Examples with DBIDs de.lmu.ifi.dbs.elki.database.ids.DBIDs used on opensource projects

Example 56 with DBIDs

use of de.lmu.ifi.dbs.elki.database.ids.DBIDs in project elki by elki-project.

the class TrivialAllNoise method run.

public Clustering<Model> run(Relation<?> relation) {
    final DBIDs ids = relation.getDBIDs();
    Clustering<Model> result = new Clustering<>("All-in-noise trivial Clustering", "allinnoise-clustering");
    Cluster<Model> c = new Cluster<Model>(ids, true, ClusterModel.CLUSTER);
    result.addToplevelCluster(c);
    return result;
}

Example 57 with DBIDs

use of de.lmu.ifi.dbs.elki.database.ids.DBIDs in project elki by elki-project.

the class TrivialAllInOne method run.

public Clustering<Model> run(Relation<?> relation) {
    final DBIDs ids = relation.getDBIDs();
    Clustering<Model> result = new Clustering<>("All-in-one trivial Clustering", "allinone-clustering");
    Cluster<Model> c = new Cluster<Model>(ids, ClusterModel.CLUSTER);
    result.addToplevelCluster(c);
    return result;
}

Example 58 with DBIDs

use of de.lmu.ifi.dbs.elki.database.ids.DBIDs in project elki by elki-project.

the class WithinClusterMeanDistanceQualityMeasure method quality.

@Override
public <V extends NumberVector> double quality(Clustering<? extends MeanModel> clustering, NumberVectorDistanceFunction<? super V> distanceFunction, Relation<V> relation) {
    double clusterDistanceSum = 0;
    for (Cluster<? extends MeanModel> cluster : clustering.getAllClusters()) {
        DBIDs ids = cluster.getIDs();
        // Compute sum of pairwise distances:
        double clusterPairwiseDistanceSum = 0;
        for (DBIDIter iter1 = ids.iter(); iter1.valid(); iter1.advance()) {
            NumberVector obj1 = relation.get(iter1);
            for (DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) {
                clusterPairwiseDistanceSum += distanceFunction.distance(obj1, relation.get(iter2));
            }
        }
        clusterDistanceSum += clusterPairwiseDistanceSum / (ids.size() * ids.size());
    }
    return clusterDistanceSum / clustering.getAllClusters().size();
}

Example 59 with DBIDs

use of de.lmu.ifi.dbs.elki.database.ids.DBIDs in project elki by elki-project.

the class StaticArrayDatabase method initialize.

/**
 * Initialize the database by getting the initial data from the database
 * connection.
 */
@Override
public void initialize() {
    if (databaseConnection != null) {
        if (LOG.isDebugging()) {
            LOG.debugFine("Loading data from database connection.");
        }
        MultipleObjectsBundle bundle = databaseConnection.loadData();
        // Run at most once.
        databaseConnection = null;
        // Find DBIDs for bundle
        {
            DBIDs bids = bundle.getDBIDs();
            if (bids instanceof ArrayStaticDBIDs) {
                this.ids = (ArrayStaticDBIDs) bids;
            } else if (bids == null) {
                this.ids = DBIDUtil.generateStaticDBIDRange(bundle.dataLength());
            } else {
                this.ids = (ArrayStaticDBIDs) DBIDUtil.makeUnmodifiable(bids);
            }
        }
        // Replace id representation (it would be nicer if we would not need
        // DBIDView at all)
        this.idrep = new DBIDView(this.ids);
        relations.add(this.idrep);
        getHierarchy().add(this, idrep);
        DBIDArrayIter it = this.ids.iter();
        int numrel = bundle.metaLength();
        for (int i = 0; i < numrel; i++) {
            SimpleTypeInformation<?> meta = bundle.meta(i);
            @SuppressWarnings("unchecked") SimpleTypeInformation<Object> ometa = (SimpleTypeInformation<Object>) meta;
            WritableDataStore<Object> store = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_DB, ometa.getRestrictionClass());
            for (it.seek(0); it.valid(); it.advance()) {
                store.put(it, bundle.data(it.getOffset(), i));
            }
            Relation<?> relation = new MaterializedRelation<>(ometa, ids, null, store);
            relations.add(relation);
            getHierarchy().add(this, relation);
            // Try to add indexes where appropriate
            for (IndexFactory<?, ?> factory : indexFactories) {
                if (factory.getInputTypeRestriction().isAssignableFromType(ometa)) {
                    @SuppressWarnings("unchecked") final IndexFactory<Object, ?> ofact = (IndexFactory<Object, ?>) factory;
                    @SuppressWarnings("unchecked") final Relation<Object> orep = (Relation<Object>) relation;
                    final Index index = ofact.instantiate(orep);
                    Duration duration = LOG.isStatistics() ? LOG.newDuration(index.getClass().getName() + ".construction").begin() : null;
                    index.initialize();
                    if (duration != null) {
                        LOG.statistics(duration.end());
                    }
                    getHierarchy().add(relation, index);
                }
            }
        }
        // fire insertion event
        eventManager.fireObjectsInserted(ids);
    }
}

Example 60 with DBIDs

use of de.lmu.ifi.dbs.elki.database.ids.DBIDs in project elki by elki-project.

the class LinearWeightedExtendedNeighborhood method getWeightedNeighbors.

@Override
public Collection<DoubleDBIDPair> getWeightedNeighbors(DBIDRef reference) {
    ModifiableDBIDs seen = DBIDUtil.newHashSet();
    List<DoubleDBIDPair> result = new ArrayList<>();
    // Add starting object
    result.add(DBIDUtil.newPair(computeWeight(0), reference));
    seen.add(reference);
    // Extend.
    DBIDs cur = DBIDUtil.deref(reference);
    for (int i = 1; i <= steps; i++) {
        final double weight = computeWeight(i);
        // Collect newly discovered IDs
        ModifiableDBIDs add = DBIDUtil.newHashSet();
        for (DBIDIter iter = cur.iter(); iter.valid(); iter.advance()) {
            for (DBIDIter iter2 = inner.getNeighborDBIDs(iter).iter(); iter2.valid(); iter2.advance()) {
                // Seen before?
                if (seen.contains(iter2)) {
                    continue;
                }
                add.add(iter2);
                result.add(DBIDUtil.newPair(weight, iter2));
            }
        }
        if (add.size() == 0) {
            break;
        }
        cur = add;
    }
    return result;
}