export flux in effective

data/input/fishTryRealBV_CC.xml

@@ -300,6 +300,12 @@
 					<fileNameOutput>lengthAgeDistribution</fileNameOutput>
 				</species.ExportLenghtAgeDistribution>
 
+				<species.ExportFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<exportSeason>SPRING</exportSeason>
+					<fileNameOutput>effectiveFluxes</fileNameOutput>
+				</species.ExportFluxes>
+
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>

src/main/java/species/ExportFluxes.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 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");
+					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()){
+						bW.write(sep+birthBasinName);
+					}
+
+				} 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 per 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 effetive 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 fisrt 2 fields of the line
+					bW.write(Time.getYear(pilot)+sep+migrationBasin.getName());
+					
+					// the cumulative effective from birth basin
+					for (String natalBasinName : group.getEnvironment().getRiverBasinNames()){
+						bW.write(sep+spawnerOriginsBeforeReproduction.get(natalBasinName));
+					}
+					// 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();
+		}
+	}
+}
+