Updating SDK examples to support new functionality for 6.3 release

Author: ajbaird

library/src/BioGearsEngineHowTo.cpp

@@ -16,29 +16,33 @@ specific language governing permissions and limitations under the License.
 #include "scenario/requests/SEDataRequest.h"
 #include "properties/SEScalarTime.h"
 
+
 int main()
 {
   // Uncomment a method to execute fuctionality!
 
-	//HowToEngineUse();
-  //HowToCreateAPatient();
-
-	//HowToAirwayObstruction();
-	//HowToAnesthesiaMachine();
-	//HowToAsthmaAttack();
-  //HowToBrainInjury();
-	//HowToBolusDrug();
-	//HowToConsumeNutrients();
-	//HowToCOPD();
-	//HowToCPR(); 
-	//HowToEnvironmentChange();
-	//HowToExercise();
-	//HowToHemorrhage();
-	//HowToLobarPneumonia();
-  HowToMechanicalVentilation();
-	//HowToPulmonaryFunctionTest();
-  //HowToSmoke();
-	//HowToTensionPneumothorax();
+//HowToEngineUse();
+//HowToCreateAPatient();
+//HowToAirwayObstruction();
+//HowToAnesthesiaMachine();
+//HowToAsthmaAttack();
+//HowToBrainInjury();
+//HowToBolusDrug();
+//HowToConsumeNutrients();
+//HowToCOPD();
+//HowToCPR(); 
+//HowToEnvironmentChange();
+//HowToExercise();
+//HowToFasciculation();
+//HowToHemorrhage();
+//HowToInfusionDrug();
+//HowToLobarPneumonia();
+//HowToMechanicalVentilation();
+//HowToPulmonaryFunctionTest();
+//HowToSarinExposure();
+//HowToSmoke();
+//HowToTensionPneumothorax();
+HowToVasopressinShockTherapy();
 
   // This one does not really run, is a pure example
   //HowToRunScenario();

library/src/BioGearsEngineHowTo.h

@@ -31,12 +31,16 @@ void HowToCOPD();
 void HowToCPR();
 void HowToEnvironmentChange();
 void HowToExercise();
+void HowToFasciculation();
 void HowToHemorrhage();
+void HowToInfusionDrug();
 void HowToLobarPneumonia();
 void HowToMechanicalVentilation();
 void HowToPulmonaryFunctionTest();
+void HowToSarinExposure();
 void HowToSmoke();
 void HowToTensionPneumothorax();
+void HowToVasopressinShockTherapy();
 
 void HowToConcurrentEngines();
 void HowToRunScenario();

library/src/HowTo-BolusDrug.cpp

@@ -15,10 +15,12 @@ specific language governing permissions and limitations under the License.
 // Include the various types you will be using in your code
 #include "utils/SEEventHandler.h"
 #include "patient/actions/SESubstanceBolus.h"
+#include "patient/actions/SESubstanceInfusion.h"
 #include "system/physiology/SEBloodChemistrySystem.h"
 #include "system/physiology/SECardiovascularSystem.h"
 #include "system/physiology/SEEnergySystem.h"
 #include "system/physiology/SERespiratorySystem.h"
+#include "system/physiology/SEDrugSystem.h"
 #include "substance/SESubstanceManager.h"
 #include "patient/SEPatient.h"
 #include "properties/SEScalarFraction.h"
@@ -28,9 +30,10 @@ specific language governing permissions and limitations under the License.
 #include "properties/SEScalarTemperature.h"
 #include "properties/SEScalarTime.h"
 #include "properties/SEScalarVolume.h"
+#include "properties/SEScalarMass.h"
 #include "properties/SEScalarVolumePerTime.h"
+#include "properties/SEScalarOsmolality.h"
 #include "engine/PhysiologyEngineTrack.h"
-#include "compartment/SECompartmentManager.h"
 
 //--------------------------------------------------------------------------------------------------
 /// \brief

library/src/HowTo-Fasciculation.cpp

@@ -0,0 +1,106 @@
+/**************************************************************************************
+Copyright 2015 Applied Research Associates, Inc.
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use
+this file except in compliance with the License. You may obtain a copy of the License
+at:
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software distributed under
+the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.
+**************************************************************************************/
+
+#include "BioGearsEngineHowTo.h"
+
+// Include the various types you will be using in your code
+#include "patient/actions/SEExercise.h"
+#include "patient/SEPatient.h"
+#include "system/physiology/SEBloodChemistrySystem.h"
+#include "system/physiology/SECardiovascularSystem.h"
+#include "system/physiology/SEEnergySystem.h"
+#include "system/physiology/SERespiratorySystem.h"
+#include "substance/SESubstanceManager.h"
+#include "substance/SESubstanceCompound.h"
+#include "properties/SEScalarAmountPerVolume.h"
+#include "properties/SEScalarFraction.h"
+#include "properties/SEScalarFrequency.h"
+#include "properties/SEScalarMass.h"
+#include "properties/SEScalarMassPerVolume.h"
+#include "properties/SEScalarPressure.h"
+#include "properties/SEScalarTemperature.h"
+#include "properties/SEScalarTime.h"
+#include "properties/SEScalarVolume.h"
+#include "properties/SEScalarVolumePerTime.h"
+#include "properties/SEScalarPower.h"
+#include "properties/SEScalar0To1.h"
+#include "engine/PhysiologyEngineTrack.h"
+#include "compartment/SECompartmentManager.h"
+
+//--------------------------------------------------------------------------------------------------
+/// \brief
+/// Demonstrates how to set concentrations of ionic compounds in bloodstream and tissue and call events
+/// based on changes in concentrations
+///
+/// \details
+/// Refer to the SEEnvironmentChange class
+/// Refer to the SEDrug Class
+//--------------------------------------------------------------------------------------------------
+
+void HowToFasciculation()
+{
+	// Create the engine and load the patient
+	std::unique_ptr<PhysiologyEngine> bg = CreateBioGearsEngine("HowToFasciculation.log");
+	bg->GetLogger()->Info("HowToFasciculation");
+
+	if (!bg->LoadState("./states/[email protected]"))
+	{
+		bg->GetLogger()->Error("Could not load state, check the error");
+		return;
+	}
+
+	//---Initialize all variables needed for scenario
+	SESubstance* Na = bg->GetSubstanceManager().GetSubstance("Sodium");
+	SESubstance* K = bg->GetSubstanceManager().GetSubstance("Potassium");
+	SESubstance* Cl = bg->GetSubstanceManager().GetSubstance("Chloride");
+	SESubstance* Ca = bg->GetSubstanceManager().GetSubstance("Calcium");
+
+	double monitorTime = 200.0;			//how long we're going to be on the look out for ion imbalances in the blood
+	CDM::enumOnOff::value lowKActive;
+	lowKActive = CDM::enumOnOff::Off;
+
+	// The tracker is responsible for advancing the engine time and outputting the data requests below at each time step
+	HowToTracker tracker(*bg);
+
+	bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("VenaCava", *Na, "Molarity", AmountPerVolumeUnit::mmol_Per_L);
+	bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("VenaCava", *K, "Molarity", AmountPerVolumeUnit::mmol_Per_L);
+	bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("VenaCava", *Cl, "Molarity", AmountPerVolumeUnit::mmol_Per_L);
+	bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("VenaCava", *Ca, "Molarity", AmountPerVolumeUnit::mmol_Per_L);
+
+	bg->GetEngineTrack()->GetDataRequestManager().SetResultsFilename("HowToFasciculation.txt");
+
+	// Advance some time to get some resting data
+	tracker.AdvanceModelTime(60);
+
+	bg->GetLogger()->Info("The patient is nice and healthy");
+	std::string message = "";
+	message = "Increase membrane resistance to potassium";
+	bg->GetLogger()->Info(message);
+	K->GetMembraneResistance().SetValue(5.0, ElectricResistanceUnit::Ohm);
+
+
+	while (bg->GetSimulationTime(TimeUnit::s) < monitorTime + 60.0)
+	{
+		if (bg->GetPatient().IsEventActive(CDM::enumPatientEvent::MildHypokalemia) && (lowKActive == CDM::enumOnOff::Off))
+		{
+			lowKActive = CDM::enumOnOff::On;
+			message = "Patient has low serum potassium, muscle fasciculation may occur";
+			bg->GetLogger()->Info(message);
+		}
+		tracker.AdvanceModelTime(10.0);
+	}
+	message = "Return membrane resistance to potassium to baseline";
+	bg->GetLogger()->Info(message);
+	K->GetMembraneResistance().SetValue(0.248, ElectricResistanceUnit::Ohm);
+
+	tracker.AdvanceModelTime(300);
+}

library/src/HowTo-Hemorrhage.cpp

@@ -30,18 +30,21 @@ specific language governing permissions and limitations under the License.
 #include "properties/SEScalarTime.h"
 #include "properties/SEScalarVolume.h"
 #include "properties/SEScalarVolumePerTime.h"
+#include "properties/SEScalar0To1.h"
 #include "engine/PhysiologyEngineTrack.h"
 #include "compartment/SECompartmentManager.h"
 
 //--------------------------------------------------------------------------------------------------
 /// \brief
-/// Usage for applying a Hemorrhage insult to the patient
+/// Usage for applying a Hemorrhage insult to the patient and also demonstrate how injury code can be used to initiate a hemorrhage if desired
 ///
 /// \details
 /// Refer to the SEHemorrhage class
 /// Refer to the SESubstanceManager class
 /// Refer to the SESubstanceIVFluids class for applying an IV to the patient
 //--------------------------------------------------------------------------------------------------
+std::string ParseMCIS(std::vector<unsigned int> &mcis);
+
 void HowToHemorrhage() 
 {
   // Create the engine and load the patient
@@ -78,26 +81,35 @@ void HowToHemorrhage()
 	bg->GetLogger()->Info(std::stringstream() <<"Diastolic Pressure : " << bg->GetCardiovascularSystem()->GetDiastolicArterialPressure(PressureUnit::mmHg) << PressureUnit::mmHg);
 	bg->GetLogger()->Info(std::stringstream() <<"Heart Rate : " << bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min) << "bpm");;
 
-	// Hemorrhage Starts - instantiate a hemorrhage action and have the engine process it
-	/*MCIS Code Brief : 
-	Digit 1 = Severity 
-	Digit 2 = Body Region(1 = Head, 2 = Torso, 3 = Arms, 4 = Legs, 5 = Multiple(not currently supported) 
-	Digit 3 = Subregion(not requied for arms or legs) 
-		In Head : 6 = Vessels 
-		In Torso : 6 = Vessels, 7 = Chest, 8 = Abdomen, 9 = Pelvis(not currently supported) 
-	Digit 4 
-		In Vessels : 1 = Intracranial, 3 - 5 = Carotid / Thoracic / Abdominal arteries(all currently removed from aorta compartment), 6 = VenaCava 
-		In Chest : 1 = Lungs, 2 = Heart In Abdomen : 1 = Liver, 2 = Spleen, 3 = Pancreas(Splanchnic), 4 = Kidney, 5 = SmallIntestine, 6 = LargeIntestine 
-	Digit 5 : Wound information too specific for BioGears(any number fine, 0 used here) 
-	
-	Stopping a hemorrhage requires Severity = 0 and remainder of code consistent with original wound*/
+	//We are going to create a hemorrhage in two different ways.  One way will be to specify the location and a severity on a scale of 0-1.
+	//The other way will be to parse an injury code and derive the location and severity
+	//Set the choice variable below either to 1 to run with location/severity or to 2 to run with injury code 
+	int choice = 2;
 
-	SEHemorrhage hemorrhageAbdominal;
-	std::vector<unsigned int> hemorrhageStart = {4,2,6,5,0 };
-	hemorrhageAbdominal.SetMCIS(hemorrhageStart);
-	hemorrhageAbdominal.ProcessMCIS();  //Extracts the injury severity and injury location from the mcis code
+	//Create variables for scenario
+	SEHemorrhage hemorrhageSpleen;			//hemorrhage object
+	std::string location;					//location of hemorrhage, valid options are "Major Artery", "Vena Cava", "Head", "Myocardium", "Lung", "Spleen", "Splanchnic", "Small Intestine", "Large Intestine", "Kidney", "Liver", "Arm", "Leg"
+	double severity;						//severity (scale 0-1)
+	std::vector<unsigned int> mcisCode;		//injury code if using option 2, see ParseMCIS method below for more details
+	//Let's create an internal hemorrhage in the spleen (maybe it ruptured...)
+	switch (choice) {
+	case 1:
+		location = "Spleen";
+		severity = 0.8;
+		break;
+	case 2:
+		mcisCode = { 4,2,8,2,0 };			//This injury code is a high severity hemorrhage in the spleen
+		severity = mcisCode[0] / 5.0;		//Digit 1 of mcis is severity on 0-5 scale.  Convert it to a 0-1 scale
+		location = ParseMCIS(mcisCode);
+		break;
+	}
+	//Set up hemorrhage with the location and severity info
+	hemorrhageSpleen.SetCompartment(location);
+	hemorrhageSpleen.GetSeverity().SetValue(severity);
+	hemorrhageSpleen.SetBleedPath();		//This is needed to tell engine which circuit pathway to set the hemorrhage on
 
-	bg->ProcessAction(hemorrhageAbdominal);
+	// Hemorrhage Starts - instantiate a hemorrhage action and have the engine process it.  Note that BioGears will output the injury code regardless of which method was used
+	bg->ProcessAction(hemorrhageSpleen);
 
 	// Advance some time to let the body bleed out a bit
 	tracker.AdvanceModelTime(300);
@@ -111,11 +123,10 @@ void HowToHemorrhage()
 	bg->GetLogger()->Info(std::stringstream() <<"Diastolic Pressure : " << bg->GetCardiovascularSystem()->GetDiastolicArterialPressure(PressureUnit::mmHg) << PressureUnit::mmHg);
 	bg->GetLogger()->Info(std::stringstream() <<"Heart Rate : " << bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min) << "bpm");;
 
-	// Hemorrhage is sealed
-	std::vector<unsigned int> hemorrhageEnd = { 0,2,6,5,0 };
-	hemorrhageAbdominal.SetMCIS(hemorrhageEnd);
-	hemorrhageAbdominal.ProcessMCIS();
-	bg->ProcessAction(hemorrhageAbdominal);
+	//Assume that the hemorrhage has been stopped somehow.  We do this by setting the severity of our hemorrhage object to 0
+	hemorrhageSpleen.GetSeverity().SetValue(0);
+	//Process update to hemorrhage action
+	bg->ProcessAction(hemorrhageSpleen);
 
 
 	// Advance some time while the medic gets the drugs ready
@@ -151,3 +162,57 @@ void HowToHemorrhage()
 	bg->GetLogger()->Info(std::stringstream() <<"Heart Rate : " << bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min) << "bpm");;
   bg->GetLogger()->Info("Finished");
 }
+
+std::string ParseMCIS(std::vector<unsigned int> &mcis)
+{
+	/*MCIS Code Brief :
+	Digit 1 = Severity
+	Digit 2 = Body Region(1 = Head, 2 = Torso, 3 = Arms, 4 = Legs, 5 = Multiple(not currently supported)
+	Digit 3 = Subregion(not required for arms or legs)
+	In Head : 6 = Vessels
+	In Torso : 6 = Vessels, 7 = Chest, 8 = Abdomen, 9 = Pelvis(not currently supported)
+	Digit 4
+	In Vessels : 1 = Intracranial (if in head), 4 = Major Artery (if in torso), 6 = "Vena Cava" (if in torso)
+	In Chest : 1 = Lungs, 2 = Heart In Abdomen : 1 = Liver, 2 = Spleen, 3 = Pancreas(Splanchnic), 4 = Kidney, 5 = SmallIntestine, 6 = LargeIntestine
+	Digit 5 : Wound information too specific for BioGears(any number fine, 0 used here) */
+
+	std::string comp = "";
+	enum region {Head =1, Torso = 2, Arm = 3, Leg = 4};		//This will decide which region to look for compartment based on digit 2 of code
+	std::map<std::vector<unsigned int>, std::string> torsoMap;	//There are so many compartments in the torso, it is easier to map them
+	//Populate torso map (codes with second digit = 2) so that digits 3-4 of code are key to correct compartment
+	torsoMap[{6, 4}] = "Major Artery";
+	torsoMap[{6, 6}] = "Vena Cava";
+	torsoMap[{7, 1}] = "Lung";
+	torsoMap[{7, 2}] = "Myocardium";
+	torsoMap[{8, 1}] = "Liver";
+	torsoMap[{8, 2}] = "Spleen";
+	torsoMap[{8, 3}] = "Splanchnic";
+	torsoMap[{8, 4}] = "Kidney";
+	torsoMap[{8, 5}] = "Small Intestine";
+	torsoMap[{8, 6}] = "Large Intestine";
+
+	int caseKey = mcis[1];		//Need 2nd digit of mcis code to decide in which region to place hemorrhage
+
+	switch (caseKey) {
+	case Head:
+		comp = "Head";
+		break;
+	case Torso:
+		if (torsoMap.find({ mcis.begin() + 2,mcis.end() - 1 }) != torsoMap.end())  //Check to see if subvector made from digits 3-4 is in map.
+			comp = torsoMap[{mcis.begin() + 2, mcis.end() - 1}];  // If yes, get compartment that goes with these digits
+		else
+			comp = "Major Artery";	//If no, we messed up somewhere and we'll put it on the artery so that the sim doesn't crash
+		break;
+	case Arm:
+		comp = "Arm";
+		break;
+	case Leg:
+		comp = "Leg";
+		break;
+	default:
+		comp = "Major Artery";	//Default to artery in case anything goes wrong
+	}
+
+
+	return comp;
+}