Spatial index in graph view (#202)

* Move spatial index to Graph so it can be used in graph views * Fix * Add documentation --------- Co-authored-by: Eduardo Ramos <[email protected]>
gephi · Jun 12, 2024 · 2bbedf3 · 2bbedf3
1 parent d006714
commit 2bbedf3
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Showing 10 changed files with 110 additions and 45 deletions.
diff --git a/src/main/java/org/gephi/graph/api/Configuration.java b/src/main/java/org/gephi/graph/api/Configuration.java
@@ -322,7 +322,7 @@ public boolean isEnableEdgeProperties() {
          * If enabled, the spatial index is updated while node positions are updated. If
          * unused, disabling it is recommended as it adds some overhead.
          * <p>
-         * The spatial index can be retrieved from {@link GraphModel#getSpatialIndex()}.
+         * The spatial index can be retrieved from {@link Graph#getSpatialIndex()}.
          * <p>
          * Default is <code>false</code>.
          *

diff --git a/src/main/java/org/gephi/graph/api/Graph.java b/src/main/java/org/gephi/graph/api/Graph.java
@@ -557,4 +557,11 @@ public interface Graph {
      * @return graph lock
      */
     GraphLock getLock();
+
+    /**
+     * Returns the spatial index.
+     *
+     * @return spatial index
+     */
+    SpatialIndex getSpatialIndex();
 }
diff --git a/src/main/java/org/gephi/graph/api/GraphModel.java b/src/main/java/org/gephi/graph/api/GraphModel.java
@@ -683,13 +683,6 @@ public static interface DefaultColumns {
      */
     public GraphObserver createGraphObserver(Graph graph, boolean withGraphDiff);
 
-    /**
-     * Returns the spatial index.
-     *
-     * @return spatial index
-     */
-    public SpatialIndex getSpatialIndex();
-
     /**
      * Returns the time format used to display time.
      *

diff --git a/src/main/java/org/gephi/graph/api/Rect2D.java b/src/main/java/org/gephi/graph/api/Rect2D.java
@@ -66,18 +66,39 @@ public Rect2D(float minX, float minY, float maxX, float maxY) {
         this.maxY = maxY;
     }
 
+    /**
+     * Return the rectangle's width.
+     *
+     * @return the rectangle's width
+     */
     public float width() {
         return maxX - minX;
     }
 
+    /**
+     * Return the rectangle's height.
+     *
+     * @return the rectangle's height
+     */
     public float height() {
         return maxY - minY;
     }
 
+    /**
+     * Return the rectangle's center, as an array where the first element is the x
+     * coordinate and the second element is the y coordinate.
+     *
+     * @return the rectangle's center
+     */
     public float[] center() {
         return new float[] { (maxX + minX) / 2, (maxY + minY) / 2 };
     }
 
+    /**
+     * Return the rectangle's radius.
+     *
+     * @return the rectangle's radius
+     */
     public float radius() {
         float width = width();
         float height = height();
@@ -92,11 +113,17 @@ public String toString() {
         return toString(FORMAT);
     }
 
-    public String toString(NumberFormat formatter) {
+    private String toString(NumberFormat formatter) {
         return "(" + formatter.format(minX) + " " + formatter.format(minY) + ") < " + "(" + formatter
                 .format(maxX) + " " + formatter.format(maxY) + ")";
     }
 
+    /**
+     * Returns true if this rectangle contains the given rectangle.
+     *
+     * @param rect the rectangle to check
+     * @return true if this rectangle contains, false otherwise
+     */
     public boolean contains(Rect2D rect) {
         if (rect == this) {
             return true;
@@ -105,6 +132,12 @@ public boolean contains(Rect2D rect) {
         return contains(rect.minX, rect.minY, rect.maxX, rect.maxY);
     }
 
+    /**
+     * Returns true if this rectangle intersects the given rectangle.
+     *
+     * @param rect the rectangle to check
+     * @return true if this rectangle intersects, false otherwise
+     */
     public boolean intersects(Rect2D rect) {
         if (rect == this) {
             return true;
@@ -113,10 +146,30 @@ public boolean intersects(Rect2D rect) {
         return intersects(rect.minX, rect.minY, rect.maxX, rect.maxY);
     }
 
+    /**
+     * Returns true if this rectangle contains the given rectangle.
+     *
+     * @param minX the x coordinate of the minimum corner
+     * @param minY the y coordinate of the minimum corner
+     * @param maxX the x coordinate of the maximum corner
+     * @param maxY the y coordinate of the maximum corner
+     *
+     * @return true if this rectangle contains, false otherwise
+     */
     public boolean contains(float minX, float minY, float maxX, float maxY) {
         return this.minX <= minX && this.minY <= minY && this.maxX >= maxX && this.maxY >= maxY;
     }
 
+    /**
+     * Returns true if this rectangle intersects the given rectangle.
+     *
+     * @param minX the x coordinate of the minimum corner
+     * @param minY the y coordinate of the minimum corner
+     * @param maxX the x coordinate of the maximum corner
+     * @param maxY the y coordinate of the maximum corner
+     *
+     * @return true if this rectangle intersects, false otherwise
+     */
     public boolean intersects(float minX, float minY, float maxX, float maxY) {
         return this.minX <= maxX && minX <= this.maxX && this.maxY >= minY && maxY >= this.minY;
     }

diff --git a/src/main/java/org/gephi/graph/api/SpatialIndex.java b/src/main/java/org/gephi/graph/api/SpatialIndex.java
@@ -22,7 +22,19 @@
  */
 public interface SpatialIndex {
 
+    /**
+     * Returns the nodes in the given area.
+     *
+     * @param rect area to query
+     * @return nodes in the area
+     */
     NodeIterable getNodesInArea(Rect2D rect);
 
+    /**
+     * Returns the edges in the given area.
+     *
+     * @param rect area to query
+     * @return edges in the area
+     */
     EdgeIterable getEdgesInArea(Rect2D rect);
 }
diff --git a/src/main/java/org/gephi/graph/impl/GraphModelImpl.java b/src/main/java/org/gephi/graph/impl/GraphModelImpl.java
@@ -369,14 +369,6 @@ public TimeIndex<Edge> getEdgeTimeIndex(GraphView view) {
         return null;
     }
 
-    @Override
-    public SpatialIndex getSpatialIndex() {
-        if (!configuration.isEnableSpatialIndex()) {
-            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
-        }
-        return store.spatialIndex;
-    }
-
     @Override
     public GraphObserver createGraphObserver(Graph graph, boolean withGraphDiff) {
         store.autoWriteLock();

diff --git a/src/main/java/org/gephi/graph/impl/GraphStore.java b/src/main/java/org/gephi/graph/impl/GraphStore.java
@@ -23,23 +23,8 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Set;
-import org.gephi.graph.api.Configuration;
-import org.gephi.graph.api.DirectedGraph;
-import org.gephi.graph.api.DirectedSubgraph;
-import org.gephi.graph.api.Edge;
-import org.gephi.graph.api.EdgeIterable;
-import org.gephi.graph.api.ElementIterable;
-import org.gephi.graph.api.Graph;
-import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.Interval;
-import org.gephi.graph.api.Node;
-import org.gephi.graph.api.NodeIterable;
-import org.gephi.graph.api.Origin;
-import org.gephi.graph.api.Subgraph;
-import org.gephi.graph.api.Table;
-import org.gephi.graph.api.TimeFormat;
-import org.gephi.graph.api.TimeRepresentation;
+
+import org.gephi.graph.api.*;
 import org.gephi.graph.api.types.IntervalSet;
 import org.gephi.graph.api.types.TimestampSet;
 
@@ -721,6 +706,14 @@ public GraphLockImpl getLock() {
         return lock;
     }
 
+    @Override
+    public SpatialIndex getSpatialIndex() {
+        if (spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
+        }
+        return spatialIndex;
+    }
+
     protected void autoReadLock() {
         if (configuration.isEnableAutoLocking()) {
             readLock();

diff --git a/src/main/java/org/gephi/graph/impl/GraphViewDecorator.java b/src/main/java/org/gephi/graph/impl/GraphViewDecorator.java
@@ -752,6 +752,14 @@ public Graph getRootGraph() {
         return graphStore;
     }
 
+    @Override
+    public SpatialIndex getSpatialIndex() {
+        if (graphStore.spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
+        }
+        return this;
+    }
+
     void checkWriteLock() {
         if (graphStore.lock != null) {
             graphStore.lock.checkHoldWriteLock();
@@ -821,12 +829,18 @@ boolean isUndirectedToIgnore(final EdgeImpl edge) {
 
     @Override
     public NodeIterable getNodesInArea(Rect2D rect) {
+        if (graphStore.spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
+        }
         Iterator<Node> iterator = graphStore.spatialIndex.getNodesInArea(rect).iterator();
         return new NodeIterableWrapper(new NodeViewIterator(iterator), graphStore.spatialIndex.nodesTree.lock);
     }
 
     @Override
     public EdgeIterable getEdgesInArea(Rect2D rect) {
+        if (graphStore.spatialIndex == null) {
+            throw new UnsupportedOperationException("Spatial index is disabled (from Configuration)");
+        }
         Iterator<Edge> iterator = graphStore.spatialIndex.getEdgesInArea(rect).iterator();
         return new EdgeIterableWrapper(new EdgeViewIterator(iterator), graphStore.spatialIndex.nodesTree.lock);
     }

diff --git a/src/main/java/org/gephi/graph/impl/UndirectedDecorator.java b/src/main/java/org/gephi/graph/impl/UndirectedDecorator.java
@@ -17,17 +17,8 @@
 
 import java.util.Collection;
 import java.util.Set;
-import org.gephi.graph.api.Edge;
-import org.gephi.graph.api.EdgeIterable;
-import org.gephi.graph.api.Graph;
-import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.Interval;
-import org.gephi.graph.api.Node;
-import org.gephi.graph.api.NodeIterable;
-import org.gephi.graph.api.Subgraph;
-import org.gephi.graph.api.UndirectedGraph;
-import org.gephi.graph.api.UndirectedSubgraph;
+
+import org.gephi.graph.api.*;
 
 public class UndirectedDecorator implements UndirectedGraph, UndirectedSubgraph {
 
@@ -422,4 +413,9 @@ public void not() {
     public Graph getRootGraph() {
         return this;
     }
+
+    @Override
+    public SpatialIndex getSpatialIndex() {
+        return store.getSpatialIndex();
+    }
 }
diff --git a/src/test/java/org/gephi/graph/impl/BasicGraphStore.java b/src/test/java/org/gephi/graph/impl/BasicGraphStore.java
@@ -1712,4 +1712,9 @@ public void doBreak() {
             // Not used because no locking
         }
     }
+
+    @Override
+    public SpatialIndex getSpatialIndex() {
+        return null;
+    }
 }