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package de.lmu.ifi.dbs.elki.algorithm;
/*
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.Collection;
import de.lmu.ifi.dbs.elki.data.type.TypeInformation;
import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
import de.lmu.ifi.dbs.elki.database.Database;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
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.NumberDistance;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.result.CollectionResult;
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.pairs.CTriple;
/**
* Algorithm to materialize all the distances in a data set.
*
* The result can then be used with the DoubleDistanceParser and
* MultipleFileInput to use cached distances.
*
* Symmetry is assumed.
*
* @param <O> Object type
* @param <D> Distance type
*/
@Title("MaterializeDistances")
@Description("Materialize all distances in the data set to use as cached/precalculated data.")
public class MaterializeDistances<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm<O, D, CollectionResult<CTriple<DBID, DBID, Double>>> {
/**
* The logger for this class.
*/
private static final Logging logger = Logging.getLogger(MaterializeDistances.class);
/**
* Constructor.
*
* @param distanceFunction Parameterization
*/
public MaterializeDistances(DistanceFunction<? super O, D> distanceFunction) {
super(distanceFunction);
}
/**
* Iterates over all points in the database.
*/
public CollectionResult<CTriple<DBID, DBID, Double>> run(Database database, Relation<O> relation) {
DistanceQuery<O, D> distFunc = database.getDistanceQuery(relation, getDistanceFunction());
final int size = relation.size();
Collection<CTriple<DBID, DBID, Double>> r = new ArrayList<CTriple<DBID, DBID, Double>>(size * (size + 1) / 2);
for(DBID id1 : relation.iterDBIDs()) {
for(DBID id2 : relation.iterDBIDs()) {
// skip inverted pairs
if(id2.compareTo(id1) > 0) {
continue;
}
double d = distFunc.distance(id1, id2).doubleValue();
r.add(new CTriple<DBID, DBID, Double>(id1, id2, d));
}
}
return new CollectionResult<CTriple<DBID, DBID, Double>>("Distance Matrix", "distance-matrix", r);
}
@Override
protected Logging getLogger() {
return logger;
}
@Override
public TypeInformation[] getInputTypeRestriction() {
return TypeUtil.array(getDistanceFunction().getInputTypeRestriction());
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm.Parameterizer<O, D> {
@Override
protected MaterializeDistances<O, D> makeInstance() {
return new MaterializeDistances<O, D>(distanceFunction);
}
}
}
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