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package de.lmu.ifi.dbs.elki.index.preprocessed.knn;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2011
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 java.util.HashMap;
import java.util.List;
import de.lmu.ifi.dbs.elki.data.NumberVector;
import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory;
import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
import de.lmu.ifi.dbs.elki.database.ids.DBIDPair;
import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
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.index.tree.LeafEntry;
import de.lmu.ifi.dbs.elki.index.tree.Node;
import de.lmu.ifi.dbs.elki.index.tree.metrical.MetricalIndexTree;
import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.MTreeEntry;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
import de.lmu.ifi.dbs.elki.math.MeanVariance;
import de.lmu.ifi.dbs.elki.result.ResultUtil;
import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil;
import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.KNNHeap;
import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
/**
* A preprocessor for annotation of the k nearest neighbors (and their
* distances) to each database object.
*
* Used for example by {@link de.lmu.ifi.dbs.elki.algorithm.outlier.LOF}.
*
* TODO correct handling of datastore events
*
* @author Erich Schubert
*
* @apiviz.uses MetricalIndexTree
*
* @param <O> the type of database objects the preprocessor can be applied to
* @param <D> the type of distance the used distance function will return
* @param <N> the type of spatial nodes in the spatial index
* @param <E> the type of spatial entries in the spatial index
*/
@Title("Spatial Approximation Materialize kNN Preprocessor")
@Description("Caterializes the (approximate) k nearest neighbors of objects of a database using a spatial approximation.")
public class MetricalIndexApproximationMaterializeKNNPreprocessor<O extends NumberVector<? super O, ?>, D extends Distance<D>, N extends Node<E>, E extends MTreeEntry<D>> extends AbstractMaterializeKNNPreprocessor<O, D> {
/**
* Logger to use
*/
private static final Logging logger = Logging.getLogger(MetricalIndexApproximationMaterializeKNNPreprocessor.class);
/**
* Constructor
*
* @param relation Relation to preprocess
* @param distanceFunction the distance function to use
* @param k query k
*/
public MetricalIndexApproximationMaterializeKNNPreprocessor(Relation<O> relation, DistanceFunction<? super O, D> distanceFunction, int k) {
super(relation, distanceFunction, k);
}
@Override
protected void preprocess() {
DistanceQuery<O, D> distanceQuery = relation.getDatabase().getDistanceQuery(relation, distanceFunction);
MetricalIndexTree<O, D, N, E> index = getMetricalIndex(relation);
storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC, List.class);
MeanVariance pagesize = new MeanVariance();
MeanVariance ksize = new MeanVariance();
if(getLogger().isVerbose()) {
getLogger().verbose("Approximating nearest neighbor lists to database objects");
}
List<E> leaves = index.getLeaves();
FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes.", leaves.size(), getLogger()) : null;
for(E leaf : leaves) {
N node = index.getNode(leaf);
int size = node.getNumEntries();
pagesize.put(size);
if(getLogger().isDebuggingFinest()) {
getLogger().debugFinest("NumEntires = " + size);
}
// Collect the ids in this node.
DBID[] ids = new DBID[size];
for(int i = 0; i < size; i++) {
ids[i] = ((LeafEntry) node.getEntry(i)).getDBID();
}
HashMap<DBIDPair, D> cache = new HashMap<DBIDPair, D>(size * size * 3 / 8);
for(DBID id : ids) {
KNNHeap<D> kNN = new KNNHeap<D>(k, distanceQuery.infiniteDistance());
for(DBID id2 : ids) {
DBIDPair key = DBIDUtil.newPair(id, id2);
D d = cache.remove(key);
if(d != null) {
// consume the previous result.
kNN.add(d, id2);
}
else {
// compute new and store the previous result.
d = distanceQuery.distance(id, id2);
kNN.add(d, id2);
// put it into the cache, but with the keys reversed
key = DBIDUtil.newPair(id2, id);
cache.put(key, d);
}
}
ksize.put(kNN.size());
storage.put(id, kNN.toSortedArrayList());
}
if(getLogger().isDebugging()) {
if(cache.size() > 0) {
getLogger().warning("Cache should be empty after each run, but still has " + cache.size() + " elements.");
}
}
if(progress != null) {
progress.incrementProcessed(getLogger());
}
}
if(progress != null) {
progress.ensureCompleted(getLogger());
}
if(getLogger().isVerbose()) {
getLogger().verbose("Average page size = " + pagesize.getMean() + " +- " + pagesize.getSampleStddev());
getLogger().verbose("On average, " + ksize.getMean() + " +- " + ksize.getSampleStddev() + " neighbors returned.");
}
}
/**
* Do some (limited) type checking, then cast the database into a spatial
* database.
*
* @param relation Database
* @return Metrical index
* @throws IllegalStateException when the cast fails.
*/
private MetricalIndexTree<O, D, N, E> getMetricalIndex(Relation<O> relation) throws IllegalStateException {
Class<MetricalIndexTree<O, D, N, E>> mcls = ClassGenericsUtil.uglyCastIntoSubclass(MetricalIndexTree.class);
ArrayList<MetricalIndexTree<O, D, N, E>> indexes = ResultUtil.filterResults(relation.getDatabase(), mcls);
// FIXME: check we got the right the representation
if(indexes.size() == 1) {
return indexes.get(0);
}
if(indexes.size() > 1) {
throw new IllegalStateException("More than one metrical index found - this is not supported!");
}
throw new IllegalStateException("No metrical index found!");
}
@Override
public String getLongName() {
return "Metrical index knn approximation";
}
@Override
public String getShortName() {
return "metrical-knn-approximation";
}
@Override
protected Logging getLogger() {
return logger;
}
/**
* The parameterizable factory.
*
* @author Erich Schubert
*
* @apiviz.stereotype factory
* @apiviz.uses MetricalIndexApproximationMaterializeKNNPreprocessor oneway -
* - «create»
*
* @param <O> the type of database objects the preprocessor can be applied to
* @param <D> the type of distance the used distance function will return
* @param <N> the type of spatial nodes in the spatial index
* @param <E> the type of spatial entries in the spatial index
*/
public static class Factory<O extends NumberVector<? super O, ?>, D extends Distance<D>, N extends Node<E>, E extends MTreeEntry<D>> extends AbstractMaterializeKNNPreprocessor.Factory<O, D> {
/**
* Constructor.
*
* @param k k
* @param distanceFunction distance function
*/
public Factory(int k, DistanceFunction<? super O, D> distanceFunction) {
super(k, distanceFunction);
}
@Override
public MetricalIndexApproximationMaterializeKNNPreprocessor<O, D, N, E> instantiate(Relation<O> relation) {
MetricalIndexApproximationMaterializeKNNPreprocessor<O, D, N, E> instance = new MetricalIndexApproximationMaterializeKNNPreprocessor<O, D, N, E>(relation, distanceFunction, k);
return instance;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer<O extends NumberVector<? super O, ?>, D extends Distance<D>, N extends Node<E>, E extends MTreeEntry<D>> extends AbstractMaterializeKNNPreprocessor.Factory.Parameterizer<O, D> {
@Override
protected Factory<O, D, N, E> makeInstance() {
return new Factory<O, D, N, E>(k, distanceFunction);
}
}
}
}
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