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Commit aa39fab2 authored by Lambert Patrick's avatar Lambert Patrick
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typing correction

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src/main/java/species/DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin.java
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package species;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
import environment.Basin;
import org.openide.util.lookup.ServiceProvider;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.BasinNetwork;
import environment.RiverBasin;
import environment.SeaBasin;
......@@ -16,15 +19,7 @@ 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;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import miscellaneous.BinomialForSuperIndividualGen;
import miscellaneous.Duo;
/**
*
......@@ -32,86 +27,103 @@ import miscellaneous.Duo;
@ServiceProvider(service = AquaNismsGroupProcess.class)
public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends DisperseAndMigrateToRiverBasic {
/**
* the season when fish migrate to the river to reproduce
*
* @unit
*/
private Season riverMigrationSeason = Season.SPRING;
/**
* the homing probalilty during the installation of new populations ( to reach kind of equilibrium)
* the homing probalilty during the installation of new populations ( to reach kind of equilibrium)
*
* @unit
*/
private double pHomingForReachEquil = 1.0;
/**
* the homing probalilty after the installation of new populations ( after reaching an equilibrium)
* the homing probalilty after the installation of new populations ( after reaching an equilibrium)
*
* @unit
*/
private double pHomingAfterEquil = 0.8;
/**
* Number of year for newly created populations to be installed ( to reach an equilibrium)
*
* @unit
*/
private long NbYearForInstallPop = 50;
/** the coefficient associated with the fish size in the logistic function used to calculate the probability to disperse
/**
* the coefficient associated with the fish size in the logistic function used to calculate the probability to
* disperse
*
* @unit -
*/
private double alpha2Rep = 0.;
/**
* the mean length used to standardize the fish length in the logistic function that calculates the probability to disperse
/**
* the mean length used to standardize the fish length in the logistic function that calculates the probability to
* disperse
*
* @unit -
*/
private double meanSpawnersLengthAtRepro = 45.;
/**
* the length standard deviation used to standardize the fish length in the logistic function that calculates the probability to disperse
/**
* the length standard deviation used to standardize the fish length in the logistic function that calculates the
* probability to disperse
*
* @unit -
*/
private double standardDeviationOfSpawnersLengthAtRepro = 2.; // for standard core values...
/**
* the weigth of the death bassin ( for strayers that do not find a catcment) used to calculate the probability to disperse
* the weigth of the death bassin ( for strayers that do not find a catcment) used to calculate the probability to
* disperse
*
* @unit
*/
private double weightOfDeathBasin = 0.2;
/**
* a bollean to kill of the strayers (used to determine if a catchment is a souce or a sink) the year given by yearOfTheKilling
* a bollean to kill of the strayers (used to determine if a catchment is a souce or a sink) the year given by
* yearOfTheKilling
*
* @unit
*/
private boolean killStrayers;
/**
* the year when the strayers are killed (used to determine if a catchment is a souce or a sink) if killStrayers is true
* the year when the strayers are killed (used to determine if a catchment is a souce or a sink) if killStrayers is
* true
*
* @unit
*/
private long yearOfTheKillings;
/**
* 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 DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin()));
System.out.println(
(new XStream(new DomDriver())).toXML(new DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin()));
}
@Override
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
}
@Override
public void doProcess(DiadromousFishGroup group) {
Time time = group.getEnvironment().getTime();
......@@ -135,67 +147,80 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
List<DiadromousFish> fishes = departure.getFishs(group);
if (fishes != null) {
//for (DiadromousFish fish : fishes) {
// for (DiadromousFish fish : fishes) {
ListIterator<DiadromousFish> fishIterator = fishes.listIterator();
while (fishIterator.hasNext()) {
DiadromousFish fish=fishIterator.next();
DiadromousFish fish = fishIterator.next();
if (fish.isMature()) {
// fish with homing
//homingAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50
homingAmount = aleaGen.getSuccessNumber2(fish.getAmount(), pHoming);
// strayed fish
// homingAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(),
// fish.getAmount(), pHoming);
homingAmount = aleaGen.getSuccessNumber(fish.getAmount(), pHoming);
// strayed fish
if (killStrayers == true && time.getYear(group.getPilot()) >= yearOfTheKillings) {
strayedAmount = 0;
}
else {
} else {
strayedAmount = fish.getAmount() - homingAmount;
}
// influence of the fish length on the probability to disperse
if (strayedAmount != 0) {
// calcula the weight associated with the fish length in the probabaility to disperse
double weightFishLength = -(alpha2Rep * ((fish.getLength() - meanSpawnersLengthAtRepro) / standardDeviationOfSpawnersLengthAtRepro));
double weightFishLength = -(alpha2Rep * ((fish.getLength() - meanSpawnersLengthAtRepro)
/ standardDeviationOfSpawnersLengthAtRepro));
// We fill the weight table
double totalWeight = 0.;
double probToGo = 0.;
long amountToGo = 0;
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)));
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 (group.isThereBasinToUpdate()) {
if (time.getYear(group.getPilot()) >= group.getYearOfTheUpdate()
&& group.getPattractive(entry.getKey().getName()) == 0){
//TODO use correctely getPaccessible
accBasinWeight = 0 ;
&& group.getPattractive(entry.getKey().getName()) == 0) {
// TODO use correctely getPaccessible
accBasinWeight = 0;
}
}
totalWeight += accBasinWeight;
basinWeightsFromDeparture.put (entry.getKey(),accBasinWeight );
basinWeightsFromDeparture.put(entry.getKey(), accBasinWeight);
}
// sum the deathBasin weight in the list
totalWeight = totalWeight + weightOfDeathBasin;
// compute sequentially the prob to go into a basin
for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {
// Afficher le contenu du MAP
Iterator<RiverBasin> iterateur = basinWeightsFromDeparture.keySet().iterator();
// Parcourir les clés et afficher les entrées de chaque clé;
while (iterateur.hasNext()) {
RiverBasin key = iterateur.next();
System.out.println(key.getName() + "=>" + basinWeightsFromDeparture.get(key));
}
System.out.println();
// compute sequentially the prob to go into a basin
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);
amountToGo = aleaGen.getSuccessNumber2(strayedAmount, probToGo);
// amountToGo = Miscellaneous.binomialForSuperIndividual(group.getPilot(),
// strayedAmount, probToGo);
amountToGo = aleaGen.getSuccessNumber(strayedAmount, probToGo);
if (amountToGo > 0) {
strayerDestination.addFish(fish.duplicateWithNewPositionAndAmount(group.getPilot(), strayerDestination, amountToGo), group);
strayerDestination.addFish(fish.duplicateWithNewPositionAndAmount(
group.getPilot(), strayerDestination, amountToGo), group);
}
totalWeight -= weight;
strayedAmount -= amountToGo;
if (strayedAmount <= 0) {
//CHECK if it occurs and for which basins
// CHECK if it occurs and for which basins
break;
}
}
......@@ -205,10 +230,10 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
if (homingAmount > 0) {
fish.setAmount(homingAmount);
fish.setPosition(homingDestination);
// retour soit dans le bassin de naissance pour les semelpares
// retour soit dans le bassin de naissance pour les semelpares
// soit dans le dernier bassin de reproduction pour les it�ropares
homingDestination.addFish(fish, group);
}
}
// remove fish from the departure basin
fishIterator.remove();
......
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