From e403278f92874dd0b69ecadb38efd588f3eb526d Mon Sep 17 00:00:00 2001
From: Poulet Camille <camille.poulet@irstea.priv>
Date: Fri, 2 Aug 2019 17:15:26 +0200
Subject: [PATCH] Add coloumnn abundance in csv file
---
data/input/fishTryRealBV_CC.xml | 6 +++---
data/input/fishTryRealBV_PL.xml | 4 ++--
src/main/java/species/DiadromousFishGroup.java | 4 ++--
src/main/java/species/MigrateToSea.java | 2 +-
src/main/java/species/NutrientRoutine.java | 12 ++++++------
...uceAndSurviveAfterReproductionWithDiagnose.java | 14 ++++++++------
6 files changed, 22 insertions(+), 20 deletions(-)
diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index d0a9a1a..3cbb97a 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -307,13 +307,13 @@
<maxNumberOfSuperIndividualPerReproduction>50.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
- <displayFluxesOnConsole>false</displayFluxesOnConsole>
+ <displayFluxesOnConsole>true</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <displayFluxesOnConsole>false</displayFluxesOnConsole>
+ <displayFluxesOnConsole>true</displayFluxesOnConsole>
</species.MigrateToSea>
<environment.updateTemperatureInRealBasin>
@@ -331,7 +331,7 @@
<long>2000</long>
<long>2100</long>
</years>
- <fileNameOutput>fluxes</fileNameOutput>
+ <fileNameOutput>JeuParam100_2100RCP85_A_essai</fileNameOutput>
</species.IdentifyPopulation>
<species.TypeTrajectoryCV>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
diff --git a/data/input/fishTryRealBV_PL.xml b/data/input/fishTryRealBV_PL.xml
index 34f20e8..4f3b80d 100644
--- a/data/input/fishTryRealBV_PL.xml
+++ b/data/input/fishTryRealBV_PL.xml
@@ -127,7 +127,7 @@
<long>2100</long>
</years>
<fluxesSeason>SPRING</fluxesSeason>
- <fileNameOutput>fluxes</fileNameOutput>
+ <fileNameOutput>JeuParam100_20100RCP85_A_essai</fileNameOutput>
</species.IdentifyPopulation>
<species.ExportRecruitment>
@@ -144,7 +144,7 @@
<species.ExportPopulationStatus>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <fileNameMortality>mortalty</fileNameMortality>
+ <fileNameMortality>mortality</fileNameMortality>
<fileNameMortalityCrash>mortalityCrash</fileNameMortalityCrash>
<fileNameStockTrap>stockTrap</fileNameStockTrap>
<fileNamePopulationStatus>populationStatus</fileNamePopulationStatus>
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 4ad4c7b..6cb3acf 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -409,10 +409,10 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
new File(this.outputPath +fileNameFluxes).getParentFile().mkdirs();
try {
bWForFluxes = new BufferedWriter(new FileWriter(new File(this.outputPath+
- fileNameFluxes +this.getSimulationId()+ ".csv")));
+ fileNameFluxes +this.getSimulationId() + ".csv")));
bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
- +sep+"fluxType"+sep+"origine"+sep+"biomass");
+ +sep+"abundance" + sep + "fluxType"+sep+"origine"+sep+"biomass");
for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
bWForFluxes.write(sep+nutrient);
}
diff --git a/src/main/java/species/MigrateToSea.java b/src/main/java/species/MigrateToSea.java
index e5887e2..65720a7 100644
--- a/src/main/java/species/MigrateToSea.java
+++ b/src/main/java/species/MigrateToSea.java
@@ -84,7 +84,7 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
try {
bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
- +";"+ basin.getName() + ";IMPORT; NONE");
+ +";"+ basin.getName() + ";" + basin.getJuvenileNumber() + ";EXPORT; NONE");
bW.write(";" + totalOutputFluxes.get("biomass"));
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
bW.write(";" + totalOutputFluxes.get(nutrient));
diff --git a/src/main/java/species/NutrientRoutine.java b/src/main/java/species/NutrientRoutine.java
index f3f26a3..d026eb9 100644
--- a/src/main/java/species/NutrientRoutine.java
+++ b/src/main/java/species/NutrientRoutine.java
@@ -356,8 +356,8 @@ public class NutrientRoutine {
Map <String, Double> anExcretionRate = new Hashtable <String, Double>();
- anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
- anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
+ anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alewifes in ug/g wet mass/hour : convertit en g
+ anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alewifes in ug/g wet mass/hour: convertit en g
System.out.println("anExcretionRate: " + anExcretionRate.toString()); //
@@ -431,13 +431,13 @@ public class NutrientRoutine {
// carcass composition for fish before spawning
Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
Map<String,Double> aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.958 / 100.); //On remplit une collection avec un put.
- aCompo.put("P", 0.673 / 100.);
+ aCompo.put("N", 2.958 / 100.); //On remplit une collection avec un put. Values from Haskell (2018) Alosa sapidissima (%)
+ aCompo.put("P", 0.673 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.941 / 100.);
- aCompo.put("P", 0.666 / 100.);
+ aCompo.put("N", 2.941 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
+ aCompo.put("P", 0.666 / 100.);// Values from Haskell (2018) Alosa sapidissima (%)
aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 5bebd92..3d54e84 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -169,6 +169,7 @@ 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){
@@ -310,7 +311,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
}
}
- System.out.println("\t"+message);
+ //System.out.println("\t"+message);
}
// --------------------------------------------------------------------------------------------------
@@ -401,18 +402,17 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
deadFish.clear();
-
if (displayFluxesOnConsole)
System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
- + riverBasin.getName() + "; " + totalInputFluxes);
-
+ + riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + "; " + totalInputFluxes);
BufferedWriter bW = group.getbWForFluxes();
if ( bW != null) {
try {
for (fluxOrigin origin : totalInputFluxes.keySet()) {
bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
- +";"+ riverBasin.getName() + ";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));
}
@@ -429,11 +429,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
- // System.out.println("("+numberOfGenitors+")");
+ //System.out.println("("+numberOfGenitors+")");
//System.out.println(" BEFORE " +riverBasin.getSpawnerOrigins().keySet());
riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
//System.out.println(" AFTER " +riverBasin.getSpawnerOrigins().keySet());
}
+
+
// --------------------------------------------------------------------------------------------------
// update the observers
// --------------------------------------------------------------------------------------------------
--
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