/* * #%L * IsisFish data * %% * Copyright (C) 2009 - 2014 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 * published by the Free Software Foundation, either version 3 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 * . * #L% */ package simulators; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import fr.ifremer.isisfish.simulator.SimulationContext; import scripts.SiMatrix; import scripts.SiMatrixEffortByCell; import scripts.SiMatrixEffortByCell_Sid; import org.nuiton.topia.TopiaException; import fr.ifremer.isisfish.IsisFishException; import fr.ifremer.isisfish.datastore.StorageException; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationSeasonInfo; import fr.ifremer.isisfish.rule.Rule; import fr.ifremer.isisfish.simulator.MetierMonitor; import fr.ifremer.isisfish.simulator.PopulationMonitor; import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.RuleMonitor; import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.Simulator; import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; import org.nuiton.math.matrix.MatrixFactory; import org.nuiton.math.matrix.MatrixND; import org.nuiton.topia.TopiaContext; import org.nuiton.topia.TopiaException; import scripts.GravityModel; import scripts.ResultName; import java.util.List; import static org.nuiton.i18n.I18n.t; import static org.nuiton.i18n.I18n.n; /** * Simulateur qui fixe la valeur de effortByCell a true pour force * l'utilisation des calculs par cellule plutot que par zone. * * @author poussin */ public class SimulatorEffortByCell_Sid extends DefaultSimulator { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(SimulatorEffortByCell_Sid.class); protected SiMatrixEffortByCell_Sid siMatrix; @Override protected SiMatrix newSiMatrix(SimulationContext context) throws TopiaException { siMatrix = new SiMatrixEffortByCell_Sid(context); return siMatrix; } /** * Use custom "siMatrix" instead of provided _siMatrix. */ protected void computeMonth(SimulationContext context, SiMatrix _siMatrix, TimeStep step, Population pop) throws IsisFishException, TopiaException { // to add result ResultManager resManager = context.getResultManager(); PopulationMonitor popMon = context.getPopulationMonitor(); MatrixND N = popMon.getN(pop); if (log.isInfoEnabled()) { log.info("====================== begin " + step + " - " + pop + " =========================== " + System.currentTimeMillis()); //log.info("N: " + N); } // add N and biomass result now, before computation // N is reassigned during computation resManager.addResult(step, pop, N); MatrixND biomass = siMatrix.matrixBiomass(N, pop, step); if (resManager.isEnabled(ResultName.MATRIX_BIOMASS)) { resManager.addResult(step, pop, biomass); } Month month = step.getMonth(); PopulationSeasonInfo info = pop.getPopulationSeasonInfo(month); // group change MatrixND CA; if (step.getStep() == 0) { CA = MatrixFactory.getInstance().matrixId( pop.sizePopulationGroup() * pop.sizePopulationZone()); } else { CA = info.getGroupChangeMatrix(month); } log.debug("CA: " + CA); //migration MatrixND M = info.getMigrationMatrix(month, N); //log.info(M); //log.debug("M: " + M); //emigration MatrixND EM = info.getEmigrationMatrix(month, N); //log.debug("EM: " + EM); //immigration MatrixND IM = info.getImmigrationMatrix(month, N).transpose(); //log.debug("IM: " + IM); // pour les premiers calculs on met N en une matrice 1D MatrixND N1D = pop.N2DToN1D(N); //log.debug("N1D: " + N1D); MatrixND tmp0 = N1D.mult(CA); MatrixND tmp1 = M.minus(EM); MatrixND tmp2 = tmp0.mult(tmp1); MatrixND tmp3 = tmp2.add(IM); //log.debug("N1D after mig: " + tmp3); // On reconvertie en une matrice Semantique N = pop.split2D(tmp3); //log.debug("N after mig: " + N); // reproduction MatrixND R = info.getReproductionMatrix(month, N); //log.debug("R: " + R); // ajout de la matrice R dans le suivi de la pop comme etant // la reproduction pour le mois courant. popMon.setReproduction(step, pop, N, biomass, R); // recrutement MatrixND recruitment = popMon.getRecruitment(step, pop); //log.debug("recruitment: " + recruitment); // mortalite de la reproduction popMon.applyReproductionMortality(pop); N = N.add(recruitment); //log.info("rec matrice"+recruitment); //log.debug("N after recru: " + N); if (resManager.isEnabled(ResultName.MATRIX_ABUNDANCE_BEGIN_MONTH)) { MatrixND abondanceBM = siMatrix.matrixAbondanceBeginMonth(N, pop, step); resManager.addResult(step, pop, abondanceBM); } if (resManager.isEnabled(ResultName.MATRIX_BIOMASS_BEGIN_MONTH)) { MatrixND biomassBM = siMatrix.matrixBiomassBeginMonth(N, pop, step); resManager.addResult(step, pop, biomassBM); } MatrixND abundance; // compute fishing matrix only if there are one or more strategy if (siMatrix.getStrategies(step).size() > 0) { // compute some Matrix and add result // this matrix is necessary for PopulationMonitor.holdCatch (reused in rule) MatrixND catchPerStrategyMetPerZonePop; if (isEffortByCell(context)) { abundance = siMatrix.matrixAbundance(N, pop, step); catchPerStrategyMetPerZonePop = siMatrix .matrixCatchPerStrategyMetPerZonePop(N, pop, step); } else { // en zone MatrixND matrixFishingMortality = siMatrix .matrixFishingMortality(step, pop); resManager.addResult(step, pop, matrixFishingMortality); abundance = siMatrix.matrixAbundance(N, pop, step, matrixFishingMortality); // this matrix is necessary for matrixCatchPerStrategyMet MatrixND catchRatePerStrategyMet = siMatrix .matrixCatchRatePerStrategyMetPerZone(pop, step, matrixFishingMortality); resManager.addResult(step, pop, catchRatePerStrategyMet); catchPerStrategyMetPerZonePop = siMatrix .matrixCatchPerStrategyMetPerZone(N, pop, step, catchRatePerStrategyMet); } popMon.holdCatch(pop, catchPerStrategyMetPerZonePop); resManager.addResult(step, pop, catchPerStrategyMetPerZonePop); if (resManager .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP)) { MatrixND catchWeightPerStrategyMet = siMatrix .matrixCatchWeightPerStrategyMetPerZonePop(step, pop, catchPerStrategyMetPerZonePop); resManager.addResult(step, pop, catchWeightPerStrategyMet); } if (isEffortByCell(context)) { MatrixND catchPerStrategyMetPerZoneMet = siMatrix .matrixCatchPerStrategyMetPerZoneMet(N, pop, step); resManager.addResult(step, pop, catchPerStrategyMetPerZoneMet); if (resManager .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET)) { MatrixND catchWeightPerStrategyMet = siMatrix .matrixCatchWeightPerStrategyMetPerZoneMet(step, pop, catchPerStrategyMetPerZoneMet); resManager.addResult(step, pop, catchWeightPerStrategyMet); } } 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); } log.debug("abundance: " + abundance); if (resManager.isEnabled(ResultName.MATRIX_ABUNDANCE_END_MONTH)) { MatrixND abondanceEM = siMatrix.matrixAbondanceEndMonth(abundance, pop, step); resManager.addResult(step, pop, abondanceEM); } if (resManager.isEnabled(ResultName.MATRIX_BIOMASS_END_MONTH)) { MatrixND biomassEM = siMatrix.matrixBiomassEndMonth(abundance, pop, step); resManager.addResult(step, pop, biomassEM); } // Keep new N popMon.setN(pop, abundance); log.debug("====================== end " + step + " - " + pop + " ==========================="); } }