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Commit 43df1645 authored by Poulet Camille's avatar Poulet Camille
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Quantification of Fluxes with value for Post spawning

parent c429ef1f
master BasinImprovement Camille DeplacementBasin Script SpawnerRunAnalysis atlantic_area develop exploration_GR3D_process hotfix3.2.1 v3.2.1 v3.2.1.b v3.2.0 v3.1 V3.2.1.a
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src/main/java/species/FishNutrient.java
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...@@ -31,9 +31,9 @@ import java.util.Hashtable; ...@@ -31,9 +31,9 @@ import java.util.Hashtable;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
/** import com.thoughtworks.xstream.XStream;
* import com.thoughtworks.xstream.io.xml.DomDriver;
*/
/** /**
* @author camille.poulet * @author camille.poulet
...@@ -41,6 +41,7 @@ import java.util.Map; ...@@ -41,6 +41,7 @@ import java.util.Map;
*/ */
public class FishNutrient { public class FishNutrient {
private ArrayList<String> nutrientsOfInterest;
/** /**
* Main feature for weight computation before spawning i.e. gametes expelling //Voir pour un retour la ligne lors du commentaire * Main feature for weight computation before spawning i.e. gametes expelling //Voir pour un retour la ligne lors du commentaire
* key gender * key gender
...@@ -48,20 +49,13 @@ public class FishNutrient { ...@@ -48,20 +49,13 @@ public class FishNutrient {
* key feature * key feature
* value value * value value
*/ */
private Map <Gender,Map<String, Double>> fishFeatures; private Map <Gender,Map<String, Double>> fishFeaturesPreSpawning;
// Si on ne possede pas wT post reproduction private Map <Gender, Map<String, Double>> fishFeaturesPostSpawning;
private double aLWfemalePost = 0.; private Map <String, Double> juvenileFeatures;
private double bLWfemalePost = 0.;
private double GSIfemalePost=0.10;
private double aLWmalePost = 0.;
private double bLWmalePost = 0.;
private double GSImalePost =.07;
// Valeurs de Haskell pour A. sapidissima -- A rechercher pour Alosa alosa
/** /**
* chemical composition of carcass before gametes expelling (before spawning) i.e. carcass + gonads + gametes * chemical composition of carcass before gametes expelling (before spawning) i.e. carcass + gonads + gametes
* <key> gender * <key> gender
...@@ -83,7 +77,7 @@ public class FishNutrient { ...@@ -83,7 +77,7 @@ public class FishNutrient {
* <value> value * <value> value
*/ */
private Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning; private Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning;
/** /**
* chemical composition of gametes * chemical composition of gametes
* <key> gender * <key> gender
...@@ -105,8 +99,6 @@ public class FishNutrient { ...@@ -105,8 +99,6 @@ public class FishNutrient {
private Map<String,Double> compoJuvenile; private Map<String,Double> compoJuvenile;
private double aLWjuveniles = -11.942 ; // parametre "a" de la relation taille/poids avec Lt en cm - Traduit la condition
private double bLWjuveniles = 3.0306; // parametre "b" de la relation taille/poids - Coefficient d'allometrie
/** /**
* *
...@@ -118,24 +110,28 @@ public class FishNutrient { ...@@ -118,24 +110,28 @@ public class FishNutrient {
/** /**
* Constructor based on the 5 Map of fish composition * Constructor based on the 5 Map of fish composition
* @param fishFeatures * @param fishFeaturesPreSpawning
* @param compoCarcassPreSpawning * @param compoCarcassPreSpawning
* @param compoCarcassPostSpawning * @param compoCarcassPostSpawning
* @param compoGametes * @param compoGametes
* @param compoJuvenile * @param compoJuvenile
*/ */
public FishNutrient(Map<Gender, Map<String, Double>> fishFeatures, public FishNutrient(ArrayList<String> nutrientsOfInterest, Map<Gender, Map<String, Double>> fishFeaturesPreSpawning,
Map<Gender, Map<String, Double>> fishFeaturesPostSpawning,
Map<Gender, Map<String, Double>> compoCarcassPreSpawning, Map<Gender, Map<String, Double>> compoCarcassPreSpawning,
Map<Gender, Map<String, Double>> compoCarcassPostSpawning, Map<Gender, Map<String, Double>> compoGametes, Map<Gender, Map<String, Double>> compoCarcassPostSpawning, Map<Gender, Map<String, Double>> compoGametes,
Map<String, Double> compoJuvenile,double aLWjuveniles, double bLWjuveniles ) { Map<String, Double> juvenileFeatures,
Map<String, Double> compoJuvenile) {
super(); super();
this.fishFeatures = fishFeatures; this.nutrientsOfInterest = nutrientsOfInterest;
this.fishFeaturesPreSpawning = fishFeaturesPreSpawning;
this.fishFeaturesPostSpawning = fishFeaturesPostSpawning;
this.compoCarcassPreSpawning = compoCarcassPreSpawning; this.compoCarcassPreSpawning = compoCarcassPreSpawning;
this.compoCarcassPostSpawning = compoCarcassPostSpawning; this.compoCarcassPostSpawning = compoCarcassPostSpawning;
this.compoGametes = compoGametes; this.compoGametes = compoGametes;
this.juvenileFeatures = juvenileFeatures;
this.compoJuvenile = compoJuvenile; this.compoJuvenile = compoJuvenile;
this.aLWjuveniles = aLWjuveniles;
this.bLWjuveniles = bLWjuveniles;
} }
/** /**
...@@ -149,7 +145,7 @@ public class FishNutrient { ...@@ -149,7 +145,7 @@ public class FishNutrient {
for (String nutrient : nutrientsOfInterest) { for (String nutrient : nutrientsOfInterest) {
if (fish.getStage()== Stage.MATURE) { if (fish.getStage()== Stage.MATURE) {
double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW")); double totalWeightPre = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW"));
//totalWeightPost = totalWeightPre * (1-GSIfemalePost)+ totalWeightPost * GSIfemalePost * CoeffLossWeight //totalWeightPost = totalWeightPre * (1-GSIfemalePost)+ totalWeightPost * GSIfemalePost * CoeffLossWeight
nutrientsInput.put(nutrient, totalWeightPre * compoCarcassPreSpawning.get(fish.getGender()).get(nutrient)); nutrientsInput.put(nutrient, totalWeightPre * compoCarcassPreSpawning.get(fish.getGender()).get(nutrient));
} }
...@@ -160,6 +156,11 @@ public class FishNutrient { ...@@ -160,6 +156,11 @@ public class FishNutrient {
return nutrientsInput; return nutrientsInput;
} }
public Map<String,Double> computeNutrientsInputForDeathBeforeSpawning(DiadromousFish fish) {
return computeNutrientsInputForDeathBeforeSpawning(fish,this.nutrientsOfInterest);
}
/** /**
* compute the nutrient fluxes for a single fish (in the super individual) * compute the nutrient fluxes for a single fish (in the super individual)
* that dies after spawning (gametes expelling) * that dies after spawning (gametes expelling)
...@@ -173,10 +174,12 @@ public class FishNutrient { ...@@ -173,10 +174,12 @@ public class FishNutrient {
if (fish.getStage()== Stage.MATURE) { if (fish.getStage()== Stage.MATURE) {
double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW")); double totalWeightPre = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW") *
//TODO Fix the new data Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW"));
double totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost); double totalWeightPost = fishFeaturesPostSpawning.get(fish.getGender()).get("aLW") *
nutrientsInput.put(nutrient,(totalWeightPre - totalWeightPost) * compoCarcassPostSpawning.get(fish.getGender()).get(nutrient)); Math.pow(fish.getLength(), fishFeaturesPostSpawning.get(fish.getGender()).get("bLW"));
nutrientsInput.put(nutrient,(totalWeightPre - totalWeightPost) *
compoCarcassPostSpawning.get(fish.getGender()).get(nutrient));
} }
else { else {
nutrientsInput.put(nutrient,0.); nutrientsInput.put(nutrient,0.);
...@@ -185,7 +188,10 @@ public class FishNutrient { ...@@ -185,7 +188,10 @@ public class FishNutrient {
return nutrientsInput; return nutrientsInput;
} }
public Map<String, Double> computeNutrientsInputForDeathAfterSpawning(DiadromousFish fish){
return computeNutrientsInputForDeathAfterSpawning(fish, this.nutrientsOfInterest);
}
/** /**
* compute the nutrient fluxes for a single fish (in the super individual) * compute the nutrient fluxes for a single fish (in the super individual)
* that survives after spawning * that survives after spawning
...@@ -198,10 +204,13 @@ public class FishNutrient { ...@@ -198,10 +204,13 @@ public class FishNutrient {
for (String nutrient: nutrientsOfInterest) { for (String nutrient: nutrientsOfInterest) {
if (fish.getStage()==Stage.MATURE) { if (fish.getStage()==Stage.MATURE) {
double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW")); double totalWeightPre = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW")
//TODO Fix with new data * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW"));
double totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost); //TODO Fix with new data
nutrientsInput.put(nutrient, (totalWeightPre - totalWeightPost) * compoGametes.get(fish.getGender()).get(nutrient)); double totalWeightPost = fishFeaturesPostSpawning.get(fish.getGender()).get("aLW")
* Math.pow(fish.getLength(), fishFeaturesPostSpawning.get(fish.getGender()).get("bLW"));
nutrientsInput.put(nutrient, (totalWeightPre - totalWeightPost) *
compoGametes.get(fish.getGender()).get(nutrient));
} }
else { else {
nutrientsInput.put(nutrient,0.); nutrientsInput.put(nutrient,0.);
...@@ -210,36 +219,66 @@ public class FishNutrient { ...@@ -210,36 +219,66 @@ public class FishNutrient {
return nutrientsInput; return nutrientsInput;
} }
public Map<String,Double> computeNutrientsExportForJuveniles (DiadromousFish juvenileFish, ArrayList<String>nutrientsOfInterest) { public Map<String,Double>computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish) {
return computeNutrientsInputForSurvivalAfterSpawning(fish, this.nutrientsOfInterest);
}
public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish, ArrayList<String>nutrientsOfInterest) {
Map<String,Double> nutrientsExport = new Hashtable<String,Double>(); Map<String,Double> nutrientsExport = new Hashtable<String,Double>();
for(String nutrient: nutrientsOfInterest) { for(String nutrient: nutrientsOfInterest) {
if(juvenileFish.getStage()==Stage.IMMATURE) { if(juvenileFish.getStage()==Stage.IMMATURE) {
double JuvenileMass = aLWjuveniles * Math.pow(juvenileFish.getLength(), bLWjuveniles); double JuvenileMass = juvenileFeatures.get("aLW") *
Math.pow(juvenileFish.getLength(), juvenileFeatures.get("bLW"));
nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient)); nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient));
} }
} }
return nutrientsExport; return nutrientsExport;
} }
public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish){
return computeNutrientsExportForJuveniles(juvenileFish, this.nutrientsOfInterest);
}
/**
* @param args
*/
public static void main(String[] args) { public static void main(String[] args) {
Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>(); Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
Map<String,Double> aFeature = new Hashtable<String,Double>(); Map<String,Double> aFeature = new Hashtable<String,Double>();
aFeature.put("aLW",1.2102E-6); // parametre "a" de la relation taille/poids avec Lt en cm - Traduit la condition
aFeature.put("bLW",3.3429);// parametre "b" de la relation taille/poids - Coefficient d'allometrie aFeature.put("bLW",3.3429);// parametre "b" de la relation taille/poids - Coefficient d'allometrie
aFeature.put("aLW",1.2102E-6 * Math.pow(10., aFeature.get("bLW"))); // parametre "a" de la relation taille/poids en kg/cm- Traduit la condition
aFeature.put("GSI",0.15); aFeature.put("GSI",0.15);
aFeaturePreSpawning.put(Gender.FEMALE, aFeature); aFeaturePreSpawning.put(Gender.FEMALE, aFeature);
aFeature = new Hashtable<String,Double>(); aFeature = new Hashtable<String,Double>();
aFeature.put("aLW",2.4386E-6);
aFeature.put("bLW",3.2252); aFeature.put("bLW",3.2252);
aFeature.put("aLW",2.4386E-6 * Math.pow(10, aFeature.get("bLW"))); // Conversion des g/mm en g.cm (from Taverny, 1991)
aFeature.put("GSI",.07); aFeature.put("GSI",.07);
aFeaturePreSpawning.put(Gender.MALE,aFeature); aFeaturePreSpawning.put(Gender.MALE,aFeature);
System.out.println(aFeaturePreSpawning.toString()); // System.out.println("aFeaturePreSpawning: " + aFeaturePreSpawning.toString()); //
Map<Gender, Map<String, Double>> aFeaturePostSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
aFeature = new Hashtable<String,Double>();
aFeature.put("GSI",0.15);
aFeature.put("aLW",aFeaturePreSpawning.get(Gender.FEMALE).get("aLW")/(1+aFeature.get("GSI"))); // parametre "a" de la relation taille/poids avec Lt en cm - Traduit la condition
aFeature.put("bLW",aFeaturePreSpawning.get(Gender.FEMALE).get("bLW"));// parametre "b" de la relation taille/poids - Coefficient d'allometrie
aFeaturePostSpawning.put(Gender.FEMALE, aFeature);
aFeature = new Hashtable<String,Double>();
aFeature.put("GSI",.07);
aFeature.put("aLW",aFeaturePreSpawning.get(Gender.MALE).get("aLW")/(1+aFeature.get("GSI")));
aFeature.put("bLW",aFeaturePreSpawning.get(Gender.MALE).get("bLW"));
aFeaturePostSpawning.put(Gender.MALE,aFeature);
System.out.println("aFeaturePostSpawning: " + aFeaturePostSpawning.toString());
// carcass composition for fish before spawning // carcass composition for fish before spawning
Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>(); Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
Map<String,Double> aCompo = new Hashtable<String,Double>(); Map<String,Double> aCompo = new Hashtable<String,Double>();
...@@ -252,7 +291,7 @@ public class FishNutrient { ...@@ -252,7 +291,7 @@ public class FishNutrient {
aCompo.put("P",0.662); aCompo.put("P",0.662);
aCompoCarcassPreSpawning.put(Gender.MALE,aCompo); aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
System.out.println(aCompoCarcassPreSpawning.toString()); // System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //
// carcass composition for fish after spawning // carcass composition for fish after spawning
Map<Gender, Map<String, Double>> aCompoCarcassPostSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>(); Map<Gender, Map<String, Double>> aCompoCarcassPostSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
...@@ -262,55 +301,70 @@ public class FishNutrient { ...@@ -262,55 +301,70 @@ public class FishNutrient {
aCompoCarcassPostSpawning.put(Gender.FEMALE,aCompo); aCompoCarcassPostSpawning.put(Gender.FEMALE,aCompo);
aCompo = new Hashtable<String,Double>(); aCompo = new Hashtable<String,Double>();
aCompo.put("N", 2.790); aCompo.put("N", 2.790); // From Haskel et al, 2017
aCompo.put("P",0.961); aCompo.put("P",0.961);
aCompoCarcassPostSpawning.put(Gender.MALE,aCompo); aCompoCarcassPostSpawning.put(Gender.MALE,aCompo);
System.out.println(aCompoCarcassPostSpawning.toString()); // System.out.println("aCompoCarcassPostSpawning: " + aCompoCarcassPostSpawning.toString()); //
// carcass composition for fish gametes // Gametes composition approximated by the difference between gonads weight before and after spawning.
Map<Gender, Map<String, Double>> aCompoGametes = new Hashtable<DiadromousFish.Gender,Map<String,Double>>(); Map<Gender, Map<String, Double>> aCompoGametes = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
aCompo = new Hashtable<String,Double>(); aCompo = new Hashtable<String,Double>();
aCompo.put("N", 0.); //On remplit une collection avec un put. aCompo.put("N", 3.242); //On remplit une collection avec un put. From Haskel et al, 2018.
aCompo.put("P", 0.); aCompo.put("P", 0.320);
aCompoGametes.put(Gender.FEMALE,aCompo); aCompoGametes.put(Gender.FEMALE,aCompo);
aCompo = new Hashtable<String,Double>(); aCompo = new Hashtable<String,Double>();
aCompo.put("N", 0.); aCompo.put("N", 3.250);
aCompo.put("P",0.); aCompo.put("P", 0.724);
aCompoGametes.put(Gender.MALE,aCompo); aCompoGametes.put(Gender.MALE,aCompo);
System.out.println(aCompoGametes.toString()); // System.out.println("aCompoGametes:" + aCompoGametes.toString()); //
// features for juveniles
Map<String,Double> aJuvenileFeatures = new Hashtable<String, Double>();
aJuvenileFeatures.put("aLW",Math.exp(-11.942));
aJuvenileFeatures.put("bLW",3.0306);
System.out.println(aJuvenileFeatures.toString());
// carcass composition for juveniles fish // carcass composition for juveniles fish
Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>(); Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>();
aCompoJuveniles.put("N", 0.); //On remplit une collection avec un put. aCompoJuveniles.put("N", 2.803); //On remplit une collection avec un put. %N in wet weight (Haskell et al, 2017) on Alosa sapidissima
aCompoJuveniles.put("P", 0.); aCompoJuveniles.put("P", 0.887); //%P in wet weight (from Haskell et al, 2017) on Alosa sapidissima
System.out.println(aCompoJuveniles.toString()); System.out.println("aCompoJuveniles: " + aCompoJuveniles.toString());
ArrayList <String> nutrientsOfInterest= new ArrayList <String>();
nutrientsOfInterest.add("N");
nutrientsOfInterest.add("P");
System.out.println("nutrientsOfInterest: " + nutrientsOfInterest);
FishNutrient fn = new FishNutrient(nutrientsOfInterest, aFeaturePreSpawning, aFeaturePostSpawning,
aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
aJuvenileFeatures, aCompoJuveniles);
FishNutrient fn = new FishNutrient(aFeaturePreSpawning, aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes, aCompoJuveniles,
-11.942, 3.0306);
SeaBasin basin = new SeaBasin(0,"Bidon",10.,12., 14.,12.); //il faut aller dans "SeaBasin" dans "environement et regarder comment est construit le constructeur. Il lui faut ici un rang, un nom de bassin versant, et des temprature pour chaque saison SeaBasin basin = new SeaBasin(0,"Bidon",10.,12., 14.,12.); //il faut aller dans "SeaBasin" dans "environement et regarder comment est construit le constructeur. Il lui faut ici un rang, un nom de bassin versant, et des temprature pour chaque saison
Pilot pilot = new Pilot (); Pilot pilot = new Pilot ();
DiadromousFish fish = new DiadromousFish (pilot, basin, 40., 1L, Gender.FEMALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande. DiadromousFish fish = new DiadromousFish (pilot, basin, 40., 1L, Gender.FEMALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
fish.setStage(Stage.MATURE); fish.setStage(Stage.MATURE);
DiadromousFish juvenileFish = new DiadromousFish(pilot,basin,2.0,1L,Gender.UNDIFFERENCIED); DiadromousFish juvenileFish = new DiadromousFish(pilot,basin,2.0,1L,Gender.UNDIFFERENCIED);
fish.setStage(Stage.IMMATURE); juvenileFish.setStage(Stage.IMMATURE);
ArrayList <String> nutrientsOfInterest= new ArrayList <String>();
nutrientsOfInterest.add("N");
nutrientsOfInterest.add("P");
System.out.println(nutrientsOfInterest);
System.out.println("Nutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fish, nutrientsOfInterest).toString()); System.out.println(fish.toString());
System.out.println("Nutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fish, nutrientsOfInterest).toString()); System.out.println("Nutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fish).toString());
System.out.println("Nutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fish, nutrientsOfInterest).toString()); System.out.println("Nutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fish).toString());
System.out.println("Nutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish, nutrientsOfInterest).toString()); System.out.println("Nutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fish).toString());
System.out.println("Nutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish).toString());
/* Create XML file
*
*/
//System.out.println((new XStream(new DomDriver())).toXML(fn));
} }
} }
......
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