diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
index 177e4b4fd382c5953d1e1f31ba78c3474ed47433..2678c280162c0308b89d371e7ea114427ca5eacf 100644
--- a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
+++ b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
@@ -288,7 +288,14 @@
<analysisSeason>SPRING</analysisSeason>
<memorySize>30</memorySize>
</species.AnalyseSpawnerFeatures>
-
+
+ <species.AnalyseFishDistribution>
+ <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+ <analysisSeason>SPRING</analysisSeason>
+ <memorySize>30</memorySize>
+ <minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
+ </species.AnalyseFishDistribution>
+
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
@@ -311,11 +318,6 @@
<displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
- <species.AnalyseFishDistribution>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <analysisSeason>SPRING</analysisSeason>
- <minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
- </species.AnalyseFishDistribution>
<species.MigrateFromRiverToInshore>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
@@ -340,11 +342,13 @@
</processesEachStep>
<processesAtEnd>
- <species.WriteBiomassFluxes>
+ <species.AnalyseLikelihoodOfPresence>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <exportSeason>SPRING</exportSeason>
- <fileNameOutput>biomassFluxes</fileNameOutput>
- </species.WriteBiomassFluxes>
+ <presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
+ <period>obs_1900_1950</period>
+ <minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
+ <epsilon>0.001</epsilon>
+ </species.AnalyseLikelihoodOfPresence>
<species.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
diff --git a/src/main/java/miscellaneous/EasyRun.java b/src/main/java/miscellaneous/EasyRun.java
index 2993abe42980a0ab5807bf23603179f67000d4fc..72bc04ca5fcd4b341cca391256bd7421eafda5b4 100644
--- a/src/main/java/miscellaneous/EasyRun.java
+++ b/src/main/java/miscellaneous/EasyRun.java
@@ -16,7 +16,6 @@
*/
package miscellaneous;
-import java.util.Arrays;
import java.util.List;
import fr.cemagref.simaqualife.extensions.pilot.BatchRunner;
@@ -37,8 +36,8 @@ public class EasyRun {
pilot.load();
// update the simulation parameters
- ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0),
- "processes.processesAtEnd.0.fileNameOutput", outputfilename);
+ // ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0),
+ // "processes.processesAtEnd.0.fileNameOutput", outputfilename);
for (int i = 0; i < paramNames.length; i++) {
ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), paramNames[i],
paramValues[i]);
@@ -75,36 +74,49 @@ public class EasyRun {
}
+ public static double getSingleValueFromAquanismGroupProcess(String targetPath) throws Exception {
+ return (double) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), targetPath);
+ }
+
+
public static void main(String[] args) throws Exception {
- String[] batchArguments = ("-simDuration 100 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
+ String[] batchArguments = ("-simDuration 150 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
+ "-groups data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml "
+ "-env data/input/northeastamerica/RIOBNneaBasins_Rjava.xml "
+ "-observers data/input/northeastamerica/RIO_obs_empty.xml").split("\\ ");
- String[] parameterNames = new String[] { "processes.processesEachStep.9.tempMinRep",
- "processes.processesEachStep.9.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
+ String[] parameterNames = new String[] { "processes.processesEachStep.10.tempMinRep",
+ "processes.processesEachStep.10.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
double[] parameterValues = new double[] { 10, 2, 0.7 };
runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
- 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));
- }
-
- // List truc = getAListFromAquanismGroupProcess("processes.processesAtEnd.1.getRecords");
+ // System.out.println("\nAnalyseSpawnerFeatures");
+ // System.out.println("basin_id, female_mean_age, male_mean_age, percent_primiparous");
+ // double[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.8.exportToR");
+ // for (double[] result : spawnerRunResults) {
+ // System.out.println(Arrays.toString(result));
+ // }
+ //
+ // System.out.println("\nAnalyseFishDistribution");
+ // System.out.println("southern_basin_id, northern_basin_id, basin_centroid_latitude,
+ // effective_centroid_latitude");
+ // double[][] distributionResults =
+ // getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
+ // for (double[] result : distributionResults) {
+ // System.out.println(Arrays.toString(result));
+ // }
+
+ System.out.println("\nAnalyseLikelihoodOfPresence");
+ System.out.println(getSingleValueFromAquanismGroupProcess("processes.processesAtEnd.0.getLogLikelihood"));
+
+ // List truc = getAListFromAquanismGroupProcess("processes.processesAtEnd.0.getRecords");
// System.out.println(truc.get(0).toString());
// System.out.println(getAListFromAquanismGroupProcess("processes.processesAtEnd.1.getRecords"));
- System.out.println(Arrays.toString(getValuesFromEnvironment("getMeanLastPercOfAut")));
-
- System.out.println(Arrays.toString(getValuesFromAquanismGroup("getRangeDistribution")));
+ // System.out.println("\ngetMeanLastPercOfAut");
+ // System.out.println(Arrays.toString(getValuesFromEnvironment("getMeanLastPercOfAut")));
}
}
diff --git a/src/main/java/species/AnalyseFishDistribution.java b/src/main/java/species/AnalyseFishDistribution.java
index 4d8d337cda5889b0202a582d58fdb48444f2b9fb..70681aba2ecffae4529ab246df98cd419388db7b 100644
--- a/src/main/java/species/AnalyseFishDistribution.java
+++ b/src/main/java/species/AnalyseFishDistribution.java
@@ -19,8 +19,9 @@
*/
package species;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
@@ -30,6 +31,7 @@ import environment.RiverBasin;
import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
+import miscellaneous.QueueMemory;
import miscellaneous.TreeMapForCentile;
import observer.ObservableRecord;
@@ -40,6 +42,8 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
private Season analysisSeason = Season.SPRING;
+ private int memorySize = 30;
+
/**
* The minimum number of recruits to consider a basin as populated
*
@@ -47,16 +51,18 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
*/
private int minimumRecruitsForPopulatedBasin = 50;
- private transient List<FishDistributionRecord> records;
+ // private transient List<FishDistributionRecord> records;
private transient double southernLimit;
private transient double northernLimit;
+ private transient Map<RiverBasin, QueueMemory<Double>> lastSpawnerNumbersMemory;
+
@Override
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
- records = new ArrayList<FishDistributionRecord>();
+ // records = new ArrayList<FishDistributionRecord>();
// define the latitude range of basin network
southernLimit = 90.;
@@ -71,78 +77,88 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
@Override
public void doProcess(DiadromousFishGroup group) {
- if (records == null)
- initTransientParameters(group.getPilot());
+ // first passage
+ if (lastSpawnerNumbersMemory == null) {
+ lastSpawnerNumbersMemory = new HashMap<RiverBasin, QueueMemory<Double>>();
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ lastSpawnerNumbersMemory.put(riverBasin, new QueueMemory<>(memorySize));
+ }
+ }
- 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();
+ // if (records == null)
+ // initTransientParameters(group.getPilot());
+ if (group.getEnvironment().getTime().getSeason(group.getPilot()) == analysisSeason) {
for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ double fluxBefore = riverBasin.getSpawnerNumberPerGroup(group);
- 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);
- }
- }
- // if the universe is empty
- if (southernEdge == northernLimit & northernEdge == southernLimit) {
- southernEdge = (northernLimit + southernLimit) / 2.;
- northernEdge = southernEdge;
+ lastSpawnerNumbersMemory.get(riverBasin).push(fluxBefore);
}
- // 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);
-
- records.add(record);
}
}
public double[][] exportToR() {
- double[][] export = new double[records.size()][4];
- for (int i = 0; i < records.size(); i++) {
- export[i][0] = records.get(i).southern_basin_id;
- export[i][1] = records.get(i).northern_basin_id;
- export[i][2] = records.get(i).basinCentroid_latitude;
- export[i][3] = records.get(i).effectiveCentroid_latitude;
+
+ // 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();
+
+ double[][] export = new double[1][4];
+ int i = 0;
+ for (Entry<RiverBasin, QueueMemory<Double>> entry : lastSpawnerNumbersMemory.entrySet()) {
+
+ if (entry.getValue().getMean() > minimumRecruitsForPopulatedBasin) {
+ // the river basin is considered populated
+
+ // NOTE : recruiit number is calulated after thermal tolerance impact
+ // (which is intreaged in the stock-recruitment relationship)
+
+ // southern edge
+ if (entry.getKey().getLatitude() < southernEdge) {
+ // the basin is the new southern edge
+ southernEdge = entry.getKey().getLatitude();
+ southernId = entry.getKey().getBasin_id();
+ // southernName = entry.getKey().getName();
+ }
+
+ // northern edge
+ if (entry.getKey().getLatitude() > northernEdge) {
+ // the basin is the new northern edge
+ northernEdge = entry.getKey().getLatitude();
+ northernId = entry.getKey().getBasin_id();
+ // northernName = entry.getKey().getName();
+ }
+
+ // for distribution centroide computation
+ latitudePresence.putWithAdding(entry.getKey().getLatitude(), 1L);
+ long effective = ((Double) entry.getValue().getMean()).longValue();
+ latitudeEffective.putWithAdding(entry.getKey().getLatitude(), effective);
+ }
+ }
+
+ // if the universe is empty (none of basins is populated)
+ if (southernEdge == northernLimit & northernEdge == southernLimit) {
+ southernEdge = (northernLimit + southernLimit) / 2.;
+ northernEdge = southernEdge;
}
+
+ // distribution centroids computation
+ double basinCentroid = latitudePresence.calculateMedian();
+ double effectiveCentroid = latitudeEffective.calculateMedian();
+
+ export[0][0] = southernId;
+ export[0][1] = northernId;
+ export[0][2] = basinCentroid;
+ export[0][3] = effectiveCentroid;
return export;
}
diff --git a/src/main/java/species/AnalyseLikelihoodOfPresence.java b/src/main/java/species/AnalyseLikelihoodOfPresence.java
index fa663d89d0331e6be1ec357736dc7d57f9587c99..ca4a12344da3d34812486036a6b46d445f774415 100644
--- a/src/main/java/species/AnalyseLikelihoodOfPresence.java
+++ b/src/main/java/species/AnalyseLikelihoodOfPresence.java
@@ -47,6 +47,11 @@ public class AnalyseLikelihoodOfPresence extends AquaNismsGroupProcess<Diadromou
*/
private int minimumRecruitsForPopulatedBasin = 50;
+ /**
+ * to avoid log(0) in log-lokelihood
+ *
+ * @unit
+ */
private double epsilon = 1e-3;
// map with presence
@@ -62,6 +67,7 @@ public class AnalyseLikelihoodOfPresence extends AquaNismsGroupProcess<Diadromou
if (Double.isNaN(epsilon))
epsilon = 1e-3;
+ // read the file of presence in river basin
try {
// open the file
FileReader reader = new FileReader(presenceFileName);
@@ -74,10 +80,16 @@ public class AnalyseLikelihoodOfPresence extends AquaNismsGroupProcess<Diadromou
// read the headers
String[] headers = scanner.nextLine().split(",");
presences = new TreeMap<String, Map<String, Integer>>();
+ boolean periodTest = false;
for (int i = 2; i < headers.length; i++) {
+ if (period.equals(headers[i]))
+ periodTest = true;
presences.put(headers[i], new TreeMap<String, Integer>());
}
+ // TODO send the error
+ if (periodTest == false)
+ System.out.println("The period " + period + " is not present in the file " + presenceFileName);
// read the lines
while (scanner.hasNextLine()) {
String[] fields = scanner.nextLine().split(",");
@@ -94,8 +106,8 @@ public class AnalyseLikelihoodOfPresence extends AquaNismsGroupProcess<Diadromou
}
}
}
- // reader.close();
- // scanner.close();
+ reader.close();
+ scanner.close();
} catch (Exception e) {
e.printStackTrace();
}
@@ -104,18 +116,24 @@ public class AnalyseLikelihoodOfPresence extends AquaNismsGroupProcess<Diadromou
@Override
public void doProcess(DiadromousFishGroup group) {
+
+ // first passage for processesAtEnd
+ if (presences == null)
+ initTransientParameters(group.getPilot());
+
logLikelihood = 0.;
for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
double p_predit = (double) riverBasin.getLastRecruitments()
.getNumberOfStriclyHigherValue(minimumRecruitsForPopulatedBasin)
/ (double) riverBasin.getLastRecruitments().size();
- int presence = presences.get(riverBasin.getName()).get(period);
+ int presence = presences.get(period).get(riverBasin.getName());
+ // System.out.println(riverBasin.getName() + " " + presence + " " + p_predit);
if (presence == 1)
- logLikelihood += Math.log(p_predit) + epsilon;
+ logLikelihood += Math.log(p_predit + epsilon);
else
- logLikelihood += 1 - Math.log(p_predit) + epsilon;
+ logLikelihood += 1 - Math.log(p_predit + epsilon);
}
}
diff --git a/src/main/java/species/AnalyseSpawnerFeatures.java b/src/main/java/species/AnalyseSpawnerFeatures.java
index 8640ceda8845d830ca624ca0d260782bc40a4483..d3ddb75f99f6ba9184caead4df3dec284ace3277 100644
--- a/src/main/java/species/AnalyseSpawnerFeatures.java
+++ b/src/main/java/species/AnalyseSpawnerFeatures.java
@@ -130,6 +130,8 @@ public class AnalyseSpawnerFeatures extends AquaNismsGroupProcess<DiadromousFish
result[i][1] = entry.getValue().getMean();
result[i][2] = maleAgeMemories.get(entry.getKey()).getMean();
result[i][3] = primiparousMemories.get(entry.getKey()).getMean();
+
+ i++;
}
return result;