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

r107 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 16, 2009

April 16, 2009

Author: jcouteau Date: 2009-04-16 12:00:03 +0000 (Thu, 16 Apr 2009) New Revision: 107 Modified: trunk/exports/SensitivityBiomassRelativeY6.java trunk/exports/SensitivityBiomassY3.java trunk/exports/SensitivityCapturesWeightRelativeY4.java trunk/exports/SensitivityCapturesWeightY1.java trunk/exports/SensitivityGenitorBiomassRelativeY5.java trunk/exports/SensitivityGenitorBiomassY2.java Log: Refactoring of sensitivity standards exports Modified: trunk/exports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-16 12:00:03 UTC (rev 107) @@ -6,10 +6,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.export.SensitivityExport; @@ -20,7 +20,8 @@ public class SensitivityBiomassRelativeY6 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityBiomassRelativeY6.class); + static private Log log = LogFactory + .getLog(SensitivityBiomassRelativeY6.class); protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; @@ -31,48 +32,27 @@ public void export(SimulationStorage simulation, Writer out) throws Exception { Date lastDate = simulation.getResultStorage().getLastDate(); - Date firstDate = new Date (11); + Date firstDate = new Date(11); double biomass = 0.0; double firstbiomass = 0.0; - - //Calculate the biomass on last time step - + for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultStorage resultStorage = simulation.getResultStorage(); + + //Get the biomass on december of the first year + MatrixND matfirstdate = resultStorage.getMatrix(firstDate, pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; + firstbiomass = matfirstdate.sumAll(); - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue(); - } - } - } - } - - //Calculate the biomass on december of first year - - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; + biomass = matlastdate.sumAll(); - if (date.equals(firstDate)) { - firstbiomass = firstbiomass + i.getValue(); - } - } } } - - out.write(Double.toString(biomass/firstbiomass)); - + out.write(Double.toString(biomass / firstbiomass)); } @Override @@ -82,7 +62,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomassRelative"; + return "SensitivityBiomassRelativeY6"; } @Override Modified: trunk/exports/SensitivityBiomassY3.java =================================================================== --- trunk/exports/SensitivityBiomassY3.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityBiomassY3.java 2009-04-16 12:00:03 UTC (rev 107) @@ -6,10 +6,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.export.SensitivityExport; @@ -30,25 +30,19 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); double biomass = 0.0; for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, - ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue(); - } - } + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); } } out.write(Double.toString(biomass)); - } @Override @@ -58,7 +52,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomass"; + return "SensitivityBiomassY3"; } @Override Modified: trunk/exports/SensitivityCapturesWeightRelativeY4.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-16 12:00:03 UTC (rev 107) @@ -6,10 +6,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.export.SensitivityExport; @@ -20,7 +20,8 @@ public class SensitivityCapturesWeightRelativeY4 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityCapturesWeightRelativeY4.class); + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightRelativeY4.class); protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; @@ -30,55 +31,36 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); Double capturesWeight = 0.0; Double capturesWeightfirst = 0.0; for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - for (Date date = new Date(0); !date.after(lastDate); date = date - .next()) { - MatrixND mat = simulation - .getResultStorage() + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage .getMatrix( - date, + new Date(lastDate.getDate() - i), pop, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - if (mat != null) { // can be null if simulation is stopped before last year simulation - mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - double val = i.getValue(); - capturesWeight = capturesWeight + val; - } - } - } - } - } - - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals(param_pop.getName())) { - for (Date date = new Date(0); date.beforeOrEquals(new Date(11)); date = date - .next()) { - MatrixND mat = simulation - .getResultStorage() + capturesWeight += matlastdate.sumAll(); + + //Get the captures Weight of each month of the first year + MatrixND matfirstdate = resultStorage .getMatrix( - date, + new Date(i), pop, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - if (mat != null) { // can be null if simulation is stopped before last year simulation - mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - double val = i.getValue(); - capturesWeightfirst = capturesWeightfirst + val; - } - } + capturesWeightfirst += matfirstdate.sumAll(); } + } } - - out.write(Double.toString(capturesWeight/capturesWeightfirst)); + + out.write(Double.toString(capturesWeight / capturesWeightfirst)); } @Override @@ -88,7 +70,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeightRelative"; + return "SensitivityCapturesWeightRelativeY4"; } @Override Modified: trunk/exports/SensitivityCapturesWeightY1.java =================================================================== --- trunk/exports/SensitivityCapturesWeightY1.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityCapturesWeightY1.java 2009-04-16 12:00:03 UTC (rev 107) @@ -6,10 +6,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.export.SensitivityExport; @@ -20,7 +20,8 @@ public class SensitivityCapturesWeightY1 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityCapturesWeightY1.class); + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightY1.class); protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; @@ -30,30 +31,26 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); Double capturesWeight = 0.0; for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - for (Date date = new Date(0); !date.after(lastDate); date = date - .next()) { - MatrixND mat = simulation - .getResultStorage() + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage .getMatrix( - date, + new Date(lastDate.getDate() - i), pop, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - if (mat != null) { // can be null if simulation is stopped before last year simulation - mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - double val = i.getValue(); - capturesWeight = capturesWeight + val; - } - } + capturesWeight += matlastdate.sumAll(); } + } } + out.write(Double.toString(capturesWeight)); } @@ -64,7 +61,7 @@ @Override public String getExportFilename() { - return "SensitivityCapturesWeight"; + return "SensitivityCapturesWeightY1"; } @Override Modified: trunk/exports/SensitivityGenitorBiomassRelativeY5.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassRelativeY5.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityGenitorBiomassRelativeY5.java 2009-04-16 12:00:03 UTC (rev 107) @@ -10,6 +10,7 @@ import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationGroup; @@ -33,46 +34,41 @@ public void export(SimulationStorage simulation, Writer out) throws Exception { Date lastDate = simulation.getResultStorage().getLastDate(); - Date firstDate = new Date (11); + Date firstDate = new Date(11); double biomass = 0.0; double firstbiomass = 0.0; - + for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultStorage resultStorage = simulation.getResultStorage(); + + //Get the biomass of the last time step + MatrixND matfirstdate = resultStorage.getMatrix(pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { + for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; PopulationGroup group = (PopulationGroup) sems[1]; - - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue() + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomass += i.getValue() * group.getReproductionRate(); } } - } - } - //Calculate the biomass on december of first year - - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; Date date = (Date) sems[0]; - - if (date.equals(firstDate)) { - firstbiomass = firstbiomass + i.getValue(); - } + if (date.equals(lastDate)) + biomass += i.getValue() * group.getReproductionRate(); } } } - out.write(Double.toString(biomass / firstbiomass)); } @@ -83,7 +79,7 @@ @Override public String getExportFilename() { - return "SensitivityGenitorBiomassRelative"; + return "SensitivityGenitorBiomassRelativeY5"; } @Override Modified: trunk/exports/SensitivityGenitorBiomassY2.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassY2.java 2009-04-14 17:45:33 UTC (rev 106) +++ trunk/exports/SensitivityGenitorBiomassY2.java 2009-04-16 12:00:03 UTC (rev 107) @@ -10,6 +10,7 @@ import org.codelutin.math.matrix.MatrixND; import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationGroup; @@ -21,7 +22,8 @@ public class SensitivityGenitorBiomassY2 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityGenitorBiomassY2.class); + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassY2.class); protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; @@ -33,18 +35,21 @@ throws Exception { Date lastDate = simulation.getResultStorage().getLastDate(); double biomass = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultStorage resultStorage = simulation.getResultStorage(); + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { + for (MatrixIterator i = matlastdate.iterator(); i.hasNext();) { i.next(); Object[] sems = i.getSemanticsCoordinates(); Date date = (Date) sems[0]; PopulationGroup group = (PopulationGroup) sems[1]; - - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue()*group.getReproductionRate(); + if (date.equals(lastDate)) { + biomass += i.getValue() * group.getReproductionRate(); } } } @@ -59,7 +64,7 @@ @Override public String getExportFilename() { - return "SensitivityGenitorBiomass"; + return "SensitivityGenitorBiomassY2"; } @Override

1 0

r106 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 14, 2009

April 14, 2009

Author: jcouteau Date: 2009-04-14 17:45:33 +0000 (Tue, 14 Apr 2009) New Revision: 106 Modified: trunk/exports/SensitivityCapturesWeightRelativeY4.java Log: Modified: trunk/exports/SensitivityCapturesWeightRelativeY4.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-14 17:41:56 UTC (rev 105) +++ trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-14 17:45:33 UTC (rev 106) @@ -1,4 +1,4 @@ -ppackage exports; +package exports; import static org.codelutin.i18n.I18n._;

1 0

r105 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 14, 2009

April 14, 2009

Author: jcouteau Date: 2009-04-14 17:41:56 +0000 (Tue, 14 Apr 2009) New Revision: 105 Added: trunk/exports/SensitivityBiomassReferenceY9.java trunk/exports/SensitivityCapturesWeightRelativeY4.java trunk/exports/SensitivityCapturesWeightY1.java trunk/exports/SensitivityGenitorBiomassRelativeY5.java Removed: trunk/exports/SensitivityCapturesPoids.java Modified: trunk/exports/SensitivityGenitorBiomassY2.java Log: Adding exports. Fixing bugs on exports. Added: trunk/exports/SensitivityBiomassReferenceY9.java =================================================================== --- trunk/exports/SensitivityBiomassReferenceY9.java (rev 0) +++ trunk/exports/SensitivityBiomassReferenceY9.java 2009-04-14 17:41:56 UTC (rev 105) @@ -0,0 +1,80 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.File; +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityBiomass") +public class SensitivityBiomassReferenceY9 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityBiomassReferenceY9.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Path to the reference simulation exports") + public String param_referenceExports; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + File referenceExports=new File (param_referenceExports); + Date lastDate = simulation.getResultStorage().getLastDate(); + double biomass = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + + if (date.afterOrEquals(lastDate)) { + biomass = biomass + i.getValue(); + } + } + } + } + out.write(Double.toString(biomass)); + + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomass"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Deleted: trunk/exports/SensitivityCapturesPoids.java =================================================================== --- trunk/exports/SensitivityCapturesPoids.java 2009-04-13 11:42:54 UTC (rev 104) +++ trunk/exports/SensitivityCapturesPoids.java 2009-04-14 17:41:56 UTC (rev 105) @@ -1,78 +0,0 @@ -package exports; - -import static org.codelutin.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; -import org.codelutin.math.matrix.MatrixND; - -import scripts.ResultName; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.entities.Population; -import fr.ifremer.isisfish.export.SensitivityExport; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.util.Doc; - -@Doc("Doc for SensitivityCapturesPoids") -public class SensitivityCapturesPoids implements SensitivityExport { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityCapturesPoids.class); - - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; - - @Doc("Population") - public Population param_pop; - - @Override - public void export(SimulationStorage simulation, Writer out) - throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - Double capturesWeight = 0.0; - - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals(param_pop.getName())) { - for (Date date = new Date(0); !date.after(lastDate); date = date - .next()) { - MatrixND mat = simulation - .getResultStorage() - .getMatrix( - date, - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - if (mat != null) { // can be null if simulation is stopped before last year simulation - mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - capturesWeight = capturesWeight + i.getValue(); - } - } - } - } - } - } - - @Override - public String getDescription() { - return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); - } - - @Override - public String getExportFilename() { - return "SensitivityCapturesPoids"; - } - - @Override - public String getExtensionFilename() { - return ".csv"; - } - - @Override - public String[] getNecessaryResult() { - return this.necessaryResult; - } - -} Added: trunk/exports/SensitivityCapturesWeightRelativeY4.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeY4.java (rev 0) +++ trunk/exports/SensitivityCapturesWeightRelativeY4.java 2009-04-14 17:41:56 UTC (rev 105) @@ -0,0 +1,104 @@ +ppackage exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityCapturesPoids") +public class SensitivityCapturesWeightRelativeY4 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityCapturesWeightRelativeY4.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightfirst = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation + .getResultStorage() + .getMatrix( + date, + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + if (mat != null) { // can be null if simulation is stopped before last year simulation + mat = mat.sumOverDim(0); //sum on strategy + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + double val = i.getValue(); + capturesWeight = capturesWeight + val; + } + } + } + } + } + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (Date date = new Date(0); date.beforeOrEquals(new Date(11)); date = date + .next()) { + MatrixND mat = simulation + .getResultStorage() + .getMatrix( + date, + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + if (mat != null) { // can be null if simulation is stopped before last year simulation + mat = mat.sumOverDim(0); //sum on strategy + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + double val = i.getValue(); + capturesWeightfirst = capturesWeightfirst + val; + } + } + } + } + } + + out.write(Double.toString(capturesWeight/capturesWeightfirst)); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeightRelative"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Copied: trunk/exports/SensitivityCapturesWeightY1.java (from rev 102, trunk/exports/SensitivityCapturesPoids.java) =================================================================== --- trunk/exports/SensitivityCapturesWeightY1.java (rev 0) +++ trunk/exports/SensitivityCapturesWeightY1.java 2009-04-14 17:41:56 UTC (rev 105) @@ -0,0 +1,80 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityCapturesPoids") +public class SensitivityCapturesWeightY1 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityCapturesWeightY1.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + Double capturesWeight = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (Date date = new Date(0); !date.after(lastDate); date = date + .next()) { + MatrixND mat = simulation + .getResultStorage() + .getMatrix( + date, + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + if (mat != null) { // can be null if simulation is stopped before last year simulation + mat = mat.sumOverDim(0); //sum on strategy + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + double val = i.getValue(); + capturesWeight = capturesWeight + val; + } + } + } + } + } + out.write(Double.toString(capturesWeight)); + } + + @Override + public String getDescription() { + return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); + } + + @Override + public String getExportFilename() { + return "SensitivityCapturesWeight"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: trunk/exports/SensitivityCapturesWeightY1.java ___________________________________________________________________ Name: svn:mergeinfo + Added: trunk/exports/SensitivityGenitorBiomassRelativeY5.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassRelativeY5.java (rev 0) +++ trunk/exports/SensitivityGenitorBiomassRelativeY5.java 2009-04-14 17:41:56 UTC (rev 105) @@ -0,0 +1,99 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityBiomass") +public class SensitivityGenitorBiomassRelativeY5 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassRelativeY5.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + Date firstDate = new Date (11); + double biomass = 0.0; + double firstbiomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + PopulationGroup group = (PopulationGroup) sems[1]; + + if (date.afterOrEquals(lastDate)) { + biomass = biomass + i.getValue() + * group.getReproductionRate(); + } + } + } + } + + //Calculate the biomass on december of first year + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + + if (date.equals(firstDate)) { + firstbiomass = firstbiomass + i.getValue(); + } + } + } + } + + out.write(Double.toString(biomass / firstbiomass)); + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomassRelative"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Modified: trunk/exports/SensitivityGenitorBiomassY2.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassY2.java 2009-04-13 11:42:54 UTC (rev 104) +++ trunk/exports/SensitivityGenitorBiomassY2.java 2009-04-14 17:41:56 UTC (rev 105) @@ -50,7 +50,6 @@ } } out.write(Double.toString(biomass)); - } @Override

1 0

r104 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 13, 2009

April 13, 2009

Author: jcouteau Date: 2009-04-13 11:42:54 +0000 (Mon, 13 Apr 2009) New Revision: 104 Removed: trunk/exports/SensitivityBiomass.java Modified: trunk/exports/SensitivityBiomassRelativeY6.java Log: Fixed Y6 export Deleted: trunk/exports/SensitivityBiomass.java =================================================================== --- trunk/exports/SensitivityBiomass.java 2009-04-13 08:49:24 UTC (rev 103) +++ trunk/exports/SensitivityBiomass.java 2009-04-13 11:42:54 UTC (rev 104) @@ -1,74 +0,0 @@ -package exports; - -import static org.codelutin.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; -import org.codelutin.math.matrix.MatrixND; - -import scripts.ResultName; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.entities.Population; -import fr.ifremer.isisfish.export.SensitivityExport; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.util.Doc; - -@Doc("Doc for SensitivityBiomass") -public class SensitivityBiomass implements SensitivityExport { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityBiomass.class); - - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; - - @Doc("Population") - public Population param_pop; - - @Override - public void export(SimulationStorage simulation, Writer out) - throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - double biomass = 0.0; - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals(param_pop.getName())) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, - ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; - - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue(); - } - } - } - } - out.write(Double.toString(biomass)); - - } - - @Override - public String getDescription() { - return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); - } - - @Override - public String getExportFilename() { - return "SensitivityBiomass"; - } - - @Override - public String getExtensionFilename() { - return ".csv"; - } - - @Override - public String[] getNecessaryResult() { - return this.necessaryResult; - } - -} Modified: trunk/exports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-13 08:49:24 UTC (rev 103) +++ trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-13 11:42:54 UTC (rev 104) @@ -82,7 +82,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomass"; + return "SensitivityBiomassRelative"; } @Override

1 0

r103 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 13, 2009

April 13, 2009

Author: jcouteau Date: 2009-04-13 08:49:24 +0000 (Mon, 13 Apr 2009) New Revision: 103 Modified: trunk/exports/SensitivityBiomassRelativeY6.java Log: Fix bad copy/paste Modified: trunk/exports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-13 08:30:32 UTC (rev 102) +++ trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-13 08:49:24 UTC (rev 103) @@ -17,10 +17,10 @@ import fr.ifremer.isisfish.util.Doc; @Doc("Doc for SensitivityBiomass") -public class SensitivityBiomassY3 implements SensitivityExport { +public class SensitivityBiomassRelativeY6 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityBiomassY3.class); + static private Log log = LogFactory.getLog(SensitivityBiomassRelativeY6.class); protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS };

1 0

r102 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 13, 2009

April 13, 2009

Author: jcouteau Date: 2009-04-13 08:30:32 +0000 (Mon, 13 Apr 2009) New Revision: 102 Added: trunk/exports/SensitivityBiomassRelativeY6.java trunk/exports/SensitivityBiomassY3.java trunk/exports/SensitivityGenitorBiomassY2.java Log: Added: trunk/exports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeY6.java (rev 0) +++ trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-13 08:30:32 UTC (rev 102) @@ -0,0 +1,98 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityBiomass") +public class SensitivityBiomassY3 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityBiomassY3.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + Date firstDate = new Date (11); + double biomass = 0.0; + double firstbiomass = 0.0; + + //Calculate the biomass on last time step + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + + if (date.afterOrEquals(lastDate)) { + biomass = biomass + i.getValue(); + } + } + } + } + + //Calculate the biomass on december of first year + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + + if (date.equals(firstDate)) { + firstbiomass = firstbiomass + i.getValue(); + } + } + } + } + + out.write(Double.toString(biomass/firstbiomass)); + + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomass"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Copied: trunk/exports/SensitivityBiomassY3.java (from rev 101, trunk/exports/SensitivityBiomass.java) =================================================================== --- trunk/exports/SensitivityBiomassY3.java (rev 0) +++ trunk/exports/SensitivityBiomassY3.java 2009-04-13 08:30:32 UTC (rev 102) @@ -0,0 +1,74 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityBiomass") +public class SensitivityBiomassY3 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityBiomassY3.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + double biomass = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + + if (date.afterOrEquals(lastDate)) { + biomass = biomass + i.getValue(); + } + } + } + } + out.write(Double.toString(biomass)); + + } + + @Override + public String getDescription() { + return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityBiomass"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: trunk/exports/SensitivityBiomassY3.java ___________________________________________________________________ Name: svn:mergeinfo + Added: trunk/exports/SensitivityGenitorBiomassY2.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassY2.java (rev 0) +++ trunk/exports/SensitivityGenitorBiomassY2.java 2009-04-13 08:30:32 UTC (rev 102) @@ -0,0 +1,76 @@ +package exports; + +import static org.codelutin.i18n.I18n._; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.codelutin.math.matrix.MatrixIterator; +import org.codelutin.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.Date; +import fr.ifremer.isisfish.util.Doc; + +@Doc("Doc for SensitivityBiomass") +public class SensitivityGenitorBiomassY2 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityGenitorBiomassY2.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + Date lastDate = simulation.getResultStorage().getLastDate(); + double biomass = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + Date date = (Date) sems[0]; + PopulationGroup group = (PopulationGroup) sems[1]; + + if (date.afterOrEquals(lastDate)) { + biomass = biomass + i.getValue()*group.getReproductionRate(); + } + } + } + } + out.write(Double.toString(biomass)); + + } + + @Override + public String getDescription() { + return _("Biomass of the genitors for the last time step. Biomass is the sum on the groups and zones"); + } + + @Override + public String getExportFilename() { + return "SensitivityGenitorBiomass"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +}

1 0

r101 - trunk
by chatellier＠users.labs.libre-entreprise.org April 9, 2009

April 9, 2009

Author: chatellier Date: 2009-04-09 12:41:26 +0000 (Thu, 09 Apr 2009) New Revision: 101 Modified: trunk/pom.xml Log: Fix xsd location Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2009-04-08 12:44:22 UTC (rev 100) +++ trunk/pom.xml 2009-04-09 12:41:26 UTC (rev 101) @@ -1,5 +1,5 @@ <?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/maven-v4_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>

1 0

r100 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 8, 2009

April 8, 2009

Author: jcouteau Date: 2009-04-08 12:44:22 +0000 (Wed, 08 Apr 2009) New Revision: 100 Modified: trunk/sensitivity/SensitivityCalculatorRSobol.java Log: adding factors name support on sobol sensitivity analysis Modified: trunk/sensitivity/SensitivityCalculatorRSobol.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-04-08 10:19:07 UTC (rev 99) +++ trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-04-08 12:44:22 UTC (rev 100) @@ -127,6 +127,23 @@ + "a<-sobol(model=NULL,X1=X1,X2=X2,order=" + param_order + ",nboot=" + param_nboot + ")"); + // Creating the factors vector. + String rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + // Export the sobol object for the second run in a .sobol file engine.voidEval("dput(a,file=\".sobol\")"); log.info("Message sent to R" + "dput(a,file=\".sobol\")"); @@ -137,6 +154,11 @@ engine.voidEval("dput(X2,file=\".X2\")"); log.info("Message sent to R" + "dput(a,file=\".sobol\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + // Get back experiment plan /*dataframe = (double[]) engine.eval("a$X");*/ @@ -214,10 +236,26 @@ // Get the .X2 file engine.voidEval("X2<-dget(\".X2\")"); log.info("Message sent to R : " + "X2<-dget(\".X2\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Set X1 names + engine.voidEval("names(X1)<-factornames"); + log.info("Message sent to R : " + "names(X1)<-factornames"); + //Set X2 names + engine.voidEval("names(X2)<-factornames"); + log.info("Message sent to R : " + "names(X2)<-factornames"); + // Get the .sobol file engine.voidEval("a<-dget(\".sobol\")"); log.info("Message sent to R : " + "a<-dget(\".sobol\")"); + //Set a$X names + engine.voidEval("names(a$X)<-factornames"); + log.info("Message sent to R : " + "names(a$X)<-factornames"); + int scenariosNumber = (Integer) engine.eval("length(a$X[,1])"); log.info("Message sent to R : " + "length(a$X[,1])");

1 0

r99 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org April 8, 2009

April 8, 2009

Author: jcouteau Date: 2009-04-08 10:19:07 +0000 (Wed, 08 Apr 2009) New Revision: 99 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 Log: Set factor names in sensitivity exports Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-08 10:19:07 UTC (rev 99) @@ -105,11 +105,12 @@ .getMaxBound(); Double min = ((ContinuousDomain<Double>) factor.getDomain()) .getMinBound(); - int card = ((ContinuousDomain<? extends Serializable>) factor.getDomain()).getCardinality(); + int card = ((ContinuousDomain<? extends Serializable>) factor + .getDomain()).getCardinality(); result = (int) Math.floor(rest / card); rest = rest - (card * result); - Double value = min + ((max - min) / (card-1) * rest); + Double value = min + ((max - min) / (card - 1) * rest); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { factor.setValueForIdentifier(value.toString()); @@ -118,7 +119,8 @@ } } if (factor.getDomain() instanceof DiscreteDomain) { - int card = ((DiscreteDomain<? extends Serializable>) factor.getDomain()).getValues().size(); + int card = ((DiscreteDomain<? extends Serializable>) factor + .getDomain()).getValues().size(); result = (int) Math.floor(rest / card); rest = rest - (card * result); factor.setValueForIdentifier(rest); @@ -130,9 +132,9 @@ } thisExperiment.setScenarios(thisExperimentScenarios); - - thisExperimentScenarios=thisExperiment.getScenarios(); + thisExperimentScenarios = thisExperiment.getScenarios(); + /* * Call R to save the data for result analysis */ @@ -143,21 +145,21 @@ //Create the factors vectors for (int j = 0; j < factorNumber; j++) { Factor<? extends Serializable> factor = thisExperimentScenarios - .get(0).getFactors().get(j); - if (factor - .getDomain() instanceof EquationContinuousDomain) { + .get(0).getFactors().get(j); + if (factor.getDomain() instanceof EquationContinuousDomain) { String vector = "factor" + j + "<-c("; for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector - + ((EquationContinuousDomain<?>)thisExperimentScenarios - .get(i).getFactors().get(j).getDomain()).getValue() - + ","; + + ((EquationContinuousDomain<?>) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue() + ","; } else { vector = vector - + ((EquationContinuousDomain<?>)thisExperimentScenarios - .get(i).getFactors().get(j).getDomain()).getValue(); + + ((EquationContinuousDomain<?>) thisExperimentScenarios + .get(i).getFactors().get(j) + .getDomain()).getValue(); } } @@ -220,6 +222,23 @@ engine.voidEval(dataframe); log.info("Message sent to R : " + dataframe); + // Creating the factors vector. + String rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); @@ -231,6 +250,11 @@ log .info("Message sent to R : write.csv(data,file=\".expandgrid\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + engine.terminate(); } catch (Exception e) { @@ -268,6 +292,11 @@ log .info("Message sent to R : factors<-read.csv(\".expandgrid.csv\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + //Get back the factors number int factorNumber = ((Double) engine.eval("length(factors)-1")) .intValue(); @@ -348,7 +377,20 @@ .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); log .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + /*Set the export directory *Export directory is the first simulation export directory. */ Modified: trunk/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFast.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorRFast.java 2009-04-08 10:19:07 UTC (rev 99) @@ -80,13 +80,13 @@ } public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { - - if(param_n==0){ - param_n=17; + + if (param_n == 0) { + param_n = 17; } - - if(param_M==0){ - param_M=1; + + if (param_M == 0) { + param_M = 1; } double[] dataframe = new double[0]; @@ -106,17 +106,6 @@ String rInstruction = "a<-fast99(model=NULL,factors=c(" + factors.size(); - /* // Creating the factors vector. - for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\","; - } else { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\""; - } - }*/ - rInstruction = rInstruction + "), n=" + param_n + ",M=" + param_M; rInstruction = rInstruction @@ -133,6 +122,23 @@ engine.voidEval(rInstruction); log.info("Message sent to R" + rInstruction); + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); @@ -143,6 +149,11 @@ engine.voidEval("dput(a,file=\".fast99\")"); log.info("Message sent to R" + "dput(a,file=\".fast99\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + // Get back experiment plan Vector<REXP> dataframeVector = (Vector<REXP>) engine.eval("a$X"); @@ -201,13 +212,13 @@ public void analyzeResult(List<SimulationStorage> simulationStorages, File outputdirectory) { - - if(param_n==0){ - param_n=17; + + if (param_n == 0) { + param_n = 17; } - - if(param_M==0){ - param_M=1; + + if (param_M == 0) { + param_M = 1; } REngine engine = new RProxy(); @@ -229,9 +240,13 @@ engine.voidEval("a<-dget(\".fast99\")"); log.info("Message sent to R : " + "a<-dget(\".fast99\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + /*int scenariosNumber = sensitivityScenarios.getScenarios().size();*/ - int scenariosNumber = (Integer)engine - .eval("length(a$X[,1])"); + int scenariosNumber = (Integer) engine.eval("length(a$X[,1])"); log.info("Message sent to R : " + "length(a$X[,1])"); int sensitivityNumber = simulationStorages.get(0).getParameter() @@ -275,6 +290,7 @@ engine.voidEval("dfresults=data.frame(a$X,results)"); log.info("Message sent to R : " + "dfresults=data.frame(a$X,results)"); + //Set working directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() @@ -282,18 +298,30 @@ log.info("Message sent to R : setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + + //Set V names + engine.voidEval("names(a$V)<-factornames"); + log.info("Message sent to R : " + "names(a$V)<-factornames"); + //Export V engine.voidEval("write.csv(a$V,\"" + simulationStorages.get(0).getParameter() .getSensitivityExport().get(k) - .getExportFilename() - + "_V.csv\")"); + .getExportFilename() + "_V.csv\")"); log.info("Message sent to R : " + "write.csv(a$V,\"" + simulationStorages.get(0).getParameter() .getSensitivityExport().get(k) .getExportFilename() + "_V.csv\")"); + //Set D1 names + engine.voidEval("names(a$D1)<-factornames"); + log.info("Message sent to R : " + "names(a$D1)<-factornames"); + //Export D1 engine.voidEval("write.csv(a$D1,\"" + simulationStorages.get(0).getParameter() @@ -305,6 +333,10 @@ .getSensitivityExport().get(k) .getExportFilename() + "_D1.csv\")"); + //Set Dt names + engine.voidEval("names(a$Dt)<-factornames"); + log.info("Message sent to R : " + "names(a$Dt)<-factornames"); + //Export Dt engine.voidEval("write.csv(a$Dt,\"" + simulationStorages.get(0).getParameter() @@ -315,6 +347,15 @@ + simulationStorages.get(0).getParameter() .getSensitivityExport().get(k) .getExportFilename() + "_Dt.csv\")"); + //Set dfresults names + engine + .voidEval("resultsnames<-c(factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + log.info("Message sent to R : " + + "names(dfresults)<-resultsnames"); //Export results engine.voidEval("write.csv(dfresults,\"" Modified: trunk/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-08 10:19:07 UTC (rev 99) @@ -21,6 +21,7 @@ import java.io.File; import java.io.Serializable; import java.util.List; +import java.util.Vector; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -30,6 +31,7 @@ import org.codelutin.math.matrix.MatrixFactory; import org.codelutin.math.matrix.MatrixND; import org.codelutin.util.FileUtil; +import org.rosuda.JRI.REXP; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; @@ -52,7 +54,7 @@ * Last update : $Date: 2009-04-03 13:13:35 +0200 (ven., 03 avr. 2009) $ By : * $Author: chatellier $ */ -@Doc("FrF2 method") +@Doc("FrF2 method, at least 4 factors need to be declared") public class SensitivityCalculatorRFrF2 implements SensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ @@ -112,8 +114,39 @@ // Get back experiment plan dataframe = (double[]) engine.eval("a$desnum"); + /*Vector<REXP> dataframeVector = (Vector<REXP>) engine.eval("a$X"); + dataframe = new double[dataframeVector.size() + * dataframeVector.get(0).asDoubleArray().length]; + for (int i = 0; i < dataframeVector.size(); i++) { + for (int j = 0; j < dataframeVector.get(0).asDoubleArray().length; j++) { + dataframe[i * dataframeVector.get(0).asDoubleArray().length + + j] = dataframeVector.get(i).asDoubleArray()[j]; + } + }*/ log.info("Message sent to R : " + "a$desnum"); + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R : " + + "dput(factornames,file=\".factornames\")"); + } catch (RException e) { e.printStackTrace(); } @@ -286,6 +319,11 @@ log .info("Message sent to R : factors<-read.csv(\".FrF2.csv\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + //Get back the factors number int factorNumber = ((Double) engine.eval("length(factors)-1")) .intValue(); @@ -323,7 +361,6 @@ //get back the resolution int resolution = (Integer) engine.eval("res.catlg(a$catentry)"); log.info("Message sent to R : " + "res.catlg(a$catentry)"); - log.info(resolution); String aovCall; @@ -355,13 +392,31 @@ } } } - aovCall = aovCall.substring(0, aovCall.length()-1); + aovCall = aovCall.substring(0, aovCall.length() - 1); aovCall = aovCall + ",data=dataforaov)"; engine.voidEval(aovCall); log.info("Message sent to R : " + aovCall); break; + case 5: + aovCall = "aovresult<-aov(result~"; + for (int j = 0; j < factorNumber; j++) { + aovCall = aovCall + "factor" + j + "+"; + } + for (int i = 0; i < factorNumber; i++) { + for (int j = 0; j < factorNumber; j++) { + if (i < j) { + aovCall = aovCall + "factor" + i + "*factor" + + j + "+"; + } + } + } + aovCall = aovCall.substring(0, aovCall.length() - 1); + aovCall = aovCall + ",data=dataforaov)"; + engine.voidEval(aovCall); + log.info("Message sent to R : " + aovCall); + break; default: - log.info("pas bien"); + log.info("This resolution is not managed"); break; } @@ -398,9 +453,11 @@ .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); log .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); - - - + + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); + /*Set the export directory *Export directory is the first simulation export directory. */ @@ -409,6 +466,17 @@ log.info("Message sent to R : setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + + //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" + simulationStorages.get(0).getParameter() @@ -442,6 +510,6 @@ } public String getDescription() { - return "Implementation of FrF2 method method using R"; + return "Implementation of FrF2 method method using R, at least 4 factors need to be declared"; } } Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-08 10:19:07 UTC (rev 99) @@ -227,6 +227,22 @@ engine.voidEval(rInstruction); log.info("Message sent to R" + rInstruction); + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factorNumber; i++) { + if (i != (factorNumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); @@ -237,6 +253,11 @@ engine.voidEval("dput(a,file=\".morris\")"); log.info("Message sent to R" + "dput(a,file=\".morris\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + // Get back experiment plan dataframe = (double[]) engine.eval("a$X"); log.info("Message sent to R" + "a$X"); @@ -302,6 +323,11 @@ engine.voidEval("a<-dget(\".morris\")"); log.info("Message sent to R : " + "a<-dget(\".morris\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + /*int scenariosNumber = sensitivityScenarios.getScenarios().size();*/ int scenariosNumber = ((Double) engine .eval("length(a$X)/length(a$factors)")).intValue(); @@ -361,12 +387,24 @@ engine.voidEval("df=data.frame(mu,mu.star,sigma)"); log.info("Message sent to R : " + "df=data.frame(mu,mu.star,sigma)"); + engine.voidEval("row.names(df)<-factornames"); + log.info("Message sent to R : " + "row.names(df)<-factornames"); //Create the data.frame of scenarios and results for export purpose engine.voidEval("dfresults=data.frame(a$X,results)"); log.info("Message sent to R : " - + "df=data.frame(mu,mu.star,sigma)"); + + "dfresults=data.frame(a$X,results)"); + //Set dfresults names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dfresults)<-resultsnames"); + log.info("Message sent to R : " + + "names(dfresults)<-resultsnames"); + //Set working directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); Modified: trunk/sensitivity/SensitivityCalculatorROptimumLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-04-08 10:19:07 UTC (rev 99) @@ -77,6 +77,7 @@ throws SensitivityException { int factornumber = plan.getFactors().size(); + List<Factor<? extends Serializable>> factors = plan.getFactors(); double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); @@ -111,12 +112,10 @@ // Get back experiment plan dataframe = (double[]) engine.eval("x"); log.info("Message sent to R : " + "x"); - log.info(dataframe); // Transform the result from R in a matrix MatrixND morris = MatrixFactory.getInstance().create(dataframe, new int[] { factornumber, param_simulationNumber }); - log.info(morris); // Setting up the scenarios. for (int j = 0; j < param_simulationNumber; j++) { @@ -222,6 +221,23 @@ engine.voidEval(data); log.info("Message sent to R : " + data); + // Creating the factors vector. + rInstruction = "factornames<-c("; + for (int i = 0; i < factornumber; i++) { + if (i != (factornumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R : " + rInstruction); + // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); @@ -233,6 +249,11 @@ log.info("Message sent to R : " + "write.csv(data,file=\".optimumlhs.csv\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + engine.terminate(); } catch (Exception e) { @@ -277,6 +298,11 @@ log .info("Message sent to R : factors<-read.csv(\".optimumlhs.csv\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + //Get back the factors number int factorNumber = ((Double) engine.eval("length(factors)-1")) .intValue(); @@ -357,6 +383,9 @@ .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); log .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); /*Set the export directory *Export directory is the first simulation export directory. @@ -366,6 +395,16 @@ log.info("Message sent to R : setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" + simulationStorages.get(0).getParameter() Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-07 15:25:54 UTC (rev 98) +++ trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-08 10:19:07 UTC (rev 99) @@ -76,6 +76,7 @@ double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); + List<Factor<? extends Serializable>> factors = plan.getFactors(); if ((Integer) param_simulationNumber == 0) { param_simulationNumber = 10; @@ -206,6 +207,23 @@ engine.voidEval(data); log.info("Message sent to R : " + data); + // Creating the factors vector. + String rInstruction = "factornames<-c("; + for (int i = 0; i < factornumber; i++) { + if (i != (factornumber - 1)) { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\","; + } else { + rInstruction = rInstruction + "\"" + + factors.get(i).getName() + "\""; + } + } + + rInstruction += ")"; + + engine.voidEval(rInstruction); + log.info("Message sent to R" + rInstruction); + // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); @@ -217,6 +235,11 @@ log.info("Message sent to R : " + "write.csv(data,file=\".randomlhs.csv\")"); + // Export the factornames object for the second run in a .factornames file + engine.voidEval("dput(factornames,file=\".factornames\")"); + log.info("Message sent to R" + + "dput(factornames,file=\".factornames\")"); + engine.terminate(); } catch (Exception e) { @@ -254,6 +277,11 @@ log .info("Message sent to R : factors<-read.csv(\".randomlhs.csv\")"); + // Get the factornames object in the .factornames file + engine.voidEval("factornames<-dget(\".factornames\")"); + log.info("Message sent to R : " + + "factornames<-dget(\".factornames\")"); + //Get back the factors number int factorNumber = ((Double) engine.eval("length(factors)-1")) .intValue(); @@ -334,6 +362,9 @@ .voidEval("names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); log .info("Message sent to R : names(exportsensitivity)<-c(\"Sum Of Squares\",\"Sensitivity indices\")"); + engine.voidEval("row.names(exportsensitivity)<-factornames"); + log.info("Message sent to R : " + + "row.names(exportsensitivity)<-factornames"); /*Set the export directory *Export directory is the first simulation export directory. @@ -343,6 +374,16 @@ log.info("Message sent to R : setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); + //Set dataforaov names + engine + .voidEval("resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + log + .info("Message sent to R : " + + "resultsnames<-c(\"Simulation\",factornames,\"Result\")"); + engine.voidEval("names(dataforaov)<-resultsnames"); + log.info("Message sent to R : " + + "names(dataforaov)<-resultsnames"); + //Save the results with the scenarios. engine.voidEval("write.csv(dataforaov,\"" + simulationStorages.get(0).getParameter()

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r98 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org April 7, 2009

April 7, 2009

Author: jcouteau Date: 2009-04-07 15:25:54 +0000 (Tue, 07 Apr 2009) New Revision: 98 Removed: trunk/exports/SensitivityBiomassPopage.java trunk/exports/SensitivityCapturesPoidsPopage.java Log: Remove unused exports Deleted: trunk/exports/SensitivityBiomassPopage.java =================================================================== --- trunk/exports/SensitivityBiomassPopage.java 2009-04-07 15:09:00 UTC (rev 97) +++ trunk/exports/SensitivityBiomassPopage.java 2009-04-07 15:25:54 UTC (rev 98) @@ -1,71 +0,0 @@ -package exports; - -import static org.codelutin.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; -import org.codelutin.math.matrix.MatrixND; - -import scripts.ResultName; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.entities.Population; -import fr.ifremer.isisfish.export.SensitivityExport; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.util.Doc; - -@Doc("Doc for SensitivityBiomassPopage") -public class SensitivityBiomassPopage implements SensitivityExport { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityBiomassPopage.class); - - protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; - - @Override - public void export(SimulationStorage simulation, Writer out) - throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - double biomass = 0.0; - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals("popage")) { - MatrixND mat = simulation.getResultStorage().getMatrix(pop, - ResultName.MATRIX_BIOMASS); - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - Object[] sems = i.getSemanticsCoordinates(); - Date date = (Date) sems[0]; - - if (date.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue(); - } - } - } - } - out.write(Double.toString(biomass)); - - } - - @Override - public String getDescription() { - return _("Biomass for the last time step. Biomass is the sum on the groups and zones"); - } - - @Override - public String getExportFilename() { - return "SensitivityBiomassPopage"; - } - - @Override - public String getExtensionFilename() { - return ".csv"; - } - - @Override - public String[] getNecessaryResult() { - return this.necessaryResult; - } - -} Deleted: trunk/exports/SensitivityCapturesPoidsPopage.java =================================================================== --- trunk/exports/SensitivityCapturesPoidsPopage.java 2009-04-07 15:09:00 UTC (rev 97) +++ trunk/exports/SensitivityCapturesPoidsPopage.java 2009-04-07 15:25:54 UTC (rev 98) @@ -1,75 +0,0 @@ -package exports; - -import static org.codelutin.i18n.I18n._; - -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.codelutin.math.matrix.MatrixIterator; -import org.codelutin.math.matrix.MatrixND; - -import scripts.ResultName; -import fr.ifremer.isisfish.datastore.SimulationStorage; -import fr.ifremer.isisfish.entities.Population; -import fr.ifremer.isisfish.export.SensitivityExport; -import fr.ifremer.isisfish.types.Date; -import fr.ifremer.isisfish.util.Doc; - -@Doc("Doc for SensitivityCapturesPoidsPopage") -public class SensitivityCapturesPoidsPopage implements SensitivityExport { - - /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityCapturesPoidsPopage.class); - - protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; - - @Override - public void export(SimulationStorage simulation, Writer out) - throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); - Double capturesWeight = 0.0; - - for (Population pop : simulation.getParameter().getPopulations()) { - if (pop.getName().equals("popage")) { - for (Date date = new Date(0); !date.after(lastDate); date = date - .next()) { - MatrixND mat = simulation - .getResultStorage() - .getMatrix( - date, - pop, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); - if (mat != null) { // can be null if simulation is stopped before last year simulation - mat = mat.sumOverDim(0); //sum on strategy - for (MatrixIterator i = mat.iterator(); i.hasNext();) { - i.next(); - capturesWeight=capturesWeight+i.getValue(); - } - } - } - } - } - } - - @Override - public String getDescription() { - return _("Captures in weight for the last year for the popage population. Captures is the sum of zones, groups, metiers and strategies"); - } - - @Override - public String getExportFilename() { - return "SensitivityCapturesPoidsPopage"; - } - - @Override - public String getExtensionFilename() { - return ".csv"; - } - - @Override - public String[] getNecessaryResult() { - return this.necessaryResult; - } - -}

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