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Poulet Camille authored
Export the effective fluxes between watersheds
dd081b0a
package species;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Basin;
import environment.BasinNetwork;
import environment.BasinNetworkReal;
import environment.RiverBasin;
import fr.cemagref.observation.kernel.Observable;
import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
import fr.cemagref.simaqualife.kernel.Processes;
import fr.cemagref.simaqualife.pilot.Pilot;
import java.awt.Color;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Scanner;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import miscellaneous.Duo;
import miscellaneous.TreeMapForCentile;
import species.DiadromousFish.Gender;
import org.openide.util.lookup.ServiceProvider;
@ServiceProvider(service = AquaNismsGroup.class)
public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNetwork> implements Comparable<DiadromousFishGroup> {
public String name = "species A";
public Color color = Color.RED;
/**
* L infinity of the van Bertalanffy growth curve
* L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public double linfVonBert = 60.;
/**
* ????
* @unit
*/
public double dMaxDisp = 300.;
/**
* length at first maturity. At that length the fish become Stage.MATURE
* @unit cm
*/
public double lFirstMaturity = 40.;
/**
* Routine to compute nutrient fluxes operated by a single individual (TODO by a single super individual).
*
*/
private NutrientRoutine nutrientRoutine;
public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
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/**
* centile to calucale the range of species distribution
* @unit
*/
public double centileForRange = 0.95;
/**
* file with the calibated parameters (from baysian approach)
* @unit
*/
private String parameterSetfileName= "data/input/reality/parameterSet.csv";
/**
* line to use in the calibrated parameters file
* @unit
*/
private int parameterSetLine =0;
/**
* year when the update of the basin should occur
* @unit
*/
private long yearOfTheUpdate;
/**
* list of the basins to be updated
* column 1: name of the basin
* column 2: Pattractive: how the bassin become attractive (0 not attractive, 1 ??? normal weight associated to catchment size)
* column 3: Paccessible: how the bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
* @unit
*/
private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
private String outputPath = "data/output/";
private String fileNameFluxes = "fluxes";
private transient BufferedWriter bWForFluxes;
private transient String sep;
/**
* map
* <key> basin name
* <value> Duo
* <first> pAttractive
* <second> pAccessible
* @unit
*/
private transient Map<String, Duo<Double, Double>> basinsToUpdate;
/**
* Brody growth coefficient of the von Bertalanffy growth curve (from the parameterset file)
* * L = Linf *(1-exp(-K*(t-t0))
* @unit year-1
*/
private transient double kOpt;
/**
* minimum temperature for the reproduction (from the parameterset file)
* @unit °C
*/
private transient double tempMinRep; //parametre de reproduction
/**
* list of the parameters provided by the calibration
* @unit
*/
private transient List<Duo<Double, Double>> parameterSets;
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public static void main(String[] args) {
DiadromousFishGroup diadromousFishGroup = new DiadromousFishGroup(new Pilot(), null, null);
double aResidenceTime =30;
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
/*
* A feature pre spawning
*/
Map<DiadromousFish.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);
/*
* a Feature post Spawning
*/
Map<DiadromousFish.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);
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Map<DiadromousFish.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
// carcass composition for fish before spawning
Map<DiadromousFish.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);
// carcass composition for fish after spawning
Map<DiadromousFish.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);
// Gametes composition approximated by the difference between gonads weight before and after spawning.
Map<DiadromousFish.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);
// 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")));
// 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
ArrayList <String> nutrientsOfInterest= new ArrayList <String>();
nutrientsOfInterest.add("N");
nutrientsOfInterest.add("P");
diadromousFishGroup.nutrientRoutine = new NutrientRoutine(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning,
aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
aJuvenileFeatures, aCompoJuveniles);
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System.out.println((new XStream(new DomDriver())).toXML(diadromousFishGroup));
}
public DiadromousFishGroup(Pilot pilot, BasinNetwork environment, Processes processes) {
super(pilot, environment, processes);
}
public double getPattractive(String basinName){
// TODO pass in argument a Basin
// remove "-s" of the sea basin name
String shortBasinName = basinName.substring(0, basinName.length()-2);
if (basinsToUpdate.containsKey(shortBasinName))
return basinsToUpdate.get(shortBasinName).getFirst();
else
return Double.NaN;
}
public double getPaccessible(String basinName){
// TODO pass in argument a Basin
//WHY not a short name
if (basinsToUpdate.containsKey(basinName))
return basinsToUpdate.get(basinName).getSecond();
else
return Double.NaN;
}
/**
* @return the yearOfTheUpdate
*/
public long getYearOfTheUpdate() {
return yearOfTheUpdate;
}
/* (non-Javadoc)
* @see fr.cemagref.simaqualife.kernel.AquaNismsGroup#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
*/
@Override
public void initTransientParameters(Pilot pilot)
throws IllegalArgumentException, IllegalAccessException,
InvocationTargetException {
super.initTransientParameters(pilot);
// basin to be updated
if ( basinsToUpdate != null){
String subDir=basinsToUpdateFile;
if (basinsToUpdateFile.lastIndexOf("/")!=-1)
subDir=basinsToUpdateFile.substring(basinsToUpdateFile.lastIndexOf("/")+1,
basinsToUpdateFile.length());
if (subDir.lastIndexOf(".")!=-1)
subDir=subDir.substring(0, subDir.lastIndexOf("."));
outputPath= outputPath.concat(subDir).concat("/");
System.out.println(outputPath);
basinsToUpdate = new HashMap<String, Duo<Double, Double>>();
FileReader reader;
Scanner scanner;
String basins;
double pAttractive;
double pAccessible;
try {
// open the file
reader = new FileReader(basinsToUpdateFile);
// Parsing the file
scanner = new Scanner(reader);
scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
scanner.useDelimiter(Pattern.compile("[;\r]"));
scanner.nextLine();
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while (scanner.hasNext()) {
basins = scanner.next();
if (basins!= null) {
pAttractive = scanner.nextDouble();
pAccessible = scanner.nextDouble();
scanner.nextLine();
Duo<Double, Double> duo=new Duo<Double, Double>(pAttractive, pAccessible);
basinsToUpdate.put(basins, duo);
}
}
reader.close();
} catch (Exception e) {
e.printStackTrace();
}
}
// charge kopt et temMinRep depuis le fichier de parametre. Sinon (parameterSetLine<=0), ce sont les
// valeur dasn le procoessus de reroduction qui sont utilis�
kOpt=Double.NaN;
tempMinRep =Double.NaN;
if (parameterSetLine>0){
parameterSets = new ArrayList<Duo<Double,Double>>(10);
// open the file
FileReader reader1;
Scanner scanner1;
try {
reader1 = new FileReader(parameterSetfileName);
// Parsing the file
scanner1 = new Scanner(reader1);
scanner1.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
scanner1.useDelimiter(Pattern.compile("[;\r]"));
scanner1.nextLine(); // skip the first line
while (scanner1.hasNext()) {
String rien= scanner1.next(); // skip id
//System.out.println(rien.compareTo("\n"));
if(rien.compareTo("\n")!=0){
Duo<Double, Double> duo=new Duo<Double, Double>(scanner1.nextDouble(), scanner1.nextDouble());
//System.out.println(duo.toString());
parameterSets.add(duo);
}
}
scanner1.close();
reader1.close();
} catch (Exception e) {
e.printStackTrace();
}
kOpt = parameterSets.get(parameterSetLine-1).getFirst();
tempMinRep = parameterSets.get(parameterSetLine-1).getSecond();
}
// open an bufferad writer to export fluxes
if (fileNameFluxes != null){
sep = ";";
new File(this.outputPath +fileNameFluxes).getParentFile().mkdirs();
try {
bWForFluxes = new BufferedWriter(new FileWriter(new File(this.outputPath+
fileNameFluxes +this.getSimulationId() + ".csv")));
bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
+sep+"abundance" + sep + "fluxType"+ sep + "origin" +sep+"biomass");
for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
bWForFluxes.write(sep+nutrient);
}
bWForFluxes.write("\n");