From b80a5ab7c791383e9d4fa17e7d72f5e1f1e266b9 Mon Sep 17 00:00:00 2001
From: "patrick.lambert" <patrick.lambert@irstea.fr>
Date: Fri, 25 Oct 2019 16:49:05 +0200
Subject: [PATCH] writing nutrient export fluxes
---
data/input/fishTryRealBV_CC.xml | 23 ++-----
src/main/java/species/MigrateToSea.java | 6 +-
.../species/WriteNutrientExportFluxes.java | 68 +++++++++++++++++++
3 files changed, 78 insertions(+), 19 deletions(-)
create mode 100644 src/main/java/species/WriteNutrientExportFluxes.java
diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index b5df39b..629e62e 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -214,9 +214,9 @@
<processesEachStep>
<environment.InformTime>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <consoleDisplay>true</consoleDisplay>
+ <consoleDisplay>true</consoleDisplay>
</environment.InformTime>
-
+
<species.PlopProcess>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<temporisation>0</temporisation>
@@ -280,7 +280,7 @@
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
-
+
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
@@ -321,21 +321,10 @@
<fileName>fluxes</fileName>
</species.WriteImportNutrientFluxes>
- <species.IdentifyPopulation>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <consoleDisplay>false</consoleDisplay>
- <fluxesSeason>SPRING</fluxesSeason>
- <years>
- <long>2000</long>
- <long>2100</long>
- </years>
- <fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
- </species.IdentifyPopulation>
-
- <species.TypeTrajectoryCV>
+ <species.WriteNutrientExportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
- </species.TypeTrajectoryCV>
+ <fileName>nutrientExportFluxes</fileName>
+ </species.WriteNutrientExportFluxes>
</processesAtEnd>
</processes>
diff --git a/src/main/java/species/MigrateToSea.java b/src/main/java/species/MigrateToSea.java
index 5362bd7..4e16a73 100644
--- a/src/main/java/species/MigrateToSea.java
+++ b/src/main/java/species/MigrateToSea.java
@@ -42,8 +42,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>();
List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
- for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
- RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
+ for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
+
//Fish move to sea and compute the related export of nutrients
List<DiadromousFish> fishes = basin.getFishs(group);
@@ -64,6 +64,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish);
for (String nutrient: aFluxExportedByJuveniles.keySet()) {
totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount());
+
+ group.getNutrientRoutine().getNutrientExportFluxesCollection().put(Time.getYear(group.getPilot()), nutrient, basin.getName(), aFluxExportedByJuveniles.get(nutrient) * fish.getAmount());
}
totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass);
diff --git a/src/main/java/species/WriteNutrientExportFluxes.java b/src/main/java/species/WriteNutrientExportFluxes.java
new file mode 100644
index 0000000..adf39b3
--- /dev/null
+++ b/src/main/java/species/WriteNutrientExportFluxes.java
@@ -0,0 +1,68 @@
+package species;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+ private String fileName= "nutrientExportFluxes";
+
+ public static void main(String[] args) {
+ System.out.println((new XStream(new DomDriver()))
+ .toXML(new WriteNutrientExportFluxes()));
+
+ }
+
+ @Override
+ public void doProcess(DiadromousFishGroup group) {
+
+ BufferedWriter bW;
+
+ String outputPath = "data/output/" ;
+ String sep = ";";
+ new File(outputPath + fileName).getParentFile().mkdirs();
+ try {
+ bW = new BufferedWriter(new FileWriter(new File(outputPath+
+ fileName + group.getSimulationId() + ".csv")));
+
+ bW.write("year"+sep+"nutrient" + sep + "originBasin" + sep + "value" + "\n");
+
+ Map<Long, Map <String, Map<String, Double>>> fluxesCollection = group.getNutrientRoutine().getNutrientExportFluxesCollection().getExportFluxesCollection();
+
+ // to iterate on sorted years
+ List<Long> years = new ArrayList<Long>(fluxesCollection.keySet());
+ Collections.sort(years);
+
+ for (long year :years) {
+ if (year >= group.getMinYearToWrite()) {
+
+ for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+
+ for (String originBasinName : group.getEnvironment().getRiverBasinNames()) {
+ bW.write(year+ sep+ nutrient + sep + originBasinName );
+ bW.write( sep + fluxesCollection.get(year).get(nutrient).get(originBasinName) + '\n');
+ }
+
+ }
+ }
+ }
+
+ bW.flush();
+ bW.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+}
--
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