diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
index 3925a60f892405add402592cbc24674b419f83cc..39977935441a569bcd8f7fb3d1accf7782f4781f 100644
--- a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
+++ b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
@@ -333,6 +333,16 @@
<exportSeason>SPRING</exportSeason>
<fileNameOutput>biomassFluxes</fileNameOutput>
</species.WriteBiomassFluxes>
+
+ <species.IdentifyPopulation>
+ <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+ <consoleDisplay>false</consoleDisplay>
+ <years>
+ <long>1813</long>
+ </years>
+ <fluxesSeason>SPRING</fluxesSeason>
+ <fileNameOutput>effectiveFluxes</fileNameOutput>
+ </species.IdentifyPopulation>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
diff --git a/exploration/NEA_sensitivity_analysis/tryFromRougier.R b/exploration/NEA_sensitivity_analysis/tryFromJava.R
similarity index 78%
rename from exploration/NEA_sensitivity_analysis/tryFromRougier.R
rename to exploration/NEA_sensitivity_analysis/tryFromJava.R
index fc903b0e77e85a12f9ce960b56bd716946bd635a..25e773922814aa504825b6e6bf6a4f00cac1726f 100644
--- a/exploration/NEA_sensitivity_analysis/tryFromRougier.R
+++ b/exploration/NEA_sensitivity_analysis/tryFromJava.R
@@ -32,13 +32,11 @@ timeStepDuration =1
seed = 1
-
parametersNames = c("processes.processesEachStep.8.tempMinRep",
"processes.processesEachStep.8.ratioS95_S50",
"processes.processesEachStep.6.pHomingAfterEquil")
thetas = c(10, 2, 0.7)
-
arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
'-timeStepDuration',timeStepDuration,
'-RNGStatusIndex', format(seed,scientific = FALSE),
@@ -46,12 +44,21 @@ arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
'-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
'-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
-outputFile = paste0("Avirer",seed)
-.jinit(classpath = "", force.init = TRUE)
+outputFile = paste0("SA/",seed)
.jinit(classpath = jarfile, force.init = TRUE)
.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(parametersNames),.jarray(thetas))
.jcall("miscellaneous.EasyRun","[D","getValuesFromEnvironement","getMeanLastPercOfAut")
.jcall("miscellaneous.EasyRun","[D","getValuesFromAquanismGroup","getRangeDistribution")
-
-
-
+# truc = .jcall("miscellaneous.EasyRun","Ljava/util/List;",
+# "getAListFromAquanismGroupProcess","processes.processesAtEnd.1.getRecords")
+#
+# trucMieux = .jcast(truc, "ljava/util/ArrayList", convert.array = FALSE)
+#
+# i <- .jnew("java/lang/Integer", as.integer(10))
+# print(i)
+# print(.jsimplify(i))
+# .jcall(trucMieux, "java/lang/Object", "get", i)
+#
+# with(trucMieux, {get(0)})
+# ArrayList = J("java.util.ArrayList")
+# .jclassPath()
diff --git a/src/main/java/miscellaneous/EasyRun.java b/src/main/java/miscellaneous/EasyRun.java
index 1beb5fda3895a266d203b3e55d4553481863ea3d..c29a463ddd9c644f8cb7893471b3806b0fe19298 100644
--- a/src/main/java/miscellaneous/EasyRun.java
+++ b/src/main/java/miscellaneous/EasyRun.java
@@ -1,6 +1,6 @@
/*
- * Copyright (C) 2014 dumoulin
- *
+ * Copyright (C) 2021 lambert Dumoulin
+ * *
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
@@ -17,6 +17,7 @@
package miscellaneous;
import java.util.Arrays;
+import java.util.List;
import fr.cemagref.simaqualife.extensions.pilot.BatchRunner;
import fr.cemagref.simaqualife.pilot.Pilot;
@@ -25,7 +26,6 @@ public class EasyRun {
static Pilot pilot;
-
public static void runSimulation(String[] batchArgs, String outputfilename, String[] paramNames, double[] paramValues)
throws Exception {
@@ -55,13 +55,18 @@ public class EasyRun {
}
- public static double[] getValuesFromEnvironement(String outputName) throws Exception {
- return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getEnvironment(), outputName);
+ public static double[] getValuesFromEnvironement(String targetName) throws Exception {
+ return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getEnvironment(), targetName);
+ }
+
+
+ public static double[] getValuesFromAquanismGroup(String targetName) throws Exception {
+ return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), targetName);
}
- public static double[] getValuesFromAquanismGroup(String outputName) throws Exception {
- return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), outputName);
+ public static List getAListFromAquanismGroupProcess(String targetPath) throws Exception {
+ return (List) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), targetPath);
}
@@ -78,6 +83,10 @@ public class EasyRun {
runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
+ List truc = getAListFromAquanismGroupProcess("processes.processesAtEnd.1.getRecords");
+ System.out.println(truc.get(0).toString());
+ // System.out.println(getAListFromAquanismGroupProcess("processes.processesAtEnd.1.getRecords"));
+
System.out.println(Arrays.toString(getValuesFromEnvironement("getMeanLastPercOfAut")));
System.out.println(Arrays.toString(getValuesFromAquanismGroup("getRangeDistribution")));
diff --git a/src/main/java/species/IdentifyPopulation.java b/src/main/java/species/IdentifyPopulation.java
index a1ef3a7f3b8254b730d76caf618beb37d3eacc98..d6d5961157ba0dc8f7e01e5120a39b1aa6818e33 100644
--- a/src/main/java/species/IdentifyPopulation.java
+++ b/src/main/java/species/IdentifyPopulation.java
@@ -23,12 +23,13 @@ import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.io.Serializable;
+import java.util.ArrayList;
import java.util.List;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
-import environment.RIOBasinNetwork;
import environment.RiverBasin;
import environment.Time;
import environment.Time.Season;
@@ -39,17 +40,76 @@ import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
*/
public class IdentifyPopulation extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+ /**
+ *
+ */
+ public class Record implements Serializable {
+ long year;
+ String migrationBasin;
+ String originBasin;
+ long effective;
+
+ public Record(long year, String migrationBasin, String originBasin, long effective) {
+ super();
+ this.year = year;
+ this.migrationBasin = migrationBasin;
+ this.originBasin = originBasin;
+ this.effective = effective;
+ }
+
+
+ @Override
+ public String toString() {
+ return "[" + this.year + "; " + this.migrationBasin + "; " + this.originBasin + "; " + this.effective + "]";
+ }
+
+
+ /**
+ * @return the year
+ */
+ public long getYear() {
+ return this.year;
+ }
+
+
+ /**
+ * @return the migrationBasin
+ */
+ public String getMigrationBasin() {
+ return this.migrationBasin;
+ }
+
+
+ /**
+ * @return the originBasin
+ */
+ public String getOriginBasin() {
+ return this.originBasin;
+ }
+
+
+ /**
+ * @return the effective
+ */
+ public long getEffective() {
+ return this.effective;
+ }
+
+ }
+
private boolean consoleDisplay = false;
private List<Long> years;
private Season fluxesSeason = Season.SPRING;
- private String fileNameOutput = "data/output/fluxes";
+ private String fileNameOutput = "effectiveFluxes";
+
+ private transient List<Record> records;
private transient BufferedWriter bW;
- private String sep;
+ private transient String sep;
+
// @Observable(description = "fluxes")
// private transient long[] fluxes;
-
public static void main(String[] args) {
System.out.println((new XStream(new DomDriver())).toXML(new IdentifyPopulation()));
}
@@ -64,18 +124,13 @@ public class IdentifyPopulation extends AquaNismsGroupProcess<DiadromousFish, Di
public void doProcess(DiadromousFishGroup group) {
if (bW == null) {
if (fileNameOutput != null) {
- sep = ";";
+ sep = ",";
try {
new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
bW = new BufferedWriter(
new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
- // BasinNetworkReal nbr= (BasinNetworkReal) pilot.getAquaticWorld().getEnvironment();
- RIOBasinNetwork nbr = group.getEnvironment();
- bW.write("year" + sep + "migrationBasin");
- for (String basinName : nbr.getRiverBasinNames()) {
- bW.write(sep + basinName);
- }
+ bW.write("year" + sep + "migrationBasin" + sep + "originBasin" + sep + "effective");
bW.write("\n");
} catch (IOException e) {
e.printStackTrace();
@@ -87,20 +142,33 @@ public class IdentifyPopulation extends AquaNismsGroupProcess<DiadromousFish, Di
String[] basinNames = group.getEnvironment().getRiverBasinNames();
+ // put in hasmap
+ if (records == null)
+ records = new ArrayList<Record>();
+
+ for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
+ for (RiverBasin originBasin : group.getEnvironment().getRiverBasins()) {
+ long effective = Math.round(basin.getSpawnerOrigins().getMeans().get(originBasin.getName()));
+ records.add(new Record(time.getYear(group.getPilot()), basin.getName(), originBasin.getName(), effective));
+ }
+ }
+
+ // write in file
if (fileNameOutput != null) {
try {
- for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
- bW.write(time.getYear(group.getPilot()) + sep + basin.getName());
-
- for (String basinName : basinNames) {
- bW.write(sep + Math.round(basin.getSpawnerOrigins().getMeans().get(basinName)));
+ for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
+ for (String originBasinName : basinNames) {
+ bW.write(time.getYear(group.getPilot()) + sep + migrationBasin.getName() + sep + originBasinName);
+ bW.write(sep + Math.round(migrationBasin.getSpawnerOrigins().getMeans().get(originBasinName)));
+ bW.write("\n");
}
- bW.write("\n");
}
+ bW.flush();
} catch (IOException e) {
e.printStackTrace();
}
+ // display in console
if (consoleDisplay) {
System.out.print("MIGRATION" + "\t");
for (String basinName : basinNames) {
@@ -128,4 +196,13 @@ public class IdentifyPopulation extends AquaNismsGroupProcess<DiadromousFish, Di
}
}
}
+
+
+ /**
+ * @return the records
+ */
+ public List<Record> getRecords() {
+ return this.records;
+ }
+
}