Import Upstream version 0.6.5~20141030

1 files changed, 286 insertions, 0 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java b/src/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java
new file mode 100644
index 00000000..086b5f69
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/database/ids/integer/DoubleIntegerDBIDPairKNNListHeap.java
@@ -0,0 +1,286 @@
+package de.lmu.ifi.dbs.elki.database.ids.integer;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2014
+ 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.database.ids.DBIDIter;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
+import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter;
+import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDPair;
+import de.lmu.ifi.dbs.elki.database.ids.KNNHeap;
+import de.lmu.ifi.dbs.elki.database.ids.KNNList;
+
+/**
+ * KNN Heap implemented using a list of DoubleInt pair objects.
+ * 
+ * Currently unused, needs benchmarking.
+ * 
+ * @author Erich Schubert
+ * 
+ * @apiviz.composedOf DoubleIntegerDBIDPair
+ */
+class DoubleIntegerDBIDPairKNNListHeap implements IntegerDBIDKNNList, KNNHeap {
+  /**
+   * The value of k this was materialized for.
+   */
+  private final int k;
+
+  /**
+   * The actual data array.
+   */
+  private DoubleIntegerDBIDPair[] data;
+
+  /**
+   * Current size
+   */
+  private int size;
+
+  /**
+   * Constructor.
+   * 
+   * @param k K parameter
+   */
+  protected DoubleIntegerDBIDPairKNNListHeap(int k) {
+    super();
+    this.data = new DoubleIntegerDBIDPair[k + 5];
+    this.k = k;
+    this.size = 0;
+  }
+
+  @Override
+  public void clear() {
+    for(int i = 0; i < size; i++) {
+      data[i] = null; // discard
+    }
+    size = 0;
+  }
+
+  @Override
+  public double insert(double distance, DBIDRef id) {
+    final int kminus1 = k - 1;
+    if(size < k || distance <= data[kminus1].doubleValue()) {
+      // Ensure we have enough space.
+      if(size > data.length) {
+        grow();
+      }
+      insertionSort(new DoubleIntegerDBIDPair(distance, id.internalGetIndex()));
+      // Truncate if necessary:
+      if(size > k && data[k].doubleValue() > data[kminus1].doubleValue()) {
+        truncate();
+      }
+    }
+    return (size < k) ? Double.POSITIVE_INFINITY : get(kminus1).doubleValue();
+  }
+
+  private void truncate() {
+    for(int i = k; i < size; i++) {
+      data[i] = null; // discard
+    }
+    size = k;
+  }
+
+  @Override
+  public void insert(DoubleDBIDPair e) {
+    final int kminus1 = k - 1;
+    final double dist = e.doubleValue();
+    if(size < k || dist <= data[kminus1].doubleValue()) {
+      // Ensure we have enough space.
+      if(size > data.length) {
+        grow();
+      }
+      if(e instanceof DoubleIntegerDBIDPair) {
+        insertionSort((DoubleIntegerDBIDPair) e);
+      }
+      else {
+        insertionSort(new DoubleIntegerDBIDPair(dist, e.internalGetIndex()));
+      }
+      // Truncate if necessary:
+      if(size > k && data[k].doubleValue() > data[kminus1].doubleValue()) {
+        truncate();
+      }
+    }
+  }
+
+  /**
+   * Perform insertion sort.
+   * 
+   * @param obj Object to insert
+   */
+  private void insertionSort(DoubleIntegerDBIDPair obj) {
+    // Insertion sort:
+    int pos = size;
+    while(pos > 0) {
+      final int prev = pos - 1;
+      DoubleIntegerDBIDPair pobj = data[prev];
+      if(pobj.doubleValue() <= obj.doubleValue()) {
+        break;
+      }
+      data[pos] = pobj;
+      pos = prev;
+    }
+    data[pos] = obj;
+    ++size;
+  }
+
+  private void grow() {
+    final DoubleIntegerDBIDPair[] old = data;
+    data = new DoubleIntegerDBIDPair[data.length + (data.length >> 1)];
+    System.arraycopy(old, 0, data, 0, old.length);
+  }
+
+  @Override
+  public DoubleIntegerDBIDPair poll() {
+    assert (size > 0);
+    return data[size--];
+  }
+
+  @Override
+  public DoubleIntegerDBIDPair peek() {
+    assert (size > 0);
+    return data[size - 1];
+  }
+
+  @Override
+  public KNNList toKNNList() {
+    return this;
+  }
+
+  @Override
+  public int getK() {
+    return k;
+  }
+
+  @Override
+  public double getKNNDistance() {
+    return (size >= k) ? get(k - 1).doubleValue() : Double.POSITIVE_INFINITY;
+  }
+
+  @Override
+  public String toString() {
+    StringBuilder buf = new StringBuilder();
+    buf.append("kNNList[");
+    for(DoubleDBIDListIter iter = this.iter(); iter.valid();) {
+      buf.append(iter.doubleValue()).append(':').append(DBIDUtil.toString(iter));
+      iter.advance();
+      if(iter.valid()) {
+        buf.append(',');
+      }
+    }
+    buf.append(']');
+    return buf.toString();
+  }
+
+  @Override
+  public DoubleIntegerDBIDPair get(int index) {
+    return data[index];
+  }
+
+  @Override
+  public Itr iter() {
+    return new Itr();
+  }
+
+  @Override
+  public int size() {
+    return size;
+  }
+
+  @Override
+  public boolean contains(DBIDRef o) {
+    for(DBIDIter iter = iter(); iter.valid(); iter.advance()) {
+      if(DBIDUtil.equal(iter, o)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  @Override
+  public boolean isEmpty() {
+    return size == 0;
+  }
+
+  /**
+   * Iterator.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  private class Itr implements DoubleIntegerDBIDListIter, IntegerDBIDArrayIter {
+    /**
+     * Cursor position.
+     */
+    private int pos = 0;
+
+    @Override
+    public int internalGetIndex() {
+      return get(pos).internalGetIndex();
+    }
+
+    @Override
+    public boolean valid() {
+      return pos < size && pos >= 0;
+    }
+
+    @Override
+    public Itr advance() {
+      pos++;
+      return this;
+    }
+
+    @Override
+    public double doubleValue() {
+      return get(pos).doubleValue();
+    }
+
+    @Override
+    public DoubleIntegerDBIDPair getPair() {
+      return get(pos);
+    }
+
+    @Override
+    public int getOffset() {
+      return pos;
+    }
+
+    @Override
+    public Itr advance(int count) {
+      pos += count;
+      return this;
+    }
+
+    @Override
+    public Itr retract() {
+      --pos;
+      return this;
+    }
+
+    @Override
+    public Itr seek(int off) {
+      pos = off;
+      return this;
+    }
+  }
+}