Examples with PrimitiveDistanceQuery de.lmu.ifi.dbs.elki.database.query.distance.PrimitiveDistanceQuery used on opensource projects

Example 1 with PrimitiveDistanceQuery

use of de.lmu.ifi.dbs.elki.database.query.distance.PrimitiveDistanceQuery in project elki by elki-project.

the class ReferenceBasedOutlierDetection method run.

/**
 * Run the algorithm on the given relation.
 *
 * @param database Database
 * @param relation Relation to process
 * @return Outlier result
 */
public OutlierResult run(Database database, Relation<? extends NumberVector> relation) {
    @SuppressWarnings("unchecked") PrimitiveDistanceQuery<? super NumberVector> distq = (PrimitiveDistanceQuery<? super NumberVector>) database.getDistanceQuery(relation, distanceFunction);
    Collection<? extends NumberVector> refPoints = refp.getReferencePoints(relation);
    if (refPoints.isEmpty()) {
        throw new AbortException("Cannot compute ROS without reference points!");
    }
    DBIDs ids = relation.getDBIDs();
    if (k >= ids.size()) {
        throw new AbortException("k must not be chosen larger than the database size!");
    }
    // storage of distance/score values.
    WritableDoubleDataStore rbod_score = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC | DataStoreFactory.HINT_HOT, Double.NaN);
    // Compute density estimation:
    for (NumberVector refPoint : refPoints) {
        DoubleDBIDList referenceDists = computeDistanceVector(refPoint, relation, distq);
        updateDensities(rbod_score, referenceDists);
    }
    // compute maximum density
    DoubleMinMax mm = new DoubleMinMax();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        mm.put(rbod_score.doubleValue(iditer));
    }
    // compute ROS
    double scale = mm.getMax() > 0. ? 1. / mm.getMax() : 1.;
    // Reuse
    mm.reset();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        double score = 1 - (rbod_score.doubleValue(iditer) * scale);
        mm.put(score);
        rbod_score.putDouble(iditer, score);
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Reference-points Outlier Scores", "reference-outlier", rbod_score, relation.getDBIDs());
    OutlierScoreMeta scoreMeta = new BasicOutlierScoreMeta(mm.getMin(), mm.getMax(), 0., 1., 0.);
    OutlierResult result = new OutlierResult(scoreMeta, scoreResult);
    // adds reference points to the result. header information for the
    // visualizer to find the reference points in the result
    result.addChildResult(new ReferencePointsResult<>("Reference points", "reference-points", refPoints));
    return result;
}