Author: jcouteau Date: 2009-03-03 16:10:13 +0000 (Tue, 03 Mar 2009) New Revision: 68 Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java Log: Simplify the scenario creation. Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-03-03 10:53:32 UTC (rev 67) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-03-03 16:10:13 UTC (rev 68) @@ -24,7 +24,6 @@ import java.io.FileWriter; import java.io.IOException; import java.io.Serializable; -import java.util.ArrayList; import java.util.List; import org.codelutin.j2r.REngine; @@ -54,250 +53,247 @@ */ public class SensitivityCalculatorRMorris implements SensitivityCalculator { - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; - public SensitivityScenarios compute(DesignPlan plan) { - double[] dataframe = new double[0]; - int nbExperiments = 0; - int factorNumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + public SensitivityScenarios compute(DesignPlan plan) { + double[] dataframe = new double[0]; + int nbExperiments = 0; + int factorNumber = plan.getFactors().size(); + List<Factor<? extends Serializable>> factors = plan.getFactors(); - String rInstruction = "a<-morris(model=NULL,factors=c("; + String rInstruction = "a<-morris(model=NULL,factors=c("; - // Creating the factors vector. - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\","; - } else { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\""; - } - } + // Creating the factors vector. + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + factors.get(i).getName() + + "\","; + } else { + rInstruction = rInstruction + "\"" + factors.get(i).getName() + + "\""; + } + } - // Adding the number of repetition parameter (r), the morris type - // (type="oat") and the level vector - rInstruction = rInstruction - + "),r=4,design=list(type=\"oat\",levels=c("; + // Adding the number of repetition parameter (r), the morris type + // (type="oat") and the level vector + rInstruction = rInstruction + + "),r=4,design=list(type=\"oat\",levels=c("; - // Creating the levels vector. - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((DiscreteDomain<? extends Serializable>) domain) - .getValues().size() + ","; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction + "4" + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((DiscreteDomain<? extends Serializable>) domain) - .getValues().size(); - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction + "4"; - } - } - } + // Creating the levels vector. + for (int i = 0; i < factorNumber; i++) { + Domain<? extends Serializable> domain = factors.get(i).getDomain(); + if (i != (factorNumber - 1)) { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + + ((DiscreteDomain<? extends Serializable>) domain) + .getValues().size() + ","; + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + "4" + ","; + } + } else { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + + ((DiscreteDomain<? extends Serializable>) domain) + .getValues().size(); + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + "4"; + } + } + } - // Adding the grid.jump parameter - rInstruction = rInstruction + "),grid.jump=1),binf=c("; + // Adding the grid.jump parameter + rInstruction = rInstruction + "),grid.jump=1),binf=c("; - // Adding the binf parameter - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction + "0,"; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMinBound() + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction + "0"; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMinBound(); - } - } - } + // Adding the binf parameter + for (int i = 0; i < factorNumber; i++) { + Domain<? extends Serializable> domain = factors.get(i).getDomain(); + if (i != (factorNumber - 1)) { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + "0,"; + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + + ((ContinuousDomain<? extends Serializable>) domain) + .getMinBound() + ","; + } + } else { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + "0"; + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + + ((ContinuousDomain<? extends Serializable>) domain) + .getMinBound(); + } + } + } - // Adding the bsup parameter - rInstruction = rInstruction + "),bsup=c("; - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((((DiscreteDomain<? extends Serializable>) domain) - .getValues().size()) - 1) + ","; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMaxBound() + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((((DiscreteDomain<? extends Serializable>) domain) - .getValues().size()) - 1); - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMaxBound(); - } - } - } - rInstruction = rInstruction + "))"; + // Adding the bsup parameter + rInstruction = rInstruction + "),bsup=c("; + for (int i = 0; i < factorNumber; i++) { + Domain<? extends Serializable> domain = factors.get(i).getDomain(); + if (i != (factorNumber - 1)) { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + + ((((DiscreteDomain<? extends Serializable>) domain) + .getValues().size()) - 1) + ","; + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + + ((ContinuousDomain<? extends Serializable>) domain) + .getMaxBound() + ","; + } + } else { + if (domain instanceof DiscreteDomain) { + rInstruction = rInstruction + + ((((DiscreteDomain<? extends Serializable>) domain) + .getValues().size()) - 1); + } else if (domain instanceof ContinuousDomain) { + rInstruction = rInstruction + + ((ContinuousDomain<? extends Serializable>) domain) + .getMaxBound(); + } + } + } + rInstruction = rInstruction + "))"; - REngine engine = new RProxy(); - try { - // Load sensitivity package into R (if package already loaded, - // nothing happens. - engine.voidEval("library(sensitivity)"); - // Run sensitivity analysis - engine.voidEval(rInstruction); - // Get back experiment plan - dataframe = (double[]) engine.eval("a$X"); + REngine engine = new RProxy(); + try { + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + // Run sensitivity analysis + engine.voidEval(rInstruction); + // Get back experiment plan + dataframe = (double[]) engine.eval("a$X"); - nbExperiments = dataframe.length / factorNumber; + nbExperiments = dataframe.length / factorNumber; - } catch (RException e) { - e.printStackTrace(); - // Error while retrieving scenario - } + } catch (RException e) { + e.printStackTrace(); + // Error while retrieving scenario + } - // Transform the result from R in a matrix - MatrixND morris = MatrixFactory.getInstance().create(dataframe, - new int[] { factorNumber, nbExperiments }); + // Transform the result from R in a matrix + MatrixND morris = MatrixFactory.getInstance().create(dataframe, + new int[] { factorNumber, nbExperiments }); - // Setting up the scenarios. - SensitivityScenarios thisExperiment = new SensitivityScenarios(); - List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - for (int j = 0; j < nbExperiments; j++) { - Scenario experimentScenario = new Scenario(); - List<Factor<? extends Serializable>> factorslist = new ArrayList(); - for (int i = 0; i < factorNumber; i++) { - Factor<? extends Serializable> factor = (Factor<? extends Serializable>) factors - .get(i).clone(); - factor.setValueForIdentifier(morris - .getValue(new int[] { i, j })); - factorslist.add(factor); - } - experimentScenario.setFactors(factorslist); - thisExperimentScenarios.add(experimentScenario); - thisExperiment.setScenarios(thisExperimentScenarios); - } - return thisExperiment; + // Setting up the scenarios. + SensitivityScenarios thisExperiment = new SensitivityScenarios(); + List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + for (int j = 0; j < nbExperiments; j++) { + Scenario experimentScenario = new Scenario(); + for (int i = 0; i < factorNumber; i++) { + Factor<? extends Serializable> factor = factors.get(i); + factor.setValueForIdentifier(morris + .getValue(new int[] { i, j })); + experimentScenario.addFactor(factor); + } + thisExperimentScenarios.add(experimentScenario); + thisExperiment.setScenarios(thisExperimentScenarios); + } + return thisExperiment; - } + } - public void analyzeResult(SensitivityScenarios sensitivityScenarios, - List<SimulationStorage> simulationStorages) { + public void analyzeResult(SensitivityScenarios sensitivityScenarios, + List<SimulationStorage> simulationStorages) { - // This is is an analysis example with biomass analysis. + // This is is an analysis example with biomass analysis. - // Creates the R expression. - String rInstruction = "tell(x,y=c("; + // Creates the R expression. + String rInstruction = "tell(x,y=c("; - for (int i = 0; i < sensitivityScenarios.getScenarios().size(); i++) { - try { - File biomass; - MatrixND matrixBiomass; - biomass = new File(simulationStorages.get(i) - .getSimulationDirectory().toString(), "Biomasses.csv"); - /* - * biomass = FileUtil.getFile(".*.csv", "fichier csv séparateur - * ';'"); - */ - matrixBiomass = MatrixFactory.getInstance().create( - new int[] { 0 }); + for (int i = 0; i < sensitivityScenarios.getScenarios().size(); i++) { + try { + File biomass; + MatrixND matrixBiomass; + biomass = new File(simulationStorages.get(i) + .getSimulationDirectory().toString(), "Biomasses.csv"); + /* + * biomass = FileUtil.getFile(".*.csv", "fichier csv séparateur + * ';'"); + */ + matrixBiomass = MatrixFactory.getInstance().create( + new int[] { 0 }); - matrixBiomass.importCSV(new FileReader(biomass), - new int[] { 0 }); + matrixBiomass.importCSV(new FileReader(biomass), + new int[] { 0 }); - // uses the very last value of the matrix to check sensitivity + // uses the very last value of the matrix to check sensitivity - int[] dimensions = matrixBiomass.getDim(); - if (i == sensitivityScenarios.getScenarios().size() - 1) { - rInstruction = rInstruction - + (double) matrixBiomass.getValue(dimensions) - + "))"; - } else { - rInstruction = rInstruction - + (double) matrixBiomass.getValue(dimensions) + ","; - } + int[] dimensions = matrixBiomass.getDim(); + if (i == sensitivityScenarios.getScenarios().size() - 1) { + rInstruction = rInstruction + + (double) matrixBiomass.getValue(dimensions) + + "))"; + } else { + rInstruction = rInstruction + + (double) matrixBiomass.getValue(dimensions) + ","; + } - } catch (Exception e) { - e.printStackTrace(); - } - } + } catch (Exception e) { + e.printStackTrace(); + } + } - double[] mu = { 0 }; - double[] mustar = { 0 }; - double[] sigma = { 0 }; + double[] mu = { 0 }; + double[] mustar = { 0 }; + double[] sigma = { 0 }; - // Call R - REngine engine = new RProxy(); - try { - // Load sensitivity package into R (if package already loaded, - // nothing happens. - engine.voidEval("library(sensitivity)"); - // Send the simulation results - engine.voidEval(rInstruction); - // Get back the sensitivity results, mu, mu star and sigma. - engine.voidEval("mu<-apply(x$ee, 2, mean)"); - mu = (double[]) engine.eval("mu"); - engine - .voidEval("mu.star <- apply(x$ee, 2, function(x) mean(abs(x)))"); - mustar = (double[]) engine.eval("mu.star"); - engine.voidEval("sigma <- apply(x$ee, 2, sd)"); - sigma = (double[]) engine.eval("sigma"); + // Call R + REngine engine = new RProxy(); + try { + // Load sensitivity package into R (if package already loaded, + // nothing happens. + engine.voidEval("library(sensitivity)"); + // Send the simulation results + engine.voidEval(rInstruction); + // Get back the sensitivity results, mu, mu star and sigma. + engine.voidEval("mu<-apply(x$ee, 2, mean)"); + mu = (double[]) engine.eval("mu"); + engine + .voidEval("mu.star <- apply(x$ee, 2, function(x) mean(abs(x)))"); + mustar = (double[]) engine.eval("mu.star"); + engine.voidEval("sigma <- apply(x$ee, 2, sd)"); + sigma = (double[]) engine.eval("sigma"); - } catch (RException e) { - e.printStackTrace(); - // Error while retrieving the results - } + } catch (RException e) { + e.printStackTrace(); + // Error while retrieving the results + } - // Treat the sensitivity results as wished. - // Create the content for export - String exportContent = ""; - for (int i = 0; i < sigma.length; i++) { - exportContent = exportContent - + "Factor : " - + sensitivityScenarios.getScenarios().get(0).getFactors() - .get(i).getName() + "\n mu = " + mu[i] - + "\n mu.star = " + mustar[i] + "\n sigma = " + sigma[i] - + "\n\n\n"; - } + // Treat the sensitivity results as wished. + // Create the content for export + String exportContent = ""; + for (int i = 0; i < sigma.length; i++) { + exportContent = exportContent + + "Factor : " + + sensitivityScenarios.getScenarios().get(0).getFactors() + .get(i).getName() + "\n mu = " + mu[i] + + "\n mu.star = " + mustar[i] + "\n sigma = " + sigma[i] + + "\n\n\n"; + } - // export in the first simulation storage - try { - File export; - export = new File(simulationStorages.get(0) - .getSimulationDirectory().toString(), "sensitivity.txt"); + // export in the first simulation storage + try { + File export; + export = new File(simulationStorages.get(0) + .getSimulationDirectory().toString(), "sensitivity.txt"); - FileWriter fstream = new FileWriter(export); - BufferedWriter out = new BufferedWriter(fstream); - out.write(exportContent); - out.close(); - } catch (IOException e) { - e.printStackTrace(); - } + FileWriter fstream = new FileWriter(export); + BufferedWriter out = new BufferedWriter(fstream); + out.write(exportContent); + out.close(); + } catch (IOException e) { + e.printStackTrace(); + } - } + } - public String getDescription() { - return "Implementation of Morris method using R"; - } + public String getDescription() { + return "Implementation of Morris method using R"; + } - public String[] getNecessaryResult() { - return this.necessaryResult; - } + public String[] getNecessaryResult() { + return this.necessaryResult; + } }