Merge pull request #1391 from kernc/fixups

Fixups

Author: astaric

.coveragerc

@@ -11,3 +11,4 @@ exclude_lines =
     pragma: no cover
     raise NotImplementedError
     if __name__ == .__main__.:
+    except MemoryError

Orange/clustering/kmeans.py

@@ -14,17 +14,21 @@ class KMeans(SklProjector):
     __wraps__ = skl_cluster.KMeans
 
     def __init__(self, n_clusters=8, init='k-means++', n_init=10, max_iter=300,
-                 tol=0.0001, random_state=None, preprocessors=None):
+                 tol=0.0001, random_state=None, preprocessors=None,
+                 compute_silhouette_score=False):
         super().__init__(preprocessors=preprocessors)
         self.params = vars()
+        self._compute_silhouette = compute_silhouette_score
 
     def fit(self, X, Y=None):
         proj = skl_cluster.KMeans(**self.params)
         proj = proj.fit(X, Y)
-        if 2 <= proj.n_clusters < X.shape[0]:
-            proj.silhouette = silhouette_score(X, proj.labels_)
-        else:
-            proj.silhouette = 0
+        proj.silhouette = np.nan
+        try:
+            if self._compute_silhouette and 2 <= proj.n_clusters < X.shape[0]:
+                proj.silhouette = silhouette_score(X, proj.labels_)
+        except MemoryError:  # Pairwise dist in silhouette fails for large data
+            pass
         proj.inertia = proj.inertia_ / X.shape[0]
         cluster_dist = Euclidean(proj.cluster_centers_)
         proj.inter_cluster = np.mean(cluster_dist[np.triu_indices_from(cluster_dist, 1)])

Orange/tests/test_clustering_kmeans.py

@@ -25,7 +25,8 @@ def test_kmeans_parameters(self):
                         max_iter=10,
                         random_state=42,
                         tol=0.001,
-                        init='random')
+                        init='random',
+                        compute_silhouette_score=True)
         c = kmeans(self.iris)
 
     def test_predict_single_instance(self):

Orange/widgets/unsupervised/owkmeans.py

@@ -218,7 +218,8 @@ def run_optimization(self):
             k_to = min(self.k_to, len(self.data))
             kmeans = KMeans(
                 init=['random', 'k-means++'][self.smart_init],
-                n_init=self.n_init, max_iter=self.max_iterations)
+                n_init=self.n_init, max_iter=self.max_iterations,
+                compute_silhouette_score=self.scoring == self.SILHOUETTE)
             with self.progressBar(k_to - self.k_from + 1) as progress:
                 for k in range(self.k_from, k_to + 1):
                     progress.advance()
@@ -264,7 +265,7 @@ def show_results(self):
         best_run = scores.index(best_score)
         score_span = (best_score - worst_score) or 1
         max_score = max(scores)
-        nplaces = min(5, int(abs(math.log(max(max_score, 1e-10)))) + 2)
+        nplaces = min(5, np.floor(abs(math.log(max(max_score, 1e-10)))) + 2)
         fmt = "{{:.{}f}}".format(nplaces)
         model = self.table_model
         model.setRowCount(len(k_scores))
@@ -278,7 +279,8 @@ def show_results(self):
             item = model.item(i, 1)
             if item is None:
                 item = QStandardItem()
-            item.setData(fmt.format(score), Qt.DisplayRole)
+            item.setData(fmt.format(score) if not np.isnan(score) else 'out-of-memory error',
+                         Qt.DisplayRole)
             bar_ratio = 0.95 * (score - worst_score) / score_span
             item.setData(bar_ratio, gui.TableBarItem.BarRole)
             model.setItem(i, 1, item)

Orange/widgets/widget.py

@@ -614,7 +614,7 @@ def progressBarSet(self, value, processEvents=QEventLoop.AllEvents):
                 text = "{}:{:02}:{:02}".format(hrs, mins, secs)
             else:
                 text = "{}:{}:{:02}".format(hrs, mins, secs)
-            self.setWindowTitle("{} ({:.2f}% complete, remaining time: {})"
+            self.setWindowTitle("{} ({:d}%, ETA: {})"
                                 .format(self.captionTitle, value, text))
         else:
             self.setWindowTitle(self.captionTitle + " (0% complete)")