Examples with SpatialDirectoryEntry de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry used on opensource projects

Example 1 with SpatialDirectoryEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry in project elki by elki-project.

the class RStarTreeKNNQuery method expandNode.

private double expandNode(O object, KNNHeap knnList, DoubleIntegerMinHeap pq, double maxDist, final int nodeID) {
    AbstractRStarTreeNode<?, ?> node = tree.getNode(nodeID);
    // data node
    if (node.isLeaf()) {
        for (int i = 0; i < node.getNumEntries(); i++) {
            SpatialPointLeafEntry entry = (SpatialPointLeafEntry) node.getEntry(i);
            double distance = distanceFunction.minDist(entry, object);
            tree.statistics.countDistanceCalculation();
            if (distance <= maxDist) {
                maxDist = knnList.insert(distance, entry.getDBID());
            }
        }
    } else // directory node
    {
        for (int i = 0; i < node.getNumEntries(); i++) {
            SpatialDirectoryEntry entry = (SpatialDirectoryEntry) node.getEntry(i);
            double distance = distanceFunction.minDist(entry, object);
            tree.statistics.countDistanceCalculation();
            // Greedy expand, bypassing the queue
            if (distance <= 0) {
                expandNode(object, knnList, pq, maxDist, entry.getPageID());
            } else {
                if (distance <= maxDist) {
                    pq.add(distance, entry.getPageID());
                }
            }
        }
    }
    return maxDist;
}

Example 2 with SpatialDirectoryEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry in project elki by elki-project.

the class DeLiClu method run.

public ClusterOrder run(Database database, Relation<NV> relation) {
    Collection<DeLiCluTreeIndex<NV>> indexes = ResultUtil.filterResults(database.getHierarchy(), relation, DeLiCluTreeIndex.class);
    if (indexes.size() != 1) {
        throw new MissingPrerequisitesException("DeLiClu found " + indexes.size() + " DeLiCluTree indexes. DeLiClu needs a special index to operate, therefore you need to add this index to your database.");
    }
    DeLiCluTreeIndex<NV> index = indexes.iterator().next();
    if (!(getDistanceFunction() instanceof SpatialPrimitiveDistanceFunction<?>)) {
        throw new IllegalArgumentException("Distance Function must be an instance of " + SpatialPrimitiveDistanceFunction.class.getName());
    }
    @SuppressWarnings("unchecked") SpatialPrimitiveDistanceFunction<NV> distFunction = (SpatialPrimitiveDistanceFunction<NV>) getDistanceFunction();
    // first do the knn-Join
    if (LOG.isVerbose()) {
        LOG.verbose("knnJoin...");
    }
    Relation<KNNList> knns = knnJoin.run(relation);
    DBIDs ids = relation.getDBIDs();
    final int size = ids.size();
    FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("DeLiClu", size, LOG) : null;
    ClusterOrder clusterOrder = new ClusterOrder(ids, "DeLiClu Clustering", "deliclu-clustering");
    heap = new UpdatableHeap<>();
    // add start object to cluster order and (root, root) to priority queue
    DBID startID = DBIDUtil.deref(ids.iter());
    clusterOrder.add(startID, Double.POSITIVE_INFINITY, null);
    int numHandled = 1;
    index.setHandled(startID, relation.get(startID));
    SpatialDirectoryEntry rootEntry = (SpatialDirectoryEntry) index.getRootEntry();
    SpatialObjectPair spatialObjectPair = new SpatialObjectPair(0., rootEntry, rootEntry, true);
    heap.add(spatialObjectPair);
    while (numHandled < size) {
        if (heap.isEmpty()) {
            throw new AbortException("DeLiClu heap was empty when it shouldn't have been.");
        }
        SpatialObjectPair dataPair = heap.poll();
        // pair of nodes
        if (dataPair.isExpandable) {
            expandNodes(index, distFunction, dataPair, knns);
        } else // pair of objects
        {
            // set handled
            LeafEntry e1 = (LeafEntry) dataPair.entry1;
            LeafEntry e2 = (LeafEntry) dataPair.entry2;
            final DBID e1id = e1.getDBID();
            IndexTreePath<DeLiCluEntry> path = index.setHandled(e1id, relation.get(e1id));
            if (path == null) {
                throw new RuntimeException("snh: parent(" + e1id + ") = null!!!");
            }
            // add to cluster order
            clusterOrder.add(e1id, dataPair.distance, e2.getDBID());
            numHandled++;
            // reinsert expanded leafs
            reinsertExpanded(distFunction, index, path, knns);
            if (progress != null) {
                progress.setProcessed(numHandled, LOG);
            }
        }
    }
    LOG.ensureCompleted(progress);
    return clusterOrder;
}

Example 3 with SpatialDirectoryEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry in project elki by elki-project.

the class AbstractXTreeNode method readSuperNode.

/**
 * Reads the id of this supernode, the numEntries and the entries array from
 * the specified stream.
 *
 * @param in the stream to read data from in order to restore the object
 * @param tree the tree this supernode is to be assigned to
 * @throws java.io.IOException if I/O errors occur
 * @throws ClassNotFoundException If the class for an object being restored
 *         cannot be found.
 * @throws IllegalStateException if the parameters of the file's supernode do
 *         not match this
 */
public <T extends AbstractXTree<N>> void readSuperNode(ObjectInput in, T tree) throws IOException, ClassNotFoundException {
    readExternal(in);
    if (capacity_to_be_filled <= 0 || !isSuperNode()) {
        throw new IllegalStateException("This node does not appear to be a supernode");
    }
    if (isLeaf) {
        throw new IllegalStateException("A supernode is cannot be a leaf");
    }
    // TODO: verify
    entries = new Entry[capacity_to_be_filled];
    // old way:
    // entries = (E[]) new XDirectoryEntry[capacity_to_be_filled];
    capacity_to_be_filled = 0;
    for (int i = 0; i < numEntries; i++) {
        SpatialEntry s = new SpatialDirectoryEntry();
        s.readExternal(in);
        entries[i] = s;
    }
    N n = tree.getSupernodes().put((long) getPageID(), (N) this);
    if (n != null) {
        Logging.getLogger(this.getClass()).fine("Warning: this supernode should only be read once. Now a node of size " + entries.length + " has replaced a node of size " + n.entries.length + " for id " + getPageID());
    }
}

Example 4 with SpatialDirectoryEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry in project elki by elki-project.

the class IndexPurity method processNewResult.

@Override
public void processNewResult(ResultHierarchy hier, Result newResult) {
    Database database = ResultUtil.findDatabase(hier);
    final ArrayList<SpatialIndexTree<?, ?>> indexes = ResultUtil.filterResults(hier, newResult, SpatialIndexTree.class);
    if (indexes == null || indexes.isEmpty()) {
        return;
    }
    Relation<String> lblrel = DatabaseUtil.guessLabelRepresentation(database);
    for (SpatialIndexTree<?, ?> index : indexes) {
        List<? extends SpatialEntry> leaves = index.getLeaves();
        MeanVariance mv = new MeanVariance();
        for (SpatialEntry e : leaves) {
            SpatialDirectoryEntry leaf = (SpatialDirectoryEntry) e;
            Node<?> n = index.getNode(leaf.getPageID());
            final int total = n.getNumEntries();
            HashMap<String, Integer> map = new HashMap<>(total);
            for (int i = 0; i < total; i++) {
                DBID id = ((SpatialPointLeafEntry) n.getEntry(i)).getDBID();
                String label = lblrel.get(id);
                Integer val = map.get(label);
                if (val == null) {
                    val = 1;
                } else {
                    val += 1;
                }
                map.put(label, val);
            }
            double gini = 0.0;
            for (Entry<String, Integer> ent : map.entrySet()) {
                double rel = ent.getValue() / (double) total;
                gini += rel * rel;
            }
            mv.put(gini);
        }
        Collection<double[]> col = new ArrayList<>();
        col.add(new double[] { mv.getMean(), mv.getSampleStddev() });
        database.getHierarchy().add((Result) index, new CollectionResult<>("Gini coefficient of index", "index-gini", col));
    }
}

Example 5 with SpatialDirectoryEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialDirectoryEntry in project elki by elki-project.

the class EuclideanRStarTreeKNNQuery method expandNode.

private double expandNode(O object, KNNHeap knnList, DoubleIntegerMinHeap pq, double maxDist, final int nodeID) {
    AbstractRStarTreeNode<?, ?> node = tree.getNode(nodeID);
    // data node
    if (node.isLeaf()) {
        for (int i = 0; i < node.getNumEntries(); i++) {
            SpatialPointLeafEntry entry = (SpatialPointLeafEntry) node.getEntry(i);
            double distance = SQUARED.minDist(entry, object);
            tree.statistics.countDistanceCalculation();
            if (distance <= maxDist) {
                maxDist = knnList.insert(distance, entry.getDBID());
            }
        }
    } else // directory node
    {
        for (int i = 0; i < node.getNumEntries(); i++) {
            SpatialDirectoryEntry entry = (SpatialDirectoryEntry) node.getEntry(i);
            double distance = SQUARED.minDist(entry, object);
            tree.statistics.countDistanceCalculation();
            // Greedy expand, bypassing the queue
            if (distance <= 0) {
                expandNode(object, knnList, pq, maxDist, entry.getPageID());
            } else {
                if (distance <= maxDist) {
                    pq.add(distance, entry.getPageID());
                }
            }
        }
    }
    return maxDist;
}