Examples with DoubleVector de.lmu.ifi.dbs.elki.data.DoubleVector used on opensource projects

Example 46 with DoubleVector

use of de.lmu.ifi.dbs.elki.data.DoubleVector in project elki by elki-project.

the class SpacefillingMaterializeKNNPreprocessorTest method testPreprocessor.

@Test
public void testPreprocessor() {
    Database db = AbstractSimpleAlgorithmTest.makeSimpleDatabase(dataset, shoulds);
    Relation<DoubleVector> rel = db.getRelation(TypeUtil.DOUBLE_VECTOR_FIELD);
    DistanceQuery<DoubleVector> distanceQuery = db.getDistanceQuery(rel, EuclideanDistanceFunction.STATIC);
    // get linear queries
    LinearScanDistanceKNNQuery<DoubleVector> lin_knn_query = new LinearScanDistanceKNNQuery<>(distanceQuery);
    // get preprocessed queries
    ListParameterization config = new ListParameterization();
    // 
    config.addParameter(// 
    SpacefillingMaterializeKNNPreprocessor.Factory.Parameterizer.CURVES_ID, // 
    HilbertSpatialSorter.class.getName() + "," + PeanoSpatialSorter.class.getName() + "," + ZCurveSpatialSorter.class.getName() + "," + BinarySplitSpatialSorter.class.getName());
    config.addParameter(SpacefillingMaterializeKNNPreprocessor.Factory.K_ID, k);
    config.addParameter(SpacefillingMaterializeKNNPreprocessor.Factory.Parameterizer.VARIANTS_ID, 10);
    config.addParameter(SpacefillingMaterializeKNNPreprocessor.Factory.Parameterizer.WINDOW_ID, 1.);
    config.addParameter(SpacefillingMaterializeKNNPreprocessor.Factory.Parameterizer.RANDOM_ID, 0L);
    SpacefillingMaterializeKNNPreprocessor.Factory<DoubleVector> preprocf = ClassGenericsUtil.parameterizeOrAbort(SpacefillingMaterializeKNNPreprocessor.Factory.class, config);
    SpacefillingMaterializeKNNPreprocessor<DoubleVector> preproc = preprocf.instantiate(rel);
    preproc.initialize();
    // add as index
    db.getHierarchy().add(rel, preproc);
    KNNQuery<DoubleVector> preproc_knn_query = preproc.getKNNQuery(distanceQuery, k);
    assertFalse("Preprocessor knn query class incorrect.", preproc_knn_query instanceof LinearScanDistanceKNNQuery);
    // test queries
    testKNNQueries(rel, lin_knn_query, preproc_knn_query, k);
    // also test partial queries, forward only
    testKNNQueries(rel, lin_knn_query, preproc_knn_query, k / 2);
}

Example 47 with DoubleVector

use of de.lmu.ifi.dbs.elki.data.DoubleVector in project elki by elki-project.

the class CloseReinsert method computeReinserts.

@Override
public <A> int[] computeReinserts(A entries, ArrayAdapter<? extends SpatialComparable, ? super A> getter, SpatialComparable page) {
    DoubleVector centroid = DoubleVector.wrap(SpatialUtil.centroid(page));
    final int size = getter.size(entries);
    double[] dist = new double[size];
    int[] idx = MathUtil.sequence(0, size);
    for (int i = 0; i < size; i++) {
        dist[i] = distanceFunction.minDist(DoubleVector.wrap(SpatialUtil.centroid(getter.get(entries, i))), centroid);
    }
    DoubleIntegerArrayQuickSort.sort(dist, idx, size);
    return Arrays.copyOf(idx, (int) (reinsertAmount * size));
}

Example 48 with DoubleVector

use of de.lmu.ifi.dbs.elki.data.DoubleVector in project elki by elki-project.

the class FarReinsert method computeReinserts.

@Override
public <A> int[] computeReinserts(A entries, ArrayAdapter<? extends SpatialComparable, ? super A> getter, SpatialComparable page) {
    DoubleVector centroid = DoubleVector.wrap(SpatialUtil.centroid(page));
    final int size = getter.size(entries);
    double[] dist = new double[size];
    int[] idx = MathUtil.sequence(0, size);
    for (int i = 0; i < size; i++) {
        dist[i] = distanceFunction.minDist(DoubleVector.wrap(SpatialUtil.centroid(getter.get(entries, i))), centroid);
    }
    DoubleIntegerArrayQuickSort.sortReverse(dist, idx, size);
    return Arrays.copyOf(idx, (int) (reinsertAmount * size));
}

Example 49 with DoubleVector

use of de.lmu.ifi.dbs.elki.data.DoubleVector 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 50 with DoubleVector

use of de.lmu.ifi.dbs.elki.data.DoubleVector 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);
}