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

r296 - in trunk: . scripts simulators
by echatellier＠users.forge.codelutin.com Sept. 25, 2012

Sept. 25, 2012

Author: echatellier Date: 2012-09-25 16:51:25 +0200 (Tue, 25 Sep 2012) New Revision: 296 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/296 Log: Ajout des scripts utilisant groupMin/groupMax permettant de calculer la mortalit?\195?\169 totale par p?\195?\170che (ftot). Added: trunk/scripts/MinimisationUtil.java trunk/scripts/ObjectiveFunction.java trunk/scripts/ObjectiveFunctionBaranov.java Modified: trunk/pom.xml trunk/scripts/ResultName.java trunk/scripts/RuleUtil.java trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-14 14:12:39 UTC (rev 295) +++ trunk/pom.xml 2012-09-25 14:51:25 UTC (rev 296) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.2.0</version> + <version>4.2.1</version>  <description>Data for Isis-fish</description> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.0.0</version> + <version>4.2.1.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Added: trunk/scripts/MinimisationUtil.java =================================================================== --- trunk/scripts/MinimisationUtil.java (rev 0) +++ trunk/scripts/MinimisationUtil.java 2012-09-25 14:51:25 UTC (rev 296) @@ -0,0 +1,176 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2012 Ifremer, CodeLutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ + +package scripts; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import fr.ifremer.isisfish.util.Nocache; + +public class MinimisationUtil { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(RuleUtil.class); + + /** + * Algo de minimisation de fmin(step, x,C,M,N) sur x. + * + * en prenant une valeur initiale de x dans [a,b] et une tolerance = tol + * Reference de l'algo : http://www1.fpl.fs.fed.us/optimization.html + * Algorithme de Brent qui approxime la fonction a minimiser par une + * parabole si possible et fait du "golden step" sinon + * + * @param a + * @param b + * @param tol tolérance + * @param f fonction d'objectif + * @return + */ + @Nocache + public static double fmin(double a, double b, double tol, ObjectiveFunction f) { + + double c, d, e, eps, xm, p, q, r, tol1, t2, u, v, w, fu, fv, fw, fx, x, tol3; + + c = .5 * (3.0 - Math.sqrt(5.0)); + d = 0.0; + eps = 1.2e-16; // 1.1102e-16 is machine precision + tol1 = eps + 1.0; + eps = Math.sqrt(eps); + v = a + c * (b - a); + // log.info("Finit=" + v); + w = v; + x = v; + e = 0.0; + fx = 0.0; + fu = 0.0; + + fx = f.compute(x); + // log.info("fx= " + fx); + + fv = fx; + fw = fx; + tol3 = tol / 3.0; + xm = .5 * (a + b); + tol1 = eps * Math.abs(x) + tol3; + t2 = 2.0 * tol1; + + while (Math.abs(x - xm) > (t2 - .5 * (b - a))) { // main loop; + // ///// De là... + p = q = r = 0.0; + if (Math.abs(e) > tol1) { // fit the parabola; + r = (x - w) * (fx - fv); + q = (x - v) * (fx - fw); + p = (x - v) * q - (x - w) * r; + q = 2.0 * (q - r); + if (q > 0.0) { + p = -p; + } else { + q = -q; + } + r = e; + e = d; + } + if ((Math.abs(p) < Math.abs(.5 * q * r)) && (p > q * (a - x)) + && (p < q * (b - x))) { // parabolic interpolation step; + d = p / q; + u = x + d; + if (((u - a) < t2) || ((b - u) < t2)) { // f must not be + // evaluated too close + // to a or b; + d = tol1; + if (x >= xm) + d = -d; + } + } else { // a golden-section step; + if (x < xm) { + e = b - x; + } else { + e = a - x; + } + d = c * e; + } + if (Math.abs(d) >= tol1) { // f must not be evaluated too close to x; + u = x + d; + } else { + if (d > 0.0) { + u = x + tol1; + } else { + u = x - tol1; + } + } + // ... à ici : ne sert qu'à calculer un u (selon 2 manières + // différentes) afin de comparer fx a fu + // --> On peut très bien prendre u à partir d'une autre simu a + // la place (?) + + fu = f.compute(u); + //log.info("fu= " + fu); + + // Update a, b, v, w, and x + if (fx <= fu) { + if (u < x) { + a = u; + } else { + b = u; + } + } + if (fu <= fx) { + if (u < x) { + b = x; + } else { + a = x; + } + v = w; + fv = fw; + w = x; + fw = fx; + x = u; + fx = fu; + xm = .5 * (a + b); + tol1 = eps * Math.abs(x) + tol3; + t2 = 2.0 * tol1; + } else { + if ((fu <= fw) || (w == x)) { + v = w; + fv = fw; + w = u; + fw = fu; + xm = .5 * (a + b); + tol1 = eps * Math.abs(x) + tol3; + t2 = 2.0 * tol1; + } else if ((fu > fv) && (v != x) && (v != w)) { + xm = .5 * (a + b); + tol1 = eps * Math.abs(x) + tol3; + t2 = 2.0 * tol1; + } else { + v = u; + fv = fu; + xm = .5 * (a + b); + tol1 = eps * Math.abs(x) + tol3; + t2 = 2.0 * tol1; + } + } + } + return x; + } +} Property changes on: trunk/scripts/MinimisationUtil.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: trunk/scripts/ObjectiveFunction.java =================================================================== --- trunk/scripts/ObjectiveFunction.java (rev 0) +++ trunk/scripts/ObjectiveFunction.java 2012-09-25 14:51:25 UTC (rev 296) @@ -0,0 +1,40 @@ +/* + * Copyright (C) 2012 lgasche + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + */ + +package scripts; + +/** + * ObjectiveFunction.java + * + * Created: 10 aout 2012 + * + * @author lgasche + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ +public abstract class ObjectiveFunction { + + /** + * Compute value depending on objective function implementation + * @param x + * @return + */ + public abstract double compute(double x); +} \ No newline at end of file Property changes on: trunk/scripts/ObjectiveFunction.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: trunk/scripts/ObjectiveFunctionBaranov.java =================================================================== --- trunk/scripts/ObjectiveFunctionBaranov.java (rev 0) +++ trunk/scripts/ObjectiveFunctionBaranov.java 2012-09-25 14:51:25 UTC (rev 296) @@ -0,0 +1,49 @@ +/* + * Copyright (C) 2012 lgasche + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + */ + +package scripts; + +import fr.ifremer.isisfish.util.Nocache; + +/** + * FonctionObjectif_Baranov.java + * + * Created: 10 aout 2012 + * + * @author lgasche <user.name(a)vcs.hostName> + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ +@Nocache +public class ObjectiveFunctionBaranov extends ObjectiveFunction { + + protected double C, M, N; + + public ObjectiveFunctionBaranov(double C, double M, double N) { // step ?? + this.C = C; + this.M = M; + this.N = N; + } + + public double compute(double xx) { + double ff = Math.pow((C - (xx/(xx+M))*(1-Math.exp(-(xx+M)))*N),2); + return ff; + } +} \ No newline at end of file Property changes on: trunk/scripts/ObjectiveFunctionBaranov.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Modified: trunk/scripts/ResultName.java =================================================================== --- trunk/scripts/ResultName.java 2012-09-14 14:12:39 UTC (rev 295) +++ trunk/scripts/ResultName.java 2012-09-25 14:51:25 UTC (rev 296) @@ -159,6 +159,21 @@ @Doc(value = "Disponible uniquement avec les simulations par Zone. do the doc of Result matrixFishingMortality") static final public String MATRIX_FISHING_MORTALITY = n_("matrixFishingMortality"); + /** + * Matrix with 1 dimension + * Dimension 1 : TimeStep + */ + @Doc(value = "do the doc of Result matrixTotalFishingMortality") + static final public String MATRIX_TOTAL_FISHING_MORTALITY = n_("matrixTotalFishingMortality"); + + /** + * Matrix with 2 dimensions + * Dimension 1 : TimeStep + * Dimension 2 : Group + */ + @Doc(value = "do the doc of Result matrixFishingMortalityPerGroup") + static final public String MATRIX_FISHING_MORTALITY_PER_GROUP = n_("matrixFishingMortalityPerGroup"); + /** * Matrix with three dimensions * Dimension 1 : TimeStep Modified: trunk/scripts/RuleUtil.java =================================================================== --- trunk/scripts/RuleUtil.java 2012-09-14 14:12:39 UTC (rev 295) +++ trunk/scripts/RuleUtil.java 2012-09-25 14:51:25 UTC (rev 296) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * Copyright (C) 2006 - 2012 Ifremer, CodeLutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -25,9 +25,8 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; -import org.nuiton.math.matrix.*; - import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationGroup; import fr.ifremer.isisfish.entities.Species; @@ -78,4 +77,24 @@ } return result; } + + public static double getTotalCatchTonsPop(SimulationContext context, Population pop, TimeStep step) { + double result = 0; + MatrixND mat = context.getPopulationMonitor().getHoldCatch(pop); + if (mat != null) { + mat = mat.copy(); + mat = mat.sumOverDim(0); // sum over Strategies + mat = mat.sumOverDim(1); // sum over metiers + mat = mat.sumOverDim(3); // sum over zones + + List<PopulationGroup> groups = pop.getPopulationGroup(); + + for (int c = 0; c < groups.size(); c++) { + PopulationGroup group = groups.get(c); + double weight = group.getMeanWeight(); + result += mat.getValue(0, 0, c, 0) * weight / 1000.0; + } + } + return result; + } } Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2012-09-14 14:12:39 UTC (rev 295) +++ trunk/scripts/SiMatrix.java 2012-09-25 14:51:25 UTC (rev 296) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -26,9 +26,11 @@ import java.util.ArrayList; import java.util.Collection; +import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; +import java.util.Arrays; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -57,12 +59,19 @@ import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.datastore.ResultStorage; +import scripts.RuleUtil; /** - * SiMatrix calcul simplement des résultats ne dependant que des parametres - * de simulation et des données du modèle. + * SiMatrix.java * + * Created: 21 aout 2006 15:53:01 + * * @author poussin + * @version $Revision: 1.18 $ + * + * Last update: $Date: 2007-11-02 17:53:20 $ + * by : $Author: bpoussin $ */ public class SiMatrix { @@ -1381,8 +1390,8 @@ Zone zone, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { double F = totalFishingMortality(step, matrixFishingMortality) - .getValue(group, zone); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcul� - double M = group.getNaturalDeathRate(zone) + .getValue(group, zone); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule + double M = group.getNaturalDeathRate(zone) / (double) Month.NUMBER_OF_MONTH; double result = Math.exp(-(F + M)); @@ -1402,9 +1411,9 @@ throws TopiaException, IsisFishException { double F = totalFishingMortalityPerCell(step, - matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcul� + matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule double M = group.getNaturalDeathRate(zone) - / (double) Month.NUMBER_OF_MONTH; + / (double) Month.NUMBER_OF_MONTH; double result = (double) Math.exp(-(F + M)); return result; @@ -1554,9 +1563,9 @@ // // /////////////////////////////////////////////////////////////////////////// - public MatrixND matrixEffortNominalPerStrategyMet(TimeStep step) throws TopiaException { + public MatrixND matrixEffortNominalPerStrategyMet(TimeStep step) throws TopiaException { - List<Strategy> strategies = getStrategies(step); + List<Strategy> strategies = getStrategies(step); List<Metier> metiers = getMetiers(step); MatrixND result = MatrixFactory.getInstance().create( @@ -1576,4 +1585,127 @@ return result; } + + /** + * Ce morceau de script sert a calculer la mortalite par peche par espece et + * par groupe d'age sur l'ensemble de la zone d'etude, + * en minimisant la difference entre les captures d'ISIS et celles calculees + * a partir de l'equation de Baranov. + * + * @param step pas de temps + * @param pop population + * @return Fishing mortality per group per year (computed in December) + */ + public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultStorage resManager) throws TopiaException { + double Fgroup=0; + double Cgroup=0; + double Mgroup=0; + double NgroupJan=0; + + List<Population> populations = Collections.singletonList(pop); + List<PopulationGroup> groups = pop.getPopulationGroup(); + + MatrixND tfgMatrix = MatrixFactory.getInstance().create( + ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP, + new List[]{populations, groups}, // On travaille sur les pops ET les groupes + new String[]{n_("Population"), n_("Group")}); + + for (PopulationGroup group : groups) { + + if (step.getMonth() == Month.DECEMBER) { + + MatrixND catchPerStrategy = null; + + for (TimeStep loopstep = new TimeStep(step.getYear() * 12); loopstep.beforeOrEquals(step); loopstep=loopstep.next()){ + // On fait cette boucle pour contourner les aspects de cache qui font que les resultats ne sont pas recuperes + //s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) + // beforeOrEquals sert a bien prendre Decembre aussi + + MatrixND catchPerStrategyTemp = resManager.getMatrix(loopstep, pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + if (catchPerStrategy == null){ + catchPerStrategy = catchPerStrategyTemp.clone(); + // On clone la matrice car si on fait les operations sur celle contenue dans le cache on la modifie et donc on recupere des resultats faux. + } else { + catchPerStrategy = catchPerStrategy.add(catchPerStrategyTemp); // Pour avoir la somme des captures sur les 12 mois + } + } + + //log.info("catchPerStrategy = " + catchPerStrategy); + catchPerStrategy = catchPerStrategy.sumOverDim(0); // Strategy + catchPerStrategy = catchPerStrategy.sumOverDim(1); // Metier + catchPerStrategy = catchPerStrategy.sumOverDim(3); // Zone : une pop peut avoir plusieurs zonespop dans ISIS + List semgroup = catchPerStrategy.getSemantic(2); + catchPerStrategy = catchPerStrategy.reduce(); // Enleve les dimensions de taille 1 + catchPerStrategy.setSemantic(0, semgroup); // Ne plait pas a Eric + Cgroup = catchPerStrategy.getValue(group); + //log.info("Cgroup = " + Cgroup + "Year=" + step.getYear()); + //log.info("catchPerStrategy = " + catchPerStrategy + "Year=" + step.getYear()); + + MatrixND naturalDeathRatePop = pop.getNaturalDeathRateMatrix(); + naturalDeathRatePop = naturalDeathRatePop.meanOverDim(1); // moyenne sur Zone + naturalDeathRatePop = naturalDeathRatePop.reduce(); // Enleve les dimensions de taille 1 + Mgroup = naturalDeathRatePop.getValue(group); + //log.info("Mgroup= " + Mgroup + "Year=" + step.getYear()); + + MatrixND abundancePopJan = resManager.getMatrix(new TimeStep(12*step.getYear()), pop, ResultName.MATRIX_ABUNDANCE); // Le timestep 0 correspond a janvier de la premiere annee et les annees sont numerotees a partir de zero abundancePopJan = abundancePopJan.sumOverDim(1); // somme sur Zone + abundancePopJan = abundancePopJan.reduce(); + NgroupJan = abundancePopJan.getValue(group); + //log.info("NgroupJan = " + NgroupJan + "Year=" + step.getYear()); + + ObjectiveFunction f = new ObjectiveFunctionBaranov(Cgroup, Mgroup, NgroupJan); + Fgroup = MinimisationUtil.fmin(0.0,2.0,1.0e-10, f); // step ?? + + //log.info("Fgroup = " + Fgroup); + + tfgMatrix.setValue(pop, group, Fgroup); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? + + } else { + //Fgroup = 0; // Ce n'est plus une valeur unique mais une matrice, est-ce que cette notation peut fonctionner ? + tfgMatrix.setValue(pop, group, 0); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? + } + } + + //log.info("tfgMatrix = " + tfgMatrix); + //log.info("tfg.DimensionNames = " + Arrays.toString(tfgMatrix.getDimensionNames())); + //log.info("tfg.Semantics = " + Arrays.toString(tfgMatrix.getSemantics())); + + return tfgMatrix; + } + + /** + * Ce morceau de script sert a calculer la mortalite par peche par espece et + * par groupe representatif a partir de la mortalite par peche par groupe + * calculee precedemment. + */ + public MatrixND totalFishingMortality (TimeStep step, Population pop, MatrixND FishingMortalityPerGroup) throws TopiaException { + MatrixND tfmMatrix = FishingMortalityPerGroup.copy(); + tfmMatrix.setName(ResultName.MATRIX_TOTAL_FISHING_MORTALITY); + //log.info("tfmMatrix = " + tfmMatrix); + + List<PopulationGroup> groups = pop.getPopulationGroup(); + + int groupMin = pop.getGroupMin(); + int groupMax = pop.getGroupMax(); + int Nbre = (int)groupMax - (int)groupMin + 1; + //log.info("Nbre = " + Nbre); + + if (groupMin != groupMax){ + for (PopulationGroup group : groups) { + if (group.getId() == groupMin) { + // MatrixND getSubMatrix(int dim, Object, int nb) + tfmMatrix = tfmMatrix.getSubMatrix(1, group, Nbre); + tfmMatrix = tfmMatrix.meanOverDim(1); + tfmMatrix = tfmMatrix.reduce(); + //log.info("tfm.DimensionNames = " + Arrays.toString(tfmMatrix.getDimensionNames())); + //log.info("tfm.Semantics = " + Arrays.toString(tfmMatrix.getSemantics())); + } + } + } else { + tfmMatrix = tfmMatrix.reduce(); + //log.info("tfm.DimensionNames = " + Arrays.toString(tfmMatrix.getDimensionNames())); + //log.info("tfm.Semantics = " + Arrays.toString(tfmMatrix.getSemantics())); + } + + return tfmMatrix; + } } Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2012-09-14 14:12:39 UTC (rev 295) +++ trunk/simulators/DefaultSimulator.java 2012-09-25 14:51:25 UTC (rev 296) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -19,7 +19,6 @@ * <http://www.gnu.org/licenses/gpl-2.0.html>. * #L% */ - package simulators; import fr.ifremer.isisfish.IsisFishException; @@ -56,7 +55,7 @@ /** * DefaultSimulator.java * - * Created: 21 août 2006 10:57:46 + * Created: 21 aout 2006 10:57:46 * * @author poussin * @version $Revision: 1.19 $ @@ -216,11 +215,12 @@ for (Population pop : siMatrix.getPopulations(step)) { computeMonth(context, siMatrix, step, pop); } - + // // Add some result not population dependante // + // only if there are one or more strategy if (siMatrix.getStrategies(step).size() > 0) { @@ -326,10 +326,11 @@ db.rollbackTransaction(); // - // clear cache + // commit result // - control.setText("Clear cache"); - context.clearCache(step); + control.setText("Commit results"); + TopiaContext tx = context.getDbResult(); + tx.commitTransaction(); // // Go next step @@ -479,7 +480,7 @@ .matrixCatchWeightPerStrategyMetPerZonePop(step, pop, catchPerStrategyMetPerZonePop); resManager.addResult(step, pop, catchWeightPerStrategyMet); - } + } if (isEffortByCell(context)) { MatrixND catchPerStrategyMetPerZoneMet = siMatrix @@ -495,6 +496,21 @@ } } + if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || + resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { + MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, + pop, context.getSimulationStorage().getResultStorage()); + + if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { + resManager.addResult(step, pop, fishingMortalityPerGroup); + } + + if (resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { + MatrixND totalFishingMortality = siMatrix.totalFishingMortality(step, pop, fishingMortalityPerGroup); + resManager.addResult(step, pop, totalFishingMortality); + } + } + } else { // no strategies // compute only if fishing mortality =0 to apply Natural Mortality abundance = siMatrix.matrixAbundanceSsF(N, pop, step); @@ -553,10 +569,6 @@ .matrixSharedNotFixedCostsPerVessel(step); resManager.addResult(step, mat); } - // if (resManager.isEnabled(ResultName.MATRIX_SHARED_FIXED_COSTS_PER_VESSEL_PER_MET)) { - // MatrixND mat = gravityModel.matrixSharedFixedCostsPerVesselPerMet(date); - // resManager.addResult(date, mat); - // } if (resManager .isEnabled(ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_SPECIES_PER_STRATEGY_MET)) { MatrixND mat = gravityModel

1 0

r295 - tags
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 16:12:39 +0200 (Fri, 14 Sep 2012) New Revision: 295 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/295 Log: Tag 4.2.0 Added: tags/4.2.0/

1 0

r294 - trunk
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 16:11:58 +0200 (Fri, 14 Sep 2012) New Revision: 294 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/294 Log: Prepare next tag Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-06 12:55:57 UTC (rev 293) +++ trunk/pom.xml 2012-09-14 14:11:58 UTC (rev 294) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.1.1</version> + <version>4.2.0</version>  <description>Data for Isis-fish</description> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.1.0</version> + <version>4.2.0.0</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r293 - tags/4.1.1/rules
by echatellier＠users.forge.codelutin.com Sept. 6, 2012

Sept. 6, 2012

Author: echatellier Date: 2012-09-06 14:55:57 +0200 (Thu, 06 Sep 2012) New Revision: 293 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/293 Log: Mise ?\195?\160 jour de TailleMin Modified: tags/4.1.1/rules/TailleMin.java Modified: tags/4.1.1/rules/TailleMin.java =================================================================== --- tags/4.1.1/rules/TailleMin.java 2012-09-06 12:54:46 UTC (rev 292) +++ tags/4.1.1/rules/TailleMin.java 2012-09-06 12:55:57 UTC (rev 293) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * Copyright (C) 2006 - 2012 Ifremer, CodeLutin, Stéphanie Mahevas, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -23,15 +23,12 @@ import static org.nuiton.i18n.I18n._; -import java.util.List; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; import scripts.ResultName; -import scripts.SiMatrix; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.MetierSeasonInfo; import fr.ifremer.isisfish.entities.Population; @@ -45,15 +42,20 @@ import fr.ifremer.isisfish.util.Doc; /** - * Cette methode remplace aussi TailleMinSurvieRejet si propSurvie est > 0 + * Cette regles tient compte de la taille minimum des poissons capturable. * + * Les captures ne sont pas impactées, mais des rejets sont générés si la + * taille des poissons est inférieures à TailleMin. + * + * En cas de propSurvie positif, la matrice d'effectif est modifié + * pour tenir compte de la partie de poisson rejeté qui survi. + * * Created: 30 novembre 2006 - * - * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * + * @author smahevas * @version $Revision: 1.1 $ - * - * Last update: $Date: 2007-01-24 18:25:34 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-01-24 18:25:34 $ by : $Author: bpoussin $ */ public class TailleMin extends AbstractRule { @@ -74,12 +76,14 @@ @Doc(value = "Proportion de survie") public double param_propSurvie = 0; - + + protected boolean affectation = true; + public String[] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override @@ -94,19 +98,20 @@ */ @Override public String getDescription() throws Exception { - return _("Tous les poissons dont la taille est inférieure à TailleMin" + - " ne seront pas capturés. Ils sont placés en rejets et rejetés" + - " suivant la proportion de survie."); + return _("Tous les poissons dont la taille est inférieure à TailleMin" + + " ne seront pas capturés. Ils sont placés en rejets et rejetés" + + " suivant la proportion de survie."); } /** - * Appelé au démarrage de la simulation, cette méthode permet d'initialiser - * des valeurs + * Appele au demarrage de la simulation, cette methode permet + * d'initialiser des valeurs de la règle. * - * @param context La simulation pour lequel on utilise cette regle + * @param context La simulation pour laquelle on utilise cette regle */ @Override public void init(SimulationContext context) throws Exception { + } /** @@ -135,12 +140,12 @@ * * @param context la simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne * @return vrai si on souhaite que les actions soit faites */ @Override - public boolean condition(SimulationContext context, TimeStep step, Metier metier) - throws Exception { + public boolean condition(SimulationContext context, TimeStep step, + Metier metier) throws Exception { log.info("Recherche si la taille Minimale s'applique"); boolean result = true; if (step.before(param_beginStep)) { @@ -156,79 +161,74 @@ } /** - * Si la condition est vrai alors cette action est executee avant le pas - * de temps de la simulation. + * Si la condition est vrai alors cette action est executee avant le pas de + * temps de la simulation. * * @param context la simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne */ @Override - public void preAction(SimulationContext context, TimeStep step, Metier metier) - throws Exception { - // nothing + public void preAction(SimulationContext context, TimeStep step, + Metier metier) throws Exception { + + affectation = true; // pour que affectation soit vraie au debut de + // chaque pas de temps pour rentrer au moins une + // fois dans postaction } /** - * Si la condition est vrai alors cette action est executée apres le pas + * Si la condition est vrai alors cette action est executee apres le pas * de temps de la simulation. * * @param context La simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne */ @Override - public void postAction(SimulationContext context, TimeStep step, Metier metier) - throws Exception { - log.info("*$*$*$* TailleMin.actionApres:" + step + " metapop:" + - param_species + " metier:" + metier); + public void postAction(SimulationContext context, TimeStep step, + Metier metier) throws Exception { + //log.info("*$*$*$* TailleMin.actionApres:" + step + " metapop:" + // + param_species + " metier:" + metier); - if (isCaptureDate(step, param_species, metier)) { - log.info( - "*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); - // ATTENTION - // les captures pour cette metapop ne sont plus du qu'au metier pour qui - // l'espece est secondaire: elles sont affectees aux rejets + if (affectation) { + log.info("*$*$*$* ok affecte capture inferieure a TailleMin au rejet"); + // ATTENTION + // les captures pour cette metapop ne sont plus du qu'au metier pour + // qui l'espece est secondaire: elles sont affectees aux rejets - //pb : ne se fait pas par metier - //il faut une matrice pour chaques pas de temps qui stocke les rejets - //par metier, par metapop et par classes d'age (comme pour les captures) - ////// - log.info("deb de affecterCaptureREJETTailleMin"); + // pb : ne se fait pas par metier + // il faut une matrice pour chaques pas de temps qui stocke les + // rejets par metier, par metapop et par classes d'age (comme pour + // les captures) + //log.info("deb de affecterCaptureREJETTailleMin"); PopulationMonitor popMon = context.getPopulationMonitor(); - SiMatrix siMatrix = SiMatrix.getSiMatrix(context); - List<Population> pops = siMatrix.getPopulations(step); - for (Population pop : pops) { - if (pop.getSpecies().equals(param_species)) { - if (popMon.getDiscard(step, pop) == null) { - MatrixND discard = popMon.getCatch(pop).copy(); - MatrixND eff = popMon.getN(pop); + for (Population pop : param_species.getPopulation()) { + MatrixND discard = popMon.getCatch(pop).copy(); + MatrixND eff = popMon.getN(pop); - for (MatrixIterator i = discard.iterator(); i.next();) { - Object[] coordonnees = i.getSemanticsCoordinates(); - PopulationGroup group = - (PopulationGroup) coordonnees[2]; - if (group.getLength() >= param_TailleMin) { - i.setValue(0); - } else if (param_propSurvie > 0) { - eff.setValue(coordonnees[2], coordonnees[3], - eff.getValue(coordonnees[2], - coordonnees[3]) + i.getValue() * - param_propSurvie); - } - } - discard.setName( - ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); - popMon.addDiscard(step, pop, discard); + for (MatrixIterator i = discard.iterator(); i.next();) { + Object[] coordonnees = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) coordonnees[2]; + if (group.getLength() >= param_TailleMin) { + i.setValue(0); + } else if (param_propSurvie > 0) { + eff.setValue(coordonnees[2], coordonnees[3], + eff.getValue(coordonnees[2], coordonnees[3]) + + i.getValue() * param_propSurvie); } } + discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); + popMon.addDiscard(step, pop, discard); } - log.info("fin de affecterCaptureRejetTailleMin"); + //log.info("fin de affecterCaptureRejetTailleMin"); - //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire + // on a affecte une fois cette meta pop au rejet il ne faut pas le + // refaire pour ce pas de temps + affectation = false; } } }

1 0

r292 - trunk/rules
by echatellier＠users.forge.codelutin.com Sept. 6, 2012

Sept. 6, 2012

Author: echatellier Date: 2012-09-06 14:54:46 +0200 (Thu, 06 Sep 2012) New Revision: 292 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/292 Log: Mise ?\195?\160 jour de TailleMin Modified: trunk/rules/TailleMin.java Modified: trunk/rules/TailleMin.java =================================================================== --- trunk/rules/TailleMin.java 2012-08-27 19:58:16 UTC (rev 291) +++ trunk/rules/TailleMin.java 2012-09-06 12:54:46 UTC (rev 292) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * Copyright (C) 2006 - 2012 Ifremer, CodeLutin, Stéphanie Mahevas, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -23,15 +23,12 @@ import static org.nuiton.i18n.I18n._; -import java.util.List; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; import scripts.ResultName; -import scripts.SiMatrix; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.MetierSeasonInfo; import fr.ifremer.isisfish.entities.Population; @@ -45,15 +42,20 @@ import fr.ifremer.isisfish.util.Doc; /** - * Cette methode remplace aussi TailleMinSurvieRejet si propSurvie est > 0 + * Cette regles tient compte de la taille minimum des poissons capturable. * + * Les captures ne sont pas impactées, mais des rejets sont générés si la + * taille des poissons est inférieures à TailleMin. + * + * En cas de propSurvie positif, la matrice d'effectif est modifié + * pour tenir compte de la partie de poisson rejeté qui survi. + * * Created: 30 novembre 2006 - * - * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * + * @author smahevas * @version $Revision: 1.1 $ - * - * Last update: $Date: 2007-01-24 18:25:34 $ - * by : $Author: bpoussin $ + * + * Last update: $Date: 2007-01-24 18:25:34 $ by : $Author: bpoussin $ */ public class TailleMin extends AbstractRule { @@ -74,12 +76,14 @@ @Doc(value = "Proportion de survie") public double param_propSurvie = 0; - + + protected boolean affectation = true; + public String[] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override @@ -94,19 +98,20 @@ */ @Override public String getDescription() throws Exception { - return _("Tous les poissons dont la taille est inférieure à TailleMin" + - " ne seront pas capturés. Ils sont placés en rejets et rejetés" + - " suivant la proportion de survie."); + return _("Tous les poissons dont la taille est inférieure à TailleMin" + + " ne seront pas capturés. Ils sont placés en rejets et rejetés" + + " suivant la proportion de survie."); } /** - * Appelé au démarrage de la simulation, cette méthode permet d'initialiser - * des valeurs + * Appele au demarrage de la simulation, cette methode permet + * d'initialiser des valeurs de la règle. * - * @param context La simulation pour lequel on utilise cette regle + * @param context La simulation pour laquelle on utilise cette regle */ @Override public void init(SimulationContext context) throws Exception { + } /** @@ -135,12 +140,12 @@ * * @param context la simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne * @return vrai si on souhaite que les actions soit faites */ @Override - public boolean condition(SimulationContext context, TimeStep step, Metier metier) - throws Exception { + public boolean condition(SimulationContext context, TimeStep step, + Metier metier) throws Exception { log.info("Recherche si la taille Minimale s'applique"); boolean result = true; if (step.before(param_beginStep)) { @@ -156,79 +161,74 @@ } /** - * Si la condition est vrai alors cette action est executee avant le pas - * de temps de la simulation. + * Si la condition est vrai alors cette action est executee avant le pas de + * temps de la simulation. * * @param context la simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne */ @Override - public void preAction(SimulationContext context, TimeStep step, Metier metier) - throws Exception { - // nothing + public void preAction(SimulationContext context, TimeStep step, + Metier metier) throws Exception { + + affectation = true; // pour que affectation soit vraie au debut de + // chaque pas de temps pour rentrer au moins une + // fois dans postaction } /** - * Si la condition est vrai alors cette action est executée apres le pas + * Si la condition est vrai alors cette action est executee apres le pas * de temps de la simulation. * * @param context La simulation pour lequel on utilise cette regle * @param step le pas de temps courant - * @param metier le metier concerné + * @param metier le metier concerne */ @Override - public void postAction(SimulationContext context, TimeStep step, Metier metier) - throws Exception { - log.info("*$*$*$* TailleMin.actionApres:" + step + " metapop:" + - param_species + " metier:" + metier); + public void postAction(SimulationContext context, TimeStep step, + Metier metier) throws Exception { + //log.info("*$*$*$* TailleMin.actionApres:" + step + " metapop:" + // + param_species + " metier:" + metier); - if (isCaptureDate(step, param_species, metier)) { - log.info( - "*$*$*$* ok affecte capture infÃ?rieure Ã? TailleMin au rejet"); - // ATTENTION - // les captures pour cette metapop ne sont plus du qu'au metier pour qui - // l'espece est secondaire: elles sont affectees aux rejets + if (affectation) { + log.info("*$*$*$* ok affecte capture inferieure a TailleMin au rejet"); + // ATTENTION + // les captures pour cette metapop ne sont plus du qu'au metier pour + // qui l'espece est secondaire: elles sont affectees aux rejets - //pb : ne se fait pas par metier - //il faut une matrice pour chaques pas de temps qui stocke les rejets - //par metier, par metapop et par classes d'age (comme pour les captures) - ////// - log.info("deb de affecterCaptureREJETTailleMin"); + // pb : ne se fait pas par metier + // il faut une matrice pour chaques pas de temps qui stocke les + // rejets par metier, par metapop et par classes d'age (comme pour + // les captures) + //log.info("deb de affecterCaptureREJETTailleMin"); PopulationMonitor popMon = context.getPopulationMonitor(); - SiMatrix siMatrix = SiMatrix.getSiMatrix(context); - List<Population> pops = siMatrix.getPopulations(step); - for (Population pop : pops) { - if (pop.getSpecies().equals(param_species)) { - if (popMon.getDiscard(step, pop) == null) { - MatrixND discard = popMon.getCatch(pop).copy(); - MatrixND eff = popMon.getN(pop); + for (Population pop : param_species.getPopulation()) { + MatrixND discard = popMon.getCatch(pop).copy(); + MatrixND eff = popMon.getN(pop); - for (MatrixIterator i = discard.iterator(); i.next();) { - Object[] coordonnees = i.getSemanticsCoordinates(); - PopulationGroup group = - (PopulationGroup) coordonnees[2]; - if (group.getLength() >= param_TailleMin) { - i.setValue(0); - } else if (param_propSurvie > 0) { - eff.setValue(coordonnees[2], coordonnees[3], - eff.getValue(coordonnees[2], - coordonnees[3]) + i.getValue() * - param_propSurvie); - } - } - discard.setName( - ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); - popMon.addDiscard(step, pop, discard); + for (MatrixIterator i = discard.iterator(); i.next();) { + Object[] coordonnees = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) coordonnees[2]; + if (group.getLength() >= param_TailleMin) { + i.setValue(0); + } else if (param_propSurvie > 0) { + eff.setValue(coordonnees[2], coordonnees[3], + eff.getValue(coordonnees[2], coordonnees[3]) + + i.getValue() * param_propSurvie); } } + discard.setName(ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP); + popMon.addDiscard(step, pop, discard); } - log.info("fin de affecterCaptureRejetTailleMin"); + //log.info("fin de affecterCaptureRejetTailleMin"); - //on a affecte une fois cette meta pop au rejet il ne faut pas le refaire + // on a affecte une fois cette meta pop au rejet il ne faut pas le + // refaire pour ce pas de temps + affectation = false; } } }

1 0

r291 - tags
by echatellier＠users.forge.codelutin.com Aug. 27, 2012

Aug. 27, 2012

Author: echatellier Date: 2012-08-27 21:58:16 +0200 (Mon, 27 Aug 2012) New Revision: 291 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/291 Log: Tag 4.1.1 Added: tags/4.1.1/

1 0

r290 - trunk
by echatellier＠users.forge.codelutin.com Aug. 27, 2012

Aug. 27, 2012

Author: echatellier Date: 2012-08-27 21:57:14 +0200 (Mon, 27 Aug 2012) New Revision: 290 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/290 Log: Use release Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-08-27 17:59:20 UTC (rev 289) +++ trunk/pom.xml 2012-08-27 19:57:14 UTC (rev 290) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.1.0-SNAPSHOT</version> + <version>4.1.1.0</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r289 - in trunk: . simulators
by echatellier＠users.forge.codelutin.com Aug. 27, 2012

Aug. 27, 2012

Author: echatellier Date: 2012-08-27 19:59:20 +0200 (Mon, 27 Aug 2012) New Revision: 289 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/289 Log: Vidage du cache ?\195?\160 la fin d'un pas de temps Modified: trunk/pom.xml trunk/simulators/DefaultSimulator.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-05-29 09:27:28 UTC (rev 288) +++ trunk/pom.xml 2012-08-27 17:59:20 UTC (rev 289) @@ -36,7 +36,7 @@ <plugins> <plugin> <artifactId>maven-compiler-plugin</artifactId> - <version>2.3.2</version> + <version>2.5.1</version> <configuration> <source>1.6</source> <target>1.6</target> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.0.1-SNAPSHOT</version> + <version>4.1.1.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2012-05-29 09:27:28 UTC (rev 288) +++ trunk/simulators/DefaultSimulator.java 2012-08-27 17:59:20 UTC (rev 289) @@ -326,11 +326,10 @@ db.rollbackTransaction(); // - // commit result + // clear cache // - control.setText("Commit results"); - TopiaContext tx = context.getDbResult(); - tx.commitTransaction(); + control.setText("Clear cache"); + context.clearCache(step); // // Go next step

1 0

r288 - in branches/4.1: . scripts sensitivityanalysis sensitivityexports
by echatellier＠users.forge.codelutin.com May 29, 2012

May 29, 2012

Author: echatellier Date: 2012-05-29 11:27:28 +0200 (Tue, 29 May 2012) New Revision: 288 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/288 Log: Merge trunk into branch Modified: branches/4.1/ branches/4.1/pom.xml branches/4.1/scripts/GravityModel.java branches/4.1/scripts/SiMatrix.java branches/4.1/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRDOptimal.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRFast.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRMorris.java branches/4.1/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRSobol.java branches/4.1/sensitivityanalysis/SensitivityCalculatorRegularFractions.java branches/4.1/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java branches/4.1/sensitivityexports/SensitivitySpawningBiomassY2.java Property changes on: branches/4.1 ___________________________________________________________________ Added: svn:mergeinfo + /trunk:272-287 Modified: branches/4.1/pom.xml =================================================================== --- branches/4.1/pom.xml 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/pom.xml 2012-05-29 09:27:28 UTC (rev 288) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.0.0</version> + <version>4.1.1</version>  <description>Data for Isis-fish</description> @@ -36,7 +36,7 @@ <plugins> <plugin> <artifactId>maven-compiler-plugin</artifactId> - <version>2.3.2</version> + <version>2.5</version> <configuration> <source>1.6</source> <target>1.6</target> @@ -49,7 +49,7 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.2</version> + <version>1.2.1</version> <executions> <execution> <goals> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.0.0.3-SNAPSHOT</version> + <version>4.1.1.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Modified: branches/4.1/scripts/GravityModel.java =================================================================== --- branches/4.1/scripts/GravityModel.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/scripts/GravityModel.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -49,15 +49,14 @@ import fr.ifremer.isisfish.types.TimeUnit; /** - * GravityModel.java - * - * Created: 4 sept. 06 15:49:08 - * + * Gravity model calcul des resultats à basés sur des resultats provenant + * de SiMatrix ou des resultat précédement calculé disponible via le + * result manager. + * + * Cette classe sert a calculer des résultats economique (prix, resultat + * servant a optimiser des cout pour les pécheurs...). + * * @author poussin - * @version $Revision: 1.9 $ - * - * Last update: $Date: 2007-03-01 17:16:12 $ - * by : $Author: bpoussin $ */ public class GravityModel { Modified: branches/4.1/scripts/SiMatrix.java =================================================================== --- branches/4.1/scripts/SiMatrix.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/scripts/SiMatrix.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -59,15 +59,10 @@ import fr.ifremer.isisfish.types.Month; /** - * SiMatrix.java + * SiMatrix calcul simplement des résultats ne dependant que des parametres + * de simulation et des données du modèle. * - * Created: 21 aout 2006 15:53:01 - * * @author poussin - * @version $Revision: 1.18 $ - * - * Last update: $Date: 2007-11-02 17:53:20 $ - * by : $Author: bpoussin $ */ public class SiMatrix { Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-05-29 09:27:28 UTC (rev 288) @@ -364,8 +364,15 @@ } //Rename R objects for saving purpose - renameObjects(engine, simulationName); + renameObjects(engine,simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + // Save Isis R session engine.saveRData(outputdirectory.getParentFile(), outputdirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-05-29 09:27:28 UTC (rev 288) @@ -238,9 +238,9 @@ "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + // Save Isis R session + engine.saveRData(outputDirectory.getParentFile(), + outputDirectory.getName()); } catch (RException eee) { @@ -376,9 +376,16 @@ } //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(firstStorageName)){ + engine.remove(object); + } + } + //Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-05-29 09:27:28 UTC (rev 288) @@ -347,9 +347,15 @@ } //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(firstStorageName)){ + engine.remove(object); + } + } + //Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRFast.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-05-29 09:27:28 UTC (rev 288) @@ -333,6 +333,13 @@ //Rename R objects for saving purpose renameObjects(engine, simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-05-29 09:27:28 UTC (rev 288) @@ -6,15 +6,15 @@ * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as - * published by the Free Software Foundation, either version 2 of the + * published by the Free Software Foundation, either version 2 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public + * + * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-2.0.html>. * #L% @@ -22,16 +22,8 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - +import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityAnalysis; import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; @@ -41,17 +33,25 @@ import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.util.Doc; +import org.nuiton.j2r.REngine; +import org.nuiton.j2r.RException; +import org.nuiton.j2r.RProxy; +import org.nuiton.j2r.types.RDataFrame; +import java.io.File; +import java.util.List; + /** * Implementation of Morris method using R. - * + * * @author jcouteau * @version $Revision$ - * + * * Last update : $Date$ By : * $Author$ */ -public class SensitivityCalculatorRMorris extends AbstractSensitivityAnalysis { +public class SensitivityCalculatorRMorris + extends AbstractSensitivityAnalysis { @Doc("Integer giving the number of repetitions of the design, i.e. the number of elementary effect computed per factor. (Default value : 4)") public int param_r = 4; @@ -62,7 +62,7 @@ /** * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs * continus. - * + * * @return <tt>true</tt> s'il sait la gerer */ @Override @@ -72,14 +72,14 @@ @Override public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { + throws SensitivityException { setIsisFactorsR(plan, outputDirectory); RDataFrame dataFrame; int nbExperiments; int factorNumber = plan.getFactors().size(); - + SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Factor> factors = plan.getFactors(); @@ -119,8 +119,8 @@ } String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s," + - "design=list(type=\"oat\",levels=c(%s),grid.jump=c(%s))," + - "binf=c(%s),bsup=c(%s))"; + "design=list(type=\"oat\",levels=c(%s),grid.jump=c(%s))," + + "binf=c(%s),bsup=c(%s))"; String rCall = String.format(rInstruction, factorNames, param_r, levels, gridJump, binf, bsup); @@ -129,12 +129,16 @@ rCall = editRInstruction(rCall); } + REngine engine = null; + try { - REngine engine = new RProxy(); + engine = new RProxy(); + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + outputDirectory.getName()); // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -157,12 +161,12 @@ dataFrame = (RDataFrame) engine.eval("expPlan"); dataFrame.setVariable("expPlan"); - nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); + nbExperiments = (Integer)engine.eval("dim(expPlan)[1]"); String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; String distribution = ""; String parameters = ""; @@ -189,7 +193,7 @@ "\"call\"=call)"); engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + "\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(expPlan)"); engine.voidEval("attr(isis.simule,\"nomModel\")<-" + "\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); @@ -221,17 +225,21 @@ @Override public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { + File outputDirectory) throws SensitivityException { SimulationStorage storage = simulationStorages.get(0); String simulationName = storage.getName().replaceAll("-", ""); + REngine engine = null; + try { - REngine engine = new RProxy(); - + engine = new RProxy(); + + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + outputDirectory.getName()); // Call R // Load sensitivity package into R (if package already loaded, @@ -278,11 +286,11 @@ //creating isis.methodAnalyse engine.voidEval("isis.methodAnalyse<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"isis.simule\"=isis.simule," + - "\"call_method\"=\"tell(a,y=" + name + ")" + "\"," + - "\"analysis_result\"=a)"); + //"\"isis.factors\"=isis.factors," + + //"\"isis.factor.distribution\"=isis.factor.distribution," + + "\"isis.simule\"=isis.simule," + + "\"call_method\"=\"tell(a,y=" + name + ")" + "\"," + + "\"analysis_result\"=a)"); //setting isis.methodAnalyse attributes engine.voidEval("attr(isis.methodAnalyse,\"nomModel\")<-" + @@ -324,9 +332,16 @@ //Rename R objects for saving purpose renameObjects(engine,simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + outputDirectory.getName()); } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); @@ -337,7 +352,7 @@ @Override public String getDescription() { return "Implementation of Morris method using R (needs the sensitivity" + - " package to work)"; + " package to work)"; } } Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-05-29 09:27:28 UTC (rev 288) @@ -381,6 +381,13 @@ //Rename R objects for saving purpose renameObjects(engine, simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + engine.terminate(); } catch (Exception e) { Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-05-29 09:27:28 UTC (rev 288) @@ -23,6 +23,7 @@ package sensitivityanalysis; import java.io.File; +import java.lang.String; import java.util.List; import fr.ifremer.isisfish.export.SensitivityExport; @@ -216,6 +217,11 @@ } rInstruction += ")"; engine.voidEval(rInstruction); + + // Clean RData + for (Factor factor:factors) { + engine.remove(factor.getName().replaceAll(" ", "")); + } // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), @@ -368,6 +374,14 @@ //Rename R objects for saving purpose renameObjects(engine, simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + + // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRSobol.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-05-29 09:27:28 UTC (rev 288) @@ -318,8 +318,15 @@ } //Rename R objects for saving purpose - renameObjects(engine, simulationName); + renameObjects(engine, simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityanalysis/SensitivityCalculatorRegularFractions.java =================================================================== --- branches/4.1/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-05-29 09:27:28 UTC (rev 288) @@ -372,6 +372,13 @@ //Rename R objects for saving purpose renameObjects(engine,simulationName); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); Modified: branches/4.1/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- branches/4.1/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -109,6 +109,7 @@ } line = reader.readLine(); } + reader.close(); for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { @@ -127,6 +128,7 @@ } } } + out.write(Double.toString(biomass / referenceBiomass)); } Property changes on: branches/4.1/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java ___________________________________________________________________ Deleted: svn:mergeinfo - Modified: branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -119,6 +119,7 @@ line = reader.readLine(); } + reader.close(); for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { @@ -152,6 +153,7 @@ } } } + out.write(Double.toString((biomass / firstbiomass) / (biomassReference / firstBiomassReference))); } Property changes on: branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java ___________________________________________________________________ Deleted: svn:mergeinfo - Modified: branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,6 +32,7 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; + import scripts.ResultName; import java.io.Writer; Property changes on: branches/4.1/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java ___________________________________________________________________ Deleted: svn:mergeinfo - Modified: branches/4.1/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- branches/4.1/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-04-26 16:22:33 UTC (rev 287) +++ branches/4.1/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-05-29 09:27:28 UTC (rev 288) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,6 +32,7 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; + import scripts.ResultName; import java.io.Writer; Property changes on: branches/4.1/sensitivityexports/SensitivitySpawningBiomassY2.java ___________________________________________________________________ Deleted: svn:mergeinfo -

1 0

r287 - trunk
by echatellier＠users.forge.codelutin.com April 26, 2012

April 26, 2012

Author: echatellier Date: 2012-04-26 18:22:33 +0200 (Thu, 26 Apr 2012) New Revision: 287 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/287 Log: Prepare next iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-04-26 16:21:51 UTC (rev 286) +++ trunk/pom.xml 2012-04-26 16:22:33 UTC (rev 287) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.1.0</version> + <version>4.1.1</version>  <description>Data for Isis-fish</description> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.0.0</version> + <version>4.1.0.1-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0