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Poulet Camille authored30b99661
/**
*
* @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
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
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;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
/**
* @author camille.poulet
*
*/
public class FishNutrient {
private static enum SpawningPosition {PRE,POST}; // on crer un static pour rserver une mme classe mmoire pour toutes les instances
private ArrayList<String> nutrientsOfInterest;
private double residenceTime;
private Map<String, Double> excretionRate;
/**
* Main feature for weight (g) computation before spawning i.e. gametes expelling according to gender, for a given length (cm)
* //Voir pour un retour la ligne lors du commentaire
* key gender
* value
* key feature
* value value
*/
private Map <Gender,Map<String, Double>> fishFeaturesPreSpawning;
private Map <Gender, Map<String, Double>> fishFeaturesPostSpawning;
private Map <String, Double> juvenileFeatures;
/**
* Weight of gametes spawned for both males and females
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* key gender
* value g
* usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
*/
private Map <Gender, Double> spawnedGametesWeight;
/**
* chemical composition of carcass before gametes expelling (before spawning) i.e. soma + gonads + gametes
* <key> gender
* <value>
* <key> chemical element
* <value> value ratio element / (total wet weight) g/g
*/
private Map<DiadromousFish.Gender,Map<String,Double>> compoCarcassPreSpawning;
//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.
/**
* chemical composition of carcass after spawning i.e. soma + spent gonad (without gametes)
* <value>
* <key> chemical element
* <value> value
*/
private Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning;
/**
* chemical composition of gametes estimated from the MIGADO dataset (BDalosesBruch)
* <key> gender
* <value>
* <key> chemical element
* <value> value
*/
private Map<DiadromousFish.Gender, Map<String,Double>> compoGametes;
// For juveniles - Based on Taverny (1991)
/**
* chemical composition of juveniles
* <key> stage
* <value>
* <key> chemical element
* <value> value
*/
private Map<String,Double> compoJuvenile;
/**
*
*/
public FishNutrient() {
// TODO Auto-generated constructor stub
}
/**
* Constructor based on the 5 Map of fish composition
* @param fishFeaturesPreSpawning
* @param compoCarcassPreSpawning
* @param compoCarcassPostSpawning
* @param compoGametes
* @param compoJuvenile
*/
public FishNutrient(ArrayList<String> nutrientsOfInterest,
double residenceTime,
Map <String, Double> excretionRate,
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Map<Gender, Map<String, Double>> fishFeaturesPreSpawning,
Map<Gender, Map<String, Double>> fishFeaturesPostSpawning,
Map<Gender, Double> gameteSpawned,
Map<Gender, Map<String, Double>> compoCarcassPreSpawning,
Map<Gender, Map<String, Double>> compoCarcassPostSpawning,
Map<Gender, Map<String, Double>> compoGametes,
Map<String, Double> juvenileFeatures,
Map<String, Double> compoJuvenile)
{
super();
this.nutrientsOfInterest = nutrientsOfInterest;
this.excretionRate = excretionRate;
this.residenceTime = residenceTime;
this.fishFeaturesPreSpawning = fishFeaturesPreSpawning;
this.fishFeaturesPostSpawning = fishFeaturesPostSpawning;
this.spawnedGametesWeight = gameteSpawned;
this.compoCarcassPreSpawning = compoCarcassPreSpawning;
this.compoCarcassPostSpawning = compoCarcassPostSpawning;
this.compoGametes = compoGametes;
this.juvenileFeatures = juvenileFeatures;
this.compoJuvenile = compoJuvenile;
}
/**
* compute the nutrient fluxes for a single fish (in the super individual)
* that dies before spawning
* @param fish
*/
public Map<String,Double> computeNutrientsInputForDeathBeforeSpawning(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
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) {
double totalWeightPre = this.getWeight(fish,SpawningPosition.PRE);
double carcass = totalWeightPre
* compoCarcassPreSpawning.get(fish.getGender()).get(nutrient);
double excretion = totalWeightPre
* residenceTime
* excretionRate.get(nutrient) ;
double nutrientImport = carcass + excretion;
nutrientsInput.put(nutrient, nutrientImport);
}
else {
nutrientsInput.put(nutrient, 0.);
}
}
//TODO Multiply by fish amount
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)
* 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) {
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if (fish.getStage()== Stage.MATURE) {
double totalWeightPost = this.getWeight(fish, SpawningPosition.POST);
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())
*compoGametes.get(fish.getGender()).get(nutrient); //TODO: FAUX ! Revoir comment calculer les gamtes
double excretion = totalWeightPost
* residenceTime
* excretionRate.get(nutrient);
double nutrientImport = carcass + gametes + excretion;
nutrientsInput.put(nutrient,nutrientImport);
}
else {
nutrientsInput.put(nutrient,0.);
}
}
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)
* 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) {
Map<String,Double> nutrientsInput = new Hashtable<String,Double>();
for (String nutrient: nutrientsOfInterest) {
if (fish.getStage()==Stage.MATURE) {
//TODO Fix with new data
double totalWeightPost = this.getWeight(fish, SpawningPosition.POST);
//Gamete compositions depends on sex.
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 {
nutrientsInput.put(nutrient,0.);
}
}
return nutrientsInput;
}
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>();
for(String nutrient: nutrientsOfInterest) {
if(juvenileFish.getStage()==Stage.IMMATURE) {