Commit 10525849 authored by patrick.lambert's avatar patrick.lambert
Browse files

code cleaning

parent bcc08e41
package species;
import java.util.List;
import org.openide.util.lookup.ServiceProvider;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Basin;
import environment.Time;
import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.Miscellaneous;
import org.openide.util.lookup.ServiceProvider;
import species.DiadromousFish.Gender;
import species.DiadromousFish.Stage;
import umontreal.iro.lecuyer.probdist.NormalDist;
......@@ -27,30 +21,32 @@ public class Grow extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGr
/**
* temperature minimum for growth
*
* @unit °C
*/
private double tempMinGrow = 3.;
/**
* temperature maximum for growth
*
* @unit °C
*/
private double tempMaxGrow = 26.;
private double tempMaxGrow = 26.;
/**
* temperature optimal for growth
*
* @unit °C
*/
private double tempOptGrow = 17.;
/**
* K, Brody growth rate at optimal temperature
* L = Linf *(1-exp(-K*(t-t0))
* K, Brody growth rate at optimal temperature L = Linf *(1-exp(-K*(t-t0))
*
* @unit year -1
*/
private double kOptForFemale= 0.3;
private double kOptForFemale = 0.3;
/**
* @return the kOptForFemale
*/
......@@ -58,13 +54,16 @@ public class Grow extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGr
return kOptForFemale;
}
/**
* @param kOptForFemale the kOptForFemale to set
* @param kOptForFemale
* the kOptForFemale to set
*/
public void setkOptForFemale(double kOptForFemale) {
this.kOptForFemale = kOptForFemale;
}
/**
* @return the kOptForMale
*/
......@@ -72,95 +71,110 @@ public class Grow extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGr
return kOptForMale;
}
/**
* @param kOptForMale the kOptForMale to set
* @param kOptForMale
* the kOptForMale to set
*/
public void setkOptForMale(double kOptForMale) {
this.kOptForMale = kOptForMale;
}
/**
* K, Brody growth rate at optimal temperature
* L = Linf *(1-exp(-K*(t-t0))
* K, Brody growth rate at optimal temperature L = Linf *(1-exp(-K*(t-t0))
*
* @unit year -1
*/
private double kOptForMale= 0.3;
private double kOptForMale = 0.3;
/**
* standart deviation for the lognormal random draw of growth increment
*
* @unit cm
*/
private double sigmaDeltaLVonBert = 0.2;
private transient NormalGen genNormal;
public static void main(String[] args) { System.out.println((new
XStream(new DomDriver())) .toXML(new Grow())); }
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver())).toXML(new Grow()));
}
@Override
@InitTransientParameters
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
genNormal = new NormalACRGen( pilot.getRandomStream(),
new NormalDist(0., 1.));
genNormal = new NormalACRGen(pilot.getRandomStream(), new NormalDist(0., 1.));
}
@Override
public void doProcess(DiadromousFishGroup group) {
for(Basin basin : group.getEnvironment().getBasins()){
if (basin.getFishs(group)!=null)
for(DiadromousFish fish : basin.getFishs(group)){
for (Basin basin : group.getEnvironment().getBasins()) {
double currentTemperature = basin.getCurrentTemperature(group.getPilot());
if (basin.getFishs(group) != null)
for (DiadromousFish fish : basin.getFishs(group)) {
double muDeltaLVonBert = 0.;
double kVonBert = 0.;
double growthIncrement = 0.;
// 1) calculate the kVonBert
//System.out.println(this.getKOpt(fish, group) );
kVonBert = this.getKOpt(fish, group) *
Miscellaneous.temperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinGrow, tempOptGrow, tempMaxGrow);
// 2) Update the fish length with a lognormal normal draw of increment
// 1) calculate the kVonBert
// System.out.println(this.getKOpt(fish, group) );
kVonBert = this.getKOpt(fish, group)
* Miscellaneous.temperatureEffect(currentTemperature, tempMinGrow, tempOptGrow, tempMaxGrow);
// 2) Update the fish length with a lognormal normal draw of increment
// limit the fish length to Linf
if (fish.getLength() < group.getLinfVonBert(fish)){
muDeltaLVonBert = Math.log((group.getLinfVonBert(fish) - fish.getLength()) * (1 - Math.exp(-kVonBert * group.getEnvironment().getTime().getSeasonDuration()))) - (sigmaDeltaLVonBert*sigmaDeltaLVonBert)/2;
growthIncrement = Math.exp(genNormal.nextDouble()*sigmaDeltaLVonBert + muDeltaLVonBert);
fish.setLength(Math.min(group.getLinfVonBert(fish), fish.getLength() + growthIncrement));
}
else {
double lengthBefore = fish.getLength();
double alea = Double.NaN;
if (fish.getLength() < group.getLinfVonBert(fish)) {
muDeltaLVonBert = Math
.log((group.getLinfVonBert(fish) - fish.getLength())
* (1 - Math.exp(-kVonBert * group.getEnvironment().getTime().getSeasonDuration())))
- (sigmaDeltaLVonBert * sigmaDeltaLVonBert) / 2;
alea = genNormal.nextDouble();
growthIncrement = Math.exp(alea * sigmaDeltaLVonBert + muDeltaLVonBert);
fish.setLength(Math.min(group.getLinfVonBert(fish), fish.getLength() + growthIncrement));
} else {
fish.setLength(group.getLinfVonBert(fish));
}
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+"): "+ growthIncrement);
System.out.println(basin.getName() + " :" + fish.getAge() + " " + fish.getGender() + " : " + lengthBefore
+ " -> " + fish.getLength() + " (" + fish.getStage() + "): " + growthIncrement + " with kVonBert = "
+ kVonBert + " (" + currentTemperature + " / " + alea + ")");
// test if fish become mature
if (fish.getStage() == Stage.IMMATURE && fish.getLength() > group.getlFirstMaturity(fish)){
fish.setStage(Stage.MATURE);
if (fish.getStage() == Stage.IMMATURE && fish.getLength() > group.getlFirstMaturity(fish)) {
fish.setStage(Stage.MATURE);
}
//System.out.println("la temp�rature du lieu de vie du poisson est :" + fish.getPosition().getCurrentTemperature() + ", la saison est :" + Time.getSeason() + " et sa nouvelle taille est :" + fish.getLength());
// System.out.println("la temp�rature du lieu de vie du poisson est :" +
// fish.getPosition().getCurrentTemperature() + ", la saison est :" + Time.getSeason() + " et sa
// nouvelle taille est :" + fish.getLength());
}
}
}
/**
* @param fish
* @param group
* @return the Brody coeff from Diadromousgroup if exists or from this grow process
* depends of the fish gender .In case of undifferentiaced fish, the mean for male and female is considered
* @return the Brody coeff from Diadromousgroup if exists or from this grow process depends of the fish gender .In
* case of undifferentiaced fish, the mean for male and female is considered
*/
public double getKOpt(DiadromousFish fish, DiadromousFishGroup group) {
double kOpt = group.getKOpt(fish);
if (Double.isNaN(kOpt)){ // no definition for the group
if (fish.getGender() == Gender.FEMALE)
kOpt = kOptForFemale;
else if (fish.getGender() == Gender.MALE)
kOpt = kOptForMale;
else
kOpt= (kOptForFemale + kOptForMale) / 2.;
}
return kOpt;
public double getKOpt(DiadromousFish fish, DiadromousFishGroup group) {
double kOpt = group.getKOpt(fish);
if (Double.isNaN(kOpt)) { // no definition for the group
if (fish.getGender() == Gender.FEMALE)
kOpt = kOptForFemale;
else if (fish.getGender() == Gender.MALE)
kOpt = kOptForMale;
else
kOpt = (kOptForFemale + kOptForMale) / 2.;
}
return kOpt;
}
}
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