Add Export Fluxes Class

Export the effective fluxes between watersheds

data/input/fishTryRealBV_CC.xml

@@ -279,6 +279,7 @@
 					<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
 					<weightOfDeathBasin>0.4</weightOfDeathBasin>
 				</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
+				
 				<species.Survive>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
@@ -289,6 +290,13 @@
 					<mortalityRateInSea>0.4</mortalityRateInSea>
 					<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
 				</species.Survive>
+				
+				<species.ExportFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<exportSeason>SPRING</exportSeason>
+					<fileNameOutput>EffectiveFluxes</fileNameOutput>
+				</species.ExportFluxes>
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>

src/main/java/species/DiadromousFishGroup.java

@@ -412,7 +412,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 						fileNameFluxes +this.getSimulationId() + ".csv")));
 
 				bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
-						+sep+"abundance" + sep + "fluxType"+sep+"origine"+sep+"biomass");
+						+sep+"abundance" + sep + "fluxType"+ sep + "origin" +sep+"biomass");
 				for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
 					bWForFluxes.write(sep+nutrient);
 				}

src/main/java/species/ExportFluxes.java

+
+package species;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import environment.RiverBasin;
+import environment.Time;
+import environment.Time.Season;
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish.Stage;
+
+/**
+ *
+ */
+public class ExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private Season exportSeason = Season.SPRING;
+
+	private String fileNameOutput = "EffectiveFluxes";
+
+	private transient BufferedWriter bW;
+	private transient String sep=";";
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver()))
+				.toXML(new ExportFluxes()));
+	}
+
+	/* (non-Javadoc)
+	 * @see fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
+	 */
+	@Override
+	public void initTransientParameters(Pilot pilot) {
+		super.initTransientParameters(pilot);
+		sep=";";
+
+	}
+
+	@Override
+	public void doProcess(DiadromousFishGroup group) {
+
+		if (bW==null){
+			if (fileNameOutput != null){
+				new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+				try {
+					bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
+							fileNameOutput +group.getSimulationId()+ ".csv")));
+
+					bW.write("year"+sep+"migrationBasin"); //create the field of the column
+					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
+						bW.write(sep + birthBasinName); // write each basin name in the file 
+					}
+
+				} catch (IOException e) {
+					e.printStackTrace();
+				}
+			}
+		}
+
+		try {
+			if (Time.getSeason(pilot) == exportSeason & Time.getYear(pilot)>1900) {
+
+
+				for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
+					//Create the map to get the abundance in each birth basin
+					Map<String, Long> spawnerOriginsBeforeReproduction = new HashMap<String, Long>(group.getEnvironment().getRiverBasinNames().length); 
+					for (String basinName : group.getEnvironment().getRiverBasinNames()){
+						spawnerOriginsBeforeReproduction.put(basinName,  0L);			
+					}
+
+					//compute the cumulative effective per birth basin 
+					if (migrationBasin.getFishs(group) != null) {
+						for (DiadromousFish fish : migrationBasin.getFishs(group)) {
+							if (fish.getStage() == Stage.MATURE) {
+								String birthBasinName = fish.getBirthBasin().getName();
+								spawnerOriginsBeforeReproduction.put(birthBasinName, spawnerOriginsBeforeReproduction.get(birthBasinName) + fish.getAmount());
+
+
+							}
+
+						}
+					}
+
+					//write the first two fields of the line 
+					bW.write(Time.getYear(pilot)+sep+migrationBasin.getName());
+
+					//write the cumulative effective from birth basin 
+					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
+						bW.write(sep+spawnerOriginsBeforeReproduction.get(birthBasinName));
+					}
+					//write an end-of(line
+					bW.write("\n");
+				}
+			}
+			if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1)
+				bW.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+}
\ No newline at end of file

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -3,6 +3,7 @@ package species;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
+import java.io.ObjectInputStream.GetField;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Hashtable;
@@ -169,7 +170,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					// age of autochnonous spawnser
 					Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>(); 
 
-					
+
 					// compute the number of spawners and keep the origines of the spawners
 					for (DiadromousFish fish : fishInBasin){
 
@@ -410,9 +411,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 						try {
 							for (fluxOrigin origin : totalInputFluxes.keySet()) {
 								bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) 
-								+";"+ riverBasin.getName() +  ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin);
+								+";"+ riverBasin.getName() +  ";" + riverBasin.getSpawnerNumber() + ";" + "IMPORT"+ ";" + origin);
 								bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
-						
+
 								for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 									bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
 								}
@@ -434,8 +435,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 				riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
 				//System.out.println("  AFTER " +riverBasin.getSpawnerOrigins().keySet());
 			}
-			
-			
+
+
 			// --------------------------------------------------------------------------------------------------
 			// update the observers
 			// --------------------------------------------------------------------------------------------------