Run PCA in a separate thread

Orange/widgets/unsupervised/owpca.py

@@ -12,6 +12,7 @@
 from Orange.preprocess import preprocess
 from Orange.projection import PCA
 from Orange.widgets import widget, gui, settings
+from Orange.widgets.utils.concurrent import ConcurrentWidgetMixin
 from Orange.widgets.utils.slidergraph import SliderGraph
 from Orange.widgets.utils.widgetpreview import WidgetPreview
 from Orange.widgets.widget import Input, Output
@@ -21,7 +22,7 @@
 LINE_NAMES = ["component variance", "cumulative variance"]
 
 
-class OWPCA(widget.OWWidget):
+class OWPCA(widget.OWWidget, ConcurrentWidgetMixin):
     name = "PCA"
     description = "Principal component analysis with a scree-diagram."
     icon = "icons/PCA.svg"
@@ -57,8 +58,9 @@ class Error(widget.OWWidget.Error):
 
     def __init__(self):
         super().__init__()
-        self.data = None
+        ConcurrentWidgetMixin.__init__(self)
 
+        self.data = None
         self._pca = None
         self._transformed = None
         self._variance_ratio = None
@@ -113,6 +115,7 @@ def __init__(self):
 
     @Inputs.data
     def set_data(self, data):
+        self.cancel()
         self.clear_messages()
         self.clear()
         self.information()
@@ -141,6 +144,7 @@ def set_data(self, data):
         self.fit()
 
     def fit(self):
+        self.cancel()
         self.clear()
         self.Warning.trivial_components.clear()
         if self.data is None:
@@ -151,20 +155,34 @@ def fit(self):
         projector = self._create_projector()
 
         if not isinstance(data, SqlTable):
-            pca = projector(data)
-            variance_ratio = pca.explained_variance_ratio_
-            cumulative = numpy.cumsum(variance_ratio)
-
-            if numpy.isfinite(cumulative[-1]):
-                self.components_spin.setRange(0, len(cumulative))
-                self._pca = pca
-                self._variance_ratio = variance_ratio
-                self._cumulative = cumulative
-                self._setup_plot()
-            else:
-                self.Warning.trivial_components()
+            self.start(self._call_projector, data, projector)
+
+    @staticmethod
+    def _call_projector(data: Table, projector, _):
+        return projector(data)
+
+    def on_done(self, result):
+        pca = result
+        variance_ratio = pca.explained_variance_ratio_
+        cumulative = numpy.cumsum(variance_ratio)
+
+        if numpy.isfinite(cumulative[-1]):
+            self.components_spin.setRange(0, len(cumulative))
+            self._pca = pca
+            self._variance_ratio = variance_ratio
+            self._cumulative = cumulative
+            self._setup_plot()
+        else:
+            self.Warning.trivial_components()
+
+        self.commit.now()
+
+    def on_partial_result(self, result):
+        pass
 
-            self.commit.now()
+    def onDeleteWidget(self):
+        self.shutdown()
+        super().onDeleteWidget()
 
     def clear(self):
         self._pca = None

Orange/widgets/unsupervised/tests/test_owpca.py

@@ -32,7 +32,7 @@ def test_constant_data(self):
         # Ignore the warning: the test checks whether the widget shows
         # Warning.trivial_components when this happens
         with np.errstate(invalid="ignore"):
-            self.send_signal(self.widget.Inputs.data, data)
+            self.send_signal(self.widget.Inputs.data, data, wait=5000)
         self.assertTrue(self.widget.Warning.trivial_components.is_shown())
         self.assertIsNone(self.get_output(self.widget.Outputs.transformed_data))
         self.assertIsNone(self.get_output(self.widget.Outputs.components))
@@ -55,12 +55,12 @@ def test_limit_components(self):
         X = np.random.RandomState(0).rand(101, 101)
         data = Table.from_numpy(None, X)
         self.widget.ncomponents = 100
-        self.send_signal(self.widget.Inputs.data, data)
+        self.send_signal(self.widget.Inputs.data, data, wait=5000)
         tran = self.get_output(self.widget.Outputs.transformed_data)
         self.assertEqual(len(tran.domain.attributes), 100)
         self.widget.ncomponents = 101  # should not be accesible
         with self.assertRaises(IndexError):
-            self.send_signal(self.widget.Inputs.data, data)
+            self.widget._setup_plot()  # pylint: disable=protected-access
 
     def test_migrate_settings_limits_components(self):
         settings = dict(ncomponents=10)
@@ -83,9 +83,11 @@ def test_variance_shown(self):
         self.send_signal(self.widget.Inputs.data, self.iris)
         self.widget.maxp = 2
         self.widget._setup_plot()
+        self.wait_until_finished()
         var2 = self.widget.variance_covered
         self.widget.ncomponents = 3
         self.widget._update_selection_component_spin()
+        self.wait_until_finished()
         var3 = self.widget.variance_covered
         self.assertGreater(var3, var2)
 
@@ -97,10 +99,11 @@ def test_unique_domain_components(self):
 
     def test_variance_attr(self):
         self.widget.ncomponents = 2
-        self.send_signal(self.widget.Inputs.data, self.iris)
+        self.send_signal(self.widget.Inputs.data, self.iris, wait=5000)
         self.wait_until_stop_blocking()
         self.widget._variance_ratio = np.array([0.5, 0.25, 0.2, 0.05])
         self.widget.commit.now()
+        self.wait_until_finished()
 
         result = self.get_output(self.widget.Outputs.transformed_data)
         pc1, pc2 = result.domain.attributes
@@ -162,7 +165,7 @@ def test_normalize_data(self, prepare_table):
         self.widget.controls.normalize.setChecked(True)
         self.assertTrue(self.widget.controls.normalize.isChecked())
         with patch.object(preprocess.Normalize, "__call__", wraps=lambda x: x) as normalize:
-            self.send_signal(self.widget.Inputs.data, data)
+            self.send_signal(self.widget.Inputs.data, data, wait=5000)
             self.wait_until_stop_blocking()
             self.assertTrue(self.widget.controls.normalize.isEnabled())
             normalize.assert_called_once()
@@ -171,7 +174,7 @@ def test_normalize_data(self, prepare_table):
         self.widget.controls.normalize.setChecked(False)
         self.assertFalse(self.widget.controls.normalize.isChecked())
         with patch.object(preprocess.Normalize, "__call__", wraps=lambda x: x) as normalize:
-            self.send_signal(self.widget.Inputs.data, data)
+            self.send_signal(self.widget.Inputs.data, data, wait=5000)
             self.wait_until_stop_blocking()
             self.assertTrue(self.widget.controls.normalize.isEnabled())
             normalize.assert_not_called()
@@ -184,13 +187,14 @@ def test_normalization_variance(self, prepare_table):
         # Enable normalization
         self.widget.controls.normalize.setChecked(True)
         self.assertTrue(self.widget.normalize)
-        self.send_signal(self.widget.Inputs.data, data)
+        self.send_signal(self.widget.Inputs.data, data, wait=5000)
         self.wait_until_stop_blocking()
         variance_normalized = self.widget.variance_covered
 
         # Disable normalization
         self.widget.controls.normalize.setChecked(False)
         self.assertFalse(self.widget.normalize)
+        self.wait_until_finished()
         self.wait_until_stop_blocking()
         variance_unnormalized = self.widget.variance_covered