Examples with WritableDoubleDataStore de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore used on opensource projects

Example 56 with WritableDoubleDataStore

use of de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore in project elki by elki-project.

the class HiCS method run.

/**
 * Perform HiCS on a given database.
 *
 * @param relation the database
 * @return The aggregated resulting scores that were assigned by the given
 *         outlier detection algorithm
 */
public OutlierResult run(Relation<V> relation) {
    final DBIDs ids = relation.getDBIDs();
    ArrayList<ArrayDBIDs> subspaceIndex = buildOneDimIndexes(relation);
    Set<HiCSSubspace> subspaces = calculateSubspaces(relation, subspaceIndex, rnd.getSingleThreadedRandom());
    if (LOG.isVerbose()) {
        LOG.verbose("Number of high-contrast subspaces: " + subspaces.size());
    }
    List<DoubleRelation> results = new ArrayList<>();
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Calculating Outlier scores for high Contrast subspaces", subspaces.size(), LOG) : null;
    // relation instead of SubspaceEuclideanDistanceFunction?)
    for (HiCSSubspace dimset : subspaces) {
        if (LOG.isVerbose()) {
            LOG.verbose("Performing outlier detection in subspace " + dimset);
        }
        ProxyDatabase pdb = new ProxyDatabase(ids);
        pdb.addRelation(new ProjectedView<>(relation, new NumericalFeatureSelection<V>(dimset)));
        // run LOF and collect the result
        OutlierResult result = outlierAlgorithm.run(pdb);
        results.add(result.getScores());
        LOG.incrementProcessed(prog);
    }
    LOG.ensureCompleted(prog);
    WritableDoubleDataStore scores = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    DoubleMinMax minmax = new DoubleMinMax();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        double sum = 0.0;
        for (DoubleRelation r : results) {
            final double s = r.doubleValue(iditer);
            if (!Double.isNaN(s)) {
                sum += s;
            }
        }
        scores.putDouble(iditer, sum);
        minmax.put(sum);
    }
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax());
    DoubleRelation scoreres = new MaterializedDoubleRelation("HiCS", "HiCS-outlier", scores, relation.getDBIDs());
    return new OutlierResult(meta, scoreres);
}

Example 57 with WritableDoubleDataStore

use of de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore in project elki by elki-project.

the class SimpleOutlierEnsemble method run.

@Override
public OutlierResult run(Database database) throws IllegalStateException {
    int num = algorithms.size();
    // Run inner outlier algorithms
    ModifiableDBIDs ids = DBIDUtil.newHashSet();
    ArrayList<OutlierResult> results = new ArrayList<>(num);
    {
        FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Inner outlier algorithms", num, LOG) : null;
        for (Algorithm alg : algorithms) {
            Result res = alg.run(database);
            List<OutlierResult> ors = OutlierResult.getOutlierResults(res);
            for (OutlierResult or : ors) {
                results.add(or);
                ids.addDBIDs(or.getScores().getDBIDs());
            }
            LOG.incrementProcessed(prog);
        }
        LOG.ensureCompleted(prog);
    }
    // Combine
    WritableDoubleDataStore sumscore = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC);
    DoubleMinMax minmax = new DoubleMinMax();
    {
        FiniteProgress cprog = LOG.isVerbose() ? new FiniteProgress("Combining results", ids.size(), LOG) : null;
        for (DBIDIter id = ids.iter(); id.valid(); id.advance()) {
            double[] scores = new double[num];
            int i = 0;
            for (OutlierResult r : results) {
                double score = r.getScores().doubleValue(id);
                if (!Double.isNaN(score)) {
                    scores[i] = score;
                    i++;
                } else {
                    LOG.warning("DBID " + id + " was not given a score by result " + r);
                }
            }
            if (i > 0) {
                // Shrink array if necessary.
                if (i < scores.length) {
                    scores = Arrays.copyOf(scores, i);
                }
                double combined = voting.combine(scores);
                sumscore.putDouble(id, combined);
                minmax.put(combined);
            } else {
                LOG.warning("DBID " + id + " was not given any score at all.");
            }
            LOG.incrementProcessed(cprog);
        }
        LOG.ensureCompleted(cprog);
    }
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax());
    DoubleRelation scores = new MaterializedDoubleRelation("Simple Outlier Ensemble", "ensemble-outlier", sumscore, ids);
    return new OutlierResult(meta, scores);
}

Example 58 with WritableDoubleDataStore

use of de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore in project elki by elki-project.

the class CTLuGLSBackwardSearchAlgorithm method run.

/**
 * Run the algorithm
 *
 * @param database Database to process
 * @param relationx Spatial relation
 * @param relationy Attribute relation
 * @return Algorithm result
 */
public OutlierResult run(Database database, Relation<V> relationx, Relation<? extends NumberVector> relationy) {
    WritableDoubleDataStore scores = DataStoreUtil.makeDoubleStorage(relationx.getDBIDs(), DataStoreFactory.HINT_STATIC);
    DoubleMinMax mm = new DoubleMinMax(0.0, 0.0);
    // Outlier detection loop
    {
        ModifiableDBIDs idview = DBIDUtil.newHashSet(relationx.getDBIDs());
        ProxyView<V> proxy = new ProxyView<>(idview, relationx);
        double phialpha = NormalDistribution.standardNormalQuantile(1.0 - alpha * .5);
        // Detect outliers while significant.
        while (true) {
            Pair<DBIDVar, Double> candidate = singleIteration(proxy, relationy);
            if (candidate.second < phialpha) {
                break;
            }
            scores.putDouble(candidate.first, candidate.second);
            if (!Double.isNaN(candidate.second)) {
                mm.put(candidate.second);
            }
            idview.remove(candidate.first);
        }
        // Remaining objects are inliers
        for (DBIDIter iter = idview.iter(); iter.valid(); iter.advance()) {
            scores.putDouble(iter, 0.0);
        }
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("GLSSODBackward", "GLSSODbackward-outlier", scores, relationx.getDBIDs());
    OutlierScoreMeta scoreMeta = new BasicOutlierScoreMeta(mm.getMin(), mm.getMax(), 0, Double.POSITIVE_INFINITY, 0);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 59 with WritableDoubleDataStore

use of de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore in project elki by elki-project.

the class CTLuMoranScatterplotOutlier method run.

/**
 * Main method.
 *
 * @param database Database
 * @param nrel Neighborhood relation
 * @param relation Data relation (1d!)
 * @return Outlier detection result
 */
public OutlierResult run(Database database, Relation<N> nrel, Relation<? extends NumberVector> relation) {
    final NeighborSetPredicate npred = getNeighborSetPredicateFactory().instantiate(database, nrel);
    // Compute the global mean and variance
    MeanVariance globalmv = new MeanVariance();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        globalmv.put(relation.get(iditer).doubleValue(0));
    }
    DoubleMinMax minmax = new DoubleMinMax();
    WritableDoubleDataStore scores = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    // calculate neighborhood average of normalized attribute values.
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        // Compute global z score
        final double globalZ = (relation.get(iditer).doubleValue(0) - globalmv.getMean()) / globalmv.getNaiveStddev();
        // Compute local average z score
        Mean localm = new Mean();
        for (DBIDIter iter = npred.getNeighborDBIDs(iditer).iter(); iter.valid(); iter.advance()) {
            if (DBIDUtil.equal(iditer, iter)) {
                continue;
            }
            localm.put((relation.get(iter).doubleValue(0) - globalmv.getMean()) / globalmv.getNaiveStddev());
        }
        // if neighors.size == 0
        final double localZ;
        if (localm.getCount() > 0) {
            localZ = localm.getMean();
        } else {
            // if s has no neighbors => Wzi = zi
            localZ = globalZ;
        }
        // compute score
        // Note: in the original moran scatterplot, any object with a score < 0 would be an outlier.
        final double score = Math.max(-globalZ * localZ, 0);
        minmax.put(score);
        scores.putDouble(iditer, score);
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("MoranOutlier", "Moran Scatterplot Outlier", scores, relation.getDBIDs());
    OutlierScoreMeta scoreMeta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, 0);
    OutlierResult or = new OutlierResult(scoreMeta, scoreResult);
    or.addChildResult(npred);
    return or;
}

Example 60 with WritableDoubleDataStore

use of de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore in project elki by elki-project.

the class ParallelSimplifiedLOF method run.

public OutlierResult run(Database database, Relation<O> relation) {
    DBIDs ids = relation.getDBIDs();
    DistanceQuery<O> distq = database.getDistanceQuery(relation, getDistanceFunction());
    KNNQuery<O> knnq = database.getKNNQuery(distq, k + 1);
    // Phase one: KNN and k-dist
    WritableDataStore<KNNList> knns = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_DB, KNNList.class);
    {
        // Compute kNN
        KNNProcessor<O> knnm = new KNNProcessor<>(k + 1, knnq);
        SharedObject<KNNList> knnv = new SharedObject<>();
        WriteDataStoreProcessor<KNNList> storek = new WriteDataStoreProcessor<>(knns);
        knnm.connectKNNOutput(knnv);
        storek.connectInput(knnv);
        ParallelExecutor.run(ids, knnm, storek);
    }
    // Phase two: simplified-lrd
    WritableDoubleDataStore lrds = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_DB);
    {
        SimplifiedLRDProcessor lrdm = new SimplifiedLRDProcessor(knns);
        SharedDouble lrdv = new SharedDouble();
        WriteDoubleDataStoreProcessor storelrd = new WriteDoubleDataStoreProcessor(lrds);
        lrdm.connectOutput(lrdv);
        storelrd.connectInput(lrdv);
        ParallelExecutor.run(ids, lrdm, storelrd);
    }
    // Phase three: Simplified-LOF
    WritableDoubleDataStore lofs = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_DB);
    DoubleMinMax minmax;
    {
        LOFProcessor lofm = new LOFProcessor(knns, lrds, true);
        SharedDouble lofv = new SharedDouble();
        DoubleMinMaxProcessor mmm = new DoubleMinMaxProcessor();
        WriteDoubleDataStoreProcessor storelof = new WriteDoubleDataStoreProcessor(lofs);
        lofm.connectOutput(lofv);
        mmm.connectInput(lofv);
        storelof.connectInput(lofv);
        ParallelExecutor.run(ids, lofm, storelof, mmm);
        minmax = mmm.getMinMax();
    }
    DoubleRelation scoreres = new MaterializedDoubleRelation("Simplified Local Outlier Factor", "simplified-lof-outlier", lofs, ids);
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
    return new OutlierResult(meta, scoreres);
}