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Commit cf8b9eb0 authored by Lambert Patrick's avatar Lambert Patrick
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typing correction

parent 0923cfcc
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src/main/java/species/Survive.java
View file @ cf8b9eb0
package species;
import java.io.BufferedWriter;
import java.io.IOException;
import java.util.ArrayList;
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.Basin;
import environment.Basin;
import environment.Basin.TypeBassin;
import environment.Time;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
......@@ -21,28 +18,29 @@ import miscellaneous.BinomialForSuperIndividualGen;
import miscellaneous.Miscellaneous;
import species.DiadromousFish.SpawnerOrigin;
import org.openide.util.lookup.ServiceProvider;
@ServiceProvider(service = AquaNismsGroupProcess.class)
public class Survive extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
public double tempMinSurvivalSpawnerInRiv = 10. ;
public double tempMaxSurvivalSpawnerInRiv = 23. ; // DEFINIR TROIS AUTRES POUR MORTALITE
public double tempMinSurvivalSpawnerInRiv = 10.;
public double tempMaxSurvivalSpawnerInRiv = 23.; // DEFINIR TROIS AUTRES POUR MORTALITE
public double tempOptSurvivalSpawnerInRiv = 20.;
public double survivalProbOptSpawnerInRiv = 1.;
//public double mortalityRateInRiver = 0.4;
// public double mortalityRateInRiver = 0.4;
public double mortalityRateInSea = 0.4;
public double mortalityRateInOffshore = 0.4;
/**
* 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 Survive())); }
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver())).toXML(new Survive()));
}
@Override
......@@ -51,106 +49,123 @@ public class Survive extends AquaNismsGroupProcess<DiadromousFish, DiadromousFis
aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
}
@Override
public void doProcess(DiadromousFishGroup group) {
Time time = group.getEnvironment().getTime();
double survivalProbability=1.;
double survivalProbability = 1.;
long survivalAmount;
long deathAmount;
Map<SpawnerOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<SpawnerOrigin, Map <String, Double>>(); //On cr�er la Map pour stocker les flux
totalInputFluxes.put(SpawnerOrigin.AUTOCHTONOUS, new Hashtable < String, Double>());
totalInputFluxes.put(SpawnerOrigin.ALLOCHTONOUS, new Hashtable < String, Double>());
for (SpawnerOrigin origin: totalInputFluxes.keySet()) {
long deathAmount;
Map<SpawnerOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<SpawnerOrigin, Map<String, Double>>(); // On
// cr�er
// la
// Map
// pour
// stocker
// les
// flux
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(nutrient, 0.); // ON MET A JOUR NOTRE map
}
totalInputFluxes.get(origin).put("biomass",0.);
totalInputFluxes.get(origin).put("biomass", 0.);
}
//double sumNGuadalquivir = 0.;
// double sumNGuadalquivir = 0.;
for(Basin basin : group.getEnvironment().getBasins()){
//System.out.print(basin.getName());
for (Basin basin : group.getEnvironment().getBasins()) {
// System.out.print(basin.getName());
if (basin.getFishs(group)!=null) {
//System.out.println(" y a des poissons");
if (basin.getFishs(group) != null) {
// System.out.println(" y a des poissons");
ListIterator<DiadromousFish> fishIterator = basin.getFishs(group).listIterator();
while (fishIterator.hasNext()) {
DiadromousFish fish = fishIterator.next();
DiadromousFish fish = fishIterator.next();
survivalProbability = 1.;
//Compute the survival probability according to the fish position
if(fish.getPosition().getType() == TypeBassin.RIVER && fish.isMature()){ //Survive in river before spawning
//double tempEffectSurv = Miscellaneous.temperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinSurvivalSpawnerInRiv, tempOptSurvivalSpawnerInRiv, tempMaxSurvivalSpawnerInRiv);
double tempEffectSurv = Miscellaneous.rectangularTemperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinSurvivalSpawnerInRiv, tempMaxSurvivalSpawnerInRiv);
if (tempEffectSurv == 0.){
// Compute the survival probability according to the fish position
if (fish.getPosition().getType() == TypeBassin.RIVER && fish.isMature()) { // Survive in river
// before spawning
// double tempEffectSurv =
// Miscellaneous.temperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()),
// tempMinSurvivalSpawnerInRiv, tempOptSurvivalSpawnerInRiv, tempMaxSurvivalSpawnerInRiv);
double tempEffectSurv = Miscellaneous.rectangularTemperatureEffect(
fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinSurvivalSpawnerInRiv,
tempMaxSurvivalSpawnerInRiv);
if (tempEffectSurv == 0.) {
survivalProbability = 0.;
//System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en " + Time.getSeason() +" a un coeff de mortalit� de " + fish.getMortalityRateInRiver() + " mais � cause de la temp�rature une prob de survie de " + survivalProbability);
}else{
// System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + "
// en " + Time.getSeason() +" a un coeff de mortalit� de " + fish.getMortalityRateInRiver()
// + " mais � cause de la temp�rature une prob de survie de " + survivalProbability);
} else {
survivalProbability = survivalProbOptSpawnerInRiv * tempEffectSurv;
//System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en " + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInRiver() + " et donc une prob de survie de " + survivalProbability);
}
//TODO:add nutrientFluxesRoutine
// System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + "
// en " + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInRiver()
// + " et donc une prob de survie de " + survivalProbability);
}
// TODO:add nutrientFluxesRoutine
}else if (fish.getPosition().getType() == TypeBassin.SEA){ //Survive at sea
} else if (fish.getPosition().getType() == TypeBassin.SEA) { // Survive at sea
survivalProbability = Math.exp(-mortalityRateInSea * time.getSeasonDuration());
//System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en " + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInSea() + " et donc une prob de survie de " + survivalProbability);
// System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en "
// + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInSea() + " et
// donc une prob de survie de " + survivalProbability);
}else if (fish.getPosition().getType() == TypeBassin.OFFSHORE){ //Survive offshore
} else if (fish.getPosition().getType() == TypeBassin.OFFSHORE) { // Survive offshore
survivalProbability = Math.exp(-mortalityRateInOffshore * time.getSeasonDuration());
//System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en " + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInOffshore() + " et donc une prob de survie de " + survivalProbability);
// System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en "
// + Time.getSeason() + " a un coeff de mortalit� de " + fish.getMortalityRateInOffshore() + "
// et donc une prob de survie de " + survivalProbability);
}else{
} else {
survivalProbability = 1.;
}
//Compute survival amount in the SI for one fish whatever its position
deathAmount = 0L;
if (survivalProbability<1.){
survivalAmount = aleaGen.getSuccessNumber2(fish.getAmount(), survivalProbability);
// Compute survival amount in the SI for one fish whatever its position
deathAmount = 0L;
if (survivalProbability < 1.) {
survivalAmount = aleaGen.getSuccessNumber(fish.getAmount(), survivalProbability);
deathAmount = fish.getAmount() - survivalAmount;
if (survivalAmount > 0)
if (survivalAmount > 0)
fish.setAmount(survivalAmount);
else
else
fishIterator.remove();
if (deathAmount > 0L && fish.getPosition().getType() == TypeBassin.RIVER) { //Compute the fluxes for dead fish in river in the SI.
if (deathAmount > 0L && fish.getPosition().getType() == TypeBassin.RIVER) { // Compute the
// fluxes for dead
// fish in river in
// the SI.
SpawnerOrigin spawnerOrigin;
if (fish.getBirthBasin() == basin)
spawnerOrigin = SpawnerOrigin.AUTOCHTONOUS;
SpawnerOrigin spawnerOrigin;
if (fish.getBirthBasin() == basin)
spawnerOrigin = SpawnerOrigin.AUTOCHTONOUS;
else
spawnerOrigin = SpawnerOrigin.ALLOCHTONOUS;
Map<String, Double> aFluxForDeadFishBeforeSpawning = group.getNutrientRoutine().computeNutrientsInputForDeathBeforeSpawning(fish); //
Map<String, Double> aFluxForDeadFishBeforeSpawning = group.getNutrientRoutine()
.computeNutrientsInputForDeathBeforeSpawning(fish); //
for (String nutrient: aFluxForDeadFishBeforeSpawning.keySet()) {
group.getNutrientRoutine().getNutrientImportFluxesCollection().
put(time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(), basin.getName(), aFluxForDeadFishBeforeSpawning.get(nutrient) * deathAmount);
for (String nutrient : aFluxForDeadFishBeforeSpawning.keySet()) {
group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
basin.getName(), aFluxForDeadFishBeforeSpawning.get(nutrient) * deathAmount);
}
/*
* if
* (basin.getName().equalsIgnoreCase("Guadalquivir")
* ) { sumNGuadalquivir +=
* aFluxForDeadFishBeforeSpawning.get("N") *
* deathAmount;
* System.out.println(Time.getYear(group.getPilot())
* + " : " + sumNGuadalquivir); }
* if (basin.getName().equalsIgnoreCase("Guadalquivir") ) { sumNGuadalquivir +=
* aFluxForDeadFishBeforeSpawning.get("N") * deathAmount;
* System.out.println(Time.getYear(group.getPilot()) + " : " + sumNGuadalquivir); }
*/
}
}
}//end on loop of fish
} // end on loop of fish
}
} //end loop on basin
}//end of doprocess
}//end of class
} // end loop on basin
}// end of doprocess
}// end of class
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