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

r276 - tags/4.0.0/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 29, 2012

Feb. 29, 2012

Author: jcouteau Date: 2012-02-29 11:33:39 +0100 (Wed, 29 Feb 2012) New Revision: 276 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/276 Log: Clean RData for sensitivity analyses Modified: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRDOptimal.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRFast.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRMorris.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRSobol.java tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRegularFractions.java Modified: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,22 +22,21 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - +import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.sensitivity.*; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; - -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.simulator.SimulationParameter; 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; +import org.nuiton.j2r.REngine; +import org.nuiton.j2r.RProxy; +import java.io.File; +import java.util.List; + /** * Implementation of ExpandGrid method using Java * @@ -366,6 +365,13 @@ //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:33:39 UTC (rev 276) @@ -80,6 +80,9 @@ try { REngine engine = new RProxy(); + //Clear session + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -258,6 +261,9 @@ REngine engine = new RProxy(); + //Clear session + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -379,6 +385,14 @@ 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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-02-29 10:33:39 UTC (rev 276) @@ -80,6 +80,9 @@ try { REngine engine = new RProxy(); + //Clear session + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -235,6 +238,9 @@ REngine engine = new RProxy(); + //Clear session + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -347,9 +353,16 @@ } //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRFast.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,24 +22,23 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - -import fr.ifremer.isisfish.simulator.sensitivity.*; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; - import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.*; 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; +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 Fast method using R. * @@ -113,7 +112,9 @@ REngine engine = new RProxy(); + //Clear session engine.clearSession(); + engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -333,6 +334,14 @@ //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,25 +22,19 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - +import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.*; +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 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; -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.util.Doc; +import java.io.File; +import java.util.List; /** * Implementation of Morris method using R. @@ -132,6 +126,9 @@ try { REngine engine = new RProxy(); + //Clear session + engine.clearSession(); + //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), outputDirectory.getName()); @@ -228,6 +225,8 @@ try { REngine engine = new RProxy(); + + engine.clearSession(); //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), @@ -324,6 +323,13 @@ //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,25 +22,19 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; - import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.simulator.SimulationParameter; -import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityAnalysis; -import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; -import fr.ifremer.isisfish.simulator.sensitivity.Factor; -import fr.ifremer.isisfish.simulator.sensitivity.Scenario; -import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; -import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; +import fr.ifremer.isisfish.simulator.sensitivity.*; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.util.Doc; +import org.nuiton.j2r.REngine; +import org.nuiton.j2r.RProxy; import org.nuiton.j2r.types.RDataFrame; +import java.io.File; +import java.util.List; + /** * Implementation of Optimum Latin Hypercube method using R. * @@ -381,6 +375,13 @@ //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,24 +22,18 @@ package sensitivityanalysis; -import java.io.File; -import java.util.List; - +import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.simulator.SimulationParameter; +import fr.ifremer.isisfish.simulator.sensitivity.*; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.util.Doc; import org.nuiton.j2r.REngine; 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; -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.util.Doc; +import java.io.File; +import java.util.List; /** * Implementation of Random Latin Hypercube method using R. @@ -372,6 +366,13 @@ engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName()); + //Clean temporary R objects + for (String object:engine.ls()) { + if (!object.startsWith(simulationName)){ + engine.remove(object); + } + } + engine.terminate(); } catch (Exception e) { Modified: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRSobol.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,26 +22,19 @@ 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.RProxy; - -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; -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.*; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.util.Doc; +import org.nuiton.j2r.REngine; +import org.nuiton.j2r.RProxy; import org.nuiton.j2r.types.RDataFrame; +import java.io.File; +import java.util.List; + /** * Implementation of Sobol method using R. * @@ -318,8 +311,15 @@ } //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: tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRegularFractions.java =================================================================== --- tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-02-29 10:11:19 UTC (rev 275) +++ tags/4.0.0/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-02-29 10:33:39 UTC (rev 276) @@ -22,30 +22,23 @@ 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; -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.*; 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; +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; + public class SensitivityCalculatorRegularFractions extends AbstractSensitivityAnalysis { @@ -372,6 +365,14 @@ //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());

1 0

r275 - trunk/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 29, 2012

Feb. 29, 2012

Author: jcouteau Date: 2012-02-29 11:11:19 +0100 (Wed, 29 Feb 2012) New Revision: 275 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/275 Log: Fix build 2 le retour Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:03:35 UTC (rev 274) +++ trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:11:19 UTC (rev 275) @@ -384,7 +384,7 @@ //Clean temporary R objects for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ + if (!object.startsWith(firstStorageName)){ engine.remove(object); } }

1 0

r274 - trunk/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 29, 2012

Feb. 29, 2012

Author: jcouteau Date: 2012-02-29 11:03:35 +0100 (Wed, 29 Feb 2012) New Revision: 274 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/274 Log: Fix compil Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-28 16:26:12 UTC (rev 273) +++ trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:03:35 UTC (rev 274) @@ -241,18 +241,11 @@ //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()); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -386,9 +379,16 @@ } //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + + //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());

1 0

r273 - trunk/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 28, 2012

Feb. 28, 2012

Author: jcouteau Date: 2012-02-28 17:26:12 +0100 (Tue, 28 Feb 2012) New Revision: 273 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/273 Log: Clean AS Modified: trunk/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java trunk/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java trunk/sensitivityanalysis/SensitivityCalculatorRFast.java trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java trunk/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java trunk/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java trunk/sensitivityanalysis/SensitivityCalculatorRSobol.java trunk/sensitivityanalysis/SensitivityCalculatorRegularFractions.java Modified: trunk/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-28 16:26:12 UTC (rev 273) @@ -238,6 +238,16 @@ "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + //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: trunk/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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]]"); @@ -213,6 +217,10 @@ } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); + } finally { + if (engine != null) { + engine.terminate(); + } } return thisExperiment; @@ -221,17 +229,21 @@ @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 +290,11 @@ //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\")<-" + @@ -324,12 +336,23 @@ //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); + } finally { + if (engine != null) { + engine.terminate(); + } } } @@ -337,7 +360,7 @@ @Override public String getDescription() { return "Implementation of Morris method using R (needs the sensitivity" + - " package to work)"; + " package to work)"; } } Modified: trunk/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRSobol.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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: trunk/sensitivityanalysis/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-02-28 16:05:51 UTC (rev 272) +++ trunk/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-02-28 16:26:12 UTC (rev 273) @@ -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());

1 0

r272 - branches
by echatellier＠users.forge.codelutin.com Feb. 28, 2012

Feb. 28, 2012

Author: echatellier Date: 2012-02-28 17:05:51 +0100 (Tue, 28 Feb 2012) New Revision: 272 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/272 Log: New branche for Added: branches/4.1/

1 0

r271 - trunk
by echatellier＠users.forge.codelutin.com Feb. 28, 2012

Feb. 28, 2012

Author: echatellier Date: 2012-02-28 17:04:50 +0100 (Tue, 28 Feb 2012) New Revision: 271 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/271 Log: Update deps Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2011-12-09 16:29:25 UTC (rev 270) +++ trunk/pom.xml 2012-02-28 16:04:50 UTC (rev 271) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.0.0.0-SNAPSHOT</version> + <version>4.0.0.3-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r270 - trunk/exports
by jcouteau＠users.forge.codelutin.com Dec. 9, 2011

Dec. 9, 2011

Author: jcouteau Date: 2011-12-09 17:29:25 +0100 (Fri, 09 Dec 2011) New Revision: 270 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/270 Log: #411 : Garder l'info strategy dans les exports de captures - Nouveaux exports avec strat?\195?\169gie Added: trunk/exports/CapturesNombreStrategies.java trunk/exports/CapturesPoidsStrategies.java Modified: trunk/exports/CapturesNombre.java trunk/exports/CapturesPoids.java Modified: trunk/exports/CapturesNombre.java =================================================================== --- trunk/exports/CapturesNombre.java 2011-12-02 19:19:55 UTC (rev 269) +++ trunk/exports/CapturesNombre.java 2011-12-09 16:29:25 UTC (rev 270) @@ -21,16 +21,6 @@ */ package exports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -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 fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; @@ -38,12 +28,22 @@ import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.TimeStep; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + /** * CapturesNombre.java * - * Created: 23 novembre 2006 - * + * Export des captures en nombre de la forme : + * Population ; Métier ; Groupe ; Zone ; Pas de temps ; Valeur + * * @author anonymous <anonymous(a)labs.libre-entreprise.org> * @version $Revision: 1.4 $ * Added: trunk/exports/CapturesNombreStrategies.java =================================================================== --- trunk/exports/CapturesNombreStrategies.java (rev 0) +++ trunk/exports/CapturesNombreStrategies.java 2011-12-09 16:29:25 UTC (rev 270) @@ -0,0 +1,110 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * %% + * 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 exports; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.types.TimeStep; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + +/** + * CapturesNombreStrategies.java + * + * Export des captures en nombre de la forme : + * Population ; Stratégie ; Métier ; Groupe ; Zone ; Pas de temps ; Valeur + * + * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * @version $Revision: 1.4 $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ + */ +public class CapturesNombreStrategies implements Export { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(CapturesNombre.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + @Override + public String getExportFilename() { + return "CapturesNombreStrategies"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String getDescription() { + return _("Export les captures en nombre de la simulation. tableau pop;strategie;metier;id;zone;nombre"); + } + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + TimeStep lastStep = simulation.getResultStorage().getLastStep(); + + for (Population pop : simulation.getParameter().getPopulations()) { + for (TimeStep step = new TimeStep(0); !step.after(lastStep); step = step + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(step, + pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + if (mat != null) { // can be null if simulation is stopped before last year simulation + //mat = mat.sumOverDim(0); //sum on strategy + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; + Strategy strategy = (Strategy) sems[0]; + + double val = i.getValue(); + out.write(pop.getName() + ";" + strategy.getName() + ";" + + metier.getName() + ";" + group.getId() + ";" + + zone.getName() + ";" + step.getStep() + ";" + + val + "\n"); + } + } + } + } + } +} Modified: trunk/exports/CapturesPoids.java =================================================================== --- trunk/exports/CapturesPoids.java 2011-12-02 19:19:55 UTC (rev 269) +++ trunk/exports/CapturesPoids.java 2011-12-09 16:29:25 UTC (rev 270) @@ -21,16 +21,6 @@ */ package exports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -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 fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; @@ -38,11 +28,21 @@ import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.types.TimeStep; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + /** * CapturesPoids.java * - * Created: 23 novembre 2006 + * Export des captures en poids de la forme : + * Population ; Métier ; Groupe ; Zone ; Pas de temps ; Valeur * * @author anonymous <anonymous(a)labs.libre-entreprise.org> * @version $Revision: 1.4 $ Added: trunk/exports/CapturesPoidsStrategies.java =================================================================== --- trunk/exports/CapturesPoidsStrategies.java (rev 0) +++ trunk/exports/CapturesPoidsStrategies.java 2011-12-09 16:29:25 UTC (rev 270) @@ -0,0 +1,110 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * %% + * 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 exports; + +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.types.TimeStep; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + +/** + * CapturesPoidsStrategies.java + * + * Export des captures en poids de la forme : + * Population ; Stratégie ; Métier ; Groupe ; Zone ; Pas de temps ; Valeur + * + * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * @version $Revision: 1.4 $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ by : $Author: bpoussin $ + */ +public class CapturesPoidsStrategies implements Export { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(CapturesPoids.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + @Override + public String getExportFilename() { + return "CapturesPoidsStrategies"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String getDescription() { + return _("Export les captures en poids de la simulation. tableau pop;strategie;metier;id;zone;nombre"); + } + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + TimeStep lastStep = simulation.getResultStorage().getLastStep(); + + for (Population pop : simulation.getParameter().getPopulations()) { + for (TimeStep step = new TimeStep(0); !step.after(lastStep); step = step + .next()) { + MatrixND mat = simulation.getResultStorage().getMatrix(step, + pop, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + if (mat != null) { // can be null if simulation is stopped before last year simulation + //mat = mat.sumOverDim(0); //sum on strategy + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Metier metier = (Metier) sems[1]; + PopulationGroup group = (PopulationGroup) sems[2]; + Zone zone = (Zone) sems[3]; + Strategy strategy = (Strategy) sems[0]; + + double val = i.getValue(); + out.write(pop.getName() + ";" + strategy.getName() + ";" + + metier.getName() + ";" + group.getId() + ";" + + zone.getName() + ";" + step.getStep() + ";" + + val + "\n"); + } + } + } + } + } +}

1 0

r269 - tags
by echatellier＠users.forge.codelutin.com Dec. 2, 2011

Dec. 2, 2011

Author: echatellier Date: 2011-12-02 20:19:55 +0100 (Fri, 02 Dec 2011) New Revision: 269 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/269 Log: Create tag 4.0.0 Added: tags/4.0.0/

1 0

r268 - trunk/simulators
by jcouteau＠users.forge.codelutin.com Nov. 30, 2011

Nov. 30, 2011

Author: jcouteau Date: 2011-11-30 14:02:08 +0100 (Wed, 30 Nov 2011) New Revision: 268 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/268 Log: Fix build Modified: trunk/simulators/DefaultSimulator.java Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2011-11-30 09:37:50 UTC (rev 267) +++ trunk/simulators/DefaultSimulator.java 2011-11-30 13:02:08 UTC (rev 268) @@ -22,21 +22,6 @@ package simulators; -import static org.nuiton.i18n.I18n._; -import static org.nuiton.i18n.I18n.n_; - -import java.util.List; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -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 scripts.SiMatrix; import fr.ifremer.isisfish.IsisFishException; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.entities.Metier; @@ -51,9 +36,23 @@ import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.Simulator; -import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.TimeStep; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +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 scripts.SiMatrix; +import java.util.List; + +import static org.nuiton.i18n.I18n._; +import static org.nuiton.i18n.I18n.n_; + /** * DefaultSimulator.java * @@ -80,7 +79,7 @@ SimulationControl control = context.getSimulationControl(); int lastYear = param.getNumberOfYear(); int lastStep = lastYear * Month.NUMBER_OF_MONTH; - TimeStep step = control.getTimeStep(); + TimeStep step = control.getStep(); ResultManager resManager = context.getResultManager(); TopiaContext db = context.getDB(); @@ -132,7 +131,7 @@ break; } - control.setTimeStep(step); + control.setStep(step); control.setProgress(step.getStep()); control.setText(_("begin step " + step)); @@ -375,7 +374,7 @@ PopulationSeasonInfo info = pop.getPopulationSeasonInfo(month); // group change - MatrixND CA = null; + MatrixND CA; if (step.getStep() == 0) { CA = MatrixFactory.getInstance().matrixId( pop.sizePopulationGroup() * pop.sizePopulationZone()); @@ -440,7 +439,7 @@ resManager.addResult(step, pop, biomassBM); } - MatrixND abundance = N; + 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 @@ -512,7 +511,7 @@ } /** - * @param date + * @param step * @param resManager * @throws IsisFishException * @throws TopiaException

1 0

r267 - trunk/sensitivityexports
by jcouteau＠users.forge.codelutin.com Nov. 30, 2011

Nov. 30, 2011

Author: jcouteau Date: 2011-11-30 10:37:50 +0100 (Wed, 30 Nov 2011) New Revision: 267 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/267 Log: #555 : Remplacer reproductionRate par MaturityOgive dans l'export d'AS SpawningBiomass Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java trunk/sensitivityexports/SensitivitySpawningBiomassY2.java Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,22 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.File; -import java.io.Writer; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -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 org.nuiton.topia.TopiaContext; -import org.nuiton.util.ReverseFileReader; -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -44,7 +28,22 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +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 org.nuiton.topia.TopiaContext; +import org.nuiton.util.ReverseFileReader; +import scripts.ResultName; +import java.io.File; +import java.io.Writer; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassReferenceY8 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -78,7 +77,7 @@ Map<Integer, Double> map =new HashMap<Integer,Double>(); for (PopulationGroup group:groups) { - map.put(group.getId(),group.getReproductionRate()); + map.put(group.getId(),group.getMaturityOgive()); } tx.closeContext(); @@ -123,7 +122,7 @@ PopulationGroup group = (PopulationGroup) sems[1]; TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) { - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,22 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.File; -import java.io.Writer; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -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 org.nuiton.topia.TopiaContext; - -import org.nuiton.util.ReverseFileReader; -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -44,7 +28,22 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +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 org.nuiton.topia.TopiaContext; +import org.nuiton.util.ReverseFileReader; +import scripts.ResultName; +import java.io.File; +import java.io.Writer; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassRelativeReferenceY11 implements SensitivityExport { @@ -83,7 +82,7 @@ Map<Integer, Double> map =new HashMap<Integer,Double>(); for (PopulationGroup group:groups) { - map.put(group.getId(),group.getReproductionRate()); + map.put(group.getId(),group.getMaturityOgive()); } tx.closeContext(); @@ -134,7 +133,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(firstStep)) { firstbiomass += i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } @@ -148,7 +147,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) { biomass = biomass + i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,16 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -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 fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -38,7 +28,16 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassRelativeY5 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -72,7 +71,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(firstStep)) { firstbiomass += i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } @@ -85,7 +84,7 @@ PopulationGroup group = (PopulationGroup) sems[1]; TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,16 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -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 fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -38,7 +28,16 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +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 java.io.Writer; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassY2 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -69,7 +68,7 @@ TimeStep step = (TimeStep) sems[0]; PopulationGroup group = (PopulationGroup) sems[1]; if (step.equals(lastStep)) { - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } }

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