MATH-1278

Deep copy of "Neuron", "Network" and "NeuronSquareMesh2D".

src/main/java/org/apache/commons/math3/ml/neuralnet/Network.java

@@ -28,6 +28,7 @@ import java.util.Collection;
 import java.util.Iterator;
 import java.util.Comparator;
 import java.util.Collections;
+import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicLong;
 import org.apache.commons.math3.exception.DimensionMismatchException;
@@ -134,6 +135,29 @@ public class Network
         this.featureSize = featureSize;
     }
 
+    /**
+     * Performs a deep copy of this instance.
+     * Upon return, the copied and original instances will be independent:
+     * Updating one will not affect the other.
+     *
+     * @return a new instance with the same state as this instance.
+     */
+    public synchronized Network copy() {
+        final Network copy = new Network(nextId.get(),
+                                         featureSize);
+
+
+        for (Map.Entry<Long, Neuron> e : neuronMap.entrySet()) {
+            copy.neuronMap.put(e.getKey(), e.getValue().copy());
+        }
+
+        for (Map.Entry<Long, Set<Long>> e : linkMap.entrySet()) {
+            copy.linkMap.put(e.getKey(), new HashSet<Long>(e.getValue()));
+        }
+
+        return copy;
+    }
+
     /**
      * {@inheritDoc}
      */

src/main/java/org/apache/commons/math3/ml/neuralnet/Neuron.java

@@ -66,6 +66,22 @@ public class Neuron implements Serializable {
         this.features = new AtomicReference<double[]>(features.clone());
     }
 
+    /**
+     * Performs a deep copy of this instance.
+     * Upon return, the copied and original instances will be independent:
+     * Updating one will not affect the other.
+     *
+     * @return a new instance with the same state as this instance.
+     */
+    public synchronized Neuron copy() {
+        final Neuron copy = new Neuron(getIdentifier(),
+                                       getFeatures());
+        copy.numberOfAttemptedUpdates.set(numberOfAttemptedUpdates.get());
+        copy.numberOfSuccessfulUpdates.set(numberOfSuccessfulUpdates.get());
+
+        return copy;
+    }
+
     /**
      * Gets the neuron's identifier.
      *

src/main/java/org/apache/commons/math3/ml/neuralnet/twod/NeuronSquareMesh2D.java

@@ -197,6 +197,54 @@ public class NeuronSquareMesh2D
         createLinks();
     }
 
+    /**
+     * Constructor with restricted access, solely used for making a
+     * {@link #copy() deep copy}.
+     *
+     * @param wrapRowDim Whether to wrap the first dimension (i.e the first
+     * and last neurons will be linked together).
+     * @param wrapColDim Whether to wrap the second dimension (i.e the first
+     * and last neurons will be linked together).
+     * @param neighbourhoodType Neighbourhood type.
+     * @param net Underlying network.
+     * @param idGrid Neuron identifiers.
+     */
+    private NeuronSquareMesh2D(boolean wrapRowDim,
+                               boolean wrapColDim,
+                               SquareNeighbourhood neighbourhoodType,
+                               Network net,
+                               long[][] idGrid) {
+        numberOfRows = idGrid.length;
+        numberOfColumns = idGrid[0].length;
+        wrapRows = wrapRowDim;
+        wrapColumns = wrapColDim;
+        neighbourhood = neighbourhoodType;
+        network = net;
+        identifiers = idGrid;
+    }
+
+    /**
+     * Performs a deep copy of this instance.
+     * Upon return, the copied and original instances will be independent:
+     * Updating one will not affect the other.
+     *
+     * @return a new instance with the same state as this instance.
+     */
+    public synchronized NeuronSquareMesh2D copy() {
+        final long[][] idGrid = new long[numberOfRows][numberOfColumns];
+        for (int r = 0; r < numberOfRows; r++) {
+            for (int c = 0; c < numberOfColumns; c++) {
+                idGrid[r][c] = identifiers[r][c];
+            }
+        }
+
+        return new NeuronSquareMesh2D(wrapRows,
+                                      wrapColumns,
+                                      neighbourhood,
+                                      network.copy(),
+                                      idGrid);
+    }
+
     /** {@inheritDoc} */
     public Iterator<Neuron> iterator() {
         return network.iterator();

src/test/java/org/apache/commons/math3/ml/neuralnet/NetworkTest.java

@@ -127,6 +127,47 @@ public class NetworkTest {
         Assert.assertFalse(isUnspecifiedOrder);
     }
 
+    /*
+     * Test assumes that the network is
+     *
+     *  0-----1
+     *  |     |
+     *  |     |
+     *  2-----3
+     */
+    @Test
+    public void testCopy() {
+        final FeatureInitializer[] initArray = { init };
+        final Network net = new NeuronSquareMesh2D(2, false,
+                                                   2, false,
+                                                   SquareNeighbourhood.VON_NEUMANN,
+                                                   initArray).getNetwork();
+
+        final Network copy = net.copy();
+        
+        final Neuron netNeuron0 = net.getNeuron(0);
+        final Neuron copyNeuron0 = copy.getNeuron(0);
+        final Neuron netNeuron1 = net.getNeuron(1);
+        final Neuron copyNeuron1 = copy.getNeuron(1);
+        Collection<Neuron> netNeighbours;
+        Collection<Neuron> copyNeighbours;
+        
+        // Check that both networks have the same connections.
+        netNeighbours = net.getNeighbours(netNeuron0);
+        copyNeighbours = copy.getNeighbours(copyNeuron0);
+        Assert.assertTrue(netNeighbours.contains(netNeuron1));
+        Assert.assertTrue(copyNeighbours.contains(copyNeuron1));
+
+        // Delete neuron 1 from original.
+        net.deleteNeuron(netNeuron1);
+
+        // Check that the networks now differ.
+        netNeighbours = net.getNeighbours(netNeuron0);
+        copyNeighbours = copy.getNeighbours(copyNeuron0);
+        Assert.assertFalse(netNeighbours.contains(netNeuron1));
+        Assert.assertTrue(copyNeighbours.contains(copyNeuron1));
+    }
+
     @Test
     public void testSerialize()
         throws IOException,

src/test/java/org/apache/commons/math3/ml/neuralnet/NeuronTest.java

@@ -85,6 +85,32 @@ public class NeuronTest {
         Assert.assertEquals(update[0],  n.getFeatures()[0], 0d);
     }
 
+    @Test
+    public void testCopy() {
+        final Neuron n = new Neuron(1, new double[] { 9.87 });
+
+        // Update original.
+        double[] update = new double[] { n.getFeatures()[0] + 2.34 };
+        n.compareAndSetFeatures(n.getFeatures(), update);
+
+        // Create a copy.
+        final Neuron copy = n.copy();
+
+        // Check that original and copy have the same value.
+        Assert.assertTrue(n.getFeatures()[0] == copy.getFeatures()[0]);
+        Assert.assertEquals(n.getNumberOfAttemptedUpdates(),
+                            copy.getNumberOfAttemptedUpdates());
+
+        // Update original.
+        update = new double[] { 1.23 * n.getFeatures()[0] };
+        n.compareAndSetFeatures(n.getFeatures(), update);
+
+        // Check that original and copy differ.
+        Assert.assertFalse(n.getFeatures()[0] == copy.getFeatures()[0]);
+        Assert.assertNotEquals(n.getNumberOfSuccessfulUpdates(),
+                               copy.getNumberOfSuccessfulUpdates());
+    }
+
     @Test
     public void testSerialize()
         throws IOException,