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

r147 - in trunk: . sensitivity
by chatellier＠users.labs.libre-entreprise.org June 12, 2009

June 12, 2009

Author: chatellier Date: 2009-06-12 08:27:01 +0000 (Fri, 12 Jun 2009) New Revision: 147 Modified: trunk/pom.xml 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: Passage des datas sur la derniere version d'isis. Simplification du pom. Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/pom.xml 2009-06-12 08:27:01 UTC (rev 147) @@ -1,17 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">  <modelVersion>4.0.0</modelVersion> -  -  <artifactId>isis-fish-data</artifactId> <name>IsisFish data</name> @@ -27,34 +20,27 @@ <description>Data for Isis-fish</description> <inceptionYear>2000</inceptionYear> -  - <issueManagement> - <url>http://labs.libre-entreprise.org/tracker/?group_id=8</url> - </issueManagement> + <properties> + <maven.test.skip>true</maven.test.skip> + <maven.compiler.source>1.6</maven.compiler.source> + <maven.compiler.target>1.6</maven.compiler.target> + </properties> <build> <sourceDirectory>${basedir}</sourceDirectory> - <plugins> - <plugin> - <artifactId>maven-compiler-plugin</artifactId> - <version>2.0.2</version> - <configuration> - <source>1.6</source> - <target>1.6</target> - <excludes> - <exclude>**/simulations/**</exclude> - </excludes> - </configuration> - </plugin> - </plugins> </build> +  + <issueManagement> + <url>http://labs.libre-entreprise.org/tracker/?group_id=132</url> + </issueManagement> +  <dependencies> <dependency> <groupId>ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>3.2.0.4-rc4-SNAPSHOT</version> + <version>3.2.0.5-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> @@ -66,40 +52,17 @@ </site> </distributionManagement> -  - <profiles> - <profile> - <id>codelutin-repository</id> + <repositories> + <repository> + <id>codelutin-lib</id> + <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> + </repository> + </repositories> - <activation> - <activeByDefault>true</activeByDefault> - </activation> - - <properties> - <maven.src.dir>${basedir}/src</maven.src.dir> - <maven.test.skip>true</maven.test.skip> - <maven.compile.source>1.5</maven.compile.source> - <maven.compile.target>1.5</maven.compile.target> - </properties> - - <repositories> - <repository> - <id>codelutin-lib</id> - <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> - </repository> - </repositories> - - <pluginRepositories> - <pluginRepository> - <id>codelutin-plugin</id> - <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> - </pluginRepository> - </pluginRepositories> - </profile> - </profiles> - -  -  + <pluginRepositories> + <pluginRepository> + <id>codelutin-plugin</id> + <url>http://lutinbuilder.labs.libre-entreprise.org/maven2</url> + </pluginRepository> + </pluginRepositories> </project> Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-06-12 08:27:01 UTC (rev 147) @@ -73,7 +73,7 @@ int k = 1; //number of sensitivity scenarios (initialization) int factorNumber = plan.getFactors().size(); //number of factors - List<Factor> factors = plan.getFactors(); //list of factors + List<Factor<?, ?>> factors = plan.getFactors(); //list of factors for (int i = 0; i < factorNumber; i++) { if (factors.get(i).getDomain() instanceof ContinuousDomain) { Modified: trunk/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFast.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRFast.java 2009-06-12 08:27:01 UTC (rev 147) @@ -96,7 +96,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); Modified: trunk/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-06-12 08:27:01 UTC (rev 147) @@ -77,7 +77,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-06-12 08:27:01 UTC (rev 147) @@ -90,7 +90,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); if (param_r == 0) { param_r = 4; Modified: trunk/sensitivity/SensitivityCalculatorROptimumLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-06-12 08:27:01 UTC (rev 147) @@ -90,7 +90,7 @@ setIsisFactorsR(plan, outputdirectory); int factornumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-06-12 08:27:01 UTC (rev 147) @@ -89,7 +89,7 @@ double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); //Test all factors, if one is discrete, return null for (int i = 0; i < factors.size(); i++) { Modified: trunk/sensitivity/SensitivityCalculatorRSobol.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-06-12 08:27:01 UTC (rev 147) @@ -93,7 +93,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-06-12 08:14:51 UTC (rev 146) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-06-12 08:27:01 UTC (rev 147) @@ -72,7 +72,7 @@ double[] dataframeplan = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor> factors = plan.getFactors(); + List<Factor<?, ?>> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios();

1 0

r146 - trunk/rules
by chatellier＠users.labs.libre-entreprise.org June 12, 2009

June 12, 2009

Author: chatellier Date: 2009-06-12 08:14:51 +0000 (Fri, 12 Jun 2009) New Revision: 146 Modified: trunk/rules/Cantonnement.java trunk/rules/CantonnementPreSimu.java Log: Le rechargement des parametres dans l'init n'est plus nec?\195?\169ssaire. Modified: trunk/rules/Cantonnement.java =================================================================== --- trunk/rules/Cantonnement.java 2009-06-05 09:49:57 UTC (rev 145) +++ trunk/rules/Cantonnement.java 2009-06-12 08:14:51 UTC (rev 146) @@ -85,17 +85,7 @@ * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { - - ZoneDAO zoneDao = IsisFishDAOHelper.getZoneDAO(context.getDB()); - GearDAO gearDao = IsisFishDAOHelper.getGearDAO(context.getDB()); - - // Rechargement du param_zone depuis le context courant - if (param_zone != null) { - param_zone = zoneDao.findByTopiaId(param_zone.getTopiaId()); - } - if (param_gear != null) { - param_gear = gearDao.findByTopiaId(param_gear.getTopiaId()); - } + } /** Modified: trunk/rules/CantonnementPreSimu.java =================================================================== --- trunk/rules/CantonnementPreSimu.java 2009-06-05 09:49:57 UTC (rev 145) +++ trunk/rules/CantonnementPreSimu.java 2009-06-12 08:14:51 UTC (rev 146) @@ -10,10 +10,7 @@ import scripts.SiMatrix; import java.util.ArrayList; -import java.util.Collection; -import java.util.Collections; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; @@ -117,22 +114,15 @@ /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { SiMatrix siMatrix = SiMatrix.getSiMatrix(context); // MetierDAO metierDao = IsisFishDAOHelper.getMetierDAO(context.getDB()); ZoneDAO zoneDao = IsisFishDAOHelper.getZoneDAO(context.getDB()); - GearDAO gearDao = IsisFishDAOHelper.getGearDAO(context.getDB()); MetierSeasonInfoDAO metierSeasonInfoDao = IsisFishDAOHelper.getMetierSeasonInfoDAO(context.getDB()); - - // Rechargement du param_zone depuis le context courant - param_zone = zoneDao.findByTopiaId(param_zone.getTopiaId()); - if (param_gear!=null){ - param_gear = gearDao.findByTopiaId(param_gear.getTopiaId()); - } - + // List<Metier> metiers = metierDao.findAll(); List<Month> SaisonFermee = Month.getMonths(param_beginMonth, param_endMonth); List<Cell> maillefermee = param_zone.getCell();

1 0

r145 - trunk/rules
by chatellier＠users.labs.libre-entreprise.org June 5, 2009

June 5, 2009

Author: chatellier Date: 2009-06-05 09:49:57 +0000 (Fri, 05 Jun 2009) New Revision: 145 Modified: trunk/rules/Cantonnement.java Log: Rechargement des entit?\195?\169s parametres (session was closed) Modified: trunk/rules/Cantonnement.java =================================================================== --- trunk/rules/Cantonnement.java 2009-05-15 13:00:50 UTC (rev 144) +++ trunk/rules/Cantonnement.java 2009-06-05 09:49:57 UTC (rev 145) @@ -82,9 +82,20 @@ /** * Appelé au démarrage de la simulation, cette méthode permet d'initialiser * des valeurs - * @param simulation La simulation pour lequel on utilise cette regle + * @param context La simulation pour lequel on utilise cette regle */ public void init(SimulationContext context) throws Exception { + + ZoneDAO zoneDao = IsisFishDAOHelper.getZoneDAO(context.getDB()); + GearDAO gearDao = IsisFishDAOHelper.getGearDAO(context.getDB()); + + // Rechargement du param_zone depuis le context courant + if (param_zone != null) { + param_zone = zoneDao.findByTopiaId(param_zone.getTopiaId()); + } + if (param_gear != null) { + param_gear = gearDao.findByTopiaId(param_gear.getTopiaId()); + } } /**

1 0

r144 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org May 15, 2009

May 15, 2009

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()");

1 0

r143 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org May 14, 2009

May 14, 2009

Author: jcouteau Date: 2009-05-14 14:25:53 +0000 (Thu, 14 May 2009) New Revision: 143 Modified: trunk/sensitivity/SensitivityCalculatorRFast.java Log: Display an error message in case of NaN values in R fast object. Modified: trunk/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFast.java 2009-05-14 07:40:17 UTC (rev 142) +++ trunk/sensitivity/SensitivityCalculatorRFast.java 2009-05-14 14:25:53 UTC (rev 143) @@ -106,10 +106,9 @@ JOptionPane .showMessageDialog( null, - "Error", factors.get(i).getName() + " has a discrete domain, this is not acceptable for this method.", - JOptionPane.ERROR_MESSAGE); + "Error", JOptionPane.ERROR_MESSAGE); return null; } } @@ -194,6 +193,18 @@ * dataframeVector.get(0).asDoubleArray().length]; for (int i = 0; i < dataframeVector.size(); i++) { for (int j = 0; j < dataframeVector.get(0).asDoubleArray().length; j++) { + if (String.valueOf( + dataframeVector.get(i).asDoubleArray()[j]) + .toString().equals("NaN")) { + log + .error("Wrong parameters for the fast method, non-numeric values were generated"); + JOptionPane + .showMessageDialog( + null, + "The parameters for this method need to be changed, non-numeric values where generated (you may want to increase the n parameter)", + "Error", JOptionPane.ERROR_MESSAGE); + return null; + } dataframe[i * dataframeVector.get(0).asDoubleArray().length + j] = dataframeVector.get(i).asDoubleArray()[j]; }

1 0

r142 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org May 14, 2009

May 14, 2009

Author: jcouteau Date: 2009-05-14 07:40:17 +0000 (Thu, 14 May 2009) New Revision: 142 Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java Log: Adding name of the sensitivity result in R object Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-11 13:51:57 UTC (rev 141) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-14 07:40:17 UTC (rev 142) @@ -539,10 +539,10 @@ 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 + "\"" + ",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 + "\"" + ",aovresult)"); + + aovCall + "\"" + ",\"analysis_result\"=aovresult)"); log .info("Message sent to R : "

1 0

r141 - trunk/scripts
by jcouteau＠users.labs.libre-entreprise.org May 11, 2009

May 11, 2009

Author: jcouteau Date: 2009-05-11 13:51:57 +0000 (Mon, 11 May 2009) New Revision: 141 Modified: trunk/scripts/SiMatrix.java Log: Back to normal (matrixCatchWeightPerStrategyMetPerZonePop well calculated) Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2009-05-11 09:53:41 UTC (rev 140) +++ trunk/scripts/SiMatrix.java 2009-05-11 13:51:57 UTC (rev 141) @@ -251,7 +251,7 @@ List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZoneMet.copy(); - result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); + result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET); for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1); @@ -282,7 +282,7 @@ .getSemantics(4)); MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP, + ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET, new List[] { strategies, metiers, groups, zones }, new String[] { n_("Strategies"), n_("Metiers"), n_("Groups"), n_("Zones") }); @@ -344,7 +344,7 @@ List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND result = matrixCatchPerStrategyMetPerZonePop.copy(); - result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET); + result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); for (PopulationGroup group : groups) { MatrixND sub = result.getSubMatrix(2, group, 1);

1 0

r140 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org May 11, 2009

May 11, 2009

Author: jcouteau Date: 2009-05-11 09:53:41 +0000 (Mon, 11 May 2009) New Revision: 140 Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java Log: Fix bug when not full run of regularfractions Modified: trunk/sensitivity/SensitivityCalculatorRegularFractions.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-07 20:20:50 UTC (rev 139) +++ trunk/sensitivity/SensitivityCalculatorRegularFractions.java 2009-05-11 09:53:41 UTC (rev 140) @@ -175,12 +175,12 @@ + "dput(factornames,file=\".factornames\")"); // Get back experiment plan - dataframeplan = (double[]) engine.eval("x$plan"); - log.info("Message sent to R : " + "x$plan"); + dataframeplan = (double[]) engine.eval("x[[1]]"); + log.info("Message sent to R : " + "x[[1]]"); //Get back the simulation number - log.info("length(x[,1])"); - int simulationNumber = (Integer) engine.eval("length(x$plan[,1])"); + log.info("length(x[[1]][,1])"); + int simulationNumber = (Integer) engine.eval("length(x[[1]][,1])"); // Transform the result from R in a matrix MatrixND morris = MatrixFactory.getInstance().create(dataframeplan,

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r139 - trunk/exports
by chatellier＠users.labs.libre-entreprise.org May 7, 2009

May 7, 2009

Author: chatellier Date: 2009-05-07 20:20:50 +0000 (Thu, 07 May 2009) New Revision: 139 Added: trunk/exports/GrossValueOfLandingsOtherSpecies.java Log: Add export Added: trunk/exports/GrossValueOfLandingsOtherSpecies.java =================================================================== --- trunk/exports/GrossValueOfLandingsOtherSpecies.java (rev 0) +++ trunk/exports/GrossValueOfLandingsOtherSpecies.java 2009-05-07 20:20:50 UTC (rev 139) @@ -0,0 +1,98 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import java.io.Writer; + +import org.codelutin.math.matrix.*; + +import scripts.ResultName; + +import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.datastore.ResultStorage; + +import fr.ifremer.isisfish.util.Doc; // pour pouvoir afficher une aide contextuelle (BUG#1605) + +/** + * VesselMargin.java + * + * Created: 23 novembre 2006 + * + * @author anonymous <anonymous(a)labs.libre-entreprise.org> + * @version $Revision: 1.3 $ + * + * Last update: $Date: 2007-05-24 09:30:07 $ + * by : $Author: bpoussin $ + */ + @Doc(value="do the doc of class VesselMargin") +public class GrossValueOfLandingsOtherSpecies implements Export { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(GrossValueOfLandingsOtherSpecies.class); + + protected String [] necessaryResult = { + ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET + }; + + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + public String getExportFilename() { + return "GrossValueOfLandingsOtherSpecies"; + } + + public String getExtensionFilename() { + return ".csv"; + } + + public String getDescription() { + return _("cvs out strategy;date;value"); + } + + public void export(SimulationStorage simulation, Writer out) throws Exception { + MatrixND mat = simulation.getResultStorage().getMatrix(ResultName.MATRIX_GROSS_VALUE_OF_LANDINGS_OTHER_SPECIES_PER_STRATEGY_MET); + for (MatrixIterator i=mat.iterator(); i.hasNext();) { + i.next(); + Object [] sems = i.getSemanticsCoordinates(); + Date date = (Date)sems[0]; + Strategy str = (Strategy)sems[1]; + Metier met = (Metier) sems[2]; + double val = i.getValue(); + out.write(str.getName() +";"+met.getName() +";"+ date.getDate() +";"+ val +"\n"); + } + /* +var Parametre=sim.getParametre(); +var PDate=Packages.fr.ifremer.nodb.Date; +var finsimu=resultats.getLastDate().getDate(); + + +var result=""; +writeln("debut export vesselmargin"); +var dateexport=new Packages.java.util.Date(); +var formatteur= new Packages.java.text.SimpleDateFormat(); +writeln("heure de debut: "+formatteur.format(dateexport)); + + +for (var idate=0;idate<=finsimu;idate++){ + var date=new PDate(idate); + var matrice=resultats.getMatrix(date, "matriceVesselMarginOverVariableCostsPerStrategyPerVessel"); + for(var iiterateur=matrice.iterator(); iiterateur.next();){ + var coordonnees=iiterateur.getSemanticsCoordinates(); + var str=coordonnees[0]; + result+=str.getName()+";"+idate+";"+iiterateur.getValue()+"\n"; + } +} +writeln("fin export vesselmargin"); + +return ""+result; +*/ + } + +}

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r138 - in trunk: scripts simulators
by chatellier＠users.labs.libre-entreprise.org May 7, 2009

May 7, 2009

Author: chatellier Date: 2009-05-07 20:14:16 +0000 (Thu, 07 May 2009) New Revision: 138 Modified: trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java Log: Re ajout de effort nominal matrix Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2009-05-07 17:07:20 UTC (rev 137) +++ trunk/scripts/SiMatrix.java 2009-05-07 20:14:16 UTC (rev 138) @@ -1226,6 +1226,66 @@ * @param date * @return */ + private double effortNominalPerStrategyMet(Strategy str, Metier metier, Date date) { + Month month = date.getMonth(); + StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + + double propSetOfVessels = str.getProportionSetOfVessels(); + int nbOfVessels = str.getSetOfVessels().getNumberOfVessels(); + double propStrMet = smi.getProportionMetier(metier); + double effortNominalPerVessel = effortNominalPerStrategyPerVessel(str, metier, date); + + if(log.isDebugEnabled()) { + log.debug( + " strategy=" + str + + " metier=" + metier + + " propSetOfVessels=" + propSetOfVessels + + " nbOfVessels=" + nbOfVessels + + " propStrMet=" + propStrMet + + " effortPerVessel=" + effortNominalPerVessel + ); + } + + double result = propSetOfVessels * nbOfVessels * propStrMet * effortNominalPerVessel; + + return result; + } + + /** + * @param str + * @param metier + * @param date + * @return + */ + private double effortNominalPerStrategyPerVessel(Strategy str, Metier metier, Date date) { + Month month = date.getMonth(); + StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + double nbTrips = smi.getNumberOfTrips(); + double fishingTime = fishingTimePerTrip(str, metier, date); + + + if(log.isDebugEnabled()) { + log.debug( + " strategy=" + str + + " metier=" + metier + + " nbTrips=" + nbTrips + + " fishingTime=" + fishingTime + + ); + } + // nominal timeAtSea = nbTrips * fishingTime; + // + double result = nbTrips * fishingTime; + + return result; + } + + /** + * @param str + * @param metier + * @param date + * @return + */ private double effortPerStrategyMet(Strategy str, Metier metier, Date date) { Month month = date.getMonth(); StrategyMonthInfo smi = str.getStrategyMonthInfo(month); @@ -1812,4 +1872,39 @@ return result; } +/////////////////////////////////////////////////////////////////////////// + // + // + // + /////////////////////////////////////////////////////////////////////////// + public MatrixND matrixEffortNominalPerStrategyMet(Date date) throws TopiaException { + + List<Strategy> strategies = getStrategies(date); + List<Metier> metiers = getMetiers(date); + + MatrixND result = MatrixFactory.getInstance().create( + ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET, + new List[]{strategies, metiers}, + new String[]{n_("Strategies"), n_("Metiers")}); + + for (int s=0; s < strategies.size(); s++) { + Strategy str = strategies.get(s); + metiers = getMetiers(str, date); + for (int m=0; m < metiers.size(); m++) { + Metier metier = metiers.get(m); + double value = effortNominalPerStrategyMet(str, metier, date); + result.setValue(str, metier, value); + } + } + +// for(Strategy str : strategies){ +// List<Metier> metierStr = getMetiers(str, date); +// for(Metier metier : metierStr) { +// double val = effortPerStrategyMet(str, metier, date); // rem perf: effortPerStrategyMet a deja ete calculé +// result.setValue(str, metier, val); +// } +// } + + return result; + } } Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2009-05-07 17:07:20 UTC (rev 137) +++ trunk/simulators/DefaultSimulator.java 2009-05-07 20:14:16 UTC (rev 138) @@ -225,6 +225,11 @@ resManager.addResult(date, effortPerStrategyMet); } + if (resManager.isEnabled(ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET)) { + MatrixND effortNominalPerStrategyMet = siMatrix.matrixEffortNominalPerStrategyMet(date); + resManager.addResult(date, effortNominalPerStrategyMet); + } + if (resManager .isEnabled(ResultName.MATRIX_STD_TRAVEL_EFFORT_PER_STRATEGY_MET)) { MatrixND stdTravelEffortPerStrategyMet = siMatrix

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