survival after reproduction as a independant process

data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml

@@ -296,7 +296,7 @@
 					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
 				</analysis.AnalyseFishDistribution>
 
-				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
+				<species.ReproduceWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>
 					<tempMinRep>10</tempMinRep>
@@ -312,13 +312,17 @@
 					<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
 					<initialLength>2.8</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
-					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
 					<maxNumberOfSuperIndividualPerReproduction>100.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>
-				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
+				</species.ReproduceWithDiagnose>
 
+				<species.SurviveAfterReproduction>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<afterReproductionSeason>SPRING</afterReproductionSeason>
+					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
+				</species.SurviveAfterReproduction>
 
 				<species.MigrateFromRiverToInshore>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>

src/main/java/species/SurviveAfterReproduction.java

+package species;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+
+import org.openide.util.lookup.ServiceProvider;
+
+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.kernel.util.TransientParameters.InitTransientParameters;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import miscellaneous.BinomialForSuperIndividualGen;
+import species.DiadromousFish.SpawnerOrigin;
+import umontreal.iro.lecuyer.probdist.NormalDist;
+import umontreal.iro.lecuyer.randvar.NormalGen;
+
+@ServiceProvider(service = AquaNismsGroupProcess.class)
+
+public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private Season afterReproductionSeason = Season.SUMMER;
+
+	private double survivalRateAfterReproduction = 0.1;
+
+	private transient NormalGen genNormal;
+
+	/**
+	 * the random numbers generator for binomial draws
+	 * 
+	 * @unit --
+	 */
+	private transient BinomialForSuperIndividualGen aleaGen;
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver())).toXML(new SurviveAfterReproduction()));
+	}
+
+
+	@Override
+	@InitTransientParameters
+	public void initTransientParameters(Pilot pilot) {
+		super.initTransientParameters(pilot);
+		genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
+
+		aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+
+	}
+
+
+	@Override
+	public void doProcess(DiadromousFishGroup group) {
+		Time time = group.getEnvironment().getTime();
+		if (time.getSeason(group.getPilot()) == afterReproductionSeason) {
+
+			for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+
+				long survivalAmount;
+
+				List<DiadromousFish> fishInBasin = riverBasin.getFishs(group);
+				if (fishInBasin != null) {
+
+					// Initiate the total fluxes for this basin
+					Map<SpawnerOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<SpawnerOrigin, Map<String, Double>>(); // On
+					totalInputFluxes.put(SpawnerOrigin.AUTOCHTONOUS, new Hashtable<String, Double>());
+					totalInputFluxes.put(SpawnerOrigin.ALLOCHTONOUS, new Hashtable<String, Double>());
+					for (SpawnerOrigin origin : totalInputFluxes.keySet()) {
+						for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+							totalInputFluxes.get(origin).put(nutrient, 0.); // ON MET A JOUR NOTRE map
+						}
+						totalInputFluxes.get(origin).put("biomass", 0.);
+					}
+
+					// iterate on the fish
+					ListIterator<DiadromousFish> fishIterator = fishInBasin.listIterator();
+					while (fishIterator.hasNext()) {
+						DiadromousFish fish = fishIterator.next();
+
+						if (fish.isMature()) {
+
+							// origin of the spwaner
+							SpawnerOrigin spawnerOrigin = (fish.getBirthBasin() == riverBasin ? SpawnerOrigin.AUTOCHTONOUS
+									: SpawnerOrigin.ALLOCHTONOUS);
+
+							// survival amount of fish
+							double biomass = 0.;
+							survivalAmount = aleaGen.getSuccessNumber(fish.getAmount(), survivalRateAfterReproduction);
+
+							// at least one fish in the SI survive, the other die
+							if (survivalAmount > 0) {
+
+								// ---------------------------------------------------------- start of nutrient routine
+								// nutrient fluxes for one fish surviving after spawning (fish.getAmount):
+								// excretion + gametes
+								Map<String, Double> aFluxAfterSurvival = group.getNutrientRoutine()
+										.computeNutrientsInputForSurvivalAfterSpawning(fish);
+
+								// nutrient fluxes for one fish dying after spawning (fish.getAmount):
+								// carcasses + excretion + gametes
+								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine()
+										.computeNutrientsInputForDeathAfterSpawning(fish);
+
+								for (String nutrient : aFluxAfterSurvival.keySet()) {
+									// For all survival fish in the SI
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(), aFluxAfterSurvival.get(nutrient) * survivalAmount);
+
+									// For all dead fish in the SI
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(),
+											aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+
+								// take into account the fish origine
+								for (String nutrient : aFluxAfterSurvival.keySet()) {
+									// For all survival fish
+									totalInputFluxes.get(spawnerOrigin).put(nutrient,
+											totalInputFluxes.get(spawnerOrigin).get(nutrient)
+													+ aFluxAfterSurvival.get(nutrient) * survivalAmount);
+
+									// For all dead fish
+									totalInputFluxes.get(spawnerOrigin).put(nutrient,
+											totalInputFluxes.get(spawnerOrigin).get(nutrient)
+													+ aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+								// compute biomass for dead fish
+								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount);
+								totalInputFluxes.get(spawnerOrigin).put("biomass",
+										totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// ------------------------------------------------------ end of nutrient routine
+
+								// update the amount of individual in the super-individual
+								fish.setAmount(survivalAmount);
+
+							} else { // the superindividual dies !!!
+								// ------------------------------------------------------ start of nutrient routine
+								// nutrient fluxes for one fish dying after spawning (fish.getAmount):
+								// carcasses + excretion + gametes
+								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine()
+										.computeNutrientsInputForDeathAfterSpawning(fish); //
+
+								for (String nutrient : aFluxForDeadFish.keySet()) {
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(),
+											aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
+								totalInputFluxes.get(spawnerOrigin).put("biomass",
+										totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// ------------------------------------------------------ end of nutrient routine
+
+								// remove fish because fish is dead
+								fishIterator.remove();
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+}