add zlp argument to spikes_removal_tool

hyperspy · Feb 1, 2017 · 1f35812 · 1f35812
1 parent 92d7c63
commit 1f35812
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Showing 2 changed files with 26 additions and 1 deletion.
diff --git a/hyperspy/_signals/eels.py b/hyperspy/_signals/eels.py
@@ -299,6 +299,31 @@ def estimate_zero_loss_peak_centre(s, mask, signal_range):
             substract_from_offset(without_nans(zlpc.data).mean(),
                                   also_align + [self])
 
+    def spikes_removal_tool(self, signal_mask=None,
+                            navigation_mask=None,
+                            signal_start=None,
+                            signal_end=None,
+                            filter_zero_loss=False,
+                            zero_loss_width=5.0):
+        if filter_zero_loss:
+            zlpc = self.estimate_zero_loss_peak_centre()
+            (signal_axis, ) = self.axes_manager[self.axes_manager.signal_axes]
+            axis = signal_axis.axis
+            mini_value = zlpc.data.mean() - zero_loss_width/2
+            maxi_value = zlpc.data.mean() + zero_loss_width/2
+            mask = -((mini_value <= axis) & (axis <= maxi_value))
+            if signal_mask:
+                signal_mask = mask & signal_mask
+            else:
+                signal_mask = mask
+            import matplotlib.pyplot as plt
+            plt.figure()
+            plt.plot(axis, signal_mask)
+        super().spikes_removal_tool(signal_mask=signal_mask,
+             navigation_mask=navigation_mask,
+             signal_start=signal_start,
+             signal_end=signal_end)    
+
     def estimate_elastic_scattering_intensity(
             self, threshold, show_progressbar=None):
         """Rough estimation of the elastic scattering intensity by

diff --git a/hyperspy/gui/egerton_quantification.py b/hyperspy/gui/egerton_quantification.py
@@ -324,7 +324,7 @@ def __init__(self, signal, navigation_mask=None, signal_mask=None,
                 signal_end = axis.max()
             elif isinstance(signal_end, int):
                 signal_start = axis[signal_end]
-            signal_mask = -((signal_start <= axis) & (axis <= signal_end))
+            signal_mask = -((signal_start <= axis) & (axis <= signal_end)) & signal_mask
         self.signal_mask = signal_mask
         self.navigation_mask = navigation_mask
         md = self.signal.metadata