Add Svn history

.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//data/input=ISO-8859-1

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

data/input/fish.xml

+<list>
+  <pikelake.pikes.PikesGroup>
+    <weightAtAgeThreshold>5.0</weightAtAgeThreshold>
+    <monthOfBirth>6</monthOfBirth>
+    <processes>
+      <processesAtBegin>
+        <pikelake.pikes.PikesPopulateProcess>
+          <initialNumberOfPikes>5</initialNumberOfPikes>
+        </pikelake.pikes.PikesPopulateProcess>
+      </processesAtBegin>
+      <processesEachStep>
+        <pikelake.pikes.PikeMovement/>
+        <pikelake.pikes.PikeHuntProcess>
+          <satiety>0.5</satiety>
+        </pikelake.pikes.PikeHuntProcess>
+        <pikelake.pikes.PikeGrowthProcess>
+          <convertionFactor>0.25</convertionFactor>
+          <slimRate>0.9</slimRate>
+        </pikelake.pikes.PikeGrowthProcess>
+        <pikelake.pikes.PikeMortalityProcess/>
+        <pikelake.pikes.PikeReproductionProcess>
+        		<ageAtFirstReproduction>5</ageAtFirstReproduction>
+        		<pikeFertility>1.3</pikeFertility>
+        </pikelake.pikes.PikeReproductionProcess>        
+        <pikelake.pikes.PikeObservationProcess/>
+        <fr.cemagref.simaqualife.kernel.processes.FireAquaNismsChangesToObservers/>
+       </processesEachStep>
+    </processes>
+    <useCemetery>false</useCemetery>
+  </pikelake.pikes.PikesGroup>
+</list>
\ No newline at end of file

data/input/fishLight.xml

+<list>
+  <pikelake.pikes.PikesGroup>
+    <weightAtAgeThreshold>5.0</weightAtAgeThreshold>
+    <monthOfBirth>6</monthOfBirth>
+    <processes>
+      <processesAtBegin>
+        <pikelake.pikes.PikesPopulateProcess>
+          <initialNumberOfPikes>1</initialNumberOfPikes>
+        </pikelake.pikes.PikesPopulateProcess>
+      </processesAtBegin>
+      <processesEachStep>
+        <pikelake.pikes.PikeMovement/>
+        <pikelake.pikes.PikeHuntProcess>
+          <satiety>0.5</satiety>
+        </pikelake.pikes.PikeHuntProcess>
+        <pikelake.pikes.PikeGrowthProcess>
+          <convertionFactor>0.25</convertionFactor>
+          <slimRate>0.9</slimRate>
+        </pikelake.pikes.PikeGrowthProcess>
+        <pikelake.pikes.PikeObservationProcess/>
+        <fr.cemagref.simaqualife.kernel.processes.FireAquaNismsChangesToObservers/>
+       </processesEachStep>
+    </processes>
+    <useCemetery>false</useCemetery>
+  </pikelake.pikes.PikesGroup>
+</list>
\ No newline at end of file

data/input/grid.xml

+<?xml version="1.0" encoding="ISO-8859-1"?> 
+<pikelake.Grid>
+	<torusType>BOTH</torusType>
+	<neighborsType>NEIGHBORHOOD_VON_NEUMANN</neighborsType>
+  <preyCarryingCapacity>50</preyCarryingCapacity>
+  <gridWidth>10</gridWidth>
+  <gridHeight>10</gridHeight>
+  <habitatValue0>0.25</habitatValue0>
+  <habitatValue1>0.5</habitatValue1>
+  <habitatValue2>1</habitatValue2>
+</pikelake.Grid>
\ No newline at end of file

data/input/observersBatch.xml

+<hashtable>
+  <entry>
+    <java-class>pikeprey.pikes.PikesGroup</java-class>
+    <fr.cemagref.observation.kernel.ObservablesHandler>
+      <observers>
+      	<fr.cemagref.observation.observers.CSVObserver>
+          <separator>;</separator>
+          <sysout>false</sysout>
+          <outputFile>data/pikes.txt</outputFile>
+        </fr.cemagref.observation.observers.CSVObserver>
+      </observers>
+    </fr.cemagref.observation.kernel.ObservablesHandler>
+  </entry>
+</hashtable>

data/input/observersCharts.xml

+<hashtable>
+  <entry>
+    <java-class>pikelake.pikes.PikesGroup</java-class>
+    <fr.cemagref.observation.kernel.ObservablesHandler>
+      <observers>
+      	<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+      		<graphType>LINE</graphType>
+      		<title>Observation of pikes biomass</title>
+      		<xAxisLabel>Time (month)</xAxisLabel>
+      		<yAxisLabel>pikes biomass</yAxisLabel>
+    	</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+      </observers>
+    </fr.cemagref.observation.kernel.ObservablesHandler>
+  </entry>
+  <entry>
+    <java-class>pikelake.pikes.Pike</java-class>
+    <fr.cemagref.observation.kernel.ObservablesHandler>
+      <observers>
+      	<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+      		<graphType>LINE</graphType>
+      		<title>Observation of pikes</title>
+      		<xAxisLabel>Time (month)</xAxisLabel>
+      		<yAxisLabel></yAxisLabel>
+    	</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
+      </observers>
+    </fr.cemagref.observation.kernel.ObservablesHandler>
+  </entry>
+</hashtable>

src/main/java/pikelake/pikes/Pike.java

+package pikelake.pikes;
+
+import fr.cemagref.simaqualife.pilot.Pilot;
+import Pike.Cell;
+import Pike.Individual;
+
+public class Pike extends Individual {
+
+	private double ingestedFood=0.;
+	
+    public Pike(Pilot pilot, Cell cell) {
+    	//TODO fix weight according to the weightAtAgeThreshold
+        // Default value of weight at birth
+    	this(pilot, cell, 0, 10.);
+    }
+    
+    public Pike(Pilot pilot, Cell cell, int age, double weight) {
+        super(pilot, cell);
+        this.age =age;
+        this.weight = weight;
+    }
+    
+
+	public double getIngestedFood() {
+		return ingestedFood;
+	}
+
+	public void setIngestedFood(double ingestedFood) {
+		this.ingestedFood = ingestedFood;
+	}
+	public void addIngestedFood(double ingestedFood) {
+		this.ingestedFood += ingestedFood;
+	}
+	
+	public double getSuitabilityForPike(Cell cell){
+		if (cell.getPikes().size()>1)
+			return 0.; // at least an other pike in the cell
+		else
+			return 1.; /////////////////////////////////////////////////////////
+			//return((double) cell.getPreys().size()) * cell.getHabitatQuality(); // number of preys accessible
+	}
+	
+	
+}
+

src/main/java/pikelake/pikes/PikeGrowthProcess.java

+package pikelake.pikes;
+
+import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
+import fr.cemagref.simaqualife.kernel.processes.LoopAquaNismsGroupProcess;
+
+public class PikeGrowthProcess extends LoopAquaNismsGroupProcess<Pike,AquaNismsGroup<Pike,?>> {
+
+	/**
+	 * <code>convertionFactor</code> proportion of the ingested food transformed into pike weight 
+	 */
+	private double convertionFactor = 0.25;
+	private double slimRate = 0.90;
+	
+	@Override
+	protected void doProcess(Pike pike, AquaNismsGroup<Pike, ?> group) {
+		pike.incAge();
+		//System.out.print("  "+ (double) pike.getAge()/12. +"y "+pike.getWeight()+ " " );
+		pike.setWeight( pike.getWeight() * slimRate + pike.getIngestedFood()* convertionFactor);
+		//System.out.print(pike.getIngestedFood() +" " + pike.getWeight());
+		//double ratio = 12* pike.getWeight()/(pike.getAge()+12);
+		//System.out.println("("+ ((double) Math.round(ratio*100))/100 +")");
+		pike.setIngestedFood(0.0);
+	}
+
+}

src/main/java/pikelake/pikes/PikeHuntProcess.java

+package pikelake.pikes;
+
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import pikelake.Cell;
+//	import predatorprey.preys.Prey;	////////////////////////////////////////////////////////////
+//	import predatorprey.preys.PreysGroup;	////////////////////////////////////////////////////
+import umontreal.iro.lecuyer.probdist.UniformDist;
+import umontreal.iro.lecuyer.randvar.UniformGen;
+import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
+import fr.cemagref.simaqualife.kernel.processes.LoopAquaNismsGroupProcess;
+import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
+import fr.cemagref.simaqualife.pilot.Pilot;
+
+/**
+ * @author patrick.lambert
+ * 
+ */
+public class PikeHuntProcess extends
+LoopAquaNismsGroupProcess<Pike, AquaNismsGroup<Pike, ?>> {
+
+	/**
+	 * <code>satiety</code> ratio of the pike weigth which stops eating
+	 * preys
+	 */
+	private double satiety = 0.10;
+
+	transient private UniformGen uniformGen;
+
+	@Override
+	protected void doProcess(Pike pike,
+			AquaNismsGroup<Pike, ?> group) {
+		Cell pikeCell = pike.getPosition();
+/*		if (pikeCell.getPreys().size() > 0) {
+			//System.out.print(" " +  pikeCell.getPreys().size() +" preys available in cell ");
+			//System.out.print("("+pikeCell.getX()+","+pikeCell.getY()+")");
+			
+			// sort the preys list according to the weigth
+			List<Prey> sortedPreys = pikeCell.getPreys();
+			Collections.sort(sortedPreys);
+
+			double ratio = pike.getIngestedFood()/pike.getWeight();
+			int idx = 0;
+			int idxMax =  sortedPreys.size();
+			int target=0;
+			int eaten=0;
+			while ((pike.getIngestedFood()/pike.getWeight() < satiety) && (idx < idxMax)) {
+
+				// the probability for a prey to be eaten depends 
+				// on the habitat quality in the cell
+				if (uniformGen.nextDouble() < pikeCell.getHabitatQuality()){
+					// eat the prey
+					Prey eatenPrey = sortedPreys.get(target);
+					pike.addIngestedFood(eatenPrey.getWeight());
+
+					// and the prey dies
+					
+					((PreysGroup)group.getPilot().getAquaticWorld().getAquaNismsGroupsList().get(0)).removeAquaNism(eatenPrey);
+					//this.interAquanism(eatenPrey);
+					pikeCell.removePrey(eatenPrey);
+					eaten ++;
+				}
+				else
+					target ++;
+
+				idx++;
+				ratio = pike.getIngestedFood()/pike.getWeight();
+			}
+			ratio= ((double) Math.round(100*ratio))/100;
+			//System.out.println(", " + eaten + " preys eaten ("+ ratio +" ), still " +  pikeCell.getPreys().size());
+		}	*/
+
+	}
+
+	@InitTransientParameters
+	public void initTransientParameters(Pilot pilot) {
+		sorted = true;
+		comparator = new Comparator<Pike>() {
+			public int compare(Pike o1, Pike o2) {
+				return (int) Math.signum(o2.getWeight() - o1.getWeight());
+			}
+		};
+
+		uniformGen = new UniformGen(pilot.getRandomStream(), new UniformDist());
+	}
+
+}

src/main/java/pikelake/pikes/PikeMortalityProcess.java

+package pikelake.pikes;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+
+public class PikeMortalityProcess extends AquaNismsGroupProcess<Pike, PikesGroup>{
+
+	public void doProcess(PikesGroup group) {
+		List<Pike> deadPike = new ArrayList<Pike>();
+		for (Pike pike: group.getAquaNismsList()){
+			double ratio = (12. * pike.getWeight() / (double) (pike.getAge()+12));
+
+			if (ratio < group.getWeightAtAgeThreshold())
+				deadPike.add(pike);
+		}
+	    // update the pikesGroup
+		for (Pike pike: deadPike){
+			group.getAquaNismsList().remove(pike);
+			//ASK WHY
+			pike.getPosition().removePike(pike);
+		}
+	}
+}

src/main/java/pikelake/pikes/PikeMovement.java

+package pikelake.pikes;
+
+import fr.cemagref.simaqualife.kernel.processes.LoopAquaNismsGroupProcess;
+import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import pikelake.Cell;
+import umontreal.iro.lecuyer.probdist.UniformDist;
+import umontreal.iro.lecuyer.randvar.UniformGen;
+import fr.cemagref.simaqualife.pilot.Pilot;
+
+public class PikeMovement extends LoopAquaNismsGroupProcess<Pike, PikesGroup> {
+
+    transient private UniformGen uniformGen;
+
+    public PikeMovement(Pilot pilot) {
+        uniformGen = new UniformGen(pilot.getRandomStream(), new UniformDist());
+    }
+	@InitTransientParameters
+	public void initTransientParameters(Pilot pilot) {
+		uniformGen = new UniformGen(pilot.getRandomStream(), new UniformDist(0,1));
+	}
+    
+    
+    @Override
+    protected void doProcess(Pike pike, PikesGroup group) {
+
+        final List<Cell> surrounding = group.getEnvironment().
+        getNeighbours(pike.getPosition());
+
+        // the first possiblity is the cell where the prey is
+        List<Cell> possibilities = new ArrayList<Cell>();
+        possibilities.add(pike.getPosition());
+        double cellSuitability = pike.getSuitabilityForPike(pike.getPosition());
+
+        // identify the destination possibilities in the neighbouring
+        // with the highest suitability
+        for (Cell cell : surrounding) {
+            double currentCellSuitability = pike.getSuitabilityForPike(cell);
+            if (currentCellSuitability > cellSuitability) {
+                cellSuitability = currentCellSuitability;
+                possibilities.clear();
+                possibilities.add(cell);
+            } else if (currentCellSuitability == cellSuitability) {
+                possibilities.add(cell);
+            }
+        }
+
+        // choose the destination cell
+        int possibilitiesNumber = possibilities.size();
+        if (possibilitiesNumber == 1) {
+            pike.moveTo(group.getPilot(), possibilities.get(0), group);
+        } else {
+            int idx = (int) Math.floor(uniformGen.nextDouble() * (double) possibilitiesNumber);
+            pike.moveTo(group.getPilot(), possibilities.get(idx), group);
+        }
+    }
+}

src/main/java/pikelake/pikes/PikeObservationProcess.java

+package pikelake.pikes;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+public class PikeObservationProcess extends AquaNismsGroupProcess<Pike,PikesGroup> {
+
+	public void doProcess(PikesGroup pikesGroup) {
+		pikesGroup.calculatePikesBiomass();
+		pikesGroup.calculatePikesNumber();
+		
+	}
+
+}

src/main/java/pikelake/pikes/PikePlopProcess.java

+package pikelake.pikes;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+public class PlopProcess extends AquaNismsGroupProcess<Pike,PikesGroup> {
+
+	private int temporisation = 3000; // in ms
+	
+	public void doProcess(PikesGroup object) {
+    	try {
+			Thread.sleep(temporisation);
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		}
+		
+	}
+
+}

src/main/java/pikelake/pikes/PikeReproductionProcess.java

+/**
+ * 
+ */
+package pikelake.pikes;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import umontreal.iro.lecuyer.probdist.PoissonDist;
+import umontreal.iro.lecuyer.randvar.PoissonGen;
+
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import fr.cemagref.simaqualife.pilot.Pilot;
+
+/**
+ * @author patrick.lambert
+ *
+ */
+public class PikeReproductionProcess extends AquaNismsGroupProcess<Pike,PikesGroup> {
+	
+	/**
+	 * <code>ageAtFirstReproduction</code> age at first reproduction (in year)
+	 */
+	private int ageAtFirstReproduction = 5;
+	
+	/**
+	 * <code>pikeFertility</code> mean number of offsprings per pike
+	 */
+	private double pikeFertility = 1.1;
+	
+	transient private PoissonGen poissonGen;
+
+	
+
+	public void initTransientParameters(Pilot pilot) {
+		poissonGen = new PoissonGen(pilot.getRandomStream(), new PoissonDist(pikeFertility));
+		
+	}
+	
+	public void doProcess(PikesGroup group) {
+		int offspring;
+		if (1+ ((group.getPilot().getCurrentTime()-1) % 12) == group.getMonthOfBirth()){
+			List<Pike> offsprings = new ArrayList<Pike>();
+			List<Pike> deadSpwaners = new ArrayList<Pike>();
+			for (Pike pike: group.getAquaNismsList()){
+				if (Math.floor((double) pike.getAge()/12.) >= ageAtFirstReproduction){
+					// number of offspring
+					offspring = poissonGen.nextInt();
+
+					System.out.println("  offspring #: "+ offspring);
+					for (int i=0; i<offspring ;i++)
+						offsprings.add(new Pike(group.getPilot(), pike.getPosition()));
+					// die after reproduction
+					//if (offspring > 0) // only if reproduce
+						deadSpwaners.add(pike);		
+				}	
+			}
+	    // update the pikesGroup
+		for (Pike pike: deadSpwaners){
+			group.getAquaNismsList().remove(pike);
+			//ASK WHY
+			pike.getPosition().removePike(pike);
+		}
+
+		for (Pike pike: offsprings)
+			group.addAquaNism(pike);
+			
+		}
+	}
+	
+	
+}