Merge pull request #6536 from PrimozGodec/fix-pca

[FIX] PCA - Output instance of table subclass when instance of table subclass on input

Author: markotoplak

Orange/widgets/unsupervised/owpca.py

@@ -5,13 +5,15 @@
 from AnyQt.QtCore import Qt
 
 from orangewidget.report import bool_str
+from orangewidget.settings import Setting
 
 from Orange.data import Table, Domain, StringVariable, ContinuousVariable
 from Orange.data.util import get_unique_names
 from Orange.data.sql.table import SqlTable, AUTO_DL_LIMIT
 from Orange.preprocess import preprocess
 from Orange.projection import PCA
-from Orange.widgets import widget, gui, settings
+from Orange.widgets import widget, gui
+from Orange.widgets.utils.annotated_data import add_columns
 from Orange.widgets.utils.concurrent import ConcurrentWidgetMixin
 from Orange.widgets.utils.slidergraph import SliderGraph
 from Orange.widgets.utils.widgetpreview import WidgetPreview
@@ -38,12 +40,12 @@ class Outputs:
         components = Output("Components", Table)
         pca = Output("PCA", PCA, dynamic=False)
 
-    ncomponents = settings.Setting(2)
-    variance_covered = settings.Setting(100)
-    auto_commit = settings.Setting(True)
-    normalize = settings.Setting(True)
-    maxp = settings.Setting(20)
-    axis_labels = settings.Setting(10)
+    ncomponents = Setting(2)
+    variance_covered = Setting(100)
+    auto_commit = Setting(True)
+    normalize = Setting(True)
+    maxp = Setting(20)
+    axis_labels = Setting(10)
 
     graph_name = "plot.plotItem"  # QGraphicsView (pg.PlotWidget -> SliderGraph)
 
@@ -222,8 +224,7 @@ def _setup_plot(self):
         self._update_axis()
 
     def _on_cut_changed(self, components):
-        if components == self.ncomponents \
-                or self.ncomponents == 0:
+        if self.ncomponents in (components, 0):
             return
 
         self.ncomponents = components
@@ -333,9 +334,9 @@ def commit(self):
             proposed = [a.name for a in self._pca.orig_domain.attributes]
             meta_name = get_unique_names(proposed, 'components')
             meta_vars = [StringVariable(name=meta_name)]
-            metas = numpy.array([['PC{}'.format(i + 1)
-                                  for i in range(self.ncomponents)]],
-                                dtype=object).T
+            metas = numpy.array(
+                [[f"PC{i + 1}"for i in range(self.ncomponents)]], dtype=object
+            ).T
             if self._variance_ratio is not None:
                 variance_name = get_unique_names(proposed, "variance")
                 meta_vars.append(ContinuousVariable(variance_name))
@@ -351,14 +352,8 @@ def commit(self):
                                metas=metas)
             components.name = 'components'
 
-            data_dom = Domain(
-                self.data.domain.attributes,
-                self.data.domain.class_vars,
-                self.data.domain.metas + domain.attributes)
-            data = Table.from_numpy(
-                data_dom, self.data.X, self.data.Y,
-                numpy.hstack((self.data.metas, transformed.X)),
-                ids=self.data.ids)
+            data_dom = add_columns(self.data.domain, metas=domain.attributes)
+            data = self.data.transform(data_dom)
 
         self.Outputs.transformed_data.send(transformed)
         self.Outputs.components.send(components)
@@ -371,7 +366,7 @@ def send_report(self):
         self.report_items((
             ("Normalize data", bool_str(self.normalize)),
             ("Selected components", self.ncomponents),
-            ("Explained variance", "{:.3f} %".format(self.variance_covered))
+            ("Explained variance", f"{self.variance_covered:.3f} %")
         ))
         self.report_plot()
 

Orange/widgets/unsupervised/tests/test_owpca.py

@@ -4,15 +4,15 @@
 from unittest.mock import patch, Mock
 
 import numpy as np
+from sklearn.utils import check_random_state
+from sklearn.utils.extmath import svd_flip
 
 from Orange.data import Table, Domain, ContinuousVariable, TimeVariable
 from Orange.preprocess import preprocess
 from Orange.widgets.tests.base import WidgetTest
 from Orange.widgets.tests.utils import table_dense_sparse, possible_duplicate_table
 from Orange.widgets.unsupervised.owpca import OWPCA
 from Orange.tests import test_filename
-from sklearn.utils import check_random_state
-from sklearn.utils.extmath import svd_flip
 
 
 class TestOWPCA(WidgetTest):
@@ -63,19 +63,19 @@ def test_limit_components(self):
             self.widget._setup_plot()  # pylint: disable=protected-access
 
     def test_migrate_settings_limits_components(self):
-        settings = dict(ncomponents=10)
+        settings = {"ncomponents": 10}
         OWPCA.migrate_settings(settings, 0)
         self.assertEqual(settings['ncomponents'], 10)
-        settings = dict(ncomponents=101)
+        settings = {"ncomponents": 101}
         OWPCA.migrate_settings(settings, 0)
         self.assertEqual(settings['ncomponents'], 100)
 
     def test_migrate_settings_changes_variance_covered_to_int(self):
-        settings = dict(variance_covered=17.5)
+        settings = {"variance_covered": 17.5}
         OWPCA.migrate_settings(settings, 0)
         self.assertEqual(settings["variance_covered"], 17)
 
-        settings = dict(variance_covered=float('nan'))
+        settings = {"variance_covered": float('nan')}
         OWPCA.migrate_settings(settings, 0)
         self.assertEqual(settings["variance_covered"], 100)
 
@@ -277,6 +277,21 @@ def test_output_data(self):
         output = self.get_output(widget.Outputs.data)
         self.assertIsNone(output)
 
+    def test_table_subclass(self):
+        """
+        When input table is instance of Table's subclass (e.g. Corpus) resulting
+        tables should also be an instance subclasses
+        """
+        class TableSub(Table):  # pylint: disable=abstract-method
+            pass
+
+        table_subclass = TableSub(self.iris)
+        self.send_signal(self.widget.Inputs.data, table_subclass)
+        data_out = self.get_output(self.widget.Outputs.data)
+        trans_data_out = self.get_output(self.widget.Outputs.transformed_data)
+        self.assertIsInstance(data_out, TableSub)
+        self.assertIsInstance(trans_data_out, TableSub)
+
 
 if __name__ == "__main__":
     unittest.main()