package de.lmu.ifi.dbs.elki.application.cache;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2012
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.io.File;
import java.io.IOException;
import de.lmu.ifi.dbs.elki.application.AbstractApplication;
import de.lmu.ifi.dbs.elki.database.Database;
import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase;
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.distancefunction.external.DiskCacheBasedDoubleDistanceFunction;
import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
/**
* Wrapper to convert a traditional text-serialized result into a on-disk matrix
* for random access.
*
* @author Erich Schubert
*
* @apiviz.has OnDiskUpperTriangleMatrix
* @apiviz.has DistanceFunction
*
* @param <O> Object type
* @param <D> Distance type
*/
public class CacheDoubleDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>> extends AbstractApplication {
/**
* The logger for this class.
*/
private static final Logging logger = Logging.getLogger(CacheDoubleDistanceInOnDiskMatrix.class);
/**
* Parameter that specifies the name of the directory to be re-parsed.
* <p>
* Key: {@code -loader.diskcache}
* </p>
*/
public static final OptionID CACHE_ID = OptionID.getOrCreateOptionID("loader.diskcache", "File name of the disk cache to create.");
/**
* Parameter that specifies the name of the directory to be re-parsed.
* <p>
* Key: {@code -loader.distance}
* </p>
*/
public static final OptionID DISTANCE_ID = OptionID.getOrCreateOptionID("loader.distance", "Distance function to cache.");
/**
* Debug flag, to double-check all write operations.
*/
private static final boolean debugExtraCheckSymmetry = false;
/**
* Holds the database connection to have the algorithm run with.
*/
private Database database;
/**
* Distance function that is to be cached.
*/
private DistanceFunction<O, D> distance;
/**
* Output file.
*/
private File out;
/**
* Constructor.
*
* @param verbose Verbose flag
* @param database Database
* @param distance Distance function
* @param out Matrix output file
*/
public CacheDoubleDistanceInOnDiskMatrix(boolean verbose, Database database, DistanceFunction<O, D> distance, File out) {
super(verbose);
this.database = database;
this.distance = distance;
this.out = out;
}
@Override
public void run() {
database.initialize();
Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
DistanceQuery<O, D> distanceQuery = database.getDistanceQuery(relation, distance);
int matrixsize = 0;
for(DBID id : relation.iterDBIDs()) {
matrixsize = Math.max(matrixsize, id.getIntegerID() + 1);
if(id.getIntegerID() < 0) {
throw new AbortException("OnDiskMatrixCache does not allow negative DBIDs.");
}
}
OnDiskUpperTriangleMatrix matrix;
try {
matrix = new OnDiskUpperTriangleMatrix(out, DiskCacheBasedDoubleDistanceFunction.DOUBLE_CACHE_MAGIC, 0, 8, matrixsize);
}
catch(IOException e) {
throw new AbortException("Error creating output matrix.", e);
}
for(DBID id1 : relation.iterDBIDs()) {
for(DBID id2 : relation.iterDBIDs()) {
if(id2.getIntegerID() >= id1.getIntegerID()) {
double d = distanceQuery.distance(id1, id2).doubleValue();
if(debugExtraCheckSymmetry) {
double d2 = distanceQuery.distance(id2, id1).doubleValue();
if(Math.abs(d - d2) > 0.0000001) {
logger.warning("Distance function doesn't appear to be symmetric!");
}
}
try {
matrix.getRecordBuffer(id1.getIntegerID(), id2.getIntegerID()).putDouble(d);
}
catch(IOException e) {
throw new AbortException("Error writing distance record " + id1 + "," + id2 + " to matrix.", e);
}
}
}
}
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractApplication.Parameterizer {
/**
* Holds the database connection to have the algorithm run with.
*/
private Database database = null;
/**
* Distance function that is to be cached.
*/
private DistanceFunction<O, D> distance = null;
/**
* Output file.
*/
private File out = null;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
// Database connection parameter
final ObjectParameter<Database> dbpar = new ObjectParameter<Database>(OptionID.DATABASE_CONNECTION, Database.class, StaticArrayDatabase.class);
if(config.grab(dbpar)) {
database = dbpar.instantiateClass(config);
}
// Distance function parameter
final ObjectParameter<DistanceFunction<O, D>> dpar = new ObjectParameter<DistanceFunction<O, D>>(DISTANCE_ID, DistanceFunction.class);
if(config.grab(dpar)) {
distance = dpar.instantiateClass(config);
}
// Output file parameter
final FileParameter cpar = new FileParameter(CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
if(config.grab(cpar)) {
out = cpar.getValue();
}
}
@Override
protected CacheDoubleDistanceInOnDiskMatrix<O, D> makeInstance() {
return new CacheDoubleDistanceInOnDiskMatrix<O, D>(verbose, database, distance, out);
}
}
/**
* Main method, delegate to super class.
*
* @param args Command line arguments
*/
public static void main(String[] args) {
runCLIApplication(CacheDoubleDistanceInOnDiskMatrix.class, args);
}
}