Merge pull request #2152 from jerneju/value-scatterplot

[FIX] Scatter Plot: dealing with scipy sparse matrix

Author: nikicc

Orange/widgets/visualize/owscatterplot.py

@@ -1,4 +1,5 @@
 import numpy as np
+import scipy.sparse as sp
 
 from AnyQt.QtCore import Qt, QTimer
 from AnyQt.QtGui import (
@@ -394,7 +395,8 @@ def set_subset_data(self, subset_data):
 
     # called when all signals are received, so the graph is updated only once
     def handleNewSignals(self):
-        self.graph.new_data(self.data_metas_X, self.subset_data)
+        self.graph.new_data(self.sparse_to_dense(self.data_metas_X),
+                            self.sparse_to_dense(self.subset_data))
         if self.attribute_selection_list and \
                 all(attr in self.graph.domain
                         for attr in self.attribute_selection_list):
@@ -407,6 +409,37 @@ def handleNewSignals(self):
         self.apply_selection()
         self.unconditional_commit()
 
+    def prepare_data(self):
+        """
+        Only when dealing with sparse matrices.
+        GH-2152
+        """
+        self.graph.new_data(self.sparse_to_dense(self.data_metas_X),
+                            self.sparse_to_dense(self.subset_data),
+                            new=False)
+
+    def sparse_to_dense(self, input_data=None):
+        self.vizrank_button.setEnabled(not (self.data and self.data.is_sparse()))
+        if input_data is None or not input_data.is_sparse():
+            return input_data
+        keys = []
+        attrs = {self.attr_x,
+                 self.attr_y,
+                 self.graph.attr_color,
+                 self.graph.attr_shape,
+                 self.graph.attr_size,
+                 self.graph.attr_label}
+        for i, attr in enumerate(input_data.domain):
+            if attr in attrs:
+                keys.append(i)
+        new_domain = input_data.domain.select_columns(keys)
+        dmx = Table.from_table(new_domain, input_data)
+        dmx.X = dmx.X.toarray()
+        # TODO: remove once we make sure Y is always dense.
+        if sp.issparse(dmx.Y):
+            dmx.Y = dmx.Y.toarray()
+        return dmx
+
     def apply_selection(self):
         """Apply selection saved in workflow."""
         if self.data is not None and self.selection is not None:
@@ -441,12 +474,14 @@ def set_attr(self, attr_x, attr_y):
         self.update_attr()
 
     def update_attr(self):
+        self.prepare_data()
         self.update_graph()
         self.cb_class_density.setEnabled(self.graph.can_draw_density())
         self.cb_reg_line.setEnabled(self.graph.can_draw_regresssion_line())
         self.send_features()
 
     def update_colors(self):
+        self.prepare_data()
         self.cb_class_density.setEnabled(self.graph.can_draw_density())
 
     def update_density(self):

Orange/widgets/visualize/owscatterplotgraph.py

@@ -591,17 +591,18 @@ def update_tooltip(self, modifiers):
         text = self.tiptexts.get(int(modifiers), self.tiptexts[0])
         self.tip_textitem.setHtml(text)
 
-    def new_data(self, data, subset_data=None, **args):
-        self.plot_widget.clear()
-        self.remove_legend()
+    def new_data(self, data, subset_data=None, new=True, **args):
+        if new:
+            self.plot_widget.clear()
+            self.remove_legend()
 
-        self.density_img = None
-        self.scatterplot_item = None
-        self.scatterplot_item_sel = None
-        self.reg_line_item = None
-        self.labels = []
-        self.selection = None
-        self.valid_data = None
+            self.density_img = None
+            self.scatterplot_item = None
+            self.scatterplot_item_sel = None
+            self.reg_line_item = None
+            self.labels = []
+            self.selection = None
+            self.valid_data = None
 
         self.subset_indices = set(e.id for e in subset_data) if subset_data else None
 
@@ -776,13 +777,15 @@ def compute_sizes(self):
         return size_data
 
     def update_sizes(self):
+        self.master.prepare_data()
+        self.update_point_size()
+
+    def update_point_size(self):
         if self.scatterplot_item:
             size_data = self.compute_sizes()
             self.scatterplot_item.setSize(size_data)
             self.scatterplot_item_sel.setSize(size_data + SELECTION_WIDTH)
 
-    update_point_size = update_sizes
-
     def get_color_index(self):
         if self.attr_color is None:
             return -1
@@ -907,6 +910,9 @@ def make_pen(color, width):
 
     def update_colors(self, keep_colors=False):
         self.master.update_colors()
+        self.update_alpha_value(keep_colors)
+
+    def update_alpha_value(self, keep_colors=False):
         if self.scatterplot_item:
             pen_data, brush_data = self.compute_colors(keep_colors)
             pen_data_sel, brush_data_sel = self.compute_colors_sel(keep_colors)
@@ -922,8 +928,6 @@ def update_colors(self, keep_colors=False):
                 elif self.density_img:
                     self.plot_widget.removeItem(self.density_img)
 
-    update_alpha_value = update_colors
-
     def create_labels(self):
         for x, y in zip(*self.scatterplot_item.getData()):
             ti = TextItem()
@@ -937,6 +941,7 @@ def update_labels(self):
             for label in self.labels:
                 label.setText("")
             return
+        self.assure_attribute_present(self.attr_label)
         if not self.labels:
             self.create_labels()
         label_column = self.data.get_column_view(self.attr_label)[0]
@@ -972,11 +977,16 @@ def compute_symbols(self):
         return shape_data
 
     def update_shapes(self):
+        self.assure_attribute_present(self.attr_shape)
         if self.scatterplot_item:
             shape_data = self.compute_symbols()
             self.scatterplot_item.setSymbol(shape_data)
         self.make_legend()
 
+    def assure_attribute_present(self, attr):
+        if attr not in self.data.domain:
+            self.master.prepare_data()
+
     def update_grid(self):
         self.plot_widget.showGrid(x=self.show_grid, y=self.show_grid)
 

Orange/widgets/visualize/tests/test_owscatterplot.py

@@ -2,6 +2,7 @@
 # pylint: disable=missing-docstring
 from unittest.mock import MagicMock
 import numpy as np
+import scipy.sparse as sp
 
 from AnyQt.QtCore import QRectF, Qt
 
@@ -268,6 +269,23 @@ def test_set_strings_settings(self):
         self.assertEqual(w.graph.attr_shape.name, "iris")
         self.assertEqual(w.graph.attr_size.name, "petal width")
 
+    def test_sparse(self):
+        """
+        Test sparse data.
+        GH-2152
+        GH-2157
+        """
+        table = Table("iris")
+        table.X = sp.csr_matrix(table.X)
+        self.assertTrue(sp.issparse(table.X))
+        table.Y = sp.csr_matrix(table._Y)  # pylint: disable=protected-access
+        self.assertTrue(sp.issparse(table.Y))
+        self.send_signal("Data", table)
+        self.widget.set_subset_data(table[:30])
+        data = self.get_output("Data")
+        self.assertTrue(data.is_sparse())
+        self.assertEqual(len(data.domain), 5)
+
 
 if __name__ == "__main__":
     import unittest