- Isis-fish-docs-commits - mailman.cloud.codelutin.com

r183 - trunk/src/site/rst/v4/user
by echatellier＠users.forge.codelutin.com Dec. 6, 2013

Dec. 6, 2013

Author: echatellier Date: 2013-12-06 09:28:00 +0100 (Fri, 06 Dec 2013) New Revision: 183 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/183 Log: >From scmwebeditor -- Modified: trunk/src/site/rst/v4/user/installation.rst Modified: trunk/src/site/rst/v4/user/installation.rst =================================================================== --- trunk/src/site/rst/v4/user/installation.rst 2013-12-06 08:22:03 UTC (rev 182) +++ trunk/src/site/rst/v4/user/installation.rst 2013-12-06 08:28:00 UTC (rev 183) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2011 Ifremer, Code Lutin, Chatellier Eric +.. * Copyright (C) 1999 - 2013 Ifremer, Code Lutin, Chatellier Eric .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as @@ -30,14 +30,14 @@ --------------- Afin de pouvoir faire tourner ISIS-Fish sur votre machine, il est -nécessaire d'avoir au moins la version 1.6.0_18 de Java d'installée. Il est +nécessaire d'avoir au moins la version *1.7* de Java d'installée. Il est possible de connaître la version actuellement installée sur votre ordinateur en tapant dans une commande DOS : «java -version». Si vous aboutissez à un message d'erreur, cela signifie que Java n'est pas -installé. Si la version installée est antérieure à la version 1.6.0_18 ou +installé. Si la version installée est antérieure à la version 1.7 ou que Java n'est pas installé, vous devez télécharger la dernière version de Java SE Development Kit (JDK). Ceci peut se faire -directement à cette adresse : http://java.sun.com/javase/downloads/index.jsp +directement à cette adresse : http://www.oracle.com/technetwork/java/javase/downloads/index.html Comment se procurer ISIS-Fish ----------------------------- @@ -69,7 +69,7 @@ Par défaut ISIS-Fish peut allouer au maximum 1Go de Ram pour son utilisation. Si votre région contient de très nombreux métiers, stratégies et populations vous pouvez devoir augmenter cette valeur -pour cela éditez le fichier *isisfish.bat* ou *isisfish.sh* suivant votre +pour cela éditez le fichier *isis-fish.bat* ou *isis-fish.sh* suivant votre plateforme (Windows, Unix/Linux). Par défaut les fichiers de lancement redirigent les sorties vers un @@ -97,17 +97,17 @@ Lancer ISIS-Fish sous Unix/Linux ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Placez-vous dans le répertoire contenant le fichier go.sh et exécutez +Placez-vous dans le répertoire contenant le fichier isis-fish.sh et exécutez le avec:: - ./isisfish.sh + ./isis-fish.sh Option de la ligne de commande ------------------------------ Il est possible de passer des paramètres à la ligne de commande par exemple:: - ./isisfish.sh --help + ./isis-fish.sh --help l'option ``--help`` permet d'afficher la liste des options disponibles

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r182 - trunk/src/site/rst
by echatellier＠users.forge.codelutin.com Dec. 6, 2013

Dec. 6, 2013

Author: echatellier Date: 2013-12-06 09:22:03 +0100 (Fri, 06 Dec 2013) New Revision: 182 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/182 Log: Fix synthax Modified: trunk/src/site/rst/publications.rst Modified: trunk/src/site/rst/publications.rst =================================================================== --- trunk/src/site/rst/publications.rst 2013-12-05 15:06:01 UTC (rev 181) +++ trunk/src/site/rst/publications.rst 2013-12-06 08:22:03 UTC (rev 182) @@ -41,7 +41,7 @@ 2013 **Iooss, B.**, Mahévas, S. 2013. Revue et objectifs des méthodes d’analyse de sensibilité globale. Dans Analyse de sensibilité et exploration de modèles - Applications aux modèles environnementaux. Quae. Ed. Robert Faivre, Bertrand Iooss, David Makowski, Stéphanie Mahévas, Hervé Monod. 2013 **R. Faivre, B. Iooss, S. Mahévas, D. Makowski, H. Monod,** editors. Analyse de sensibilité et exploration de modèles. Applications aux modèles environnementaux. Editions Quae, 2013.(http://www.quae.com/fr/r2142-analyse-de-sensibilite-et-exploration-de… 2012 **Deporte N.**, C.Ulrich, S. Mahévas, S.Demanèche, F. Bastardie. 2012. Regional me´tier definition: a comparative investigation of statistical methods using a workflow applied to internationalotter trawl fisheries in the North Sea.ICES Journal of Marine Science 69(2): 331-342 -2011 **Mahévas, S ** et al., (2011) « An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets », Ices Journal Of Marine Science 68, no. 10 : 2252-2263. +2011 **Mahévas, S** et al., (2011) « An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets », Ices Journal Of Marine Science 68, no. 10 : 2252-2263. 2011 **Hussein, C.**, M.Verdoit-Jarraya, J.Pastor, A.Ibrahim, G.Saragoni, D.Pelletier, S. Mahévas, P.Lenfant, 2011. 'Assessing the impact of artisanal and recreational fishing and protection on a white seabream (Diplodus sargussargus) population in the north-western Mediterranean Sea using a simulation model. Part2: Sensitivity analysis and management measures.' **Fisheries Research** 108, Issue 1, Pages 174-183 `Ici <https://w3.ifremer.fr/archimer/doc/00030/14115/11337.pdf>`__ `Fisheries research <http://www.journals.elsevier.com/fisheries-research/>`_ 2011 **Hussein, C.**, M.Verdoit-Jarraya, J.Pastor, A.Ibrahim, G.Saragoni, D.Pelletier, S. Mahévas, P.Lenfant (2011) 'Assessing the impact of artisanal and recreational fishing and protection on a white seabream (Diplodus sargussargus) population in the north-western Mediterranean Sea using a simulation model. Part1: Parameterization and simulations.' **Fisheries Research** 108, Issue 1, Pages 163-173 `Ici <https://w3.ifremer.fr/archimer/doc/00030/14114/11351.pdf>`__ `Fisheries research <http://www.journals.elsevier.com/fisheries-research/>`_ 2011 **Marchal, P.**, Little, L.R., and Thébaud, O., 2011. 'Quota allocation in mixed-fisheries: a bioeconomic modelling approach applied to the Channel flatfish fisheries.' **ICES Journal of Marine Science**, 68, 1580–1591. `Ici <https://w3.ifremer.fr/archimer/doc/00044/15492/12971.pdf>`__ `sciencedirect <http://www.sciencedirect.com/>`_

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r181 - in trunk/src/site/en/rst/v4: . user/tutorials
by echatellier＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: echatellier Date: 2013-12-05 16:06:01 +0100 (Thu, 05 Dec 2013) New Revision: 181 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/181 Log: Fix doc Modified: trunk/src/site/en/rst/v4/index.rst trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst Modified: trunk/src/site/en/rst/v4/index.rst =================================================================== --- trunk/src/site/en/rst/v4/index.rst 2013-12-05 15:02:58 UTC (rev 180) +++ trunk/src/site/en/rst/v4/index.rst 2013-12-05 15:06:01 UTC (rev 181) @@ -45,7 +45,7 @@ .. _Tutorials: user/tutorials.html .. _FAQ: user/FAQ.html .. _Developer manual: devel/index.html -.. _APIs documentation: user/tutorial/useAPI.html +.. _APIs documentation: user/tutorials/useAPI.html .. _ISIS scripts examples: user/scripts.html .. _R scripts examples: user/scriptsR.html .. _Changes in version 4.0: user/changements40.html Modified: trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst 2013-12-05 15:02:58 UTC (rev 180) +++ trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst 2013-12-05 15:06:01 UTC (rev 181) @@ -137,7 +137,7 @@ `Parameter files and matrix`_ -.. _Parameter files and matrix: ../../downloads/Exemple_directory.zip +.. _Parameter files and matrix: ../../../../downloads/Exemple_directory.zip *The script for the simulation plan* (written from the editor) allows to read and modify the values of the parameters depending on the simulation matrix. (Please refer to the manual for a description of @@ -150,7 +150,7 @@ `Script sensitivity analysis`_ -.. _Script sensitivity analysis: ../../downloads/Example_SimulationPlan_en.java +.. _Script sensitivity analysis: ../../../downloads/Example_SimulationPlan_en.java Sequential simulation designs: an example of calibration using the simplex method --------------------------------------------------------------------------------- @@ -169,7 +169,7 @@ `Calibration script`_ -.. _Calibration script: ../../downloads/CalibrationEspeceq1q2Export_en.java +.. _Calibration script: ../../../downloads/CalibrationEspeceq1q2Export_en.java Launching a simulation plan --------------------------- Modified: trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 2013-12-05 15:02:58 UTC (rev 180) +++ trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 2013-12-05 15:06:01 UTC (rev 181) @@ -24,7 +24,7 @@ .. - Tutorial for the use of APIs -========================== +============================ Before you start... First, don't panic!

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r180 - in trunk/src/site/en/rst: . v4
by echatellier＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: echatellier Date: 2013-12-05 16:02:58 +0100 (Thu, 05 Dec 2013) New Revision: 180 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/180 Log: Fix links Modified: trunk/src/site/en/rst/index.rst trunk/src/site/en/rst/v4/index.rst Modified: trunk/src/site/en/rst/index.rst =================================================================== --- trunk/src/site/en/rst/index.rst 2013-12-05 15:00:47 UTC (rev 179) +++ trunk/src/site/en/rst/index.rst 2013-12-05 15:02:58 UTC (rev 180) @@ -5,7 +5,7 @@ .. * $Id: index.rst 3124 2010-11-29 18:14:09Z chatellier $ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2010 Ifremer, Code Lutin +.. * Copyright (C) 1999 - 2013 Ifremer, Code Lutin, Chatellier Eric .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as Modified: trunk/src/site/en/rst/v4/index.rst =================================================================== --- trunk/src/site/en/rst/v4/index.rst 2013-12-05 15:00:47 UTC (rev 179) +++ trunk/src/site/en/rst/v4/index.rst 2013-12-05 15:02:58 UTC (rev 180) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 2011 Ifremer, CodeLutin, Chatellier Eric +.. * Copyright (C) 2011 - 2013 Ifremer, CodeLutin, Chatellier Eric .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as @@ -45,7 +45,7 @@ .. _Tutorials: user/tutorials.html .. _FAQ: user/FAQ.html .. _Developer manual: devel/index.html -.. _APIs documentation: user/useAPI.html +.. _APIs documentation: user/tutorial/useAPI.html .. _ISIS scripts examples: user/scripts.html .. _R scripts examples: user/scriptsR.html .. _Changes in version 4.0: user/changements40.html

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r179 - in trunk/src/site/en: resources/downloads rst/v4/user/tutorials
by echatellier＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: echatellier Date: 2013-12-05 16:00:47 +0100 (Thu, 05 Dec 2013) New Revision: 179 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/179 Log: Traduction de la page simulation plan par Sigrid Added: trunk/src/site/en/resources/downloads/CalibrationEspeceq1q2Export_en.java trunk/src/site/en/resources/downloads/Example_SimulationPlan_en.java Modified: trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst Added: trunk/src/site/en/resources/downloads/CalibrationEspeceq1q2Export_en.java =================================================================== --- trunk/src/site/en/resources/downloads/CalibrationEspeceq1q2Export_en.java (rev 0) +++ trunk/src/site/en/resources/downloads/CalibrationEspeceq1q2Export_en.java 2013-12-05 15:00:47 UTC (rev 179) @@ -0,0 +1,447 @@ +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.*;// to use methode StringUtil.toDouble() +import org.codelutin.util.*;// to use 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 $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ + + +/////***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_en 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_en.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/Sigrid/work/ISIS-FISH/Calibration/Historic.csv"); + protected String exportHisto = ""; + + +//initial points of the simplex + public Population param_Population = null; + public String param_M1 = "2.42e-5;2.11e-6";// devient un parametre du plan d analyse + public String param_M2 = "2.34e-5;2.59e-6";// devient un parametre du plan d analyse + public String param_M3 = "2.59e-5;2.41e-6";// devient un parametre du plan d analyse + //public String param_pas = "1e-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 = "Q:/work/ISIS-FISH/Simu/Calibration/Observedlandings2001-2003.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_WEIGHT_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 s�parateur ';'"); + } 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 = 4 ; +/////*** enter number of observation per year (if you have observation by quarter put 4) / lines of the observations file + int nbTrim = nbYear * 4; + 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 = nextSimulation.getParameter().getAnalysePlanNumber(); + +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 { +/// Here is the simplex algorithm, nothing to change here + 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"); + +//ranks the first three experiments according to the value of the objectif function +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); + + +//computes and evaluates 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"); + + // Run fifth experiments with parameters which depends on the fourth +//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 +//fill in the table of experiments (keeps track of the simulation runs) + experiences.getExperience(number).q1 = q1; + experiences.getExperience(number).q2 = q2; + +log.info("on change Q dans la DB avec : q1 = " + q1 + " " + "q2 = " + q2); + +// Changes the value of q in the database + 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 = lastSimulation.getParameter().getAnalysePlanNumber(); + ResultStorage result = lastSimulation.getResultStorage(); + +/////*** Simulated catches are cumulated over strategies, areas and metiers + + MatrixND L2 = result.getMatrix(param_Population, ResultName.MATRIX_CATCH_WEIGHT_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 +//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,a); + + L = L.reduce(); + + +/////////////////// Computation of the objective function ////////////////// +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(); +//loop over quarters and size classes + + 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 ); + +//add the value of the objective function in the table of experiments + experiences.getExperience(number).criteria = crit; + +// writes the results of the last simulation in a csv file +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 { +//method called to change the database + TopiaContext db = nextSimulation.getStorage().beginTransaction(); + Population pop = (Population)db.findByTopiaId(param_Population.getTopiaId()); //get the target population + MatrixND c = pop.getCapturability(); // get the catchability matrix + +//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); + } + +/////*** 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(); + db.closeContext(); +} + + + + + static public class Experiences { +// create the table of experiments where simulations are stored + + /** 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; + } + } + + +} \ No newline at end of file Property changes on: trunk/src/site/en/resources/downloads/CalibrationEspeceq1q2Export_en.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: trunk/src/site/en/resources/downloads/Example_SimulationPlan_en.java =================================================================== --- trunk/src/site/en/resources/downloads/Example_SimulationPlan_en.java (rev 0) +++ trunk/src/site/en/resources/downloads/Example_SimulationPlan_en.java 2013-12-05 15:00:47 UTC (rev 179) @@ -0,0 +1,310 @@ +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.io.File; +import java.io.FileReader; +import java.io.Writer; +import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Properties; + +import org.codelutin.math.matrix.*; +import org.codelutin.util.*; +import org.codelutin.topia.*; + +import fr.ifremer.isisfish.*; +import fr.ifremer.isisfish.types.*; +import fr.ifremer.isisfish.rule.Rule; +import fr.ifremer.isisfish.rule.RuleHelper; +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.RegionStorage; +import fr.ifremer.isisfish.datastore.RuleStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.datastore.ResultStorage; + +/* + * Exemple_PlanAnalyse.java + * + * Created: 6 juin 2007 + * + * @author sl + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ + +/** + * The way it works is that you create text files containing the simulation matrix (matrix.txt) and + * one text file per parameter modified by the plan, containing the different values taken by the parameter at each simulation. + * For instance if the TAC is modified the file will be named tac.txt. + * For parameters that are double files should look like this: + * <pre> + * -1=0.8 + * 1=1.2 + * </pre> + * + * For parameters that are String files should look like this: + * <pre> + * -1=equation written on a single line + * 1=another equation written on a single line + * </pre> + * + * For parameters that are management rules files should look like this: + * <pre> +-1=Cantonnement +rule.-1.parameter.gear=fr.ifremer.isisfish.entities.Gear\#11690286646709\#0.5814158398678262 +rule.-1.parameter.zone=fr.ifremer.isisfish.entities.Zone\#11690286645767\#0.37798185123822536 +rule.-1.parameter.beginDate=0 +rule.-1.parameter.endDate=119 +rule.-1.parameter.enginSelectivite=false +rule.-1.parameter.beginMonth=8 +rule.-1.parameter.endMonth=11 +1=Cantonnement +rule.1.parameter.gear=fr.ifremer.isisfish.entities.Gear\#11690286646709\#0.5814158398678262 +rule.1.parameter.zone=fr.ifremer.isisfish.entities.Zone\#11690286645767\#0.37798185123822536 +rule.1.parameter.beginDate=0 +rule.1.parameter.endDate=119 +rule.1.parameter.enginSelectivite=false +rule.1.parameter.beginMonth=3 +rule.1.parameter.endMonth=11 + * </pre> + */ +public class Example_SimulationPlan_en implements AnalysePlan { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(Example_SimulationPlan_en.class); + + /// Enter here the names of the matrix and parameter files + /// In this example, we change the bounds of size classes (growth), + /// catchability, selectivity and the parameters of the Marine protected area. + + static private final String MATRIX = "matrix"; /// The file is names matrix.txt + static private final String VBGF = "growth"; + static private final String SELECTIVITY = "selectivity"; + static private final String CATCHABILITY = "capturabilite"; + static private final String AMP = "amp"; + + /// Here are the public parameters of the simulation plan (the parameters you can change in the interface) + + public int param_parameterNumber = 4; /// This parameter is normally not modify, it is the number of column in the simulation matrix + public int param_first = 0; /// We use this parameter to indicate at which line of the matrix the simulations should start. + /// It's useful if the plan has been interrupted and you don't want to start all over again. + public int param_simulationNumber = 16;/// this parameter is also not modified in theory, this is the number of lines in the simulation matrix. + public String param_directory = "Exemple_directory/"; /// Here enter the path to th efolder where the text files are stored, + /// by default the same folder where the launch file is. + + + /// Declaration of the matrix of experiments + private MatrixND matrix = null; + + public String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_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 _("Do the experiments of a full factorial design for 4 parameters with 2 modalities"); + } + + /** + * Appel� au d�marrage de la simulation, cette m�thode permet d'initialiser + * des valeurs + * @param simulation La simulation pour lequel on utilise ce plan + */ + public void init(AnalysePlanContext context) throws Exception { + /// Create the matrix of experiements and load the values from the text file: + File dir = new File(param_directory); + matrix = MatrixFactory.getInstance().create(new int[]{param_simulationNumber, param_parameterNumber}); + matrix.importCSV(new FileReader(new File(dir, MATRIX + ".txt")), new int[]{0,0}); + matrix.setSemantics(1, Arrays.asList(new String[]{VBGF,CATCHABILITY, SELECTIVITY,AMP})); +System.out.println(matrix); +System.out.println("amp 0 : "+ matrix.getValue(0,AMP)); + /// add the management rules modified by the simulation plan + context.getParam().addExtraRules("Cantonnement"); + } + + + /// Here we create a method to read the value of the modality of a parameter in the matrix of experiments for the ongoing simulation + /// The arguments for this method are the name of the text file and the rank of the simulation in the simulation design + /// For a parameter that is a double + /** + * @param name name of the file + * @param simulation rank of the simulation + * @return + */ + private double getDouble(String name, int simulation) throws Exception { + File dir = new File(param_directory); + Properties prop = new Properties(); + prop.load(new BufferedReader(new FileReader(new File(dir, name + ".txt")))); + int ligne = simulation + param_first; + int mod = (int)matrix.getValue(ligne, name); +System.out.println("mod et ligne : "+ mod+" "+ligne); + double result = Double.parseDouble(prop.getProperty(""+mod)); +System.out.println("result : "+ result); + return result; + } + + /// for a list of doubles + /** + * @param name name of the file + * @param simulation rank of the simulation + * @return + */ + private double [] getList(String name, int simulation) throws Exception { + File dir = new File(param_directory); + Properties prop = new Properties(); + prop.load(new BufferedReader(new FileReader(new File(dir, name + ".txt")))); + int ligne = simulation + param_first; + int mod = (int)matrix.getValue(ligne, name); + double [] result = StringUtil.toArrayDouble(prop.getProperty(""+mod).split(";")); // ""+ builds a character string + return result; + } + + /// for a character string (equation) + /** + * @param name name of the file + * @param simulation rank of the simulation + * @return + */ + private String getString(String name, int simulation) throws Exception { + File dir = new File(param_directory); + Properties prop = new Properties(); + prop.load(new BufferedReader(new FileReader(new File(dir, name + ".txt")))); + int ligne = simulation + param_first; + int mod = (int)matrix.getValue(ligne , name); + String result = prop.getProperty(""+mod); + return result; + } + /// for the parameters of a management rule + /** + * @param name name of the file + * @param simulation rank of the simulation + * @return + */ + private Rule getRule(RegionStorage regionStorage, String name, int simulation) throws Exception { + File dir = new File(param_directory); + Properties prop = new Properties(); + prop.load(new BufferedReader(new FileReader(new File(dir, name+".txt")))); + int ligne = simulation + param_first; + int mod = (int)matrix.getValue(ligne , name); + String ruleName = prop.getProperty(""+mod); + RuleStorage ruleStorage = RuleStorage.getRule(ruleName); + Rule rule = ruleStorage.getNewRuleInstance(); + RuleHelper.populateRule(mod, regionStorage, rule, prop); + return rule; + } + + + + /** + * 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 + */ + public boolean beforeSimulation(AnalysePlanContext context, SimulationStorage nextSimulation) throws Exception { + + int simNum = nextSimulation.getParameter().getAnalysePlanNumber()+ param_first; + + if (simNum < param_simulationNumber+1) { /// check if the end of the plan is reached + + /// Use of the methods to read parameter values in the matrix of experiments + double [] croissance = getList (VBGF , simNum); + double catchability = getDouble (CATCHABILITY, simNum); + String selectivity = getString (SELECTIVITY, simNum); + Rule amp = getRule(nextSimulation.getStorage(), AMP, simNum); + + /// Write information in the log + nextSimulation.getInformation().addInformation("Growth ("+context.getNumber()+")= " + croissance); + nextSimulation.getInformation().addInformation("Selectivity ("+context.getNumber()+")= " + selectivity); + + + /// Here the values of the parameters in the database are modified according to the modality in the matrix of experiments + /// For management rules + + // remove the previous management rule(it is stored under the name "LastAMP") + List<Rule> paramRules = nextSimulation.getParameter().getRules(); + // add the new rule to the simulation + paramRules.add(amp); + + /// Modify parameters in the database: + TopiaContext tx = nextSimulation.getStorage().beginTransaction(); + /// get the objects to modify in the database + PopulationDAO popDAO = IsisFishDAOHelper.getPopulationDAO(tx); + Population pop = popDAO.findByName("test population"); + List<PopulationGroup> groups = pop.getPopulationGroup(); + GearDAO gearDAO = IsisFishDAOHelper.getGearDAO(tx); + List<Gear> gears = gearDAO.findAll(); + + ///Modify bounds of size classes + /// replace with the elements in the list + for (PopulationGroup group : groups) { + group.setMinLength(croissance[group.getId()]) ; + group.setMaxLength(croissance[group.getId()+1]) ; + } + + /// modify catchability + /// the value in the database is changed by multiplying by the value of the modality + MatrixND c = pop.getCapturability(); + for (MatrixIterator i = c.iterator(); i.hasNext();){ + i.next(); + i.setValue(i.getValue()* catchability); + } + + /// modify selectivity + /// replace the existing equation with the new one + for (Gear gear : gears) { + Selectivity sel = gear.getPopulationSelectivity(pop); + Equation eq = sel.getEquation(); + eq.setContent(selectivity); + } + + tx.commitTransaction(); + return true; + } else { + return false; + } + + } + + /** + * Call after 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 + */ + public boolean afterSimulation(AnalysePlanContext context, SimulationStorage lastSimulation) throws Exception { + return true; + } + +} Property changes on: trunk/src/site/en/resources/downloads/Example_SimulationPlan_en.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Modified: trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst 2013-12-05 14:44:36 UTC (rev 178) +++ trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst 2013-12-05 15:00:47 UTC (rev 179) @@ -14,183 +14,175 @@ .. * .. * 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 +.. * 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 +.. * License along with this program. If not, see .. * <http://www.gnu.org/licenses/gpl-3.0.html>. .. * #L% .. - -Tutorial to use simulation plans -================================ +Tutorial for the use of Simulation plans +======================================== -This tutorial have not been translated yet. Here is the French version +An experimental design is a statistically chosen set of experiments (simulations) which differ by the +values taken by certain parameters of the model with the objective of answering a specific question. -Un plan d'analyse est un ensemble d'expériences (simulations) pour lesquelles on -va modifier la valeur de certains paramètres selon un protocole défini pour -répondre à une question. On distingue des plans de simulations pour lesquels +Two kinds of simulation plans must be distinguished : -* *les expériences sont indépendantes* . C'est à dire que l'ordre des - simulations n'a pas d'importance et que l'on pourrait par exemple les lancer - sur des ordinateurs différents. Les valeurs que les paramètres devront prendre - à chaque nouvelle simulation sont déterminées au préalable. +* *experiments are independent* . That is to say that the order in which simulations are run doesn’t + matter, and they could possibly ber un on different computers. The values taken by the parameters + at each simulation are previously determined. -* *les expériences sont séquentielles* . Les valeurs des paramètres de la - simulation n+1 dépendent des résultats de la simulation n. +* *sequential experiments*. In this case, parameter values in simulation n+1 depend on the results + of simulation n. -Expériences Indépendantes : exemple d'une analyse de sensibilité ----------------------------------------------------------------- +Independent Experiments: the example of sensitivity analysis +------------------------------------------------------------ -Dans le cas d'expériences indépendantes, la première étape est de définir les -paramètres à modifier et les différentes valeurs qu'ils devront prendre -(appelées « modalités »). On les organise ensuite selon un plan d'expérience -adéquat (plan complet, factoriel, optimisé...) qu'on écrit sous forme de matrice. -Des méthodes sont déjà disponibles pour réaliser ce type de plans sous -ISIS-Fish. Ils sont décrits ici mais libre à l'utilisateur d'écrire ses propres -scripts si la méthode actuellement utilisée ne répond pas à ses besoins. Voici -la description et le fonctionnement des scripts existants : ils nécessitent -l'écriture de 3 types de fichiers : un script de plan d'analyse, une matrice -d'expérience et des fichiers paramètre : +In the case of independent simulations, first step is to identy the parameters which are modified +at each simulation and the values they take (“modalities”). An adequate simulation plan is then +designed (full factorial design, Latin hypercube…) which translates into a matrix. -La matrice d'expérience -~~~~~~~~~~~~~~~~~~~~~~~ +Methods are available in ISIS-Fish to design these kinds of simulation plans without any coding +(scripts available and interface sensitivity analysis), however if the proposed methods do not cover +the user’s needs, he is encouraged to adapt the scripts, or write and share his own scripts. -*La matrice d'expérience* est une matrice [expériences x paramètres] : chaque -colonne correspond à l'un des paramètres à modifier et chaque ligne contient -les modalités des paramètres pour une expérience donnée. Les modalités sont -codées par des entiers (-1 ;0 ;1 etc). Cette matrice est copiée dans un -fichier .txt sans en-tête de colonnes ni de lignes. +Here is how a simulation plan works: Three types of files are required: -Les fichiers paramètres -~~~~~~~~~~~~~~~~~~~~~~~ +A script of simulation plan, a matrix of experiment, and parameters files. -*Les fichiers paramètres* : un fichier .txt par paramètre donnant la -correspondance entre la valeur de la modalité (-1 ;0 ;1) dans la matrice et la -valeur du paramètre. Ce paramètre peut être un réel, une liste de réels, une -équation… Si l'on nomme les modalités –1 et 1, le fichier est de la forme +The matrix of experiments +~~~~~~~~~~~~~~~~~~~~~~~~~ -Pour un paramètre qui est une liste +* *The matrix of experiments* is a matrix [experiments x parameters] : each column corresponds to + one of the parameters modified in the analysis with its modalities and each line corresponds to one + simulation. Usually, discrete modalities are coded using integers (-1 ;0 ;1 etc) but the value taken by + the parameter can as well be listed. + +The matrix must be copied in a text file (.txt) without row names nor column names. + +Parameter files +~~~~~~~~~~~~~~~ + +*Parameter files*: If the modalities are coded with integers, a text file (.txt) per parameter (or +column of the matrix) which gives the correspondence between the modality (-1 ;0 ;1) in the matrix +and the value of the parameter to enter in the database. It is mostly useful if the parameter is an +equation, a list, a matrix, or a management rule... + +For instance if the modalities are –1 and 1, the file looks like : + +For a parameter which is a list + ___________________________________ :: - -1=0.5;0.8;0.9;0.11 - 1=0.5;0.11;0.15;0.41 + -1=0.5;0.8;0.9;0.11 -Pour un paramètre qui est une équation + 1=0.5;0.11;0.15;0.41 + +For a parameter which is a list an equation + ______________________________________ :: - -1=if(condition = true) return 5 ; else return 3 ; - 1=if(condition = true) return 7 ; else return 3 ; + -1=if(condition = true) return 5 ; else return 3 ; -Pour un paramètre qui est un réel + 1=if(condition = true) return 7 ; else return 3 ; + +For a parameter which is a real + _________________________________ :: - -1=0.8 - 1=1.2 + -1=0.8 -Autres + 1=1.2 + +Other… + ______ -On peut aussi modifier les paramètres des règles de gestion...(voir -exemple). Il faut alors indiquer dans le .txt tous les paramètres public de -la règle. Attention pour certaines règles de gestion il faut définir la -population, l'engin, la zone... ciblée par la règle dans les paramètres. -Pour ce faire il n'est pas possible d'écrire le nom de la population, de la -zone... il faut déterminer le code correspondant qui est du genre +It’s possible for instance to change the management rules and their parameters… (see example). +In this case, you need to fill the .txt with all the public parameters of the rule. Be aware +that for some rules the public parameters are population or zone, in this case you will need to find +the code corresponding to the pop or zone, which looks like this: :: - fr.ifremer.isisfish.entities.Zone#1169028645767#0.37798185123822536 + fr.ifremer.isisfish.entities.Zone#1169028645767#0.37798185123822536 -Pour cela on peut faire tourner une simulation avec la règle en question -correctement paramétrée et aller voir dans les logs (fichier debug.txt dans -le même dossier que le .bat de lancement), ces codes sont inscrits à coté du -nom du paramètre au moment de l'initialisation des règle de gestion. +The easiest way, is to run a simulation with the rule correctly filed and look in the logs (debug.txt) for +the codes, which appear after the name of the parameter when the rule is initiated. -*Attention !!!!* dans ces fichiers la syntaxe est importante: +*Warning !!!!* in these files the syntax is of importance : -* Pas d'espace -* Pas de « ; » à la fin des lignes -* Pas de « + » devant un chiffre quand il désigne une modalité (+1=NON ; 1=OUI) +* no space +* no « ; » at the end of the lines +* no « + » in front of a number when it refers to a modality (+1=NO ; 1=YES) -Les fichier matrix.txt et les fichiers paramètres.txt doivent être placés *dans -un même dossier* de préférence localisé dans le dossier contenant le .bat de -lancement d'ISIS-Fish (qui est la racine pour le logiciel). +For practical reasons, place the matrix.txt and parameters files *in the same folder*, at best in the +same folder when the lauching file for ISIS is (.bat). This is the root for the software which avoid +problems with paths. -Exemple +Example ~~~~~~~ -On propose ici la matrice et les fichiers paramètres d'une analyse -de sensibilité sur les paramètres de croissance, capturabilité, selectivité et -la période de fermeture d'un cantonnement. +As an example, we want here to carry out a sensitivity analysis on growth, catchability, selectivity +and time period for a spatial closure. -`Fichiers parametres et matrice`_ +`Parameter files and matrix`_ -.. _Fichiers parametres et matrice: ../../downloads/Exemple_directory.zip +.. _Parameter files and matrix: ../../downloads/Exemple_directory.zip -*Le script de plan de simulation* (écrit à partir de l'éditeur de scripts) -permet de récupérer et modifier les valeurs des paramètres en fonction de la -matrice d'expérience pour chaque simulation. (Voir le manuel pour l'explication -de la structure des scripts de plans de simulation.) +*The script for the simulation plan* (written from the editor) allows to read and modify the values of +the parameters depending on the simulation matrix. (Please refer to the manual for a description of +the structure of the scripts for simulation plans). -On joint ici le script commenté correspondant à l'analyse de sensibilité -précédante. Le script contient les méthodes nécessaires à lire les fichiers -matrice.txt et les fichiers contenant les modalités des paramètres. Il contient -aussi le code servant à modifier les valeurs de ces paramètres dans la base de -donnée (pour connaitre les méthodes permettant d'accéder aux différents -paramètres de la base de donnée, se référer aux APIs). +Download here the commented program for this sensitivity analysis -`Script d'analyse de sensibilite`_ +The code contains methods required to read the text files and modify the database (to learn how to +access parameters of the database, please refer to the tutorial on APIs). -.. _Script d'analyse de sensibilite: ../../downloads/Exemple_PlanSimulation.java +`Script sensitivity analysis`_ -Plans sequentiels : exemple de calibration par la méthode du simplexe ---------------------------------------------------------------------- +.. _Script sensitivity analysis: ../../downloads/Example_SimulationPlan_en.java -Dans ce cas, les modalités prises par les paramètres à la simulation suivante -dépendent des résultats des simulations précédentes. Il faut donc écrire -l'algorithme de calcul de ces nouvelles valeurs en fonction des résultats de -simulation dans le script du plan d'analyse. Il faut également écrire le code -permettant de modifier la valeur des paramètres pour la remplacer par la -nouvelle valeur calculée. +Sequential simulation designs: an example of calibration using the simplex method +--------------------------------------------------------------------------------- -Exemple +In the case of sequential designs, le values taken by a parameter in simulation n+1 depend on +the results of simulation n, n-1, n-2... The script of the simulation plan contains the algorithm of +computation of these news values. In addition the script contains the code to modify the parameters +in the database. + +Example ~~~~~~~ -L'exemple reprend un script qui permet de calibrer deux paramètres (ici la -capturabilité) par la méthode du simplexe à pas variable à partir des -débarquements trimestriels. +This example is available in the software when downloaded. It allows for the calibration of two +parameters (usually two catchability parameters)using the simplex method, the objective function +being the mean squared error between catch per quarter simulated and observed. -`Script de calibration`_ +`Calibration script`_ -.. _Script de calibration: ../../downloads/calibration.java +.. _Calibration script: ../../downloads/CalibrationEspeceq1q2Export_en.java -Lancement d'un Plan d'analyse ------------------------------ +Launching a simulation plan +--------------------------- -Quand les scripts sont écrits, c'est tout simple ! +As soon as scripts as written and checked it’s simple ! +In the simulation interface, prepare your simulation as usual, except if your simulation plan modifies +management rules: If a rule is modified it must not be loaded in the interface (the simulation plan +will add it). Check the box “use a simulation plan”. In the corresponding tab, select your simulation +plan in the list, and clic “add”. Fill in the parameters. Go back to the simulation tab and clic simulate. -Dans l'interface de lancement de simulation on prépare sa simulation comme -d'habitude à l'exception des règles de gestion : il ne faut pas charger une -règle si elle doit être modifiée par le plan car elle sera ajoutée par le plan -d'analyse à la suite des règles entrées dans l'interface. On coche la case -« Utiliser le plan d'analyse ». On sélectionne le plan Exemple_PlanAnalyse ou -CalibrationExpeceq1q2 dans la liste déroulante. On remplit les paramètres du -plan et on lance la simulation. +References +---------- -PS : Attention à bien vérifier les différentes étapes listées dans le Pense-Bête -sinon gare aux 500 simulations sans effectifs initiaux... ;-) - -Biblio intéressante -------------------- - * Drouineau, H., Mahévas, S., Pelletier, D. and Beliaeff, B. 2006. Assessing the impact of different management options using ISIS-Fish: the French Hake-Nephrops mixed fishery of the Bay of Biscay. Aquatic living resource, @@ -205,4 +197,5 @@ Simplex optimization: a technique for improving quality and productivity in research, development, and manufacturing (Chemometrics series). B.R. CRC Press LLC. 402 pp. -* Nocedal, J., and Wright, S.J. 2006. Numerical Optimization. Mikosch, T. V., Resnick, S. I. , andRobinson, S. M. (Eds.). 2nd Ed., Springer Series in Operations Research, New York. \ No newline at end of file +* Nocedal, J., and Wright, S.J. 2006. Numerical Optimization. Mikosch, T. V., Resnick, S. I. , + andRobinson, S. M. (Eds.). 2nd Ed., Springer Series in Operations Research, New York.

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r178 - in trunk/src/site/en/rst/v4: . user/tutorials
by echatellier＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: echatellier Date: 2013-12-05 15:44:36 +0100 (Thu, 05 Dec 2013) New Revision: 178 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/178 Log: Traduction de la page API par Sigrid Modified: trunk/src/site/en/rst/v4/index.rst trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst Modified: trunk/src/site/en/rst/v4/index.rst =================================================================== --- trunk/src/site/en/rst/v4/index.rst 2013-12-05 14:31:10 UTC (rev 177) +++ trunk/src/site/en/rst/v4/index.rst 2013-12-05 14:44:36 UTC (rev 178) @@ -45,7 +45,7 @@ .. _Tutorials: user/tutorials.html .. _FAQ: user/FAQ.html .. _Developer manual: devel/index.html -.. _APIs documentation: user/API.html +.. _APIs documentation: user/useAPI.html .. _ISIS scripts examples: user/scripts.html .. _R scripts examples: user/scriptsR.html .. _Changes in version 4.0: user/changements40.html Modified: trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 2013-12-05 14:31:10 UTC (rev 177) +++ trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 2013-12-05 14:44:36 UTC (rev 178) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2010 Ifremer, Code Lutin +.. * Copyright (C) 1999 - 2013 Ifremer, Code Lutin, Sigrid Lehuta .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as @@ -23,115 +23,88 @@ .. * #L% .. - -Tutorial on APIs use -==================== +Tutorial for the use of APIs +========================== -This tutorial have not been translated to english yet. +Before you start... +First, don't panic! +You need to know that all the values entered in the interface by users are stored in corresponding ISIS objects. To modify those values, that is to say, the attributes of the objects, you need to know their nature and structure, how to access and modify them. To do so, the dependency between objects must be understood. The architecture of the database is available here ( `Modele ISIS-Fish`_ ) but also reflected by the architecture of the tree in the input interface. -Avant tout il faut savoir, que toutes les valeurs saisies dans l'interface de -saisie par l'utilisateur sont stoquées dans les objets d'ISIS correspondants. -Pour modifier ces valeurs avant ou en cours de simulation, il faut connaitre -leur nature et leur structure, savoir comment y accéder et les modifier. -Pour savoir comment y accéder il faut connaitre les dépendances entre objets -(objets qui sont des attributs d'autres objets). Pour cela on consulte -l'architecture de la base de donnée ( `Modele ISIS-Fish`_ ) qui se reflète dans -l'architecture de l'interface de saisie. +To know how to pass from an object to another you need to find the corresponding method in the API. -Pour savoir comment passer d'un objet a un autre il faut connaitre les méthodes -appliquables aux objets : tout est dans l'API. +Remark: Start by getting to know the various Java objects (double, boolean, string, integer, equation, matrix,...)(cf tutoriaux JAVA). -Remarque : Il vaut mieux commencer par se familiariser avec les differents types -d'objets JAVA (double, boolean, string, integer, equation, matrix,...), les -attributs et les methodes (cf tutoriaux JAVA). +Here is an example « step by step » in the case where you want to modify the natural mortality equation (in a simulation plan for instance). We want to replace temporarily the equation in the database with another one. +You need to create an object equation. +First start by creating an object String containing the new equation:: -Voici un exemple "pas à pas" pour le cas ou l'on voudrait modifier l'equation de -mortalité naturelle dans un plan d'analyse par exemple. On veut remplacer -provisoirement la valeur de la base par une autre. On crée un objet String -rempli avec l'autre valeur par exemple:: - String mortalitenaturelle = "if (groupe.getId() == 0) return 1.5; else return 0.2;" -Se poser la question : "Dans la base de donnée où se trouve la mortalité naturelle ?" +Then ask yourself: "In the database where is natural mortality?" ------------------------------------------------------------------------------------- -Réponse : dans l'interface de saisie, elle est dans la branche "population" et -l'onglet "equations". -(au passage le titre de l'onglet nous renseigne sur le type d'objet auquel on a -affaire : ya de grandes chances pour que parmi la batterie d'objets possibles -(int, double, matrice...) la mortalité naturelle soit une equation ;-) ) +Answer: In the input interface, in the branch for "population" and the equation tab. +(here the name of the tab inform on the type of objects listed here, most likely equations). -En francais on dirait "dans population, va chercher l'objet equation de -mortalité naturelle, et attribut lui la valeur du string mortalitenaturelle", ya -pu qu'a le dire en java. +In English, you would say, in population, get the equation for natural mortality which is filled with a string. -Ouvrir la page des APIs +Open API pages ----------------------- -Dans la colonne de gauche de l'API (sous "all classes") on cherche l'entite -"population" et on clique dessus. +On the left, under « all classes », look for th entity « population » (the one in italic), clic on it. -Les méthodes disponibles +Available methods ------------------------ -Toutes méthodes que l'on peut appliquer à un objet population (colonne de -droite) s'affichent , et le type d'objet qu'elles renvoient (colonne de gauche). +All the methods available for an object of type « population » appear in a table. The second column tells the method name and arguments it takes, the first column tells the type of object the method returns. +The code you will write should look like this:: +Type_of_object_returned_by_the_method_on_left_side objectName = population.method(method arguments); + +There are mostly 2 kinds of methods : -c'est a dire que les lignes de commandes qu'on ecrira seront de la forme:: +* methods "get" : get an object +* methods "set" : set the value of an object. - objet_renvoyé_indiqué_à_gauche nomObjet = population.methode_ecrite_à_droite(argument de la methode); +In our example we eventually want to change a value, so "set". -Il y a surtout deux grands types de méthodes : - -* les méthodes "get" : qui vont chercher un objet -* les méthodes "set" : qui assignent une valeur a un objet. - -Dans notre exemple on veut changer l'equation de mortalité naturelle, c est donc -un set ! - -On cherche une méthode qui parle de mortalité naturelle... +Look for a method dealing with natural mortality ---------------------------------------------------------- -On trouve getNaturalDeathRate() qui renvoit un objet equation (c'est l'objet -equation qui contient la valeur de l'equation de mortalite naturelle remplie par -l'utilisateur) et setNaturalDeathRate(Equation naturalDeathRate) pour laquelle -on doit passer un objet equation (une equation de naturalDeathRate) en argument. +You find getNaturalDeathRate() which returns an equation (it is the object equation which contains the value of the equation of natural mortality filled by the user in the interface) and setNaturalDeathRate(Equation naturalDeathRate) which receives as argument an equation. -(en cliquant sur le nom de la méthode on a une description sommaire de ce -qu'elle fait) +(Note: a clic on the method name gives you further information on the method) -setNaturalDeathRate() parait être ce qu'on veut faire... -mais la méthode setNaturalDeathRate prend en argument une equation, on ne peut -donc pas faire:: +setNaturalDeathRate() seems appropriate... +However the method takes an equation as argument and not a String, we thus cannot write:: pop.setNaturalDeathRate(mortalitenaturelle); -puisque mortalitenaturelle n'est pas une equation mais un string. - - -Créer une équation +Create an equation ------------------ -Du coup il faut trouver autre chose qui fasse le lien entre un string et une -equation. En cliquant sur "equation" dans la page d'API on tombe sur la page des -méthodes qui s'appliquent aux objets qui sont des equations. On trouve une -méthode .setContent(String ) qui prend en argument un string. Ca veut dire que -si on a une equation, on peut lui changer sa valeur en utilisant cette methode -avec un string en argument. -L'equation dont on veut changer la valeur on sait la récupérer:: +So next step, how to transform a string into an equation. +Clic on « equation » on the API page, you are re-directed toward the pages of methods for equations. You will find a method .setContent(String ) which takes a string as argument and returns an equation. So that means that applied to an equation this method changes the value of the equation according to whats written in the string. +We know how to GET the equation we want to change:: +Equation eqMortalite = pop.getNaturalDeathRate(); - Equation eqMortalite = pop.getNaturalDeathRate(); - -L'objet eqMortalite est un objet equation:: - +Then to change its content:: eqMortalite.setContent(mortalitenaturelle); -et là on a le droit vu que mortalitenaturelle est un string et que la méthode -prend un string en argument. +Voilà ! +Note it could also be done in a single line:: +pop.getNaturalDeathRate().setContent(mortalitenaturelle); -et voilà c'est fait ! +Note too that even if the equation is stored in another object with a new name (eqMortalite) the original equation in the database is modified. So be careful if you want to work on equations or matrices from the database without changing them, start by making copies and work on the copy, not on the original object. -remarque : on pourrait le faire en 1 ligne:: +Exercise: +------------ - pop.getNaturalDeathRate().setContent(mortalitenaturelle); +How do you change the selectivity of the gear used by métier métier for population POP? +Ans:: +métier.getGear().getPopulationSelectivity(POP).getEquation() .setContent("return 1;") +How to change the proportion of effort spent by strategy str on métier met in september to 0.1? +Ans:: +str.getStrategyMonthInfo(Month.SEPTEMBER).setProportionMetier(met,0.1); + .. _Modele ISIS-Fish: ../isisFishModel.html

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r177 - trunk/src/site/resources/images
by echatellier＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: echatellier Date: 2013-12-05 15:31:10 +0100 (Thu, 05 Dec 2013) New Revision: 177 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/177 Log: fixes #570: Mod?\195?\168le de donn?\195?\169es pas ?\195?\160 jour Modified: trunk/src/site/resources/images/IsisFishModel.png Modified: trunk/src/site/resources/images/IsisFishModel.png =================================================================== (Binary files differ)

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r176 - in trunk/src/site/rst: . applications
by bpoussin＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: bpoussin Date: 2013-12-05 15:18:18 +0100 (Thu, 05 Dec 2013) New Revision: 176 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/176 Log: change header Modified: trunk/src/site/rst/applications.rst trunk/src/site/rst/applications/gdg.rst trunk/src/site/rst/applications/manche.rst trunk/src/site/rst/applications/other.rst Modified: trunk/src/site/rst/applications/gdg.rst =================================================================== --- trunk/src/site/rst/applications/gdg.rst 2013-12-05 14:15:17 UTC (rev 175) +++ trunk/src/site/rst/applications/gdg.rst 2013-12-05 14:18:18 UTC (rev 176) @@ -1,29 +1,28 @@ -<?xml version="1.0" encoding="UTF-8"?> - - Publications Golfe de Gascogne ============================== Modified: trunk/src/site/rst/applications/manche.rst =================================================================== --- trunk/src/site/rst/applications/manche.rst 2013-12-05 14:15:17 UTC (rev 175) +++ trunk/src/site/rst/applications/manche.rst 2013-12-05 14:18:18 UTC (rev 176) @@ -1,29 +1,28 @@ -<?xml version="1.0" encoding="UTF-8"?> - - Publications Manche =================== Modified: trunk/src/site/rst/applications/other.rst =================================================================== --- trunk/src/site/rst/applications/other.rst 2013-12-05 14:15:17 UTC (rev 175) +++ trunk/src/site/rst/applications/other.rst 2013-12-05 14:18:18 UTC (rev 176) @@ -1,29 +1,28 @@ -<?xml version="1.0" encoding="UTF-8"?> - - Autres publications =================== Modified: trunk/src/site/rst/applications.rst =================================================================== --- trunk/src/site/rst/applications.rst 2013-12-05 14:15:17 UTC (rev 175) +++ trunk/src/site/rst/applications.rst 2013-12-05 14:18:18 UTC (rev 176) @@ -1,29 +1,28 @@ -<?xml version="1.0" encoding="UTF-8"?> - - Publications ============

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r175 - trunk/src/site/rst/applications
by bpoussin＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: bpoussin Date: 2013-12-05 15:15:17 +0100 (Thu, 05 Dec 2013) New Revision: 175 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/175 Log: add other application Added: trunk/src/site/rst/applications/other.rst Added: trunk/src/site/rst/applications/other.rst =================================================================== --- trunk/src/site/rst/applications/other.rst (rev 0) +++ trunk/src/site/rst/applications/other.rst 2013-12-05 14:15:17 UTC (rev 175) @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> + + +Autres publications +=================== + Property changes on: trunk/src/site/rst/applications/other.rst ___________________________________________________________________ Added: svn:mime-type + text/plain Added: svn:keywords + Author Date Id Revision HeadURL

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r174 - trunk/src/site/rst/applications
by bpoussin＠users.forge.codelutin.com Dec. 5, 2013

Dec. 5, 2013

Author: bpoussin Date: 2013-12-05 15:13:49 +0100 (Thu, 05 Dec 2013) New Revision: 174 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/174 Log: change mime-type Modified: trunk/src/site/rst/applications/gdg.rst trunk/src/site/rst/applications/manche.rst Property changes on: trunk/src/site/rst/applications/gdg.rst ___________________________________________________________________ Modified: svn:mime-type - application/xml + text/plain Property changes on: trunk/src/site/rst/applications/manche.rst ___________________________________________________________________ Modified: svn:mime-type - application/xml + text/plain

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