MDS: Show Kruskal stress

Author: janezd

Orange/widgets/unsupervised/owmds.py

@@ -200,6 +200,7 @@ def __init__(self):
 
         self.embedding = None  # type: Optional[np.ndarray]
         self.effective_matrix = None  # type: Optional[DistMatrix]
+        self.stress = None
 
         self.size_model = self.gui.points_models[2]
         self.size_model.order = \
@@ -241,6 +242,8 @@ def _add_controls_optimization(self):
                 sizePolicy=(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed),
                 callback=self.__refresh_rate_combo_changed),
             1, 1)
+        self.stress_label = QLabel("Kruskal Stress: -")
+        grid.addWidget(self.stress_label, 2, 0, 1, 3)
 
     def __refresh_rate_combo_changed(self):
         if self.task is not None:
@@ -392,17 +395,32 @@ def on_partial_result(self, result: Result):
             if need_update:
                 self.graph.update_coordinates()
                 self.graph.update_density()
+                self.update_stress()
 
     def on_done(self, result: Result):
         assert isinstance(result.embedding, np.ndarray)
         assert len(result.embedding) == len(self.effective_matrix)
         self.embedding = result.embedding
         self.graph.update_coordinates()
         self.graph.update_density()
+        self.update_stress()
         self.run_button.setText("Start")
         self.step_button.setEnabled(True)
         self.commit.deferred()
 
+    def update_stress(self):
+        self.stress = self._compute_stress()
+        stress_val = "-" if self.stress is None else f"{self.stress:.3f}"
+        self.stress_label.setText(f"Kruskal Stress: {stress_val}")
+
+    def _compute_stress(self):
+        if self.embedding is None or self.effective_matrix is None:
+            return None
+        actual = scipy.spatial.distance.pdist(self.embedding)
+        actual = scipy.spatial.distance.squareform(actual)
+        return np.sqrt(np.sum((actual - self.effective_matrix) ** 2)
+                       / (np.sum(self.effective_matrix ** 2) or 1))
+
     def on_exception(self, ex: Exception):
         if isinstance(ex, MemoryError):
             self.Error.out_of_memory()
@@ -436,6 +454,7 @@ def jitter_coord(part):
         # (Random or PCA), restarting the optimization if necessary.
         if self.effective_matrix is None:
             self.graph.reset_graph()
+            self.update_stress()
             return
 
         X = self.effective_matrix
@@ -451,6 +470,8 @@ def jitter_coord(part):
         # restart the optimization if it was interrupted.
         if self.task is not None:
             self._run()
+        else:
+            self.update_stress()
 
     def handleNewSignals(self):
         self._initialize()
@@ -473,12 +494,12 @@ def setup_plot(self):
 
     def get_size_data(self):
         if self.attr_size == "Stress":
-            return self.stress(self.embedding, self.effective_matrix)
+            return self.get_stress(self.embedding, self.effective_matrix)
         else:
             return super().get_size_data()
 
     @staticmethod
-    def stress(X, distD):
+    def get_stress(X, distD):
         assert X.shape[0] == distD.shape[0] == distD.shape[1]
         D1_c = scipy.spatial.distance.pdist(X, metric="euclidean")
         D1 = scipy.spatial.distance.squareform(D1_c, checks=False)

Orange/widgets/unsupervised/tests/test_owmds.py

@@ -1,5 +1,5 @@
 # Test methods with long descriptive names can omit docstrings
-# pylint: disable=missing-docstring
+# pylint: disable=missing-docstring,protected-access
 import os
 from itertools import chain
 import unittest
@@ -320,6 +320,25 @@ def test_matrix_columns_default_label(self):
         label_text = self.widget.controls.attr_label.currentText()
         self.assertEqual(label_text, "labels")
 
+    def test_update_stress(self):
+        w = self.widget
+        w.effective_matrix = np.array([[0, 4, 1],
+                                       [4, 0, 1],
+                                       [1, 1, 0]])  # sum of squares is 36
+        w.embedding = [[0, 0],                       [0, 3],
+                       [4, 3]]
+        # dists [[0, 3, 5], diff [[0, 1, 4],  sqr  [[0, 1, 16],  sum = 52
+        #        [3, 0, 4],       [1, 0, 3],        [1, 0, 9],
+        #        [5, 4, 0]]       [4, 3, 0]]        [16, 9, 0]]
+        w.update_stress()
+        expected = np.sqrt(52 / 36)
+        self.assertAlmostEqual(w._compute_stress(), expected)
+        self.assertIn(f"{expected:.3f}", w.stress_label.text())
+
+        w.embedding = None
+        w.update_stress()
+        self.assertIsNone(w._compute_stress())
+        self.assertIn("-", w.stress_label.text())
 
 class TestOWMDSRunner(unittest.TestCase):
     @classmethod