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Commit e7b0c7ba authored by Lambert Patrick's avatar Lambert Patrick
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with listIterator in DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin

parent c955e4de
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src/main/java/species/DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin.java
View file @ e7b0c7ba
package species;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.ListIterator;
import java.util.Map;
......@@ -14,7 +15,6 @@ import environment.SeaBasin;
import environment.Time;
import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.Miscellaneous;
import org.openide.util.lookup.ServiceProvider;
......@@ -96,14 +96,6 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
.toXML(new DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin()));
}
@Override
public void initTransientParameters(Pilot pilot) {
// TODO Auto-generated method stub
super.initTransientParameters(pilot);
}
@Override
public void doProcess(DiadromousFishGroup group) {
Time time = group.getEnvironment().getTime();
......@@ -121,21 +113,17 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
pHoming = pHomingAfterEquil;
}
//List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
//List<DiadromousFish> newFish = new ArrayList<DiadromousFish>();
//List<Duo<DiadromousFish, Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish, Basin>>();
for (SeaBasin departure : group.getEnvironment().getSeaBasins()) {
RiverBasin homingDestination = (RiverBasin) bn.getAssociatedRiverBasin(departure);
RiverBasin homingDestination = (RiverBasin) bn.getAssociatedRiverBasin(departure);
List<DiadromousFish> fishes = departure.getFishs(group);
if (fishes != null) {
ListIterator<DiadromousFish> fishIterator = fishes .listIterator();
while (fishIterator.hasNext()) {
DiadromousFish fish = fishIterator.next();
//for (DiadromousFish fish : fishes) {
ListIterator<DiadromousFish> fishIterator = fishes.listIterator();
while (fishIterator.hasNext()) {
DiadromousFish fish=fishIterator.next();
//for (DiadromousFish fish : fishes) {
if (fish.isMature()) {
// fish with homing
homingAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50
......@@ -147,69 +135,50 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
strayedAmount = fish.getAmount() - homingAmount;
}
// manage strayed fish
// influence of the fish length on the probability to disperse
if (strayedAmount != 0) {
// calculate the weight associated with the fish length in the probabaility to disperse
// calcula the weight associated with the fish length in the probabaility to disperse
double weightFishLength = -(alpha2Rep * ((fish.getLength() - meanSpawnersLengthAtRepro) / standardDeviationOfSpawnersLengthAtRepro));
Map<RiverBasin, Double> basinWeightswithDeathWeight = new TreeMap<RiverBasin,Double>();
// We fill the weight table
double totalWeight = 0.;
double probToGo = 0.;
long amountToGo = 0;
// TODO manage the case when AccBasOfFish is empty
//for (Duo<Basin, Double> accBasin : accBasOfFish) {
for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {
// total weight for the basins
RiverBasin destination = entry.getKey();
double weight = entry.getValue();
double accBasinWeight = 1 / (1 + Math.exp(-(weight + weightFishLength)));
Map<RiverBasin, Double> basinWeightsFromDeparture = new HashMap<RiverBasin, Double>();
for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {
double accBasinWeight = 1. / (1. + Math.exp(-(entry.getValue() + weightFishLength)));
// put weight to 0 for unused basins
if (group.isThereBasinToUpdate()){
if (time.getYear(group.getPilot()) >= group.getYearOfTheUpdate()
&& group.getPattractive(destination.getName()) == 0){
&& group.getPattractive(entry.getKey().getName()) == 0){
//TODO use correctely getPaccessible
accBasinWeight = 0 ;
}
}
totalWeight += accBasinWeight;
basinWeightswithDeathWeight.put(destination, accBasinWeight);
basinWeightsFromDeparture.put (entry.getKey(),accBasinWeight );
}
// add the deathBasin in the map
//accBasOfFish.add(new Duo<Basin, Double>(deathBasin, weightOfDeathBasin));
//basinWeightswithDeathWeight.put(deathBasin, weightOfDeathBasin);
// sum the deathBasin weight in the list
totalWeight = totalWeight + weightOfDeathBasin;
// compute sequentially the prob to go into a basin
for (Entry<RiverBasin, Double> entry : basinWeightswithDeathWeight.entrySet()) {
RiverBasin destination = entry.getKey();
double weight = entry.getValue();
for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {
RiverBasin strayerDestination = entry.getKey();
Double weight = entry.getValue();
probToGo = weight / totalWeight;
amountToGo = Miscellaneous.binomialForSuperIndividual(group.getPilot(), strayedAmount, probToGo);
if (amountToGo > 0) {
// add a "duplicated" fish in the destination basin
DiadromousFish duplicatedFish = fish.duplicateWithNewPositionAndAmount(group.getPilot(), destination, amountToGo);
destination.addFish(duplicatedFish, group);
//newFish.add(fish.duplicateWithNewPositionAndAmount(group.getPilot(), bn.getAssociatedRiverBasin(b), amountToGo));
strayerDestination.addFish(fish.duplicateWithNewPositionAndAmount(group.getPilot(), strayerDestination, amountToGo), group);
}
//else{
//TODO add to the cemetery
//deadFish.add(fish.duplicateWithNewPositionAndAmount(accBasin, amountToGo));
//}
totalWeight -= weight;
strayedAmount -= amountToGo;
if (strayedAmount <= 0) {
//CHECK if it not alwalys the northorn catcments that do not receive fish
//CHECK if it occurs and for which basins
break;
}
}
......@@ -218,32 +187,18 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
// update fish with homing
if (homingAmount > 0) {
fish.setAmount(homingAmount);
fish.setPosition(homingDestination);
// retour soit dans le bassin de naissance pour les semelpares
// soit dans le dernier bassin de reproduction pour les it�ropares
//fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
fish.setPosition(homingDestination);
homingDestination.addFish(fish, group);
}
/*else {
deadFish.add(fish);
}*/
// remove from the list of departure basin
fishIterator.remove();
} // end if mature
} // end of listiterator
// remove fish from the departure basin
fishIterator.remove();
}
}
}
}
/* for (Duo<DiadromousFish, Basin> duo : fishesToMove) {
duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group);
}
for (DiadromousFish fish : deadFish) {
group.removeAquaNism(fish);
}
for (DiadromousFish fish : newFish) {
group.addAquaNism(fish);
}*/
}
}
}
\ No newline at end of file
}
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