Merge pull request #2918 from LMSC-NTappy/fix_spikes_removal_tool

Fixed spikes_removal_tool bug when no navigator is present

hyperspy/signal_tools.py

@@ -1807,8 +1807,9 @@ def find(self, back=False):
                     minimum),
                 self.signal.axes_manager.signal_axes[0].index2value(
                     maximum))
-            self.signal._plot.pointer._set_indices(
-                self.coordinates[self.index])
+            if self.signal._plot.navigator_plot is not None:
+                self.signal._plot.pointer._set_indices(
+                    self.coordinates[self.index])
             self.update_plot()
             self.create_interpolation_line()
 

hyperspy/tests/signals/test_spike_removal_tool.py

@@ -66,6 +66,24 @@ def test_spikes_removal_tool():
 ]
 
 
+def test_spikes_removal_tool_navigation_dimension_0():
+    #Artificial Signal
+    s = Signal1D(np.ones(1234))
+    #Add a spike
+    s.data[333] = 666
+
+    assert s.axes_manager.navigation_dimension == 0
+
+    sr = SpikesRemovalInteractive(s)
+    sr.threshold = 1.5
+    sr.add_noise = False
+    sr.find()
+
+    sr.apply()
+
+    np.testing.assert_allclose(s.data[333], 1, atol=1e-4)
+
+
 @pytest.mark.parametrize(("add_noise, decimal"), [(True, 1), (False, 5)])
 def test_spikes_removal_tool_non_interactive(add_noise, decimal):
     s = Signal1D(np.ones((2, 3, 30)))

upcoming_changes/2918.bugfix.rst

@@ -0,0 +1 @@
+Fix bug when the spikes_removal_tool would not work interactively for signal with 0-dimension navigation space.