write biomass and effective fluxes

data/input/fishTryRealBV_CC.xml

@@ -214,7 +214,9 @@
 			<processesEachStep>
 				<environment.InformTime>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					  <consoleDisplay>true</consoleDisplay>
 				</environment.InformTime>
+				
 				<species.PlopProcess>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<temporisation>0</temporisation>
@@ -273,18 +275,12 @@
 					<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
 				</species.Survive>
 
-				<species.WriteEffectivesFluxes>
+				<species.WriteEffectiveAndBiomassFluxes>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<exportSeason>SPRING</exportSeason>
-					<fileNameOutput>effectiveFluxes</fileNameOutput>
-				</species.WriteEffectivesFluxes>
-
-				<species.WriteBiomassFluxes>
-					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
-					<exportSeason>SPRING</exportSeason>
-					<fileNameOutput>BiomassFluxessBeforeReproduction</fileNameOutput>
-				</species.WriteBiomassFluxes>
-
+					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
+				</species.WriteEffectiveAndBiomassFluxes>
+				
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>

src/main/java/species/NutrientRoutine.java

@@ -116,11 +116,11 @@ public class NutrientRoutine {
 
 	private Map<String,Double> compoJuvenile;
 
-	private transient NutrientFluxesCollection nutrientFluxesCollection;
+	private transient NutrientImportFluxesCollection nutrientImportFluxesCollection;
 
 
 	public NutrientRoutine() {
-		this.nutrientFluxesCollection = new NutrientFluxesCollection();
+		this.nutrientImportFluxesCollection = new NutrientImportFluxesCollection();
 	}
 
 	/**
@@ -155,17 +155,17 @@ public class NutrientRoutine {
 		this.juvenileFeatures = juvenileFeatures;
 		this.compoJuvenile = compoJuvenile; 
 
-		this.nutrientFluxesCollection = new NutrientFluxesCollection();
+		this.nutrientImportFluxesCollection = new NutrientImportFluxesCollection();
 
 	}
 
 	public void createNutrienFluxesCollection(String[] basinNames) {
-		nutrientFluxesCollection = new NutrientFluxesCollection();
-		nutrientFluxesCollection.setBasinNames(basinNames);
+		nutrientImportFluxesCollection = new NutrientImportFluxesCollection();
+		nutrientImportFluxesCollection.setBasinNames(basinNames);
 	}
 
-	public NutrientFluxesCollection getNutrientFluxesCollection() {
-		return nutrientFluxesCollection;
+	public NutrientImportFluxesCollection getNutrientFluxesCollection() {
+		return nutrientImportFluxesCollection;
 	}
 
 	/**
@@ -546,9 +546,10 @@ public class NutrientRoutine {
 
 	} 
 
-	public class NutrientFluxesCollection { 
+	public class NutrientImportFluxesCollection { 
 
 		/* 
+		 * collection of import fluxes (from sea to rivers)
 		 * <key> Year
 		 * <value> 
 		 * 	<key> Nutrient
@@ -558,21 +559,37 @@ public class NutrientRoutine {
 		 * 			<key> destination basin name 
 		 * 			<value> flux 
 		 */
-		//  
-		private Map<Long, Map <String, Map<String, Map<String, Double>>>> fluxesCollection ;
+		private Map<Long, Map <String, Map<String, Map<String, Double>>>> importFluxesCollection ;
+		
+		/* 
+		 * collection of export fluxes (from river to sea)
+		 * <key> Year
+		 * <value> 
+		 * 	<key> Nutrient
+		 * 	<value>	
+		 * 		<key> origin basin name 
+		 * 		<value> flux
+		 */
+		private Map<Long, Map <String,  Map<String, Double>>> exportFluxesCollection ;
+		
 		private transient String[] basinNames; 
 
-		NutrientFluxesCollection() {
+		NutrientImportFluxesCollection() {
 
-			fluxesCollection  = new HashMap <Long, Map <String, Map<String, Map<String, Double>>>> (); 
+			importFluxesCollection  = new HashMap <Long, Map <String, Map<String, Map<String, Double>>>> ();
+			exportFluxesCollection = new HashMap <Long, Map <String,  Map<String, Double>>> ();
 		}
 
 
-		public Map<Long, Map<String, Map<String, Map<String, Double>>>> getFluxesCollection() {
-			return fluxesCollection;
+		public Map<Long, Map<String, Map<String, Map<String, Double>>>> getImportFluxesCollection() {
+			return importFluxesCollection;
 		}
 
-
+		
+		public Map<Long, Map<String,  Map<String, Double>>> getExportFluxesCollection() {
+			return exportFluxesCollection;
+		}
+		
 		public void setBasinNames(String[] basinNames) {
 			this.basinNames = basinNames;
 		}
@@ -580,7 +597,7 @@ public class NutrientRoutine {
 
 		public void put(Long year,String nutrient, String originBasinName, String destinationBasinName, Double flux ) {
 
-			if(!fluxesCollection.containsKey(year)) {
+			if(!importFluxesCollection.containsKey(year)) {
 
 				Map <String, Map <String, Map <String, Double>>> nutrientsMap = new TreeMap <String, Map <String, Map <String, Double>>>();
 
@@ -600,15 +617,69 @@ public class NutrientRoutine {
 					nutrientsMap.put(nutrientOfInterest, originsMap); 
 				}
 
-				fluxesCollection.put(year,nutrientsMap); 
+				importFluxesCollection.put(year,nutrientsMap); 
 			} 
 
-			double previousFlux = fluxesCollection.get(year).get(nutrient).get(originBasinName).get(destinationBasinName); 
-			fluxesCollection.get(year).get(nutrient).get(originBasinName).put(destinationBasinName, previousFlux + flux);
+			double previousFlux = importFluxesCollection.get(year).get(nutrient).get(originBasinName).get(destinationBasinName); 
+			importFluxesCollection.get(year).get(nutrient).get(originBasinName).put(destinationBasinName, previousFlux + flux);
 
 		} 
 	}
 
+	public class NutrientExportFluxesCollection { 
+
+		/* 
+		 * <key> Year
+		 * <value> 
+		 * 	<key> Nutrient
+		 * 	<value>	
+		 * 		<key> origin basin name 
+		 * 		<value>  flux 
+		 */
+		//  
+		private Map<Long, Map<String, Map<String, Double>>> exportFluxesCollection ;
+		private transient String[] basinNames; 
+
+		NutrientExportFluxesCollection() {
+
+			exportFluxesCollection  = new HashMap <Long,  Map<String, Map<String, Double>>> (); 
+		}
+
+
+		public Map<Long,  Map<String, Map<String, Double>>> getFluxesCollection() {
+			return exportFluxesCollection;
+		}
+
+
+		public void setBasinNames(String[] basinNames) {
+			this.basinNames = basinNames;
+		}
+
+
+		public void put(Long year,String nutrient, String originBasinName, Double flux ) {
+
+			if(!exportFluxesCollection.containsKey(year)) {
+
+				Map <String,  Map <String, Double>> nutrientsMap = new TreeMap <String,  Map <String, Double>>();
+
+				for (String nutrientOfInterest : nutrientsOfInterest) {
+
+					Map <String, Double> originsMap = new TreeMap <String,  Double>();
+					for (String originName : basinNames) {
+						originsMap.put(originName, 0.); 
+					}
+
+					nutrientsMap.put(nutrientOfInterest, originsMap); 
+				}
+
+				exportFluxesCollection.put(year,nutrientsMap); 
+			} 
+
+			double previousFlux = exportFluxesCollection.get(year).get(nutrient).get(originBasinName); 
+			exportFluxesCollection.get(year).get(nutrient).put(originBasinName, previousFlux + flux);
+
+		} 
+	}
 }
 
 

src/main/java/species/WriteEffectiveAndBiomassFluxes.java

+/**
+ * patrick.lambert
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2018, Irstea
+ *
+ * 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
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+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 WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private Season exportSeason = Season.SPRING;
+
+	private String fileNameOutput = "effectiveBiomassFluxes";
+
+	private transient BufferedWriter bW;
+	private transient String sep=";";
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver()))
+				.toXML(new WriteEffectiveAndBiomassFluxes()));
+	}
+
+	/* (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+"type"+ sep+"originBasin" ); //create the field of the column
+					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
+						bW.write(sep + birthBasinName); // write each basin name in the file 
+					}
+					bW.write("\n");
+
+				} catch (IOException e) {
+					e.printStackTrace();
+				}
+			}
+		}
+
+		if (Time.getSeason(pilot) == exportSeason & Time.getYear(pilot) >= group.getMinYearToWrite()) {
+
+			//Create the map to get the biomass in each migration basin and birth basin
+			Map<String, Map<String, Long>> spawnerEffectivePerDestination = new HashMap<String,  Map<String, Long>>(group.getEnvironment().getRiverBasinNames().length); 
+			//Create the map to get the abundance in each migration and birth birth basin
+			Map<String,  Map<String, Double>> spawnerBiomassPerDestination = new HashMap<String,  Map<String, Double>>(group.getEnvironment().getRiverBasinNames().length); 
+
+			// initialise maps with 0
+			for (String destinationName: group.getEnvironment().getRiverBasinNames()) {
+				Map<String, Long> spawnerEffectivePerOrigin =  new HashMap<String, Long>(group.getEnvironment().getRiverBasinNames().length); 
+				Map<String, Double> spawnerBiomassPerOrigin =  new HashMap<String, Double>(group.getEnvironment().getRiverBasinNames().length); 
+				for (String originName : group.getEnvironment().getRiverBasinNames()){
+					spawnerEffectivePerOrigin.put(originName,  0L);		
+					spawnerBiomassPerOrigin.put(originName, 0.);
+				}
+
+				spawnerEffectivePerDestination.put(destinationName,spawnerEffectivePerOrigin );
+				spawnerBiomassPerDestination.put(destinationName,spawnerBiomassPerOrigin );
+			}
+
+			for (RiverBasin destinationBasin: group.getEnvironment().getRiverBasins()) {
+				//compute the cumulative effective and biomass per birth basin 
+				if (destinationBasin.getFishs(group) != null) {
+					for (DiadromousFish fish : destinationBasin.getFishs(group)) {
+						if (fish.getStage() == Stage.MATURE) {
+							String originBasinName = fish.getBirthBasin().getName();
+
+							spawnerEffectivePerDestination.get(destinationBasin.getName()).
+							put(originBasinName, spawnerEffectivePerDestination.get(destinationBasin.getName()).get(originBasinName) + fish.getAmount() );
+
+							double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
+							spawnerBiomassPerDestination.get(destinationBasin.getName()).
+							put(originBasinName, spawnerBiomassPerDestination.get(destinationBasin.getName()).get(originBasinName) + biomass );
+						}
+					}
+				}
+			}
+
+			try {
+				// write effective
+				for (String originBasinName: group.getEnvironment().getRiverBasinNames()) {
+					bW.write(Time.getYear(pilot)+ sep + "effective" + sep + originBasinName );
+
+					for (String destinationBasinName : group.getEnvironment().getRiverBasinNames()) {
+						bW.write(sep+spawnerEffectivePerDestination.get(destinationBasinName).get(originBasinName));
+					}
+					// write an end-of-line
+					bW.write("\n");
+				}
+
+				// write biomass
+				for (String originBasinName: group.getEnvironment().getRiverBasinNames()) {
+					bW.write(Time.getYear(pilot)+ sep + "biomass"+ sep + originBasinName );
+
+					for (String destinationBasinName : group.getEnvironment().getRiverBasinNames()) {
+						bW.write(sep+spawnerBiomassPerDestination.get(destinationBasinName).get(originBasinName));
+					}
+					// write an end-of-line
+					bW.write("\n");
+				}
+
+
+				if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1) {
+					bW.flush();
+					bW.close();
+				}
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}
+	}
+}
+

src/main/java/species/WriteImportNutrientFluxes.java

@@ -47,7 +47,7 @@ public class WriteImportNutrientFluxes extends AquaNismsGroupProcess<DiadromousF
 
 			bW.write("\n");
 
-			Map<Long, Map <String, Map<String, Map<String, Double>>>> fluxesCollection = group.getNutrientRoutine().getNutrientFluxesCollection().getFluxesCollection();
+			Map<Long, Map <String, Map<String, Map<String, Double>>>> fluxesCollection = group.getNutrientRoutine().getNutrientFluxesCollection().getImportFluxesCollection();
 
 			// to iterate on sorted years
 			List<Long> years =  new ArrayList<Long>(fluxesCollection.keySet());