FishNutrient.java 20.06 KiB
/**
 * 
 * @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) {