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

r315 - branches/4.2.2/sensitivityanalysis
by echatellier＠users.forge.codelutin.com April 10, 2014

April 10, 2014

Author: echatellier Date: 2014-04-10 18:44:50 +0200 (Thu, 10 Apr 2014) New Revision: 315 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/315 Log: Mise ?\195?\160 jour dans la gestion des ouverture/fermeture et nettoyage des sessions Modified: branches/4.2.2/sensitivityanalysis/DOptimal.java branches/4.2.2/sensitivityanalysis/Fast.java branches/4.2.2/sensitivityanalysis/Morris.java branches/4.2.2/sensitivityanalysis/OptimumLHS.java branches/4.2.2/sensitivityanalysis/RandomLHS.java branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java branches/4.2.2/sensitivityanalysis/RegularFractions.java branches/4.2.2/sensitivityanalysis/Sobol.java Modified: branches/4.2.2/sensitivityanalysis/DOptimal.java =================================================================== --- branches/4.2.2/sensitivityanalysis/DOptimal.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/DOptimal.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,7 +32,6 @@ import org.apache.commons.lang.StringUtils; import org.nuiton.j2r.REngine; import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; import org.nuiton.j2r.types.RDataFrame; import java.io.File; @@ -77,12 +76,8 @@ int factorsNb = factors.size(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - engine.voidEval("library(AlgDesign)"); //Create a list of the factors under the form factor1=factor1,... @@ -211,7 +206,7 @@ Map<Object, Object> values = discDomain.getValues(); int count=0; Collection<Object> collecValues = values.values(); - for (Object value:collecValues){ + for (Object value:collecValues) { if (count!=0){ parameters += ","; } @@ -236,11 +231,8 @@ "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory, false); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -254,22 +246,16 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number int factorNumber = (Integer)engine.eval("dim(x$design)[2]"); SimulationParameter param = simulationStorages.get(0).getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - SimulationStorage firstStorage = simulationStorages.get(0); + String firstStorageName = outputDirectory.getName().replaceAll("-", ""); - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - for (int k = 0; k < sensitivityNumber; k++) { SensitivityExport sensitivityExport = @@ -318,7 +304,7 @@ *Sensitivity Indices export name is sensitivityExportName_SensitivityIndices.csv */ -//Compute Sum of Squares and Sensitivity indices + //Compute Sum of Squares and Sensitivity indices engine.voidEval("SoS<-summary(aovresult)[[1]][1:dim(summary(aovresult)[[1]])[1],2]"); engine.voidEval("names(SoS)<-dimnames(summary(aovresult)[[1]])[[1]][1:dim(summary(aovresult)[[1]])[1]]"); engine.voidEval("IndSensibilite<-SoS/sum(SoS)"); @@ -373,23 +359,8 @@ } - //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + closeEngine(engine, outputDirectory); - - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(firstStorageName)){ - engine.remove(object); - } - } - - //Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/Fast.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Fast.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/Fast.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -28,7 +28,6 @@ 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; @@ -102,12 +101,8 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); @@ -156,10 +151,6 @@ 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(); @@ -171,6 +162,8 @@ thisExperimentScenarios.add(experimentScenario); thisExperiment.setScenarios(thisExperimentScenarios); } + + closeEngine(engine, outputDirectory, false); } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -182,20 +175,13 @@ public void analyzeResult(List<SimulationStorage> simulationStorages, File outputDirectory) throws SensitivityException { - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - + // for export engine.setwd(outputDirectory); // Call R @@ -284,21 +270,9 @@ simulationName + "." + name)); } + + closeEngine(engine, outputDirectory); - //Rename R objects for saving purpose - renameObjects(engine, simulationName); - - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/Morris.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Morris.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/Morris.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -123,17 +123,9 @@ rCall = editRInstruction(rCall); } - REngine engine; - try { - engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); @@ -200,10 +192,6 @@ "\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Setting up the scenarios. List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); for (int j = 0; j < nbExperiments; j++) { @@ -216,6 +204,8 @@ thisExperimentScenarios.add(experimentScenario); thisExperiment.setScenarios(thisExperimentScenarios); } + + closeEngine(engine, outputDirectory, false); } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); @@ -229,20 +219,11 @@ public void analyzeResult(List<SimulationStorage> simulationStorages, File outputDirectory) throws SensitivityException { - SimulationStorage storage = simulationStorages.get(0); - String simulationName = storage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); - REngine engine = null; - try { - engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Call R // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -331,20 +312,8 @@ } - //Rename R objects for saving purpose - renameObjects(engine,simulationName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/OptimumLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -26,7 +26,6 @@ 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; @@ -69,10 +68,10 @@ } @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) throws SensitivityException { - setIsisFactorsR(plan, outputdirectory); + setIsisFactorsR(plan, outputDirectory); int factorNumber = plan.getFactors().size(); List<Factor> factors = plan.getFactors(); @@ -84,15 +83,8 @@ checkAllFactorContinuous(factors); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Set working directory to get Isis R session - engine.loadRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - //Load the lhs library engine.voidEval("library(lhs)"); @@ -200,12 +192,8 @@ engine.voidEval(rInstruction); - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); + closeEngine(engine, outputDirectory, false); - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't generate scenarios", e); } @@ -219,20 +207,12 @@ //The first storage to get the name and parameters all along the method SimulationStorage storage = simulationStorages.get(0); + String simulationName = outputDirectory.getName().replaceAll("-", ""); - String simulationName = storage.getName().replaceAll("-", ""); - try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - engine.voidEval("factors<-data.frame(x)"); engine.voidEval("names(factors)<-factornames"); @@ -349,18 +329,8 @@ } - //Rename R objects for saving purpose - renameObjects(engine, simulationName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/RandomLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RandomLHS.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/RandomLHS.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -28,7 +28,6 @@ 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; @@ -81,15 +80,8 @@ try { - REngine engine = new RProxy(); //The R engine + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Load the lhs library engine.voidEval("library(lhs)"); @@ -190,16 +182,13 @@ engine.voidEval(rInstruction); // Clean RData - for (Factor factor:factors) { - engine.remove(factor.getName().replaceAll(" ", "")); + for (Factor factor : factors) { + String factorName = factor.getName().replaceAll(" ", ""); + engine.remove(factorName); } - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory, false); - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't generate scenarios", e); } @@ -212,22 +201,14 @@ File outputDirectory) throws SensitivityException { SimulationStorage simulationStorage1 = simulationStorages.get(0); - String simName = simulationStorage1.getName(); - String simulationName = simName.replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); SimulationParameter param = simulationStorage1.getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); //List<SensitivityExport> export = param.getSensitivityExport(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - engine.voidEval("factors<-data.frame(x)"); //Get back the factors number @@ -339,26 +320,10 @@ "isis.methodAnalyse"; engine.voidEval(String.format(renameIsisMethodAnalyse, simulationName + "." + name)); - } - //Rename R objects for saving purpose - renameObjects(engine, simulationName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,7 +32,6 @@ import org.apache.commons.lang.StringUtils; import org.nuiton.j2r.REngine; import org.nuiton.j2r.RException; -import org.nuiton.j2r.RProxy; import org.nuiton.j2r.types.RDataFrame; import java.io.File; @@ -77,7 +76,7 @@ int factorsNb = factors.size(); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); //Get Isis R session engine.loadRData(outputDirectory.getParentFile(), @@ -213,11 +212,8 @@ "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory, false); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -231,22 +227,16 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number int factorNumber = (Integer)engine.eval("dim(x)[2]"); SimulationParameter param = simulationStorages.get(0).getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - SimulationStorage firstStorage = simulationStorages.get(0); + String firstStorageName = outputDirectory.getName().replaceAll("-", ""); - String firstStorageName = firstStorage.getName().replaceAll("-", ""); - for (int k = 0; k < sensitivityNumber; k++) { SensitivityExport sensitivityExport = @@ -344,22 +334,8 @@ } - //Rename R objects for saving purpose - renameObjects(engine, firstStorageName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(firstStorageName)){ - engine.remove(object); - } - } - - //Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); } Modified: branches/4.2.2/sensitivityanalysis/RegularFractions.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularFractions.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/RegularFractions.java 2014-04-10 16:44:50 UTC (rev 315) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2014 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -28,7 +28,6 @@ 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; @@ -97,7 +96,7 @@ try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); //Clear session engine.clearSession(); @@ -204,12 +203,8 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory, false); - engine.terminate(); - } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); } @@ -226,19 +221,12 @@ SimulationParameter param = firstStorage.getParameter(); List<SensitivityExport> exports = param.getSensitivityExport(); int sensitivityNumber = exports.size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - //Get back the factors number int factorNumber = (Integer) engine.eval("dim(data)[2]"); @@ -347,22 +335,8 @@ } - //Rename R objects for saving purpose - renameObjects(engine,simulationName); + closeEngine(engine, outputDirectory); - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - - engine.terminate(); - } catch (Exception eee) { throw new SensitivityException("Can't evaluate results", eee); } Modified: branches/4.2.2/sensitivityanalysis/Sobol.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Sobol.java 2014-04-10 14:19:27 UTC (rev 314) +++ branches/4.2.2/sensitivityanalysis/Sobol.java 2014-04-10 16:44:50 UTC (rev 315) @@ -29,7 +29,6 @@ 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; @@ -68,10 +67,10 @@ } @Override - public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) + public SensitivityScenarios compute(DesignPlan plan, File outputDirectory) throws SensitivityException { - setIsisFactorsR(plan, outputdirectory); + setIsisFactorsR(plan, outputDirectory); RDataFrame dataFrame; int nbExperiments; @@ -90,15 +89,8 @@ } try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - engine.voidEval("library(sensitivity)"); String x = "<-data.frame(matrix(c("; @@ -156,11 +148,7 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - // Save Isis R session - engine.saveRData(outputdirectory.getParentFile(), - outputdirectory.getName()); - - // Setting up the scenarios. + // Setting up the scenarios. for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { @@ -171,11 +159,13 @@ } thisExperimentScenarios.add(experimentScenario); } + + closeEngine(engine, outputDirectory, false); } catch (Exception e) { - throw new SensitivityException("Can't generate scenarios", e);} + throw new SensitivityException("Can't generate scenarios", e); + } - thisExperiment.setScenarios(thisExperimentScenarios); return thisExperiment; @@ -188,19 +178,12 @@ SimulationStorage firstStorage = simulationStorages.get(0); SimulationParameter param = firstStorage.getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); - String simulationName = firstStorage.getName().replaceAll("-", ""); + String simulationName = outputDirectory.getName().replaceAll("-", ""); try { - REngine engine = new RProxy(); + REngine engine = openEngine(outputDirectory); - //Clear session - engine.clearSession(); - - //Get Isis R session - engine.loadRData(outputDirectory.getParentFile(), - outputDirectory.getName()); - // Call R // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -291,19 +274,7 @@ } - //Rename R objects for saving purpose - renameObjects(engine, simulationName); - - //Clean temporary R objects - for (String object:engine.ls()) { - if (!object.startsWith(simulationName)){ - engine.remove(object); - } - } - - // Save Isis R session - engine.saveRData(outputDirectory.getParentFile(), - outputDirectory.getName()); + closeEngine(engine, outputDirectory); } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); }

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r314 - branches/4.2.2/scripts
by echatellier＠users.forge.codelutin.com April 10, 2014

April 10, 2014

Author: echatellier Date: 2014-04-10 16:19:27 +0200 (Thu, 10 Apr 2014) New Revision: 314 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/314 Log: Fix javadoc Modified: branches/4.2.2/scripts/RuleUtil.java branches/4.2.2/scripts/SiMatrix.java Modified: branches/4.2.2/scripts/RuleUtil.java =================================================================== --- branches/4.2.2/scripts/RuleUtil.java 2013-12-01 22:05:23 UTC (rev 313) +++ branches/4.2.2/scripts/RuleUtil.java 2014-04-10 14:19:27 UTC (rev 314) @@ -52,7 +52,7 @@ /** * @param context le context de simulation * @param species l'espece sur lequel on souhaite le total - * @param date la date pour laquel on veut le calcul, cet argument est + * @param step le pas de temps pour lequel on veut le calcul, cet argument est * passe seulement pour que le cache ne retourne pas toujours la meme valeur * @return total catch in tons */ Modified: branches/4.2.2/scripts/SiMatrix.java =================================================================== --- branches/4.2.2/scripts/SiMatrix.java 2013-12-01 22:05:23 UTC (rev 313) +++ branches/4.2.2/scripts/SiMatrix.java 2014-04-10 14:19:27 UTC (rev 314) @@ -101,13 +101,9 @@ } /** - * * @param context - * Simulation context - * @param db - * TopiaContext with transaction opened. You must used this - * TopiaContext and not used - * SimulationContext.getSimulationStorage().getStorage() + * Simulation context transaction opened. You must used this + * TopiaContext and not used SimulationContext.getSimulationStorage().getStorage() * @throws TopiaException */ public SiMatrix(SimulationContext context) throws TopiaException { @@ -1080,8 +1076,8 @@ /** * - * @param setOfVessels - * @param zone + * @param sov + * @param zoneMetier * @return */ protected double travelTimePerTrip(SetOfVessels sov,

1 0

Build failed in Jenkins: isis-fish-data-nightly #1
by admin+ci-codelutin.com＠codelutin.com Feb. 17, 2014

Feb. 17, 2014

See <http://ci.codelutin.com/jenkins/job/isis-fish-data-nightly/1/> ------------------------------------------ [...truncated 1429 lines...] <div id="members"> <ul> <li><a href="http://www.easter-eggs.com/">Easter-eggs</a></li> <li><a href="http://www.codelutin.com/">Code Lutin</a></li> <li><a href="http://www.entrouvert.com/">Entr'ouvert</a></li> <li><a href="http://www.ldd.fr/">Les Développements Durables</a></li> <li><a href="http://www.nereide.fr">Néréide</a></li> <li><a href="http://www.syloe.com/">Syloé</a></li> <li><a href="http://www.labor-liber.com/">labor-liber</a></li> <li><a href="http://www.cliss21.com/">Cliss XXI</a></li> <li><a href="http://www.silecs.info/">SILECS</a></li> <li><a href="http://www.libricks.fr/">Libricks</a></li> <li><a href="http://azae.net/">Azaé</a></li> <li><a href="http://www.scil.coop">SCIL</a></li> <li><a href="https://www.cadoles.com/">Cadoles</a></li> </ul> </div> </div> </div> </div> <div id="warpperhome" class="clearfix"> <div class="menu"> <div class="rightmenu"> <ul> <li class="level1"><div class="li"> <a href="/accueil" class="wikilink1" title="accueil">Accueil</a></div> </li> <li class="level1"><div class="li"> <a href="/nos_metiers" class="wikilink1" title="nos_metiers">Nos métiers</a></div> </li> <li class="level1"><div class="li"> <a href="/nos_valeurs" class="wikilink1" title="nos_valeurs">Nos valeurs</a></div> </li> <li class="level1"><div class="li"> <a href="/references" class="wikilink1" title="references"> Nos références</a></div> </li> <li class="level1"><div class="li"> <a href="/le_laboratoire" class="wikilink1" title="le_laboratoire">Le laboratoire</a></div> </li> <li class="level1"><div class="li"> <a href="/contact" class="wikilink1" title="contact">Contact</a></div> </li> </ul> </div> </div> <div id="warpper2"> <div class="maincontent"> <div class="margin">  <div class="page_left"> <h1 class="sectionedit1"><a name="cette_page_n_existe_pas_encore" id="cette_page_n_existe_pas_encore">Cette page n'existe pas encore</a></h1> <div class="level1"> <p> Vous avez suivi un lien vers une page qui n'existe pas encore. 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r313 - in branches/4.2.2: exports rules scripts sensitivityanalysis sensitivityexports simulationplans simulators
by echatellier＠users.forge.codelutin.com Dec. 1, 2013

Dec. 1, 2013

Author: echatellier Date: 2013-12-01 23:05:23 +0100 (Sun, 01 Dec 2013) New Revision: 313 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/313 Log: Format and correct some codes Modified: branches/4.2.2/exports/Abundances.java branches/4.2.2/exports/Biomasses.java branches/4.2.2/exports/CapturesNombre.java branches/4.2.2/exports/CapturesNombreStrategies.java branches/4.2.2/exports/CapturesPoids.java branches/4.2.2/exports/CapturesPoidsStrategies.java branches/4.2.2/exports/CellsDefinition.java branches/4.2.2/exports/EffortsMetier.java branches/4.2.2/exports/MetierZone.java branches/4.2.2/exports/NonActivite.java branches/4.2.2/exports/OwnerMargin.java branches/4.2.2/exports/RegionDefinition.java branches/4.2.2/exports/RejetsNombre.java branches/4.2.2/exports/RejetsPoids.java branches/4.2.2/exports/VesselMargin.java branches/4.2.2/exports/ZonesDefinition.java branches/4.2.2/rules/Cantonnement.java branches/4.2.2/rules/CantonnementPreSimu.java branches/4.2.2/rules/ChangementParamControlablePresimu.java branches/4.2.2/rules/EffortReduction.java branches/4.2.2/rules/GraviteVPUE1.java branches/4.2.2/rules/InterdictionEngin.java branches/4.2.2/rules/InterdictionEnginPreSimu.java branches/4.2.2/rules/TACpoids.java branches/4.2.2/rules/TailleMin.java branches/4.2.2/rules/TotalClosure.java branches/4.2.2/scripts/GravityModel.java branches/4.2.2/scripts/MinimisationUtil.java branches/4.2.2/scripts/ObjectiveFunction.java branches/4.2.2/scripts/ObjectiveFunctionBaranov.java branches/4.2.2/scripts/ResultName.java branches/4.2.2/scripts/RuleUtil.java branches/4.2.2/scripts/SiMatrix.java branches/4.2.2/sensitivityanalysis/DOptimal.java branches/4.2.2/sensitivityanalysis/Fast.java branches/4.2.2/sensitivityanalysis/Morris.java branches/4.2.2/sensitivityanalysis/OptimumLHS.java branches/4.2.2/sensitivityanalysis/RandomLHS.java branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java branches/4.2.2/sensitivityanalysis/RegularFractions.java branches/4.2.2/sensitivityanalysis/Sobol.java branches/4.2.2/sensitivityexports/SensitivityBiomassReferenceY9.java branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeY6.java branches/4.2.2/sensitivityexports/SensitivityBiomassY3.java branches/4.2.2/sensitivityexports/SensitivityCatchWeightReferenceY7.java branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeY4.java branches/4.2.2/sensitivityexports/SensitivityCatchWeightY1.java branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassY2.java branches/4.2.2/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java branches/4.2.2/simulationplans/SimulationNumberRestriction.java branches/4.2.2/simulators/DefaultSimulator.java branches/4.2.2/simulators/SimulatorEffortByCell.java Modified: branches/4.2.2/exports/Abundances.java =================================================================== --- branches/4.2.2/exports/Abundances.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/Abundances.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -37,7 +37,7 @@ import fr.ifremer.isisfish.datastore.SimulationStorage; /** - * Abundance.java + * Abundances.java * * Created: 1 septembre 2006 * @@ -52,8 +52,8 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(Abundances.class); - protected String [] necessaryResult = { - ResultName.MATRIX_ABUNDANCE + protected String[] necessaryResult = { + ResultName.MATRIX_ABUNDANCE }; @Override @@ -80,15 +80,15 @@ public void export(SimulationStorage simulation, Writer out) throws Exception { for (Population pop : simulation.getParameter().getPopulations()) { MatrixND mat = simulation.getResultStorage().getMatrix(pop, ResultName.MATRIX_ABUNDANCE); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - TimeStep step = (TimeStep)sems[0]; - PopulationGroup group = (PopulationGroup)sems[1]; - Zone zone = (Zone)sems[2]; + Object[] sems = i.getSemanticsCoordinates(); + TimeStep step = (TimeStep) sems[0]; + PopulationGroup group = (PopulationGroup) sems[1]; + Zone zone = (Zone) sems[2]; double val = i.getValue(); - out.write(pop.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ step.getStep() +";"+ val +"\n"); + out.write(pop.getName() + ";" + group.getId() + ";" + zone.getName() + ";" + step.getStep() + ";" + val + "\n"); } } } Modified: branches/4.2.2/exports/Biomasses.java =================================================================== --- branches/4.2.2/exports/Biomasses.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/Biomasses.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -53,8 +53,8 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(Biomasses.class); - protected String [] necessaryResult = { - ResultName.MATRIX_BIOMASS + protected String[] necessaryResult = { + ResultName.MATRIX_BIOMASS }; @Override @@ -81,15 +81,15 @@ public void export(SimulationStorage simulation, Writer out) throws Exception { for (Population pop : simulation.getParameter().getPopulations()) { MatrixND mat = simulation.getResultStorage().getMatrix(pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); - TimeStep step = (TimeStep)sems[0]; - PopulationGroup group = (PopulationGroup)sems[1]; - Zone zone = (Zone)sems[2]; - + Object[] sems = i.getSemanticsCoordinates(); + TimeStep step = (TimeStep) sems[0]; + PopulationGroup group = (PopulationGroup) sems[1]; + Zone zone = (Zone) sems[2]; + double val = i.getValue(); - out.write(pop.getName() +";"+ group.getId() +";"+ zone.getName() +";"+ step.getStep() +";"+ val +"\n"); + out.write(pop.getName() + ";" + group.getId() + ";" + zone.getName() + ";" + step.getStep() + ";" + val + "\n"); } } } Modified: branches/4.2.2/exports/CapturesNombre.java =================================================================== --- branches/4.2.2/exports/CapturesNombre.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/CapturesNombre.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,9 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesNombre.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP + }; @Override public String[] getNecessaryResult() { @@ -82,8 +84,7 @@ TimeStep lastStep = simulation.getResultStorage().getLastStep(); for (Population pop : simulation.getParameter().getPopulations()) { - for (TimeStep step = new TimeStep(0); !step.after(lastStep); step = step - .next()) { + for (TimeStep step = new TimeStep(0); !step.after(lastStep); step = step.next()) { MatrixND mat = simulation.getResultStorage().getMatrix(step, pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); if (mat != null) { // can be null if simulation is stopped before last year simulation Modified: branches/4.2.2/exports/CapturesNombreStrategies.java =================================================================== --- branches/4.2.2/exports/CapturesNombreStrategies.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/CapturesNombreStrategies.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -55,7 +55,9 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesNombreStrategies.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP + }; @Override public String[] getNecessaryResult() { @@ -78,8 +80,7 @@ } @Override - public void export(SimulationStorage simulation, Writer out) - throws Exception { + public void export(SimulationStorage simulation, Writer out) throws Exception { TimeStep lastStep = simulation.getResultStorage().getLastStep(); for (Population pop : simulation.getParameter().getPopulations()) { Modified: branches/4.2.2/exports/CapturesPoids.java =================================================================== --- branches/4.2.2/exports/CapturesPoids.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/CapturesPoids.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,9 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesPoids.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + }; @Override public String[] getNecessaryResult() { Modified: branches/4.2.2/exports/CapturesPoidsStrategies.java =================================================================== --- branches/4.2.2/exports/CapturesPoidsStrategies.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/CapturesPoidsStrategies.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -55,7 +55,9 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CapturesPoidsStrategies.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + }; @Override public String[] getNecessaryResult() { Modified: branches/4.2.2/exports/CellsDefinition.java =================================================================== --- branches/4.2.2/exports/CellsDefinition.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/CellsDefinition.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -50,11 +50,11 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(CellsDefinition.class); - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override Modified: branches/4.2.2/exports/EffortsMetier.java =================================================================== --- branches/4.2.2/exports/EffortsMetier.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/EffortsMetier.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,7 @@ static private Log log = LogFactory.getLog(EffortsMetier.class); protected String [] necessaryResult = { - ResultName.MATRIX_EFFORT_PER_STRATEGY_MET + ResultName.MATRIX_EFFORT_PER_STRATEGY_MET }; @Override @@ -80,7 +80,7 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { MatrixND mat = simulation.getResultStorage().getMatrix(ResultName.MATRIX_EFFORT_PER_STRATEGY_MET); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); Object [] sems = i.getSemanticsCoordinates(); TimeStep step = (TimeStep)sems[0]; Modified: branches/4.2.2/exports/MetierZone.java =================================================================== --- branches/4.2.2/exports/MetierZone.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/MetierZone.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -51,8 +51,8 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(MetierZone.class); - public String [] necessaryResult = { - ResultName.MATRIX_METIER_ZONE, + protected String [] necessaryResult = { + ResultName.MATRIX_METIER_ZONE, }; @Override @@ -82,7 +82,7 @@ for (TimeStep step = new TimeStep(0); !step.after(lastStep); step = step.next() ) { MatrixND mat = simulation.getResultStorage().getMatrix(step, ResultName.MATRIX_METIER_ZONE); if (mat != null) { // can be null if simulation is stopped before last year simulation - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); if (i.getValue() == 1) { Object metier = i.getSemanticsCoordinates()[0]; Modified: branches/4.2.2/exports/NonActivite.java =================================================================== --- branches/4.2.2/exports/NonActivite.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/NonActivite.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,7 @@ static private Log log = LogFactory.getLog(NonActivite.class); protected String [] necessaryResult = { - ResultName.MATRIX_NO_ACTIVITY + ResultName.MATRIX_NO_ACTIVITY }; @Override @@ -80,7 +80,7 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { MatrixND mat = simulation.getResultStorage().getMatrix(ResultName.MATRIX_NO_ACTIVITY); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); Object [] sems = i.getSemanticsCoordinates(); TimeStep step = (TimeStep)sems[0]; Modified: branches/4.2.2/exports/OwnerMargin.java =================================================================== --- branches/4.2.2/exports/OwnerMargin.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/OwnerMargin.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,7 @@ static private Log log = LogFactory.getLog(OwnerMargin.class); protected String [] necessaryResult = { - ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL + ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL }; @Override @@ -80,9 +80,9 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { MatrixND mat = simulation.getResultStorage().getMatrix(ResultName.MATRIX_OWNER_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); - Object [] sems = i.getSemanticsCoordinates(); + Object[] sems = i.getSemanticsCoordinates(); TimeStep step = (TimeStep)sems[0]; Strategy str = (Strategy)sems[1]; Modified: branches/4.2.2/exports/RegionDefinition.java =================================================================== --- branches/4.2.2/exports/RegionDefinition.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/RegionDefinition.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -49,11 +49,11 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(RegionDefinition.class); - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override Modified: branches/4.2.2/exports/RejetsNombre.java =================================================================== --- branches/4.2.2/exports/RejetsNombre.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/RejetsNombre.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,9 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(RejetsNombre.class); - protected String[] necessaryResult = { ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP + }; @Override public String[] getNecessaryResult() { Modified: branches/4.2.2/exports/RejetsPoids.java =================================================================== --- branches/4.2.2/exports/RejetsPoids.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/RejetsPoids.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,8 +54,8 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(RejetsPoids.class); - protected String[] necessaryResult = { ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP - + protected String[] necessaryResult = { + ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP }; @Override Modified: branches/4.2.2/exports/VesselMargin.java =================================================================== --- branches/4.2.2/exports/VesselMargin.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/VesselMargin.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -54,7 +54,7 @@ static private Log log = LogFactory.getLog(VesselMargin.class); protected String [] necessaryResult = { - ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL + ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL }; @Override @@ -80,7 +80,7 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { MatrixND mat = simulation.getResultStorage().getMatrix(ResultName.MATRIX_VESSEL_MARGIN_OVER_VARIABLE_COSTS_PER_STRATEGY_PER_VESSEL); - for (MatrixIterator i=mat.iterator(); i.hasNext();) { + for (MatrixIterator i = mat.iterator(); i.hasNext();) { i.next(); Object [] sems = i.getSemanticsCoordinates(); TimeStep step = (TimeStep)sems[0]; Modified: branches/4.2.2/exports/ZonesDefinition.java =================================================================== --- branches/4.2.2/exports/ZonesDefinition.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/exports/ZonesDefinition.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -51,11 +51,11 @@ /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(ZonesDefinition.class); - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override Modified: branches/4.2.2/rules/Cantonnement.java =================================================================== --- branches/4.2.2/rules/Cantonnement.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/Cantonnement.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -50,6 +50,8 @@ /** * Cantonnement.java * + * Remplace aussi Cantonnement Engin + * * Created: 30 novembre 2006 * * @author anonymous <anonymous(a)labs.libre-entreprise.org> @@ -58,10 +60,6 @@ * Last update: $Date: 2007-11-02 17:41:41 $ * by : $Author: bpoussin $ */ - -/** - * Remplace aussi Cantonnement Engin - */ public class Cantonnement extends AbstractRule { /** to use log facility, just put in your code: log.info("..."); */ @@ -80,12 +78,12 @@ @Doc(value="End month") public Month param_endMonth = Month.DECEMBER; - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - ResultName.MATRIX_NO_ACTIVITY, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + ResultName.MATRIX_NO_ACTIVITY, }; @Override @@ -126,7 +124,7 @@ public boolean condition(SimulationContext context, TimeStep step, Metier metier) throws Exception { if (step.before(param_beginStep)) { return false; - } else if(step.after(param_endStep)) { + } else if (step.after(param_endStep)) { return false; } @@ -204,7 +202,7 @@ zoneCantonnement.addAllCell(tmpCells); i.remove(); } - List<Zone> newZone = new ArrayList<Zone>(); + List<Zone> newZone = new ArrayList<>(); newZone.add(zoneCantonnement); infoMetier.setZone(newZone); } else { @@ -219,10 +217,10 @@ metierMon.addforbiddenMetier(metier); List<Strategy> strategies = siMatrix.getStrategies(step); - for(Strategy str : strategies){ + for (Strategy str : strategies) { StrategyMonthInfo info = str.getStrategyMonthInfo(step.getMonth()); double prop = info.getProportionMetier(metier); - if (prop != 0){ + if (prop != 0) { noActivity.setValue(str , metier, prop); info.setProportionMetier(metier, 0); } Modified: branches/4.2.2/rules/CantonnementPreSimu.java =================================================================== --- branches/4.2.2/rules/CantonnementPreSimu.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/CantonnementPreSimu.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -73,15 +73,15 @@ @Doc(value="End month") public Month param_endMonth = Month.DECEMBER; - protected Map<Month, MatrixND> tableNonActivite = new HashMap<Month, MatrixND>(); + protected Map<Month, MatrixND> tableNonActivite = new HashMap<>(); protected boolean affectNonActivite = false; - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - ResultName.MATRIX_NO_ACTIVITY, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + ResultName.MATRIX_NO_ACTIVITY, }; @Override @@ -107,7 +107,8 @@ if (effort != null){ for (Month month : chomageMonth) { StrategyMonthInfo InfoMois = strategy.getStrategyMonthInfo(month); -//this.p.tableNonActivite=Regle_action_lib.reportNonActivite(this.p.tableNonActivite, listestrategies.get(i), metier, mois, InfoMois.getProportionMetier(metier)); + // this.p.tableNonActivite=Regle_action_lib.reportNonActivite(this.p.tableNonActivite, + // listestrategies.get(i), metier, mois, InfoMois.getProportionMetier(metier)); log.info("debut reportNonActivite"); // on regarde si on a déjà une entrée pour le mois courant @@ -160,16 +161,16 @@ else { log.info("l engin du métier est bien concerné"); List<MetierSeasonInfo> saisons = metier.getMetierSeasonInfo(); - for (MetierSeasonInfo saisonmetier: saisons){ + for (MetierSeasonInfo saisonmetier : saisons){ int inter = siMatrix.nbCellInter(saisonmetier.getZone(), param_zone); - if (inter != 0){ + if (inter != 0) { List<Cell> MailleMetier = siMatrix.getCells(saisonmetier.getZone()); // les mailles qui reste dans la zone metier - List<Cell> newCellMetier = new ArrayList<Cell>(MailleMetier); + List<Cell> newCellMetier = new ArrayList<>(MailleMetier); newCellMetier.removeAll(maillefermee); - List<Month> saison=saisonmetier.getMonths(); + List<Month> saison = saisonmetier.getMonths(); if (saison.containsAll(SaisonFermee)){ log.info("il y a bien intersection entre la zone métier et le cantonnement pour la saison "+saison.toString()); // calcule de la zone restante: Modified: branches/4.2.2/rules/ChangementParamControlablePresimu.java =================================================================== --- branches/4.2.2/rules/ChangementParamControlablePresimu.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/ChangementParamControlablePresimu.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -77,11 +77,11 @@ @Doc(value="New param controlable value") public String param_newParamValue = "80"; - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override Modified: branches/4.2.2/rules/EffortReduction.java =================================================================== --- branches/4.2.2/rules/EffortReduction.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/EffortReduction.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -57,9 +57,13 @@ @Doc("Pourcentage de reduction d effort applique.") public double param_PercentReduction = 0.5; - boolean first = true; + protected boolean first = true; - protected String[] necessaryResult = {}; + protected String[] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + }; /** * @return the necessaryResult Modified: branches/4.2.2/rules/GraviteVPUE1.java =================================================================== --- branches/4.2.2/rules/GraviteVPUE1.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/GraviteVPUE1.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -59,21 +59,20 @@ static private Log log = LogFactory.getLog(GraviteVPUE1.class); /** stocke la somme des prop initiales [str x month] */ - private MatrixND SommePropInitial = null; - /** stocke par strat*met, la dernière attractivite pour chaque mois [str x met x month] */ + protected MatrixND SommePropInitial = null; /** permet de stocker les CPUE nominales [str x met] */ - private MatrixND valuePerUnitOfEffort = null; + protected MatrixND valuePerUnitOfEffort = null; - public String[] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET, - //ResultName.MATRIX_EFFORT_PER_STRATEGY_MET, - ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET, // garder la , + // Booleen permettant que ne boucler que sur un seul metier dans la preaction : + protected boolean first = true; + protected String[] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET }; @Override @@ -146,7 +145,6 @@ SommePropInitial.setValue(str, info.getMonth(), somme); } } - } /** @@ -164,8 +162,6 @@ return step.getYear() > 0; } - // Booleen permettant que ne boucler que sur un seul metier dans la preaction : - boolean first = true; /** * Si la condition est vrai alors cette action est executee avant le pas Modified: branches/4.2.2/rules/InterdictionEngin.java =================================================================== --- branches/4.2.2/rules/InterdictionEngin.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/InterdictionEngin.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -71,11 +71,11 @@ @Doc(value="do the doc of param endMonth") public Month param_endMonth = Month.DECEMBER; - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override @@ -167,7 +167,7 @@ // 1er cas:l'effort est reporte sur un metier de la meme strategie, // n'ayant pas l'espece comme capture principale et pechant avec le meme engin - List<EffortDescription> MetiersPossibles = new ArrayList<EffortDescription>(Strat.getSetOfVessels().getPossibleMetiers()); + List<EffortDescription> MetiersPossibles = new ArrayList<>(Strat.getSetOfVessels().getPossibleMetiers()); // on verifie que les metiers sont bien pratiques au mois courant, // qu'ils n'ont pas le meme engin et qu'ils ne sont pas @@ -184,7 +184,7 @@ // on repartit maintenant l'effort entre les differents metiers // possibles dans la meme strategie si un metier possible existe bien - if (MetiersPossibles.size() != 0){ + if (MetiersPossibles.size() != 0) { int NbMetier=MetiersPossibles.size(); for (EffortDescription effort : MetiersPossibles) { Metier met = effort.getPossibleMetiers(); @@ -203,7 +203,7 @@ siMatrix.getMetiers(step)); matNonActivite.setValue(Strat, metier, StratMonthInfo.getProportionMetier(metier)); - StratMonthInfo.setProportionMetier(metier,0); + StratMonthInfo.setProportionMetier(metier, 0); } } Modified: branches/4.2.2/rules/InterdictionEnginPreSimu.java =================================================================== --- branches/4.2.2/rules/InterdictionEnginPreSimu.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/InterdictionEnginPreSimu.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -70,14 +70,14 @@ @Doc(value="do the doc of param endMonth") public Month param_endMonth = Month.DECEMBER; - protected Map<Month, MatrixND> tableNonActivite = new HashMap<Month, MatrixND>(); + protected Map<Month, MatrixND> tableNonActivite = new HashMap<>(); protected boolean affectNonActivite = false; - public String [] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String [] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override @@ -207,7 +207,7 @@ @Override public void preAction(SimulationContext context, TimeStep step, Metier metier) throws Exception { // on ne doit le faire qu'une seul fois quelque soit le nombre de metier - affectNonActivite=true; + affectNonActivite = true; MatrixND mat = tableNonActivite.get(step.getMonth()); MetierMonitor metierMon = context.getMetierMonitor(); @@ -215,8 +215,7 @@ if (noActivity == null) { metierMon.setNoActivity(step, mat.copy()); - } - else { + } else { noActivity = noActivity.add(mat); } // fin Modified: branches/4.2.2/rules/TACpoids.java =================================================================== --- branches/4.2.2/rules/TACpoids.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/TACpoids.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -87,13 +87,13 @@ @Doc("TAC in tons") public double param_tacInTons = 900; - boolean affectation = false; + protected boolean affectation = false; protected String[] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; /** Modified: branches/4.2.2/rules/TailleMin.java =================================================================== --- branches/4.2.2/rules/TailleMin.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/TailleMin.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin, Stéphanie Mahevas, Chatellier Eric + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin, Stéphanie Mahevas, 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 @@ -79,7 +79,7 @@ protected boolean affectation = true; - public String[] necessaryResult = { + protected String[] necessaryResult = { // put here all necessary result for this rule // example: // ResultName.MATRIX_BIOMASS, Modified: branches/4.2.2/rules/TotalClosure.java =================================================================== --- branches/4.2.2/rules/TotalClosure.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/rules/TotalClosure.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -57,8 +57,8 @@ public Month param_beginMonth = Month.JANUARY; public Month param_endMonth = Month.JANUARY; - public String[] necessaryResult = { - ResultName.MATRIX_NO_ACTIVITY + protected String[] necessaryResult = { + ResultName.MATRIX_NO_ACTIVITY }; @Override @@ -77,6 +77,7 @@ */ @Override public void init(SimulationContext context) throws Exception { + } /** Modified: branches/4.2.2/scripts/GravityModel.java =================================================================== --- branches/4.2.2/scripts/GravityModel.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/GravityModel.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 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 Modified: branches/4.2.2/scripts/MinimisationUtil.java =================================================================== --- branches/4.2.2/scripts/MinimisationUtil.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/MinimisationUtil.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2012 Ifremer, CodeLutin, Chatellier Eric + * Copyright (C) 2012, 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 Modified: branches/4.2.2/scripts/ObjectiveFunction.java =================================================================== --- branches/4.2.2/scripts/ObjectiveFunction.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/ObjectiveFunction.java 2013-12-01 22:05:23 UTC (rev 313) @@ -1,6 +1,9 @@ /* - * Copyright (C) 2012 lgasche - * + * #%L + * IsisFish data + * %% + * Copyright (C) 2012, 2013 Ifremer, CodeLutin, lgasche + * %% * 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 @@ -14,6 +17,7 @@ * 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 scripts; Modified: branches/4.2.2/scripts/ObjectiveFunctionBaranov.java =================================================================== --- branches/4.2.2/scripts/ObjectiveFunctionBaranov.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/ObjectiveFunctionBaranov.java 2013-12-01 22:05:23 UTC (rev 313) @@ -1,6 +1,9 @@ /* - * Copyright (C) 2012 lgasche - * + * #%L + * IsisFish data + * %% + * Copyright (C) 2012, 2013 Ifremer, CodeLutin, lgasche + * %% * 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 @@ -14,6 +17,7 @@ * 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 scripts; Modified: branches/4.2.2/scripts/ResultName.java =================================================================== --- branches/4.2.2/scripts/ResultName.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/ResultName.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as Modified: branches/4.2.2/scripts/RuleUtil.java =================================================================== --- branches/4.2.2/scripts/RuleUtil.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/RuleUtil.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, CodeLutin, Chatellier Eric + * Copyright (C) 2006 - 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 Modified: branches/4.2.2/scripts/SiMatrix.java =================================================================== --- branches/4.2.2/scripts/SiMatrix.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/scripts/SiMatrix.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -1493,12 +1493,6 @@ return result; } - /////////////////////////////////////////////////////////////////////////// - // - // - // - /////////////////////////////////////////////////////////////////////////// - /** * @param step * @return @@ -1526,12 +1520,6 @@ return result; } - /////////////////////////////////////////////////////////////////////////// - // - // - // - /////////////////////////////////////////////////////////////////////////// - /** * * @@ -1556,11 +1544,6 @@ return result; } - /////////////////////////////////////////////////////////////////////////// - // - // - // - /////////////////////////////////////////////////////////////////////////// public MatrixND matrixEffortNominalPerStrategyMet(TimeStep step) throws TopiaException { List<Strategy> strategies = getStrategies(step); @@ -1614,7 +1597,7 @@ MatrixND catchPerStrategy = null; - for (TimeStep loopstep = new TimeStep(step.getYear() * 12); loopstep.beforeOrEquals(step); loopstep=loopstep.next()){ + for (TimeStep loopstep = new TimeStep(step.getYear() * 12); loopstep.beforeOrEquals(step); loopstep=loopstep.next()) { // On fait cette boucle pour contourner les aspects de cache qui font que les resultats ne sont pas recuperes //s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) // beforeOrEquals sert a bien prendre Decembre aussi Modified: branches/4.2.2/sensitivityanalysis/DOptimal.java =================================================================== --- branches/4.2.2/sensitivityanalysis/DOptimal.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/DOptimal.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityanalysis/Fast.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Fast.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/Fast.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -24,10 +24,8 @@ import java.io.File; import java.util.List; -import java.util.Map; import fr.ifremer.isisfish.simulator.sensitivity.*; -import org.apache.commons.lang3.StringUtils; import org.nuiton.j2r.REngine; import org.nuiton.j2r.RException; import org.nuiton.j2r.RProxy; @@ -35,8 +33,6 @@ import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.simulator.SimulationParameter; -import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; import fr.ifremer.isisfish.util.Doc; import org.nuiton.j2r.types.RDataFrame; Modified: branches/4.2.2/sensitivityanalysis/Morris.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Morris.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/Morris.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityanalysis/OptimumLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -37,7 +37,6 @@ 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; Modified: branches/4.2.2/sensitivityanalysis/RandomLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RandomLHS.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/RandomLHS.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -39,7 +39,6 @@ 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; /** Modified: branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityanalysis/RegularFractions.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularFractions.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/RegularFractions.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -35,13 +35,10 @@ 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; public class RegularFractions extends AbstractSensitivityAnalysis { Modified: branches/4.2.2/sensitivityanalysis/Sobol.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Sobol.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityanalysis/Sobol.java 2013-12-01 22:05:23 UTC (rev 313) @@ -24,7 +24,6 @@ import java.io.File; import java.util.List; -import java.util.Map; import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.simulator.sensitivity.*; @@ -34,7 +33,6 @@ import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.SimulationParameter; -import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.util.Doc; import org.nuiton.j2r.types.RDataFrame; Modified: branches/4.2.2/sensitivityexports/SensitivityBiomassReferenceY9.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityBiomassReferenceY9.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityBiomassReferenceY9.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeY6.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeY6.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityBiomassRelativeY6.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityexports/SensitivityBiomassY3.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityBiomassY3.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityBiomassY3.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityexports/SensitivityCatchWeightReferenceY7.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityCatchWeightReferenceY7.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityCatchWeightReferenceY7.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 Modified: branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -39,14 +39,15 @@ import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; -public class SensitivityCatchWeightRelativeReferenceY10 implements - SensitivityExport { +public class SensitivityCatchWeightRelativeReferenceY10 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory .getLog(SensitivityCatchWeightRelativeReferenceY10.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + }; @Doc("Population") public Population param_pop; Modified: branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeY4.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeY4.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityCatchWeightRelativeY4.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -43,7 +43,9 @@ static private Log log = LogFactory .getLog(SensitivityCatchWeightRelativeY4.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + }; @Doc("Population") public Population param_pop; Modified: branches/4.2.2/sensitivityexports/SensitivityCatchWeightY1.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivityCatchWeightY1.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivityCatchWeightY1.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2013 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 @@ -43,7 +43,9 @@ static private Log log = LogFactory .getLog(SensitivityCatchWeightY1.class); - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + protected String[] necessaryResult = { + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP + }; @Doc("Population") public Population param_pop; Modified: branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau, 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 @@ -50,13 +50,15 @@ static private Log log = LogFactory .getLog(SensitivitySpawningBiomassReferenceY8.class); - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + protected String[] necessaryResult = { + ResultName.MATRIX_BIOMASS + }; @Doc("Population") public Population param_pop; @Doc("URL of the Biomasses.csv reference export file") - public String param_referenceBiomassCSV =""; + public String param_referenceBiomassCSV = ""; @Override public void export(SimulationStorage simulation, Writer out) Modified: branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau, 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 @@ -57,7 +57,7 @@ public Population param_pop; @Doc("URL of the Biomasses.csv reference export file") - public String param_referenceBiomassCSV =""; + public String param_referenceBiomassCSV = ""; @Override public void export(SimulationStorage simulation, Writer out) Modified: branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau, 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 @@ -45,7 +45,9 @@ static private Log log = LogFactory .getLog(SensitivitySpawningBiomassRelativeY5.class); - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + protected String[] necessaryResult = { + ResultName.MATRIX_BIOMASS + }; @Doc("Population") public Population param_pop; Modified: branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassY2.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/sensitivityexports/SensitivitySpawningBiomassY2.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Jean Couteau, 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 @@ -45,7 +45,9 @@ static private Log log = LogFactory .getLog(SensitivitySpawningBiomassY2.class); - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + protected String[] necessaryResult = { + ResultName.MATRIX_BIOMASS + }; @Doc("Population") public Population param_pop; Modified: branches/4.2.2/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java =================================================================== --- branches/4.2.2/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/simulationplans/CalibrationSimplexePasVariable2Capturabilite.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2007 - 2011 Ifremer, CodeLutin, Sigrid Lehuta + * Copyright (C) 2007 - 2013 Ifremer, CodeLutin, Sigrid Lehuta * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -110,7 +110,7 @@ //*** write the name of the simulated matrix that contains the data corresponding // to your observations (here MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP) - public String[] necessaryResult = { + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; Modified: branches/4.2.2/simulationplans/SimulationNumberRestriction.java =================================================================== --- branches/4.2.2/simulationplans/SimulationNumberRestriction.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/simulationplans/SimulationNumberRestriction.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, CodeLutin + * Copyright (C) 2006 - 2013 Ifremer, CodeLutin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -49,11 +49,11 @@ @Doc(value = "do the doc of param max") public int param_max = 10; - public String[] necessaryResult = { - // put here all necessary result for this rule - // example: - // ResultName.MATRIX_BIOMASS, - // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, + protected String[] necessaryResult = { + // put here all necessary result for this rule + // example: + // ResultName.MATRIX_BIOMASS, + // ResultName.MATRIX_NET_VALUE_OF_LANDINGS_PER_STRATEGY_MET, }; @Override Modified: branches/4.2.2/simulators/DefaultSimulator.java =================================================================== --- branches/4.2.2/simulators/DefaultSimulator.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/simulators/DefaultSimulator.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Cedric 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 Modified: branches/4.2.2/simulators/SimulatorEffortByCell.java =================================================================== --- branches/4.2.2/simulators/SimulatorEffortByCell.java 2013-11-28 09:19:52 UTC (rev 312) +++ branches/4.2.2/simulators/SimulatorEffortByCell.java 2013-12-01 22:05:23 UTC (rev 313) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as

1 0

r312 - branches/4.2.2
by echatellier＠users.forge.codelutin.com Nov. 28, 2013

Nov. 28, 2013

Author: echatellier Date: 2013-11-28 10:19:52 +0100 (Thu, 28 Nov 2013) New Revision: 312 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/312 Log: Update deps. Build with java7. Modified: branches/4.2.2/pom.xml Modified: branches/4.2.2/pom.xml =================================================================== --- branches/4.2.2/pom.xml 2013-11-28 09:19:27 UTC (rev 311) +++ branches/4.2.2/pom.xml 2013-11-28 09:19:52 UTC (rev 312) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.2.2</version> + <version>4.3.0</version>  <description>Data for Isis-fish</description> @@ -36,10 +36,10 @@ <plugins> <plugin> <artifactId>maven-compiler-plugin</artifactId> - <version>2.5.1</version> + <version>3.1</version> <configuration> - <source>1.6</source> - <target>1.6</target> + <source>1.7</source> + <target>1.7</target> <excludes> <exclude>**/simulations/**</exclude> <exclude>**/formules/**</exclude> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.2.0-SNAPSHOT</version> + <version>4.3.0.0-beta1-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r311 - branches/4.2.2/sensitivityanalysis
by echatellier＠users.forge.codelutin.com Nov. 28, 2013

Nov. 28, 2013

Author: echatellier Date: 2013-11-28 10:19:27 +0100 (Thu, 28 Nov 2013) New Revision: 311 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/311 Log: Update AS scripts Modified: branches/4.2.2/sensitivityanalysis/DOptimal.java branches/4.2.2/sensitivityanalysis/Fast.java branches/4.2.2/sensitivityanalysis/Morris.java branches/4.2.2/sensitivityanalysis/OptimumLHS.java branches/4.2.2/sensitivityanalysis/RandomLHS.java branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java branches/4.2.2/sensitivityanalysis/RegularFractions.java branches/4.2.2/sensitivityanalysis/Sobol.java Modified: branches/4.2.2/sensitivityanalysis/DOptimal.java =================================================================== --- branches/4.2.2/sensitivityanalysis/DOptimal.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/DOptimal.java 2013-11-28 09:19:27 UTC (rev 311) @@ -109,16 +109,15 @@ 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(); + int nbValues = ((DiscreteDomain) domain).getValuesCount(); for (int i = 0; i < nbValues; i++) { vector += "as.integer(" + i + "),"; } @@ -202,9 +201,9 @@ 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/4.2.2/sensitivityanalysis/Fast.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Fast.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/Fast.java 2013-11-28 09:19:27 UTC (rev 311) @@ -24,8 +24,10 @@ import java.io.File; import java.util.List; +import java.util.Map; import fr.ifremer.isisfish.simulator.sensitivity.*; +import org.apache.commons.lang3.StringUtils; import org.nuiton.j2r.REngine; import org.nuiton.j2r.RException; import org.nuiton.j2r.RProxy; @@ -35,8 +37,6 @@ 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; @@ -44,9 +44,9 @@ * Implementation of Fast method using R. * * @author jcouteau - * @version $Revision: 89 $ + * @version $Revision: 3842 $ * - * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : + * Last update : $Date: 2013-11-22 18:52:48 +0100 (ven., 22 nov. 2013) $ By : * $Author: jcouteau $ */ public class Fast extends AbstractSensitivityAnalysis { @@ -87,14 +87,9 @@ 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, " + @@ -145,33 +140,8 @@ nbExperiments = (Integer)engine.eval("dim(a$X)[1]"); - String factorDistribution = "isis.factor.distribution<-data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; + engine.voidEval(getIsisFactorDistribution(factors)); - // Creating the vectors. - String distribution = ""; - String parameters = ""; - String factorNames = ""; - - for (int i = 0; i < factorNumber; i++) { - Factor factor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); - if (i != 0) { - distribution += ","; - parameters += ","; - factorNames += ","; - } - - distribution += "\"qunif\""; - parameters += "\"[" + domain.getMinBound() + ";" + - domain.getMaxBound() + "]\""; - factorNames += "\"" + factor.getName() + "\""; - } - engine.voidEval(String.format(factorDistribution, factorNames, - distribution, parameters)); - engine.voidEval("call<-a$call"); @@ -199,18 +169,7 @@ 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); - } + factor.setValueForIdentifier(dataFrame.get(i,j)); experimentScenario.addFactor(factor); } thisExperimentScenarios.add(experimentScenario); Modified: branches/4.2.2/sensitivityanalysis/Morris.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Morris.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/Morris.java 2013-11-28 09:19:27 UTC (rev 311) @@ -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); + checkAllUniformDistribution(factors); // Creating the vectors. String factorNames = ""; @@ -97,7 +94,6 @@ String bsup = ""; for (int i = 0; i < factorNumber; i++) { Factor factor = factors.get(i); - ContinuousDomain domain = (ContinuousDomain) factor.getDomain(); if (i != 0) { factorNames += ","; levels += ","; @@ -112,9 +108,8 @@ gridJump += factor.getCardinality() / 2; - binf += domain.getCalculatorMinBound(); - - bsup += domain.getCalculatorMaxBound(); + binf += 0; + bsup += 1; } String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s," + @@ -128,7 +123,7 @@ rCall = editRInstruction(rCall); } - REngine engine = null; + REngine engine; try { engine = new RProxy(); @@ -178,9 +173,17 @@ 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/4.2.2/sensitivityanalysis/OptimumLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2013-11-28 09:19:27 UTC (rev 311) @@ -45,7 +45,7 @@ * Implementation of Optimum Latin Hypercube method using R. * * @author jcouteau - * @version $Revision: 1.0 $ + * @version $Revision: 3842 $ */ public class OptimumLHS extends AbstractSensitivityAnalysis { @@ -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(); @@ -126,34 +126,7 @@ 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(getIsisFactorDistribution(factors)); engine.voidEval("call<-" + "\"x<-optimumLHS(" + "n=" + param_simulationNumber Modified: branches/4.2.2/sensitivityanalysis/RandomLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RandomLHS.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/RandomLHS.java 2013-11-28 09:19:27 UTC (rev 311) @@ -46,7 +46,7 @@ * Implementation of Random Latin Hypercube method using R. * * @author jcouteau - * @version $Revision: 1.0 $ + * @version $Revision: 3842 $ */ public class RandomLHS extends AbstractSensitivityAnalysis { @@ -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 { @@ -122,35 +122,8 @@ thisExperiment.setScenarios(thisExperimentScenarios); } - String isisFactorDistribution = "isis.factor.distribution<-" + - "data.frame(" + - "NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; + engine.voidEval(getIsisFactorDistribution(factors)); - 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 + ")\""); Modified: branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2013-11-28 09:19:27 UTC (rev 311) @@ -100,20 +100,19 @@ Domain domain = factor.getDomain(); if (domain instanceof ContinuousDomain) { - ContinuousDomain contDomain = (ContinuousDomain) domain; - int card = factor.getCardinality(); - Double min = contDomain.getCalculatorMinBound(); - Double max = contDomain.getCalculatorMaxBound(); - - for (int i = 0; i < card; i++) { - //add the ith value - vector += (min + (i * (max - min) / (card - 1))) + ","; - } +// ContinuousDomain contDomain = (ContinuousDomain) domain; +// int card = factor.getCardinality(); +// Double min = 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(); + int nbValues = ((DiscreteDomain) domain).getValuesCount(); for (int i = 0; i < nbValues; i++) { vector += "as.integer(" + i + "),"; } @@ -178,9 +177,9 @@ 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/4.2.2/sensitivityanalysis/RegularFractions.java =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularFractions.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/RegularFractions.java 2013-11-28 09:19:27 UTC (rev 311) @@ -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 { @@ -89,20 +87,15 @@ 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(); 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 { @@ -157,18 +150,7 @@ 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); - } + factor.setValueForIdentifier(dataFrame.get(i,j)); experimentScenario.addFactor(factor); } thisExperimentScenarios.add(experimentScenario); @@ -207,7 +189,7 @@ } engine.voidEval(dataframe); - engine.voidEval("isis.factor.distribution<-c(0.0)"); + engine.voidEval(getIsisFactorDistribution(factors)); engine.voidEval("isis.MethodExp<-list(" + "\"isis.factors\"=isis.factors," + Modified: branches/4.2.2/sensitivityanalysis/Sobol.java =================================================================== --- branches/4.2.2/sensitivityanalysis/Sobol.java 2013-11-08 10:22:14 UTC (rev 310) +++ branches/4.2.2/sensitivityanalysis/Sobol.java 2013-11-28 09:19:27 UTC (rev 311) @@ -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; @@ -46,9 +42,9 @@ * Implementation of Sobol method using R. * * @author jcouteau - * @version $Revision: 89 $ + * @version $Revision: 3842 $ * - * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : + * Last update : $Date: 2013-11-22 18:52:48 +0100 (ven., 22 nov. 2013) $ By : * $Author: jcouteau $ */ public class Sobol extends AbstractSensitivityAnalysis { @@ -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 +103,19 @@ 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++) { + x += "runif("+param_n+"),"; + } + + x = StringUtils.removeEnd(x, ","); + + x+="),nrow="+param_n+"))"; + + engine.voidEval("X1"+x); + engine.voidEval("X2"+x); + engine.voidEval(rCall); // Creating the factors vector. @@ -135,36 +139,8 @@ nbExperiments = dataFrame.dim()[0]; - String isisFactorDistribution = "isis.factor.distribution<-" + - "data.frame(NomFacteur=c(%s)," + - "NomDistribution=c(%s)," + - "ParametreDistribution=c(%s))"; + engine.voidEval(getIsisFactorDistribution(factors)); - // 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(" +

1 0

r310 - trunk/scripts
by echatellier＠users.forge.codelutin.com Nov. 8, 2013

Nov. 8, 2013

Author: echatellier Date: 2013-11-08 11:22:14 +0100 (Fri, 08 Nov 2013) New Revision: 310 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/310 Log: AJout d'un commentaire sur un resultat Modified: trunk/scripts/ResultName.java Modified: trunk/scripts/ResultName.java =================================================================== --- trunk/scripts/ResultName.java 2013-11-07 14:21:30 UTC (rev 309) +++ trunk/scripts/ResultName.java 2013-11-08 10:22:14 UTC (rev 310) @@ -136,6 +136,9 @@ * Dimension 3 : Metier * Dimension 4 : Group * Dimension 5 : Zone + * + * N'est calculé que si l'effort est calculé par cellule et non par zone. + * @see SimulatorEffortByCell */ @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZoneMet") static final public String MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchWeightPerStrategyMetPerZoneMet");

1 0

r309 - in trunk: scripts simulators
by echatellier＠users.forge.codelutin.com Nov. 7, 2013

Nov. 7, 2013

Author: echatellier Date: 2013-11-07 15:21:30 +0100 (Thu, 07 Nov 2013) New Revision: 309 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/309 Log: AJout d'un commentaire sur un resultat Modified: trunk/scripts/ResultName.java trunk/simulators/SimulatorEffortByCell.java Modified: trunk/scripts/ResultName.java =================================================================== --- trunk/scripts/ResultName.java 2013-11-02 10:38:07 UTC (rev 308) +++ trunk/scripts/ResultName.java 2013-11-07 14:21:30 UTC (rev 309) @@ -111,6 +111,9 @@ * Dimension 3 : Metier * Dimension 4 : Group * Dimension 5 : Zone + * + * N'est calculé que si l'effort est calculé par cellule et non par zone. + * @see SimulatorEffortByCell */ @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZoneMet") static final public String MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET = n_("matrixCatchPerStrategyMetPerZoneMet"); Modified: trunk/simulators/SimulatorEffortByCell.java =================================================================== --- trunk/simulators/SimulatorEffortByCell.java 2013-11-02 10:38:07 UTC (rev 308) +++ trunk/simulators/SimulatorEffortByCell.java 2013-11-07 14:21:30 UTC (rev 309) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2009 - 2013 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -31,7 +31,7 @@ /** * Simulateur qui fixe la valeur de effortByCell a true pour force - * l'utilisation des calcules par cellule plutot que par zone. + * l'utilisation des calculs par cellule plutot que par zone. * * @author poussin */

1 0

r308 - branches
by echatellier＠users.forge.codelutin.com Nov. 2, 2013

Nov. 2, 2013

Author: echatellier Date: 2013-11-02 11:38:07 +0100 (Sat, 02 Nov 2013) New Revision: 308 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/308 Log: Remove old branches Removed: branches/3.2/ branches/4.0.1/ branches/4.1/

1 0

r307 - branches/4.2.2/sensitivityanalysis
by echatellier＠users.forge.codelutin.com Nov. 7, 2012

Nov. 7, 2012

Author: echatellier Date: 2012-11-07 15:18:20 +0100 (Wed, 07 Nov 2012) New Revision: 307 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/307 Log: Rename sensitivy scripts with prefix Added: branches/4.2.2/sensitivityanalysis/DOptimal.java branches/4.2.2/sensitivityanalysis/Fast.java branches/4.2.2/sensitivityanalysis/Morris.java branches/4.2.2/sensitivityanalysis/OptimumLHS.java branches/4.2.2/sensitivityanalysis/RandomLHS.java branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java branches/4.2.2/sensitivityanalysis/RegularFractions.java branches/4.2.2/sensitivityanalysis/Sobol.java Removed: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRDOptimal.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFast.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFrF2.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRMorris.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRSobol.java branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRegularFractions.java Copied: branches/4.2.2/sensitivityanalysis/DOptimal.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRDOptimal.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/DOptimal.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/DOptimal.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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"; + } +} Copied: branches/4.2.2/sensitivityanalysis/Fast.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFast.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/Fast.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/Fast.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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: 89 $ + * + * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : + * $Author: jcouteau $ + */ +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)"; + } + +} Copied: branches/4.2.2/sensitivityanalysis/Morris.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRMorris.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/Morris.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/Morris.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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)"; + } + +} Copied: branches/4.2.2/sensitivityanalysis/OptimumLHS.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/OptimumLHS.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/OptimumLHS.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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: 1.0 $ + */ +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)"; + } + +} Copied: branches/4.2.2/sensitivityanalysis/RandomLHS.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/RandomLHS.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/RandomLHS.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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: 1.0 $ + */ +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)"; + } + +} Copied: branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/RegularExpandGrid.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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"; + } +} Copied: branches/4.2.2/sensitivityanalysis/RegularFractions.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRegularFractions.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/RegularFractions.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/RegularFractions.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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"; + } + +} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorJavaExpandGrid.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,393 +0,0 @@ -/* - * #%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 fr.ifremer.isisfish.simulator.sensitivity.*; -import org.nuiton.j2r.REngine; -import org.nuiton.j2r.RProxy; - -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.simulator.SimulationParameter; -import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain; -import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; -import fr.ifremer.isisfish.util.Doc; - -/** - * 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); - - //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 Expand Grid method using Java"; - } - -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,406 +0,0 @@ -/* - * #%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 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 += 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"; - } -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRExpandGrid.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,375 +0,0 @@ -/* - * #%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 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 += 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"; - } -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFast.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFast.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,358 +0,0 @@ -/* - * #%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: 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); - - //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)"; - } - -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFrF2.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFrF2.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRFrF2.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,389 +0,0 @@ -/* - * #%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.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; - -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; - -/** - * 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/4.2.2/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,358 +0,0 @@ -/* - * #%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 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); - } - - 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)"; - } - -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorROptimumLHS.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,405 +0,0 @@ -/* - * #%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: 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); - - //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)"; - } - -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRRandomLHS.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,403 +0,0 @@ -/* - * #%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: 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); - - // 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)"; - } - -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRSobol.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRSobol.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,343 +0,0 @@ -/* - * #%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: 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); - - //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)"; - } -} Deleted: branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRegularFractions.java =================================================================== --- branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-11-06 10:23:44 UTC (rev 306) +++ branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRegularFractions.java 2012-11-07 14:18:20 UTC (rev 307) @@ -1,399 +0,0 @@ -/* - * #%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 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); - - //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"; - } - -} Copied: branches/4.2.2/sensitivityanalysis/Sobol.java (from rev 305, branches/4.2.2/sensitivityanalysis/SensitivityCalculatorRSobol.java) =================================================================== --- branches/4.2.2/sensitivityanalysis/Sobol.java (rev 0) +++ branches/4.2.2/sensitivityanalysis/Sobol.java 2012-11-07 14:18:20 UTC (rev 307) @@ -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: 89 $ + * + * Last update : $Date: 2009-03-25 13:45:16 +0100 (mer., 25 mars 2009) $ By : + * $Author: jcouteau $ + */ +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)"; + } +}

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