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

r286 - tags
by echatellier＠users.forge.codelutin.com April 26, 2012

April 26, 2012

Author: echatellier Date: 2012-04-26 18:21:51 +0200 (Thu, 26 Apr 2012) New Revision: 286 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/286 Log: Tag 4.1.0 release Added: tags/4.1.0/

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r285 - trunk
by echatellier＠users.forge.codelutin.com April 26, 2012

April 26, 2012

Author: echatellier Date: 2012-04-26 18:20:47 +0200 (Thu, 26 Apr 2012) New Revision: 285 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/285 Log: Use released version Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-04-26 16:02:07 UTC (rev 284) +++ trunk/pom.xml 2012-04-26 16:20:47 UTC (rev 285) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.0.0-SNAPSHOT</version> + <version>4.1.0.0</version> <scope>compile</scope> </dependency> </dependencies>

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r284 - trunk/sensitivityexports
by echatellier＠users.forge.codelutin.com April 26, 2012

April 26, 2012

Author: echatellier Date: 2012-04-26 18:02:07 +0200 (Thu, 26 Apr 2012) New Revision: 284 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/284 Log: Revert : Get result within an valid transaction to avoid lazyexceptions Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java trunk/sensitivityexports/SensitivitySpawningBiomassY2.java Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-04-26 13:32:21 UTC (rev 283) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-04-26 16:02:07 UTC (rev 284) @@ -80,6 +80,8 @@ map.put(group.getId(),group.getMaturityOgive()); } + tx.closeContext(); + //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -114,7 +116,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -127,8 +129,6 @@ } } - tx.closeContext(); - out.write(Double.toString(biomass / referenceBiomass)); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-04-26 13:32:21 UTC (rev 283) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-04-26 16:02:07 UTC (rev 284) @@ -85,6 +85,8 @@ map.put(group.getId(),group.getMaturityOgive()); } + tx.closeContext(); + //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -124,7 +126,7 @@ //Get the biomass of the first time step MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -138,7 +140,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -152,8 +154,6 @@ } } - tx.closeContext(); - out.write(Double.toString((biomass / firstbiomass) / (biomassReference / firstBiomassReference))); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-04-26 13:32:21 UTC (rev 283) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-04-26 16:02:07 UTC (rev 284) @@ -32,7 +32,6 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; -import org.nuiton.topia.TopiaContext; import scripts.ResultName; @@ -64,9 +63,8 @@ ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the first time step - TopiaContext tx = simulation.getStorage().beginTransaction(); MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -80,7 +78,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -89,8 +87,6 @@ if (step.equals(lastStep)) biomass += i.getValue() * group.getMaturityOgive(); } - - tx.closeContext(); } } out.write(Double.toString(biomass / firstbiomass)); Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-04-26 13:32:21 UTC (rev 283) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-04-26 16:02:07 UTC (rev 284) @@ -32,7 +32,6 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; -import org.nuiton.topia.TopiaContext; import scripts.ResultName; @@ -62,9 +61,8 @@ ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the last time step - TopiaContext tx = simulation.getStorage().beginTransaction(); MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS, tx); + ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -74,7 +72,6 @@ biomass += i.getValue() * group.getMaturityOgive(); } } - tx.closeContext(); } } out.write(Double.toString(biomass));

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r283 - trunk/sensitivityexports
by echatellier＠users.forge.codelutin.com April 26, 2012

April 26, 2012

Author: echatellier Date: 2012-04-26 15:32:21 +0200 (Thu, 26 Apr 2012) New Revision: 283 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/283 Log: Get result within an valid transaction to avoid lazyexceptions Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java trunk/sensitivityexports/SensitivitySpawningBiomassY2.java Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-04-03 15:59:20 UTC (rev 282) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2012-04-26 13:32:21 UTC (rev 283) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -80,8 +80,6 @@ map.put(group.getId(),group.getMaturityOgive()); } - tx.closeContext(); - //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -109,13 +107,14 @@ } line = reader.readLine(); } + reader.close(); for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -127,6 +126,9 @@ } } } + + tx.closeContext(); + out.write(Double.toString(biomass / referenceBiomass)); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-04-03 15:59:20 UTC (rev 282) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2012-04-26 13:32:21 UTC (rev 283) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -85,8 +85,6 @@ map.put(group.getId(),group.getMaturityOgive()); } - tx.closeContext(); - //instantiate a reader that starts reading from the file end. ReverseFileReader reader = new ReverseFileReader(referenceFile); @@ -119,13 +117,14 @@ line = reader.readLine(); } + reader.close(); for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { //Get the biomass of the first time step MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -139,7 +138,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -152,6 +151,9 @@ } } } + + tx.closeContext(); + out.write(Double.toString((biomass / firstbiomass) / (biomassReference / firstBiomassReference))); } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-04-03 15:59:20 UTC (rev 282) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2012-04-26 13:32:21 UTC (rev 283) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,6 +32,8 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; + import scripts.ResultName; import java.io.Writer; @@ -62,8 +64,9 @@ ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the first time step + TopiaContext tx = simulation.getStorage().beginTransaction(); MatrixND matfirstdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -77,7 +80,7 @@ //Get the biomass of the last time step MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -86,6 +89,8 @@ if (step.equals(lastStep)) biomass += i.getValue() * group.getMaturityOgive(); } + + tx.closeContext(); } } out.write(Double.toString(biomass / firstbiomass)); Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-04-03 15:59:20 UTC (rev 282) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2012-04-26 13:32:21 UTC (rev 283) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2009 - 2011 Ifremer, Code Lutin, Jean Couteau + * Copyright (C) 2009 - 2012 Ifremer, Code Lutin, Jean Couteau, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -32,6 +32,8 @@ import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixIterator; import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; + import scripts.ResultName; import java.io.Writer; @@ -60,8 +62,9 @@ ResultStorage resultStorage = simulation.getResultStorage(); //Get the biomass of the last time step + TopiaContext tx = simulation.getStorage().beginTransaction(); MatrixND matlastdate = resultStorage.getMatrix(pop, - ResultName.MATRIX_BIOMASS); + ResultName.MATRIX_BIOMASS, tx); for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); @@ -71,6 +74,7 @@ biomass += i.getValue() * group.getMaturityOgive(); } } + tx.closeContext(); } } out.write(Double.toString(biomass));

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r282 - trunk
by echatellier＠users.forge.codelutin.com April 3, 2012

April 3, 2012

Author: echatellier Date: 2012-04-03 17:59:20 +0200 (Tue, 03 Apr 2012) New Revision: 282 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/282 Log: Update plugin version Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-04-03 15:54:09 UTC (rev 281) +++ trunk/pom.xml 2012-04-03 15:59:20 UTC (rev 282) @@ -49,7 +49,7 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.2</version> + <version>1.2.1</version> <executions> <execution> <goals>

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r281 - trunk
by echatellier＠users.forge.codelutin.com April 3, 2012

April 3, 2012

Author: echatellier Date: 2012-04-03 17:54:09 +0200 (Tue, 03 Apr 2012) New Revision: 281 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/281 Log: Update next version Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-03-30 08:17:23 UTC (rev 280) +++ trunk/pom.xml 2012-04-03 15:54:09 UTC (rev 281) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.0.0</version> + <version>4.1.0</version>  <description>Data for Isis-fish</description> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.0.0.3-SNAPSHOT</version> + <version>4.1.0.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

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r280 - trunk/scripts
by echatellier＠users.forge.codelutin.com March 30, 2012

March 30, 2012

Author: echatellier Date: 2012-03-30 10:17:23 +0200 (Fri, 30 Mar 2012) New Revision: 280 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/280 Log: Add doc about simatrix and gravitymodel Modified: trunk/scripts/GravityModel.java trunk/scripts/SiMatrix.java Modified: trunk/scripts/GravityModel.java =================================================================== --- trunk/scripts/GravityModel.java 2012-03-22 10:38:45 UTC (rev 279) +++ trunk/scripts/GravityModel.java 2012-03-30 08:17:23 UTC (rev 280) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -49,15 +49,14 @@ import fr.ifremer.isisfish.types.TimeUnit; /** - * GravityModel.java - * - * Created: 4 sept. 06 15:49:08 - * + * Gravity model calcul des resultats à basés sur des resultats provenant + * de SiMatrix ou des resultat précédement calculé disponible via le + * result manager. + * + * Cette classe sert a calculer des résultats economique (prix, resultat + * servant a optimiser des cout pour les pécheurs...). + * * @author poussin - * @version $Revision: 1.9 $ - * - * Last update: $Date: 2007-03-01 17:16:12 $ - * by : $Author: bpoussin $ */ public class GravityModel { Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2012-03-22 10:38:45 UTC (rev 279) +++ trunk/scripts/SiMatrix.java 2012-03-30 08:17:23 UTC (rev 280) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2011 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2006 - 2012 Ifremer, Code Lutin, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -59,15 +59,10 @@ import fr.ifremer.isisfish.types.Month; /** - * SiMatrix.java + * SiMatrix calcul simplement des résultats ne dependant que des parametres + * de simulation et des données du modèle. * - * Created: 21 aout 2006 15:53:01 - * * @author poussin - * @version $Revision: 1.18 $ - * - * Last update: $Date: 2007-11-02 17:53:20 $ - * by : $Author: bpoussin $ */ public class SiMatrix {

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r279 - branches
by jcouteau＠users.forge.codelutin.com March 22, 2012

March 22, 2012

Author: jcouteau Date: 2012-03-22 11:38:45 +0100 (Thu, 22 Mar 2012) New Revision: 279 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/279 Log: Branche pour changement mod?\195?\168le facteurs Added: branches/4.0.1/

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r278 - trunk/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 29, 2012

Feb. 29, 2012

Author: jcouteau Date: 2012-02-29 12:05:43 +0100 (Wed, 29 Feb 2012) New Revision: 278 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/278 Log: termminate not necessary Modified: trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java Modified: trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-29 11:04:50 UTC (rev 277) +++ trunk/sensitivityanalysis/SensitivityCalculatorRMorris.java 2012-02-29 11:05:43 UTC (rev 278) @@ -217,10 +217,6 @@ } catch (RException eee) { throw new SensitivityException("Can't generate scenarios", eee); - } finally { - if (engine != null) { - engine.terminate(); - } } return thisExperiment; @@ -349,10 +345,6 @@ } catch (Exception e) { throw new SensitivityException("Can't evaluate results", e); - } finally { - if (engine != null) { - engine.terminate(); - } } }

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r277 - trunk/sensitivityanalysis
by jcouteau＠users.forge.codelutin.com Feb. 29, 2012

Feb. 29, 2012

Author: jcouteau Date: 2012-02-29 12:04:50 +0100 (Wed, 29 Feb 2012) New Revision: 277 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/277 Log: This code should not be here Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java Modified: trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java =================================================================== --- trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 10:33:39 UTC (rev 276) +++ trunk/sensitivityanalysis/SensitivityCalculatorRDOptimal.java 2012-02-29 11:04:50 UTC (rev 277) @@ -238,9 +238,6 @@ "\"nomModel\")<-\"isis-fish-externe-R\""); engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); - //Rename R objects for saving purpose - renameObjects(engine,simulationName); - // Save Isis R session engine.saveRData(outputDirectory.getParentFile(), outputDirectory.getName());

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