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diff --git a/src/de/lmu/ifi/dbs/elki/index/preprocessed/subspaceproj/FourCSubspaceIndex.java b/src/de/lmu/ifi/dbs/elki/index/preprocessed/subspaceproj/FourCSubspaceIndex.java
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--- a/src/de/lmu/ifi/dbs/elki/index/preprocessed/subspaceproj/FourCSubspaceIndex.java
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@@ -1,260 +0,0 @@
-package de.lmu.ifi.dbs.elki.index.preprocessed.subspaceproj;
-
-/*
- This file is part of ELKI:
- Environment for Developing KDD-Applications Supported by Index-Structures
-
- Copyright (C) 2013
- Ludwig-Maximilians-Universität München
- Lehr- und Forschungseinheit für Datenbanksysteme
- ELKI Development Team
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU Affero General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Affero General Public License for more details.
-
- You should have received a copy of the GNU Affero General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-import java.util.ArrayList;
-
-import de.lmu.ifi.dbs.elki.data.NumberVector;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
-import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DistanceDBIDList;
-import de.lmu.ifi.dbs.elki.database.relation.Relation;
-import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.Distance;
-import de.lmu.ifi.dbs.elki.logging.Logging;
-import de.lmu.ifi.dbs.elki.logging.LoggingUtil;
-import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.LimitEigenPairFilter;
-import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.PCAFilteredResult;
-import de.lmu.ifi.dbs.elki.math.linearalgebra.pca.PCAFilteredRunner;
-import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil;
-import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
-import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.WrongParameterValueException;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GlobalParameterConstraint;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterConstraint;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.ParameterFlagGlobalConstraint;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag;
-
-/**
- * Preprocessor for 4C local dimensionality and locally weighted matrix
- * assignment to objects of a certain database.
- *
- * @author Arthur Zimek
- *
- * @apiviz.composedOf PCAFilteredRunner
- *
- * @param <V> Vector type
- * @param <D> Distance type
- */
-@Title("4C Preprocessor")
-@Description("Computes the local dimensionality and locally weighted matrix of objects of a certain database according to the 4C algorithm.\n" + "The PCA is based on epsilon range queries.")
-public class FourCSubspaceIndex<V extends NumberVector<?>, D extends Distance<D>> extends AbstractSubspaceProjectionIndex<V, D, PCAFilteredResult> {
- /**
- * Our logger
- */
- private static final Logging LOG = Logging.getLogger(FourCSubspaceIndex.class);
-
- /**
- * The Filtered PCA Runner
- */
- private PCAFilteredRunner<V> pca;
-
- /**
- * Full constructor.
- *
- * @param relation Relation
- * @param epsilon Epsilon value
- * @param rangeQueryDistanceFunction
- * @param minpts MinPts value
- * @param pca PCA runner
- */
- public FourCSubspaceIndex(Relation<V> relation, D epsilon, DistanceFunction<V, D> rangeQueryDistanceFunction, int minpts, PCAFilteredRunner<V> pca) {
- super(relation, epsilon, rangeQueryDistanceFunction, minpts);
- this.pca = pca;
- }
-
- @Override
- protected PCAFilteredResult computeProjection(DBIDRef id, DistanceDBIDList<D> neighbors, Relation<V> database) {
- ModifiableDBIDs ids = DBIDUtil.newArray(neighbors.size());
- for(DBIDIter neighbor = neighbors.iter(); neighbor.valid(); neighbor.advance()) {
- ids.add(neighbor);
- }
- PCAFilteredResult pcares = pca.processIds(ids, database);
-
- if(LOG.isDebugging()) {
- StringBuilder msg = new StringBuilder();
- msg.append(id).append(' '); // .append(database.getObjectLabelQuery().get(id));
- msg.append("\ncorrDim ").append(pcares.getCorrelationDimension());
- LOG.debugFine(msg.toString());
- }
- return pcares;
- }
-
- @Override
- protected Logging getLogger() {
- return LOG;
- }
-
- @Override
- public String getLongName() {
- return "4C local Subspaces";
- }
-
- @Override
- public String getShortName() {
- return "4C-subspaces";
- }
-
- @Override
- public void logStatistics() {
- // No statistics to log.
- }
-
- /**
- * Factory class for 4C preprocessors.
- *
- * @author Erich Schubert
- *
- * @apiviz.stereotype factory
- * @apiviz.uses FourCSubspaceIndex oneway - - «creates»
- *
- * @param <V> Vector type
- * @param <D> Distance type
- */
- public static class Factory<V extends NumberVector<?>, D extends Distance<D>> extends AbstractSubspaceProjectionIndex.Factory<V, D, FourCSubspaceIndex<V, D>> {
- /**
- * The default value for delta.
- */
- public static final double DEFAULT_DELTA = LimitEigenPairFilter.DEFAULT_DELTA;
-
- /**
- * The Filtered PCA Runner
- */
- private PCAFilteredRunner<V> pca;
-
- /**
- * Constructor.
- *
- * @param epsilon
- * @param rangeQueryDistanceFunction
- * @param minpts
- * @param pca
- */
- public Factory(D epsilon, DistanceFunction<V, D> rangeQueryDistanceFunction, int minpts, PCAFilteredRunner<V> pca) {
- super(epsilon, rangeQueryDistanceFunction, minpts);
- this.pca = pca;
- }
-
- @Override
- public FourCSubspaceIndex<V, D> instantiate(Relation<V> relation) {
- return new FourCSubspaceIndex<>(relation, epsilon, rangeQueryDistanceFunction, minpts, pca);
- }
-
- /**
- * Parameterization class.
- *
- * @author Erich Schubert
- *
- * @apiviz.exclude
- */
- public static class Parameterizer<V extends NumberVector<?>, D extends Distance<D>> extends AbstractSubspaceProjectionIndex.Factory.Parameterizer<V, D, Factory<V, D>> {
- /**
- * The Filtered PCA Runner
- */
- private PCAFilteredRunner<V> pca;
-
- @Override
- protected void makeOptions(Parameterization config) {
- super.makeOptions(config);
- // flag absolute
- boolean absolute = false;
- Flag absoluteF = new Flag(LimitEigenPairFilter.EIGENPAIR_FILTER_ABSOLUTE);
- if(config.grab(absoluteF)) {
- absolute = absoluteF.isTrue();
- }
-
- // Parameter delta
- double delta = 0.0;
- DoubleParameter deltaP = new DoubleParameter(LimitEigenPairFilter.EIGENPAIR_FILTER_DELTA, DEFAULT_DELTA);
- deltaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE);
- if(config.grab(deltaP)) {
- delta = deltaP.doubleValue();
- }
- // Absolute flag doesn't have a sensible default value for delta.
- if(absolute && deltaP.tookDefaultValue()) {
- config.reportError(new WrongParameterValueException("Illegal parameter setting: " + "Flag " + absoluteF.getName() + " is set, " + "but no value for " + deltaP.getName() + " is specified."));
- }
-
- // if (optionHandler.isSet(DELTA_P)) {
- // delta = (Double) optionHandler.getOptionValue(DELTA_P);
- // try {
- // if (!absolute && delta < 0 || delta > 1)
- // throw new WrongParameterValueException(DELTA_P, "delta", DELTA_D);
- // } catch (NumberFormatException e) {
- // throw new WrongParameterValueException(DELTA_P, "delta", DELTA_D, e);
- // }
- // } else if (!absolute) {
- // delta = LimitEigenPairFilter.DEFAULT_DELTA;
- // } else {
- // throw new WrongParameterValueException("Illegal parameter setting: "
- // +
- // "Flag " + ABSOLUTE_F + " is set, " + "but no value for " + DELTA_P +
- // " is specified.");
- // }
-
- // Parameterize PCA
- ListParameterization pcaParameters = new ListParameterization();
- // eigen pair filter
- pcaParameters.addParameter(PCAFilteredRunner.PCA_EIGENPAIR_FILTER, LimitEigenPairFilter.class.getName());
- // abs
- if(absolute) {
- pcaParameters.addFlag(LimitEigenPairFilter.EIGENPAIR_FILTER_ABSOLUTE);
- }
- // delta
- pcaParameters.addParameter(LimitEigenPairFilter.EIGENPAIR_FILTER_DELTA, delta);
- // big value
- pcaParameters.addParameter(PCAFilteredRunner.BIG_ID, 50);
- // small value
- pcaParameters.addParameter(PCAFilteredRunner.SMALL_ID, 1);
- Class<PCAFilteredRunner<V>> cls = ClassGenericsUtil.uglyCastIntoSubclass(PCAFilteredRunner.class);
- pca = pcaParameters.tryInstantiate(cls);
- for(ParameterException e : pcaParameters.getErrors()) {
- LoggingUtil.warning("Error in internal parameterization: " + e.getMessage());
- }
-
- final ArrayList<ParameterConstraint<? super Double>> deltaCons = new ArrayList<>();
- // TODO: this constraint is already set in the parameter itself, since
- // it
- // also applies to the relative case, right? -- erich
- // deltaCons.add(CommonConstraints.NONNEGATIVE_DOUBLE);
- deltaCons.add(CommonConstraints.LESS_EQUAL_ONE_DOUBLE);
-
- GlobalParameterConstraint gpc = new ParameterFlagGlobalConstraint<>(deltaP, deltaCons, absoluteF, false);
- config.checkConstraint(gpc);
- }
-
- @Override
- protected Factory<V, D> makeInstance() {
- return new Factory<>(epsilon, rangeQueryDistanceFunction, minpts, pca);
- }
- }
- }
-}
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