April 2009 - Isis-fish-data-commits - mailman.cloud.codelutin.com

r122 - trunk/scripts
by jcouteau＠users.labs.libre-entreprise.org April 28, 2009

April 28, 2009

Author: jcouteau Date: 2009-04-28 13:25:06 +0000 (Tue, 28 Apr 2009) New Revision: 122 Modified: trunk/scripts/SiMatrix.java Log: Adaptation aux scripts de St?\195?\169phanie Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2009-04-28 13:19:55 UTC (rev 121) +++ trunk/scripts/SiMatrix.java 2009-04-28 13:25:06 UTC (rev 122) @@ -246,7 +246,7 @@ List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZoneMet.copy(); - result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET); + result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); @@ -271,7 +271,7 @@ Set<Cell> cellPops = new HashSet(matrixCatchPerStrategyMetPerCell.getSemantics(4)); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET, + ResultName.MATRIX_CATCH_PER_STRATEGY_MET, new List[]{strategies, metiers, groups, zones}, new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); @@ -316,7 +316,7 @@ // on somme sur les cellules MatrixND result = matrixCatchPerStrategyMetPerCell.sumOverDim(4); result = result.reduceDims(4); - result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET); return result; } @@ -326,7 +326,7 @@ List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZonePop.copy(); - result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); @@ -359,7 +359,7 @@ // on le passe en argument ce qui evite de le calculer 2 fois // MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMet(pop, date); MatrixND result = matrixCatchRatePerStrategyMet.copy(); - result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET); for(PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); @@ -390,7 +390,7 @@ List<Zone> zones = pop.getPopulationZone(); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_CATCH_RATE_PER_STRATEGY_MET_PER_ZONE_POP, + ResultName.MATRIX_CATCH_RATE_PER_STRATEGY_MET, new List[]{strategies, metiers, groups, zones}, new String[]{n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones")}); @@ -1624,7 +1624,7 @@ List<Zone> zones = N.getSemantics(1); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_BIOMASS_BEGIN_MONTH, + ResultName.MATRIX_BIOMASS, new List[]{groups, zones}, new String[]{n_("Groups"), n_("Zones")}); @@ -1646,7 +1646,7 @@ List<Zone> zones = N.getSemantics(1); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_ABONDANCE_BEGIN_MONTH, + ResultName.MATRIX_ABUNDANCE, new List[]{groups, zones}, new String[]{n_("Groups"), n_("Zones")}); @@ -1742,7 +1742,7 @@ List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixDiscardPerStrategyMetPerZonePop.copy(); - result.setName(ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP); + result.setName(ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET); for(PopulationGroup group : groups){ MatrixND sub = result.getSubMatrix(2, group, 1);

1 0

r121 - in trunk: exports rules scripts
by jcouteau＠users.labs.libre-entreprise.org April 28, 2009

April 28, 2009

Author: jcouteau Date: 2009-04-28 13:19:55 +0000 (Tue, 28 Apr 2009) New Revision: 121 Added: trunk/rules/GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD.java Modified: trunk/exports/SensitivityCapturesWeightReferenceY7.java trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java trunk/exports/SensitivityCapturesWeightRelativeY4.java trunk/exports/SensitivityCapturesWeightY1.java trunk/rules/GraviteCPUE.java trunk/rules/TACpoids.java trunk/scripts/ResultName.java Log: Commit des scripts modifi?\195?\169s par St?\195?\169phanie adaptation des scripts existants Refactoring des scripts de st?\195?\169phanie (rajouts des @Doc sur les param?\195?\168tres, plus de system.out.println, organize imports et format du code) Modified: trunk/exports/SensitivityCapturesWeightReferenceY7.java =================================================================== --- trunk/exports/SensitivityCapturesWeightReferenceY7.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/exports/SensitivityCapturesWeightReferenceY7.java 2009-04-28 13:19:55 UTC (rev 121) @@ -24,7 +24,7 @@ static private Log log = LogFactory .getLog(SensitivityCapturesWeightReferenceY7.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET }; @Doc("Population") public Population param_pop; @@ -53,7 +53,7 @@ .getMatrix( new Date(lastDate.getDate() - i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeight += matlastdate.sumAll(); //Get the reference captures Weight of each month of the last year @@ -62,7 +62,7 @@ MatrixND matlastdatereference = referenceResultStorage .getMatrix( new Date(lastDate.getDate() - i), - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET + " " + pop, tx); capturesWeightReference += matlastdatereference.sumAll(); tx.commitTransaction(); Modified: trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-04-28 13:19:55 UTC (rev 121) @@ -25,7 +25,7 @@ static private Log log = LogFactory .getLog(SensitivityCapturesWeightRelativeReferenceY10.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET }; @Doc("Population") public Population param_pop; @@ -56,7 +56,7 @@ .getMatrix( new Date(lastDate.getDate() - i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeight += matlastdate.sumAll(); //Get the captures Weight of each month of the first year @@ -64,7 +64,7 @@ .getMatrix( new Date(i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeightfirst += matfirstdate.sumAll(); //Get the reference captures Weight of each month of the last year @@ -75,7 +75,7 @@ MatrixND matlastdatereference = referenceResultStorage .getMatrix( new Date(lastDate.getDate() - i), - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET + " " + pop, tx); capturesWeightreference += matlastdatereference.sumAll(); @@ -83,7 +83,7 @@ MatrixND matfirstdatereference = referenceResultStorage .getMatrix( new Date(i), - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET + " " + pop, tx); capturesWeightfirstreference += matfirstdatereference .sumAll(); Modified: trunk/exports/SensitivityCapturesWeightRelativeY4.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-28 13:19:55 UTC (rev 121) @@ -23,7 +23,7 @@ static private Log log = LogFactory .getLog(SensitivityCapturesWeightRelativeY4.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET }; @Doc("Population") public Population param_pop; @@ -45,7 +45,7 @@ .getMatrix( new Date(lastDate.getDate() - i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeight += matlastdate.sumAll(); //Get the captures Weight of each month of the first year @@ -53,7 +53,7 @@ .getMatrix( new Date(i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeightfirst += matfirstdate.sumAll(); } Modified: trunk/exports/SensitivityCapturesWeightY1.java =================================================================== --- trunk/exports/SensitivityCapturesWeightY1.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/exports/SensitivityCapturesWeightY1.java 2009-04-28 13:19:55 UTC (rev 121) @@ -23,7 +23,7 @@ static private Log log = LogFactory .getLog(SensitivityCapturesWeightY1.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET }; @Doc("Population") public Population param_pop; @@ -44,7 +44,7 @@ .getMatrix( new Date(lastDate.getDate() - i), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); capturesWeight += matlastdate.sumAll(); } Modified: trunk/rules/GraviteCPUE.java =================================================================== --- trunk/rules/GraviteCPUE.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/rules/GraviteCPUE.java 2009-04-28 13:19:55 UTC (rev 121) @@ -57,7 +57,7 @@ // 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_CATCH_WEIGHT_PER_STRATEGY_MET, ResultName.MATRIX_EFFORT_PER_STRATEGY_MET, }; @@ -186,7 +186,7 @@ MatrixND temp = resultmanager.getMatrix( date.previousYear(), pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); // on somme sur les zones temp=temp.sumOverDim(3); // on somme sur les groupes Added: trunk/rules/GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD.java =================================================================== --- trunk/rules/GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD.java (rev 0) +++ trunk/rules/GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD.java 2009-04-28 13:19:55 UTC (rev 121) @@ -0,0 +1,542 @@ +package rules; + +import static org.codelutin.i18n.I18n._; +import static org.codelutin.i18n.I18n.n_; + +import java.io.File; +import java.io.FileReader; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MapFunction; +import org.codelutin.math.matrix.MatrixFactory; +import org.codelutin.math.matrix.MatrixND; +import org.codelutin.util.FileUtil; + +import scripts.ResultName; +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; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.StrategyMonthInfo; +import fr.ifremer.isisfish.rule.AbstractRule; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.types.Month; + +/** + * GraviteVPUE1Anchois.java + * + * Created: 26 aout 2008 + * + * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * @version $Revision: 1.2 $ + * + * Last update: $Date: 2008-10-23 08:59:38 $ by : $Author: Stephanie $ + */ +public class GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD extends + AbstractRule { + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD.class); + + public String param_nomfichier_coeffOthers0 = "Inputs_Langoustine/CoeffOthers_Intercept_Langoustine/CoeffOthersNephrops.csv"; + public String param_nomfichier_coeffOthers1 = "Inputs_Langoustine/CoeffOthers_Intercept_Langoustine/CoeffOthersHake.csv"; + public String param_nomfichier_coeffOthers2 = "Inputs_Langoustine/CoeffOthers_Intercept_Langoustine/CoeffOthersBenthic.csv"; + public boolean param_gravite = false; + // doit �tre � vrai si gravite s'applique sinon la methode calcul uniquement les grossvalue otherspecies + + static final protected String BETA_O = "BetaOthers"; + static final protected String ALPHA_O = "AlphaOthers"; + + protected File CoeffOthers0; + protected File CoeffOthers1; + protected File CoeffOthers2; + + protected MatrixND matrixCoeffOthers; + + protected List<Metier> metiers; + // interdit de faire des set sur les strategies de la map, il faut recuperer les strategies de la date courante + protected Map<String, Strategy> mesStrategies; + + /** stocke la somme des prop initiales [str x month] */ + private MatrixND SommePropInitial = null; + /** + * stocke par strat*met, la derni�re 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 m�tier chaque mois en fonction de la VPUE du m�tier l'ann�e pr�c�dante et les gross Values otherSpecies"); + /*"HYPOTHESES GRAVITE" + " attention cette r�gle doit toujours �tre mise avant les mesures de gestion"+ + " si pour un metier Effort (m�tier annee-1,mois) = 0 et propinitiale (m�tier, mois) !=0 (ie m�tier potentiellement pratiqu�), alors "+ + on remet propInitiale pour tous les m�tiers (premiere vue complete pour tous les metiers de la strategie - graviteVPUE1-, une alternative + pourrait �tre de chercher lapremiere ann�e avant ann�e -1 pour laquelle le m�tier, ayant une propInitiale non nulle , aurait une VPUE (metier,mois) non nulle + et recuperer la propStr (metier,mois) pour cette ann�e et on l'affecte ann�e courante - mois, les autres m�tiers se partageant la proportion d'effort restante + en fonction de leur VPUE - graviteVPUE2-, une alternative pourrait etre de chercher la premiere ann�e avant ann�e -1 pour laquelle tous les m�tiers, + ayant une propInitiale non nulle, auraient eu une propStr non nulle, (surement difficile � trouver) - - graviteVPUE3- d'autres hypoth�ses pourraient etre envisag�es) + "*/ + /*Calcul des gross Value Other Species en fonction de l'effort par strategie et par m�tier � date + Avant ann�e 1 (premiere ann�e d'appliaction de Gravit�) - il faut deja faire les calculs des grossValues des autres esp�ces + A partir de l'ann�e 1 : Gravit� s'applique, il faut donc attendre de connaitre l'allocation de l'effort � date (dependant des gross values species et otherspecies � date - 1) + pour pouvoir calculer les grossValueOtherSpecies � date + + */ + } + + /** + * function used to initialise MatrixND to NaN double + */ + private MapFunction nanFunction = new MapFunction() { + public double apply(double value) { + return Double.NaN; + } + }; + + /** + * 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(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); + } + } + + // load coefficients of relation others file in a matrix + if (param_nomfichier_coeffOthers0 == null + || "".equals(param_nomfichier_coeffOthers0)) { + CoeffOthers0 = FileUtil.getFile(".*.csv", + "fichier 0 csv s�parateur ';'"); + CoeffOthers1 = FileUtil.getFile(".*.csv", + "fichier 1 csv s�parateur ';'"); + CoeffOthers2 = FileUtil.getFile(".*.csv", + "fichier 2 csv s�parateur ';'"); + } else { + CoeffOthers0 = new File(param_nomfichier_coeffOthers0); + CoeffOthers1 = new File(param_nomfichier_coeffOthers1); + CoeffOthers2 = new File(param_nomfichier_coeffOthers2); + } + + // reccuperation des metiers et strategies + SiMatrix siMatrix = SiMatrix.getSiMatrix(context); + List<String> coeffs = Arrays.asList(new String[] { ALPHA_O, BETA_O }); + + // creation de mes strategies qui ne contient pas les espagnols + //mesStrategies = new HashMap<String, Strategy>(); + //for(Strategy str : strs) { + // mesStrategies.put(str.getName(), str); + //} + + MatrixND matCoeffOthers0 = MatrixFactory.getInstance().create( + "matCoeffOthers0", new List[] { metiers, coeffs }, + new String[] { "Metiers", "Coeff" }); + MatrixND matCoeffOthers1 = MatrixFactory.getInstance().create( + "matCoeffOthers1", new List[] { metiers, coeffs }, + new String[] { "Metiers", "Coeff" }); + MatrixND matCoeffOthers2 = MatrixFactory.getInstance().create( + "matCoeffOthers2", new List[] { metiers, coeffs }, + new String[] { "Metiers", "Coeff" }); + + matCoeffOthers0.importCSV(new FileReader(CoeffOthers0), new int[] { 0, + 0 }); + matCoeffOthers1.importCSV(new FileReader(CoeffOthers1), new int[] { 0, + 0 }); + matCoeffOthers2.importCSV(new FileReader(CoeffOthers2), new int[] { 0, + 0 }); + + // captures non simulees + matrixCoeffOthers = MatrixFactory.getInstance().create( + "matrixCoeffOthers", new List[] { strs, metiers, coeffs }, + new String[] { "Strategies", "Metiers", "Coeff" }); + + MatrixND matImport = MatrixFactory.getInstance().create( + new int[] { 14, 2 }); + ; + for (Strategy str : strs) { + log.info("str =" + str.getName()); + for (Metier met : metiers) { + for (String coeff : coeffs) { + if ("NephropsLargeLesSables".equals(str.getName()) + || "NephropsLargeGuilvinec".equals(str.getName()) + || "NephropsIntermediateLesSables".equals(str + .getName()) + || "NephropsIntermediateGuilvinec".equals(str + .getName())) { + matImport = matCoeffOthers0; + } else if ("HakeLargeLesSables".equals(str.getName()) + || "HakeLargeGuilvinec".equals(str.getName()) + || "HakeIntermediateLesSables" + .equals(str.getName()) + || "HakeIntermediateGuilvinec" + .equals(str.getName())) { + matImport = matCoeffOthers1; + } else if ("BenthicLargeLesSables".equals(str.getName()) + || "BenthicLargeGuilvinec".equals(str.getName()) + || "BenthicIntermediateLesSables".equals(str + .getName()) + || "BenthicIntermediateGuilvinec".equals(str + .getName())) { + matImport = matCoeffOthers2; + } + matrixCoeffOthers.setValue(str, met, coeff, matImport + .getValue(met, coeff)); + }// fin de for coeff + }// fin de for met + }// fin de for strategy + log.info("matrixCoeffOthers : " + matrixCoeffOthers); + + } + + /** + * 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 { + + return true; // on y passe a chaque pas de temps + } + + /** + * Si la condition est vrai alors cette action est execut�e avant le pas de + * temps de la simulation. + * + * @param simulation + * La simulation pour lequel on utilise cette regle + */ + // Booleen permettant que ne boucler que sur un seul metier dans la preaction : + boolean first = true; + + public void preAction(SimulationContext context, Date date, Metier metier) + throws Exception { + if (log.isDebugEnabled()) { + log.debug("first = " + first + "date:" + date); + } + log.info("first = " + first + " ,on passe dans la preaction ?"); + if (first) { // on passe dans preaction pour la premiere fois + + log.info("Oui, preaction : "); + + List<Strategy> strs = SiMatrix.getSiMatrix(context).getStrategies( + date); + List<Population> populations = SiMatrix.getSiMatrix(context) + .getPopulations(date); + List<Metier> metiers = SiMatrix.getSiMatrix(context).getMetiers( + date); + ResultStorage resultmanager = context.getSimulationStorage() + .getResultStorage(); + //on commence par creer une instance de resultats de matrice GrossValuesOtherSpecies + MatrixND GrossValueOtherSpeciesPerStrMet = MatrixFactory + .getInstance() + .create( + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET, + new List[] { strs, metiers }, + new String[] { n_("Strategies"), n_("Metiers") }); + log.info("GrossValueOtherSpeciesPerStrMet initialisee " + + GrossValueOtherSpeciesPerStrMet); + + // si ann�e>=1 alors on fait le calcul des gravit� puis on met � jour les gross value otherspecies + if ((date.getYear() > 0) & (param_gravite == true)) { + ////////Initialisation des matrices qui resultent de la simulation//////////////////////////////////////////////////////////// + log.info("calcul de Gravite"); + //Calcul de l effort nominal par strategy met + MatrixND EffortNominalPerStrMet = null; + EffortNominalPerStrMet = resultmanager.getMatrix(date + .previousYear(), + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET); + log.info("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) + .copy(); + log.info("GrossValuePerStrMet calculee " + GrossValuePerStrMet); + + //ajouter pour tous les m�tiers les valeurs li�es qux autres esp�ces calcul�es par modele lineaire + // Boucle sur les strategies de mes strategies + //List <Strategy> mStr = strs; + for (Strategy strIndex : strs) { + // interdit de faire des set sur les strategies de la semantique de la matrice, il faut recuperer les strategies de la date courante + Strategy str = (Strategy) context.getDB().findByTopiaId( + strIndex.getTopiaId()); + + StrategyMonthInfo smi = str.getStrategyMonthInfo(date + .getMonth()); + Collection<EffortDescription> strMet = str + .getSetOfVessels().getPossibleMetiers(); + //2) calcul les valeurs non simulees du mois l ann�e pr�c�dante + for (EffortDescription effort : strMet) { + Metier met = effort.getPossibleMetiers(); + log.info("Boucle metier 1, metier possible: " + + met.getName()); + double eff = EffortNominalPerStrMet.getValue(str, met); + log.info("effort str" + str.getName() + met.getName() + + " : " + eff); + + //GrossValueAutres par strat�gie + // Hypothese 1 = pas de distinction entre les m�tiers n'agira donc pas sur la gravit�) + // Hypothese 2 = a distinguer selon les m�tiers - agira sur la gravit� + // l'hypothese est le resultat des coef dans la matrice en entr�e si tous identiques quelque soit le metier dans la strat�gie alors H1 + // sinon H2 + double valMetOther = matrixCoeffOthers.getValue(str, + met, ALPHA_O) + + matrixCoeffOthers.getValue(str, met, BETA_O) + * eff; + if (valMetOther < 0) { + valMetOther = 0; + } + double valMet = valMetOther + + GrossValuePerStrMet.getValue(str, met); + //log.info("valOtherMetAnchois :"+matrixCoeffOthers.getValue(str,met)*eff); + //log.info("GrossValuePerStrMet avant : "+GrossValuePerStrMet.getValue(str,met)); + GrossValuePerStrMet.setValue(str, met, valMet); + log.info("valOtherMetLangoustine : " + valMet); + log.info("GrossValuePerStrMet apres : " + + GrossValuePerStrMet.getValue(str, met)); + + } + } + + ////////////////////////////////////////////////////////////////////////////////////////////////////////// + valuePerUnitOfEffort.map(nanFunction); //r�initialisation avant calcul pour date + + for (Strategy str : strs) { + log.info("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(); + log.info("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 m�tier 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 pech� au mois, annee-1 + //on recupere la capture tot + double value = GrossValuePerStrMet.getValue(str, + strMetier); + log.info("DEBUG: value : " + value); + log.info("DEBUG: effort : " + effort); + double vpue = value / effort; + valuePerUnitOfEffort.setValue(str, strMetier, vpue); + log.info("value/effort= " + vpue); + somme += value / effort; + } else if ((effort == 0) + & (smi.getProportionMetier(strMetier) == 0)) {// n'a jamais p�che avec ce metier + valuePerUnitOfEffort.setValue(str, strMetier, 0); + log.info("n'a jamais p�che 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 incompl�te mais pas grave car on mettra PropInitiale � tous les metiers + log + .info("n'a pas peche au mois, annee -1, mais avait une prop d'effort non nul a l'annee=0"); + } + } + log.info("testCondition pour str" + str.getName() + ":" + + testCondition); + // � partir des VPUE stockees dans valuePerUnitOfEffort, on calcule la gravit� + double newProp = 0; + log + .info("� partir des VPUE stockees dans valuePerUnitOfEffort, on calcule la gravit�"); + if (!testCondition) { + double SommeVPUEstrat = somme; + log.info("SommeVPUEstrat=" + SommeVPUEstrat); + for (EffortDescription ed : strMet) { + Metier strMetier = ed.getPossibleMetiers(); + log.info("PropStrInitiale(metier=" + + strMetier.getName() + ")" + + smi.getProportionMetier(strMetier)); + log + .info("SommePropInitial.getValue(str, date.getMonth()=" + + SommePropInitial.getValue(str, + date.getMonth())); + log + .info("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; + } + log.info("newProp(metier=" + strMetier.getName() + + ")" + newProp); + smi.setProportionMetier(strMetier, newProp); + log.info("PropStrNouvelle(metier=" + + strMetier.getName() + ")" + + smi.getProportionMetier(strMetier)); + // annee>= 1 calcul des gross Value otherSpecies avec les nouvelles valeurs d'effort calcul�es par gravite + //avec la nouvelle proportion on en d�duit la gross Value of Species de date pour ce str-met + double valMetOtherSpecies = matrixCoeffOthers + .getValue(str, strMetier, ALPHA_O) + + matrixCoeffOthers.getValue(str, + strMetier, BETA_O) * newProp; + //tester si valMetOtherSpecies <= alors mettre � 0 + if (valMetOtherSpecies < 0) { + valMetOtherSpecies = 0; + } + GrossValueOtherSpeciesPerStrMet.setValue(str, + strMetier, valMetOtherSpecies); + log.info("valOtherMetLangoustine : " + + valMetOtherSpecies); + log.info("GrossValuePerStrMet apres : " + + GrossValueOtherSpeciesPerStrMet.getValue( + str, 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 d�faut initialis� � la valeur de la base de donn�es (val initiales) + }//fin de boucle sur strategy + // r�sultats grossvalue otherspecies mis dans le resultManager + resultmanager + .addResult( + date, + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET, + GrossValueOtherSpeciesPerStrMet); + + } else if ((date.getYear() == 0) || (param_gravite == false)) { + //si ann�e==0 alors on ne fait que le calcul des gross value other species + for (Strategy str : strs) { + log.info("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(); + for (EffortDescription ed : strMet) { + Metier strMetier = ed.getPossibleMetiers(); + log.info("PropStrInitiale(metier=" + + strMetier.getName() + ")" + + smi.getProportionMetier(strMetier)); + double valMetOtherSpecies = matrixCoeffOthers.getValue( + str, strMetier, ALPHA_O) + + matrixCoeffOthers.getValue(str, strMetier, + BETA_O) + * smi.getProportionMetier(strMetier); + //tester si valMetOtherSpecies <= alors mettre � 0 + if (valMetOtherSpecies < 0) { + valMetOtherSpecies = 0; + } + GrossValueOtherSpeciesPerStrMet.setValue(str, + strMetier, valMetOtherSpecies); + log.info("valOtherMetLangoustine : " + + valMetOtherSpecies); + log.info("GrossValuePerStrMet apres : " + + GrossValueOtherSpeciesPerStrMet.getValue(str, + strMetier)); + } + } + // r�sultats grossvalue otherspecies mis dans le resultManager + resultmanager + .addResult( + date, + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET, + GrossValueOtherSpeciesPerStrMet); + } // fin de calcul pour ann�e ==0 + first = false; + + }// fin de first= true + + if (log.isDebugEnabled()) { + log.debug("fin Gravite CPUEAction avant"); + } + + } + + /** + * Si la condition est vrai alors cette action est execut�e 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 { + first = true; + + } + +} Modified: trunk/rules/TACpoids.java =================================================================== --- trunk/rules/TACpoids.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/rules/TACpoids.java 2009-04-28 13:19:55 UTC (rev 121) @@ -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 +27,119 @@ 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 * * Created: 7 septembre 2006 * * @author anonymous <anonymous(a)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 + * TAC peut-etre utilis� pour les diff�rents 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 - * + * <li>Pour utiliser le tac proportionnel, il faut mettre dans le parametre + * propTac une valeur > 0, le TAC sera alors recalcul� a chaque mois de janvier. + * <li>Pour utiliser la survie il faut mettre dans le param�tre propSurvie une + * valeur > 0, automatiquement les suvie seront ajout� 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(value = "do the doc of param species") public Species param_species = null; - @Doc(value="do the doc of param beginDate") + @Doc(value = "do the doc of param beginDate") 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(value = "do the doc of param endDate") + public Date param_endDate = new Date(90); + @Doc(value = "do the doc of param propSurvie") public double param_propSurvie = 0; - @Doc(value="do the doc of param propTac") + @Doc(value = "do the doc of param propTac") public double param_propTac = 0; - /** TAC in tonne */ - public double param_tacInTons = 0; - + /** TAC in tonnes */ + @Doc(value = "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 + * 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 + * + * @param simulation + * 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 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 { + 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 n�cessaire + 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 +147,47 @@ } 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 execut�e 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 { + 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 + + //r�cupere toutes les strat�gies pratiquant le m�tier 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 +199,38 @@ // 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 Activit�") + && !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 +240,52 @@ // 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 execut�e 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 { + 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 +297,46 @@ // 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_PER_ZONE_POP); - 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); + 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 r�ajoute 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: trunk/scripts/ResultName.java =================================================================== --- trunk/scripts/ResultName.java 2009-04-22 16:32:05 UTC (rev 120) +++ trunk/scripts/ResultName.java 2009-04-28 13:19:55 UTC (rev 121) @@ -1,6 +1,6 @@ /* *##% * Copyright (C) 2006 - * Code Lutin, Cédric Pineau, Benjamin Poussin + * Code Lutin, C�dric 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 ao�t 2006 15:09:37 * * @author poussin * @version $Revision: 1.10 $ @@ -37,54 +37,48 @@ /** * 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 r�sultat est d'ajouter une constante ici, et de l'utiliser + * ensuite lors de la cr�ation 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 r�sultats + * potentiellement disponible et de ne pas ce tromper en �crivent le nom + * d'un r�sultat * <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 + * afficher l'ensemble des r�sultats 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 = n_("matrixDiscardsWeightPerStrMet"); @Doc(value = "do the doc of Result matrixDiscardsPerStrMet") - static final public String MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP = n_("matrixDiscardsPerStrMet"); + static final public String MATRIX_DISCARDS_PER_STR_MET = n_("matrixDiscardsPerStrMet"); @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") static final public String MATRIX_EFFORT_PER_STRATEGY_MET = n_("matrixEffortPerStrategyMet"); + @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") 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") - static final public String MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchPerStrategyMetPerZoneMet"); - @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") - static final public String MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchWeightPerStrategyMetPerZoneMet"); - @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") + @Doc(value = "do the doc of Result matrixCatchRatePerStrategyMet") + static final public String MATRIX_CATCH_RATE_PER_STRATEGY_MET = n_("matrixCatchRatePerStrategyMet"); + @Doc(value = "do the doc of Result matrixCatchPerStrategyMet") + static final public String MATRIX_CATCH_PER_STRATEGY_MET = n_("matrixCatchPerStrategyMet"); + @Doc(value = "do the doc of Result matrixFishingMortality") static final public String MATRIX_FISHING_MORTALITY = n_("matrixFishingMortality"); + @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMet") + static final public String MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET = n_("matrixCatchWeightPerStrategyMet"); @Doc(value = "do the doc of Result matrixAbundance") static final public String MATRIX_ABUNDANCE = n_("matrixAbundance"); @Doc(value = "do the doc of Result matrixBiomass") static final public String MATRIX_BIOMASS = n_("matrixBiomass"); - @Doc(value = "do the doc of Result matrixBiomassBeginMonth") - 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") static final public String MATRIX_FISHING_TIME_PER_MONTH_PER_VESSEL = n_("matrixFishingTimePerMonthPerVessel"); @@ -105,6 +99,8 @@ static final public String MATRIX_GROSS_VALUE_OF_LANDINGS_PER_SPECIES_PER_STRATEGY_MET = n_("matrixGrossValueOfLandingsPerSpeciesPerStrategyMet"); @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 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")

1 0

r120 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 22, 2009

April 22, 2009

Author: jcouteau Date: 2009-04-22 16:32:05 +0000 (Wed, 22 Apr 2009) New Revision: 120 Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivity/SensitivityCalculatorRFrF2.java Log: Code formatting and some corrections Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-22 16:31:17 UTC (rev 119) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-22 16:32:05 UTC (rev 120) @@ -392,14 +392,7 @@ + ")"); log.info("Message sent to R : " + "isis.simule<-data.frame(isis.simule," + name + ")"); - } - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - String name = simulationStorages.get(0).getParameter() - .getSensitivityExport().get(k).getExportFilename(); - //Create the dataforaov data.frame String dataframe = "dataforaov<-data.frame(factors," + name + "=" + name + ")"; Modified: trunk/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-22 16:31:17 UTC (rev 119) +++ trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-22 16:32:05 UTC (rev 120) @@ -19,9 +19,7 @@ package sensitivity; import java.io.File; -import java.io.Serializable; import java.util.List; -import java.util.Vector; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -31,15 +29,12 @@ 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.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.SensitivityCalculator; - -import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -163,8 +158,7 @@ for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors() - .get(i); + Factor factor = plan.getFactors().get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { if (frf2.getValue(new int[] { i, j }) == -1) { @@ -178,15 +172,13 @@ } } else { if (frf2.getValue(new int[] { i, j }) == -1) { - factor - .setValueForIdentifier(((ContinuousDomain) factor - .getDomain()).getMinBound()); + factor.setValueForIdentifier(((ContinuousDomain) factor + .getDomain()).getMinBound()); } if (frf2.getValue(new int[] { i, j }) == 1) { - factor - .setValueForIdentifier(((ContinuousDomain) factor - .getDomain()).getMaxBound()); + factor.setValueForIdentifier(((ContinuousDomain) factor + .getDomain()).getMaxBound()); } } experimentScenario.addFactor(factor); @@ -197,8 +189,8 @@ try { //Create the factors vectors for (int j = 0; j < factorNumber; j++) { - Factor factor = thisExperimentScenarios - .get(0).getFactors().get(j); + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { String vector = "factor" + j + "<-c("; @@ -477,7 +469,6 @@ 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,\""

1 0

r119 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 22, 2009

April 22, 2009

Author: jcouteau Date: 2009-04-22 16:31:17 +0000 (Wed, 22 Apr 2009) New Revision: 119 Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java Log: RandomLHS conform to new CDC Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-22 14:33:10 UTC (rev 118) +++ trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-22 16:31:17 UTC (rev 119) @@ -19,9 +19,10 @@ package sensitivity; import java.io.File; -import java.io.Serializable; import java.util.List; +import javax.swing.JOptionPane; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.codelutin.j2r.REngine; @@ -31,14 +32,15 @@ import org.codelutin.util.FileUtil; import fr.ifremer.isisfish.datastore.SimulationStorage; +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.SensitivityCalculator; -import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; 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; @@ -51,14 +53,15 @@ * */ @Doc("Random Latin Hypercube") -public class SensitivityCalculatorRRandomLHS extends AbstractSensitivityCalculator { +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; + public int param_simulationNumber = 10; /** * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs @@ -73,12 +76,28 @@ 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; } @@ -86,6 +105,14 @@ REngine engine = new RProxy(); try { + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + //Load the lhs library engine.voidEval("library(lhs)"); log.info("Message sent to R : " + "library(lhs)"); @@ -108,8 +135,7 @@ 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); + Factor factor = plan.getFactors().get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { factor @@ -131,13 +157,74 @@ thisExperiment.setScenarios(thisExperimentScenarios); } - //Create the factors vectors - for (int j = 0; j < factornumber; j++) { - Factor factor = thisExperimentScenarios - .get(0).getFactors().get(j); + 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" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; for (int i = 0; i < param_simulationNumber; i++) { if (i < (param_simulationNumber - 1)) { vector = vector @@ -156,7 +243,9 @@ engine.voidEval(vector); log.info("Message sent to R : " + vector); } else if (factor.getDomain() instanceof MatrixContinuousDomain) { - String vector = "factor" + j + "<-c("; + //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 @@ -175,7 +264,9 @@ engine.voidEval(vector); log.info("Message sent to R : " + vector); } else { - String vector = "factor" + j + "<-c("; + //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 @@ -193,15 +284,13 @@ 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 + "),"; + if (j < factors.size() - 1) { + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; } else { - data = data + "factor" + j + "=factor(factor" + j + "))"; + data += factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "))"; } } @@ -241,6 +330,14 @@ log.info("Message sent to R" + "dput(factornames,file=\".factornames\")"); + //Set working directory to save Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + engine.terminate(); } catch (Exception e) { @@ -261,36 +358,44 @@ REngine engine = new RProxy(); try { - param_simulationNumber = simulationStorages.get(0).getParameter() - .getSensitivityExport().size(); + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); - for (int k = 0; k < param_simulationNumber; k++) { + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); - // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); - log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + // Set output directory + engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); - //Get back the scenarios - //engine.voidEval("factors<-read.csv(\".expandgrid.csv\",row.names=1,col.names=1)"); - engine.voidEval("factors<-read.csv(\".randomlhs.csv\")"); - log - .info("Message sent to R : factors<-read.csv(\".randomlhs.csv\")"); + //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 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(); - //factorNumber=factorNumber-1; + //Get back the factors number + int factorNumber = ((Double) engine.eval("length(factors)-1")) + .intValue(); - //Create the results vectors - String result = "result<-c("; - for (int l = 0; l < simulationStorages.size(); l++) { + param_simulationNumber = simulationStorages.get(0).getParameter() + .getSensitivityExport().size(); + + for (int k = 0; k < param_simulationNumber; k++) { + + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .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 @@ -304,27 +409,64 @@ String simulResult = FileUtil.readAsString(importFile); double simulationResult = Double.valueOf(simulResult); if (l < simulationStorages.size() - 1) { - result = result + simulationResult + ","; + rInstruction = rInstruction + simulationResult + ","; } else { - result = result + simulationResult; + rInstruction = rInstruction + simulationResult; } } - result = result + ")"; - engine.voidEval(result); - log.info("Message sent to R : " + result); + 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 < param_simulationNumber; k++) { + + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); + //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(factors,result=result)"; + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; engine.voidEval(dataframe); log.info("Message sent to R : " + dataframe); //Call aov() - String aovCall = "aovresult<-aov(result~"; + 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 + "factor" + j + "+"; + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; } else { - aovCall = aovCall + "factor" + j + ",data=dataforaov)"; + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ",data=dataforaov)"; } } engine.voidEval(aovCall); @@ -367,14 +509,6 @@ 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() - + "\")"); - log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); - //Set dataforaov names engine .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); @@ -385,6 +519,14 @@ 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() + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); + //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" + simulationStorages.get(0).getParameter() @@ -407,10 +549,71 @@ .getExportFilename() + "_SensitivityIndices.csv\")"); //FIXME export through java to enable export when using Rserve (when distant Rserve). - engine.terminate(); + + //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 + "\"" + ",aovresult)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + ",aovresult)"); + + 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)); + } - log.info("end"); + //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() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + + engine.terminate(); + } catch (Exception e) { e.printStackTrace(); // Error while processing

1 0

r118 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 22, 2009

April 22, 2009

Author: jcouteau Date: 2009-04-22 14:33:10 +0000 (Wed, 22 Apr 2009) New Revision: 118 Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivity/SensitivityCalculatorRegularFractions.java Log: Changing attributes instruction in R Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-21 12:27:21 UTC (rev 117) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-22 14:33:10 UTC (rev 118) @@ -284,9 +284,9 @@ log .info("Message sent to R : " - + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); //Create isis.Simule log.info("Message sent to R : " + "isis.simule<-data.frame(data)"); @@ -294,9 +294,9 @@ log .info("Message sent to R : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); log.info("Message sent to R : " + "names(isis.simule)<-isis.factors[[1]]"); @@ -394,13 +394,6 @@ + "isis.simule<-data.frame(isis.simule," + name + ")"); } - //adding attribute to isis.Simule - log - .info("Message sent to R : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); - engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); - for (int k = 0; k < sensitivityNumber; k++) { // Creates the R expression to import results in R @@ -521,6 +514,12 @@ .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + aovCall + "\"" + ",aovresult)"); + 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("-", ""); Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-04-21 12:27:21 UTC (rev 117) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-04-22 14:33:10 UTC (rev 118) @@ -303,9 +303,9 @@ log .info("Message sent to R : " - + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + .voidEval("attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); //Create isis.Simule log.info("Message sent to R : " + "isis.simule<-data.frame(data)"); @@ -313,20 +313,18 @@ log .info("Message sent to R : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + .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 .expandgrid file + + // Export the data.frame object for the second run in a .expandgrid file engine.voidEval("write.csv(data,file=\".data.csv\")"); - log - .info("Message sent to R : 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() + "\")"); engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); @@ -374,11 +372,10 @@ engine.voidEval("factornames<-dget(\".factornames\")"); log.info("Message sent to R : " + "factornames<-dget(\".factornames\")"); - - //Get back the scenarios + + //Get back the scenarios engine.voidEval("factors<-read.csv(\".data.csv\")"); - log - .info("Message sent to R : 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")) @@ -427,9 +424,9 @@ //adding attribute to isis.Simule log .info("Message sent to R : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); for (int k = 0; k < sensitivityNumber; k++) { @@ -551,6 +548,12 @@ .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + aovCall + "\"" + ",aovresult)"); + 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("-", "");

1 0

r117 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 21, 2009

April 21, 2009

Author: jcouteau Date: 2009-04-21 12:27:21 +0000 (Tue, 21 Apr 2009) New Revision: 117 Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java Log: Fixed attributes bug in R Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-20 16:25:44 UTC (rev 116) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-21 12:27:21 UTC (rev 117) @@ -209,9 +209,29 @@ 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 : " - + "isis.factor.distribution<-c(0.0)"); - engine.voidEval("isis.factor.distribution<-c(0.0)"); + + 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"); @@ -224,18 +244,18 @@ log .info("Message sent to R : " - + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.MethodExp,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + .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 : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + .voidEval("attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); log.info("Message sent to R : " + "names(isis.simule)<-isis.factors[[1]]"); @@ -318,7 +338,7 @@ 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)"); @@ -368,9 +388,15 @@ //adding attribute to isis.Simule log .info("Message sent to R : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + "attr(isis.simule,\"nomModel\")<-\"isis-fish-externe-R\""); engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + .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++) { @@ -386,11 +412,17 @@ 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 + ")" + "\",a)"); + + 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 + ")" + "\",a)"); + + 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)");

1 0

r116 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 20, 2009

April 20, 2009

Author: jcouteau Date: 2009-04-20 16:25:44 +0000 (Mon, 20 Apr 2009) New Revision: 116 Added: trunk/sensitivity/SensitivityCalculatorRegularFractions.java trunk/sensitivity/regularfractions.R Log: Regular Fractions method working, conform to the new CDC. Added: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java (rev 0) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-04-20 16:25:44 UTC (rev 116) @@ -0,0 +1,614 @@ +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.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") + 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 + */ + public boolean canManageCardinality() { + return true; + } + + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan, outputdirectory); + + double[] dataframeplan = 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(); + + 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 { + + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + + //Set the working directory (to import the R function) + engine.voidEval("setwd(\"" + param_pathToFunction + "\")"); + log.info("Message sent to R : " + "setwd(\"" + param_pathToFunction + + "\")"); + + //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() + + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); + + // Export the morris object for the second run in a .morris 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$plan"); + log.info("Message sent to R : " + "x$plan"); + + //Get back the simulation number + log.info("length(x[,1])"); + int simulationNumber = (Integer) engine.eval("length(x$plan[,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 : " + + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.MethodExp)<-list(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 : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(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 .expandgrid 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() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + + engine.terminate(); + + } catch (RException eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + } + + return thisExperiment; + + } + + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputdirectory) throws SensitivityException { + + REngine engine = new RProxy(); + try { + + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); + + // 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(); + + int sensitivityNumber = simulationStorages.get(0).getParameter() + .getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); + + //Create the results vectors + String result = 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, + simulationStorages.get(l).getParameter() + .getSensitivityExport().get(k) + .getExportFilename() + + simulationStorages.get(l).getParameter() + .getSensitivityExport().get(k) + .getExtensionFilename()); + String simulResult = FileUtil.readAsString(importFile); + double simulationResult = Double.valueOf(simulResult); + if (l < simulationStorages.size() - 1) { + result = result + simulationResult + ","; + } else { + result = result + simulationResult; + } + } + result = result + ")"; + engine.voidEval(result); + log.info("Message sent to R : " + result); + + //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 : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .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() + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + log.info("Message sent to R : write.csv(dataforaov,\"" + + simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k) + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + log.info("Message sent to R : write.csv(exportsensitivity,\"" + + simulationStorages.get(0).getParameter() + .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 + "\"" + ",aovresult)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + ",aovresult)"); + + 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() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + + engine.terminate(); + + } catch (Exception eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); + } + + } + + public String getDescription() { + return "Implementation of Regular fractions method using R"; + } + +} Added: trunk/sensitivity/regularfractions.R =================================================================== --- trunk/sensitivity/regularfractions.R (rev 0) +++ trunk/sensitivity/regularfractions.R 2009-04-20 16:25:44 UTC (rev 116) @@ -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) +} +#--------------------------------------------------------------------------- +

1 0

r115 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 20, 2009

April 20, 2009

Author: jcouteau Date: 2009-04-20 13:40:15 +0000 (Mon, 20 Apr 2009) New Revision: 115 Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivity/SensitivityCalculatorRMorris.java Log: Expand Grid conform to CDC, fixed bug on Morris (in R). Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-20 08:28:32 UTC (rev 114) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-20 13:40:15 UTC (rev 115) @@ -28,10 +28,10 @@ import org.codelutin.util.FileUtil; import fr.ifremer.isisfish.datastore.SimulationStorage; +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.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; @@ -68,24 +68,26 @@ 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) { + if (((ContinuousDomain) factors.get(i).getDomain()) + .getCardinality() != 0) { k = k - * ((ContinuousDomain) factors - .get(i).getDomain()).getCardinality(); + * ((ContinuousDomain) factors.get(i).getDomain()) + .getCardinality(); } } else if (factors.get(i).getDomain() instanceof DiscreteDomain) { - if (((DiscreteDomain) factors.get(i) - .getDomain()).getValues().size() != 0) { + if (((DiscreteDomain) factors.get(i).getDomain()).getValues() + .size() != 0) { k = k - * ((DiscreteDomain) factors - .get(i).getDomain()).getValues().size(); + * ((DiscreteDomain) factors.get(i).getDomain()) + .getValues().size(); } } } @@ -104,8 +106,8 @@ .getMaxBound(); Double min = ((ContinuousDomain) factor.getDomain()) .getMinBound(); - int card = ((ContinuousDomain) factor - .getDomain()).getCardinality(); + int card = ((ContinuousDomain) factor.getDomain()) + .getCardinality(); result = (int) Math.floor(rest / card); rest = rest - (card * result); @@ -118,8 +120,8 @@ } } if (factor.getDomain() instanceof DiscreteDomain) { - int card = ((DiscreteDomain) factor - .getDomain()).getValues().size(); + int card = ((DiscreteDomain) factor.getDomain()) + .getValues().size(); result = (int) Math.floor(rest / card); rest = rest - (card * result); factor.setValueForIdentifier(rest); @@ -141,13 +143,26 @@ REngine engine = new RProxy(); try { - //Create the factors vectors + + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".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); + Factor factor = thisExperimentScenarios.get(0).getFactors() + .get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { - String vector = "factor" + j + "<-c("; + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector @@ -166,7 +181,9 @@ engine.voidEval(vector); log.info("Message sent to R : " + vector); } else if (factor.getDomain() instanceof MatrixContinuousDomain) { - String vector = "factor" + j + "<-c("; + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector @@ -185,7 +202,9 @@ engine.voidEval(vector); log.info("Message sent to R : " + vector); } else { - String vector = "factor" + j + "<-c("; + //String vector = "factor" + j + "<-c("; + String vector = factor.getName().replaceAll(" ", "") + + "<-c("; for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector @@ -204,16 +223,13 @@ log.info("Message sent to R : " + vector); } - } - - //Create the data data.frame from the factors - String dataframe = "data<-data.frame("; - for (int j = 0; j < factorNumber; j++) { if (j < factorNumber - 1) { - dataframe = dataframe + "factor" + j + "=factor(factor" + j - + "),"; + dataframe = dataframe + + factor.getName().replaceAll(" ", "") + "=factor(" + + factor.getName().replaceAll(" ", "") + "),"; } else { - dataframe = dataframe + "factor" + j + "=factor(factor" + j + dataframe += factor.getName().replaceAll(" ", "") + + "=factor(" + factor.getName().replaceAll(" ", "") + "))"; } @@ -254,6 +270,46 @@ 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 : " + + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.MethodExp)<-list(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 : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(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() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + engine.terminate(); } catch (Exception e) { @@ -270,39 +326,44 @@ REngine engine = new RProxy(); try { - /*int scenariosNumber = sensitivityScenarios.getScenarios().size(); - int factorNumber = sensitivityScenarios.getScenarios().get(0) - .getFactors().size();*/ + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + + // Set output directory + engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + + "\")"); + log.info("Message sent to R : setwd(\"" + + outputdirectory.getAbsolutePath() + "\")"); + + //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(); + int sensitivityNumber = simulationStorages.get(0).getParameter() .getSensitivityExport().size(); for (int k = 0; k < sensitivityNumber; k++) { - // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); - log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); - //Get back the scenarios - //engine.voidEval("factors<-read.csv(\".expandgrid.csv\",row.names=1,col.names=1)"); - 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(); - //factorNumber=factorNumber-1; - //Create the results vectors - String result = "result<-c("; + String result = name + "<-c("; for (int l = 0; l < simulationStorages.size(); l++) { File importFile = new File(simulationStorages.get(l) .getDirectory().toString() @@ -326,18 +387,48 @@ engine.voidEval(result); log.info("Message sent to R : " + result); + //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 : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); + //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(factors,result=result)"; + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; engine.voidEval(dataframe); log.info("Message sent to R : " + dataframe); //Call aov() - String aovCall = "aovresult<-aov(result~"; + 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 + "factor" + j + "+"; + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + "+"; } else { - aovCall = aovCall + "factor" + j + ",data=dataforaov)"; + aovCall = aovCall + + engine + .eval("names(factors)[" + (j + 2) + "]") + + ",data=dataforaov)"; } } engine.voidEval(aovCall); @@ -420,10 +511,65 @@ .getExportFilename() + "_SensitivityIndices.csv\")"); //FIXME export through java to enable export when using Rserve (when distant Rserve). - engine.terminate(); + + //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 + "\"" + ",aovresult)"); + engine + .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" + + aovCall + "\"" + ",aovresult)"); + + 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)); + } - log.info("end"); + //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() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + + engine.terminate(); + } catch (Exception e) { e.printStackTrace(); // Error while processing Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-20 08:28:32 UTC (rev 114) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-20 13:40:15 UTC (rev 115) @@ -318,8 +318,7 @@ engine.voidEval("factornames<-dget(\".factornames\")"); log.info("Message sent to R : " + "factornames<-dget(\".factornames\")"); - - /*int scenariosNumber = sensitivityScenarios.getScenarios().size();*/ + int scenariosNumber = ((Double) engine .eval("length(a$X)/length(a$factors)")).intValue(); log.info("Message sent to R : " + "length(a$X)/length(a$factors)"); @@ -359,10 +358,39 @@ // 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 : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .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 + ")" + "\",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 + ")" + "\",a)"); + // 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)"); @@ -429,35 +457,6 @@ .getExportFilename() + "_Results.csv\")"); //FIXME export through java to enable export when using Rserve - //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 : " - + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); - engine - .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); - - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - String name = simulationStorages.get(0).getParameter() - .getSensitivityExport().get(k).getExportFilename(); - - //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 + ")" + "\",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 + ")" + "\",a)"); - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; String simulationName = simulationStorages.get(0).getName() .replaceAll("-", "");

1 0

r114 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 20, 2009

April 20, 2009

Author: jcouteau Date: 2009-04-20 08:28:32 +0000 (Mon, 20 Apr 2009) New Revision: 114 Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java Log: Morris method managing more than one export (in R) Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-18 13:12:30 UTC (rev 113) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-20 08:28:32 UTC (rev 114) @@ -58,6 +58,7 @@ * Last update : $Date$ By : * $Author$ */ + @Doc("Morris method") public class SensitivityCalculatorRMorris extends AbstractSensitivityCalculator { @@ -217,9 +218,9 @@ log .info("Message sent to R : " - + "isis.MethodExp<-list(isis.factors,isis.factor.distribution,call)"); + + "isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); engine - .voidEval("isis.MethodExp<-list(isis.factors,isis.factor.distribution,call)"); + .voidEval("isis.MethodExp<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"call\"=call)"); log .info("Message sent to R : " @@ -359,8 +360,8 @@ engine.voidEval(rInstruction); //Compute results - engine.voidEval("tell(a,y=name)"); - log.info("Message sent to R : " + "tell(a,y=name)"); + engine.voidEval("tell(a,y=" + name + ")"); + log.info("Message sent to R : " + "tell(a,y=" + name + ")"); // Get back the sensitivity results, mu, mu star and sigma. engine.voidEval("mu<-apply(a$ee, 2, mean)"); @@ -433,7 +434,6 @@ + ")"); log.info("Message sent to R : " + "isis.simule<-data.frame(isis.simule," + name + ")"); - } //adding attribute to isis.Simule @@ -443,20 +443,38 @@ engine .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); - //creating isis.methodAnalyse - log - .info("Message sent to R : " - + "isis.methodAnalyse<-list(isis.factor,isis.factor.distribution,isis.simule,call_method=\"tell(a,results)\",a)"); - engine - .voidEval("isis.methodAnalyse<-list(isis.factor,isis.factor.distribution,isis.simule,call_method=\"tell(a,results)\",a)"); + for (int k = 0; k < sensitivityNumber; k++) { + // Creates the R expression to import results in R + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); + + //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 + ")" + "\",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 + ")" + "\",a)"); + + 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 renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; - String renameIsisFactor = "%s.isis.factor<-isis.factor"; - String renameIsisMethodExp = "%s.isis.methodExp<-isis.methodExp"; + String renameIsisFactor = "%s.isis.factor<-isis.factors"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.MethodExp"; String simulationName = simulationStorages.get(0).getName() .replaceAll("-", ""); @@ -466,11 +484,6 @@ engine.voidEval(String.format(renameIsisSimule, simulationName)); log.info("Message sent to R : " - + String.format(renameIsisMethodAnalyse, simulationName)); - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName)); - - log.info("Message sent to R : " + String.format(renameIsisFactorDistribution, simulationName)); engine.voidEval(String.format(renameIsisFactorDistribution,

1 0

r113 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 18, 2009

April 18, 2009

Author: jcouteau Date: 2009-04-18 13:12:30 +0000 (Sat, 18 Apr 2009) New Revision: 113 Modified: trunk/exports/SensitivityBiomassReferenceY9.java trunk/exports/SensitivityBiomassRelativeReferenceY12.java trunk/exports/SensitivityCapturesWeightReferenceY7.java trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java trunk/exports/SensitivityGenitorBiomassReferenceY8.java trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java Log: Fixed resultStorage bug on exports Modified: trunk/exports/SensitivityBiomassReferenceY9.java =================================================================== --- trunk/exports/SensitivityBiomassReferenceY9.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityBiomassReferenceY9.java 2009-04-18 13:12:30 UTC (rev 113) @@ -7,6 +7,7 @@ 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; @@ -43,6 +44,8 @@ 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())) { @@ -50,14 +53,26 @@ MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, ResultName.MATRIX_BIOMASS); biomass = matlastdate.sumAll(); + System.out.println("matlastdate:" + (Object) matlastdate); - //Get the reference biomass of the last time step + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); + MatrixND matreferencelastdate = referenceResultStorage - .getMatrix(lastDate, pop, ResultName.MATRIX_BIOMASS); + .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)); Modified: trunk/exports/SensitivityBiomassRelativeReferenceY12.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeReferenceY12.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityBiomassRelativeReferenceY12.java 2009-04-18 13:12:30 UTC (rev 113) @@ -7,6 +7,7 @@ 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; @@ -30,7 +31,7 @@ public Population param_pop; @Doc("Name of the reference simulation") - public String param_referenceSimulation=""; + public String param_referenceSimulation = ""; @Override public void export(SimulationStorage simulation, Writer out) @@ -61,14 +62,23 @@ biomass = matlastdate.sumAll(); //Get the biomass on december of the first year + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); MatrixND matfirstdatereference = referenceResultStorage - .getMatrix(firstDate, pop, ResultName.MATRIX_BIOMASS); + .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, pop, ResultName.MATRIX_BIOMASS); + .getMatrix(lastDate, ResultName.MATRIX_BIOMASS + " " + + pop, tx); biomassReference = matlastdatereference.sumAll(); + tx.commitTransaction(); + tx.closeContext(); } } Modified: trunk/exports/SensitivityCapturesWeightReferenceY7.java =================================================================== --- trunk/exports/SensitivityCapturesWeightReferenceY7.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityCapturesWeightReferenceY7.java 2009-04-18 13:12:30 UTC (rev 113) @@ -7,6 +7,7 @@ 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; @@ -29,7 +30,7 @@ public Population param_pop; @Doc("Name of the reference simulation") - public String param_referenceSimulation=""; + public String param_referenceSimulation = ""; @Override public void export(SimulationStorage simulation, Writer out) @@ -56,12 +57,16 @@ 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), - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + + " " + pop, tx); capturesWeightReference += matlastdatereference.sumAll(); + tx.commitTransaction(); + tx.closeContext(); } Modified: trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-04-18 13:12:30 UTC (rev 113) @@ -7,6 +7,7 @@ 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; @@ -67,21 +68,27 @@ 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), - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + 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), - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + + " " + pop, tx); capturesWeightfirstreference += matfirstdatereference .sumAll(); + tx.commitTransaction(); + tx.closeContext(); } } } Modified: trunk/exports/SensitivityGenitorBiomassReferenceY8.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassReferenceY8.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityGenitorBiomassReferenceY8.java 2009-04-18 13:12:30 UTC (rev 113) @@ -8,6 +8,7 @@ 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; @@ -62,8 +63,10 @@ } //Get the reference biomass of the last time step + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); MatrixND matlastdatereference = referenceResultStorage - .getMatrix(pop, ResultName.MATRIX_BIOMASS); + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); for (MatrixIterator i = matlastdatereference.iterator(); i .hasNext();) { i.next(); @@ -75,6 +78,8 @@ * group.getReproductionRate(); } } + tx.commitTransaction(); + tx.closeContext(); } } out.write(Double.toString(biomass / referenceBiomass)); Modified: trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java 2009-04-17 13:51:32 UTC (rev 112) +++ trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java 2009-04-18 13:12:30 UTC (rev 113) @@ -8,6 +8,7 @@ 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; @@ -81,8 +82,10 @@ } //Get the reference biomass of the first time step + TopiaContext tx = referenceSimulation.getStorage() + .beginTransaction(); MatrixND matfirstdatereference = referenceResultStorage - .getMatrix(pop, ResultName.MATRIX_BIOMASS); + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); for (MatrixIterator i = matfirstdatereference.iterator(); i .hasNext();) { i.next(); @@ -97,7 +100,7 @@ //Get the reference biomass of the last time step MatrixND matlastdatereference = referenceResultStorage - .getMatrix(pop, ResultName.MATRIX_BIOMASS); + .getMatrix(ResultName.MATRIX_BIOMASS + " " + pop, tx); for (MatrixIterator i = matlastdatereference.iterator(); i .hasNext();) { i.next(); @@ -109,6 +112,8 @@ * group.getReproductionRate(); } } + tx.commitTransaction(); + tx.closeContext(); } } out.write(Double.toString((biomass / firstbiomass)

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