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Example 11 with ListParameterization

use of de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization in project elki by elki-project.

the class MaterializedKNNAndRKNNPreprocessorTest method testPreprocessor.

@Test
public void testPreprocessor() {
    UpdatableDatabase db;
    // get database
    try (InputStream is = AbstractSimpleAlgorithmTest.open(dataset)) {
        ListParameterization params = new ListParameterization();
        // Setup parser and data loading
        NumberVectorLabelParser<DoubleVector> parser = new NumberVectorLabelParser<>(DoubleVector.FACTORY);
        InputStreamDatabaseConnection dbc = new InputStreamDatabaseConnection(is, new ArrayList<>(), parser);
        // We want to allow the use of indexes via "params"
        params.addParameter(AbstractDatabase.Parameterizer.DATABASE_CONNECTION_ID, dbc);
        db = ClassGenericsUtil.parameterizeOrAbort(HashmapDatabase.class, params);
        db.initialize();
    } catch (IOException e) {
        fail("Test data " + dataset + " not found.");
        return;
    }
    Relation<DoubleVector> rep = db.getRelation(TypeUtil.DOUBLE_VECTOR_FIELD);
    DistanceQuery<DoubleVector> distanceQuery = db.getDistanceQuery(rep, EuclideanDistanceFunction.STATIC);
    // verify data set size.
    assertEquals("Data set size doesn't match parameters.", shoulds, rep.size());
    // get linear queries
    LinearScanDistanceKNNQuery<DoubleVector> lin_knn_query = new LinearScanDistanceKNNQuery<>(distanceQuery);
    LinearScanRKNNQuery<DoubleVector> lin_rknn_query = new LinearScanRKNNQuery<>(distanceQuery, lin_knn_query, k);
    // get preprocessed queries
    ListParameterization config = new ListParameterization();
    config.addParameter(MaterializeKNNPreprocessor.Factory.DISTANCE_FUNCTION_ID, distanceQuery.getDistanceFunction());
    config.addParameter(MaterializeKNNPreprocessor.Factory.K_ID, k);
    MaterializeKNNAndRKNNPreprocessor<DoubleVector> preproc = new MaterializeKNNAndRKNNPreprocessor<>(rep, distanceQuery.getDistanceFunction(), k);
    KNNQuery<DoubleVector> preproc_knn_query = preproc.getKNNQuery(distanceQuery, k);
    RKNNQuery<DoubleVector> preproc_rknn_query = preproc.getRKNNQuery(distanceQuery);
    // add as index
    db.getHierarchy().add(rep, preproc);
    assertFalse("Preprocessor knn query class incorrect.", preproc_knn_query instanceof LinearScanDistanceKNNQuery);
    assertFalse("Preprocessor rknn query class incorrect.", preproc_rknn_query instanceof LinearScanDistanceKNNQuery);
    // test queries
    testKNNQueries(rep, lin_knn_query, preproc_knn_query, k);
    testRKNNQueries(rep, lin_rknn_query, preproc_rknn_query, k);
    // also test partial queries, forward only
    testKNNQueries(rep, lin_knn_query, preproc_knn_query, k / 2);
    // insert new objects
    List<DoubleVector> insertions = new ArrayList<>();
    NumberVector.Factory<DoubleVector> o = RelationUtil.getNumberVectorFactory(rep);
    int dim = RelationUtil.dimensionality(rep);
    Random random = new Random(seed);
    for (int i = 0; i < updatesize; i++) {
        DoubleVector obj = VectorUtil.randomVector(o, dim, random);
        insertions.add(obj);
    }
    // System.out.println("Insert " + insertions);
    DBIDs deletions = db.insert(MultipleObjectsBundle.makeSimple(rep.getDataTypeInformation(), insertions));
    // test queries
    testKNNQueries(rep, lin_knn_query, preproc_knn_query, k);
    testRKNNQueries(rep, lin_rknn_query, preproc_rknn_query, k);
    // delete objects
    // System.out.println("Delete " + deletions);
    db.delete(deletions);
    // test queries
    testKNNQueries(rep, lin_knn_query, preproc_knn_query, k);
    testRKNNQueries(rep, lin_rknn_query, preproc_rknn_query, k);
}
Also used : UpdatableDatabase(de.lmu.ifi.dbs.elki.database.UpdatableDatabase) ArrayList(java.util.ArrayList) NumberVectorLabelParser(de.lmu.ifi.dbs.elki.datasource.parser.NumberVectorLabelParser) Random(java.util.Random) ListParameterization(de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization) LinearScanDistanceKNNQuery(de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery) InputStream(java.io.InputStream) HashmapDatabase(de.lmu.ifi.dbs.elki.database.HashmapDatabase) ArrayDBIDs(de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs) DBIDs(de.lmu.ifi.dbs.elki.database.ids.DBIDs) InputStreamDatabaseConnection(de.lmu.ifi.dbs.elki.datasource.InputStreamDatabaseConnection) IOException(java.io.IOException) MaterializeKNNAndRKNNPreprocessor(de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNAndRKNNPreprocessor) NumberVector(de.lmu.ifi.dbs.elki.data.NumberVector) DoubleVector(de.lmu.ifi.dbs.elki.data.DoubleVector) LinearScanRKNNQuery(de.lmu.ifi.dbs.elki.database.query.rknn.LinearScanRKNNQuery) AbstractSimpleAlgorithmTest(de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest) Test(org.junit.Test)

Example 12 with ListParameterization

use of de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization in project elki by elki-project.

the class SpacefillingKNNPreprocessorTest method testGaussian.

@Test
public void testGaussian() {
    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(// 
    SpacefillingKNNPreprocessor.Factory.Parameterizer.CURVES_ID, // 
    HilbertSpatialSorter.class.getName() + "," + PeanoSpatialSorter.class.getName() + "," + ZCurveSpatialSorter.class.getName() + "," + BinarySplitSpatialSorter.class.getName());
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.DIM_ID, 7);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.PROJECTION_ID, GaussianRandomProjectionFamily.class);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.VARIANTS_ID, 10);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.WINDOW_ID, 5.);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.RANDOM_ID, 0L);
    config.addParameter(GaussianRandomProjectionFamily.Parameterizer.RANDOM_ID, 0L);
    SpacefillingKNNPreprocessor.Factory<DoubleVector> preprocf = ClassGenericsUtil.parameterizeOrAbort(SpacefillingKNNPreprocessor.Factory.class, config);
    SpacefillingKNNPreprocessor<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);
}
Also used : SpacefillingKNNPreprocessor(de.lmu.ifi.dbs.elki.index.preprocessed.knn.SpacefillingKNNPreprocessor) LinearScanDistanceKNNQuery(de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery) Database(de.lmu.ifi.dbs.elki.database.Database) DoubleVector(de.lmu.ifi.dbs.elki.data.DoubleVector) HilbertSpatialSorter(de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter) ListParameterization(de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization) Test(org.junit.Test) AbstractSimpleAlgorithmTest(de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest)

Example 13 with ListParameterization

use of de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization in project elki by elki-project.

the class SpacefillingKNNPreprocessorTest method testHenzinger.

@Test
public void testHenzinger() {
    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(// 
    SpacefillingKNNPreprocessor.Factory.Parameterizer.CURVES_ID, // 
    HilbertSpatialSorter.class.getName() + "," + PeanoSpatialSorter.class.getName() + "," + ZCurveSpatialSorter.class.getName() + "," + BinarySplitSpatialSorter.class.getName());
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.DIM_ID, 7);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.PROJECTION_ID, SimplifiedRandomHyperplaneProjectionFamily.class);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.VARIANTS_ID, 10);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.WINDOW_ID, 5.);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.RANDOM_ID, 0L);
    config.addParameter(SimplifiedRandomHyperplaneProjectionFamily.Parameterizer.RANDOM_ID, 1L);
    SpacefillingKNNPreprocessor.Factory<DoubleVector> preprocf = ClassGenericsUtil.parameterizeOrAbort(SpacefillingKNNPreprocessor.Factory.class, config);
    SpacefillingKNNPreprocessor<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);
}
Also used : SpacefillingKNNPreprocessor(de.lmu.ifi.dbs.elki.index.preprocessed.knn.SpacefillingKNNPreprocessor) LinearScanDistanceKNNQuery(de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery) Database(de.lmu.ifi.dbs.elki.database.Database) DoubleVector(de.lmu.ifi.dbs.elki.data.DoubleVector) HilbertSpatialSorter(de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter) ListParameterization(de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization) Test(org.junit.Test) AbstractSimpleAlgorithmTest(de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest)

Example 14 with ListParameterization

use of de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization in project elki by elki-project.

the class SpacefillingKNNPreprocessorTest method testAchlioptas.

@Test
public void testAchlioptas() {
    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(// 
    SpacefillingKNNPreprocessor.Factory.Parameterizer.CURVES_ID, // 
    HilbertSpatialSorter.class.getName() + "," + PeanoSpatialSorter.class.getName() + "," + ZCurveSpatialSorter.class.getName() + "," + BinarySplitSpatialSorter.class.getName());
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.DIM_ID, 7);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.PROJECTION_ID, AchlioptasRandomProjectionFamily.class);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.VARIANTS_ID, 10);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.WINDOW_ID, 5.);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.RANDOM_ID, 0L);
    config.addParameter(AchlioptasRandomProjectionFamily.Parameterizer.RANDOM_ID, 0L);
    SpacefillingKNNPreprocessor.Factory<DoubleVector> preprocf = ClassGenericsUtil.parameterizeOrAbort(SpacefillingKNNPreprocessor.Factory.class, config);
    SpacefillingKNNPreprocessor<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);
}
Also used : SpacefillingKNNPreprocessor(de.lmu.ifi.dbs.elki.index.preprocessed.knn.SpacefillingKNNPreprocessor) LinearScanDistanceKNNQuery(de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery) Database(de.lmu.ifi.dbs.elki.database.Database) DoubleVector(de.lmu.ifi.dbs.elki.data.DoubleVector) HilbertSpatialSorter(de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter) ListParameterization(de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization) Test(org.junit.Test) AbstractSimpleAlgorithmTest(de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest)

Example 15 with ListParameterization

use of de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization in project elki by elki-project.

the class SpacefillingKNNPreprocessorTest method testSubset.

@Test
public void testSubset() {
    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(// 
    SpacefillingKNNPreprocessor.Factory.Parameterizer.CURVES_ID, // 
    HilbertSpatialSorter.class.getName() + "," + PeanoSpatialSorter.class.getName() + "," + ZCurveSpatialSorter.class.getName() + "," + BinarySplitSpatialSorter.class.getName());
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.DIM_ID, 7);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.PROJECTION_ID, RandomSubsetProjectionFamily.class);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.VARIANTS_ID, 10);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.WINDOW_ID, 5.);
    config.addParameter(SpacefillingKNNPreprocessor.Factory.Parameterizer.RANDOM_ID, 0L);
    config.addParameter(RandomSubsetProjectionFamily.Parameterizer.RANDOM_ID, 0L);
    SpacefillingKNNPreprocessor.Factory<DoubleVector> preprocf = ClassGenericsUtil.parameterizeOrAbort(SpacefillingKNNPreprocessor.Factory.class, config);
    SpacefillingKNNPreprocessor<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);
}
Also used : SpacefillingKNNPreprocessor(de.lmu.ifi.dbs.elki.index.preprocessed.knn.SpacefillingKNNPreprocessor) LinearScanDistanceKNNQuery(de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery) Database(de.lmu.ifi.dbs.elki.database.Database) DoubleVector(de.lmu.ifi.dbs.elki.data.DoubleVector) HilbertSpatialSorter(de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter) ListParameterization(de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization) Test(org.junit.Test) AbstractSimpleAlgorithmTest(de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest)

Aggregations

ListParameterization (de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization)76 Test (org.junit.Test)68 AbstractIndexStructureTest (de.lmu.ifi.dbs.elki.index.AbstractIndexStructureTest)26 Database (de.lmu.ifi.dbs.elki.database.Database)10 AbstractSimpleAlgorithmTest (de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest)9 DoubleVector (de.lmu.ifi.dbs.elki.data.DoubleVector)9 LinearScanDistanceKNNQuery (de.lmu.ifi.dbs.elki.database.query.knn.LinearScanDistanceKNNQuery)8 HilbertSpatialSorter (de.lmu.ifi.dbs.elki.math.spacefillingcurves.HilbertSpatialSorter)6 SpacefillingKNNPreprocessor (de.lmu.ifi.dbs.elki.index.preprocessed.knn.SpacefillingKNNPreprocessor)5 Random (java.util.Random)3 AbstractClusterAlgorithmTest (de.lmu.ifi.dbs.elki.algorithm.clustering.AbstractClusterAlgorithmTest)2 Model (de.lmu.ifi.dbs.elki.data.model.Model)2 StaticArrayDatabase (de.lmu.ifi.dbs.elki.database.StaticArrayDatabase)2 InputStreamDatabaseConnection (de.lmu.ifi.dbs.elki.datasource.InputStreamDatabaseConnection)2 MaterializeKNNAndRKNNPreprocessor (de.lmu.ifi.dbs.elki.index.preprocessed.knn.MaterializeKNNAndRKNNPreprocessor)2 NormalDistribution (de.lmu.ifi.dbs.elki.math.statistics.distribution.NormalDistribution)2 NormalMOMEstimator (de.lmu.ifi.dbs.elki.math.statistics.distribution.estimator.NormalMOMEstimator)2 IOException (java.io.IOException)2 InputStream (java.io.InputStream)2 ByLabelClustering (de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelClustering)1