diff --git a/src/main/java/species/FishNutrient.java b/src/main/java/species/FishNutrient.java
index 930f2abffe93925788f5ecc31e859df546f725ef..1883634e8a4b072626b1c2b1dfb534b503abbcef 100644
--- a/src/main/java/species/FishNutrient.java
+++ b/src/main/java/species/FishNutrient.java
@@ -43,7 +43,8 @@ public class FishNutrient {
private ArrayList<String> nutrientsOfInterest;
/**
- * Main feature for weight computation before spawning i.e. gametes expelling //Voir pour un retour à la ligne lors du commentaire
+ * Main feature for weight (g) computation before spawning i.e. gametes expelling according to gender, for a given length (cm)
+ * //Voir pour un retour à la ligne lors du commentaire
* key gender
* value
* key feature
@@ -61,7 +62,7 @@ public class FishNutrient {
* <key> gender
* <value>
* <key> chemical element
- * <value> value
+ * <value> value ratio element / (total wet weight) g/g
*/
private Map<DiadromousFish.Gender,Map<String,Double>> compoCarcassPreSpawning;
@@ -153,6 +154,8 @@ public class FishNutrient {
nutrientsInput.put(nutrient, 0.);
}
}
+
+ //TODO Multiply by fish amount
return nutrientsInput;
}
@@ -243,129 +246,146 @@ public class FishNutrient {
return computeNutrientsExportForJuveniles(juvenileFish, this.nutrientsOfInterest);
}
-
/**
- * @param args
+ * Compute the weight for a fish with length (cm)
+ * @param fish
+ * @return weight (g)
*/
- public static void main(String[] args) {
-
- Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
- Map<String,Double> aFeature = new Hashtable<String,Double>();
- 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);
- aFeaturePreSpawning.put(Gender.FEMALE, aFeature);
-
- aFeature = new Hashtable<String,Double>();
- 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);
- aFeaturePreSpawning.put(Gender.MALE,aFeature);
-
- 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
- Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
- Map<String,Double> aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.917); //On remplit une collection avec un put.
- aCompo.put("P", 0.725);
- aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.921);
- aCompo.put("P",0.662);
- aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
-
- System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //
-
- // carcass composition for fish after spawning
- Map<Gender, Map<String, Double>> aCompoCarcassPostSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 3.216); //On remplit une collection avec un put.
- aCompo.put("P", 0.997);
- aCompoCarcassPostSpawning.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.790); // From Haskel et al, 2017
- aCompo.put("P",0.961);
- aCompoCarcassPostSpawning.put(Gender.MALE,aCompo);
-
- System.out.println("aCompoCarcassPostSpawning: " + aCompoCarcassPostSpawning.toString()); //
-
- // 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>>();
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 3.242); //On remplit une collection avec un put. From Haskel et al, 2018.
- aCompo.put("P", 0.320);
- aCompoGametes.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 3.250);
- aCompo.put("P", 0.724);
- aCompoGametes.put(Gender.MALE,aCompo);
-
- 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
- Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>();
- 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", 0.887); //%P in wet weight (from Haskell et al, 2017) on Alosa sapidissima
-
- 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);
-
- 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 température pour chaque saison
- 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.
- fish.setStage(Stage.MATURE);
- DiadromousFish juvenileFish = new DiadromousFish(pilot,basin,2.0,1L,Gender.UNDIFFERENCIED);
- juvenileFish.setStage(Stage.IMMATURE);
-
- System.out.println(fish.toString());
- System.out.println("Nutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fish).toString());
- System.out.println("Nutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fish).toString());
- System.out.println("Nutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fish).toString());
- System.out.println("Nutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish).toString());
+ public double getWeight (DiadromousFish fish) {
+
+ double weight = 0.;
+ if (fish.getStage()==Stage.IMMATURE)
+ weight = juvenileFeatures.get("aLW") * Math.pow(fish.getLength(),juvenileFeatures.get("bLW"));
+ else //Stage.MATURE
+ weight = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW")
+ * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW") );
+
+ return weight;
+ }
+/**
+ * @param args
+ */
+public static void main(String[] args) {
+
+ Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
+ Map<String,Double> aFeature = new Hashtable<String,Double>();
+ 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);
+ aFeaturePreSpawning.put(Gender.FEMALE, aFeature);
+
+ aFeature = new Hashtable<String,Double>();
+ 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);
+ aFeaturePreSpawning.put(Gender.MALE,aFeature);
+
+ 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
+ Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
+ Map<String,Double> aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 2.917 / 100.); //On remplit une collection avec un put.
+ aCompo.put("P", 0.725 / 100.);
+ aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
+
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 2.921 / 100.);
+ aCompo.put("P", 0.662 / 100.);
+ aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
+
+ System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //
+
+ // carcass composition for fish after spawning
+ Map<Gender, Map<String, Double>> aCompoCarcassPostSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 3.216 / 100.); //On remplit une collection avec un put.
+ aCompo.put("P", 0.997 / 100.);
+ aCompoCarcassPostSpawning.put(Gender.FEMALE,aCompo);
+
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 2.790 / 100.); // From Haskel et al, 2017
+ aCompo.put("P", 0.9610 / 100.);
+ aCompoCarcassPostSpawning.put(Gender.MALE,aCompo);
+
+ System.out.println("aCompoCarcassPostSpawning: " + aCompoCarcassPostSpawning.toString()); //
+
+ // 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>>();
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 3.242 / 100.); //On remplit une collection avec un put. From Haskel et al, 2018.
+ aCompo.put("P", 0.320 / 100.); // Haskel = %P, N, ici ratio donc divise par 100
+ aCompoGametes.put(Gender.FEMALE,aCompo);
+
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 3.250 / 100.);
+ aCompo.put("P", 0.724 / 100.);
+ aCompoGametes.put(Gender.MALE,aCompo);
+
+ System.out.println("aCompoGametes:" + aCompoGametes.toString()); //
+
+ // features for juveniles
+
+ Map<String,Double> aJuvenileFeatures = new Hashtable<String, Double>();
+ aJuvenileFeatures.put("bLW",3.0306);
+ aJuvenileFeatures.put("aLW",Math.exp(-11.942) * Math.pow(10., aJuvenileFeatures.get("bLW")));
+
+ System.out.println("aJuvenileFeatures: " + aJuvenileFeatures.toString());
+ // carcass composition for juveniles fish
+ Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>();
+ aCompoJuveniles.put("N", 2.803 / 100.); //On remplit une collection avec un put. %N in wet weight (Haskell et al, 2017) on Alosa sapidissima
+ aCompoJuveniles.put("P", 0.887 / 100.); //%P in wet weight (from Haskell et al, 2017) on Alosa sapidissima
- /* Create XML file
- *
- */
- //System.out.println((new XStream(new DomDriver())).toXML(fn));
+ 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);
+
+ 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 température pour chaque saison
+ Pilot pilot = new Pilot ();
+ DiadromousFish fish = new DiadromousFish (pilot, basin, 55., 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);
+ DiadromousFish juvenileFish = new DiadromousFish(pilot,basin,7.0,1L,Gender.UNDIFFERENCIED);
+ juvenileFish.setStage(Stage.IMMATURE);
+
+ System.out.println(); // affiche une ligne blanche
+ System.out.println(fish.getGender() + ": " + fish.getLength() + " cm " + fn.getWeight(fish)+ " g ");
+ System.out.println("\tNutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fish).toString());
+ System.out.println("\tNutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fish).toString());
+ System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fish).toString());
+ System.out.println(juvenileFish.getStage() + ": " + juvenileFish.getLength() + " cm " + fn.getWeight(juvenileFish)+ " g ");
+ System.out.println("\tNutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish).toString());
+
+
+ /* Create XML file
+ *
+ */
+ //System.out.println((new XStream(new DomDriver())).toXML(fn));
- }
+}
}