diff --git a/src/main/java/species/FishNutrient.java b/src/main/java/species/FishNutrient.java
index e1befab90ba189217cad6e113d2b7b7d8b4fe365..337b9c7d162a2a17d4103eed733768fc2e7d0f6a 100644
--- a/src/main/java/species/FishNutrient.java
+++ b/src/main/java/species/FishNutrient.java
@@ -69,7 +69,7 @@ public class FishNutrient {
* value g
* usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
*/
- private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
+ //private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
/**
@@ -128,7 +128,7 @@ public class FishNutrient {
Map <String, Double> excretionRate,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning,
- Map<DiadromousFish.Gender, Double> gameteSpawned,
+ //Map<DiadromousFish.Gender, Double> gameteSpawned,
Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> compoGametes,
@@ -141,7 +141,7 @@ public class FishNutrient {
this.residenceTime = residenceTime;
this.fishFeaturesPreSpawning = fishFeaturesPreSpawning;
this.fishFeaturesPostSpawning = fishFeaturesPostSpawning;
- this.spawnedGametesWeight = gameteSpawned;
+ //this.spawnedGametesWeight = gameteSpawned;
this.compoCarcassPreSpawning = compoCarcassPreSpawning;
this.compoCarcassPostSpawning = compoCarcassPostSpawning;
this.compoGametes = compoGametes;
@@ -202,7 +202,7 @@ public class FishNutrient {
double carcass = totalWeightPost
* compoCarcassPostSpawning.get(fish.getGender()).get(nutrient);
//double gametes = (totalWeightPre - totalWeightPost) FAUX car perte de poids somatique due a la reproduction
- double gametes = spawnedGametesWeight.get(fish.getGender())
+ double gametes = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
*compoGametes.get(fish.getGender()).get(nutrient);
double excretion = totalWeightPost
* residenceTime
@@ -237,15 +237,15 @@ public class FishNutrient {
//TODO Fix with new data
double totalWeightPost = this.getWeight(fish, SpawningPosition.POST);
//Gamete compositions depends on sex.
- double gametes = spawnedGametesWeight.get(fish.getGender())
+
+ double gametes = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
* compoGametes.get(fish.getGender()).get(nutrient);
+ // double gametes = spawnedGametesWeight.get(fish.getGender()) * compoGametes.get(fish.getGender()).get(nutrient);
double excretion = totalWeightPost
* residenceTime
* excretionRate.get(nutrient);
double nutrientImport = gametes + excretion;
-
-
nutrientsInput.put(nutrient, nutrientImport);
}
else {
@@ -297,6 +297,7 @@ public class FishNutrient {
return weight;
}
+
/**
* Compute the weight for a fish with length (cm)
@@ -308,9 +309,35 @@ public class FishNutrient {
return getWeight (fish, SpawningPosition.PRE);
}
+ public double getGonadWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
+
+ double gonadWeight = 0.;
+ if (fish.getStage()==Stage.MATURE);
+ if (spawningPosition == SpawningPosition.PRE)
+ gonadWeight = Math.exp(fishFeaturesPreSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPreSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+ else
+ gonadWeight = Math.exp(fishFeaturesPostSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPostSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+
+ return gonadWeight;
+ }
+
+ /**
+ * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ * @param fish
+ * @return weight (g)
+ */
+ public double getGonadWeight (DiadromousFish fish) {
+
+ return getGonadWeight (fish, SpawningPosition.PRE);
+ }
-public ArrayList<String> getNutrientsOfInterest() {
+
+
+
+ public ArrayList<String> getNutrientsOfInterest() {
return nutrientsOfInterest;
}
@@ -349,6 +376,8 @@ public static void main(String[] args) {
aFeature.put("aLW", Math.exp(-4.9078)); //weight size relationship computed from BDalosesBruch
aFeature.put("bLW", 3.147);
+ aFeature.put("aLW_Gonad", -5.2425); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.6729); // issu de la relation taille - poids des gonades Bruch
//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);
@@ -360,6 +389,8 @@ public static void main(String[] args) {
aFeature = new Hashtable<String,Double>();
aFeature.put("aLW", Math.exp(-1.304));
aFeature.put("bLW", 2.1774);
+ aFeature.put("aLW_Gonad", -8.8744);
+ aFeature.put("bLW_Gonad", 3.3838);
//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",.08);
aFeaturePreSpawning.put(Gender.MALE,aFeature);
@@ -377,6 +408,8 @@ public static void main(String[] args) {
aFeature = new Hashtable<String,Double>();
aFeature.put("aLW", Math.exp(-4.3276)); //weight size relationship computed from BDalosesBruch
aFeature.put("bLW", 2.9418);
+ aFeature.put("aLW_Gonad", -6.6234); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.8545); // issu de la relation taille - poids des gonades Bruch
//aFeature.put("GSI",0.10); //From BDalosesBruch
//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
@@ -389,6 +422,8 @@ public static void main(String[] args) {
aFeature.put("aLW", Math.exp(-4.5675));// parametre "a" de la relation taille/poids - Coefficient d'allometrie
aFeature.put("bLW", 2.9973);
+ aFeature.put("aLW_Gonad", -11.285); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 3.8331); // issu de la relation taille - poids des gonades Bruch
//aFeature.put("GSI",.05); From BDalosesBruch
//aFeature.put("aLW",aFeaturePreSpawning.get(Gender.MALE).get("aLW")/(1+aFeature.get("GSI")));
//aFeature.put("bLW",aFeaturePreSpawning.get(Gender.MALE).get("bLW"));
@@ -396,11 +431,12 @@ public static void main(String[] args) {
System.out.println("aFeaturePostSpawning: " + aFeaturePostSpawning.toString());
- Map<Gender, Double> aGameteSpawned = new Hashtable <DiadromousFish.Gender,Double>();
- aGameteSpawned.put(Gender.FEMALE, 131.); // Compute from the difference between spawned and unspawned ovaries ie correspond to a mean weight of eggs spawned
- aGameteSpawned.put(Gender.MALE, 44.8); // Compute from the difference between spawned and unspawned testes ie correspond to a mean weight of sperm spawned
- System.out.println("aGameteSpawned: " + aGameteSpawned.toString());
+ //Map<Gender, Double> aGameteSpawned = new Hashtable <DiadromousFish.Gender,Double>();
+ //aGameteSpawned.put(Gender.FEMALE, 131.); // Compute from the difference between spawned and unspawned ovaries ie correspond to a mean weight of eggs spawned
+ //aGameteSpawned.put(Gender.MALE, 44.8); // Compute from the difference between spawned and unspawned testes ie correspond to a mean weight of sperm spawned
+
+ //System.out.println("aGameteSpawned: " + aGameteSpawned.toString());
// carcass composition for fish before spawning
Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
@@ -466,7 +502,7 @@ public static void main(String[] args) {
System.out.println("nutrientsOfInterest: " + nutrientsOfInterest);
- FishNutrient fn = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, aGameteSpawned,
+ FishNutrient fn = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning,
aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
aJuvenileFeatures, aCompoJuveniles);