Re-enabled volume constraint with revised method taking into account

both model and feedback forces

.classpath

@@ -16,5 +16,7 @@
 	<classpathentry kind="var" path="ICY_PLUGINS/nchenouard/spot/DetectionResult.jar"/>
 	<classpathentry kind="var" path="ICY_PLUGINS/adufour/blocks/Blocks.jar"/>
 	<classpathentry kind="var" path="ICY_PLUGINS/adufour/roi/mesh/ROI3DMeshPlugin.jar"/>
+	<classpathentry kind="var" path="ICY_PLUGINS/adufour/thresholder/Thresholder.jar"/>
+	<classpathentry kind="var" path="ICY_PLUGINS/adufour/roi/LabelExtractor.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

src/plugins/adufour/activecontours/ActiveContour.java

@@ -145,7 +145,7 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
 
     abstract void computeInternalForces(double weight);
 
-    abstract void computeVolumeConstraint(double targetVolume);
+    abstract void computeVolumeConstraint(double targetVolume, double weight);
 
     /**
      * Computes the feedback forces yielded by the penetration of the current contour into the

src/plugins/adufour/activecontours/ActiveContours.java

@@ -338,9 +338,8 @@ public class ActiveContours extends EzPlug implements EzStoppable, Block
     public final EzVarBoolean tracking_newObjects = new EzVarBoolean("Watch entering objects", false);
 
     private final HashMap<TrackSegment, Double> volumes = new HashMap<TrackSegment, Double>();
-    // TODO: we disabled volume constraint feature as it doesn't work and sometime end to crazy contour (Stephane)
-    public final EzVarBoolean volume_constraint = new EzVarBoolean("Volume constraint (disabled)", false);
-//    public final EzVarBoolean volume_constraint = new EzVarBoolean("Volume constraint", false);
+    public final EzVarBoolean volume_constraint = new EzVarBoolean("Volume constraint", false);
+    public final EzVarDouble volume_weight = new EzVarDouble("Volume weight", 0.01, 0,1, 0.01);
 
     public final EzButton showTrackManager;
 
@@ -515,7 +514,7 @@ public class ActiveContours extends EzPlug implements EzStoppable, Block
     {
         super.loadParameters(file);
 
-        // TODO: we disabled volume constraint feature as it doesn't work and sometime end to crazy contour (Stephane)
+        // TODO: disabled as the feature is broken (Stephane)
         volume_constraint.setValue(Boolean.FALSE);
     }
 
@@ -1430,7 +1429,7 @@ public class ActiveContours extends EzPlug implements EzStoppable, Block
 
             if (volume_constraint.getValue() && volumes.containsKey(segment))
             {
-                contour.computeVolumeConstraint(volumes.get(segment));
+                contour.computeVolumeConstraint(volumes.get(segment), volume_weight.getValue());
             }
 
             contour.move(boundField, contour_timeStep.getValue());
@@ -1491,10 +1490,12 @@ public class ActiveContours extends EzPlug implements EzStoppable, Block
                                 contour.computeFeedbackForces(otherContour);
                             }
 
+                            // we disabled volume constraint feature as it doesn't work and sometime end to crazy contour (Stephane)
+							// re-enabled volume constraint after taking into account both shrinking and growing contours instead of just growing ones(Daniel)
                             if (volume_constraint.getValue() && volumes.containsKey(segment))
-                            {
-                                contour.computeVolumeConstraint(volumes.get(segment));
-                            }
+							{
+								contour.computeVolumeConstraint(volumes.get(segment), volume_weight.getValue());
+							}
                         }
                         else
                         {
@@ -1863,9 +1864,8 @@ public class ActiveContours extends EzPlug implements EzStoppable, Block
         inputMap.add("tracking", tracking.getVariable());
         inputMap.add("division sensitivity", division_sensitivity.getVariable());
         inputMap.add("axis constraint", axis_weight.getVariable());
-        // TODO: we disabled volume constraint feature as it doesn't work and sometime end to crazy contour (Stephane)
-        inputMap.add("volume constraint (disabled)", volume_constraint.getVariable());
-//        inputMap.add("volume constraint", volume_constraint.getVariable());
+        volume_constraint.setValue(true);
+        inputMap.add("Volume weight", volume_weight.getVariable());
         inputMap.add("watch entering objects", tracking_newObjects.getVariable());
     }
 

src/plugins/adufour/activecontours/Mesh3D.java

@@ -335,7 +335,8 @@ public class Mesh3D extends ActiveContour
         }
     }
 
-    void computeVolumeConstraint(double targetVolume)
+    // TODO take into account weight
+    void computeVolumeConstraint(double targetVolume, double weight)
     {
         // 1) compute the difference between target and current volume
         final double volumeDiff = targetVolume - getDimension(2);

src/plugins/adufour/activecontours/Polygon2D.java

@@ -417,7 +417,7 @@ public class Polygon2D extends ActiveContour
             Polygon2D child1 = new Polygon2D(sampling, new SlidingWindow(this.convergence.getSize()));
             for (int p = 0; p < nPoints; p++)
             {
-                Point3d pp = points.get(p + i);
+                Point3d pp = points.get((p + i) % n);
                 center.add(pp);
                 child1.addPoint(pp);
             }
@@ -689,40 +689,26 @@ public class Polygon2D extends ActiveContour
 
         weight /= sampling.getValue();
 
-        // first point
-        prev = points.get(n - 1);
-        curr = points.get(0);
-        next = points.get(1);
-
-        force = feedbackForces[0];
-
-        force.x += weight * (prev.x - 2 * curr.x + next.x);
-        force.y += weight * (prev.y - 2 * curr.y + next.y);
+        // initialize points
+        prev = points.get(n - 2);
+        curr = points.get(n - 1);
+        next = points.get(0);
 
         // middle points
-        for (int i = 1; i < n - 1; i++)
+        for (int i = 0; i < n; i++)
         {
-            force = feedbackForces[i];
-            prev = points.get(i - 1);
-            curr = points.get(i);
-            next = points.get(i + 1);
+            prev = curr;
+            curr = next;
+            next = points.get((i + 1)%n);
 
+            force = feedbackForces[i];
             force.x += weight * (prev.x - 2 * curr.x + next.x);
             force.y += weight * (prev.y - 2 * curr.y + next.y);
         }
-
-        // last point
-        force = feedbackForces[n - 1];
-        prev = points.get(n - 2);
-        curr = points.get(n - 1);
-        next = points.get(0);
-
-        force.x += weight * (prev.x - 2 * curr.x + next.x);
-        force.y += weight * (prev.y - 2 * curr.y + next.y);
     }
 
     @Override
-    void computeVolumeConstraint(double targetVolume)
+    void computeVolumeConstraint(double targetVolume, double weight)
     {
         // 1) compute the difference between target and current volume
         double volumeDiff = targetVolume - getDimension(2);
@@ -731,46 +717,18 @@ public class Polygon2D extends ActiveContour
 
         int n = points.size();
 
-        Vector3d avgFeedback = new Vector3d();
-        int nbFeedbackForces = 0;
-
+        Vector3d totalForce = new Vector3d();
         for (int i = 0; i < n; i++)
         {
-            Vector3d mf = modelForces[i];
+        	totalForce.add(feedbackForces[i],  modelForces[i]);
 
             // 2) check whether the final force has same direction as the outer normal
-            double forceNorm = mf.dot(contourNormals[i]);
-
-            // if forces have same direction (forceNorm > 0): contour is growing
-            // if forces have opposite direction (forceNorm < 0): contour is shrinking
-
-            // if (forceNorm * volumeDiff < 0)
-            // {
-            // // forceNorm and volumeDiff have opposite signs because:
-            // // - contour too small (volumeDiff > 0) and shrinking (forceNorm < 0)
-            // // or
-            // // - contour too large (volumeDiff < 0) and growing (forceNorm > 0)
-            // // => in both cases, constrain the final force accordingly
-            // mf.scale(1.0 / (1.0 + Math.abs(volumeDiff) / 10));
-            // }
-
-            // estimate an average feedback
-            if (forceNorm > 0 && volumeDiff < 0)
-            {
-                avgFeedback.add(feedbackForces[i]);
-                nbFeedbackForces++;
-            }
-        }
-
-        if (avgFeedback.length() > 0)
-        {
-            avgFeedback.scale(1.0 / nbFeedbackForces);
-            avgFeedback.scale(Math.abs(volumeDiff / targetVolume) / 0.5);
+            double forceNorm = totalForce.dot(contourNormals[i]);
 
-            // move the entire mesh (ugly, but amazingly efficient!!)
-            for (int i = 0; i < n; i++)
-            {
-                volumeConstraintForces[i].add(avgFeedback);
+            if (forceNorm * volumeDiff < 0) {
+            	totalForce.set(contourNormals[i]);
+            	totalForce.scale(volumeDiff * weight / targetVolume);
+            	volumeConstraintForces[i].set(totalForce);
             }
         }
     }
@@ -1570,28 +1528,17 @@ public class Polygon2D extends ActiveContour
     protected void updateNormals()
     {
         int n = points.size();
+        Point3d p1 = points.get(n - 2);
+        Point3d p = points.get(n - 1);
+        Point3d p2 = points.get(0);
 
-        // first point
-        {
-            Point3d p1 = points.get(n - 1);
-            Point3d p2 = points.get(1);
-            contourNormals[0].normalize(new Vector3d(p2.y - p1.y, p1.x - p2.x, 0));
-        }
-
-        // middle points
-        for (int i = 1; i < n - 1; i++)
+        for (int i = 0; i < n; i++)
         {
-            Point3d p1 = points.get(i - 1);
-            Point3d p2 = points.get(i + 1);
+            p1 = p;
+            p = p2;
+            p2 = points.get((i + 1) % n);
             contourNormals[i].normalize(new Vector3d(p2.y - p1.y, p1.x - p2.x, 0));
         }
-
-        // last point
-        {
-            Point3d p1 = points.get(n - 2);
-            Point3d p2 = points.get(0);
-            contourNormals[n - 1].normalize(new Vector3d(p2.y - p1.y, p1.x - p2.x, 0));
-        }
     }
 
     @Override
@@ -1633,7 +1580,6 @@ public class Polygon2D extends ActiveContour
         this.path = newPath;
     }
 
-    @SuppressWarnings("deprecation")
     @Deprecated
     @Override
     public ROI2D toROI()