Skip to content

GitLab

Commit 6bf85149 authored by patrick.lambert's avatar patrick.lambert
Browse files

update of analyse AquaNismGroupProcesses

parent db793f43
Hide whitespace changes
Inline Side-by-side
data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
View file @ 6bf85149
......@@ -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>
......
src/main/java/miscellaneous/EasyRun.java
View file @ 6bf85149
......@@ -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")));
}
}
src/main/java/species/AnalyseFishDistribution.java
View file @ 6bf85149
......@@ -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;
}
......
src/main/java/species/AnalyseLikelihoodOfPresence.java
View file @ 6bf85149
......@@ -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);
}
}
......
src/main/java/species/AnalyseSpawnerFeatures.java
View file @ 6bf85149
......@@ -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;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment