Examples with DoubleMinMax de.lmu.ifi.dbs.elki.math.DoubleMinMax used on opensource projects

Example 21 with DoubleMinMax

use of de.lmu.ifi.dbs.elki.math.DoubleMinMax in project elki by elki-project.

the class LocalIsolationCoefficient method run.

/**
 * Runs the algorithm in the timed evaluation part.
 *
 * @param database Database context
 * @param relation Data relation
 */
public OutlierResult run(Database database, Relation<O> relation) {
    final DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, getDistanceFunction());
    // + query point
    KNNQuery<O> knnQuery = database.getKNNQuery(distanceQuery, k + 1);
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Compute Local Isolation Coefficients", relation.size(), LOG) : null;
    DoubleMinMax minmax = new DoubleMinMax();
    WritableDoubleDataStore lic_score = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        // + query point
        final KNNList knn = knnQuery.getKNNForDBID(iditer, k + 1);
        // sum of the distances to the k nearest neighbors
        double skn = 0;
        // number of neighbors so far
        int i = 0;
        for (DoubleDBIDListIter neighbor = knn.iter(); i < k && neighbor.valid(); neighbor.advance()) {
            if (DBIDUtil.equal(iditer, neighbor)) {
                continue;
            }
            skn += neighbor.doubleValue();
            ++i;
        }
        double lic = knn.getKNNDistance() + (i > 0 ? skn / i : 0);
        lic_score.putDouble(iditer, lic);
        minmax.put(skn);
        LOG.incrementProcessed(prog);
    }
    LOG.ensureCompleted(prog);
    DoubleRelation res = new MaterializedDoubleRelation("Local Isolation Coefficient", "lic-outlier", lic_score, relation.getDBIDs());
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), 0., Double.POSITIVE_INFINITY, 0.);
    return new OutlierResult(meta, res);
}

Example 22 with DoubleMinMax

use of de.lmu.ifi.dbs.elki.math.DoubleMinMax 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;
}

Example 23 with DoubleMinMax

use of de.lmu.ifi.dbs.elki.math.DoubleMinMax in project elki by elki-project.

the class ParallelKNNOutlier method run.

public OutlierResult run(Database database, Relation<O> relation) {
    DBIDs ids = relation.getDBIDs();
    WritableDoubleDataStore store = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_DB);
    DistanceQuery<O> distq = database.getDistanceQuery(relation, getDistanceFunction());
    KNNQuery<O> knnq = database.getKNNQuery(distq, k + 1);
    // Compute the kNN
    KNNProcessor<O> knnm = new KNNProcessor<>(k + 1, knnq);
    SharedObject<KNNList> knnv = new SharedObject<>();
    knnm.connectKNNOutput(knnv);
    // Extract the k-distance
    KDistanceProcessor kdistm = new KDistanceProcessor(k + 1);
    SharedDouble kdistv = new SharedDouble();
    kdistm.connectKNNInput(knnv);
    kdistm.connectOutput(kdistv);
    // Store in outlier scores
    WriteDoubleDataStoreProcessor storem = new WriteDoubleDataStoreProcessor(store);
    storem.connectInput(kdistv);
    // Gather statistics
    DoubleMinMaxProcessor mmm = new DoubleMinMaxProcessor();
    mmm.connectInput(kdistv);
    ParallelExecutor.run(ids, knnm, kdistm, storem, mmm);
    DoubleMinMax minmax = mmm.getMinMax();
    DoubleRelation scoreres = new MaterializedDoubleRelation("kNN Outlier Score", "knn-outlier", store, ids);
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 0.0);
    return new OutlierResult(meta, scoreres);
}

Example 24 with DoubleMinMax

use of de.lmu.ifi.dbs.elki.math.DoubleMinMax in project elki by elki-project.

the class ISOS method transformScores.

/**
 * Transform scores
 *
 * @param scores Scores to transform
 * @param ids DBIDs to process
 * @param logPerp log perplexity
 * @param phi Expected outlier rate
 * @return Minimum and maximum scores
 */
public static DoubleMinMax transformScores(WritableDoubleDataStore scores, DBIDs ids, double logPerp, double phi) {
    DoubleMinMax minmax = new DoubleMinMax();
    double adj = (1 - phi) / phi;
    for (DBIDIter it = ids.iter(); it.valid(); it.advance()) {
        double or = FastMath.exp(-scores.doubleValue(it) * logPerp) * adj;
        double s = 1. / (1 + or);
        scores.putDouble(it, s);
        minmax.put(s);
    }
    return minmax;
}

Example 25 with DoubleMinMax

use of de.lmu.ifi.dbs.elki.math.DoubleMinMax in project elki by elki-project.

the class SimplifiedLOF method run.

/**
 * Run the Simple LOF algorithm.
 *
 * @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("Simplified LOF", 3) : null;
    DBIDs ids = relation.getDBIDs();
    LOG.beginStep(stepprog, 1, "Materializing neighborhoods w.r.t. distance function.");
    KNNQuery<O> knnq = DatabaseUtil.precomputedKNNQuery(database, relation, getDistanceFunction(), k);
    // Compute LRDs
    LOG.beginStep(stepprog, 2, "Computing densities.");
    WritableDoubleDataStore dens = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    computeSimplifiedLRDs(ids, knnq, dens);
    // compute LOF_SCORE of each db object
    LOG.beginStep(stepprog, 3, "Computing SLOFs.");
    WritableDoubleDataStore lofs = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC);
    DoubleMinMax lofminmax = new DoubleMinMax();
    computeSimplifiedLOFs(ids, knnq, dens, lofs, lofminmax);
    LOG.setCompleted(stepprog);
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Simplified Local Outlier Factor", "simplified-lof-outlier", lofs, ids);
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(lofminmax.getMin(), lofminmax.getMax(), 0., Double.POSITIVE_INFINITY, 1.);
    OutlierResult result = new OutlierResult(scoreMeta, scoreResult);
    return result;
}