diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index 3cbb97ae8ddaacea54d3db8e380b55a25aff5fb8..8dfc85d26ce78d9fa3e2c30c313fb9fce14c8cd5 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -279,6 +279,7 @@
<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
<weightOfDeathBasin>0.4</weightOfDeathBasin>
</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
+
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
@@ -289,6 +290,13 @@
<mortalityRateInSea>0.4</mortalityRateInSea>
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
+
+ <species.ExportFluxes>
+ <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+ <exportSeason>SPRING</exportSeason>
+ <fileNameOutput>EffectiveFluxes</fileNameOutput>
+ </species.ExportFluxes>
+
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 6cb3acfad0d24d85a70448e63849bbcef830144b..bd6fb457c0a1cdef793d1e930414139caef05194 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -412,7 +412,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
fileNameFluxes +this.getSimulationId() + ".csv")));
bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
- +sep+"abundance" + sep + "fluxType"+sep+"origine"+sep+"biomass");
+ +sep+"abundance" + sep + "fluxType"+ sep + "origin" +sep+"biomass");
for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
bWForFluxes.write(sep+nutrient);
}
diff --git a/src/main/java/species/ExportFluxes.java b/src/main/java/species/ExportFluxes.java
new file mode 100644
index 0000000000000000000000000000000000000000..da3a2940de2c31bf40bb1cf865680cf07ba9118b
--- /dev/null
+++ b/src/main/java/species/ExportFluxes.java
@@ -0,0 +1,110 @@
+
+package species;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import environment.RiverBasin;
+import environment.Time;
+import environment.Time.Season;
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish.Stage;
+
+/**
+ *
+ */
+public class ExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+ private Season exportSeason = Season.SPRING;
+
+ private String fileNameOutput = "EffectiveFluxes";
+
+ private transient BufferedWriter bW;
+ private transient String sep=";";
+
+ public static void main(String[] args) {
+ System.out.println((new XStream(new DomDriver()))
+ .toXML(new ExportFluxes()));
+ }
+
+ /* (non-Javadoc)
+ * @see fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
+ */
+ @Override
+ public void initTransientParameters(Pilot pilot) {
+ super.initTransientParameters(pilot);
+ sep=";";
+
+ }
+
+ @Override
+ public void doProcess(DiadromousFishGroup group) {
+
+ if (bW==null){
+ if (fileNameOutput != null){
+ new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+ try {
+ bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
+ fileNameOutput +group.getSimulationId()+ ".csv")));
+
+ bW.write("year"+sep+"migrationBasin"); //create the field of the column
+ for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
+ bW.write(sep + birthBasinName); // write each basin name in the file
+ }
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ try {
+ if (Time.getSeason(pilot) == exportSeason & Time.getYear(pilot)>1900) {
+
+
+ for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
+ //Create the map to get the abundance in each birth basin
+ Map<String, Long> spawnerOriginsBeforeReproduction = new HashMap<String, Long>(group.getEnvironment().getRiverBasinNames().length);
+ for (String basinName : group.getEnvironment().getRiverBasinNames()){
+ spawnerOriginsBeforeReproduction.put(basinName, 0L);
+ }
+
+ //compute the cumulative effective per birth basin
+ if (migrationBasin.getFishs(group) != null) {
+ for (DiadromousFish fish : migrationBasin.getFishs(group)) {
+ if (fish.getStage() == Stage.MATURE) {
+ String birthBasinName = fish.getBirthBasin().getName();
+ spawnerOriginsBeforeReproduction.put(birthBasinName, spawnerOriginsBeforeReproduction.get(birthBasinName) + fish.getAmount());
+
+
+ }
+
+ }
+ }
+
+ //write the first two fields of the line
+ bW.write(Time.getYear(pilot)+sep+migrationBasin.getName());
+
+ //write the cumulative effective from birth basin
+ for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
+ bW.write(sep+spawnerOriginsBeforeReproduction.get(birthBasinName));
+ }
+ //write an end-of(line
+ bW.write("\n");
+ }
+ }
+ if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1)
+ bW.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 3d54e84fe305847ebcdcc4ea97fe8656ff2d37d6..7b508000fbdfd7f8aac5507ce98ecc7d831df782 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -3,6 +3,7 @@ package species;
import java.io.BufferedWriter;
import java.io.IOException;
+import java.io.ObjectInputStream.GetField;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
@@ -169,7 +170,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// age of autochnonous spawnser
Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>();
-
+
// compute the number of spawners and keep the origines of the spawners
for (DiadromousFish fish : fishInBasin){
@@ -410,9 +411,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
try {
for (fluxOrigin origin : totalInputFluxes.keySet()) {
bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
- +";"+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin);
+ +";"+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + ";" + "IMPORT"+ ";" + origin);
bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
-
+
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
}
@@ -434,8 +435,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
//System.out.println(" AFTER " +riverBasin.getSpawnerOrigins().keySet());
}
-
-
+
+
// --------------------------------------------------------------------------------------------------
// update the observers
// --------------------------------------------------------------------------------------------------