diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index 6236237886728ab546c03a51417852ddee2d881b..d0a9a1a6bcaeb1730f94f96d66573c485346b430 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -227,6 +227,7 @@
<yearOfTheUpdate>0</yearOfTheUpdate>
<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
<outputPath>data/output/</outputPath>
+ <fileNameFluxes>nutrientFluxes</fileNameFluxes>
<processes>
<processesAtBegin>
<species.PopulateBasinNetworkWithANorthLimit>
@@ -306,11 +307,13 @@
<maxNumberOfSuperIndividualPerReproduction>50.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
+ <displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+ <displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.MigrateToSea>
<environment.updateTemperatureInRealBasin>
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 67d2454f4b121b10f28ba7867b4a79d72e9e141a..4ad4c7b26cb5694452a1f0d587c714732a016eff 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -13,7 +13,10 @@ import fr.cemagref.simaqualife.kernel.Processes;
import fr.cemagref.simaqualife.pilot.Pilot;
import java.awt.Color;
+import java.io.BufferedWriter;
+import java.io.File;
import java.io.FileReader;
+import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -65,7 +68,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
private NutrientRoutine nutrientRoutine;
public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
-
+
/**
* centile to calucale the range of species distribution
* @unit
@@ -100,6 +103,11 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
private String outputPath = "data/output/";
+
+ private String fileNameFluxes = "fluxes";
+
+ private transient BufferedWriter bWForFluxes;
+ private transient String sep;
/**
* map
@@ -394,6 +402,35 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
kOpt = parameterSets.get(parameterSetLine-1).getFirst();
tempMinRep = parameterSets.get(parameterSetLine-1).getSecond();
}
+
+ // open an bufferad writer to export fluxes
+ if (fileNameFluxes != null){
+ sep = ";";
+ new File(this.outputPath +fileNameFluxes).getParentFile().mkdirs();
+ try {
+ bWForFluxes = new BufferedWriter(new FileWriter(new File(this.outputPath+
+ fileNameFluxes +this.getSimulationId()+ ".csv")));
+
+ bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
+ +sep+"fluxType"+sep+"origine"+sep+"biomass");
+ for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
+ bWForFluxes.write(sep+nutrient);
+ }
+ bWForFluxes.write("\n");
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+
+ /**
+ * @return the bWForFluxes
+ */
+ public BufferedWriter getbWForFluxes() {
+ return bWForFluxes;
}
public double getKOpt(){
diff --git a/src/main/java/species/MigrateToSea.java b/src/main/java/species/MigrateToSea.java
index 206043342e5bf624554daa588f8c98e9f6c507ae..e5887e23e4d81eef860b9370f8e10de482cf99fd 100644
--- a/src/main/java/species/MigrateToSea.java
+++ b/src/main/java/species/MigrateToSea.java
@@ -8,6 +8,9 @@ import environment.RiverBasin;
import environment.Time;
import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
@@ -15,7 +18,6 @@ import java.util.Map;
import miscellaneous.Duo;
import species.DiadromousFish.Stage;
-
import org.openide.util.lookup.ServiceProvider;
@ServiceProvider(service = AquaNismsGroupProcess.class)
@@ -23,6 +25,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
private Season seaMigrationSeason = Season.SUMMER;
+ private boolean displayFluxesOnConsole = true;
+
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver()))
.toXML(new MigrateToSea()));
@@ -33,48 +37,65 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
if (Time.getSeason(group.getPilot()) == seaMigrationSeason ){
Basin destination;
-
- //On créer la Map pour stocker les flux d'export
+
+ //On cr�er la Map pour stocker les flux d'export
Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>();
-
+
List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
//Fish move to sea and compute the related export of nutrients
List<DiadromousFish> fishes = basin.getFishs(group);
-
- // ON ré-initialise notre map pour chauqe bassin
+
+ // ON r�-initialise notre map pour chauqe bassin
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
totalOutputFluxes.put(nutrient, 0.);
}
- totalOutputFluxes.put("biomass", 0.); //création de la biomasse
-
+ totalOutputFluxes.put("biomass", 0.); //cr�ation de la biomasse
+
if (fishes!=null) {
for (DiadromousFish fish : fishes) {
destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination)); //Mentionne la sortie d'un poisson de la boucle
-
+
double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
-
+
if (fish.getStage()==Stage.IMMATURE) {
Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish);
for (String nutrient: aFluxExportedByJuveniles.keySet()) {
totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount());
}
-
+
totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass);
}
}
}
-
+
for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
- duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on déplace les poissons dans le fichier MoveTo et on dénote la destination du poisson.
+ duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on d�place les poissons dans le fichier MoveTo et on d�note la destination du poisson.
+ }
+
+ if (displayFluxesOnConsole)
+ System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
+ + basin.getName() + "; " + totalOutputFluxes);
+
+ BufferedWriter bW = group.getbWForFluxes();
+ if ( bW != null) {
+ try {
+
+ bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
+ +";"+ basin.getName() + ";IMPORT; NONE");
+ bW.write(";" + totalOutputFluxes.get("biomass"));
+ for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+ bW.write(";" + totalOutputFluxes.get(nutrient));
+ }
+ bW.write("\n");
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
}
- System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
- + basin.getName() + "; " + totalOutputFluxes);
}
}
-
-
}
}
\ No newline at end of file
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 20dd84d3ec092eacd6f6af7037d4e2241487290d..5bebd92294b095d9bc34f8c377e9cbd53065ae50 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -1,6 +1,8 @@
package species;
+import java.io.BufferedWriter;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
@@ -59,9 +61,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private double maxNumberOfSuperIndividualPerReproduction = 50.;
private boolean withDiagnose = true;
+ private boolean displayFluxesOnConsole = true;
+
private transient NormalGen genNormal;
private transient MortalityFunction mortalityFunction;
+
+ private enum fluxOrigin {AUTOCHTONOUS, ALLOCHTONOUS};
/**
* relationship between
* recruitment in number of juvenile on spawning grounds
@@ -110,10 +116,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
if (fishInBasin != null){
//Initiate the total fluxes for this basin
- Map<String, Map<String, Double>> totalInputFluxes = new Hashtable<String, Map <String, Double>>(); //On créer la Map pour stocker les flux
- totalInputFluxes.put("autochtonous", new Hashtable < String, Double>());
- totalInputFluxes.put("allochtonous", new Hashtable < String, Double>());
- for (String origin: totalInputFluxes.keySet()) {
+ Map<fluxOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<fluxOrigin, Map <String, Double>>(); //On cr�er la Map pour stocker les flux
+ totalInputFluxes.put(fluxOrigin.AUTOCHTONOUS, new Hashtable < String, Double>());
+ totalInputFluxes.put(fluxOrigin.ALLOCHTONOUS, new Hashtable < String, Double>());
+ for (fluxOrigin origin: totalInputFluxes.keySet()) {
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
totalInputFluxes.get(origin).put(nutrient, 0.); // ON MET A JOUR NOTRE map
}
@@ -195,11 +201,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
double biomass = 0.;
- String origin;
+ fluxOrigin origin;
if(fish.getBirthBasin()== riverBasin)
- origin = "autochtonous";
+ origin = fluxOrigin.AUTOCHTONOUS;
else
- origin = "allochtonous";
+ origin = fluxOrigin.ALLOCHTONOUS;
if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs
//Export for fishes survived after spawning (survivalAmount) : excretion + gametes
@@ -395,9 +401,28 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
deadFish.clear();
- System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
- + riverBasin.getName() + "; " + totalInputFluxes);
+ if (displayFluxesOnConsole)
+ System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
+ + riverBasin.getName() + "; " + totalInputFluxes);
+
+ BufferedWriter bW = group.getbWForFluxes();
+ if ( bW != null) {
+ try {
+ for (fluxOrigin origin : totalInputFluxes.keySet()) {
+ bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
+ +";"+ riverBasin.getName() + ";IMPORT;"+origin);
+ bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
+ for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+ bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
+ }
+ bW.write("\n");
+ }
+ } catch (IOException e) {
+
+ e.printStackTrace();
+ }
+ }
}
else {
riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));