Merge pull request #3316 from janezd/remove-overlap

[ENH] projections: Remove sizing by overlap

Author: lanzagar

Orange/widgets/tests/base.py

@@ -848,7 +848,7 @@ def test_attr_models(self):
         controls = self.widget.controls
         self.assertEqual(len(controls.attr_color.model()), 8)
         self.assertEqual(len(controls.attr_shape.model()), 3)
-        self.assertTrue(7 < len(controls.attr_size.model()) < 10)
+        self.assertTrue(5 < len(controls.attr_size.model()) < 8)
         self.assertEqual(len(controls.attr_label.model()), 8)
 
         # color and label should contain all variables
@@ -864,14 +864,6 @@ def test_attr_models(self):
                 self.assertNotIn(var, controls.attr_size.model())
                 self.assertIn(var, controls.attr_shape.model())
 
-    def test_overlap(self):
-        """Test option 'Overlap' in 'Size' combo box"""
-        self.send_signal(self.widget.Inputs.data, self.data)
-        self.assertEqual(len(set(self.widget.graph.get_sizes())), 1)
-        simulate.combobox_activate_item(self.widget.controls.attr_size,
-                                        OWPlotGUI.SizeByOverlap)
-        self.assertGreater(len(set(self.widget.graph.get_sizes())), 1)
-
     def test_attr_label_metas(self, timeout=DEFAULT_TIMEOUT):
         """Set 'Label' from string meta attribute"""
         cont = Continuize(multinomial_treatment=Continuize.AsOrdinal)

Orange/widgets/unsupervised/tests/test_owmds.py

@@ -7,8 +7,6 @@
 
 import numpy as np
 
-from AnyQt.QtTest import QSignalSpy
-
 from Orange.data import Table
 from Orange.distance import Euclidean
 from Orange.misc import DistMatrix
@@ -18,7 +16,6 @@
 )
 from Orange.widgets.tests.utils import simulate
 from Orange.widgets.unsupervised.owmds import OWMDS
-from Orange.widgets.utils.plot import OWPlotGUI
 
 
 class TestOWMDS(WidgetTest, ProjectionWidgetTestMixin,
@@ -275,16 +272,6 @@ def test_saved_matrix_and_data(self):
         self.send_signal(self.widget.Inputs.data, towns_data)
         self.assertIn(towns_data.domain["label"], attr_label.model())
 
-    def test_overlap(self):
-        self.send_signal(self.signal_name, self.signal_data)
-        if self.widget.isBlocking():
-            spy = QSignalSpy(self.widget.blockingStateChanged)
-            self.assertTrue(spy.wait(5000))
-        self.assertEqual(len(set(self.widget.graph.get_sizes())), 1)
-        simulate.combobox_activate_item(self.widget.controls.attr_size,
-                                        OWPlotGUI.SizeByOverlap)
-        self.assertEqual(len(set(self.widget.graph.get_sizes())), 1)
-
 
 if __name__ == "__main__":
     unittest.main()

Orange/widgets/utils/plot/owplotgui.py

@@ -28,10 +28,8 @@
 import os
 
 import unicodedata
-from functools import reduce
-from operator import itemgetter
 
-from Orange.data import ContinuousVariable, DiscreteVariable, Variable
+from Orange.data import ContinuousVariable, DiscreteVariable
 from Orange.widgets import gui
 from Orange.widgets.utils import itemmodels
 from Orange.widgets.utils.listfilter import variables_filter
@@ -430,19 +428,16 @@ class OWPlotGUI:
 
     def __init__(self, plot):
         self._plot = plot
-        self.color_model = DomainModel(placeholder="(Same color)",
-                                       valid_types=DomainModel.PRIMITIVE)
-        self.shape_model = DomainModel(placeholder="(Same shape)",
-                                       valid_types=DiscreteVariable)
-        self.size_model = DomainModel(placeholder="(Same size)",
-                                      order=(self.SizeByOverlap,) + DomainModel.SEPARATED,
-                                      valid_types=ContinuousVariable)
+        self.color_model = DomainModel(
+            placeholder="(Same color)", valid_types=DomainModel.PRIMITIVE)
+        self.shape_model = DomainModel(
+            placeholder="(Same shape)", valid_types=DiscreteVariable)
+        self.size_model = DomainModel(
+            placeholder="(Same size)", valid_types=ContinuousVariable)
         self.label_model = DomainModel(placeholder="(No labels)")
         self.points_models = [self.color_model, self.shape_model,
                               self.size_model, self.label_model]
 
-    SizeByOverlap = "Overlap"
-
     Spacing = 0
 
     ShowLegend = 2

Orange/widgets/visualize/utils/widget.py

@@ -1,6 +1,4 @@
-from collections import Counter, defaultdict
 from xml.sax.saxutils import escape
-from math import log2
 
 import numpy as np
 
@@ -22,7 +20,6 @@
 from Orange.widgets.utils.colorpalette import (
     ColorPaletteGenerator, ContinuousPaletteGenerator, DefaultRGBColors
 )
-from Orange.widgets.utils.plot import OWPlotGUI
 from Orange.widgets.utils.sql import check_sql_input
 from Orange.widgets.visualize.owscatterplotgraph import OWScatterPlotBase
 from Orange.widgets.visualize.utils.component import OWGraphWithAnchors
@@ -98,13 +95,6 @@ def get_subset_mask(self):
         """
         return None
 
-    @staticmethod
-    def __get_overlap_groups(x, y):
-        coord_to_id = defaultdict(list)
-        for i, xy in enumerate(zip(x, y)):
-            coord_to_id[xy].append(i)
-        return coord_to_id
-
     def get_column(self, attr, filter_valid=True,
                    merge_infrequent=False, return_labels=False):
         """
@@ -172,11 +162,6 @@ def get_column(self, attr, filter_valid=True,
     # Sizes
     def get_size_data(self):
         """Return the column corresponding to `attr_size`"""
-        if self.attr_size == OWPlotGUI.SizeByOverlap:
-            x, y = self.get_coordinates_data()
-            coord_to_id = self.__get_overlap_groups(x, y)
-            overlaps = [len(coord_to_id[xy]) for xy in zip(x, y)]
-            return [1 + log2(o) for o in overlaps]
         return self.get_column(self.attr_size)
 
     def impute_sizes(self, size_data):
@@ -195,22 +180,11 @@ def impute_sizes(self, size_data):
 
     def sizes_changed(self):
         self.graph.update_sizes()
-        self.graph.update_colors()  # Needed for overlapping
 
     # Colors
     def get_color_data(self):
         """Return the column corresponding to color data"""
-        colors = self.get_column(self.attr_color, merge_infrequent=True)
-        if self.attr_size == OWPlotGUI.SizeByOverlap:
-            # color overlapping points by most frequent color
-            x, y = self.get_coordinates_data()
-            coord_to_id = self.__get_overlap_groups(x, y)
-            majority_colors = np.empty(len(x))
-            for i, xy in enumerate(zip(x, y)):
-                cnt = Counter(colors[j] for j in coord_to_id[xy])
-                majority_colors[i] = cnt.most_common(1)[0][0]
-            return majority_colors
-        return colors
+        return self.get_column(self.attr_color, merge_infrequent=True)
 
     def get_color_labels(self):
         """

doc/visual-programming/source/widgets/visualize/scatterplot.rst

@@ -41,8 +41,7 @@ the left side of the widget. A snapshot below shows the scatterplot of the
 2. Set the color of the displayed points (you will get colors for discrete
    values and grey-scale points for continuous). Set label, shape and
    size to differentiate between points. Set symbol size and opacity for
-   all data points. Set the desired colors scale. To visualize the number
-   of overlapping points use *Overlap* for size.
+   all data points. Set the desired colors scale.
 3. Adjust *plot properties*:
 
    -  *Show legend* displays a legend on the right. Click and drag the legend to move it.