writing nutrient export fluxes

data/input/fishTryRealBV_CC.xml

@@ -214,9 +214,9 @@
 			<processesEachStep>
 				<environment.InformTime>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					  <consoleDisplay>true</consoleDisplay>
+					<consoleDisplay>true</consoleDisplay>
 				</environment.InformTime>
-				
+
 				<species.PlopProcess>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<temporisation>0</temporisation>
@@ -280,7 +280,7 @@
 					<exportSeason>SPRING</exportSeason>
 					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
 				</species.WriteEffectiveAndBiomassFluxes>
-				
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>
@@ -321,21 +321,10 @@
 					<fileName>fluxes</fileName>
 				</species.WriteImportNutrientFluxes>
 
-				<species.IdentifyPopulation>
-					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<consoleDisplay>false</consoleDisplay>
-					<fluxesSeason>SPRING</fluxesSeason>
-					<years>
-						<long>2000</long>
-						<long>2100</long>
-					</years>
-					<fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
-				</species.IdentifyPopulation>
-
-				<species.TypeTrajectoryCV>
+				<species.WriteNutrientExportFluxes>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
-				</species.TypeTrajectoryCV>
+					<fileName>nutrientExportFluxes</fileName>
+				</species.WriteNutrientExportFluxes>
 
 			</processesAtEnd>
 		</processes>

src/main/java/species/MigrateToSea.java

@@ -42,8 +42,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 			Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>(); 
 
 			List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
-			for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
-				RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
+			for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
+		
 				//Fish move to sea and compute the related export of nutrients 
 				List<DiadromousFish> fishes = basin.getFishs(group);
 
@@ -64,6 +64,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 							Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish); 
 							for (String nutrient: aFluxExportedByJuveniles.keySet()) {
 								totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount()); 	
+								
+								group.getNutrientRoutine().getNutrientExportFluxesCollection().put(Time.getYear(group.getPilot()), nutrient, basin.getName(),  aFluxExportedByJuveniles.get(nutrient) * fish.getAmount());
 							}
 
 							totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass); 

src/main/java/species/WriteNutrientExportFluxes.java

+package species;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private String fileName= "nutrientExportFluxes";
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver()))
+				.toXML(new WriteNutrientExportFluxes()));
+
+	}
+
+	@Override
+	public void doProcess(DiadromousFishGroup group) {
+
+		BufferedWriter bW;
+
+		String outputPath = "data/output/" ;
+		String sep = ";"; 
+		new File(outputPath + fileName).getParentFile().mkdirs();
+		try {
+			bW = new BufferedWriter(new FileWriter(new File(outputPath+
+					fileName + group.getSimulationId() + ".csv")));
+
+			bW.write("year"+sep+"nutrient" + sep + "originBasin" + sep + "value" + "\n");
+
+			Map<Long, Map <String,  Map<String, Double>>> fluxesCollection = group.getNutrientRoutine().getNutrientExportFluxesCollection().getExportFluxesCollection();
+
+			// to iterate on sorted years
+			List<Long> years =  new ArrayList<Long>(fluxesCollection.keySet());
+			Collections.sort(years);
+
+			for (long year :years) {
+				if (year >= group.getMinYearToWrite()) {
+
+					for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+
+						for (String originBasinName : group.getEnvironment().getRiverBasinNames()) {
+							bW.write(year+ sep+ nutrient + sep + originBasinName );
+							bW.write( sep + fluxesCollection.get(year).get(nutrient).get(originBasinName) + '\n');
+						}
+
+					}
+				}
+			}
+
+			bW.flush();
+			bW.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+}