Compute total fluxes for import and export

src/main/java/species/MigrateToSea.java

@@ -9,8 +9,13 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import java.util.ArrayList;
+import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
+
 import miscellaneous.Duo;
+import species.DiadromousFish.Stage;
+
 import org.openide.util.lookup.ServiceProvider;
 
 @ServiceProvider(service = AquaNismsGroupProcess.class)
@@ -28,19 +33,48 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 
 		if (Time.getSeason(group.getPilot()) == seaMigrationSeason ){
 			Basin destination;
-                        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];
-                            
-                                List<DiadromousFish> fishes = basin.getFishs(group);
-                                if (fishes!=null) for (DiadromousFish fish : fishes) {
-                                        destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
-                                        fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination));
-                                }       
-                        }
-                        for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
-                                duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group);
-                        }
-                }
+			
+			//On crer la Map pour stocker les flux d'export
+			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];
+				//Fish move to sea and compute the related export of nutrients 
+				List<DiadromousFish> fishes = basin.getFishs(group);
+				
+				// ON r-initialise notre map pour chauqe bassin 
+				for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
+					totalOutputFluxes.put(nutrient, 0.); 
+				}
+				totalOutputFluxes.put("biomass", 0.); //cration de la biomasse 
+				
+				if (fishes!=null) {
+					for (DiadromousFish fish : fishes) {
+						destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
+						fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination)); //Mentionne la sortie d'un poisson de la boucle 
+					
+						double biomass = group.getFishNutrient().getWeight(fish) * fish.getAmount(); 
+						
+						if (fish.getStage()==Stage.IMMATURE) {
+							Map <String, Double> aFluxExportedByJuveniles= group.getFishNutrient().computeNutrientsExportForJuveniles(fish); 
+							for (String nutrient: aFluxExportedByJuveniles.keySet()) {
+								totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount()); 	
+							}
+							
+							totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass); 
+						}
+					}     
+				}
+				
+				for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
+					duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on dplace les poissons dans le fichier MoveTo et on dnote la destination du poisson.
+				}
+				System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
+						+ basin.getName() + "; " + totalOutputFluxes);
+			}
+		}
+		
+		
 	}
-}
+}
\ No newline at end of file

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -110,11 +110,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 				if (fishInBasin != null){
 
 					//Initiate the total fluxes for this basin 
-					Map<String, Double> totalFluxes = new Hashtable<String, Double>(); //On crer la Map pour stocker les flux 
+					Map<String, Double> totalInputFluxes = new Hashtable<String, Double>(); //On crer la Map pour stocker les flux 
 					for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
-						totalFluxes.put(nutrient, 0.); // ON MET A JOUR NOTRE map 
+						totalInputFluxes.put(nutrient, 0.); // ON MET A JOUR NOTRE map 
 					}
 
+					totalInputFluxes.put("biomass",0.); 
 					// --------------------------------------------------------------------------------------------------
 					// definition of the stock recruiment relationship
 					// --------------------------------------------------------------------------------------------------
@@ -188,30 +189,44 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 							// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
 							survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction); 
-							if (survivalAmount > 0) {
+							double biomass = 0.; 
+							if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs 
 
 								//Export for fishes survived after spawning (survivalAmount) : excretion + gametes
 								Map <String, Double> aFluxAfterSurvival = group.getFishNutrient().computeNutrientsInputForSurvivalAfterSpawning(fish); 
+
+								//Export for fishes that dies after spawning (fish.getAmount - survivalAmount): excretion + gametes + carcasse 
+								Map<String, Double> aFluxForDeadFish = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); 
+
 								for (String nutrient: aFluxAfterSurvival.keySet()) {
-									totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount); 	
+									//For survival fish
+									totalInputFluxes.put(nutrient,totalInputFluxes.get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount); 
+
+									//For dead fish
+									totalInputFluxes.put(nutrient,totalInputFluxes.get(nutrient) + aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount)); 
 								}
-								fish.setAmount(survivalAmount); }
+								
+								//compute biomass for dead fish 
+								biomass = group.getFishNutrient().getWeight(fish) * (fish.getAmount() - survivalAmount); 
+								totalInputFluxes.put("biomass", totalInputFluxes.get("biomass") + biomass);
+								
+								//update the amount of individual in the super-individual 
+								fish.setAmount(survivalAmount); 
+							}
 							else {
-
+								//Le superinvidu est mort !!! 
 								deadFish.add(fish);
 
 								//Export for fished died before spawning (fish.getAmount): carcasses + excretion + gametes 
 								Map<String, Double> aFlux = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); // 
+								
 								for (String nutrient: aFlux.keySet()) {
-									totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFlux.get(nutrient) * (fish.getAmount()) - survivalAmount); //Fish.getAmount - survivalAmount = total fishes died. 
-
+									totalInputFluxes.put(nutrient,totalInputFluxes.get(nutrient) + aFlux.get(nutrient) * fish.getAmount()); //Fish.getAmount - survivalAmount = total fishes died. 
 								}
-
-
+								 biomass = group.getFishNutrient().getWeight(fish) * (fish.getAmount());
+								 totalInputFluxes.put("biomass", totalInputFluxes.get("biomass") + biomass); 
 							}
-
 						}
-
 					}
 
 					// keep the spawner number
@@ -366,15 +381,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					// Remove deadfish and compute the related nutrient fluxes 
 					// --------------------------------------------------------------------------------------------------
 					for (DiadromousFish fish : deadFish){
-
-
-
 						group.removeAquaNism(fish);
 					}
 					deadFish.clear();
 
-					System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";"
-							+ riverBasin.getName() + "; " + totalFluxes);
+					System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
+							+ riverBasin.getName() + "; " + totalInputFluxes);
 
 				}
 				else {