From 309bb45c3c3bcb8c9423b4e473cb89abce13f411 Mon Sep 17 00:00:00 2001
From: "camille.poulet" <camille.poulet@BXP1829.bordeaux.irstea.priv>
Date: Fri, 3 May 2019 17:42:56 +0200
Subject: [PATCH] Fish nutrient with Array list and Hashtable implementation
---
src/main/java/species/FishNutrient.java | 407 ++++++++++++++----------
1 file changed, 236 insertions(+), 171 deletions(-)
diff --git a/src/main/java/species/FishNutrient.java b/src/main/java/species/FishNutrient.java
index 7b6703c..c9f56a0 100644
--- a/src/main/java/species/FishNutrient.java
+++ b/src/main/java/species/FishNutrient.java
@@ -1,7 +1,7 @@
/**
- * patrick.lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2018, Irstea
+ *
+ * @author Camille Poulet, Patrick Lambert
+ * @copyright Copyright (c) 2019, Irstea
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -20,55 +20,93 @@
package species;
import environment.SeaBasin;
+import environment.Time.Season;
import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish.Gender;
import species.DiadromousFish.Stage;
+import species.ReproduceAndSurviveAfterReproduction;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
/**
*
*/
-public class FishNutrient {
-
- private double aLWfemalePre = 0.0221; // param�tre "a" de la relation taille/poids avec Lt en cm
- private double bLWfemalePre = 2.8147; // param�tre "b" de la relation taille/poids
- private double GSIfemalePre =.15;
- private double aLWmalePre = 0.0221; // param�tre "a" de la relation taille/poids avec Lt en cm
- private double bLWmalePre = 2.8147; // param�tre "b" de la relation taille/poids
- private double GSImalePre =.07;
- // Si on ne possède pas wT post reproduction
+/**
+ * @author camille.poulet
+ *
+ */
+public class FishNutrient {
/**
- * param�tre "a" de la relation taille/poids avec Lt en cm
+ * Main feature for weight computation before spawning i.e. gametes expelling //Voir pour un retour à la ligne lors du commentaire
+ * key gender
+ * value
+ * key feature
+ * value value
*/
- private double aLWfemalePost = 0.; // param�tre "a" de la relation taille/poids avec Lt en cm
- private double bLWfemalePost = 0.; // param�tre "b" de la relation taille/poids
+ private Map <Gender,Map<String, Double>> fishFeatures;
+
+ // Si on ne possede pas wT post reproduction
+
+ private double aLWfemalePost = 0.;
+ private double bLWfemalePost = 0.;
private double GSIfemalePost=0.10;
- private double aLWmalePost = 0.; // param�tre "a" de la relation taille/poids avec Lt en cm
- private double bLWmalePost = 0.; // param�tre "b" de la relation taille/poids
+ private double aLWmalePost = 0.;
+ private double bLWmalePost = 0.;
private double GSImalePost =.07;
- //Si on possede WT post reproduction
- private double CoeffLossWeight = 0.;
+ // Valeurs de Haskell pour A. sapidissima -- A rechercher pour Alosa alosa
- //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
+ * <key> gender
+ * <value>
+ * <key> chemical element
+ * <value> value
+ */
+ private Map<DiadromousFish.Gender,Map<String,Double>> compoCarcassPreSpawning;
- private double compoNpreMale = 2.921;
- private double compoPpreMale = 0.662;
- private double compoNpreFemale = 2.917;
- private double compoPpreFemale = 0.725;
+ //package permettant la création d'une table de hachage ie fonctionnant en clé -valeur. Clé unique, mais valeur peut être associée à plusieurs clés;
+ //La class d'objet Map a pour point faible la taille des données à stocker. Plus on a de valeur dans la table, plus c'est lourd et lent! Donc, trouver un compromis entre temps de calcul et espace.
+ //N'accepte pas la valeur nulle et thread safe i.e. utilisable simultanément par plusieurs éléments du programme.
- private double compoNpostMale = 2.790 ;
- private double compoPpostMale = 0.961;
- private double compoNpostFemale = 3.216 ;
- private double compoPpostFemale = 0.997;
+ /**
+ * chemical composition of carcass after spawning i.e. gonads without gametes
+ * <key> gender
+ * <value>
+ * <key> chemical element
+ * <value> value
+ */
+ private Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning;
+
+ /**
+ * chemical composition of gametes
+ * <key> gender
+ * <value>
+ * <key> chemical element
+ * <value> value
+ */
+ private Map<DiadromousFish.Gender, Map<String,Double>> compoGametes;
- private double compoNoocyte =0.0;
- private double compoNsperm =0.0;
- private double compoPoocyte =0.0;
- private double compoPsperm =0.0;
+ // For juveniles - Based on Taverny (1991)
+ /**
+ * chemical composition of juveniles
+ * <key> stage
+ * <value>
+ * <key> chemical element
+ * <value> value
+ */
+
+ 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
/**
*
@@ -76,175 +114,202 @@ public class FishNutrient {
public FishNutrient() {
// TODO Auto-generated constructor stub
}
-
- public FishNutrient(double aLWfemalePre, double bLWfemalePre, double gSIfemalePre, double aLWmalePre,
- double bLWmalePre, double gSImalePre, double aLWfemalePost, double bLWfemalePost, double gSIfemalePost,
- double aLWmalePost, double bLWmalePost, double gSImalePost, double coeffLossWeight, double compoNpreMale,
- double compoPpreMale, double compoNpreFemale, double compoPpreFemale, double compoNpostMale,
- double compoPpostMale, double compoNpostFemale, double compoPpostFemale, double compoNoocyte,
- double compoNsperm, double compoPoocyte, double compoPsperm) {
+
+ /**
+ * Constructor based on the 5 Map of fish composition
+ * @param fishFeatures
+ * @param compoCarcassPreSpawning
+ * @param compoCarcassPostSpawning
+ * @param compoGametes
+ * @param compoJuvenile
+ */
+ public FishNutrient(Map<Gender, Map<String, Double>> fishFeatures,
+ Map<Gender, Map<String, Double>> compoCarcassPreSpawning,
+ Map<Gender, Map<String, Double>> compoCarcassPostSpawning, Map<Gender, Map<String, Double>> compoGametes,
+ Map<String, Double> compoJuvenile,double aLWjuveniles, double bLWjuveniles ) {
super();
- this.aLWfemalePre = aLWfemalePre;
- this.bLWfemalePre = bLWfemalePre;
- GSIfemalePre = gSIfemalePre;
- this.aLWmalePre = aLWmalePre;
- this.bLWmalePre = bLWmalePre;
- GSImalePre = gSImalePre;
- this.aLWfemalePost = aLWfemalePost;
- this.bLWfemalePost = bLWfemalePost;
- GSIfemalePost = gSIfemalePost;
- this.aLWmalePost = aLWmalePost;
- this.bLWmalePost = bLWmalePost;
- GSImalePost = gSImalePost;
- CoeffLossWeight = coeffLossWeight;
- this.compoNpreMale = compoNpreMale;
- this.compoPpreMale = compoPpreMale;
- this.compoNpreFemale = compoNpreFemale;
- this.compoPpreFemale = compoPpreFemale;
- this.compoNpostMale = compoNpostMale;
- this.compoPpostMale = compoPpostMale;
- this.compoNpostFemale = compoNpostFemale;
- this.compoPpostFemale = compoPpostFemale;
- this.compoNoocyte = compoNoocyte;
- this.compoNsperm = compoNsperm;
- this.compoPoocyte = compoPoocyte;
- this.compoPsperm = compoPsperm;
+ this.fishFeatures = fishFeatures;
+ this.compoCarcassPreSpawning = compoCarcassPreSpawning;
+ this.compoCarcassPostSpawning = compoCarcassPostSpawning;
+ this.compoGametes = compoGametes;
+ this.compoJuvenile = compoJuvenile;
+ this.aLWjuveniles = aLWjuveniles;
+ this.bLWjuveniles = bLWjuveniles;
}
-
/**
- * compute the N and P fluxes for a single fish (in the super individual)
- * that dies after spawning (gametes expelling)
+ * compute the nutrient fluxes for a single fish (in the super individual)
+ * that dies before spawning
* @param fish
*/
- public double[] computeInportNPforDeathBeforeSpawning(DiadromousFish fish) {
- double totalWeightPre;
+ public Map<String,Double> computeNutrientsInputForDeathBeforeSpawning(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
- double [] inportNP = new double[2]; //Declare an array with two coloumns
- inportNP[0] = 0; // create the colomn
- inportNP[1] = 0;
+ Map<String,Double> nutrientsInput = new Hashtable<String, Double>(); // On créer ici une Map, classe mère des hashtable (Homme = classe mere ie Map//Jules = hashtable)
+ for (String nutrient : nutrientsOfInterest) {
- if (fish.getStage()== Stage.MATURE) {
- if(fish.getGender()== Gender.FEMALE) {
- totalWeightPre = aLWfemalePre * Math.pow(fish.getLength(), bLWfemalePre);
+ if (fish.getStage()== Stage.MATURE) {
+ double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW"));
//totalWeightPost = totalWeightPre * (1-GSIfemalePost)+ totalWeightPost * GSIfemalePost * CoeffLossWeight
- inportNP[0] = totalWeightPre * compoNpreFemale;
- inportNP[1] = totalWeightPre * compoPpreFemale;
+ nutrientsInput.put(nutrient, totalWeightPre * compoCarcassPreSpawning.get(fish.getGender()).get(nutrient));
}
- else if (fish.getGender()== Gender.MALE) {
- totalWeightPre = aLWmalePre * Math.pow(fish.getLength(), bLWmalePre);
- //totalWeightPost = totalWeightPre * (1-GSImalePost)+ totalWeightPost * GSImalePost * CoeffLossWeight
- inportNP[0] = totalWeightPre * compoNpreMale;
- inportNP[1] = totalWeightPre * compoPpreMale;
- }
- else {
- totalWeightPre= Double.NaN;
- inportNP[0] = 0.;
- inportNP[1] = 0;
+ else {
+ nutrientsInput.put(nutrient, 0.);
}
}
- return inportNP;
-
+ return nutrientsInput;
}
- public double[] computeInportNPforDeathAfterSpawning(DiadromousFish fish) {
- double totalWeightPre, totalWeightPost;
+ /**
+ * compute the nutrient fluxes for a single fish (in the super individual)
+ * that dies after spawning (gametes expelling)
+ * @param fish
+ * @return nutrientsInput
+ */
+ public Map<String, Double> computeNutrientsInputForDeathAfterSpawning(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
+
+ Map<String,Double> nutrientsInput = new Hashtable<String,Double>();
+ for (String nutrient : nutrientsOfInterest) {
- double[] inportNP = new double[2];
- inportNP[0] = 0.;
- inportNP[1] = 0.;
+ if (fish.getStage()== Stage.MATURE) {
- if (fish.getStage() == Stage.MATURE) {
- if (fish.getGender() == Gender.FEMALE ) {
- totalWeightPre = aLWfemalePre * Math.pow(fish.getLength(), bLWfemalePre);
- totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost);
- //totalWeightPost = totalWeightPre * (1-GSIfemalePost)+ totalWeightPost * GSIfemalePost * CoeffLossWeight
- inportNP[0] = totalWeightPost * compoNpostFemale + (totalWeightPre - totalWeightPost) * compoNoocyte;
- inportNP[1] = totalWeightPost * compoPpostFemale + (totalWeightPre - totalWeightPost) * compoPoocyte;
- }
- else if (fish.getGender() == Gender.MALE) {
- totalWeightPre = aLWmalePre * Math.pow(fish.getLength(), bLWmalePre);
- totalWeightPost = aLWmalePost * Math.pow(fish.getLength(), bLWmalePost);
- //totalWeightPost = totalWeightPre * (1-GSImalePost)+ totalWeightPost * GSImalePost * CoeffLossWeight
- inportNP[0] = totalWeightPost * compoNpostMale + (totalWeightPre - totalWeightPost) * compoNsperm;
- inportNP[1] = totalWeightPost * compoPpostMale + (totalWeightPre - totalWeightPost) * compoPsperm;
+ double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW"));
+ //TODO Fix the new data
+ double totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost);
+ nutrientsInput.put(nutrient,(totalWeightPre - totalWeightPost) * compoCarcassPostSpawning.get(fish.getGender()).get(nutrient));
}
else {
- totalWeightPre = Double.NaN;
- totalWeightPost = 0.;
- inportNP[0]=0.;
- inportNP[1]=0.;
- }
+ nutrientsInput.put(nutrient,0.);
+ }
}
-
- return inportNP;
+ return nutrientsInput;
}
- public double [] computeInportNPforSurvivalAfterSpawning(DiadromousFish fish) {
- double totalWeightPre, totalWeightPost;
-
- double[]inportNP = new double [2];
- inportNP[0]= 0;
- inportNP[1] = 0;
-
- if (fish.getStage()== Stage.MATURE) {
- if (fish.getGender()==Gender.FEMALE){
- totalWeightPre = aLWfemalePre * Math.pow(fish.getLength(), bLWfemalePre);
- totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost);
- //totalWeightPost = totalWeightPre * (1-GSImalePost)+ totalWeightPost * GSImalePost * CoeffLossWeight
- inportNP[0] = (totalWeightPre - totalWeightPost)* compoNoocyte;
- inportNP[1] = (totalWeightPre - totalWeightPost)* compoPoocyte;
- }
- else if (fish.getGender()== Gender.MALE) {
+
+ /**
+ * compute the nutrient fluxes for a single fish (in the super individual)
+ * that survives after spawning
+ * Map: model output = element of interest ie string + double ie the quantification of this fluxes.
+ * @return nutrientsInput
+ */
+ public Map<String,Double>computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
- totalWeightPre = aLWfemalePre * Math.pow(fish.getLength(), bLWmalePre);
- totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWmalePost);
- //totalWeightPost = totalWeightPre * (1-GSImalePost)+ totalWeightPost * GSImalePost * CoeffLossWeight
- inportNP[0] = (totalWeightPre - totalWeightPost)* compoNsperm;
- inportNP[1] = (totalWeightPre - totalWeightPost)* compoPsperm;
+ Map<String,Double> nutrientsInput = new Hashtable<String,Double>();
+ for (String nutrient: nutrientsOfInterest) {
+ if (fish.getStage()==Stage.MATURE) {
+ double totalWeightPre = fishFeatures.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeatures.get(fish.getGender()).get("bLW"));
+ //TODO Fix with new data
+ double totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost);
+ nutrientsInput.put(nutrient, (totalWeightPre - totalWeightPost) * compoGametes.get(fish.getGender()).get(nutrient));
}
else {
- totalWeightPre= Double.NaN;
- totalWeightPost = 0.;
- inportNP[0] = 0.;
- inportNP[1] = 0;
-
+ nutrientsInput.put(nutrient,0.);
}
}
-
- return inportNP;
+ return nutrientsInput;
+ }
+
+ public Map<String,Double> computeNutrientsExportForJuveniles (DiadromousFish juvenileFish, ArrayList<String>nutrientsOfInterest) {
+ Map<String,Double> nutrientsExport = new Hashtable<String,Double>();
+ for(String nutrient: nutrientsOfInterest) {
+ if(juvenileFish.getStage()==Stage.IMMATURE) {
+
+ double JuvenileMass = aLWjuveniles * Math.pow(juvenileFish.getLength(), bLWjuveniles);
+ nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient));
+ }
+ }
+
+ return nutrientsExport;
}
-public static void main(String[] args) {
-
- FishNutrient fn = new FishNutrient(0.0221, 2.8147, .15, 0.0221, 2.8147, .07, 0., 0., 0.10, 0., 0., 0.07, 0., 2.921, 0.662, 2.917, 0.725, 2.790, 0.961, 3.216, 0.997, 0., 0., 0., 0.); //On lui passe les valeurs utilisés ici dans le programme
- 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);
- double[] np = fn.computeInportNPforDeathAfterSpawning(fish);
- System.out.println("N = " + np[0]+ "P = "+ np[1]); // on met des + à la place des "," car l'ordinateur n'est pas capable detraiter des objets ddifférent de "String". Or on a un double ici.
-
-
-
-
-
-
-
-
-
-
-
-
+ 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("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("GSI",0.15);
+ aFeaturePreSpawning.put(Gender.FEMALE, aFeature);
+
+ aFeature = new Hashtable<String,Double>();
+ aFeature.put("aLW",2.4386E-6);
+ aFeature.put("bLW",3.2252);
+ aFeature.put("GSI",.07);
+ aFeaturePreSpawning.put(Gender.MALE,aFeature);
+
+ System.out.println(aFeaturePreSpawning.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.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);
+ aCompo.put("P",0.961);
+ aCompoCarcassPostSpawning.put(Gender.MALE,aCompo);
+
+ System.out.println(aCompoCarcassPostSpawning.toString()); //
+
+ // carcass composition for fish gametes
+ Map<Gender, Map<String, Double>> aCompoGametes = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 0.); //On remplit une collection avec un put.
+ aCompo.put("P", 0.);
+ aCompoGametes.put(Gender.FEMALE,aCompo);
+
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 0.);
+ aCompo.put("P",0.);
+ aCompoGametes.put(Gender.MALE,aCompo);
+
+ System.out.println(aCompoGametes.toString()); //
+
+ // carcass composition for juveniles fish
+ Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>();
+ aCompoJuveniles.put("N", 0.); //On remplit une collection avec un put.
+ aCompoJuveniles.put("P", 0.);
+
+ System.out.println(aCompoJuveniles.toString());
+
+ 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 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);
+ fish.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("Nutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fish, nutrientsOfInterest).toString());
+ System.out.println("Nutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fish, nutrientsOfInterest).toString());
+ System.out.println("Nutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish, nutrientsOfInterest).toString());
+
+
+ }
}
-
-
-
-}
-
-
-
--
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