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

Example 1 with MaterializedRelation

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

the class CenterOfMassMetaClustering method runClusteringAlgorithm.

/**
 * Run a clustering algorithm on a single instance.
 *
 * @param parent Parent result to attach to
 * @param ids Object IDs to process
 * @param store Input data
 * @param dim Dimensionality
 * @param title Title of relation
 * @return Clustering result
 */
protected C runClusteringAlgorithm(ResultHierarchy hierarchy, Result parent, DBIDs ids, DataStore<DoubleVector> store, int dim, String title) {
    SimpleTypeInformation<DoubleVector> t = new VectorFieldTypeInformation<>(DoubleVector.FACTORY, dim);
    Relation<DoubleVector> sample = new MaterializedRelation<>(t, ids, title, store);
    ProxyDatabase d = new ProxyDatabase(ids, sample);
    C clusterResult = inner.run(d);
    d.getHierarchy().remove(sample);
    d.getHierarchy().remove(clusterResult);
    hierarchy.add(parent, sample);
    hierarchy.add(sample, clusterResult);
    return clusterResult;
}

Example 2 with MaterializedRelation

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

the class TSNE method run.

public Relation<DoubleVector> run(Relation<O> relation) {
    AffinityMatrix pij = affinity.computeAffinityMatrix(relation, EARLY_EXAGGERATION);
    // Create initial solution.
    final int size = pij.size();
    double[][] sol = randomInitialSolution(size, dim, random.getSingleThreadedRandom());
    projectedDistances.setLong(0L);
    optimizetSNE(pij, sol);
    LOG.statistics(projectedDistances);
    // Remove the original (unprojected) data unless configured otherwise.
    removePreviousRelation(relation);
    // Transform into output data format.
    DBIDs ids = relation.getDBIDs();
    WritableDataStore<DoubleVector> proj = DataStoreFactory.FACTORY.makeStorage(ids, DataStoreFactory.HINT_DB | DataStoreFactory.HINT_SORTED, DoubleVector.class);
    VectorFieldTypeInformation<DoubleVector> otype = new VectorFieldTypeInformation<>(DoubleVector.FACTORY, dim);
    for (DBIDArrayIter it = pij.iterDBIDs(); it.valid(); it.advance()) {
        proj.put(it, DoubleVector.wrap(sol[it.getOffset()]));
    }
    return new MaterializedRelation<>("tSNE", "t-SNE", otype, proj, ids);
}

Example 3 with MaterializedRelation

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

the class KNNJoin method run.

/**
 * Joins in the given spatial database to each object its k-nearest neighbors.
 *
 * @param relation Relation to process
 * @return result
 */
public Relation<KNNList> run(Relation<V> relation) {
    DBIDs ids = relation.getDBIDs();
    WritableDataStore<KNNList> knnLists = run(relation, ids);
    // Wrap as relation:
    return new MaterializedRelation<>("k nearest neighbors", "kNNs", TypeUtil.KNNLIST, knnLists, ids);
}

Example 4 with MaterializedRelation

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

the class CASH method buildDB.

/**
 * Builds a dim-1 dimensional database where the objects are projected into
 * the specified subspace.
 *
 * @param dim the dimensionality of the database
 * @param basis the basis defining the subspace
 * @param ids the ids for the new database
 * @param relation the database storing the parameterization functions
 * @return a dim-1 dimensional database where the objects are projected into
 *         the specified subspace
 */
private MaterializedRelation<ParameterizationFunction> buildDB(int dim, double[][] basis, DBIDs ids, Relation<ParameterizationFunction> relation) {
    ProxyDatabase proxy = new ProxyDatabase(ids);
    SimpleTypeInformation<ParameterizationFunction> type = new SimpleTypeInformation<>(ParameterizationFunction.class);
    WritableDataStore<ParameterizationFunction> prep = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_HOT, ParameterizationFunction.class);
    // Project
    for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
        prep.put(iter, project(basis, relation.get(iter)));
    }
    if (LOG.isDebugging()) {
        LOG.debugFine("db fuer dim " + (dim - 1) + ": " + ids.size());
    }
    MaterializedRelation<ParameterizationFunction> prel = new MaterializedRelation<>(type, ids, null, prep);
    proxy.addRelation(prel);
    return prel;
}

Example 5 with MaterializedRelation

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

the class BarnesHutTSNE method run.

public Relation<DoubleVector> run(Database database, Relation<O> relation) {
    AffinityMatrix neighbors = affinity.computeAffinityMatrix(relation, EARLY_EXAGGERATION);
    double[][] solution = randomInitialSolution(neighbors.size(), dim, random.getSingleThreadedRandom());
    projectedDistances.setLong(0L);
    optimizetSNE(neighbors, solution);
    LOG.statistics(projectedDistances);
    // Remove the original (unprojected) data unless configured otherwise.
    removePreviousRelation(relation);
    DBIDs ids = relation.getDBIDs();
    WritableDataStore<DoubleVector> proj = DataStoreFactory.FACTORY.makeStorage(ids, DataStoreFactory.HINT_DB | DataStoreFactory.HINT_SORTED, DoubleVector.class);
    VectorFieldTypeInformation<DoubleVector> otype = new VectorFieldTypeInformation<>(DoubleVector.FACTORY, dim);
    for (DBIDArrayIter it = neighbors.iterDBIDs(); it.valid(); it.advance()) {
        proj.put(it, DoubleVector.wrap(solution[it.getOffset()]));
    }
    return new MaterializedRelation<>("tSNE", "t-SNE", otype, proj, ids);
}