September 2009 - Isis-fish-commits - mailman.cloud.codelutin.com

r2594 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/metier
by chatellier＠users.labs.libre-entreprise.org 10 Sep '09

10 Sep '09

Author: chatellier Date: 2009-09-10 07:47:36 +0000 (Thu, 10 Sep 2009) New Revision: 2594 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/metier/MetierSeasonInfoTargetSpeciesModel.java Log: Fix impossible cast Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/metier/MetierSeasonInfoTargetSpeciesModel.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/metier/MetierSeasonInfoTargetSpeciesModel.java 2009-09-10 07:44:26 UTC (rev 2593) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/input/metier/MetierSeasonInfoTargetSpeciesModel.java 2009-09-10 07:47:36 UTC (rev 2594) @@ -1,5 +1,5 @@ /* *##% - * Copyright (C) 2009 Code Lutin + * Copyright (C) 2009 Ifremer, Code Lutin * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -20,7 +20,6 @@ import static org.codelutin.i18n.I18n._; -import java.awt.Checkbox; import java.awt.Component; import java.util.List; @@ -229,7 +228,7 @@ case 2: Boolean bValue = (Boolean)value; c = new JCheckBox(); - ((Checkbox)c).setState(bValue); + ((JCheckBox)c).setSelected(bValue); break; default: throw new IndexOutOfBoundsException("No such column " + column);

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r2593 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity
by chatellier＠users.labs.libre-entreprise.org 10 Sep '09

10 Sep '09

Author: chatellier Date: 2009-09-10 07:44:26 +0000 (Thu, 10 Sep 2009) New Revision: 2593 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java Log: Fix potential NPE Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java 2009-09-10 07:42:43 UTC (rev 2592) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EditorHelper.java 2009-09-10 07:44:26 UTC (rev 2593) @@ -524,7 +524,7 @@ result = ((MetierSeasonInfoSpeciesEditorUI) c) .getMetierSeasonInfo().getSpeciesTargetSpecies(); - } else if (result instanceof PopulationZonesEditorUI) { + } else if (c instanceof PopulationZonesEditorUI) { result = ((PopulationZonesEditorUI) c) .getFieldPopulationMappingZoneReproZoneRecru().getMatrix();

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r2592 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher
by chatellier＠users.labs.libre-entreprise.org 10 Sep '09

10 Sep '09

Author: chatellier Date: 2009-09-10 07:42:43 +0000 (Thu, 10 Sep 2009) New Revision: 2592 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationExecutor.java Log: Fix impossible cast Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationExecutor.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationExecutor.java 2009-09-09 16:27:51 UTC (rev 2591) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationExecutor.java 2009-09-10 07:42:43 UTC (rev 2592) @@ -122,7 +122,7 @@ // un simple suspend du thread n'est pas bon, car la tache ne // serait alors jamais executer et ce n'est pas forcement ce que // l'on souhaite - if (r instanceof SimulationItem) { + if (r instanceof SimulationJob) { SimulationService.getService().resubmit((SimulationJob) r); } throw new RuntimeException(

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r2591 - in isis-fish/trunk/src/test: java/fr/ifremer/isisfish/util resources/test-database resources/test-database/analyseplans resources/test-database/exports resources/test-database/rules resources/test-database/scripts resources/test-database/sensitivity resources/test-database/sensitivityexports
by chatellier＠users.labs.libre-entreprise.org 09 Sep '09

09 Sep '09

Author: chatellier Date: 2009-09-09 16:27:51 +0000 (Wed, 09 Sep 2009) New Revision: 2591 Added: isis-fish/trunk/src/test/resources/test-database/analyseplans/CalibrationSimplexePasVariable2Capturabilite.java isis-fish/trunk/src/test/resources/test-database/analyseplans/SimulationNumberRestriction.java isis-fish/trunk/src/test/resources/test-database/rules/EffortReduction.java isis-fish/trunk/src/test/resources/test-database/rules/GraviteVPUE1.java isis-fish/trunk/src/test/resources/test-database/rules/TotalClosure.java isis-fish/trunk/src/test/resources/test-database/sensitivity/ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorJavaExpandGrid.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFast.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFrF2.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRMorris.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorROptimumLHS.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRRandomLHS.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRSobol.java isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRegularFractions.java isis-fish/trunk/src/test/resources/test-database/sensitivity/regularfractions.R isis-fish/trunk/src/test/resources/test-database/sensitivityexports/ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassReferenceY9.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeY6.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassY3.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightReferenceY7.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeReferenceY10.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeY4.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightY1.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassReferenceY8.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeReferenceY11.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeY5.java isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassY2.java Removed: isis-fish/trunk/src/test/resources/test-database/analyseplans/Calibration.java isis-fish/trunk/src/test/resources/test-database/analyseplans/Max.java isis-fish/trunk/src/test/resources/test-database/rules/GraviteCPUE.java isis-fish/trunk/src/test/resources/test-database/rules/RecrutementLangoustine.java Modified: isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/JavadocHelperTest.java isis-fish/trunk/src/test/resources/test-database/exports/Abundances.java isis-fish/trunk/src/test/resources/test-database/exports/Biomasses.java isis-fish/trunk/src/test/resources/test-database/exports/CapturesNombre.java isis-fish/trunk/src/test/resources/test-database/exports/CapturesPoids.java isis-fish/trunk/src/test/resources/test-database/exports/CellsDefinition.java isis-fish/trunk/src/test/resources/test-database/exports/EffortsMetier.java isis-fish/trunk/src/test/resources/test-database/exports/MetierZone.java isis-fish/trunk/src/test/resources/test-database/exports/NonActivite.java isis-fish/trunk/src/test/resources/test-database/exports/OwnerMargin.java isis-fish/trunk/src/test/resources/test-database/exports/RegionDefinition.java isis-fish/trunk/src/test/resources/test-database/exports/RejetsNombre.java isis-fish/trunk/src/test/resources/test-database/exports/RejetsPoids.java isis-fish/trunk/src/test/resources/test-database/exports/VesselMargin.java isis-fish/trunk/src/test/resources/test-database/exports/ZonesDefinition.java isis-fish/trunk/src/test/resources/test-database/rules/Cantonnement.java isis-fish/trunk/src/test/resources/test-database/rules/CantonnementPreSimu.java isis-fish/trunk/src/test/resources/test-database/rules/ChangementParamControlablePresimu.java isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEngin.java isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEnginPreSimu.java isis-fish/trunk/src/test/resources/test-database/rules/TACpoids.java isis-fish/trunk/src/test/resources/test-database/rules/TailleMin.java isis-fish/trunk/src/test/resources/test-database/scripts/GravityModel.java isis-fish/trunk/src/test/resources/test-database/scripts/ResultName.java isis-fish/trunk/src/test/resources/test-database/scripts/RuleUtil.java isis-fish/trunk/src/test/resources/test-database/scripts/SiMatrix.java Log: Mise ?\195?\160 jour de la database de test. Modified: isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/JavadocHelperTest.java =================================================================== --- isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/JavadocHelperTest.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/JavadocHelperTest.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -57,7 +57,7 @@ File currentDirectory = getCurrentDatabaseDirectory(); File destinationDirectory = new File(getTestDirectory(), "isis-docs"); - File testJavaFile = new File(currentDirectory, "analyseplans" + File.separatorChar + "Calibration.java"); + File testJavaFile = new File(currentDirectory, "analyseplans" + File.separatorChar + "CalibrationSimplexePasVariable2Capturabilite.java"); PrintWriter out = new PrintWriter(System.out); int result = JavadocHelper.generateJavadoc(currentDirectory, testJavaFile, Deleted: isis-fish/trunk/src/test/resources/test-database/analyseplans/Calibration.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/analyseplans/Calibration.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/analyseplans/Calibration.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,342 +0,0 @@ -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; - -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) -/** - * Calibration_bidon.java - * - * Created: 8 mars 2007 - * - * @author <> - * @version $Revision: 1.2 $ - * - * Last update: $Date: 2007-11-02 17:43:14 $ - * by : $Author: bpoussin $ - */ -public class Calibration implements AnalysePlan { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(Calibration.class); - - enum State {STATE_INIT, STATE_0, STATE_1, STATE_2, STATE_3, STATE_4}; - - //parametres de la simu 3 points initiaux d un simplex d ordre 2 - @Doc(value="do the doc of param Population") - public Population param_Population = null; - @Doc(value="do the doc of param M1 (devient un parametre du plan d analyse)") - public String param_M1 = "1e-5;1e-6";// devient un parametre du plan d analyse - @Doc(value="do the doc of param M2 (devient un parametre du plan d analyse)") - public String param_M2 = "2e-4;2e-5";// devient un parametre du plan d analyse - - @Doc(value="do the doc of param M3 (devient un parametre du plan d analyse)") - public String param_M3 = "1e-4;1e-6";// devient un parametre du plan d analyse - @Doc(value="do the doc of param pas (devient un parametre du plan d analyse)") - public String param_pas = "1e-5";// devient un parametre du plan d analyse - @Doc(value="nom + chemin du fichier contenant les debarquements observes par groupe pour la derniere annee") - public String param_nomfichier_debarquements = "";//nom + chemin du fichier contenant les debarquements observes par groupe pour la derniere annee - - protected File debarquementsObserves; - protected MatrixND matrixDebarquement; - - protected State state = State.STATE_INIT; - protected Experiences experiences = new Experiences(); - - - /** - * @return the experiences - */ - public Experiences getExperiences() { - return this.experiences; - } - - public String [] necessaryResult = { - ResultName.MATRIX_LANDING_PER_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 _("Simplexe"); - } - - /** - * 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()); - - int nbGroup = pop.sizePopulationGroup(); - 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}); - 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 - */ - public boolean beforeSimulation(AnalysePlanContext context, SimulationStorage nextSimulation) throws Exception { - boolean doNext = true; - - int number = context.getNumber(); - - if (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 = 0; - double q2 = 0; - - double lastCritere = experiences.getExperience(number-1).criteria; - double g1 = (experiences.current.get(2).q1 + experiences.current.get(1).q1) / 2.0; - double g2 = (experiences.current.get(2).q2 + experiences.current.get(1).q2) / 2.0; - - double worst1 = experiences.current.get(0).q1; - double worst2 = experiences.current.get(0).q2; - - - if (state == State.STATE_INIT) { - // on fait la 4eme simulation dans tous les cas - state = State.STATE_0; - Collections.sort(experiences.current); - q1 = 2 * g1 - worst1; - q2 = 2 * g2 - worst2; - } else if (state == State.STATE_0) { - // on fait la 5eme avec des q qui dependent de la 4eme dans le dernier cas - if (lastCritere < experiences.current.get(0).criteria) { - state = State.STATE_1; - q1 = g1 - ( g1 - worst1 ) / 2.0; - q2 = g2 - ( g2 - worst2 ) / 2.0; - } else if (lastCritere < experiences.current.get(1).criteria) { - state = State.STATE_2; - q1 = g1 + ( g1 - worst1 ) / 2.0; - q2 = g2 + ( g2 - worst2 ) / 2.0; - } else if (lastCritere < experiences.current.get(2).criteria) { - state = State.STATE_INIT; - experiences.current.remove(3); - } else { // dernier cas possible: if (lastCritere > experiences.current.get(2).critere) { - state = State.STATE_4; - q1 = experiences.current.get(3).q1 + g1 - worst1; - q2 = experiences.current.get(3).q2 + g2 - worst2; - } - } else if (state == State.STATE_1) { - // la derniere simulation a ete faite - if (lastCritere > experiences.current.get(0).criteria) { - experiences.current.remove(3); - experiences.current.remove(0); - } else { - // FIXME on supprime les 2 derniere qui vient d'etre faite, on risque donc de boucler - experiences.current.remove(4); - experiences.current.remove(3); - doNext = false; - } - state = State.STATE_INIT; - } else if (state == State.STATE_2) { - if (lastCritere > experiences.current.get(0).criteria) { - experiences.current.remove(3); - experiences.current.remove(0); - } else { - // FIXME on supprime les 2 derniere qui vient d'etre faite, on risque donc de boucler - experiences.current.remove(4); - experiences.current.remove(3); - doNext = false; - } - state = State.STATE_INIT; - } else if (state == State.STATE_4) { - if (lastCritere > experiences.current.get(3).criteria) { - experiences.current.remove(3); - experiences.current.remove(0); - } else { - experiences.current.remove(4); - experiences.current.remove(0); - } - state = State.STATE_INIT; - } - - experiences.getExperience(number).q1 = q1; - experiences.getExperience(number).q2 = q2; - - changeDB(experiences.getExperience(number), nextSimulation); - } - - return doNext; - } - - /** - * 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; - - int number = context.getNumber(); - - ResultStorage result = lastSimulation.getResultStorage(); - log.fatal("sim: " + lastSimulation + " result: " + result); - MatrixND L = result.getMatrix(param_Population, ResultName.MATRIX_LANDING_PER_MET); - L = L.sumOverDim(0);// sum sur les mois, si on ajoute le pas (12) on peut sommer sur les annees - L = L.sumOverDim(1);// sum sur les strategies - L = L.sumOverDim(3);// sum sur les metiers - L = L.sumOverDim(4);// sum sur les zones - L = L.reduce(); // supprime les dim qui n ont qu un element - - double crit = 0; - for ( MatrixIterator g = L.iterator(); g.hasNext();){ - g.next(); - int [] dim = g.getCoordinates(); - double obs = matrixDebarquement.getValue(dim); - double simules = g.getValue(); - crit += Math.pow(obs-simules, 2); - } - experiences.getExperience(number).criteria = crit; - - return doNext; - } - - /** - * Modify nextSimulation database with q1 and q2 in exp. - * @param exp - * @param nextSimulation - * @throws Exception - */ - protected void changeDB(Experience exp, SimulationStorage nextSimulation) throws Exception { - TopiaContext db = nextSimulation.getStorage().beginTransaction();//ouvrir un context pour modifier les donnees - Population pop = (Population)db.findByTopiaId(param_Population.getTopiaId()); -// autre solution moins efficace: -// PopulationDAO popDAO = IsisFishDAOHelper.getPopulationDAO(db); -// Population Nephrops = dao.findByName(param_Population.getName()); - - MatrixND c = pop.getCapturability(); - - for (MatrixIterator i = c.iterator(); i.hasNext();){ - i.next(); - - Object [] sem = i.getSemanticsCoordinates(); - PopulationGroup group = (PopulationGroup)sem[0]; - PopulationSeasonInfo season = (PopulationSeasonInfo)sem[1]; - - if (season.getFirstMonth().after(Month.JULY) && group.getId() >=18){ //mois >= aout - i.setValue(exp.q2); - } - else { - i.setValue(exp.q1); - } - } - db.commitTransaction(); - db.closeContext(); - } - - public class Experiences { - /** contains last simplex and potentialy 2 more simulation */ - protected List<Experience> current = new ArrayList<Experience>(); - /** contains all experience done */ - protected List<Experience> history = new ArrayList<Experience>(); - - /** - * @return the history - */ - public List<Experience> getHistory() { - return this.history; - } - - /** - * 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; - } - } - - /** - * Use to keep q1, q2 and criteria of simulation - * @author poussin - */ - 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; - } - } - -} - Added: isis-fish/trunk/src/test/resources/test-database/analyseplans/CalibrationSimplexePasVariable2Capturabilite.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/analyseplans/CalibrationSimplexePasVariable2Capturabilite.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/analyseplans/CalibrationSimplexePasVariable2Capturabilite.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,481 @@ +package analyseplans; + +import static org.codelutin.i18n.I18n._; + +import java.io.File; +import java.io.FileReader; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; +import org.codelutin.util.FileUtil; +import org.codelutin.util.StringUtil; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.PopulationSeasonInfo; +import fr.ifremer.isisfish.simulator.AnalysePlan; +import fr.ifremer.isisfish.simulator.AnalysePlanContext; +import fr.ifremer.isisfish.util.Doc; + +/** + * CalibrationSimplexePasVariable2Capturabilite. + * + * Created: 17 septembre 2007 + * + * @author <> + * @version $Revision$ + * + * Last update: $Date$ + * 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 : "CalibrationSimplexePasVariable2Capturabilite" +public class CalibrationSimplexePasVariable2Capturabilite implements + AnalysePlan { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(CalibrationSimplexePasVariable2Capturabilite.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 + protected File exportHistoric = new File("Historic.csv"); + protected String exportHisto = ""; + + @Doc("Population which parameters are calibrated") + public Population param_Population = null; + @Doc("First initial point of the simplex: de la forme(\"xx;yy\")") + public String param_M1 = "2.42e-5;2.11e-6";// devient un parametre du plan d analyse + @Doc("Second initial point of the simplex") + public String param_M2 = "2.34e-5;2.59e-6";// devient un parametre du plan d analyse + @Doc("Third initial point of the simplex") + public String param_M3 = "2.59e-5;2.41e-6";// 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) + @Doc(value = "file name and path of observed landings") + public String param_nomfichier_debarquements = "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_PER_ZONE_POP }; + + 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 context 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 = 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(); + } + + double g1; + double g2; + double worst1; + double worst2; + + /** + * 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 { + 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 lastSimulation 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_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + // 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 put 3, over year 12, else put "//" at the beginning of the following line + L = L.sumOverDim(0, 3); + + 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); + } + + /////*** 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<Experience> { + 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(Experience other) { + int result = Double.compare(this.criteria, other.criteria); + return result; + } + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/analyseplans/CalibrationSimplexePasVariable2Capturabilite.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Deleted: isis-fish/trunk/src/test/resources/test-database/analyseplans/Max.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/analyseplans/Max.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/analyseplans/Max.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,97 +0,0 @@ -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.Writer; - -import org.codelutin.math.matrix.*; - -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; - -import fr.ifremer.isisfish.simulator.AnalysePlanIndependent; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - -/** - * Max.java - * - * Created: 2 mars 2007 - * - * @author bpoussin <bpoussin at labs.libre-entreprise.org> - * @version $Revision: 1.2 $ - * - * Last update: $Date: 2007-03-09 15:27:21 $ - * by : $Author: bpoussin $ - */ -public class Max implements AnalysePlanIndependent { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(Max.class); - - @Doc(value="do the doc of param max") - public int param_max = 10; - - - 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 _("Permit to specify maximum simulation numbers"); - } - - /** - * Appel? au d?marrage de la simulation, cette m?thode permet d'initialiser - * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void init(AnalysePlanContext context) throws Exception { - - } - - /** - * 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 { - boolean result = context.getNumber() <= param_max; - return result; - } - - /** - * 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; - } - -} Added: isis-fish/trunk/src/test/resources/test-database/analyseplans/SimulationNumberRestriction.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/analyseplans/SimulationNumberRestriction.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/analyseplans/SimulationNumberRestriction.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,96 @@ +package analyseplans; + +import static org.codelutin.i18n.I18n._; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.AnalysePlanContext; +import fr.ifremer.isisfish.simulator.AnalysePlanIndependent; +import fr.ifremer.isisfish.util.Doc; + +/** + * ExempleSimulationsIndependantes.java + * + * Created: 2 mars 2007 + * + * @author bpoussin <bpoussin at labs.libre-entreprise.org> + * @version $Revision$ + * + * Last update: $Date$ by : $Author: bpoussin $ + */ +public class SimulationNumberRestriction implements AnalysePlanIndependent { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SimulationNumberRestriction.class); + + @Doc(value = "do the doc of param max") + public int param_max = 10; + + public String[] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + }; + + @Override + 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 + */ + @Override + public String getDescription() throws Exception { + return _("Permit to specify maximum simulation numbers"); + } + + /** + * Appelé au démarrage de la simulation, cette méthode permet d'initialiser + * des valeurs + * + * @param context La simulation pour lequel on utilise cette regle + */ + @Override + public void init(AnalysePlanContext context) throws Exception { + + } + + /** + * 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 + */ + @Override + public boolean beforeSimulation(AnalysePlanContext context, + SimulationStorage nextSimulation) throws Exception { + boolean result = context.getNumber() < param_max; + return result; + } + + /** + * Call after each simulation + * + * @param context + * plan context + * @param lastSimulation storage used for last simulation + * @return true if we must do next simulation, false to stop plan + * @throws Exception + */ + @Override + public boolean afterSimulation(AnalysePlanContext context, + SimulationStorage lastSimulation) throws Exception { + return true; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/analyseplans/SimulationNumberRestriction.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Modified: isis-fish/trunk/src/test/resources/test-database/exports/Abundances.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/Abundances.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/Abundances.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -14,10 +14,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * Abundance.java * @@ -29,7 +26,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - at Doc(value="do the doc of class Abundances") public class Abundances implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -52,7 +48,7 @@ } public String getDescription() { - return _("Export les abondances en nombre tableau avec des lignes pop;id;zone;date;nombre."); + return _("Exporte les abondances en nombre tableau avec des lignes pop;id;zone;date;nombre."); } public void export(SimulationStorage simulation, Writer out) throws Exception { Modified: isis-fish/trunk/src/test/resources/test-database/exports/Biomasses.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/Biomasses.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/Biomasses.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -15,10 +15,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * Biomasses.java * @@ -30,7 +27,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class Biomasses") public class Biomasses implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -53,7 +49,7 @@ } public String getDescription() { - return _("Export les biomasses tableau avec des lignes pop;id;zone;date;nombre"); + return _("Exporte les biomasses tableau avec des lignes pop;id;zone;date;nombre"); } public void export(SimulationStorage simulation, Writer out) throws Exception { Modified: isis-fish/trunk/src/test/resources/test-database/exports/CapturesNombre.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/CapturesNombre.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/CapturesNombre.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,44 +2,39 @@ import static org.codelutin.i18n.I18n._; +import java.io.Writer; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; -import java.io.Writer; - -import org.codelutin.math.matrix.*; - import scripts.ResultName; - -import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * CapturesNombre.java - * + * * Created: 23 novembre 2006 - * + * * @author anonymous <anonymous at labs.libre-entreprise.org> * @version $Revision: 1.4 $ - * - * Last update: $Date: 2007-05-24 09:30:07 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ */ - @Doc(value="do the doc of class CaptureNombre") public class CapturesNombre implements Export { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesNombre.class); - protected String [] necessaryResult = { - ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP - }; - + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP }; + public String[] getNecessaryResult() { return this.necessaryResult; } @@ -47,76 +42,80 @@ public String getExportFilename() { return "CapturesNombre"; } - + public String getExtensionFilename() { return ".csv"; } - + public String getDescription() { return _("Export les captures en nombre de la simulation. tableau pop;metier;id;zone;nombre"); } - public void export(SimulationStorage simulation, Writer out) throws Exception { + public void export(SimulationStorage simulation, Writer out) + throws Exception { Date lastDate = simulation.getResultStorage().getLastDate(); - + for (Population pop : simulation.getParameter().getPopulations()) { - for (Date date = new Date(0); !date.after(lastDate); date = date.next() ) { - MatrixND mat = simulation.getResultStorage().getMatrix(date, pop, - ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(date, + pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); if (mat != null) { // can be null if simulation is stopped before last year simulation mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - Metier metier = (Metier)sems[1]; - PopulationGroup group = (PopulationGroup)sems[2]; - Zone zone = (Zone)sems[3]; + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; double val = i.getValue(); - out.write(pop.getName() +";"+ metier.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ date.getDate() +";"+ val +"\n"); + out.write(pop.getName() + ";" + metier.getName() + ";" + + group.getId() + ";" + zone.getName() + ";" + + date.getDate() + ";" + val + "\n"); } } } } /* -var Parametre=sim.getParametre(); -var Populations=Parametre.getPopulations(); -var PDate=Packages.fr.ifremer.nodb.Date; + var Parametre=sim.getParametre(); + var Populations=Parametre.getPopulations(); + var PDate=Packages.fr.ifremer.nodb.Date; -var capture=0.0; -var result=""; + var capture=0.0; + var result=""; -writeln("debut de export captures nombre"); -var dateexport=new Packages.java.util.Date(); -var formatteur= new Packages.java.text.SimpleDateFormat(); -writeln("heure de debut: "+formatteur.format(dateexport)); -var finsimu=resultats.getLastDate().getDate(); + writeln("debut de export captures nombre"); + var dateexport=new Packages.java.util.Date(); + var formatteur= new Packages.java.text.SimpleDateFormat(); + writeln("heure de debut: "+formatteur.format(dateexport)); + var finsimu=resultats.getLastDate().getDate(); -for (var ipop=Populations.iterator();ipop.hasNext();){ - var pop=ipop.next(); - for (var idate=0;idate<=finsimu;idate++){ - var date=new PDate(idate); - var matrice=resultats.getMatrix(date,pop, "matriceCatchPerStrategyMet"); - var temp=matrice.sumOverDim(0); - writeln("on a la matrice"); - for (var iiterateur=temp.iterator();iiterateur.next();){ - var coordonnees=iiterateur.getSemanticsCoordinates(); - var metier=coordonnees[1]; - var c=coordonnees[2]; - var z=coordonnees[3]; - capture=iiterateur.getValue(); - result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; - } - } -} + for (var ipop=Populations.iterator();ipop.hasNext();){ + var pop=ipop.next(); + for (var idate=0;idate<=finsimu;idate++){ + var date=new PDate(idate); + var matrice=resultats.getMatrix(date,pop, "matriceCatchPerStrategyMet"); + var temp=matrice.sumOverDim(0); + writeln("on a la matrice"); + for (var iiterateur=temp.iterator();iiterateur.next();){ + var coordonnees=iiterateur.getSemanticsCoordinates(); + var metier=coordonnees[1]; + var c=coordonnees[2]; + var z=coordonnees[3]; + capture=iiterateur.getValue(); + result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; + } + } + } -writeln("fin de CapturesNombre"); + writeln("fin de CapturesNombre"); -return ""+result; + return ""+result; -*/ + */ } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/CapturesPoids.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/CapturesPoids.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/CapturesPoids.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,44 +2,39 @@ import static org.codelutin.i18n.I18n._; +import java.io.Writer; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; -import java.io.Writer; - -import org.codelutin.math.matrix.*; - import scripts.ResultName; - -import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * CapturesPoids.java - * + * * Created: 23 novembre 2006 - * + * * @author anonymous <anonymous at labs.libre-entreprise.org> * @version $Revision: 1.4 $ - * - * Last update: $Date: 2007-05-24 09:30:07 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ */ - @Doc(value="do the doc of class CapturesPoids") public class CapturesPoids implements Export { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesPoids.class); - protected String [] necessaryResult = { - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP - }; - + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + public String[] getNecessaryResult() { return this.necessaryResult; } @@ -47,72 +42,76 @@ public String getExportFilename() { return "CapturesPoids"; } - + public String getExtensionFilename() { return ".csv"; } - + public String getDescription() { return _("Export les captures en poids de la simulation. tableau pop;metier;id;zone;nombre"); } - public void export(SimulationStorage simulation, Writer out) throws Exception { + public void export(SimulationStorage simulation, Writer out) + throws Exception { Date lastDate = simulation.getResultStorage().getLastDate(); for (Population pop : simulation.getParameter().getPopulations()) { - for (Date date = new Date(0); !date.after(lastDate); date = date.next() ) { - MatrixND mat = simulation.getResultStorage().getMatrix(date, pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(date, + pop, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); if (mat != null) { // can be null if simulation is stopped before last year simulation mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - Metier metier = (Metier)sems[1]; - PopulationGroup group = (PopulationGroup)sems[2]; - Zone zone = (Zone)sems[3]; + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; double val = i.getValue(); - out.write(pop.getName() +";"+ metier.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ date.getDate() +";"+ val +"\n"); + out.write(pop.getName() + ";" + metier.getName() + ";" + + group.getId() + ";" + zone.getName() + ";" + + date.getDate() + ";" + val + "\n"); } } } } -/* -var Parametre=sim.getParametre(); -var Populations=Parametre.getPopulations(); -var PDate=Packages.fr.ifremer.nodb.Date; + /* + var Parametre=sim.getParametre(); + var Populations=Parametre.getPopulations(); + var PDate=Packages.fr.ifremer.nodb.Date; -var capture=0.0; -var result=""; -writeln("debut de export captures poids"); -var dateexport=new Packages.java.util.Date(); -var formatteur= new Packages.java.text.SimpleDateFormat(); -writeln("heure de debut: "+formatteur.format(dateexport)); -var finsimu=resultats.getLastDate().getDate(); + var capture=0.0; + var result=""; + writeln("debut de export captures poids"); + var dateexport=new Packages.java.util.Date(); + var formatteur= new Packages.java.text.SimpleDateFormat(); + writeln("heure de debut: "+formatteur.format(dateexport)); + var finsimu=resultats.getLastDate().getDate(); -for (var ipop=Populations.iterator();ipop.hasNext();){ - var pop=ipop.next(); - for (var idate=0;idate<=finsimu;idate++){ - var date=new PDate(idate); - var matrice=resultats.getMatrix(date,pop, "matriceCatchWeightPerStrategyMet"); - var temp=matrice.sumOverDim(0); - writeln("on a la matrice"); - for (var iiterateur=temp.iterator();iiterateur.next();){ - var coordonnees=iiterateur.getSemanticsCoordinates(); - var metier=coordonnees[1]; - var c=coordonnees[2]; - var z=coordonnees[3]; - capture=iiterateur.getValue(); - result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; - } - } -} + for (var ipop=Populations.iterator();ipop.hasNext();){ + var pop=ipop.next(); + for (var idate=0;idate<=finsimu;idate++){ + var date=new PDate(idate); + var matrice=resultats.getMatrix(date,pop, "matriceCatchWeightPerStrategyMet"); + var temp=matrice.sumOverDim(0); + writeln("on a la matrice"); + for (var iiterateur=temp.iterator();iiterateur.next();){ + var coordonnees=iiterateur.getSemanticsCoordinates(); + var metier=coordonnees[1]; + var c=coordonnees[2]; + var z=coordonnees[3]; + capture=iiterateur.getValue(); + result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; + } + } + } -writeln("fin de CapturesPoids"); -return ""+result; + writeln("fin de CapturesPoids"); + return ""+result; -*/ + */ } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/CellsDefinition.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/CellsDefinition.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/CellsDefinition.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,22 +1,18 @@ package exports; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import static org.codelutin.i18n.I18n._; import java.io.Writer; import java.util.List; -import static org.codelutin.i18n.I18n._; -import org.codelutin.math.matrix.*; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.topia.TopiaContext; -import fr.ifremer.isisfish.entities.*; -import fr.ifremer.isisfish.export.Export; -import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.entities.Cell; +import fr.ifremer.isisfish.export.Export; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * CellsDefinition.java * @@ -28,7 +24,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class CellsDefinition") public class CellsDefinition implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -58,11 +53,14 @@ } public void export(SimulationStorage simulation, Writer out) throws Exception { - List<Cell> cells = simulation.getFisheryRegion().getCell(); + TopiaContext tx = simulation.getStorage().beginTransaction(); + List<Cell> cells = SimulationStorage.getFisheryRegion(tx).getCell(); for (Cell cell : cells) { out.write(cell + ";" + cell.getLongitude() + ";" + cell.getLatitude() + "\n"); } + + tx.closeContext(); } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/EffortsMetier.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/EffortsMetier.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/EffortsMetier.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -15,10 +15,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * EffortsMetier.java * @@ -30,7 +27,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class EffortsMetier") public class EffortsMetier implements Export { /** to use log facility, just put in your code: log.info("..."); */ Modified: isis-fish/trunk/src/test/resources/test-database/exports/MetierZone.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/MetierZone.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/MetierZone.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -10,14 +10,10 @@ import scripts.ResultName; -import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * MetierZone.java * @@ -29,7 +25,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class MetierZone") public class MetierZone implements Export { /** to use log facility, just put in your code: log.info("..."); */ Modified: isis-fish/trunk/src/test/resources/test-database/exports/NonActivite.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/NonActivite.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/NonActivite.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -17,8 +17,6 @@ import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * NonActivite.java * @@ -30,7 +28,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class NonActivite") public class NonActivite implements Export { /** to use log facility, just put in your code: log.info("..."); */ Modified: isis-fish/trunk/src/test/resources/test-database/exports/OwnerMargin.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/OwnerMargin.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/OwnerMargin.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -15,10 +15,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * OwnerMargin.java * @@ -30,7 +27,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class OwnerMargin") public class OwnerMargin implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -53,7 +49,7 @@ } public String getDescription() { - return _("cvs out strategy;date;value"); + return _("Exporte les profits du patrons, retourne un tableau strategy;date;value"); } public void export(SimulationStorage simulation, Writer out) throws Exception { Modified: isis-fish/trunk/src/test/resources/test-database/exports/RegionDefinition.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/RegionDefinition.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/RegionDefinition.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -6,15 +6,12 @@ import java.io.Writer; import static org.codelutin.i18n.I18n._; -import org.codelutin.math.matrix.*; +import org.codelutin.topia.TopiaContext; import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * RegionDefinition.java * @@ -26,7 +23,6 @@ * Last update: $Date: 2007-05-24 10:05:22 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class RegionDefinition") public class RegionDefinition implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -57,7 +53,9 @@ public void export(SimulationStorage simulation, Writer out) throws Exception { // NomRegion LatituteMin LatitudeMax LongitudeMin LongitudeMax PasLatitude PasLongitude - FisheryRegion region = simulation.getFisheryRegion(); + TopiaContext tx = simulation.getStorage().beginTransaction(); + FisheryRegion region = SimulationStorage.getFisheryRegion(tx); + out.write(region.getName() + ";" + region.getMinLatitude() + ";" + region.getMaxLatitude() + ";" @@ -66,6 +64,8 @@ + region.getCellLengthLatitude() + ";" + region.getCellLengthLongitude() + "\n"); + + tx.closeContext(); } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/RejetsNombre.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/RejetsNombre.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/RejetsNombre.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,44 +2,39 @@ import static org.codelutin.i18n.I18n._; +import java.io.Writer; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; -import java.io.Writer; - -import org.codelutin.math.matrix.*; - import scripts.ResultName; - -import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * RejetsNombre.java - * + * * Created: 23 novembre 2006 - * + * * @author anonymous <anonymous at labs.libre-entreprise.org> * @version $Revision: 1.4 $ - * - * Last update: $Date: 2007-05-24 09:30:07 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ */ - @Doc(value="do the doc of class RejetsNombre") public class RejetsNombre implements Export { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(RejetsNombre.class); - protected String [] necessaryResult = { - ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP - }; - + protected String[] necessaryResult = { ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP }; + public String[] getNecessaryResult() { return this.necessaryResult; } @@ -47,74 +42,79 @@ public String getExportFilename() { return "RejetsNombre"; } - + public String getExtensionFilename() { return ".csv"; } - + public String getDescription() { return _("Export les rejets en nombre de la simulation. tableau pop;metier;id;zone;date;nombre"); } - public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + for (Population pop : simulation.getParameter().getPopulations()) { - for (Date date = new Date(0); !date.after(lastDate); date = date.next() ) { - MatrixND mat = simulation.getResultStorage().getMatrix(date, pop, ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(date, + pop, ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); if (mat != null) { // can be null if simulation is stopped before last year simulation mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - Metier metier = (Metier)sems[1]; - PopulationGroup group = (PopulationGroup)sems[2]; - Zone zone = (Zone)sems[3]; - + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; + double val = i.getValue(); - out.write(pop.getName() +";"+ metier.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ date.getDate() +";"+ val +"\n"); + out.write(pop.getName() + ";" + metier.getName() + ";" + + group.getId() + ";" + zone.getName() + ";" + + date.getDate() + ";" + val + "\n"); } } } } -/* -var Parametre=sim.getParametre(); -var Populations=Parametre.getPopulations(); -var PDate=Packages.fr.ifremer.nodb.Date; + /* + var Parametre=sim.getParametre(); + var Populations=Parametre.getPopulations(); + var PDate=Packages.fr.ifremer.nodb.Date; -var capture=0.0; -var result=""; -writeln("debut de export rejets nombre"); -var dateexport=new Packages.java.util.Date(); -var formatteur= new Packages.java.text.SimpleDateFormat(); -writeln("heure de debut: "+formatteur.format(dateexport)); -var finsimu=resultats.getLastDate().getDate(); + var capture=0.0; + var result=""; + writeln("debut de export rejets nombre"); + var dateexport=new Packages.java.util.Date(); + var formatteur= new Packages.java.text.SimpleDateFormat(); + writeln("heure de debut: "+formatteur.format(dateexport)); + var finsimu=resultats.getLastDate().getDate(); -for (var ipop=Populations.iterator();ipop.hasNext();){ - var pop=ipop.next(); - for (var idate=0;idate<=finsimu;idate++){ - var date=new PDate(idate); - var matrice=resultats.getMatrix(date,pop ,"Rejet par metier"); - if (matrice==null){ - matrice=MatrixFactory.create(resultats.getMatrix(new PDate(0),pop ,"Rejet par metier")); - matrice.mults(0); - } - var temp=matrice.sumOverDim(0); - writeln("on a la matrice"); - for (var iiterateur=temp.iterator();iiterateur.next();){ - var coordonnees=iiterateur.getSemanticsCoordinates(); - var metier=coordonnees[1]; - var c=coordonnees[2]; - var z=coordonnees[3]; - capture=iiterateur.getValue(); - result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; - } - } -} + for (var ipop=Populations.iterator();ipop.hasNext();){ + var pop=ipop.next(); + for (var idate=0;idate<=finsimu;idate++){ + var date=new PDate(idate); + var matrice=resultats.getMatrix(date,pop ,"Rejet par metier"); + if (matrice==null){ + matrice=MatrixFactory.create(resultats.getMatrix(new PDate(0),pop ,"Rejet par metier")); + matrice.mults(0); + } + var temp=matrice.sumOverDim(0); + writeln("on a la matrice"); + for (var iiterateur=temp.iterator();iiterateur.next();){ + var coordonnees=iiterateur.getSemanticsCoordinates(); + var metier=coordonnees[1]; + var c=coordonnees[2]; + var z=coordonnees[3]; + capture=iiterateur.getValue(); + result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; + } + } + } -writeln("fin de RejetsNombre"); -return ""+result; -*/ + writeln("fin de RejetsNombre"); + return ""+result; + */ } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/RejetsPoids.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/RejetsPoids.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/RejetsPoids.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,45 +2,41 @@ import static org.codelutin.i18n.I18n._; +import java.io.Writer; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; -import java.io.Writer; - -import org.codelutin.math.matrix.*; - import scripts.ResultName; - -import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * RejetsPoids.java - * + * * Created: 23 novembre 2006 - * + * * @author anonymous <anonymous at labs.libre-entreprise.org> * @version $Revision: 1.4 $ - * - * Last update: $Date: 2007-05-24 09:30:07 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ */ - @Doc(value="do the doc of class RejetsPoids") public class RejetsPoids implements Export { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(RejetsPoids.class); - protected String [] necessaryResult = { - ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP - + protected String[] necessaryResult = { ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP + }; - + public String[] getNecessaryResult() { return this.necessaryResult; } @@ -48,73 +44,78 @@ public String getExportFilename() { return "RejetsPoids"; } - + public String getExtensionFilename() { return ".csv"; } - + public String getDescription() { return _("Export les rejets en poids de la simulation. tableau pop;metier;id;zone;date;nombre"); } - public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + for (Population pop : simulation.getParameter().getPopulations()) { - for (Date date = new Date(0); !date.after(lastDate); date = date.next() ) { - MatrixND mat = simulation.getResultStorage().getMatrix(date, pop, ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(date, + pop, ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); if (mat != null) { // can be null if simulation is stopped before last year simulation mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - Metier metier = (Metier)sems[1]; - PopulationGroup group = (PopulationGroup)sems[2]; - Zone zone = (Zone)sems[3]; + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; double val = i.getValue(); - out.write(pop.getName() +";"+ metier.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ date.getDate() +";"+ val +"\n"); + out.write(pop.getName() + ";" + metier.getName() + ";" + + group.getId() + ";" + zone.getName() + ";" + + date.getDate() + ";" + val + "\n"); } } } } -/* -var Parametre=sim.getParametre(); -var Populations=Parametre.getPopulations(); -var PDate=Packages.fr.ifremer.nodb.Date; + /* + var Parametre=sim.getParametre(); + var Populations=Parametre.getPopulations(); + var PDate=Packages.fr.ifremer.nodb.Date; -var capture=0.0; -var result=""; -writeln("debut de export rejets poids"); -var dateexport=new Packages.java.util.Date(); -var formatteur= new Packages.java.text.SimpleDateFormat(); -writeln("heure de debut: "+formatteur.format(dateexport)); -var finsimu=resultats.getLastDate().getDate(); + var capture=0.0; + var result=""; + writeln("debut de export rejets poids"); + var dateexport=new Packages.java.util.Date(); + var formatteur= new Packages.java.text.SimpleDateFormat(); + writeln("heure de debut: "+formatteur.format(dateexport)); + var finsimu=resultats.getLastDate().getDate(); -for (var ipop=Populations.iterator();ipop.hasNext();){ - var pop=ipop.next(); - for (var idate=0;idate<=finsimu;idate++){ - var date=new PDate(idate); - var matrice=resultats.getMatrix(date, pop, "Rejet par metier"); - if (matrice==null){ - matrice=MatrixFactory.create(resultats.getMatrix(new PDate(0),pop ,"Rejet par metier")); - matrice.mults(0); - } - var temp=matrice.sumOverDim(0); - for (var iiterateur=temp.iterator();iiterateur.next();){ - var coordonnees=iiterateur.getSemanticsCoordinates(); - var metier=coordonnees[1]; - var c=coordonnees[2]; - var z=coordonnees[3]; - capture=iiterateur.getValue()*c.getPoidsMoyen(); - result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; - } - } -} + for (var ipop=Populations.iterator();ipop.hasNext();){ + var pop=ipop.next(); + for (var idate=0;idate<=finsimu;idate++){ + var date=new PDate(idate); + var matrice=resultats.getMatrix(date, pop, "Rejet par metier"); + if (matrice==null){ + matrice=MatrixFactory.create(resultats.getMatrix(new PDate(0),pop ,"Rejet par metier")); + matrice.mults(0); + } + var temp=matrice.sumOverDim(0); + for (var iiterateur=temp.iterator();iiterateur.next();){ + var coordonnees=iiterateur.getSemanticsCoordinates(); + var metier=coordonnees[1]; + var c=coordonnees[2]; + var z=coordonnees[3]; + capture=iiterateur.getValue()*c.getPoidsMoyen(); + result+=pop.getNom()+";"+metier.getNom()+";"+c.getId()+";"+z.getNom()+";"+idate+";"+capture+"\n"; + } + } + } -writeln("fin de RejetsPoids"); -return ""+result; -*/ + writeln("fin de RejetsPoids"); + return ""+result; + */ } } Modified: isis-fish/trunk/src/test/resources/test-database/exports/VesselMargin.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/VesselMargin.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/VesselMargin.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -15,10 +15,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * VesselMargin.java * @@ -30,7 +27,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class VesselMargin") public class VesselMargin implements Export { /** to use log facility, just put in your code: log.info("..."); */ Modified: isis-fish/trunk/src/test/resources/test-database/exports/ZonesDefinition.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/exports/ZonesDefinition.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/exports/ZonesDefinition.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -7,16 +7,13 @@ import java.util.List; import static org.codelutin.i18n.I18n._; -import org.codelutin.math.matrix.*; +import org.codelutin.topia.TopiaContext; import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** * ZonesDefinition.java * @@ -28,7 +25,6 @@ * Last update: $Date: 2007-05-24 09:30:07 $ * by : $Author: bpoussin $ */ - @Doc(value="do the doc of class ZoneDefinition") public class ZonesDefinition implements Export { /** to use log facility, just put in your code: log.info("..."); */ @@ -58,7 +54,9 @@ } public void export(SimulationStorage simulation, Writer out) throws Exception { - List<Zone> zones = simulation.getFisheryRegion().getZone(); + TopiaContext tx = simulation.getStorage().beginTransaction(); + List<Zone> zones = SimulationStorage.getFisheryRegion(tx).getZone(); + Date lastDate = simulation.getResultStorage().getLastDate(); for (Date date = new Date(0); !date.after(lastDate); date = date.next() ) { @@ -68,6 +66,8 @@ } } } + + tx.closeContext(); } } Modified: isis-fish/trunk/src/test/resources/test-database/rules/Cantonnement.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/Cantonnement.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/Cantonnement.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -46,17 +46,17 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(Cantonnement.class); - @Doc(value="do the doc of param zone") + @Doc(value="Zone de fermeture") public Zone param_zone = null; - @Doc(value="do the doc of param gear") + @Doc(value="Engin concernés") public Gear param_gear = null; - @Doc(value="do the doc of param beginDate") + @Doc(value="Begin date") public Date param_beginDate = new Date(0); - @Doc(value="do the doc of param endDate") + @Doc(value="End date") public Date param_endDate = new Date(119); - @Doc(value="do the doc of param beginMonth") + @Doc(value="Begin month") public Month param_beginMonth = Month.JANUARY; - @Doc(value="do the doc of param endMonth") + @Doc(value="End month") public Month param_endMonth = Month.DECEMBER; public String [] necessaryResult = { @@ -76,20 +76,23 @@ * @return L'aide ou la description de la regle */ public String getDescription() throws Exception { + // fermeture saisiniere de zone qui peut être réduite à un engin + // et a certaines années de la simulation return _("Cantonnement: can be used to Cantonnement with gear if you put gear in parameter"); } /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { + } /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { @@ -149,7 +152,7 @@ /** * Si la condition est vrai alors cette action est executée avant le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { MetierMonitor metierMon = context.getMetierMonitor(); @@ -320,7 +323,7 @@ /** * Si la condition est vrai alors cette action est executée apres le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { // nothing Modified: isis-fish/trunk/src/test/resources/test-database/rules/CantonnementPreSimu.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/CantonnementPreSimu.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/CantonnementPreSimu.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -10,10 +10,7 @@ import scripts.SiMatrix; import java.util.ArrayList; -import java.util.Collection; -import java.util.Collections; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; @@ -31,7 +28,7 @@ import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) /** - * Cantonnement.java + * CantonnementPreSimu.java * * Created: 30 novembre 2006 * @@ -46,15 +43,13 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CantonnementPreSimu.class); - @Doc(value="do the doc of param zone") + @Doc(value="Zone de fermature") public Zone param_zone = null; - @Doc(value="do the doc of param gear") + @Doc(value="Engin concernés") public Gear param_gear = null; - @Doc(value="do the doc of param enginSelective") - public boolean param_enginSelective = true; - @Doc(value="do the doc of param beginMonth") + @Doc(value="Begin month") public Month param_beginMonth = Month.JANUARY; - @Doc(value="do the doc of param endMonth") + @Doc(value="End month") public Month param_endMonth = Month.DECEMBER; protected Map<Month, MatrixND> tableNonActivite = new HashMap<Month, MatrixND>(); @@ -117,7 +112,7 @@ /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { SiMatrix siMatrix = SiMatrix.getSiMatrix(context); @@ -125,7 +120,7 @@ // MetierDAO metierDao = IsisFishDAOHelper.getMetierDAO(context.getDB()); ZoneDAO zoneDao = IsisFishDAOHelper.getZoneDAO(context.getDB()); MetierSeasonInfoDAO metierSeasonInfoDao = IsisFishDAOHelper.getMetierSeasonInfoDAO(context.getDB()); - + // List<Metier> metiers = metierDao.findAll(); List<Month> SaisonFermee = Month.getMonths(param_beginMonth, param_endMonth); List<Cell> maillefermee = param_zone.getCell(); @@ -641,7 +636,7 @@ /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { @@ -668,7 +663,7 @@ /** * Si la condition est vrai alors cette action est executée avant le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { // on ne doit le faire qu'une seul fois quelque soit le nombre de metier @@ -704,7 +699,7 @@ /** * Si la condition est vrai alors cette action est executée apres le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { affectNonActivite = false; Modified: isis-fish/trunk/src/test/resources/test-database/rules/ChangementParamControlablePresimu.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/ChangementParamControlablePresimu.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/ChangementParamControlablePresimu.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,32 +2,35 @@ import static org.codelutin.i18n.I18n._; +import java.util.ArrayList; +import java.util.List; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import scripts.ResultName; import scripts.SiMatrix; - -import java.io.Writer; -import java.util.ArrayList; -import java.util.List; - -import org.codelutin.math.matrix.*; - import fr.ifremer.isisfish.IsisFishDAOHelper; +import fr.ifremer.isisfish.datastore.RegionStorage; +import fr.ifremer.isisfish.entities.EffortDescription; +import fr.ifremer.isisfish.entities.EffortDescriptionDAO; +import fr.ifremer.isisfish.entities.FisheryRegion; +import fr.ifremer.isisfish.entities.Gear; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.MetierDAO; +import fr.ifremer.isisfish.entities.MetierSeasonInfo; +import fr.ifremer.isisfish.entities.MetierSeasonInfoDAO; +import fr.ifremer.isisfish.entities.SetOfVessels; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.StrategyMonthInfo; +import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.rule.AbstractRule; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.entities.*; -import fr.ifremer.isisfish.rule.AbstractRule; -import fr.ifremer.isisfish.datastore.RegionStorage; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.util.Doc; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** - * TailleMin.java + * ChangementParamControlablePresimu.java * * Created: 30 novembre 2006 * @@ -42,15 +45,15 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(ChangementParamControlablePresimu.class); - @Doc(value="do the doc of param zone") + @Doc(value="Zone de fermeture") public Zone param_zone = null; - @Doc(value="do the doc of param gear") + @Doc(value="Engin concernés") public Gear param_gear = null; - @Doc(value="do the doc of param beginMonth") + @Doc(value="Begin month") public Month param_beginMonth = Month.JANUARY; - @Doc(value="do the doc of param endMonth") + @Doc(value="End month") public Month param_endMonth = Month.DECEMBER; - @Doc(value="do the doc of param newParamValue") + @Doc(value="New param controlable value") public String param_newParamValue = "80"; public String [] necessaryResult = { @@ -75,7 +78,7 @@ /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { SiMatrix siMatrix = SiMatrix.getSiMatrix(context); @@ -134,7 +137,8 @@ MetierSeasonInfo NouveauInfoSaison = infoDao.create(); NouveauInfoSaison.setMetier(NouveauMetier); NouveauInfoSaison.setMonths(sais); - NouveauInfoSaison.setZone(infsais.getZone()); + // EC : new ArrayList<Zone>() fix error "Found shared references to a collection" + NouveauInfoSaison.setZone(new ArrayList<Zone>(infsais.getZone())); NouveauInfoSaison.setComment("créé durant la simulation"); NouveauMetier.addMetierSeasonInfo(NouveauInfoSaison); } @@ -294,8 +298,8 @@ } /** - * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * La condition qui doit etre vrai pour faire les actions. + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { @@ -303,18 +307,18 @@ } /** - * Si la condition est vrai alors cette action est executée avant le pas + * Si la condition est vrai alors cette action est executée avant le pas. * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { // nothing } /** - * Si la condition est vrai alors cette action est executée apres le pas + * Si la condition est vrai alors cette action est executée apres le pas. * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { // nothing Added: isis-fish/trunk/src/test/resources/test-database/rules/EffortReduction.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/EffortReduction.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/rules/EffortReduction.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,139 @@ +package rules; + +import static org.codelutin.i18n.I18n._; + +import java.util.List; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import scripts.SiMatrix; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.rule.AbstractRule; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +/** + * EffortReduction.java + * + * Created: 3 septembre 2008 + * + * @author anonymous <anonymous at labs.libre-entreprise.org> + * @version $Revision$ + */ +public class EffortReduction extends AbstractRule { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(EffortReduction.class); + + @Doc("Begin date") + public Date param_beginDate = new Date(0); + @Doc("End date") + public Date param_endDate = new Date(59); + + @Doc("Pourcentage de reduction d effort applique.") + public double param_PercentReduction = 0.5; + + boolean first = true; + + protected String[] necessaryResult = {}; + + /** + * @return the necessaryResult + */ + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + /** + * Permet d'afficher a l'utilisateur une aide sur la regle. + * @return L'aide ou la description de la regle + */ + public String getDescription() { + return _("Reduce monthly effort of each strategy of the percent indicated"); + } + + /** + * Appele au demarrage de la simulation, cette methode permet d'initialiser + * des valeurs. + * @param context La simulation pour lequel on utilise cette regle + */ + public void init(SimulationContext context) throws Exception { + } + + /** + * La condition qui doit etre vrai pour faire les actions + * @param context La simulation pour lequel on utilise cette regle + * @return vrai si on souhaite que les actions soit faites + */ + public boolean condition(SimulationContext context, Date date, Metier metier) + throws Exception { + + boolean result = true; + if (date.before(param_beginDate)) { + result = false; + } else if (date.after(param_endDate)) { + result = false; + } + if (result) + System.out.println("condition vraie"); + return result; + } + + /** + * Si la condition est vrai alors cette action est executee avant le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { + // shinte la boucle metier + if (first) { + first = false; + SiMatrix siMatrix = SiMatrix.getSiMatrix(context); + List<Strategy> strs = siMatrix.getStrategies(date); + for (Strategy str : strs) { + System.out.println("strategy evaluee : " + str.getName()); + + /* Dans un premiere temps tant que l inactivit? est un entier on utilise + * la proportion du nombre de bateaux de la strategie pour reduire l effort + * ce qu on ferait aussi pour une mesure de reduction du nombre de bateaux mais + * comme actuellement on ne tient pas compte de l economie... ca revient au meme + * En fait passer par l inactivit? n est pas la meilleure facon de modifier + * l effort le mieux serait d agir sur un autre coeff qui est multipli? a + * l effort (Fstd ou ciblage) car comme ca le code serait generique mais on + * ne verrait pas que l effort nominal est modifi?... + */ + + double propOld = str.getProportionSetOfVessels(); + double newProp = propOld * (1 - param_PercentReduction); + str.setProportionSetOfVessels(newProp); + + /* int Inact = str.getStrategyMonthInfo(date.getMonth()).getMinInactivityDays(); + System.out.println("inactivity old = "+ Inact); + int nbDays = date.getMonth().getNumbersOfDays(); + System.out.println("nbDays = "+nbDays); + double newInact = nbDays-((nbDays-Inact)*(1-param_PercentReduction)); + System.out.println("newInact = "+newInact); + int ni = (int) newInact ; + System.out.println("ni = "+ ni); + str.getStrategyMonthInfo(date.getMonth()).setMinInactivityDays(ni); + System.out.println("setMinInactivityDays : " + str.getStrategyMonthInfo(date.getMonth()).getMinInactivityDays()); + */ + } + } + } + + /** + * Si la condition est vrai alors cette action est executee apres le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void postAction(SimulationContext context, Date date, Metier metier) + throws Exception { + first = true; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/rules/EffortReduction.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Deleted: isis-fish/trunk/src/test/resources/test-database/rules/GraviteCPUE.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/GraviteCPUE.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/GraviteCPUE.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,484 +0,0 @@ -package rules; - -import static org.codelutin.i18n.I18n._; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import scripts.GravityModel; -import scripts.ResultName; -import scripts.SiMatrix; - -import java.util.Arrays; -import java.util.List; - -import org.codelutin.math.matrix.*; - -import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.entities.*; -import fr.ifremer.isisfish.rule.AbstractRule; -import fr.ifremer.isisfish.datastore.ResultStorage; - -/** - * GraviteCPUE.java - * - * Created: 30 novembre 2006 - * - * @author anonymous <anonymous at labs.libre-entreprise.org> - * @version $Revision: 1.2 $ - * - * Last update: $Date: 2007-07-18 08:59:38 $ - * by : $Author: hilaire $ - */ -public class GraviteCPUE extends AbstractRule { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(GraviteCPUE.class); - - /** stocke la somme des prop initiales [str x month] */ - private MatrixND SommePropInitial = null; - /** stocke par strat*met, la dernière attractivite pour chaque mois - * [str x met x month] */ - private MatrixND HistoriqueCPUE = null; - - /** va permettre de stocker a chaque pas de temps la somme des attractivite [str] */ - MatrixND SommeCPUEstrat = null; - /** va permettre de stocker a chaque pas de temps la somme des proportions - * pour les metiers n'ayant pas d'attractivite [str] */ - MatrixND SommeProp = null; - - /** permet de stocker les CPUE standardiser [str x met] */ - private MatrixND catchPerUnitOfEffort = 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, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP, - ResultName.MATRIX_EFFORT_PER_STRATEGY_MET, - }; - - public String[] getNecessaryResult() { - return this.necessaryResult; - } - - /** - * Permet d'afficher a l'utilisateur une aide sur la regle. - * @return L'aide ou la description de la regle - */ - public String getDescription() throws Exception { - // TODO - return _("GraviteCPUE"); - } - - /** - * function used to initialise MatrixND to NaN double - */ - private MapFunction nanFunction = new MapFunction() { - public double apply(double value) { - return Double.NaN; - } - }; - - /** - * Appelé au démarrage de la simulation, cette méthode permet d'initialiser - * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void init(SimulationContext context) throws Exception { - Date date = new Date(0); - - List<Strategy> strs = SiMatrix.getSiMatrix(context).getStrategies(date); - List<Metier> metiers = SiMatrix.getSiMatrix(context).getMetiers(date); - List<Month> months = Arrays.asList(Month.MONTH); - - SommePropInitial = MatrixFactory.getInstance().create("SommePropInitial", - new List[]{strs, months}, new String[]{"Strategies", "Months"}); - SommePropInitial.map(nanFunction); - - HistoriqueCPUE = MatrixFactory.getInstance().create("HistoriqueCPUE", - new List[]{strs, metiers, months}, new String[]{"Strategies", "Metiers", "Months"}); - HistoriqueCPUE.map(nanFunction); - - - SommeCPUEstrat = MatrixFactory.getInstance().create("SommeCPUEstrat", - new List[]{strs}, new String[]{"Strategies"}); - SommeCPUEstrat.map(nanFunction); - - SommeProp = MatrixFactory.getInstance().create("SommeProp", - new List[]{strs}, new String[]{"Strategies"}); - SommeProp.map(nanFunction); - - catchPerUnitOfEffort = MatrixFactory.getInstance().create("ValuePerUnitOfEffort", - new List[]{strs, metiers}, new String[]{"Strategies", "Metiers"}); - catchPerUnitOfEffort.map(nanFunction); - - for (Strategy str : strs) { - List<Metier> strMetiers = SiMatrix.getSiMatrix(context).getMetiers(str, date); - List<StrategyMonthInfo> infos = str.getStrategyMonthInfo(); - for (StrategyMonthInfo info : infos) { - double somme = 0; - for (Metier strMetier : strMetiers) { - somme += info.getProportionMetier(strMetier); - } - // FIXME soit on somme pour toutes les str le meme metier; donc pas de notion de str.getName dans la cle - // soit pour une str on somme tous ces metiers (mais ce doit etre 1; donc pas de notion de metier.getName dans la cle - SommePropInitial.setValue(str, info.getMonth(), somme); - } - } - -/* -var allStr = SiMatrice.getListStrategies(); - -for(var i=0; i<allStr.size(); i++){ - var str=allStr.get(i); - var metiers=str.getSetOfVessels().getMetiers(); - var ListeStrMonthInfos=str.getStrategyMonthInfos(); - for (var j=0; j<ListeStrMonthInfos.size();j++){ - var somme=0; - var StrMonthInfo=ListeStrMonthInfos.get(j); - for (var k=0;k<metiers.size();k++){ - var metier=metiers.get(k); - somme+=StrMonthInfo.getProportionMetier(metier); - } - this.p.SommePropInitial.put(new Chaine(str.getName()+"-"+metier.getNom()+"-"+StrMonthInfo.getMonth().getNumMois()),somme); - } -} - - //permet de stocker les CPUE standardiser -CatchperUnitOfEffort = MatrixFactory.create("ValuePerUnitOfEffort",new Array(allStr,SiMatrice.getListMetiers()),new Array("Strategies","Metiers")); -*/ - } - /** - * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle - * @return vrai si on souhaite que les actions soit faites - */ - public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { - // Il faut etre au moins au deuxieme pas de temps. - // FIXME 2eme pas de temps ou 2eme annee ? ici c 2eme annee et non pas 2eme mois - return date.getYear() > 0; - } - - /** - * Si la condition est vrai alors cette action est executée avant le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { - if (log.isDebugEnabled()) { - log.debug("Gravite Action avant metier:"+ metier + "date:"+ date); - } - - List<Strategy> strs = SiMatrix.getSiMatrix(context).getStrategies(date); - List<Population> populations = SiMatrix.getSiMatrix(context).getPopulations(date); - - double newPropDiv = 0; - - ResultStorage resultmanager = context.getSimulationStorage().getResultStorage(); - - //on commence par creer une matrice de capture par strategie met - MatrixND catchWeigthPerStrMet = null; - for (Population pop : populations){ - MatrixND temp = resultmanager.getMatrix( - date.previousYear(), - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - // on somme sur les zones - temp=temp.sumOverDim(3); - // on somme sur les groupes - temp=temp.sumOverDim(2); - if (catchWeigthPerStrMet == null) { - catchWeigthPerStrMet = temp; - } else { - catchWeigthPerStrMet.add(temp); - } - } - - MatrixND effortPerStrMet = resultmanager.getMatrix( - date.previousYear(), - ResultName.MATRIX_EFFORT_PER_STRATEGY_MET); - - for (Strategy str : strs){ - List<Metier> strMetiers = SiMatrix.getSiMatrix(context).getMetiers(str, date); - for (Metier strMetier : strMetiers){ - double effort = effortPerStrMet.getValue(str, strMetier); - if (effort > 0){ - EffortDescription effortdesc = str.getSetOfVessels().getPossibleMetiers(strMetier); - int nombreop=effortdesc.getFishingOperation(); - int nombregear=effortdesc.getGearsNumberPerOperation(); - double param=strMetier.getGearParameterValueAsDouble(); - double facteur = param * nombreop * nombregear*strMetier.getGear().getStandardisationFactor() / 24.0; - //on restandardise l'effort - effort /= facteur; - //on recupere la capture tot - Object group = catchWeigthPerStrMet.getSemantics(2).get(0); - Object zone = catchWeigthPerStrMet.getSemantics(3).get(0); - - double capture = catchWeigthPerStrMet.getValue(str, strMetier, group, zone); - - catchPerUnitOfEffort.setValue(str, strMetier, capture/effort); - } - } - } - - - - for (Strategy str : strs){ - List<Metier> strMetiers = SiMatrix.getSiMatrix(context).getMetiers(str, date); - StrategyMonthInfo info = str.getStrategyMonthInfo(date.getMonth()); - - if(strMetiers.contains(metier)){ - // on verifie que le metier est bien un metier possible - double CPUE = Double.NaN; - if (SommeCPUEstrat.getValue(str) == Double.NaN){ - if (effortPerStrMet.getValue(str, metier) > 0){ - CPUE = catchPerUnitOfEffort.getValue(str, metier); - } - } - - if (CPUE != Double.NaN){ - if (log.isDebugEnabled()) { - log.debug("on a une CPUE l'année n-1, on la met dans l'historique\n" + info + " " + metier); - } - HistoriqueCPUE.setValue(str, metier, info.getMonth(), CPUE); - } else { - if (log.isDebugEnabled()) { - log.debug("ou calcul déjà fait ou pas de CPUE à l'année n-1"); - } - CPUE = HistoriqueCPUE.getValue(str, metier, info.getMonth()); - if (CPUE != Double.NaN) { - if (log.isDebugEnabled()) { - log.debug("on a une CPUE dans le passé: " + CPUE); - } - } else{ - if (log.isDebugEnabled()) { - log.debug("on a pas de CPUE dans le passé, on remet donc la poportion initiale"); - } - } - } - if (CPUE != Double.NaN) { - // si on a une CPUE, il faut aller voir l'attractivite des autres metiers: 2 cas de figure: - // soit on en retrouve une dans le passe qui est son attractivite - // soit on en retrouve pas et dans ce cas le, la proportion d'effort sera celle initiale de la db - // on a alors newProp=(1-sum(pmet1))*CPUE/somme(CPUEmet2) - // avec pmet1 la proprtion initiale pour les metiers pour lesquels on a pas retrouve de CPUE, CPUEmet2, la CPUE pour les - // metiers qui ont eu une CPUE dans le passe, et CPUE la CPUE du metier courant - if (SommeCPUEstrat.getValue(str) == Double.NaN){ - double SommeCPUE=0; - double PropTot=0; - for (Metier strMetier : strMetiers){ - double temp = Double.NaN; - if (effortPerStrMet.getValue(str, strMetier) > 0){ - temp = catchPerUnitOfEffort.getValue(str, strMetier); - } - if (temp != Double.NaN){ - if (log.isDebugEnabled()) { - log.debug("on a une CPUE l'année n-1, on l'ajoute à p.SommeCPUEstrat"); - } - HistoriqueCPUE.setValue(str, metier, info.getMonth(), temp); - SommeCPUE += temp; - } - else{ - if (log.isDebugEnabled()) { - log.debug("on a pas de CPUE l'année n-1, on regarde si il y en a dans le passé"); - } - temp = HistoriqueCPUE.getValue(str, metier, info.getMonth()); - if (temp != Double.NaN){ - if (log.isDebugEnabled()) { - log.debug("on a une CPUE dans le passé: "+temp); - } - SommeCPUE+=temp; - } - else{ - if (log.isDebugEnabled()) { - log.debug("on a pas de CPUE dans le passé, on l'ajoute donc à p.SommeProp"); - } - PropTot += info.getProportionMetier(strMetier); - } - } - } - SommeCPUEstrat.setValue(str, SommeCPUE); - SommeProp.setValue(str, PropTot); - } - - if (SommeCPUEstrat.getValue(str) > 0){ - newPropDiv = (SommePropInitial.getValue(str, info.getMonth()) - SommeProp.getValue(str)) - * CPUE / SommeCPUEstrat.getValue(str); - if (log.isDebugEnabled()) { - log.debug("newpropdiv: " + newPropDiv); - } - info.setProportionMetier(metier, newPropDiv); - } - else { // c'est le cas e priori quasi impossible oe y a toujours eu une CPUE nulle quelquesoit le metier, dans ce cas le on remet aussi la prop iniitiale - if (log.isDebugEnabled()) { - log.debug("aucun metier n'a d'attractivite, on remet la prop initiale"); - } - } - } - } - } - - if (log.isDebugEnabled()) { - log.debug("fin Gravite CPUEAction avant"); - } - -/* -writeln("Gravite Action avant metier:"+p.metier+ "date:"+ p.date); -var Chaine=Packages.java.lang.String; - - - -var month=p.date.getMois(); -var allStr = SiMatrice.getListStrategies(); -var newPropDiv=0.0; - -if (!p.CalculCatch){ - var resultmanager=control.getResultatManager(); - - //on commence par creer une matrice de capture par strategie met - var ListePopulation=SiMatrice.getListPopulations(); - pop=ListePopulation.get(0); - var CaptureParStrMet=resultmanager.getMatrix(new Packages.fr.ifremer.nodb.Date(p.date.getDate()-12),pop,"matriceCatchWeightPerStrategyMet"); - CaptureParStrMet=CaptureParStrMet.sumOverDim(3); - CaptureParStrMet=CaptureParStrMet.sumOverDim(2); - writeln(CaptureParStrMet); - for (var ipop=1;ipop<ListePopulation.size();ipop++){ - var pop=ListePopulation.get(ipop); - var temp=resultmanager.getMatrix(new Packages.fr.ifremer.nodb.Date(p.date.getDate()-12),pop,"matriceCatchWeightPerStrategyMet"); - temp=temp.sumOverDim(3); - temp=temp.sumOverDim(2); - writeln(temp); - CaptureParStrMet.add(temp); - writeln(CaptureParStrMet); - } - - var Effort=resultmanager.getMatrix(new Packages.fr.ifremer.nodb.Date(p.date.getDate()-12),"matriceEffortPerStrategyMet"); - writeln("on récupère la matrice d'effort"); - for (var iStrategie=allStr.iterator();iStrategie.hasNext();){ - var Strategie=iStrategie.next(); - var listeMet=Strategie.getSetOfVessels().getMetiers(); - for (imetier=listeMet.iterator();imetier.hasNext();){ - var metier=imetier.next(); - var effort=Effort.getValue(Strategie,metier); - if (effort>0){ - var effortdesc=Strategie.getSetOfVessels().getEffort(metier); - var nombreop=effortdesc.getFishingOperation(); - var nombregear=effortdesc.getGearsNumberPerOperation(); - var param=metier.getValeurParamControlable(); - var facteur=metier.getValeurParamControlable()*nombreop*nombregear/24.0; - //on restandardise l'effort - effort/=facteur; - //on recupere la capture tot - var dim3=new Packages.java.util.ArrayList(CaptureParStrMet.getSemantics(3)); - var dim2=new Packages.java.util.ArrayList(CaptureParStrMet.getSemantics(2)); - - var capture=CaptureParStrMet.getValue(Strategie,metier,dim2.get(0),dim3.get(0)); - - p.CatchperUnitOfEffort.setValue(Strategie,metier,capture/effort); - } - } - } - p.CalculCatch=true; -} - - - -for(var i=0; i<allStr.size(); i++){ - var str = allStr.get(i); - var strMonthInfo = str.getStrategyMonthInfo(month); - var propStrMet = strMonthInfo.getPropStrMetier(p.metier); - - if(str.getSetOfVessels().getMetiers().contains(p.metier)){ -//on verifie que le metier est bien un metier possible - var CPUE=null; - if (!p.SommeCPUEstrat.containsKey(new Chaine(str.getName()))){ - if (GravityModel.getEffortPerStrategyMet(str, p.metier, new Packages.fr.ifremer.nodb.Date(p.date.getDate()-12))>0){ - CPUE=p.CatchperUnitOfEffort.getValue(str,p.metier); - } - } - if (CPUE!=null){ - writeln("on a une CPUE l'année n-1, on la met dans l'historique"); - writeln(strMonthInfo+" "+p.metier); - p.HistoriqueCPUE.put(new Chaine(str.getName()+"-"+p.metier.getNom()+"-"+strMonthInfo.getMonth().getNumMois()),CPUE); - } - else{ - writeln ("ou calcul déjà fait ou pas de CPUE à l'année n-1"); - CPUE=p.HistoriqueCPUE.get(new Chaine(str.getName()+"-"+p.metier.getNom()+"-"+strMonthInfo.getMonth().getNumMois())); - if (CPUE!=null){ - writeln ("on a une CPUE dans le passé: "+CPUE); - } - else{ - writeln ("on a pas de CPUE dans le passé, on remet donc la poportion initiale"); - } - } - if (CPUE!=null) { -//si on a une CPUE, il faut aller voir l'attractivite des autres metiers: 2 cas de figure: -// soit on en retrouve une dans le passe qui est son attractivite -// soit on en retrouve pas et dans ce cas le, la proportion d'effort sera celle initiale de la db -//on a alors newProp=(1-sum(pmet1))*CPUE/somme(CPUEmet2) -//avec pmet1 la proprtion initiale pour les metiers pour lesquels on a pas retrouve de CPUE, CPUEmet2, la CPUE pour les -//metiers qui ont eu une CPUE dans le passe, et CPUE la CPUE du metier courant - if (!p.SommeCPUEstrat.containsKey(str.getName())){ - var SommeCPUE=0; - var PropTot=0; - var metiers=str.getSetOfVessels().getMetiers(); - for (var imetiers=metiers.iterator();imetiers.hasNext();){ - var metier=imetiers.next(); - var temp=null; - if (GravityModel.getEffortPerStrategyMet(str, metier, new Packages.fr.ifremer.nodb.Date(p.date.getDate()-12))>0){ - temp=p.CatchperUnitOfEffort.getValue(str,metier); - } - if (temp!=null){ - writeln("on a une CPUE l'année n-1, on l'ajoute à p.SommeCPUEstrat"); - p.HistoriqueCPUE.put(new Chaine(str.getName()+"-"+metier.getNom()+"-"+strMonthInfo.getMonth().getNumMois()),CPUE); - SommeCPUE+=temp; - } - else{ - writeln ("on a pas de CPUE l'année n-1, on regarde si il y en a dans le passé"); - temp=p.HistoriqueCPUE.get(new Chaine(str.getName()+"-"+metier.getNom()+"-"+strMonthInfo.getMonth().getNumMois())); - if (temp!=null){ - writeln ("on a une CPUE dans le passé: "+temp); - SommeCPUE+=temp; - } - else{ - writeln ("on a pas de CPUE dans le passé, on l'ajoute donc à p.SommeProp"); - PropTot+=strMonthInfo.getProportionMetier(metier); - } - } - } - p.SommeCPUEstrat.put(new Chaine(str.getName()),SommeCPUE); - p.SommeProp.put(new Chaine(str.getName()),PropTot); - } - if (p.SommeCPUEstrat.get(new Chaine(str.getName()))>0){ - newPropDiv = (p.SommePropInitial.get(new Chaine(str.getName()+"-"+strMonthInfo.getMonth().getNumMois()))-p.SommeProp.get(new Chaine(str.getName())))*CPUE/ p.SommeCPUEstrat.get(new Chaine(str.getName())); - writeln("newpropdiv: "+newPropDiv); - strMonthInfo.setProportionMetier(p.metier, new Packages.java.lang.Float(newPropDiv)); - } - else { // c'est le cas e priori quasi impossible oe y a toujours eu une CPUE nulle quelquesoit le metier, dans ce cas le on remet aussi la prop iniitiale - writeln("aucun metier n'a d'attractivite, on remet la prop initiale"); - } - } - } -} - -writeln("fin Gravite CPUEAction avant"); -return p.gestionMetier; -*/ - } - - /** - * Si la condition est vrai alors cette action est executée apres le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { - SommeCPUEstrat.map(nanFunction); - SommeProp.map(nanFunction); - catchPerUnitOfEffort.map(nanFunction); - } - -} Added: isis-fish/trunk/src/test/resources/test-database/rules/GraviteVPUE1.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/GraviteVPUE1.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/rules/GraviteVPUE1.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,291 @@ +package rules; + +import static org.codelutin.i18n.I18n._; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import scripts.ResultName; +import scripts.SiMatrix; + +import java.util.Arrays; +import java.util.List; +import java.util.Collection; + +import org.codelutin.math.matrix.*; + +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.rule.AbstractRule; +import fr.ifremer.isisfish.datastore.ResultStorage; + +/** + * GraviteVPUE1.java + * + * Created: 26 aout 2008 + * + * @author anonymous <anonymous at labs.libre-entreprise.org> + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author: 2SY- Sigrid+Youen+Stephanie $ + */ +public class GraviteVPUE1 extends AbstractRule { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(GraviteVPUE1.class); + + /** stocke la somme des prop initiales [str x month] */ + private MatrixND SommePropInitial = null; + /** stocke par strat*met, la dernière attractivite pour chaque mois [str x met x month] */ + + /** permet de stocker les CPUE nominales [str x met] */ + private MatrixND valuePerUnitOfEffort = 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, + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + //ResultName.MATRIX_EFFORT_PER_STRATEGY_MET, + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET, // garder la , + + }; + + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + /** + * Permet d'afficher a l'utilisateur une aide sur la regle. + * @return L'aide ou la description de la regle + */ + public String getDescription() throws Exception { + return _("Calcule les proportion par métier chaque mois en fonction de la VPUE du métier l'année précédante"); + /*"HYPOTHESES GRAVITE" + " attention cette règle doit toujours être mise avant les mesures de gestion"+ + " si pour un metier Effort (métier annee-1,mois) = 0 et propinitiale (métier, mois) !=0 (ie métier potentiellement pratiqué), alors "+ + on remet propInitiale pour tous les métiers (premiere vue complete pour tous les metiers de la strategie - graviteVPUE1-, une alternative + pourrait être de chercher lapremiere année avant année -1 pour laquelle le métier, ayant une propInitiale non nulle , aurait une VPUE (metier,mois) non nulle + et recuperer la propStr (metier,mois) pour cette année et on l'affecte année courante - mois, les autres métiers se partageant la proportion d'effort restante + en fonction de leur VPUE - graviteVPUE2-, une alternative pourrait etre de chercher la premiere année avant année -1 pour laquelle tous les métiers, + ayant une propInitiale non nulle, auraient eu une propStr non nulle, (surement difficile à trouver) - - graviteVPUE3- d'autres hypothèses pourraient etre envisagées) + "*/ + } + + /** + * function used to initialise MatrixND to NaN double + */ + private MapFunction nanFunction = new MapFunction() { + public double apply(double value) { + return Double.NaN; + } + }; + + /** + * Appelé au démarrage de la simulation, cette méthode permet d'initialiser + * des valeurs + * @param context La simulation pour lequel on utilise cette regle + */ + public void init(SimulationContext context) throws Exception { + Date date = new Date(0); + + List<Strategy> strs = SiMatrix.getSiMatrix(context).getStrategies(date); + List<Metier> metiers = SiMatrix.getSiMatrix(context).getMetiers(date); + List<Month> months = Arrays.asList(Month.MONTH); + + SommePropInitial = MatrixFactory.getInstance().create( + "SommePropInitial", new List[] { strs, months }, + new String[] { "Strategies", "Months" }); + SommePropInitial.map(nanFunction); + + valuePerUnitOfEffort = MatrixFactory.getInstance().create( + "ValuePerUnitOfEffort", new List[] { strs, metiers }, + new String[] { "Strategies", "Metiers" }); + valuePerUnitOfEffort.map(nanFunction); + + for (Strategy str : strs) { + List<Metier> strMetiers = SiMatrix.getSiMatrix(context).getMetiers( + str, date); + List<StrategyMonthInfo> infos = str.getStrategyMonthInfo(); + for (StrategyMonthInfo info : infos) { + double somme = 0; + for (Metier strMetier : strMetiers) { + somme += info.getProportionMetier(strMetier); + } + // FIXME soit on somme pour toutes les str le meme metier; donc pas de notion de str.getName dans la cle + // soit pour une str on somme tous ces metiers (mais ce doit etre 1; donc pas de notion de metier.getName dans la cle + SommePropInitial.setValue(str, info.getMonth(), somme); + } + } + + } + + /** + * La condition qui doit etre vrai pour faire les actions + * @param context La simulation pour lequel on utilise cette regle + * @return vrai si on souhaite que les actions soit faites + */ + public boolean condition(SimulationContext context, Date date, Metier metier) + throws Exception { + // Il faut etre au moins au deuxieme pas de temps. + return date.getYear() > 0; + } + + // Booleen permettant que ne boucler que sur un seul metier dans la preaction : + boolean first = true; + + /** + * Si la condition est vrai alors cette action est executée avant le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { + if (log.isDebugEnabled()) { + log.debug("first = " + first + "date:" + date); + } + System.out.println("first = " + first + + " ,on passe dans la preaction ?"); + if (first) { // on passe dans preaction pour la premiere fois + System.out.println("Oui, preaction : "); + + List<Strategy> strs = SiMatrix.getSiMatrix(context).getStrategies( + date); + //List<Population> populations = SiMatrix.getSiMatrix(context) + // .getPopulations(date); + ResultStorage resultmanager = context.getSimulationStorage() + .getResultStorage(); + + ////////Initialisation des matrices qui resultent de la simulation//////////////////////////////////////////////////////////// + + //Calcul de l effort nominal par strategy met + MatrixND EffortNominalPerStrMet = null; + EffortNominalPerStrMet = resultmanager.getMatrix(date + .previousYear(), + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET); + System.out.println("EffortNominalPerStrMet calculee " + + EffortNominalPerStrMet); + + //on commence par creer une matrice de valeurs (somme sur ttes les especes capturees) par strategie met + MatrixND GrossValuePerStrMet = null; + GrossValuePerStrMet = resultmanager.getMatrix(date.previousYear(), + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET); + + System.out.println("GrossValuePerStrMet calculee " + + GrossValuePerStrMet); + + //ajouter pour tous les métiers les valeurs liées qux autres espèces calculées par modele lineaire + + ////////////////////////////////////////////////////////////////////////////////////////////////////////// + valuePerUnitOfEffort.map(nanFunction); //réinitialisation avant calcul pour date + + for (Strategy str : strs) { + System.out + .println("INFO: Boucle creation valuePerUnitEffort : " + + str.getName()); + // log.info("Boucle creation catchperuniteffort : "+ str.getName()); + StrategyMonthInfo smi = str.getStrategyMonthInfo(date + .getMonth()); + Collection<EffortDescription> strMet = str.getSetOfVessels() + .getPossibleMetiers(); + //SiMatrix.getSiMatrix(context).getMetiers(str, date); + + // boucle pour tester s'il existe un metier pour lequel effort(metier)=0 et PropInitiale(metier)=0 (Condition) + boolean testCondition = false; + double somme = 0;//initialisation de la somme des VPUE des metiers de la strategie + for (EffortDescription ed : strMet) { + Metier strMetier = ed.getPossibleMetiers(); + System.out.println("Pour str=" + str.getName() + + " et metier=" + strMetier.getName()); + double effort = EffortNominalPerStrMet.getValue(str, + strMetier); + // on teste effort pour le calcul des VPUE + // si effort != 0 , valeur/effort + //sinon (effort =0) , deux cas de figure : + // 1. soit propInitiale =0 pour ce métier et dans ce cas VPUE =0 et ca ne doit pas impacter le calcul de la gravite pour les autres metiers de str + // 2. soit propInitiale! =0 et dans ce cas, on mettra PropInitiale pour tous les metiers de str + if (effort > 0) {// a peché au mois, annee-1 + //on recupere la capture tot + double value = GrossValuePerStrMet.getValue(str, + strMetier); + System.out.println("DEBUG: value : " + value); + System.out.println("DEBUG: effort : " + effort); + double vpue = value / effort; + valuePerUnitOfEffort.setValue(str, strMetier, vpue); + System.out.println("value/effort= " + vpue); + somme += value / effort; + } else if ((effort == 0) + & (smi.getProportionMetier(strMetier) == 0)) {// n'a jamais pêche avec ce metier + valuePerUnitOfEffort.setValue(str, strMetier, 0); + System.out.println("n'a jamais pêche avec ce metier"); + } else {// n'a pas peche au mois, annee -1, mais avait une prop d'effort non nul a l'annee=0 + testCondition = true;// ie somme est incomplète mais pas grave car on mettra PropInitiale à tous les metiers + System.out.println("n'a pas peche au mois, annee -1, mais avait une prop d'effort non nul a l'annee=0"); + } + } + System.out.println("testCondition pour str" + str.getName() + + ":" + testCondition); + // A partir des VPUE stockees dans valuePerUnitOfEffort, on calcule la gravité + double newProp = 0; + System.out + .println("A partir des VPUE stockees dans valuePerUnitOfEffort, on calcule la gravité"); + if (!testCondition) { + double SommeVPUEstrat = somme; + System.out.println("SommeVPUEstrat=" + SommeVPUEstrat); + for (EffortDescription ed : strMet) { + Metier strMetier = ed.getPossibleMetiers(); + System.out.println("PropStrInitiale(metier=" + + strMetier.getName() + ")" + + smi.getProportionMetier(strMetier)); + System.out.println("SommePropInitial.getValue(str, date.getMonth()=" + + SommePropInitial.getValue(str, date + .getMonth())); + System.out.println("valuePerUnitOfEffort.getValue(str, strMetier)" + + valuePerUnitOfEffort.getValue(str, + strMetier)); + if (SommeVPUEstrat == 0) { + newProp = 0; + } else { + newProp = SommePropInitial.getValue(str, date + .getMonth()) + * valuePerUnitOfEffort.getValue(str, + strMetier) / SommeVPUEstrat; + } + System.out.println("newProp(metier=" + + strMetier.getName() + ")" + newProp); + smi.setProportionMetier(strMetier, newProp); + System.out.println("PropStrNouvelle(metier=" + + strMetier.getName() + ")" + + smi.getProportionMetier(strMetier)); + } + } + // else ie on met propInitiale dans PropStr(str,annee,mois) + // rien n'a faire car au debut de chaque pas de temps, PropStr + // est par défaut initialisé à la valeur de la base de données (val initiales) + + }//fin de boucle sur strategy + + first = false; + + }// fin de first= true + + if (log.isDebugEnabled()) { + log.debug("fin Gravite CPUEAction avant"); + } + + } + + /** + * Si la condition est vrai alors cette action est executée apres le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void postAction(SimulationContext context, Date date, Metier metier) + throws Exception { + first = true; + } +} Property changes on: isis-fish/trunk/src/test/resources/test-database/rules/GraviteVPUE1.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Modified: isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEngin.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEngin.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEngin.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,7 +1,6 @@ package rules; import static org.codelutin.i18n.I18n._; -import static org.codelutin.i18n.I18n.n_; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -9,7 +8,6 @@ import scripts.ResultName; import scripts.SiMatrix; -import java.io.Writer; import java.util.ArrayList; import java.util.Iterator; import java.util.List; @@ -22,9 +20,6 @@ import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.rule.AbstractRule; -import fr.ifremer.isisfish.datastore.RegionStorage; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) @@ -44,13 +39,13 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(InterdictionEngin.class); - @Doc(value="do the doc of param gear") + @Doc(value="Prohibited gear") public Gear param_gear = null; - @Doc(value="do the doc of param beginDate") + @Doc(value="Begin date") public Date param_beginDate = new Date(0); - @Doc(value="do the doc of param endDate") + @Doc(value="End date") public Date param_endDate = new Date(119); - @Doc(value="do the doc of param beginMonth") + @Doc(value="Begin month") public Month param_beginMonth = Month.JANUARY; @Doc(value="do the doc of param endMonth") public Month param_endMonth = Month.DECEMBER; @@ -71,20 +66,22 @@ * @return L'aide ou la description de la regle */ public String getDescription() throws Exception { + // interdiction des metiers utilisant cet engin return _("Prohibited gear"); } /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { - // TODO + // nothing } + /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { @@ -133,7 +130,7 @@ /** * Si la condition est vrai alors cette action est executée avant le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { log.info("le metier vise par l'interdiction : " + metier); @@ -158,12 +155,12 @@ // 1er cas:l'effort est reporte sur un metier de la meme strategie, // n'ayant pas l'espece comme capture principale et pechant avec le meme engin - List<EffortDescription> MetiersPossibles= new ArrayList<EffortDescription>(Strat.getSetOfVessels().getPossibleMetiers()); + List<EffortDescription> MetiersPossibles = new ArrayList<EffortDescription>(Strat.getSetOfVessels().getPossibleMetiers()); // on verifie que les metiers sont bien pratiques au mois courant, // qu'ils n'ont pas le meme engin et qu'ils ne sont pas // interdits par ailleurs - for (Iterator<EffortDescription> effort=MetiersPossibles.iterator(); effort.hasNext();) { + for (Iterator<EffortDescription> effort = MetiersPossibles.iterator(); effort.hasNext();) { Metier met = effort.next().getPossibleMetiers(); if (StratMonthInfo.getProportionMetier(met) == 0 || met.getGear().equals(metier.getGear()) @@ -187,7 +184,7 @@ StratMonthInfo.setProportionMetier(metier, 0); //le metier vise a alors une proportion nulle } // s'il n'y a pas de metier alternatif, on passe a nonActivite - else{ + else { MatrixND matNonActivite = metierMon.getOrCreateNoActivity(date, ResultName.MATRIX_NO_ACTIVITY, siMatrix.getStrategies(date), @@ -270,7 +267,7 @@ /** * Si la condition est vrai alors cette action est executée apres le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { // nothing Modified: isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEnginPreSimu.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEnginPreSimu.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/InterdictionEnginPreSimu.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -8,7 +8,6 @@ import scripts.ResultName; -import java.io.Writer; import java.util.ArrayList; import java.util.HashMap; import java.util.Iterator; @@ -24,13 +23,11 @@ import fr.ifremer.isisfish.entities.*; import fr.ifremer.isisfish.rule.AbstractRule; import fr.ifremer.isisfish.datastore.RegionStorage; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) /** - * InterdictionEngin.java + * InterdictionEnginPreSimu. * * Created: 30 novembre 2006 * @@ -77,13 +74,13 @@ /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { MetierMonitor metierMon = context.getMetierMonitor(); - Month moisDeb = param_beginMonth; - Month moisFin = param_endMonth; + //Month moisDeb = param_beginMonth; + //Month moisFin = param_endMonth; Gear EnginInterdit = param_gear; log.info("nom de l'engin interdit "+EnginInterdit.getName()); @@ -224,7 +221,7 @@ } /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { @@ -251,7 +248,7 @@ /** * Si la condition est vrai alors cette action est executée avant le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { // on ne doit le faire qu'une seul fois quelque soit le nombre de metier @@ -261,10 +258,10 @@ MetierMonitor metierMon = context.getMetierMonitor(); MatrixND noActivity = metierMon.getNoActivity(date); - if (noActivity == null){ + if (noActivity == null) { metierMon.setNoActivity(date, mat.copy()); } - else{ + else { noActivity = noActivity.add(mat); } // fin @@ -287,7 +284,7 @@ /** * Si la condition est vrai alors cette action est executée apres le pas * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { affectNonActivite = false; Deleted: isis-fish/trunk/src/test/resources/test-database/rules/RecrutementLangoustine.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/RecrutementLangoustine.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/RecrutementLangoustine.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,184 +0,0 @@ -package rules; - -import static org.codelutin.i18n.I18n._; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import scripts.ResultName; - -import java.io.Writer; - -import org.codelutin.math.matrix.*; -import org.codelutin.topia.TopiaContext; -import org.codelutin.util.StringUtil; - -import fr.ifremer.isisfish.IsisFishDAOHelper; -import fr.ifremer.isisfish.simulator.PopulationMonitor; -import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.entities.*; -import fr.ifremer.isisfish.rule.AbstractRule; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; - -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - -/** - * RecrutementLangoustine.java - * - * Created: 22 mars 2007 - * - * @author stephanie MAHEVAS <smahevas at ifremer.fr> - * @version $Revision: 1.1 $ - * - * Last update: $Date: 2007-03-22 17:33:56 $ - * by : $Author: bpoussin $ - */ -public class RecrutementLangoustine extends AbstractRule { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(RecrutementLangoustine.class); - - @Doc(value="do the doc of param recrut1998") - public double param_recrut1998 =0; - @Doc(value="do the doc of param recrut1999") - public double param_recrut1999 =0; - @Doc(value="do the doc of param recrut2000") - public double param_recrut2000 =0; - @Doc(value="do the doc of param recrut2001") - public double param_recrut2001 =0; - @Doc(value="do the doc of param recrut2002") - public double param_recrut2002 =0; - @Doc(value="do the doc of param recrut2003") - public double param_recrut2003 =0; - @Doc(value="do the doc of param recrut2004") - public double param_recrut2004 =0; - @Doc(value="do the doc of param recrut2005") - public double param_recrut2005 =0; - - public double [] recru = 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 la regle. - * @return L'aide ou la description de la regle - */ - public String getDescription() throws Exception { - // TODO - return _("TODO description rule"); - } - - /** - * Appelé au démarrage de la simulation, cette méthode permet d'initialiser - * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void init(SimulationContext context) throws Exception { - // remarque on pourrait aussi avoir un seul parametre de regle - // par exemple param_recru_depuis_1998 = "0;0;0;0;0;0;0;0"; - // on ferait alors - // recru = StringUtil.toArrayDouble(param_recru_depuis_1998.split(";")); - - recru = new double[]{ - param_recrut1998, - param_recrut1999, - param_recrut2000, - param_recrut2001, - param_recrut2002, - param_recrut2003, - param_recrut2004, - param_recrut2005, - }; - } - /** - * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle - * @return vrai si on souhaite que les actions soit faites - */ - public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { - boolean result = false; - if (date.getMonth().equals(Month.SEPTEMBER) || - date.getMonth().equals(Month.OCTOBER) - || date.getMonth().equals(Month.NOVEMBER) - ||date.getMonth().equals(Month.DECEMBER)) { - result = true; - } - return result; -/* -writeln("recrutement CIEM"); -var mois = p.date.getMois().getNumMois(); -//si le recrutement a lieu en octobre -if( mois==8 ||mois==9 || mois==10 || mois==11){ -//??&& p.oprfaite==false{ -var result = true; -} - return result ; -*/ - - } - - /** - * Si la condition est vrai alors cette action est executée avant -le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { - TopiaContext db = context.getDB(); - - PopulationDAO popDao = IsisFishDAOHelper.getPopulationDAO(db); - Population pop = popDao.findByName("nephrops"); - PopulationGroup group0 = pop.getPopulationGroup().get(0); - - ZoneDAO zoneDao = IsisFishDAOHelper.getZoneDAO(db); - Zone zone1 = zoneDao.findByName("zone L21E7"); - Zone zone2 = zoneDao.findByName("zone L21E8"); - Zone zone3 = zoneDao.findByName("zone L22E6"); - Zone zone4 = zoneDao.findByName("zone L22E7"); - Zone zone5 = zoneDao.findByName("zone L23E5"); - Zone zone6 = zoneDao.findByName("zone L23E6"); - Zone zone7 = zoneDao.findByName("zone L23E7"); - Zone zone8 = zoneDao.findByName("zone L24E5"); - Zone zone9 = zoneDao.findByName("zone L24E6"); - - int year = date.getYear(); - MatrixND matN = context.getPopulationMonitor().getN(pop); - - double coefR =4/(Math.exp(-0.6/12))*(1+ Math.exp(-0.3/12)+ Math.exp(-0.6/12)+ Math.exp(-0.9/12)); - - double R = recru[year] * coefR / 9.0; - - matN.setValue(group0, zone1, R); - matN.setValue(group0, zone2, R); - matN.setValue(group0, zone3, R); - matN.setValue(group0, zone4, R); - matN.setValue(group0, zone5, R); - matN.setValue(group0, zone6, R); - matN.setValue(group0, zone7, R); - matN.setValue(group0, zone8, R); - matN.setValue(group0, zone9, R); - - } - - /** - * Si la condition est vrai alors cette action est executée apres le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle - */ - public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { - // TODO - } - -} \ No newline at end of file Modified: isis-fish/trunk/src/test/resources/test-database/rules/TACpoids.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/TACpoids.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/TACpoids.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,21 +1,19 @@ package rules; +import static org.codelutin.i18n.I18n._; + import java.util.HashSet; -import java.util.List; import java.util.Set; -import static org.codelutin.i18n.I18n._; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixFactory; import org.codelutin.math.matrix.MatrixIterator; import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; import scripts.RuleUtil; import scripts.SiMatrix; - +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.entities.EffortDescription; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; @@ -29,107 +27,112 @@ import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.util.Doc; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** - * TAC.java - * + * TAC peut-etre utilise pour les differents TAC, en proportion des effectifs + * et/ou avec survie ou non. + * + * <li>Pour utiliser le tac proportionnel, il faut mettre dans le parametre + * propTac une valeur > 0, le TAC sera alors recalcule a chaque mois de janvier. + * <li>Pour utiliser la survie il faut mettre dans le parametre propSurvie une + * valeur > 0, automatiquement les suvie seront ajoute aux effectifs + * * Created: 7 septembre 2006 * * @author anonymous <anonymous at labs.libre-entreprise.org> - * @version $Revision: 1.5 $ + * @version $Revision: 1.3 $ * - * Last update: $Date: 2007-11-20 15:50:09 $ - * by : $Author: bpoussin $ + * Last update: $Date: 290607 $ + * by : $Author: sigrid $ */ - -/** - * TAC peut-etre utilisé pour les différents TAC, en proportion des effectifs - * et/ou avec survie ou non. - * - * <li>Pour utiliser le tac proportionnel, il faut mettre dans le parametre propTac - * une valeur > 0, le TAC sera alors recalculé a chaque mois de janvier. - * <li>Pour utiliser la survie il faut mettre dans le paramètre propSurvie - * une valeur > 0, automatiquement les suvie seront ajouté aux effectifs - * - */ public class TACpoids extends AbstractRule { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(TACpoids.class); - @Doc(value="do the doc of param species") + @Doc("Affected species") public Species param_species = null; - @Doc(value="do the doc of param beginDate") + @Doc("Debin date") public Date param_beginDate = new Date(0); - @Doc(value="do the doc of param endDate") - public Date param_endDate = new Date(22); - @Doc(value="do the doc of param propSurvie") + @Doc("End date") + public Date param_endDate = new Date(90); + @Doc("Proportion de survie") public double param_propSurvie = 0; - @Doc(value="do the doc of param propTac") + @Doc("Proportionnal TAC") public double param_propTac = 0; - /** TAC in tonne */ - public double param_tacInTons = 0; - + /** TAC in tonnes */ + @Doc("TAC in tons") + public double param_tacInTons = 900; + boolean affectation = false; - - protected String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + + protected String[] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; - + /** * @return the necessaryResult */ public String[] getNecessaryResult() { return this.necessaryResult; } - + /** * Permet d'afficher a l'utilisateur une aide sur la regle. + * * @return L'aide ou la description de la regle */ public String getDescription() { - return _("TAC weight in tons.\nIf you want survival discard use propSurvie other than 0.\nIf you wish TAC computed use propTac other than 0."); + return _("TAC weight in tons.\nIf you want survival discard use propSurvie other than 0.\nIf you wish TAC computed as a proportion of the biomass use propTac other than 0."); } - + /** - * Appelé au démarrage de la simulation, cette méthode permet d'initialiser + * Appele au demarrage de la simulation, cette methode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * + * @param context La simulation pour lequel on utilise cette regle */ - public void init(SimulationContext context) throws Exception { + public void init(SimulationContext context) throws Exception { } - + /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ - public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { + public boolean condition(SimulationContext context, Date date, Metier metier) + throws Exception { + + log.info("test si TAC atteint"); // read species in current session - param_species = (Species)context.getDB().findByTopiaId(param_species.getTopiaId()); - - // on fait le calcul du tac si nécessaire - if (param_propTac > 0 && date.getMonth().equals(Month.JANUARY)){ + param_species = (Species) context.getDB().findByTopiaId( + param_species.getTopiaId()); + + // on fait le calcul du tac si necessaire + if (param_propTac > 0 && date.getMonth().equals(Month.JANUARY)) { PopulationMonitor popMon = context.getPopulationMonitor(); param_tacInTons = popMon.getBiomass(param_species) * param_propTac; - } - + } + boolean result = false; - if(date.before(param_beginDate)) { + if (date.before(param_beginDate)) { result = false; - } else if(date.after(param_endDate)) { - result = false; + } else if (date.after(param_endDate)) { + result = false; } else { - TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()).getSpeciesTargetSpecies(param_species); + TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()) + .getSpeciesTargetSpecies(param_species); if (ts != null) { - double catchTons = RuleUtil.getTotalCatchTons(context, param_species, date); - log.info("[TAC] catchTons = " + catchTons + " >= param_tacInTons:" + param_tacInTons ); + double catchTons = RuleUtil.getTotalCatchTons(context, + param_species, date); + log.info("[TAC] catchTons = " + catchTons + + " >= param_tacInTons:" + param_tacInTons); if (catchTons >= param_tacInTons) { result = true; } @@ -137,39 +140,46 @@ } return result; } - + /** - * Si la condition est vrai alors cette action est executée avant le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * Si la condition est vrai alors cette action est executee avant le pas de + * temps de la simulation. + * + * @param context La simulation pour lequel on utilise cette regle */ - public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { affectation = false; + log.info("[TAC] preAction for: " + metier); - - TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()).getSpeciesTargetSpecies(param_species); - if(ts != null && ts.getPrimaryCatch()) { + log.info(" TAC atteint [TAC] preAction for: " + metier); + TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()) + .getSpeciesTargetSpecies(param_species); + if (ts != null && ts.getPrimaryCatch()) { // recupere tous les metiers qui ont l'espece en capture principale =>metiers vises - List<Metier> aimedMetiers = context.getDB().find("select distinct(metierSeasonInfo.metier) " + - "from fr.ifremer.isisfish.entities.TargetSpecies " + - "where species=? and primaryCatch=true", param_species); + // aimedMetiers ne fonctionne pas je ne sais pas pourquoi ! mais au final forbiddenMetier aura le meme effet + /*List<Metier> aimedMetiers = context.getDB().find("select distinct(metierSeasonInfo.metier) " + + "from fr.ifremer.isisfish.entities.TargetSpecies" + + "where species=? and primaryCatch=true", param_species); - log.info("aimed Metier: " + aimedMetiers); + log.info("aimed Metier: " + aimedMetiers);*/ context.getMetierMonitor().addforbiddenMetier(metier); - - //récupere toutes les stratégies pratiquant le métier et pour lesquelles la proportion !=0 + + //recupere toutes les strategies pratiquant le metier et pour lesquelles la proportion !=0 SiMatrix siMatrix = SiMatrix.getSiMatrix(context); Set<Strategy> strs = new HashSet<Strategy>(); for (Strategy str : siMatrix.getStrategies(date)) { - double prop = str.getStrategyMonthInfo(date.getMonth()).getProportionMetier(metier); + double prop = str.getStrategyMonthInfo(date.getMonth()) + .getProportionMetier(metier); if (prop != 0) { strs.add(str); } } - - for (Strategy str : strs){ - StrategyMonthInfo smi = str.getStrategyMonthInfo(date.getMonth()); - + + for (Strategy str : strs) { + StrategyMonthInfo smi = str.getStrategyMonthInfo(date + .getMonth()); + // 1er cas de figure: l'effort est reporte sur un metier de la // meme strategie, n'ayant pas l'espece comme capture principale // et pechant avec le meme engin @@ -181,35 +191,38 @@ // sans consideration sur les engins, et pour lesquels la // proportion peut etre nulle Set<Metier> possibleMetierCase3 = new HashSet<Metier>(); - - for (EffortDescription effort : str.getSetOfVessels().getPossibleMetiers()) { + + for (EffortDescription effort : str.getSetOfVessels() + .getPossibleMetiers()) { Metier newMetier = effort.getPossibleMetiers(); if ( - !aimedMetiers.contains(newMetier) - && !metier.getName().equalsIgnoreCase("nonActiviy") + /*!aimedMetiers.contains(newMetier) + &&*/!metier.getName().equalsIgnoreCase("nonActiviy") && !metier.getName().equalsIgnoreCase("nonActivie") - && !context.getMetierMonitor().getForbiddenMetier().contains(newMetier) - ) { + && !metier.getName().equalsIgnoreCase( + "non Activite") + && !context.getMetierMonitor().getForbiddenMetier() + .contains(newMetier)) { possibleMetierCase3.add(newMetier); - + if (smi.getProportionMetier(newMetier) != 0) { possibleMetierCase2.add(newMetier); - + if (metier.getGear().equals(newMetier.getGear())) { possibleMetierCase1.add(newMetier); } } } } - + Set<Metier> possibleMetier = null; - if (possibleMetierCase1.size() != 0){ + if (possibleMetierCase1.size() != 0) { log.info("[TAC] Use case 1"); possibleMetier = possibleMetierCase1; } else if (possibleMetierCase2.size() != 0) { log.info("[TAC] Use case 2"); possibleMetier = possibleMetierCase2; - } else if (possibleMetierCase3.size() != 0){ + } else if (possibleMetierCase3.size() != 0) { log.info("[TAC] Use case 3"); possibleMetier = possibleMetierCase3; } @@ -219,46 +232,51 @@ // possibles dans la meme strategie si un metier possible existe // bien la repartion est proportionnelle a l'effort deja alloue // dans la strategie - - double somme=0; - for (Metier met : possibleMetierCase1) { + + double somme = 0; + for (Metier met : possibleMetier) { somme += smi.getProportionMetier(met); } - for (Metier met : possibleMetierCase1) { - double newProportion = - smi.getProportionMetier(met) - + (smi.getProportionMetier(metier) - * smi.getProportionMetier(met) / somme); + for (Metier met : possibleMetier) { + double newProportion = smi.getProportionMetier(met) + + (smi.getProportionMetier(metier) + * smi.getProportionMetier(met) / somme); smi.setProportionMetier(met, newProportion); } - smi.setProportionMetier(metier, 0); //le metier vise a alors une proportion nulle - } else{ + smi.setProportionMetier(metier, 0); //le metier vise a alors une proportion nulle + log.info("[TAC] il y a des metiers possibles"); + } else { log.info("[TAC] Use no activity"); - + // sinon on met tout dans le metier nonActivite MetierMonitor metierMon = context.getMetierMonitor(); MatrixND mat = metierMon.getOrCreateNoActivity(date, - ResultName.MATRIX_NO_ACTIVITY, - siMatrix.getStrategies(date), - siMatrix.getMetiers(date)); + ResultName.MATRIX_NO_ACTIVITY, siMatrix + .getStrategies(date), siMatrix + .getMetiers(date)); mat.setValue(str, metier, smi.getProportionMetier(metier)); - + smi.getProportionMetier().setValue(metier, 0); - } + } } } } - + /** - * Si la condition est vrai alors cette action est executée apres le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * Si la condition est vrai alors cette action est executee apres le pas de + * temps de la simulation. + * + * @param context La simulation pour lequel on utilise cette regle */ - public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { + public void postAction(SimulationContext context, Date date, Metier metier) + throws Exception { + ResultStorage resultmanager = context.getSimulationStorage() + .getResultStorage(); log.info("[TAC] postAction for: " + metier); - TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()).getSpeciesTargetSpecies(param_species); - if(ts != null){ - if (!affectation){ + TargetSpecies ts = metier.getMetierSeasonInfo(date.getMonth()) + .getSpeciesTargetSpecies(param_species); + if (ts != null) { + if (!affectation) { // ATTENTION // les captures pour cette metapop ne sont plus du qu'au metier // pour qui l'espece est secondaire: elles sont affectees aux @@ -270,36 +288,46 @@ // pour les captures) ////// PopulationMonitor popMon = context.getPopulationMonitor(); + log.info("popMon biomass" + popMon.getBiomass(param_species)); for (Population pop : param_species.getPopulation()) { - // si on a deja une matrice rejet on le vide (elle vient - // forcement de la regle taille minimale or si le tac est - // atteint, tout va dorenavent dans les rejets et on mais - // TOUTES les captures dans les rejets - MatrixND discard = popMon.getDiscard(date, pop); - if (discard != null) { - discard.mults(0); - } - - discard = popMon.getCatch(pop).copy(); - discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET); - popMon.addDiscard(date, pop, discard); - log.info("[TAC] add discard for " + pop + ": " + discard); - - if (param_propSurvie > 0) { - MatrixND eff = popMon.getN(pop); - //on réajoute les survivants aux effectifs - for (MatrixIterator i=discard.iterator(); i.next();){ - Object [] coord = i.getSemanticsCoordinates(); - eff.setValue(coord[2],coord[3], - eff.getValue(coord[2],coord[3])+i.getValue()*param_propSurvie); + if (!pop.getName().equals("Population_new")) { + log.info("pop : " + pop.getName()); + // si on a deja une matrice rejet on le vide (elle vient + // forcement de la regle taille minimale or si le tac est + // atteint, tout va dorenavent dans les rejets et on mais + // TOUTES les captures dans les rejets + MatrixND discard = popMon.getDiscard(date, pop); + log.info("discard : " + discard); + if (discard != null) { + discard.mults(0); } + log.info("catch = " + popMon.getCatch(pop)); + discard = popMon.getCatch(pop).copy(); + // ca ne doit pas pouvoir marcher car MATRIX_DISCARDS_PER_STR_MET est de dimension pop groupe str met - et discard n'a plus la dimension pop + discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); + popMon.addDiscard(date, pop, discard); + log.info("[TAC] add discard for " + pop + ": " + + discard); + // ne manquerait-il pas + resultmanager.addResult(date, pop, discard); + if (param_propSurvie > 0) { + MatrixND eff = popMon.getN(pop); + //on réajoute les survivants aux effectifs + for (MatrixIterator i = discard.iterator(); i + .next();) { + Object[] coord = i.getSemanticsCoordinates(); + eff.setValue(coord[2], coord[3], eff.getValue( + coord[2], coord[3]) + + i.getValue() * param_propSurvie); + } + } + } + // on a affecte une fois cette meta pop au rejet il ne faut pas + // le refaire + affectation = true; } - - // on a affecte une fois cette meta pop au rejet il ne faut pas - // le refaire - affectation=true; } } } Modified: isis-fish/trunk/src/test/resources/test-database/rules/TailleMin.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/TailleMin.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/rules/TailleMin.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -2,30 +2,30 @@ import static org.codelutin.i18n.I18n._; +import java.util.List; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; import scripts.SiMatrix; - -import java.io.Writer; -import java.util.List; - -import org.codelutin.math.matrix.*; - +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.MetierSeasonInfo; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Species; +import fr.ifremer.isisfish.entities.TargetSpecies; +import fr.ifremer.isisfish.rule.AbstractRule; import fr.ifremer.isisfish.simulator.PopulationMonitor; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.entities.*; -import fr.ifremer.isisfish.rule.AbstractRule; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.util.Doc; -import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) - /** - * TailleMin.java - * + * Cette methode remplace aussi TailleMinSurvieRejet si propSurvie est > 0 + * * Created: 30 novembre 2006 * * @author anonymous <anonymous at labs.libre-entreprise.org> @@ -34,27 +34,23 @@ * Last update: $Date: 2007-01-24 18:25:34 $ * by : $Author: bpoussin $ */ - -/** - * Cette methode remplace aussi TailleMinSurvieRejet si propSurvie est > 0 - */ public class TailleMin extends AbstractRule { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(TailleMin.class); - @Doc(value="do the doc of param beginDate") + @Doc(value = "Begin date") public Date param_beginDate = new Date(0); - @Doc(value="do the doc of param endDate") + @Doc(value = "End date") public Date param_endDate = new Date(119); - @Doc(value="do the doc of param species") + @Doc(value = "Affected species") public Species param_species = null; - @Doc(value="do the doc of param TailleMin") + @Doc(value = "Taille minimale") public double param_TailleMin = 27; - @Doc(value="do the doc of param propSurvie") + @Doc(value = "Proportion de survie") public double param_propSurvie = 0; - public String [] necessaryResult = { + public String[] necessaryResult = { // put here all necessary result for this rule // example: // ResultName.MATRIX_BIOMASS, @@ -67,21 +63,22 @@ /** * Permet d'afficher a l'utilisateur une aide sur la regle. + * * @return L'aide ou la description de la regle */ public String getDescription() throws Exception { - // TODO - return _("TODO description rule"); + return _(""); } - + /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { } - + /** * @param context * @param date @@ -93,16 +90,18 @@ MetierSeasonInfo info = metier.getMetierSeasonInfo(date.getMonth()); TargetSpecies target = info.getSpeciesTargetSpecies(species); boolean result = target != null; - + return result; } - + /** * La condition qui doit etre vrai pour faire les actions - * @param simulation La simulation pour lequel on utilise cette regle + * + * @param context La simulation pour lequel on utilise cette regle * @return vrai si on souhaite que les actions soit faites */ - public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception { + public boolean condition(SimulationContext context, Date date, Metier metier) + throws Exception { log.info("Recherche si la taille Minimale s'applique"); boolean result = true; if (date.before(param_beginDate)) { @@ -110,56 +109,62 @@ } else if (date.after(param_endDate)) { result = false; } else if (isCaptureDate(date, param_species, metier) != true) { - result=false; + result = false; } log.info("fin de condition TailleMin:" + result); return result; - + // fin - + /* -writeln("Recherche si la taille Minimale s'applique (oldValue="+oldValue); -var metier=p.metier; -var result = true; -if(oldValue != undefined) - result = oldValue; -else if (Regle_libUtil.isCaptureDate(p.date,p.metapop, metier)!=true) - result=false; -else if(p.date.before(p.dateDeb)) - result = false; -else if(p.date.after(p.dateFin)) - result = false; + writeln("Recherche si la taille Minimale s'applique (oldValue="+oldValue); + var metier=p.metier; + var result = true; + if(oldValue != undefined) + result = oldValue; + else if (Regle_libUtil.isCaptureDate(p.date,p.metapop, metier)!=true) + result=false; + else if(p.date.before(p.dateDeb)) + result = false; + else if(p.date.after(p.dateFin)) + result = false; -writeln("fin de condition TailleMin:"+result); -return result; -*/ + writeln("fin de condition TailleMin:"+result); + return result; + */ } - + /** - * Si la condition est vrai alors cette action est executée avant le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * Si la condition est vrai alors cette action est executée avant le pas de + * temps de la simulation. + * + * @param context La simulation pour lequel on utilise cette regle */ - public void preAction(SimulationContext context, Date date, Metier metier) throws Exception { + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { // nothing } - + /** - * Si la condition est vrai alors cette action est executée apres le pas - * de temps de la simulation. - * @param simulation La simulation pour lequel on utilise cette regle + * Si la condition est vrai alors cette action est executée apres le pas de + * temps de la simulation. + * + * @param context La simulation pour lequel on utilise cette regle */ - public void postAction(SimulationContext context, Date date, Metier metier) throws Exception { - log.info("*$*$*$* TailleMin.actionApres:" + date + " metapop:" + param_species + " metier:" + metier); + public void postAction(SimulationContext context, Date date, Metier metier) + throws Exception { + log.info("*$*$*$* TailleMin.actionApres:" + date + " metapop:" + + param_species + " metier:" + metier); - if(isCaptureDate(date, param_species, metier)){ - log.info("*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); + if (isCaptureDate(date, param_species, metier)) { + log + .info("*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); // ATTENTION // les captures pour cette metapop ne sont plus du qu'au metier pour qui // l'espece est secondaire: elles sont affectees aux rejets - + //pb : ne se fait pas par metier //il faut une matrice pour chaques pas de temps qui stocke les rejets //par metier, par metapop et par classes d'age (comme pour les captures) @@ -169,67 +174,69 @@ PopulationMonitor popMon = context.getPopulationMonitor(); SiMatrix siMatrix = SiMatrix.getSiMatrix(context); List<Population> pops = siMatrix.getPopulations(date); - + for (Population pop : pops) { if (pop.getSpecies().equals(param_species)) { if (popMon.getDiscard(date, pop) == null) { MatrixND discard = popMon.getCatch(pop).copy(); MatrixND eff = popMon.getN(pop); - - for (MatrixIterator i=discard.iterator(); i.next();) { - Object [] coordonnees = i.getSemanticsCoordinates(); - PopulationGroup group = (PopulationGroup)coordonnees[2]; + + for (MatrixIterator i = discard.iterator(); i.next();) { + Object[] coordonnees = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) coordonnees[2]; if (group.getLength() >= param_TailleMin) { i.setValue(0); } else if (param_propSurvie > 0) { eff.setValue(coordonnees[2], coordonnees[3], - eff.getValue(coordonnees[2], coordonnees[3]) - + i.getValue() * param_propSurvie); + eff.getValue(coordonnees[2], + coordonnees[3]) + + i.getValue() + * param_propSurvie); } } - discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET); + discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); popMon.addDiscard(date, pop, discard); } } } - + log.info("fin de affecterCaptureRejetTailleMin"); - - //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire + + //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire } // fin - + /* -writeln("*$*$*$* TailleMin.actionApres:"+p.date+" metapop:"+p.metapop+" metier:"+p.metier); -if(Regle_libUtil.isCaptureDate(p.date,p.metapop, p.metier)){ - writeln("*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); - // ATTENTION - // les captures pour cette metapop ne sont plus du qu'au metier pour qui - // l'espece est secondaire: elles sont affectees aux rejets + writeln("*$*$*$* TailleMin.actionApres:"+p.date+" metapop:"+p.metapop+" metier:"+p.metier); + if(Regle_libUtil.isCaptureDate(p.date,p.metapop, p.metier)){ + writeln("*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); + // ATTENTION + // les captures pour cette metapop ne sont plus du qu'au metier pour qui + // l'espece est secondaire: elles sont affectees aux rejets - //pb : ne se fait pas par metier - //il faut une matrice pour chaques pas de temps qui stocke les rejets - //par metier, par metapop et par classes d'age (comme pour les captures) - ////// -writeln("deb de affecterCaptureREJETTailleMin"); -var suivi = null; + //pb : ne se fait pas par metier + //il faut une matrice pour chaques pas de temps qui stocke les rejets + //par metier, par metapop et par classes d'age (comme pour les captures) + ////// + writeln("deb de affecterCaptureREJETTailleMin"); + var suivi = null; -//recherche du suivi pour les pop qui ont une certaine meta pop -for(var i=0; i< suiviePop.size(); i++){ - if(suiviePop.get(i).getPop().getMetaPopulation().equals(metapop)){ + //recherche du suivi pour les pop qui ont une certaine meta pop + for(var i=0; i< suiviePop.size(); i++){ + if(suiviePop.get(i).getPop().getMetaPopulation().equals(metapop)){ suivi = suiviePop.get(i); var populations=suivi.getPop(); - //si on a pas deja creer le rejet on le cree et on en fait un resultat + //si on a pas deja creer le rejet on le cree et on en fait un resultat var matRejet = suivi.getRejet(date); if (matRejet==null){ var matRejetBis = MatrixFactory.create(suivi.getCapture()); var eff=suivi.getN(); -//on encapsule les objets des 4 dimensions de la matrice capture + //on encapsule les objets des 4 dimensions de la matrice capture for (var iiterateur=matRejetBis.iterator();iiterateur.next();){ var coordonnees=iiterateur.getSemanticsCoordinates(); var classe=coordonnees[2]; @@ -243,18 +250,18 @@ matRejetBis.setName("Rejet par metier"); suivi.addRejet(date,matRejetBis); } - } -} + } + } -writeln("fin de affecterCaptureRejetTailleMin"); + writeln("fin de affecterCaptureRejetTailleMin"); - //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire -} + //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire + } -return p.gestionMetier; -*/ + return p.gestionMetier; + */ } } Added: isis-fish/trunk/src/test/resources/test-database/rules/TotalClosure.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/rules/TotalClosure.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/rules/TotalClosure.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,119 @@ +package rules; + +import static org.codelutin.i18n.I18n._; + +import java.util.List; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import scripts.SiMatrix; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.StrategyMonthInfo; +import fr.ifremer.isisfish.rule.AbstractRule; +import fr.ifremer.isisfish.simulator.MetierMonitor; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.types.Month; + +/** + * Remplace aussi Cantonnement Engin. + * + * Created: 29 aout 2007 + * @author sigrid + * @version $Revision$ + */ +public class TotalClosure extends AbstractRule { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(TotalClosure.class); + + public Date param_beginDate = new Date(100); + public Date param_endDate = new Date(119); + public Month param_beginMonth = Month.JANUARY; + public Month param_endMonth = Month.JANUARY; + + public String[] necessaryResult = { + ResultName.MATRIX_NO_ACTIVITY + }; + + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + public String getDescription() throws Exception { + return _("Total closure of the fishery"); + } + + /** + * Appelé au démarrage de la simulation, cette methode permet d'initialiser des valeurs. + * @param context La simulation pour lequel on utilise cette regle + */ + public void init(SimulationContext context) throws Exception { + } + + /** + * La condition qui doit etre vrai pour faire les actions. + * @param context La simulation pour lequel on utilise cette regle + * @return vrai si on souhaite que les actions soit faites + */ + public boolean condition(SimulationContext context, Date date, Metier metier) + throws Exception { + boolean result = true; + if (date.before(param_beginDate)) { + result = false; + } else if (date.after(param_endDate)) { + result = false; + } + + if (date.getMonth().before(param_beginMonth)) { + result = false; + } else if (date.getMonth().after(param_endMonth)) { + result = false; + } + return result; + } + + /** + * Si la condition est vrai alors cette action est executee avant le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { + MetierMonitor metierMon = context.getMetierMonitor(); + + //MetierSeasonInfo infoMetier = metier.getMetierSeasonInfo(date + // .getMonth()); + + SiMatrix siMatrix = SiMatrix.getSiMatrix(context); + MatrixND noActivity = metierMon.getOrCreateNoActivity(date, + ResultName.MATRIX_NO_ACTIVITY, siMatrix.getStrategies(date), + siMatrix.getMetiers(date)); + metierMon.addforbiddenMetier(metier); + List<Strategy> strategies = siMatrix.getStrategies(date); + + for (Strategy str : strategies) { + StrategyMonthInfo info = str.getStrategyMonthInfo(date.getMonth()); + double prop = info.getProportionMetier(metier); + if (prop != 0) { + noActivity.setValue(str, metier, prop); + info.setProportionMetier(metier, 0); + } + } + } + + /** + * Si la condition est vrai alors cette action est executee apres le pas + * de temps de la simulation. + * @param context La simulation pour lequel on utilise cette regle + */ + public void postAction(SimulationContext context, Date date, Metier metier) + throws Exception { + // nothing + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/rules/TotalClosure.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Modified: isis-fish/trunk/src/test/resources/test-database/scripts/GravityModel.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/scripts/GravityModel.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/scripts/GravityModel.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,6 +1,6 @@ /* *##% - * Copyright (C) 2006 - * Code Lutin, C?dric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2009 + * Code Lutin, Cédric Pineau, Benjamin Poussin * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -17,21 +17,8 @@ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *##%*/ -/* * - * GravityModel.java - * - * Created: 4 sept. 06 15:49:08 - * - * @author poussin - * @version $Revision: 1.9 $ - * - * Last update: $Date: 2007-03-01 17:16:12 $ - * by : $Author: bpoussin $ - */ - package scripts; -import static org.codelutin.i18n.I18n._; import static org.codelutin.i18n.I18n.n_; import java.util.Collection; @@ -58,17 +45,22 @@ import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeUnit; - /** + * GravityModel.java + * + * Created: 4 sept. 06 15:49:08 + * * @author poussin + * @version $Revision: 1.9 $ * + * Last update: $Date: 2007-03-01 17:16:12 $ + * by : $Author: bpoussin $ */ - public class GravityModel { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(GravityModel.class); - + protected SimulationContext context = null; protected TopiaContext db = null; protected SiMatrix siMatrix = null; @@ -76,20 +68,24 @@ /** * Method used to get GravityModel used for simulation - * @param context context simulation + * + * @param context + * context simulation * @return GravityModel or null if no GravityModel created for simulation */ public static GravityModel getGravityModel(SimulationContext context) { - GravityModel result = (GravityModel)context.getValue(GravityModel.class.getName()); + GravityModel result = (GravityModel) context + .getValue(GravityModel.class.getName()); return result; } - - private static void setGravityModel(SimulationContext context, GravityModel gravityModel) { + + private static void setGravityModel(SimulationContext context, + GravityModel gravityModel) { context.setValue(GravityModel.class.getName(), gravityModel); } - - - public GravityModel(SimulationContext context, SiMatrix siMatrix) throws TopiaException, StorageException{ + + public GravityModel(SimulationContext context, SiMatrix siMatrix) + throws TopiaException, StorageException { this.context = context; this.db = context.getDB(); this.resultManager = context.getSimulationStorage().getResultStorage(); @@ -105,103 +101,95 @@ // MatrixFishingTimePerMonthPerVessel ////////////////////////////////////////////////////////////////////// - public MatrixND matrixFishingTimePerMonthPerVessel(Date date) throws TopiaException{ + public MatrixND matrixFishingTimePerMonthPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_FISHING_TIME_PER_MONTH_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = fishingTimePerMonthPerVessel(str, metier, date); result.setValue(str, metier, value); } } - -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = fishingTimePerMonthPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * FishingTimePerMonthPerVessel[str,met,month] = FishingTimePerTrip[str,met,month]NbTripsPerMonth[str,month] - + * implante suivant document ModifTable3PourBP25-07-2006.doc + * FishingTimePerMonthPerVessel[str,met,month] = + * FishingTimePerTrip[str,met,month]NbTripsPerMonth[str,month] + * * @param str * @param metier * @param date * @return */ - private double fishingTimePerMonthPerVessel(Strategy str, Metier metier, Date date) { - Month month = date.getMonth(); - double timePerTrip = siMatrix.fishingTimePerTrip(str, metier, date); - double nbTrip = str.getStrategyMonthInfo(month).getNumberOfTrips(); - return timePerTrip * nbTrip; - } + private double fishingTimePerMonthPerVessel(Strategy str, Metier metier, + Date date) { + Month month = date.getMonth(); + double timePerTrip = siMatrix.fishingTimePerTrip(str, metier, date); + double nbTrip = str.getStrategyMonthInfo(month).getNumberOfTrips(); + return timePerTrip * nbTrip; + } - ////////////////////////////////////////////////////////////////////// // matrixFuelCostsOfTravelPerVessel ////////////////////////////////////////////////////////////////////// - public MatrixND matrixFuelCostsOfTravelPerVessel(Date date) throws TopiaException{ + public MatrixND matrixFuelCostsOfTravelPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_FUEL_COSTS_OF_TRAVEL_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = fuelCostsOfTravelPerVessel(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = fuelCostsOfTravelPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * FuelCostsOfTravelPerVessel[sov,met,month]?=?NbTripsPerMonth[str,month]*TravelTimePerTrip[sov,met,month]*UnitFuelCostsOfTravel[vt] - * + * implante suivant document ModifTable3PourBP25-07-2006.doc + * FuelCostsOfTravelPerVessel[sov,met,month] = + * NbTripsPerMonth[str,month]*TravelTimePerTrip[sov,met,month]*UnitFuelCostsOfTravel[vt] + * * @param str * @param metier * @param date * @return */ - private double fuelCostsOfTravelPerVessel(Strategy str, Metier metier, Date date) { + private double fuelCostsOfTravelPerVessel(Strategy str, Metier metier, + Date date) { Month month = date.getMonth(); double nbTrip = str.getStrategyMonthInfo(month).getNumberOfTrips(); Collection<Zone> zone = metier.getMetierSeasonInfo(month).getZone(); // TODO: verifier que travelTime est bien en heure, car le unitFuelCost est l'unite par heure - double travelTime = siMatrix.travelTimePerTrip(str.getSetOfVessels(), zone); - double unitFuelCost = str.getSetOfVessels().getVesselType().getUnitFuelCostOfTravel(); + double travelTime = siMatrix.travelTimePerTrip(str.getSetOfVessels(), + zone); + double unitFuelCost = str.getSetOfVessels().getVesselType() + .getUnitFuelCostOfTravel(); return nbTrip * travelTime * unitFuelCost; } @@ -210,94 +198,87 @@ // matrixCostsOfFishingPerVessel ////////////////////////////////////////////////////////////////////// - public MatrixND matrixCostsOfFishingPerVessel(Date date) throws TopiaException{ + public MatrixND matrixCostsOfFishingPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_COSTS_OF_FISHING_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = costsOfFishingPerVessel(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = costsOfFishingPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * CostsOfFishingPerVessel[str,met,month]= FishingTimePerMonthPerVessel [str,met,month] {NbFishingOperationsPerDay[sov,met] UnitCostsOfFishing[sov,met] / 24} + * implante suivant document ModifTable3PourBP25-07-2006.doc + * CostsOfFishingPerVessel[str,met,month]= FishingTimePerMonthPerVessel + * [str,met,month] {NbFishingOperationsPerDay[sov,met] + * UnitCostsOfFishing[sov,met] / 24} * * @param str * @param metier * @param date * @return */ - private double costsOfFishingPerVessel(Strategy str, Metier metier, Date date) { + private double costsOfFishingPerVessel(Strategy str, Metier metier, + Date date) { double fishingTime = fishingTimePerMonthPerVessel(str, metier, date); - EffortDescription effort = str.getSetOfVessels().getPossibleMetiers(metier); + EffortDescription effort = str.getSetOfVessels().getPossibleMetiers( + metier); int nbOperation = 0; double unitCostOfFishing = 0; - if(effort != null){ + if (effort != null) { nbOperation = effort.getFishingOperation(); unitCostOfFishing = effort.getUnitCostOfFishing(); } - return fishingTime * ( nbOperation * unitCostOfFishing / TimeUnit.HOUR_PER_DAY); + return fishingTime + * (nbOperation * unitCostOfFishing / TimeUnit.HOUR_PER_DAY); } ////////////////////////////////////////////////////////////////////// // matrixFuelCostsPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixFuelCostsPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixFuelCostsPerVessel(Date date) throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_FUEL_COSTS_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = fuelCostsPerVessel(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = fuelCostsPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * FuelCostsPerVessel[str,met,month] = FuelCostsOfTravelPerVessel [sov,met,month] + CostsOfFishingPerVessel [str,met,month] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * FuelCostsPerVessel[str,met,month] = FuelCostsOfTravelPerVessel + * [sov,met,month] + CostsOfFishingPerVessel [str,met,month] * * @param str * @param metier @@ -314,52 +295,58 @@ ////////////////////////////////////////////////////////////////////// // matrixRepairAndMaintenanceGearCostsPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixRepairAndMaintenanceGearCostsPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixRepairAndMaintenanceGearCostsPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_REPAIR_AND_MAINTENANCE_GEAR_COSTS_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = repairAndMaintenanceGearCostsPerVessel(str, metier, date); + double value = repairAndMaintenanceGearCostsPerVessel(str, + metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = repairAndMaintenanceGearCostsPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } + // for(Strategy str : strategies){ + // metiers = siMatrix.getMetiers(str, date); + // for(Metier metier : metiers) { + // double value = repairAndMaintenanceGearCostsPerVessel(str, metier, date); + // result.setValue(str, metier, value); + // } + // } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * RepairAndMaintenanceGearCostsPerVessel[str,met,month]?=?FishingTimePerMonthPerVessel[str,met,month] *RepairAndMaintenanceGearCostsPerDay[sov,met]/NbHoursPerDay + * implante suivant document ModifTable3PourBP25-07-2006.doc + * RepairAndMaintenanceGearCostsPerVessel[str,met,month] = + * FishingTimePerMonthPerVessel[str,met,month] + * *RepairAndMaintenanceGearCostsPerDay[sov,met]/NbHoursPerDay * * @param str * @param metier * @param date * @return */ - private double repairAndMaintenanceGearCostsPerVessel(Strategy str, Metier metier, Date date) { + private double repairAndMaintenanceGearCostsPerVessel(Strategy str, + Metier metier, Date date) { double fishingTime = fishingTimePerMonthPerVessel(str, metier, date); - EffortDescription effort = str.getSetOfVessels().getPossibleMetiers(metier); + EffortDescription effort = str.getSetOfVessels().getPossibleMetiers( + metier); double repair = 0; - if(effort != null){ + if (effort != null) { repair = effort.getRepairAndMaintenanceGearCost(); } // FIXME verifier qu'il faut bien retourner 0, si pas d'effort @@ -369,52 +356,50 @@ ////////////////////////////////////////////////////////////////////// // matrixOtherRunningCostsPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixOtherRunningCostsPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixOtherRunningCostsPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_OTHER_RUNNING_COSTS_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = otherRunningCostsPerVessel(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = otherRunningCostsPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * OtherRunningCostsPerVessel[str,met,month]=?FishingTimePerMonthPerVessel[str,met,month]*OtherRunningCostsPerDay[sov,met]/ NbHoursPerDay + * implante suivant document ModifTable3PourBP25-07-2006.doc + * OtherRunningCostsPerVessel[str,met,month] = + * FishingTimePerMonthPerVessel[str,met,month]*OtherRunningCostsPerDay[sov,met]/ + * NbHoursPerDay * * @param str * @param metier * @param date * @return */ - private double otherRunningCostsPerVessel(Strategy str, Metier metier, Date date) { + private double otherRunningCostsPerVessel(Strategy str, Metier metier, + Date date) { double fishingTime = fishingTimePerMonthPerVessel(str, metier, date); - EffortDescription effort = str.getSetOfVessels().getPossibleMetiers(metier); + EffortDescription effort = str.getSetOfVessels().getPossibleMetiers( + metier); double otherCosts = 0; - if(effort != null){ + if (effort != null) { otherCosts = effort.getOtherRunningCost(); } // FIXME verifier qu'il faut bien retourner 0, si pas d'effort @@ -424,156 +409,112 @@ ////////////////////////////////////////////////////////////////////// // matrixSharedNotFixedCostsPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixSharedNotFixedCostsPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixSharedNotFixedCostsPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_SHARED_NOT_FIXED_COSTS_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = sharedNotFixedCostsPerVessel(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = sharedNotFixedCostsPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * SharedNotFixedCostsPerVessel[str,met,month]=?FuelCostsPerVessel[str,met,month] +?OtherRunningCostsPerVessel[str,met,month] - * + * implante suivant document ModifTable3PourBP25-07-2006.doc + * SharedNotFixedCostsPerVessel[str,met,month]=FuelCostsPerVessel[str,met,month] + * +OtherRunningCostsPerVessel[str,met,month] + * * @param str * @param metier * @param date * @return */ - private double sharedNotFixedCostsPerVessel(Strategy str, Metier metier, Date date) { + private double sharedNotFixedCostsPerVessel(Strategy str, Metier metier, + Date date) { double fuelCostsPerVessel = fuelCostsPerVessel(str, metier, date); - double otherRunningCostsPerVessel = otherRunningCostsPerVessel(str, metier, date); + double otherRunningCostsPerVessel = otherRunningCostsPerVessel(str, + metier, date); return fuelCostsPerVessel + otherRunningCostsPerVessel; - } + } ////////////////////////////////////////////////////////////////////// - // matrixSharedFixedCostsPerVesselPerMet - ////////////////////////////////////////////////////////////////////// -// Supprime avec Steph le 20070227 -// public MatrixND matrixSharedFixedCostsPerVesselPerMet(Date date) throws TopiaException{ -// List<Strategy> strategies = siMatrix.getStrategies(date); -// -// MatrixND result = MatrixFactory.getInstance().create( -// ResultName.MATRIX_SHARED_FIXED_COSTS_PER_VESSEL_PER_MET, -// new List[]{strategies}, -// new String[]{n_("Strategies")}); -// -// for (int s=0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// double value = sharedFixedCostsPerVesselPerMet(str, date); -// result.setValue(s, value); -// } -//// for(Strategy str : strategies){ -//// double value = sharedFixedCostsPerVesselPerMet(str, date); -//// result.setValue(str, value); -//// } -// -// return result; -// } -// -// /** -// * implant? suivant document ModifTable3PourBP25-07-2006.doc -// * SharedFixedCostsPerVesselPerMet [str,month]=FixedCostsPerMonth[sov]/NbMet[sov] -// * -// * @param str -// * @param date -// * @return -// */ -// private double sharedFixedCostsPerVesselPerMet(Strategy str, Date date) { -// SetOfVessels sov = str.getSetOfVessels(); -// double fixedCosts = sov.getFixedCosts(); -// int nbMet = sov.sizePossibleMetiers(); -// -// return fixedCosts / (double)nbMet; -// } - - ////////////////////////////////////////////////////////////////////// // matrixGrossValueOfLandingsPerSpeciesPerStrategyMet ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixGrossValueOfLandingsPerSpeciesPerStrategyMet(Date date) throws TopiaException{ + public MatrixND matrixGrossValueOfLandingsPerSpeciesPerStrategyMet(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); List<Population> pops = siMatrix.getPopulations(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_SPECIES_PER_STRATEGY_MET, - new List[]{strategies, metiers, pops}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Populations")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_SPECIES_PER_STRATEGY_MET, + new List[] { strategies, metiers, pops }, + new String[] { n_("Strategies"), n_("Metiers"), + n_("Populations") }); - for (int p=0; p < pops.size(); p++) { + for (int p = 0; p < pops.size(); p++) { Population pop = pops.get(p); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = grossValueOfLandingsPerSpeciesPerStrategyMet(str, metier, pop, date); + double value = grossValueOfLandingsPerSpeciesPerStrategyMet( + str, metier, pop, date); result.setValue(str, metier, pop, value); } } } -// for(Population pop : pops){ -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = grossValueOfLandingsPerSpeciesPerStrategyMet(str, metier, pop, date); -// result.setValue(str, metier, pop, value); -// } -// } -// } - return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * GrossValueOfLandingsPerSpeciesPerStrategyMet[str,met,pop,month]?=?sum over classes_cl of [PricePerKg(pop,cl, t)* (CatchWeightPerStrategyMet [str,met,pop,cl,month] ?DiscardsWeightPerStrategyMet [str,met,pop,cl,mo -nth] - * GrossValueOfLandingsPerSpeciesPerStrategyMet[str,met,pop,month] = sum over classes_cl of [PricePerKg(pop,cl, t)* (CatchWeightPerStrategyMet [str,met,pop,cl,month] -DiscardsWeightPerStrategyMet [str,met,pop,cl,mo -nth])] - * + * implante suivant document ModifTable3PourBP25-07-2006.doc + * GrossValueOfLandingsPerSpeciesPerStrategyMet[str,met,pop,month]=sum over + * classes_cl of [PricePerKg(pop,cl, t)* (CatchWeightPerStrategyMet + * [str,met,pop,cl,month] ?DiscardsWeightPerStrategyMet [str,met,pop,cl,mo + * nth] GrossValueOfLandingsPerSpeciesPerStrategyMet[str,met,pop,month] = + * sum over classes_cl of [PricePerKg(pop,cl, t)* (CatchWeightPerStrategyMet + * [str,met,pop,cl,month] -DiscardsWeightPerStrategyMet [str,met,pop,cl,mo + * nth])] + * * @param str * @param metier * @param pop * @param date * @return */ - private double grossValueOfLandingsPerSpeciesPerStrategyMet(Strategy str, Metier metier, Population pop, Date date) { + private double grossValueOfLandingsPerSpeciesPerStrategyMet(Strategy str, + Metier metier, Population pop, Date date) { List<PopulationGroup> groups = pop.getPopulationGroup(); double result = 0; - for(PopulationGroup group : groups){ + for (PopulationGroup group : groups) { double price = group.getPrice(); Collection<Zone> zones = pop.getPopulationZone(); - for(Zone zone : zones){ - double catchWeight = getCatchWeightPerStrMetPerZonePop(str, metier, group, zone, date); - double discardsWeight = getDiscardsWeightPerStrMet(str, metier, group, zone, date); + for (Zone zone : zones) { + double catchWeight = getCatchWeightPerStrMetPerZonePop(str, + metier, group, zone, date); + double discardsWeight = getDiscardsWeightPerStrMet(str, metier, + group, zone, date); // FIXME demander/verifier que ce le bon calcule result += price * (catchWeight - discardsWeight); } @@ -589,10 +530,12 @@ * @param date * @return */ - private double getCatchWeightPerStrMetPerZonePop(Strategy str, Metier metier, PopulationGroup group, Zone zone, Date date) { - MatrixND mat = resultManager.getMatrix(date, group.getPopulation(), ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - double result = 0; - if(mat != null){ + private double getCatchWeightPerStrMetPerZonePop(Strategy str, + Metier metier, PopulationGroup group, Zone zone, Date date) { + MatrixND mat = resultManager.getMatrix(date, group.getPopulation(), + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + double result = 0; + if (mat != null) { result = mat.getValue(str, metier, group, zone); } return result; @@ -606,10 +549,12 @@ * @param date * @return */ - private double getDiscardsWeightPerStrMet(Strategy str, Metier metier, PopulationGroup group, Zone zone, Date date) { - MatrixND mat = resultManager.getMatrix(date, group.getPopulation(), ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); - double result = 0; - if(mat != null){ + private double getDiscardsWeightPerStrMet(Strategy str, Metier metier, + PopulationGroup group, Zone zone, Date date) { + MatrixND mat = resultManager.getMatrix(date, group.getPopulation(), + ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); + double result = 0; + if (mat != null) { result = mat.getValue(str, metier, group, zone); } return result; @@ -618,33 +563,28 @@ ////////////////////////////////////////////////////////////////////// // matrixGrossValueOfLandingsPerStrategyMet ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixGrossValueOfLandingsPerStrategyMet(Date date) throws TopiaException{ + + public MatrixND matrixGrossValueOfLandingsPerStrategyMet(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = grossValueOfLandingsPerStrategyMet(str, metier, date); + double value = grossValueOfLandingsPerStrategyMet(str, metier, + date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = grossValueOfLandingsPerStrategyMet(str, metier, date); -// result.setValue(str, metier, value); -// } -// } - + return result; } @@ -653,14 +593,16 @@ * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double grossValueOfLandingsPerStrategyMet(Strategy str, Metier metier, Date date) throws TopiaException { + private double grossValueOfLandingsPerStrategyMet(Strategy str, + Metier metier, Date date) throws TopiaException { List<Population> pops = siMatrix.getPopulations(date); double result = 0; - for(int i=0; i<pops.size(); i++){ - Population pop = (Population)pops.get(i); - result += grossValueOfLandingsPerSpeciesPerStrategyMet(str, metier, pop, date); + for (int i = 0; i < pops.size(); i++) { + Population pop = (Population) pops.get(i); + result += grossValueOfLandingsPerSpeciesPerStrategyMet(str, metier, + pop, date); } return result; } @@ -668,433 +610,450 @@ ////////////////////////////////////////////////////////////////////// // matrixGrossValueOfLandingsPerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixGrossValueOfLandingsPerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixGrossValueOfLandingsPerStrategyMetPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL, + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = grossValueOfLandingsPerStrategyMetPerVessel(str, metier, date); + double value = grossValueOfLandingsPerStrategyMetPerVessel(str, + metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = grossValueOfLandingsPerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * GrossValueOfLandingsPerStrategyMetPerVessel[str,met,month]?= GrossValueOfLandingsPerStrategyMet[str,met,month]?/[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * GrossValueOfLandingsPerStrategyMetPerVessel[str,met,month]= + * GrossValueOfLandingsPerStrategyMet[str,met,month]/[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double grossValueOfLandingsPerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double grossValueOfLandingsPerStrategyMet = grossValueOfLandingsPerStrategyMet(str, metier, date); + private double grossValueOfLandingsPerStrategyMetPerVessel(Strategy str, + Metier metier, Date date) throws TopiaException { + double grossValueOfLandingsPerStrategyMet = grossValueOfLandingsPerStrategyMet( + str, metier, date); // FIXME verifier que c bien cette donn?e qu'il faut utiliser dans le doc: PropNbVessels(str, sov) double proportionSetOfVessels = str.getProportionSetOfVessels(); double numberOfVessels = str.getSetOfVessels().getNumberOfVessels(); - double grossValueOfLandingsOtherSpeciesPerStrategyMet = grossValueOfLandingsOtherSpeciesPerStrategyMet(str,metier,date); + double grossValueOfLandingsOtherSpeciesPerStrategyMet = grossValueOfLandingsOtherSpeciesPerStrategyMet( + str, metier, date); - - return (grossValueOfLandingsPerStrategyMet + grossValueOfLandingsOtherSpeciesPerStrategyMet) / (proportionSetOfVessels * numberOfVessels); + return (grossValueOfLandingsPerStrategyMet + grossValueOfLandingsOtherSpeciesPerStrategyMet) + / (proportionSetOfVessels * numberOfVessels); } ////////////////////////////////////////////////////////////////////// // matrixNetValueOfLandingsPerStrategyMet ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixNetValueOfLandingsPerStrategyMet(Date date) throws TopiaException{ + + public MatrixND matrixNetValueOfLandingsPerStrategyMet(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = netValueOfLandingsPerStrategyMet(str, metier, date); + double value = netValueOfLandingsPerStrategyMet(str, metier, + date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = netValueOfLandingsPerStrategyMet(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * NetValueOfLandingsPerStrategyMet[str,met,month]?=?GrossValueOfLandingsPerStrategyMet[str,met,month]?(1-LandingCostRate[str,met]?) + * implante suivant document ModifTable3PourBP25-07-2006.doc + * NetValueOfLandingsPerStrategyMet[str,met,month] = + * GrossValueOfLandingsPerStrategyMet[str,met,month] + * (1-LandingCostRate[str,met]) * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double netValueOfLandingsPerStrategyMet(Strategy str, Metier metier, Date date) throws TopiaException { - double grossValue = grossValueOfLandingsPerStrategyMet(str, metier, date); - EffortDescription effort = str.getSetOfVessels().getPossibleMetiers(metier); + private double netValueOfLandingsPerStrategyMet(Strategy str, + Metier metier, Date date) throws TopiaException { + double grossValue = grossValueOfLandingsPerStrategyMet(str, metier, + date); + EffortDescription effort = str.getSetOfVessels().getPossibleMetiers( + metier); double landingCost = 1; // FIXME demander si le metier n'a pas d'effort s'il faut que landingCost soit bien a 1 - if(effort != null){ + if (effort != null) { landingCost -= effort.getLandingCosts(); } - double grossValueOfLandingsOtherSpeciesPerStrategyMet = grossValueOfLandingsOtherSpeciesPerStrategyMet(str,metier,date); - - double result = (grossValue + grossValueOfLandingsOtherSpeciesPerStrategyMet)* landingCost; + double grossValueOfLandingsOtherSpeciesPerStrategyMet = grossValueOfLandingsOtherSpeciesPerStrategyMet( + str, metier, date); + + double result = (grossValue + grossValueOfLandingsOtherSpeciesPerStrategyMet) + * landingCost; return result; - } + } - private double grossValueOfLandingsOtherSpeciesPerStrategyMet(Strategy str, Metier metier, Date date) throws TopiaException { + private double grossValueOfLandingsOtherSpeciesPerStrategyMet(Strategy str, + Metier metier, Date date) throws TopiaException { // FIXME evaluer l'equation dans suivant le doc des equations return 0; } - + ////////////////////////////////////////////////////////////////////// // matrixNetValueOfLandingsPerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixNetValueOfLandingsPerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixNetValueOfLandingsPerStrategyMetPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL, + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = netValueOfLandingsPerStrategyMetPerVessel(str, metier, date); + double value = netValueOfLandingsPerStrategyMetPerVessel(str, + metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = netValueOfLandingsPerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } - /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * NetValueOfLandingsPerStrategyMetPerVessel[str,met,month]?=?NetValueOfLandingsPerStrategyMet[str,met,month]?/[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * NetValueOfLandingsPerStrategyMetPerVessel[str,met,month] = + * NetValueOfLandingsPerStrategyMet[str,met,month] + * /[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double netValueOfLandingsPerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double netValueOfLandingsPerStrategyMet = netValueOfLandingsPerStrategyMet(str, metier, date); - // FIXME verifier que c bien cette donn?e qu'il faut utiliser dans le doc: PropNbVessels(str, sov) + private double netValueOfLandingsPerStrategyMetPerVessel(Strategy str, + Metier metier, Date date) throws TopiaException { + double netValueOfLandingsPerStrategyMet = netValueOfLandingsPerStrategyMet( + str, metier, date); + // FIXME verifier que c bien cette donnée qu'il faut utiliser dans le doc: PropNbVessels(str, sov) double proportionSetOfVessels = str.getProportionSetOfVessels(); double numberOfVessels = str.getSetOfVessels().getNumberOfVessels(); - return netValueOfLandingsPerStrategyMet / (proportionSetOfVessels * numberOfVessels); + return netValueOfLandingsPerStrategyMet + / (proportionSetOfVessels * numberOfVessels); } ////////////////////////////////////////////////////////////////////// // matrixNetRenevueToSharePerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixNetRenevueToSharePerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixNetRenevueToSharePerStrategyMetPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_NET_RENEVUE_TO_SHARE_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_NET_RENEVUE_TO_SHARE_PER_STRATEGY_MET_PER_VESSEL, + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = netRenevueToSharePerStrategyMetPerVessel(str, metier, date); + double value = netRenevueToSharePerStrategyMetPerVessel(str, + metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = netRenevueToSharePerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * NetRevenueToSharePerStrategyMetPerVessel[str,met,month]?=?NetValueOfLandingsPerStrategyMetPerVessel[str,met,month]?-?SharedNotFixedCostsPerVessel [str,met,month]*PropStr(str,met,month) - SharedFixedCostsPerVessel -PerMet[str,month] - * + * implante suivant document ModifTable3PourBP25-07-2006.doc + * NetRevenueToSharePerStrategyMetPerVessel[str,met,month] = + * NetValueOfLandingsPerStrategyMetPerVessel[str,met,month] - + * SharedNotFixedCostsPerVessel [str,met,month]*PropStr(str,met,month) - + * SharedFixedCostsPerVessel PerMet[str,month] + * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double netRenevueToSharePerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double netRenevueToSharePerStrategyMetPerVessel = netValueOfLandingsPerStrategyMetPerVessel(str, metier, date); - double sharedNotFixedCostsPerVessel = sharedNotFixedCostsPerVessel(str, metier, date); - double propStr = str.getStrategyMonthInfo(date.getMonth()).getProportionMetier(metier); + private double netRenevueToSharePerStrategyMetPerVessel(Strategy str, + Metier metier, Date date) throws TopiaException { + double netRenevueToSharePerStrategyMetPerVessel = netValueOfLandingsPerStrategyMetPerVessel( + str, metier, date); + double sharedNotFixedCostsPerVessel = sharedNotFixedCostsPerVessel(str, + metier, date); + double propStr = str.getStrategyMonthInfo(date.getMonth()) + .getProportionMetier(metier); - double result = netRenevueToSharePerStrategyMetPerVessel - sharedNotFixedCostsPerVessel * propStr; + double result = netRenevueToSharePerStrategyMetPerVessel + - sharedNotFixedCostsPerVessel * propStr; return result; } ////////////////////////////////////////////////////////////////////// // matrixCrewSharePerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixCrewSharePerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixCrewSharePerStrategyMetPerVessel(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_CREW_SHARE_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = crewSharePerStrategyMetPerVessel(str, metier, date); + double value = crewSharePerStrategyMetPerVessel(str, metier, + date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = crewSharePerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } - /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * CrewSharePerStrategyMetPerVessel[str,met,month]?=?NetRevenueToSharePerStrategyMetPerVessel[str,met,month]*CrewShareRate[sov,met] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * CrewSharePerStrategyMetPerVessel[str,met,month] = + * NetRevenueToSharePerStrategyMetPerVessel[str,met,month]*CrewShareRate[sov,met] * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double crewSharePerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel(str, metier, date); + private double crewSharePerStrategyMetPerVessel(Strategy str, + Metier metier, Date date) throws TopiaException { + double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel( + str, metier, date); - EffortDescription effort = str.getSetOfVessels().getPossibleMetiers(metier); + EffortDescription effort = str.getSetOfVessels().getPossibleMetiers( + metier); double crewShareRate = 0; - if(effort != null){ + if (effort != null) { crewShareRate = effort.getCrewShareRate(); } // FIXME verifier qu'il faut bien retourner 0, si pas d'effort return netRenevueToShare * crewShareRate; - } + } ////////////////////////////////////////////////////////////////////// // matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel( + Date date) throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL, + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = ownerMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); + double value = ownerMarginOverVariableCostsPerStrategyMetPerVessel( + str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = ownerMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } - /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * OwnerMarginOverVariableCostsPerStrategyMetPerVessel[str,met,month] = NetRevenueToSharePerStrategyMetPerVessel[str,met,month]?- CrewSharePerStrategyMetPerVessel[str,met,month]?- RepairAndMaintenanceGearCostsPerVes -sel[str,met,month]?* PropStr(str,met,month) + * implante suivant document ModifTable3PourBP25-07-2006.doc + * OwnerMarginOverVariableCostsPerStrategyMetPerVessel[str,met,month] = + * NetRevenueToSharePerStrategyMetPerVessel[str,met,month] - + * CrewSharePerStrategyMetPerVessel[str,met,month] - + * RepairAndMaintenanceGearCostsPerVes sel[str,met,month] * + * PropStr(str,met,month) * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double ownerMarginOverVariableCostsPerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel(str, metier, date); + private double ownerMarginOverVariableCostsPerStrategyMetPerVessel( + Strategy str, Metier metier, Date date) throws TopiaException { + double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel( + str, metier, date); double crewShare = crewSharePerStrategyMetPerVessel(str, metier, date); - double repair = repairAndMaintenanceGearCostsPerVessel(str, metier, date); - double propStr = str.getStrategyMonthInfo(date.getMonth()).getProportionMetier(metier); + double repair = repairAndMaintenanceGearCostsPerVessel(str, metier, + date); + double propStr = str.getStrategyMonthInfo(date.getMonth()) + .getProportionMetier(metier); return netRenevueToShare - crewShare - repair * propStr; - } + } - ////////////////////////////////////////////////////////////////////// // matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel( + Date date) throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); List<Metier> metiers = siMatrix.getMetiers(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL, + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = siMatrix.getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - double value = vesselMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); + double value = vesselMarginOverVariableCostsPerStrategyMetPerVessel( + str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// metiers = siMatrix.getMetiers(str, date); -// for(Metier metier : metiers) { -// double value = vesselMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); -// result.setValue(str, metier, value); -// } -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * VesselMarginOverVariableCostsPerStrategyMetPerVessel?[str,met,month]?=NetRevenueToSharePerStrategyMetPerVessel[str,met,month]- RepairAndMaintenanceGearCostsPerVessel [str,met,month]?* PropStr(str,met,month) + * implante suivant document ModifTable3PourBP25-07-2006.doc + * VesselMarginOverVariableCostsPerStrategyMetPerVessel [str,met,month] + * =NetRevenueToSharePerStrategyMetPerVessel[str,met,month]- + * RepairAndMaintenanceGearCostsPerVessel [str,met,month] * + * PropStr(str,met,month) * * @param str * @param metier * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double vesselMarginOverVariableCostsPerStrategyMetPerVessel(Strategy str, Metier metier, Date date) throws TopiaException { - double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel(str, metier, date); - double repair = repairAndMaintenanceGearCostsPerVessel(str, metier, date); - double propStr = str.getStrategyMonthInfo(date.getMonth()).getProportionMetier(metier); + private double vesselMarginOverVariableCostsPerStrategyMetPerVessel( + Strategy str, Metier metier, Date date) throws TopiaException { + double netRenevueToShare = netRenevueToSharePerStrategyMetPerVessel( + str, metier, date); + double repair = repairAndMaintenanceGearCostsPerVessel(str, metier, + date); + double propStr = str.getStrategyMonthInfo(date.getMonth()) + .getProportionMetier(metier); return netRenevueToShare - repair * propStr; - } - + } + ////////////////////////////////////////////////////////////////////// // matrixOwnerMarginOverVariableCostsPerStrategyPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixOwnerMarginOverVariableCostsPerStrategyPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixOwnerMarginOverVariableCostsPerStrategyPerVessel( + Date date) throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL, - new List[]{strategies}, - new String[]{n_("Strategies")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL, + new List[] { strategies }, + new String[] { n_("Strategies") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); - double value = ownerMarginOverVariableCostsPerStrategyPerVessel(str, date); + double value = ownerMarginOverVariableCostsPerStrategyPerVessel( + str, date); result.setValue(s, value); } -// for(Strategy str : strategies){ -// double value = ownerMarginOverVariableCostsPerStrategyPerVessel(str, date); -// result.setValue(str, value); -// } return result; } - + /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * OwnerMarginOverVariableCostsPerStrategyPerVessel[str,month]?=?somme sur tous les m?tiers de OwnerMarginOverVariableCostsPerStrategyMetPerVessel [str,met,month] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * OwnerMarginOverVariableCostsPerStrategyPerVessel[str,month] = somme sur + * tous les metiers de OwnerMarginOverVariableCostsPerStrategyMetPerVessel + * [str,met,month] * * @param str * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double ownerMarginOverVariableCostsPerStrategyPerVessel(Strategy str, Date date) throws TopiaException { + private double ownerMarginOverVariableCostsPerStrategyPerVessel( + Strategy str, Date date) throws TopiaException { SetOfVessels sov = str.getSetOfVessels(); Collection<EffortDescription> efforts = sov.getPossibleMetiers(); float result = 0; - + for (EffortDescription effort : efforts) { Metier metier = effort.getPossibleMetiers(); - result += ownerMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); + result += ownerMarginOverVariableCostsPerStrategyMetPerVessel(str, + metier, date); } return result; } @@ -1102,80 +1061,87 @@ ////////////////////////////////////////////////////////////////////// // matrixOwnerMarginOverVariableCostsPerStrategy ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixOwnerMarginOverVariableCostsPerStrategy(Date date) throws TopiaException{ + + public MatrixND matrixOwnerMarginOverVariableCostsPerStrategy(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY, - new List[]{strategies}, - new String[]{n_("Strategies")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY, + new List[] { strategies }, + new String[] { n_("Strategies") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); double value = ownerMarginOverVariableCostsPerStrategy(str, date); result.setValue(s, value); } -// for(Strategy str : strategies){ -// double value = ownerMarginOverVariableCostsPerStrategy(str, date); -// result.setValue(str, value); -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * OwnerMarginOverVariableCostsPerStrategy[str,month]?=?OwnerMarginOverVariableCostsPerStrategyPerVessel[str,month]?*[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * OwnerMarginOverVariableCostsPerStrategy[str,month] = + * OwnerMarginOverVariableCostsPerStrategyPerVessel[str,month] + * *[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] * * @param str * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double ownerMarginOverVariableCostsPerStrategy(Strategy str, Date date) throws TopiaException { - double ownerMarginOverVariableCostsPerStrategyPerVessel = ownerMarginOverVariableCostsPerStrategyPerVessel(str, date); + private double ownerMarginOverVariableCostsPerStrategy(Strategy str, + Date date) throws TopiaException { + double ownerMarginOverVariableCostsPerStrategyPerVessel = ownerMarginOverVariableCostsPerStrategyPerVessel( + str, date); double proportionSetOfVessels = str.getProportionSetOfVessels(); double numberOfVessels = str.getSetOfVessels().getNumberOfVessels(); - return ownerMarginOverVariableCostsPerStrategyPerVessel * (proportionSetOfVessels * numberOfVessels); - } + return ownerMarginOverVariableCostsPerStrategyPerVessel + * (proportionSetOfVessels * numberOfVessels); + } ////////////////////////////////////////////////////////////////////// // matrixVesselMarginOverVariableCostsPerStrategyPerVessel ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixVesselMarginOverVariableCostsPerStrategyPerVessel(Date date) throws TopiaException{ + + public MatrixND matrixVesselMarginOverVariableCostsPerStrategyPerVessel( + Date date) throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL, - new List[]{strategies}, - new String[]{n_("Strategies")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL, + new List[] { strategies }, + new String[] { n_("Strategies") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); - double value = vesselMarginOverVariableCostsPerStrategyPerVessel(str, date); + double value = vesselMarginOverVariableCostsPerStrategyPerVessel( + str, date); result.setValue(s, value); } -// for(Strategy str : strategies){ -// double value = vesselMarginOverVariableCostsPerStrategyPerVessel(str, date); -// result.setValue(str, value); -// } return result; } - + /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * VesselMarginOverVariableCostsPerStrategyPerVessel[str,month]?= somme sur tous les m?tiers de VesselMarginOverVariableCostsPerStrategyMetPerVessel? [str,met,month] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * VesselMarginOverVariableCostsPerStrategyPerVessel[str,month] = somme sur + * tous les metiers de VesselMarginOverVariableCostsPerStrategyMetPerVessel + * [str,met,month] * * @param str * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double vesselMarginOverVariableCostsPerStrategyPerVessel(Strategy str, Date date) throws TopiaException { + private double vesselMarginOverVariableCostsPerStrategyPerVessel( + Strategy str, Date date) throws TopiaException { SetOfVessels sov = str.getSetOfVessels(); Collection<EffortDescription> efforts = sov.getPossibleMetiers(); @@ -1183,74 +1149,80 @@ for (EffortDescription effort : efforts) { Metier metier = effort.getPossibleMetiers(); - result += vesselMarginOverVariableCostsPerStrategyMetPerVessel(str, metier, date); + result += vesselMarginOverVariableCostsPerStrategyMetPerVessel(str, + metier, date); } return result; - } + } - ////////////////////////////////////////////////////////////////////// // matrixVesselMarginOverVariableCostsPerStrategy ////////////////////////////////////////////////////////////////////// - - public MatrixND matrixVesselMarginOverVariableCostsPerStrategy(Date date) throws TopiaException{ + + public MatrixND matrixVesselMarginOverVariableCostsPerStrategy(Date date) + throws TopiaException { List<Strategy> strategies = siMatrix.getStrategies(date); - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY, - new List[]{strategies}, - new String[]{n_("Strategies")}); + MatrixND result = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY, + new List[] { strategies }, + new String[] { n_("Strategies") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); double value = vesselMarginOverVariableCostsPerStrategy(str, date); result.setValue(s, value); } -// for(Strategy str : strategies){ -// double value = vesselMarginOverVariableCostsPerStrategy(str, date); -// result.setValue(str, value); -// } return result; } /** - * implant? suivant document ModifTable3PourBP25-07-2006.doc - * VesselMarginOverVariableCostsPerStrategy[str,month]?=VesselMarginOverVariableCostsPerStrategyPerVessel?[str,month] *[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] + * implante suivant document ModifTable3PourBP25-07-2006.doc + * VesselMarginOverVariableCostsPerStrategy[str,month] + * =VesselMarginOverVariableCostsPerStrategyPerVessel [str,month] + * *[PropNbVessels(str,sov)*NbVesselsSetOfVessels(sov)] * * @param str * @param date * @return - * @throws TopiaException + * @throws TopiaException */ - private double vesselMarginOverVariableCostsPerStrategy(Strategy str, Date date) throws TopiaException { - double vesselMarginOverVariableCostsPerStrategyPerVessel = vesselMarginOverVariableCostsPerStrategyPerVessel(str, date); + private double vesselMarginOverVariableCostsPerStrategy(Strategy str, + Date date) throws TopiaException { + double vesselMarginOverVariableCostsPerStrategyPerVessel = vesselMarginOverVariableCostsPerStrategyPerVessel( + str, date); double proportionSetOfVessels = str.getProportionSetOfVessels(); double numberOfVessels = str.getSetOfVessels().getNumberOfVessels(); - return vesselMarginOverVariableCostsPerStrategyPerVessel * (proportionSetOfVessels * numberOfVessels); + return vesselMarginOverVariableCostsPerStrategyPerVessel + * (proportionSetOfVessels * numberOfVessels); } - /////////////////////////////////////////////////////////////////////////// // - // Methode non utilis?e directement dans GravityModel, mais dans les rules + // Methode non utilisee directement dans GravityModel, mais dans les rules // /////////////////////////////////////////////////////////////////////////// - public double valuePerUnitFishingEffort(Strategy str, Metier metier, Date date) throws TopiaException{ - List<Population> pops = siMatrix.getPopulations(date); + public double valuePerUnitFishingEffort(Strategy str, Metier metier, + Date date) throws TopiaException { + List<Population> pops = siMatrix.getPopulations(date); - double result = 0; + double result = 0; - for(Population pop : pops){ + for (Population pop : pops) { List<PopulationGroup> groups = pop.getPopulationGroup(); Collection<Zone> zones = pop.getPopulationZone(); - for(PopulationGroup group : groups){ + for (PopulationGroup group : groups) { double price = group.getPrice(); - for(Zone zone : zones){ - double catchValue = getCatchWeightPerStrMetPerZonePop(str, metier, group, zone, date); - double discards = getDiscardsWeightPerStrMet(str, metier, group, zone, date); + for (Zone zone : zones) { + double catchValue = getCatchWeightPerStrMetPerZonePop(str, + metier, group, zone, date); + double discards = getDiscardsWeightPerStrMet(str, metier, + group, zone, date); result += price * (catchValue - discards); } } @@ -1258,7 +1230,7 @@ double effort = getEffortPerStrategyMet(str, metier, date); - if(effort == 0){ + if (effort == 0) { result = 0; } else { result = result / effort; @@ -1274,28 +1246,32 @@ * @return */ public double getEffortPerStrategyMet(Strategy str, Metier metier, Date date) { - MatrixND mat = resultManager.getMatrix(date, ResultName.MATRIX_EFFORT_PER_STRATEGY_MET); + MatrixND mat = resultManager.getMatrix(date, + ResultName.MATRIX_EFFORT_PER_STRATEGY_MET); double result = 0; - if(mat != null){ + if (mat != null) { result = mat.getValue(str, metier); } return result; } - public double landingPerUnitFishingEffort(Strategy str, Metier metier, Date date) throws TopiaException{ + public double landingPerUnitFishingEffort(Strategy str, Metier metier, + Date date) throws TopiaException { List<Population> pops = siMatrix.getPopulations(date); double effort = getEffortPerStrategyMet(str, metier, date); double result = 0; - if(effort != 0){ // s'il n'y a pas d'effort on retournera 0 - for(Population pop : pops){ + if (effort != 0) { // s'il n'y a pas d'effort on retournera 0 + for (Population pop : pops) { List<PopulationGroup> groups = pop.getPopulationGroup(); Collection<Zone> zones = pop.getPopulationZone(); - for(PopulationGroup group : groups){ - for(Zone zone : zones){ - double catchValue = getCatchWeightPerStrMetPerZonePop(str, metier, group, zone, date); - double discards = getDiscardsWeightPerStrMet(str, metier, group, zone, date); + for (PopulationGroup group : groups) { + for (Zone zone : zones) { + double catchValue = getCatchWeightPerStrMetPerZonePop( + str, metier, group, zone, date); + double discards = getDiscardsWeightPerStrMet(str, + metier, group, zone, date); result += catchValue - discards; } } @@ -1305,7 +1281,4 @@ return result; } - } - - Modified: isis-fish/trunk/src/test/resources/test-database/scripts/ResultName.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/scripts/ResultName.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/scripts/ResultName.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,6 +1,6 @@ /* *##% * Copyright (C) 2006 - * Code Lutin, Cédric Pineau, Benjamin Poussin + * Code Lutin, Cedric Pineau, Benjamin Poussin * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -20,7 +20,7 @@ /* * * ResultName.java * - * Created: 23 août 2006 15:09:37 + * Created: 23 aout 2006 15:09:37 * * @author poussin * @version $Revision: 1.10 $ @@ -37,103 +37,105 @@ /** * Contient l'ensemble des noms des differents resultats. Le mieux lorsque l'on - * veut un nouveau résultat est d'ajouter une constante ici, et de l'utiliser - * ensuite lors de la création de la matrice. + * veut un nouveau resultat est d'ajouter une constante ici, et de l'utiliser + * ensuite lors de la creation de la matrice. * <p> - * Ceci permet d'avoir un endroit unique ou l'on voit l'ensemble des résultats - * potentiellement disponible et de ne pas ce tromper en écrivent le nom - * d'un résultat + * Ceci permet d'avoir un endroit unique ou l'on voit l'ensemble des resultats + * potentiellement disponible et de ne pas ce tromper en ecrivent le nom d'un + * resultat * <p> - * Cette classe ne doit contenir que des noms de resultat en static public String - * l'interface de lancement de simulation se base sur cette classe pour - * afficher l'ensemble des résultats disponible + * Cette classe ne doit contenir que des noms de resultat en static public + * String l'interface de lancement de simulation se base sur cette classe pour + * afficher l'ensemble des resultats disponible * * @author poussin */ public class ResultName { @Doc(value = "do the doc of Result matrixDiscardsWeightPerStrMet") - static final public String MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP = n_("matrixDiscardsWeightPerStrMet"); + static final public String MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP = n_("matrixDiscardsWeightPerStrMetPerZonePop"); - @Doc(value = "do the doc of Result matrixDiscardsPerStrMet") - static final public String MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP = n_("matrixDiscardsPerStrMet"); - @Doc(value = "do the doc of Result matrixLandingPerMet") + @Doc(value = "do the doc of Result matrixDiscardsPerStrMet") + static final public String MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP = n_("matrixDiscardsPerStrMetPerZonePop"); + @Doc(value = "do the doc of Result matrixLandingPerMet") static final public String MATRIX_LANDING_PER_MET = n_("matrixLandingPerMet"); - @Doc(value = "do the doc of Result matrixEffortPerStrategyMet") + @Doc(value = "do the doc of Result matrixEffortPerStrategyMet") static final public String MATRIX_EFFORT_PER_STRATEGY_MET = n_("matrixEffortPerStrategyMet"); - @Doc(value = "do the doc of Result matrixStdTravelEffortPerStrategyMet") + @Doc(value = "do the doc of Result matrixEffortNominalPerStrategyMet") + static final public String MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET = n_("matrixEffortNominalPerStrategyMet"); + @Doc(value = "do the doc of Result matrixStdTravelEffortPerStrategyMet") static final public String MATRIX_STD_TRAVEL_EFFORT_PER_STRATEGY_MET = n_("matrixStdTravelEffortPerStrategyMet"); - @Doc(value = "do the doc of Result matrixEffortPerZonePop") + @Doc(value = "do the doc of Result matrixEffortPerZonePop") static final public String MATRIX_EFFORT_PER_ZONE_POP = n_("matrixEffortPerZonePop"); @Doc(value = "Disponible uniquement avec les simulations par Zone. do the doc of Result matrixCatchRatePerStrategyMet") static final public String MATRIX_CATCH_RATE_PER_STRATEGY_MET_PER_ZONE_POP = n_("matrixCatchRatePerStrategyMet"); - @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZoneMet") + @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZoneMet") static final public String MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchPerStrategyMetPerZoneMet"); - @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZonePop") + @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZonePop") static final public String MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP = n_("matrixCatchPerStrategyMetPerZonePop"); - @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZoneMet") + @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZoneMet") static final public String MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchWeightPerStrategyMetPerZoneMet"); - @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZonePop") + @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZonePop") static final public String MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP = n_("matrixCatchWeightPerStrategyMetPerZonePop"); @Doc(value = "Disponible uniquement avec les simulations par Zone. do the doc of Result matrixFishingMortality") static final public String MATRIX_FISHING_MORTALITY = n_("matrixFishingMortality"); - @Doc(value = "do the doc of Result matrixAbundance") + @Doc(value = "do the doc of Result matrixAbundance") static final public String MATRIX_ABUNDANCE = n_("matrixAbundance"); - @Doc(value = "do the doc of Result matrixBiomass") + @Doc(value = "do the doc of Result matrixBiomass") + static final public String MATRIX_ABUNDANCE_BEGIN_MONTH = n_("matrixAbundanceBeginMonth"); + @Doc(value = "do the doc of Result matrixBiomass") static final public String MATRIX_BIOMASS = n_("matrixBiomass"); - @Doc(value = "do the doc of Result matrixBiomassBeginMonth") + @Doc(value = "do the doc of Result matrixBiomass") static final public String MATRIX_BIOMASS_BEGIN_MONTH = n_("matrixBiomassBeginMonth"); - @Doc(value = "do the doc of Result matrixBiomassBeginMonth") - static final public String MATRIX_ABONDANCE_BEGIN_MONTH = n_("matrixAbondanceBeginMonth"); - @Doc(value = "do the doc of Result matrixFishingTimePerMonthPerVessel") + @Doc(value = "do the doc of Result matrixFishingTimePerMonthPerVessel") static final public String MATRIX_FISHING_TIME_PER_MONTH_PER_VESSEL = n_("matrixFishingTimePerMonthPerVessel"); - @Doc(value = "do the doc of Result matrixFuelCostsOfTravelPerVessel") + @Doc(value = "do the doc of Result matrixFuelCostsOfTravelPerVessel") static final public String MATRIX_FUEL_COSTS_OF_TRAVEL_PER_VESSEL = n_("matrixFuelCostsOfTravelPerVessel"); - @Doc(value = "do the doc of Result matrixCostsOfFishingPerVessel") + @Doc(value = "do the doc of Result matrixCostsOfFishingPerVessel") static final public String MATRIX_COSTS_OF_FISHING_PER_VESSEL = n_("matrixCostsOfFishingPerVessel"); - @Doc(value = "do the doc of Result matrixFuelCostsPerVessel") + @Doc(value = "do the doc of Result matrixFuelCostsPerVessel") static final public String MATRIX_FUEL_COSTS_PER_VESSEL = n_("matrixFuelCostsPerVessel"); - @Doc(value = "do the doc of Result matrixRepairAndMaintenanceGearCostsPerVessel") + @Doc(value = "do the doc of Result matrixRepairAndMaintenanceGearCostsPerVessel") static final public String MATRIX_REPAIR_AND_MAINTENANCE_GEAR_COSTS_PER_VESSEL = n_("matrixRepairAndMaintenanceGearCostsPerVessel"); - @Doc(value = "do the doc of Result matrixOtherRunningCostsPerVessel") + @Doc(value = "do the doc of Result matrixOtherRunningCostsPerVessel") static final public String MATRIX_OTHER_RUNNING_COSTS_PER_VESSEL = n_("matrixOtherRunningCostsPerVessel"); - @Doc(value = "do the doc of Result matrixSharedNotFixedCostsPerVessel") + @Doc(value = "do the doc of Result matrixSharedNotFixedCostsPerVessel") static final public String MATRIX_SHARED_NOT_FIXED_COSTS_PER_VESSEL = n_("matrixSharedNotFixedCostsPerVessel"); -// static final public String MATRIX_SHARED_FIXED_COSTS_PER_VESSEL_PER_MET = n_("matrixSharedFixedCostsPerVesselPerMet"); - @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerSpeciesPerStrategyMet") + // static final public String MATRIX_SHARED_FIXED_COSTS_PER_VESSEL_PER_MET = n_("matrixSharedFixedCostsPerVesselPerMet"); + @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerSpeciesPerStrategyMet") static final public String MATRIX_GROSS_VALUE_OF_LANDINGS_PER_SPECIES_PER_STRATEGY_MET = n_("matrixGrossValueOfLandingsPerSpeciesPerStrategyMet"); - @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerStrategyMet") + @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerStrategyMet") static final public String MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET = n_("matrixGrossValueOfLandingsPerStrategyMet"); - @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerStrategyMetPerVessel") + @Doc(value = "do the doc of Result matrixGrossValueOfLandingsOtherSpeciesPerStrategyMet") + static final public String MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET = n_("matrixGrossValueOfLandingsOtherSpeciesPerStrategyMet"); + @Doc(value = "do the doc of Result matrixGrossValueOfLandingsPerStrategyMetPerVessel") static final public String MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL = n_("matrixGrossValueOfLandingsPerStrategyMetPerVessel"); - @Doc(value = "do the doc of Result matrixNetValueOfLandingsPerStrategyMet") + @Doc(value = "do the doc of Result matrixNetValueOfLandingsPerStrategyMet") static final public String MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET = n_("matrixNetValueOfLandingsPerStrategyMet"); - @Doc(value = "do the doc of Result matrixNetValueOfLandingsPerStrategyMetPerVessel") + @Doc(value = "do the doc of Result matrixNetValueOfLandingsPerStrategyMetPerVessel") static final public String MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET_PER_VESSEL = n_("matrixNetValueOfLandingsPerStrategyMetPerVessel"); - @Doc(value = "do the doc of Result matrixNetRenevueToSharePerStrategyMetPerVessel") + @Doc(value = "do the doc of Result matrixNetRenevueToSharePerStrategyMetPerVessel") static final public String MATRIX_NET_RENEVUE_TO_SHARE_PER_STRATEGY_MET_PER_VESSEL = n_("matrixNetRenevueToSharePerStrategyMetPerVessel"); - @Doc(value = "do the doc of Result matrixCrewSharePerStrategyPerVessel") + @Doc(value = "do the doc of Result matrixCrewSharePerStrategyPerVessel") static final public String MATRIX_CREW_SHARE_PER_STRATEGY_MET_PER_VESSEL = n_("matrixCrewSharePerStrategyPerVessel"); - @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel") + @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel") static final public String MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL = n_("matrixOwnerMarginOverVariableCostsPerStrategyMetPerVessel"); - @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel") + @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel") static final public String MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_MET_PER_VESSEL = n_("matrixVesselMarginOverVariableCostsPerStrategyMetPerVessel"); - @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategyPerVessel") + @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategyPerVessel") static final public String MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL = n_("matrixOwnerMarginOverVariableCostsPerStrategyPerVessel"); - @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategy") + @Doc(value = "do the doc of Result matrixOwnerMarginOverVariableCostsPerStrategy") static final public String MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY = n_("matrixOwnerMarginOverVariableCostsPerStrategy"); - @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategyPerVessel") + @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategyPerVessel") static final public String MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL = n_("matrixVesselMarginOverVariableCostsPerStrategyPerVessel"); - @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategy") + @Doc(value = "do the doc of Result matrixVesselMarginOverVariableCostsPerStrategy") static final public String MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY = n_("matrixVesselMarginOverVariableCostsPerStrategy"); - @Doc(value = "do the doc of Result matrixNoActivity") + @Doc(value = "do the doc of Result matrixNoActivity") static final public String MATRIX_NO_ACTIVITY = n_("matrixNoActivity"); - @Doc(value = "do the doc of Result matrixMetierZone") + @Doc(value = "do the doc of Result matrixMetierZone") static final public String MATRIX_METIER_ZONE = n_("matrixMetierZone"); - @Doc(value = "do the doc of Result matrixPrice") + @Doc(value = "do the doc of Result matrixPrice") static final public String MATRIX_PRICE = n_("matrixPrice"); } - - Modified: isis-fish/trunk/src/test/resources/test-database/scripts/RuleUtil.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/scripts/RuleUtil.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/scripts/RuleUtil.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -14,7 +14,7 @@ import fr.ifremer.isisfish.types.Date; /** - * ChangeMatrixBackend.java + * RuleUtil. * * Created: 6 septembre 2006 * @@ -34,22 +34,21 @@ * @param species l'espece sur lequel on souhaite le total * @param date la date pour laquel on veut le calcul, cet argument est * passe seulement pour que le cache ne retourne pas toujours la meme valeur - * @return + * @return total catch in tons */ public static double getTotalCatchTons(SimulationContext context, Species species, Date date) { double result = 0; for (Population pop : species.getPopulation()) { MatrixND mat = context.getPopulationMonitor().getHoldCatch(pop); - if(mat!=null) { + if (mat != null) { mat = mat.copy(); mat = mat.sumOverDim(0); // sum over Strategies mat = mat.sumOverDim(1); // sum over metiers mat = mat.sumOverDim(3); // sum over zones -// List<PopulationGroup> groups = mat.getSemantics(2); List<PopulationGroup> groups = pop.getPopulationGroup(); - - for (int c=0; c<groups.size(); c++) { + + for (int c = 0; c < groups.size(); c++) { PopulationGroup group = groups.get(c); double weight = group.getMeanWeight(); result += mat.getValue(0, 0, c, 0) * weight / 1000.0; @@ -58,8 +57,4 @@ } return result; } - - - - } Modified: isis-fish/trunk/src/test/resources/test-database/scripts/SiMatrix.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/scripts/SiMatrix.java 2009-09-09 15:35:02 UTC (rev 2590) +++ isis-fish/trunk/src/test/resources/test-database/scripts/SiMatrix.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -1,6 +1,6 @@ /* *##% - * Copyright (C) 2006 - * Code Lutin, Benjamin Poussin + * Copyright (C) 2006 - 2009 + * Ifremer, Code Lutin, Benjamin Poussin * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -17,28 +17,15 @@ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *##%*/ -/* * - * SiMatrix.java - * - * Created: 21 ao?t 2006 15:53:01 - * - * @author poussin - * @version $Revision: 1.18 $ - * - * Last update: $Date: 2007-11-02 17:53:20 $ - * by : $Author: bpoussin $ - */ - package scripts; -import static org.codelutin.i18n.I18n._; import static org.codelutin.i18n.I18n.n_; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; -import java.util.Iterator; import java.util.List; +import java.util.Set; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -67,56 +54,66 @@ import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.Date; import fr.ifremer.isisfish.types.Month; -import java.util.Arrays; -import java.util.Set; /** + * SiMatrix.java + * + * Created: 21 aout 2006 15:53:01 + * * @author poussin + * @version $Revision: 1.18 $ * + * Last update: $Date: 2007-11-02 17:53:20 $ + * by : $Author: bpoussin $ */ - public class SiMatrix { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(SiMatrix.class); - + protected SimulationContext context = null; protected TopiaContext db = null; - + /** * Method used to get SiMatrix used for simulation - * @param context context simulation + * + * @param context + * context simulation * @return SiMatrix or null if no SiMatrix created for simulation + * @throws TopiaException */ - public static SiMatrix getSiMatrix(SimulationContext context) throws TopiaException { - SiMatrix result = (SiMatrix)context.getValue(SiMatrix.class.getName()); + public static SiMatrix getSiMatrix(SimulationContext context) + throws TopiaException { + SiMatrix result = (SiMatrix) context.getValue(SiMatrix.class.getName()); if (result == null) { result = new SiMatrix(context); } return result; } - + private static void setSiMatrix(SimulationContext context, SiMatrix siMatrix) { context.setValue(SiMatrix.class.getName(), siMatrix); } - + /** * - * @param context Simulation context - * @param db TopiaContext with transaction opened. You must used this - * TopiaContext and not used - * SimulationContext.getSimulationStorage().getStorage() - * @throws TopiaException + * @param context + * Simulation context + * @param db + * TopiaContext with transaction opened. You must used this + * TopiaContext and not used + * SimulationContext.getSimulationStorage().getStorage() + * @throws TopiaException */ public SiMatrix(SimulationContext context) throws TopiaException { this.context = context; this.db = context.getDB(); setSiMatrix(context, this); } - + /** * @return - * @throws TopiaException + * @throws TopiaException */ public List<Zone> getZones(Date date) throws TopiaException { ZoneDAO dao = IsisFishDAOHelper.getZoneDAO(db); @@ -126,12 +123,13 @@ /** * @return - * @throws TopiaException + * @throws TopiaException */ public List<Population> getPopulations(Date date) throws TopiaException { List<Population> populations = new ArrayList<Population>(); - for (Population pop : context.getSimulationStorage().getParameter().getPopulations()) { - Population tmp = (Population)db.findByTopiaId(pop.getTopiaId()); + for (Population pop : context.getSimulationStorage().getParameter() + .getPopulations()) { + Population tmp = (Population) db.findByTopiaId(pop.getTopiaId()); populations.add(tmp); } return populations; @@ -139,39 +137,40 @@ /** * @return - * @throws TopiaException + * @throws TopiaException */ public List<Strategy> getStrategies(Date date) throws TopiaException { -// if (strategies == null) { + // if (strategies == null) { List<Strategy> strategies = new ArrayList<Strategy>(); - for (Strategy str : context.getSimulationStorage().getParameter().getStrategies()) { - Strategy tmp = (Strategy)db.findByTopiaId(str.getTopiaId()); - strategies.add(tmp); - } -// } + for (Strategy str : context.getSimulationStorage().getParameter() + .getStrategies()) { + Strategy tmp = (Strategy) db.findByTopiaId(str.getTopiaId()); + strategies.add(tmp); + } + // } return strategies; } public List<Metier> getMetiers(Date date) throws TopiaException { -// if (metiers == null) { - List<Metier> metiers = new ArrayList<Metier>(); - HashSet<Metier> tmp = new HashSet<Metier>(); - for (Strategy str : getStrategies(date)) { - SetOfVessels sov = str.getSetOfVessels(); - for (EffortDescription effort : sov.getPossibleMetiers()) { - Metier metier = effort.getPossibleMetiers(); - if (tmp.add(metier)) { - metiers.add(metier); - } + // if (metiers == null) { + List<Metier> metiers = new ArrayList<Metier>(); + HashSet<Metier> tmp = new HashSet<Metier>(); + for (Strategy str : getStrategies(date)) { + SetOfVessels sov = str.getSetOfVessels(); + for (EffortDescription effort : sov.getPossibleMetiers()) { + Metier metier = effort.getPossibleMetiers(); + if (tmp.add(metier)) { + metiers.add(metier); } } -// } + } + // } return metiers; } /** - * Retourne les metiers pratiqu?s par une Strategie ? une date donn?e - * Un metier est pratiqu? si le PropStrMet est diff?rent de 0 + * Retourne les metiers pratiques par une Strategie a une date donnee Un + * metier est pratique si le PropStrMet est different de 0 * * @param str * @param date @@ -180,13 +179,13 @@ public List<Metier> getMetiers(Strategy str, Date date) { StrategyMonthInfo info = str.getStrategyMonthInfo(date.getMonth()); MatrixND props = info.getProportionMetier(); - + List<Metier> result = new ArrayList<Metier>(); - - for (MatrixIterator i=props.iterator(); i.hasNext();) { + + for (MatrixIterator i = props.iterator(); i.hasNext();) { i.next(); if (i.getValue() != 0) { - Metier metier = (Metier)i.getSemanticsCoordinates()[0]; + Metier metier = (Metier) i.getSemanticsCoordinates()[0]; result.add(metier); } } @@ -194,26 +193,26 @@ } /** - * Retourne la matrix Metier x Zone qui correspond au zone utilis? par - * un m?tier pour une date donn?e. Si la valeur de la matrice est 1 alors - * la zone est utilis? par le m?tier, si elle vaut 0 alors elle n'est pas - * utilis?e. + * Retourne la matrix Metier x Zone qui correspond au zone utilise par un + * metier pour une date donnee. Si la valeur de la matrice est 1 alors la + * zone est utilise par le metier, si elle vaut 0 alors elle n'est pas + * utilisee. * * @param date * @return - * @throws TopiaException + * @throws TopiaException */ public MatrixND getMetierZone(Date date) throws TopiaException { List<Metier> metiers = getMetiers(date); List<Zone> zones = getZones(date); - + MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_METIER_ZONE, - new List[]{metiers, zones}, - new String[]{n_("Metiers"), n_("Zones")}); + ResultName.MATRIX_METIER_ZONE, new List[] { metiers, zones }, + new String[] { n_("Metiers"), n_("Zones") }); for (Metier metier : metiers) { - Collection<Zone> zoneMetier = metier.getMetierSeasonInfo(date.getMonth()).getZone(); + Collection<Zone> zoneMetier = metier.getMetierSeasonInfo( + date.getMonth()).getZone(); for (Zone zone : zoneMetier) { result.setValue(metier, zone, 1); } @@ -224,25 +223,26 @@ public MatrixND matrixPrice(Date date, Population pop) { List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_PRICE, - new List[]{groups}, - new String[]{n_("PopulationGroup")}); - + ResultName.MATRIX_PRICE, new List[] { groups }, + new String[] { n_("PopulationGroup") }); + for (PopulationGroup group : groups) { result.setValue(group, group.getPrice()); } - + return result; } - - /////////////////////////////////////////////////////////////////////////// + + /////////////////////////////////////////////////////////////////////////// // // Toutes les methodes suivantes ne sont utiles que pour // matrixCatchPerStrategyMet // /////////////////////////////////////////////////////////////////////////// - - public MatrixND matrixCatchWeightPerStrategyMetPerZoneMet(Date date, Population pop, MatrixND matrixCatchPerStrategyMetPerZoneMet) throws TopiaException, IsisFishException { + + public MatrixND matrixCatchWeightPerStrategyMetPerZoneMet(Date date, + Population pop, MatrixND matrixCatchPerStrategyMetPerZoneMet) + throws TopiaException, IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZoneMet.copy(); @@ -257,35 +257,43 @@ return result; } - public MatrixND matrixCatchPerStrategyMetPerZoneMet(MatrixND N, Population pop, Date date) throws TopiaException, IsisFishException { - - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell(date, pop); - MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell(pop, date, matrixFishingMortalityPerCell); - MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell(N, pop, date, matrixCatchRatePerStrategyMetPerCell); - + public MatrixND matrixCatchPerStrategyMetPerZoneMet(MatrixND N, + Population pop, Date date) throws TopiaException, IsisFishException { + + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + date, pop); + MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( + pop, date, matrixFishingMortalityPerCell); + MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( + N, pop, date, matrixCatchRatePerStrategyMetPerCell); + List<Strategy> strategies = getStrategies(date); List<Metier> metiers = getMetiers(date); - List<PopulationGroup> groups = matrixCatchPerStrategyMetPerCell.getSemantics(2); + List<PopulationGroup> groups = matrixCatchPerStrategyMetPerCell + .getSemantics(2); List<Zone> zones = getZones(date); - Set<Cell> cellPops = new HashSet(matrixCatchPerStrategyMetPerCell.getSemantics(4)); - + Set<Cell> cellPops = new HashSet(matrixCatchPerStrategyMetPerCell + .getSemantics(4)); + MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET, - new List[]{strategies, metiers, groups, zones}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); - + new List[] { strategies, metiers, groups, zones }, + new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), + n_("Zones") }); + // matrice temporaire ou les zones pops sont sommees MatrixND tmp = matrixCatchPerStrategyMetPerCell.sumOverDim(3); tmp = tmp.reduceDims(3); - + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); - for(int g = 0; g<groups.size(); g++) { + for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(date.getMonth()); + MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(date + .getMonth()); Collection<Zone> zoneMet = infoMet.getZone(); for (Zone z : zoneMet) { double value = 0; @@ -304,15 +312,19 @@ } } } - + return result; } - - public MatrixND matrixCatchPerStrategyMetPerZonePop(MatrixND N, Population pop, Date date) throws TopiaException, IsisFishException { - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell(date, pop); - MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell(pop, date, matrixFishingMortalityPerCell); - MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell(N, pop, date, matrixCatchRatePerStrategyMetPerCell); - + + public MatrixND matrixCatchPerStrategyMetPerZonePop(MatrixND N, + Population pop, Date date) throws TopiaException, IsisFishException { + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + date, pop); + MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( + pop, date, matrixFishingMortalityPerCell); + MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( + N, pop, date, matrixCatchRatePerStrategyMetPerCell); + // on somme sur les cellules MatrixND result = matrixCatchPerStrategyMetPerCell.sumOverDim(4); result = result.reduceDims(4); @@ -320,9 +332,10 @@ return result; } - + public MatrixND matrixCatchWeightPerStrategyMetPerZonePop(Date date, - Population pop, MatrixND matrixCatchPerStrategyMetPerZonePop) throws TopiaException, IsisFishException { + Population pop, MatrixND matrixCatchPerStrategyMetPerZonePop) + throws TopiaException, IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZonePop.copy(); @@ -337,33 +350,33 @@ return result; } - /** * Utilise pour le calcul en Zone - * - * Matrice des captures en nombre - * dim [ Strategy x Metier x Classe x zonePop ] - * + * + * Matrice des captures en nombre dim [ Strategy x Metier x Classe x zonePop ] + * * @param N l'abondance sous forme de matrice 2D [class x zone] * @param pop * @param date + * @param matrixCatchRatePerStrategyMet * @return * @throws TopiaException * @throws IsisFishException */ - public MatrixND matrixCatchPerStrategyMetPerZone(MatrixND N, Population pop, - Date date, MatrixND matrixCatchRatePerStrategyMet) throws TopiaException, IsisFishException { + public MatrixND matrixCatchPerStrategyMetPerZone(MatrixND N, + Population pop, Date date, MatrixND matrixCatchRatePerStrategyMet) + throws TopiaException, IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); // on le passe en argument ce qui evite de le calculer 2 fois -// MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMet(pop, date); + // MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMet(pop, date); MatrixND result = matrixCatchRatePerStrategyMet.copy(); result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); - for(PopulationGroup group : groups) { + for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); - for(Zone zone : zones){ + for (Zone zone : zones) { MatrixND subsub = sub.getSubMatrix(3, zone, 1); double val = N.getValue(group, zone); subsub.mults(val); @@ -373,17 +386,19 @@ } /** - * Utilise pour le calcul en Zone - * Matrice des captures en poids - * dim [ Strategy x Metier x Classe x zonePop ] - * + * Utilise pour le calcul en Zone Matrice des captures en poids dim [ + * Strategy x Metier x Classe x zonePop ] + * * @param pop * @param date + * @param matrixFishingMortality * @return * @throws TopiaException * @throws IsisFishException */ - public MatrixND matrixCatchRatePerStrategyMetPerZone(Population pop, Date date, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { + public MatrixND matrixCatchRatePerStrategyMetPerZone(Population pop, + Date date, MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { List<Strategy> strategies = getStrategies(date); List<Metier> metiers = getMetiers(date); List<PopulationGroup> groups = pop.getPopulationGroup(); @@ -391,52 +406,53 @@ MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_CATCH_RATE_PER_STRATEGY_MET_PER_ZONE_POP, - new List[]{strategies, metiers, groups, zones}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); + new List[] { strategies, metiers, groups, zones }, + new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), + n_("Zones") }); - // Optimisation Hilaire - for (int s=0; s < strategies.size(); s++) { - Strategy str = strategies.get(s); - metiers = getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { - Metier metier = metiers.get(m); - for (int z=0; z < zones.size(); z++) { - Zone zone = zones.get(z); - double effort = effortPerZonePop(str,metier,date,zone); - if (effort > 0){ - for (int g=0; g < groups.size(); g++) { - PopulationGroup group = groups.get(g); - double value = catchRatePerStrategyMet(str, metier, date, group, zone, matrixFishingMortality); - result.setValue(str, metier, group, zone, value); - } + // Optimisation Hilaire + for (int s = 0; s < strategies.size(); s++) { + Strategy str = strategies.get(s); + metiers = getMetiers(str, date); + for (int m = 0; m < metiers.size(); m++) { + Metier metier = metiers.get(m); + for (int z = 0; z < zones.size(); z++) { + Zone zone = zones.get(z); + double effort = effortPerZonePop(str, metier, date, zone); + if (effort > 0) { + for (int g = 0; g < groups.size(); g++) { + PopulationGroup group = groups.get(g); + double value = catchRatePerStrategyMet(str, metier, + date, group, zone, matrixFishingMortality); + result.setValue(str, metier, group, zone, value); } } } } + } return result; } - /** + /** * @param str * @param metier * @param date * @param zone * @return */ - private double effortPerZonePop(Strategy str, Metier metier, Date date, Zone zonePop) { + private double effortPerZonePop(Strategy str, Metier metier, Date date, + Zone zonePop) { Month month = date.getMonth(); Collection<Zone> zoneMet = metier.getMetierSeasonInfo(month).getZone(); double inter = nbCellInter(zoneMet, zonePop); - double effortPerStrategyPerCell = effortPerStrategyPerCell(str, metier, date); + double effortPerStrategyPerCell = effortPerStrategyPerCell(str, metier, + date); - if(log.isDebugEnabled()) { - log.debug( - " strategy=" + str + - " metier=" + metier + - " inter=" + inter + - " effortPerStrategyPerCell=" + effortPerStrategyPerCell - ); + if (log.isDebugEnabled()) { + log.debug(" strategy=" + str + " metier=" + metier + " inter=" + + inter + " effortPerStrategyPerCell=" + + effortPerStrategyPerCell); } double result = effortPerStrategyPerCell * inter; @@ -444,29 +460,37 @@ } // Optimisation Hilaire - private double catchRatePerStrategyMet(Strategy str, Metier metier, Date date, PopulationGroup group, Zone zone, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { - double totalFishingMortality = totalFishingMortality(date, matrixFishingMortality).getValue(group, zone); + private double catchRatePerStrategyMet(Strategy str, Metier metier, + Date date, PopulationGroup group, Zone zone, + MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { + double totalFishingMortality = totalFishingMortality(date, + matrixFishingMortality).getValue(group, zone); - if(totalFishingMortality == 0){ - if(log.isDebugEnabled()) {log.debug("pas de totalFishingMortality pour (" + group + ", " + zone +")");} + if (totalFishingMortality == 0) { + if (log.isDebugEnabled()) { + log.debug("pas de totalFishingMortality pour (" + group + ", " + + zone + ")"); + } return 0; } - double fishingMortality = matrixFishingMortality.getValue(str, metier, group, zone); - double totalCatchRate = totalCatchRate(date, group, zone, totalFishingMortality); + double fishingMortality = matrixFishingMortality.getValue(str, metier, + group, zone); + double totalCatchRate = totalCatchRate(date, group, zone, + totalFishingMortality); - if(log.isDebugEnabled()) { - log.debug( - " totalFishingMortality=" + totalFishingMortality + - " fishingMortality=" + fishingMortality + - " totalCatchRate=" + totalCatchRate); + if (log.isDebugEnabled()) { + log.debug(" totalFishingMortality=" + totalFishingMortality + + " fishingMortality=" + fishingMortality + + " totalCatchRate=" + totalCatchRate); } - double result = fishingMortality / totalFishingMortality * totalCatchRate; + double result = fishingMortality / totalFishingMortality + * totalCatchRate; return result; } - /** * @param date * @param group @@ -475,35 +499,37 @@ * @return * @throws TopiaException */ - private double totalCatchRate(Date date, PopulationGroup group, - Zone zone, double totalFishingMortality) throws TopiaException { + private double totalCatchRate(Date date, PopulationGroup group, Zone zone, + double totalFishingMortality) throws TopiaException { double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; - if(M == 0){ + if (M == 0) { // normalement il devrait y avoir de la mortalite naturelle if (log.isWarnEnabled()) { - log.warn("Pas de mortalit? naturelle pour: " + group); + log.warn("Pas de mortalite naturelle pour: " + group); } } double F = totalFishingMortality; double result = 0; - if( M != 0 || F != 0){ - result = F/(F+M) * (1 - Math.exp(-(F+M))); + if (M != 0 || F != 0) { + result = F / (F + M) * (1 - Math.exp(-(F + M))); } return result; } /** - * Returne une matrice de mortalite group x zone, donc somme sur str et metier - * + * Returne une matrice de mortalite group x zone, donc somme sur str et + * metier + * * @param date * @param matrixFishingMortality * @param group * @param zone * @return */ - private MatrixND totalFishingMortality(Date date, MatrixND matrixFishingMortality) { + private MatrixND totalFishingMortality(Date date, + MatrixND matrixFishingMortality) { MatrixND result = matrixFishingMortality.sumOverDim(0); result = result.sumOverDim(1); result = result.reduceDims(0, 1); @@ -511,16 +537,16 @@ } /** - * Matrice fishing mortality - * dim [ Strategy x Metier x Classe x zonePop ] - * + * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop ] + * * @param pop * @param date * @return * @throws TopiaException * @throws IsisFishException */ - public MatrixND matrixFishingMortality(Date date, Population pop) throws TopiaException, IsisFishException { + public MatrixND matrixFishingMortality(Date date, Population pop) + throws TopiaException, IsisFishException { List<Strategy> strategies = getStrategies(date); List<Metier> metiers = getMetiers(date); List<PopulationGroup> groups = pop.getPopulationGroup(); @@ -529,8 +555,9 @@ // default value in matrix is 0 MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_FISHING_MORTALITY, - new List[]{strategies, metiers, groups, zones}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); + new List[] { strategies, metiers, groups, zones }, + new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), + n_("Zones") }); Month month = date.getMonth(); PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); @@ -545,28 +572,35 @@ for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(month); + MetierSeasonInfo infoMet = metier + .getMetierSeasonInfo(month); // getTargetFactor seem to be simple double ciblage = infoMet.getTargetFactor(group); if (ciblage != 0) { // check 0, this prevent next call, for default value Gear gear = metier.getGear(); - Selectivity selectivity = gear.getPopulationSelectivity(pop); + Selectivity selectivity = gear + .getPopulationSelectivity(pop); if (selectivity != null) { // getCoefficient is equation evaluation - double coeff = selectivity.getCoefficient(pop, group, metier); + double coeff = selectivity.getCoefficient(pop, + group, metier); if (coeff != 0) { // check 0, this prevent next call, for default value for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); - double effort = effortPerZonePop(str, metier, date, zone); + double effort = effortPerZonePop(str, + metier, date, zone); if (effort > 0) { // put value only if <> 0 - double value = coeff * capturability * ciblage * effort; - result.setValue(str, metier, group, zone, value); + double value = coeff + * capturability * ciblage + * effort; + result.setValue(str, metier, group, + zone, value); } } } @@ -580,31 +614,33 @@ } /** - * Matrice des captures en nombre - * dim [ Strategy x Metier x Classe x zonePop ] + * Matrice des captures en nombre dim [ Strategy x Metier x Classe x zonePop ] * - * @param N l'abondance sous forme de matrice 2D [class x zone] + * @param N + * l'abondance sous forme de matrice 2D [class x zone] * @param pop * @param date * @return - * @throws TopiaException - * @throws IsisFishException + * @throws TopiaException + * @throws IsisFishException */ - private MatrixND matrixCatchPerStrategyMetPerCell(MatrixND N, Population pop, - Date date, MatrixND matrixCatchRatePerStrategyMetPerCell) throws TopiaException, IsisFishException { + private MatrixND matrixCatchPerStrategyMetPerCell(MatrixND N, + Population pop, Date date, + MatrixND matrixCatchRatePerStrategyMetPerCell) + throws TopiaException, IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); // on le passe en argument ce qui evite de le calculer 2 fois -// MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMet(pop, date); + // MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMet(pop, date); MatrixND result = matrixCatchRatePerStrategyMetPerCell.copy(); result.setName("matrixCatchPerStrategyMetPerCell"); - for(PopulationGroup group : groups) { + for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); - for(Zone zone : zones){ + for (Zone zone : zones) { MatrixND subsub = sub.getSubMatrix(3, zone, 1); - double val = N.getValue(group, zone) / (double)zone.sizeCell(); + double val = N.getValue(group, zone) / (double) zone.sizeCell(); subsub.mults(val); } } @@ -612,16 +648,17 @@ } /** - * Matrice des captures en poids - * dim [ Strategy x Metier x Classe x zonePop ] + * Matrice des captures en poids dim [ Strategy x Metier x Classe x zonePop ] * * @param pop * @param date * @return - * @throws TopiaException - * @throws IsisFishException + * @throws TopiaException + * @throws IsisFishException */ - private MatrixND matrixCatchRatePerStrategyMetPerCell(Population pop, Date date, MatrixND matrixFishingMortalityPerCell) throws TopiaException, IsisFishException { + private MatrixND matrixCatchRatePerStrategyMetPerCell(Population pop, + Date date, MatrixND matrixFishingMortalityPerCell) + throws TopiaException, IsisFishException { List<Strategy> strategies = getStrategies(date); List<Metier> metiers = getMetiers(date); List<PopulationGroup> groups = pop.getPopulationGroup(); @@ -630,33 +667,16 @@ MatrixND result = MatrixFactory.getInstance().create( "matrixCatchRatePerStrategyMetPerCell", - new List[]{strategies, metiers, groups, zones, cells}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones"), n_("Cells")}); - -// for (int s=0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// metiers = getMetiers(str, date); -// for (int m=0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// for (int g=0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); -// for (int z=0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// double value = catchRatePerStrategyMet(str, metier, date, group, zone); -// result.setValue(str, metier, group, zone, value); -// } -// } -// } -// } - -// if(totalFishingMortality == 0){ -// if(log.isDebugEnabled()) {log.debug("pas de totalFishingMortality pour (" + pop + ")");} -// } else { - // Optimisation Hilaire - - MatrixND matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCell.sumOverDim(2); - matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCellSumOverGroup.reduceDims(2); - + new List[] { strategies, metiers, groups, zones, cells }, + new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), + n_("Zones"), n_("Cells") }); + + // Optimisation Hilaire + MatrixND matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCell + .sumOverDim(2); + matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCellSumOverGroup + .reduceDims(2); + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = getMetiers(str, date); @@ -667,130 +687,107 @@ List<Cell> cellZones = zone.getCell(); for (int c = 0; c < cellZones.size(); c++) { Cell cell = cellZones.get(c); - double effort = matrixFishingMortalityPerCellSumOverGroup.getValue( - str, metier, zone, cell); + double effort = matrixFishingMortalityPerCellSumOverGroup + .getValue(str, metier, zone, cell); if (effort > 0) { for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); double value = catchRatePerStrategyMetPerCell( str, metier, date, group, zone, cell, matrixFishingMortalityPerCell); - result.setValue(new Object[]{str, metier, group, - zone, cell}, value); + result.setValue(new Object[] { str, metier, + group, zone, cell }, value); } } } } } } -// } -// for (Strategy str : strategies) { -// List<Metier> metierStr = getMetiers(str, date); -// for (Metier metier : metierStr) { -// for (PopulationGroup group : groups) { -// for (Zone zone : zones) { -// double val = catchRatePerStrategyMet(str, metier, date, group, zone); -// result.setValue(str, metier, group, zone, val); -// } -// } -// } -// } return result; } /** + * catchRatePerStrategyMetPerCell. + * + * Optimisation Hilaire + * * @param str * @param metier * @param date * @param group * @param zone + * @param cell + * @param matrixFishingMortalityPerCell * @return - * @throws TopiaException - * @throws IsisFishException + * @throws TopiaException + * @throws IsisFishException */ -// private double catchRatePerStrategyMet(Strategy str, Metier metier, Date date, PopulationGroup group, Zone zone) throws TopiaException, IsisFishException { -// double totalFishingMortality = totalFishingMortality(date, group, zone); -// -// if(totalFishingMortality == 0){ -// if(log.isDebugEnabled()) {log.debug("pas de totalFishingMortality pour (" + group + ", " + zone +")");} -// return 0; -// } -// -// double fishingMortality = fishingMortality(str, metier, date, group, zone); -// double totalCatchRate = totalCatchRate(date, group, zone, totalFishingMortality); -// -// if(log.isDebugEnabled()) { -// log.debug( -// " totalFishingMortality=" + totalFishingMortality + -// " fishingMortality=" + fishingMortality + -// " totalCatchRate=" + totalCatchRate); -// } -// double result = fishingMortality / totalFishingMortality * totalCatchRate; -// -// return result; -// } - - // Optimisation Hilaire private double catchRatePerStrategyMetPerCell(Strategy str, Metier metier, Date date, PopulationGroup group, Zone zone, Cell cell, - MatrixND matrixFishingMortalityPerCell) throws TopiaException, IsisFishException { + MatrixND matrixFishingMortalityPerCell) throws TopiaException, + IsisFishException { - double totalFishingMortality = totalFishingMortalityPerCell(date, - matrixFishingMortalityPerCell).getValue(group, zone); + MatrixND totalFishingMortalityPerCell = totalFishingMortalityPerCell( + date, matrixFishingMortalityPerCell); + double totalFishingMortality = totalFishingMortalityPerCell.getValue( + group, zone, cell); - if(totalFishingMortality == 0){ - if(log.isDebugEnabled()) {log.debug("pas de totalFishingMortality pour (" + group + ", " + zone +")");} + if (totalFishingMortality == 0) { + if (log.isDebugEnabled()) { + log.debug("pas de totalFishingMortality pour (" + group + ", " + + zone + ")"); + } return 0; } - double fishingMortalityPerCell = matrixFishingMortalityPerCell.getValue( - new Object[]{str, metier, group, zone, cell}); - double totalCatchRatePerCell = - totalCatchRatePerCell(date, group, zone, totalFishingMortality); + double fishingMortalityPerCell = matrixFishingMortalityPerCell + .getValue(new Object[] { str, metier, group, zone, cell }); + double totalCatchRatePerCell = totalCatchRatePerCell(date, group, zone, + totalFishingMortality); - if(log.isDebugEnabled()) { - log.debug( - " totalFishingMortality=" + totalFishingMortality + - " fishingMortality=" + fishingMortalityPerCell + - " totalCatchRate=" + totalCatchRatePerCell); + if (log.isDebugEnabled()) { + log.debug(" totalFishingMortality=" + totalFishingMortality + + " fishingMortality=" + fishingMortalityPerCell + + " totalCatchRate=" + totalCatchRatePerCell); } - double result = - fishingMortalityPerCell / totalFishingMortality * totalCatchRatePerCell; + double result = fishingMortalityPerCell / totalFishingMortality + * totalCatchRatePerCell; return result; } - /** * @param date * @param group * @param zone * @param totalFishingMortality * @return - * @throws TopiaException + * @throws TopiaException */ private double totalCatchRatePerCell(Date date, PopulationGroup group, - Zone zone, double totalFishingMortalityPerCell) throws TopiaException { + Zone zone, double totalFishingMortalityPerCell) + throws TopiaException { double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; - if(M == 0){ + if (M == 0) { // normalement il devrait y avoir de la mortalite naturelle if (log.isWarnEnabled()) { - log.warn("Pas de mortalit? naturelle pour: " + group); + log.warn("Pas de mortalite naturelle pour: " + group); } } double F = totalFishingMortalityPerCell; double result = 0; - if( M != 0 || F != 0){ - result = F/(F+M) * (1 - Math.exp(-(F+M))); + if (M != 0 || F != 0) { + result = F / (F + M) * (1 - Math.exp(-(F + M))); } return result; } /** - * Returne une matrice de mortalite group x zone, donc somme sur str et metier + * Returne une matrice de mortalite group x zone, donc somme sur str et + * metier * * @param date * @param matrixFishingMortality @@ -798,26 +795,28 @@ * @param zone * @return */ - private MatrixND totalFishingMortalityPerCell(Date date, MatrixND matrixFishingMortalityPerCell) { + private MatrixND totalFishingMortalityPerCell(Date date, + MatrixND matrixFishingMortalityPerCell) { MatrixND result = matrixFishingMortalityPerCell.sumOverDim(0); result = result.sumOverDim(1); result = result.reduceDims(0, 1); return result; } - - // Nouvelle implantation suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) /** - * Matrice fishing mortality - * dim [ Strategy x Metier x Classe x zonePop x cellPop] + * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop x + * cellPop] * + * Nouvelle implantation suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) + * * @param pop * @param date * @return - * @throws TopiaException - * @throws IsisFishException + * @throws TopiaException + * @throws IsisFishException */ - public MatrixND matrixFishingMortalityPerCell(Date date, Population pop) throws TopiaException, IsisFishException { + public MatrixND matrixFishingMortalityPerCell(Date date, Population pop) + throws TopiaException, IsisFishException { List<Strategy> strategies = getStrategies(date); List<Metier> metiers = getMetiers(date); List<PopulationGroup> groups = pop.getPopulationGroup(); @@ -827,8 +826,9 @@ // default value in matrix is 0 MatrixND result = MatrixFactory.getInstance().create( "matrixFishingMortalityPerCell", - new List[]{strategies, metiers, groups, zones, cells}, - new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones"), n_("Cells")}); + new List[] { strategies, metiers, groups, zones, cells }, + new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), + n_("Zones"), n_("Cells") }); Month month = date.getMonth(); PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); @@ -843,7 +843,8 @@ for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); - MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(month); + MetierSeasonInfo infoMet = metier + .getMetierSeasonInfo(month); // getTargetFactor seem to be simple double ciblage = infoMet.getTargetFactor(group); @@ -854,13 +855,14 @@ if (selectivity != null) { // getCoefficient is equation evaluation - double coeff = selectivity.getCoefficient(pop, group, metier); + double coeff = selectivity.getCoefficient(pop,group, metier); if (coeff != 0) { // check 0, this prevent next call, for default value for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); // l'effort d'une cellule du metier - double effort = effortPerStrategyPerCell(str, metier, date); + double effort = effortPerStrategyPerCell( + str, metier, date); if (effort > 0) { // put value only if <> 0 for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); @@ -868,7 +870,13 @@ for (Cell cellMet : infoMet.getCells()) { if (cellPops.contains(cellMet)) { double value = coeff * capturability * ciblage * effort; - result.setValue(new Object[]{str, metier, group, zone, cellMet}, value); + result.setValue( + new Object[] { str, + metier, + group, + zone, + cellMet }, + value); } } } @@ -883,278 +891,37 @@ return result; } - // Supprimee suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) -// /** -// * Matrice fishing mortality -// * dim [ Strategy x Metier x Classe x zonePop ] -// * -// * @param pop -// * @param date -// * @return -// * @throws TopiaException -// * @throws IsisFishException -// */ -// public MatrixND matrixFishingMortalityPerCell(Date date, Population pop) throws TopiaException, IsisFishException { -// List<Strategy> strategies = getStrategies(date); -// List<Metier> metiers = getMetiers(date); -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// -// // default value in matrix is 0 -// MatrixND result = MatrixFactory.getInstance().create( -// ResultName.MATRIX_FISHING_MORTALITY, -// new List[]{strategies, metiers, groups, zones}, -// new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); -// -// Month month = date.getMonth(); -// PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); -// -// for (int g=0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); -// -// // getCapturability is check matrix validity and create matrix if needed and get one value in -// double capturability = infoPop.getCapturability(group); -// if (capturability != 0) { // check 0, this prevent next call, for default value -// -// for (int m=0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// -// MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(month); -// // getTargetFactor seem to be simple -// double ciblage = infoMet.getTargetFactor(group); -// -// if (ciblage != 0) { // check 0, this prevent next call, for default value -// -// Gear gear = metier.getGear(); -// Selectivity selectivity = gear.getPopulationSelectivity(pop); -// if (selectivity != null) { -// -// // getCoefficient is equation evaluation -// double coeff = selectivity.getCoefficient(pop, group, metier); -// if (coeff != 0) { // check 0, this prevent next call, for default value -// -// for (int s=0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// for (int z=0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// double effort = effortPerZonePop(str,metier,date,zone); -// if (effort > 0){ // put value only if <> 0 -// double value = coeff * capturability * ciblage * effort; -// result.setValue(str, metier, group, zone, value); -// } -// } -// } -// } -// } -// } -// } -// } -// } -// return result; -// } - - // ne prendre que les metiers pratiqu? semble une bonne idee, mais en fait non, car cela oblige l'ordre des boucles - // et donc ne permet pas autant d'optimisation que souhait? -// public MatrixND matrixFishingMortality2(Date date, Population pop) throws TopiaException, IsisFishException { -// List<Strategy> strategies = getStrategies(date); -// List<Metier> metiers = getMetiers(date); -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); - -// // default value in matrix is 0 -// MatrixND result = MatrixFactory.getInstance().create( -// ResultName.MATRIX_FISHING_MORTALITY, -// new List[]{strategies, metiers, groups, zones}, -// new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); - -// Month month = date.getMonth(); -// PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); - -// for (int s=0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// metiers = getMetiers(str, date); -// for (int m=0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// Gear gear = metier.getGear(); -// Selectivity selectivity = gear.getPopulationSelectivity(pop); -// if (selectivity != null) { -// MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(month); -// for (int z=0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// double effort = effortPerZonePop(str,metier,date,zone); -// if (effort > 0){ // put value only if <> 0 -// for (int g=0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); - -// // getTargetFactor seem to be simple -// double ciblage = infoMet.getTargetFactor(group); -// if (ciblage != 0) { // check 0, this prevent next call, for default value -// // getCapturability is check matrix validity and create matrix if needed and get one value in -// double capturability = infoPop.getCapturability(group); -// if (capturability != 0) { // check 0, this prevent next call, for default value -// // getCoefficient is equation evaluation -// double coeff = selectivity.getCoefficient(pop, group, metier); -// if (coeff != 0) { // check 0, this prevent next call, for default value -// double value = coeff * capturability * ciblage * effort; -// result.setValue(str, metier, group, zone, value); -// } -// } -// } -// } -// } -// } -// } -// } -// } -// return result; -// } - -// /** -// * @param date -// * @param group -// * @param zone -// * @return -// * @throws TopiaException -// * @throws IsisFishException -// */ -// private double totalFishingMortality(Date date, PopulationGroup group, Zone zone) throws TopiaException, IsisFishException { -// List<Strategy> strategies = getStrategies(date); -// -// float result = 0; -// -//// for(Strategy str : strategies){ -//// List<Metier> metierStr = getMetiers(str, date); -//// for (Metier metier : metierStr) { -//// // TODO peut etre ne pas le faire si classe.pop n'est pas -//// /// peche par le metier -//// result += fishingMortality(str, metier, date, group, zone); -//// } -//// } -// -// // Optimisation Hilaire -// for(Strategy str : strategies){ -// List<Metier> metierStr = getMetiers(str, date); -// for (Metier metier : metierStr) { -// double effort=effortPerZonePop(str,metier,date,zone); -// if (effort>0) -// result += fishingMortality(str, metier, date, group, zone, effort); -// } -// } -// -// return result; -// } - - - // fusion fishingMortality and matrixFishingMortality for performance reason -// /** -// * @param str -// * @param metier -// * @param date -// * @param group -// * @param zone -// * @return -// * @throws IsisFishException -// */ -// private double fishingMortality(Strategy str, Metier metier, Date date, PopulationGroup group, Zone zone, double effort) throws IsisFishException { -// Month month = date.getMonth(); -// Population pop = group.getPopulation(); -// Gear gear = metier.getGear(); -// -// Selectivity selectivity = gear.getPopulationSelectivity(pop); -// -// double result = 0; -// -// if (selectivity != null) { -// MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(month); -// double ciblage = infoMet.getTargetFactor(group); -// -// PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); -// double capturability = infoPop.getCapturability(group); -// -// double coeff = selectivity.getCoefficient(pop, group, metier); -// -// // Optimisation Hilaire -//// double effort = effortPerZonePop(str, metier, date, zone); -// -// // la methode est appeler des millions de fois, donc meme si -// // on ne perd pas beaucoup de temps avec le if, on en perd deja -// // trop -//// if(log.isDebugEnabled()) { -//// log.debug( -//// " strategy=" + str + -//// " metier=" + metier + -//// " ciblage=" + ciblage + -//// " capturabilite=" + capturability + -//// " selectivity=" + coeff + -//// " effort=" + effort); -//// } -// -// result = coeff * capturability * ciblage * effort; -// } -// -// return result; -// } - - // Supprimee suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) -// /** -// * @param str -// * @param metier -// * @param date -// * @param zone -// * @return -// */ -// private double effortPerZonePop(Strategy str, Metier metier, Date date, Zone zonePop) { -// Month month = date.getMonth(); -// Collection<Zone> zoneMet = metier.getMetierSeasonInfo(month).getZone(); -// double inter = nbCellInter(zoneMet, zonePop); -// -// double effortPerStrategyPerCell = effortPerStrategyPerCell(str, metier, date); -// -// if(log.isDebugEnabled()) { -// log.debug( -// " strategy=" + str + -// " metier=" + metier + -// " inter=" + inter + -// " effortPerStrategyPerCell=" + effortPerStrategyPerCell -// ); -// } -// -// double result = effortPerStrategyPerCell * inter; -// return result; -// } - /** * @param str * @param metier * @param date * @return */ - private double effortPerStrategyPerCell(Strategy str, Metier metier, Date date) { + private double effortPerStrategyPerCell(Strategy str, Metier metier, + Date date) { Month month = date.getMonth(); - StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + //StrategyMonthInfo smi = str.getStrategyMonthInfo(month); Collection<Zone> zones = metier.getMetierSeasonInfo(month).getZone(); double nbCell = getCells(zones).size(); - if(nbCell == 0){ + if (nbCell == 0) { // normalement il devrait y avoir des mailles, mais pour les // ancienne zone AuPort, il n'y en avait pas - if(log.isWarnEnabled()) log.warn("Calcul d'une distance pour le metier "+metier+" pour le mois "+month+" avec une zone sans maille: " + zones); + if (log.isWarnEnabled()) + log.warn("Calcul d'une distance pour le metier " + metier + + " pour le mois " + month + + " avec une zone sans maille: " + zones); return 0; } + double effortPerStrategy = effortPerStrategyMet(str, metier, date); - double effortPerStrategy = effortPerStrategyMet(str, metier, date); - - if(log.isDebugEnabled()) { - log.debug( - " strategy=" + str + - " metier=" + metier + - " nbCell=" + nbCell + - " effortPerStrategy=" + effortPerStrategy - ); + if (log.isDebugEnabled()) { + log.debug(" strategy=" + str + " metier=" + metier + " nbCell=" + + nbCell + " effortPerStrategy=" + effortPerStrategy); } - double result = effortPerStrategy/nbCell; + double result = effortPerStrategy / nbCell; return result; } @@ -1165,14 +932,14 @@ * @param date * @return */ - private double effortPerStrategyMet(Strategy str, Metier metier, Date date) { + private double effortNominalPerStrategyMet(Strategy str, Metier metier, Date date) { Month month = date.getMonth(); StrategyMonthInfo smi = str.getStrategyMonthInfo(month); - + double propSetOfVessels = str.getProportionSetOfVessels(); int nbOfVessels = str.getSetOfVessels().getNumberOfVessels(); double propStrMet = smi.getProportionMetier(metier); - double effortPerVessel = effortPerStrategyPerVessel(str, metier, date); + double effortNominalPerVessel = effortNominalPerStrategyPerVessel(str, metier, date); if(log.isDebugEnabled()) { log.debug( @@ -1181,38 +948,93 @@ " propSetOfVessels=" + propSetOfVessels + " nbOfVessels=" + nbOfVessels + " propStrMet=" + propStrMet + - " effortPerVessel=" + effortPerVessel + " effortPerVessel=" + effortNominalPerVessel ); } - double result = propSetOfVessels * nbOfVessels * propStrMet * effortPerVessel; + double result = propSetOfVessels * nbOfVessels * propStrMet * effortNominalPerVessel; return result; } - + /** * @param str * @param metier * @param date * @return */ - private double effortPerStrategyPerVessel(Strategy str, Metier metier, Date date) { + private double effortNominalPerStrategyPerVessel(Strategy str, Metier metier, Date date) { Month month = date.getMonth(); StrategyMonthInfo smi = str.getStrategyMonthInfo(month); double nbTrips = smi.getNumberOfTrips(); double fishingTime = fishingTimePerTrip(str, metier, date); - double stdEffortPerHour = stdEffortPerHour(date, str.getSetOfVessels(), metier); + if(log.isDebugEnabled()) { log.debug( " strategy=" + str + " metier=" + metier + " nbTrips=" + nbTrips + - " fishingTime=" + fishingTime + - " stdEffortPerHour=" + stdEffortPerHour + " fishingTime=" + fishingTime + ); } - + // nominal timeAtSea = nbTrips * fishingTime; + // + double result = nbTrips * fishingTime; + + return result; + } + + /** + * @param str + * @param metier + * @param date + * @return + */ + private double effortPerStrategyMet(Strategy str, Metier metier, Date date) { + Month month = date.getMonth(); + StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + + double propSetOfVessels = str.getProportionSetOfVessels(); + int nbOfVessels = str.getSetOfVessels().getNumberOfVessels(); + double propStrMet = smi.getProportionMetier(metier); + double effortPerVessel = effortPerStrategyPerVessel(str, metier, date); + + if (log.isDebugEnabled()) { + log.debug(" strategy=" + str + " metier=" + metier + + " propSetOfVessels=" + propSetOfVessels + " nbOfVessels=" + + nbOfVessels + " propStrMet=" + propStrMet + + " effortPerVessel=" + effortPerVessel); + } + + double result = propSetOfVessels * nbOfVessels * propStrMet + * effortPerVessel; + + return result; + } + + /** + * @param str + * @param metier + * @param date + * @return + */ + private double effortPerStrategyPerVessel(Strategy str, Metier metier, + Date date) { + Month month = date.getMonth(); + StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + double nbTrips = smi.getNumberOfTrips(); + double fishingTime = fishingTimePerTrip(str, metier, date); + double stdEffortPerHour = stdEffortPerHour(date, str.getSetOfVessels(), + metier); + + if (log.isDebugEnabled()) { + log.debug(" strategy=" + str + " metier=" + metier + " nbTrips=" + + nbTrips + " fishingTime=" + fishingTime + + " stdEffortPerHour=" + stdEffortPerHour); + } + double result = nbTrips * fishingTime * stdEffortPerHour; return result; @@ -1232,38 +1054,36 @@ Collection<Zone> zone = metier.getMetierSeasonInfo(month).getZone(); if (zone == null) { - if(log.isWarnEnabled()) log.warn( - "missing zone for metier =" + metier + - " for month" + month - ); + if (log.isWarnEnabled()) + log.warn("missing zone for metier =" + metier + " for month" + + month); } - double tripDuration = smi.getTripType().getTripDuration().getHour(); + double tripDuration = smi.getTripType().getTripDuration().getHour(); double travelTime = travelTimePerTrip(str.getSetOfVessels(), zone); double result = tripDuration - travelTime; - if (result < 0 ) { - if(log.isWarnEnabled()) log.warn( - " strategy=" + str + - " metier=" + metier + - " tripDuration=" + tripDuration + - " travelTime=" + travelTime - ); + if (result < 0) { + if (log.isWarnEnabled()) + log.warn(" strategy=" + str + " metier=" + metier + + " tripDuration=" + tripDuration + " travelTime=" + + travelTime); } return result; } /** - * + * * @param setOfVessels * @param zone * @return */ - protected double travelTimePerTrip(SetOfVessels sov, Collection<Zone> zoneMetier) { + protected double travelTimePerTrip(SetOfVessels sov, + Collection<Zone> zoneMetier) { Cell maille = sov.getPort().getCell(); - double result = - 2 * distance(zoneMetier, maille) / sov.getVesselType().getSpeed(); + double result = 2 * distance(zoneMetier, maille) + / sov.getVesselType().getSpeed(); return result; } @@ -1277,24 +1097,24 @@ double result = 0; List<Cell> cells = getCells(zones); - if(cells.size() == 0){ + if (cells.size() == 0) { // normalement il devrait y avoir des mailles, mais pour les // ancienne zone AuPort, il n'y en avait pas - if(log.isWarnEnabled()) { + if (log.isWarnEnabled()) { log.warn("Calcul d'une distance avec une zone sans maille"); } return 0; } - for(Cell c : cells){ + for (Cell c : cells) { result += distance(c, cell); } - if(log.isDebugEnabled()) { - log.debug(" result=" + result + " nbMaille="+cells.size()); + if (log.isDebugEnabled()) { + log.debug(" result=" + result + " nbMaille=" + cells.size()); } - - result = result / (double)cells.size(); + + result = result / (double) cells.size(); return result; } @@ -1305,61 +1125,54 @@ */ private double distance(Cell m1, Cell m2) { double earthRadius = 6378.388; - double p = 180/Math.PI; + double p = 180 / Math.PI; - if(log.isDebugEnabled()) log.debug("p: " + p); + if (log.isDebugEnabled()) + log.debug("p: " + p); double m1lat = m1.getLatitude(); double m2lat = m2.getLatitude(); double m1lon = m1.getLongitude(); double m2lon = m2.getLongitude(); - if(log.isDebugEnabled()) log.debug( - " m1lat=" + m1lat + - " m2lat=" + m2lat + - " m1lon=" + m1lon + - " m2lonx=" + m2lon - ); + if (log.isDebugEnabled()) + log.debug(" m1lat=" + m1lat + " m2lat=" + m2lat + " m1lon=" + m1lon + + " m2lonx=" + m2lon); - double m1lat_div_p = m1lat/p; - double m2lat_div_p = m2lat/p; - double m1lon_div_p = m1lon/p; - double m2lon_div_p = m2lon/p; + double m1lat_div_p = m1lat / p; + double m2lat_div_p = m2lat / p; + double m1lon_div_p = m1lon / p; + double m2lon_div_p = m2lon / p; - if(log.isDebugEnabled()) log.debug( - " m1lat_div_p=" + m1lat_div_p + - " m2lat_div_p=" + m2lat_div_p + - " m1lon_div_p=" + m1lon_div_p + - " m2lon_div_p=" + m2lon_div_p - ); + if (log.isDebugEnabled()) + log.debug(" m1lat_div_p=" + m1lat_div_p + " m2lat_div_p=" + + m2lat_div_p + " m1lon_div_p=" + m1lon_div_p + + " m2lon_div_p=" + m2lon_div_p); double sin_m1lat_div_p = Math.sin(m1lat_div_p); double sin_m2lat_div_p = Math.sin(m2lat_div_p); double cos_m1lat_div_p = Math.cos(m1lat_div_p); double cos_m2lat_div_p = Math.cos(m2lat_div_p); - if(log.isDebugEnabled()) log.debug( - " sin_m1lat_div_p=" + sin_m1lat_div_p + - " sin_m2lat_div_p=" + sin_m2lat_div_p + - " cos_m1lat_div_p=" + cos_m1lat_div_p + - " cos_m2lat_div_p=" + cos_m2lat_div_p - ); + if (log.isDebugEnabled()) + log.debug(" sin_m1lat_div_p=" + sin_m1lat_div_p + + " sin_m2lat_div_p=" + sin_m2lat_div_p + + " cos_m1lat_div_p=" + cos_m1lat_div_p + + " cos_m2lat_div_p=" + cos_m2lat_div_p); - double cos_m1lon_div_p_minus_m2lon_div_p = Math.cos(m1lon_div_p - m2lon_div_p); + double cos_m1lon_div_p_minus_m2lon_div_p = Math.cos(m1lon_div_p + - m2lon_div_p); - if(log.isDebugEnabled()) log.debug( - " cos_m1lon_div_p_minus_m2lon_div_p=" + cos_m1lon_div_p_minus_m2lon_div_p); + if (log.isDebugEnabled()) + log.debug(" cos_m1lon_div_p_minus_m2lon_div_p=" + + cos_m1lon_div_p_minus_m2lon_div_p); - double acos = Math.acos( - sin_m1lat_div_p - * sin_m2lat_div_p - + - cos_m1lat_div_p - * cos_m2lat_div_p - * cos_m1lon_div_p_minus_m2lon_div_p - ); + double acos = Math.acos(sin_m1lat_div_p * sin_m2lat_div_p + + cos_m1lat_div_p * cos_m2lat_div_p + * cos_m1lon_div_p_minus_m2lon_div_p); - if(log.isDebugEnabled()) log.debug(" acos=" + acos); + if (log.isDebugEnabled()) + log.debug(" acos=" + acos); double result = earthRadius * acos; @@ -1374,19 +1187,18 @@ private double stdEffortPerHour(Date date, SetOfVessels sov, Metier metier) { double result = 0; EffortDescription ed = sov.getPossibleMetiers(metier); - if(ed != null){ + if (ed != null) { double fstd = metier.getGear().getStandardisationFactor(); double etp = sov.getTechnicalEfficiency(date, metier); - double val = - fstd * etp * ed.getFishingOperation() * ed.getGearsNumberPerOperation(); + double val = fstd * etp * ed.getFishingOperation() + * ed.getGearsNumberPerOperation(); result = val; } - result = result/24; // 24 heures + result = result / 24; // 24 heures return result; } - /** * used here and in Rule (CantonnementPreSimu) * @@ -1400,7 +1212,7 @@ } return result; } - + /** * used here and in Rule (CantonnementPreSimu) * @@ -1414,97 +1226,105 @@ tmp.retainAll(zonePop.getCell()); return tmp.size(); } - + /////////////////////////////////////////////////////////////////////////// // // // /////////////////////////////////////////////////////////////////////////// - + /** * @param N * @param pop * @param date * @return - * @throws IsisFishException - * @throws TopiaException + * @throws IsisFishException + * @throws TopiaException */ private MatrixND matrixAbundancePerCell(MatrixND N, Population pop, - Date date, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { + Date date, MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); List<Cell> allCells = getCells(zones); - + MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_ABUNDANCE + "_PER_CELL", - new List[]{groups, zones, allCells}, - new String[]{n_("Groups"), n_("Zones"), n_("Cells")}); + new List[] { groups, zones, allCells }, + new String[] { n_("Groups"), n_("Zones"), n_("Cells") }); - for (int g=0; g < groups.size(); g++) { + for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); - for (int z=0; z < zones.size(); z++) { + for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); List<Cell> cells = zone.getCell(); - for (int c=0; c<cells.size(); c++) { + for (int c = 0; c < cells.size(); c++) { Cell cell = cells.get(c); - double value = survivalRatePerCell(date, group, zone, - cell, matrixFishingMortality); + double value = survivalRatePerCell(date, group, zone, cell, + matrixFishingMortality); double n = N.getValue(g, z) / zone.sizeCell(); value *= n; result.setValue(g, z, c, value); } } } - + return result; } - + /** - * Utilise pour le calcule en Cell + * Utilise pour le calcule en Cell. + * * @param N * @param pop * @param date * @return - * @throws IsisFishException - * @throws TopiaException + * @throws IsisFishException + * @throws TopiaException */ public MatrixND matrixAbundance(MatrixND N, Population pop, Date date) throws TopiaException, IsisFishException { - - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell(date, pop); - - MatrixND result = matrixAbundancePerCell(N, pop, date, matrixFishingMortalityPerCell); + + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + date, pop); + + MatrixND result = matrixAbundancePerCell(N, pop, date, + matrixFishingMortalityPerCell); result = result.sumOverDim(2); result = result.reduceDims(2); result.setName(ResultName.MATRIX_ABUNDANCE); - - return result; + + return result; } /** - * Utilise pour le calcule en Zone + * Utilise pour le calcule en Zone. + * * @param N * @param pop * @param date + * @param matrixFishingMortality * @return * @throws IsisFishException * @throws TopiaException */ - public MatrixND matrixAbundance(MatrixND N, Population pop, Date date, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { + public MatrixND matrixAbundance(MatrixND N, Population pop, Date date, + MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_ABUNDANCE, - new List[]{groups, zones}, - new String[]{n_("Groups"), n_("Zones")}); + ResultName.MATRIX_ABUNDANCE, new List[] { groups, zones }, + new String[] { n_("Groups"), n_("Zones") }); - for (int g=0; g < groups.size(); g++) { + for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); - for (int z=0; z < zones.size(); z++) { + for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); - double value = survivalRatePerZone(date, group, zone, matrixFishingMortality); + double value = survivalRatePerZone(date, group, zone, + matrixFishingMortality); double n = N.getValue(g, z); value *= n; result.setValue(g, z, value); @@ -1517,6 +1337,7 @@ /** * Utilise pour la mortalite des poissons, lorsqu'aucune strategie n'est * selectionnee. + * * @param N * @param pop * @param date @@ -1524,21 +1345,23 @@ * @throws IsisFishException * @throws TopiaException */ - public MatrixND matrixAbundanceSsF(MatrixND N, Population pop, Date date) throws TopiaException, IsisFishException { + public MatrixND matrixAbundanceSsF(MatrixND N, Population pop, Date date) + throws TopiaException, IsisFishException { List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_ABUNDANCE, - new List[]{groups, zones}, - new String[]{n_("Groups"), n_("Zones")}); + ResultName.MATRIX_ABUNDANCE, new List[] { groups, zones }, + new String[] { n_("Groups"), n_("Zones") }); - for (int g=0; g < groups.size(); g++) { + for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); - for (int z=0; z < zones.size(); z++) { + for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); - double M = group.getNaturalDeathRate(zone)/(double)Month.NUMBER_OF_MONTH; - double value = (double)Math.exp(-M);; + double M = group.getNaturalDeathRate(zone) + / (double) Month.NUMBER_OF_MONTH; + double value = (double) Math.exp(-M); + ; double n = N.getValue(g, z); value *= n; result.setValue(g, z, value); @@ -1556,31 +1379,36 @@ * @throws IsisFishException * @throws TopiaException */ - private double survivalRatePerZone(Date date, PopulationGroup group, Zone zone, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { - double F = totalFishingMortality(date, matrixFishingMortality).getValue(group, zone); //totalFishingMortality(date, group, zone); // rem perf: totalFishingMortality a deja ete calcul? - double M = group.getNaturalDeathRate(zone)/(double)Month.NUMBER_OF_MONTH; - double result = Math.exp(-(F+M)); + private double survivalRatePerZone(Date date, PopulationGroup group, + Zone zone, MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { + double F = totalFishingMortality(date, matrixFishingMortality) + .getValue(group, zone); //totalFishingMortality(date, group, zone); // rem perf: totalFishingMortality a deja ete calcul? + double M = group.getNaturalDeathRate(zone) + / (double) Month.NUMBER_OF_MONTH; + double result = Math.exp(-(F + M)); return result; } - /** * @param date * @param group * @param zone * @return - * @throws IsisFishException - * @throws TopiaException + * @throws IsisFishException + * @throws TopiaException */ - private double survivalRatePerCell(Date date, PopulationGroup group, Zone zone, - Cell cell, MatrixND matrixFishingMortalityPerCell) throws TopiaException, IsisFishException { - - double F = totalFishingMortalityPerCell(date, matrixFishingMortalityPerCell) - .getValue(group, zone, cell); //totalFishingMortality(date, group, zone); // rem perf: totalFishingMortality a deja ete calcul? - double M = group.getNaturalDeathRate(zone)/(double)Month.NUMBER_OF_MONTH; - double result = (double)Math.exp(-(F+M)); + private double survivalRatePerCell(Date date, PopulationGroup group, + Zone zone, Cell cell, MatrixND matrixFishingMortalityPerCell) + throws TopiaException, IsisFishException { + double F = totalFishingMortalityPerCell(date, + matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(date, group, zone); // rem perf: totalFishingMortality a deja ete calcul? + double M = group.getNaturalDeathRate(zone) + / (double) Month.NUMBER_OF_MONTH; + double result = (double) Math.exp(-(F + M)); + return result; } @@ -1589,9 +1417,9 @@ // // /////////////////////////////////////////////////////////////////////////// - + /** - * @param n + * @param N * @param pop * @param date * @return @@ -1601,32 +1429,31 @@ List<Zone> zones = N.getSemantics(1); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_BIOMASS, - new List[]{groups, zones}, - new String[]{n_("Groups"), n_("Zones")}); + ResultName.MATRIX_BIOMASS, new List[] { groups, zones }, + new String[] { n_("Groups"), n_("Zones") }); - for (int g=0; g < groups.size(); g++) { + for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); double meanWeight = group.getMeanWeight(); - for (int z=0; z < zones.size(); z++) { + for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); double n = N.getValue(group, zone); double value = n * meanWeight; result.setValue(group, zone, value); } } - + return result; } - public MatrixND matrixBiomassBeginMonth(MatrixND N, Population pop, Date date) { + public MatrixND matrixBiomassBeginMonth(MatrixND N, Population pop, + Date date) { List<PopulationGroup> groups = N.getSemantics(0); List<Zone> zones = N.getSemantics(1); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_BIOMASS_BEGIN_MONTH, - new List[]{groups, zones}, - new String[]{n_("Groups"), n_("Zones")}); + ResultName.MATRIX_BIOMASS_BEGIN_MONTH, new List[] { groups, zones }, + new String[] { n_("Groups"), n_("Zones") }); for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); @@ -1641,14 +1468,14 @@ return result; } - public MatrixND matrixAbondanceBeginMonth(MatrixND N, Population pop, Date date) { + public MatrixND matrixAbondanceBeginMonth(MatrixND N, Population pop, + Date date) { List<PopulationGroup> groups = N.getSemantics(0); List<Zone> zones = N.getSemantics(1); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_ABONDANCE_BEGIN_MONTH, - new List[]{groups, zones}, - new String[]{n_("Groups"), n_("Zones")}); + ResultName.MATRIX_ABUNDANCE_BEGIN_MONTH, new List[] { groups, zones }, + new String[] { n_("Groups"), n_("Zones") }); for (int g = 0; g < groups.size(); g++) { PopulationGroup group = groups.get(g); @@ -1661,17 +1488,16 @@ return result; } - /////////////////////////////////////////////////////////////////////////// // // // /////////////////////////////////////////////////////////////////////////// - + /** * @param date * @return - * @throws TopiaException + * @throws TopiaException */ public MatrixND matrixEffortPerStrategyMet(Date date) throws TopiaException { List<Strategy> strategies = getStrategies(date); @@ -1679,27 +1505,19 @@ MatrixND result = MatrixFactory.getInstance().create( ResultName.MATRIX_EFFORT_PER_STRATEGY_MET, - new List[]{strategies, metiers}, - new String[]{n_("Strategies"), n_("Metiers")}); + new List[] { strategies, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); - for (int s=0; s < strategies.size(); s++) { + for (int s = 0; s < strategies.size(); s++) { Strategy str = strategies.get(s); metiers = getMetiers(str, date); - for (int m=0; m < metiers.size(); m++) { + for (int m = 0; m < metiers.size(); m++) { Metier metier = metiers.get(m); double value = effortPerStrategyMet(str, metier, date); result.setValue(str, metier, value); } } -// for(Strategy str : strategies){ -// List<Metier> metierStr = getMetiers(str, date); -// for(Metier metier : metierStr) { -// double val = effortPerStrategyMet(str, metier, date); // rem perf: effortPerStrategyMet a deja ete calcul? -// result.setValue(str, metier, val); -// } -// } - return result; } @@ -1708,49 +1526,56 @@ // // /////////////////////////////////////////////////////////////////////////// - -// /** -// * @param pop -// * @param date -// * @return -// */ -// public MatrixND matrixCatchWeightPerStrategyMet(Population pop, -// Date date, MatrixND matrixCatchPerStrategyMet) { -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// -// MatrixND result = matrixCatchPerStrategyMet.copy(); -// result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); -// -// for(PopulationGroup group : groups){ -// MatrixND sub = result.getSubMatrix(2, group, 1); -// double meanWeight = group.getMeanWeight(); -// sub.mults(meanWeight); -// } -// -// return result; -// } /** * * * @param pop * @param date + * @param matrixDiscardPerStrategyMetPerZonePop * @return */ public MatrixND matrixDiscardWeightPerStrategyMetPerZonePop(Population pop, Date date, MatrixND matrixDiscardPerStrategyMetPerZonePop) { - List<PopulationGroup> groups = pop.getPopulationGroup(); + List<PopulationGroup> groups = pop.getPopulationGroup(); - MatrixND result = matrixDiscardPerStrategyMetPerZonePop.copy(); - result.setName(ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); + MatrixND result = matrixDiscardPerStrategyMetPerZonePop.copy(); + result.setName(ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); - for(PopulationGroup group : groups){ - MatrixND sub = result.getSubMatrix(2, group, 1); - double meanWeight = group.getMeanWeight(); - sub.mults(meanWeight); - } + for (PopulationGroup group : groups) { + MatrixND sub = result.getSubMatrix(2, group, 1); + double meanWeight = group.getMeanWeight(); + sub.mults(meanWeight); + } - return result; + return result; } + /////////////////////////////////////////////////////////////////////////// + // + // + // + /////////////////////////////////////////////////////////////////////////// + public MatrixND matrixEffortNominalPerStrategyMet(Date date) throws TopiaException { + + List<Strategy> strategies = getStrategies(date); + List<Metier> metiers = getMetiers(date); + + MatrixND result = MatrixFactory.getInstance().create( + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET, + new List[]{strategies, metiers}, + new String[]{n_("Strategies"), n_("Metiers")}); + + for (int s=0; s < strategies.size(); s++) { + Strategy str = strategies.get(s); + metiers = getMetiers(str, date); + for (int m=0; m < metiers.size(); m++) { + Metier metier = metiers.get(m); + double value = effortNominalPerStrategyMet(str, metier, date); + result.setValue(str, metier, value); + } + } + + return result; + } } Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorJavaExpandGrid.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,623 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RProxy; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of ExpandGrid method using Java + * + * @author jcouteau + * @version $Revision$ + * + */ +public class SensitivityCalculatorJavaExpandGrid extends + AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCalculatorJavaExpandGrid.class); + + @Doc("Interaction order") + public int param_order = 2; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return false; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputdirectory); + + int k = 1; //number of sensitivity scenarios (initialization) + int factorNumber = plan.getFactors().size(); //number of factors + List<Factor<?, ?>> factors = plan.getFactors(); //list of factors + + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof ContinuousDomain) { + if (((ContinuousDomain) factors.get(i).getDomain()) + .getCardinality() != 0) { + k = k + * ((ContinuousDomain) factors.get(i).getDomain()) + .getCardinality(); + } + } else if (factors.get(i).getDomain() instanceof DiscreteDomain) { + if (((DiscreteDomain) factors.get(i).getDomain()).getValues() + .size() != 0) { + k = k + * ((DiscreteDomain) factors.get(i).getDomain()) + .getValues().size(); + } + } + } + + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + for (int i = 0; i < k; i++) { + int result = 0; //used for the euclidian division + int rest = i; //used for the euclidian division + Scenario experimentScenario = new Scenario(); + for (int j = 0; j < factorNumber; j++) { + Factor factor = factors.get(j); + if (factor.getDomain() instanceof ContinuousDomain) { + Double max = ((ContinuousDomain) factor.getDomain()) + .getMaxBound(); + Double min = ((ContinuousDomain) factor.getDomain()) + .getMinBound(); + int card = ((ContinuousDomain) factor.getDomain()) + .getCardinality(); + result = (int) Math.floor(rest / card); + rest = rest - (card * result); + + Double value = min + ((max - min) / (card - 1) * rest); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(value); + } else { + factor.setValueForIdentifier(value); + } + } + if (factor.getDomain() instanceof DiscreteDomain) { + int card = ((DiscreteDomain) factor.getDomain()) + .getValues().size(); + result = (int) Math.floor(rest / card); + rest = rest - (card * result); + factor.setValueForIdentifier(rest); + } + rest = result; + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + + } + thisExperiment.setScenarios(thisExperimentScenarios); + + thisExperimentScenarios = thisExperiment.getScenarios(); + + /* + * Call R to save the data for result analysis + */ + int scenariosNumber = thisExperimentScenarios.size(); + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + String dataframe = "data<-data.frame("; + + //Create the factors vectors and the dataframe instruction + for (int j = 0; j < factorNumber; j++) { + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { + + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < scenariosNumber; i++) { + if (i < (scenariosNumber - 1)) { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else if (factor.getDomain() instanceof MatrixContinuousDomain) { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < scenariosNumber; i++) { + if (i < (scenariosNumber - 1)) { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < scenariosNumber; i++) { + if (i < (scenariosNumber - 1)) { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue() + + ","; + } else { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } + + if (j < factorNumber - 1) { + dataframe = dataframe + + factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; + } else { + dataframe += factor.getName().replaceAll(" ", "") + + "=factor(" + factor.getName().replaceAll(" ", "") + + "))"; + } + + } + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + // Creating the factors vector. + String rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the data.frame object for the second run in a .expandgrid file + engine.voidEval("write.csv(data,file=\".expandgrid.csv\")"); + log + .info("Message sent to R : write.csv(data,file=\".expandgrid\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + + //Create the isis.factor.distribution + log.info("Message sent to R : " + + "isis.factor.distribution<-c(0.0)"); + engine.voidEval("isis.factor.distribution<-c(0.0)"); + + //Create isis.MethodExp + log + .info("Message sent to R : " + + "isis.MethodExp<-list(isis.factor,isis.factor.distribution,call_méthode=\"isis-fish-externeR\")"); + engine + .voidEval("isis.MethodExp<-list(isis.factor,isis.factor.distribution,call_méthode=\"isis-fish-externeR\")"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + //Create isis.Simule + log.info("Message sent to R : " + "isis.simule<-data.frame(data)"); + engine.voidEval("isis.simule<-data.frame(data)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) throws SensitivityException { + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + //Get back the scenarios + engine.voidEval("factors<-read.csv(\".expandgrid.csv\")"); + log + .info("Message sent to R : factors<-read.csv(\".expandgrid.csv\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < simulationStorages.size(); l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~("; + for (int j = 0; j < factorNumber; j++) { + log.info("Message sent to R : " + "names(factors)[" + + (j + 2) + "]"); + + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; + } else { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ")"; + if(param_order>1){ + aovCall+="^" + param_order + ",data=dataforaov)"; + }else{ + aovCall+=",data=dataforaov)"; + } + } + } + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + log.info("Message sent to R : SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + engine + .voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + log + .info("Message sent to R : names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + log.info("Message sent to R : IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity=data.frame(SoS[1:" + + factorNumber + "],IndSensibilite[1:" + factorNumber + + "])"); + log + .info("Message sent to R : exportsensitivity=data.frame(SoS[1:" + + factorNumber + + "],IndSensibilite[1:" + + factorNumber + "])"); + engine + .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + log + .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + + log + .info("Message sent to R : " + + "attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + } + + @Override + public String getDescription() { + return "Implementation of Expand Grid method using Java"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorJavaExpandGrid.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFast.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFast.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,609 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; +import java.util.Vector; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RException; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; +import org.rosuda.JRI.REXP; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of Fast method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author: jcouteau $ + */ +public class SensitivityCalculatorRFast extends AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory + .getLog(SensitivityCalculatorRFast.class); + + @Doc("an integer giving the sample size, i.e. the length of the discretization of the s-space (see Cukier et al.). (default=20)") + public int param_n = 20; + + @Doc("an integer specifying the interference parameter, i.e. the number of harmonics to sum in the Fourier series decomposition (see Cukier et al.). (default=6)") + public int param_M = 6; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + //public int[] param_omega; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan, outputdirectory); + + double[] dataframe = new double[0]; + int nbExperiments = 0; + int factorNumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + "Error", JOptionPane.ERROR_MESSAGE); + return null; + } + } + String rInstruction = "a<-fast99(model=NULL,factors=%s, n=%s, M=%s, q = \"qunif\", q.arg=list(min=0,max=1))"; + String rCall = String.format(rInstruction, factors.size(), param_n, + param_M); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R" + "library(sensitivity)"); + + // Run sensitivity analysis + engine.voidEval(rCall); + log.info("Message sent to R" + rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R" + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the fast99 object for the second run in a .fast99 file + engine.voidEval("dput(a,file=\".fast99\")"); + log.info("Message sent to R" + "dput(a,file=\".fast99\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + + // Get back experiment plan + + Vector<REXP> dataframeVector = (Vector<REXP>) engine.eval("a$X"); + dataframe = new double[dataframeVector.size() + * dataframeVector.get(0).asDoubleArray().length]; + for (int i = 0; i < dataframeVector.size(); i++) { + for (int j = 0; j < dataframeVector.get(0).asDoubleArray().length; j++) { + if (String.valueOf( + dataframeVector.get(i).asDoubleArray()[j]) + .toString().equals("NaN")) { + log + .error("Wrong parameters for the fast method, non-numeric values were generated"); + JOptionPane + .showMessageDialog( + null, + "The parameters for this method need to be changed, non-numeric values where generated (you may want to increase the n parameter)", + "Error", JOptionPane.ERROR_MESSAGE); + return null; + } + dataframe[i * dataframeVector.get(0).asDoubleArray().length + + j] = dataframeVector.get(i).asDoubleArray()[j]; + } + } + + log.info("Message sent to R" + "a$X"); + + if (log.isDebugEnabled()) { + log.debug("rInstruction = " + rInstruction); + } + + nbExperiments = dataframe.length / factorNumber; + + String isisFactorDistribution = "isis.factor.distribution<-data.frame(NomFacteur=c(%s),NomDistribution=c(%s),ParametreDistribution=c(%s))"; + + // Creating the vectors. + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + factorNames += ","; + } + + distribution += "\"qunif\""; + parameters += "\"[" + ((ContinuousDomain) domain).getMinBound() + + ";" + ((ContinuousDomain) domain).getMaxBound() + + "]\""; + factorNames += "\"" + factors.get(i).getName() + "\""; + } + + log.info("Message sent to R : " + + String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + log.info("Message sent to R : " + "call<-a$call"); + engine.voidEval("call<-a$call"); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + "isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(a$X)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + } catch (RException eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + // Error while retrieving scenario + } + + // Transform the result from R in a matrix + MatrixND fast = MatrixFactory.getInstance().create(dataframe, + new int[] { factorNumber, nbExperiments }); + + // Setting up the scenarios. + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(fast + .getValue(new int[] { i, j })); + } else { + Double value = (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound() + + ((Double) ((ContinuousDomain) factor.getDomain()) + .getMaxBound() - (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound()) + * fast.getValue(new int[] { i, j }); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) { + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Call R + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); + + //Set the working directory (for import and exports) + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the morris object for the second run in a .morris file + engine.voidEval("a<-dget(\".fast99\")"); + log.info("Message sent to R : " + "a<-dget(\".fast99\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + /*int scenariosNumber = sensitivityScenarios.getScenarios().size();*/ + int scenariosNumber = (Integer) engine.eval("length(a$X[,1])"); + log.info("Message sent to R : " + "length(a$X[,1])"); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < scenariosNumber; l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Compute results + engine.voidEval("tell(a,y=" + name + ")"); + log.info("Message sent to R : " + "tell(a,y=" + name + ")"); + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + + //setting isis.methodAnalyse attributes + log + .info("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + + //Create the data.frame of scenarios and results for export purpose + engine.voidEval("dfresults=data.frame(a$X,results)"); + log.info("Message sent to R : " + + "dfresults=data.frame(a$X,results)"); + + //Set working directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Set V names + engine.voidEval("names(a$V)<-factornames"); + log.info("Message sent to R : " + "names(a$V)<-factornames"); + + //Export V + engine.voidEval("write.csv(a$V,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_V.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$V,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_V.csv\")"); + + //Set D1 names + engine.voidEval("names(a$D1)<-factornames"); + log.info("Message sent to R : " + "names(a$D1)<-factornames"); + + //Export D1 + engine.voidEval("write.csv(a$D1,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_D1.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$D1,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_D1.csv\")"); + + //Set Dt names + engine.voidEval("names(a$Dt)<-factornames"); + log.info("Message sent to R : " + "names(a$Dt)<-factornames"); + + //Export Dt + engine.voidEval("write.csv(a$Dt,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Dt.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$Dt,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Dt.csv\")"); + //Set dfresults names + engine.voidEval("resultsnames<-c(factornames,\"Result\")"); + log.info("Message sent to R : " + + "resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + log.info("Message sent to R : " + + "names(dfresults)<-resultsnames"); + + //Export results + engine.voidEval("write.csv(dfresults,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : " + + "write.csv(results,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + //FIXME export through java to enable export when using Rserve + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + } catch (Exception e) { + e.printStackTrace(); + } + } + + @Override + public String getDescription() { + return "Implementation of FAST method using R"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFast.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFrF2.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFrF2.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,525 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RException; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of FrF2 method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author: chatellier $ + */ +public class SensitivityCalculatorRFrF2 extends AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory + .getLog(SensitivityCalculatorRFrF2.class); + + @Doc("is the arabic numeral for the requested resolution of the design( 3 <= resolution <= 5). (if resolution=3, model = sum(Xi), if resolution = 4 or 5, model = sum(Xi)+sum(XiXj)") + public int param_resolution; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + double[] dataframe = new double[0]; + int nbExperiments = 0; + int factorNumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + return null; + } + } + + REngine engine = new RProxy(); + + try { + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + engine.voidEval("library(FrF2)"); + log.info("Message sent to R : " + "library(FrF2)"); + + //Set the working directory (for import and exports) + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + String rInstruction = "a<-FrF2(nfactors=" + factorNumber + + ",resolution=" + param_resolution + ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + + // Export the FrF2 object for the second run in a .FrF2 file + engine.voidEval("dput(a,file=\".FrF2\")"); + log.info("Message sent to R" + "dput(a,file=\".FrF2\")"); + + // Get back experiment plan + dataframe = (double[]) engine.eval("a$desnum"); + /*Vector<REXP> dataframeVector = (Vector<REXP>) engine.eval("a$X"); + dataframe = new double[dataframeVector.size() + * dataframeVector.get(0).asDoubleArray().length]; + for (int i = 0; i < dataframeVector.size(); i++) { + for (int j = 0; j < dataframeVector.get(0).asDoubleArray().length; j++) { + dataframe[i * dataframeVector.get(0).asDoubleArray().length + + j] = dataframeVector.get(i).asDoubleArray()[j]; + } + }*/ + log.info("Message sent to R : " + "a$desnum"); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + + } catch (RException e) { + e.printStackTrace(); + } + + nbExperiments = dataframe.length / factorNumber; + + // Transform the result from R in a matrix + MatrixND frf2 = MatrixFactory.getInstance().create(dataframe, + new int[] { factorNumber, nbExperiments }); + + // Setting up the scenarios. + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + if (frf2.getValue(new int[] { i, j }) == -1) { + factor.setValueForIdentifier(0); + } + + if (frf2.getValue(new int[] { i, j }) == 1) { + factor.setValueForIdentifier(1); + } + } else { + if (frf2.getValue(new int[] { i, j }) == -1) { + factor.setValueForIdentifier(((ContinuousDomain) factor + .getDomain()).getMinBound()); + } + + if (frf2.getValue(new int[] { i, j }) == 1) { + factor.setValueForIdentifier(((ContinuousDomain) factor + .getDomain()).getMaxBound()); + } + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + try { + //Create the factors vectors + for (int j = 0; j < factorNumber; j++) { + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { + + String vector = "factor" + j + "<-c("; + for (int i = 0; i < nbExperiments; i++) { + if (i < (nbExperiments - 1)) { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else if (factor.getDomain() instanceof MatrixContinuousDomain) { + String vector = "factor" + j + "<-c("; + for (int i = 0; i < nbExperiments; i++) { + if (i < (nbExperiments - 1)) { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else { + String vector = "factor" + j + "<-c("; + for (int i = 0; i < nbExperiments; i++) { + if (i < (nbExperiments - 1)) { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue() + + ","; + } else { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } + } + + //Create the data data.frame from the factors + String data = "data<-data.frame("; + for (int j = 0; j < factorNumber; j++) { + if (j < factorNumber - 1) { + data = data + "factor" + j + "=factor(factor" + j + "),"; + } else { + data = data + "factor" + j + "=factor(factor" + j + "))"; + } + + } + engine.voidEval(data); + log.info("Message sent to R : " + data); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the scenario matrix for the second run in a .FrF2.csv file + engine.voidEval("write.csv(data,file=\".FrF2.csv\")"); + log.info("Message sent to R : " + + "write.csv(data,file=\".FrF2.csv\")"); + + engine.terminate(); + + } catch (RException e) { + e.printStackTrace(); + } + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) { + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + engine.voidEval("library(FrF2)"); + log.info("Message sent to R : " + "library(FrF2)"); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Get back the FrF2 object + engine.voidEval("a<-dget(\".FrF2\")"); + log.info("Message sent to R : a<-dget(\".FrF2\")"); + + //Get back the scenarios + engine.voidEval("factors<-read.csv(\".FrF2.csv\")"); + log + .info("Message sent to R : factors<-read.csv(\".FrF2.csv\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < simulationStorages.size(); l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors,result=result)"; + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + //get back the resolution + int resolution = (Integer) engine.eval("res.catlg(a$catentry)"); + log.info("Message sent to R : " + "res.catlg(a$catentry)"); + + String aovCall; + + switch (resolution) { + case 3: + //Call aov() + aovCall = "aovresult<-aov(result~"; + for (int j = 0; j < factorNumber; j++) { + if (j < (factorNumber - 1)) { + aovCall = aovCall + "factor" + j + "+"; + } else { + aovCall = aovCall + "factor" + j + + ",data=dataforaov)"; + } + } + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + break; + case 4: + aovCall = "aovresult<-aov(result~"; + for (int j = 0; j < factorNumber; j++) { + aovCall = aovCall + "factor" + j + "+"; + } + for (int i = 0; i < factorNumber; i++) { + for (int j = 0; j < factorNumber; j++) { + if (i < j) { + aovCall = aovCall + "factor" + i + "*factor" + + j + "+"; + } + } + } + aovCall = aovCall.substring(0, aovCall.length() - 1); + aovCall = aovCall + ",data=dataforaov)"; + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + break; + case 5: + aovCall = "aovresult<-aov(result~"; + for (int j = 0; j < factorNumber; j++) { + aovCall = aovCall + "factor" + j + "+"; + } + for (int i = 0; i < factorNumber; i++) { + for (int j = 0; j < factorNumber; j++) { + if (i < j) { + aovCall = aovCall + "factor" + i + "*factor" + + j + "+"; + } + } + } + aovCall = aovCall.substring(0, aovCall.length() - 1); + aovCall = aovCall + ",data=dataforaov)"; + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + break; + default: + log.info("This resolution is not managed"); + break; + } + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + log.info("Message sent to R : SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + engine + .voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + log + .info("Message sent to R : names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + log.info("Message sent to R : IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity=data.frame(SoS[1:" + + factorNumber + "],IndSensibilite[1:" + factorNumber + + "])"); + log + .info("Message sent to R : exportsensitivity=data.frame(SoS[1:" + + factorNumber + + "],IndSensibilite[1:" + + factorNumber + "])"); + engine + .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + log + .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + engine.terminate(); + } + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + } + + @Override + public String getDescription() { + return "Implementation of FrF2 method method using R, at least 4 factors need to be declared"; + } +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRFrF2.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRMorris.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRMorris.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,572 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RException; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of Morris method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author: jcouteau $ + */ +public class SensitivityCalculatorRMorris extends AbstractSensitivityCalculator { + + @Doc("Integer giving the number of repetitions of the design, i.e. the number of elementary effect computed per factor. (Default value : 4)") + public int param_r = 4; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory + .getLog(SensitivityCalculatorRMorris.class); + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return false; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan, outputdirectory); + + double[] dataframe = new double[0]; + int nbExperiments = 0; + int factorNumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + + if (param_r == 0) { + param_r = 4; + } + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); + return null; + } + } + + // Creating the vectors. + String factorNames = ""; + String levels = ""; + String gridJump = ""; + String binf = ""; + String bsup = ""; + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + factorNames += ","; + levels += ","; + gridJump += ","; + binf += ","; + bsup += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + + levels += ((ContinuousDomain) domain).getCardinality(); + + gridJump += (Integer) (((ContinuousDomain) domain).getCardinality() / 2); + + binf += ((ContinuousDomain) domain).getMinBound(); + + bsup += ((ContinuousDomain) domain).getMaxBound(); + } + + String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s,design=list(type=\"oat\",levels=c(%s),grid.jump=c(%s)),binf=c(%s),bsup=c(%s))"; + + String rCall = String.format(rInstruction, factorNames, param_r, + levels, gridJump, binf, bsup); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + REngine engine = new RProxy(); + try { + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); + + // Run sensitivity analysis + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c(%s)"; + rCall = String.format(rInstruction, factorNames); + + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the morris object for the second run in a .morris file + engine.voidEval("dput(a,file=\".morris\")"); + log.info("Message sent to R : " + "dput(a,file=\".morris\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + + // Get back experiment plan + dataframe = (double[]) engine.eval("a$X"); + log.info("Message sent to R : " + "a$X"); + + if (log.isDebugEnabled()) { + log.debug("rInstruction = " + rInstruction); + } + + nbExperiments = dataframe.length / factorNumber; + + String isisFactorDistribution = "isis.factor.distribution<-data.frame(NomFacteur=c(%s),NomDistribution=c(%s),ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + } + + distribution += "\"qunif\""; + parameters += "\"[" + ((ContinuousDomain) domain).getMinBound() + + ";" + ((ContinuousDomain) domain).getMaxBound() + + "]\""; + } + + log.info("Message sent to R : " + + String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + log.info("Message sent to R : " + "call<-a$call"); + engine.voidEval("call<-a$call"); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + "isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(a$X)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + } catch (RException eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + // Error while retrieving scenario + } + + // Transform the result from R in a matrix + MatrixND morris = MatrixFactory.getInstance().create(dataframe, + new int[] { factorNumber, nbExperiments }); + + // Setting up the scenarios. + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor + .setValueForIdentifier((Double) morris.getValue(i, + j)); + } else { + factor.setValueForIdentifier(morris.getValue(new int[] { i, + j })); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) { + + REngine engine = new RProxy(); + try { + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Call R + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); + + //Set the working directory (for import and exports) + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the morris object for the second run in a .morris file + engine.voidEval("a<-dget(\".morris\")"); + log.info("Message sent to R : " + "a<-dget(\".morris\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + int scenariosNumber = ((Double) engine + .eval("length(a$X)/length(a$factors)")).intValue(); + log.info("Message sent to R : " + "length(a$X)/length(a$factors)"); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < scenariosNumber; l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Compute results + engine.voidEval("tell(a,y=" + name + ")"); + log.info("Message sent to R : " + "tell(a,y=" + name + ")"); + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + + //setting isis.methodAnalyse attributes + log + .info("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + + // Get back the sensitivity results, mu, mu star and sigma. + engine.voidEval("mu<-apply(a$ee, 2, mean)"); + log.info("Message sent to R : " + "mu<-apply(a$ee, 2, mean)"); + engine + .voidEval("mu.star <- apply(a$ee, 2, function(a) mean(abs(a)))"); + log + .info("Message sent to R : " + + "mu.star <- apply(a$ee, 2, function(a) mean(abs(a)))"); + engine.voidEval("sigma <- apply(a$ee, 2, sd)"); + log + .info("Message sent to R : " + + "sigma <- apply(a$ee, 2, sd)"); + + //Create the data.frame of sensitivity indices for export purpose + engine.voidEval("df=data.frame(mu,mu.star,sigma)"); + log.info("Message sent to R : " + + "df=data.frame(mu,mu.star,sigma)"); + engine.voidEval("row.names(df)<-factornames"); + log.info("Message sent to R : " + "row.names(df)<-factornames"); + + //Create the data.frame of scenarios and results for export purpose + engine.voidEval("dfresults=data.frame(a$X,name)"); + log.info("Message sent to R : " + + "dfresults=data.frame(a$X,name)"); + + //Set dfresults names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + log.info("Message sent to R : " + + "names(dfresults)<-resultsnames"); + + //Set working directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Export sensitivity indices + engine.voidEval("write.csv(df,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : " + + "write.csv(df,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + + //Export results + engine.voidEval("write.csv(dfresults,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : " + + "write.csv(results,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + //FIXME export through java to enable export when using Rserve + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + } catch (Exception e) { + e.printStackTrace(); + } + + } + + @Override + public String getDescription() { + return "Implementation of Morris method using R"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRMorris.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorROptimumLHS.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorROptimumLHS.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,724 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * save.image() Implementation of Optimum Latin Hypercube method using R. + * + * @author jcouteau + * @version $Revision$ + */ +public class SensitivityCalculatorROptimumLHS extends + AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCalculatorROptimumLHS.class); + + @Doc("Number of simulations (default=10)") + public int param_simulationNumber = 10; + @Doc("The maximum number of times the Columnwise Pairwise algorithm is applied to all the columns(default=2).") + public int param_MaxSweeps = 2; + @Doc("The optimal stopping criterion (between 0 and 1) (default=0.1).") + public double param_eps = 0.1; + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputdirectory); + + int factornumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + double[] dataframe = new double[0]; + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factornumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); + return null; + } + } + + REngine engine = new RProxy(); + + if ((Integer) param_simulationNumber == 0) { + param_simulationNumber = 10; + } + if ((Integer) param_MaxSweeps == 0) { + param_MaxSweeps = 2; + } + + if ((Double) param_eps == 0) { + param_eps = 0.1; + } + + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + //Load the lhs library + engine.voidEval("library(lhs)"); + log.info("Message sent to R : " + "library(lhs)"); + + //Remove all objects that will be used + engine.voidEval("remove(\"isis.factor.distribution\")"); + engine.voidEval("remove(\"isis.simule\")"); + engine.voidEval("remove(\"isis.MethodExp\")"); + engine.voidEval("remove(\"isis.methodAnalyse\")"); + + String rInstruction = "x<-optimumLHS(n=%s,k=%s,maxSweeps=%s,eps=%s)"; + + String rCall = String.format(rInstruction, param_simulationNumber, + factornumber, param_MaxSweeps, param_eps); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + //Create the scenarios + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Get back experiment plan + dataframe = (double[]) engine.eval("x"); + log.info("Message sent to R : " + "x"); + + // Transform the result from R in a matrix + MatrixND morris = MatrixFactory.getInstance().create(dataframe, + new int[] { factornumber, param_simulationNumber }); + + // Setting up the scenarios. + for (int j = 0; j < param_simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factornumber; i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(morris.getValue(new int[] { + i, j })); + } else { + Double value = (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound() + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound()) + * morris.getValue(new int[] { i, j }); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String isisFactorDistribution = "isis.factor.distribution<-data.frame(NomFacteur=c(%s),NomDistribution=c(%s),ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factors.size(); i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + factorNames += ","; + parameters += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + distribution += "\"qunif\""; + parameters += "\"[" + ((ContinuousDomain) domain).getMinBound() + + ";" + ((ContinuousDomain) domain).getMaxBound() + + "]\""; + } + + log.info("Message sent to R : " + + String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + log.info("Message sent to R : " + "call<-" + "\"x<-optimumLHS(n=" + + param_simulationNumber + ",k=" + factornumber + + ",maxSweeps=" + param_MaxSweeps + ",eps=" + param_eps + + ")\""); + engine.voidEval("call<-" + "\"x<-optimumLHS(n=" + + param_simulationNumber + ",k=" + factornumber + + ",maxSweeps=" + param_MaxSweeps + ",eps=" + param_eps + + ")\""); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + "isis.simule<-data.frame(x)"); + engine.voidEval("isis.simule<-data.frame(x)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + String data = "data<-data.frame("; + + //Create the factors vectors and the dataframe instruction + for (int j = 0; j < factors.size(); j++) { + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { + + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else if (factor.getDomain() instanceof MatrixContinuousDomain) { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue() + + ","; + } else { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } + + if (j < factors.size() - 1) { + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; + } else { + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "))"; + } + + } + engine.voidEval(data); + log.info("Message sent to R : " + data); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factornumber; i++) { + if (i != (factornumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the scenario matrix for the second run in a .optimumlhs.csv file + engine.voidEval("write.csv(data,file=\".optimumlhs.csv\")"); + log.info("Message sent to R : " + + "write.csv(data,file=\".optimumlhs.csv\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) throws SensitivityException { + + if ((Integer) param_simulationNumber == 0) { + param_simulationNumber = 10; + } + if ((Integer) param_MaxSweeps == 0) { + param_MaxSweeps = 2; + } + + if ((Double) param_eps == 0) { + param_eps = 0.1; + } + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + //Get back the scenarios + engine.voidEval("factors<-read.csv(\".optimumlhs.csv\")"); + log + .info("Message sent to R : factors<-read.csv(\".optimumlhs.csv\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); + + //Get back the simulation number + param_simulationNumber = (Integer) (engine + .eval("length(factors[,1])")); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < param_simulationNumber; l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~"; + for (int j = 0; j < factorNumber; j++) { + log.info("Message sent to R : " + "names(factors)[" + + (j + 2) + "]"); + + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; + } else { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ",data=dataforaov)"; + } + } + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + log.info("Message sent to R : SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + engine + .voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + log + .info("Message sent to R : names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + log.info("Message sent to R : IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity=data.frame(SoS[1:" + + factorNumber + "],IndSensibilite[1:" + factorNumber + + "])"); + log + .info("Message sent to R : exportsensitivity=data.frame(SoS[1:" + + factorNumber + + "],IndSensibilite[1:" + + factorNumber + "])"); + engine + .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + log + .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + + log + .info("Message sent to R : " + + "attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + } + + @Override + public String getDescription() { + return "Implementation of Random Latin Hypercube method method using R"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorROptimumLHS.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRRandomLHS.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,699 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of Random Latin Hypercube method using R. + * + * @author jcouteau + * @version $Revision$ + */ +public class SensitivityCalculatorRRandomLHS extends + AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCalculatorRRandomLHS.class); + + @Doc("Simulation number (default=10)") + public int param_simulationNumber = 10; + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputdirectory); + + int factornumber = plan.getFactors().size(); + double[] dataframe = new double[0]; + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + List<Factor<?, ?>> factors = plan.getFactors(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factors.size(); i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); + return null; + } + } + + if ((Integer) param_simulationNumber == 0) { + param_simulationNumber = 10; + } + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + //Set working directory for other results + log.info("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + //Load the lhs library + engine.voidEval("library(lhs)"); + log.info("Message sent to R : " + "library(lhs)"); + + //Create the scenarios + String rInstruction = "x<-randomLHS(%s,%s)"; + String rCall = String.format(rInstruction, param_simulationNumber, + factornumber); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Get back experiment plan + dataframe = (double[]) engine.eval("x"); + log.info("Message sent to R" + "x"); + + // Transform the result from R in a matrix + MatrixND morris = MatrixFactory.getInstance().create(dataframe, + new int[] { factornumber, param_simulationNumber }); + + // Setting up the scenarios. + for (int j = 0; j < param_simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factornumber; i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(morris.getValue(new int[] { + i, j })); + } else { + Double value = (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound() + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound()) + * morris.getValue(new int[] { i, j }); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String isisFactorDistribution = "isis.factor.distribution<-data.frame(NomFacteur=c(%s),NomDistribution=c(%s),ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factors.size(); i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + factorNames += ","; + parameters += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + distribution += "\"qunif\""; + parameters += "\"[" + ((ContinuousDomain) domain).getMinBound() + + ";" + ((ContinuousDomain) domain).getMaxBound() + + "]\""; + } + + log.info("Message sent to R : " + + String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + log.info("Message sent to R : " + "call<-" + "\"x<-randomLHS(" + + param_simulationNumber + "," + factornumber + ")\""); + engine.voidEval("call<-" + "\"x<-randomLHS(" + + param_simulationNumber + "," + factornumber + ")\""); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + "isis.simule<-data.frame(x)"); + engine.voidEval("isis.simule<-data.frame(x)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + String data = "data<-data.frame("; + + //Create the factors vectors and the dataframe instruction + for (int j = 0; j < factors.size(); j++) { + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { + + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else if (factor.getDomain() instanceof MatrixContinuousDomain) { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else { + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + if (i < (param_simulationNumber - 1)) { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue() + + ","; + } else { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } + + if (j < factors.size() - 1) { + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; + } else { + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "))"; + } + + } + engine.voidEval(data); + log.info("Message sent to R : " + data); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factornumber; i++) { + if (i != (factornumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the scenario matrix for the second run in a .randomlhs.csv file + engine.voidEval("write.csv(data,file=\".randomlhs.csv\")"); + log.info("Message sent to R : " + + "write.csv(data,file=\".randomlhs.csv\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) throws SensitivityException { + + if ((Integer) param_simulationNumber == 0) { + param_simulationNumber = 10; + } + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + //Get back the scenarios + engine.voidEval("factors<-read.csv(\".randomlhs.csv\")"); + log + .info("Message sent to R : factors<-read.csv(\".randomlhs.csv\")"); + + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); + + //Get back the simulation number + param_simulationNumber = (Integer) (engine + .eval("length(factors[,1])")); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < simulationStorages.size(); l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~"; + for (int j = 0; j < factorNumber; j++) { + log.info("Message sent to R : " + "names(factors)[" + + (j + 2) + "]"); + + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; + } else { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ",data=dataforaov)"; + } + } + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + log.info("Message sent to R : SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + engine + .voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + log + .info("Message sent to R : names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + log.info("Message sent to R : IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity=data.frame(SoS[1:" + + factorNumber + "],IndSensibilite[1:" + factorNumber + + "])"); + log + .info("Message sent to R : exportsensitivity=data.frame(SoS[1:" + + factorNumber + + "],IndSensibilite[1:" + + factorNumber + "])"); + engine + .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + log + .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + + log + .info("Message sent to R : " + + "attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception e) { + e.printStackTrace(); + // Error while processing + } + + } + + @Override + public String getDescription() { + return "Implementation of Random Latin Hypercube method method using R"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRRandomLHS.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRSobol.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRSobol.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRSobol.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,596 @@ +/* *##% + * Copyright (C) 2006 - 2009 Code Lutin + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + *##%*/ + +package sensitivity; + +import java.io.File; +import java.util.List; +import java.util.Vector; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; +import org.rosuda.JRI.REXP; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +/** + * Implementation of Sobol method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author: jcouteau $ + */ +public class SensitivityCalculatorRSobol extends AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory + .getLog(SensitivityCalculatorRFast.class); + + @Doc("the size of the 2 random samples") + public int param_n = 20; + + @Doc("the number of bootstrap replicates.") + public int param_nboot = 20; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan, outputdirectory); + + double[] dataframe = new double[0]; + int nbExperiments = 0; + int factorNumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); + return null; + } + } + + String rInstruction = "a<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; + String rCall = String.format(rInstruction, param_nboot); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + REngine engine = new RProxy(); + + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); + + //Set the working directory (for import and exports) + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + engine.voidEval("X1<-data.frame(matrix(runif(" + factorNumber + "*" + + param_n + "),nrow=" + param_n + "))"); + log + .info("Message sent to R : " + + "X1<-data.frame(matrix(runif(" + factorNumber + + "*" + param_n + "),nrow=" + param_n + "))"); + engine.voidEval("X2<-data.frame(matrix(runif(" + factorNumber + "*" + + param_n + "),nrow=" + param_n + "))"); + log + .info("Message sent to R : " + + "X2<-data.frame(matrix(runif(" + factorNumber + + "*" + param_n + "),nrow=" + param_n + "))"); + + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + + // Export the sobol object for the second run in a .sobol file + engine.voidEval("dput(a,file=\".sobol\")"); + log.info("Message sent to R" + "dput(a,file=\".sobol\")"); + // Export the X1 object for the second run in a .X1 file + engine.voidEval("dput(X1,file=\".X1\")"); + log.info("Message sent to R" + "dput(a,file=\".sobol\")"); + // Export the X2 object for the second run in a .X2 file + engine.voidEval("dput(X2,file=\".X2\")"); + log.info("Message sent to R" + "dput(a,file=\".sobol\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + + // Get back experiment plan + /*dataframe = (double[]) engine.eval("a$X");*/ + + Vector<REXP> dataframeVector = (Vector<REXP>) engine.eval("a$X"); + int dataframevectorsize = dataframeVector.size(); + int dataframevectorlength = dataframeVector.get(0).asDoubleArray().length; + dataframe = new double[dataframevectorsize * dataframevectorlength]; + for (int i = 0; i < dataframeVector.size(); i++) { + for (int j = 0; j < dataframeVector.get(0).asDoubleArray().length; j++) { + dataframe[i * dataframeVector.get(0).asDoubleArray().length + + j] = dataframeVector.get(i).asDoubleArray()[j]; + } + } + log.info("Message sent to R : " + "a$X"); + + nbExperiments = dataframe.length / factorNumber; + + String isisFactorDistribution = "isis.factor.distribution<-data.frame(NomFacteur=c(%s),NomDistribution=c(%s),ParametreDistribution=c(%s))"; + + // Creating the vectors. + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + factorNames += ","; + } + + distribution += "\"qunif\""; + parameters += "\"[" + ((ContinuousDomain) domain).getMinBound() + + ";" + ((ContinuousDomain) domain).getMaxBound() + + "]\""; + factorNames += "\"" + factors.get(i).getName() + "\""; + } + + log.info("Message sent to R : " + + String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + log.info("Message sent to R : " + "call<-a$call"); + engine.voidEval("call<-a$call"); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + "isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(a$X)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + } catch (Exception e) { + e.printStackTrace(); + } + + // Transform the result from R in a matrix + MatrixND fast = MatrixFactory.getInstance().create(dataframe, + new int[] { factorNumber, nbExperiments }); + + // Setting up the scenarios. + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(fast + .getValue(new int[] { i, j })); + } else { + Double value = (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound() + + ((Double) ((ContinuousDomain) factor.getDomain()) + .getMaxBound() - (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound()) + * fast.getValue(new int[] { i, j }); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) { + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Call R + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); + + //Set the working directory (for import and exports) + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Get the .X1 file + engine.voidEval("X1<-dget(\".X1\")"); + log.info("Message sent to R : " + "X1<-dget(\".X1\")"); + // Get the .X2 file + engine.voidEval("X2<-dget(\".X2\")"); + log.info("Message sent to R : " + "X2<-dget(\".X2\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Set X1 names + engine.voidEval("names(X1)<-factornames"); + log.info("Message sent to R : " + "names(X1)<-factornames"); + //Set X2 names + engine.voidEval("names(X2)<-factornames"); + log.info("Message sent to R : " + "names(X2)<-factornames"); + + // Get the .sobol file + engine.voidEval("a<-dget(\".sobol\")"); + log.info("Message sent to R : " + "a<-dget(\".sobol\")"); + + //Set a$X names + engine.voidEval("names(a$X)<-factornames"); + log.info("Message sent to R : " + "names(a$X)<-factornames"); + + int scenariosNumber = (Integer) engine.eval("length(a$X[,1])"); + log.info("Message sent to R : " + "length(a$X[,1])"); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < scenariosNumber; l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Compute results + engine.voidEval("tell(a,y=" + name + ")"); + log.info("Message sent to R : " + "tell(a,y=" + name + ")"); + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"tell(a,y=" + + name + ")" + "\",\"analysis_result\"=a)"); + + //setting isis.methodAnalyse attributes + log + .info("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\")"); + + //Create the data.frame of scenarios and results for export purpose + engine.voidEval("dfresults=data.frame(a$X,results)"); + log.info("Message sent to R : " + + "dfresults=data.frame(a$X,results)"); + + //Set working directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Export V + engine.voidEval("write.csv(a$V,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$V,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_V.csv\")"); + + //Export DD + engine.voidEval("write.csv(a$D,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_D.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$D,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_D.csv\")"); + + //Export S + engine.voidEval("write.csv(a$S,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_S.csv\")"); + log.info("Message sent to R : " + + "write.csv(a$S,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_S.csv\")"); + + //Export results + engine.voidEval("write.csv(dfresults,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : " + + "write.csv(results,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + //FIXME export through java to enable export when using Rserve + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + } catch (Exception e) { + e.printStackTrace(); + } + } + + @Override + public String getDescription() { + return "Implementation of Sobol method using R (use of the R sobol2002 method)"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRSobol.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRegularFractions.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRegularFractions.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,664 @@ +package sensitivity; + +import java.io.File; +import java.util.List; + +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.j2r.REngine; +import org.codelutin.j2r.RException; +import org.codelutin.j2r.RProxy; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; +import fr.ifremer.isisfish.simulator.sensitivity.Domain; +import fr.ifremer.isisfish.simulator.sensitivity.Factor; +import fr.ifremer.isisfish.simulator.sensitivity.Scenario; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; +import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityCalculatorRegularFractions extends + AbstractSensitivityCalculator { + + /** to use log facility, just put in your code: log.info("..."); */ + private static Log log = LogFactory + .getLog(SensitivityCalculatorRFrF2.class); + + @Doc("the path of the directory where the R function is stored (do not indicate the RegularFractions.R file name)") + public String param_pathToFunction = ""; + + @Doc("unique prime number of levels of all input and unit factors") + public int param_p = 2; + + @Doc("number of unit factors (so that there are N=p^r units)") + public int param_r = 2; + + @Doc("resolution of the fraction") + public int param_resolution = 2; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan, outputdirectory); + + double[] dataframeplan = new double[0]; + int factorNumber = plan.getFactors().size(); + List<Factor<?, ?>> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + String factorNames = ""; + + //Test all factors, if one is discrete, return null + //Create a string with all factors names + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + factorNames += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + + if (domain instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); + return null; + } + } + + REngine engine = new RProxy(); + + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //outputdirectory.getName(); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + //Set the working directory (to import the R function) + engine.voidEval("setwd(\"" + + param_pathToFunction.replaceAll("\\\\", "/") + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + param_pathToFunction.replaceAll("\\\\", "/") + "\")"); + + //Import the function + log.info("source(\"regularfractions.R\")"); + engine.voidEval("source(\"regularfractions.R\")"); + + //Create the instruction + String rInstruction = "x<-regular.fraction(%s,%s,%s,%s)"; + String rCall = String.format(rInstruction, factors.size(), param_p, + param_r, param_resolution); + + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); + } + + // Run function + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Run function + engine.voidEval("call<-\"" + rCall + "\""); + log.info("Message sent to R : " + "call<-\"" + rCall + "\""); + + // Creating the factors vector. + rInstruction = "factornames<-c(%s)"; + rCall = String.format(rInstruction, factorNames); + + engine.voidEval(rCall); + log.info("Message sent to R : " + rCall); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Export the result object for the second run in a .regularfractions file + engine.voidEval("dput(x,file=\".regularfractions\")"); + log.info("Message sent to R : " + + "dput(x,file=\".regularfractions\")"); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + + // Get back experiment plan + dataframeplan = (double[]) engine.eval("x[[1]]"); + log.info("Message sent to R : " + "x[[1]]"); + + //Get back the simulation number + log.info("length(x[[1]][,1])"); + int simulationNumber = (Integer) engine.eval("length(x[[1]][,1])"); + + // Transform the result from R in a matrix + MatrixND morris = MatrixFactory.getInstance().create(dataframeplan, + new int[] { factors.size(), simulationNumber }); + + // Setting up the scenarios. + for (int j = 0; j < simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factors.size(); i++) { + Factor factor = plan.getFactors().get(i); + if ((factor.getDomain() instanceof MatrixContinuousDomain) + || (factor.getDomain() instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(morris.getValue(new int[] { + i, j })); + } else { + Double value = (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound() + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor + .getDomain()).getMinBound()) + * (morris.getValue(new int[] { i, j }) / (param_p - 1)); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String dataframe = "data<-data.frame("; + + //Create the factors vectors and the dataframe instruction + for (int j = 0; j < factorNumber; j++) { + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { + + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < simulationNumber; i++) { + if (i < (simulationNumber - 1)) { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((EquationContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else if (factor.getDomain() instanceof MatrixContinuousDomain) { + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < simulationNumber; i++) { + if (i < (simulationNumber - 1)) { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; + } else { + vector = vector + + ((MatrixContinuousDomain) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } else { + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; + for (int i = 0; i < simulationNumber; i++) { + if (i < (simulationNumber - 1)) { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue() + + ","; + } else { + vector = vector + + thisExperimentScenarios.get(i) + .getFactors().get(j).getValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + log.info("Message sent to R : " + vector); + } + + if (j < factorNumber - 1) { + dataframe = dataframe + + factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; + } else { + dataframe += factor.getName().replaceAll(" ", "") + + "=factor(" + factor.getName().replaceAll(" ", "") + + "))"; + } + + } + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + log.info("Message sent to R : " + + "isis.factor.distribution<-c(0.0)"); + engine.voidEval("isis.factor.distribution<-c(0.0)"); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + engine + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); + + log + .info("Message sent to R : " + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); + + //Create isis.Simule + log.info("Message sent to R : " + "isis.simule<-data.frame(data)"); + engine.voidEval("isis.simule<-data.frame(data)"); + + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + // Export the data.frame object for the second run in a .data file + engine.voidEval("write.csv(data,file=\".data.csv\")"); + log.info("Message sent to R : write.csv(data,file=\".data.csv\")"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (RException eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + } + + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) throws SensitivityException { + + REngine engine = new RProxy(); + try { + + //Clear session + log.info("rm(list=ls())"); + engine.voidEval("rm(list=ls())"); + + //Set working directory to get Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + //Get Isis R session + log.info("load(\"" + outputdirectory.getName() + ".RData\")"); + engine + .voidEval("load(\"" + outputdirectory.getName() + + ".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + + // Get the regularfractions object from the .regularfractions file + engine.voidEval("x<-dget(\".regularfractions\")"); + log.info("Message sent to R : " + "x<-dget(\".regularfractions\")"); + + // Get the factornames object from the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Get back the scenarios + engine.voidEval("factors<-read.csv(\".data.csv\")"); + log.info("Message sent to R : factors<-read.csv(\".data.csv\")"); + + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + String rInstruction = name + "<-c("; + for (int l = 0; l < simulationStorages.size(); l++) { + File importFile = new File(simulationStorages.get(l) + .getDirectory().toString() + + File.separator + + SimulationStorage.RESULT_EXPORT_DIRECTORY, param + .getSensitivityExport().get(k).getExportFilename() + + param.getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + rInstruction = rInstruction + simulationResult + ","; + } else { + rInstruction = rInstruction + simulationResult; + } + } + rInstruction = rInstruction + ")"; + + log.info("Message sent to R : " + rInstruction); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; + engine.voidEval(dataframe); + log.info("Message sent to R : " + dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~("; + for (int j = 0; j < factorNumber; j++) { + log.info("Message sent to R : " + "names(factors)[" + + (j + 2) + "]"); + + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; + } else { + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ")"; + if (param_resolution <= 4) { + aovCall += ",data=dataforaov)"; + } else { + aovCall += "^2,data=dataforaov)"; + } + } + } + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + log.info("Message sent to R : SoS<-summary(aovresult)[[1]][1:" + + factorNumber + ",2]"); + engine + .voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + log + .info("Message sent to R : names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" + + factorNumber + "]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + log.info("Message sent to R : IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity=data.frame(SoS[1:" + + factorNumber + "],IndSensibilite[1:" + factorNumber + + "])"); + log + .info("Message sent to R : exportsensitivity=data.frame(SoS[1:" + + factorNumber + + "],IndSensibilite[1:" + + factorNumber + "])"); + engine + .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + log + .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + + "\"" + + ",\"analysis_result\"=list(aovresult,IndSensibilite))"); + + log + .info("Message sent to R : " + + "attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + engine + .voidEval("attr(isis.methodAnalyse,\"nomModel\")<-\"isis-fish-externe-R\""); + + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName + + "." + name)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName + "." + name)); + + } + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + + // Save Isis R session + log.info("save.image(file=\"" + outputdirectory.getName() + ".RData\")"); + engine.voidEval("save.image(file=\"" + outputdirectory.getName() + + ".RData\")"); + + engine.terminate(); + + } catch (Exception eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + } + + } + + @Override + public String getDescription() { + return "Implementation of Regular fractions method using R"; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivity/SensitivityCalculatorRegularFractions.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivity/regularfractions.R =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivity/regularfractions.R (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivity/regularfractions.R 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,211 @@ +#================================================================================ +# FONCTIONS DE CALCUL D'UNE FRACTION REGULIERE DE RESOLUTION DONNEE +# Auteur: H. Monod, INRA Jouy en Josas +# Copyright INRA 2009 +# Ce programme est une version preliminaire et simplifiee d'une librairie R +# en preparation par A. Kobilinsky, H. Monod, A. Bouvier +#================================================================================ +regular.fraction <- function(s,p,r,resolution){ + # DESCRIPTION + # generates a regular fractional factorial design of given resolution, + # for s factors at p levels in p^r units + # ARGUMENTS + # s : number of input factors + # p : unique prime number of levels of all input and unit factors + # r : number of unit factors (so that there are N=p^r units) + # resolution : resolution of the fraction + # max.sol : maximum number of solutions + # DETAILS + # This is a simplified version of a more general library in preparation. + # In this version, all factors must have the same prime number of levels + # and only fractions with a given resolution can be constructed. The first + # q factors are used as basic factors. The first solution is kept although + # it may not be the most interesting one (no control of aberration). This + # function is programmed entirely in R and so it is not efficient with respect + # to computer time. There is no explicit check on the arguments and so it + # is up to the user to restrict p to a prime number such as 2, 3, 5 or 7. + # OUTPUT: + # a list with two components: plan (the design in base p) and matrice.cle + # (the design key). The design has N=p^r rows (units) and s columns (factors). + # All its elements are integers modulo p that represent the factor levels. + + # ensemble ineligible + cat("Determination des termes ineligibles: ") + ineligible <- diag(s) + for(reso in 2:(resolution-1)){ + combis <- combn(s,reso) + ncombi <- ncol(combis) + select <- cbind( c(combis), rep(seq(ncombi),rep(reso,ncombi)) ) + ineli <- matrix(0,s,ncombi) + ineli[select] <- 1 + ineligible <- cbind(ineligible,ineli) + } + cat(ncol(ineligible)," termes ineligibles.\n") + if( (p!=2) ){ + ineligible <- representative.basep(ineligible,p) + } + # Identification of the last non-zero coefficients in each ineligible trt character + ineligible.lnz <- apply(ineligible, 2, function(x){max(seq(along=x)[x!=0])}) + # initialisation of PhiStar by using the first q factors as basic factors + PhiStar <- diag(r) + # + f <- ncol(PhiStar) + if(s == f){ + check <- !any(apply(((PhiStar %*% ineligible)%%p)==0, 2, all)) + if(check) return(list(PhiStar)) + } + # Calculation of the set of initially admissible elements of U* + admissible <- t(convertinto.basep(seq((p^r)-1),p)) + nb.admissible <- ncol(admissible) + # Backtrack search - preliminaries + eeU <- list(length=s-f) + leeU <- rep(NA,s-f) + neeU <- rep(0,s-f) + # Backtrack search + cat("Recherche d'une solution (algorithme backtrack).\n") + jprev <- 0 ; j <- 1 + solved <- FALSE + while((j > 0)&(!solved)){ + PhiStar <- PhiStar[,seq(f+j-1), drop=FALSE] + if(jprev < j){ + ineligible.j <- ineligible[ seq(f+j-1), ineligible.lnz==(f+j), drop=FALSE ] + admissible.keep <- planor.kernelcheck.basep(PhiStar, admissible, ineligible.j, p) + eeU[[j]] <- seq(nb.admissible)[admissible.keep] + leeU[j] <- length(eeU[[j]]) + neeU[j] <- 0 + } + if(neeU[j] < leeU[j]){ + neeU[j] <- neeU[j]+1 + newcolj <- (eeU[[j]])[neeU[j]] + PhiStar <- cbind(PhiStar,admissible[,newcolj]) + if(j == (s-f)){ + cat("Solution obtenue. ") + solved <- TRUE + jprev <- j ; j <- j + } + else{ + jprev <- j ; j <- j+1 + } + } + else{ + jprev <- j ; j <- j-1 + } + } + if(solved){ + # Construction du plan + plan <- crossing(rep(p,r),start=0) %*% PhiStar %%p + # Sortie + out <- list(plan=plan, matrice.cle=PhiStar, p=p) + } + else{ + cat("Pas de solution. ") + out <- NULL + } + cat("Recherche terminee.\n") + return(out) +} +#--------------------------------------------------------------------------- +planor.kernelcheck.basep <- function(PhiStar, admissible, IneligibleSet, p){ + ImagesIS <- (- PhiStar %*% IneligibleSet)%%p + avoid <- convertfrom.basep( t(ImagesIS), p) + candidate <- convertfrom.basep( t(admissible), p) + test <- !(candidate %in% avoid) + return(test) +} +#--------------------------------------------------------------------------- +convertinto.basep <- function (x, p) { + # Conversion of an integer or integer vector x into base p + # The coefficients are ordered by increasing powers of p + if (!is.numeric(x)) + stop("cannot decompose non-numeric arguments") + if (length(x) > 1) { + l <- matrix(0, length(x), length(Recall(max(x),p))) + for(i in seq(along = x)){ + dec.i <- Recall(x[i],p) + l[i, seq(along=dec.i) ] <- dec.i + } + return(l) + } + if (x != round(x) || x < 0) + return(x) + val <- x%%p + while ( (x <- x%/%p) > 0 ) { + newval <- x%%p + val <- c(val,newval) + } + return(val) +} +#--------------------------------------------------------------------------- +convertfrom.basep <- function (x, p) { + # Conversion of integers x coded as vectors of coefficients in base p + # to classical integers in base 10 + + if (!is.numeric(x)) + stop("cannot recompose non-numeric arguments") + if( (max(x)>p) || (min(x)<0) ) + stop("x must be reduced modulo p") + if (is.matrix(x)) { + l <- rep(NA, nrow(x)) + for(i in seq(along = l)){ + l[i] <- Recall(x[i,],p) + } + return(l) + } + val <- sum( x * p^(seq(along=x)-1) ) + return(val) +} +#--------------------------------------------------------------------------- +inverses.basep <- function(p){ + # Raw calculation of the inverses modulo p + + if(p==2) return(1) + else if(p==3) return(c(1,2)) + products <- outer(seq(2,p-2), seq(2,p-2), "*")%%p + inverses <- 1 + apply(products, 1, function(x){ seq(along=x)[x==1] }) + return( c(1,inverses,p-1) ) +} +#--------------------------------------------------------------------------- +representative.basep <- function(mat,p){ + # generates the minimal set of representatives in base p + # of the columns x of matrix mat + + mat <- as.matrix(mat) + # + if(p==2) return(mat %%2) + # + representative <- NULL + for(j in seq(ncol(mat))){ + x <- mat[,j] + select <- seq(x)[x != 0] + nbtocross <- length(select)-1 + if( nbtocross <= 0 ) mat.j <- x + else{ + select <- select[seq(nbtocross)] + N <- (p-1)^nbtocross + mat.j <- matrix(x, nrow(mat), N) + mat.j[select,] <- t( crossing(rep(p-1,nbtocross),start=1) ) + } + representative <- cbind(representative, mat.j) + } + return(representative %%p) +} +#--------------------------------------------------------------------------- +crossing <- function(n,start=1){ + # Generates all n1 x n2 x ... x ns combinations of size s with n1,...,ns integers + + N <- prod(n) + s <- length(n) + n <- c(n,1) + crosses <- matrix(NA, N, s) + for(i in seq(s)) + { + motif <- start + seq(n[s+1-i])-1 + repet1 <- rep( prod(n[s+1-i+seq(i)]), n[s+1-i] ) + if(i==s){ repet2 <- 1 } + else{ repet2 <- prod(n[seq(s-i)]) } + crosses[,s-i+1] <- rep( rep( motif, repet1 ), repet2 ) + } + return(crosses) +} +#--------------------------------------------------------------------------- + Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassReferenceY9.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassReferenceY9.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassReferenceY9.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,100 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityBiomassReferenceY9 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityBiomassReferenceY9.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double biomass = 0.0; + Double referenceBiomass = 0.0; + + System.out.println("reference simul : " + param_referenceSimulation); + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); + System.out.println("matlastdate:" + (Object) matlastdate); + + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + + MatrixND matreferencelastdate = referenceResultStorage + .getMatrix(lastDate, ResultName.MATRIX_BIOMASS + " " + + pop, tx); + referenceBiomass = matreferencelastdate.sumAll(); + + tx.commitTransaction(); + tx.closeContext(); + } + } + System.out.println("simulationStorage:" + simulation); + System.out.println("referenece simulation:" + referenceSimulation); + System.out.println("resultStorage:" + resultStorage); + System.out.println("referenceStroagr:" + referenceResultStorage); + System.out.println("biomass:" + biomass); + System.out.println("referenceBiomass:" + referenceBiomass); + + out.write(Double.toString(biomass / referenceBiomass)); + + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomassReferenceY9"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassReferenceY9.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,110 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityBiomassRelativeReferenceY12 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityBiomassRelativeReferenceY12.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage resultStorage = simulation.getResultStorage(); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + double biomassReference = 0.0; + double firstbiomassReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass on december of the first year + MatrixND matfirstdate = resultStorage.getMatrix(firstDate, pop, + ResultName.MATRIX_BIOMASS); + firstbiomass = matfirstdate.sumAll(); + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); + + //Get the biomass on december of the first year + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix(firstDate, ResultName.MATRIX_BIOMASS + " " + + pop, tx); + firstbiomassReference = matfirstdatereference.sumAll(); + tx.commitTransaction(); + tx.closeContext(); + + //Get the biomass of the last time step + tx = referenceSimulation.getStorage().beginTransaction(); + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(lastDate, ResultName.MATRIX_BIOMASS + " " + + pop, tx); + biomassReference = matlastdatereference.sumAll(); + tx.commitTransaction(); + tx.closeContext(); + + } + } + + out.write(Double.toString((biomass / firstbiomass) + / (biomassReference / firstbiomassReference))); + + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomassRelativeReferenceY12"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeY6.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeY6.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeY6.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,77 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityBiomassRelativeY6 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityBiomassRelativeY6.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass on december of the first year + MatrixND matfirstdate = resultStorage.getMatrix(firstDate, pop, + ResultName.MATRIX_BIOMASS); + firstbiomass = matfirstdate.sumAll(); + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); + + } + } + out.write(Double.toString(biomass / firstbiomass)); + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomassRelativeY6"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassRelativeY6.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassY3.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassY3.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassY3.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,67 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityBiomassY3 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityBiomassY3.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + double biomass = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); + } + } + out.write(Double.toString(biomass)); + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomassY3"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityBiomassY3.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightReferenceY7.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightReferenceY7.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightReferenceY7.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,98 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityCapturesWeightReferenceY7 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightReferenceY7.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + + //Get the reference captures Weight of each month of the last year + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + MatrixND matlastdatereference = referenceResultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + + " " + pop, tx); + capturesWeightReference += matlastdatereference.sumAll(); + tx.commitTransaction(); + tx.closeContext(); + + } + + } + } + + out.write(Double.toString(capturesWeight / capturesWeightReference)); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeightReferenceY7"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightReferenceY7.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeReferenceY10.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeReferenceY10.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,118 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityCapturesWeightRelativeReferenceY10 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightRelativeReferenceY10.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightfirst = 0.0; + Double capturesWeightreference = 0.0; + Double capturesWeightfirstreference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + + //Get the captures Weight of each month of the first year + MatrixND matfirstdate = resultStorage + .getMatrix( + new Date(i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightfirst += matfirstdate.sumAll(); + + //Get the reference captures Weight of each month of the last year + + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + + MatrixND matlastdatereference = referenceResultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + + " " + pop, tx); + capturesWeightreference += matlastdatereference.sumAll(); + + //Get the reference captures Weight of each month of the first year + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix( + new Date(i), + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + + " " + pop, tx); + capturesWeightfirstreference += matfirstdatereference + .sumAll(); + tx.commitTransaction(); + tx.closeContext(); + } + } + } + out.write(Double.toString((capturesWeight / capturesWeightfirst) + / (capturesWeightreference / capturesWeightfirstreference))); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeightRelativeReferenceY10"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeReferenceY10.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeY4.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeY4.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeY4.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,85 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityCapturesWeightRelativeY4 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightRelativeY4.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightfirst = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + + //Get the captures Weight of each month of the first year + MatrixND matfirstdate = resultStorage + .getMatrix( + new Date(i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightfirst += matfirstdate.sumAll(); + } + + } + } + + out.write(Double.toString(capturesWeight / capturesWeightfirst)); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeightRelativeY4"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightRelativeY4.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightY1.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightY1.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightY1.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,76 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityCapturesWeightY1 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightY1.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + } + + } + } + + out.write(Double.toString(capturesWeight)); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeightY1"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityCapturesWeightY1.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassReferenceY8.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassReferenceY8.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassReferenceY8.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,107 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityGenitorBiomassReferenceY8 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassReferenceY8.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double biomass = 0.0; + Double referenceBiomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + biomass += i.getValue() * group.getReproductionRate(); + } + } + + //Get the reference biomass of the last time step + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); + for (MatrixIterator i = matlastdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + referenceBiomass += i.getValue() + * group.getReproductionRate(); + } + } + tx.commitTransaction(); + tx.closeContext(); + } + } + out.write(Double.toString(biomass / referenceBiomass)); + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomassReferenceY8"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassReferenceY8.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeReferenceY11.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeReferenceY11.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeReferenceY11.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,142 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.topia.TopiaContext; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityGenitorBiomassRelativeReferenceY11 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassRelativeReferenceY11.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage resultStorage = simulation.getResultStorage(); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + double biomassReference = 0.0; + double firstbiomassReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the first time step + MatrixND matfirstdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomass += i.getValue() + * group.getReproductionRate(); + } + } + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + biomass = biomass + i.getValue() + * group.getReproductionRate(); + } + } + + //Get the reference biomass of the first time step + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); + for (MatrixIterator i = matfirstdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomassReference += i.getValue() + * group.getReproductionRate(); + } + } + + //Get the reference biomass of the last time step + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); + for (MatrixIterator i = matlastdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + biomassReference += i.getValue() + * group.getReproductionRate(); + } + } + tx.commitTransaction(); + tx.closeContext(); + } + } + out.write(Double.toString((biomass / firstbiomass) + / (biomassReference / firstbiomassReference))); + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomassRelativeReferenceY11"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeReferenceY11.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeY5.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeY5.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeY5.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,94 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityGenitorBiomassRelativeY5 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassRelativeY5.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + ResultStorage resultStorage = simulation.getResultStorage(); + + //Get the biomass of the first time step + MatrixND matfirstdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomass += i.getValue() + * group.getReproductionRate(); + } + } + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) + biomass += i.getValue() * group.getReproductionRate(); + } + } + } + out.write(Double.toString(biomass / firstbiomass)); + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomassRelativeY5"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassRelativeY5.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL" Added: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassY2.java =================================================================== --- isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassY2.java (rev 0) +++ isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassY2.java 2009-09-09 16:27:51 UTC (rev 2591) @@ -0,0 +1,79 @@ +package sensitivityexports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityGenitorBiomassY2 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassY2.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + double biomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + ResultStorage resultStorage = simulation.getResultStorage(); + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + PopulationGroup group = (PopulationGroup) sems[1]; + if (date.equals(lastDate)) { + biomass += i.getValue() * group.getReproductionRate(); + } + } + } + } + out.write(Double.toString(biomass)); + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomassY2"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: isis-fish/trunk/src/test/resources/test-database/sensitivityexports/SensitivityGenitorBiomassY2.java ___________________________________________________________________ Added: svn:keywords + "Author Date Id Revision HeadURL"

1 0

r2590 - isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util
by chatellier＠users.labs.libre-entreprise.org 09 Sep '09

09 Sep '09

Author: chatellier Date: 2009-09-09 15:35:02 +0000 (Wed, 09 Sep 2009) New Revision: 2590 Modified: isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/EvaluateHelperTest.java Log: Ajout d'un test sur la compilation des equations (ne fonctionne pas) Modified: isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/EvaluateHelperTest.java =================================================================== --- isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/EvaluateHelperTest.java 2009-09-04 17:43:44 UTC (rev 2589) +++ isis-fish/trunk/src/test/java/fr/ifremer/isisfish/util/EvaluateHelperTest.java 2009-09-09 15:35:02 UTC (rev 2590) @@ -21,8 +21,8 @@ import java.util.HashMap; import java.util.Map; -import junit.framework.Assert; - +import org.junit.Assert; +import org.junit.Ignore; import org.junit.Test; import fr.ifremer.isisfish.AbstractIsisFishTest; @@ -75,7 +75,7 @@ args.put("context", null); args.put("age", 2.0); args.put("group", null); - Object result = EvaluatorHelper.evaluate("org.codelutin.equation", + Object result = EvaluatorHelper.evaluate("fr.isisfish.equation", "TestEvaluate", PopulationGrowth.class, equationContent, args); Assert.assertNotNull(result); @@ -95,17 +95,37 @@ args.put("group", null); String equationContent = "return length * 2.0;"; - Object result = EvaluatorHelper.evaluate("org.codelutin.equation", + Object result = EvaluatorHelper.evaluate("fr.isisfish.equation", "TestDoubleContentEvaluate", PopulationGrowthReverse.class, equationContent, args); Assert.assertNotNull(result); Assert.assertEquals("4.0", result.toString()); equationContent = "return length * 3.0;"; - result = EvaluatorHelper.evaluate("org.codelutin.equation", + result = EvaluatorHelper.evaluate("fr.isisfish.equation", "TestDoubleContentEvaluate", PopulationGrowthReverse.class, equationContent, args); Assert.assertNotNull(result); Assert.assertEquals("6.0", result.toString()); } + + /** + * Test que le repertoire des scripts en bien présent + * dans le classpath de compilation. + */ + @Ignore + public void testEquationWithDatabaseContent() { + Map<String, Object> args = new HashMap<String, Object>(); + args.put("context", null); + args.put("length", 2.0); + args.put("group", null); + + String equationContent = "String name = scripts.ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP;"; + equationContent += "return length * 2.0;"; + Object result = EvaluatorHelper.evaluate("fr.isisfish.equation", + "TestEquationWithDatabaseContent", PopulationGrowthReverse.class, + equationContent, args); + Assert.assertNotNull(result); + Assert.assertEquals("4.0", result.toString()); + } }

1 0

r2589 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org 04 Sep '09

04 Sep '09

Author: chatellier Date: 2009-09-04 17:43:44 +0000 (Fri, 04 Sep 2009) New Revision: 2589 Modified: isis-fish/trunk/changelog.txt Log: Update changelog Modified: isis-fish/trunk/changelog.txt =================================================================== --- isis-fish/trunk/changelog.txt 2009-09-04 17:42:32 UTC (rev 2588) +++ isis-fish/trunk/changelog.txt 2009-09-04 17:43:44 UTC (rev 2589) @@ -1,3 +1,7 @@ +isis-fish (3.2.0.6) stable; urgency=low + + -- + isis-fish (3.2.0.5) stable; urgency=low * Fix export loaded too early (not in correct classloader) @@ -5,7 +9,7 @@ * Fix a date comparison problem (frequent in windows) * Restore running status progress bar indeterminate state - -- + -- ven. sept. 4 19:41:17 CEST 2009 isis-fish (3.2.0.5-rc3) stable; urgency=low

1 0

r2588 - isis-fish/trunk/src/main/java/fr/ifremer/isisfish
by chatellier＠users.labs.libre-entreprise.org 04 Sep '09

04 Sep '09

Author: chatellier Date: 2009-09-04 17:42:32 +0000 (Fri, 04 Sep 2009) New Revision: 2588 Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java Log: Next version Modified: isis-fish/trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- isis-fish/trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2009-09-04 16:57:15 UTC (rev 2587) +++ isis-fish/trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2009-09-04 17:42:32 UTC (rev 2588) @@ -119,7 +119,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static VersionNumber version = new VersionNumber(3, 2, 0, 5); + protected final static VersionNumber version = new VersionNumber(3, 2, 0, 6); protected final static VersionNumber databaseVersion = new VersionNumber( version.getNumber(0), version.getNumber(1)); protected final static VersionNumber apiVersion = new VersionNumber(

1 0

r2587 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org 04 Sep '09

04 Sep '09

Author: chatellier Date: 2009-09-04 16:57:15 +0000 (Fri, 04 Sep 2009) New Revision: 2587 Modified: isis-fish/trunk/pom.xml Log: [maven-release-plugin] prepare for next development iteration Modified: isis-fish/trunk/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2009-09-04 16:57:11 UTC (rev 2586) +++ isis-fish/trunk/pom.xml 2009-09-04 16:57:15 UTC (rev 2587) @@ -13,7 +13,7 @@ <groupId>ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>3.2.0.5</version> + <version>3.2.0.6-SNAPSHOT</version>  <dependencies> @@ -585,9 +585,9 @@   <scm> - <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</connection> - <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</developerConnection> - <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/tags/…</url> + <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</connection> + <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</developerConnection> + <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/trunk…</url> </scm>

1 0

r2586 - in isis-fish/tags: . isis-fish-3.2.0.5
by chatellier＠users.labs.libre-entreprise.org 04 Sep '09

04 Sep '09

Author: chatellier Date: 2009-09-04 16:57:11 +0000 (Fri, 04 Sep 2009) New Revision: 2586 Added: isis-fish/tags/isis-fish-3.2.0.5/ isis-fish/tags/isis-fish-3.2.0.5/pom.xml Removed: isis-fish/tags/isis-fish-3.2.0.5/pom.xml Log: [maven-release-plugin] copy for tag isis-fish-3.2.0.5 Deleted: isis-fish/tags/isis-fish-3.2.0.5/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2009-09-04 16:43:48 UTC (rev 2584) +++ isis-fish/tags/isis-fish-3.2.0.5/pom.xml 2009-09-04 16:57:11 UTC (rev 2586) @@ -1,770 +0,0 @@ -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> - - <modelVersion>4.0.0</modelVersion> - -  -  -  - <parent> - <groupId>org.codelutin</groupId> - <artifactId>lutinproject</artifactId> - <version>3.5</version> - </parent> - - <groupId>ifremer</groupId> - <artifactId>isis-fish</artifactId> - <version>3.2.0.5-SNAPSHOT</version> - -  - <dependencies> - -  - - <dependency> - <groupId>log4j</groupId> - <artifactId>log4j</artifactId> - <version>1.2.14</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>org.codelutin</groupId> - <artifactId>lutinutil</artifactId> - <version>${lutinutil.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin.topia</groupId> - <artifactId>topia-persistence</artifactId> - <version>${topia.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin</groupId> - <artifactId>topia-service</artifactId> - <version>${topia.service.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin</groupId> - <artifactId>lutinmatrix</artifactId> - <version>${lutinmatrix.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin</groupId> - <artifactId>lutinwidget</artifactId> - <version>${lutinwidget.version}</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>org.codelutin.jaxx</groupId> - <artifactId>jaxx-runtime-swing</artifactId> - <version>${jaxx.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin.jaxx</groupId> - <artifactId>jaxx-runtime-validator</artifactId> - <version>${jaxx.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.codelutin.jaxx</groupId> - <artifactId>jaxx-runtime-swing-widget</artifactId> - <version>${jaxx.version}</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>org.codelutin</groupId> - <artifactId>lutinj2r</artifactId> - <version>${lutinj2r.version}</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>commons-jxpath</groupId> - <artifactId>commons-jxpath</artifactId> - <version>1.2</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>commons-lang</groupId> - <artifactId>commons-lang</artifactId> - <version>2.4</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.apache.commons</groupId> - <artifactId>commons-math</artifactId> - <version>2.0</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>commons-collections</groupId> - <artifactId>commons-collections</artifactId> - <version>3.2.1</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>commons-beanutils</groupId> - <artifactId>commons-beanutils</artifactId> - <version>1.8.0</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>commons-io</groupId> - <artifactId>commons-io</artifactId> - <version>1.4</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>dom4j</groupId> - <artifactId>dom4j</artifactId> - <version>1.6.1</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>jfreechart</groupId> - <artifactId>jfreechart</artifactId> - <version>0.9.3</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>jcommon</groupId> - <artifactId>jcommon</artifactId> - <version>0.7.0</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>org.apache.xmlrpc</groupId> - <artifactId>xmlrpc-client</artifactId> - <version>${xmlrpc.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.apache.xmlrpc</groupId> - <artifactId>xmlrpc-server</artifactId> - <version>${xmlrpc.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>commons-httpclient</groupId> - <artifactId>commons-httpclient</artifactId> - <version>3.1</version> - <scope>runtime</scope> - </dependency> - -  - <dependency> - <groupId>org.beanshell</groupId> - <artifactId>bsh</artifactId> - <version>2.0b4</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>openmap</groupId> - <artifactId>openmap</artifactId> - <version>${openmap.version}</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>org.fife</groupId> - <artifactId>rsyntaxtextarea</artifactId> - <version>1.3.4</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>com.jcraft</groupId> - <artifactId>jsch</artifactId> - <version>0.1.42</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>jaxen</groupId> - <artifactId>jaxen</artifactId> - <version>1.1.1</version> - <scope>runtime</scope> - </dependency> - -  - <dependency> - <groupId>com.h2database</groupId> - <artifactId>h2</artifactId> - <version>1.1.117</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz</artifactId> - <version>${aspectwerkz.version}</version> - <scope>compile</scope> - </dependency> - <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz-jdk5</artifactId> - <version>${aspectwerkz.version}</version> - <scope>compile</scope> - </dependency> - <dependency> - <groupId>aspectwerkz</groupId> - <artifactId>aspectwerkz-core</artifactId> - <version>${aspectwerkz.version}</version> - <scope>compile</scope> - </dependency> - -  - <dependency> - <groupId>ssj</groupId> - <artifactId>ssj</artifactId> - <version>2.1.1</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>Blas</artifactId> - <version>20081007</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>colt</artifactId> - <version>20081007</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>interpreter</artifactId> - <version>1.6.8</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>language</artifactId> - <version>1.6.7</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>logger</artifactId> - <version>1.6.4</version> - <scope>runtime</scope> - </dependency> - - <dependency> - <groupId>ssj</groupId> - <artifactId>optimization</artifactId> - <version>20081007</version> - <scope>runtime</scope> - </dependency> -  - -  - <dependency> - <groupId>org.tmatesoft</groupId> - <artifactId>svnkit</artifactId> - <version>1.2.3.5521</version> - <scope>compile</scope> - </dependency> - <dependency> - <groupId>com.trilead</groupId> - <artifactId>trilead-ssh2</artifactId> - <version>build213-svnkit-1.2</version> - <scope>runtime</scope> - </dependency> -  - - <dependency> - <groupId>org.freemarker</groupId> - <artifactId>freemarker</artifactId> - <version>2.3.15</version> - </dependency> - - <dependency> - <groupId>net.sourceforge.cpdetector</groupId> - <artifactId>cpdetector</artifactId> - <version>1.0.7</version> - <scope>compile</scope> - </dependency> - - <dependency> - <groupId>com.sun</groupId> - <artifactId>tools</artifactId> - <version>1.6.0</version> - </dependency> - </dependencies> - -  -  -  - <name>IsisFish</name> - <description>Simulateur de pecherie complexe.</description> - <inceptionYear>1999</inceptionYear> - - <licenses> - <license> - <name>GPL</name> - <url>http://www.gnu.org/copyleft/gpl.html</url> - <distribution>repo</distribution> - </license> - </licenses> - -  -  -  - <packaging>jar</packaging> - - <properties> -  - <labs.id>8</labs.id> - -  - <labs.project>isis-fish</labs.project> - -  - <jaxx.version>1.5.1</jaxx.version> - <topia.version>2.1.6.1</topia.version> - <topia.service.version>1.0.3</topia.service.version> - <lutinmatrix.version>1.3</lutinmatrix.version> - <lutinutil.version>1.0.6</lutinutil.version> - <i18n.version>0.9</i18n.version> - <lutinwidget.version>0.14.1</lutinwidget.version> - <generator.version>0.64</generator.version> - <lutinj2r.version>0.4</lutinj2r.version> - <jrst.version>0.8.4</jrst.version> - <license-switcher.version>0.6</license-switcher.version> - <openmap.version>4.6.4</openmap.version> - <aspectwerkz.version>2.0</aspectwerkz.version> - <xmlrpc.version>3.1.2</xmlrpc.version> - -  - <maven.test.forkMode>once</maven.test.forkMode> - -  - <maven.jar.main.class>fr.ifremer.isisfish.IsisFish</maven.jar.main.class> - -  - <keystorepath>${codelutin.keystorepath}</keystorepath> - <keystorealias>CodeLutin</keystorealias> - <keystorepass>codelutin</keystorepass> - <jnlp.build.directory>${project.build.directory}/jnlp</jnlp.build.directory> - - <jnlpCodebase>${project.url}</jnlpCodebase> -  - <jnlpCodebase>file://${jnlp.build.directory}</jnlpCodebase> - </properties> - - <build> - <plugins> - - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-generator-plugin</artifactId> - <version>${generator.version}</version> - <executions> - <execution> - <id>Generator</id> - <phase>generate-sources</phase> - <configuration> - <srcDirZuml>${project.basedir}/src/main/xmi</srcDirZuml> - <srcXmiDest>${maven.gen.dir}/xmi/</srcXmiDest> - <fullPackagePath>fr.ifremer.isisfish</fullPackagePath> - <extractedPackages>fr.ifremer.isisfish</extractedPackages> -  - <srcGenDest>${maven.gen.dir}/objectmodel/</srcGenDest> - <includes>**/*.objectmodel</includes> - <templates>org.codelutin.topia.generator.TopiaMetaGenerator</templates> - <excludeTemplates> - <value>org.codelutin.topia.generator.EntityEnumGenerator</value> - <value>org.codelutin.topia.generator.EntityProviderGenerator</value> - </excludeTemplates> - <destDirGen>${maven.gen.dir}/java</destDirGen> - <defaultPackage>fr.ifremer.isisfish</defaultPackage> - <copyVersionDir>${project.basedir}/src/main/resources/oldmappings/%MODELNAME% - </copyVersionDir> - <copyVersionFiles>**/*.hbm.xml</copyVersionFiles> - <copyOverwrite>true</copyOverwrite> - </configuration> - <goals> - <goal>zargo2xmi</goal> - <goal>xmi2objectmodel</goal> - <goal>generate</goal> - <goal>copyVersionFiles</goal> - </goals> - </execution> - </executions> - <dependencies> - <dependency> - <groupId>org.codelutin.topia</groupId> - <artifactId>topia-persistence</artifactId> - <version>${topia.version}</version> - <scope>runtime</scope> - </dependency> - </dependencies> - </plugin> - - <plugin> - <groupId>org.codelutin.jaxx</groupId> - <artifactId>maven-jaxx-plugin</artifactId> - <version>${jaxx.version}</version> - <executions> - <execution> - <goals> - <goal>generate</goal> - </goals> - <configuration> - <extraImportList>jaxx.runtime.SwingUtil,static jaxx.runtime.Util.getStringValue</extraImportList> - <addSourcesToClassPath>true</addSourcesToClassPath> - <addProjectClassPath>true</addProjectClassPath> - </configuration> - </execution> - </executions> - </plugin> - - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-i18n-plugin</artifactId> - <version>${i18n.version}</version> - <configuration> - <entries> - <entry> - <basedir>${maven.gen.dir}/java/</basedir> - <specificGoal>parserJava</specificGoal> - <includes> - <param>**\/**UI.java</param> - </includes> - </entry> - </entries> - </configuration> - <executions> - <execution> - <goals> - <goal>parserJava</goal> - <goal>gen</goal> - </goals> - </execution> - </executions> - </plugin> - -  - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-jrst-plugin</artifactId> - <version>${jrst.version}</version> - <configuration> - <defaultLocale>fr</defaultLocale> - </configuration> - <executions> - <execution> - <phase>pre-site</phase> - <goals> - <goal>jrst</goal> - </goals> - </execution> - </executions> - </plugin> - - <plugin> - <artifactId>maven-dependency-plugin</artifactId> - <executions> - <execution> - <id>copy-dependencies</id> - </execution> - </executions> - </plugin> - - <plugin> - <artifactId>maven-assembly-plugin</artifactId> - <version>2.2-beta-4</version> - <configuration> - <descriptors> - <descriptor>src/main/assembly/bin.xml</descriptor> - </descriptors> - <attach>false</attach> - </configuration> - <executions> - <execution> - <phase>verify</phase> - <goals> - <goal>single</goal> - </goals> - </execution> - </executions> - </plugin> - </plugins> - - <pluginManagement> - <plugins> - <plugin> - <artifactId>maven-jar-plugin</artifactId> - <configuration> - <archive> - <manifest> - <addClasspath>true</addClasspath> - <classpathPrefix>lib/</classpathPrefix> - </manifest> - </archive> - </configuration> - </plugin> - <plugin> - <artifactId>maven-surefire-plugin</artifactId> - <configuration> - <systemProperties> - <property> - <name>java.io.tmpdir</name> - <value>${project.build.directory}/surefire-workdir</value> - </property> - </systemProperties> - </configuration> - </plugin> - </plugins> - </pluginManagement> - </build> - - <reporting> - <plugins> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-javadoc-plugin</artifactId> - <version>2.6</version> - <configuration> - <links> - <link>http://java.sun.com/javase/6/docs/api/</link> - <link>http://lutinutil.labs.libre-entreprise.org/lutinutil/apidocs/</link> - <link>http://lutinmatrix.labs.libre-entreprise.org/lutinmatrix/apidocs/</link> - <link>http://topia.labs.libre-entreprise.org/topia/topia-persistence/apidocs/</link> - </links> - </configuration> - </plugin> - <plugin> - <groupId>org.codehaus.mojo</groupId> - <artifactId>findbugs-maven-plugin</artifactId> - <version>2.1</version> - </plugin> - </plugins> - </reporting> - -  -  -  - <scm> - <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</connection> - <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</developerConnection> - <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/trunk…</url> - </scm> - -  - <repositories> - <repository> - <id>codelutin-repository</id> - <name>CodeLutinRepository</name> - <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> - <snapshots> - <enabled>true</enabled> - <checksumPolicy>warn</checksumPolicy> - </snapshots> - <releases> - <enabled>true</enabled> - <checksumPolicy>warn</checksumPolicy> - </releases> - </repository> - </repositories> - - <profiles> - <profile> - <id>release-profile</id> - <activation> - <property> - <name>performRelease</name> - <value>true</value> - </property> - </activation> - <build> - <plugins> - -  - <plugin> - <groupId>org.codelutin</groupId> - <artifactId>maven-license-switcher-plugin</artifactId> - <version>${license-switcher.version}</version> - <configuration> - <licenseName>${license-switcher.licenseName}</licenseName> - </configuration> - <executions> - <execution> - <id>attach-licenses</id> - <goals> -  - <goal>third-party</goal> - </goals> - </execution> - </executions> - </plugin> - - <plugin> - <artifactId>maven-antrun-plugin</artifactId> - <executions> -  - <execution> - <id>JnlpSun</id> - <phase>verify</phase> - <configuration> - <tasks> - <mkdir dir="${jnlp.build.directory}" /> - <copy file="${project.basedir}/src/main/jnlp/sun.jnlp" verbose="${maven.verbose}" todir="${jnlp.build.directory}" failonerror="false"> - <filterset> - <filter token="lib-javahelp" value="javahelp-2.0.02.jar" /> - <filter token="lib-activation" value="activation-1.1.jar" /> - <filter token="lib-mail" value="mail-1.4.jar" /> - <filter token="url" value="${jnlpCodebase}" /> - </filterset> - </copy> - <copy file="${project.basedir}/src/main/jnlp/jxlayer.jnlp" verbose="${maven.verbose}" todir="${jnlp.build.directory}" failonerror="false"> - <filterset> - <filter token="lib" value="jxlayer-3.0.1.jar" /> - <filter token="url" value="${jnlpCodebase}" /> - </filterset> - </copy> - - <copy verbose="${maven.verbose}" todir="${jnlp.build.directory}/lib" failonerror="false"> - <fileset dir="${project.build.directory}/lib"> - <include name="javahelp-2.0.02.jar" /> - <include name="activation-1.1.jar" /> - <include name="mail-1.4.jar" /> - <include name="jxlayer-3.0.1.jar" /> - </fileset> - </copy> - </tasks> - </configuration> - <goals> - <goal>run</goal> - </goals> - </execution> - - <execution> - <id>JnlpToSite</id> - <phase>pre-site</phase> - <configuration> - <tasks> - <mkdir dir="${maven.site.gen.dir}/resources" /> - <copy todir="${maven.site.gen.dir}/resources" verbose="true" failonerror="false" overwrite="false"> - <fileset dir="${jnlp.build.directory}"> - <include name="**" /> - </fileset> -  - <fileset dir="target"> - <include name="${project.build.finalName}-bin.zip" /> - </fileset> - - </copy> - </tasks> - </configuration> - <goals> - <goal>run</goal> - </goals> - </execution> - </executions> - </plugin> - <plugin> - <groupId>org.codehaus.mojo.webstart</groupId> - <artifactId>webstart-maven-plugin</artifactId> - <version>1.0-alpha-2-cl_20090204</version> - <executions> - <execution> - <phase>verify</phase> - <goals> - <goal>jnlp-inline</goal> - </goals> - </execution> - </executions> - <configuration> - <force>false</force> - <dependencies> - <excludes> - <exclude>javax.help:javahelp</exclude> - <exclude>javax.mail:mail</exclude> - <exclude>javax.activation:activation</exclude> - <exclude>org.swinglabs:jxlayer</exclude> - </excludes> - </dependencies> - <libPath>lib</libPath> - <extensions> - <sun>sun.jnlp</sun> - <jxlayer>jxlayer.jnlp</jxlayer> - </extensions> - <jnlp> - <outputFile>isis-fish-v3.jnlp</outputFile> - <mainClass>${maven.jar.main.class}</mainClass> - <allPermissions>true</allPermissions> - <offlineAllowed>true</offlineAllowed> - </jnlp> - - <sign> - <keystore>${keystorepath}</keystore> - <keypass /> - <storepass>${keystorepass}</storepass> - <storetype /> - <alias>${keystorealias}</alias> - <validity /> - <dnameCn /> - <dnameOu /> - <dnameO /> - <dnameL /> - <dnameSt /> - <dnameC /> - <verify>true</verify> - <keystoreConfig> - <delete>false</delete> - <gen>false</gen> - </keystoreConfig> - </sign> - <pack200>false</pack200> - <gzip>true</gzip> - <verbose>false</verbose> - </configuration> - </plugin> - - </plugins> - </build> - </profile> - - </profiles> - -</project> Copied: isis-fish/tags/isis-fish-3.2.0.5/pom.xml (from rev 2585, isis-fish/trunk/pom.xml) =================================================================== --- isis-fish/tags/isis-fish-3.2.0.5/pom.xml (rev 0) +++ isis-fish/tags/isis-fish-3.2.0.5/pom.xml 2009-09-04 16:57:11 UTC (rev 2586) @@ -0,0 +1,770 @@ +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> + + <modelVersion>4.0.0</modelVersion> + +  +  +  + <parent> + <groupId>org.codelutin</groupId> + <artifactId>lutinproject</artifactId> + <version>3.5</version> + </parent> + + <groupId>ifremer</groupId> + <artifactId>isis-fish</artifactId> + <version>3.2.0.5</version> + +  + <dependencies> + +  + + <dependency> + <groupId>log4j</groupId> + <artifactId>log4j</artifactId> + <version>1.2.14</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>org.codelutin</groupId> + <artifactId>lutinutil</artifactId> + <version>${lutinutil.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin.topia</groupId> + <artifactId>topia-persistence</artifactId> + <version>${topia.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin</groupId> + <artifactId>topia-service</artifactId> + <version>${topia.service.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin</groupId> + <artifactId>lutinmatrix</artifactId> + <version>${lutinmatrix.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin</groupId> + <artifactId>lutinwidget</artifactId> + <version>${lutinwidget.version}</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>org.codelutin.jaxx</groupId> + <artifactId>jaxx-runtime-swing</artifactId> + <version>${jaxx.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin.jaxx</groupId> + <artifactId>jaxx-runtime-validator</artifactId> + <version>${jaxx.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.codelutin.jaxx</groupId> + <artifactId>jaxx-runtime-swing-widget</artifactId> + <version>${jaxx.version}</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>org.codelutin</groupId> + <artifactId>lutinj2r</artifactId> + <version>${lutinj2r.version}</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>commons-jxpath</groupId> + <artifactId>commons-jxpath</artifactId> + <version>1.2</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>commons-lang</groupId> + <artifactId>commons-lang</artifactId> + <version>2.4</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.apache.commons</groupId> + <artifactId>commons-math</artifactId> + <version>2.0</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>commons-collections</groupId> + <artifactId>commons-collections</artifactId> + <version>3.2.1</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>commons-beanutils</groupId> + <artifactId>commons-beanutils</artifactId> + <version>1.8.0</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>commons-io</groupId> + <artifactId>commons-io</artifactId> + <version>1.4</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>dom4j</groupId> + <artifactId>dom4j</artifactId> + <version>1.6.1</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>jfreechart</groupId> + <artifactId>jfreechart</artifactId> + <version>0.9.3</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>jcommon</groupId> + <artifactId>jcommon</artifactId> + <version>0.7.0</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>org.apache.xmlrpc</groupId> + <artifactId>xmlrpc-client</artifactId> + <version>${xmlrpc.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.apache.xmlrpc</groupId> + <artifactId>xmlrpc-server</artifactId> + <version>${xmlrpc.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>commons-httpclient</groupId> + <artifactId>commons-httpclient</artifactId> + <version>3.1</version> + <scope>runtime</scope> + </dependency> + +  + <dependency> + <groupId>org.beanshell</groupId> + <artifactId>bsh</artifactId> + <version>2.0b4</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>openmap</groupId> + <artifactId>openmap</artifactId> + <version>${openmap.version}</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>org.fife</groupId> + <artifactId>rsyntaxtextarea</artifactId> + <version>1.3.4</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>com.jcraft</groupId> + <artifactId>jsch</artifactId> + <version>0.1.42</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>jaxen</groupId> + <artifactId>jaxen</artifactId> + <version>1.1.1</version> + <scope>runtime</scope> + </dependency> + +  + <dependency> + <groupId>com.h2database</groupId> + <artifactId>h2</artifactId> + <version>1.1.117</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>aspectwerkz</groupId> + <artifactId>aspectwerkz</artifactId> + <version>${aspectwerkz.version}</version> + <scope>compile</scope> + </dependency> + <dependency> + <groupId>aspectwerkz</groupId> + <artifactId>aspectwerkz-jdk5</artifactId> + <version>${aspectwerkz.version}</version> + <scope>compile</scope> + </dependency> + <dependency> + <groupId>aspectwerkz</groupId> + <artifactId>aspectwerkz-core</artifactId> + <version>${aspectwerkz.version}</version> + <scope>compile</scope> + </dependency> + +  + <dependency> + <groupId>ssj</groupId> + <artifactId>ssj</artifactId> + <version>2.1.1</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>Blas</artifactId> + <version>20081007</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>colt</artifactId> + <version>20081007</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>interpreter</artifactId> + <version>1.6.8</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>language</artifactId> + <version>1.6.7</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>logger</artifactId> + <version>1.6.4</version> + <scope>runtime</scope> + </dependency> + + <dependency> + <groupId>ssj</groupId> + <artifactId>optimization</artifactId> + <version>20081007</version> + <scope>runtime</scope> + </dependency> +  + +  + <dependency> + <groupId>org.tmatesoft</groupId> + <artifactId>svnkit</artifactId> + <version>1.2.3.5521</version> + <scope>compile</scope> + </dependency> + <dependency> + <groupId>com.trilead</groupId> + <artifactId>trilead-ssh2</artifactId> + <version>build213-svnkit-1.2</version> + <scope>runtime</scope> + </dependency> +  + + <dependency> + <groupId>org.freemarker</groupId> + <artifactId>freemarker</artifactId> + <version>2.3.15</version> + </dependency> + + <dependency> + <groupId>net.sourceforge.cpdetector</groupId> + <artifactId>cpdetector</artifactId> + <version>1.0.7</version> + <scope>compile</scope> + </dependency> + + <dependency> + <groupId>com.sun</groupId> + <artifactId>tools</artifactId> + <version>1.6.0</version> + </dependency> + </dependencies> + +  +  +  + <name>IsisFish</name> + <description>Simulateur de pecherie complexe.</description> + <inceptionYear>1999</inceptionYear> + + <licenses> + <license> + <name>GPL</name> + <url>http://www.gnu.org/copyleft/gpl.html</url> + <distribution>repo</distribution> + </license> + </licenses> + +  +  +  + <packaging>jar</packaging> + + <properties> +  + <labs.id>8</labs.id> + +  + <labs.project>isis-fish</labs.project> + +  + <jaxx.version>1.5.1</jaxx.version> + <topia.version>2.1.6.1</topia.version> + <topia.service.version>1.0.3</topia.service.version> + <lutinmatrix.version>1.3</lutinmatrix.version> + <lutinutil.version>1.0.6</lutinutil.version> + <i18n.version>0.9</i18n.version> + <lutinwidget.version>0.14.1</lutinwidget.version> + <generator.version>0.64</generator.version> + <lutinj2r.version>0.4</lutinj2r.version> + <jrst.version>0.8.4</jrst.version> + <license-switcher.version>0.6</license-switcher.version> + <openmap.version>4.6.4</openmap.version> + <aspectwerkz.version>2.0</aspectwerkz.version> + <xmlrpc.version>3.1.2</xmlrpc.version> + +  + <maven.test.forkMode>once</maven.test.forkMode> + +  + <maven.jar.main.class>fr.ifremer.isisfish.IsisFish</maven.jar.main.class> + +  + <keystorepath>${codelutin.keystorepath}</keystorepath> + <keystorealias>CodeLutin</keystorealias> + <keystorepass>codelutin</keystorepass> + <jnlp.build.directory>${project.build.directory}/jnlp</jnlp.build.directory> + + <jnlpCodebase>${project.url}</jnlpCodebase> +  + <jnlpCodebase>file://${jnlp.build.directory}</jnlpCodebase> + </properties> + + <build> + <plugins> + + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-generator-plugin</artifactId> + <version>${generator.version}</version> + <executions> + <execution> + <id>Generator</id> + <phase>generate-sources</phase> + <configuration> + <srcDirZuml>${project.basedir}/src/main/xmi</srcDirZuml> + <srcXmiDest>${maven.gen.dir}/xmi/</srcXmiDest> + <fullPackagePath>fr.ifremer.isisfish</fullPackagePath> + <extractedPackages>fr.ifremer.isisfish</extractedPackages> +  + <srcGenDest>${maven.gen.dir}/objectmodel/</srcGenDest> + <includes>**/*.objectmodel</includes> + <templates>org.codelutin.topia.generator.TopiaMetaGenerator</templates> + <excludeTemplates> + <value>org.codelutin.topia.generator.EntityEnumGenerator</value> + <value>org.codelutin.topia.generator.EntityProviderGenerator</value> + </excludeTemplates> + <destDirGen>${maven.gen.dir}/java</destDirGen> + <defaultPackage>fr.ifremer.isisfish</defaultPackage> + <copyVersionDir>${project.basedir}/src/main/resources/oldmappings/%MODELNAME% + </copyVersionDir> + <copyVersionFiles>**/*.hbm.xml</copyVersionFiles> + <copyOverwrite>true</copyOverwrite> + </configuration> + <goals> + <goal>zargo2xmi</goal> + <goal>xmi2objectmodel</goal> + <goal>generate</goal> + <goal>copyVersionFiles</goal> + </goals> + </execution> + </executions> + <dependencies> + <dependency> + <groupId>org.codelutin.topia</groupId> + <artifactId>topia-persistence</artifactId> + <version>${topia.version}</version> + <scope>runtime</scope> + </dependency> + </dependencies> + </plugin> + + <plugin> + <groupId>org.codelutin.jaxx</groupId> + <artifactId>maven-jaxx-plugin</artifactId> + <version>${jaxx.version}</version> + <executions> + <execution> + <goals> + <goal>generate</goal> + </goals> + <configuration> + <extraImportList>jaxx.runtime.SwingUtil,static jaxx.runtime.Util.getStringValue</extraImportList> + <addSourcesToClassPath>true</addSourcesToClassPath> + <addProjectClassPath>true</addProjectClassPath> + </configuration> + </execution> + </executions> + </plugin> + + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-i18n-plugin</artifactId> + <version>${i18n.version}</version> + <configuration> + <entries> + <entry> + <basedir>${maven.gen.dir}/java/</basedir> + <specificGoal>parserJava</specificGoal> + <includes> + <param>**\/**UI.java</param> + </includes> + </entry> + </entries> + </configuration> + <executions> + <execution> + <goals> + <goal>parserJava</goal> + <goal>gen</goal> + </goals> + </execution> + </executions> + </plugin> + +  + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-jrst-plugin</artifactId> + <version>${jrst.version}</version> + <configuration> + <defaultLocale>fr</defaultLocale> + </configuration> + <executions> + <execution> + <phase>pre-site</phase> + <goals> + <goal>jrst</goal> + </goals> + </execution> + </executions> + </plugin> + + <plugin> + <artifactId>maven-dependency-plugin</artifactId> + <executions> + <execution> + <id>copy-dependencies</id> + </execution> + </executions> + </plugin> + + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>2.2-beta-4</version> + <configuration> + <descriptors> + <descriptor>src/main/assembly/bin.xml</descriptor> + </descriptors> + <attach>false</attach> + </configuration> + <executions> + <execution> + <phase>verify</phase> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + + <pluginManagement> + <plugins> + <plugin> + <artifactId>maven-jar-plugin</artifactId> + <configuration> + <archive> + <manifest> + <addClasspath>true</addClasspath> + <classpathPrefix>lib/</classpathPrefix> + </manifest> + </archive> + </configuration> + </plugin> + <plugin> + <artifactId>maven-surefire-plugin</artifactId> + <configuration> + <systemProperties> + <property> + <name>java.io.tmpdir</name> + <value>${project.build.directory}/surefire-workdir</value> + </property> + </systemProperties> + </configuration> + </plugin> + </plugins> + </pluginManagement> + </build> + + <reporting> + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-javadoc-plugin</artifactId> + <version>2.6</version> + <configuration> + <links> + <link>http://java.sun.com/javase/6/docs/api/</link> + <link>http://lutinutil.labs.libre-entreprise.org/lutinutil/apidocs/</link> + <link>http://lutinmatrix.labs.libre-entreprise.org/lutinmatrix/apidocs/</link> + <link>http://topia.labs.libre-entreprise.org/topia/topia-persistence/apidocs/</link> + </links> + </configuration> + </plugin> + <plugin> + <groupId>org.codehaus.mojo</groupId> + <artifactId>findbugs-maven-plugin</artifactId> + <version>2.1</version> + </plugin> + </plugins> + </reporting> + +  +  +  + <scm> + <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</connection> + <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</developerConnection> + <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/tags/…</url> + </scm> + +  + <repositories> + <repository> + <id>codelutin-repository</id> + <name>CodeLutinRepository</name> + <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> + <snapshots> + <enabled>true</enabled> + <checksumPolicy>warn</checksumPolicy> + </snapshots> + <releases> + <enabled>true</enabled> + <checksumPolicy>warn</checksumPolicy> + </releases> + </repository> + </repositories> + + <profiles> + <profile> + <id>release-profile</id> + <activation> + <property> + <name>performRelease</name> + <value>true</value> + </property> + </activation> + <build> + <plugins> + +  + <plugin> + <groupId>org.codelutin</groupId> + <artifactId>maven-license-switcher-plugin</artifactId> + <version>${license-switcher.version}</version> + <configuration> + <licenseName>${license-switcher.licenseName}</licenseName> + </configuration> + <executions> + <execution> + <id>attach-licenses</id> + <goals> +  + <goal>third-party</goal> + </goals> + </execution> + </executions> + </plugin> + + <plugin> + <artifactId>maven-antrun-plugin</artifactId> + <executions> +  + <execution> + <id>JnlpSun</id> + <phase>verify</phase> + <configuration> + <tasks> + <mkdir dir="${jnlp.build.directory}" /> + <copy file="${project.basedir}/src/main/jnlp/sun.jnlp" verbose="${maven.verbose}" todir="${jnlp.build.directory}" failonerror="false"> + <filterset> + <filter token="lib-javahelp" value="javahelp-2.0.02.jar" /> + <filter token="lib-activation" value="activation-1.1.jar" /> + <filter token="lib-mail" value="mail-1.4.jar" /> + <filter token="url" value="${jnlpCodebase}" /> + </filterset> + </copy> + <copy file="${project.basedir}/src/main/jnlp/jxlayer.jnlp" verbose="${maven.verbose}" todir="${jnlp.build.directory}" failonerror="false"> + <filterset> + <filter token="lib" value="jxlayer-3.0.1.jar" /> + <filter token="url" value="${jnlpCodebase}" /> + </filterset> + </copy> + + <copy verbose="${maven.verbose}" todir="${jnlp.build.directory}/lib" failonerror="false"> + <fileset dir="${project.build.directory}/lib"> + <include name="javahelp-2.0.02.jar" /> + <include name="activation-1.1.jar" /> + <include name="mail-1.4.jar" /> + <include name="jxlayer-3.0.1.jar" /> + </fileset> + </copy> + </tasks> + </configuration> + <goals> + <goal>run</goal> + </goals> + </execution> + + <execution> + <id>JnlpToSite</id> + <phase>pre-site</phase> + <configuration> + <tasks> + <mkdir dir="${maven.site.gen.dir}/resources" /> + <copy todir="${maven.site.gen.dir}/resources" verbose="true" failonerror="false" overwrite="false"> + <fileset dir="${jnlp.build.directory}"> + <include name="**" /> + </fileset> +  + <fileset dir="target"> + <include name="${project.build.finalName}-bin.zip" /> + </fileset> + + </copy> + </tasks> + </configuration> + <goals> + <goal>run</goal> + </goals> + </execution> + </executions> + </plugin> + <plugin> + <groupId>org.codehaus.mojo.webstart</groupId> + <artifactId>webstart-maven-plugin</artifactId> + <version>1.0-alpha-2-cl_20090204</version> + <executions> + <execution> + <phase>verify</phase> + <goals> + <goal>jnlp-inline</goal> + </goals> + </execution> + </executions> + <configuration> + <force>false</force> + <dependencies> + <excludes> + <exclude>javax.help:javahelp</exclude> + <exclude>javax.mail:mail</exclude> + <exclude>javax.activation:activation</exclude> + <exclude>org.swinglabs:jxlayer</exclude> + </excludes> + </dependencies> + <libPath>lib</libPath> + <extensions> + <sun>sun.jnlp</sun> + <jxlayer>jxlayer.jnlp</jxlayer> + </extensions> + <jnlp> + <outputFile>isis-fish-v3.jnlp</outputFile> + <mainClass>${maven.jar.main.class}</mainClass> + <allPermissions>true</allPermissions> + <offlineAllowed>true</offlineAllowed> + </jnlp> + + <sign> + <keystore>${keystorepath}</keystore> + <keypass /> + <storepass>${keystorepass}</storepass> + <storetype /> + <alias>${keystorealias}</alias> + <validity /> + <dnameCn /> + <dnameOu /> + <dnameO /> + <dnameL /> + <dnameSt /> + <dnameC /> + <verify>true</verify> + <keystoreConfig> + <delete>false</delete> + <gen>false</gen> + </keystoreConfig> + </sign> + <pack200>false</pack200> + <gzip>true</gzip> + <verbose>false</verbose> + </configuration> + </plugin> + + </plugins> + </build> + </profile> + + </profiles> + +</project>

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r2585 - isis-fish/trunk
by chatellier＠users.labs.libre-entreprise.org 04 Sep '09

04 Sep '09

Author: chatellier Date: 2009-09-04 16:57:07 +0000 (Fri, 04 Sep 2009) New Revision: 2585 Modified: isis-fish/trunk/pom.xml Log: [maven-release-plugin] prepare release isis-fish-3.2.0.5 Modified: isis-fish/trunk/pom.xml =================================================================== --- isis-fish/trunk/pom.xml 2009-09-04 16:43:48 UTC (rev 2584) +++ isis-fish/trunk/pom.xml 2009-09-04 16:57:07 UTC (rev 2585) @@ -13,7 +13,7 @@ <groupId>ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>3.2.0.5-SNAPSHOT</version> + <version>3.2.0.5</version>  <dependencies> @@ -585,9 +585,9 @@   <scm> - <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</connection> - <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/trunk</developerConnection> - <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/trunk…</url> + <connection>scm:svn:svn://anonymous at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</connection> + <developerConnection>scm:svn:svn+ssh://chatellier at labs.libre-entreprise.org/svnroot/isis-fish/isis-fish/tags/isis-fish-3.2.0.5</developerConnection> + <url>http://labs.libre-entreprise.org/plugins/scmsvn/viewcvs.php/isis-fish/tags/…</url> </scm>

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