je veux bien passer te voir car je suis à Brest, faut-juste que tu me dises ou est ton bureau? stephanie Delphine.Rocklin@ifremer.fr a écrit :

Bonjour tout le monde,

bon ISIS me fais encore des siennes. J'ai modifié le script de Calibration afin de l'adapter à mes données et mon cas d'étude, mais ça ne semble pas vraiment fonctionner.

Le script tourne apparemment (je le sélectionne dans la fenêtre de simulations et il me donne les bons paramètres), de même lorsque je clique sur "vérifier" (de l'éditeur de script), il me dit que c'est ok. Mais lorsque je lance la simu en utilisant le plan d'analyse (simu qui tourne sans soucis apparent), il ne créé aucun fichier Historic. De même, dans le lanceur de simulation, onglet "queue", il indique "0" dans la cellule "plan". Est-ce que cela signifie que mon plan d'analyse n'est pas pris en compte ? (je sélectionne pourtant "CalibrationEspeceq1q2Export" dans l'onglet "Analyse de sensibilité").

Ou alors manque-t-il une info à la base ? Dans le script ? Un document manquant ?

Je vous envoie en pièces jointes le script de la calibration & le fichier csv contenant mes débarquements observés (abondances).J'ai 14 groupes de pop. et 3 mois (mai, juin, juillet) donc 14 colonnes, et 3 lignes. J'ai indiqué dans le script qu'il doit créer une ss-matrice contenant uniquement ces 3 mois (MatrixND L = L2.getSubMatrix(0,4,3).copy(); ) comme m'avait montré Sigrid (merci bcp d'ailleurs pour les explications !). "0" pour signaler qu'on s'intéresse aux mois, "4" pour signaler qu'on ne commence qu'au mois de mai et "3" pour ne considérer que 3 mois à partir de là.

Si quelqu'un peut m'éclairer.....merci !

delphine

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package analyseplans; import static org.codelutin.i18n.I18n._; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import scripts.ResultName; import java.io.*; import java.util.*; import org.codelutin.math.matrix.*; import org.codelutin.topia.*;// pour pouvoir utiliser la methode StringUtil.toDouble() import org.codelutin.util.*;// pour pouvoir utiliser la methode StringUtil.toDouble() import fr.ifremer.isisfish.*; import fr.ifremer.isisfish.types.*; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.simulator.AnalysePlan; import fr.ifremer.isisfish.simulator.AnalysePlanContext; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.datastore.ResultStorage;

/** * /////***File must be copied in isis-database-3/ analyseplans/ * File name : CalibrationEspeceq1q2Export.java * /////*** File name could be modified if needed * /////*** BUT class name must be identical to file name (without the extention ".java") see below * * Created: 17 septembre 2007 * * @author <> * @version $Revision: 1.27 $ * * Last update: $Date: 2007/05/24 09:29:18 $ * by : $Author: bpoussin $ */

/////***You can modify class name if you want /////***BUT attention : file name and class name must be the same (without the extention ".java"), ie here : "CalibrationEspeceq1q2Export" public class CalibrationEspeceq1q2Export implements AnalysePlan {

/** to use log facility, just put in your code: log.info("..."); */

/////***class name to check here static private Log log = LogFactory.getLog(CalibrationEspeceq1q2Export.class);

enum State {STATE_INIT, STATE_0, STATE_1, STATE_2, STATE_3, STATE_4};

/////***here must appear the path to export the historic file ("Historic.csv") where q1, q2 and criteria computed at each simulation are written /////***Attention : before beginning a new calibration rename your eventual old file Historic.csv otherwise it will be lost File exportHistoric = new File ("C:/Documents and Settings/drocklin/Bureau/Calibration/Historic.csv"); protected String exportHisto = "";

//initial points of the simplex public Population param_Population = null; public String param_M1 = "2.0e-4;2.0e-6";// devient un parametre du plan d analyse public String param_M2 = "1.5e-4;2.5e-6";// devient un parametre du plan d analyse public String param_M3 = "2.5e-4;2.4e-6";// devient un parametre du plan d analyse public String param_pas = "2e-5";// devient un parametre du plan d analyse ///// ***put here the path and name of the file containing the data on which you calibrate your fichery ( here observed catches) public String param_nomfichier_debarquements = "C:/Documents and Settings/drocklin/Bureau/ObservedLandings/Observedlandings2008.csv";//in row : time ; in columns : age or length group protected File debarquementsObserves; protected MatrixND matrixDebarquement;

protected State state = State.STATE_INIT; public Experiences experiences = new Experiences(); public String [] necessaryResult = { ResultName.MATRIX_CATCH_PER_STRATEGY_MET };

public String[] getNecessaryResult() { return this.necessaryResult; }

/** * Permet d'afficher a l'utilisateur une aide sur le plan. * @return L'aide ou la description du plan */ public String getDescription() throws Exception { return _("Calibration using variable step Simplex method (Walters): user gives a file of observations (here catches) by time step and group (.csv), output will try to approach oservations by changing the values of catchability"); }

/** * Appele au demarrage de la simulation, cette methode permet d'initialiser * des valeurs * @param simulation La simulation pour lequel on utilise cette regle */ public void init(AnalysePlanContext context) throws Exception { if (param_nomfichier_debarquements==null || "".equals(param_nomfichier_debarquements)){ debarquementsObserves = FileUtil.getFile(".*.csv", "fichier csv séparateur ';'"); } else { debarquementsObserves = new File(param_nomfichier_debarquements); } int nbYear = context.getParam().getNumberOfYear();

TopiaContext db = context.getParam().getRegion().getStorage().beginTransaction(); Population pop = (Population)db.findByTopiaId(param_Population.getTopiaId());

/////*** specify dimention of the matrix containning observations (observed landings for instance) /////*** numbers of group/columns : could be equal to your number of classes in ISIS but may also be different if your had only aggregated data int nbGroup = 14 ; /////*** enter number of observation per year (if you have observation by quarter put 4) / lines of the observations file int nbTrim = nbYear * 3; int [] dimMatrix = {nbTrim,nbGroup}; matrixDebarquement = MatrixFactory.getInstance().create(dimMatrix); //matrixDebarquement = MatrixFactory.getInstance().create(new int[]{nbGroup}); // List<PopulationGroup> groups = pop.getPopulationGroup(); // matrixDebarquement = MatrixFactory.getInstance().create(new List[]{groups}); matrixDebarquement.importCSV(new FileReader(debarquementsObserves),new int []{0,0}); log.info("MatrixDebarquement : " + matrixDebarquement); db.closeContext(); }

/** * Call before each simulation * @param context plan context * @param nextSimulation storage used for next simulation * @return true if we must do next simulation, false to stop plan * @throws Exception */ double g1; double g2; double worst1; double worst2;

public boolean beforeSimulation(AnalysePlanContext context, SimulationStorage nextSimulation) throws Exception { boolean doNext = true; boolean doBoucle = true; log.info("before simulation");

int number = context.getNumber();

if (number <3) { log.info("number<3");

String [] M1 = param_M1.split(";"); String [] M2 = param_M2.split(";"); String [] M3 = param_M3.split(";");

double [] q1 = StringUtil.toArrayDouble(M1[0], M2[0], M3[0]); double [] q2 = StringUtil.toArrayDouble(M1[1], M2[1], M3[1]); experiences.getExperience(number).q1 = q1[number]; experiences.getExperience(number).q2 = q2[number];

changeDB(experiences.getExperience(number), nextSimulation);

} else {

double q1 = 1000; double q2 = 1000; double lastCritere = experiences.getExperience(number-1).criteria; while (doBoucle){ doBoucle = false; if (state == State.STATE_INIT) { doBoucle = false ; log.info("state init");

//ordonne les 3 premieres experiences selon leur critere Collections.sort(experiences.current); //log.info("SIMPLEXE : current 0 = " + experiences.current.get(0).criteria + "current 1 = " + experiences.current.get(1).criteria + "current 2 = " + experiences.current.get(2).criteria ); log.info("SIMPLEXE : current 0 = " + experiences.current.get(0).criteria + "current 1 = " + experiences.current.get(1).criteria + "current 2 = " + experiences.current.get(2).criteria ); log.info("SIMPLEXE : Best q1 = " + experiences.current.get(0).q1 + " q2 = " + experiences.current.get(0).q2); log.info("SIMPLEXE : NextBest q1 = " + experiences.current.get(1).q1 + " q2 = " + experiences.current.get(1).q2); log.info("SIMPLEXE : Worst q1 = " + experiences.current.get(2).q1 + " q2 = " + experiences.current.get(2).q2);

//Calcul et evaluation de R double g1 = (experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0; double g2 = (experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0; double worst1 = experiences.current.get(2).q1; double worst2 = experiences.current.get(2).q2;

state = State.STATE_0;

q1 = 2 * g1 - worst1; q2 = 2 * g2 - worst2;

log.info ("R : q1 = " + q1 + " q2 = " + q2 );

} else if (state == State.STATE_0) { doBoucle = false; log.info("state 0");

// on fait la 5eme avec des q qui dependent de la 4eme dans le dernier cas //log.info("g1 = " + g1 + " " + "g2 = " + g2); //log.info("worst1 = " + worst1 + " " + "worst2 = " + worst2);

if (lastCritere > experiences.current.get(2).criteria) { log.info("State 0 : R : lastCtritere > current2 : R pire de W"); state = State.STATE_1; //calcul de Cw q1 = ((experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0) - ( ((experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0) - experiences.current.get(2).q1 ) / 2.0; q2 = ((experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0) - ( ((experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0) - experiences.current.get(2).q2 ) / 2.0; log.info("Cw : q1 = " + q1 + " q2 = " + q2);

} else if (lastCritere > experiences.current.get(1).criteria) { log.info("State 0 :R : lastCritere > current 1 : R meilleur que W et moins bon que N"); state = State.STATE_2; // calcul de Cr q1 = ((experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0) + ( ((experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0) - experiences.current.get(2).q1 ) / 2.0; q2 = ((experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0) + ( ((experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0) - experiences.current.get(2).q2 ) / 2.0; log.info("Cr : q1 = " + q1 + " q2 = " + q2);

} else if (lastCritere > experiences.current.get(0).criteria) { log.info("State 0 :R : lastCritere > current0 : R meilleur que N et moins bon que B"); state = State.STATE_INIT; experiences.current.remove(2);//remove(3)avant doBoucle = true; log.info("remove W, simplex BNR");

} else { // dernier cas possible: if (lastCritere < experiences.current.get(0).critere) { log.info("State 0 :R : lastCritere < current 0 : R meilleur que B, calcul de E"); state = State.STATE_4;

q1 = experiences.getExperience(number-1).q1 + (experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0 - experiences.current.get(2).q1; q2 = experiences.getExperience(number-1).q2 + (experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0 - experiences.current.get(2).q2; //q1 = experiences.current.get(3).q1 + (experiences.current.get(0).q1 + experiences.current.get(1).q1) / 2.0 - experiences.current.get(2).q1; //q2 = experiences.current.get(3).q2 + (experiences.current.get(0).q2 + experiences.current.get(1).q2) / 2.0 - experiences.current.get(2).q2; log.info("E : q1 = " + q1 + " q2 = " + q2); }

} else if (state == State.STATE_1) { log.info("state 1, simplex BNCw"); experiences.current.remove(3); experiences.current.remove(2); state = State.STATE_INIT; doBoucle = true;

} else if (state == State.STATE_2) { log.info("state 2, simplex BNCr"); experiences.current.remove(3); experiences.current.remove(2); state = State.STATE_INIT; doBoucle = true;

} else if (state == State.STATE_4) { log.info("state 4 :comparaison de E a B"); doBoucle = true; if (lastCritere < experiences.current.get(0).criteria) { log.info("E meilleur que B, remove 2 et 3 : simplex BNE"); experiences.current.remove(3); experiences.current.remove(2); } else { log.info("E moins bon que B, remove 2 et 4, simplex BNR"); experiences.current.remove(4); experiences.current.remove(2); }

state = State.STATE_INIT; }

}//fin du while //on remplit la table experiences experiences.getExperience(number).q1 = q1; experiences.getExperience(number).q2 = q2;

log.info("on change Q dans la DB avec : q1 = " + q1 + " " + "q2 = " + q2);

// on change la valeur de q dans la DB changeDB(experiences.getExperience(number), nextSimulation); }// fin du else (number > 3) return doNext; }// fin du before simulation

/**

* Call after each simulation, compute criteria for last simulation * @param context plan context * @param nextSimulation storage used for next simulation * @return true if we must do next simulation, false to stop plan * @throws Exception */

public boolean afterSimulation(AnalysePlanContext context, SimulationStorage lastSimulation) throws Exception { boolean doNext = true; log.info("after simulation"); int number = context.getNumber(); ResultStorage result = lastSimulation.getResultStorage();

/////*** Simulated catches are cumulated over strategies, areas and metiers

MatrixND L2 = result.getMatrix(param_Population, ResultName.MATRIX_CATCH_PER_STRATEGY_MET);

// log.info("dim de L2" + " " + Arrays.toString(L2.getDim())); /////*** If some strategies, metiers or areas must not be included in the cumulated catches see below else put "//" at the beginning of line 297 and replace "L2" by "L" at line 289 /////*** the strategies or so to exclude must be at the begining or end of the list you enter in the parameters interface /////*** fill the line MatrixND L = L2.getSubMatrix(a,b,c).copy(); as follow : /////*** a = 1 if you want to exclude strategies, 2 if metiers and 4 if areas /////*** b = indice of the first object considered /////*** c = number of object to keep after b, b included // MatrixND L = L2.getSubMatrix(1,2,4).copy(); // for instance : keep strategies 2,3,4,5

MatrixND L = L2.getSubMatrix(0,4,3).copy();

//log.info("sous matrice extraite"); L = L.sumOverDim(1);// sum over strategies L = L.sumOverDim(2);// sum over metiers L = L.sumOverDim(4);// sum over zones log.info("sommes sur les strategies, metiers et zones faites");

/////*** if observations are cumulated by groups else put "//" at the beginning of the following line //L = L.sumOverDim(3); /////*** else if number of groups in your database differs from number of groups in observations ... write me an e-mail

////*** if observations are cumulated over quarter a = 3, over year a = 12, else put "//" at the beginning of the following line //L = L.sumOverDim(0,1);

L = L.reduce();

///////////////////Calcul du critere////////////////// log.info("calcul du critere"); log.info("dim de L" + " " + Arrays.toString(L.getDim())); log.info("dim de obs" + " " + Arrays.toString(matrixDebarquement.getDim())); double crit = 0; for ( MatrixIterator g = L.iterator(); g.hasNext();){ g.next(); //boucle sur les trimestres et les classes d age

int [] dim = g.getCoordinates();

double obs = matrixDebarquement.getValue(dim); double simules = g.getValue();

crit += Math.pow(obs-simules, 2); // crit = crit + (obs-simules)^2 }// fin du for log.info("critere " + number + " = " + crit );

//ajoute le critere dans la table experiences experiences.getExperience(number).criteria = crit;

//ecriture de la table historic exportHisto += experiences.getExperience(number).q1 +";"+ experiences.getExperience(number).q2 +";"+ experiences.getExperience(number).criteria + "\n"; org.codelutin.util.FileUtil.writeString(exportHistoric, exportHisto);

return doNext;

}// fin du after simulation

/** * Modify nextSimulation database with q1 and q2 in exp. * @param exp * @param nextSimulation * @throws Exception */

protected void changeDB(Experience exp, SimulationStorage nextSimulation) throws Exception { //methode appelee dans before simualtion TopiaContext db = nextSimulation.getStorage().beginTransaction();//ouvrir un context pour modifier les donnees Population pop = (Population)db.findByTopiaId(param_Population.getTopiaId()); //reccupere la pop ciblee MatrixND c = pop.getCapturability(); // reccupere la matrice de capturabilité

//log.info("Pour cette simulation : q1 = " + exp.q1 + ";" + "q2 = " + exp.q2 );

/////*** that is where you explain how to fill the catchability matrix with q1 and q2 for (MatrixIterator i = c.iterator(); i.hasNext();){ i.next(); Object [] sem = i.getSemanticsCoordinates(); PopulationGroup group = (PopulationGroup)sem[0]; PopulationSeasonInfo season = (PopulationSeasonInfo)sem[1];

////*** exemple when q2 corresponds to the 12 first groups (groups 0 to 11) // if (group.getId() < 12){ // i.setValue(exp.q2); //}else { //i.setValue(exp.q1); //} if (group.getId() == 3){ i.setValue(exp.q1); }else if (group.getId() == 6){ i.setValue(exp.q2); } /////*** exemple when it depends on seasons and groups /* if (season.getFirstMonth().after(Month.JULY) && group.getId() >=18){ //month >= aout && groupID >= 18 i.setValue(exp.q2); }else { i.setValue(exp.q1); } */

}//fin du for

db.commitTransaction(); // effectue la modification db.closeContext(); // ferme le context }

static public class Experiences { // cree la liste experiences ou sont stoqués q1,q2 et critere pour chaque simulation

/** contains last simplex and potentialy 2 more simulation */ public List<Experience> current = new ArrayList<Experience>();

/** contains all experience done */ public List<Experience> history = new ArrayList<Experience>(); /** * return experience requested, if this experience doesn't exist * create it. * * @param i simulation number * @return experience with simulation number fixed if new experience * is returned */ public Experience getExperience(int i) { Experience result; if (i<history.size()) { result = history.get(i); } else { result = new Experience(); result.simNumber = i; history.add(i, result); current.add(result); } return result; }//fin de la definition de getExperience

/** * @return the history */ public List<Experience> getHistory() { return this.history; } }// fin de la creation des listes experiences

static public class Experience implements Comparable { public int simNumber; public double criteria; public double q1; public double q2; /** * Permit to order experience, first is experience with smallest criteria */ public int compareTo(Object arg0) { Experience other = (Experience)arg0; int result = Double.compare(this.criteria, other.criteria); return result; } }

}

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-- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas@ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: 02 40 37 41 81 Fax: 02 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................