easyRun in java

src/main/java/analysis/EasyRun.java

@@ -26,7 +26,7 @@ public class EasyRun {
 
 	static Pilot pilot;
 
-	public static void runSimulation(String[] batchArgs, String[] paramNames, double[] paramValues) throws Exception {
+	public static void runSimulation(String[] batchArgs, String[] paramNameaANG, double[] paramValuesANG) throws Exception {
 
 		try {
 			pilot = new Pilot();
@@ -35,12 +35,10 @@ public class EasyRun {
 			runner.parseArgs(batchArgs, false, true, false);
 			pilot.load();
 
-			// update the simulation parameters
-			// ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0),
-			// "processes.processesAtEnd.0.fileNameOutput", outputfilename);
-			for (int i = 0; i < paramNames.length; i++) {
-				ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), paramNames[i],
-						paramValues[i]);
+			// update the simulation parameters in AquaNismGroup
+			for (int i = 0; i < paramNameaANG.length; i++) {
+				ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), paramNameaANG[i],
+						paramValuesANG[i]);
 			}
 			// run the simulation
 			pilot.run();
@@ -54,6 +52,40 @@ public class EasyRun {
 	}
 
 
+	public static void runSimulation(String[] batchArgs, String[] paramNameaANG, double[] paramValuesANG, String[] paramNameaENV,
+			String[] paramValuesENV) throws Exception {
+
+		// TODO parse string to other type if needed
+		try {
+			pilot = new Pilot();
+			BatchRunner runner = new BatchRunner(pilot);
+			pilot.init();
+			runner.parseArgs(batchArgs, false, true, false);
+			pilot.load();
+
+			// update the simulation parameters in AquaNismGroup
+			for (int i = 0; i < paramNameaANG.length; i++) {
+				ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), paramNameaANG[i],
+						paramValuesANG[i]);
+			}
+
+			// update the simulation parameters in Environment
+			for (int i = 0; i < paramNameaENV.length; i++) {
+				ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getEnvironment(), paramNameaENV[i], paramValuesENV[i]);
+			}
+
+			// run the simulation
+			pilot.run();
+
+			// For forcing resources releasing (like shp files)
+			System.gc();
+		} catch (Throwable e) {
+			System.out.println(e.getMessage());
+			e.printStackTrace();
+		}
+	}
+
+
 	public static double[] getValuesFromEnvironment(String targetName) throws Exception {
 		return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getEnvironment(), targetName);
 	}
@@ -85,20 +117,28 @@ public class EasyRun {
 
 
 	public static void main(String[] args) throws Exception {
-		String[] batchArguments = ("-simDuration 150 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
-				+ "-groups data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml "
-				+ "-env data/input/northeastamerica/RIOBNneaBasins_Rjava.xml "
+		// blank are important
+		String[] batchArguments = ("-simDuration 40 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
+				+ "-groups data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml" + " "
+				+ "-env data/input/northeastamerica/RIOBNneaBasins_Rjava.xml" + " "
 				+ "-observers data/input/northeastamerica/RIO_obs_empty.xml").split("\\ ");
 
-		String[] parameterNames = new String[] { "processes.processesEachStep.10.tempMinRep",
-				"processes.processesEachStep.10.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
-
-		double[] parameterValues = new double[] { 10, 2, 0.7 };
+		// String[] parameterNames = new String[] { "processes.processesEachStep.10.tempMinRep",
+		// "processes.processesEachStep.10.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
+		//
+		// double[] parameterValues = new double[] { 10, 2, 0.7 };
 
-		runSimulation(batchArguments, parameterNames, parameterValues);
+		// =====================================================
+		System.out.println("WITHOUT ALLEE EFFECT");
+		String[] parameterNamesANG = new String[] { "processes.processesEachStep.11.Soffset" };
+		double[] parameterValuesANG = new double[] { 0. };
+		// runSimulation(batchArguments, parameterNamesANG, parameterValuesANG);
+		String[] parameterNamesENV = new String[] { "simulationName" };
+		String[] parameterValuesENV = new String[] { "noAllee" };
+		runSimulation(batchArguments, parameterNamesANG, parameterValuesANG, parameterNamesENV, parameterValuesENV);
 
 		System.out.println("\n== AnalyseSpawnerFeatures ==");
-		String[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.8.exportToR");
+		String[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
 		for (String[] record : spawnerRunResults) {
 			for (String value : record)
 				System.out.print(value + "\t");
@@ -106,7 +146,7 @@ public class EasyRun {
 		}
 
 		System.out.println("\n== AnalyseFishDistribution ==");
-		String[][] distributionResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
+		String[][] distributionResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.10.exportToR");
 		for (String[] record : distributionResults) {
 			for (String value : record)
 				System.out.print(value + "\t");