path: root/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/FastOPTICS.java

package de.lmu.ifi.dbs.elki.algorithm.clustering.optics;

/*
 Copyright (C) 2015
 Johannes Schneider, ABB Research,Switzerland, johannes.schneider@alumni.ethz.ch

 This file is part of ELKI:
 Environment for Developing KDD-Applications Supported by Index-Structures

 Copyright (C) 2015
 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 de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm;
import de.lmu.ifi.dbs.elki.data.NumberVector;
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.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.DoubleDataStore;
import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
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.ids.ModifiableDBIDs;
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.minkowski.EuclideanDistanceFunction;
import de.lmu.ifi.dbs.elki.index.preprocessed.fastoptics.RandomProjectedNeighborsAndDensities;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil;
import de.lmu.ifi.dbs.elki.utilities.datastructures.heap.UpdatableHeap;
import de.lmu.ifi.dbs.elki.utilities.documentation.Reference;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;

/**
 * FastOPTICS algorithm (Fast approximation of OPTICS)
 *
 * Note that this is <em>not</em> FOPTICS as in "Fuzzy OPTICS"!
 *
 * Reference:
 * <p>
 * J. Schneider and M. Vlachos<br />
 * Fast parameterless density-based clustering via random projections<br />
 * Proc. 22nd ACM international conference on Conference on Information &
 * Knowledge Management (CIKM)
 * </p>
 *
 * This is based on the original code provided by Johannes Schneider, with
 * ELKIfications and optimizations by Erich Schubert.
 *
 * @author Johannes Schneider
 * @author Erich Schubert
 *
 * @apiviz.composedOf RandomProjectedNeighborsAndDensities
 */
@Reference(authors = "J. Schneider and M. Vlachos", //
title = "Fast parameterless density-based clustering via random projections", //
booktitle = "Proc. 22nd ACM international conference on Conference on Information & Knowledge Management (CIKM)", //
url = "http://dx.doi.org/10.1145/2505515.2505590")
public class FastOPTICS<V extends NumberVector> extends AbstractAlgorithm<ClusterOrder> implements OPTICSTypeAlgorithm {
  /**
   * Class logger.
   */
  private static final Logging LOG = Logging.getLogger(FastOPTICS.class);

  /**
   * undefined value for (reachability/average) distance
   */
  public static final double UNDEFINED_DISTANCE = -0.1f;

  /**
   * Result: output order of points
   */
  ClusterOrder order;

  /**
   * Result: reachability distances
   */
  WritableDoubleDataStore reachDist;

  /**
   * processed points
   */
  ModifiableDBIDs processed;

  /**
   * neighbors of a point
   */
  DataStore<? extends DBIDs> neighs;

  /**
   * Inverse Densities correspond to average distances in point set of
   * projections
   */
  DoubleDataStore inverseDensities;

  /**
   * MinPts parameter.
   */
  int minPts;

  /**
   * Index.
   */
  RandomProjectedNeighborsAndDensities<V> index;

  /**
   * Constructor.
   *
   * @param minpts Minimum number of neighbors.
   * @param index Index
   */
  public FastOPTICS(int minpts, RandomProjectedNeighborsAndDensities<V> index) {
    super();
    this.minPts = minpts;
    this.index = index;
  }

  /**
   * Run the algorithm.
   *
   * @param db Database
   * @param rel Relation
   */
  public ClusterOrder run(Database db, Relation<V> rel) {
    DBIDs ids = rel.getDBIDs();
    DistanceQuery<V> dq = db.getDistanceQuery(rel, EuclideanDistanceFunction.STATIC);

    // initialize points used and reachability distance
    reachDist = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, UNDEFINED_DISTANCE);

    // compute projections, density estimates and neighborhoods
    index.computeSetsBounds(rel, minPts, ids); // project points
    inverseDensities = index.computeAverageDistInSet(); // compute densities
    neighs = index.getNeighs(); // get neighbors of points

    // compute ordering as for OPTICS
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("OPTICS clustering.", ids.size(), LOG) : null;
    processed = DBIDUtil.newHashSet(ids.size());
    order = new ClusterOrder(ids, "FastOPTICS Cluster Order", "fast-optics");
    for(DBIDIter it = ids.iter(); it.valid(); it.advance()) {
      if(!processed.contains(it)) {
        expandClusterOrder(DBIDUtil.deref(it), order, dq, prog);
      }
    }
    index.logStatistics();
    LOG.ensureCompleted(prog);
    return order;
  }

  /**
   * OPTICS algorithm for processing a point, but with different density
   * estimates
   *
   * @param ipt Point
   * @param order Cluster order (output)
   * @param dq Distance query
   * @param prog Progress for logging.
   */
  protected void expandClusterOrder(DBID ipt, ClusterOrder order, DistanceQuery<V> dq, FiniteProgress prog) {
    UpdatableHeap<OPTICSHeapEntry> heap = new UpdatableHeap<>();
    heap.add(new OPTICSHeapEntry(ipt, null, 1e6f));
    while(!heap.isEmpty()) {
      final OPTICSHeapEntry current = heap.poll();
      DBID currPt = current.objectID;
      order.add(currPt, current.reachability, current.predecessorID);
      processed.add(currPt);
      double coredist = inverseDensities.doubleValue(currPt);
      for(DBIDIter it = neighs.get(currPt).iter(); it.valid(); it.advance()) {
        if(processed.contains(it)) {
          continue;
        }
        double nrdist = dq.distance(currPt, it);
        if(coredist > nrdist) {
          nrdist = coredist;
        }
        if(reachDist.doubleValue(it) == UNDEFINED_DISTANCE) {
          reachDist.put(it, nrdist);
        }
        else if(nrdist < reachDist.doubleValue(it)) {
          reachDist.put(it, nrdist);
        }
        heap.add(new OPTICSHeapEntry(DBIDUtil.deref(it), currPt, nrdist));
      }
      LOG.incrementProcessed(prog);
    }
  }

  @Override
  public int getMinPts() {
    return minPts;
  }

  @Override
  public TypeInformation[] getInputTypeRestriction() {
    return TypeUtil.array(EuclideanDistanceFunction.STATIC.getInputTypeRestriction());
  }

  @Override
  protected Logging getLogger() {
    return LOG;
  }

  /**
   * Parameterization class.
   *
   * @author Erich Schubert
   *
   * @apiviz.exclude
   *
   * @param <V> Vector type
   */
  public static class Parameterizer<V extends NumberVector> extends AbstractParameterizer {
    /**
     * Minimum number of neighbors for density estimation.
     */
    int minpts;

    /**
     * Random projection index.
     */
    RandomProjectedNeighborsAndDensities<V> index;

    @Override
    protected void makeOptions(Parameterization config) {
      super.makeOptions(config);
      IntParameter minptsP = new IntParameter(AbstractOPTICS.Parameterizer.MINPTS_ID) //
      .addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
      if(config.grab(minptsP)) {
        minpts = minptsP.intValue();
      }
      Class<RandomProjectedNeighborsAndDensities<V>> clz = ClassGenericsUtil.uglyCastIntoSubclass(RandomProjectedNeighborsAndDensities.class);
      index = config.tryInstantiate(clz);
    }

    @Override
    protected FastOPTICS<V> makeInstance() {
      return new FastOPTICS<V>(minpts, index);
    }
  }
}