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

Example 41 with MaterializedDoubleRelation

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

the class ParallelKNNWeightOutlier method run.

/**
 * Run the parallel kNN weight outlier detector.
 *
 * @param database Database to process
 * @param relation Relation to analyze
 * @return Outlier detection result
 */
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);
    // Find kNN
    KNNProcessor<O> knnm = new KNNProcessor<>(k + 1, knnq);
    SharedObject<KNNList> knnv = new SharedObject<>();
    knnm.connectKNNOutput(knnv);
    // Extract outlier score
    KNNWeightProcessor kdistm = new KNNWeightProcessor(k + 1);
    SharedDouble kdistv = new SharedDouble();
    kdistm.connectKNNInput(knnv);
    kdistm.connectOutput(kdistv);
    // Store in output result
    WriteDoubleDataStoreProcessor storem = new WriteDoubleDataStoreProcessor(store);
    storem.connectInput(kdistv);
    // And gather statistics for metadata
    DoubleMinMaxProcessor mmm = new DoubleMinMaxProcessor();
    mmm.connectInput(kdistv);
    ParallelExecutor.run(ids, knnm, kdistm, storem, mmm);
    DoubleMinMax minmax = mmm.getMinMax();
    DoubleRelation scoreres = new MaterializedDoubleRelation("kNN weight Outlier Score", "knnw-outlier", store, ids);
    OutlierScoreMeta meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax(), 0., Double.POSITIVE_INFINITY, 0.);
    return new OutlierResult(meta, scoreres);
}

Example 42 with MaterializedDoubleRelation

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

the class IDOS method run.

/**
 * Run the algorithm
 *
 * @param database Database
 * @param relation Data relation
 * @return Outlier result
 */
public OutlierResult run(Database database, Relation<O> relation) {
    StepProgress stepprog = LOG.isVerbose() ? new StepProgress("IDOS", 3) : null;
    if (stepprog != null) {
        stepprog.beginStep(1, "Precomputing neighborhoods", LOG);
    }
    KNNQuery<O> knnQ = DatabaseUtil.precomputedKNNQuery(database, relation, getDistanceFunction(), Math.max(k_c, k_r) + 1);
    DBIDs ids = relation.getDBIDs();
    if (stepprog != null) {
        stepprog.beginStep(2, "Computing intrinsic dimensionalities", LOG);
    }
    DoubleDataStore intDims = computeIDs(ids, knnQ);
    if (stepprog != null) {
        stepprog.beginStep(3, "Computing IDOS scores", LOG);
    }
    DoubleMinMax idosminmax = new DoubleMinMax();
    DoubleDataStore ldms = computeIDOS(ids, knnQ, intDims, idosminmax);
    if (stepprog != null) {
        stepprog.setCompleted(LOG);
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Intrinsic Dimensionality Outlier Score", "idos", ldms, ids);
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(idosminmax.getMin(), idosminmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 43 with MaterializedDoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.MaterializedDoubleRelation 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 44 with MaterializedDoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.MaterializedDoubleRelation 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 45 with MaterializedDoubleRelation

use of de.lmu.ifi.dbs.elki.database.relation.MaterializedDoubleRelation 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);
}