new version of AnalyseFishDistribution

src/main/java/environment/RiverBasin.java

@@ -106,6 +106,7 @@ public class RiverBasin extends Basin {
 
 	// private int memorySize; // size of the queue
 	// TODO define as many QueueMemory as populations
+	private QueueMemory<Double> lastSpawnerNumbersBeforeReproduction;
 	private QueueMemory<Long> lastRecruitments;
 	private QueueMemory<Long> lastRecruitmentExpectations;
 	private QueueMemory<Double> lastProdCapacities; // keep the production capacities of the basin (parameter alpha of
@@ -133,7 +134,6 @@ public class RiverBasin extends Basin {
 
 	protected static transient ObservablesHandler cobservable;
 
-
 	public ObservablesHandler getCobservable() {
 		return cobservable;
 	}
@@ -235,6 +235,7 @@ public class RiverBasin extends Basin {
 		this.yearOfLastNulRep = 0;
 		this.type = Basin.BasinType.RIVER;
 		// this.memorySize = memoryAllQueues;
+		this.lastSpawnerNumbersBeforeReproduction = new QueueMemory<Double>(memorySize);
 		this.lastRecruitments = new QueueMemory<Long>(memorySize);
 		this.lastRecruitmentExpectations = new QueueMemory<Long>(memorySize);
 		this.lastProdCapacities = new QueueMemory<Double>(memorySize);
@@ -429,6 +430,14 @@ public class RiverBasin extends Basin {
 	}
 
 
+	/**
+	 * @return the lastSpawnerNumbersBeforeReproduction
+	 */
+	public QueueMemory<Double> getLastSpawnerNumbersBeforeReproduction() {
+		return this.lastSpawnerNumbersBeforeReproduction;
+	}
+
+
 	public QueueMemory<Long> getLastRecruitments() {
 		return lastRecruitments;
 	}
@@ -453,12 +462,12 @@ public class RiverBasin extends Basin {
 		return numberOfNonNulRecruitmentDuringLastYears;
 	}
 
-
 	/*
 	 * public QueueMemory<Double> getFemaleSpawnersForFirstTimeMeanAges() { return
 	 * spawnersForFirstTimeMeanAges.get(Gender.FEMALE); }
 	 */
 
+
 	public QueueMemory<Double> getSpawnersForFirstTimeMeanLengths(DiadromousFish.Gender gender) {
 		if (gender == Gender.FEMALE)
 			return femaleSpawnersForFirstTimeMeanLengths;

src/main/java/species/AnalyseFishDistribution.java

@@ -27,8 +27,6 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
 
 import environment.RIOBasinNetwork;
 import environment.RiverBasin;
-import environment.Time;
-import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import miscellaneous.TreeMapForCentile;
@@ -39,17 +37,6 @@ import observer.ObservableRecord;
  */
 public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 
-	private Season fishDistributionAnalysisSeason = Season.SPRING;
-
-	private long fishDistributionAnalysisStartYear = 1920;
-
-	private long fishDistributionAnalysisEndYear = 1950;
-
-	private transient List<FishDistributionRecord> records;
-
-	private transient double southernLimit;
-	private transient double northernLimit;
-
 	/**
 	 * The minimum number of recruits to consider a basin as populated
 	 * 
@@ -57,53 +44,11 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
 	 */
 	private int minimumRecruitsForPopulatedBasin = 50;
 
-	private class FishDistributionRecord implements ObservableRecord {
-		@Information(unit = "year")
-		private long year;
-
-		@Information(unit = "-")
-		private int southern_basin_id;
-		@Information(unit = "-")
-		private String southern_basin_name;
-		@Information(unit = "°")
-		private double southern_latitude;
-
-		@Information(unit = "-")
-		private int northern_basin_id;
-		@Information(unit = "-")
-		private String northern_basin_name;
-		@Information(unit = "°")
-		private double northern_latitude;
-
-		@Information(unit = "°")
-		private double centroide_latitude;
-
-		public FishDistributionRecord(long year, int southern_basin_id, String southern_basin_name, double southern_latitude,
-				int northern_basin_id, String northern_basin_name, double northern_latitude, double centroide_latitude) {
-			this.year = year;
-			this.southern_basin_id = southern_basin_id;
-			this.southern_basin_name = southern_basin_name;
-			this.southern_latitude = southern_latitude;
-			this.northern_basin_id = northern_basin_id;
-			this.northern_basin_name = northern_basin_name;
-			this.northern_latitude = northern_latitude;
-			this.centroide_latitude = centroide_latitude;
-		}
-
-
-		@Override
-		public String toString() {
-			return "FishDistributionRecord [year=" + this.year + ", southern_basin_id=" + this.southern_basin_id
-					+ ", southern_basin_name=" + this.southern_basin_name + ", southern_latitude=" + this.southern_latitude
-					+ ", northern_basin_id=" + this.northern_basin_id + ", northern_basin_name=" + this.northern_basin_name
-					+ ", northern_latitude=" + this.northern_latitude + ", centroide_latitude=" + this.centroide_latitude + "]";
-		}
-	}
+	private transient List<FishDistributionRecord> records;
 
-	public static void main(String[] args) {
-		System.out.println((new XStream(new DomDriver())).toXML(new AnalyseFishDistribution()));
-	}
+	private transient double southernLimit;
 
+	private transient double northernLimit;
 
 	@Override
 	public void initTransientParameters(Pilot pilot) {
@@ -126,76 +71,123 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
 		if (records == null)
 			initTransientParameters(group.getPilot());
 
-		Time time = group.getEnvironment().getTime();
-		if (time.getSeason(group.getPilot()) == fishDistributionAnalysisSeason
-				& time.getYear(group.getPilot()) >= fishDistributionAnalysisStartYear
-				& time.getYear(group.getPilot()) <= fishDistributionAnalysisEndYear) {
-
-			// initialise the distribution range
-			double southernEdge = northernLimit;
-			double northernEdge = southernLimit;
-			int southernId = -1;
-			int northernId = -1;
-			String southernName = "";
-			String northernName = "";
-			// initialise for centroid
-			TreeMapForCentile latitudeEffective = new TreeMapForCentile();
-			for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
-
-				if (riverBasin.getLastRecruitments().getLastItem() > minimumRecruitsForPopulatedBasin) {
-					// the basin is considerd as populated
-
-					// southern edge
-					if (riverBasin.getLatitude() < southernEdge) {
-						// the basin is the new southern edge
-						southernEdge = riverBasin.getLatitude();
-						southernId = riverBasin.getBasin_id();
-						southernName = riverBasin.getName();
-					}
-
-					// northern edge
-					if (riverBasin.getLatitude() > southernEdge) {
-						// the basin is the new northern edge
-						northernEdge = riverBasin.getLatitude();
-						northernId = riverBasin.getBasin_id();
-						northernName = riverBasin.getName();
-					}
-
-					// for distribution centroide computation
-					long effective = 0;
-					for (DiadromousFish fish : riverBasin.getFishs(group)) {
-						effective += fish.getAmount();
-					}
-					latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
+		// initialise the distribution range
+		double southernEdge = northernLimit;
+		double northernEdge = southernLimit;
+		int southernId = -1;
+		int northernId = -1;
+		String southernName = "";
+		String northernName = "";
+		// initialise for centroid
+		TreeMapForCentile latitudeEffective = new TreeMapForCentile();
+		TreeMapForCentile latitudePresence = new TreeMapForCentile();
+
+		for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+
+			if (riverBasin.getLastRecruitments().getMean() > minimumRecruitsForPopulatedBasin) {
+				// the river basin is consdered populated
+
+				// NOTE : recruiit number is calulated after thermal tolerance impact
+				// (which is intreaged in the stock-recruitment relationship)
+
+				// southern edge
+				if (riverBasin.getLatitude() < southernEdge) {
+					// the basin is the new southern edge
+					southernEdge = riverBasin.getLatitude();
+					southernId = riverBasin.getBasin_id();
+					southernName = riverBasin.getName();
+				}
+
+				// northern edge
+				if (riverBasin.getLatitude() > southernEdge) {
+					// the basin is the new northern edge
+					northernEdge = riverBasin.getLatitude();
+					northernId = riverBasin.getBasin_id();
+					northernName = riverBasin.getName();
 				}
-			}
-			// if the universe is empty
-			if (southernEdge == northernLimit & northernEdge == southernLimit) {
-				southernEdge = (northernLimit + southernLimit) / 2.;
-				northernEdge = southernEdge;
-			}
-			// distribution centroide computation
-			double centroide = latitudeEffective.calculateMedian();
 
-			// add a record
-			FishDistributionRecord record = new FishDistributionRecord(time.getYear(group.getPilot()), southernId, southernName,
-					southernEdge, northernId, northernName, northernEdge, centroide);
-			records.add(record);
+				// for distribution centroide computation
+				latitudePresence.putWithAdding(riverBasin.getLatitude(), 1L);
+				long effective = ((Double) riverBasin.getLastSpawnerNumbersBeforeReproduction().getMean()).longValue();
+				latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
+			}
+		}
+		// if the universe is empty
+		if (southernEdge == northernLimit & northernEdge == southernLimit) {
+			southernEdge = (northernLimit + southernLimit) / 2.;
+			northernEdge = southernEdge;
 		}
+
+		// distribution centroids computation
+		double basinCentroid = latitudePresence.calculateMedian();
+		double effectiveCentroid = latitudeEffective.calculateMedian();
+
+		// add a record
+		FishDistributionRecord record = new FishDistributionRecord(southernId, southernName, southernEdge, northernId,
+				northernName, northernEdge, basinCentroid, effectiveCentroid);
+
+		records.add(record);
 	}
 
 
 	public double[][] exportToR() {
-
 		double[][] export = new double[records.size()][4];
-
 		for (int i = 0; i < records.size(); i++) {
-			export[i][0] = records.get(i).year;
-			export[i][1] = records.get(i).southern_basin_id;
-			export[i][2] = records.get(i).northern_basin_id;
-			export[i][3] = records.get(i).centroide_latitude;
+			export[i][0] = records.get(i).southern_basin_id;
+			export[i][1] = records.get(i).northern_basin_id;
+			export[i][2] = records.get(i).basinCentroid_latitude;
+			export[i][3] = records.get(i).effectiveCentroid_latitude;
 		}
 		return export;
+	}
+
+	private class FishDistributionRecord implements ObservableRecord {
+
+		@Information(unit = "-")
+		private int southern_basin_id;
+		@Information(unit = "-")
+		private String southern_basin_name;
+		@Information(unit = "°")
+		private double southern_latitude;
+
+		@Information(unit = "-")
+		private int northern_basin_id;
+		@Information(unit = "-")
+		private String northern_basin_name;
+		@Information(unit = "°")
+		private double northern_latitude;
+
+		@Information(unit = "°")
+		private double basinCentroid_latitude;
+		@Information(unit = "°")
+		private double effectiveCentroid_latitude;
 
+		public FishDistributionRecord(int southern_basin_id, String southern_basin_name, double southern_latitude,
+				int northern_basin_id, String northern_basin_name, double northern_latitude, double basinCentroid_latitude,
+				double effectiveCentroid_latitude) {
+			super();
+			this.southern_basin_id = southern_basin_id;
+			this.southern_basin_name = southern_basin_name;
+			this.southern_latitude = southern_latitude;
+			this.northern_basin_id = northern_basin_id;
+			this.northern_basin_name = northern_basin_name;
+			this.northern_latitude = northern_latitude;
+			this.basinCentroid_latitude = basinCentroid_latitude;
+			this.effectiveCentroid_latitude = effectiveCentroid_latitude;
+		}
+
+
+		@Override
+		public String toString() {
+			return "FishDistributionRecord [southern_basin_id=" + this.southern_basin_id + ", southern_basin_name="
+					+ this.southern_basin_name + ", southern_latitude=" + this.southern_latitude + ", northern_basin_id="
+					+ this.northern_basin_id + ", northern_basin_name=" + this.northern_basin_name + ", northern_latitude="
+					+ this.northern_latitude + ", basinCentroide_latitude=" + this.basinCentroid_latitude
+					+ ", effectiveCentroide_latitude=" + this.effectiveCentroid_latitude + "]";
+		}
+	}
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver())).toXML(new AnalyseFishDistribution()));
 	}
 }

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

 package species;
 
-import java.io.BufferedWriter;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Hashtable;
@@ -82,7 +80,6 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	private transient StockRecruitmentRelationship stockRecruitmentRelationship;
 	// private transient UniformGen genUniform;
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new ReproduceAndSurviveAfterReproductionWithDiagnose()));
 	}
@@ -128,7 +125,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 			for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
 
 				// before the party !!!!
-				double fluxBefore = riverBasin.getSpawnerNumber();
+				double fluxBefore = riverBasin.getSpawnerNumberPerGroup(group);
+				riverBasin.getLastSpawnerNumbersBeforeReproduction().add(fluxBefore);
 
 				double b, c, alpha, beta, amountPerSuperIndividual, S95, S50;
 				double numberOfFemaleSpawners = 0.;
@@ -520,16 +518,16 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 									/ riverBasin.getLastProdCapacities().getLastItem());
 
 							// keep the no null recruitment
-							if (numberOfAutochtones > 0) {
-								riverBasin.getNumberOfNonNulRecruitmentForFinalProbOfPres().push(1.);
-								riverBasin.getNumberOfNonNulRecruitmentDuringLastYears().push(1.);
-							} else {
-								riverBasin.getNumberOfNonNulRecruitmentForFinalProbOfPres().push(0.);
-								riverBasin.getNumberOfNonNulRecruitmentDuringLastYears().push(0.);
-							}
+							// if (numberOfAutochtones > 0) {
+							riverBasin.getNumberOfNonNulRecruitmentForFinalProbOfPres().push(1.);
+							riverBasin.getNumberOfNonNulRecruitmentDuringLastYears().push(1.);
+							// } else {
+							// riverBasin.getNumberOfNonNulRecruitmentForFinalProbOfPres().push(0.);
+							// riverBasin.getNumberOfNonNulRecruitmentDuringLastYears().push(0.);
+							// }
 
 						} else {
-							// stock the last year of null recruitment
+							// stock the null recruitment of the last year
 							riverBasin.setYearOfLastNulRep(time.getYear(group.getPilot()));
 							riverBasin.getLastRecruitmentExpectations().push((long) 0);
 							riverBasin.getLastRecruitments().push((long) 0);
@@ -567,26 +565,18 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					 * ";" + riverBasin.getSpawnerNumberPerGroup(group)+ "; " + totalInputFluxes);
 					 */
 					/*
-					BufferedWriter bW = group.getbWForFluxes();
-					if (bW != null) {
-						try {
-							for (SpawnerOrigin origin : totalInputFluxes.keySet()) {
-								bW.write(group.getPilot().getCurrentTime() + "; " + time.getYear(group.getPilot()) + ";"
-										+ time.getSeason(group.getPilot()) + ";" + riverBasin.getName() + ";" + fluxBefore + ";"
-										+ "IMPORT" + ";" + origin);
-								bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
-
-								for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
-									bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
-								}
-								bW.write("\n");
-							}
-						} catch (IOException e) {
+					 * BufferedWriter bW = group.getbWForFluxes(); if (bW != null) { try { for (SpawnerOrigin origin :
+					 * totalInputFluxes.keySet()) { bW.write(group.getPilot().getCurrentTime() + "; " +
+					 * time.getYear(group.getPilot()) + ";" + time.getSeason(group.getPilot()) + ";" +
+					 * riverBasin.getName() + ";" + fluxBefore + ";" + "IMPORT" + ";" + origin); bW.write(";" +
+					 * totalInputFluxes.get(origin).get("biomass"));
+					 * 
+					 * for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) { bW.write(";" +
+					 * totalInputFluxes.get(origin).get(nutrient)); } bW.write("\n"); } } catch (IOException e) {
+					 * 
+					 * e.printStackTrace(); } }
+					 */
 
-							e.printStackTrace();
-						}
-					}*/
-					
 				} else {
 					riverBasin.setYearOfLastNulRep(time.getYear(group.getPilot()));
 				}
@@ -657,7 +647,6 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 		 */
 		double sigmaZ; //
 
-
 		public void init(double alpha, double beta, double S50, double S95) {
 			this.alpha = alpha;
 			this.beta = beta;
@@ -752,7 +741,6 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 		// third: effective of corresponding recruitment
 		List<Trio<Integer, Long, Long>> data; // WHY age as integer
 
-
 		public void init(List<Trio<Integer, Long, Long>> data) {
 			this.data = data;
 		}