November 2013 - Isis-fish-commits - mailman.cloud.codelutin.com

r3833 - in branches/4.0.1/src: main/java/fr/ifremer/isisfish/simulator/sensitivity main/java/fr/ifremer/isisfish/simulator/sensitivity/domain test/java/fr/ifremer/isisfish/simulator/sensitivity test/resources/test-database/sensitivityanalysis
by echatellier＠users.forge.codelutin.com Nov. 14, 2013

Nov. 14, 2013

Author: echatellier Date: 2013-11-14 22:01:30 +0100 (Thu, 14 Nov 2013) New Revision: 3833 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3833 Log: Sensitivity Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Domain.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorGroup.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/DiscreteDomain.java branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.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/RegularExpandGrid.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityAnalysis.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -346,67 +346,61 @@ * Get factor domain min bound depending on distribution. */ protected double getMinBound(Factor factor) { - ContinuousDomain domain = (ContinuousDomain)factor.getDomain(); - Distribution distribution = domain.getDistribution(); - double result = 0; - if (distribution == Distribution.QUNIFPC) { - Object reference = (Double)domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); - if (reference instanceof MatrixND) { - result = 1; - } else { - Double coefficient = (Double)domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[1].getName()); - result = (Double)reference - ((Double)reference * coefficient); - } - } else if (distribution == Distribution.QUNIFMM) { - Object min = domain.getDistributionParameter(Distribution.QUNIFMM.getDistibutionParams()[0].getName()); - // pour les matrices, on prend 1 et on multipliera le retour - // de R sur la matrice pour faire varier la matrice completement - // note: on ne fait pas ca pour les réels car les utilisateurs - // prefere avoir les valeurs réelles dans le RData. - if (min instanceof MatrixND) { - result = 1; - } else { - result = (Double)min; - } - } else { - if (log.isWarnEnabled()) { - log.warn("Can't call getMinBound for distribution " + distribution); - } - } - return result; + return getBound(factor, true); } - + /** * Get factor domain max bound depending on distribution. */ protected double getMaxBound(Factor factor) { + return getBound(factor, false); + } + + /** + * Get factor domain bound depending on distribution. + * + * @param min min or max + */ + protected double getBound(Factor factor, boolean min) { ContinuousDomain domain = (ContinuousDomain)factor.getDomain(); Distribution distribution = domain.getDistribution(); double result = 0; if (distribution == Distribution.QUNIFPC) { Object reference = (Double)domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[0].getName()); if (reference instanceof MatrixND) { - result = 1; + result = min ? 0 : 1; } else { Double coefficient = (Double)domain.getDistributionParameter(Distribution.QUNIFPC.getDistibutionParams()[1].getName()); - result = (Double)reference + ((Double)reference * coefficient); + if (min) { + result = (Double)reference - ((Double)reference * coefficient); + } else { + result = (Double)reference + ((Double)reference * coefficient); + } } } else if (distribution == Distribution.QUNIFMM) { - Object max = domain.getDistributionParameter(Distribution.QUNIFMM.getDistibutionParams()[1].getName()); + Object value = domain.getDistributionParameter(Distribution.QUNIFMM.getDistibutionParams()[min ? 0 : 1].getName()); // pour les matrices, on prend 1 et on multipliera le retour // de R sur la matrice pour faire varier la matrice completement // note: on ne fait pas ca pour les réels car les utilisateurs // prefere avoir les valeurs réelles dans le RData. - if (max instanceof MatrixND) { - result = 1; + if (value instanceof MatrixND) { + result = min ? 0 : 1; } else { - result = (Double)max; + result = (Double)value; } } else { if (log.isWarnEnabled()) { - log.warn("Can't call getMaxBound for distribution " + distribution); + log.warn("Can't call getBound for distribution " + distribution); } } return result; } + + /** + * + * @param value + */ + protected void setFactorValue(double value) { + + } } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Domain.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Domain.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Domain.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -52,13 +52,13 @@ */ public interface Domain extends Serializable, Cloneable { - /** + /* * Return value associated to identifier. * * @param identifier * @return found value or <tt>null</tt> if not found - */ - Object getValueForIdentifier(Object identifier); + * + Object getValueForIdentifier(Object identifier);*/ /** * Accept a new visitor. Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -183,35 +183,32 @@ * @return the value */ public Object getDisplayedValue() { - // FIXME echatellier 20120313 EquationContinuousDomain removed - /*if (domain instanceof EquationDiscreteDomain || - domain instanceof EquationContinuousDomain) { + // add quotes for equation, but why ? + if (equationVariableName != null) { return "\"" + getValue() + "\""; - } else {*/ + } else { return getValue(); - //} + } } /** * Set value. * - * FIXME JC 2011-10-24 Unused (or only for test ?). - * * @param value new value */ public void setValue(Object value) { this.value = value; } - /** + /* * Set value for label. * * @param valueIdentifier new value identifier to get - */ + * public void setValueForIdentifier(Object valueIdentifier) { identifier = valueIdentifier; value = domain.getValueForIdentifier(valueIdentifier); - } + }*/ /** * Get path. Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorGroup.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorGroup.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/FactorGroup.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -254,8 +254,7 @@ domain = new ContinuousDomain(Distribution.QUNIFMM); ((ContinuousDomain)domain).addDistributionParam("min", 0.0); ((ContinuousDomain)domain).addDistributionParam("max", 1.0); - } - else if (isDiscrete()) { + } else if (isDiscrete()) { // les domaines doivent avoir les même domaines // et pour l'utilisation quand fera l'appelant // de getDomain(), on peut en retourner un au hazard @@ -286,20 +285,20 @@ public String toString() { return "FactorGroup(" + name + ")"; } - - /** + + /* * Set value for label. * * @param valueIdentifier new value identifier to get - */ + * @Override public void setValueForIdentifier(Object valueIdentifier) { identifier = valueIdentifier; for (Factor factor : factors) { factor.setValueForIdentifier(valueIdentifier); } - } - + }*/ + /** * Get the factor value for displaying (for example in R). * Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -162,26 +162,23 @@ distributionParameters.put(name, value); } - /** - * {@inheritDoc}. - */ + /*@Override public Object getValueForIdentifier(Object identifier) { Double result = 0d; - // FIXME - /*if (isPercentageType()) { + if (isPercentageType()) { // since 3.4.0.0, operator is always * result = ((Double)referenceValue + (((Double)referenceValue * coefficient) * ((2 * (Double)identifier - 1)))); } else { result = ((Double)identifier * ((Double)maxBound - (Double)minBound)) + (Double)minBound; - }*/ + } return result; - } - + }*/ + /** * Accept a new visitor. * Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/DiscreteDomain.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/DiscreteDomain.java 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/DiscreteDomain.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -35,7 +35,7 @@ /** * Un domain discret a un ensemble de valeur. - * Chaque valeur est identifiée par un label pour sont utilisation par les + * Chaque valeur est identifiée par un label pour son utilisation par les * script d'AS. * * @author chatellier @@ -62,7 +62,7 @@ } /** - * Get domaine values. + * Get domain values. * * @return the values */ @@ -80,10 +80,29 @@ } /** + * Set domain value. + * + * @param key the key + * @param value the value + */ + public void putValue(Object key, Object value) { + this.values.put(key, value); + } + + /** + * Get domain value count. + * + * @return domain value count + */ + public int getValuesCount() { + return values.size(); + } + + /* * {@inheritDoc}. * * @throws IllegalArgumentException if identifier is not a valid key - */ + * public Object getValueForIdentifier(Object identifier) throws IllegalArgumentException { @@ -93,7 +112,7 @@ } return values.get(identifier); - } + }*/ /** * Accept a new visitor. 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -35,7 +35,6 @@ import org.junit.Assert; import org.junit.Assume; import org.junit.Before; -import org.junit.BeforeClass; import org.junit.Test; import org.nuiton.j2r.RException; import org.nuiton.j2r.RProxy; @@ -80,11 +79,11 @@ } /** - * Build a test design plan with only continuous factors. + * Build a test design plan with continuous factors unsing uniform distribution. * * @return test design plan */ - protected DesignPlan getContinuousDesignPlan() { + protected DesignPlan getPlanUniformDistrib() { DesignPlan result = new DesignPlan(); @@ -106,34 +105,97 @@ factor2.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); result.addFactor(factor2); -// // 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); -// -// // factor -// Factor factor2 = new Factor("testmatrix"); -// ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); -// domain2.addDistributionParam("reference", matrix1); -// domain2.addDistributionParam("coefficient", 0.1); -// factor2.setDomain(domain2); -// factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); -// result.addFactor(factor2); + return result; + } + + /** + * Build a test design plan with continuous factors uning uniform distribution + * and matrix. + * + * @return test design plan + */ + protected DesignPlan getPlanUniformDistribMatrix() { + DesignPlan result = new DesignPlan(); + + // factor 1, min/max on int + Factor factor1 = new Factor("testint"); + ContinuousDomain domain1 = new ContinuousDomain(Distribution.QUNIFMM); + domain1.addDistributionParam("min", 0.0); + domain1.addDistributionParam("max", 2.0); + factor1.setDomain(domain1); + factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor1); + + // 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); + + // factor + Factor factor2 = new Factor("testmatrix"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); + domain2.addDistributionParam("reference", matrix1); + domain2.addDistributionParam("coefficient", 0.1); + factor2.setDomain(domain2); + factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); + result.addFactor(factor2); + return result; } /** + * Build a test design plan with continuous factors uning uniform distribution + * and matrix. + * + * @return test design plan + */ + protected DesignPlan getPlanNormCauchyDistribMatrix() { + + DesignPlan result = new DesignPlan(); + + // factor 1, min/max on int + Factor factor1 = new Factor("testint"); + ContinuousDomain domain1 = new ContinuousDomain(Distribution.DCHISQ); + domain1.addDistributionParam("df", 1.0); + domain1.addDistributionParam("ncp", 3.0); + factor1.setDomain(domain1); + factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor1); + + // 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); + + // factor + Factor factor2 = new Factor("testmatrix"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFMM); + domain2.addDistributionParam("min", matrix1); + domain2.addDistributionParam("max", matrix1); + factor2.setDomain(domain2); + factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); + result.addFactor(factor2); + + return result; + } + + /** * Build a test design plan with only continuous factors. * * @return test design plan */ - protected DesignPlan getOtherDistribDesignPlan() { + protected DesignPlan getPlanNormCauchyDistrib() { DesignPlan result = new DesignPlan(); @@ -155,25 +217,32 @@ factor2.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); result.addFactor(factor2); -// // 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); -// -// // factor -// Factor factor2 = new Factor("testmatrix"); -// ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); -// domain2.addDistributionParam("reference", matrix1); -// domain2.addDistributionParam("coefficient", 0.1); -// factor2.setDomain(domain2); -// factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); -// result.addFactor(factor2); + return result; + } + + protected DesignPlan getPlanDiscreteInt() { + DesignPlan result = new DesignPlan(); + + // factor 1, min/max on int + Factor factor1 = new Factor("lnorm"); + DiscreteDomain domain1 = new DiscreteDomain(); + Map<Object> obj = new Hash + domain1.setValues(values); + domain1.addDistributionParam("sdlog", 1.0); + factor1.setDomain(domain1); + factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor1); + + // factor 1, min/max on int + Factor factor2 = new Factor("cauchy"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.DCAUCHY); + domain2.addDistributionParam("location", 0.0); + domain2.addDistributionParam("scale", 1.0); + factor2.setDomain(domain2); + factor2.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor2); + return result; } @@ -194,13 +263,28 @@ * @throws SensitivityException */ @Test - public void testMorris() throws IsisFishException, SensitivityException { + public void testMorrisUniform() throws IsisFishException, SensitivityException { SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Morris").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("Morris script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + Assert.assertEquals(3, scenarii.getScenarios().size()); + } + + /** + * Test de génération des scenarios via la methode Morris. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test(expected=SensitivityException.class) + public void testMorrisNorm() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Morris").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("Morris script not found in test data", script); + DesignPlan designPlan = getPlanNormCauchyDistrib(); + script.compute(designPlan, simulationsDir); } /** @@ -214,7 +298,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("DOptimal").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("DOptimal script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -230,7 +314,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Fast").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("Fast script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -246,7 +330,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("OptimumLHS").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("OptimumLHS script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -262,7 +346,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RandomLHS").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("RandomLHS script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -278,7 +362,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RegularExpandGrid").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("RegularExpandGrid script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -294,7 +378,7 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RegularFractions").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("RegularFractions script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); } @@ -310,12 +394,12 @@ SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Sobol").getNewSensitivityAnalysisInstance(); Assert.assertNotNull("Sobol script not found in test data", script); - DesignPlan designPlan = getContinuousDesignPlan(); + DesignPlan designPlan = getPlanUniformDistrib(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); Assert.assertEquals(80, scenarii.getScenarios().size()); - designPlan = getOtherDistribDesignPlan(); + designPlan = getPlanNormCauchyDistrib(); scenarii = script.compute(designPlan, simulationsDir); Assert.assertEquals(80, scenarii.getScenarios().size()); 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -117,8 +117,7 @@ // vector += (min + (i * (max - min) / (card - 1))) + ","; // } } else { - Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); - int nbValues = values.size(); + int nbValues = ((DiscreteDomain) domain).getValuesCount(); for (int i = 0; i < nbValues; i++) { vector += "as.integer(" + i + "),"; } 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -85,14 +85,9 @@ SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - //Test all factors, if one is discrete, return null - for (int i = 0; i < factorNumber; i++) { - if (factors.get(i).getDomain() instanceof DiscreteDomain) { - throw new SensitivityException(factors.get(i).getName() + - " has a discrete domain, this is not acceptable for fast " + - "method."); - } - } + // only run with continuous + checkAllFactorContinuous(factors); + String rInstruction = "a<-fast99(" + "model=NULL," + "factors=%s, " + 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -84,7 +84,7 @@ param_r = 4; } - checkAllFactorContinuous(factors); + checkAllUniformDistribution(factors); // Creating the vectors. String factorNames = ""; 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -112,8 +112,7 @@ } if (domain instanceof DiscreteDomain) { - Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); - int nbValues = values.size(); + int nbValues = ((DiscreteDomain) domain).getValuesCount(); for (int i = 0; i < nbValues; i++) { vector += "as.integer(" + i + "),"; } 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 2013-11-08 16:51:41 UTC (rev 3832) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java 2013-11-14 21:01:30 UTC (rev 3833) @@ -87,6 +87,8 @@ String factorNames = ""; //Test all factors, if one is discrete, return null + checkAllFactorContinuous(factors); + //Create a string with all factors names for (int i = 0; i < factorNumber; i++) { Domain domain = factors.get(i).getDomain(); @@ -95,12 +97,6 @@ } factorNames += "\"" + factors.get(i).getName() + "\""; - - if (domain instanceof DiscreteDomain) { - throw new SensitivityException(factors.get(i).getName() + - " has a discrete domain, this is not acceptable for " + - "this method."); - } } try {

1 0

r3832 - in branches/4.0.1/src/test: java/fr/ifremer/isisfish/simulator/sensitivity resources/test-database/sensitivityanalysis resources/test-database/simulationplans
by jcouteau＠users.forge.codelutin.com Nov. 8, 2013

Nov. 8, 2013

Author: jcouteau Date: 2013-11-08 17:51:41 +0100 (Fri, 08 Nov 2013) New Revision: 3832 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3832 Log: Make Sobol work with all distributions (no equation, no matrix) Modified: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.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 branches/4.0.1/src/test/resources/test-database/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -60,17 +60,14 @@ /** Simulation dir used to save Rdata files. */ protected File simulationsDir; - @BeforeClass - public static void init() { - System.setProperty("R.type", "jni"); - } - /** * Ces tests utilisent directement le moteur R, s'il n'est pas disponible, * on va eviter de faire les tests. */ @Before public void setUp() { + + System.setProperty("R.type", "jni"); try { new RProxy(); } catch (RException e) { @@ -95,34 +92,92 @@ Factor factor1 = new Factor("testint"); ContinuousDomain domain1 = new ContinuousDomain(Distribution.QUNIFMM); domain1.addDistributionParam("min", 0.0); - domain1.addDistributionParam("max", 50.0); + domain1.addDistributionParam("max", 2.0); factor1.setDomain(domain1); factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); result.addFactor(factor1); - // 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); - - // factor - Factor factor2 = new Factor("testmatrix"); - ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); - domain2.addDistributionParam("reference", matrix1); - domain2.addDistributionParam("coefficient", 0.1); + // factor 1, min/max on int + Factor factor2 = new Factor("testint 2"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFMM); + domain2.addDistributionParam("min", 40.0); + domain2.addDistributionParam("max", 50.0); factor2.setDomain(domain2); - factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); + factor2.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); result.addFactor(factor2); + +// // 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); +// +// // factor +// Factor factor2 = new Factor("testmatrix"); +// ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); +// domain2.addDistributionParam("reference", matrix1); +// domain2.addDistributionParam("coefficient", 0.1); +// factor2.setDomain(domain2); +// factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); +// result.addFactor(factor2); return result; } /** + * Build a test design plan with only continuous factors. + * + * @return test design plan + */ + protected DesignPlan getOtherDistribDesignPlan() { + + DesignPlan result = new DesignPlan(); + + // factor 1, min/max on int + Factor factor1 = new Factor("lnorm"); + ContinuousDomain domain1 = new ContinuousDomain(Distribution.DLNORM); + domain1.addDistributionParam("meanlog", 0.0); + domain1.addDistributionParam("sdlog", 1.0); + factor1.setDomain(domain1); + factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor1); + + // factor 1, min/max on int + Factor factor2 = new Factor("cauchy"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.DCAUCHY); + domain2.addDistributionParam("location", 0.0); + domain2.addDistributionParam("scale", 1.0); + factor2.setDomain(domain2); + factor2.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor2); + +// // 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); +// +// // factor +// Factor factor2 = new Factor("testmatrix"); +// ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); +// domain2.addDistributionParam("reference", matrix1); +// domain2.addDistributionParam("coefficient", 0.1); +// factor2.setDomain(domain2); +// factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); +// result.addFactor(factor2); + + return result; + } + + /** * Test tmp files/dir. * * @throws IOException @@ -257,6 +312,13 @@ DesignPlan designPlan = getContinuousDesignPlan(); SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); - + + Assert.assertEquals(80, scenarii.getScenarios().size()); + + designPlan = getOtherDistribDesignPlan(); + scenarii = script.compute(designPlan, simulationsDir); + + Assert.assertEquals(80, scenarii.getScenarios().size()); + } } 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -109,13 +109,13 @@ 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))) + ","; - } +// 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))) + ","; +// } } else { Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); int nbValues = values.size(); @@ -202,9 +202,9 @@ if (domain instanceof ContinuousDomain){ ContinuousDomain contDomain = (ContinuousDomain)domain; distribution += "\"qunif\""; - parameters += "\"[" + contDomain.getMinBound() - + ";" + contDomain.getMaxBound() - + "]\""; +// parameters += "\"[" + contDomain.getMinBound() +// + ";" + contDomain.getMaxBound() +// + "]\""; } else { DiscreteDomain discDomain = (DiscreteDomain)domain; distribution += "\"discrete\""; 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -35,8 +35,6 @@ 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.types.RDataFrame; @@ -165,8 +163,8 @@ } distribution += "\"qunif\""; - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; +// parameters += "\"[" + domain.getMinBound() + ";" + +// domain.getMaxBound() + "]\""; factorNames += "\"" + factor.getName() + "\""; } engine.voidEval(String.format(factorDistribution, factorNames, @@ -200,17 +198,17 @@ for (int i = 0; i < factorNumber; i++) { Factor factor = plan.getFactors().get(i); Domain domain = factor.getDomain(); - if ((domain instanceof MatrixContinuousDomain) - || (domain instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(dataFrame.get(i,j)); - } else { - ContinuousDomain continuousDomain = (ContinuousDomain)domain; - Double min = continuousDomain.getCalculatorMinBound(); - Double max = continuousDomain.getCalculatorMaxBound(); - Double dFValue = (Double)dataFrame.get(i,j); - Double value = min + (max - min) * dFValue; - factor.setValueForIdentifier(value); - } +// if ((domain instanceof MatrixContinuousDomain) +// || (domain instanceof EquationContinuousDomain)) { +// factor.setValueForIdentifier(dataFrame.get(i,j)); +// } else { +// ContinuousDomain continuousDomain = (ContinuousDomain)domain; +// Double min = continuousDomain.getCalculatorMinBound(); +// Double max = continuousDomain.getCalculatorMaxBound(); +// Double dFValue = (Double)dataFrame.get(i,j); +// Double value = min + (max - min) * dFValue; +// factor.setValueForIdentifier(value); +// } experimentScenario.addFactor(factor); } thisExperimentScenarios.add(experimentScenario); 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -25,14 +25,10 @@ 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.apache.commons.lang3.StringUtils; import org.nuiton.j2r.REngine; import org.nuiton.j2r.RException; import org.nuiton.j2r.RProxy; @@ -40,6 +36,7 @@ import java.io.File; import java.util.List; +import java.util.Map; /** * Implementation of Morris method using R. @@ -87,7 +84,7 @@ param_r = 4; } - testNoDiscrete(factors); + checkAllFactorContinuous(factors); // Creating the vectors. String factorNames = ""; @@ -112,9 +109,10 @@ gridJump += factor.getCardinality() / 2; - binf += domain.getCalculatorMinBound(); - - bsup += domain.getCalculatorMaxBound(); + //binf += domain.getCalculatorMinBound(); + binf+=0; + bsup+=0; + //bsup += domain.getCalculatorMaxBound(); } String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s," + @@ -128,7 +126,7 @@ rCall = editRInstruction(rCall); } - REngine engine = null; + REngine engine; try { engine = new RProxy(); @@ -178,9 +176,17 @@ parameters += ","; } - distribution += "\"qunif\""; - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; + Distribution r_distribution = domain.getDistribution(); + + distribution += "\""+ r_distribution.getInstruction() +"\""; + parameters += "\"["; + + for (Map.Entry<String,Object> param:domain.getDistributionParameters().entrySet()){ + parameters += param.getKey() + "=" + param.getValue() + ";"; + } + + parameters = StringUtils.removeEnd(parameters,";"); + parameters += "]\""; } engine.voidEval(String.format(factorDistribution, factorNames, distribution, parameters)); 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -82,7 +82,7 @@ List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); //Test all factors, if one is discrete, return null - testNoDiscrete(factors); + checkAllFactorContinuous(factors); try { REngine engine = new RProxy(); @@ -148,8 +148,8 @@ factorNames += "\"" + factors.get(i).getName() + "\""; distribution += "\"qunif\""; //add [min;max] to parameters - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; +// parameters += "\"[" + domain.getMinBound() + ";" + +// domain.getMaxBound() + "]\""; } engine.voidEval(String.format(isisFactorDistribution, factorNames, 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -78,7 +78,7 @@ List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); //The list of scenarios List<Factor> factors = plan.getFactors(); //The factors - testNoDiscrete(factors); + checkAllFactorContinuous(factors); try { @@ -144,9 +144,9 @@ factorNames += "\"" + factors.get(i).getName() + "\""; distribution += "\"qunif\""; //all distributions are qunif - double min = domain.getCalculatorMinBound(); - double max = domain.getCalculatorMaxBound(); - parameters += "\"[" + min + ";" + max + "]\""; +// double min = domain.getCalculatorMinBound(); +// double max = domain.getCalculatorMaxBound(); +// parameters += "\"[" + min + ";" + max + "]\""; } engine.voidEval(String.format(isisFactorDistribution, factorNames, distribution, parameters)); 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -102,13 +102,13 @@ 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))) + ","; - } +// 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))) + ","; +// } } if (domain instanceof DiscreteDomain) { @@ -178,9 +178,9 @@ if (domain instanceof ContinuousDomain){ ContinuousDomain contDomain = (ContinuousDomain)domain; distribution += "\"qunif\""; - parameters += "\"[" + contDomain.getMinBound() - + ";" + contDomain.getMaxBound() - + "]\""; +// parameters += "\"[" + contDomain.getMinBound() +// + ";" + contDomain.getMaxBound() +// + "]\""; } else { DiscreteDomain discDomain = (DiscreteDomain)domain; distribution += "\"discrete\""; 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -42,8 +42,6 @@ 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.domain.EquationContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; import fr.ifremer.isisfish.util.Doc; public class RegularFractions extends AbstractSensitivityAnalysis { @@ -159,16 +157,16 @@ Factor factor = plan.getFactors().get(i); Domain domain = factor.getDomain(); Double dFValue = (Double)dataFrame.get(i,j); - if ((domain instanceof MatrixContinuousDomain) - || (domain instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(dFValue); - } else { - ContinuousDomain contDomain = (ContinuousDomain)domain; - Double max = contDomain.getCalculatorMaxBound(); - Double min = contDomain.getCalculatorMinBound(); - Double value = min + (max - min) * dFValue / (param_p - 1); - factor.setValueForIdentifier(value); - } +// if ((domain instanceof MatrixContinuousDomain) +// || (domain instanceof EquationContinuousDomain)) { +// factor.setValueForIdentifier(dFValue); +// } else { +// ContinuousDomain contDomain = (ContinuousDomain)domain; +// Double max = contDomain.getCalculatorMaxBound(); +// Double min = contDomain.getCalculatorMinBound(); +// Double value = min + (max - min) * dFValue / (param_p - 1); +// factor.setValueForIdentifier(value); +// } experimentScenario.addFactor(factor); } thisExperimentScenarios.add(experimentScenario); 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 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -24,20 +24,16 @@ 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.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.util.Doc; import org.nuiton.j2r.types.RDataFrame; @@ -86,7 +82,7 @@ SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - testNoDiscrete(factors); + checkAllFactorContinuous(factors); String rInstruction = "a<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; String rCall = String.format(rInstruction, param_nboot); @@ -107,11 +103,32 @@ engine.voidEval("library(sensitivity)"); - engine.voidEval("X1<-data.frame(matrix(runif(" + factorNumber + "*" - + param_n + "),nrow=" + param_n + "))"); - engine.voidEval("X2<-data.frame(matrix(runif(" + factorNumber + "*" - + param_n + "),nrow=" + param_n + "))"); + String x = "<-data.frame(matrix(c("; + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + ContinuousDomain domain = (ContinuousDomain)factor.getDomain(); + + Distribution r_distribution = domain.getDistribution(); + + x += r_distribution.getInstruction() +"("+param_n+","; + + for (Map.Entry<String,Object> param:domain.getDistributionParameters().entrySet()){ + x += param.getKey() + "=" + param.getValue() + ","; + } + + x = StringUtils.removeEnd(x, ","); + + x+= "),"; + } + + x = StringUtils.removeEnd(x, ","); + + x+="),nrow="+param_n+"))"; + + engine.voidEval("X1"+x); + engine.voidEval("X2"+x); + engine.voidEval(rCall); // Creating the factors vector. @@ -147,18 +164,25 @@ for (int i = 0; i < factorNumber; i++) { Factor factor = factors.get(i); - Domain domain = factor.getDomain(); + ContinuousDomain domain = (ContinuousDomain)factor.getDomain(); if (i != 0) { distribution += ","; parameters += ","; factorNames += ","; } - distribution += "\"qunif\""; - ContinuousDomain continuousDomain = (ContinuousDomain) domain; - double min = continuousDomain.getCalculatorMinBound(); - double max = continuousDomain.getCalculatorMaxBound(); - parameters += "\"[" + min + ";" + max + "]\""; + Distribution r_distribution = domain.getDistribution(); + + distribution += "\""+ r_distribution.getInstruction() +"\""; + parameters += "\"["; + + for (Map.Entry<String,Object> param:domain.getDistributionParameters().entrySet()){ + parameters += param.getKey() + "=" + param.getValue() + ";"; + } + + parameters = StringUtils.removeEnd(parameters, ";"); + parameters += "]\""; + factorNames += "\"" + factor.getName() + "\""; } Modified: branches/4.0.1/src/test/resources/test-database/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java 2013-11-08 14:25:47 UTC (rev 3831) +++ branches/4.0.1/src/test/resources/test-database/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java 2013-11-08 16:51:41 UTC (rev 3832) @@ -29,6 +29,7 @@ import java.util.Collections; import java.util.List; +import fr.ifremer.isisfish.util.ScriptUtil; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; @@ -384,7 +385,7 @@ exportHisto += experiences.getExperience(number).q1 + ";" + experiences.getExperience(number).q2 + ";" + experiences.getExperience(number).criteria + "\n"; - org.nuiton.util.FileUtil.writeString(exportHistoric, exportHisto); + ScriptUtil.writeString(exportHistoric, exportHisto); return doNext; }// fin du after simulation

1 0

r3831 - branches/4.0.1/src/test/resources/test-database/sensitivityanalysis
by echatellier＠users.forge.codelutin.com Nov. 8, 2013

Nov. 8, 2013

Author: echatellier Date: 2013-11-08 15:25:47 +0100 (Fri, 08 Nov 2013) New Revision: 3831 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3831 Log: Use renamed AS scripts Added: 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 Removed: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRDOptimal.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFast.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFrF2.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRMorris.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRSobol.java branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRegularFractions.java Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,405 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +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.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; +import java.util.Collection; +import java.util.List; +import java.util.Map; + +/** + * User: couteau + * Date: 14 janv. 2010 + * Time: 11:58:09 + */ +public class DOptimal extends AbstractSensitivityAnalysis { + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + @Doc("Order") + public int param_order=1; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return false; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + + setIsisFactorsR(plan, outputDirectory); + + //extract the factors from the design plan + List<Factor> factors = plan.getFactors(); + int factorsNb = factors.size(); + + try { + REngine engine = new RProxy(); + + //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,... + String factorsNames = ""; + + //Create a list of the factors under the form factor1,factor2,... + String factorNames = ""; + + //Create a list of the factors under the form factor1+factor2+... + String factorPlus=""; + + //create the factors vectors + for (Factor factor : factors) { + //The factor values vector + String factorName = factor.getName().replaceAll(" ", ""); + factorsNames += factorName + "=" + factorName + ","; + factorNames += factorName + ","; + factorPlus += factorName + "+"; + + String vector = factorName + "<-c("; + + 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))) + ","; + } + } else { + Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); + int nbValues = values.size(); + for (int i = 0; i < nbValues; i++) { + vector += "as.integer(" + i + "),"; + } + } + + vector = vector.substring(0, vector.length() - 1); + + vector += ")"; + + engine.voidEval(vector); + + + } + + factorsNames = factorsNames.substring(0,factorsNames.length()-1); + factorNames = factorNames.substring(0,factorNames.length()-1); + factorPlus = factorPlus.substring(0,factorPlus.length()-1); + + + //X<-expand.grid(vector=???,weight=???) + String expandGrid = "expandgrid<-expand.grid(%s)"; + + + + String rCall = String.format(expandGrid,factorsNames); + + engine.voidEval(rCall); + + if (param_order ==1 ){ + rCall = "x<-optFederov(~(%s),data=expandgrid, " + + "approximate =FALSE, center=F, criterion = \"D\"," + + "nRepeats=10)"; + } else { + rCall = "x<-optFederov(~(%s)^"+param_order+",data=expandgrid, " + + "approximate =FALSE, center=F, criterion = \"D\"," + + "nRepeats=10)"; + } + + rCall = String.format(rCall,factorPlus); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + engine.voidEval("runif(1)"); + + engine.voidEval(rCall); + + engine.eval("expPlan<-as.data.frame(x$design)"); + RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + int nbExperiments = (Integer)engine.eval("dim(x$design)[1]"); + + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorsNb; i++) { + Factor factor = factors.get(i); + factor.setValueForIdentifier(dataFrame.get(i, j)); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + + String factorDistribution = "isis.factor.distribution<-data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + + for (int i = 0; i < factorsNb; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + } + if (domain instanceof ContinuousDomain){ + ContinuousDomain contDomain = (ContinuousDomain)domain; + distribution += "\"qunif\""; + parameters += "\"[" + contDomain.getMinBound() + + ";" + contDomain.getMaxBound() + + "]\""; + } else { + DiscreteDomain discDomain = (DiscreteDomain)domain; + distribution += "\"discrete\""; + parameters+="\"["; + Map<Object, Object> values = discDomain.getValues(); + int count=0; + Collection<Object> collecValues = values.values(); + for (Object value:collecValues){ + if (count!=0){ + parameters += ","; + } + parameters += StringUtils.replace(value.toString(), "\"", "\\\"") ; + count++; + } + parameters+="]\""; + } + } + engine.voidEval(String.format(factorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-\"" + rCall + "\""); + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + engine.voidEval("isis.simule<-x$design"); + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + // Save Isis R session + engine.saveRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + + } catch (RException eee) { + throw new SensitivityException("Can't generate scenarios", eee); + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + try { + + REngine engine = new RProxy(); + + //Get Isis R session + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + //Get back the factors number + int factorNumber = (Integer)engine.eval("dim(x$design)[2]"); + + SimulationParameter param = simulationStorages.get(0).getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + SimulationStorage firstStorage = simulationStorages.get(0); + + String firstStorageName = firstStorage.getName().replaceAll("-", ""); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String name = sensitivityExport.getExportFilename(); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + name + ")"); + + //Create the dataforaov data.frame + String dataFrame = "dataforaov<-data.frame(x$design," + + name + "=" + name + ")"; + engine.voidEval(dataFrame); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~("; + for (int j = 0; j < factorNumber; j++) { + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine.eval("names(x$design)[" + (j + 1) + "]") + + "+"; + } else { + aovCall = aovCall + + engine.eval("names(x$design)[" + (j + 1) + "]") + + ")"; + if(param_order>1){ + aovCall+="^" + param_order + ",data=dataforaov)"; + }else{ + aovCall+=",data=dataforaov)"; + } + } + } + engine.voidEval(aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + +//Compute Sum of Squares and Sensitivity indices + engine.voidEval("SoS<-summary(aovresult)[[1]][1:dim(summary(aovresult)[[1]])[1],2]"); + engine.voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:dim(summary(aovresult)[[1]])[1]]"); + engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity<-data.frame(" + + "SoS[1:dim(summary(aovresult)[[1]])[1]]," + + "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); + engine.voidEval("names(exportsensitivity)<-c(" + + "\"Sum Of Squares\"," + + "\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); + + + //Set dataforaov names + engine.voidEval("resultsnames<-c(names(x$design),\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.setwd(outputDirectory); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-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," + + "\"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); + + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of D optimal method method using R, needs" + + "AlgDesign package to work"; + } +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/DOptimal.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,358 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +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.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.types.RDataFrame; + +/** + * Implementation of Fast method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author$ + */ +public class Fast extends AbstractSensitivityAnalysis { + + @Doc("an integer giving the sample size, i.e. the length of the " + + "discretization of the s-space (see Cukier et al.). (default=20)") + public int param_n = 20; + + @Doc("an integer specifying the interference parameter, i.e. the number " + + "of harmonics to sum in the Fourier series decomposition (see Cukier et " + + "al.). (default=6)") + public int param_M = 6; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputDirectory); + + RDataFrame dataFrame; + int nbExperiments; + int factorNumber = plan.getFactors().size(); + List<Factor> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + for (int i = 0; i < factorNumber; i++) { + if (factors.get(i).getDomain() instanceof DiscreteDomain) { + throw new SensitivityException(factors.get(i).getName() + + " has a discrete domain, this is not acceptable for fast " + + "method."); + } + } + String rInstruction = "a<-fast99(" + + "model=NULL," + + "factors=%s, " + + "n=%s, " + + "M=%s, " + + "q = \"qunif\", " + + "q.arg=list(min=0,max=1))"; + String rCall = String.format(rInstruction, factors.size(), param_n, + param_M); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + try { + + REngine engine = new RProxy(); + + engine.clearSession(); + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + + // Run sensitivity analysis + engine.voidEval(rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + String factorName = factors.get(i).getName(); + if (i != (factorNumber - 1)) { + rInstruction += "\"" + factorName + "\","; + } else { + rInstruction += "\"" + factorName + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + + // Get back experiment plan + dataFrame = (RDataFrame) engine.eval("a$X"); + dataFrame.setVariable("a$X"); + + nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); + + String factorDistribution = "isis.factor.distribution<-data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + // Creating the vectors. + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + factorNames += ","; + } + + distribution += "\"qunif\""; + parameters += "\"[" + domain.getMinBound() + ";" + + domain.getMaxBound() + "]\""; + factorNames += "\"" + factor.getName() + "\""; + } + engine.voidEval(String.format(factorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-a$call"); + + + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + + engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + + "\"isis-fish-externe-R\""); + + engine.voidEval("isis.simule<-data.frame(a$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(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + Domain domain = factor.getDomain(); + if ((domain instanceof MatrixContinuousDomain) + || (domain instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(dataFrame.get(i,j)); + } else { + ContinuousDomain continuousDomain = (ContinuousDomain)domain; + Double min = continuousDomain.getCalculatorMinBound(); + Double max = continuousDomain.getCalculatorMaxBound(); + Double dFValue = (Double)dataFrame.get(i,j); + Double value = min + (max - min) * dFValue; + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + } catch (RException eee) { + throw new SensitivityException("Can't generate scenarios", eee); + } + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + SimulationStorage storage = simulationStorages.get(0); + String simulationName = storage.getName().replaceAll("-", ""); + + try { + + REngine engine = new RProxy(); + + //Clear session + engine.clearSession(); + + //Get Isis R session + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + engine.setwd(outputDirectory); + + // Call R + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + + SimulationParameter param = simulationStorages.get(0).getParameter(); + + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule,\"nomModel\")<-" + + "\"isis-fish-externe-R\""); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Compute results + engine.voidEval("tell(a,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"); + + //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)"); + + //setting isis.methodAnalyse attributes + engine.voidEval("attr(isis.methodAnalyse,\"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)"); + + //Set working directory + engine.setwd(outputDirectory); + + //Export V + engine.voidEval("write.csv(a$V,\"" + name + "_V.csv\")"); + + //Export D1 + engine.voidEval("write.csv(a$D1,\"" + name + "_D1.csv\")"); + + //Export Dt + engine.voidEval("write.csv(a$Dt,\"" + name + "_Dt.csv\")"); + //Set dfresults names + engine.voidEval("resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + + //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)); + + } + + //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); + } + } + + @Override + public String getDescription() { + return "Implementation of FAST method using R (needs the sensitivity " + + "package to work)"; + } + +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Fast.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,357 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +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.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 Morris 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; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continus. + * + * @return {@code true} s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return false; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputDirectory); + + RDataFrame dataFrame; + int nbExperiments; + int factorNumber = plan.getFactors().size(); + + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + + List<Factor> factors = plan.getFactors(); + + if (param_r == 0) { + param_r = 4; + } + + testNoDiscrete(factors); + + // Creating the vectors. + String factorNames = ""; + String levels = ""; + String gridJump = ""; + String binf = ""; + String bsup = ""; + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); + if (i != 0) { + factorNames += ","; + levels += ","; + gridJump += ","; + binf += ","; + bsup += ","; + } + + factorNames += "\"" + factor.getName() + "\""; + + levels += factor.getCardinality(); + + gridJump += factor.getCardinality() / 2; + + binf += domain.getCalculatorMinBound(); + + bsup += domain.getCalculatorMaxBound(); + } + + 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))"; + + String rCall = String.format(rInstruction, factorNames, param_r, + levels, gridJump, binf, bsup); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + REngine engine = null; + + try { + engine = new RProxy(); + + 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)"); + + // Run sensitivity analysis + engine.voidEval(rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c(%s)"; + rCall = String.format(rInstruction, factorNames); + + engine.voidEval(rCall); + + // Set output directory + engine.setwd(outputDirectory); + + // Get back experiment plan + engine.eval("expPlan<-as.data.frame(a$X)"); + dataFrame = (RDataFrame) engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + + nbExperiments = (Integer)engine.eval("dim(expPlan)[1]"); + + String factorDistribution = "isis.factor.distribution<-data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + } + + distribution += "\"qunif\""; + parameters += "\"[" + domain.getMinBound() + ";" + + domain.getMaxBound() + "]\""; + } + engine.voidEval(String.format(factorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-a$call"); + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + 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++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + factor.setValueForIdentifier(dataFrame.get(i, j)); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + } catch (RException eee) { + throw new SensitivityException("Can't generate scenarios", eee); + } + + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + SimulationStorage storage = simulationStorages.get(0); + String simulationName = storage.getName().replaceAll("-", ""); + + REngine engine = null; + + try { + engine = new RProxy(); + + 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. + engine.voidEval("library(sensitivity)"); + + //Set the working directory (for exports) + engine.setwd(outputDirectory); + + SimulationParameter param = simulationStorages.get(0) + .getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule,\"nomModel\")<-" + + "\"isis-fish-externe-R\""); + + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Compute results + engine.voidEval("tell(a,y=" + name + ")"); + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-list(" + + //"\"isis.factors\"=isis.factors," + + //"\"isis.factor.distribution\"=isis.factor.distribution," + + "\"isis.simule\"=isis.simule," + + "\"call_method\"=\"tell(a,y=" + name + ")" + "\"," + + "\"analysis_result\"=a)"); + + //setting isis.methodAnalyse attributes + engine.voidEval("attr(isis.methodAnalyse,\"nomModel\")<-" + + "\"isis-fish-externe-R\""); + + // Get back the sensitivity results, mu, mu star and sigma. + engine.voidEval("mu<-apply(a$ee, 2, mean)"); + engine.voidEval("mu.star <- apply(a$ee, 2, function(a) mean(abs(a)))"); + engine.voidEval("sigma <- apply(a$ee, 2, sd)"); + + //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"); + + //Create the data.frame of scenarios and results for export purpose + engine.voidEval("dfresults<-data.frame(a$X," + name + ")"); + + //Set dfresults names + engine.voidEval("resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + + //Export sensitivity indices + engine.voidEval("write.csv(df," + + "\"" + name + "_SensitivityIndices.csv\")"); + + //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)); + + } + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of Morris method using R (needs the sensitivity" + + " package to work)"; + } + +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Morris.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,404 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +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.domain.ContinuousDomain; +import fr.ifremer.isisfish.util.Doc; +import org.nuiton.j2r.types.RDataFrame; + +/** + * Implementation of Optimum Latin Hypercube method using R. + * + * @author jcouteau + * @version $Revision$ + */ +public class OptimumLHS extends AbstractSensitivityAnalysis { + + @Doc("Number of simulations (default=10)") + public int param_simulationNumber = 10; + @Doc("The maximum number of times the Columnwise Pairwise algorithm is applied to all the columns(default=2).") + public int param_MaxSweeps = 2; + @Doc("The optimal stopping criterion (between 0 and 1) (default=0.1).") + public double param_eps = 0.1; + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputdirectory); + + int factorNumber = plan.getFactors().size(); + List<Factor> factors = plan.getFactors(); + RDataFrame dataFrame; + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + //Test all factors, if one is discrete, return null + testNoDiscrete(factors); + + try { + REngine engine = new RProxy(); + + //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 rCall = String.format(rInstruction, param_simulationNumber, + factorNumber, param_MaxSweeps, param_eps); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + //Create the scenarios + engine.voidEval(rCall); + + // Get back experiment plan + engine.eval("expPlan<-as.data.frame(x)"); + dataFrame = (RDataFrame)engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + + // Setting up the scenarios. + for (int j = 0; j < param_simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + factor.setValueForIdentifier(dataFrame.get(i, j)); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String isisFactorDistribution = "isis.factor.distribution<-" + + "data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factors.size(); i++) { + Factor tempFactor = factors.get(i); + ContinuousDomain domain = (ContinuousDomain) tempFactor.getDomain(); + if (i != 0) { + distribution += ","; + factorNames += ","; + parameters += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + distribution += "\"qunif\""; + //add [min;max] to parameters + parameters += "\"[" + domain.getMinBound() + ";" + + domain.getMaxBound() + "]\""; + } + + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-" + "\"x<-optimumLHS(" + + "n=" + param_simulationNumber + + ",k=" + factorNumber + + ",maxSweeps=" + param_MaxSweeps + + ",eps=" + param_eps + ")\""); + + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("isis.simule<-data.frame(x)"); + + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + String data = "data<-data.frame("; + + //Create the factors vectors and the dataFrame instruction + for (int j = 0; j < factors.size(); j++) { + //The factor values vector + String vector; + //Get back the factor + Scenario scenario = thisExperimentScenarios.get(0); + Factor factor = scenario.getFactors().get(j); + String factorName = factor.getName().replaceAll(" ", ""); + + vector = factorName + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + //Get back the displayed value the factor + Scenario tempScenario = thisExperimentScenarios.get(i); + Factor tempFactor = tempScenario.getFactors().get(j); + Object value = tempFactor.getDisplayedValue(); + + if (i < (param_simulationNumber - 1)) { + vector = vector + value + ","; + } else { + vector += value; + } + + } + vector += ")"; + engine.voidEval(vector); + + if (j < factors.size() - 1) { + data += factorName + "=factor(" + factorName + "),"; + } else { + data += factorName + "=factor(" + factorName + "))"; + } + } + engine.voidEval(data); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + + // Save Isis R session + engine.saveRData(outputdirectory.getParentFile(), + outputdirectory.getName()); + + engine.terminate(); + + } catch (Exception e) { + throw new SensitivityException("Can't generate scenarios", e); + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + //The first storage to get the name and parameters all along the method + SimulationStorage storage = simulationStorages.get(0); + + String simulationName = storage.getName().replaceAll("-", ""); + + try { + + REngine engine = new RProxy(); + + //Clear session + engine.clearSession(); + + //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 + param_simulationNumber = (Integer) (engine.eval("length(factors[,1])")); + + SimulationParameter param = storage.getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + SensitivityExport export = param.getSensitivityExport().get(k); + String name = export.getExportFilename(); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + + name + "=" + name + ")"; + engine.voidEval(dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~"; + for (int j = 0; j < factorNumber; j++) { + + String factorName = (String) engine.eval("names(factors)[" + (j + 1) + "]"); + factorName = factorName.replaceAll(" ", "."); + + if (j < (factorNumber - 1)) { + aovCall += factorName + + "+"; + } else { + aovCall += factorName + ",data=dataforaov)"; + } + } + engine.voidEval(aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //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)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity<-data.frame(" + + "SoS[1:dim(summary(aovresult)[[1]])[1]]," + + "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); + engine.voidEval("names(exportsensitivity)<-c(" + + "\"Sum Of Squares\"," + + "\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); + + + //Set dataforaov names + engine.voidEval("names(dataforaov)<-c(factornames,\"Result\")"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.setwd(outputDirectory); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + name + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + name + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-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," + + "\"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); + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of Random Latin Hypercube method method " + + "using R (needs 'lhs' package to work)"; + } + +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/OptimumLHS.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,402 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +import java.io.File; +import java.lang.String; +import java.util.List; + +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.util.Doc; + +/** + * Implementation of Random Latin Hypercube method using R. + * + * @author jcouteau + * @version $Revision$ + */ +public class RandomLHS extends AbstractSensitivityAnalysis { + + @Doc("Simulation number (default=10)") + public int param_simulationNumber = 10; + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputDirectory); + + int factorNumber = plan.getFactors().size(); + RDataFrame dataFrame; //The dataframe to get back the scenarios from R + SensitivityScenarios thisExperiment = new SensitivityScenarios(); //The experiment we will build + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); //The list of scenarios + List<Factor> factors = plan.getFactors(); //The factors + + testNoDiscrete(factors); + + try { + + REngine engine = new RProxy(); //The R engine + + //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 rCall = String.format(rInstruction, param_simulationNumber, + factorNumber); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + engine.voidEval(rCall); + + // Get back experiment plan + engine.eval("expPlan<-as.data.frame(x)"); + dataFrame = (RDataFrame)engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + + // Setting up the scenarios. + for (int j = 0; j < param_simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); //The factor we are setting + factor.setValueForIdentifier(dataFrame.get(i,j)); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String isisFactorDistribution = "isis.factor.distribution<-" + + "data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + + //Create the strings for the isis.MethodExp instruction + for (int i = 0; i < factors.size(); i++) { + ContinuousDomain domain = (ContinuousDomain)factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; //the distribution + factorNames += ","; //the factor names + parameters += ","; //the parameters + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + distribution += "\"qunif\""; //all distributions are qunif + double min = domain.getCalculatorMinBound(); + double max = domain.getCalculatorMaxBound(); + parameters += "\"[" + min + ";" + max + "]\""; + } + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-" + "\"x<-randomLHS(" + + param_simulationNumber + "," + factorNumber + ")\""); + + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("isis.simule<-data.frame(x)"); + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + String data = "data<-data.frame("; + + //Create the factors vectors and the dataFrame instruction + for (int j = 0; j < factors.size(); j++) { + Scenario firstScenario = thisExperimentScenarios.get(0); + Factor factor = firstScenario.getFactors().get(j); + String factorName = factor.getName().replaceAll(" ", ""); + + //the vector of the factor values + //read all the values one by one from the already created + //scenarios. + String vector = factorName + "<-c("; + for (int i = 0; i < param_simulationNumber; i++) { + Scenario scenario = thisExperimentScenarios.get(i); + List<Factor> factorList = scenario.getFactors(); + Factor factor1 = factorList.get(j); + if (i < (param_simulationNumber - 1)) { + vector += factor1.getDisplayedValue() + ","; + } else { + vector += factor1.getDisplayedValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + + //add factor1=factor(factor1) for each factor... + if (j < factors.size() - 1) { + data += factorName + "=factor(" + factorName + "),"; + } else { + data += factorName + "=factor(" + factorName + "))"; + } + + } + engine.voidEval(data); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + rInstruction += ")"; + engine.voidEval(rInstruction); + + // Clean RData + for (Factor factor:factors) { + engine.remove(factor.getName().replaceAll(" ", "")); + } + + // Save Isis R session + engine.saveRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + engine.terminate(); + + } catch (Exception e) { + throw new SensitivityException("Can't generate scenarios", e); + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + SimulationStorage simulationStorage1 = simulationStorages.get(0); + String simName = simulationStorage1.getName(); + String simulationName = simName.replaceAll("-", ""); + SimulationParameter param = simulationStorage1.getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + //List<SensitivityExport> export = param.getSensitivityExport(); + + try { + REngine engine = new RProxy(); + + //Clear session + engine.clearSession(); + + //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)"); + + //Get back the simulation number + param_simulationNumber = (Integer) (engine.eval("length(factors[,1])")); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + // Creates the R expression to import results in R + String name = param.getSensitivityExport().get(k) + .getExportFilename(); + + //Create the dataforaov data.frame + String dataframe = "dataforaov<-data.frame(factors," + name + + "=" + name + ")"; + engine.voidEval(dataframe); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~"; + for (int j = 0; j < factorNumber; j++) { + + if (j < (factorNumber - 1)) { + aovCall += engine.eval("names(factors)[" + (j + 1) + "]") + + "+"; + } else { + aovCall += engine.eval("names(factors)[" + (j + 1) + "]") + + ",data=dataforaov)"; + } + } + engine.voidEval(aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //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)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity<-data.frame(" + + "SoS[1:dim(summary(aovresult)[[1]])[1]]," + + "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); + engine.voidEval("names(exportsensitivity)<-c(" + + "\"Sum Of Squares\"," + + "\"Sensitivity indices\")"); + 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"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.setwd(outputDirectory); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k).getExportFilename() + + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k).getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-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," + + "\"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); + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of Random Latin Hypercube method method using" + + " R needs the 'lhs' package to work)"; + } + +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RandomLHS.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,374 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +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.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; +import java.util.Collection; +import java.util.List; +import java.util.Map; + +/** + * User: couteau + * Date: 6 janv. 2010 + * Time: 14:31:09 + */ +public class RegularExpandGrid extends AbstractSensitivityAnalysis { + + @Doc("Interaction order") + public int param_order = 2; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return false; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + + setIsisFactorsR(plan, outputDirectory); + + //extract the factors from the design plan + List<Factor> factors = plan.getFactors(); + int factorsNb = factors.size(); + + try { + REngine engine = new RProxy(); + + //Get Isis R session + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + //Create a list of the factors under the form factor1=factor1,... + String factorsNames = ""; + + //Create a list of the factors under the form factor1,factor2,... + String factorNames = ""; + + //create the factors vectors + for (Factor factor : factors) { + //The factor values vector + String factorName = factor.getName().replaceAll(" ", ""); + factorsNames += factorName + "=" + factorName + ","; + factorNames += factorName + ","; + String vector = factorName + "<-c("; + + 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))) + ","; + } + } + + if (domain instanceof DiscreteDomain) { + Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); + int nbValues = values.size(); + for (int i = 0; i < nbValues; i++) { + vector += "as.integer(" + i + "),"; + } + } + + vector = vector.substring(0, vector.length() - 1); + + vector += ")"; + + engine.voidEval(vector); + + + } + + factorsNames = factorsNames.substring(0,factorsNames.length()-1); + factorNames = factorNames.substring(0,factorNames.length()-1); + + + //X<-expand.grid(vector=???,weight=???) + String expandGrid = "x<-expand.grid(%s)"; + + String rCall = String.format(expandGrid,factorsNames); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + engine.voidEval(rCall); + + engine.eval("expPlan<-as.data.frame(x)"); + RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + int nbExperiments = (Integer)engine.eval("dim(x)[1]"); + + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorsNb; i++) { + Factor factor = factors.get(i); + factor.setValueForIdentifier(dataFrame.get(i, j)); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + + String factorDistribution = "isis.factor.distribution<-data.frame(" + + "NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + String distribution = ""; + String parameters = ""; + + for (int i = 0; i < factorsNb; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + } + if (domain instanceof ContinuousDomain){ + ContinuousDomain contDomain = (ContinuousDomain)domain; + distribution += "\"qunif\""; + parameters += "\"[" + contDomain.getMinBound() + + ";" + contDomain.getMaxBound() + + "]\""; + } else { + DiscreteDomain discDomain = (DiscreteDomain)domain; + distribution += "\"discrete\""; + parameters+="\"["; + Map<Object, Object> values = discDomain.getValues(); + int count=0; + Collection<Object> collecValues = values.values(); + for (Object value:collecValues){ + if (count!=0){ + parameters += ","; + } + parameters += StringUtils.replace(value.toString(), "\"", "\\\"") ; + count++; + } + parameters+="]\""; + } + } + engine.voidEval(String.format(factorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-\"" + + String.format(expandGrid,factorsNames) + "\""); + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + engine.voidEval("isis.simule<-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()); + + + } catch (RException eee) { + throw new SensitivityException("Can't generate scenarios", eee); + } + + return thisExperiment; + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + try { + + REngine engine = new RProxy(); + + //Get Isis R session + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + //Get back the factors number + int factorNumber = (Integer)engine.eval("dim(x)[2]"); + + SimulationParameter param = simulationStorages.get(0).getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + + SimulationStorage firstStorage = simulationStorages.get(0); + + String firstStorageName = firstStorage.getName().replaceAll("-", ""); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String name = sensitivityExport.getExportFilename(); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + name + ")"); + + //Create the dataforaov data.frame + String dataFrame = "dataforaov<-data.frame(x," + + name + "=" + name + ")"; + engine.voidEval(dataFrame); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~("; + for (int j = 0; j < factorNumber; j++) { + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine.eval("names(x)[" + (j + 1) + "]") + + "+"; + } else { + aovCall = aovCall + + engine.eval("names(x)[" + (j + 1) + "]") + + ")"; + if(param_order>1){ + aovCall+="^" + param_order + ",data=dataforaov)"; + }else{ + aovCall+=",data=dataforaov)"; + } + } + } + engine.voidEval(aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //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)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity<-data.frame(" + + "SoS[1:dim(summary(aovresult)[[1]])[1]]," + + "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); + engine.voidEval("names(exportsensitivity)<-c(" + + "\"Sum Of Squares\"," + + "\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.setwd(outputDirectory); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + + param.getSensitivityExport().get(k) + + .getExportFilename() + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + + param.getSensitivityExport().get(k) + .getExportFilename() + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-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," + + "\"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); + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of Expand Grid method using R"; + } +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularExpandGrid.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,398 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +import java.io.File; +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.domain.EquationContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; +import fr.ifremer.isisfish.util.Doc; + +public class RegularFractions extends AbstractSensitivityAnalysis { + + @Doc("the path of the directory where the R function is stored (do not indicate the RegularFractions.R file name)") + public String param_pathToFunction = ""; + + @Doc("unique prime number of levels of all input and unit factors") + public int param_p = 2; + + @Doc("number of unit factors (so that there are N=p^r units)") + public int param_r = 2; + + @Doc("resolution of the fraction") + public int param_resolution = 2; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputDirectory); + + RDataFrame dataFrame; + int factorNumber = plan.getFactors().size(); + List<Factor> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + String factorNames = ""; + + //Test all factors, if one is discrete, return null + //Create a string with all factors names + for (int i = 0; i < factorNumber; i++) { + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + factorNames += ","; + } + + factorNames += "\"" + factors.get(i).getName() + "\""; + + if (domain instanceof DiscreteDomain) { + throw new SensitivityException(factors.get(i).getName() + + " has a discrete domain, this is not acceptable for " + + "this method."); + } + } + + try { + + REngine engine = new RProxy(); + + //Clear session + engine.clearSession(); + + //Get Isis R session + engine.loadRData(outputDirectory.getParentFile(), + outputDirectory.getName()); + + //Set the working directory (to import the R function) + engine.setwd(new File(param_pathToFunction)); + + //Import the function + engine.voidEval("source(\"regularfractions.R\")"); + + //Create the instruction + String rInstruction = "x<-regular.fraction(%s,%s,%s,%s)"; + String rCall = String.format(rInstruction, factors.size(), param_p, + param_r, param_resolution); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + // Run function + engine.voidEval(rCall); + + // Run function + engine.voidEval("call<-\"" + rCall + "\""); + + // Creating the factors vector. + rInstruction = "factornames<-c(%s)"; + rCall = String.format(rInstruction, factorNames); + + engine.voidEval(rCall); + + + // Get back experiment plan + engine.eval("expPlan<-as.data.frame(x[[1]])"); + dataFrame = (RDataFrame)engine.eval("expPlan"); + dataFrame.setVariable("expPlan"); + + //Get back the simulation number + int simulationNumber = (Integer) engine.eval("length(x[[1]][,1])"); + + // Setting up the scenarios. + for (int j = 0; j < simulationNumber; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factors.size(); i++) { + Factor factor = plan.getFactors().get(i); + Domain domain = factor.getDomain(); + Double dFValue = (Double)dataFrame.get(i,j); + if ((domain instanceof MatrixContinuousDomain) + || (domain instanceof EquationContinuousDomain)) { + factor.setValueForIdentifier(dFValue); + } else { + ContinuousDomain contDomain = (ContinuousDomain)domain; + Double max = contDomain.getCalculatorMaxBound(); + Double min = contDomain.getCalculatorMinBound(); + Double value = min + (max - min) * dFValue / (param_p - 1); + factor.setValueForIdentifier(value); + } + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + + String dataframe = "data<-data.frame("; + + //Create the factors vectors and the dataframe instruction + for (int j = 0; j < factorNumber; j++) { + Factor factor = factors.get(j); + String factorName = factor.getName().replaceAll(" ", ""); + + String vector = factorName + "<-c("; + for (int i = 0; i < simulationNumber; i++) { + Scenario scenario = thisExperimentScenarios.get(i); + List<Factor> newFactors = scenario.getFactors(); + Factor factor1 = newFactors.get(j); + + if (i < (simulationNumber - 1)) { + vector += factor1.getDisplayedValue() + ","; + } else { + vector += factor1.getDisplayedValue(); + } + + } + vector = vector + ")"; + engine.voidEval(vector); + + if (j < factorNumber - 1) { + dataframe += factorName + "=factor(" + factorName + "),"; + } else { + dataframe += factorName + "=factor(" + factorName + "))"; + } + + } + engine.voidEval(dataframe); + + engine.voidEval("isis.factor.distribution<-c(0.0)"); + + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + //Create isis.Simule + engine.voidEval("isis.simule<-data.frame(data)"); + + 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()); + + engine.terminate(); + + } catch (RException eee) { + throw new SensitivityException("Can't generate scenarios", eee); + } + + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + SimulationStorage firstStorage = simulationStorages.get(0); + SimulationParameter param = firstStorage.getParameter(); + List<SensitivityExport> exports = param.getSensitivityExport(); + int sensitivityNumber = exports.size(); + String simulationName = firstStorage.getName().replaceAll("-", ""); + + try { + + REngine engine = new RProxy(); + + //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]"); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + for (SensitivityExport export : exports) { + + String name = export.getExportFilename(); + + //Create the dataforaov data.frame + String dataFrame = "dataforaov<-data.frame(data," + + name + "=" + name + ")"; + engine.voidEval(dataFrame); + + //Call aov() + String aovCall = "aovresult<-aov(" + name + "~("; + for (int j = 0; j < factorNumber; j++) { + + if (j < (factorNumber - 1)) { + aovCall = aovCall + + engine.eval("names(data)[" + (j + 1) + "]") + + "+"; + } else { + aovCall = aovCall + + engine.eval("names(data)[" + (j + 1) + "]") + + ")"; + if (param_resolution <= 4) { + aovCall += ",data=dataforaov)"; + } else { + aovCall += "^2,data=dataforaov)"; + } + } + } + engine.voidEval(aovCall); + + /*Export the results + *Export format is csv, data separated by ',' + *Results Export name is sensitivityExportName_Results.csv + *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv + */ + + //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)"); + + //Create a data.frame to export sensitivity important results in one file. + engine.voidEval("exportsensitivity<-data.frame(" + + "SoS[1:dim(summary(aovresult)[[1]])[1]]," + + "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); + engine.voidEval("names(exportsensitivity)<-c(" + + "\"Sum Of Squares\"," + + "\"Sensitivity indices\")"); + 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"); + + /*Set the export directory + *Export directory is the first simulation export directory. + */ + engine.setwd(outputDirectory); + + //Save the results with the scenarios. + engine.voidEval("write.csv(dataforaov,\"" + name + + "_Results.csv\")"); + + //Save the sensitivity indices + engine.voidEval("write.csv(exportsensitivity,\"" + name + + "_SensitivityIndices.csv\")"); + //FIXME export through java to enable export when using Rserve (when distant Rserve). + + //creating isis.methodAnalyse + engine.voidEval("isis.methodAnalyse<-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," + + "\"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); + + //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); + } + + } + + @Override + public String getDescription() { + return "Implementation of Regular fractions method using R"; + } + +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/RegularFractions.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,390 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.domain.EquationContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; -import fr.ifremer.isisfish.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; - -/** - * Implementation of ExpandGrid method using Java - * - * @author jcouteau - * @version $Revision: 1.0 $ - * - */ -public class SensitivityCalculatorJavaExpandGrid extends - AbstractSensitivityAnalysis { - - @Doc("Interaction order") - public int param_order = 2; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return false; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputDirectory); - - int k = 1; //number of sensitivity scenarios (initialization) - int factorNumber = plan.getFactors().size(); //number of factors - List<Factor> factors = plan.getFactors(); //list of factors - - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - Domain domain = factor.getDomain(); - - //calculate the number of scenarios - if (domain instanceof ContinuousDomain) { - if (factor.getCardinality() != 0) { - k = k * factor.getCardinality(); - } - } else if (domain instanceof DiscreteDomain) { - DiscreteDomain discreteDomain = (DiscreteDomain)domain; - if (discreteDomain.getValues().size() != 0) { - k = k * discreteDomain.getValues().size(); - } - } - } - - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - for (int i = 0; i < k; i++) { - int result = 0; //used for the euclidian division - int rest = i; //used for the euclidian division - Scenario experimentScenario = new Scenario(); - for (int j = 0; j < factorNumber; j++) { - Factor factor = factors.get(j); - Domain domain = factor.getDomain(); - if (domain instanceof ContinuousDomain) { - ContinuousDomain continuousDomain = (ContinuousDomain)domain; - Double max = continuousDomain.getCalculatorMaxBound(); - Double min = continuousDomain.getCalculatorMinBound(); - int card = factor.getCardinality(); - - //Do the euclidian division - result = (int) Math.floor(rest / card); - rest = rest - (card * result); - - //Calculate the value of the factor - Double value = min + ((max - min) / (card - 1) * rest); - if ((domain instanceof MatrixContinuousDomain) - || (domain instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(value); - } else { - factor.setValueForIdentifier(value); - } - } - if (factor.getDomain() instanceof DiscreteDomain) { - DiscreteDomain discreteDomain = (DiscreteDomain)domain; - int card = discreteDomain.getValues().size(); - - //Do the euclidian division - result = (int) Math.floor(rest / card); - rest = rest - (card * result); - - //Select the value of the factor - factor.setValueForIdentifier(rest); - } - rest = result; - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - - } - thisExperiment.setScenarios(thisExperimentScenarios); - - thisExperimentScenarios = thisExperiment.getScenarios(); - - /* - * Call R to save the data for result analysis - */ - int scenariosNumber = thisExperimentScenarios.size(); - - try { - - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - String dataframe = "data<-data.frame("; - - //Create the factors vectors and the dataframe instruction - for (int j = 0; j < factorNumber; j++) { - - Factor factor = factors.get(j); - String factorName = factor.getName().replaceAll(" ", ""); - - //String vector = "factor" + j + "<-c("; - String vector = factorName + "<-c("; - for (int i = 0; i < scenariosNumber; i++) { - Scenario scenario = thisExperimentScenarios.get(i); - List<Factor> newFactors = scenario.getFactors(); - Factor factor1 = newFactors.get(j); - - if (i < (scenariosNumber - 1)) { - vector += factor1.getDisplayedValue() + ","; - } else { - vector += factor1.getDisplayedValue(); - } - - } - vector = vector + ")"; - engine.voidEval(vector); - - if (j < factorNumber - 1) { - dataframe += factorName + "=factor(" + factorName + "),"; - } else { - dataframe += factorName + "=factor(" + factorName + "))"; - } - - } - engine.voidEval(dataframe); - - // Creating the factors vector. - String rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\","; - } else { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\""; - } - } - - rInstruction += ")"; - - engine.voidEval(rInstruction); - - //Create the isis.factor.distribution - engine.voidEval("isis.factor.distribution<-c(0.0)"); - - //Create isis.MethodExp - engine.voidEval("isis.MethodExp<-list(" + - "isis.factors," + - "isis.factor.distribution," + - "call_method=\"isis-fish-externeR\")"); - - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - //Create isis.Simule - engine.voidEval("isis.simule<-data.frame(data)"); - - 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()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e); - } - - return thisExperiment; - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputdirectory) throws SensitivityException { - - SimulationStorage firstStorage = simulationStorages.get(0); - String simulationName = firstStorage.getName().replaceAll("-", ""); - SimulationParameter param = firstStorage.getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - try { - - REngine engine = new RProxy(); - - //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]"); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String name = sensitivityExport.getExportFilename(); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," - + name + ")"); - - //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(data," + - name + "=" + name + ")"; - engine.voidEval(dataframe); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~("; - for (int j = 0; j < factorNumber; j++) { - if (j < (factorNumber - 1)) { - aovCall = aovCall + - engine.eval("names(data)[" + (j + 1) + "]") + - "+"; - } else { - aovCall = aovCall + - engine.eval("names(data)[" + (j + 1) + "]") + - ")"; - if(param_order>1){ - aovCall+="^" + param_order + ",data=dataforaov)"; - }else{ - aovCall+=",data=dataforaov)"; - } - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //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)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - 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"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputdirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" - + param.getSensitivityExport().get(k).getExportFilename() + "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" - + param.getSensitivityExport().get(k).getExportFilename() - + "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of Expand Grid method using Java"; - } - -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,403 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.util.Doc; -import java.io.File; -import java.util.Collection; -import java.util.List; -import java.util.Map; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * User: couteau - * Date: 14 janv. 2010 - * Time: 11:58:09 - */ -public class SensitivityCalculatorRDOptimal - extends AbstractSensitivityAnalysis { - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - @Doc("Order") - public int param_order=1; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return false; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - - setIsisFactorsR(plan, outputDirectory); - - //extract the factors from the design plan - List<Factor> factors = plan.getFactors(); - int factorsNb = factors.size(); - - try { - REngine engine = new RProxy(); - - //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,... - String factorsNames = ""; - - //Create a list of the factors under the form factor1,factor2,... - String factorNames = ""; - - //Create a list of the factors under the form factor1+factor2+... - String factorPlus=""; - - //create the factors vectors - for (Factor factor : factors) { - //The factor values vector - String factorName = factor.getName().replaceAll(" ", ""); - factorsNames += factorName + "=" + factorName + ","; - factorNames += factorName + ","; - factorPlus += factorName + "+"; - - String vector = factorName + "<-c("; - - 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))) + ","; - } - } else { - Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); - int nbValues = values.size(); - for (int i = 0; i < nbValues; i++) { - vector += "as.integer(" + i + "),"; - } - } - - vector = vector.substring(0, vector.length() - 1); - - vector += ")"; - - engine.voidEval(vector); - - - } - - factorsNames = factorsNames.substring(0,factorsNames.length()-1); - factorNames = factorNames.substring(0,factorNames.length()-1); - factorPlus = factorPlus.substring(0,factorPlus.length()-1); - - - //X<-expand.grid(vector=???,weight=???) - String expandGrid = "expandgrid<-expand.grid(%s)"; - - - - String rCall = String.format(expandGrid,factorsNames); - - engine.voidEval(rCall); - - if (param_order ==1 ){ - rCall = "x<-optFederov(~(%s),data=expandgrid, " + - "approximate =FALSE, center=F, criterion = \"D\"," + - "nRepeats=10)"; - } else { - rCall = "x<-optFederov(~(%s)^"+param_order+",data=expandgrid, " + - "approximate =FALSE, center=F, criterion = \"D\"," + - "nRepeats=10)"; - } - - rCall = String.format(rCall,factorPlus); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - engine.voidEval("runif(1)"); - - engine.voidEval(rCall); - - engine.eval("expPlan<-as.data.frame(x$design)"); - RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - int nbExperiments = (Integer)engine.eval("dim(x$design)[1]"); - - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - for (int j = 0; j < nbExperiments; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorsNb; i++) { - Factor factor = factors.get(i); - factor.setValueForIdentifier(dataFrame.get(i, j)); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - - String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - String distribution = ""; - String parameters = ""; - - for (int i = 0; i < factorsNb; i++) { - Domain domain = factors.get(i).getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - } - if (domain instanceof ContinuousDomain){ - ContinuousDomain contDomain = (ContinuousDomain)domain; - distribution += "\"qunif\""; - parameters += "\"[" + contDomain.getMinBound() - + ";" + contDomain.getMaxBound() - + "]\""; - } else { - DiscreteDomain discDomain = (DiscreteDomain)domain; - distribution += "\"discrete\""; - parameters+="\"["; - Map<Object, Object> values = discDomain.getValues(); - int count=0; - Collection<Object> collecValues = values.values(); - for (Object value:collecValues){ - if (count!=0){ - parameters += ","; - } - parameters += value; - count++; - } - parameters+="]\""; - } - } - engine.voidEval(String.format(factorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-\"" + rCall + "\""); - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-x$design"); - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - - } catch (RException eee) { - throw new SensitivityException("Can't generate scenarios", eee); - } - - return thisExperiment; - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - try { - - REngine engine = new RProxy(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - //Get back the factors number - int factorNumber = (Integer)engine.eval("dim(x$design)[2]"); - - SimulationParameter param = simulationStorages.get(0).getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - SimulationStorage firstStorage = simulationStorages.get(0); - - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String name = sensitivityExport.getExportFilename(); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," - + name + ")"); - - //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(x$design," - + name + "=" + name + ")"; - engine.voidEval(dataFrame); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~("; - for (int j = 0; j < factorNumber; j++) { - if (j < (factorNumber - 1)) { - aovCall = aovCall - + engine.eval("names(x$design)[" + (j + 1) + "]") - + "+"; - } else { - aovCall = aovCall - + engine.eval("names(x$design)[" + (j + 1) + "]") - + ")"; - if(param_order>1){ - aovCall+="^" + param_order + ",data=dataforaov)"; - }else{ - aovCall+=",data=dataforaov)"; - } - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - -//Compute Sum of Squares and Sensitivity indices - engine.voidEval("SoS<-summary(aovresult)[[1]][1:dim(summary(aovresult)[[1]])[1],2]"); - engine.voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:dim(summary(aovresult)[[1]])[1]]"); - engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); - - - //Set dataforaov names - engine.voidEval("resultsnames<-c(names(x$design),\"Result\")"); - engine.voidEval("names(dataforaov)<-resultsnames"); - - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputDirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" - + param.getSensitivityExport().get(k) - - .getExportFilename() + "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" - + param.getSensitivityExport().get(k) - .getExportFilename() - + "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - //Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of D optimal method method using R, needs" + - "AlgDesign package to work"; - } -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,373 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.util.Doc; -import java.io.File; -import java.util.Collection; -import java.util.List; -import java.util.Map; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * User: couteau - * Date: 6 janv. 2010 - * Time: 14:31:09 - */ -public class SensitivityCalculatorRExpandGrid - extends AbstractSensitivityAnalysis { - - @Doc("Interaction order") - public int param_order = 2; - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return false; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - - setIsisFactorsR(plan, outputDirectory); - - //extract the factors from the design plan - List<Factor> factors = plan.getFactors(); - int factorsNb = factors.size(); - - try { - REngine engine = new RProxy(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - //Create a list of the factors under the form factor1=factor1,... - String factorsNames = ""; - - //Create a list of the factors under the form factor1,factor2,... - String factorNames = ""; - - //create the factors vectors - for (Factor factor : factors) { - //The factor values vector - String factorName = factor.getName().replaceAll(" ", ""); - factorsNames += factorName + "=" + factorName + ","; - factorNames += factorName + ","; - String vector = factorName + "<-c("; - - 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))) + ","; - } - } - - if (domain instanceof DiscreteDomain) { - Map<Object, Object> values = ((DiscreteDomain) domain).getValues(); - int nbValues = values.size(); - for (int i = 0; i < nbValues; i++) { - vector += "as.integer(" + i + "),"; - } - } - - vector = vector.substring(0, vector.length() - 1); - - vector += ")"; - - engine.voidEval(vector); - - - } - - factorsNames = factorsNames.substring(0,factorsNames.length()-1); - factorNames = factorNames.substring(0,factorNames.length()-1); - - - //X<-expand.grid(vector=???,weight=???) - String expandGrid = "x<-expand.grid(%s)"; - - String rCall = String.format(expandGrid,factorsNames); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - engine.voidEval(rCall); - - engine.eval("expPlan<-as.data.frame(x)"); - RDataFrame dataFrame = (RDataFrame)engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - int nbExperiments = (Integer)engine.eval("dim(x)[1]"); - - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - for (int j = 0; j < nbExperiments; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorsNb; i++) { - Factor factor = factors.get(i); - factor.setValueForIdentifier(dataFrame.get(i, j)); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - - String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - String distribution = ""; - String parameters = ""; - - for (int i = 0; i < factorsNb; i++) { - Domain domain = factors.get(i).getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - } - if (domain instanceof ContinuousDomain){ - ContinuousDomain contDomain = (ContinuousDomain)domain; - distribution += "\"qunif\""; - parameters += "\"[" + contDomain.getMinBound() - + ";" + contDomain.getMaxBound() - + "]\""; - } else { - DiscreteDomain discDomain = (DiscreteDomain)domain; - distribution += "\"discrete\""; - parameters+="\"["; - Map<Object, Object> values = discDomain.getValues(); - int count=0; - Collection<Object> collecValues = values.values(); - for (Object value:collecValues){ - if (count!=0){ - parameters += ","; - } - parameters += value; - count++; - } - parameters+="]\""; - } - } - engine.voidEval(String.format(factorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-\"" + - String.format(expandGrid,factorsNames) + "\""); - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-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()); - - - } catch (RException eee) { - throw new SensitivityException("Can't generate scenarios", eee); - } - - return thisExperiment; - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - try { - - REngine engine = new RProxy(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - //Get back the factors number - int factorNumber = (Integer)engine.eval("dim(x)[2]"); - - SimulationParameter param = simulationStorages.get(0).getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - SimulationStorage firstStorage = simulationStorages.get(0); - - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String name = sensitivityExport.getExportFilename(); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," - + name + ")"); - - //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(x," - + name + "=" + name + ")"; - engine.voidEval(dataFrame); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~("; - for (int j = 0; j < factorNumber; j++) { - if (j < (factorNumber - 1)) { - aovCall = aovCall - + engine.eval("names(x)[" + (j + 1) + "]") - + "+"; - } else { - aovCall = aovCall - + engine.eval("names(x)[" + (j + 1) + "]") - + ")"; - if(param_order>1){ - aovCall+="^" + param_order + ",data=dataforaov)"; - }else{ - aovCall+=",data=dataforaov)"; - } - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //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)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputDirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" - + param.getSensitivityExport().get(k) - - .getExportFilename() + "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" - + param.getSensitivityExport().get(k) - .getExportFilename() - + "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - //Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of Expand Grid method using R"; - } -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFast.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFast.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFast.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,355 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.domain.EquationContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; -import fr.ifremer.isisfish.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * Implementation of Fast method using R. - * - * @author jcouteau - * @version $Revision: 89 $ - * - * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : - * $Author: jcouteau $ - */ -public class SensitivityCalculatorRFast extends AbstractSensitivityAnalysis { - - @Doc("an integer giving the sample size, i.e. the length of the " + - "discretization of the s-space (see Cukier et al.). (default=20)") - public int param_n = 20; - - @Doc("an integer specifying the interference parameter, i.e. the number " + - "of harmonics to sum in the Fourier series decomposition (see Cukier et " + - "al.). (default=6)") - public int param_M = 6; - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputDirectory); - - RDataFrame dataFrame; - int nbExperiments; - int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - //Test all factors, if one is discrete, return null - for (int i = 0; i < factorNumber; i++) { - if (factors.get(i).getDomain() instanceof DiscreteDomain) { - throw new SensitivityException(factors.get(i).getName() + - " has a discrete domain, this is not acceptable for fast " + - "method."); - } - } - String rInstruction = "a<-fast99(" + - "model=NULL," + - "factors=%s, " + - "n=%s, " + - "M=%s, " + - "q = \"qunif\", " + - "q.arg=list(min=0,max=1))"; - String rCall = String.format(rInstruction, factors.size(), param_n, - param_M); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - try { - - REngine engine = new RProxy(); - - engine.clearSession(); - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - // Load sensitivity package into R (if package already loaded, - // nothing happens. - engine.voidEval("library(sensitivity)"); - - // Run sensitivity analysis - engine.voidEval(rCall); - - // Creating the factors vector. - rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - String factorName = factors.get(i).getName(); - if (i != (factorNumber - 1)) { - rInstruction += "\"" + factorName + "\","; - } else { - rInstruction += "\"" + factorName + "\""; - } - } - - rInstruction += ")"; - - engine.voidEval(rInstruction); - - // Get back experiment plan - dataFrame = (RDataFrame) engine.eval("a$X"); - dataFrame.setVariable("a$X"); - - nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); - - String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - // Creating the vectors. - String distribution = ""; - String parameters = ""; - String factorNames = ""; - - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - factorNames += ","; - } - - distribution += "\"qunif\""; - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; - factorNames += "\"" + factor.getName() + "\""; - } - engine.voidEval(String.format(factorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-a$call"); - - - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - - engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + - "\"isis-fish-externe-R\""); - - engine.voidEval("isis.simule<-data.frame(a$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(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors().get(i); - Domain domain = factor.getDomain(); - if ((domain instanceof MatrixContinuousDomain) - || (domain instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(dataFrame.get(i,j)); - } else { - ContinuousDomain continuousDomain = (ContinuousDomain)domain; - Double min = continuousDomain.getCalculatorMinBound(); - Double max = continuousDomain.getCalculatorMaxBound(); - Double dFValue = (Double)dataFrame.get(i,j); - Double value = min + (max - min) * dFValue; - factor.setValueForIdentifier(value); - } - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - } catch (RException eee) { - throw new SensitivityException("Can't generate scenarios", eee); - } - return thisExperiment; - - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); - - try { - - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.setwd(outputDirectory); - - // Call R - // Load sensitivity package into R (if package already loaded, - // nothing happens. - engine.voidEval("library(sensitivity)"); - - SimulationParameter param = simulationStorages.get(0).getParameter(); - - int sensitivityNumber = param.getSensitivityExport().size(); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule,\"nomModel\")<-" + - "\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); - - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k) - .getExportFilename(); - - //Compute results - engine.voidEval("tell(a,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"); - - //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)"); - - //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse,\"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)"); - - //Set working directory - engine.setwd(outputDirectory); - - //Export V - engine.voidEval("write.csv(a$V,\"" + name + "_V.csv\")"); - - //Export D1 - engine.voidEval("write.csv(a$D1,\"" + name + "_D1.csv\")"); - - //Export Dt - engine.voidEval("write.csv(a$Dt,\"" + name + "_Dt.csv\")"); - //Set dfresults names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); - engine.voidEval("names(dfresults)<-resultsnames"); - - //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)); - - } - - //Rename R objects for saving purpose - renameObjects(engine, simulationName); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - } - - @Override - public String getDescription() { - return "Implementation of FAST method using R (needs the sensitivity " + - "package to work)"; - } - -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFrF2.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFrF2.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRFrF2.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,387 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.util.Doc; -import java.io.File; -import java.util.List; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.math.matrix.MatrixFactory; -import org.nuiton.math.matrix.MatrixND; -import org.nuiton.util.FileUtil; - -/** - * Implementation of FrF2 method using R. - * - * @author jcouteau - * @version $Revision: 94 $ - * - * Last update : $Date: 2009-04-03 13:13:35 +0200 (ven., 03 avr. 2009) $ By : - * $Author: chatellier $ - */ -public class SensitivityCalculatorRFrF2 extends AbstractSensitivityAnalysis { - - //TODO jcouteau 20110607 need to use new ethods on REngine instead of coding R sentences by hand. - - /** to use log facility, just put in your code: log.info("..."); */ - private static Log log = LogFactory - .getLog(SensitivityCalculatorRFrF2.class); - - @Doc("is the arabic numeral for the requested resolution of the design( 3 <= resolution <= 5). (if resolution=3, model = sum(Xi), if resolution = 4 or 5, model = sum(Xi)+sum(XiXj)") - public int param_resolution; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) - throws SensitivityException { - - double[] dataframe; - int nbExperiments; - int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - testNoDiscrete(factors); - - try { - REngine engine = new RProxy(); - - //Clear session - engine.voidEval("rm(list=ls())"); - - engine.voidEval("library(FrF2)"); - - //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" - + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") - + "\")"); - - String rInstruction = "a<-FrF2(nfactors=" + factorNumber - + ",resolution=" + param_resolution + ")"; - - engine.voidEval(rInstruction); - - // Export the FrF2 object for the second run in a .FrF2 file - engine.voidEval("dput(a,file=\".FrF2\")"); - - // Get back experiment plan - dataframe = (double[]) engine.eval("a$desnum"); - - // Creating the factors vector. - rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\","; - } else { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\""; - } - } - - rInstruction += ")"; - - engine.voidEval(rInstruction); - - // Export the factornames object for the second run in a .factornames file - engine.voidEval("dput(factornames,file=\".factornames\")"); - - - nbExperiments = dataframe.length / factorNumber; - - // Transform the result from R in a matrix - MatrixND frf2 = MatrixFactory.getInstance().create(dataframe, - new int[] { factorNumber, nbExperiments }); - - // Setting up the scenarios. - for (int j = 0; j < nbExperiments; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors().get(i); - - if (frf2.getValue(new int[]{i, j}) == -1) { - factor.setValueForIdentifier(0); - } else if (frf2.getValue(new int[]{i, j}) == 1) { - factor.setValueForIdentifier(1); - } - - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - //Create the factors vectors - for (int j = 0; j < factorNumber; j++) { - Factor factor = thisExperimentScenarios.get(0).getFactors() - .get(j); - - String vector = "factor" + j + "<-c("; - for (int i = 0; i < nbExperiments; i++) { - if (i < (nbExperiments - 1)) { - vector = vector + factor.getDisplayedValue() + ","; - } else { - vector = vector + factor.getDisplayedValue(); - } - - } - vector = vector + ")"; - engine.voidEval(vector); - } - - //Create the data data.frame from the factors - String data = "data<-data.frame("; - for (int j = 0; j < factorNumber; j++) { - if (j < factorNumber - 1) { - data = data + "factor" + j + "=factor(factor" + j + "),"; - } else { - data = data + "factor" + j + "=factor(factor" + j + "))"; - } - - } - engine.voidEval(data); - - // Set output directory - engine.voidEval("setwd(\"" - + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") - + "\")"); - - // Export the scenario matrix for the second run in a .FrF2.csv file - engine.voidEval("write.csv(data,file=\".FrF2.csv\")"); - - engine.terminate(); - - } catch (RException e) { - throw new SensitivityException("Can't generate scenarios", e); - } - return thisExperiment; - - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputdirectory) throws SensitivityException { - - try { - - REngine engine = new RProxy(); - - //Clear session - engine.voidEval("rm(list=ls())"); - - SimulationParameter param = simulationStorages.get(0) - .getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - for (int k = 0; k < sensitivityNumber; k++) { - - engine.voidEval("library(FrF2)"); - - // Set output directory - engine.voidEval("setwd(\"" - + outputdirectory.getAbsolutePath().replaceAll("\\\\", - "/") + "\")"); - - //Get back the FrF2 object - engine.voidEval("a<-dget(\".FrF2\")"); - - //Get back the scenarios - engine.voidEval("factors<-read.csv(\".FrF2.csv\")"); - - // Get the factornames object in the .factornames file - engine.voidEval("factornames<-dget(\".factornames\")"); - - //Get back the factors number - int factorNumber = ((Double) engine.eval("length(factors)-1")) - .intValue(); - - // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k) - .getExportFilename(); - String rInstruction = name + "<-c("; - for (int l = 0; l < simulationStorages.size(); l++) { - File importFile = new File(simulationStorages.get(l) - .getDirectory().toString() - + File.separator - + SimulationStorage.RESULT_EXPORT_DIRECTORY, param - .getSensitivityExport().get(k).getExportFilename() - + param.getSensitivityExport().get(k) - .getExtensionFilename()); - String simulResult = FileUtil.readAsString(importFile); - double simulationResult = Double.valueOf(simulResult); - if (l < simulationStorages.size() - 1) { - rInstruction = rInstruction + simulationResult + ","; - } else { - rInstruction = rInstruction + simulationResult; - } - } - rInstruction = rInstruction + ")"; - - // Send the simulation results - engine.voidEval(rInstruction); - - //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(factors,result=result)"; - engine.voidEval(dataframe); - - //get back the resolution - int resolution = (Integer) engine.eval("res.catlg(a$catentry)"); - - String aovCall; - - switch (resolution) { - case 3: - //Call aov() - aovCall = "aovresult<-aov(result~"; - for (int j = 0; j < factorNumber; j++) { - if (j < (factorNumber - 1)) { - aovCall = aovCall + "factor" + j + "+"; - } else { - aovCall = aovCall + "factor" + j - + ",data=dataforaov)"; - } - } - engine.voidEval(aovCall); - break; - case 4: - aovCall = "aovresult<-aov(result~"; - for (int j = 0; j < factorNumber; j++) { - aovCall = aovCall + "factor" + j + "+"; - } - for (int i = 0; i < factorNumber; i++) { - for (int j = 0; j < factorNumber; j++) { - if (i < j) { - aovCall = aovCall + "factor" + i + "*factor" - + j + "+"; - } - } - } - aovCall = aovCall.substring(0, aovCall.length() - 1); - aovCall = aovCall + ",data=dataforaov)"; - engine.voidEval(aovCall); - break; - case 5: - aovCall = "aovresult<-aov(result~"; - for (int j = 0; j < factorNumber; j++) { - aovCall = aovCall + "factor" + j + "+"; - } - for (int i = 0; i < factorNumber; i++) { - for (int j = 0; j < factorNumber; j++) { - if (i < j) { - aovCall = aovCall + "factor" + i + "*factor" - + j + "+"; - } - } - } - aovCall = aovCall.substring(0, aovCall.length() - 1); - aovCall = aovCall + ",data=dataforaov)"; - engine.voidEval(aovCall); - break; - default: - log.info("This resolution is not managed"); - break; - } - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //Compute Sum of Squares and Sensitivity indices - engine.voidEval("SoS<-summary(aovresult)[[1]][1:" - + factorNumber + ",2]"); - engine.voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:" - + factorNumber + "]"); - engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity=data.frame(SoS[1:" - + factorNumber + "],IndSensibilite[1:" + factorNumber - + "])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\",\"Sensitivity indices\")"); - - engine.voidEval("row.names(exportsensitivity)<-factornames"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.voidEval("setwd(\"" - + outputdirectory.getAbsolutePath().replaceAll("\\\\", - "/") + "\")"); - - //Set dataforaov names - engine.voidEval("resultsnames<-c(\"Simulation\"," + - "factornames,\"Result\")"); - engine.voidEval("names(dataforaov)<-resultsnames"); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" - + param.getSensitivityExport().get(k) - .getExportFilename() + "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" - + param.getSensitivityExport().get(k) - .getExportFilename() - + "_SensitivityIndices.csv\")"); - - //FIXME export through java to enable export when using Rserve (when distant Rserve). - engine.terminate(); - } - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of FrF2 method method using R, at least 4 factors need to be declared (nneds the 'sensitivity' package to work)"; - } -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRMorris.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRMorris.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,341 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * Implementation of Morris method using R. - * - * @author jcouteau - * @version $Revision: 253 $ - * - * Last update : $Date: 2011-07-07 14:31:31 +0200 (jeu. 07 juil. 2011) $ By : - * $Author: chatellier $ - */ -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; - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continus. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return false; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputDirectory); - - RDataFrame dataFrame; - int nbExperiments; - int factorNumber = plan.getFactors().size(); - - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - - List<Factor> factors = plan.getFactors(); - - if (param_r == 0) { - param_r = 4; - } - - testNoDiscrete(factors); - - // Creating the vectors. - String factorNames = ""; - String levels = ""; - String gridJump = ""; - String binf = ""; - String bsup = ""; - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); - if (i != 0) { - factorNames += ","; - levels += ","; - gridJump += ","; - binf += ","; - bsup += ","; - } - - factorNames += "\"" + factor.getName() + "\""; - - levels += factor.getCardinality(); - - gridJump += factor.getCardinality() / 2; - - binf += domain.getCalculatorMinBound(); - - bsup += domain.getCalculatorMaxBound(); - } - - 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))"; - - String rCall = String.format(rInstruction, factorNames, param_r, - levels, gridJump, binf, bsup); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - try { - REngine engine = new RProxy(); - - //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)"); - - // Run sensitivity analysis - engine.voidEval(rCall); - - // Creating the factors vector. - rInstruction = "factornames<-c(%s)"; - rCall = String.format(rInstruction, factorNames); - - engine.voidEval(rCall); - - // Set output directory - engine.setwd(outputDirectory); - - // Get back experiment plan - engine.eval("expPlan<-as.data.frame(a$X)"); - dataFrame = (RDataFrame) engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - - nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); - - String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - String distribution = ""; - String parameters = ""; - - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - } - - distribution += "\"qunif\""; - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; - } - engine.voidEval(String.format(factorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-a$call"); - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - engine.voidEval("attr(isis.MethodExp,\"nomModel\")<-" + - "\"isis-fish-externe-R\""); - engine.voidEval("isis.simule<-data.frame(a$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. - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - for (int j = 0; j < nbExperiments; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - factor.setValueForIdentifier(dataFrame.get(i, j)); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - } catch (RException eee) { - throw new SensitivityException("Can't generate scenarios", eee); - } - - return thisExperiment; - - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); - - try { - REngine engine = new RProxy(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - // Call R - // Load sensitivity package into R (if package already loaded, - // nothing happens. - engine.voidEval("library(sensitivity)"); - - //Set the working directory (for exports) - engine.setwd(outputDirectory); - - SimulationParameter param = simulationStorages.get(0) - .getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule,\"nomModel\")<-" + - "\"isis-fish-externe-R\""); - - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); - - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k) - .getExportFilename(); - - //Compute results - engine.voidEval("tell(a,y=" + name + ")"); - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"isis.simule\"=isis.simule," + - "\"call_method\"=\"tell(a,y=" + name + ")" + "\"," + - "\"analysis_result\"=a)"); - - //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse,\"nomModel\")<-" + - "\"isis-fish-externe-R\""); - - // Get back the sensitivity results, mu, mu star and sigma. - engine.voidEval("mu<-apply(a$ee, 2, mean)"); - engine.voidEval("mu.star <- apply(a$ee, 2, function(a) mean(abs(a)))"); - engine.voidEval("sigma <- apply(a$ee, 2, sd)"); - - //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"); - - //Create the data.frame of scenarios and results for export purpose - engine.voidEval("dfresults<-data.frame(a$X," + name + ")"); - - //Set dfresults names - engine.voidEval("resultsnames<-c(factornames,\"Result\")"); - engine.voidEval("names(dfresults)<-resultsnames"); - - //Export sensitivity indices - engine.voidEval("write.csv(df," + - "\"" + name + "_SensitivityIndices.csv\")"); - - //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)); - - } - - //Rename R objects for saving purpose - renameObjects(engine,simulationName); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of Morris method using R (needs the sensitivity" + - " package to work)"; - } - -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,396 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * Implementation of Optimum Latin Hypercube method using R. - * - * @author jcouteau - * @version $Revision: 1.0 $ - */ -public class SensitivityCalculatorROptimumLHS extends - AbstractSensitivityAnalysis { - - @Doc("Number of simulations (default=10)") - public int param_simulationNumber = 10; - @Doc("The maximum number of times the Columnwise Pairwise algorithm is applied to all the columns(default=2).") - public int param_MaxSweeps = 2; - @Doc("The optimal stopping criterion (between 0 and 1) (default=0.1).") - public double param_eps = 0.1; - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputdirectory); - - int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); - RDataFrame dataFrame; - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - //Test all factors, if one is discrete, return null - testNoDiscrete(factors); - - try { - REngine engine = new RProxy(); - - //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 rCall = String.format(rInstruction, param_simulationNumber, - factorNumber, param_MaxSweeps, param_eps); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - //Create the scenarios - engine.voidEval(rCall); - - // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x)"); - dataFrame = (RDataFrame)engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - - // Setting up the scenarios. - for (int j = 0; j < param_simulationNumber; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors().get(i); - factor.setValueForIdentifier(dataFrame.get(i, j)); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - String isisFactorDistribution = "isis.factor.distribution<-" + - "data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - String distribution = ""; - String parameters = ""; - String factorNames = ""; - - for (int i = 0; i < factors.size(); i++) { - Factor tempFactor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) tempFactor.getDomain(); - if (i != 0) { - distribution += ","; - factorNames += ","; - parameters += ","; - } - - factorNames += "\"" + factors.get(i).getName() + "\""; - distribution += "\"qunif\""; - //add [min;max] to parameters - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; - } - - engine.voidEval(String.format(isisFactorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-" + "\"x<-optimumLHS(" - + "n=" + param_simulationNumber - + ",k=" + factorNumber - + ",maxSweeps=" + param_MaxSweeps - + ",eps=" + param_eps + ")\""); - - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("isis.simule<-data.frame(x)"); - - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - - String data = "data<-data.frame("; - - //Create the factors vectors and the dataFrame instruction - for (int j = 0; j < factors.size(); j++) { - //The factor values vector - String vector; - //Get back the factor - Scenario scenario = thisExperimentScenarios.get(0); - Factor factor = scenario.getFactors().get(j); - String factorName = factor.getName().replaceAll(" ", ""); - - vector = factorName + "<-c("; - for (int i = 0; i < param_simulationNumber; i++) { - //Get back the displayed value the factor - Scenario tempScenario = thisExperimentScenarios.get(i); - Factor tempFactor = tempScenario.getFactors().get(j); - Object value = tempFactor.getDisplayedValue(); - - if (i < (param_simulationNumber - 1)) { - vector = vector + value + ","; - } else { - vector += value; - } - - } - vector += ")"; - engine.voidEval(vector); - - if (j < factors.size() - 1) { - data += factorName + "=factor(" + factorName + "),"; - } else { - data += factorName + "=factor(" + factorName + "))"; - } - } - engine.voidEval(data); - - // Creating the factors vector. - rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\","; - } else { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\""; - } - } - - rInstruction += ")"; - - engine.voidEval(rInstruction); - - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e); - } - - return thisExperiment; - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - //The first storage to get the name and parameters all along the method - SimulationStorage storage = simulationStorages.get(0); - - String simulationName = storage.getName().replaceAll("-", ""); - - try { - - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //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 - param_simulationNumber = (Integer) (engine.eval("length(factors[,1])")); - - SimulationParameter param = storage.getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); - - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - SensitivityExport export = param.getSensitivityExport().get(k); - String name = export.getExportFilename(); - - //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(factors," + - name + "=" + name + ")"; - engine.voidEval(dataframe); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~"; - for (int j = 0; j < factorNumber; j++) { - - String factorName = (String) engine.eval("names(factors)[" + (j + 1) + "]"); - factorName = factorName.replaceAll(" ", "."); - - if (j < (factorNumber - 1)) { - aovCall += factorName + - "+"; - } else { - aovCall += factorName + ",data=dataforaov)"; - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //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)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - engine.voidEval("row.names(exportsensitivity)<-dimnames(summary(aovresult)[[1]])[1][[1]][1:dim(summary(aovresult)[[1]])[1]]"); - - - //Set dataforaov names - engine.voidEval("names(dataforaov)<-c(factornames,\"Result\")"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputDirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" + - name + "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" + - name + "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of Random Latin Hypercube method method " + - "using R (needs 'lhs' package to work)"; - } - -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,387 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * Implementation of Random Latin Hypercube method using R. - * - * @author jcouteau - * @version $Revision: 1.0 $ - */ -public class SensitivityCalculatorRRandomLHS extends - AbstractSensitivityAnalysis { - - @Doc("Simulation number (default=10)") - public int param_simulationNumber = 10; - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputDirectory); - - int factorNumber = plan.getFactors().size(); - RDataFrame dataFrame; //The dataframe to get back the scenarios from R - SensitivityScenarios thisExperiment = new SensitivityScenarios(); //The experiment we will build - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); //The list of scenarios - List<Factor> factors = plan.getFactors(); //The factors - - testNoDiscrete(factors); - - try { - - REngine engine = new RProxy(); //The R engine - - //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 rCall = String.format(rInstruction, param_simulationNumber, - factorNumber); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - engine.voidEval(rCall); - - // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x)"); - dataFrame = (RDataFrame)engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - - // Setting up the scenarios. - for (int j = 0; j < param_simulationNumber; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors().get(i); //The factor we are setting - factor.setValueForIdentifier(dataFrame.get(i,j)); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - String isisFactorDistribution = "isis.factor.distribution<-" + - "data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - String distribution = ""; - String parameters = ""; - String factorNames = ""; - - - //Create the strings for the isis.MethodExp instruction - for (int i = 0; i < factors.size(); i++) { - ContinuousDomain domain = (ContinuousDomain)factors.get(i).getDomain(); - if (i != 0) { - distribution += ","; //the distribution - factorNames += ","; //the factor names - parameters += ","; //the parameters - } - - factorNames += "\"" + factors.get(i).getName() + "\""; - distribution += "\"qunif\""; //all distributions are qunif - double min = domain.getCalculatorMinBound(); - double max = domain.getCalculatorMaxBound(); - parameters += "\"[" + min + ";" + max + "]\""; - } - engine.voidEval(String.format(isisFactorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-" + "\"x<-randomLHS(" - + param_simulationNumber + "," + factorNumber + ")\""); - - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("isis.simule<-data.frame(x)"); - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - - String data = "data<-data.frame("; - - //Create the factors vectors and the dataFrame instruction - for (int j = 0; j < factors.size(); j++) { - Scenario firstScenario = thisExperimentScenarios.get(0); - Factor factor = firstScenario.getFactors().get(j); - String factorName = factor.getName().replaceAll(" ", ""); - - //the vector of the factor values - //read all the values one by one from the already created - //scenarios. - String vector = factorName + "<-c("; - for (int i = 0; i < param_simulationNumber; i++) { - Scenario scenario = thisExperimentScenarios.get(i); - List<Factor> factorList = scenario.getFactors(); - Factor factor1 = factorList.get(j); - if (i < (param_simulationNumber - 1)) { - vector += factor1.getDisplayedValue() + ","; - } else { - vector += factor1.getDisplayedValue(); - } - - } - vector = vector + ")"; - engine.voidEval(vector); - - //add factor1=factor(factor1) for each factor... - if (j < factors.size() - 1) { - data += factorName + "=factor(" + factorName + "),"; - } else { - data += factorName + "=factor(" + factorName + "))"; - } - - } - engine.voidEval(data); - - // Creating the factors vector. - rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\","; - } else { - rInstruction = rInstruction + "\"" - + factors.get(i).getName() + "\""; - } - } - rInstruction += ")"; - engine.voidEval(rInstruction); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e); - } - - return thisExperiment; - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - SimulationStorage simulationStorage1 = simulationStorages.get(0); - String simName = simulationStorage1.getName(); - String simulationName = simName.replaceAll("-", ""); - SimulationParameter param = simulationStorage1.getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - //List<SensitivityExport> export = param.getSensitivityExport(); - - try { - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //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)"); - - //Get back the simulation number - param_simulationNumber = (Integer) (engine.eval("length(factors[,1])")); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); - - for (int k = 0; k < sensitivityNumber; k++) { - - // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k) - .getExportFilename(); - - //Create the dataforaov data.frame - String dataframe = "dataforaov<-data.frame(factors," + name - + "=" + name + ")"; - engine.voidEval(dataframe); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~"; - for (int j = 0; j < factorNumber; j++) { - - if (j < (factorNumber - 1)) { - aovCall += engine.eval("names(factors)[" + (j + 1) + "]") - + "+"; - } else { - aovCall += engine.eval("names(factors)[" + (j + 1) + "]") - + ",data=dataforaov)"; - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //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)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - 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"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputDirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" + - param.getSensitivityExport().get(k).getExportFilename() + - "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" + - param.getSensitivityExport().get(k).getExportFilename() + - "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - - } - - @Override - public String getDescription() { - return "Implementation of Random Latin Hypercube method method using" + - " R needs the 'lhs' package to work)"; - } - -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRSobol.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRSobol.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRSobol.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,334 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -/** - * Implementation of Sobol method using R. - * - * @author jcouteau - * @version $Revision: 89 $ - * - * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : - * $Author: jcouteau $ - */ -public class SensitivityCalculatorRSobol extends AbstractSensitivityAnalysis { - - @Doc("the size of the 2 random samples") - public int param_n = 20; - - @Doc("the number of bootstrap replicates.") - public int param_nboot = 20; - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputdirectory); - - RDataFrame dataFrame; - int nbExperiments; - int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - testNoDiscrete(factors); - - String rInstruction = "a<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; - String rCall = String.format(rInstruction, param_nboot); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - try { - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - - engine.voidEval("library(sensitivity)"); - - engine.voidEval("X1<-data.frame(matrix(runif(" + factorNumber + "*" - + param_n + "),nrow=" + param_n + "))"); - engine.voidEval("X2<-data.frame(matrix(runif(" + factorNumber + "*" - + param_n + "),nrow=" + param_n + "))"); - - engine.voidEval(rCall); - - // Creating the factors vector. - rInstruction = "factornames<-c("; - for (int i = 0; i < factorNumber; i++) { - String factorName = factors.get(i).getName(); - if (i != (factorNumber - 1)) { - rInstruction += "\"" + factorName + "\","; - } else { - rInstruction += "\"" + factorName + "\""; - } - } - - rInstruction += ")"; - - engine.voidEval(rInstruction); - - // Get back experiment plan - dataFrame = (RDataFrame) engine.eval("a$X"); - dataFrame.setVariable("a$X"); - - nbExperiments = dataFrame.dim()[0]; - - String isisFactorDistribution = "isis.factor.distribution<-" + - "data.frame(NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; - - // Creating the vectors. - String distribution = ""; - String parameters = ""; - String factorNames = ""; - - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - Domain domain = factor.getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - factorNames += ","; - } - - distribution += "\"qunif\""; - ContinuousDomain continuousDomain = (ContinuousDomain) domain; - double min = continuousDomain.getCalculatorMinBound(); - double max = continuousDomain.getCalculatorMaxBound(); - parameters += "\"[" + min + ";" + max + "]\""; - factorNames += "\"" + factor.getName() + "\""; - } - - engine.voidEval(String.format(isisFactorDistribution, factorNames, - distribution, parameters)); - - engine.voidEval("call<-a$call"); - - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("isis.simule<-data.frame(a$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(); - for (int i = 0; i < factorNumber; i++) { - Factor factor = plan.getFactors().get(i); - Double dFValue = (Double) dataFrame.get(i, j); - factor.setValueForIdentifier(dFValue); - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - } - - } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e);} - - - thisExperiment.setScenarios(thisExperimentScenarios); - return thisExperiment; - - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - SimulationStorage firstStorage = simulationStorages.get(0); - SimulationParameter param = firstStorage.getParameter(); - int sensitivityNumber = param.getSensitivityExport().size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); - - try { - - REngine engine = new RProxy(); - - //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. - engine.voidEval("library(sensitivity)"); - - //Set X1 names - engine.voidEval("names(X1)<-factornames"); - //Set X2 names - engine.voidEval("names(X2)<-factornames"); - - //Set a$X names - engine.voidEval("names(a$X)<-factornames"); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = param.getSensitivityExport().get(k); - String name = sensitivityExport.getExportFilename(); - - //Compute results - engine.voidEval("tell(a,y=" + name + ")"); - - engine.voidEval("row.names(a$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=\"\"))"); - - //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)"); - - //setting isis.methodAnalyse attributes - engine.voidEval("attr(isis.methodAnalyse," + - "\"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)"); - - //Set working directory - engine.setwd(outputDirectory); - - //Export V - engine.voidEval("write.csv(a$V,\"" - + name - + "_SensitivityIndices.csv\")"); - //Export DD - engine.voidEval("write.csv(a$D,\"" - + name + "_D.csv\")"); - - //Export S - engine.voidEval("write.csv(a$S,\"" - + name + "_S.csv\")"); - - //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)); - - } - - //Rename R objects for saving purpose - renameObjects(engine, simulationName); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - } catch (Exception e) { - throw new SensitivityException("Can't evaluate results", e); - } - } - - @Override - public String getDescription() { - return "Implementation of Sobol method using R (use of the R " + - "sobol2002 method, needs the 'sensitivity' package to work)"; - } -} Deleted: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRegularFractions.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2013-11-07 22:42:17 UTC (rev 3830) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -1,390 +0,0 @@ -/* - * #%L - * IsisFish data - * %% - * Copyright (C) 2009 - 2011 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 - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public - * License along with this program. If not, see - * <http://www.gnu.org/licenses/gpl-3.0.html>. - * #L% - */ - -package sensitivityanalysis; - -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.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.domain.EquationContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; -import fr.ifremer.isisfish.util.Doc; -import java.io.File; -import java.util.List; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; -import org.nuiton.j2r.types.RDataFrame; - -public class SensitivityCalculatorRegularFractions extends - AbstractSensitivityAnalysis { - - @Doc("the path of the directory where the R function is stored (do not indicate the RegularFractions.R file name)") - public String param_pathToFunction = ""; - - @Doc("unique prime number of levels of all input and unit factors") - public int param_p = 2; - - @Doc("number of unit factors (so that there are N=p^r units)") - public int param_r = 2; - - @Doc("resolution of the fraction") - public int param_resolution = 2; - - @Doc("True to be able to modify the code sent to R") - public boolean param_modifR = false; - - /** - * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs - * continue. - * - * @return <tt>true</tt> s'il sait la gerer - */ - @Override - public boolean canManageCardinality() { - return true; - } - - @Override - public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) - throws SensitivityException { - - setIsisFactorsR(plan, outputDirectory); - - RDataFrame dataFrame; - int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - - String factorNames = ""; - - //Test all factors, if one is discrete, return null - //Create a string with all factors names - for (int i = 0; i < factorNumber; i++) { - Domain domain = factors.get(i).getDomain(); - if (i != 0) { - factorNames += ","; - } - - factorNames += "\"" + factors.get(i).getName() + "\""; - - if (domain instanceof DiscreteDomain) { - throw new SensitivityException(factors.get(i).getName() + - " has a discrete domain, this is not acceptable for " + - "this method."); - } - } - - try { - - REngine engine = new RProxy(); - - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - //Set the working directory (to import the R function) - engine.setwd(new File(param_pathToFunction)); - - //Import the function - engine.voidEval("source(\"regularfractions.R\")"); - - //Create the instruction - String rInstruction = "x<-regular.fraction(%s,%s,%s,%s)"; - String rCall = String.format(rInstruction, factors.size(), param_p, - param_r, param_resolution); - - if (param_modifR) { - rCall = editRInstruction(rCall); - } - - // Run function - engine.voidEval(rCall); - - // Run function - engine.voidEval("call<-\"" + rCall + "\""); - - // Creating the factors vector. - rInstruction = "factornames<-c(%s)"; - rCall = String.format(rInstruction, factorNames); - - engine.voidEval(rCall); - - - // Get back experiment plan - engine.eval("expPlan<-as.data.frame(x[[1]])"); - dataFrame = (RDataFrame)engine.eval("expPlan"); - dataFrame.setVariable("expPlan"); - - //Get back the simulation number - int simulationNumber = (Integer) engine.eval("length(x[[1]][,1])"); - - // Setting up the scenarios. - for (int j = 0; j < simulationNumber; j++) { - Scenario experimentScenario = new Scenario(); - for (int i = 0; i < factors.size(); i++) { - Factor factor = plan.getFactors().get(i); - Domain domain = factor.getDomain(); - Double dFValue = (Double)dataFrame.get(i,j); - if ((domain instanceof MatrixContinuousDomain) - || (domain instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(dFValue); - } else { - ContinuousDomain contDomain = (ContinuousDomain)domain; - Double max = contDomain.getCalculatorMaxBound(); - Double min = contDomain.getCalculatorMinBound(); - Double value = min + (max - min) * dFValue / (param_p - 1); - factor.setValueForIdentifier(value); - } - experimentScenario.addFactor(factor); - } - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - - String dataframe = "data<-data.frame("; - - //Create the factors vectors and the dataframe instruction - for (int j = 0; j < factorNumber; j++) { - Factor factor = factors.get(j); - String factorName = factor.getName().replaceAll(" ", ""); - - String vector = factorName + "<-c("; - for (int i = 0; i < simulationNumber; i++) { - Scenario scenario = thisExperimentScenarios.get(i); - List<Factor> newFactors = scenario.getFactors(); - Factor factor1 = newFactors.get(j); - - if (i < (simulationNumber - 1)) { - vector += factor1.getDisplayedValue() + ","; - } else { - vector += factor1.getDisplayedValue(); - } - - } - vector = vector + ")"; - engine.voidEval(vector); - - if (j < factorNumber - 1) { - dataframe += factorName + "=factor(" + factorName + "),"; - } else { - dataframe += factorName + "=factor(" + factorName + "))"; - } - - } - engine.voidEval(dataframe); - - engine.voidEval("isis.factor.distribution<-c(0.0)"); - - engine.voidEval("isis.MethodExp<-list(" + - "\"isis.factors\"=isis.factors," + - "\"isis.factor.distribution\"=isis.factor.distribution," + - "\"call\"=call)"); - - engine.voidEval("attr(isis.MethodExp," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - //Create isis.Simule - engine.voidEval("isis.simule<-data.frame(data)"); - - 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()); - - engine.terminate(); - - } catch (RException eee) { - throw new SensitivityException("Can't generate scenarios", eee); - } - - return thisExperiment; - - } - - @Override - public void analyzeResult(List<SimulationStorage> simulationStorages, - File outputDirectory) throws SensitivityException { - - SimulationStorage firstStorage = simulationStorages.get(0); - SimulationParameter param = firstStorage.getParameter(); - List<SensitivityExport> exports = param.getSensitivityExport(); - int sensitivityNumber = exports.size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); - - try { - - REngine engine = new RProxy(); - - //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]"); - - for (int k = 0; k < sensitivityNumber; k++) { - - SensitivityExport sensitivityExport = - param.getSensitivityExport().get(k); - - String rInstruction = createImportInstruction(sensitivityExport, - simulationStorages); - - // Send the simulation results - engine.voidEval(rInstruction); - - //Put results in isis.simule - engine.voidEval("isis.simule<-data.frame(isis.simule," + - sensitivityExport.getExportFilename() + ")"); - } - - //adding attribute to isis.Simule - engine.voidEval("attr(isis.simule," + - "\"nomModel\")<-\"isis-fish-externe-R\""); - - for (SensitivityExport export : exports) { - - String name = export.getExportFilename(); - - //Create the dataforaov data.frame - String dataFrame = "dataforaov<-data.frame(data," + - name + "=" + name + ")"; - engine.voidEval(dataFrame); - - //Call aov() - String aovCall = "aovresult<-aov(" + name + "~("; - for (int j = 0; j < factorNumber; j++) { - - if (j < (factorNumber - 1)) { - aovCall = aovCall - + engine.eval("names(data)[" + (j + 1) + "]") - + "+"; - } else { - aovCall = aovCall - + engine.eval("names(data)[" + (j + 1) + "]") - + ")"; - if (param_resolution <= 4) { - aovCall += ",data=dataforaov)"; - } else { - aovCall += "^2,data=dataforaov)"; - } - } - } - engine.voidEval(aovCall); - - /*Export the results - *Export format is csv, data separated by ',' - *Results Export name is sensitivityExportName_Results.csv - *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv - */ - - //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)"); - - //Create a data.frame to export sensitivity important results in one file. - engine.voidEval("exportsensitivity<-data.frame(" + - "SoS[1:dim(summary(aovresult)[[1]])[1]]," + - "IndSensibilite[1:dim(summary(aovresult)[[1]])[1]])"); - engine.voidEval("names(exportsensitivity)<-c(" + - "\"Sum Of Squares\"," + - "\"Sensitivity indices\")"); - 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"); - - /*Set the export directory - *Export directory is the first simulation export directory. - */ - engine.setwd(outputDirectory); - - //Save the results with the scenarios. - engine.voidEval("write.csv(dataforaov,\"" + name + - "_Results.csv\")"); - - //Save the sensitivity indices - engine.voidEval("write.csv(exportsensitivity,\"" + name + - "_SensitivityIndices.csv\")"); - //FIXME export through java to enable export when using Rserve (when distant Rserve). - - //creating isis.methodAnalyse - engine.voidEval("isis.methodAnalyse<-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," + - "\"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); - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - - } catch (Exception eee) { - throw new SensitivityException("Can't evaluate results", eee); - } - - } - - @Override - public String getDescription() { - return "Implementation of Regular fractions method using R"; - } - -} Added: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java =================================================================== --- branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java (rev 0) +++ branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java 2013-11-08 14:25:47 UTC (rev 3831) @@ -0,0 +1,343 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2009 - 2012 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 + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + +package sensitivityanalysis; + +import java.io.File; +import java.util.List; + +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.domain.ContinuousDomain; +import fr.ifremer.isisfish.util.Doc; +import org.nuiton.j2r.types.RDataFrame; + +/** + * Implementation of Sobol method using R. + * + * @author jcouteau + * @version $Revision$ + * + * Last update : $Date$ By : + * $Author$ + */ +public class Sobol extends AbstractSensitivityAnalysis { + + @Doc("the size of the 2 random samples") + public int param_n = 20; + + @Doc("the number of bootstrap replicates.") + public int param_nboot = 20; + + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + + /** + * Retourne vrai si le calculateur sait gerer la cardinalité des facteurs + * continue. + * + * @return <tt>true</tt> s'il sait la gerer + */ + @Override + public boolean canManageCardinality() { + return true; + } + + @Override + public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + throws SensitivityException { + + setIsisFactorsR(plan, outputdirectory); + + RDataFrame dataFrame; + int nbExperiments; + int factorNumber = plan.getFactors().size(); + List<Factor> factors = plan.getFactors(); + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + + testNoDiscrete(factors); + + String rInstruction = "a<-sobol2002(model=NULL,X1=X1,X2=X2,nboot=%s)"; + String rCall = String.format(rInstruction, param_nboot); + + if (param_modifR) { + rCall = editRInstruction(rCall); + } + + try { + REngine engine = new RProxy(); + + //Clear session + engine.clearSession(); + + //Get Isis R session + engine.loadRData(outputdirectory.getParentFile(), + outputdirectory.getName()); + + engine.voidEval("library(sensitivity)"); + + engine.voidEval("X1<-data.frame(matrix(runif(" + factorNumber + "*" + + param_n + "),nrow=" + param_n + "))"); + engine.voidEval("X2<-data.frame(matrix(runif(" + factorNumber + "*" + + param_n + "),nrow=" + param_n + "))"); + + engine.voidEval(rCall); + + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + String factorName = factors.get(i).getName(); + if (i != (factorNumber - 1)) { + rInstruction += "\"" + factorName + "\","; + } else { + rInstruction += "\"" + factorName + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + + // Get back experiment plan + dataFrame = (RDataFrame) engine.eval("a$X"); + dataFrame.setVariable("a$X"); + + nbExperiments = dataFrame.dim()[0]; + + String isisFactorDistribution = "isis.factor.distribution<-" + + "data.frame(NomFacteur=c(%s)," + + "NomDistribution=c(%s)," + + "ParametreDistribution=c(%s))"; + + // Creating the vectors. + String distribution = ""; + String parameters = ""; + String factorNames = ""; + + for (int i = 0; i < factorNumber; i++) { + Factor factor = factors.get(i); + Domain domain = factor.getDomain(); + if (i != 0) { + distribution += ","; + parameters += ","; + factorNames += ","; + } + + distribution += "\"qunif\""; + ContinuousDomain continuousDomain = (ContinuousDomain) domain; + double min = continuousDomain.getCalculatorMinBound(); + double max = continuousDomain.getCalculatorMaxBound(); + parameters += "\"[" + min + ";" + max + "]\""; + factorNames += "\"" + factor.getName() + "\""; + } + + engine.voidEval(String.format(isisFactorDistribution, factorNames, + distribution, parameters)); + + engine.voidEval("call<-a$call"); + + engine.voidEval("isis.MethodExp<-list(" + + "\"isis.factors\"=isis.factors," + + "\"isis.factor.distribution\"=isis.factor.distribution," + + "\"call\"=call)"); + + engine.voidEval("attr(isis.MethodExp," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("isis.simule<-data.frame(a$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(); + for (int i = 0; i < factorNumber; i++) { + Factor factor = plan.getFactors().get(i); + Double dFValue = (Double) dataFrame.get(i, j); + factor.setValueForIdentifier(dFValue); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + } + + } catch (Exception e) { + throw new SensitivityException("Can't generate scenarios", e);} + + + thisExperiment.setScenarios(thisExperimentScenarios); + return thisExperiment; + + } + + @Override + public void analyzeResult(List<SimulationStorage> simulationStorages, + File outputDirectory) throws SensitivityException { + + SimulationStorage firstStorage = simulationStorages.get(0); + SimulationParameter param = firstStorage.getParameter(); + int sensitivityNumber = param.getSensitivityExport().size(); + String simulationName = firstStorage.getName().replaceAll("-", ""); + + try { + + REngine engine = new RProxy(); + + //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. + engine.voidEval("library(sensitivity)"); + + //Set X1 names + engine.voidEval("names(X1)<-factornames"); + //Set X2 names + engine.voidEval("names(X2)<-factornames"); + + //Set a$X names + engine.voidEval("names(a$X)<-factornames"); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = + param.getSensitivityExport().get(k); + + String rInstruction = createImportInstruction(sensitivityExport, + simulationStorages); + + // Send the simulation results + engine.voidEval(rInstruction); + + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + + sensitivityExport.getExportFilename() + ")"); + } + + //adding attribute to isis.Simule + engine.voidEval("attr(isis.simule," + + "\"nomModel\")<-\"isis-fish-externe-R\""); + + engine.voidEval("attr(isis.simule,\"call\")<-isis.MethodExp$call"); + + for (int k = 0; k < sensitivityNumber; k++) { + + SensitivityExport sensitivityExport = param.getSensitivityExport().get(k); + String name = sensitivityExport.getExportFilename(); + + //Compute results + engine.voidEval("tell(a,y=" + name + ")"); + + engine.voidEval("row.names(a$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=\"\"))"); + + //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)"); + + //setting isis.methodAnalyse attributes + engine.voidEval("attr(isis.methodAnalyse," + + "\"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)"); + + //Set working directory + engine.setwd(outputDirectory); + + //Export V + engine.voidEval("write.csv(a$V,\"" + + name + + "_SensitivityIndices.csv\")"); + //Export DD + engine.voidEval("write.csv(a$D,\"" + + name + "_D.csv\")"); + + //Export S + engine.voidEval("write.csv(a$S,\"" + + name + "_S.csv\")"); + + //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)); + + } + + //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); + } + } + + @Override + public String getDescription() { + return "Implementation of Sobol method using R (use of the R " + + "sobol2002 method, needs the 'sensitivity' package to work)"; + } +} Property changes on: branches/4.0.1/src/test/resources/test-database/sensitivityanalysis/Sobol.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native

1 0

r3830 - in branches/4.0.1/src/main: java/fr/ifremer/isisfish/ui java/fr/ifremer/isisfish/ui/calibration java/fr/ifremer/isisfish/ui/widget resources/i18n
by echatellier＠users.forge.codelutin.com Nov. 7, 2013

Nov. 7, 2013

Author: echatellier Date: 2013-11-07 23:42:17 +0100 (Thu, 07 Nov 2013) New Revision: 3830 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3830 Log: Ajout des interfaces de calibration (maquette) Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationHandler.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationMethodUI.jaxx branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationUI.jaxx branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/widget/DummyLayerUI.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/SimulationUI.jaxx branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomePanelUI.jaxx branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomeTabUI.jaxx branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/SimulationUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/SimulationUI.jaxx 2013-11-03 20:47:26 UTC (rev 3829) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/SimulationUI.jaxx 2013-11-07 22:42:17 UTC (rev 3830) @@ -111,5 +111,5 @@ <JMenuItem id="miImport" text="isisfish.simulation.menu.import" onActionPerformed="importSimulation()"/> </JMenu> </JMenuBar> - <JTabbedPane id="bodyTabbedPane" constraints='BorderLayout.CENTER'/> + <JTabbedPane id="bodyTabbedPane" constraints='BorderLayout.CENTER' decorator="boxed"/> </JPanel> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomePanelUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomePanelUI.jaxx 2013-11-03 20:47:26 UTC (rev 3829) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomePanelUI.jaxx 2013-11-07 22:42:17 UTC (rev 3830) @@ -5,7 +5,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2006 - 2010 Ifremer, Code Lutin + Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Chatellier Eric %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomeTabUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomeTabUI.jaxx 2013-11-03 20:47:26 UTC (rev 3829) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/WelcomeTabUI.jaxx 2013-11-07 22:42:17 UTC (rev 3830) @@ -30,6 +30,7 @@ fr.ifremer.isisfish.ui.input.InputSaveVerifier fr.ifremer.isisfish.ui.sensitivity.SensitivitySaveVerifier fr.ifremer.isisfish.ui.sensitivity.SensitivityInputHandler + fr.ifremer.isisfish.ui.calibration.CalibrationHandler javax.swing.ImageIcon </import> @@ -58,6 +59,10 @@ <fr.ifremer.isisfish.ui.sensitivity.SensitivityUI id="sensitivityUI" constructorParams='new JAXXInitialContext().add(new InputAction()).add(new SensitivitySaveVerifier()).add(new SimulAction()).add(new SensitivityInputHandler()).add(this)' /> </tab> + <tab title=' ' icon='{new ImageIcon(getClass().getResource("/images/SimulationLauncher.gif"))}'> + <fr.ifremer.isisfish.ui.calibration.CalibrationUI id="calibrationUI" + constructorParams='new JAXXInitialContext().add(new InputAction()).add(new SensitivitySaveVerifier()).add(new SimulAction()).add(new CalibrationHandler()).add(this)' /> + </tab> <tab title=' ' icon='{new ImageIcon(getClass().getResource("/images/calc.gif"))}'> <fr.ifremer.isisfish.ui.result.ResultUI /> </tab> Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationHandler.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationHandler.java (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationHandler.java 2013-11-07 22:42:17 UTC (rev 3830) @@ -0,0 +1,29 @@ +/* + * #%L + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 Ifremer, Codelutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package fr.ifremer.isisfish.ui.calibration; + +import fr.ifremer.isisfish.ui.input.InputHandler; + +public class CalibrationHandler extends InputHandler { + +} Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationMethodUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationMethodUI.jaxx (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationMethodUI.jaxx 2013-11-07 22:42:17 UTC (rev 3830) @@ -0,0 +1,119 @@ + +<Table> + <import> + java.awt.CardLayout + javax.swing.ComboBoxModel + javax.swing.table.DefaultTableModel + </import> + + <script><![CDATA[ + + + ]]></script> + <row> + <cell fill="horizontal"> + <JLabel text="isisfish.calibration.select"/> + </cell> + <cell fill="horizontal" weightx="1.0"> + <JComboBox id="fieldCalibrationMethodSelect" /> + </cell> + </row> + <row> + <cell columns="2" fill="both" weightx="1.0" weighty="1.0"> + <JScrollPane> + <JTable id="simulCalibrationMethodParam" rowHeight='24'/> + </JScrollPane> + </cell> + </row> + <row> + <cell columns="2" fill="both" weightx="1.0" weighty="1.0"> + <JPanel id="factorCardinalityPanel" layout="{new CardLayout()}"> + <JLabel text="isisfish.calibration.methodfactorsupported" horizontalAlignment="center" + border="{BorderFactory.createEtchedBorder()}" font-style="italic" constraints='"factorCardinalitySupported"'/> + <JScrollPane id="factorCardinalityScrollPane" constraints='"factorCardinalityNotSupported"'> + <JTable id="factorCardinality" rowHeight='24' /> + </JScrollPane> + </JPanel> + </cell> + </row> + <row> + <cell fill="both" columns='3' weightx="1.0"> + <JLabel text="isisfish.calibration.objectives"/> + </cell> + </row> + <row> + <cell columns='2' fill="both" weightx="1.0" weighty="1.0"> + <Table> + <row> + <cell fill="both" weightx="0.5" weighty="1.0"> + <JScrollPane> + <JList id="availableCalibrationObjectives" selectionMode="{javax.swing.ListSelectionModel.MULTIPLE_INTERVAL_SELECTION}" /> + </JScrollPane> + </cell> + <cell fill="both" weighty="1.0"> + <Table> + <row> + <cell fill="both"> + <JButton id="addObjectiveButton" text="isisfish.common.add" enabled="false" /> + </cell> + </row> + <row> + <cell fill="both"> + <JButton id="removeObjectiveButton" text="isisfish.common.remove" enabled="false" /> + </cell> + </row> + <row> + <cell fill="both"> + <JButton id="clearObjectiveButton" text="isisfish.common.clear" enabled="false" /> + </cell> + </row> + </Table> + </cell> + <cell fill="both" weightx="0.5" weighty="1.0"> + <JScrollPane> + <JList id="selectedCalibrationObjectives" selectionMode="{javax.swing.ListSelectionModel.MULTIPLE_INTERVAL_SELECTION}" /> + </JScrollPane> + </cell> + </row> + </Table> + </cell> + </row> + <row> + <cell fill="both" columns='2' weightx="1.0" weighty="1.0"> + <JScrollPane> + <JTable id="objectiveParamsTable" rowHeight='24' /> + </JScrollPane> + </cell> + </row> + <row> + <cell fill="horizontal"> + <JLabel text="isisfish.calibration.optimization"/> + </cell> + <cell fill="horizontal" weightx="1.0"> + <JComboBox id="fieldCalibrationScriptSelect" /> + </cell> + </row> +</Table> Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationUI.jaxx =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationUI.jaxx (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/calibration/CalibrationUI.jaxx 2013-11-07 22:42:17 UTC (rev 3830) @@ -0,0 +1,98 @@ + +<fr.ifremer.isisfish.ui.SimulationUI> + + <import> + fr.ifremer.isisfish.ui.input.InputAction + jaxx.runtime.JAXXContext + jaxx.runtime.context.JAXXInitialContext + jaxx.runtime.SwingUtil + </import> + + <script><![CDATA[ + protected void $afterCompleteSetup() { + SwingUtil.getLayer(bodyTabbedPane).setUI(dummyLayer); + } + + /** + * Refresh all simulation launch UI. + */ + @Override + protected void regionStorageChanged() { + + } + + @Override + public void refresh() { + + } + + @Override + public void selectParametersTab() { + + } + + @Override + public void setEnabledPrescriptTab(boolean selected) { + // no prescript in AS + } + + @Override + public void setEnabledSimulationPlanTab(boolean selected) { + // no simulation plan in AS + } + + @Override + public void refreshFactorTree() { + + } + ]]></script> + + <CalibrationHandler id="handler" /> + + <fr.ifremer.isisfish.ui.widget.DummyLayerUI id="dummyLayer" /> + <JTabbedPane id="bodyTabbedPane"> + <tab title='isisfish.params.title'> + <fr.ifremer.isisfish.ui.simulator.ParamsUI id='paramsUI' sensitivity='true' regionStorage="{getRegionStorage()}" + constructorParams='new JAXXInitialContext().add(new InputAction()).add("SimulationUI", this).add(this)' /> + </tab> + <tab title='isisfish.sensitivity.title'> + <fr.ifremer.isisfish.ui.sensitivity.SensitivityTabUI id="sensitivityTabUI" + constructorParams='new JAXXInitialContext().add(new InputAction()).add("SimulationUI", this).add(this)' /> + </tab> + <tab title='isisfish.calibration.title'> + <CalibrationMethodUI id="calibrationMethodUI" constructorParams='this'/> + </tab> + <tab title='isisfish.export.title'> + <fr.ifremer.isisfish.ui.simulator.ExportUI id="exportUI" constructorParams='this'/> + </tab> + <tab title='isisfish.resultChoice.title'> + <fr.ifremer.isisfish.ui.simulator.ResultChoiceUI id="resultChoiceUI" constructorParams='this'/> + </tab> + <tab title='isisfish.advancedParameters.title'> + <fr.ifremer.isisfish.ui.simulator.AdvancedParamsUI id="advancedParamsUI" constructorParams='this'/> + </tab> + </JTabbedPane> +</fr.ifremer.isisfish.ui.SimulationUI> Added: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/widget/DummyLayerUI.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/widget/DummyLayerUI.java (rev 0) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/widget/DummyLayerUI.java 2013-11-07 22:42:17 UTC (rev 3830) @@ -0,0 +1,64 @@ +/* + * #%L + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 Ifremer, Codelutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package fr.ifremer.isisfish.ui.widget; + +import java.awt.Color; +import java.awt.Font; +import java.awt.Graphics2D; + +import javax.swing.JComponent; + +import org.jdesktop.jxlayer.JXLayer; +import org.jdesktop.jxlayer.plaf.AbstractLayerUI; + +public class DummyLayerUI extends AbstractLayerUI<JComponent> { + + /** serialVersionUID. */ + private static final long serialVersionUID = 309245880711380974L; + + @Override + protected void paintLayer(Graphics2D g2, JXLayer<? extends JComponent> l) { + super.paintLayer(g2, l); + + // position + //g2.translate(-35, 90); // top left + g2.translate(l.getBounds().getMaxX() - 160, l.getBounds().getMaxY()); // bottom right + + // yellow backgroung + g2.rotate(Math.PI * -42 / 180); + g2.setColor(Color.YELLOW); + g2.fillRect(10, 10, 200, 30); + + // text + g2.translate(70, 15); + g2.setFont(new Font("Dialog", Font.BOLD, 16)); + g2.setColor(Color.BLACK); + g2.drawString("Maquette",10,10); + + // for test only + g2.translate(-3, 10); + g2.setFont(new Font("Dialog", Font.ITALIC, 10)); + g2.setColor(Color.BLACK); + g2.drawString("(non fonctionnelle)",10,10); + } +} Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-03 20:47:26 UTC (rev 3829) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-07 22:42:17 UTC (rev 3830) @@ -97,6 +97,11 @@ isisfish.advancedParams.simulationCache=Simulation cache isisfish.advancedParams.simulationStatistique=Simulation statistics isisfish.advancedParams.simulatorUse=Simulator to Use +isisfish.calibration.methodfactorsupported= +isisfish.calibration.objectives= +isisfish.calibration.optimization= +isisfish.calibration.select= +isisfish.calibration.title= isisfish.cell.comments=Comments isisfish.cell.land=Land isisfish.cell.latitude=Latitude Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-03 20:47:26 UTC (rev 3829) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-07 22:42:17 UTC (rev 3830) @@ -97,6 +97,11 @@ isisfish.advancedParams.simulationCache=Simulation cache isisfish.advancedParams.simulationStatistique=Simulation statistique isisfish.advancedParams.simulatorUse=Simulateur à utiliser +isisfish.calibration.methodfactorsupported=La méthode de calibration choisie gère les cardinalités des facteurs +isisfish.calibration.objectives=Fonctions d'objectif +isisfish.calibration.optimization=Script d'optimisation +isisfish.calibration.select=Méthode de calibration +isisfish.calibration.title=Calibration isisfish.cell.comments=Commentaires isisfish.cell.land=Terre isisfish.cell.latitude=Latitude

1 0

r3829 - branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity
by echatellier＠users.forge.codelutin.com Nov. 3, 2013

Nov. 3, 2013

Author: echatellier Date: 2013-11-03 21:47:26 +0100 (Sun, 03 Nov 2013) New Revision: 3829 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3829 Log: Add unit test to test AS scripts Added: branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java Added: 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 (rev 0) +++ branches/4.0.1/src/test/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityAnalysisTest.java 2013-11-03 20:47:26 UTC (rev 3829) @@ -0,0 +1,262 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 Ifremer, Code Lutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package fr.ifremer.isisfish.simulator.sensitivity; + +import java.io.File; +import java.io.IOException; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.aspectj.util.FileUtil; +import org.junit.After; +import org.junit.Assert; +import org.junit.Assume; +import org.junit.Before; +import org.junit.BeforeClass; +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; +import fr.ifremer.isisfish.datastore.SensitivityAnalysisStorage; +import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; +import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; + +/** + * Test les scripts d'AS disponible dans les ressources de tests. + * + * @author Eric Chatellier + */ +public class SensitivityAnalysisTest extends AbstractIsisFishTest { + + private static final Log log = LogFactory.getLog(SensitivityAnalysisTest.class); + + /** Simulation dir used to save Rdata files. */ + protected File simulationsDir; + + @BeforeClass + public static void init() { + System.setProperty("R.type", "jni"); + } + + /** + * Ces tests utilisent directement le moteur R, s'il n'est pas disponible, + * on va eviter de faire les tests. + */ + @Before + public void setUp() { + try { + new RProxy(); + } catch (RException e) { + if (log.isDebugEnabled()) { + log.debug("R not available. Skipping current test"); + } + Assume.assumeNoException(e); + } + simulationsDir = FileUtil.getTempDir("simulations"); + } + + /** + * Build a test design plan with only continuous factors. + * + * @return test design plan + */ + protected DesignPlan getContinuousDesignPlan() { + + DesignPlan result = new DesignPlan(); + + // factor 1, min/max on int + Factor factor1 = new Factor("testint"); + ContinuousDomain domain1 = new ContinuousDomain(Distribution.QUNIFMM); + domain1.addDistributionParam("min", 0.0); + domain1.addDistributionParam("max", 50.0); + factor1.setDomain(domain1); + factor1.setPath("org.nuiton.factor#1234567890#0.12242345354#name"); + result.addFactor(factor1); + + // 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); + + // factor + Factor factor2 = new Factor("testmatrix"); + ContinuousDomain domain2 = new ContinuousDomain(Distribution.QUNIFPC); + domain2.addDistributionParam("reference", matrix1); + domain2.addDistributionParam("coefficient", 0.1); + factor2.setDomain(domain2); + factor2.setPath("org.nuiton.math.matrix.MatrixND#563456293453#2.456347646#dim"); + result.addFactor(factor2); + + return result; + } + + /** + * Test tmp files/dir. + * + * @throws IOException + */ + @After + public void clear() throws IOException { + FileUtils.deleteDirectory(simulationsDir); + } + + /** + * Test de génération des scenarios via la methode Morris. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testMorris() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Morris").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("Morris script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode DOptimal. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testDOptimal() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("DOptimal").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("DOptimal script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode Fast. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testFast() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Fast").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("Fast script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode OptimumLHS. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testOptimumLHS() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("OptimumLHS").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("OptimumLHS script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode RandomLHS. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testRandomLHS() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RandomLHS").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("RandomLHS script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode RegularExpandGrid. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testRegularExpandGrid() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RegularExpandGrid").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("RegularExpandGrid script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode RegularFractions. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testRegularFractions() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("RegularFractions").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("RegularFractions script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } + + /** + * Test de génération des scenarios via la methode RegularExpandGrid. + * + * @throws IsisFishException + * @throws SensitivityException + */ + @Test + public void testSobol() throws IsisFishException, SensitivityException { + SensitivityAnalysis script = SensitivityAnalysisStorage.getSensitivityAnalysis("Sobol").getNewSensitivityAnalysisInstance(); + Assert.assertNotNull("Sobol script not found in test data", script); + + DesignPlan designPlan = getContinuousDesignPlan(); + SensitivityScenarios scenarii = script.compute(designPlan, simulationsDir); + + } +}

1 0

r3828 - branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 11:13:56 +0100 (Sat, 02 Nov 2013) New Revision: 3828 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3828 Log: Add missing getDistribution parameter method Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-02 09:51:05 UTC (rev 3827) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java 2013-11-02 10:13:56 UTC (rev 3828) @@ -103,6 +103,16 @@ } /** + * Return distribution parameter value by parameter name. + * + * @param name name + * @return param value + */ + public Object getDistributionParameter(String name) { + return distributionParameters.get(name); + } + + /** * Set distribution parameters (clear previous). * * @param distributionParameters distribution params

1 0

r3827 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/entities src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/resources/i18n
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 10:51:05 +0100 (Sat, 02 Nov 2013) New Revision: 3827 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3827 Log: Fix some reported problems Modified: branches/4.0.1/pom.xml branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: branches/4.0.1/pom.xml =================================================================== --- branches/4.0.1/pom.xml 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/pom.xml 2013-11-02 09:51:05 UTC (rev 3827) @@ -295,17 +295,17 @@ <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjrt</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency> <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjtools</artifactId> - <version>1.7.3</version> + <version>1.7.4</version> </dependency>  @@ -321,7 +321,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.8.0-SNAPSHOT</version> + <version>1.7.8</version> <scope>compile</scope> </dependency>  @@ -476,7 +476,7 @@ <signatureVersion>1.0</signatureVersion>  - <jaxxVersion>2.5.28</jaxxVersion> + <jaxxVersion>2.5.29</jaxxVersion> <eugeneVersion>2.6.3</eugeneVersion> <topiaVersion>2.8.1.3</topiaVersion> <hibernateVersion>4.2.7.Final</hibernateVersion> @@ -679,10 +679,6 @@ <id>nuiton.public</id> <url>http://nexus.nuiton.org/nexus/content/groups/public</url> </repository> - <repository> - <id>svnkit.public</id> - <url>http://maven.tmatesoft.com/content/repositories/snapshots</url> - </repository> </repositories> <pluginRepositories> @@ -741,7 +737,7 @@ <properties>  <minimumTokens>100</minimumTokens> - <targetJdk>1.6</targetJdk> + <targetJdk>1.7</targetJdk> </properties> <build> Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/CodeSourceStorage.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -31,7 +31,6 @@ import java.util.List; import org.apache.commons.io.FileUtils; -import org.nuiton.util.FileUtil; import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/PopulationImpl.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -559,8 +559,6 @@ // matrix when capturability is null instead check validity and // create new one and paste the old } else if (!Arrays.equals(mat.getSemantics(), sems)) { - log.debug("Capturability has changed, create new matrix and copy old: " - + mat.getSemantics() + " " + sems); MatrixND newmat = MatrixFactory.getInstance().create( n_("isisfish.population.capturability"), sems, Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/entities/SeasonImpl.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -62,7 +62,7 @@ public List<Month> getMonths() { List<Month> result = new ArrayList<Month>(); Month m = getFirstMonth(); - while (m.equals(getLastMonth()) == false) { + while (!m.equals(getLastMonth())) { result.add(m); m = m.next(); } @@ -92,7 +92,7 @@ boolean result = month.equals(getLastMonth()); // check first last month, because loop don't do that Month m = getFirstMonth(); - while (result == false && m.equals(getLastMonth()) == false) { + while (!result && !m.equals(getLastMonth())) { result = m.equals(month); m = m.next(); } Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationMonitor.java 2013-11-02 09:51:05 UTC (rev 3827) @@ -425,7 +425,7 @@ waitAndCheckProgression(); } catch (Exception e) { if (log.isErrorEnabled()) { - log.error("An exception occurs durring monitoring", e); + log.error("An exception occurs during monitoring", e); } } } Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties 2013-11-02 09:51:05 UTC (rev 3827) @@ -1,4 +1,6 @@ = +%s\ has\ a\ discrete\ domain,\ this\ is\ not\ acceptable\ for\ this\ method.= +%s\ has\ a\ non\ uniform\ distribution,\ this\ is\ not\ acceptable\ for\ this\ method.= Add\ to\ default\ queue= Analyse\ plan\ error,\ too\ many\ simulation\ for\ %s\ \:\ %s= Can't\ add\ result\ '%1$s'\ at\ date\ %2$s=Can't add result '%1$s' at date %2$s @@ -39,12 +41,14 @@ Maximum\ value= Minimum\ value= Missing\ name= +Modifier\ le\ code\ R\ envoyé\ si\ vous\ le\ souhaitez= No\ port\ cell= Normal\ stop\ thread,\ this\ is\ not\ an\ error= Not\ start\ simulation\ %s\ because\ user\ ask\ stop= Process\ template\ error= QUnif\ %= QUnif\ Min/Max= +R\ modif= Reference\ value= Region\ %s\ allready\ exist\ in\ repository.\ Can't\ import= Region\ %s\ already\ inited= Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-02 09:31:48 UTC (rev 3826) +++ branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties 2013-11-02 09:51:05 UTC (rev 3827) @@ -1,4 +1,6 @@ = +%s\ has\ a\ discrete\ domain,\ this\ is\ not\ acceptable\ for\ this\ method.= +%s\ has\ a\ non\ uniform\ distribution,\ this\ is\ not\ acceptable\ for\ this\ method.= Add\ to\ default\ queue= Analyse\ plan\ error,\ too\ many\ simulation\ for\ %s\ \:\ %s= Can't\ add\ result\ '%1$s'\ at\ date\ %2$s=Can't add result '%1$s' at date %2$s @@ -39,12 +41,14 @@ Maximum\ value= Minimum\ value= Missing\ name= +Modifier\ le\ code\ R\ envoyé\ si\ vous\ le\ souhaitez= No\ port\ cell= Normal\ stop\ thread,\ this\ is\ not\ an\ error= Not\ start\ simulation\ %s\ because\ user\ ask\ stop= Process\ template\ error= QUnif\ %= QUnif\ Min/Max= +R\ modif= Reference\ value= Region\ %s\ allready\ exist\ in\ repository.\ Can't\ import= Region\ %s\ already\ inited=La région %s a déjà été initialisée

1 0

r3826 - in branches/4.0.1/src/main/java/fr/ifremer/isisfish: types/hibernate util
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 10:31:48 +0100 (Sat, 02 Nov 2013) New Revision: 3826 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3826 Log: Comment non used code non compilable since hibernate 4.2 Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-10-31 22:54:54 UTC (rev 3825) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/types/hibernate/MatrixType.java 2013-11-02 09:31:48 UTC (rev 3826) @@ -69,9 +69,6 @@ */ private static final Log log = LogFactory.getLog(MatrixType.class); - public MatrixType() { - } - public boolean isMutable() { return true; } @@ -92,7 +89,7 @@ if(str.startsWith("[") && str.endsWith("]")) { str = str.substring(1, str.length()-1); // remove [ and ] } - String [] dimAsString = StringUtil.split(str, ","); + String [] dimAsString = StringUtil.split(str, ","); int[] result = new int[dimAsString.length]; int i = 0; for (String dim : dimAsString) { @@ -285,8 +282,8 @@ private static final Type[] hibernateTypes = { StandardBasicTypes.STRING, //name (String) StandardBasicTypes.STRING, //dim (int[]) - StandardBasicTypes.CLOB, //dimNames (String[]) - StandardBasicTypes.CLOB, //semantics (List[]) + StandardBasicTypes.CLOB, //dimNames (String[]) + StandardBasicTypes.CLOB, //semantics (List[]) StandardBasicTypes.CLOB //data (List<List<...>>) }; Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java =================================================================== --- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java 2013-10-31 22:54:54 UTC (rev 3825) +++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/TopiaEntityConverter.java 2013-11-02 09:31:48 UTC (rev 3826) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,15 +32,14 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.hibernate.HibernateException; -import org.hibernate.engine.QueryParameters; -import org.hibernate.engine.SessionImplementor; +import org.hibernate.engine.spi.QueryParameters; +import org.hibernate.engine.spi.SessionImplementor; import org.hibernate.type.StandardBasicTypes; import org.nuiton.topia.TopiaContext; import org.nuiton.topia.TopiaException; import org.nuiton.topia.persistence.TopiaEntity; import org.nuiton.topia.persistence.TopiaId; - /** * Classe utilise pour convertir une chaine en un objet TopiaEntity. * @@ -50,15 +49,12 @@ */ public class TopiaEntityConverter implements Converter { - /** - * Logger for this class - */ - private static final Log log = LogFactory - .getLog(TopiaEntityConverter.class); + /** Logger for this class. */ + private static final Log log = LogFactory.getLog(TopiaEntityConverter.class); protected TopiaContext context = null; protected SessionImplementor session = null; - + public TopiaEntityConverter(TopiaContext context) { this.context = context; } @@ -67,15 +63,13 @@ this.session = session; } - /* (non-Javadoc) - * @see org.apache.commons.beanutils.Converter#convert(java.lang.Class, java.lang.Object) - */ + @Override public Object convert(Class type, Object value) { Object result = null; if (value instanceof TopiaEntity) { result = value; - } else if (value instanceof String){ - result = getTopiaEntity((String)value); + } else if (value instanceof String) { + result = getTopiaEntity((String) value); } else { throw new ConversionException("Can't convert '" + value + "' to " + type.getName()); } @@ -88,7 +82,8 @@ try { TopiaContext tx = context.beginTransaction(); result = tx.findByTopiaId(topiaId); - // FIXME when after tx.closeContext we can continu to load object, call it here + // FIXME when after tx.closeContext we can continu to load + // object, call it here tx.commitTransaction(); tx.closeContext(); } catch (TopiaException eee) { @@ -99,19 +94,21 @@ } else if (session != null) { QueryParameters params = new QueryParameters(StandardBasicTypes.STRING, topiaId); String entityClass = TopiaId.getClassNameAsString(topiaId); - + try { + /* Non compilable code since hibernate 4.2, but not a real, not usefull boolean mustCommit = false; if (!session.getJDBCContext().getTransaction().isActive()) { mustCommit = true; session.getJDBCContext().getTransaction().begin(); - } + }*/ String hql = "from " + entityClass + " where topiaId=?"; List results = session.list(hql, params); - if (mustCommit) { + + /*if (mustCommit) { session.getJDBCContext().getTransaction().commit(); - } - result = (TopiaEntity)results.get(0); + }*/ + result = (TopiaEntity) results.get(0); } catch (HibernateException eee) { if (log.isDebugEnabled()) { log.debug("Can't find TopiaEntity: " + topiaId, eee);

1 0