package de.lmu.ifi.dbs.elki.algorithm.outlier.spatial.neighborhood;
/*
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.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;
import de.lmu.ifi.dbs.elki.data.ExternalID;
import de.lmu.ifi.dbs.elki.data.LabelList;
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.datastore.DataStore;
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.datastore.WritableDataStore;
import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
import de.lmu.ifi.dbs.elki.database.relation.Relation;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.utilities.FileUtil;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
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;
/**
* A precomputed neighborhood, loaded from an external file.
*
* @author Erich Schubert
*/
public class ExternalNeighborhood extends AbstractPrecomputedNeighborhood {
/**
* Logger
*/
static final Logging logger = Logging.getLogger(ExternalNeighborhood.class);
/**
* Parameter to specify the neighborhood file
*/
public static final OptionID NEIGHBORHOOD_FILE_ID = OptionID.getOrCreateOptionID("externalneighbors.file", "The file listing the neighbors.");
/**
* Constructor.
*
* @param store Store to access
*/
public ExternalNeighborhood(DataStore<DBIDs> store) {
super(store);
}
@Override
public String getLongName() {
return "External Neighborhood";
}
@Override
public String getShortName() {
return "external-neighborhood";
}
@Override
protected Logging getLogger() {
return logger;
}
/**
* Factory class.
*
* @author Erich Schubert
*
* @apiviz.stereotype factory
* @apiviz.has ExternalNeighborhood oneway - - «produces»
*/
public static class Factory extends AbstractPrecomputedNeighborhood.Factory<Object> {
/**
* The input file.
*/
private File file;
/**
* Constructor.
*
* @param file File to load
*/
public Factory(File file) {
super();
this.file = file;
}
@Override
public NeighborSetPredicate instantiate(Relation<?> database) {
DataStore<DBIDs> store = loadNeighbors(database);
ExternalNeighborhood neighborhood = new ExternalNeighborhood(store);
return neighborhood;
}
@Override
public TypeInformation getInputTypeRestriction() {
return TypeUtil.ANY;
}
/**
* Method to load the external neighbors.
*/
private DataStore<DBIDs> loadNeighbors(Relation<?> database) {
final WritableDataStore<DBIDs> store = DataStoreUtil.makeStorage(database.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC | DataStoreFactory.HINT_TEMP, DBIDs.class);
if(logger.isVerbose()) {
logger.verbose("Loading external neighborhoods.");
}
if(logger.isDebugging()) {
logger.verbose("Building reverse label index...");
}
// Build a map label/ExternalId -> DBID
// (i.e. a reverse index!)
// TODO: move this into the database layer to share?
Map<String, DBID> lblmap = new HashMap<String, DBID>(database.size() * 2);
{
Relation<LabelList> olq = database.getDatabase().getRelation(TypeUtil.LABELLIST);
Relation<ExternalID> eidq = database.getDatabase().getRelation(TypeUtil.EXTERNALID);
for(DBID id : database.iterDBIDs()) {
if(eidq != null) {
ExternalID eid = eidq.get(id);
if(eid != null) {
lblmap.put(eid.toString(), id);
}
}
if(olq != null) {
LabelList label = olq.get(id);
if(label != null) {
for(String lbl : label) {
lblmap.put(lbl, id);
}
}
}
}
}
try {
if(logger.isDebugging()) {
logger.verbose("Loading neighborhood file.");
}
InputStream in = new FileInputStream(file);
in = FileUtil.tryGzipInput(in);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
for(String line; (line = br.readLine()) != null;) {
ArrayModifiableDBIDs neighbours = DBIDUtil.newArray();
String[] entries = line.split(" ");
DBID id = lblmap.get(entries[0]);
if(id != null) {
for(int i = 0; i < entries.length; i++) {
final DBID neigh = lblmap.get(entries[i]);
if(neigh != null) {
neighbours.add(neigh);
}
else {
if(logger.isDebugging()) {
logger.debug("No object found for label " + entries[i]);
}
}
}
store.put(id, neighbours);
}
else {
if(logger.isDebugging()) {
logger.warning("No object found for label " + entries[0]);
}
}
}
br.close();
in.close();
return store;
}
catch(IOException e) {
throw new AbortException("Loading of external neighborhood failed.", e);
}
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractParameterizer {
/**
* The input file.
*/
File file;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
file = getParameterNeighborhoodFile(config);
}
/**
* Get the neighborhood parameter.
*
* @param config Parameterization
* @return Instance or null
*/
protected static File getParameterNeighborhoodFile(Parameterization config) {
final FileParameter param = new FileParameter(NEIGHBORHOOD_FILE_ID, FileParameter.FileType.INPUT_FILE);
if(config.grab(param)) {
return param.getValue();
}
return null;
}
@Override
protected ExternalNeighborhood.Factory makeInstance() {
return new ExternalNeighborhood.Factory(file);
}
}
}
}