Commit 309bb45c authored by camille.poulet's avatar camille.poulet
Browse files

Fish nutrient with Array list and Hashtable implementation

Showing with 236 additions and 171 deletions
+236 -171
/**
* 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 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 cration d'une table de hachage ie fonctionnant en cl -valeur. Cl unique, mais valeur peut tre associe plusieurs cls;
//La class d'objet Map a pour point faible la taille des donnes 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 simultanment par plusieurs lments 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 crer ici une Map, classe mre 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 utiliss 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 temprature 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 + la place des "," car l'ordinateur n'est pas capable detraiter des objets ddiffrent 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 temprature 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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