[Isis-fish-data-commits] r144 - trunk/sensitivity

Author: jcouteau Date: 2009-05-15 13:00:50 +0000 (Fri, 15 May 2009) New Revision: 144 Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivity/SensitivityCalculatorRFast.java trunk/sensitivity/SensitivityCalculatorRFrF2.java trunk/sensitivity/SensitivityCalculatorRMorris.java trunk/sensitivity/SensitivityCalculatorROptimumLHS.java trunk/sensitivity/SensitivityCalculatorRRandomLHS.java trunk/sensitivity/SensitivityCalculatorRSobol.java trunk/sensitivity/SensitivityCalculatorRegularFractions.java Log: Adapt R scripts to windows file system Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-05-15 13:00:50 UTC (rev 144) @@ -146,8 +146,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -256,10 +260,12 @@ log.info("Message sent to R : " + rInstruction); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the data.frame object for the second run in a .expandgrid file engine.voidEval("write.csv(data,file=\".expandgrid.csv\")"); @@ -304,8 +310,12 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -328,18 +338,24 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); //Get back the scenarios engine.voidEval("factors<-read.csv(\".expandgrid.csv\")"); @@ -471,10 +487,12 @@ /*Set the export directory *Export directory is the first simulation export directory. */ - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" @@ -550,8 +568,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFast.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRFast.java 2009-05-15 13:00:50 UTC (rev 144) @@ -138,8 +138,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -172,10 +176,12 @@ log.info("Message sent to R" + rInstruction); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R" + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the fast99 object for the second run in a .fast99 file engine.voidEval("dput(a,file=\".fast99\")"); @@ -275,8 +281,12 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -326,8 +336,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -340,10 +354,12 @@ log.info("Message sent to R : " + "library(sensitivity)"); //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the morris object for the second run in a .morris file engine.voidEval("a<-dget(\".fast99\")"); @@ -444,10 +460,12 @@ + "dfresults=data.frame(a$X,results)"); //Set working directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); // Get the factornames object in the .factornames file engine.voidEval("factornames<-dget(\".factornames\")"); @@ -550,8 +568,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-05-15 13:00:50 UTC (rev 144) @@ -95,10 +95,12 @@ log.info("Message sent to R : " + "library(FrF2)"); //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); String rInstruction = "a<-FrF2(nfactors=" + factorNumber + ",resolution=" + param_resolution + ")"; @@ -264,10 +266,12 @@ log.info("Message sent to R : " + data); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the scenario matrix for the second run in a .FrF2.csv file engine.voidEval("write.csv(data,file=\".FrF2.csv\")"); @@ -299,10 +303,12 @@ log.info("Message sent to R : " + "library(FrF2)"); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Get back the FrF2 object engine.voidEval("a<-dget(\".FrF2\")"); @@ -457,10 +463,12 @@ /*Set the export directory *Export directory is the first simulation export directory. */ - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Set dataforaov names engine Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-05-15 13:00:50 UTC (rev 144) @@ -162,8 +162,12 @@ REngine engine = new RProxy(); try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -186,10 +190,12 @@ log.info("Message sent to R : " + rCall); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the morris object for the second run in a .morris file engine.voidEval("dput(a,file=\".morris\")"); @@ -263,8 +269,12 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -312,8 +322,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -326,10 +340,12 @@ log.info("Message sent to R : " + "library(sensitivity)"); //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the morris object for the second run in a .morris file engine.voidEval("a<-dget(\".morris\")"); @@ -344,23 +360,24 @@ .eval("length(a$X)/length(a$factors)")).intValue(); log.info("Message sent to R : " + "length(a$X)/length(a$factors)"); - SimulationParameter param = simulationStorages.get(0).getParameter(); + SimulationParameter param = simulationStorages.get(0) + .getParameter(); int sensitivityNumber = param.getSensitivityExport().size(); for (int k = 0; k < sensitivityNumber; k++) { // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k).getExportFilename(); + String name = param.getSensitivityExport().get(k) + .getExportFilename(); String rInstruction = name + "<-c("; for (int l = 0; l < scenariosNumber; 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()); + + 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) { @@ -397,7 +414,8 @@ for (int k = 0; k < sensitivityNumber; k++) { // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k).getExportFilename(); + String name = param.getSensitivityExport().get(k) + .getExportFilename(); //Compute results engine.voidEval("tell(a,y=" + name + ")"); @@ -454,10 +472,12 @@ + "names(dfresults)<-resultsnames"); //Set working directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Export sensitivity indices engine.voidEval("write.csv(df,\"" @@ -520,8 +540,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorROptimumLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-05-15 13:00:50 UTC (rev 144) @@ -125,8 +125,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -362,10 +366,12 @@ log.info("Message sent to R" + rInstruction); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the scenario matrix for the second run in a .optimumlhs.csv file engine.voidEval("write.csv(data,file=\".optimumlhs.csv\")"); @@ -378,8 +384,12 @@ + "dput(factornames,file=\".factornames\")"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -413,18 +423,24 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); //Get back the scenarios engine.voidEval("factors<-read.csv(\".optimumlhs.csv\")"); @@ -581,10 +597,12 @@ /*Set the export directory *Export directory is the first simulation export directory. */ - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" @@ -660,8 +678,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-05-15 13:00:50 UTC (rev 144) @@ -113,16 +113,24 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); //Set working directory for other results - log.info("setwd(\"" + outputdirectory + "\")"); - engine.voidEval("setwd(\"" + outputdirectory + "\")"); + log.info("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); //Load the lhs library engine.voidEval("library(lhs)"); @@ -343,10 +351,12 @@ log.info("Message sent to R" + rInstruction); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the scenario matrix for the second run in a .randomlhs.csv file engine.voidEval("write.csv(data,file=\".randomlhs.csv\")"); @@ -359,8 +369,12 @@ + "dput(factornames,file=\".factornames\")"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -387,18 +401,24 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); //Get back the scenarios engine.voidEval("factors<-read.csv(\".randomlhs.csv\")"); @@ -552,10 +572,12 @@ /*Set the export directory *Export directory is the first simulation export directory. */ - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" @@ -631,8 +653,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorRSobol.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-05-15 13:00:50 UTC (rev 144) @@ -136,8 +136,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -147,10 +151,12 @@ log.info("Message sent to R : " + "library(sensitivity)"); //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); engine.voidEval("X1<-data.frame(matrix(runif(" + factorNumber + "*" + param_n + "),nrow=" + param_n + "))"); @@ -274,8 +280,12 @@ engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -323,8 +333,12 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); @@ -337,10 +351,12 @@ log.info("Message sent to R : " + "library(sensitivity)"); //Set the working directory (for import and exports) - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Get the .X1 file engine.voidEval("X1<-dget(\".X1\")"); @@ -456,10 +472,12 @@ + "dfresults=data.frame(a$X,results)"); //Set working directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Export V engine.voidEval("write.csv(a$V,\"" @@ -539,8 +557,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-14 14:25:53 UTC (rev 143) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-15 13:00:50 UTC (rev 144) @@ -105,17 +105,22 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); //Set the working directory (to import the R function) - engine.voidEval("setwd(\"" + param_pathToFunction + "\")"); - log.info("Message sent to R : " + "setwd(\"" + param_pathToFunction - + "\")"); + engine.voidEval("setwd(\"" + + param_pathToFunction.replaceAll("\\\\", "/") + "\")"); + log.info("Message sent to R : " + "setwd(\"" + + param_pathToFunction.replaceAll("\\\\", "/") + "\")"); //Import the function log.info("source(\"regularfractions.R\")"); @@ -159,10 +164,12 @@ log.info("Message sent to R : " + rCall); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : " + "setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Export the morris object for the second run in a .morris file engine.voidEval("dput(x,file=\".regularfractions\")"); @@ -327,8 +334,12 @@ log.info("Message sent to R : write.csv(data,file=\".data.csv\")"); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()"); @@ -352,18 +363,24 @@ try { //Set working directory to get Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); //Get Isis R session log.info("load(\".RData\")"); engine.voidEval("load(\".RData\")"); // Set output directory - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", "/") + + "\")"); // Get the regularfractions object from the .regularfractions file engine.voidEval("x<-dget(\".regularfractions\")"); @@ -432,7 +449,8 @@ for (int k = 0; k < sensitivityNumber; k++) { // Creates the R expression to import results in R - String name = param.getSensitivityExport().get(k).getExportFilename(); + String name = param.getSensitivityExport().get(k) + .getExportFilename(); //Create the dataforaov data.frame String dataframe = "dataforaov<-data.frame(factors," + name @@ -511,10 +529,12 @@ /*Set the export directory *Export directory is the first simulation export directory. */ - engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() - + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); log.info("Message sent to R : setwd(\"" - + outputdirectory.getAbsolutePath() + "\")"); + + outputdirectory.getAbsolutePath().replaceAll("\\\\", + "/") + "\")"); //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" @@ -539,10 +559,13 @@ log .info("Message sent to R : " + "isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" - + aovCall + "\"" + ",\"analysis_result\"=aovresult)"); + + aovCall + "\"" + + ",\"analysis_result\"=aovresult)"); engine .voidEval("isis.methodAnalyse<-list(\"isis.factors\"=isis.factors,\"isis.factor.distribution\"=isis.factor.distribution,\"isis.simule\"=isis.simule,call_method=\"" - + aovCall + "\"" + ",\"analysis_result\"=aovresult)"); + + aovCall + + "\"" + + ",\"analysis_result\"=aovresult)"); log .info("Message sent to R : " @@ -590,8 +613,12 @@ engine.voidEval(String.format(renameIsisMethodExp, simulationName)); //Set working directory to save Isis R session - log.info("setwd(\"" + outputdirectory.getParent() + "\")"); - engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + log.info("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); + engine.voidEval("setwd(\"" + + outputdirectory.getParent().replaceAll("\\\\", "/") + + "\")"); // Save Isis R session log.info("save.image()");