November 2011 - Isis-fish-data-commits - mailman.cloud.codelutin.com

r268 - trunk/simulators
by jcouteau＠users.forge.codelutin.com 30 Nov '11

30 Nov '11

Author: jcouteau Date: 2011-11-30 14:02:08 +0100 (Wed, 30 Nov 2011) New Revision: 268 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/268 Log: Fix build Modified: trunk/simulators/DefaultSimulator.java Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2011-11-30 09:37:50 UTC (rev 267) +++ trunk/simulators/DefaultSimulator.java 2011-11-30 13:02:08 UTC (rev 268) @@ -22,21 +22,6 @@ package simulators; -import static org.nuiton.i18n.I18n._; -import static org.nuiton.i18n.I18n.n_; - -import java.util.List; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.math.matrix.MatrixFactory; -import org.nuiton.math.matrix.MatrixND; -import org.nuiton.topia.TopiaContext; -import org.nuiton.topia.TopiaException; - -import scripts.GravityModel; -import scripts.ResultName; -import scripts.SiMatrix; import fr.ifremer.isisfish.IsisFishException; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.entities.Metier; @@ -51,9 +36,23 @@ import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.Simulator; -import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.TimeStep; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; +import org.nuiton.topia.TopiaException; +import scripts.GravityModel; +import scripts.ResultName; +import scripts.SiMatrix; +import java.util.List; + +import static org.nuiton.i18n.I18n._; +import static org.nuiton.i18n.I18n.n_; + /** * DefaultSimulator.java * @@ -80,7 +79,7 @@ SimulationControl control = context.getSimulationControl(); int lastYear = param.getNumberOfYear(); int lastStep = lastYear * Month.NUMBER_OF_MONTH; - TimeStep step = control.getTimeStep(); + TimeStep step = control.getStep(); ResultManager resManager = context.getResultManager(); TopiaContext db = context.getDB(); @@ -132,7 +131,7 @@ break; } - control.setTimeStep(step); + control.setStep(step); control.setProgress(step.getStep()); control.setText(_("begin step " + step)); @@ -375,7 +374,7 @@ PopulationSeasonInfo info = pop.getPopulationSeasonInfo(month); // group change - MatrixND CA = null; + MatrixND CA; if (step.getStep() == 0) { CA = MatrixFactory.getInstance().matrixId( pop.sizePopulationGroup() * pop.sizePopulationZone()); @@ -440,7 +439,7 @@ resManager.addResult(step, pop, biomassBM); } - MatrixND abundance = N; + MatrixND abundance; // compute fishing matrix only if there are one or more strategy if (siMatrix.getStrategies(step).size() > 0) { // compute some Matrix and add result @@ -512,7 +511,7 @@ } /** - * @param date + * @param step * @param resManager * @throws IsisFishException * @throws TopiaException

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r267 - trunk/sensitivityexports
by jcouteau＠users.forge.codelutin.com 30 Nov '11

30 Nov '11

Author: jcouteau Date: 2011-11-30 10:37:50 +0100 (Wed, 30 Nov 2011) New Revision: 267 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/267 Log: #555 : Remplacer reproductionRate par MaturityOgive dans l'export d'AS SpawningBiomass 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 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,22 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.File; -import java.io.Writer; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.math.matrix.MatrixIterator; -import org.nuiton.math.matrix.MatrixND; - -import org.nuiton.topia.TopiaContext; -import org.nuiton.util.ReverseFileReader; -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -44,7 +28,22 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; +import org.nuiton.util.ReverseFileReader; +import scripts.ResultName; +import java.io.File; +import java.io.Writer; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassReferenceY8 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -78,7 +77,7 @@ Map<Integer, Double> map =new HashMap<Integer,Double>(); for (PopulationGroup group:groups) { - map.put(group.getId(),group.getReproductionRate()); + map.put(group.getId(),group.getMaturityOgive()); } tx.closeContext(); @@ -123,7 +122,7 @@ PopulationGroup group = (PopulationGroup) sems[1]; TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) { - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,22 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.File; -import java.io.Writer; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.math.matrix.MatrixIterator; -import org.nuiton.math.matrix.MatrixND; -import org.nuiton.topia.TopiaContext; - -import org.nuiton.util.ReverseFileReader; -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -44,7 +28,22 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaContext; +import org.nuiton.util.ReverseFileReader; +import scripts.ResultName; +import java.io.File; +import java.io.Writer; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassRelativeReferenceY11 implements SensitivityExport { @@ -83,7 +82,7 @@ Map<Integer, Double> map =new HashMap<Integer,Double>(); for (PopulationGroup group:groups) { - map.put(group.getId(),group.getReproductionRate()); + map.put(group.getId(),group.getMaturityOgive()); } tx.closeContext(); @@ -134,7 +133,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(firstStep)) { firstbiomass += i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } @@ -148,7 +147,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) { biomass = biomass + i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,16 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.math.matrix.MatrixIterator; -import org.nuiton.math.matrix.MatrixND; - -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -38,7 +28,16 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import scripts.ResultName; +import java.io.Writer; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassRelativeY5 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -72,7 +71,7 @@ TimeStep step = (TimeStep) sems[0]; if (step.equals(firstStep)) { firstbiomass += i.getValue() - * group.getReproductionRate(); + * group.getMaturityOgive(); } } @@ -85,7 +84,7 @@ PopulationGroup group = (PopulationGroup) sems[1]; TimeStep step = (TimeStep) sems[0]; if (step.equals(lastStep)) - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } } Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-11-21 10:41:33 UTC (rev 266) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-11-30 09:37:50 UTC (rev 267) @@ -21,16 +21,6 @@ */ package sensitivityexports; -import static org.nuiton.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.nuiton.math.matrix.MatrixIterator; -import org.nuiton.math.matrix.MatrixND; - -import scripts.ResultName; import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; @@ -38,7 +28,16 @@ import fr.ifremer.isisfish.export.SensitivityExport; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.Doc; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import scripts.ResultName; +import java.io.Writer; + +import static org.nuiton.i18n.I18n._; + public class SensitivitySpawningBiomassY2 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ @@ -69,7 +68,7 @@ TimeStep step = (TimeStep) sems[0]; PopulationGroup group = (PopulationGroup) sems[1]; if (step.equals(lastStep)) { - biomass += i.getValue() * group.getReproductionRate(); + biomass += i.getValue() * group.getMaturityOgive(); } } }

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r266 - trunk
by echatellier＠users.forge.codelutin.com 21 Nov '11

21 Nov '11

Author: echatellier Date: 2011-11-21 11:41:33 +0100 (Mon, 21 Nov 2011) New Revision: 266 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/266 Log: Prepare release Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2011-11-08 11:05:17 UTC (rev 265) +++ trunk/pom.xml 2011-11-21 10:41:33 UTC (rev 266) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.0.0.0-beta-1-SNAPSHOT</version> + <version>4.0.0.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

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r265 - trunk/sensitivityexports
by jcouteau＠users.forge.codelutin.com 08 Nov '11

08 Nov '11

Author: jcouteau Date: 2011-11-08 12:05:17 +0100 (Tue, 08 Nov 2011) New Revision: 265 Url: http://forge.codelutin.com/repositories/revision/isis-fish-data/265 Log: Rename sensitivity exports Modified: trunk/sensitivityexports/SensitivityBiomassReferenceY9.java trunk/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java trunk/sensitivityexports/SensitivityBiomassRelativeY6.java trunk/sensitivityexports/SensitivityBiomassY3.java trunk/sensitivityexports/SensitivityCatchWeightReferenceY7.java trunk/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java trunk/sensitivityexports/SensitivityCatchWeightRelativeY4.java trunk/sensitivityexports/SensitivityCatchWeightY1.java trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java trunk/sensitivityexports/SensitivitySpawningBiomassY2.java Modified: trunk/sensitivityexports/SensitivityBiomassReferenceY9.java =================================================================== --- trunk/sensitivityexports/SensitivityBiomassReferenceY9.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityBiomassReferenceY9.java 2011-11-08 11:05:17 UTC (rev 265) @@ -118,7 +118,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomassReferenceY9"; + return "SensitivityBiomassReferenceY9_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java =================================================================== --- trunk/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityBiomassRelativeReferenceY12.java 2011-11-08 11:05:17 UTC (rev 265) @@ -126,7 +126,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomassRelativeReferenceY12"; + return "SensitivityBiomassRelativeReferenceY12_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/sensitivityexports/SensitivityBiomassRelativeY6.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityBiomassRelativeY6.java 2011-11-08 11:05:17 UTC (rev 265) @@ -82,7 +82,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomassRelativeY6"; + return "SensitivityBiomassRelativeY6_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityBiomassY3.java =================================================================== --- trunk/sensitivityexports/SensitivityBiomassY3.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityBiomassY3.java 2011-11-08 11:05:17 UTC (rev 265) @@ -72,7 +72,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomassY3"; + return "SensitivityBiomassY3_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityCatchWeightReferenceY7.java =================================================================== --- trunk/sensitivityexports/SensitivityCatchWeightReferenceY7.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityCatchWeightReferenceY7.java 2011-11-08 11:05:17 UTC (rev 265) @@ -121,7 +121,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeightReferenceY7"; + return "SensitivityCapturesWeightReferenceY7_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java =================================================================== --- trunk/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityCatchWeightRelativeReferenceY10.java 2011-11-08 11:05:17 UTC (rev 265) @@ -134,7 +134,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeightRelativeReferenceY10"; + return "SensitivityCapturesWeightRelativeReferenceY10_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityCatchWeightRelativeY4.java =================================================================== --- trunk/sensitivityexports/SensitivityCatchWeightRelativeY4.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityCatchWeightRelativeY4.java 2011-11-08 11:05:17 UTC (rev 265) @@ -90,7 +90,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeightRelativeY4"; + return "SensitivityCapturesWeightRelativeY4_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivityCatchWeightY1.java =================================================================== --- trunk/sensitivityexports/SensitivityCatchWeightY1.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivityCatchWeightY1.java 2011-11-08 11:05:17 UTC (rev 265) @@ -81,7 +81,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeightY1"; + return "SensitivityCapturesWeightY1_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivitySpawningBiomassReferenceY8.java 2011-11-08 11:05:17 UTC (rev 265) @@ -138,7 +138,7 @@ @Override public String getExportFilename() { - return "SensitivitySpawningBiomassReferenceY8"; + return "SensitivitySpawningBiomassReferenceY8_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeReferenceY11.java 2011-11-08 11:05:17 UTC (rev 265) @@ -164,7 +164,7 @@ @Override public String getExportFilename() { - return "SensitivitySpawningBiomassRelativeReferenceY11"; + return "SensitivitySpawningBiomassRelativeReferenceY11_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivitySpawningBiomassRelativeY5.java 2011-11-08 11:05:17 UTC (rev 265) @@ -99,7 +99,7 @@ @Override public String getExportFilename() { - return "SensitivityGenitorBiomassRelativeY5"; + return "SensitivityGenitorBiomassRelativeY5_" + param_pop.getName(); } @Override Modified: trunk/sensitivityexports/SensitivitySpawningBiomassY2.java =================================================================== --- trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-10-28 11:15:57 UTC (rev 264) +++ trunk/sensitivityexports/SensitivitySpawningBiomassY2.java 2011-11-08 11:05:17 UTC (rev 265) @@ -84,7 +84,7 @@ @Override public String getExportFilename() { - return "SensitivityGenitorBiomassY2"; + return "SensitivityGenitorBiomassY2_" + param_pop.getName(); } @Override

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