Abundance_Correction

data/input/fishTryRealBV_CC.xml

@@ -83,13 +83,20 @@
 							<double>-11.285</double>
 						</entry>
 						<entry>
--							<string>bLW</string>
--							<double>2.9973</double>
--						</entry>
--						<entry>
--							<string>aLW</string>
--							<double>0.010383887012522573</double>
--						</entry>
+							-
+							<string>bLW</string>
+							-
+							<double>2.9973</double>
+							-
+						</entry>
+						-
+						<entry>
+							-
+							<string>aLW</string>
+							-
+							<double>0.010383887012522573</double>
+							-
+						</entry>
 					</hashtable>
 				</entry>
 				<entry>
@@ -104,13 +111,20 @@
 							<double>-6.6234</double>
 						</entry>
 						<entry>
--							<string>bLW</string>
--							<double>2.9418</double>
--						</entry>
--						<entry>
--							<string>aLW</string>
--							<double>0.013199187556948952</double>
--						</entry>
+							-
+							<string>bLW</string>
+							-
+							<double>2.9418</double>
+							-
+						</entry>
+						-
+						<entry>
+							-
+							<string>aLW</string>
+							-
+							<double>0.013199187556948952</double>
+							-
+						</entry>
 					</hashtable>
 				</entry>
 			</fishFeaturesPostSpawning>
@@ -279,7 +293,7 @@
 					<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
 					<weightOfDeathBasin>0.4</weightOfDeathBasin>
 				</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
-				
+
 				<species.Survive>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
@@ -290,13 +304,20 @@
 					<mortalityRateInSea>0.4</mortalityRateInSea>
 					<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
 				</species.Survive>
-				
+
 				<species.ExportFluxes>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<exportSeason>SPRING</exportSeason>
 					<fileNameOutput>EffectiveFluxes</fileNameOutput>
 				</species.ExportFluxes>
 
+				<species.ExportBiomass>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
+					<exportSeason>SPRING</exportSeason>
+					<fileNameOutput>BiomassFluxes</fileNameOutput>
+				</species.ExportBiomass>
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>

src/main/java/environment/RiverBasin.java

@@ -66,12 +66,20 @@ public class RiverBasin extends Basin {
 	public double getSpawnerNumber() {
 		long nbSpawn = 0;
 		for (DiadromousFishGroup group : this.getGroups()) {
+			nbSpawn += getSpawnerNumberPerGroup(group);
+		}
+		return nbSpawn;
+	}
+	
+
+	public double getSpawnerNumberPerGroup(DiadromousFishGroup group) {
+		long nbSpawn = 0;
+	
 			for (DiadromousFish fish : this.getFishs(group)) {
 				if (fish.isMature()) {
 					nbSpawn += fish.getAmount();
 				}
 			}
-		}
 		return nbSpawn;
 	}
 

src/main/java/species/ExportBiomass.java

@@ -37,7 +37,7 @@ public class ExportBiomass extends AquaNismsGroupProcess<DiadromousFish, Diadrom
 
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver()))
-				.toXML(new ExportFluxes()));
+				.toXML(new ExportBiomass()));
 	}
 
 	/* (non-Javadoc)

src/main/java/species/ExportFluxes.java

@@ -60,6 +60,7 @@ public class ExportFluxes extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
 						bW.write(sep + birthBasinName); // write each basin name in the file 
 					}
+					bW.write("\n");
 
 				} catch (IOException e) {
 					e.printStackTrace();

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -98,6 +98,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 			List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
 
 			for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
+				
+				// before the party !!!!
+				double fluxBefore =riverBasin.getSpawnerNumber();
+								
 				double b, c, alpha, beta, amountPerSuperIndividual ,  S95, S50 ;
 				double numberOfFemaleGenitors = 0.;
 				double numberOfAutochtones = 0.;
@@ -402,16 +406,20 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 						group.removeAquaNism(fish);
 					}
 					deadFish.clear();
-
+				
+					// -------------------------------------------------------
+					// display information
+					// -----------------------------------------------------
 					if 	(displayFluxesOnConsole)
+						
 						System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
-								+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() +  "; " + totalInputFluxes); 
+								+ riverBasin.getName() + ";" +  fluxBefore + ";" + riverBasin.getSpawnerNumberPerGroup(group)+  "; " + totalInputFluxes); 
 					BufferedWriter bW = group.getbWForFluxes();
 					if ( bW != null) {
 						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() +  ";" + fluxBefore + ";" + "IMPORT"+ ";" + origin);
 								bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
 
 								for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {