Add edge weight normalization to ForceAtlas2

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/forceAtlas2/ForceAtlas2.java

@@ -83,6 +83,7 @@ public class ForceAtlas2 implements Layout {
     private boolean barnesHutOptimize;
     private double barnesHutTheta;
     private boolean linLogMode;
+    private boolean normalizeEdgeWeights;
     private boolean strongGravityMode;
     private int threadCount;
     private int currentThreadCount;
@@ -216,13 +217,56 @@ public class ForceAtlas2 implements Layout {
                     Attraction.apply(e.getSource(), e.getTarget(), 1);
                 }
             } else if (getEdgeWeightInfluence() == 1) {
-                for (Edge e : edges) {
-                    Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
+                if (isNormalizeEdgeWeights()) {
+                    Double w;
+                    Double edgeWeightMin = Double.MAX_VALUE;
+                    Double edgeWeightMax = Double.MIN_VALUE;
+                    for (Edge e : edges) {
+                        w = getEdgeWeight(e, isDynamicWeight, interval);
+                        edgeWeightMin = Math.min(w, edgeWeightMin);
+                        edgeWeightMax = Math.max(w, edgeWeightMax);
+                    }
+                    if (edgeWeightMin < edgeWeightMax) {
+                        for (Edge e : edges) {
+                            w = (getEdgeWeight(e, isDynamicWeight, interval) - edgeWeightMin) / (edgeWeightMax - edgeWeightMin);
+                            Attraction.apply(e.getSource(), e.getTarget(), w);
+                        }
+                    } else {
+                        for (Edge e : edges) {
+                            Attraction.apply(e.getSource(), e.getTarget(), 1.);
+                        }
+                    }
+                } else {
+                    for (Edge e : edges) {
+                        Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
+                    }
                 }
             } else {
-                for (Edge e : edges) {
-                    Attraction.apply(e.getSource(), e.getTarget(),
-                        Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
+                if (isNormalizeEdgeWeights()) {
+                    Double w;
+                    Double edgeWeightMin = Double.MAX_VALUE;
+                    Double edgeWeightMax = Double.MIN_VALUE;
+                    for (Edge e : edges) {
+                        w = getEdgeWeight(e, isDynamicWeight, interval);
+                        edgeWeightMin = Math.min(w, edgeWeightMin);
+                        edgeWeightMax = Math.max(w, edgeWeightMax);
+                    }
+                    if (edgeWeightMin < edgeWeightMax) {
+                        for (Edge e : edges) {
+                            w = (getEdgeWeight(e, isDynamicWeight, interval) - edgeWeightMin) / (edgeWeightMax - edgeWeightMin);
+                            Attraction.apply(e.getSource(), e.getTarget(),
+                                Math.pow(w, getEdgeWeightInfluence()));
+                        }
+                    } else {
+                        for (Edge e : edges) {
+                            Attraction.apply(e.getSource(), e.getTarget(), 1.);
+                        }
+                    }
+                } else {
+                    for (Edge e : edges) {
+                        Attraction.apply(e.getSource(), e.getTarget(),
+                            Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
+                    }
                 }
             }
 
@@ -409,6 +453,14 @@ public class ForceAtlas2 implements Layout {
                 NbBundle.getMessage(getClass(), "ForceAtlas2.edgeWeightInfluence.desc"),
                 "getEdgeWeightInfluence", "setEdgeWeightInfluence"));
 
+            properties.add(LayoutProperty.createProperty(
+                this, Boolean.class,
+                NbBundle.getMessage(getClass(), "ForceAtlas2.normalizeEdgeWeights.name"),
+                FORCEATLAS2_BEHAVIOR,
+                "ForceAtlas2.normalizeEdgeWeights.name",
+                NbBundle.getMessage(getClass(), "ForceAtlas2.normalizeEdgeWeights.desc"),
+                "isNormalizeEdgeWeights", "setNormalizeEdgeWeights"));
+
             properties.add(LayoutProperty.createProperty(
                 this, Double.class,
                 NbBundle.getMessage(getClass(), "ForceAtlas2.jitterTolerance.name"),
@@ -470,6 +522,7 @@ public class ForceAtlas2 implements Layout {
         setLinLogMode(false);
         setAdjustSizes(false);
         setEdgeWeightInfluence(1.);
+        setNormalizeEdgeWeights(true);
 
         // Performance
         setJitterTolerance(1d);
@@ -522,6 +575,14 @@ public class ForceAtlas2 implements Layout {
         this.linLogMode = linLogMode;
     }
 
+    public Boolean isNormalizeEdgeWeights() {
+        return normalizeEdgeWeights;
+    }
+
+    public void setNormalizeEdgeWeights(Boolean normalizeEdgeWeights) {
+        this.normalizeEdgeWeights = normalizeEdgeWeights;
+    }
+
     public Double getScalingRatio() {
         return scalingRatio;
     }

modules/LayoutPlugin/src/main/resources/org/gephi/layout/plugin/forceAtlas2/Bundle.properties

@@ -16,6 +16,8 @@ ForceAtlas2.distributedAttraction.name=Dissuade Hubs
 ForceAtlas2.distributedAttraction.desc=Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
 ForceAtlas2.linLogMode.name=LinLog mode
 ForceAtlas2.linLogMode.desc=Switch ForceAtlas' model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.
+ForceAtlas2.normalizeEdgeWeights.name=Normalize edge weights
+ForceAtlas2.normalizeEdgeWeights.desc=Puts edge weights between 0 and 1.
 ForceAtlas2.adjustSizes.name=Prevent Overlap
 ForceAtlas2.adjustSizes.desc=Use only when spatialized. Should not be used with "Approximate Repulsion"
 ForceAtlas2.jitterTolerance.name=Tolerance (speed)

modules/LayoutPlugin/src/main/resources/org/gephi/layout/plugin/forceAtlas2/Bundle_fr.properties

@@ -14,6 +14,8 @@ ForceAtlas2.distributedAttraction.name=Dissuader les Hubs
 ForceAtlas2.distributedAttraction.desc=Distribue l'attraction le long des liens sortants. Les hubs attirent moins et sont ainsi poussés vers les bords.
 ForceAtlas2.linLogMode.name=Mode LinLog
 ForceAtlas2.linLogMode.desc=Bascule le modèle de lin-lin à lin-log (en hommage à Andreas Noack). Rend les clusters plus resserrés.
+ForceAtlas2.normalizeEdgeWeights.name=Normalise le poids des liens
+ForceAtlas2.normalizeEdgeWeights.desc=Fait comme si le poids des liens était compris entre 0 et 1
 ForceAtlas2.adjustSizes.name=Empêcher le Recouvrement
 ForceAtlas2.adjustSizes.desc=Utiliser seulement une fois spatialisé. Ne devrait pas être utilisé avec "Répulsion approximative"
 ForceAtlas2.jitterTolerance.name=Tolérance (vitesse)