diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
index 09400c58e601c4fd04d96c0c69a19638d1266c97..177e4b4fd382c5953d1e1f31ba78c3474ed47433 100644
--- a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
+++ b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
@@ -283,6 +283,12 @@
<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> -->
+ <species.AnalyseSpawnerFeatures>
+ <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+ <analysisSeason>SPRING</analysisSeason>
+ <memorySize>30</memorySize>
+ </species.AnalyseSpawnerFeatures>
+
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
@@ -307,12 +313,10 @@
<species.AnalyseFishDistribution>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <fishDistributionAnalysisSeason>SPRING</fishDistributionAnalysisSeason>
- <fishDistributionAnalysisStartYear>1820</fishDistributionAnalysisStartYear>
- <fishDistributionAnalysisEndYear>1850</fishDistributionAnalysisEndYear>
+ <analysisSeason>SPRING</analysisSeason>
<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
</species.AnalyseFishDistribution>
-
+
<species.MigrateFromRiverToInshore>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
diff --git a/src/main/java/miscellaneous/EasyRun.java b/src/main/java/miscellaneous/EasyRun.java
index 3a889a14eb9b898be5eced2d2e25e3ae5c25d535..2993abe42980a0ab5807bf23603179f67000d4fc 100644
--- a/src/main/java/miscellaneous/EasyRun.java
+++ b/src/main/java/miscellaneous/EasyRun.java
@@ -81,14 +81,19 @@ public class EasyRun {
+ "-env data/input/northeastamerica/RIOBNneaBasins_Rjava.xml "
+ "-observers data/input/northeastamerica/RIO_obs_empty.xml").split("\\ ");
- String[] parameterNames = new String[] { "processes.processesEachStep.8.tempMinRep",
- "processes.processesEachStep.8.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
+ String[] parameterNames = new String[] { "processes.processesEachStep.9.tempMinRep",
+ "processes.processesEachStep.9.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
double[] parameterValues = new double[] { 10, 2, 0.7 };
runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
- double[][] distributionResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
+ double[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.8.exportToR");
+ for (double[] result : spawnerRunResults) {
+ System.out.println(Arrays.toString(result));
+ }
+
+ double[][] distributionResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.10.exportToR");
for (double[] result : distributionResults) {
System.out.println(Arrays.toString(result));
}
diff --git a/src/main/java/species/AnalyseFishDistribution.java b/src/main/java/species/AnalyseFishDistribution.java
index 4ba0ecf382aa49a1b981541b00ffbda65d6e5885..4d8d337cda5889b0202a582d58fdb48444f2b9fb 100644
--- a/src/main/java/species/AnalyseFishDistribution.java
+++ b/src/main/java/species/AnalyseFishDistribution.java
@@ -27,6 +27,7 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.RIOBasinNetwork;
import environment.RiverBasin;
+import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.TreeMapForCentile;
@@ -37,6 +38,8 @@ import observer.ObservableRecord;
*/
public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+ private Season analysisSeason = Season.SPRING;
+
/**
* The minimum number of recruits to consider a basin as populated
*
@@ -71,62 +74,64 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
if (records == null)
initTransientParameters(group.getPilot());
- // initialise the distribution range
- double southernEdge = northernLimit;
- double northernEdge = southernLimit;
- int southernId = -1;
- int northernId = -1;
- String southernName = "";
- String northernName = "";
- // initialise for centroid
- TreeMapForCentile latitudeEffective = new TreeMapForCentile();
- TreeMapForCentile latitudePresence = new TreeMapForCentile();
-
- for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
-
- if (riverBasin.getLastRecruitments().getMean() > minimumRecruitsForPopulatedBasin) {
- // the river basin is consdered populated
-
- // NOTE : recruiit number is calulated after thermal tolerance impact
- // (which is intreaged in the stock-recruitment relationship)
-
- // southern edge
- if (riverBasin.getLatitude() < southernEdge) {
- // the basin is the new southern edge
- southernEdge = riverBasin.getLatitude();
- southernId = riverBasin.getBasin_id();
- southernName = riverBasin.getName();
- }
-
- // northern edge
- if (riverBasin.getLatitude() > southernEdge) {
- // the basin is the new northern edge
- northernEdge = riverBasin.getLatitude();
- northernId = riverBasin.getBasin_id();
- northernName = riverBasin.getName();
+ if (group.getEnvironment().getTime().getSeason(group.getPilot()) == analysisSeason) {
+ // initialise the distribution range
+ double southernEdge = northernLimit;
+ double northernEdge = southernLimit;
+ int southernId = -1;
+ int northernId = -1;
+ String southernName = "";
+ String northernName = "";
+ // initialise for centroid
+ TreeMapForCentile latitudeEffective = new TreeMapForCentile();
+ TreeMapForCentile latitudePresence = new TreeMapForCentile();
+
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+
+ if (riverBasin.getLastRecruitments().getMean() > minimumRecruitsForPopulatedBasin) {
+ // the river basin is consdered populated
+
+ // NOTE : recruiit number is calulated after thermal tolerance impact
+ // (which is intreaged in the stock-recruitment relationship)
+
+ // southern edge
+ if (riverBasin.getLatitude() < southernEdge) {
+ // the basin is the new southern edge
+ southernEdge = riverBasin.getLatitude();
+ southernId = riverBasin.getBasin_id();
+ southernName = riverBasin.getName();
+ }
+
+ // northern edge
+ if (riverBasin.getLatitude() > southernEdge) {
+ // the basin is the new northern edge
+ northernEdge = riverBasin.getLatitude();
+ northernId = riverBasin.getBasin_id();
+ northernName = riverBasin.getName();
+ }
+
+ // for distribution centroide computation
+ latitudePresence.putWithAdding(riverBasin.getLatitude(), 1L);
+ long effective = ((Double) riverBasin.getLastSpawnerNumbersBeforeReproduction().getMean()).longValue();
+ latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
}
-
- // for distribution centroide computation
- latitudePresence.putWithAdding(riverBasin.getLatitude(), 1L);
- long effective = ((Double) riverBasin.getLastSpawnerNumbersBeforeReproduction().getMean()).longValue();
- latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
}
- }
- // if the universe is empty
- if (southernEdge == northernLimit & northernEdge == southernLimit) {
- southernEdge = (northernLimit + southernLimit) / 2.;
- northernEdge = southernEdge;
- }
+ // if the universe is empty
+ if (southernEdge == northernLimit & northernEdge == southernLimit) {
+ southernEdge = (northernLimit + southernLimit) / 2.;
+ northernEdge = southernEdge;
+ }
- // distribution centroids computation
- double basinCentroid = latitudePresence.calculateMedian();
- double effectiveCentroid = latitudeEffective.calculateMedian();
+ // distribution centroids computation
+ double basinCentroid = latitudePresence.calculateMedian();
+ double effectiveCentroid = latitudeEffective.calculateMedian();
- // add a record
- FishDistributionRecord record = new FishDistributionRecord(southernId, southernName, southernEdge, northernId,
- northernName, northernEdge, basinCentroid, effectiveCentroid);
+ // add a record
+ FishDistributionRecord record = new FishDistributionRecord(southernId, southernName, southernEdge, northernId,
+ northernName, northernEdge, basinCentroid, effectiveCentroid);
- records.add(record);
+ records.add(record);
+ }
}
diff --git a/src/main/java/species/AnalyseSpawnerFeatures.java b/src/main/java/species/AnalyseSpawnerFeatures.java
index 57cc98119dc907221a9efa3639506a969ca8f3dd..8640ceda8845d830ca624ca0d260782bc40a4483 100644
--- a/src/main/java/species/AnalyseSpawnerFeatures.java
+++ b/src/main/java/species/AnalyseSpawnerFeatures.java
@@ -27,6 +27,7 @@ import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.RiverBasin;
+import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.QueueMemory;
@@ -38,6 +39,7 @@ import species.DiadromousFish.Gender;
public class AnalyseSpawnerFeatures extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
private int memorySize = 30;
+ private Season analysisSeason = Season.SPRING;
private transient Map<Integer, QueueMemory<Double>> femaleAgeMemories;
private transient Map<Integer, QueueMemory<Double>> maleAgeMemories;
@@ -56,47 +58,62 @@ public class AnalyseSpawnerFeatures extends AquaNismsGroupProcess<DiadromousFish
// first passage
if (femaleAgeMemories == null) {
femaleAgeMemories = new HashMap<Integer, QueueMemory<Double>>();
+ maleAgeMemories = new HashMap<Integer, QueueMemory<Double>>();
+ primiparousMemories = new HashMap<Integer, QueueMemory<Double>>();
for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
- femaleAgeMemories.put(riverBasin.getId(), new QueueMemory<>(memorySize));
+ femaleAgeMemories.put(riverBasin.getBasin_id(), new QueueMemory<>(memorySize));
+ maleAgeMemories.put(riverBasin.getBasin_id(), new QueueMemory<>(memorySize));
+ primiparousMemories.put(riverBasin.getBasin_id(), new QueueMemory<>(memorySize));
}
}
- for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ if (group.getEnvironment().getTime().getSeason(group.getPilot()) == analysisSeason) {
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
- if (riverBasin.getFishs(group) != null) {
+ if (riverBasin.getFishs(group) != null) {
- double meanAgeForFemale = 0.;
- double nbAgeForFemale = 0.;
+ double meanAgeForFemale = 0.;
+ double nbAgeForFemale = 0.;
- double meanAgeForMale = 0.;
- double nbAgeForMale = 0.;
+ double meanAgeForMale = 0.;
+ double nbAgeForMale = 0.;
- double nbOfSpawners = 0.;
- double nbOfPrimiparous = 0.;
+ double nbOfSpawners = 0.;
+ double nbOfPrimiparous = 0.;
- for (DiadromousFish fish : riverBasin.getFishs(group)) {
- if (fish.isMature()) {
+ for (DiadromousFish fish : riverBasin.getFishs(group)) {
+ if (fish.isMature()) {
- // mean age
- if (fish.getGender() == Gender.FEMALE) {
- meanAgeForFemale += fish.getAge() * fish.getAmount();
- nbAgeForFemale += fish.getAmount();
- } else if (fish.getGender() == Gender.MALE) {
- meanAgeForMale += fish.getAge() * fish.getAmount();
- nbAgeForMale += fish.getAmount();
- }
+ // mean age
+ if (fish.getGender() == Gender.FEMALE) {
+ meanAgeForFemale += fish.getAge() * fish.getAmount();
+ nbAgeForFemale += fish.getAmount();
+ } else if (fish.getGender() == Gender.MALE) {
+ meanAgeForMale += fish.getAge() * fish.getAmount();
+ nbAgeForMale += fish.getAmount();
+ }
- // primiparous
- nbOfSpawners += fish.getAmount();
- if (fish.getNumberOfReproduction() == 0)
- nbOfPrimiparous += fish.getAmount();
+ // primiparous
+ nbOfSpawners += fish.getAmount();
+ if (fish.getNumberOfReproduction() == 0)
+ nbOfPrimiparous += fish.getAmount();
+ }
}
+ // add value in the queues
+ if (nbAgeForFemale > 0.)
+ femaleAgeMemories.get(riverBasin.getBasin_id()).push(meanAgeForFemale / nbAgeForFemale);
+ else
+ femaleAgeMemories.get(riverBasin.getBasin_id()).push(Double.NaN);
+ if (nbAgeForMale > 0.)
+ maleAgeMemories.get(riverBasin.getBasin_id()).push(meanAgeForMale / nbAgeForMale);
+ else
+ maleAgeMemories.get(riverBasin.getBasin_id()).push(Double.NaN);
+ if (nbOfSpawners > 0.)
+ primiparousMemories.get(riverBasin.getBasin_id()).push(nbOfPrimiparous / nbOfSpawners);
+ else
+ primiparousMemories.get(riverBasin.getBasin_id()).push(Double.NaN);
}
- // add value in the quues
- femaleAgeMemories.get(riverBasin.getBasin_id()).add(meanAgeForFemale / nbAgeForFemale);
- maleAgeMemories.get(riverBasin.getBasin_id()).add(meanAgeForMale / nbAgeForMale);
- primiparousMemories.get(riverBasin.getBasin_id()).add(nbOfPrimiparous / nbOfSpawners);
}
}
}
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 427ab7f411a1d9d0589ebe1abfc4cce37ece4d8a..8904f0025347fb428de26461623d03a04f0f97f8 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -126,7 +126,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// before the party !!!!
double fluxBefore = riverBasin.getSpawnerNumberPerGroup(group);
- riverBasin.getLastSpawnerNumbersBeforeReproduction().add(fluxBefore);
+ riverBasin.getLastSpawnerNumbersBeforeReproduction().push(fluxBefore);
double b, c, alpha, beta, amountPerSuperIndividual, S95, S50;
double numberOfFemaleSpawners = 0.;