Examples with DoubleDBIDPair de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair used on opensource projects

Example 6 with DoubleDBIDPair

use of de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair in project elki by elki-project.

the class SOD method getNearestNeighbors.

/**
 * Get the k nearest neighbors in terms of the shared nearest neighbor
 * distance.
 *
 * The query object is excluded from the knn list.
 *
 * FIXME: move this to the database layer.
 *
 * @param relation the database holding the objects
 * @param simQ similarity function
 * @param queryObject the query object for which the kNNs should be determined
 * @return the k nearest neighbors in terms of the shared nearest neighbor
 *         distance without the query object
 */
private DBIDs getNearestNeighbors(Relation<V> relation, SimilarityQuery<V> simQ, DBIDRef queryObject) {
    Heap<DoubleDBIDPair> nearestNeighbors = new TiedTopBoundedHeap<>(knn);
    for (DBIDIter iter = relation.iterDBIDs(); iter.valid(); iter.advance()) {
        if (DBIDUtil.equal(iter, queryObject)) {
            continue;
        }
        double sim = simQ.similarity(queryObject, iter);
        if (sim > 0.) {
            nearestNeighbors.add(DBIDUtil.newPair(sim, iter));
        }
    }
    // Collect DBIDs
    ArrayModifiableDBIDs dbids = DBIDUtil.newArray(nearestNeighbors.size());
    while (nearestNeighbors.size() > 0) {
        dbids.add(nearestNeighbors.poll());
    }
    return dbids;
}

Example 7 with DoubleDBIDPair

use of de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair in project elki by elki-project.

the class UnweightedNeighborhoodAdapter method getWeightedNeighbors.

@Override
public Collection<DoubleDBIDPair> getWeightedNeighbors(DBIDRef reference) {
    DBIDs neighbors = inner.getNeighborDBIDs(reference);
    ArrayList<DoubleDBIDPair> adapted = new ArrayList<>(neighbors.size());
    for (DBIDIter iter = neighbors.iter(); iter.valid(); iter.advance()) {
        adapted.add(DBIDUtil.newPair(1.0, iter));
    }
    return adapted;
}

Example 8 with DoubleDBIDPair

use of de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair in project elki by elki-project.

the class OUTRES method refineRange.

/**
 * Refine a range query.
 *
 * @param neighc Original result
 * @param adjustedEps New epsilon
 * @return refined list
 */
private DoubleDBIDList refineRange(DoubleDBIDList neighc, double adjustedEps) {
    ModifiableDoubleDBIDList n = DBIDUtil.newDistanceDBIDList(neighc.size());
    // We don't have a guarantee for this list to be sorted
    for (DoubleDBIDListIter neighbor = neighc.iter(); neighbor.valid(); neighbor.advance()) {
        DoubleDBIDPair p = neighbor.getPair();
        double dist = p.doubleValue();
        if (dist <= adjustedEps) {
            n.add(dist, p);
        }
    }
    return n;
}

Example 9 with DoubleDBIDPair

use of de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair in project elki by elki-project.

the class MaterializeKNNAndRKNNPreprocessor method materializeKNNAndRKNNs.

/**
 * Materializes the kNNs and RkNNs of the specified object IDs.
 *
 * @param ids the IDs of the objects
 */
private void materializeKNNAndRKNNs(ArrayDBIDs ids, FiniteProgress progress) {
    // add an empty list to each rknn
    for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
        if (materialized_RkNN.get(iter) == null) {
            materialized_RkNN.put(iter, new TreeSet<DoubleDBIDPair>());
        }
    }
    // knn query
    List<? extends KNNList> kNNList = knnQuery.getKNNForBulkDBIDs(ids, k);
    int i = 0;
    for (DBIDIter id = ids.iter(); id.valid(); id.advance(), i++) {
        KNNList kNNs = kNNList.get(i);
        storage.put(id, kNNs);
        for (DoubleDBIDListIter iter = kNNs.iter(); iter.valid(); iter.advance()) {
            TreeSet<DoubleDBIDPair> rknns = materialized_RkNN.get(iter);
            rknns.add(makePair(iter, id));
        }
        getLogger().incrementProcessed(progress);
    }
    getLogger().ensureCompleted(progress);
}

Example 10 with DoubleDBIDPair

use of de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair in project elki by elki-project.

the class MaterializeKNNAndRKNNPreprocessor method updateKNNsAndRkNNs.

/**
 * Updates the kNNs and RkNNs after insertion of the specified ids.
 *
 * @param ids the ids of newly inserted objects causing a change of
 *        materialized kNNs and RkNNs
 * @return the RkNNs of the specified ids, i.e. the kNNs which have been
 *         updated
 */
private ArrayDBIDs updateKNNsAndRkNNs(DBIDs ids) {
    ArrayModifiableDBIDs rkNN_ids = DBIDUtil.newArray();
    DBIDs oldids = DBIDUtil.difference(relation.getDBIDs(), ids);
    for (DBIDIter id = oldids.iter(); id.valid(); id.advance()) {
        KNNList oldkNNs = storage.get(id);
        double knnDist = oldkNNs.getKNNDistance();
        // look for new kNNs
        KNNHeap heap = null;
        for (DBIDIter newid = ids.iter(); newid.valid(); newid.advance()) {
            double dist = distanceQuery.distance(id, newid);
            if (dist <= knnDist) {
                // New id changes the kNNs of oldid.
                if (heap == null) {
                    heap = DBIDUtil.newHeap(oldkNNs);
                }
                heap.insert(dist, newid);
            }
        }
        // kNNs for oldid have changed:
        if (heap != null) {
            KNNList newkNNs = heap.toKNNList();
            storage.put(id, newkNNs);
            // get the difference
            int i = 0;
            int j = 0;
            ModifiableDoubleDBIDList added = DBIDUtil.newDistanceDBIDList();
            ModifiableDoubleDBIDList removed = DBIDUtil.newDistanceDBIDList();
            // TODO: use iterators.
            while (i < oldkNNs.size() && j < newkNNs.size()) {
                DoubleDBIDPair drp1 = oldkNNs.get(i);
                DoubleDBIDPair drp2 = newkNNs.get(j);
                // NOTE: we assume that on ties they are ordered the same way!
                if (!DBIDUtil.equal(drp1, drp2)) {
                    added.add(drp2);
                    j++;
                } else {
                    i++;
                    j++;
                }
            }
            if (i != j) {
                for (; i < oldkNNs.size(); i++) {
                    removed.add(oldkNNs.get(i));
                }
                for (; j < newkNNs.size(); i++) {
                    added.add(newkNNs.get(i));
                }
            }
            // add new RkNN
            for (DoubleDBIDListIter newnn = added.iter(); newnn.valid(); newnn.advance()) {
                TreeSet<DoubleDBIDPair> rknns = materialized_RkNN.get(newnn);
                rknns.add(makePair(newnn, id));
            }
            // remove old RkNN
            for (DoubleDBIDListIter oldnn = removed.iter(); oldnn.valid(); oldnn.advance()) {
                TreeSet<DoubleDBIDPair> rknns = materialized_RkNN.get(oldnn);
                rknns.remove(makePair(oldnn, id));
            }
            rkNN_ids.add(id);
        }
    }
    return rkNN_ids;
}