Merge pull request #59 from biolab/fix

[FIX] Remove calls to deprecated get_column_view method
biolab · Dec 6, 2022 · bd03ab4 · bd03ab4
2 parents b276b38 + 03ad8c6
commit bd03ab4
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Showing 3 changed files with 17 additions and 21 deletions.
diff --git a/orangecontrib/survival_analysis/widgets/owchorts.py b/orangecontrib/survival_analysis/widgets/owchorts.py
@@ -76,8 +76,8 @@ def check_unique_values(split_by, values):
         cutoff = partial(check_unique_values, np.mean)
     elif splitting_criteria == SplittingCriteria.LogRankTest:
         time_var, event_var = get_survival_endpoints(data.domain)
-        durations, _ = data.get_column_view(time_var)
-        events, _ = data.get_column_view(event_var)
+        durations = data.get_column(time_var)
+        events = data.get_column(event_var)
         cutoff = partial(cutoff_by_log_rank_optimization, durations, events, callback)
     else:
         raise ValueError('Unknown splitting criteria')

diff --git a/orangecontrib/survival_analysis/widgets/owkaplanmeier.py b/orangecontrib/survival_analysis/widgets/owkaplanmeier.py
@@ -658,11 +658,11 @@ def generate_plot_curves(self) -> List[EstimatedFunctionCurve]:
             return []
 
         data = self.data
-        time, _ = data.get_column_view(self.time_var)
-        events, _ = data.get_column_view(self.event_var)
+        time = data.get_column(self.time_var)
+        events = data.get_column(self.event_var)
 
         if self.group_var:
-            groups, _ = data.get_column_view(self.group_var.name)
+            groups = data.get_column(self.group_var.name)
             group_indexes = [index for index, _ in enumerate(self.group_var.values)]
             colors = [self._get_discrete_var_color(index) for index in group_indexes]
             masks = groups == np.reshape(group_indexes, (-1, 1))
@@ -688,7 +688,7 @@ def commit(self):
 
         data = self.data
 
-        time, _ = data.get_column_view(self.time_var)
+        time = data.get_column(self.time_var)
         if self.group_var is None:
             time_interval = self.graph.selection[0].x
             start, end = time_interval[0], time_interval[-1]
@@ -697,7 +697,7 @@ def commit(self):
             )
         else:
             selection = []
-            group, _ = data.get_column_view(self.group_var.name)
+            group = data.get_column(self.group_var.name)
             for group_id, time_interval in self.graph.selection.items():
                 start, end = time_interval.x[0], time_interval.x[-1]
                 selection += (

diff --git a/orangecontrib/survival_analysis/widgets/tests/test_owkaplanmeier.py b/orangecontrib/survival_analysis/widgets/tests/test_owkaplanmeier.py
@@ -85,12 +85,8 @@ def setUp(self) -> None:
         vb.resize(200, 200)
 
     def simulate_mouse_drag(self, start: tuple, end: tuple):
-        start = self.widget.graph.view_box.mapViewToScene(
-            pg.Point(start[0], start[1])
-        ).toPoint()
-        end = self.widget.graph.view_box.mapViewToScene(
-            pg.Point(end[0], end[1])
-        ).toPoint()
+        start = self.widget.graph.view_box.mapViewToScene(pg.Point(start[0], start[1]))
+        end = self.widget.graph.view_box.mapViewToScene(pg.Point(end[0], end[1]))
 
         mouse_move(self.widget.graph, start)
         # this is somehow not respected in KaplanMeierViewBox.mouseDragEvent
@@ -166,13 +162,13 @@ def test_curve_highlight(self):
         self.widget.group_var = self.widget.data.domain['Group']
         self.widget.on_group_changed()
 
-        pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.5)).toPoint()
+        pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.5))
         mouse_move(self.widget.graph, pos)
         # We need to wait for events to process
         QTest.qWait(100)
         self.assertTrue(self.widget.graph.highlighted_curve == 1)
 
-        pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.85)).toPoint()
+        pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.85))
         mouse_move(self.widget.graph, pos)
         QTest.qWait(100)
         self.assertTrue(self.widget.graph.highlighted_curve == 0)
@@ -197,9 +193,9 @@ def test_selection(self):
 
         # check output data
         selected_data = self.get_output(self.widget.Outputs.selected_data)
-        selected_groups = selected_data.get_column_view('Group')[0]
+        selected_groups = selected_data.get_column('Group')
         self.assertEqual(12, selected_groups.size)
-        selected_groups = set(selected_data.get_column_view('Group')[0])
+        selected_groups = set(selected_data.get_column('Group'))
         self.assertEqual(2, len(selected_groups))
         self.assertIn(0, selected_groups)
         self.assertIn(1, selected_groups)
@@ -223,9 +219,9 @@ def test_selection(self):
 
         # check output data
         selected_data = self.get_output(self.widget.Outputs.selected_data)
-        selected_groups = selected_data.get_column_view('Group')[0]
+        selected_groups = selected_data.get_column('Group')
         self.assertEqual(6, selected_groups.size)
-        selected_groups = set(selected_data.get_column_view('Group')[0])
+        selected_groups = set(selected_data.get_column('Group'))
         self.assertEqual(1, len(selected_groups))
         self.assertIn(0, selected_groups)
         self.assertNotIn(1, selected_groups)
@@ -249,9 +245,9 @@ def test_selection(self):
 
         # check output data
         selected_data = self.get_output(self.widget.Outputs.selected_data)
-        selected_groups = selected_data.get_column_view('Group')[0]
+        selected_groups = selected_data.get_column('Group')
         self.assertEqual(6, selected_groups.size)
-        selected_groups = set(selected_data.get_column_view('Group')[0])
+        selected_groups = set(selected_data.get_column('Group'))
         self.assertEqual(1, len(selected_groups))
         self.assertIn(1, selected_groups)
         self.assertNotIn(0, selected_groups)