest(RenalFeedback feedback, const std::strin
   TimingProfile tmr;
   tmr.Start("Test");
   PulseController pc(sTestDirectory + "/RenalFeedbackTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::On);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -189,7 +191,6 @@ void PulseEngineTest::RenalFeedbackTest(RenalFeedback feedback, const std::strin
   pc.GetCompartments().CreateLiquidCompartment(pulse::ExtravascularCompartment::RightKidneyIntracellular);
   pc.m_Config->EnableTissue(eSwitch::On);// This needs to be on for making the tissue to extravascular mapping
   pc.GetCompartments().StateChange();
-  SEPatient* patient = (SEPatient*)&pc.GetPatient();
 
   SEFluidCircuit& rCircuit = pc.GetCircuits().GetRenalCircuit();
   SELiquidCompartmentGraph& rGraph = pc.GetCompartments().GetRenalGraph();
@@ -489,8 +490,9 @@ void PulseEngineTest::RenalSystemTest(RenalSystems systemtest, const std::string
   TimingProfile tmr;
   tmr.Start("Test");
   PulseController pc(sTestDirectory + "/RenalSystemTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::On);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -504,7 +506,6 @@ void PulseEngineTest::RenalSystemTest(RenalSystems systemtest, const std::string
   pc.GetCompartments().CreateLiquidCompartment(pulse::ExtravascularCompartment::RightKidneyIntracellular);
   pc.m_Config->EnableTissue(eSwitch::On);// This needs to be on for making the tissue to extravascular mapping
   pc.GetCompartments().StateChange();
-  SEPatient* patient = (SEPatient*)&pc.GetPatient();
   SESubstance& potassium = pc.GetSubstances().GetPotassium();
 
   // Renal needs these present for Gluconeogenesis

test/engine/cpp/RespiratoryCircuit.cpp

@@ -45,8 +45,9 @@ void PulseEngineTest::RespiratoryCircuitAndTransportTest(RespiratoryConfiguratio
   std::ofstream fAerosolGraph;
 
   PulseController pc(sTestDirectory + "/RespiratoryCircuitAndTransportTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off); 
   pc.CreateCircuitsAndCompartments();
@@ -206,8 +207,9 @@ void PulseEngineTest::RespiratoryDriverTest(const std::string& sTestDirectory)
   TimingProfile tmr;
   tmr.Start("Test");
   PulseController pc(sTestDirectory + "/RespiratoryDriverTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -276,7 +278,7 @@ void PulseEngineTest::RespiratoryDriverTest(const std::string& sTestDirectory)
       //Check to see if the circuit has stabilized
       if (std::abs(TotalVolume_L - PreviousTotalVolume_L) < 1e-10)
       {
-        if (!bRVReached && TotalVolume_L <= pc.GetPatient().GetResidualVolume(VolumeUnit::L))
+        if (!bRVReached && TotalVolume_L <= pc.GetCurrentPatient().GetResidualVolume(VolumeUnit::L))
         {
           bRVReached = true;
         }
@@ -316,7 +318,7 @@ void PulseEngineTest::RespiratoryDriverTest(const std::string& sTestDirectory)
     bSettled = false;
 
     //Check to see if we've gone all the way to the max volume
-    if (TotalVolume_L >= pc.GetPatient().GetTotalLungCapacity(VolumeUnit::L))
+    if (TotalVolume_L >= pc.GetCurrentPatient().GetTotalLungCapacity(VolumeUnit::L))
     {
       bIRVReached = true;
     }

test/engine/cpp/SolverTests.cpp

@@ -45,8 +45,9 @@ void PulseEngineTest::SolverSpeedTest(const std::string& rptDirectory)
   bool showAllOutput = true; //toggle this to show all Info outputs for all circuits, which will show first-pass solve times and fail rates
 
   PulseController pc(tsSolverSpeed.GetLogger());
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::On);
   pc.m_Config->EnableTissue(eSwitch::On);
   pc.CreateCircuitsAndCompartments();

test/engine/cpp/TemperatureCircuit.cpp

@@ -37,8 +37,9 @@
 void PulseEngineTest::InternalTemperatureVariableBMRCircuitTest(const std::string& sTestDirectory)
 {
   PulseController pc(sTestDirectory + "/InternalTemperatureVariableBMRCircuitTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -111,8 +112,9 @@ void PulseEngineTest::InternalTemperatureVariableBMRCircuitTest(const std::strin
 void PulseEngineTest::InternalTemperatureVariableSkinCircuitTest(const std::string& sTestDirectory)
 {
   PulseController pc(sTestDirectory + "/InternalTemperatureVariableSkinCircuitTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);
+  pc.SetupPatient(patient);
   pc.m_Config->EnableRenal(eSwitch::Off);
   pc.m_Config->EnableTissue(eSwitch::Off);
   pc.CreateCircuitsAndCompartments();
@@ -208,8 +210,9 @@ void PulseEngineTest::InternalTemperatureVariableSkinCircuitTest(const std::stri
 void PulseEngineTest::InternalTemperatureVariableCoreCircuitTest(const std::string& sTestDirectory)
 {
   PulseController pc(sTestDirectory + "/InternalTemperatureVariableCoreCircuitTest.log");
-  pc.GetPatient().SerializeFromFile("./patients/StandardMale.json",JSON);
-  pc.SetupPatient();
+  SEPatient patient(pc.GetLogger());
+  patient.SerializeFromFile("./patients/StandardMale.json", JSON);