r3968 - in branches/4.0.1/src: main/java/fr/ifremer/isisfish/simulator main/java/fr/ifremer/isisfish/vcs main/resources/templates/script test/java/fr/ifremer/isisfish/simulator test/java/fr/ifremer/isisfish/simulator/sensitivity test/java/fr/ifremer/isisfish/vcs test/resources/test-database/sensitivityanalysis
Author: echatellier Date: 2014-04-17 17:26:04 +0200 (Thu, 17 Apr 2014) New Revision: 3968 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3968 Log: Fix all tests Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/Optimization.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java branches/4.0.1/src/main/resources/templates/script/optimization.ftl branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/SimulationParameterTest.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/FactorTest.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/Optimization.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/Optimization.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/Optimization.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -80,7 +80,7 @@ /** * Cette methode est appelee lorsqu'il n'y a plus de simulation a faire - * (init ou getNextSimulation n'ont pas fait appel a context.addSimulation) + * (init ou nextSimulation n'ont pas fait appel a context.addSimulation) * @param context */ void finish(OptimizationContext context) throws Exception; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/vcs/VCSSVN.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -809,9 +809,9 @@ SVNDiffClient diffClient = getSVNManager().getDiffClient(); diffClient.doDiff(file, // File path1, - SVNRevision.WORKING, // SVNRevision rN, + SVNRevision.HEAD, // SVNRevision rN, file, // File path2, - SVNRevision.HEAD, // SVNRevision rM, + SVNRevision.WORKING, // SVNRevision rM, SVNDepth.IMMEDIATES, // SVNDepth depth, false, // boolean useAncestry, byte1, // OutputStream result, Modified: branches/4.0.1/src/main/resources/templates/script/optimization.ftl =================================================================== --- branches/4.0.1/src/main/resources/templates/script/optimization.ftl 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/main/resources/templates/script/optimization.ftl 2014-04-17 15:26:04 UTC (rev 3968) @@ -106,28 +106,27 @@ /** * La premiere generation doit etre construite dans cette methode - * via des appels a context.newSimulation(...) + * dans l'init. * * @param context */ public void firstSimulation(OptimizationContext context) throws Exception { - // TODO + } /** * Génère une nouvelle série de simulation suivant le context d'optimisation. - * Pour cela vous devez appeler context.newSimulation(...) pour ajouter - * des simulations pour la prochaine generation. - * + * * @param context context */ - public void getNextSimulation(OptimizationContext context) { - // TODO + public void nextSimulation(OptimizationContext context) { + } /** - * Cette methode est appelee après chaque serie de simulation - * soit apres firstSimulation et nextSimulation + * Cette methode est appelee après chaque serie de simulation soit apres firstSimulation et + * nextSimulation. + * * @param context */ public void endSimulation(OptimizationContext context) { @@ -136,9 +135,10 @@ /** * Cette methode est appelee lorsqu'il n'y a plus de simulation a faire - * (firstSimulation ou nextSimulation n'ont pas fait appel a context.newSimulation) + * (init ou nextSimulation n'ont pas fait appel a context.addSimulation) * @param context */ - public void finish(OptimizationContext context) throws Exception; - + public void finish(OptimizationContext context) throws Exception { + + } } Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/SimulationParameterTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/SimulationParameterTest.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/SimulationParameterTest.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -65,8 +65,9 @@ Assert.assertEquals("", params.getRegionName()); Assert.assertEquals(1, params.getNumberOfYear()); Assert.assertEquals("DefaultSimulator.java", params.getSimulatorName()); - Assert.assertTrue(params.getUseOptimization()); + Assert.assertTrue(params.getUseCache()); Assert.assertFalse(params.getUseStatistic()); + Assert.assertFalse(params.getUseOptimization()); Assert.assertTrue(params.getStrategies().isEmpty()); Assert.assertTrue(params.getPopulations().isEmpty()); // Not easy to test it Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/FactorTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/FactorTest.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/FactorTest.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -134,128 +134,6 @@ * @see MatrixND */ @Test - public void testMatrixContinuousFactor() { - - // matrix 1 - MatrixND matrix1 = MatrixFactory.getInstance().create("test1", - new int[] { 3, 2 }, new String[] { "col1", "col2" }); - matrix1.setValue(new int[] { 0, 0 }, 1); - matrix1.setValue(new int[] { 0, 1 }, -14); - matrix1.setValue(new int[] { 1, 0 }, 21); - matrix1.setValue(new int[] { 1, 1 }, 2); - matrix1.setValue(new int[] { 2, 0 }, 3); - matrix1.setValue(new int[] { 2, 1 }, -1); - - // matrix minBound - MatrixND minBound = MatrixFactory.getInstance().create("test1", - new int[]{3, 2}, new String[]{"col1", "col2"}); - minBound.setValue(new int[]{0, 0}, 0.9); - minBound.setValue(new int[]{0, 1}, -15.4); - minBound.setValue(new int[]{1, 0}, 18.9); - minBound.setValue(new int[]{1, 1}, 1.8); - minBound.setValue(new int[]{2, 0}, 2.7); - minBound.setValue(new int[]{2, 1}, -1.1); - - // matrix maxBound - MatrixND maxBound = MatrixFactory.getInstance().create("test1", - new int[]{3, 2}, new String[]{"col1", "col2"}); - maxBound.setValue(new int[]{0, 0}, 1.1); - maxBound.setValue(new int[]{0, 1}, -12.6); - maxBound.setValue(new int[]{1, 0}, 23.1); - maxBound.setValue(new int[]{1, 1}, 2.2); - maxBound.setValue(new int[]{2, 0}, 3.3); - maxBound.setValue(new int[]{2, 1}, -0.9); - - // factor - Factor factor = new Factor("testmatrix"); - ContinuousDomain domain = new ContinuousDomain(Distribution.QUNIFPC); - domain.addDistributionParam("reference", matrix1); - domain.addDistributionParam("coefficient", 0.1); - factor.setDomain(domain); - factor.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); - factor.setValueForIdentifier(0.1); - - Assert.assertEquals(0.92, ((MatrixND)factor.getValue()).getValue(new int[] { 0, 0 }),0.0000001); - Assert.assertEquals(2.76, ((MatrixND)factor.getValue()).getValue(new int[] { 2, 0 }),0.0000001); - Assert.assertEquals(0.1, (Double)factor.getDisplayedValue(),0); - - // matrix 2 - MatrixND matrix2 = MatrixFactory.getInstance().create("test1", - new int[] { 3, 2 }, new String[] { "col1", "col2" }); - matrix2.setValue(new int[] { 0, 0 }, 1); - matrix2.setValue(new int[] { 0, 1 }, -14); - matrix2.setValue(new int[] { 1, 0 }, 21); - matrix2.setValue(new int[] { 1, 1 }, 2); - matrix2.setValue(new int[] { 2, 0 }, 3); - matrix2.setValue(new int[] { 2, 1 }, -1); - - // factor 2 - Factor factor2 = new Factor("testmatrix"); - ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); - domain2.addDistributionParam("reference", matrix2); - domain2.addDistributionParam("coefficient", 0.1); - factor2.setDomain(domain2); - factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); - factor2.setValueForIdentifier(0.2); - - Assert.assertEquals(0.94, ((MatrixND)factor2.getValue()).getValue(new int[] { 0, 0 }),0.0000001); - Assert.assertEquals(2.82, ((MatrixND)factor2.getValue()).getValue(new int[] { 2, 0 }),0.0000001); - - // matrix 3 - MatrixND matrix3 = MatrixFactory.getInstance().create("test1", - new int[] { 3, 2 }, new String[] { "col1", "col2" }); - matrix3.setValue(new int[] { 0, 0 }, 1); - matrix3.setValue(new int[] { 0, 1 }, -14); - matrix3.setValue(new int[] { 1, 0 }, 21); - matrix3.setValue(new int[] { 1, 1 }, 2); - matrix3.setValue(new int[] { 2, 0 }, 3); - matrix3.setValue(new int[] { 2, 1 }, -1); - - // factor 3 - Factor factor3 = new Factor("testmatrix"); - ContinuousDomain domain3 = new ContinuousDomain(Distribution.QUNIFPC); - domain3.addDistributionParam("reference", matrix3); - domain3.addDistributionParam("coefficient", 0.2); - factor3.setDomain(domain3); - factor3.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); - factor3.setValueForIdentifier(0.1); - - Assert.assertEquals(0.84, ((MatrixND)factor3.getValue()).getValue(new int[] { 0, 0 }),0.0000001); - Assert.assertEquals(2.52, ((MatrixND)factor3.getValue()).getValue(new int[] { 2, 0 }),0.0000001); - - // matrix 4 - MatrixND matrix4 = MatrixFactory.getInstance().create("test1", - new int[] { 3, 2 }, new String[] { "col1", "col2" }); - matrix4.setValue(new int[] { 0, 0 }, 4); - matrix4.setValue(new int[] { 0, 1 }, -2); - matrix4.setValue(new int[] { 1, 0 }, 42); - matrix4.setValue(new int[] { 1, 1 }, 10); - matrix4.setValue(new int[] { 2, 0 }, 7); - matrix4.setValue(new int[] { 2, 1 }, 0); - - // factor 4 - Factor factor4 = new Factor("testmatrix"); - ContinuousDomain domain4 = new ContinuousDomain(Distribution.QUNIFMM); - domain4.addDistributionParam("min", matrix3); - domain4.addDistributionParam("max", matrix4); - factor4.setDomain(domain4); - factor4.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); - factor4.setValueForIdentifier(0.5); - - Assert.assertEquals(2.5, ((MatrixND)factor4.getValue()).getValue(new int[] { 0, 0 }),0.0000001); - Assert.assertEquals(5.0, ((MatrixND)factor4.getValue()).getValue(new int[] { 2, 0 }),0.0000001); - - if (log.isInfoEnabled()) { - log.info("factor#toString() = " + factor); - } - } - - /** - * Test factor with matrix. - * - * @see MatrixND - */ - @Test public void testEquationContinuousFactor() { // factor Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -41,8 +41,6 @@ import org.junit.Test; import org.nuiton.j2r.RException; import org.nuiton.j2r.RProxy; -import org.nuiton.math.matrix.MatrixFactory; -import org.nuiton.math.matrix.MatrixND; import fr.ifremer.isisfish.AbstractIsisFishTest; import fr.ifremer.isisfish.IsisFishException; @@ -123,7 +121,7 @@ return factor2; } - protected Factor getContinuousMatrixUniformPCFactor() { + /*protected Factor getContinuousMatrixUniformPCFactor() { // matrix 1 MatrixND matrix1 = MatrixFactory.getInstance().create("test1", new int[] { 3, 2 }, new String[] { "col1", "col2" }); @@ -143,7 +141,7 @@ factor2.setDomain(domain2); factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); return factor2; - } + }*/ protected Factor getContinuousDoubleCauchyFactor() { // factor 1, min/max on int @@ -235,7 +233,7 @@ } } - // matrix uniform + /* matrix uniform designPlan = getDesignPlan(getContinuousMatrixUniformPCFactor(), getContinuousMatrixUniformPCFactor()); scenarii = script.compute(designPlan, simulationsDir); Assert.assertTrue(scenarii.getScenarios().size() >= 3); // random, can be 9, 12 @@ -244,7 +242,7 @@ MatrixND value = (MatrixND)factor.getValue(); Assert.assertTrue(value.getValue(0, 0) >= 0.9 && value.getValue(0, 0) <= 1.1); } - } + }*/ // check fail is discrete designPlan = getDesignPlan(getDiscreteIntFactor(),getContinuousDoubleUniformMMFactor()); Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java =================================================================== --- branches/4.0.1/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/vcs/VCSSVNTest.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -513,10 +513,7 @@ String result = vcs.getDiff(firstFile); // quelques tests sur la sortie, pas d'égalité parfaite - // TODO echatellier 20120607 depuis svnkit 1.7, le diff - // ne mentionne plus le nom du fichier. Ca doit être un bug, mais - // dans le cas d'isis c'est pas tres grave - //Assert.assertTrue(result.indexOf("version.txt") > 0); + Assert.assertTrue(result.indexOf("version.txt") > 0); Assert.assertTrue(result.indexOf("-Version 3.1.0") > 0); Assert.assertTrue(result.indexOf("+Version 3.2.1") > 0); Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,7 +32,6 @@ import org.apache.commons.lang.StringUtils; 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; @@ -77,12 +76,8 @@ int factorsNb = factors.size(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - engine.voidEval("library(AlgDesign)"); //Create a list of the factors under the form factor1=factor1,... @@ -107,15 +102,15 @@ Domain domain = factor.getDomain(); if (domain instanceof ContinuousDomain) { - ContinuousDomain contDomain = (ContinuousDomain) domain; + //ContinuousDomain contDomain = (ContinuousDomain) domain; int card = factor.getCardinality(); -// Double min = contDomain.getCalculatorMinBound(); -// Double max = contDomain.getCalculatorMaxBound(); -// -// for (int i = 0; i < card; i++) { -// //add the ith value -// vector += (min + (i * (max - min) / (card - 1))) + ","; -// } + Double min = 0.0; + Double max = 1.0; + + for (int i = 0; i < card; i++) { + //add the ith value + vector += (min + (i * (max - min) / (card - 1))) + ","; + } } else { int nbValues = ((DiscreteDomain) domain).getValuesCount(); for (int i = 0; i < nbValues; i++) { @@ -147,11 +142,11 @@ engine.voidEval(rCall); if (param_order ==1 ){ - rCall = "x<-optFederov(~(%s),data=expandgrid, " + + rCall = "isis.methodAnalyse<-optFederov(~(%s),data=expandgrid, " + "approximate =FALSE, center=F, criterion = \"D\"," + "nRepeats=10)"; } else { - rCall = "x<-optFederov(~(%s)^"+param_order+",data=expandgrid, " + + rCall = "isis.methodAnalyse<-optFederov(~(%s)^"+param_order+",data=expandgrid, " + "approximate =FALSE, center=F, criterion = \"D\"," + "nRepeats=10)"; } @@ -166,10 +161,10 @@ engine.voidEval(rCall); - engine.eval("expPlan<-as.data.frame(x$design)"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse$design)"); RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); dataFrame.setVariable("expPlan"); - int nbExperiments = (Integer)engine.eval("dim(x$design)[1]"); + int nbExperiments = (Integer)engine.eval("dim(isis.methodAnalyse$design)[1]"); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); for (int j = 0; j < nbExperiments; j++) { @@ -199,11 +194,9 @@ parameters += ","; } if (domain instanceof ContinuousDomain){ - ContinuousDomain contDomain = (ContinuousDomain)domain; + //ContinuousDomain contDomain = (ContinuousDomain)domain; distribution += "\"qunif\""; -// parameters += "\"[" + contDomain.getMinBound() -// + ";" + contDomain.getMaxBound() -// + "]\""; + parameters += "\"[0.0;1.0]\""; } else { DiscreteDomain discDomain = (DiscreteDomain)domain; distribution += "\"discrete\""; @@ -211,7 +204,7 @@ Map<Object, Object> values = discDomain.getValues(); int count=0; Collection<Object> collecValues = values.values(); - for (Object value:collecValues){ + for (Object value:collecValues) { if (count!=0){ parameters += ","; } @@ -225,22 +218,19 @@ distribution, parameters)); engine.voidEval("call<-\"" + rCall + "\""); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-x$design"); + engine.voidEval("isis.simule<-isis.methodAnalyse$design"); engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -254,22 +244,16 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number - int factorNumber = (Integer)engine.eval("dim(x$design)[2]"); + int factorNumber = (Integer)engine.eval("dim(isis.methodAnalyse$design)[2]"); SimulationParameter param = simulationStorages.get(0).getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - SimulationStorage firstStorage = simulationStorages.get(0); + String firstStorageName = outputDirectory.getName().replaceAll("-", ""); - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - for (int k = 0; k < sensitivityNumber; k++) { SensitivityExport sensitivityExport = @@ -288,7 +272,7 @@ + name + ")"); //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(x$design," + String dataFrame = "dataforaov<-data.frame(isis.methodAnalyse$design," + name + "=" + name + ")"; engine.voidEval(dataFrame); @@ -297,11 +281,11 @@ for (int j = 0; j < factorNumber; j++) { if (j < (factorNumber - 1)) { aovCall = aovCall - + engine.eval("names(x$design)[" + (j + 1) + "]") + + engine.eval("names(isis.methodAnalyse$design)[" + (j + 1) + "]") + "+"; } else { aovCall = aovCall - + engine.eval("names(x$design)[" + (j + 1) + "]") + + engine.eval("names(isis.methodAnalyse$design)[" + (j + 1) + "]") + ")"; if(param_order>1){ aovCall+="^" + param_order + ",data=dataforaov)"; @@ -318,7 +302,7 @@ *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv */ -//Compute Sum of Squares and Sensitivity indices + //Compute Sum of Squares and Sensitivity indices engine.voidEval("SoS<-summary(aovresult)[[1]][1:dim(summary(aovresult)[[1]])[1],2]"); engine.voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:dim(summary(aovresult)[[1]])[1]]"); engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); @@ -357,39 +341,20 @@ //FIXME export through java to enable export when using Rserve (when distant Rserve). //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", firstStorageName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + "\"call_method\"=\"" + aovCall + "\"," + "\"analysis_result\"=list(aovresult,IndSensibilite))"); - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\""); - - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; - engine.voidEval(String.format(renameIsisMethodAnalyse, - firstStorageName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + closeEngine(engine, outputDirectory); - - //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()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -24,20 +24,17 @@ import java.io.File; import java.util.List; -import java.util.Map; import fr.ifremer.isisfish.simulator.sensitivity.*; -import org.apache.commons.lang3.StringUtils; + 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.domain.ContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; import fr.ifremer.isisfish.util.Doc; + import org.nuiton.j2r.types.RDataFrame; /** @@ -90,7 +87,7 @@ // only run with continuous checkAllFactorContinuous(factors); - String rInstruction = "a<-fast99(" + + String rInstruction = "isis.methodAnalyse<-fast99(" + "model=NULL," + "factors=%s, " + "n=%s, " + @@ -106,12 +103,8 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); @@ -135,35 +128,31 @@ engine.voidEval(rInstruction); // Get back experiment plan - dataFrame = (RDataFrame) engine.eval("a$X"); - dataFrame.setVariable("a$X"); + dataFrame = (RDataFrame) engine.eval("isis.methodAnalyse$X"); + dataFrame.setVariable("isis.methodAnalyse$X"); - nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); + nbExperiments = (Integer)engine.eval("dim(isis.methodAnalyse$X)[1]"); engine.voidEval(getIsisFactorDistribution(factors)); - engine.voidEval("call<-a$call"); + engine.voidEval("call<-isis.methodAnalyse$call"); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + + engine.voidEval("attr(isis.methodExp,\"nomModel\")<-" + "\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(isis.methodAnalyse$X)"); engine.voidEval("attr(isis.simule,\"nomModel\")<-" + "\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Setting up the scenarios. for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); @@ -175,6 +164,8 @@ thisExperimentScenarios.add(experimentScenario); thisExperiment.setScenarios(thisExperimentScenarios); } + + closeEngine(engine, outputDirectory); } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -186,20 +177,13 @@ public void analyzeResult(List<SimulationStorage> simulationStorages, File outputDirectory) throws SensitivityException { - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - + // for export engine.setwd(outputDirectory); // Call R @@ -230,7 +214,7 @@ //adding attribute to isis.Simule engine.voidEval("attr(isis.simule,\"nomModel\")<-" + "\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.methodExp$call"); for (int k = 0; k < sensitivityNumber; k++) { @@ -239,70 +223,52 @@ .getExportFilename(); //Compute results - engine.voidEval("tell(a,y=" + name + ")"); + engine.voidEval("tell(isis.methodAnalyse,y=" + name + ")"); - engine.voidEval("names(a$V)<-factornames"); - engine.voidEval("names(a$X)<-factornames"); - engine.voidEval("names(a$D1)<-factornames"); - engine.voidEval("names(a$Dt)<-factornames"); + engine.voidEval("names(isis.methodAnalyse$V)<-isis.factor.distribution$NomFacteur"); + engine.voidEval("names(isis.methodAnalyse$X)<-isis.factor.distribution$NomFacteur"); + engine.voidEval("names(isis.methodAnalyse$D1)<-isis.factor.distribution$NomFacteur"); + engine.voidEval("names(isis.methodAnalyse$Dt)<-isis.factor.distribution$NomFacteur"); //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + - "call_method=\"tell(a,y=" + name + ")" + "\"," + - "\"analysis_result\"=a)"); + "call_method=\"tell(isis.methodAnalyse,y=" + name + ")" + "\"," + + "\"analysis_result\"=isis.methodAnalyse)"); //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse,\"nomModel\")<-" + + engine.voidEval("attr(" + exportMethodAnalyse + ",\"nomModel\")<-" + "\"isis-fish-externe-R\")"); //Create the data.frame of scenarios and results for export purpose - engine.voidEval("dfresults<-data.frame(a$X,a$y)"); + engine.voidEval("dfresults<-data.frame(isis.methodAnalyse$X,isis.methodAnalyse$y)"); //Set working directory engine.setwd(outputDirectory); //Export V - engine.voidEval("write.csv(a$V,\"" + name + "_V.csv\")"); + engine.voidEval("write.csv(isis.methodAnalyse$V,\"" + name + "_V.csv\")"); //Export D1 - engine.voidEval("write.csv(a$D1,\"" + name + "_D1.csv\")"); + engine.voidEval("write.csv(isis.methodAnalyse$D1,\"" + name + "_D1.csv\")"); //Export Dt - engine.voidEval("write.csv(a$Dt,\"" + name + "_Dt.csv\")"); + engine.voidEval("write.csv(isis.methodAnalyse$Dt,\"" + name + "_Dt.csv\")"); //Set dfresults names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); - engine.voidEval("names(dfresults)<-resultsnames"); + engine.voidEval("resultsnames<-c(isis.factor.distribution$NomFacteur,\"Result\")"); + engine.voidEval("names(dfresults)<-isis.factor.distribution$NomFacteur"); //Export results engine.voidEval("write.csv(dfresults,\"" + name + "_Results.csv\")"); //FIXME export through java to enable export when using Rserve - - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse" + - "<-isis.methodAnalyse"; - - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } + + closeEngine(engine, outputDirectory); - //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()); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -28,10 +28,10 @@ import fr.ifremer.isisfish.simulator.sensitivity.*; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.util.Doc; + import org.apache.commons.lang3.StringUtils; 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; @@ -112,7 +112,7 @@ bsup += 1; } - String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s," + + String rInstruction = "isis.methodAnalyse<-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))"; @@ -123,17 +123,9 @@ rCall = editRInstruction(rCall); } - REngine engine; - try { - engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); @@ -151,7 +143,7 @@ engine.setwd(outputDirectory); // Get back experiment plan - engine.eval("expPlan<-as.data.frame(a$X)"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse$X)"); dataFrame = (RDataFrame) engine.eval("expPlan"); dataFrame.setVariable("expPlan"); @@ -188,22 +180,18 @@ engine.voidEval(String.format(factorDistribution, factorNames, distribution, parameters)); - engine.voidEval("call<-a$call"); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("call<-isis.methodAnalyse$call"); + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + + engine.voidEval("attr(isis.methodExp,\"nomModel\")<-" + "\"isis-fish-externe-R\""); 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]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Setting up the scenarios. List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); for (int j = 0; j < nbExperiments; j++) { @@ -216,6 +204,8 @@ thisExperimentScenarios.add(experimentScenario); thisExperiment.setScenarios(thisExperimentScenarios); } + + closeEngine(engine, outputDirectory); } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); @@ -229,20 +219,11 @@ public void analyzeResult(List<SimulationStorage> simulationStorages, File outputDirectory) throws SensitivityException { - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); - REngine engine = null; - try { - engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Call R // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -275,7 +256,7 @@ engine.voidEval("attr(isis.simule,\"nomModel\")<-" + "\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.methodExp$call"); for (int k = 0; k < sensitivityNumber; k++) { @@ -284,34 +265,35 @@ .getExportFilename(); //Compute results - engine.voidEval("tell(a,y=" + name + ")"); + engine.voidEval("tell(isis.methodAnalyse,y=" + name + ")"); //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + //"\"isis.factors\"=isis.factors," + //"\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + - "\"call_method\"=\"tell(a,y=" + name + ")" + "\"," + - "\"analysis_result\"=a)"); + "\"call_method\"=\"tell(isis.methodAnalyse,y=" + name + ")" + "\"," + + "\"analysis_result\"=isis.methodAnalyse)"); //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse,\"nomModel\")<-" + + engine.voidEval("attr(" + exportMethodAnalyse + ",\"nomModel\")<-" + "\"isis-fish-externe-R\""); // Get back the sensitivity results, mu, mu star and sigma. - engine.voidEval("mu<-apply(a$ee, 2, mean)"); - engine.voidEval("mu.star <- apply(a$ee, 2, function(a) mean(abs(a)))"); - engine.voidEval("sigma <- apply(a$ee, 2, sd)"); + engine.voidEval("mu<-apply(isis.methodAnalyse$ee, 2, mean)"); + engine.voidEval("mu.star <- apply(isis.methodAnalyse$ee, 2, function(a) mean(abs(a)))"); + engine.voidEval("sigma <- apply(isis.methodAnalyse$ee, 2, sd)"); //Create the data.frame of sensitivity indices for export purpose engine.voidEval("df<-data.frame(mu,mu.star,sigma)"); - engine.voidEval("row.names(df)<-factornames"); + engine.voidEval("row.names(df)<-isis.factor.distribution$NomFacteur"); //Create the data.frame of scenarios and results for export purpose - engine.voidEval("dfresults<-data.frame(a$X," + name + ")"); + engine.voidEval("dfresults<-data.frame(isis.methodAnalyse$X," + name + ")"); //Set dfresults names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("resultsnames<-c(isis.factor.distribution$NomFacteur,\"Result\")"); engine.voidEval("names(dfresults)<-resultsnames"); //Export sensitivity indices @@ -323,28 +305,10 @@ "\"" + name + "_Results.csv\")"); //FIXME export through java to enable export when using Rserve - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-" + - "isis.methodAnalyse"; - - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine,simulationName); + closeEngine(engine, outputDirectory); - //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()); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -26,19 +26,13 @@ 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.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.*; import fr.ifremer.isisfish.util.Doc; + import org.nuiton.j2r.types.RDataFrame; /** @@ -70,10 +64,10 @@ } @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) throws SensitivityException { - setIsisFactorsR(plan, outputdirectory); + setIsisFactorsR(plan, outputDirectory); int factorNumber = plan.getFactors().size(); List<Factor> factors = plan.getFactors(); @@ -85,19 +79,12 @@ checkAllFactorContinuous(factors); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Set working directory to get Isis R session - engine.loadRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - //Load the lhs library engine.voidEval("library(lhs)"); - String rInstruction = "x<-optimumLHS(n=%s,k=%s,maxSweeps=%s,eps=%s)"; + String rInstruction = "isis.methodAnalyse<-optimumLHS(n=%s,k=%s,maxSweeps=%s,eps=%s)"; String rCall = String.format(rInstruction, param_simulationNumber, factorNumber, param_MaxSweeps, param_eps); @@ -110,7 +97,7 @@ engine.voidEval(rCall); // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x)"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse)"); dataFrame = (RDataFrame)engine.eval("expPlan"); dataFrame.setVariable("expPlan"); @@ -128,21 +115,21 @@ engine.voidEval(getIsisFactorDistribution(factors)); - engine.voidEval("call<-" + "\"x<-optimumLHS(" + engine.voidEval("call<-" + "\"isis.methodAnalyse<-optimumLHS(" + "n=" + param_simulationNumber + ",k=" + factorNumber + ",maxSweeps=" + param_MaxSweeps + ",eps=" + param_eps + ")\""); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(x)"); + engine.voidEval("isis.simule<-data.frame(isis.methodAnalyse)"); engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); @@ -201,12 +188,8 @@ engine.voidEval(rInstruction); - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); + closeEngine(engine, outputDirectory); - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't generate scenarios", e); } @@ -220,23 +203,15 @@ //The first storage to get the name and parameters all along the method SimulationStorage storage = simulationStorages.get(0); + String simulationName = outputDirectory.getName().replaceAll("-", ""); - String simulationName = storage.getName().replaceAll("-", ""); - try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); + engine.voidEval("factors<-data.frame(isis.methodAnalyse)"); + engine.voidEval("names(factors)<-isis.factor.distribution$NomFacteur"); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.voidEval("factors<-data.frame(x)"); - engine.voidEval("names(factors)<-factornames"); - //Get back the factors number int factorNumber = (Integer) engine.eval("length(factors[1,])"); //Get back the simulation number @@ -264,7 +239,7 @@ //adding attribute to isis.Simule engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.methodExp$call"); for (int k = 0; k < sensitivityNumber; k++) { @@ -315,7 +290,7 @@ //Set dataforaov names - engine.voidEval("names(dataforaov)<-c(factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-c(isis.factor.distribution$NomFacteur,\"Result\")"); /*Set the export directory *Export directory is the first simulation export directory. @@ -332,36 +307,21 @@ //FIXME export through java to enable export when using Rserve (when distant Rserve). //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + "call_method=\"" + aovCall + "\""+ ",\"analysis_result\"=list(aovresult,IndSensibilite))"); - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\""); - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-" + - "isis.methodAnalyse"; - - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine, simulationName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -28,18 +28,11 @@ import fr.ifremer.isisfish.export.SensitivityExport; 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.simulator.sensitivity.*; import fr.ifremer.isisfish.util.Doc; /** @@ -82,20 +75,13 @@ try { - REngine engine = new RProxy(); //The R engine + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Load the lhs library engine.voidEval("library(lhs)"); //Create the scenarios - String rInstruction = "x<-randomLHS(%s,%s)"; + String rInstruction = "isis.methodAnalyse<-randomLHS(%s,%s)"; String rCall = String.format(rInstruction, param_simulationNumber, factorNumber); @@ -106,7 +92,7 @@ engine.voidEval(rCall); // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x)"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse)"); dataFrame = (RDataFrame)engine.eval("expPlan"); dataFrame.setVariable("expPlan"); @@ -124,18 +110,18 @@ engine.voidEval(getIsisFactorDistribution(factors)); - engine.voidEval("call<-" + "\"x<-randomLHS(" + engine.voidEval("call<-" + "\"isis.methodAnalyse<-randomLHS(" + param_simulationNumber + "," + factorNumber + ")\""); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(x)"); + engine.voidEval("isis.simule<-data.frame(isis.methodAnalyse)"); engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); @@ -191,16 +177,13 @@ engine.voidEval(rInstruction); // Clean RData - for (Factor factor:factors) { - engine.remove(factor.getName().replaceAll(" ", "")); + for (Factor factor : factors) { + String factorName = factor.getName().replaceAll(" ", ""); + engine.remove(factorName); } - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory); - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't generate scenarios", e); } @@ -213,24 +196,16 @@ File outputDirectory) throws SensitivityException { SimulationStorage simulationStorage1 = simulationStorages.get(0); - String simName = simulationStorage1.getName(); - String simulationName = simName.replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); SimulationParameter param = simulationStorage1.getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); //List<SensitivityExport> export = param.getSensitivityExport(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); + engine.voidEval("factors<-data.frame(isis.methodAnalyse)"); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.voidEval("factors<-data.frame(x)"); - //Get back the factors number int factorNumber = (Integer) engine.eval("length(factors)"); @@ -257,7 +232,7 @@ engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.methodExp$call"); for (int k = 0; k < sensitivityNumber; k++) { @@ -306,7 +281,7 @@ //Set dataforaov names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("resultsnames<-c(isis.factor.distribution$NomFacteur,\"Result\")"); engine.voidEval("names(dataforaov)<-resultsnames"); /*Set the export directory @@ -326,40 +301,20 @@ //FIXME export through java to enable export when using Rserve (when distant Rserve). //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + "call_method=\"" + aovCall + "\"," + "\"analysis_result\"=list(aovresult,IndSensibilite))"); - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\""); - - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-" + - "isis.methodAnalyse"; - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine, simulationName); + closeEngine(engine, outputDirectory); - //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()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -29,10 +29,10 @@ import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; import fr.ifremer.isisfish.util.Doc; + import org.apache.commons.lang.StringUtils; 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; @@ -77,7 +77,7 @@ int factorsNb = factors.size(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), @@ -100,15 +100,15 @@ Domain domain = factor.getDomain(); if (domain instanceof ContinuousDomain) { -// ContinuousDomain contDomain = (ContinuousDomain) domain; -// int card = factor.getCardinality(); -// Double min = contDomain.getCalculatorMinBound(); -// Double max = contDomain.getCalculatorMaxBound(); -// -// for (int i = 0; i < card; i++) { -// //add the ith value -// vector += (min + (i * (max - min) / (card - 1))) + ","; -// } + //ContinuousDomain contDomain = (ContinuousDomain) domain; + int card = factor.getCardinality(); + Double min = 0.0; + Double max = 1.0; + + for (int i = 0; i < card; i++) { + //add the ith value + vector += (min + (i * (max - min) / (card - 1))) + ","; + } } if (domain instanceof DiscreteDomain) { @@ -132,7 +132,7 @@ //X<-expand.grid(vector=???,weight=???) - String expandGrid = "x<-expand.grid(%s)"; + String expandGrid = "isis.methodAnalyse<-expand.grid(%s)"; String rCall = String.format(expandGrid,factorsNames); @@ -142,10 +142,10 @@ engine.voidEval(rCall); - engine.eval("expPlan<-as.data.frame(x)"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse)"); RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); dataFrame.setVariable("expPlan"); - int nbExperiments = (Integer)engine.eval("dim(x)[1]"); + int nbExperiments = (Integer)engine.eval("dim(isis.methodAnalyse)[1]"); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); for (int j = 0; j < nbExperiments; j++) { @@ -175,11 +175,9 @@ parameters += ","; } if (domain instanceof ContinuousDomain){ - ContinuousDomain contDomain = (ContinuousDomain)domain; + //ContinuousDomain contDomain = (ContinuousDomain)domain; distribution += "\"qunif\""; -// parameters += "\"[" + contDomain.getMinBound() -// + ";" + contDomain.getMaxBound() -// + "]\""; + parameters += "\"[0.0;1.0]\""; } else { DiscreteDomain discDomain = (DiscreteDomain)domain; distribution += "\"discrete\""; @@ -202,22 +200,19 @@ engine.voidEval("call<-\"" + String.format(expandGrid,factorsNames) + "\""); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-x"); + engine.voidEval("isis.simule<-isis.methodAnalyse"); engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -231,22 +226,16 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number - int factorNumber = (Integer)engine.eval("dim(x)[2]"); + int factorNumber = (Integer)engine.eval("dim(isis.methodAnalyse)[2]"); SimulationParameter param = simulationStorages.get(0).getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - SimulationStorage firstStorage = simulationStorages.get(0); + String firstStorageName = outputDirectory.getName().replaceAll("-", ""); - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - for (int k = 0; k < sensitivityNumber; k++) { SensitivityExport sensitivityExport = @@ -265,7 +254,7 @@ + name + ")"); //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(x," + String dataFrame = "dataforaov<-data.frame(isis.methodAnalyse," + name + "=" + name + ")"; engine.voidEval(dataFrame); @@ -274,11 +263,11 @@ for (int j = 0; j < factorNumber; j++) { if (j < (factorNumber - 1)) { aovCall = aovCall - + engine.eval("names(x)[" + (j + 1) + "]") + + engine.eval("names(isis.methodAnalyse)[" + (j + 1) + "]") + "+"; } else { aovCall = aovCall - + engine.eval("names(x)[" + (j + 1) + "]") + + engine.eval("names(isis.methodAnalyse)[" + (j + 1) + "]") + ")"; if(param_order>1){ aovCall+="^" + param_order + ",data=dataforaov)"; @@ -328,38 +317,20 @@ //FIXME export through java to enable export when using Rserve (when distant Rserve). //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", firstStorageName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + "\"call_method\"=\"" + aovCall + "\"," + "\"analysis_result\"=list(aovresult,IndSensibilite))"); - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\""); - - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; - engine.voidEval(String.format(renameIsisMethodAnalyse, - firstStorageName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + closeEngine(engine, outputDirectory); - //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()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -26,22 +26,14 @@ import java.util.List; 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.domain.ContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; +import fr.ifremer.isisfish.simulator.sensitivity.*; import fr.ifremer.isisfish.util.Doc; public class RegularFractions extends AbstractSensitivityAnalysis { @@ -100,7 +92,7 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); //Clear session engine.clearSession(); @@ -116,7 +108,7 @@ engine.voidEval("source(\"regularfractions.R\")"); //Create the instruction - String rInstruction = "x<-regular.fraction(%s,%s,%s,%s)"; + String rInstruction = "isis.methodAnalyse<-regular.fraction(%s,%s,%s,%s)"; String rCall = String.format(rInstruction, factors.size(), param_p, param_r, param_resolution); @@ -138,12 +130,12 @@ // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x[[1]])"); + engine.eval("expPlan<-as.data.frame(isis.methodAnalyse[[1]])"); dataFrame = (RDataFrame)engine.eval("expPlan"); dataFrame.setVariable("expPlan"); //Get back the simulation number - int simulationNumber = (Integer) engine.eval("length(x[[1]][,1])"); + int simulationNumber = (Integer) engine.eval("length(isis.methodAnalyse[[1]][,1])"); // Setting up the scenarios. for (int j = 0; j < simulationNumber; j++) { @@ -191,12 +183,12 @@ engine.voidEval(getIsisFactorDistribution(factors)); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); //Create isis.Simule @@ -207,12 +199,8 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory); - engine.terminate(); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -229,21 +217,14 @@ SimulationParameter param = firstStorage.getParameter(); List<SensitivityExport> exports = param.getSensitivityExport(); int sensitivityNumber = exports.size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number - int factorNumber = (Integer) engine.eval("dim(data)[2]"); + int factorNumber = (Integer) engine.eval("dim(isis.simule)[2]"); for (int k = 0; k < sensitivityNumber; k++) { @@ -270,7 +251,7 @@ String name = export.getExportFilename(); //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(data," + + String dataFrame = "dataforaov<-data.frame(isis.simule," + name + "=" + name + ")"; engine.voidEval(dataFrame); @@ -280,11 +261,11 @@ if (j < (factorNumber - 1)) { aovCall = aovCall - + engine.eval("names(data)[" + (j + 1) + "]") + + engine.eval("names(isis.simule)[" + (j + 1) + "]") + "+"; } else { aovCall = aovCall - + engine.eval("names(data)[" + (j + 1) + "]") + + engine.eval("names(isis.simule)[" + (j + 1) + "]") + ")"; if (param_resolution <= 4) { aovCall += ",data=dataforaov)"; @@ -316,8 +297,8 @@ engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); //Set dataforaov names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); - engine.voidEval("names(dataforaov)<-resultsnames"); + engine.voidEval("resultsnames<-c(isis.factor.distribution$NomFacteur,\"Result\")"); + engine.voidEval("names(dataforaov)<-isis.factor.distribution$NomFacteur"); /*Set the export directory *Export directory is the first simulation export directory. @@ -334,38 +315,20 @@ //FIXME export through java to enable export when using Rserve (when distant Rserve). //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + "\"call_method\"=\"" + aovCall + "\"," + "\"analysis_result\"=list(aovresult,IndSensibilite))"); - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\""); - - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine,simulationName); + closeEngine(engine, outputDirectory); - //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()); - - engine.terminate(); - } catch (Exception eee) { throw new SensitivityException("Can't evaluate results", eee); } Modified: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java 2014-04-17 15:05:25 UTC (rev 3967) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java 2014-04-17 15:26:04 UTC (rev 3968) @@ -24,18 +24,17 @@ import java.io.File; import java.util.List; -import java.util.Map; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.simulator.sensitivity.*; + import org.apache.commons.lang3.StringUtils; 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.util.Doc; + import org.nuiton.j2r.types.RDataFrame; /** @@ -70,10 +69,10 @@ } @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) throws SensitivityException { - setIsisFactorsR(plan, outputdirectory); + setIsisFactorsR(plan, outputDirectory); RDataFrame dataFrame; int nbExperiments; @@ -84,7 +83,7 @@ checkAllFactorContinuous(factors); - String rInstruction = "a<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; + String rInstruction = "isis.methodAnalyse<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; String rCall = String.format(rInstruction, param_nboot); if (param_modifR) { @@ -92,15 +91,8 @@ } try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - engine.voidEval("library(sensitivity)"); String x = "<-data.frame(matrix(c("; @@ -134,35 +126,31 @@ engine.voidEval(rInstruction); // Get back experiment plan - dataFrame = (RDataFrame) engine.eval("a$X"); - dataFrame.setVariable("a$X"); + dataFrame = (RDataFrame) engine.eval("isis.methodAnalyse$X"); + dataFrame.setVariable("isis.methodAnalyse$X"); nbExperiments = dataFrame.dim()[0]; engine.voidEval(getIsisFactorDistribution(factors)); - engine.voidEval("call<-a$call"); + engine.voidEval("call<-isis.methodAnalyse$call"); - engine.voidEval("isis.MethodExp<-list(" + + engine.voidEval("isis.methodExp<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + + engine.voidEval("attr(isis.methodExp," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(isis.methodAnalyse$X)"); engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - - // Setting up the scenarios. + // Setting up the scenarios. for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { @@ -173,11 +161,13 @@ } thisExperimentScenarios.add(experimentScenario); } + + closeEngine(engine, outputDirectory); } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e);} + throw new SensitivityException("Can't generate scenarios", e); + } - thisExperiment.setScenarios(thisExperimentScenarios); return thisExperiment; @@ -190,19 +180,12 @@ SimulationStorage firstStorage = simulationStorages.get(0); SimulationParameter param = firstStorage.getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Call R // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -236,7 +219,7 @@ engine.voidEval("attr(isis.simule," + "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + engine.voidEval("attr(isis.simule,\"call\")<-isis.methodExp$call"); for (int k = 0; k < sensitivityNumber; k++) { @@ -246,13 +229,14 @@ //Compute results engine.voidEval("tell(a,y=" + name + ")"); - engine.voidEval("row.names(a$S)<-names(a$X)"); - engine.voidEval("row.names(a$T)<-names(a$X)"); - engine.voidEval("row.names(a$V)<-c(\"global\"," + - "names(a$X),paste(\"-\",names(a$X),sep=\"\"))"); + engine.voidEval("row.names(isis.methodAnalyse$S)<-names(isis.methodAnalyse$X)"); + engine.voidEval("row.names(isis.methodAnalyse$T)<-names(isis.methodAnalyse$X)"); + engine.voidEval("row.names(isis.methodAnalyse$V)<-c(\"global\"," + + "names(isis.methodAnalyse$X),paste(\"-\",names(isis.methodAnalyse$X),sep=\"\"))"); //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + + String exportMethodAnalyse = String.format("%s.isis.methodAnalyse", simulationName + "." + name); + engine.voidEval(exportMethodAnalyse + "<-list(" + "\"isis.factors\"=isis.factors," + "\"isis.factor.distribution\"=isis.factor.distribution," + "\"isis.simule\"=isis.simule," + @@ -260,25 +244,25 @@ "\"analysis_result\"=a)"); //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse," + + engine.voidEval("attr(" + exportMethodAnalyse + "," + "\"nomModel\")<-\"isis-fish-externe-R\")"); //Create the data.frame of scenarios and results for export purpose - engine.voidEval("dfresults<-data.frame(a$X,a$y)"); + engine.voidEval("dfresults<-data.frame(isis.methodAnalyse$X,isis.methodAnalyse$y)"); //Set working directory engine.setwd(outputDirectory); //Export V - engine.voidEval("write.csv(a$V,\"" + engine.voidEval("write.csv(isis.methodAnalyse$V,\"" + name + "_SensitivityIndices.csv\")"); //Export DD - engine.voidEval("write.csv(a$D,\"" + engine.voidEval("write.csv(isis.methodAnalyse$D,\"" + name + "_D.csv\")"); //Export S - engine.voidEval("write.csv(a$S,\"" + engine.voidEval("write.csv(isis.methodAnalyse$S,\"" + name + "_S.csv\")"); //Export results @@ -286,26 +270,9 @@ + name + "_Results.csv\")"); //FIXME export through java to enable export when using Rserve - String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-" + - "isis.methodAnalyse"; - engine.voidEval(String.format(renameIsisMethodAnalyse, - simulationName + "." + name)); - } - //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()); + closeEngine(engine, outputDirectory); } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); }
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echatellier＠users.forge.codelutin.com