Refactored towards a self contained clasim

.gitignore

 builds/
+results/

clasim.cmake

@@ -2,46 +2,57 @@ cmake_minimum_required(VERSION 3.9.4)
 
 project(clasim)
 
-find_path(CONFIG++_INCLUDE_DIR libconfig.h++)
-find_library(CONFIG++_LIBRARY NAMES libconfig++.a)
+# use dpkg -L libconfig++-dev to find the location of libconfig.h++ and libconfig++.a
+find_path(CONFIG++_INCLUDE_DIR libconfig.h++ <libconfig.h++ location>)
+find_library(CONFIG++_LIBRARY NAMES libconfig++.a PATH <libconfig++.a location>)
 
+#clasim depends on pulse this will call will give you access to pulse directories
+#needed by clasim
+find_package(Pulse REQUIRED NO_MODULE)
 
-# set your simulation source directory
-set(SIM_SRC_DIR simsrc/mcps2018/algo1)
+# Variables to be used in the source files
+set(CLASIM_CONFIG_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources/)
+set(CLASIM_RESULTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/results/)
+set(PULSE_STATE_DIR ${Pulse_INSTALL}/bin/states/)
+
+# Create directory at build generation
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/results)
+
+# Generate header file to include variables
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/simsrc/mcps2018/include/configure_clasim_paths.h.in
+    ${CMAKE_CURRENT_SOURCE_DIR}/simsrc/mcps2018/include/configure_clasim_paths.h
+)
 
+# set your simulation source directory
+set(SIM_SRC_PATH simsrc/mcps2018/algo1)
 
 # *** include your source files
 # list each file individually
 set(MY_SOURCE_FILES
 
-    ${SIM_SRC_DIR}/SimEngine.cpp
-    ${SIM_SRC_DIR}/Monitor.cpp
-    ${SIM_SRC_DIR}/Controller.cpp
-    ${SIM_SRC_DIR}/Pump.cpp
-    ${SIM_SRC_DIR}/SimulationLogger.cpp
-    ${SIM_SRC_DIR}/MedicalDevice.cpp
+    ${SIM_SRC_PATH}/SimEngine.cpp
+    ${SIM_SRC_PATH}/Monitor.cpp
+    ${SIM_SRC_PATH}/Controller.cpp
+    ${SIM_SRC_PATH}/Pump.cpp
+    ${SIM_SRC_PATH}/SimulationLogger.cpp
+    ${SIM_SRC_PATH}/MedicalDevice.cpp
 
 )
 
-# set name of application created to run simulation
-set(APPNAME clasim)
-
-add_executable(${APPNAME} ${MY_SOURCE_FILES})
-
-#cmd depends on pulse this will call will give you access to pulse directories
-#needed by cmd
-find_package(Pulse REQUIRED NO_MODULE)
+add_executable(clasim ${MY_SOURCE_FILES})
 
 #include directories
-target_include_directories(${APPNAME} PRIVATE ${Pulse_INCLUDE_DIRS})
-target_include_directories(${APPNAME} PRIVATE ${CONFIG++_INCLUDE_DIR})
+target_include_directories(clasim PRIVATE ${Pulse_INCLUDE_DIRS})
+target_include_directories(clasim PRIVATE ${CONFIG++_INCLUDE_DIR})
 
 # *** include your simulation include directories here
-target_include_directories(${APPNAME} PRIVATE simsrc/mcps2018/include/)
+target_include_directories(clasim PRIVATE simsrc/mcps2018/include/)
 
 #libraries
-target_link_libraries(${APPNAME} debug "${Pulse_DEBUG_LIBS}")
-target_link_libraries(${APPNAME} optimized "${Pulse_LIBS}")
-target_link_libraries(${APPNAME} optimized "${CONFIG++_LIBRARY}")
+target_link_libraries(clasim debug "${Pulse_DEBUG_LIBS}")
+target_link_libraries(clasim optimized "${Pulse_LIBS}")
+target_link_libraries(clasim optimized "${CONFIG++_LIBRARY}")
+
 
-install(TARGETS ${APPNAME} RUNTIME DESTINATION ${Pulse_INSTALL}/bin)
+install(TARGETS clasim RUNTIME DESTINATION ${Pulse_INSTALL}/bin)

resources/scenario.cfg

+# Configuration file for Heart Rate Scenario
+
+
+## rate : Number of samples per second ## MAX: 50.0 Hz  ## Type: double
+
+monitor = {
+       
+	input_rate = 0.02;  ## MUST be multiple of 50.0
+        output_rate = 0.01; ## Must be less than monitor.rate and also multiple of 50.0 
+};
+
+
+controller = {
+
+        rate = 0.01;	
+	patientData = {
+	    enabled = ["HeartRate", "BloodPressure", "BloodVolume"];
+	}
+	algorithm= {
+	    wait_10 = 10.0; # Wait for 10 minutes
+	    wait_5  = 5.0; # Wait for 5 minutes
+	}
+};
+
+
+pump = {
+
+	rate = 1.0; # Intercommand delay -> to be used later
+	delay = 15.0;
+
+};
+
+
+simulation = {
+	patients = {
+	    names = ["Soldier", "Jeff", "Gus"];
+	}
+        time = {
+	    run = 3600.0;   	  # Time -> Seconds # How long should simulation run
+	    injury_start = 15.0; # When should injury be introduced to patient
+	    injury_stop = 700.0;  # When should injury  be stopped
+	}
+	path = "results"; # folder to store out sim output files -> to be used later
+
+};

simsrc/mcps2018/algo1/SimEngine.cpp

@@ -52,70 +52,63 @@ using namespace libconfig;
 
 int main(int argc, char * argv[]){
 
-        if(argc < 2)
-		{
-			cout << "Error: must provide a configuration file\n";
-			cout << "Usage: ./clasim configfile\n";
-		}
-		else
-		{
-
-	                string f_path = argv[1];
-                        const char* filepath = f_path.c_str();
-			clock_t t1, t2, sim_run_time;
-			vector<string> patients_list;
-			auto cf = std::make_shared<Config>();
-			float sim_time_secs, sim_time_mins;
-            string f_path = argv[1];
-            const char* filepath = f_path.c_str();
-            
-			try
-			{
-					cf->readFile(filepath);
-			}
 
-			catch(const FileIOException &fioex) {
-					std::cerr << "I/O error while reading file: " << filepath << std::endl;
-					//return(EXIT_FAILURE);
-			}
+	    clock_t t1, t2, sim_run_time;
+	    vector<string> patients_list;
+	    auto cf = std::make_shared<Config>();
+	    float sim_time_secs, sim_time_mins;
+	    string f_path = clasim_config_dir+"scenario.cfg";
+	    const char* filepath = f_path.c_str();
 
-			catch(const ParseException &pex) {
-					std::cerr << "Parse error at " << pex.getFile() << ":" << pex.getLine()
-						<< " - " << pex.getError() << std::endl;
-					//return(EXIT_FAILURE);
-			}
+	    try
+	    {
+			    cf->readFile(filepath);
+	    }
 
-			patients_list = get_global_patients(cf);
+	    catch(const FileIOException &fioex) {
+			    std::cerr << "I/O error while reading file: " << filepath << std::endl;
+			    //return(EXIT_FAILURE);
+	    }
 
-			for(auto patient: patients_list) {
-				// start timer
-				t1 = clock();
+	    catch(const ParseException &pex) {
+			    std::cerr << "Parse error at " << pex.getFile() << ":" << pex.getLine()
+				    << " - " << pex.getError() << std::endl;
+			    //return(EXIT_FAILURE);
+	    }
 
-				//Simulation input : Name of patient
-				Simulation(patient, cf);
+	    patients_list = get_global_patients(cf);
 
-				//stop timer
-				t2 = clock();
+	    for(auto patient: patients_list) {
+		    // start timer
+		    t1 = clock();
+
+		    //Simulation input : Name of patient
+		    Simulation(patient, cf);
+
+		    //stop timer
+		    t2 = clock();
+
+		    sim_run_time = t2 - t1;
+		    sim_time_secs = ((float)sim_run_time)/CLOCKS_PER_SEC;
+		    sim_time_mins = sim_time_secs/60.0;
+
+		    cout << "\nThe Simulation for " << patient;
+		    cout  << " took "<< sim_time_secs <<" seconds ";
+		    cout <<"or " << sim_time_mins <<" minutes"<<endl;
+            }
 
-				sim_run_time = t2 - t1;
-				sim_time_secs = ((float)sim_run_time)/CLOCKS_PER_SEC;
-				sim_time_mins = sim_time_secs/60.0;
 
-				cout << "\nThe Simulation for " << patient;
-				cout  << " took "<< sim_time_secs <<" seconds ";
-				cout <<"or " << sim_time_mins <<" minutes"<<endl;
-			}
-		}
 }
 
 void Simulation(const string patient_name, const std::shared_ptr<Config>& cf)
 {
 
 	  	// Create the engine and load the patient
-	  	std::unique_ptr<PhysiologyEngine> pe = CreatePulseEngine("SimulationEngine_"+patient_name+".log");
+	  	std::unique_ptr<PhysiologyEngine> pe =
+CreatePulseEngine(clasim_results_dir+"SimulationEngine_"+patient_name+".log");
 	  	pe->GetLogger()->Info("CMD Simulation");
 	  	//if (!pe->LoadStateFile("./states/StandardMale@0s.pba"))
-			if (!pe->LoadStateFile("./states/"+patient_name+"@0s.pba"))
+			if (!pe->LoadStateFile(pulse_state_dir+patient_name+"@0s.pba"))
 	  	{
 	    		pe->GetLogger()->Error("Could not load state, check the error");
 	    		return;
@@ -128,7 +121,7 @@ void Simulation(const string patient_name, const std::shared_ptr<Config>& cf)
 		  pe->GetEngineTracker()->GetDataRequestManager().CreatePhysiologyDataRequest("HeartRate", FrequencyUnit::Per_min);
 		  pe->GetEngineTracker()->GetDataRequestManager().CreatePhysiologyDataRequest("BloodVolume", VolumeUnit::mL);
 		  pe->GetEngineTracker()->GetDataRequestManager().CreatePhysiologyDataRequest("MeanArterialPressure", PressureUnit::mmHg);
-		  pe->GetEngineTracker()->GetDataRequestManager().SetResultsFilename("PulseSimEngine_"+patient_name+".txt");
+		  pe->GetEngineTracker()->GetDataRequestManager().SetResultsFilename(clasim_results_dir+"PulseSimEngine_"+patient_name+".txt");
 
 			//instatiate Hemorrhage Action
 			SEHemorrhage hemorrhageLeg;
@@ -168,7 +161,8 @@ void Simulation(const string patient_name, const std::shared_ptr<Config>& cf)
 
 
 			//logger
-			sim_env.logger = std::make_shared<SimulationLogger>("SimulationEngineLog_"+patient_name+".txt");
+			sim_env.logger =
+std::make_shared<SimulationLogger>(clasim_results_dir+"SimulationEngineLog_"+patient_name+".txt");
 
 			bool STOP = false; // Execute stop hemmorrhage only once; without this it be executed for each timestep
 			bool DEVICES_START = false;

simsrc/mcps2018/include/SimEngine.h

 
 #ifndef SIMENGINE_H
 #define SIMENGINE_H
-#include<string>
+#include <string>
+#include "configure_clasim_paths.h"
 
 void Simulation(const std::string, const std::shared_ptr<Config>& cf);
 

simsrc/mcps2018/include/configure_clasim_paths.h.in

+#ifndef CONFIGURE_SIM_PATHS_H
+#define CONFIGURE_SIM_PATHS_H
+
+#include <string>
+#include <stdio.h>
+
+// @variable@ from cmake file to be substituted with actual values
+// after generation
+const std::string clasim_config_dir = "@CLASIM_CONFIG_DIR@";
+const std::string pulse_state_dir = "@PULSE_STATE_DIR@";
+const std::string clasim_results_dir = "@CLASIM_RESULTS_DIR@";
+
+#endif