OWPCA: Output ApplyDomain preprocessor

Author: VesnaT

Orange/preprocess/preprocess.py

@@ -488,6 +488,21 @@ def transform(var):
         return data.transform(domain)
 
 
+class ApplyDomain(Preprocess):
+    def __init__(self, domain, name, max_components=None):
+        self._domain = domain
+        self._name = name
+        self._max_components = max_components
+
+    def __call__(self, data):
+        transformed = data.transform(self._domain)
+        return transformed[:, :self._max_components] \
+            if self._max_components is not None else transformed
+
+    def __str__(self):
+        return self._name
+
+
 class PreprocessorList(Preprocess):
     """
     Store a list of preprocessors and on call apply them to the dataset.

Orange/widgets/data/tests/test_owtransform.py

@@ -2,8 +2,10 @@
 # pylint: disable=missing-docstring
 from Orange.data import Table
 from Orange.preprocess import Discretize
+from Orange.preprocess.preprocess import Preprocess
 from Orange.widgets.data.owtransform import OWTransform
 from Orange.widgets.tests.base import WidgetTest
+from Orange.widgets.unsupervised.owpca import OWPCA
 
 
 class TestOWTransform(WidgetTest):
@@ -61,6 +63,19 @@ def test_output(self):
                          self.widget.preprocessor_label.text())
         self.assertEqual("", self.widget.output_label.text())
 
+    def test_input_pca_preprocessor(self):
+        owpca = self.create_widget(OWPCA)
+        self.send_signal(owpca.Inputs.data, self.data, widget=owpca)
+        owpca.components_spin.setValue(2)
+        pp = self.get_output(owpca.Outputs.preprocessor, widget=owpca)
+        self.assertIsNotNone(pp, Preprocess)
+
+        self.send_signal(self.widget.Inputs.data, self.data)
+        self.send_signal(self.widget.Inputs.preprocessor, pp)
+        output = self.get_output(self.widget.Outputs.transformed_data)
+        self.assertIsInstance(output, Table)
+        self.assertEqual(output.X.shape, (len(self.data), 2))
+
     def test_send_report(self):
         self.send_signal(self.widget.Inputs.data, self.data)
         self.widget.report_button.click()

Orange/widgets/unsupervised/owpca.py

@@ -10,6 +10,7 @@
 from Orange.data import Table, Domain, StringVariable, ContinuousVariable
 from Orange.data.sql.table import SqlTable, AUTO_DL_LIMIT
 from Orange.preprocess import Normalize
+from Orange.preprocess.preprocess import Preprocess, ApplyDomain
 from Orange.projection import PCA, TruncatedSVD
 from Orange.widgets import widget, gui, settings
 from Orange.widgets.widget import Input, Output
@@ -44,6 +45,7 @@ class Outputs:
         transformed_data = Output("Transformed data", Table)
         components = Output("Components", Table)
         pca = Output("PCA", PCA, dynamic=False)
+        preprocessor = Output("Preprocessor", Preprocess)
 
     settingsHandler = settings.DomainContextHandler()
 
@@ -290,6 +292,7 @@ def clear_outputs(self):
         self.Outputs.transformed_data.send(None)
         self.Outputs.components.send(None)
         self.Outputs.pca.send(self._pca_projector)
+        self.Outputs.preprocessor.send(None)
 
     def get_model(self):
         if self.rpca is None:
@@ -455,7 +458,7 @@ def _update_axis(self):
         axis.setTicks([[(i, str(i+1)) for i in range(0, p, d)]])
 
     def commit(self):
-        transformed = components = None
+        transformed = components = pp = None
         if self._pca is not None:
             if self._transformed is None:
                 # Compute the full transform (MAX_COMPONENTS components) only once.
@@ -479,10 +482,14 @@ def commit(self):
                                metas=metas)
             components.name = 'components'
 
+            domain = self._pca_projector(self.data).domain
+            pp = ApplyDomain(domain, "PCA", self.ncomponents)
+
         self._pca_projector.component = self.ncomponents
         self.Outputs.transformed_data.send(transformed)
         self.Outputs.components.send(components)
         self.Outputs.pca.send(self._pca_projector)
+        self.Outputs.preprocessor.send(pp)
 
     def send_report(self):
         if self.data is None:

Orange/widgets/unsupervised/tests/test_owpca.py

@@ -4,6 +4,7 @@
 import scipy.sparse as sp
 
 from Orange.data import Table, Domain, ContinuousVariable, TimeVariable
+from Orange.preprocess.preprocess import Preprocess
 from Orange.widgets.tests.base import WidgetTest
 from Orange.widgets.unsupervised.owpca import OWPCA, DECOMPOSITIONS
 
@@ -131,3 +132,16 @@ def test_do_not_mask_features(self):
         self.widget.set_data(data)
         ndata = Table("iris.tab")
         self.assertEqual(data.domain[0], ndata.domain[0])
+
+    def test_output_preprocessor(self):
+        data = Table("iris")
+        self.send_signal(self.widget.Inputs.data, data)
+        pp = self.get_output(self.widget.Outputs.preprocessor)
+        self.assertIsInstance(pp, Preprocess)
+        transformed_data = pp(data[::10])
+        self.assertIsInstance(transformed_data, Table)
+        self.assertEqual(transformed_data.X.shape, (15, 2))
+        output = self.get_output(self.widget.Outputs.transformed_data)
+        np.testing.assert_array_equal(transformed_data.X, output.X[::10])
+        self.assertEqual([a.name for a in transformed_data.domain.attributes],
+                         [m.name for m in output.domain.attributes])