October 2015 - Isis-fish-data-commits - mailman.cloud.codelutin.com

r379 - trunk/scripts
by echatellier＠users.forge.codelutin.com Oct. 28, 2015

Oct. 28, 2015

Author: echatellier Date: 2015-10-28 14:58:16 +0100 (Wed, 28 Oct 2015) New Revision: 379 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/379 Log: Remove pop dimension in F result Modified: trunk/scripts/SiMatrix.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-10-27 16:36:34 UTC (rev 378) +++ trunk/scripts/SiMatrix.java 2015-10-28 13:58:16 UTC (rev 379) @@ -1158,13 +1158,12 @@ double Mgroup = 0; double NgroupRef = 0; - List<Population> populations = Collections.singletonList(pop); List<PopulationGroup> groups = pop.getPopulationGroup(); MatrixND tfgMatrix = MatrixFactory.getInstance().create( MatrixFishingMortalityPerGroup.NAME, - new List[]{populations, groups}, // On travaille sur les pops ET les groupes - new String[]{n("Population"), n("Group")}); + new List[]{groups}, // On travaille sur les groupes + new String[]{n("Group")}); for (PopulationGroup group : groups) { @@ -1195,12 +1194,8 @@ catchPerStrategy = catchPerStrategy.sumOverDim(0); // Strategy catchPerStrategy = catchPerStrategy.sumOverDim(1); // Metier catchPerStrategy = catchPerStrategy.sumOverDim(3); // Zone : une pop peut avoir plusieurs zonespop dans ISIS - List semgroup = catchPerStrategy.getSemantic(2); - catchPerStrategy = catchPerStrategy.reduce(); // Enleve les dimensions de taille 1 - catchPerStrategy.setSemantic(0, semgroup); // Ne plait pas a Eric + catchPerStrategy = catchPerStrategy.reduceDims(0, 1, 3); // Enleve les dimensions de taille 1 Cgroup = catchPerStrategy.getValue(group); - //log.info("Cgroup = " + Cgroup + "Year=" + step.getYear()); - //log.info("catchPerStrategy = " + catchPerStrategy + "Year=" + step.getYear()); // compute total mortality by suming naturalDeathRate and fishingMortalityOtherFleetsMatrix MatrixND naturalDeathRatePop = pop.getNaturalDeathRateMatrix(); @@ -1217,7 +1212,8 @@ abundanceReferenceMonth = Month.JANUARY; } TimeStep refStep = new TimeStep(12 * step.getYear() + abundanceReferenceMonth.getMonthNumber()); - MatrixND abundancePopRef = resManager.getMatrix(refStep, pop, MatrixAbundanceBeginMonth.NAME); // Le timestep 0 correspond a janvier de la premiere annee et les annees sont numerotees a partir de zero + // Le timestep 0 correspond a janvier de la premiere annee et les annees sont numerotees a partir de zero + MatrixND abundancePopRef = resManager.getMatrix(refStep, pop, MatrixAbundanceBeginMonth.NAME); abundancePopRef = abundancePopRef.sumOverDim(1); // somme sur Zone abundancePopRef = abundancePopRef.reduce(); NgroupRef = abundancePopRef.getValue(group); @@ -1224,22 +1220,16 @@ //log.info("NgroupRef = " + NgroupJan + "Year=" + step.getYear()); ObjectiveFunction f = new ObjectiveFunctionBaranov(Cgroup, Mgroup, NgroupRef); - Fgroup = MinimisationUtil.fmin(0.0,2.0,1.0e-10, f); // step ?? + Fgroup = MinimisationUtil.fmin(0.0, 2.0, 1.0e-10, f); // step ?? - //log.info("Fgroup = " + Fgroup); + tfgMatrix.setValue(group, Fgroup); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? - tfgMatrix.setValue(pop, group, Fgroup); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? - } else { //Fgroup = 0; // Ce n'est plus une valeur unique mais une matrice, est-ce que cette notation peut fonctionner ? - tfgMatrix.setValue(pop, group, 0); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? + tfgMatrix.setValue(group, 0); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? } } - //log.info("tfgMatrix = " + tfgMatrix); - //log.info("tfg.DimensionNames = " + Arrays.toString(tfgMatrix.getDimensionNames())); - //log.info("tfg.Semantics = " + Arrays.toString(tfgMatrix.getSemantics())); - return tfgMatrix; } @@ -1251,23 +1241,19 @@ public MatrixND totalFishingMortality(TimeStep step, Population pop, MatrixND fishingMortalityPerGroup) throws TopiaException { MatrixND tfmMatrix = fishingMortalityPerGroup.copy(); tfmMatrix.setName(MatrixTotalFishingMortality.NAME); - //log.info("tfmMatrix = " + tfmMatrix); List<PopulationGroup> groups = pop.getPopulationGroup(); int groupMin = pop.getFbarGroupMin(); int groupMax = pop.getFbarGroupMax(); - int Nbre = (int)groupMax - (int)groupMin + 1; - //log.info("Nbre = " + Nbre); + int groupCount = (int)groupMax - (int)groupMin + 1; for (PopulationGroup group : groups) { if (group.getId() == groupMin) { // MatrixND getSubMatrix(int dim, Object, int nb) - tfmMatrix = tfmMatrix.getSubMatrix(1, group, Nbre); - tfmMatrix = tfmMatrix.meanOverDim(1); + tfmMatrix = tfmMatrix.getSubMatrix(0, group, groupCount); + tfmMatrix = tfmMatrix.meanOverDim(0); tfmMatrix = tfmMatrix.reduce(); - //log.info("tfm.DimensionNames = " + Arrays.toString(tfmMatrix.getDimensionNames())); - //log.info("tfm.Semantics = " + Arrays.toString(tfmMatrix.getSemantics())); } }

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r378 - trunk/scripts
by echatellier＠users.forge.codelutin.com Oct. 27, 2015

Oct. 27, 2015

Author: echatellier Date: 2015-10-27 17:36:34 +0100 (Tue, 27 Oct 2015) New Revision: 378 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/378 Log: refs #7666: Ajouter l'?\195?\169quation de mortalit?\195?\169 par p?\195?\170che Other Modified: trunk/scripts/SiMatrix.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-10-22 11:45:06 UTC (rev 377) +++ trunk/scripts/SiMatrix.java 2015-10-27 16:36:34 UTC (rev 378) @@ -1184,10 +1184,10 @@ catchPerStrategyTemp = resManager.getMatrix(loopstep, pop, MatrixCatchPerStrategyMetPerZonePop.NAME); } if (catchPerStrategy == null) { - catchPerStrategy = catchPerStrategyTemp.copy(); - // On clone la matrice car si on fait les operations sur celle contenue dans le cache on la modifie et donc on recupere des resultats faux. + catchPerStrategy = catchPerStrategyTemp.copy(); + // On clone la matrice car si on fait les operations sur celle contenue dans le cache on la modifie et donc on recupere des resultats faux. } else { - catchPerStrategy = catchPerStrategy.add(catchPerStrategyTemp); // Pour avoir la somme des captures sur les 12 mois + catchPerStrategy = catchPerStrategy.add(catchPerStrategyTemp); // Pour avoir la somme des captures sur les 12 mois } } @@ -1202,10 +1202,14 @@ //log.info("Cgroup = " + Cgroup + "Year=" + step.getYear()); //log.info("catchPerStrategy = " + catchPerStrategy + "Year=" + step.getYear()); + // compute total mortality by suming naturalDeathRate and fishingMortalityOtherFleetsMatrix MatrixND naturalDeathRatePop = pop.getNaturalDeathRateMatrix(); naturalDeathRatePop = naturalDeathRatePop.meanOverDim(1); // moyenne sur Zone naturalDeathRatePop = naturalDeathRatePop.reduce(); // Enleve les dimensions de taille 1 - Mgroup = naturalDeathRatePop.getValue(group); + MatrixND fishingMortalityOther = pop.getFishingMortalityOtherFleetsMatrix(); + fishingMortalityOther = fishingMortalityOther.meanOverDim(1); // moyenne sur Zone + fishingMortalityOther = fishingMortalityOther.reduce(); // Enleve les dimensions de taille 1 + Mgroup = naturalDeathRatePop.getValue(group) + fishingMortalityOther.getValue(group); //log.info("Mgroup= " + Mgroup + "Year=" + step.getYear()); Month abundanceReferenceMonth = pop.getAbundanceReferenceMonth();

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r377 - in trunk: . scripts
by echatellier＠users.forge.codelutin.com Oct. 22, 2015

Oct. 22, 2015

Author: echatellier Date: 2015-10-22 13:45:06 +0200 (Thu, 22 Oct 2015) New Revision: 377 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/377 Log: fixes #7666: Ajouter l'?\195?\169quation de mortalit?\195?\169 par p?\195?\170che Other Modified: trunk/pom.xml trunk/scripts/SiMatrix.java trunk/scripts/SiMatrixEffortByCell.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-10-15 08:50:55 UTC (rev 376) +++ trunk/pom.xml 2015-10-22 11:45:06 UTC (rev 377) @@ -36,7 +36,7 @@ <plugins> <plugin> <artifactId>maven-compiler-plugin</artifactId> - <version>3.2</version> + <version>3.3</version> <configuration> <source>1.7</source> <target>1.7</target> @@ -49,7 +49,7 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.3.2</version> + <version>1.4.0</version> <executions> <execution> <goals> Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-10-15 08:50:55 UTC (rev 376) +++ trunk/scripts/SiMatrix.java 2015-10-22 11:45:06 UTC (rev 377) @@ -236,6 +236,21 @@ return result; } + /** + * Since 4.4, FishingMortalityOtherFleets must be added everewhere NaturalDeathRate was + * used. + * + * @param step current step + * @param group group + * @param zone zone + * @return + */ + public double getTotalDeathRate(TimeStep step, PopulationGroup group, Zone zone) { + double n = group.getNaturalDeathRate(zone); + double o = group.getFishingMortalityOtherFleets(zone); + return n + o; + } + /////////////////////////////////////////////////////////////////////////// // // Toutes les methodes suivantes ne sont utiles que pour @@ -442,7 +457,7 @@ */ private double totalCatchRate(TimeStep step, PopulationGroup group, Zone zone, double totalFishingMortality) throws TopiaException { - double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; + double M = getTotalDeathRate(step, group, zone) / Month.NUMBER_OF_MONTH; if (M == 0) { // normalement il devrait y avoir de la mortalite naturelle if (log.isWarnEnabled()) { @@ -935,7 +950,7 @@ PopulationGroup group = groups.get(g); for (int z = 0; z < zones.size(); z++) { Zone zone = zones.get(z); - double M = group.getNaturalDeathRate(zone) + double M = getTotalDeathRate(step, group, zone) / (double) Month.NUMBER_OF_MONTH; double value = (double) Math.exp(-M); @@ -962,7 +977,7 @@ IsisFishException { double F = totalFishingMortality(step, matrixFishingMortality) .getValue(group, zone); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule - double M = group.getNaturalDeathRate(zone) + double M = getTotalDeathRate(step, group, zone) / (double) Month.NUMBER_OF_MONTH; double result = Math.exp(-(F + M)); Modified: trunk/scripts/SiMatrixEffortByCell.java =================================================================== --- trunk/scripts/SiMatrixEffortByCell.java 2015-10-15 08:50:55 UTC (rev 376) +++ trunk/scripts/SiMatrixEffortByCell.java 2015-10-22 11:45:06 UTC (rev 377) @@ -256,7 +256,7 @@ double F = totalFishingMortalityPerCell(step, matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule - double M = group.getNaturalDeathRate(zone) + double M = getTotalDeathRate(step, group, zone) / (double) Month.NUMBER_OF_MONTH; double result = (double) Math.exp(-(F + M)); @@ -499,7 +499,7 @@ private double totalCatchRatePerCell(TimeStep step, PopulationGroup group, Zone zone, double totalFishingMortalityPerCell) throws TopiaException { - double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; + double M = getTotalDeathRate(step, group, zone) / Month.NUMBER_OF_MONTH; if (M == 0) { // normalement il devrait y avoir de la mortalite naturelle if (log.isWarnEnabled()) {

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r376 - trunk/resultinfos
by echatellier＠users.forge.codelutin.com Oct. 15, 2015

Oct. 15, 2015

Author: echatellier Date: 2015-10-15 10:50:55 +0200 (Thu, 15 Oct 2015) New Revision: 376 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/376 Log: Add comment Modified: trunk/resultinfos/MatrixTotalFishingMortality.java Modified: trunk/resultinfos/MatrixTotalFishingMortality.java =================================================================== --- trunk/resultinfos/MatrixTotalFishingMortality.java 2015-10-15 08:49:28 UTC (rev 375) +++ trunk/resultinfos/MatrixTotalFishingMortality.java 2015-10-15 08:50:55 UTC (rev 376) @@ -24,6 +24,8 @@ import fr.ifremer.isisfish.result.AbstractResultInfo; /** + * F. + * * Matrix with 1 dimension * Dimension 1 : TimeStep */

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r375 - trunk/scripts
by echatellier＠users.forge.codelutin.com Oct. 15, 2015

Oct. 15, 2015

Author: echatellier Date: 2015-10-15 10:49:28 +0200 (Thu, 15 Oct 2015) New Revision: 375 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/375 Log: Fix migration error Modified: trunk/scripts/SiMatrix.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-10-15 08:36:16 UTC (rev 374) +++ trunk/scripts/SiMatrix.java 2015-10-15 08:49:28 UTC (rev 375) @@ -1035,7 +1035,7 @@ List<Zone> zones = (List<Zone>)N.getSemantic(1); MatrixND result = MatrixFactory.getInstance().create( - MatrixBiomassBeginMonth.NAME, new List[] { groups, zones }, + MatrixAbundanceBeginMonth.NAME, new List[] { groups, zones }, new String[] { n("Groups"), n("Zones") }); for (int g = 0; g < groups.size(); g++) {

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r374 - trunk/resultinfos
by echatellier＠users.forge.codelutin.com Oct. 15, 2015

Oct. 15, 2015

Author: echatellier Date: 2015-10-15 10:36:16 +0200 (Thu, 15 Oct 2015) New Revision: 374 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/374 Log: Fix result dependencies Modified: trunk/resultinfos/MatrixFishingMortalityPerGroup.java Modified: trunk/resultinfos/MatrixFishingMortalityPerGroup.java =================================================================== --- trunk/resultinfos/MatrixFishingMortalityPerGroup.java 2015-10-14 08:49:29 UTC (rev 373) +++ trunk/resultinfos/MatrixFishingMortalityPerGroup.java 2015-10-15 08:36:16 UTC (rev 374) @@ -24,6 +24,8 @@ import fr.ifremer.isisfish.result.AbstractResultInfo; /** + * Fbar. + * * Matrix with 2 dimensions * Dimension 1 : TimeStep * Dimension 2 : Group @@ -33,7 +35,7 @@ public static final String NAME = MatrixFishingMortalityPerGroup.class.getSimpleName(); protected String[] necessaryResult = { - MatrixAbundance.NAME, + MatrixAbundanceBeginMonth.NAME, MatrixCatchPerStrategyMetPerZonePop.NAME, MatrixLandingPerMet.NAME };

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r373 - trunk/scripts
by echatellier＠users.forge.codelutin.com Oct. 14, 2015

Oct. 14, 2015

Author: echatellier Date: 2015-10-14 10:49:29 +0200 (Wed, 14 Oct 2015) New Revision: 373 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/373 Log: Calcul de F avec MatrixAbundanceBeginMonth Modified: trunk/scripts/SiMatrix.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-06-25 12:26:46 UTC (rev 372) +++ trunk/scripts/SiMatrix.java 2015-10-14 08:49:29 UTC (rev 373) @@ -1198,7 +1198,7 @@ abundanceReferenceMonth = Month.JANUARY; } TimeStep refStep = new TimeStep(12 * step.getYear() + abundanceReferenceMonth.getMonthNumber()); - MatrixND abundancePopRef = resManager.getMatrix(refStep, pop, MatrixAbundance.NAME); // Le timestep 0 correspond a janvier de la premiere annee et les annees sont numerotees a partir de zero + MatrixND abundancePopRef = resManager.getMatrix(refStep, pop, MatrixAbundanceBeginMonth.NAME); // Le timestep 0 correspond a janvier de la premiere annee et les annees sont numerotees a partir de zero abundancePopRef = abundancePopRef.sumOverDim(1); // somme sur Zone abundancePopRef = abundancePopRef.reduce(); NgroupRef = abundancePopRef.getValue(group); @@ -1212,8 +1212,8 @@ tfgMatrix.setValue(pop, group, Fgroup); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? } else { - //Fgroup = 0; // Ce n'est plus une valeur unique mais une matrice, est-ce que cette notation peut fonctionner ? - tfgMatrix.setValue(pop, group, 0); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? + //Fgroup = 0; // Ce n'est plus une valeur unique mais une matrice, est-ce que cette notation peut fonctionner ? + tfgMatrix.setValue(pop, group, 0); // Bien faire attention a l'endroit ou on met cette etape (quelle boucle) ? } }

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