Examples with DoubleRelation de.lmu.ifi.dbs.elki.database.relation.DoubleRelation used on opensource projects

Example 51 with DoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.DoubleRelation in project elki by elki-project.

the class LOF method run.

/**
 * Runs the LOF algorithm on the given database.
 *
 * @param database Database to query
 * @param relation Data to process
 * @return LOF outlier result
 */
public OutlierResult run(Database database, Relation<O> relation) {
    StepProgress stepprog = LOG.isVerbose() ? new StepProgress("LOF", 3) : null;
    DBIDs ids = relation.getDBIDs();
    LOG.beginStep(stepprog, 1, "Materializing nearest-neighbor sets.");
    KNNQuery<O> knnq = DatabaseUtil.precomputedKNNQuery(database, relation, getDistanceFunction(), k);
    // Compute LRDs
    LOG.beginStep(stepprog, 2, "Computing Local Reachability Densities (LRD).");
    WritableDoubleDataStore lrds = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    computeLRDs(knnq, ids, lrds);
    // compute LOF_SCORE of each db object
    LOG.beginStep(stepprog, 3, "Computing Local Outlier Factors (LOF).");
    WritableDoubleDataStore lofs = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB);
    // track the maximum value for normalization.
    DoubleMinMax lofminmax = new DoubleMinMax();
    computeLOFScores(knnq, ids, lrds, lofs, lofminmax);
    LOG.setCompleted(stepprog);
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Local Outlier Factor", "lof-outlier", lofs, ids);
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(lofminmax.getMin(), lofminmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 52 with DoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.DoubleRelation in project elki by elki-project.

the class COF method run.

/**
 * Runs the COF algorithm on the given database.
 *
 * @param database Database to query
 * @param relation Data to process
 * @return COF outlier result
 */
public OutlierResult run(Database database, Relation<O> relation) {
    StepProgress stepprog = LOG.isVerbose() ? new StepProgress("COF", 3) : null;
    DistanceQuery<O> dq = database.getDistanceQuery(relation, getDistanceFunction());
    LOG.beginStep(stepprog, 1, "Materializing COF neighborhoods.");
    KNNQuery<O> knnq = DatabaseUtil.precomputedKNNQuery(database, relation, dq, k);
    DBIDs ids = relation.getDBIDs();
    LOG.beginStep(stepprog, 2, "Computing Average Chaining Distances.");
    WritableDoubleDataStore acds = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    computeAverageChainingDistances(knnq, dq, ids, acds);
    // compute COF_SCORE of each db object
    LOG.beginStep(stepprog, 3, "Computing Connectivity-based Outlier Factors.");
    WritableDoubleDataStore cofs = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB);
    // track the maximum value for normalization.
    DoubleMinMax cofminmax = new DoubleMinMax();
    computeCOFScores(knnq, ids, acds, cofs, cofminmax);
    LOG.setCompleted(stepprog);
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Connectivity-Based Outlier Factor", "cof-outlier", cofs, ids);
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(cofminmax.getMin(), cofminmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 53 with DoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.DoubleRelation in project elki by elki-project.

the class INFLO method run.

/**
 * Run the algorithm
 *
 * @param database Database to process
 * @param relation Relation to process
 * @return Outlier result
 */
public OutlierResult run(Database database, Relation<O> relation) {
    StepProgress stepprog = LOG.isVerbose() ? new StepProgress("INFLO", 3) : null;
    // Step one: find the kNN
    LOG.beginStep(stepprog, 1, "Materializing nearest-neighbor sets.");
    KNNQuery<O> knnq = DatabaseUtil.precomputedKNNQuery(database, relation, getDistanceFunction(), kplus1);
    // Step two: find the RkNN, minus kNN.
    LOG.beginStep(stepprog, 2, "Materialize reverse NN.");
    ModifiableDBIDs pruned = DBIDUtil.newHashSet();
    // RNNS
    WritableDataStore<ModifiableDBIDs> rnns = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_TEMP | DataStoreFactory.HINT_HOT, ModifiableDBIDs.class);
    // init the rNN
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        rnns.put(iditer, DBIDUtil.newArray());
    }
    computeNeighborhoods(relation, knnq, pruned, rnns);
    // Step three: compute INFLO scores
    LOG.beginStep(stepprog, 3, "Compute INFLO scores.");
    // Calculate INFLO for any Object
    DoubleMinMax inflominmax = new DoubleMinMax();
    WritableDoubleDataStore inflos = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    // Note: this modifies knns, by adding rknns!
    computeINFLO(relation, pruned, knnq, rnns, inflos, inflominmax);
    LOG.setCompleted(stepprog);
    LOG.statistics(new LongStatistic(INFLO.class.getName() + ".pruned", pruned.size()));
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Influence Outlier Score", "inflo-outlier", inflos, relation.getDBIDs());
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(inflominmax.getMin(), inflominmax.getMax(), 0., Double.POSITIVE_INFINITY, 1.);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 54 with DoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.DoubleRelation in project elki by elki-project.

the class LoOP method run.

/**
 * Performs the LoOP algorithm on the given database.
 *
 * @param database Database to process
 * @param relation Relation to process
 * @return Outlier result
 */
public OutlierResult run(Database database, Relation<O> relation) {
    StepProgress stepprog = LOG.isVerbose() ? new StepProgress(5) : null;
    Pair<KNNQuery<O>, KNNQuery<O>> pair = getKNNQueries(database, relation, stepprog);
    KNNQuery<O> knnComp = pair.getFirst();
    KNNQuery<O> knnReach = pair.getSecond();
    // Assert we got something
    if (knnComp == null) {
        throw new AbortException("No kNN queries supported by database for comparison distance function.");
    }
    if (knnReach == null) {
        throw new AbortException("No kNN queries supported by database for density estimation distance function.");
    }
    // FIXME: tie handling!
    // Probabilistic distances
    WritableDoubleDataStore pdists = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB);
    LOG.beginStep(stepprog, 3, "Computing pdists");
    computePDists(relation, knnReach, pdists);
    // Compute PLOF values.
    WritableDoubleDataStore plofs = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    LOG.beginStep(stepprog, 4, "Computing PLOF");
    double nplof = computePLOFs(relation, knnComp, pdists, plofs);
    // Normalize the outlier scores.
    DoubleMinMax mm = new DoubleMinMax();
    {
        // compute LOOP_SCORE of each db object
        LOG.beginStep(stepprog, 5, "Computing LoOP scores");
        FiniteProgress progressLOOPs = LOG.isVerbose() ? new FiniteProgress("LoOP for objects", relation.size(), LOG) : null;
        final double norm = 1. / (nplof * MathUtil.SQRT2);
        for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
            double loop = NormalDistribution.erf((plofs.doubleValue(iditer) - 1.) * norm);
            plofs.putDouble(iditer, loop);
            mm.put(loop);
            LOG.incrementProcessed(progressLOOPs);
        }
        LOG.ensureCompleted(progressLOOPs);
    }
    LOG.setCompleted(stepprog);
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Local Outlier Probabilities", "loop-outlier", plofs, relation.getDBIDs());
    OutlierScoreMeta scoreMeta = new ProbabilisticOutlierScore(mm.getMin(), mm.getMax(), 0.);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 55 with DoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.DoubleRelation in project elki by elki-project.

the class KNNOutlier method run.

/**
 * Runs the algorithm in the timed evaluation part.
 *
 * @param relation Data relation
 */
public OutlierResult run(Relation<O> relation) {
    final DistanceQuery<O> distanceQuery = relation.getDistanceQuery(getDistanceFunction());
    final KNNQuery<O> knnQuery = relation.getKNNQuery(distanceQuery, k);
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("kNN distance for objects", relation.size(), LOG) : null;
    DoubleMinMax minmax = new DoubleMinMax();
    WritableDoubleDataStore knno_score = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    // compute distance to the k nearest neighbor.
    for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
        // distance to the kth nearest neighbor
        // (assuming the query point is always included, with distance 0)
        final double dkn = knnQuery.getKNNForDBID(it, k).getKNNDistance();
        knno_score.putDouble(it, dkn);
        minmax.put(dkn);
        LOG.incrementProcessed(prog);
    }
    LOG.ensureCompleted(prog);
    DoubleRelation scoreres = new MaterializedDoubleRelation("kNN Outlier Score", "knn-outlier", knno_score, relation.getDBIDs());
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), 0., Double.POSITIVE_INFINITY, 0.);
    return new OutlierResult(meta, scoreres);
}