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());