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

Example 76 with KNNList

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

the class MkMaxTree method reverseKNNQuery.

/**
 * Performs a reverse k-nearest neighbor query for the given object ID. In the
 * first step the candidates are chosen by performing a reverse k-nearest
 * neighbor query with k = {@link #getKmax()}. Then these candidates are refined
 * in a second step.
 */
@Override
public DoubleDBIDList reverseKNNQuery(DBIDRef id, int k) {
    if (k > this.getKmax()) {
        throw new IllegalArgumentException("Parameter k has to be equal or less than " + "parameter k of the MkMax-Tree!");
    }
    // get the candidates
    ModifiableDoubleDBIDList candidates = DBIDUtil.newDistanceDBIDList();
    doReverseKNNQuery(id, getRoot(), null, candidates);
    if (k == this.getKmax()) {
        candidates.sort();
        // rkNNStatistics.addResults(candidates.size());
        return candidates;
    }
    // refinement of candidates
    ModifiableDBIDs candidateIDs = DBIDUtil.newArray(candidates.size());
    for (DBIDIter candidate = candidates.iter(); candidate.valid(); candidate.advance()) {
        candidateIDs.add(candidate);
    }
    Map<DBID, KNNList> knnLists = batchNN(getRoot(), candidateIDs, k);
    ModifiableDoubleDBIDList result = DBIDUtil.newDistanceDBIDList();
    for (DBIDIter iter = candidateIDs.iter(); iter.valid(); iter.advance()) {
        DBID cid = DBIDUtil.deref(iter);
        KNNList cands = knnLists.get(cid);
        for (DoubleDBIDListIter iter2 = cands.iter(); iter2.valid(); iter2.advance()) {
            if (DBIDUtil.equal(id, iter2)) {
                result.add(iter2.doubleValue(), cid);
                break;
            }
        }
    }
    // FIXME: re-add statistics.
    // rkNNStatistics.addResults(result.size());
    // rkNNStatistics.addCandidates(candidates.size());
    result.sort();
    return result;
}

Example 77 with KNNList

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

the class MkTabTreeIndex method knnDistances.

/**
 * Returns the knn distance of the object with the specified id.
 *
 * @param object the query object
 * @return the knn distance of the object with the specified id
 */
private double[] knnDistances(O object) {
    KNNList knns = knnq.getKNNForObject(object, getKmax() - 1);
    double[] distances = new double[getKmax()];
    int i = 0;
    for (DoubleDBIDListIter iter = knns.iter(); iter.valid() && i < getKmax(); iter.advance(), i++) {
        distances[i] = iter.doubleValue();
    }
    return distances;
}

Example 78 with KNNList

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

the class MaterializeKNNPreprocessor method preprocess.

/**
 * The actual preprocessing step.
 */
@Override
protected void preprocess() {
    // Could be subclass
    final Logging log = getLogger();
    createStorage();
    ArrayDBIDs ids = DBIDUtil.ensureArray(relation.getDBIDs());
    if (log.isStatistics()) {
        log.statistics(new LongStatistic(this.getClass().getName() + ".k", k));
    }
    Duration duration = log.isStatistics() ? log.newDuration(this.getClass().getName() + ".precomputation-time").begin() : null;
    FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Materializing k nearest neighbors (k=" + k + ")", ids.size(), getLogger()) : null;
    // Try bulk
    List<? extends KNNList> kNNList = null;
    if (usebulk) {
        kNNList = knnQuery.getKNNForBulkDBIDs(ids, k);
        if (kNNList != null) {
            int i = 0;
            for (DBIDIter id = ids.iter(); id.valid(); id.advance(), i++) {
                storage.put(id, kNNList.get(i));
                log.incrementProcessed(progress);
            }
        }
    } else {
        final boolean ismetric = getDistanceQuery().getDistanceFunction().isMetric();
        for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
            if (ismetric && storage.get(iter) != null) {
                log.incrementProcessed(progress);
                // Previously computed (duplicate point?)
                continue;
            }
            KNNList knn = knnQuery.getKNNForDBID(iter, k);
            storage.put(iter, knn);
            if (ismetric) {
                for (DoubleDBIDListIter it = knn.iter(); it.valid() && it.doubleValue() == 0.; it.advance()) {
                    // Reuse
                    storage.put(it, knn);
                }
            }
            log.incrementProcessed(progress);
        }
    }
    log.ensureCompleted(progress);
    if (duration != null) {
        log.statistics(duration.end());
    }
}

Example 79 with KNNList

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

the class MaterializeKNNPreprocessor method updateKNNsAfterInsertion.

/**
 * Updates the kNNs of the RkNNs of the specified ids.
 *
 * @param ids the ids of newly inserted objects causing a change of
 *        materialized kNNs
 * @return the RkNNs of the specified ids, i.e. the kNNs which have been
 *         updated
 */
private ArrayDBIDs updateKNNsAfterInsertion(DBIDs ids) {
    ArrayModifiableDBIDs rkNN_ids = DBIDUtil.newArray();
    DBIDs oldids = DBIDUtil.difference(relation.getDBIDs(), ids);
    for (DBIDIter iter = oldids.iter(); iter.valid(); iter.advance()) {
        KNNList kNNs = storage.get(iter);
        double knnDist = kNNs.getKNNDistance();
        // look for new kNNs
        KNNHeap heap = null;
        for (DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) {
            double dist = distanceQuery.distance(iter, iter2);
            if (dist <= knnDist) {
                if (heap == null) {
                    heap = DBIDUtil.newHeap(kNNs);
                }
                heap.insert(dist, iter2);
            }
        }
        if (heap != null) {
            kNNs = heap.toKNNList();
            storage.put(iter, kNNs);
            rkNN_ids.add(iter);
        }
    }
    return rkNN_ids;
}

Example 80 with KNNList

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

the class PreprocessorKNNQuery method getKNNForBulkDBIDs.

@Override
public List<KNNList> getKNNForBulkDBIDs(ArrayDBIDs ids, int k) {
    if (!warned && k > preprocessor.getK()) {
        getLogger().warning("Requested more neighbors than preprocessed: requested " + k + " preprocessed " + preprocessor.getK(), new Throwable());
        warned = true;
    }
    if (k < preprocessor.getK()) {
        List<KNNList> result = new ArrayList<>(ids.size());
        for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
            result.add(getSublist(preprocessor.get(iter), k));
        }
        return result;
    }
    List<KNNList> result = new ArrayList<>(ids.size());
    for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
        result.add(preprocessor.get(iter));
    }
    return result;
}