Examples of org.drools.core.util.bitmask.OpenBitSet

org.drools.core.util.bitmask.OpenBitSet
An "open" BitSet implementation that allows direct access to the array of words storing the bits.
Unlike java.util.bitset, the fact that bits are packed into an array of longs is part of the interface. This allows efficient implementation of other algorithms by someone other than the author. It also allows one to efficiently implement alternate serialization or interchange formats.
OpenBitSet is faster than java.util.BitSet in most operations and *much* faster at calculating cardinality of sets and results of set operations. It can also handle sets of larger cardinality (up to 64 * 2**32-1)
The goals of OpenBitSet are the fastest implementation possible, and maximum code reuse. Extra safety and encapsulation may always be built on top, but if that's built in, the cost can never be removed (and hence people re-implement their own version in order to get better performance). If you want a "safe", totally encapsulated (and slower and limited) BitSet class, use java.util.BitSet.

Performance Results
Test system: Pentium 4, Sun Java 1.5_06 -server -Xbatch -Xmx64M
BitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.

cardinality intersect_count union nextSetBit get iterator

50% full 3.36 3.96 1.44 1.46 1.99 1.58

1% full 3.31 3.90 1.04 0.99

Test system: AMD Opteron, 64 bit linux, Sun Java 1.5_06 -server -Xbatch -Xmx64M
BitSet size = 1,000,000
Results are java.util.BitSet time divided by OpenBitSet time.

cardinality intersect_count union nextSetBit get iterator

50% full 2.50 3.50 1.00 1.03 1.12 1.25

1% full 2.51 3.49 1.00 1.02

	cardinality	intersect_count	union	nextSetBit	get	iterator
50% full	3.36	3.96	1.44	1.46	1.99	1.58
1% full	3.31	3.90		1.04		0.99

	cardinality	intersect_count	union	nextSetBit	get	iterator
50% full	2.50	3.50	1.00	1.03	1.12	1.25
1% full	2.51	3.49		1.00		1.02

    public void mapNodeToCliqueFamily(OpenBitSet[] varNodeToCliques, JunctionTreeClique[] jtNodes) {
        for ( int i = 0; i < varNodeToCliques.length; i++ ) {
            GraphNode<BayesVariable> varNode = graph.getNode( i );


            // Get OpenBitSet for parents
            OpenBitSet parents = new OpenBitSet();
            int count = 0;
            for ( Edge edge : varNode.getInEdges() ) {
                parents.set( edge.getOutGraphNode().getId() );
                count++;
            }


            if ( count == 0 ) {
                // node has no parents, so simply find the smallest clique it's in.
            }


            OpenBitSet cliques = varNodeToCliques[i];
            if  ( cliques == null ) {
                throw new IllegalStateException("Node exists, that is not part of a clique. " + varNode.toString());
            }
            int bestWeight = -1;
            int clique = -1;
            // finds the smallest node, that contains all the parents
            for ( int j = cliques.nextSetBit(0); j >= 0; j = cliques.nextSetBit( j+ 1 ) ) {
                JunctionTreeClique jtNode = jtNodes[j];


                // if the node has parents, we find the small clique it's in.
                // If it has parents then is jtNode a supserset of parents, visa-vis is parents a subset of jtNode
                if ( (count == 0 || OpenBitSet.andNotCount(parents, jtNode.getBitSet()) == 0 ) && ( clique == -1 || jtNode.getBitSet().cardinality() < bestWeight ) ) {

View Full Code Here

     * @param id
     * @param clique
     */
    public void mapVarNodeToCliques(OpenBitSet[] nodeToCliques, int id, OpenBitSet clique) {
        for ( int i = clique.nextSetBit(0); i >= 0; i = clique.nextSetBit( i + 1 ) ) {
             OpenBitSet cliques = nodeToCliques[i];
            if ( cliques == null ) {
                cliques = new OpenBitSet();
                nodeToCliques[i] = cliques;
            }
            cliques.set(id);
        }
    }

View Full Code Here

        // must use the adjacency matrix, and not the vertex.getEdges() for connections,
        // as it gets updated with new connections, during elimination
        weightRequired = (int) Math.abs(v.getContent().getOutcomes().length);
        newEdgesRequired = 0;


        cliqueBitSet = new OpenBitSet(adjMatrix.length);


        cliqueBitSet.set(v.getId());


        // determine new edges added, to ensure all adjacent nodes become neighbours in a cluster
        boolean[] adjList = adjMatrix[ v.getId() ];

View Full Code Here

import static org.junit.Assert.assertTrue;


public class JunctionTreeBuilderTest {
    @Test
    public void testOpenBitSet() {
        OpenBitSet b1 = bitSet("00000111");
        OpenBitSet b2 = bitSet("00000111");
        OpenBitSet b3 = bitSet("00000110");
        OpenBitSet b4 = bitSet("00001110");


        assertEquals(0, OpenBitSet.andNotCount(b1, b2)); // b1 and b3 are equal


        assertEquals( 1,  OpenBitSet.andNotCount( b2, b3 ) ); // b2 is not a subset of b3
        assertEquals(0, OpenBitSet.andNotCount(b3, b2)); // b3 is a subset of b2

View Full Code Here

    public void testCliqueSuperSet() {
        Graph<BayesVariable> graph = new BayesNetwork();
        JunctionTreeBuilder jtBuilder = new JunctionTreeBuilder( graph );


        List<OpenBitSet> cliques = new ArrayList<OpenBitSet>();
        OpenBitSet OpenBitSet1 = bitSet("00011110");
        jtBuilder.updateCliques(cliques, OpenBitSet1);
        assertEquals( 1, cliques.size() );


        // ignore subset
        OpenBitSet OpenBitSet2 = bitSet("00000110");
        jtBuilder.updateCliques(cliques, OpenBitSet2);
        assertEquals( 1, cliques.size() );
        assertEquals( OpenBitSet1, cliques.get(0) );


        // add overlapping, as not a pure subset
        OpenBitSet OpenBitSet3 = bitSet("01000110");
        jtBuilder.updateCliques(cliques, OpenBitSet3);
        assertEquals( 2, cliques.size() );
        assertEquals( OpenBitSet1, cliques.get(0) );
        assertEquals( OpenBitSet3, cliques.get(1) );
    }

View Full Code Here

        GraphNode x4 = addNode(graph);
        GraphNode x5 = addNode(graph);
        GraphNode x6 = addNode(graph);




        OpenBitSet OpenBitSet1_1 = bitSet("00001110");
        OpenBitSet OpenBitSet1_2 = bitSet("01101100");
        SeparatorSet s1 = new SeparatorSet( OpenBitSet1_1, 0, OpenBitSet1_2, 0, graph);


        OpenBitSet OpenBitSet2_1 = bitSet("00001110");
        OpenBitSet OpenBitSet2_2 = bitSet("00100100");
        SeparatorSet s2 = new SeparatorSet( OpenBitSet2_1, 0, OpenBitSet2_2, 0, graph);


        List<SeparatorSet> list = new ArrayList<SeparatorSet>();
        list.add( s1 );
        list.add( s2 );

View Full Code Here


        x1.setContent(new BayesVariable<String>("x1", x0.getId(), new String[]{"a"}, new double[][]{{0.1 }}));
        x2.setContent(new BayesVariable<String>("x2", x0.getId(), new String[]{"a", "b"}, new double[][]{{0.1, 0.1}}));
        x3.setContent(new BayesVariable<String>("x3", x0.getId(), new String[]{"a", "b"}, new double[][]{{0.1, 0.1}}));


        OpenBitSet OpenBitSet1_1 = bitSet("00001110");
        OpenBitSet OpenBitSet1_2 = bitSet("01101100");
        SeparatorSet s1 = new SeparatorSet( OpenBitSet1_1, 0, OpenBitSet1_2, 0, graph);


        OpenBitSet OpenBitSet2_1 = bitSet("00001110");
        OpenBitSet OpenBitSet2_2 = bitSet("00100110");
        SeparatorSet s2 = new SeparatorSet( OpenBitSet2_1, 0, OpenBitSet2_2, 0, graph);


        List<SeparatorSet> list = new ArrayList<SeparatorSet>();
        list.add( s1 );
        list.add( s2 );

View Full Code Here

        GraphNode x4 = addNode(graph);
        GraphNode x5 = addNode(graph);
        GraphNode x6 = addNode(graph);




        OpenBitSet OpenBitSet1_1 = bitSet("00001110");
        OpenBitSet OpenBitSet1_2 = bitSet("01000010");
        SeparatorSet s1 = new SeparatorSet( OpenBitSet1_1, 0, OpenBitSet1_2, 0, graph);


        OpenBitSet OpenBitSet2_1 = bitSet("00001110");
        OpenBitSet OpenBitSet2_2 = bitSet("01000100");
        SeparatorSet s2 = new SeparatorSet( OpenBitSet2_1, 0, OpenBitSet2_2, 0, graph);


        List<SeparatorSet> list = new ArrayList<SeparatorSet>();
        list.add( s1 );
        list.add( s2 );

View Full Code Here


        GraphNode x4 = addNode(graph);
        GraphNode x5 = addNode(graph);
        GraphNode x6 = addNode(graph);


        OpenBitSet OpenBitSet1 = bitSet("00001110");
        OpenBitSet OpenBitSet2 = bitSet("00011100");
        OpenBitSet OpenBitSet3 = bitSet("00110000");
        OpenBitSet OpenBitSet4 = bitSet("01110000");


        List<OpenBitSet> cliques = new ArrayList<OpenBitSet>();
        cliques.add ( OpenBitSet1 );
        cliques.add ( OpenBitSet2 );
        cliques.add ( OpenBitSet3 );
        cliques.add ( OpenBitSet4 );


        List<SeparatorSet> separatorSets = new ArrayList<SeparatorSet>();
        for ( int i = 0; i < cliques.size(); i++ ) {
            OpenBitSet ci = cliques.get(i);
            for ( int j = i+1; j < cliques.size(); j++ ) {
                OpenBitSet cj = cliques.get(j);
                if ( ci.intersects( cj ) ) {
                    SeparatorSet separatorSet = new SeparatorSet( ci, 0, cj, 0, graph );
                }
            }
        }

View Full Code Here

        GraphNode x5 = addNode(graph);
        GraphNode x6 = addNode(graph);
        GraphNode x7 = addNode(graph);


        List<OpenBitSet> list = new ArrayList<OpenBitSet>();
        OpenBitSet OpenBitSet1 = bitSet("00001111");
        OpenBitSet OpenBitSet2 = bitSet("00111100");
        OpenBitSet OpenBitSet3 = bitSet("11100000"); // linear


        OpenBitSet intersect1And2 = ((OpenBitSet)OpenBitSet2.clone());
        intersect1And2.and(OpenBitSet1);


        OpenBitSet intersect2And3 = ((OpenBitSet)OpenBitSet2.clone());
        intersect2And3.and(OpenBitSet3);


        list.add(OpenBitSet1);
        list.add(OpenBitSet2);
        list.add(OpenBitSet3);

View Full Code Here

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Related Classes of org.drools.core.util.bitmask.OpenBitSet

org.drools.beliefs.bayes.EliminationCandidate

org.drools.beliefs.bayes.GraphTest

org.drools.beliefs.bayes.JunctionTreeBuilder

org.drools.beliefs.bayes.JunctionTreeBuilderTest

org.drools.beliefs.bayes.JunctionTreeTest

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Examples of org.drools.core.util.bitmask.OpenBitSet

Performance Results

Related Classes of org.drools.core.util.bitmask.OpenBitSet