Examples of ArrayModifiableDBIDs

Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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        adjustApproximatedKNNDistances(dirEntry, knnLists);
      }
    }

    // PolynomialApproximation approx1 = node.knnDistanceApproximation();
    ArrayModifiableDBIDs ids = DBIDUtil.newArray();
    leafEntryIDs(node, ids);
    PolynomialApproximation approx = approximateKnnDistances(getMeanKNNList(ids, knnLists));
    entry.setKnnDistanceApproximation(approx);
  }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    FiniteProgress progress = logger.isVerbose() ? new FiniteProgress("Processing partitions.", partitions, logger) : null;
    for(int part = 0; part < partitions; part++) {
      int size = (partitions * minsize + part >= aids.size()) ? minsize : minsize + 1;
      // Collect the ids in this node.
      ArrayModifiableDBIDs ids = DBIDUtil.newArray(size);
      for(int i = 0; i < size; i++) {
        assert (size * partitions + part < aids.size());
        ids.add(aids.get(i * partitions + part));
      }
      HashMap<DBIDPair, D> cache = new HashMap<DBIDPair, D>(size * size * 3 / 8);
      for(DBID id : ids) {
        KNNHeap<D> kNN = new KNNHeap<D>(k, distanceQuery.infiniteDistance());
        for(DBID id2 : ids) {
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    super();
    this.positiveClassName = positive_class_name;
  }

  private ROCResult computeROCResult(int size, SetDBIDs positiveids, Iterator<DBID> iter) {
    ArrayModifiableDBIDs order = DBIDUtil.newArray(size);
    while(iter.hasNext()) {
      Object o = iter.next();
      if(!(o instanceof DBID)) {
        throw new IllegalStateException("Iterable result contained non-DBID - result didn't satisfy requirements");
      }
      else {
        order.add((DBID) o);
      }
    }
    if(order.size() != size) {
      throw new IllegalStateException("Iterable result doesn't match database size - incomplete ordering?");
    }
    List<DoubleDoublePair> roccurve = ROC.materializeROC(size, positiveids, new ROC.SimpleAdapter(order.iterator()));
    double rocauc = ROC.computeAUC(roccurve);
    if(logger.isVerbose()) {
      logger.verbose(ROCAUC_LABEL +": " + rocauc);
    }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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  public static ArrayModifiableDBIDs getObjectsByLabelMatch(Database database, Pattern name_pattern) {
    Relation<String> relation = guessLabelRepresentation(database);
    if(name_pattern == null) {
      return DBIDUtil.newArray();
    }
    ArrayModifiableDBIDs ret = DBIDUtil.newArray();
    for(DBID objid : relation.iterDBIDs()) {
      if(name_pattern.matcher(relation.get(objid)).matches()) {
        ret.add(objid);
      }
    }
    return ret;
  }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    TreeSet<FCPair<Double, DBID>> minhotset = new TreeSet<FCPair<Double, DBID>>();
    TreeSet<FCPair<Double, DBID>> maxhotset = new TreeSet<FCPair<Double, DBID>>(Collections.reverseOrder());

    int randomsize = (int) Math.max(25, Math.pow(database.size(), 0.2));
    double rprob = ((double) randomsize) / size;
    ArrayModifiableDBIDs randomset = DBIDUtil.newArray(randomsize);

    Iterator<DBID> iter = database.iterDBIDs();
    if(!iter.hasNext()) {
      throw new IllegalStateException(ExceptionMessages.DATABASE_EMPTY);
    }
    DBID firstid = iter.next();
    minhotset.add(new FCPair<Double, DBID>(Double.MAX_VALUE, firstid));
    maxhotset.add(new FCPair<Double, DBID>(Double.MIN_VALUE, firstid));
    while(iter.hasNext()) {
      DBID id1 = iter.next();
      // generate candidates for min distance.
      ArrayList<FCPair<Double, DBID>> np = new ArrayList<FCPair<Double, DBID>>(k * 2 + randomsize * 2);
      for(FCPair<Double, DBID> pair : minhotset) {
        DBID id2 = pair.getSecond();
        // skip the object itself
        if(id1.compareTo(id2) == 0) {
          continue;
        }
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      for(DBID id2 : randomset) {
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      minhotset.addAll(np);
      shrinkHeap(minhotset, k);

      // generate candidates for max distance.
      ArrayList<FCPair<Double, DBID>> np2 = new ArrayList<FCPair<Double, DBID>>(k * 2 + randomsize * 2);
      for(FCPair<Double, DBID> pair : minhotset) {
        DBID id2 = pair.getSecond();
        // skip the object itself
        if(id1.compareTo(id2) == 0) {
          continue;
        }
        double d = distFunc.distance(id1, id2).doubleValue();
        np2.add(new FCPair<Double, DBID>(d, id1));
        np2.add(new FCPair<Double, DBID>(d, id2));
      }
      for(DBID id2 : randomset) {
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      maxhotset.addAll(np2);
      shrinkHeap(maxhotset, k);

      // update random set
      if(randomset.size() < randomsize) {
        randomset.add(id1);
      }
      else if(rnd.nextDouble() < rprob) {
        randomset.set((int) Math.floor(rnd.nextDouble() * randomsize), id1);
      }
    }
    return new DoubleMinMax(minhotset.first().getFirst(), maxhotset.first().getFirst());
  }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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   * @param relation Relation
   * @param iter DBID iterator
   * @return result object
   */
  private SimilarityMatrix computeSimilarityMatrixImage(Relation<O> relation, Iterator<DBID> iter) {
    ArrayModifiableDBIDs order = DBIDUtil.newArray(relation.size());
    while(iter.hasNext()) {
      Object o = iter.next();
      if(!(o instanceof DBID)) {
        throw new IllegalStateException("Iterable result contained non-DBID - result didn't satisfy requirements");
      }
      else {
        order.add((DBID) o);
      }
    }
    if(order.size() != relation.size()) {
      throw new IllegalStateException("Iterable result doesn't match database size - incomplete ordering?");
    }
    DistanceQuery<O, ? extends NumberDistance<?, ?>> dq = distanceFunction.instantiate(relation);
    final int size = order.size();

    // When the logging is in the outer loop, it's just 2*size (providing enough
    // resolution)
    final int ltotal = 2 * size; // size * (size + 1);
    FiniteProgress prog = logger.isVerbose() ? new FiniteProgress("Similarity Matrix Image", ltotal, logger) : null;

    // Note: we assume that we have an efficient distance cache available,
    // since we are using 2*O(n*n) distance computations.
    DoubleMinMax minmax = new DoubleMinMax();
    for(int x = 0; x < size; x++) {
      DBID id1 = order.get(x);
      for(int y = x; y < size; y++) {
        DBID id2 = order.get(y);
        final double dist = dq.distance(id1, id2).doubleValue();
        if(!Double.isNaN(dist) && !Double.isInfinite(dist) /* && dist > 0.0 */) {
          if(!skipzero || dist != 0.0) {
            minmax.put(dist);
          }
        }
      }
      if(prog != null) {
        prog.incrementProcessed(logger);
      }
    }

    double zoom = minmax.getMax() - minmax.getMin();
    if(zoom > 0.0) {
      zoom = 1. / zoom;
    }
    LinearScaling scale = new LinearScaling(zoom, -minmax.getMin() * zoom);
    BufferedImage img = new BufferedImage(size, size, BufferedImage.TYPE_INT_RGB);
    for(int x = 0; x < size; x++) {
      DBID id1 = order.get(x);
      for(int y = x; y < size; y++) {
        DBID id2 = order.get(y);
        double ddist = dq.distance(id1, id2).doubleValue();
        if(ddist > 0.0) {
          ddist = scale.getScaled(ddist);
        }
        // Apply extra scaling
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    TreeSet<FCPair<Double, DBID>> minhotset = new TreeSet<FCPair<Double, DBID>>();
    TreeSet<FCPair<Double, DBID>> maxhotset = new TreeSet<FCPair<Double, DBID>>(Collections.reverseOrder());

    int randomsize = (int) Math.max(25, Math.pow(database.size(), 0.2));
    double rprob = ((double) randomsize) / size;
    ArrayModifiableDBIDs randomset = DBIDUtil.newArray(randomsize);

    Iterator<DBID> iter = database.iterDBIDs();
    if(!iter.hasNext()) {
      throw new IllegalStateException(ExceptionMessages.DATABASE_EMPTY);
    }
    DBID firstid = iter.next();
    minhotset.add(new FCPair<Double, DBID>(Double.MAX_VALUE, firstid));
    maxhotset.add(new FCPair<Double, DBID>(Double.MIN_VALUE, firstid));
    while(iter.hasNext()) {
      DBID id1 = iter.next();
      // generate candidates for min distance.
      ArrayList<FCPair<Double, DBID>> np = new ArrayList<FCPair<Double, DBID>>(k * 2 + randomsize * 2);
      for(FCPair<Double, DBID> pair : minhotset) {
        DBID id2 = pair.getSecond();
        // skip the object itself
        if(id1.compareTo(id2) == 0) {
          continue;
        }
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      for(DBID id2 : randomset) {
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      minhotset.addAll(np);
      shrinkHeap(minhotset, k);

      // generate candidates for max distance.
      ArrayList<FCPair<Double, DBID>> np2 = new ArrayList<FCPair<Double, DBID>>(k * 2 + randomsize * 2);
      for(FCPair<Double, DBID> pair : minhotset) {
        DBID id2 = pair.getSecond();
        // skip the object itself
        if(id1.compareTo(id2) == 0) {
          continue;
        }
        double d = distFunc.distance(id1, id2).doubleValue();
        np2.add(new FCPair<Double, DBID>(d, id1));
        np2.add(new FCPair<Double, DBID>(d, id2));
      }
      for(DBID id2 : randomset) {
        double d = distFunc.distance(id1, id2).doubleValue();
        np.add(new FCPair<Double, DBID>(d, id1));
        np.add(new FCPair<Double, DBID>(d, id2));
      }
      maxhotset.addAll(np2);
      shrinkHeap(maxhotset, k);

      // update random set
      if(randomset.size() < randomsize) {
        randomset.add(id1);
      }
      else if(rnd.nextDouble() < rprob) {
        randomset.set((int) Math.floor(rnd.nextDouble() * randomsize), id1);
      }
    }
    return new DoubleMinMax(minhotset.first().getFirst(), maxhotset.first().getFirst());
  }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    super();
    this.positiveClassName = positive_class_name;
  }

  private ROCResult computeROCResult(int size, SetDBIDs positiveids, Iterator<DBID> iter) {
    ArrayModifiableDBIDs order = DBIDUtil.newArray(size);
    while(iter.hasNext()) {
      Object o = iter.next();
      if(!(o instanceof DBID)) {
        throw new IllegalStateException("Iterable result contained non-DBID - result didn't satisfy requirements");
      }
      else {
        order.add((DBID) o);
      }
    }
    if(order.size() != size) {
      throw new IllegalStateException("Iterable result doesn't match database size - incomplete ordering?");
    }
    List<DoubleDoublePair> roccurve = ROC.materializeROC(size, positiveids, new ROC.SimpleAdapter(order.iterator()));
    double rocauc = ROC.computeAUC(roccurve);
    if(logger.isVerbose()) {
      logger.verbose(ROCAUC_LABEL +": " + rocauc);
    }
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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   * @param relation Relation
   * @param iter DBID iterator
   * @return result object
   */
  private SimilarityMatrix computeSimilarityMatrixImage(Relation<O> relation, Iterator<DBID> iter) {
    ArrayModifiableDBIDs order = DBIDUtil.newArray(relation.size());
    while(iter.hasNext()) {
      Object o = iter.next();
      if(!(o instanceof DBID)) {
        throw new IllegalStateException("Iterable result contained non-DBID - result didn't satisfy requirements");
      }
      else {
        order.add((DBID) o);
      }
    }
    if(order.size() != relation.size()) {
      throw new IllegalStateException("Iterable result doesn't match database size - incomplete ordering?");
    }
    DistanceQuery<O, ? extends NumberDistance<?, ?>> dq = distanceFunction.instantiate(relation);
    final int size = order.size();

    // When the logging is in the outer loop, it's just 2*size (providing enough
    // resolution)
    final int ltotal = 2 * size; // size * (size + 1);
    FiniteProgress prog = logger.isVerbose() ? new FiniteProgress("Similarity Matrix Image", ltotal, logger) : null;

    // Note: we assume that we have an efficient distance cache available,
    // since we are using 2*O(n*n) distance computations.
    DoubleMinMax minmax = new DoubleMinMax();
    for(int x = 0; x < size; x++) {
      DBID id1 = order.get(x);
      for(int y = x; y < size; y++) {
        DBID id2 = order.get(y);
        final double dist = dq.distance(id1, id2).doubleValue();
        if(!Double.isNaN(dist) && !Double.isInfinite(dist) /* && dist > 0.0 */) {
          if(!skipzero || dist != 0.0) {
            minmax.put(dist);
          }
        }
      }
      if(prog != null) {
        prog.incrementProcessed(logger);
      }
    }

    double zoom = minmax.getMax() - minmax.getMin();
    if(zoom > 0.0) {
      zoom = 1. / zoom;
    }
    LinearScaling scale = new LinearScaling(zoom, -minmax.getMin() * zoom);
    BufferedImage img = new BufferedImage(size, size, BufferedImage.TYPE_INT_RGB);
    for(int x = 0; x < size; x++) {
      DBID id1 = order.get(x);
      for(int y = x; y < size; y++) {
        DBID id2 = order.get(y);
        double ddist = dq.distance(id1, id2).doubleValue();
        if(ddist > 0.0) {
          ddist = scale.getScaled(ddist);
        }
        // Apply extra scaling
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Examples of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs

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    storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, ArrayDBIDs.class);
    KNNQuery<O, D> knnquery = QueryUtil.getKNNQuery(relation, distanceFunction, numberOfNeighbors);

    FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("assigning nearest neighbor lists", relation.size(), getLogger()) : null;
    for(DBID id : relation.iterDBIDs()) {
      ArrayModifiableDBIDs neighbors = DBIDUtil.newArray(numberOfNeighbors);
      KNNResult<D> kNN = knnquery.getKNNForDBID(id, numberOfNeighbors);
      for(int i = 0; i < kNN.size(); i++) {
        final DBID nid = kNN.get(i).getDBID();
        // if(!id.equals(nid)) {
        neighbors.add(nid);
        // }
        // Size limitation to exactly numberOfNeighbors
        if(neighbors.size() >= numberOfNeighbors) {
          break;
        }
      }
      neighbors.sort();
      storage.put(id, neighbors);
      if(progress != null) {
        progress.incrementProcessed(getLogger());
      }
    }
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