Fix handling of duplicates and merge history.

Author: kno10

elki-clustering/src/main/java/elki/clustering/hierarchical/BufferedSearchSingleLink.java

@@ -223,8 +223,9 @@ private void initializeHeap() {
           final double d = pq.computeExactDistance();
           if(d == 0.) { // duplicate, merge immediately
             int cb = builder.get(b);
-            assert ca != cb;
-            ca = builder.add(ca, 0, cb);
+            if(ca != cb) {
+              ca = builder.add(ca, 0, cb);
+            }
             continue;
           }
           h.add(d, b);
@@ -256,9 +257,9 @@ private void refillNeighbors(int a, int ca) {
       DoubleIntegerMinHeap h = heaps[a];
       double thres = h.isEmpty() ? Double.POSITIVE_INFINITY : h.peekKey();
       final double skip = threshold[a];
-      if (last != a) {
-    	  pq.search(ita.seek(a)).increaseSkip(skip);
-    	  last = a;
+      if(last != a) {
+        pq.search(ita.seek(a)).increaseSkip(skip);
+        last = a;
       }
       for(; pq.valid() && pq.allLowerBound() < thres; pq.advance()) {
         final int b = ids.index(pq);

elki-clustering/src/main/java/elki/clustering/hierarchical/ClusterMergeHistoryBuilder.java

@@ -112,12 +112,12 @@ public int get(int i) {
     }
     // Follow i to its parent.
     int p = parent[i];
-    if (p == i) {
+    if(p == i) {
       return i;
     }
     while(true) {
       final int pp = parent[p];
-      if (p == pp) {
+      if(p == pp) {
         return p;
       }
       parent[i] = pp; // path halving
@@ -274,15 +274,13 @@ public int[] optimizeOrder() {
       return da < db ? -1 : da > db ? +1 : (a > b ? -1 : +1);
     });
     // Now we need to ensure merges are consistent in their order
-    byte[] seen = new byte[m];
+    boolean[] seen = new boolean[m];
     int[] order = new int[m];
     int size = 0;
     for(int it : o1) {
-      if(seen[it] > 0) {
-        continue;
+      if(!seen[it]) {
+        size = addRecursive(order, size, seen, it, n);
       }
-      size = addRecursive(order, size, seen, it, n);
-      seen[order[size++] = it] = 1;
     }
     assert size == m;
     // Rewrite the result:
@@ -346,16 +344,15 @@ private boolean checkMonotone() {
    * @param n Number of primary objects
    * @return Size after additions
    */
-  private int addRecursive(int[] order, int size, byte[] seen, int it, int n) {
+  private int addRecursive(int[] order, int size, boolean[] seen, int it, int n) {
     int a = merges[it << 1] - n, b = merges[(it << 1) + 1] - n;
-    if(a >= 0 && seen[a] == 0) {
+    if(a >= 0 && !seen[a]) {
       size = addRecursive(order, size, seen, a, n);
-      seen[order[size++] = a] = 1;
     }
-    if(b >= 0 && seen[b] == 0) {
+    if(b >= 0 && !seen[b]) {
       size = addRecursive(order, size, seen, b, n);
-      seen[order[size++] = b] = 1;
     }
+    seen[order[size++] = it] = true;
     return size;
   }
 }

elki-clustering/src/main/java/elki/clustering/hierarchical/HeapOfSearchersSingleLink.java

@@ -177,7 +177,7 @@ public void run(Relation<? extends O> relation) {
         }
         nn.poll();
         // need refill?
-        if(nn.isEmpty() || nn.peekKey() > curd) {
+        if(nn.isEmpty() || nn.peekKey() > pqs[a].allLowerBound()) {
           refillNeighbors(a, ca);
         }
         if(nn.isEmpty()) {
@@ -218,8 +218,9 @@ private void initializeHeap(Relation<? extends O> relation) {
           final double d = pq.computeExactDistance();
           if(d == 0.) { // duplicate, merge immediately
             int cb = builder.get(b);
-            assert ca != cb;
-            ca = builder.add(ca, 0, cb);
+            if (ca != cb) {
+              ca = builder.add(ca, 0, cb);
+            }
             continue;
           }
           h.add(d, b);

elki-clustering/src/main/java/elki/clustering/hierarchical/RestartingSearchSingleLink.java

@@ -234,8 +234,9 @@ private void initializeHeap() {
           final double d = pq.computeExactDistance();
           if(d == 0.) { // duplicate, merge immediately
             int cb = builder.get(b);
-            assert ca != cb;
-            ca = builder.add(ca, 0, cb);
+            if(ca != cb) {
+              ca = builder.add(ca, 0, cb);
+            }
             continue;
           }
           if(d < thresh) {