Fix prediction data not honoring cluster_selection_epsilon

hdbscan/_hdbscan_tree.pyx

@@ -705,6 +705,9 @@ cpdef tuple get_clusters(np.ndarray tree, dict stability,
 
     stabilities : ndarray (n_clusters,)
         The cluster coherence strengths of each cluster.
+    
+    selected clusters : ndarray (n_clusters,)
+        The ids of the selected clusters
     """
     cdef list node_list
     cdef np.ndarray cluster_tree
@@ -803,4 +806,4 @@ cpdef tuple get_clusters(np.ndarray tree, dict stability,
     probs = get_probabilities(tree, reverse_cluster_map, labels)
     stabilities = get_stability_scores(labels, clusters, stability, max_lambda)
 
-    return (labels, probs, stabilities)
+    return (labels, probs, stabilities, np.array(sorted(clusters)))

hdbscan/flat.py

@@ -184,7 +184,8 @@ def HDBSCAN_flat(X, n_clusters=None,
      new_clusterer.probabilities_,
      new_clusterer.cluster_persistence_,
      new_clusterer._condensed_tree,
-     new_clusterer._single_linkage_tree) = output
+     new_clusterer._single_linkage_tree,
+     new_clusterer._selected_clusters) = output
 
     # PredictionData attached to HDBSCAN should also change.
     # A function re_init is defined in this module to handle this.

hdbscan/hdbscan_.py

@@ -62,7 +62,7 @@ def _tree_to_labels(
     """
     condensed_tree = condense_tree(single_linkage_tree, min_cluster_size)
     stability_dict = compute_stability(condensed_tree)
-    labels, probabilities, stabilities = get_clusters(
+    labels, probabilities, stabilities, selected_clusters = get_clusters(
         condensed_tree,
         stability_dict,
         cluster_selection_method,
@@ -72,7 +72,8 @@ def _tree_to_labels(
         max_cluster_size,
     )
 
-    return (labels, probabilities, stabilities, condensed_tree, single_linkage_tree)
+    return (labels, probabilities, stabilities, condensed_tree, single_linkage_tree,
+            selected_clusters)
 
 
 def _hdbscan_generic(
@@ -1130,6 +1131,7 @@ def __init__(
         self._outlier_scores = None
         self._prediction_data = None
         self._relative_validity = None
+        self._selected_clusters = None
 
     def fit(self, X, y=None):
         """Perform HDBSCAN clustering from features or distance matrix.
@@ -1186,6 +1188,7 @@ def fit(self, X, y=None):
             self.cluster_persistence_,
             self._condensed_tree,
             self._single_linkage_tree,
+            self._selected_clusters,
             self._min_spanning_tree,
         ) = hdbscan(clean_data, **kwargs)
 
@@ -1248,6 +1251,7 @@ def generate_prediction_data(self):
             self._prediction_data = PredictionData(
                 self._raw_data,
                 self.condensed_tree_,
+                self._selected_clusters,
                 min_samples,
                 tree_type=tree_type,
                 metric=self.metric,

hdbscan/prediction.py

@@ -95,15 +95,14 @@ def _recurse_leaf_dfs(self, current_node):
             return sum(
                 [recurse_leaf_dfs(self.cluster_tree, child) for child in children], [])
 
-    def __init__(self, data, condensed_tree, min_samples,
+    def __init__(self, data, condensed_tree, selected_clusters, min_samples,
                  tree_type='kdtree', metric='euclidean', **kwargs):
         self.raw_data = data.astype(np.float64)
         self.tree = self._tree_type_map[tree_type](self.raw_data,
                                                    metric=metric, **kwargs)
         self.core_distances = self.tree.query(data, k=min_samples)[0][:, -1]
         self.dist_metric = DistanceMetric.get_metric(metric, **kwargs)
 
-        selected_clusters = sorted(condensed_tree._select_clusters())
         # raw_condensed_tree = condensed_tree.to_numpy()
         raw_condensed_tree = condensed_tree._raw_tree
 

hdbscan/tests/test_hdbscan.py

@@ -144,7 +144,7 @@ def test_hdbscan_distance_matrix():
     D = distance.squareform(distance.pdist(X))
     D /= np.max(D)
 
-    labels, p, persist, ctree, ltree, mtree = hdbscan(D, metric="precomputed")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(D, metric="precomputed")
     # number of clusters, ignoring noise if present
     n_clusters_1 = len(set(labels)) - int(-1 in labels)  # ignore noise
     assert n_clusters_1 == n_clusters
@@ -167,7 +167,7 @@ def test_hdbscan_sparse_distance_matrix():
     D = sparse.csr_matrix(D)
     D.eliminate_zeros()
 
-    labels, p, persist, ctree, ltree, mtree = hdbscan(D, metric="precomputed")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(D, metric="precomputed")
     # number of clusters, ignoring noise if present
     n_clusters_1 = len(set(labels)) - int(-1 in labels)  # ignore noise
     assert n_clusters_1 == n_clusters
@@ -178,7 +178,7 @@ def test_hdbscan_sparse_distance_matrix():
 
 
 def test_hdbscan_feature_vector():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X)
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(X)
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -191,7 +191,9 @@ def test_hdbscan_feature_vector():
 
 
 def test_hdbscan_prims_kdtree():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, algorithm="prims_kdtree")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        X, algorithm="prims_kdtree"
+    )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -203,7 +205,9 @@ def test_hdbscan_prims_kdtree():
 
 
 def test_hdbscan_prims_balltree():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, algorithm="prims_balltree")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        X, algorithm="prims_balltree"
+    )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -215,7 +219,9 @@ def test_hdbscan_prims_balltree():
 
 
 def test_hdbscan_boruvka_kdtree():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, algorithm="boruvka_kdtree")
+    labels, p, persist, ctree, ltree, selclstrs, mtree, = hdbscan(
+        X, algorithm="boruvka_kdtree"
+    )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -229,7 +235,9 @@ def test_hdbscan_boruvka_kdtree():
 
 
 def test_hdbscan_boruvka_balltree():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, algorithm="boruvka_balltree")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        X, algorithm="boruvka_balltree"
+    )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -243,7 +251,7 @@ def test_hdbscan_boruvka_balltree():
 
 
 def test_hdbscan_generic():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, algorithm="generic")
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(X, algorithm="generic")
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -261,7 +269,7 @@ def test_hdbscan_high_dimensional():
     H, y = make_blobs(n_samples=50, random_state=0, n_features=64)
     # H, y = shuffle(X, y, random_state=7)
     H = StandardScaler().fit_transform(H)
-    labels, p, persist, ctree, ltree, mtree = hdbscan(H)
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(H)
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -275,7 +283,7 @@ def test_hdbscan_high_dimensional():
 
 
 def test_hdbscan_best_balltree_metric():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
         X, metric="seuclidean", V=np.ones(X.shape[1])
     )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
@@ -287,7 +295,9 @@ def test_hdbscan_best_balltree_metric():
 
 
 def test_hdbscan_no_clusters():
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, min_cluster_size=len(X) + 1)
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        X, min_cluster_size=len(X) + 1
+    )
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == 0
 
@@ -298,7 +308,7 @@ def test_hdbscan_no_clusters():
 
 def test_hdbscan_min_cluster_size():
     for min_cluster_size in range(2, len(X) + 1, 1):
-        labels, p, persist, ctree, ltree, mtree = hdbscan(
+        labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
             X, min_cluster_size=min_cluster_size
         )
         true_labels = [label for label in labels if label != -1]
@@ -315,7 +325,7 @@ def test_hdbscan_callable_metric():
     # metric is the function reference, not the string key.
     metric = distance.euclidean
 
-    labels, p, persist, ctree, ltree, mtree = hdbscan(X, metric=metric)
+    labels, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(X, metric=metric)
     n_clusters_1 = len(set(labels)) - int(-1 in labels)
     assert n_clusters_1 == n_clusters
 
@@ -333,8 +343,10 @@ def test_hdbscan_boruvka_kdtree_matches():
 
     data = generate_noisy_data()
 
-    labels_prims, p, persist, ctree, ltree, mtree = hdbscan(data, algorithm="generic")
-    labels_boruvka, p, persist, ctree, ltree, mtree = hdbscan(
+    labels_prims, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        data, algorithm="generic"
+    )
+    labels_boruvka, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
         data, algorithm="boruvka_kdtree"
     )
 
@@ -354,8 +366,10 @@ def test_hdbscan_boruvka_balltree_matches():
 
     data = generate_noisy_data()
 
-    labels_prims, p, persist, ctree, ltree, mtree = hdbscan(data, algorithm="generic")
-    labels_boruvka, p, persist, ctree, ltree, mtree = hdbscan(
+    labels_prims, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
+        data, algorithm="generic"
+    )
+    labels_boruvka, p, persist, ctree, ltree, selclstrs, mtree = hdbscan(
         data, algorithm="boruvka_balltree"
     )