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

Example 1 with SpatialPointLeafEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialPointLeafEntry 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 SpatialPointLeafEntry

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

the class KNNJoin method processDataPages.

/**
 * Processes the two data pages pr and ps and determines the k-nearest
 * neighbors of pr in ps.
 *
 * @param df the distance function to use
 * @param pr the first data page
 * @param ps the second data page
 * @param pr_heaps the knn lists for each data object
 * @param ps_heaps the knn lists for each data object in ps
 */
private void processDataPages(SpatialPrimitiveDistanceFunction<? super V> df, List<KNNHeap> pr_heaps, List<KNNHeap> ps_heaps, N pr, N ps) {
    // Compare pairwise
    for (int j = 0; j < ps.getNumEntries(); j++) {
        final SpatialPointLeafEntry s_e = (SpatialPointLeafEntry) ps.getEntry(j);
        final KNNHeap hj = ps_heaps != null ? ps_heaps.get(j) : null;
        final DBID s_id = s_e.getDBID();
        for (int i = 0; i < pr.getNumEntries(); i++) {
            final SpatialPointLeafEntry r_e = (SpatialPointLeafEntry) pr.getEntry(i);
            double distance = df.minDist(s_e, r_e);
            pr_heaps.get(i).insert(distance, s_id);
            if (hj != null) {
                hj.insert(distance, r_e.getDBID());
            }
        }
    }
}

Example 3 with SpatialPointLeafEntry

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

the class AbstractXTree method initializeCapacities.

@Override
protected void initializeCapacities(SpatialEntry exampleLeaf) {
    /* Simulate the creation of a leaf page to get the page capacity */
    try {
        int cap = 0;
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        ObjectOutputStream oos = new ObjectOutputStream(baos);
        SpatialPointLeafEntry sl = new SpatialPointLeafEntry(DBIDUtil.importInteger(0), new double[exampleLeaf.getDimensionality()]);
        while (baos.size() <= getPageSize()) {
            sl.writeExternal(oos);
            oos.flush();
            cap++;
        }
        // the last one caused the page to overflow.
        leafCapacity = cap - 1;
    } catch (IOException e) {
        throw new AbortException("Error determining page sizes.", e);
    }
    /* Simulate the creation of a directory page to get the capacity */
    try {
        int cap = 0;
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        ObjectOutputStream oos = new ObjectOutputStream(baos);
        ModifiableHyperBoundingBox hb = new ModifiableHyperBoundingBox(new double[exampleLeaf.getDimensionality()], new double[exampleLeaf.getDimensionality()]);
        XTreeDirectoryEntry xl = new XTreeDirectoryEntry(0, hb);
        while (baos.size() <= getPageSize()) {
            xl.writeExternal(oos);
            oos.flush();
            cap++;
        }
        dirCapacity = cap - 1;
    } catch (IOException e) {
        throw new AbortException("Error determining page sizes.", e);
    }
    if (dirCapacity <= 1) {
        throw new IllegalArgumentException("Node size of " + getPageSize() + " Bytes is chosen too small!");
    }
    if (dirCapacity < 10) {
        getLogger().warning("Page size is choosen very small! Maximum number of entries " + "in a directory node = " + (dirCapacity - 1));
    }
    // minimum entries per directory node
    dirMinimum = (int) Math.round((dirCapacity - 1) * settings.relativeMinEntries);
    if (dirMinimum < 2) {
        dirMinimum = 2;
    }
    // minimum entries per directory node
    settings.min_fanout = (int) Math.round((dirCapacity - 1) * settings.relativeMinFanout);
    if (settings.min_fanout < 2) {
        settings.min_fanout = 2;
    }
    if (leafCapacity <= 1) {
        throw new IllegalArgumentException("Node size of " + getPageSize() + " Bytes is chosen too small!");
    }
    if (leafCapacity < 10) {
        getLogger().warning("Page size is choosen very small! Maximum number of entries " + "in a leaf node = " + (leafCapacity - 1));
    }
    // minimum entries per leaf node
    leafMinimum = (int) Math.round((leafCapacity - 1) * settings.relativeMinEntries);
    if (leafMinimum < 2) {
        leafMinimum = 2;
    }
    dimensionality = exampleLeaf.getDimensionality();
    if (getLogger().isVerbose()) {
        getLogger().verbose("Directory Capacity:  " + (dirCapacity - 1) + "\nDirectory minimum: " + dirMinimum + "\nLeaf Capacity:     " + (leafCapacity - 1) + "\nLeaf Minimum:      " + leafMinimum + "\nminimum fanout: " + settings.min_fanout);
    }
}

Example 4 with SpatialPointLeafEntry

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

the class AbstractXTreeNode method readExternal.

/**
 * Reads the id of this node, the numEntries and the entries array from the
 * specified stream. If the {@link #supernode} field is set, <code>this</code>
 * cannot be contained in <code>in</code>. Such a node has to be manually
 * filled using {@link #readSuperNode(ObjectInput, AbstractXTree)}.
 *
 * @param in the stream to read data from in order to restore the object
 * @throws java.io.IOException if I/O errors occur
 * @throws ClassNotFoundException If the class for an object being restored
 *         cannot be found.
 */
@Override
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException {
    setPageID(in.readInt());
    isLeaf = in.readBoolean();
    supernode = in.readBoolean();
    numEntries = in.readInt();
    final int capacity = in.readInt();
    if (supernode) {
        // this node is a supernode and is yet to be filled
        capacity_to_be_filled = capacity;
        return;
    }
    // entries = (E[]) java.lang.reflect.Array.newInstance(eclass, capacity);
    if (isLeaf()) {
        entries = (Entry[]) new SpatialPointLeafEntry[capacity];
    } else {
        entries = (Entry[]) new XTreeDirectoryEntry[capacity];
    }
    for (int i = 0; i < numEntries; i++) {
        SpatialEntry s = isLeaf() ? new SpatialPointLeafEntry() : new XTreeDirectoryEntry();
        s.readExternal(in);
        entries[i] = s;
    }
}

Example 5 with SpatialPointLeafEntry

use of de.lmu.ifi.dbs.elki.index.tree.spatial.SpatialPointLeafEntry 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));
    }
}