Don't give NaN positions to nodes without size

The layouts space nodes by their size, so a graph whose nodes all have size 0 (or a single such node) made the circumference 0 and the angle Infinity, giving NaN positions that graphstore rejects. Use a minimum size of 1 in the circumference and angle computations. Version 0.9.4.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>

Author: mbastian

modules/CircularLayout/pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.gephi.layout.plugin</groupId>
     <artifactId>circularlayout</artifactId>
-    <version>0.9.3</version>
+    <version>0.9.4</version>
     <packaging>nbm</packaging>
 
     <name>CircularLayout</name>

modules/CircularLayout/src/main/java/org/gephi/layout/plugin/circularlayout/circlelayout/CircleLayout.java

@@ -78,7 +78,7 @@ public void initAlgo()
       {
          if (!n.isFixed())
          {
-            tmpcirc += (n.size() * 2);
+            tmpcirc += (nodeSize(n) * 2);
          }
       }
       tmpcirc     = (tmpcirc * 1.2);
@@ -109,7 +109,7 @@ public void initAlgo()
          {
             if (this.isNodePlacementNoOverlap())
             {
-               noderadius = (n.size());
+               noderadius = (nodeSize(n));
                double noderadian = (theta * noderadius * 1.2);
                nodeCoords = this.cartCoors(radius, 1, lasttheta + noderadian);
                lasttheta += (noderadius * 2 * theta * 1.2);

modules/CircularLayout/src/main/java/org/gephi/layout/plugin/circularlayout/dualcirclelayout/DualCircleLayout.java

@@ -90,11 +90,11 @@ public void initAlgo()
          {
             if (index < this.secondarynodecount)
             {
-               tmpsecondarycirc += (n.size() * 2);
+               tmpsecondarycirc += (nodeSize(n) * 2);
             }
             else
             {
-               tmpprimarycirc += (n.size() * 2);
+               tmpprimarycirc += (nodeSize(n) * 2);
             }
             index++;
          }
@@ -137,7 +137,7 @@ public void initAlgo()
             if (index < this.secondarynodecount)
             {
                //Draw secondary circle
-               double noderadius = (n.size());
+               double noderadius = (nodeSize(n));
                //This step is hackish... but it makes small numbers of nodes symetrical on both the secondary circles.
                if (secondary_scale > 2)
                {
@@ -153,7 +153,7 @@ public void initAlgo()
             }
             else
             {
-               double noderadius = (n.size());
+               double noderadius = (nodeSize(n));
                double noderadian = (primary_theta * noderadius * 1.2 * primary_scale);
                if (index == this.secondarynodecount)
                {

modules/CircularLayout/src/main/java/org/gephi/layout/plugin/circularlayout/layouthelper/LayoutHelper.java

@@ -43,6 +43,8 @@
  */
 public abstract class LayoutHelper implements Layout
 {
+   private static final double MIN_NODE_SIZE = 1.0;
+
    private final LayoutBuilder layoutBuilder;
    protected GraphModel        graphModel;
    private boolean             converged;
@@ -284,6 +286,15 @@ public static Map getRotationMap()
       return map;
    }
 
+   /**
+    * The room a node takes on the circle. Nodes are spaced by their size, so a node without size (e.g. one that was
+    * ranked down to zero) would give a circle with no circumference and NaN positions.
+    */
+   protected static double nodeSize(Node n)
+   {
+      return Math.max(n.size(), MIN_NODE_SIZE);
+   }
+
    public float[] cartCoors(double radius, int whichInt, double theta)
    {
       float[] coOrds = new float[2];

modules/CircularLayout/src/main/java/org/gephi/layout/plugin/circularlayout/radialaxislayout/RadialAxisLayout.java

@@ -201,7 +201,7 @@ else if ("BOTTOM".equals(this.strKnockdown))
                   }
                   if (order == 0)
                   {
-                     double noderadius = n.size();
+                     double noderadius = nodeSize(n);
                      circ += noderadius * 2;
                      SparBaseList.add(n);
                   }
@@ -230,7 +230,7 @@ else if ("BOTTOM".equals(this.strKnockdown))
       double[] ArraySparTheta  = new double[(int)SparArrayCount];
       for (Node n : SparBaseList)
       {
-         double noderadius = (n.size());
+         double noderadius = (nodeSize(n));
          double noderadian = (theta * noderadius * this.dScalingWidth);
          ArraySparTheta[group]  = lasttheta + noderadian;
          ArraySparLength[group] = noderadius * this.dScalingWidth;
@@ -256,7 +256,7 @@ else if ("BOTTOM".equals(this.strKnockdown))
                tmpsparlength = ArraySparLength[position.group];
                tmpspartheta  = ArraySparTheta[position.group];
 
-               double noderadius = (n.size());
+               double noderadius = (nodeSize(n));
                if (this.boolSparSpiral)
                {
                   nodeCoords = this.cartCoors(tmpsparlength + radius + (noderadius * this.dScalingWidth), 1, tmpspartheta + (position.order * (thetainc / SparNodeCount[position.group])));