コード例 #1
0
  public Result run(Database database, Relation<O> rel) {
    DistanceQuery<O> dq = rel.getDistanceQuery(getDistanceFunction());
    int size = rel.size();
    long pairs = (size * (long) size) >> 1;

    final long ssize = sampling <= 1 ? (long) Math.ceil(sampling * pairs) : (long) sampling;
    if (ssize > Integer.MAX_VALUE) {
      throw new AbortException("Sampling size too large.");
    }
    final int qsize = quantile <= 0 ? 1 : (int) Math.ceil(quantile * ssize);

    DoubleMaxHeap heap = new DoubleMaxHeap(qsize);

    ArrayDBIDs ids = DBIDUtil.ensureArray(rel.getDBIDs());
    DBIDArrayIter i1 = ids.iter(), i2 = ids.iter();
    Random r = rand.getSingleThreadedRandom();

    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Sampling", (int) ssize, LOG) : null;
    for (long i = 0; i < ssize; i++) {
      int x = r.nextInt(size - 1) + 1, y = r.nextInt(x);
      double dist = dq.distance(i1.seek(x), i2.seek(y));
      // Skip NaN, and/or zeros.
      if (dist != dist || (nozeros && dist < Double.MIN_NORMAL)) {
        continue;
      }
      heap.add(dist, qsize);
      LOG.incrementProcessed(prog);
    }

    LOG.statistics(new DoubleStatistic(PREFIX + ".quantile", quantile));
    LOG.statistics(new LongStatistic(PREFIX + ".samplesize", ssize));
    LOG.statistics(new DoubleStatistic(PREFIX + ".distance", heap.peek()));
    LOG.ensureCompleted(prog);
    Collection<String> header = Arrays.asList(new String[] {"Distance"});
    Collection<Vector> data = Arrays.asList(new Vector[] {new Vector(heap.peek())});
    return new CollectionResult<Vector>("Distances sample", "distance-sample", data, header);
  }
コード例 #2
0
 /**
  * Constructor.
  *
  * @param prob Probability
  * @param rnd Random generator
  */
 public RandomSamplingStreamFilter(double prob, RandomFactory rnd) {
   super();
   this.prob = prob;
   this.random = rnd.getSingleThreadedRandom();
 }
コード例 #3
0
ファイル: DOC.java プロジェクト: mangwang/elki
  /**
   * Performs a single run of FastDOC, finding a single cluster.
   *
   * @param database Database context
   * @param relation used to get actual values for DBIDs.
   * @param S The set of points we're working on.
   * @param d Dimensionality of the data set we're currently working on.
   * @param r Size of random samples.
   * @param m Number of inner iterations (per seed point).
   * @param n Number of outer iterations (seed points).
   * @return a cluster, if one is found, else <code>null</code>.
   */
  private Cluster<SubspaceModel> runFastDOC(
      Database database, Relation<V> relation, ArrayModifiableDBIDs S, int d, int n, int m, int r) {
    // Relevant attributes of highest cardinality.
    long[] D = null;
    // The seed point for the best dimensions.
    DBIDVar dV = DBIDUtil.newVar();

    // Inform the user about the progress in the current iteration.
    FiniteProgress iprogress =
        LOG.isVerbose()
            ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG)
            : null;

    Random random = rnd.getSingleThreadedRandom();

    DBIDArrayIter iter = S.iter();
    outer:
    for (int i = 0; i < n; ++i) {
      // Pick a random seed point.
      iter.seek(random.nextInt(S.size()));

      for (int j = 0; j < m; ++j) {
        // Choose a set of random points.
        DBIDs randomSet = DBIDUtil.randomSample(S, r, random);

        // Initialize cluster info.
        long[] nD = BitsUtil.zero(d);

        // Test each dimension.
        for (int k = 0; k < d; ++k) {
          if (dimensionIsRelevant(k, relation, randomSet)) {
            BitsUtil.setI(nD, k);
          }
        }

        if (D == null || BitsUtil.cardinality(nD) > BitsUtil.cardinality(D)) {
          D = nD;
          dV.set(iter);

          if (BitsUtil.cardinality(D) >= d_zero) {
            if (iprogress != null) {
              iprogress.setProcessed(iprogress.getTotal(), LOG);
            }
            break outer;
          }
        }
        LOG.incrementProcessed(iprogress);
      }
    }
    LOG.ensureCompleted(iprogress);

    // If no relevant dimensions were found, skip it.
    if (D == null || BitsUtil.cardinality(D) == 0) {
      return null;
    }

    // Get all points in the box.
    SubspaceMaximumDistanceFunction df = new SubspaceMaximumDistanceFunction(D);
    DistanceQuery<V> dq = database.getDistanceQuery(relation, df);
    RangeQuery<V> rq = database.getRangeQuery(dq, DatabaseQuery.HINT_SINGLE);

    // TODO: add filtering capabilities into query API!
    DBIDs C = DBIDUtil.intersection(S, rq.getRangeForDBID(dV, w));

    // If we have a non-empty cluster, return it.
    return (C.size() > 0) ? makeCluster(relation, C, D) : null;
  }
コード例 #4
0
ファイル: DOC.java プロジェクト: mangwang/elki
  /**
   * Performs a single run of DOC, finding a single cluster.
   *
   * @param database Database context
   * @param relation used to get actual values for DBIDs.
   * @param S The set of points we're working on.
   * @param d Dimensionality of the data set we're currently working on.
   * @param r Size of random samples.
   * @param m Number of inner iterations (per seed point).
   * @param n Number of outer iterations (seed points).
   * @param minClusterSize Minimum size a cluster must have to be accepted.
   * @return a cluster, if one is found, else <code>null</code>.
   */
  private Cluster<SubspaceModel> runDOC(
      Database database,
      Relation<V> relation,
      ArrayModifiableDBIDs S,
      final int d,
      int n,
      int m,
      int r,
      int minClusterSize) {
    // Best cluster for the current run.
    DBIDs C = null;
    // Relevant attributes for the best cluster.
    long[] D = null;
    // Quality of the best cluster.
    double quality = Double.NEGATIVE_INFINITY;

    // Bounds for our cluster.
    // ModifiableHyperBoundingBox bounds = new ModifiableHyperBoundingBox(new
    // double[d], new double[d]);

    // Weights for distance (= rectangle query)
    SubspaceMaximumDistanceFunction df = new SubspaceMaximumDistanceFunction(BitsUtil.zero(d));
    DistanceQuery<V> dq = database.getDistanceQuery(relation, df);
    RangeQuery<V> rq = database.getRangeQuery(dq);

    // Inform the user about the progress in the current iteration.
    FiniteProgress iprogress =
        LOG.isVerbose()
            ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG)
            : null;

    Random random = rnd.getSingleThreadedRandom();
    DBIDArrayIter iter = S.iter();

    for (int i = 0; i < n; ++i) {
      // Pick a random seed point.
      iter.seek(random.nextInt(S.size()));

      for (int j = 0; j < m; ++j) {
        // Choose a set of random points.
        DBIDs randomSet = DBIDUtil.randomSample(S, r, random);

        // Initialize cluster info.
        long[] nD = BitsUtil.zero(d);

        // Test each dimension and build bounding box.
        for (int k = 0; k < d; ++k) {
          if (dimensionIsRelevant(k, relation, randomSet)) {
            BitsUtil.setI(nD, k);
          }
        }
        if (BitsUtil.cardinality(nD) > 0) {
          // Get all points in the box.
          df.setSelectedDimensions(nD);
          // TODO: add filtering capabilities into query API!
          DBIDs nC = DBIDUtil.intersection(S, rq.getRangeForDBID(iter, w));

          if (LOG.isDebuggingFiner()) {
            LOG.finer(
                "Testing a cluster candidate, |C| = "
                    + nC.size()
                    + ", |D| = "
                    + BitsUtil.cardinality(nD));
          }

          // Is the cluster large enough?
          if (nC.size() < minClusterSize) {
            // Too small.
            if (LOG.isDebuggingFiner()) {
              LOG.finer("... but it's too small.");
            }
          } else {
            // Better cluster than before?
            double nQuality = computeClusterQuality(nC.size(), BitsUtil.cardinality(nD));
            if (nQuality > quality) {
              if (LOG.isDebuggingFiner()) {
                LOG.finer("... and it's the best so far: " + nQuality + " vs. " + quality);
              }
              C = nC;
              D = nD;
              quality = nQuality;
            } else {
              if (LOG.isDebuggingFiner()) {
                LOG.finer("... but we already have a better one.");
              }
            }
          }
        }
        LOG.incrementProcessed(iprogress);
      }
    }
    LOG.ensureCompleted(iprogress);

    return (C != null) ? makeCluster(relation, C, D) : null;
  }