[FIX] Hierarchical Clustering: infinite distances

Author: jerneju

Orange/widgets/unsupervised/owhierarchicalclustering.py

@@ -34,7 +34,7 @@
 from Orange.widgets.utils import colorpalette, itemmodels
 from Orange.widgets.utils.annotated_data import (create_annotated_table,
                                                  ANNOTATED_DATA_SIGNAL_NAME)
-from Orange.widgets.widget import Input, Output
+from Orange.widgets.widget import Input, Output, Msg
 
 __all__ = ["OWHierarchicalClustering"]
 
@@ -763,6 +763,9 @@ class Outputs:
     cluster_roles = ["Attribute", "Class variable", "Meta variable"]
     basic_annotations = ["None", "Enumeration"]
 
+    class Error(widget.OWWidget.Error):
+        not_finite_distances = Msg("Some distances are infinite")
+
     def __init__(self):
         super().__init__()
 
@@ -962,11 +965,16 @@ def axis_view(orientation):
     @Inputs.distances
     def set_distances(self, matrix):
         self.error()
+        self.Error.clear()
         if matrix is not None:
             N, _ = matrix.shape
             if N < 2:
                 self.error("Empty distance matrix")
                 matrix = None
+        if matrix is not None:
+            if not np.all(np.isfinite(matrix)):
+                self.Error.not_finite_distances()
+                matrix = None
 
         self.matrix = matrix
         if matrix is not None:

Orange/widgets/unsupervised/tests/test_owhierarchicalclustering.py

@@ -2,6 +2,7 @@
 # pylint: disable=missing-docstring
 import numpy as np
 import Orange.misc
+from Orange.data import Table, Domain, ContinuousVariable, DiscreteVariable
 from Orange.distance import Euclidean
 from Orange.widgets.tests.base import WidgetTest, WidgetOutputsTestMixin
 from Orange.widgets.unsupervised.owhierarchicalclustering import \
@@ -102,3 +103,23 @@ def test_domain_loses_class(self):
         data = self.data[:, :4]
         distances = Euclidean(data)
         self.send_signal(self.widget.Inputs.distances, distances)
+
+    def test_infinite_distances(self):
+        """
+        Scipy does not accept infinite distances and neither does this widget.
+        Error is shown.
+        GH-2380
+        """
+        table = Table(
+            Domain(
+                [ContinuousVariable("a")],
+                [DiscreteVariable("b", values=["y"])]),
+            list(zip([1.79e308, -1e120],
+                     "yy"))
+        )
+        distances = Euclidean(table)
+        self.assertFalse(self.widget.Error.not_finite_distances.is_shown())
+        self.send_signal(self.widget.Inputs.distances, distances)
+        self.assertTrue(self.widget.Error.not_finite_distances.is_shown())
+        self.send_signal(self.widget.Inputs.distances, self.distances)
+        self.assertFalse(self.widget.Error.not_finite_distances.is_shown())