diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index ab309702b509703b1857d1b5268ffeda032e6014..6236237886728ab546c03a51417852ddee2d881b 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -10,7 +10,7 @@
<linfVonBert>60.0</linfVonBert>
<dMaxDisp>300.0</dMaxDisp>
<lFirstMaturity>40.0</lFirstMaturity>
- <fishNutrient>
+ <nutrientRoutine>
<nutrientsOfInterest>
<string>N</string>
<string>P</string>
@@ -30,6 +30,14 @@
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
+ <entry>
+ <string>bLW_Gonad</string>
+ <double>3.3838</double>
+ </entry>
+ <entry>
+ <string>aLW_Gonad</string>
+ <double>-8.8744</double>
+ </entry>
<entry>
<string>bLW</string>
<double>2.1774</double>
@@ -43,6 +51,14 @@
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
+ <entry>
+ <string>bLW_Gonad</string>
+ <double>2.6729</double>
+ </entry>
+ <entry>
+ <string>aLW_Gonad</string>
+ <double>-5.2425</double>
+ </entry>
<entry>
<string>bLW</string>
<double>3.147</double>
@@ -58,6 +74,14 @@
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
+ <entry>
+ <string>bLW_Gonad</string>
+ <double>3.8331</double>
+ </entry>
+ <entry>
+ <string>aLW_Gonad</string>
+ <double>-11.285</double>
+ </entry>
<entry>
<string>bLW</string>
<double>2.9973</double>
@@ -71,6 +95,14 @@
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
+ <entry>
+ <string>bLW_Gonad</string>
+ <double>2.8545</double>
+ </entry>
+ <entry>
+ <string>aLW_Gonad</string>
+ <double>-6.6234</double>
+ </entry>
<entry>
<string>bLW</string>
<double>2.9418</double>
@@ -92,16 +124,6 @@
<double>0.006986429759979109</double>
</entry>
</juvenileFeatures>
- <spawnedGametesWeight class="hashtable">
- <entry>
- <species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
- <double>44.8</double>
- </entry>
- <entry>
- <species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
- <double>131.0</double>
- </entry>
- </spawnedGametesWeight>
<compoCarcassPreSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
@@ -196,7 +218,8 @@
<double>0.02803</double>
</entry>
</compoJuvenile>
- </fishNutrient>
+ </nutrientRoutine>
+
<fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
<centileForRange>0.95</centileForRange>
<parameterSetfileName>data/input/reality/parameterSet.csv</parameterSetfileName>
@@ -245,19 +268,16 @@
<meanBvSurface>17351</meanBvSurface>
<standardDeviationBvSurface>35594</standardDeviationBvSurface>
<meanInterDistance>300.0</meanInterDistance>
- <standardDeviationInterDistance>978.0
- </standardDeviationInterDistance>
+ <standardDeviationInterDistance>978.0</standardDeviationInterDistance>
<pHomingForReachEquil>0.75</pHomingForReachEquil>
<pHomingAfterEquil>0.75</pHomingAfterEquil>
<NbYearForInstallPop>0</NbYearForInstallPop>
<riverMigrationSeason>SPRING</riverMigrationSeason>
<alpha2Rep>0.0</alpha2Rep>
<meanSpawnersLengthAtRepro>45.0</meanSpawnersLengthAtRepro>
- <standardDeviationOfSpawnersLengthAtRepro>2.0
- </standardDeviationOfSpawnersLengthAtRepro>
+ <standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
<weightOfDeathBasin>0.4</weightOfDeathBasin>
</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
-
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
@@ -268,8 +288,6 @@
<mortalityRateInSea>0.4</mortalityRateInSea>
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
-
-
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
@@ -314,8 +332,7 @@
</species.IdentifyPopulation>
<species.TypeTrajectoryCV>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <fileNameOutput>JeuParam100_2100RCP85_A_essai
- </fileNameOutput>
+ <fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
</species.TypeTrajectoryCV>
</processesAtEnd>
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 49dab6f5048449929c030970a63a6136c886a5b2..67d2454f4b121b10f28ba7867b4a79d72e9e141a 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -62,7 +62,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
* Routine to compute nutrient fluxes operated by a single individual (TODO by a single super individual).
*
*/
- private FishNutrient fishNutrient;
+ private NutrientRoutine nutrientRoutine;
public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
@@ -265,7 +265,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
- diadromousFishGroup.fishNutrient = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, aGameteSpawned,
+ diadromousFishGroup.nutrientRoutine = new NutrientRoutine(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning,
aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
aJuvenileFeatures, aCompoJuveniles);
@@ -507,9 +507,9 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
return lFirstMaturity;
}
- public FishNutrient getFishNutrient() {
+ public NutrientRoutine getNutrientRoutine() {
- return fishNutrient;
+ return nutrientRoutine;
}
public void setlFirstMaturity(double lFirstMaturity) {
diff --git a/src/main/java/species/FishNutrient.java b/src/main/java/species/FishNutrient.java
deleted file mode 100644
index cd09d24a14ebe30747f1a78f2f19f6fbfea29081..0000000000000000000000000000000000000000
--- a/src/main/java/species/FishNutrient.java
+++ /dev/null
@@ -1,507 +0,0 @@
-/**
- *
- * @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 fr.cemagref.simaqualife.pilot.Pilot;
-import species.DiadromousFish.Gender;
-import species.DiadromousFish.Stage;
-import java.util.ArrayList;
-import java.util.Hashtable;
-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 créer un static pour réserver une même classe mémoire pour toutes les instances
-
- //private static enum Gender {UNDIFFERENCIED, FEMALE, MALE};
-
- 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 à la ligne lors du commentaire
- * key gender
- * value
- * key feature
- * value value
- */
- private Map <DiadromousFish.Gender,Map<String, Double>> fishFeaturesPreSpawning;
-
- private Map <DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning;
-
- private Map<String, Double> juvenileFeatures;
-
-
- /**
- * Weight of gametes spawned for both males and females
- * key gender
- * value g
- * usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
- */
- private Map <DiadromousFish.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 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.
-
- /**
- * 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> chemical element
- * <value> value
- */
-
- private Map<String,Double> compoJuvenile;
-
-
-
- /**
- * 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,
- Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning,
- Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning,
- Map<DiadromousFish.Gender, Double> gameteSpawned,
- Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning,
- Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning,
- Map<DiadromousFish.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 créer ici une Map, classe mère 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) {
-
- 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 gamètes
- 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) {
-
- double JuvenileMass = this.getWeight(juvenileFish);
- nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient));
- }
- }
-
- return nutrientsExport;
- }
-
- public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish){
- return computeNutrientsExportForJuveniles(juvenileFish, this.nutrientsOfInterest);
-
- }
-
- /**
- * Compute the weight for a fish with length (cm)
- * @param fish
- * @return weight (g)
- */
- public double getWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
-
- double weight = 0.;
- if (fish.getStage()==Stage.IMMATURE)
- weight = juvenileFeatures.get("aLW") * Math.pow(fish.getLength(),juvenileFeatures.get("bLW"));
- else //Stage.MATURE
- if (spawningPosition == SpawningPosition.PRE)
- weight = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW") );
- else
- weight = fishFeaturesPostSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPostSpawning.get(fish.getGender()).get("bLW"));
-
- return weight;
- }
-
- /**
- * Compute the weight for a fish with length (cm)
- * @param fish
- * @return weight (g)
- */
- public double getWeight (DiadromousFish fish) {
-
- return getWeight (fish, SpawningPosition.PRE);
- }
-
-
-
-public ArrayList<String> getNutrientsOfInterest() {
- return nutrientsOfInterest;
- }
-
-/**
- * @param args
- */
-/**
- * @param args
- */
-/**
- * @param args
- */
-public static void main(String[] args) {
-
-
- double aResidenceTime =30;
-
- System.out.println("aResidenceTime: " + aResidenceTime); //
-
-
- Map <String, Double> anExcretionRate = new Hashtable <String, Double>();
- anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
- anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
-
- System.out.println("anExcretionRate: " + anExcretionRate.toString()); //
-
- /*
- * A feature pre spawning
- */
- Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
-
- /*
- * For females
- */
- Map<String,Double> aFeature = new Hashtable<String,Double>();
-
- aFeature.put("aLW", Math.exp(-4.9078)); //weight size relationship computed from BDalosesBruch
- aFeature.put("bLW", 3.147);
- //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);
-
- /*
- * For males
- */
- aFeature = new Hashtable<String,Double>();
- aFeature.put("aLW", Math.exp(-1.304));
- aFeature.put("bLW", 2.1774);
- //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",.08);
- aFeaturePreSpawning.put(Gender.MALE,aFeature);
-
- System.out.println("aFeaturePreSpawning: " + aFeaturePreSpawning.toString()); //
-
- /*
- * a Feature post Spawning
- */
- Map<Gender, Map<String, Double>> aFeaturePostSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
-
- /*
- * For females
- */
- aFeature = new Hashtable<String,Double>();
- aFeature.put("aLW", Math.exp(-4.3276)); //weight size relationship computed from BDalosesBruch
- aFeature.put("bLW", 2.9418);
- //aFeature.put("GSI",0.10); //From BDalosesBruch
- //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);
-
- /*
- * For males
- */
- aFeature = new Hashtable<String,Double>();
-
- aFeature.put("aLW", Math.exp(-4.5675));// parametre "a" de la relation taille/poids - Coefficient d'allometrie
- aFeature.put("bLW", 2.9973);
- //aFeature.put("GSI",.05); From BDalosesBruch
- //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());
-
- Map<Gender, Double> aGameteSpawned = new Hashtable <DiadromousFish.Gender,Double>();
- aGameteSpawned.put(Gender.FEMALE, 131.); // Compute from the difference between spawned and unspawned ovaries ie correspond to a mean weight of eggs spawned
- aGameteSpawned.put(Gender.MALE, 44.8); // Compute from the difference between spawned and unspawned testes ie correspond to a mean weight of sperm spawned
-
- System.out.println("aGameteSpawned: " + aGameteSpawned.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", 2.958 / 100.); //On remplit une collection avec un put.
- aCompo.put("P", 0.673 / 100.);
- aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.941 / 100.);
- aCompo.put("P", 0.666 / 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", 0.961 / 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
-
- 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,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, aGameteSpawned,
- 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 fishFemale = new DiadromousFish (pilot, basin, 52., 1L, Gender.FEMALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
- fishFemale.setStage(Stage.MATURE);
- DiadromousFish fishMale = new DiadromousFish (pilot, basin, 47., 1L, Gender.MALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
- fishMale.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(fishFemale.getGender() + ": " + fishFemale.getLength() + " cm " + fn.getWeight(fishFemale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishFemale, SpawningPosition.POST));
- System.out.println("\tNutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fishFemale).toString());
- System.out.println("\tNutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fishFemale).toString());
- System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishFemale).toString());
-
- System.out.println(fishMale.getGender() + ": " + fishMale.getLength() + " cm " + fn.getWeight(fishMale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishMale, SpawningPosition.POST));
- System.out.println("\tNutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fishMale).toString());
- System.out.println("\tNutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fishMale).toString());
- System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishMale).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));
-
-}
-}
-
-
diff --git a/src/main/java/species/MigrateToSea.java b/src/main/java/species/MigrateToSea.java
index 95fbddeaec73451a1213cafe3d859af86596d9a5..206043342e5bf624554daa588f8c98e9f6c507ae 100644
--- a/src/main/java/species/MigrateToSea.java
+++ b/src/main/java/species/MigrateToSea.java
@@ -9,8 +9,13 @@ import environment.Time;
import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import java.util.ArrayList;
+import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+
import miscellaneous.Duo;
+import species.DiadromousFish.Stage;
+
import org.openide.util.lookup.ServiceProvider;
@ServiceProvider(service = AquaNismsGroupProcess.class)
@@ -28,19 +33,48 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
if (Time.getSeason(group.getPilot()) == seaMigrationSeason ){
Basin destination;
- List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
- for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
- RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
-
- List<DiadromousFish> fishes = basin.getFishs(group);
- if (fishes!=null) for (DiadromousFish fish : fishes) {
- destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
- fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination));
- }
- }
- for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
- duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group);
- }
- }
+
+ //On créer la Map pour stocker les flux d'export
+ Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>();
+
+ List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
+ for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
+ RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
+ //Fish move to sea and compute the related export of nutrients
+ List<DiadromousFish> fishes = basin.getFishs(group);
+
+ // ON ré-initialise notre map pour chauqe bassin
+ for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+ totalOutputFluxes.put(nutrient, 0.);
+ }
+ totalOutputFluxes.put("biomass", 0.); //création de la biomasse
+
+ if (fishes!=null) {
+ for (DiadromousFish fish : fishes) {
+ destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
+ fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination)); //Mentionne la sortie d'un poisson de la boucle
+
+ double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
+
+ if (fish.getStage()==Stage.IMMATURE) {
+ Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish);
+ for (String nutrient: aFluxExportedByJuveniles.keySet()) {
+ totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount());
+ }
+
+ totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass);
+ }
+ }
+ }
+
+ for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
+ duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on déplace les poissons dans le fichier MoveTo et on dénote la destination du poisson.
+ }
+ System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
+ + basin.getName() + "; " + totalOutputFluxes);
+ }
+ }
+
+
}
-}
+}
\ No newline at end of file
diff --git a/src/main/java/species/NutrientRoutine.java b/src/main/java/species/NutrientRoutine.java
new file mode 100644
index 0000000000000000000000000000000000000000..f3f26a36fe1717fc09b5dda2c33dc8b0863ac308
--- /dev/null
+++ b/src/main/java/species/NutrientRoutine.java
@@ -0,0 +1,533 @@
+/**
+ *
+ * @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 fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish.Gender;
+import species.DiadromousFish.Stage;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+
+/**
+ * @author camille.poulet
+ *
+ */
+public class NutrientRoutine {
+
+
+ private static enum SpawningPosition {PRE,POST}; // on créer un static pour réserver une même classe mémoire pour toutes les instances
+
+ //private static enum Gender {UNDIFFERENCIED, FEMALE, MALE};
+
+ 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 à la ligne lors du commentaire
+ * key gender
+ * value
+ * key feature
+ * value value
+ */
+ private Map <DiadromousFish.Gender,Map<String, Double>> fishFeaturesPreSpawning;
+
+ private Map <DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning;
+
+ private Map<String, Double> juvenileFeatures;
+
+
+ /**
+ * Weight of gametes spawned for both males and females
+ * key gender
+ * value g
+ * usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
+ */
+ //private Map <DiadromousFish.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 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.
+
+ /**
+ * 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> chemical element
+ * <value> value
+ */
+
+ private Map<String,Double> compoJuvenile;
+
+
+
+ /**
+ * Constructor based on the 5 Map of fish composition
+ * @param fishFeaturesPreSpawning
+ * @param compoCarcassPreSpawning
+ * @param compoCarcassPostSpawning
+ * @param compoGametes
+ * @param compoJuvenile
+ */
+ public NutrientRoutine(ArrayList<String> nutrientsOfInterest,
+
+ double residenceTime,
+ Map <String, Double> excretionRate,
+ Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning,
+ Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning,
+ Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning,
+ Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning,
+ Map<DiadromousFish.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.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 créer ici une Map, classe mère 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) {
+
+ 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 = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
+ *compoGametes.get(fish.getGender()).get(nutrient);
+ 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 = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
+ * 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) {
+
+ double JuvenileMass = this.getWeight(juvenileFish);
+ nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient));
+ }
+ }
+
+ return nutrientsExport;
+ }
+
+ public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish){
+ return computeNutrientsExportForJuveniles(juvenileFish, this.nutrientsOfInterest);
+
+ }
+
+ /**
+ * Compute the weight for a fish with length (cm)
+ * @param fish
+ * @return weight (g)
+ */
+ public double getWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
+
+ double weight = 0.;
+ if (fish.getStage()==Stage.IMMATURE)
+ weight = juvenileFeatures.get("aLW") * Math.pow(fish.getLength(),juvenileFeatures.get("bLW"));
+ else //Stage.MATURE
+ if (spawningPosition == SpawningPosition.PRE)
+ weight = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW") );
+ else
+ weight = fishFeaturesPostSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPostSpawning.get(fish.getGender()).get("bLW"));
+
+ return weight;
+ }
+
+
+ /**
+ * Compute the weight for a fish with length (cm)
+ * @param fish
+ * @return weight (g)
+ */
+ public double getWeight (DiadromousFish fish) {
+
+ return getWeight (fish, SpawningPosition.PRE);
+ }
+
+ public double getGonadWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
+
+ double gonadWeight = 0.;
+ if (fish.getStage()==Stage.MATURE);
+ if (spawningPosition == SpawningPosition.PRE)
+ gonadWeight = Math.exp(fishFeaturesPreSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPreSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+ else
+ gonadWeight = Math.exp(fishFeaturesPostSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPostSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+
+ return gonadWeight;
+ }
+
+
+ /**
+ * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ * @param fish
+ * @return weight (g)
+ */
+ public double getGonadWeight (DiadromousFish fish) {
+
+ return getGonadWeight (fish, SpawningPosition.PRE);
+ }
+
+
+
+
+ public ArrayList<String> getNutrientsOfInterest() {
+ return nutrientsOfInterest;
+ }
+
+ /**
+ * @param args
+ */
+ /**
+ * @param args
+ */
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+
+
+ double aResidenceTime =30;
+
+ System.out.println("aResidenceTime: " + aResidenceTime); //
+
+
+ Map <String, Double> anExcretionRate = new Hashtable <String, Double>();
+ anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
+ anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
+
+ System.out.println("anExcretionRate: " + anExcretionRate.toString()); //
+
+ /*
+ * A feature pre spawning
+ */
+ Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
+
+ /*
+ * For females
+ */
+ Map<String,Double> aFeature = new Hashtable<String,Double>();
+
+ aFeature.put("aLW", Math.exp(-4.9078)); //weight size relationship computed from BDalosesBruch
+ aFeature.put("bLW", 3.147);
+ aFeature.put("aLW_Gonad", -5.2425); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.6729); // issu de la relation taille - poids des gonades Bruch
+ //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);
+
+ /*
+ * For males
+ */
+ aFeature = new Hashtable<String,Double>();
+ aFeature.put("aLW", Math.exp(-1.304));
+ aFeature.put("bLW", 2.1774);
+ aFeature.put("aLW_Gonad", -8.8744);
+ aFeature.put("bLW_Gonad", 3.3838);
+ //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",.08);
+ aFeaturePreSpawning.put(Gender.MALE,aFeature);
+
+ System.out.println("aFeaturePreSpawning: " + aFeaturePreSpawning.toString()); //
+
+ /*
+ * a Feature post Spawning
+ */
+ Map<Gender, Map<String, Double>> aFeaturePostSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
+
+ /*
+ * For females
+ */
+ aFeature = new Hashtable<String,Double>();
+ aFeature.put("aLW", Math.exp(-4.3276)); //weight size relationship computed from BDalosesBruch
+ aFeature.put("bLW", 2.9418);
+ aFeature.put("aLW_Gonad", -6.6234); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.8545); // issu de la relation taille - poids des gonades Bruch
+ //aFeature.put("GSI",0.10); //From BDalosesBruch
+ //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);
+
+ /*
+ * For males
+ */
+ aFeature = new Hashtable<String,Double>();
+
+ aFeature.put("aLW", Math.exp(-4.5675));// parametre "a" de la relation taille/poids - Coefficient d'allometrie
+ aFeature.put("bLW", 2.9973);
+ aFeature.put("aLW_Gonad", -11.285); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 3.8331); // issu de la relation taille - poids des gonades Bruch
+ //aFeature.put("GSI",.05); From BDalosesBruch
+ //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", 2.958 / 100.); //On remplit une collection avec un put.
+ aCompo.put("P", 0.673 / 100.);
+ aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
+
+ aCompo = new Hashtable<String,Double>();
+ aCompo.put("N", 2.941 / 100.);
+ aCompo.put("P", 0.666 / 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", 0.961 / 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.); // Approximée par la compo des gonades
+ 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
+
+ System.out.println("aCompoJuveniles: " + aCompoJuveniles.toString());
+
+ ArrayList <String> nutrientsOfInterest= new ArrayList <String>();
+ nutrientsOfInterest.add("N");
+ nutrientsOfInterest.add("P");
+
+ System.out.println("nutrientsOfInterest: " + nutrientsOfInterest);
+
+
+ NutrientRoutine fn = new NutrientRoutine(nutrientsOfInterest,aResidenceTime, anExcretionRate, 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 fishFemale = new DiadromousFish (pilot, basin, 52., 1L, Gender.FEMALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
+ fishFemale.setStage(Stage.MATURE);
+ DiadromousFish fishMale = new DiadromousFish (pilot, basin, 47., 1L, Gender.MALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
+ fishMale.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(fishFemale.getGender() + ": " + fishFemale.getLength() + " cm " + fn.getWeight(fishFemale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishFemale, SpawningPosition.POST));
+ System.out.println("\tNutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fishFemale).toString());
+ System.out.println("\tNutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fishFemale).toString());
+ System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishFemale).toString());
+
+ System.out.println(fishMale.getGender() + ": " + fishMale.getLength() + " cm " + fn.getWeight(fishMale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishMale, SpawningPosition.POST));
+ System.out.println("\tNutrients Fluxes for death before spawning " + fn.computeNutrientsInputForDeathBeforeSpawning(fishMale).toString());
+ System.out.println("\tNutrients Fluxes for death after spawning " + fn.computeNutrientsInputForDeathAfterSpawning(fishMale).toString());
+ System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishMale).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));
+
+ }
+}
+
+
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
index 8e8f773cbb3aa64198476c7b0995999594a281c2..21007cc5c241d066babeeea8d86a749b06d95a81 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
@@ -163,6 +163,7 @@ public class ReproduceAndSurviveAfterReproduction extends AquaNismsGroupProcess<
survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
if (survivalAmount > 0)
fish.setAmount(survivalAmount);
+
else
deadFish.add(fish);
}
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index f1ca10f624eb731cf2ff1a058f5065a97adc6429..20dd84d3ec092eacd6f6af7037d4e2241487290d 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -108,20 +108,23 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
List<DiadromousFish> fishInBasin = riverBasin.getFishs(group);
if (fishInBasin != null){
-
- Map<String, Double> totalFluxes = new Hashtable<String, Double>(); //On cr�er la Map pour stocker les flux
-
- for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
-
- totalFluxes.put(nutrient, 0.); // ON MET A JOUR NOTRE map
-
+
+ //Initiate the total fluxes for this basin
+ Map<String, Map<String, Double>> totalInputFluxes = new Hashtable<String, Map <String, Double>>(); //On créer la Map pour stocker les flux
+ totalInputFluxes.put("autochtonous", new Hashtable < String, Double>());
+ totalInputFluxes.put("allochtonous", new Hashtable < String, Double>());
+ for (String origin: totalInputFluxes.keySet()) {
+ for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+ totalInputFluxes.get(origin).put(nutrient, 0.); // ON MET A JOUR NOTRE map
+ }
+ totalInputFluxes.get(origin).put("biomass",0.);
}
// --------------------------------------------------------------------------------------------------
// definition of the stock recruiment relationship
// --------------------------------------------------------------------------------------------------
-
+
// effective temperature for reproduction (priority to the ANG value)
double tempEffectRep;
if (Double.isNaN(group.getTempMinRep())){
@@ -152,7 +155,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// initilisation of the stock recruitment relationship
stockRecruitmentRelationship.init(alpha, beta, S50, S95);
-
+
// --------------------------------------------------------------------------------------------------
// calulation of the spawner number
// --------------------------------------------------------------------------------------------------
@@ -162,15 +165,15 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// compute the number of spawners and keep the origines of the spawners
for (DiadromousFish fish : fishInBasin){
-
+
if (fish.getGender() == Gender.FEMALE & fish.isMature()){
-
+
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
if (fish.getNumberOfReproduction() < 1) {
numberOfFemaleSpawnerForFirstTime++;
femaleSpawnersForFirstTimeAgesSum += fish.getAge();
}
- numberOfFemaleGenitors += fish.getAmount() ;
+ numberOfFemaleGenitors += fish.getAmount() ; // on ajoute a chaque fois le fish.getAmount (CcumSum)
// spawner per origine
String basinName = fish.getBirthBasin().getName();
@@ -190,11 +193,49 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
fish.incNumberOfReproduction();
// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
- survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
- if (survivalAmount > 0)
- fish.setAmount(survivalAmount);
+ survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
+ double biomass = 0.;
+ String origin;
+ if(fish.getBirthBasin()== riverBasin)
+ origin = "autochtonous";
else
+ origin = "allochtonous";
+ if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs
+
+ //Export for fishes survived after spawning (survivalAmount) : excretion + gametes
+ Map <String, Double> aFluxAfterSurvival = group.getNutrientRoutine().computeNutrientsInputForSurvivalAfterSpawning(fish);
+
+ //Export for fishes that dies after spawning (fish.getAmount - survivalAmount): excretion + gametes + carcasse
+ Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish);
+
+ for (String nutrient: aFluxAfterSurvival.keySet()) {
+ //For survival fish
+ totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount);
+
+ //For dead fish
+ totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+ }
+
+ //compute biomass for dead fish
+ biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount);
+ totalInputFluxes.get(origin).put("biomass", totalInputFluxes.get(origin).get("biomass") + biomass);
+
+ //update the amount of individual in the super-individual
+ fish.setAmount(survivalAmount);
+ }
+ else {
+ //Le superindividu est mort !!!
deadFish.add(fish);
+
+ //Export for fished died before spawning (fish.getAmount): carcasses + excretion + gametes
+ Map<String, Double> aFlux = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); //
+
+ for (String nutrient: aFlux.keySet()) {
+ totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFlux.get(nutrient) * fish.getAmount()); //Fish.getAmount - survivalAmount = total fishes died.
+ }
+ biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
+ totalInputFluxes.get(origin).put("biomass", totalInputFluxes.get(origin).get("biomass") + biomass);
+ }
}
}
@@ -269,9 +310,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// --------------------------------------------------------------------------------------------------
// Reproduction process (number of recruits)
// --------------------------------------------------------------------------------------------------
-
+
if (numberOfFemaleGenitors > 0.) {
-
+
//BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors);
@@ -280,7 +321,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
long numberOfRecruit = Math.round(Math.exp(genNormal.nextDouble()*sigmaRecruitment + muRecruitment));
//System.out.println(group.getPilot().getCurrentTime()+" "+Time.getSeason(group.getPilot())+" "+ riverBasin.getName()+": " + numberOfGenitors + " spwaners \tgive "+ numberOfRecruit + " recruits");
-
+
// keep last % of autochtone
riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleGenitors);
@@ -350,28 +391,18 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Remove deadfish and compute the related nutrient fluxes
// --------------------------------------------------------------------------------------------------
for (DiadromousFish fish : deadFish){
-
- Map<String, Double> aFlux = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); //
-
- for (String nutrient: aFlux.keySet()) {
-
- totalFluxes.put(nutrient,totalFluxes.get(nutrient) + aFlux.get(nutrient) * fish.getAmount());
- }
-
-
-
group.removeAquaNism(fish);
}
deadFish.clear();
-
- //System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";"
- //+ riverBasin.getName() + "; " + totalFluxes);
-
+
+ System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
+ + riverBasin.getName() + "; " + totalInputFluxes);
+
}
else {
riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));
}
-
+
// System.out.println("("+numberOfGenitors+")");
//System.out.println(" BEFORE " +riverBasin.getSpawnerOrigins().keySet());