April 2009 - Isis-fish-data-commits - mailman.cloud.codelutin.com

r112 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org 17 Apr '09

17 Apr '09

Author: jcouteau Date: 2009-04-17 13:51:32 +0000 (Fri, 17 Apr 2009) New Revision: 112 Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java Log: Adapt Morris method to the new R CDC Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-17 12:27:11 UTC (rev 111) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-17 13:51:32 UTC (rev 112) @@ -19,7 +19,6 @@ package sensitivity; import java.io.File; -import java.io.Serializable; import java.util.List; import javax.swing.Box; @@ -38,13 +37,11 @@ import org.codelutin.util.FileUtil; import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; - import fr.ifremer.isisfish.simulator.sensitivity.Domain; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; -import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; -import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -62,7 +59,7 @@ * $Author$ */ @Doc("Morris method") -public class SensitivityCalculatorRMorris extends AbstractSensitivityCalculator { +public class SensitivityCalculatorRMorris extends AbstractSensitivityCalculator { @Doc("Integer giving the number of repetitions of the design, i.e. the number of elementary effect computed per factor. (Default value : 4)") public int param_r = 4; @@ -85,9 +82,9 @@ } public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { - - setIsisFactorsR(plan,outputdirectory); + setIsisFactorsR(plan, outputdirectory); + double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); @@ -129,17 +126,13 @@ factorNames += "\"" + factors.get(i).getName() + "\""; - levels += ((ContinuousDomain) domain) - .getCardinality(); + levels += ((ContinuousDomain) domain).getCardinality(); - gridJump += (Integer) (((ContinuousDomain) domain) - .getCardinality() / 2); + gridJump += (Integer) (((ContinuousDomain) domain).getCardinality() / 2); - binf += ((ContinuousDomain) domain) - .getMinBound(); + binf += ((ContinuousDomain) domain).getMinBound(); - bsup += ((ContinuousDomain) domain) - .getMaxBound(); + bsup += ((ContinuousDomain) domain).getMaxBound(); } String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s,design=list(type=\"oat\",levels=c(%s),grid.jump=c(%s)),binf=c(%s),bsup=c(%s))"; @@ -166,13 +159,21 @@ REngine engine = new RProxy(); try { + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); log.info("Message sent to R : " + "library(sensitivity)"); // Run sensitivity analysis - engine.voidEval(rInstruction); + engine.voidEval(rCall); log.info("Message sent to R : " + rCall); // Creating the factors vector. @@ -180,26 +181,26 @@ rCall = String.format(rInstruction, factorNames); engine.voidEval(rCall); - log.info("Message sent to R" + rCall); + log.info("Message sent to R : " + rCall); // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); - log.info("Message sent to R" + "setwd(\"" + log.info("Message sent to R : " + "setwd(\"" + outputdirectory.getAbsolutePath() + "\")"); // Export the morris object for the second run in a .morris file engine.voidEval("dput(a,file=\".morris\")"); - log.info("Message sent to R" + "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" + 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"); + log.info("Message sent to R : " + "a$X"); if (log.isDebugEnabled()) { log.debug("rInstruction = " + rInstruction); @@ -207,6 +208,46 @@ nbExperiments = dataframe.length / factorNumber; + log.info("Message sent to R : " + + "isis.factor.distribution<-c(0.0)"); + engine.voidEval("isis.factor.distribution<-c(0.0)"); + + log.info("Message sent to R : " + "call<-a$call"); + engine.voidEval("call<-a$call"); + + log + .info("Message sent to R : " + + "isis.MethodExp<-list(isis.factors,isis.factor.distribution,call)"); + engine + .voidEval("isis.MethodExp<-list(isis.factors,isis.factor.distribution,call)"); + + log + .info("Message sent to R : " + + "attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.MethodExp)<-list(nomModel=\"isis-fish-externe-R\")"); + + log.info("Message sent to R : " + "isis.simule<-data.frame(a$X)"); + engine.voidEval("isis.simule<-data.frame(a$X)"); + + log + .info("Message sent to R : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + log.info("Message sent to R : " + + "names(isis.simule)<-isis.factors[[1]]"); + engine.voidEval("names(isis.simule)<-isis.factors[[1]]"); + + //Set working directory to save Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + } catch (RException eee) { eee.printStackTrace(); throw new RuntimeException("R evaluation failed", eee); @@ -226,7 +267,9 @@ Factor factor = factors.get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier((Double)morris.getValue(i, j)); + factor + .setValueForIdentifier((Double) morris.getValue(i, + j)); } else { factor.setValueForIdentifier(morris.getValue(new int[] { i, j })); @@ -246,6 +289,14 @@ REngine engine = new RProxy(); try { + //Set working directory to get Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + //Get Isis R session + log.info("load(\".RData\")"); + engine.voidEval("load(\".RData\")"); + // Call R // Load sensitivity package into R (if package already loaded, // nothing happens. @@ -278,7 +329,9 @@ for (int k = 0; k < sensitivityNumber; k++) { // Creates the R expression to import results in R - String rInstruction = "results<-c("; + String name = simulationStorages.get(0).getParameter() + .getSensitivityExport().get(k).getExportFilename(); + String rInstruction = name + "<-c("; for (int l = 0; l < scenariosNumber; l++) { File importFile = new File(simulationStorages.get(l) .getDirectory().toString() @@ -306,8 +359,8 @@ engine.voidEval(rInstruction); //Compute results - engine.voidEval("tell(a,y=results)"); - log.info("Message sent to R : " + "tell(a,y=results)"); + engine.voidEval("tell(a,y=name)"); + log.info("Message sent to R : " + "tell(a,y=name)"); // Get back the sensitivity results, mu, mu star and sigma. engine.voidEval("mu<-apply(a$ee, 2, mean)"); @@ -330,9 +383,9 @@ 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$X,results)"); + engine.voidEval("dfresults=data.frame(a$X,name)"); log.info("Message sent to R : " - + "dfresults=data.frame(a$X,results)"); + + "dfresults=data.frame(a$X,name)"); //Set dfresults names engine @@ -375,7 +428,70 @@ .getExportFilename() + "_Results.csv\")"); //FIXME export through java to enable export when using Rserve + //Put results in isis.simule + engine.voidEval("isis.simule<-data.frame(isis.simule," + name + + ")"); + log.info("Message sent to R : " + + "isis.simule<-data.frame(isis.simule," + name + ")"); + } + + //adding attribute to isis.Simule + log + .info("Message sent to R : " + + "attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + engine + .voidEval("attributes(isis.simule)<-list(nomModel=\"isis-fish-externe-R\")"); + + //creating isis.methodAnalyse + log + .info("Message sent to R : " + + "isis.methodAnalyse<-list(isis.factor,isis.factor.distribution,isis.simule,call_method=\"tell(a,results)\",a)"); + engine + .voidEval("isis.methodAnalyse<-list(isis.factor,isis.factor.distribution,isis.simule,call_method=\"tell(a,results)\",a)"); + + //Rename R objects for saving purpose + + String renameIsisSimule = "%s.isis.simule<-isis.simule"; + String renameIsisMethodAnalyse = "%s.isis.methodAnalyse<-isis.methodAnalyse"; + String renameIsisFactorDistribution = "%s.isis.factor.distribution<-isis.factor.distribution"; + String renameIsisFactor = "%s.isis.factor<-isis.factor"; + String renameIsisMethodExp = "%s.isis.methodExp<-isis.methodExp"; + + String simulationName = simulationStorages.get(0).getName() + .replaceAll("-", ""); + + log.info("Message sent to R : " + + String.format(renameIsisSimule, simulationName)); + engine.voidEval(String.format(renameIsisSimule, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodAnalyse, simulationName)); + engine.voidEval(String.format(renameIsisMethodAnalyse, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactorDistribution, + simulationName)); + engine.voidEval(String.format(renameIsisFactorDistribution, + simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisFactor, simulationName)); + engine.voidEval(String.format(renameIsisFactor, simulationName)); + + log.info("Message sent to R : " + + String.format(renameIsisMethodExp, simulationName)); + engine.voidEval(String.format(renameIsisMethodExp, simulationName)); + + //Set working directory to save Isis R session + log.info("setwd(\"" + outputdirectory.getParent() + "\")"); + engine.voidEval("setwd(\"" + outputdirectory.getParent() + "\")"); + + // Save Isis R session + log.info("save.image()"); + engine.voidEval("save.image()"); + } catch (Exception e) { e.printStackTrace(); }

1 0

r111 - trunk
by chatellier＠users.labs.libre-entreprise.org 17 Apr '09

17 Apr '09

Author: chatellier Date: 2009-04-17 12:27:11 +0000 (Fri, 17 Apr 2009) New Revision: 111 Modified: trunk/pom.xml Log: Update dependency Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2009-04-17 10:03:06 UTC (rev 110) +++ trunk/pom.xml 2009-04-17 12:27:11 UTC (rev 111) @@ -54,7 +54,7 @@ <dependency> <groupId>ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>3.2.0.4-rc3-SNAPSHOT</version> + <version>3.2.0.4-rc4-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r110 - trunk
by jcouteau＠users.labs.libre-entreprise.org 17 Apr '09

17 Apr '09

Author: jcouteau Date: 2009-04-17 10:03:06 +0000 (Fri, 17 Apr 2009) New Revision: 110 Modified: trunk/pom.xml Log: Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2009-04-17 09:51:03 UTC (rev 109) +++ trunk/pom.xml 2009-04-17 10:03:06 UTC (rev 110) @@ -54,7 +54,7 @@ <dependency> <groupId>ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>3.2.0.4-rc2-SNAPSHOT</version> + <version>3.2.0.4-rc3-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r109 - trunk/sensitivity
by jcouteau＠users.labs.libre-entreprise.org 17 Apr '09

17 Apr '09

Author: jcouteau Date: 2009-04-17 09:51:03 +0000 (Fri, 17 Apr 2009) New Revision: 109 Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java trunk/sensitivity/SensitivityCalculatorRFast.java trunk/sensitivity/SensitivityCalculatorRFrF2.java trunk/sensitivity/SensitivityCalculatorRMorris.java trunk/sensitivity/SensitivityCalculatorROptimumLHS.java trunk/sensitivity/SensitivityCalculatorRRandomLHS.java trunk/sensitivity/SensitivityCalculatorRSobol.java Log: Adapt to isis-fish sensitivity refactoring Modified: trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorJavaExpandGrid.java 2009-04-17 09:51:03 UTC (rev 109) @@ -19,7 +19,6 @@ package sensitivity; import java.io.File; -import java.io.Serializable; import java.util.List; import org.apache.commons.logging.Log; @@ -32,7 +31,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; -import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; @@ -49,8 +48,8 @@ * */ @Doc("ExpandGrid") -public class SensitivityCalculatorJavaExpandGrid implements - SensitivityCalculator { +public class SensitivityCalculatorJavaExpandGrid extends + AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory @@ -71,21 +70,21 @@ int k = 1; //number of sensitivity scenarios (initialization) int factorNumber = plan.getFactors().size(); //number of factors - List<Factor<? extends Serializable>> factors = plan.getFactors(); //list of factors + List<Factor> factors = plan.getFactors(); //list of factors for (int i = 0; i < factorNumber; i++) { if (factors.get(i).getDomain() instanceof ContinuousDomain) { - if (((ContinuousDomain<? extends Serializable>) factors.get(i) + if (((ContinuousDomain) factors.get(i) .getDomain()).getCardinality() != 0) { k = k - * ((ContinuousDomain<? extends Serializable>) factors + * ((ContinuousDomain) factors .get(i).getDomain()).getCardinality(); } } else if (factors.get(i).getDomain() instanceof DiscreteDomain) { - if (((DiscreteDomain<? extends Serializable>) factors.get(i) + if (((DiscreteDomain) factors.get(i) .getDomain()).getValues().size() != 0) { k = k - * ((DiscreteDomain<? extends Serializable>) factors + * ((DiscreteDomain) factors .get(i).getDomain()).getValues().size(); } } @@ -99,13 +98,13 @@ int rest = i; //used for the euclidian division Scenario experimentScenario = new Scenario(); for (int j = 0; j < factorNumber; j++) { - Factor<? extends Serializable> factor = factors.get(j); + Factor factor = factors.get(j); if (factor.getDomain() instanceof ContinuousDomain) { - Double max = ((ContinuousDomain<Double>) factor.getDomain()) + Double max = ((ContinuousDomain) factor.getDomain()) .getMaxBound(); - Double min = ((ContinuousDomain<Double>) factor.getDomain()) + Double min = ((ContinuousDomain) factor.getDomain()) .getMinBound(); - int card = ((ContinuousDomain<? extends Serializable>) factor + int card = ((ContinuousDomain) factor .getDomain()).getCardinality(); result = (int) Math.floor(rest / card); rest = rest - (card * result); @@ -119,7 +118,7 @@ } } if (factor.getDomain() instanceof DiscreteDomain) { - int card = ((DiscreteDomain<? extends Serializable>) factor + int card = ((DiscreteDomain) factor .getDomain()).getValues().size(); result = (int) Math.floor(rest / card); rest = rest - (card * result); @@ -144,7 +143,7 @@ try { //Create the factors vectors for (int j = 0; j < factorNumber; j++) { - Factor<? extends Serializable> factor = thisExperimentScenarios + Factor factor = thisExperimentScenarios .get(0).getFactors().get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { @@ -152,12 +151,12 @@ for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } @@ -171,12 +170,12 @@ for (int i = 0; i < scenariosNumber; i++) { if (i < (scenariosNumber - 1)) { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } Modified: trunk/sensitivity/SensitivityCalculatorRFast.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFast.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorRFast.java 2009-04-17 09:51:03 UTC (rev 109) @@ -38,6 +38,8 @@ import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; + +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -55,7 +57,7 @@ * $Author: jcouteau $ */ -public class SensitivityCalculatorRFast implements SensitivityCalculator { +public class SensitivityCalculatorRFast extends AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ private static Log log = LogFactory @@ -92,7 +94,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); @@ -186,17 +188,17 @@ for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { - Factor<? extends Serializable> factor = plan.getFactors() + Factor factor = plan.getFactors() .get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { factor.setValueForIdentifier(Double.valueOf( fast.getValue(new int[] { i, j })).toString()); } else { - Double value = (Double) ((ContinuousDomain<?>) factor + Double value = (Double) ((ContinuousDomain) factor .getDomain()).getMinBound() - + ((Double) ((ContinuousDomain<?>) factor - .getDomain()).getMaxBound() - (Double) ((ContinuousDomain<?>) factor + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor .getDomain()).getMinBound()) * fast.getValue(new int[] { i, j }); factor.setValueForIdentifier(value); Modified: trunk/sensitivity/SensitivityCalculatorRFrF2.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorRFrF2.java 2009-04-17 09:51:03 UTC (rev 109) @@ -38,6 +38,8 @@ import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; + +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -55,7 +57,7 @@ * $Author: chatellier $ */ @Doc("FrF2 method, at least 4 factors need to be declared") -public class SensitivityCalculatorRFrF2 implements SensitivityCalculator { +public class SensitivityCalculatorRFrF2 extends AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ private static Log log = LogFactory @@ -79,7 +81,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); @@ -161,7 +163,7 @@ for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { - Factor<? extends Serializable> factor = plan.getFactors() + Factor factor = plan.getFactors() .get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { @@ -177,13 +179,13 @@ } else { if (frf2.getValue(new int[] { i, j }) == -1) { factor - .setValueForIdentifier(((ContinuousDomain<?>) factor + .setValueForIdentifier(((ContinuousDomain) factor .getDomain()).getMinBound()); } if (frf2.getValue(new int[] { i, j }) == 1) { factor - .setValueForIdentifier(((ContinuousDomain<?>) factor + .setValueForIdentifier(((ContinuousDomain) factor .getDomain()).getMaxBound()); } } @@ -195,7 +197,7 @@ try { //Create the factors vectors for (int j = 0; j < factorNumber; j++) { - Factor<? extends Serializable> factor = thisExperimentScenarios + Factor factor = thisExperimentScenarios .get(0).getFactors().get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { @@ -203,12 +205,12 @@ for (int i = 0; i < nbExperiments; i++) { if (i < (nbExperiments - 1)) { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } @@ -222,12 +224,12 @@ for (int i = 0; i < nbExperiments; i++) { if (i < (nbExperiments - 1)) { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } Modified: trunk/sensitivity/SensitivityCalculatorRMorris.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorRMorris.java 2009-04-17 09:51:03 UTC (rev 109) @@ -22,6 +22,12 @@ import java.io.Serializable; import java.util.List; +import javax.swing.Box; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JScrollPane; +import javax.swing.JTextPane; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.codelutin.j2r.REngine; @@ -33,10 +39,12 @@ import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.sensitivity.DesignPlan; + import fr.ifremer.isisfish.simulator.sensitivity.Domain; import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -54,11 +62,14 @@ * $Author$ */ @Doc("Morris method") -public class SensitivityCalculatorRMorris implements SensitivityCalculator { +public class SensitivityCalculatorRMorris extends AbstractSensitivityCalculator { @Doc("Integer giving the number of repetitions of the design, i.e. the number of elementary effect computed per factor. (Default value : 4)") - public int param_r; + public int param_r = 4; + @Doc("True to be able to modify the code sent to R") + public boolean param_modifR = false; + /** to use log facility, just put in your code: log.info("..."); */ private static Log log = LogFactory .getLog(SensitivityCalculatorRMorris.class); @@ -74,174 +85,102 @@ } public SensitivityScenarios compute(DesignPlan plan, File outputdirectory) { + + setIsisFactorsR(plan,outputdirectory); double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); - if (((Integer) param_r == null) || ((Integer) param_r == 0)) { + if (param_r == 0) { param_r = 4; } //Test all factors, if one is discrete, return null for (int i = 0; i < factorNumber; i++) { if (factors.get(i).getDomain() instanceof DiscreteDomain) { + JOptionPane + .showMessageDialog( + null, + "Error", + factors.get(i).getName() + + " has a discrete domain, this is not acceptable for this method.", + JOptionPane.ERROR_MESSAGE); return null; } } - String rInstruction = "a<-morris(model=NULL,factors=c("; - - // Creating the factors vector. + // Creating the vectors. + String factorNames = ""; + String levels = ""; + String gridJump = ""; + String binf = ""; + String bsup = ""; for (int i = 0; i < factorNumber; i++) { - if (i != (factorNumber - 1)) { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\","; - } else { - rInstruction = rInstruction + "\"" + factors.get(i).getName() - + "\""; + Domain domain = factors.get(i).getDomain(); + if (i != 0) { + factorNames += ","; + levels += ","; + gridJump += ","; + binf += ","; + bsup += ","; } - } - // Adding the number of repetition parameter (r), the morris type - // (type="oat") and the level vector - rInstruction = rInstruction + "),r=" + param_r - + ",design=list(type=\"oat\",levels=c("; + factorNames += "\"" + factors.get(i).getName() + "\""; - // Creating the levels vector. - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((DiscreteDomain<? extends Serializable>) domain) - .getValues().size() + ","; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getCardinality() + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((DiscreteDomain<? extends Serializable>) domain) - .getValues().size(); - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getCardinality(); - } - } - } + levels += ((ContinuousDomain) domain) + .getCardinality(); - // Adding the grid.jump parameter - rInstruction = rInstruction + "),grid.jump=c("; + gridJump += (Integer) (((ContinuousDomain) domain) + .getCardinality() / 2); - // Creating the grid.jump vector. - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + (Integer) (((DiscreteDomain<? extends Serializable>) domain) - .getValues().size() / 2) + ","; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + (Integer) (((ContinuousDomain<? extends Serializable>) domain) - .getCardinality() / 2) + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + (Integer) (((DiscreteDomain<? extends Serializable>) domain) - .getValues().size() / 2); - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + (Integer) (((ContinuousDomain<? extends Serializable>) domain) - .getCardinality() / 2); - } - } + binf += ((ContinuousDomain) domain) + .getMinBound(); + + bsup += ((ContinuousDomain) domain) + .getMaxBound(); } - rInstruction += ")),binf=c("; + String rInstruction = "a<-morris(model=NULL,factors=c(%s),r=%s,design=list(type=\"oat\",levels=c(%s),grid.jump=c(%s)),binf=c(%s),bsup=c(%s))"; - // Adding the binf parameter - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction + "0,"; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMinBound() + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction + "0"; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMinBound(); - } - } - } + String rCall = String.format(rInstruction, factorNames, param_r, + levels, gridJump, binf, bsup); - // Adding the bsup parameter - rInstruction = rInstruction + "),bsup=c("; - for (int i = 0; i < factorNumber; i++) { - Domain<? extends Serializable> domain = factors.get(i).getDomain(); - if (i != (factorNumber - 1)) { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((((DiscreteDomain<? extends Serializable>) domain) - .getValues().size()) - 1) + ","; - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMaxBound() + ","; - } - } else { - if (domain instanceof DiscreteDomain) { - rInstruction = rInstruction - + ((((DiscreteDomain<? extends Serializable>) domain) - .getValues().size()) - 1); - } else if (domain instanceof ContinuousDomain) { - rInstruction = rInstruction - + ((ContinuousDomain<? extends Serializable>) domain) - .getMaxBound(); - } - } + if (param_modifR) { + JLabel label = new JLabel( + "Modifier le code R envoyé si vous le souhaitez"); + JTextPane text = new JTextPane(); + text.setText(rCall); + text.setSize(400, 400); + text.setPreferredSize(text.getSize()); + + Box box = Box.createVerticalBox(); + box.add(label); + box.add(new JScrollPane(text)); + + JOptionPane.showMessageDialog(null, box, "R modif", + JOptionPane.QUESTION_MESSAGE); + rCall = text.getText(); } - rInstruction = rInstruction + "))"; REngine engine = new RProxy(); try { // Load sensitivity package into R (if package already loaded, // nothing happens. engine.voidEval("library(sensitivity)"); - log.info("Message sent to R" + "library(sensitivity)"); + log.info("Message sent to R : " + "library(sensitivity)"); // Run sensitivity analysis engine.voidEval(rInstruction); - log.info("Message sent to R" + rInstruction); + log.info("Message sent to R : " + rCall); // 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 = "factornames<-c(%s)"; + rCall = String.format(rInstruction, factorNames); - rInstruction += ")"; - engine.voidEval(rInstruction); - log.info("Message sent to R" + rInstruction); + engine.voidEval(rCall); + log.info("Message sent to R" + rCall); // Set output directory engine.voidEval("setwd(\"" + outputdirectory.getAbsolutePath() @@ -268,8 +207,9 @@ nbExperiments = dataframe.length / factorNumber; - } catch (RException e) { - e.printStackTrace(); + } catch (RException eee) { + eee.printStackTrace(); + throw new RuntimeException("R evaluation failed", eee); // Error while retrieving scenario } @@ -283,11 +223,10 @@ for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { - Factor<? extends Serializable> factor = factors.get(i); + Factor factor = factors.get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { - factor.setValueForIdentifier(Double.valueOf( - morris.getValue(new int[] { i, j })).toString()); + factor.setValueForIdentifier((Double)morris.getValue(i, j)); } else { factor.setValueForIdentifier(morris.getValue(new int[] { i, j })); Modified: trunk/sensitivity/SensitivityCalculatorROptimumLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorROptimumLHS.java 2009-04-17 09:51:03 UTC (rev 109) @@ -35,6 +35,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; @@ -42,7 +43,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain; import fr.ifremer.isisfish.util.Doc; -/** +/**save.image() * Implementation of Optimum Latin Hypercube method using R. * * @author jcouteau @@ -50,7 +51,7 @@ * */ @Doc("Optimum Latin Hypercube") -public class SensitivityCalculatorROptimumLHS implements SensitivityCalculator { +public class SensitivityCalculatorROptimumLHS extends AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory @@ -77,7 +78,7 @@ throws SensitivityException { int factornumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); @@ -121,7 +122,7 @@ for (int j = 0; j < param_simulationNumber; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factornumber; i++) { - Factor<? extends Serializable> factor = plan.getFactors() + Factor factor = plan.getFactors() .get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { @@ -130,10 +131,10 @@ morris.getValue(new int[] { i, j })) .toString()); } else { - Double value = (Double) ((ContinuousDomain<?>) factor + Double value = (Double) ((ContinuousDomain) factor .getDomain()).getMinBound() - + ((Double) ((ContinuousDomain<?>) factor - .getDomain()).getMaxBound() - (Double) ((ContinuousDomain<?>) factor + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor .getDomain()).getMinBound()) * morris.getValue(new int[] { i, j }); factor.setValueForIdentifier(value); @@ -146,7 +147,7 @@ //Create the factors vectors for (int j = 0; j < factornumber; j++) { - Factor<? extends Serializable> factor = thisExperimentScenarios + Factor factor = thisExperimentScenarios .get(0).getFactors().get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { @@ -154,12 +155,12 @@ for (int i = 0; i < param_simulationNumber; i++) { if (i < (param_simulationNumber - 1)) { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } @@ -173,12 +174,12 @@ for (int i = 0; i < param_simulationNumber; i++) { if (i < (param_simulationNumber - 1)) { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } Modified: trunk/sensitivity/SensitivityCalculatorRRandomLHS.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorRRandomLHS.java 2009-04-17 09:51:03 UTC (rev 109) @@ -35,6 +35,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityException; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; @@ -50,7 +51,7 @@ * */ @Doc("Random Latin Hypercube") -public class SensitivityCalculatorRRandomLHS implements SensitivityCalculator { +public class SensitivityCalculatorRRandomLHS extends AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory @@ -76,7 +77,7 @@ double[] dataframe = new double[0]; SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); if ((Integer) param_simulationNumber == 0) { param_simulationNumber = 10; @@ -107,7 +108,7 @@ for (int j = 0; j < param_simulationNumber; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factornumber; i++) { - Factor<? extends Serializable> factor = plan.getFactors() + Factor factor = plan.getFactors() .get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { @@ -116,10 +117,10 @@ morris.getValue(new int[] { i, j })) .toString()); } else { - Double value = (Double) ((ContinuousDomain<?>) factor + Double value = (Double) ((ContinuousDomain) factor .getDomain()).getMinBound() - + ((Double) ((ContinuousDomain<?>) factor - .getDomain()).getMaxBound() - (Double) ((ContinuousDomain<?>) factor + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor .getDomain()).getMinBound()) * morris.getValue(new int[] { i, j }); factor.setValueForIdentifier(value); @@ -132,7 +133,7 @@ //Create the factors vectors for (int j = 0; j < factornumber; j++) { - Factor<? extends Serializable> factor = thisExperimentScenarios + Factor factor = thisExperimentScenarios .get(0).getFactors().get(j); if (factor.getDomain() instanceof EquationContinuousDomain) { @@ -140,12 +141,12 @@ for (int i = 0; i < param_simulationNumber; i++) { if (i < (param_simulationNumber - 1)) { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((EquationContinuousDomain<?>) thisExperimentScenarios + + ((EquationContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } @@ -159,12 +160,12 @@ for (int i = 0; i < param_simulationNumber; i++) { if (i < (param_simulationNumber - 1)) { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue() + ","; } else { vector = vector - + ((MatrixContinuousDomain<?>) thisExperimentScenarios + + ((MatrixContinuousDomain) thisExperimentScenarios .get(i).getFactors().get(j) .getDomain()).getValue(); } Modified: trunk/sensitivity/SensitivityCalculatorRSobol.java =================================================================== --- trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-04-16 13:25:07 UTC (rev 108) +++ trunk/sensitivity/SensitivityCalculatorRSobol.java 2009-04-17 09:51:03 UTC (rev 109) @@ -37,6 +37,7 @@ import fr.ifremer.isisfish.simulator.sensitivity.Factor; import fr.ifremer.isisfish.simulator.sensitivity.Scenario; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityCalculator; +import fr.ifremer.isisfish.simulator.sensitivity.AbstractSensitivityCalculator; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityScenarios; import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain; import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain; @@ -54,7 +55,7 @@ * $Author: jcouteau $ */ -public class SensitivityCalculatorRSobol implements SensitivityCalculator { +public class SensitivityCalculatorRSobol extends AbstractSensitivityCalculator { /** to use log facility, just put in your code: log.info("..."); */ private static Log log = LogFactory @@ -84,7 +85,7 @@ double[] dataframe = new double[0]; int nbExperiments = 0; int factorNumber = plan.getFactors().size(); - List<Factor<? extends Serializable>> factors = plan.getFactors(); + List<Factor> factors = plan.getFactors(); SensitivityScenarios thisExperiment = new SensitivityScenarios(); List<Scenario> thisExperimentScenarios = thisExperiment.getScenarios(); @@ -188,17 +189,17 @@ for (int j = 0; j < nbExperiments; j++) { Scenario experimentScenario = new Scenario(); for (int i = 0; i < factorNumber; i++) { - Factor<? extends Serializable> factor = plan.getFactors() + Factor factor = plan.getFactors() .get(i); if ((factor.getDomain() instanceof MatrixContinuousDomain) || (factor.getDomain() instanceof EquationContinuousDomain)) { factor.setValueForIdentifier(Double.valueOf( fast.getValue(new int[] { i, j })).toString()); } else { - Double value = (Double) ((ContinuousDomain<?>) factor + Double value = (Double) ((ContinuousDomain) factor .getDomain()).getMinBound() - + ((Double) ((ContinuousDomain<?>) factor - .getDomain()).getMaxBound() - (Double) ((ContinuousDomain<?>) factor + + ((Double) ((ContinuousDomain) factor + .getDomain()).getMaxBound() - (Double) ((ContinuousDomain) factor .getDomain()).getMinBound()) * fast.getValue(new int[] { i, j }); factor.setValueForIdentifier(value); @@ -360,7 +361,7 @@ } public String getDescription() { - return "Implementation of FAST method using R"; + return "Implementation of Sobol method using R"; } }

1 0

r108 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org 16 Apr '09

16 Apr '09

Author: jcouteau Date: 2009-04-16 13:25:07 +0000 (Thu, 16 Apr 2009) New Revision: 108 Added: trunk/exports/SensitivityBiomassRelativeReferenceY12.java trunk/exports/SensitivityCapturesWeightReferenceY7.java trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java trunk/exports/SensitivityGenitorBiomassReferenceY8.java trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java Modified: trunk/exports/SensitivityBiomassReferenceY9.java trunk/exports/SensitivityBiomassRelativeY6.java trunk/exports/SensitivityGenitorBiomassRelativeY5.java Log: Implementation of reference exports. Modified: trunk/exports/SensitivityBiomassReferenceY9.java =================================================================== --- trunk/exports/SensitivityBiomassReferenceY9.java 2009-04-16 12:00:03 UTC (rev 107) +++ trunk/exports/SensitivityBiomassReferenceY9.java 2009-04-16 13:25:07 UTC (rev 108) @@ -2,12 +2,10 @@ 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; @@ -22,39 +20,47 @@ public class SensitivityBiomassReferenceY9 implements SensitivityExport { /** to use log facility, just put in your code: log.info("..."); */ - static private Log log = LogFactory.getLog(SensitivityBiomassReferenceY9.class); + 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; + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + @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; + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double biomass = 0.0; + Double referenceBiomass = 0.0; + 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.afterOrEquals(lastDate)) { - biomass = biomass + i.getValue(); - } - } + //Get the reference biomass of the last time step + MatrixND matreferencelastdate = referenceResultStorage + .getMatrix(lastDate, pop, ResultName.MATRIX_BIOMASS); + referenceBiomass = matreferencelastdate.sumAll(); + } } - out.write(Double.toString(biomass)); + out.write(Double.toString(biomass / referenceBiomass)); + } @Override @@ -64,7 +70,7 @@ @Override public String getExportFilename() { - return "SensitivityBiomass"; + return "SensitivityBiomassReferenceY9"; } @Override Added: trunk/exports/SensitivityBiomassRelativeReferenceY12.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeReferenceY12.java (rev 0) +++ trunk/exports/SensitivityBiomassRelativeReferenceY12.java 2009-04-16 13:25:07 UTC (rev 108) @@ -0,0 +1,101 @@ +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.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 SensitivityBiomassRelativeReferenceY12 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityBiomassRelativeReferenceY12.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation=""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage resultStorage = simulation.getResultStorage(); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + double biomassReference = 0.0; + double firstbiomassReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass on december of the first year + MatrixND matfirstdate = resultStorage.getMatrix(firstDate, pop, + ResultName.MATRIX_BIOMASS); + firstbiomass = matfirstdate.sumAll(); + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(lastDate, pop, + ResultName.MATRIX_BIOMASS); + biomass = matlastdate.sumAll(); + + //Get the biomass on december of the first year + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix(firstDate, pop, ResultName.MATRIX_BIOMASS); + firstbiomassReference = matfirstdatereference.sumAll(); + + //Get the biomass of the last time step + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(lastDate, pop, ResultName.MATRIX_BIOMASS); + biomassReference = matlastdatereference.sumAll(); + + } + } + + out.write(Double.toString((biomass / firstbiomass) + / (biomassReference / firstbiomassReference))); + + } + + @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 "SensitivityBiomassRelativeReferenceY12"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Modified: trunk/exports/SensitivityBiomassRelativeY6.java =================================================================== --- trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-16 12:00:03 UTC (rev 107) +++ trunk/exports/SensitivityBiomassRelativeY6.java 2009-04-16 13:25:07 UTC (rev 108) @@ -31,14 +31,14 @@ @Override public void export(SimulationStorage simulation, Writer out) throws Exception { - Date lastDate = simulation.getResultStorage().getLastDate(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.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())) { - ResultStorage resultStorage = simulation.getResultStorage(); + if (pop.getName().equals(param_pop.getName())) { //Get the biomass on december of the first year MatrixND matfirstdate = resultStorage.getMatrix(firstDate, pop, Added: trunk/exports/SensitivityCapturesWeightReferenceY7.java =================================================================== --- trunk/exports/SensitivityCapturesWeightReferenceY7.java (rev 0) +++ trunk/exports/SensitivityCapturesWeightReferenceY7.java 2009-04-16 13:25:07 UTC (rev 108) @@ -0,0 +1,94 @@ +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.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 SensitivityCapturesPoids") +public class SensitivityCapturesWeightReferenceY7 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightReferenceY7.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation=""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + + //Get the reference captures Weight of each month of the last year + MatrixND matlastdatereference = referenceResultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightReference += matlastdatereference.sumAll(); + + } + + } + } + + out.write(Double.toString(capturesWeight / capturesWeightReference)); + } + + @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 "SensitivityCapturesWeightReferenceY7"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Added: trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java =================================================================== --- trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java (rev 0) +++ trunk/exports/SensitivityCapturesWeightRelativeReferenceY10.java 2009-04-16 13:25:07 UTC (rev 108) @@ -0,0 +1,112 @@ +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.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 SensitivityCapturesPoids") +public class SensitivityCapturesWeightRelativeReferenceY10 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityCapturesWeightRelativeReferenceY10.class); + + protected String[] necessaryResult = { ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double capturesWeight = 0.0; + Double capturesWeightfirst = 0.0; + Double capturesWeightreference = 0.0; + Double capturesWeightfirstreference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the captures Weight of each month of the last year + MatrixND matlastdate = resultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeight += matlastdate.sumAll(); + + //Get the captures Weight of each month of the first year + MatrixND matfirstdate = resultStorage + .getMatrix( + new Date(i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightfirst += matfirstdate.sumAll(); + + //Get the reference captures Weight of each month of the last year + MatrixND matlastdatereference = referenceResultStorage + .getMatrix( + new Date(lastDate.getDate() - i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightreference += matlastdatereference.sumAll(); + + //Get the reference captures Weight of each month of the first year + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix( + new Date(i), + pop, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); + capturesWeightfirstreference += matfirstdatereference + .sumAll(); + } + } + } + out.write(Double.toString((capturesWeight / capturesWeightfirst) + / (capturesWeightreference / capturesWeightfirstreference))); + } + + @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 "SensitivityCapturesWeightRelativeReferenceY10"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Added: trunk/exports/SensitivityGenitorBiomassReferenceY8.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassReferenceY8.java (rev 0) +++ trunk/exports/SensitivityGenitorBiomassReferenceY8.java 2009-04-16 13:25:07 UTC (rev 108) @@ -0,0 +1,103 @@ +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.ResultStorage; +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 SensitivityGenitorBiomassReferenceY8 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassReferenceY8.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + ResultStorage resultStorage = simulation.getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Double biomass = 0.0; + Double referenceBiomass = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + 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(lastDate)) { + biomass += i.getValue() * group.getReproductionRate(); + } + } + + //Get the reference biomass of the last time step + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(pop, ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + referenceBiomass += i.getValue() + * group.getReproductionRate(); + } + } + } + } + out.write(Double.toString(biomass / referenceBiomass)); + } + + @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 "SensitivityGenitorBiomassReferenceY8"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Added: trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java (rev 0) +++ trunk/exports/SensitivityGenitorBiomassRelativeReferenceY11.java 2009-04-16 13:25:07 UTC (rev 108) @@ -0,0 +1,138 @@ +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.ResultStorage; +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 SensitivityGenitorBiomassRelativeReferenceY11 implements + SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory + .getLog(SensitivityGenitorBiomassRelativeReferenceY11.class); + + protected String[] necessaryResult = { ResultName.MATRIX_BIOMASS }; + + @Doc("Population") + public Population param_pop; + + @Doc("Name of the reference simulation") + public String param_referenceSimulation = ""; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + SimulationStorage referenceSimulation = SimulationStorage + .getSimulation(param_referenceSimulation); + ResultStorage resultStorage = simulation.getResultStorage(); + ResultStorage referenceResultStorage = referenceSimulation + .getResultStorage(); + Date lastDate = resultStorage.getLastDate(); + Date firstDate = new Date(11); + double biomass = 0.0; + double firstbiomass = 0.0; + double biomassReference = 0.0; + double firstbiomassReference = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the biomass of the first time step + MatrixND matfirstdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomass += i.getValue() + * group.getReproductionRate(); + } + } + + //Get the biomass of the last time step + MatrixND matlastdate = resultStorage.getMatrix(pop, + ResultName.MATRIX_BIOMASS); + 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(lastDate)) { + biomass = biomass + i.getValue() + * group.getReproductionRate(); + } + } + + //Get the reference biomass of the first time step + MatrixND matfirstdatereference = referenceResultStorage + .getMatrix(pop, ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matfirstdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(firstDate)) { + firstbiomassReference += i.getValue() + * group.getReproductionRate(); + } + } + + //Get the reference biomass of the last time step + MatrixND matlastdatereference = referenceResultStorage + .getMatrix(pop, ResultName.MATRIX_BIOMASS); + for (MatrixIterator i = matlastdatereference.iterator(); i + .hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup) sems[1]; + Date date = (Date) sems[0]; + if (date.equals(lastDate)) { + biomassReference += i.getValue() + * group.getReproductionRate(); + } + } + } + } + out.write(Double.toString((biomass / firstbiomass) + / (biomassReference / firstbiomassReference))); + } + + @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 "SensitivityGenitorBiomassRelativeReferenceY11"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} \ No newline at end of file Modified: trunk/exports/SensitivityGenitorBiomassRelativeY5.java =================================================================== --- trunk/exports/SensitivityGenitorBiomassRelativeY5.java 2009-04-16 12:00:03 UTC (rev 107) +++ trunk/exports/SensitivityGenitorBiomassRelativeY5.java 2009-04-16 13:25:07 UTC (rev 108) @@ -42,7 +42,7 @@ if (pop.getName().equals(param_pop.getName())) { ResultStorage resultStorage = simulation.getResultStorage(); - //Get the biomass of the last time step + //Get the biomass of the first time step MatrixND matfirstdate = resultStorage.getMatrix(pop, ResultName.MATRIX_BIOMASS); for (MatrixIterator i = matfirstdate.iterator(); i.hasNext();) {

1 0

r107 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org 16 Apr '09

16 Apr '09

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 14 Apr '09

14 Apr '09

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 14 Apr '09

14 Apr '09

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 13 Apr '09

13 Apr '09

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

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r103 - trunk/exports
by jcouteau＠users.labs.libre-entreprise.org 13 Apr '09

13 Apr '09

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 };

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