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− 112
.settings/org.eclipse.core.resources.prefs
+ 4
− 1
eclipse.preferences.version=1
encoding//data/input=ISO-8859-1
encoding//data/input=ISO-8859-15
encoding//src/main/java=ISO-8859-15
encoding//src/test/java=ISO-8859-15
encoding/<project>=ISO-8859-15
.settings/org.eclipse.jdt.core.prefs
+ 5
− 3
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.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.compliance=1.6
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
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.6
.settings/org.eclipse.m2e.core.prefs 0 → 100644
+ 4
− 0
activeProfiles=
eclipse.preferences.version=1
resolveWorkspaceProjects=true
version=1
.settings/org.eclipse.pde.core.prefs 0 → 100644
+ 2
− 0
BUNDLE_ROOT_PATH=target/classes
eclipse.preferences.version=1
data/input/fish.xml
+ 2
− 0
<?xml version="1.0" encoding="ISO-8859-15"?>
<!DOCTYPE xml>
<list>
<pikelake.pikes.PikesGroup>
<weightAtAgeThreshold>5.0</weightAtAgeThreshold>
data/input/fishLight.xml
+ 29
− 26
<?xml version="1.0" encoding="ISO-8859-15"?>
<!DOCTYPE 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>
<distance>10.0</distance>
</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>
<pikelake.pikes.PikesGroup>
<weightAtAgeThreshold>5.0</weightAtAgeThreshold>
<monthOfBirth>6</monthOfBirth>
<processes>
<processesAtBegin>
<pikelake.pikes.PikesPopulateProcess>
<initialNumberOfPikes>10</initialNumberOfPikes>
</pikelake.pikes.PikesPopulateProcess>
</processesAtBegin>
<processesEachStep>
<pikelake.pikes.PikeMovement>
<distance>10</distance>
</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/>
<pikelake.pikes.PikeMovement/>
<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
+ 7
− 3
<?xml version="1.0" encoding="ISO-8859-1"?>
<?xml version="1.0" encoding="ISO-8859-15"?>
<!DOCTYPE xml>
<pikelake.Grid>
<!--inputFileName>river2DShape.txt</inputFileName-->
<!--depthCoef >2.3</depthCoef-->
<!--ncFileName>data/SiAM3168.nc</ncFileName-->
<!--sectorFileName>data/shapefile.EstuarySector.txt</sectorFileName-->
<torusType>BOTH</torusType>
<neighborsType>NEIGHBORHOOD_VON_NEUMANN</neighborsType>
<gridWidth>10</gridWidth>
<gridHeight>10</gridHeight>
<gridWidth>214</gridWidth>
<gridHeight>243</gridHeight>
</pikelake.Grid>
\ No newline at end of file
data/input/observersBatch.xml
+ 2
− 0
<?xml version="1.0" encoding="ISO-8859-15"?>
<!DOCTYPE xml>
<hashtable>
<entry>
<java-class>pikeprey.pikes.PikesGroup</java-class>
data/input/observersCharts.xml
+ 90
− 26
<?xml version="1.0" encoding="ISO-8859-15"?>
<!DOCTYPE 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>
<entry>
<java-class>pikelake.GridObserver</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<fr.cemagref.simaqualife.extensions.spatial2D.Movement2DObserver>
<title>Bariousses</title>
<bgColor>
<red>168</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</bgColor>
<pikeColor>
<red>0</red>
<green>0</green>
<blue>255</blue>
<alpha>255</alpha>
</pikeColor>
<envColor>
<red>0</red>
<green>0</green>
<blue>255</blue>
<alpha>255</alpha>
</envColor>
</fr.cemagref.simaqualife.extensions.spatial2D.Movement2DObserver>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
<!--entry>
<java-class>fr.cemagref.simaqualife.kernel.AquaticWorld</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<pikelake.environment.Movement2DWithinShapeObserver>
<title>Bariousses</title>
<bgColor>
<red>168</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</bgColor>
<shapeColor>
<red>0</red>
<green>0</green>
<blue>255</blue>
<alpha>255</alpha>
</shapeColor>
<margin>1</margin>
<sizeOfDisplayedIndividuals>2</sizeOfDisplayedIndividuals>
</pikelake.environment.Movement2DWithinShapeObserver>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry-->
<!--entry>
<java-class>pikelake.Grid</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<fr.cemagref.simaqualife.extensions.spatial2D.Movement2DObserver>
<Pilot></Pilot>
<title>Bariousses</title>
<groupsColors>
<red>255</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</groupsColors>
<bgColor>
<red>0</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</bgColor>
<envColor>
<red>0</red>
<green>0</green>
<blue>255</blue>
<alpha>255</alpha>
</envColor>
<cellSizeMin>1</cellSizeMin>
</fr.cemagref.simaqualife.extensions.spatial2D.Movement2DObserver>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry-->
</hashtable>
src/main/java/pikelake/environment/Movement2DWithinShapeObserver.java 0 → 100644
+ 202
− 0
package pikelake.environment;
import fr.cemagref.observation.gui.Configurable;
import fr.cemagref.observation.gui.Drawable;
//import fr.cemagref.observation.kernel.ObservablesHandler;
import fr.cemagref.observation.kernel.ObserverListener;
import fr.cemagref.ohoui.swing.OhOUIDialog;
import fr.cemagref.ohoui.swing.OhOUI;
import fr.cemagref.ohoui.annotations.Description;
import fr.cemagref.ohoui.annotations.NoRecursive;
import fr.cemagref.ohoui.filters.NoTransientField;
import fr.cemagref.simaqualife.kernel.AquaNism;
import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
import fr.cemagref.simaqualife.pilot.Pilot;
//import fr.cemagref.simaqualife.pilot.gui.util.FileChooserField;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.awt.Shape;
import java.awt.geom.AffineTransform;
import java.awt.geom.GeneralPath;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import javax.swing.JComponent;
@SuppressWarnings({ "serial" })
@NoRecursive
public abstract class Movement2DWithinShapeObserver extends ObserverListener implements Configurable, Drawable {
// private transient FileChooserField modulesChooser;
private transient JComponent display;
private transient GeneralPath generalPath;
private transient List<AquaNismsGroup<? extends AquaNism<? extends Point2D,?>,?>> groups;
private String title;
// TODO supress transient when list will be supported by AutOUI
@Description (name="Groups colors",tooltip="Colors af aquanisms groups")
private transient List<Color> groupsColors;
@Description (name="Background color",tooltip="Background color")
private Color bgColor;
@Description (name="River color",tooltip="River color")
private Color shapeColor;
private int margin;
private int sizeOfDisplayedIndividuals;
// use for determine if generalPath must be rescaled
private transient int displayWidthBak,displayHeightBak;
// used for coordinates rescaling
private transient double repositioningTranslateX,repositioningTranslateY;
private transient double shapeOriginalWidth, shapeOriginalHeight;
private transient double shapeAspectRatio;
private transient double rescaleFactorWithOriginal;
public Movement2DWithinShapeObserver(int margin) {
this(margin,Color.BLACK,Color.BLUE);
}
public Movement2DWithinShapeObserver() {
this(Color.BLACK,Color.BLUE);
}
public Movement2DWithinShapeObserver(Color bgColor,Color shapeColor) {
this(0,bgColor,shapeColor);
}
public Movement2DWithinShapeObserver(int margin,Color bgColor,Color shapeColor) {
this.margin = margin;
this.bgColor = bgColor;
this.shapeColor = shapeColor;
}
public String getTitle() {
return title;
}
public JComponent getDisplay() {
return display;
}
public void valueChanged(ObserverListener clObservable, Object instance, int t) {
display.repaint();
}
@SuppressWarnings("unchecked")
public void init() {
Pilot pilot = new Pilot();
display = new DisplayComponent();
display.setVisible(false);
display.setDoubleBuffered(true);
displayWidthBak = 0;
displayHeightBak = 0;
// init shape
this.generalPath = new GeneralPath(((AsShapeConvertible)pilot.getAquaticWorld().getEnvironment()).getShape());
// original dimension storage
this.shapeOriginalWidth = this.generalPath.getBounds().getWidth();
this.shapeOriginalHeight = this.generalPath.getBounds().getHeight();
this.shapeAspectRatio = shapeOriginalWidth / shapeOriginalHeight;
// repositionning the shape to (0,0)
this.repositioningTranslateX = - this.generalPath.getBounds().getX();
this.repositioningTranslateY = - this.generalPath.getBounds().getY();
this.generalPath.transform(AffineTransform.getTranslateInstance(this.margin+repositioningTranslateX,this.margin+repositioningTranslateY));
// vertical flip
this.generalPath.transform(AffineTransform.getScaleInstance(1,-1));
this.generalPath.transform(AffineTransform.getTranslateInstance(0,shapeOriginalHeight));
groups = new ArrayList<AquaNismsGroup<? extends AquaNism<? extends Point2D,?>,?>>((Collection<? extends AquaNismsGroup<? extends AquaNism<? extends Point2D, ?>, ?>>)pilot.getAquaticWorld().getAquaNismsGroupsList());
if (groups!=null) {
display.setVisible(true);
}
groupsColors = new ArrayList<Color>();
groupsColors.add(Color.RED);
groupsColors.add(Color.GREEN);
groupsColors.add(Color.YELLOW);
groupsColors.add(Color.CYAN);
groupsColors.add(Color.GRAY);
display.repaint();
}
public void disable() {
display.setVisible(false);
}
public static interface AsShapeConvertible {
public Shape getShape();
}
public void configure() {
OhOUIDialog dialog = OhOUI.getDialog(null,this,new NoTransientField());
dialog.setSize(new Dimension(480, 200));
dialog.setVisible(true);
display.repaint();
}
public void addObservable(ObserverListener classObservable) {
// nothing to do
}
public void close() {
// nothing to do
}
private class DisplayComponent extends JComponent {
@Override
protected synchronized void paintComponent(Graphics g) {
super.paintComponents(g);
Graphics2D g2d = (Graphics2D)g;
// determine if generalPath must be rescaled
if ( (this.getWidth() != displayWidthBak) || (this.getHeight() != displayHeightBak) ) {
// backup for comparaison in the next loop
displayWidthBak = this.getWidth();
displayHeightBak = this.getHeight();
// compute the rescale factor with keeping the aspect ratio
double rescaleFactor;
// TODO calcul faux quand margin > 0
if ( ((double)displayWidthBak/displayHeightBak) < shapeAspectRatio ) {
rescaleFactor = displayWidthBak / (generalPath.getBounds().getWidth());
rescaleFactorWithOriginal = displayWidthBak / shapeOriginalWidth;
} else {
rescaleFactor = displayHeightBak / (generalPath.getBounds().getHeight());
rescaleFactorWithOriginal = displayHeightBak / shapeOriginalHeight;
}
// rescale the generalPath
generalPath.transform(
AffineTransform.getScaleInstance(rescaleFactor,rescaleFactor)
);
}
// Draw Background
g.setColor(bgColor);
g.fillRect(0, 0, getWidth(), getHeight());
// Draw the generalPath
g.setColor(shapeColor);
g2d.fill(generalPath);
//g.setColor(aquanismsColor);
Iterator<Color> colorsIterator = groupsColors.iterator();
// Draw aquanisms
for (AquaNismsGroup<? extends AquaNism<? extends Point2D,?>,?> group : groups) {
if (colorsIterator.hasNext()) g.setColor(colorsIterator.next());
for (AquaNism<? extends Point2D,?> aquanism : group.getAquaNismsList()) {
Rectangle rect=new Rectangle((int)((aquanism.getPosition().getX()+repositioningTranslateX) * rescaleFactorWithOriginal),
(int)(generalPath.getBounds().getHeight() /*flip vertically*/ - (aquanism.getPosition().getY()+repositioningTranslateY) * rescaleFactorWithOriginal),
sizeOfDisplayedIndividuals,sizeOfDisplayedIndividuals);
// draw the individuals after repositioning and rescaling the position
g2d.fill(rect);
}
}
}
}
}
src/main/java/pikelake/pikes/PikeHuntProcess.java
+ 2
− 4
package pikelake.pikes;
import java.util.Collections;
//import java.util.Collections;
import java.util.Comparator;
import java.util.List;
//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;
src/main/java/pikelake/pikes/PikeMovement.java
+ 1
− 1
@@ -57,4 +57,4 @@ public class PikeMovement extends LoopAquaNismsGroupProcess<Pike, PikesGroup> {
pike.moveTo(group.getPilot(), possibilities.get(idx), group);
}
}
}
}
\ No newline at end of file
src/main/java/pikelake/pikes/PikeObservationProcess.java
+ 0
− 1
@@ -9,5 +9,4 @@ public class PikeObservationProcess extends AquaNismsGroupProcess<Pike,PikesGrou
pikesGroup.calculatePikesNumber();
}
}
src/main/java/pikelake/pikes/PikesGroup.java
+ 0
− 3
@@ -28,7 +28,6 @@ public class PikesGroup extends AquaNismsGroup<Pike,Grid> {
private transient int pikesNumber;
public PikesGroup(Pilot pilot, Grid arg0, Processes arg1) {
super(pilot, arg0, arg1);
}
@@ -42,7 +41,6 @@ public class PikesGroup extends AquaNismsGroup<Pike,Grid> {
}
System.out.println(" pred: "+pikesNumber + " " + pikesNumber2);*/
return pikesNumber;
}
public double calculatePikesBiomass(){
@@ -50,7 +48,6 @@ public class PikesGroup extends AquaNismsGroup<Pike,Grid> {
for(Pike pike : this.getAquaNismsList())
pikesBiomass += pike.getWeight();
return pikesBiomass;
}
src/main/java/pikelake/Cell.java
+ 4
− 33
package pikelake;
import fr.cemagref.simaqualife.extensions.spatial2D.Grid2D;
//import fr.cemagref.simaqualife.extensions.spatial2D.Grid2D;
import fr.cemagref.simaqualife.extensions.spatial2D.IndexedCell;
import fr.cemagref.simaqualife.pilot.Pilot;
//import fr.cemagref.simaqualife.pilot.Pilot;
import java.util.ArrayList;
import java.util.List;
import pikelake.pikes.Pike;
// import predatorprey.preys.Prey; /////////////////////////////////////////////////////////////////
public class Cell extends IndexedCell {
/**
* <code>preyCarryingCapacity</code> number of preys that this place can
* support
*/
// private int preyCarryingCapacity; /////////////////////////////////////////////////////////////////
/**
* <code>habitatQuality</code> The quality of this place (pike point of
* view). A high value means that preys are vulnerable for the pikes
*/
private double habitatQuality;
/**
* <code>preys</code> The list of preys in this place
*/
// private transient List<Prey> preys; /////////////////////////////////////////////////////////////////
/**
* <code>pikes</code> The list of pikes in this place
*/
private transient List<Pike> pikes;
public Cell(int index, double habitatQuality) { // , int preyCarryingCapacity) { //////////////////////
public Cell(int index, double habitatQuality) {
super(index);
this.habitatQuality = habitatQuality;
// this.preyCarryingCapacity = preyCarryingCapacity; /////////////////////////////////////////////////////////////////
// preys = new ArrayList<Prey>(); /////////////////////////////////////////////////////////////////
pikes = new ArrayList<Pike>();
}
// public List<Prey> getPreys() { /////////////////////////////////////////////////////////////////
// return preys; /////////////////////////////////////////////////////////////////
// } /////////////////////////////////////////////////////////////////
public List<Pike> getPikes() {
return pikes;
}
// public boolean addPrey(Prey prey) { /////////////////////////////////////////////////////////////////
// return preys.add(prey); /////////////////////////////////////////////////////////////////
// } /////////////////////////////////////////////////////////////////
// public boolean removePrey(Prey prey) { /////////////////////////////////////////////////////////////////
// return preys.remove(prey); /////////////////////////////////////////////////////////////////
// } /////////////////////////////////////////////////////////////////
public boolean addPike(Pike pike) {
return pikes.add(pike);
}
@@ -71,8 +46,4 @@ public class Cell extends IndexedCell {
return habitatQuality;
}
// public int getPreyCarryingCapacity() { /////////////////////////////////////////////////////////////////
// return preyCarryingCapacity; /////////////////////////////////////////////////////////////////
// } /////////////////////////////////////////////////////////////////
}