source additions for new 6.3 release/support

src/build.properties

@@ -1,4 +1,4 @@
-biogears.version=BioGears_6.1.1-beta
+biogears.version=BioGears_6.3.0-beta
 biogears.home=${basedir}/..
 biogears.bin=${biogears.home}/bin
 biogears.config=release

src/build.xml

@@ -314,10 +314,13 @@
 		<ant antfile="build.xml" dir="${biogears.cdm}" target="jar" /> 
 		<ant antfile="build.xml" dir="${biogears.engine}" target="compile" /> 
 		<ant antfile="build.xml" dir="${biogears.engine}" target="jar" /> 
+		<ant antfile="build.xml" dir="${biogears.gui}" target="compile" /> 
+		<ant antfile="build.xml" dir="${biogears.gui}" target="jar" /> 
 		<!-- Create a jar with all dependencies -->
 		<delete file="../bin/BioGears.jar"/>
 	    <!-- Create the Jar-->
 		<jar destfile="../bin/BioGears.jar" excludes="**/Sun_micr.rsa **/Sun_micr.sf">
+			<zipfileset src="${biogears.bin}/BioGearsGUI.jar" includes="**/*.java **/*.class"/>		
 			<zipfileset src="${biogears.bin}/BioGearsEngine.jar" includes="**/*.java **/*.class"/>	
 			<zipfileset src="${biogears.bin}/CommonDataModel.jar" includes="**/*.java **/*.class"/>
 			<zipfileset src="${biogears.bin}/DataModelBindings.jar" includes="**/*.java **/*.class"/>
@@ -626,6 +629,16 @@
 	<target name="buildSDK-windows" depends="copyToSDK-windows" if="deployWindows">
 		<!-- Make sure howto files compile -->
 		<ant antfile="build.xml" dir="${biogears.SDK}" target="all" /> 
+		<!-- Zip it! -->
+		<delete file="${biogears.deploy}/${biogears.version}-sdk-windows.zip"/>
+		<zip destfile="${biogears.deploy}/${biogears.version}-sdk-windows.zip">
+      <zipfileset dir="${biogears.home}" prefix="${biogears.version}">
+        <include name="LICENSE"/>
+        <include name="NOTICE"/>
+      </zipfileset>
+			<zipfileset dir="${biogears.SDK}" excludes="howto/build/**, /cmake/msvs*/**" prefix="${biogears.version}"/>
+			<zipfileset dir="${biogears.doxy}" includes="html/**, Mainpage.html, ReadMe.txt" prefix="${biogears.version}/docs/"/>
+		</zip>
 	</target>
 	<target name="copyToSDK-windows" if="deployWindows">
 		<!-- Clean out the sdk folder of any previous deployment -->
@@ -959,7 +972,7 @@
         </java>
     </target>   
 
-	<!-- Example for pulling from the build machine : ant rebaseDebug -DrebaseFrom="\\sed-biogears\JenkinsBuild\History\MSVC-x86\374 - b5541f5b6212d8288f1ff35da996110f871292c9\Scenarios" -->
+	<!-- Example for pulling from the build machine : ant rebaseDebug -DrebaseFrom="\\sed-biogears\JenkinsBuild\History\MSVC-x86\387 - aa894de288d5147620c4e0d275fe64d8bd0f1d5f\Scenarios" -->
     <target name="rebaseDebug">
         <java classname="mil.tatrc.physiology.utilities.testing.Rebase" dir="${biogears.bin}" fork="true" failonerror="false">
             <arg value="${rebaseFrom}" unless:blank="${rebaseFrom}"/><!-- From -->

src/cdm/cpp/compartment/tissue/SETissueCompartment.cpp

@@ -27,6 +27,7 @@ SETissueCompartment::SETissueCompartment(const std::string& name, Logger* logger
 {
   m_AcidicPhospohlipidConcentration = nullptr;
   m_MatrixVolume = nullptr;
+  m_MembranePotential = nullptr;
   m_NeutralLipidsVolumeFraction = nullptr;
   m_NeutralPhospholipidsVolumeFraction = nullptr;
   m_TissueToPlasmaAlbuminRatio = nullptr;
@@ -45,6 +46,7 @@ void SETissueCompartment::Clear()
   SECompartment::Clear();
   SAFE_DELETE(m_AcidicPhospohlipidConcentration);
   SAFE_DELETE(m_MatrixVolume);
+  SAFE_DELETE(m_MembranePotential);
   SAFE_DELETE(m_NeutralLipidsVolumeFraction);
   SAFE_DELETE(m_NeutralPhospholipidsVolumeFraction);
   SAFE_DELETE(m_TissueToPlasmaAlbuminRatio);
@@ -61,6 +63,8 @@ bool SETissueCompartment::Load(const CDM::TissueCompartmentData& in, SESubstance
     GetAcidicPhospohlipidConcentration().Load(in.AcidicPhospohlipidConcentration().get());
   if (in.MatrixVolume().present())
     GetMatrixVolume().Load(in.MatrixVolume().get());
+  if (in.MembranePotential().present())
+	  GetMembranePotential().Load(in.MembranePotential().get());
   if (in.NeutralLipidsVolumeFraction().present())
     GetNeutralLipidsVolumeFraction().Load(in.NeutralLipidsVolumeFraction().get());
   if (in.NeutralPhospholipidsVolumeFraction().present())
@@ -89,6 +93,8 @@ void SETissueCompartment::Unload(CDM::TissueCompartmentData& data)
     data.AcidicPhospohlipidConcentration(std::unique_ptr<CDM::ScalarMassPerMassData>(m_AcidicPhospohlipidConcentration->Unload()));
   if (HasMatrixVolume())
     data.MatrixVolume(std::unique_ptr<CDM::ScalarVolumeData>(m_MatrixVolume->Unload())); 
+  if (HasMembranePotential())
+	  data.MembranePotential(std::unique_ptr<CDM::ScalarElectricPotentialData>(m_MembranePotential->Unload()));
   if (HasNeutralLipidsVolumeFraction())
     data.NeutralLipidsVolumeFraction(std::unique_ptr<CDM::ScalarFractionData>(m_NeutralLipidsVolumeFraction->Unload()));
   if (HasNeutralPhospholipidsVolumeFraction())
@@ -111,6 +117,8 @@ const SEScalar* SETissueCompartment::GetScalar(const std::string& name)
     return &GetAcidicPhospohlipidConcentration();
   if (name.compare("MatrixVolume") == 0)
     return &GetMatrixVolume();  
+  if (name.compare("MembranePotential") == 0)
+	  return &GetMembranePotential();
   if (name.compare("NeutralLipidsVolumeFraction") == 0)
     return &GetNeutralLipidsVolumeFraction();
   if (name.compare("NeutralPhospholipidsVolumeFraction") == 0)
@@ -165,6 +173,23 @@ double SETissueCompartment::GetMatrixVolume(const VolumeUnit& unit) const
   return m_MatrixVolume->GetValue(unit);
 }
 
+bool SETissueCompartment::HasMembranePotential() const
+{
+	return m_MembranePotential == nullptr ? false : m_MembranePotential->IsValid();
+}
+SEScalarElectricPotential& SETissueCompartment::GetMembranePotential()
+{
+	if (m_MembranePotential == nullptr)
+		m_MembranePotential = new SEScalarElectricPotential();
+	return *m_MembranePotential;
+}
+double SETissueCompartment::GetMembranePotential(const ElectricPotentialUnit& unit) const
+{
+	if (m_MembranePotential == nullptr)
+		return SEScalar::dNaN();
+	return m_MembranePotential->GetValue(unit);
+}
+
 bool SETissueCompartment::HasNeutralLipidsVolumeFraction() const
 {
   return m_NeutralLipidsVolumeFraction == nullptr ? false : m_NeutralLipidsVolumeFraction->IsValid();

src/cdm/cpp/compartment/tissue/SETissueCompartment.h

@@ -48,6 +48,10 @@ class DLL_DECL SETissueCompartment : public SECompartment
   virtual SEScalarVolume& GetMatrixVolume();
   virtual double GetMatrixVolume(const VolumeUnit& unit) const;
 
+  virtual bool HasMembranePotential() const;
+  virtual SEScalarElectricPotential& GetMembranePotential();
+  virtual double GetMembranePotential(const ElectricPotentialUnit& unit) const;
+
   virtual bool HasNeutralLipidsVolumeFraction() const;
   virtual SEScalarFraction& GetNeutralLipidsVolumeFraction();
   virtual double GetNeutralLipidsVolumeFraction() const;
@@ -76,6 +80,7 @@ class DLL_DECL SETissueCompartment : public SECompartment
 
   SEScalarMassPerMass*   m_AcidicPhospohlipidConcentration;
   SEScalarVolume*        m_MatrixVolume;
+  SEScalarElectricPotential*		m_MembranePotential;
   SEScalarFraction*      m_NeutralLipidsVolumeFraction;
   SEScalarFraction*      m_NeutralPhospholipidsVolumeFraction;
   SEScalar*              m_TissueToPlasmaAlbuminRatio;

src/cdm/cpp/engine/PhysiologyEngineTrack.cpp

@@ -37,6 +37,7 @@ specific language governing permissions and limitations under the License.
 #include "system/physiology/SERenalSystem.h"
 #include "system/physiology/SERespiratorySystem.h"
 #include "system/physiology/SETissueSystem.h"
+#include "system/physiology/SEHepaticSystem.h"
 #include "system/equipment/Anesthesia/SEAnesthesiaMachine.h"
 #include "system/equipment/ElectroCardioGram/SEElectroCardioGram.h"
 #include "system/equipment/Inhaler/SEInhaler.h"
@@ -102,6 +103,9 @@ PhysiologyEngineTrack::PhysiologyEngineTrack(PhysiologyEngine& engine) : Loggabl
   SENervousSystem* nervous = (SENervousSystem*)engine.GetNervousSystem();
   if (nervous != nullptr)
     m_PhysiologySystems.push_back(nervous);
+  SEHepaticSystem* hepatic = (SEHepaticSystem*)engine.GetHepaticSystem();
+  if (hepatic != nullptr)
+    m_PhysiologySystems.push_back(hepatic);
 
   m_Environment = (SEEnvironment*)engine.GetEnvironment();
 
@@ -155,7 +159,7 @@ void PhysiologyEngineTrack::SetupRequests()
 {
   bool isOpen = m_ResultsStream.is_open();
   if (!isOpen || m_ForceConnection)
-  {// Process/Hook up all requests with their associated scalers
+  {// Process/Hook up all requests with their associated scalars
     for (SEDataRequest* dr : m_DataRequestMgr.GetDataRequests())
     {
       if (!TrackRequest(*dr))
@@ -190,7 +194,7 @@ void PhysiologyEngineTrack::PullData()
     if (ds == nullptr)
     {
       Error("You cannot modify CSV Results file data requests in the middle of a run.");
-      Error("Ignorning data request " + dr->GetName());
+      Error("Ignoring data request " + dr->GetName());
       continue;
     }
     if (!ds->HasScalar())

src/cdm/cpp/patient/SEPatient.cpp

@@ -70,6 +70,7 @@ SEPatient::SEPatient(Logger* logger) : Loggable(logger)
 	m_InspiratoryCapacity = nullptr;
 	m_InspiratoryReserveVolume = nullptr;
 	m_LeanBodyMass = nullptr;
+  m_MuscleMass = nullptr;
   m_MeanArterialPressureBaseline = nullptr;
 	m_ResidualVolume = nullptr;
 	m_RespirationRateBaseline = nullptr;
@@ -128,6 +129,7 @@ void SEPatient::Clear()
 	SAFE_DELETE(m_InspiratoryCapacity);
 	SAFE_DELETE(m_InspiratoryReserveVolume);
 	SAFE_DELETE(m_LeanBodyMass);
+  SAFE_DELETE(m_MuscleMass);
   SAFE_DELETE(m_MeanArterialPressureBaseline);
 	SAFE_DELETE(m_ResidualVolume);
 	SAFE_DELETE(m_RespirationRateBaseline);
@@ -176,6 +178,8 @@ const SEScalar* SEPatient::GetScalar(const std::string& name)
 		return &GetInspiratoryReserveVolume();
 	if (name.compare("LeanBodyMass") == 0)
 		return &GetLeanBodyMass();
+  if (name.compare("MuscleMass") == 0)
+    return &GetMuscleMass();
   if (name.compare("MeanArterialPressureBaseline") == 0)
 		return &GetMeanArterialPressureBaseline();
 	if (name.compare("ResidualVolume") == 0)
@@ -240,6 +244,8 @@ bool SEPatient::Load(const CDM::PatientData& in)
     GetInspiratoryReserveVolume().Load(in.InspiratoryReserveVolume().get());
   if (in.LeanBodyMass().present())
 	  GetLeanBodyMass().Load(in.LeanBodyMass().get());
+  if (in.MuscleMass().present())
+    GetMuscleMass().Load(in.MuscleMass().get());
   if(in.MeanArterialPressureBaseline().present())
 		GetMeanArterialPressureBaseline().Load(in.MeanArterialPressureBaseline().get());
 	if (in.ResidualVolume().present())
@@ -318,6 +324,8 @@ void SEPatient::Unload(CDM::PatientData& data) const
 		data.InspiratoryReserveVolume(std::unique_ptr<CDM::ScalarVolumeData>(m_InspiratoryReserveVolume->Unload()));
 	if (m_LeanBodyMass != nullptr)
 		data.LeanBodyMass(std::unique_ptr<CDM::ScalarMassData>(m_LeanBodyMass->Unload()));
+  if (m_MuscleMass != nullptr)
+    data.MuscleMass(std::unique_ptr<CDM::ScalarMassData>(m_MuscleMass->Unload()));
   if(m_MeanArterialPressureBaseline!=nullptr)
 		data.MeanArterialPressureBaseline(std::unique_ptr<CDM::ScalarPressureData>(m_MeanArterialPressureBaseline->Unload())); 
 	if (m_ResidualVolume != nullptr)
@@ -468,6 +476,9 @@ 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::MuscleCatabolism:
+        m_ss << " Patient has begun muscle catabolism";
+        break;
       case CDM::enumPatientEvent::MuscleGlycogenDepleted:
         m_ss << " Patient's muscle glycogen is depleted";
         break;
@@ -496,7 +507,7 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 				m_ss << " Patient has Tachypnea";
 				break;
 			case CDM::enumPatientEvent::Fatigue:
-				m_ss << "Patient has fatigue";
+				m_ss << " Patient has fatigue";
 				break;
 			case CDM::enumPatientEvent::StartOfCardiacCycle:
 			case CDM::enumPatientEvent::StartOfExhale:
@@ -542,7 +553,7 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 				m_ss << " Patient no longer has Diuresis";
 				break;
 			case CDM::enumPatientEvent::Fasciculation:
-				m_ss << "Patient no longer has fasciculations";
+				m_ss << "Patient no longer has Fasciculation";
 				break;
 			case CDM::enumPatientEvent::FunctionalIncontinence:
 				m_ss << " Patient has an empty bladder";
@@ -635,7 +646,7 @@ void SEPatient::SetEvent(CDM::enumPatientEvent::value type, bool active, const S
 				m_ss << " Patient no longer has Tachypnea";
 				break;
 			case CDM::enumPatientEvent::Fatigue:
-				m_ss << "Patient is no longer fatigued";
+				m_ss << " Patient is no longer fatigued";
 				break;
 			case CDM::enumPatientEvent::StartOfCardiacCycle:
 			case CDM::enumPatientEvent::StartOfExhale:
@@ -1005,6 +1016,23 @@ double SEPatient::GetLeanBodyMass(const MassUnit& unit) const
 	return m_LeanBodyMass->GetValue(unit);
 }
 
+bool SEPatient::HasMuscleMass() const
+{
+  return m_MuscleMass == nullptr ? false : m_MuscleMass->IsValid();
+}
+SEScalarMass& SEPatient::GetMuscleMass()
+{
+  if (m_MuscleMass == nullptr)
+    m_MuscleMass = new SEScalarMass();
+  return *m_MuscleMass;
+}
+double SEPatient::GetMuscleMass(const MassUnit& unit) const
+{
+  if (m_MuscleMass == nullptr)
+    return SEScalar::dNaN();
+  return m_MuscleMass->GetValue(unit);
+}
+
 bool SEPatient::HasMeanArterialPressureBaseline() const
 {
 	return m_MeanArterialPressureBaseline==nullptr?false:m_MeanArterialPressureBaseline->IsValid();

src/cdm/cpp/patient/SEPatient.h

@@ -136,6 +136,10 @@ class DLL_DECL SEPatient : public Loggable
   virtual SEScalarMass& GetLeanBodyMass();
   virtual double GetLeanBodyMass(const MassUnit& unit) const;
 
+  virtual bool HasMuscleMass() const;
+  virtual SEScalarMass& GetMuscleMass();
+  virtual double GetMuscleMass(const MassUnit& unit) const;
+
 	virtual bool HasMeanArterialPressureBaseline() const;
 	virtual SEScalarPressure& GetMeanArterialPressureBaseline();
   virtual double GetMeanArterialPressureBaseline(const PressureUnit& unit) const;		
@@ -187,6 +191,7 @@ class DLL_DECL SEPatient : public Loggable
   SEScalarMassPerVolume*     m_BodyDensity;
   SEScalarFraction*		       m_BodyFatFraction;
   SEScalarMass*              m_LeanBodyMass;
+  SEScalarMass*              m_MuscleMass;
 
   SEScalarArea*              m_AlveoliSurfaceArea;
   SEScalarFraction*          m_RightLungRatio;