Functions adapted to hyperspy-based methods

lumispy/signals/cl_sem_spectrum.py

@@ -29,14 +29,20 @@
 class CLSEMSpectrum(CLSpectrum):
     _signal_type = "CL_SEM"
 
-    def correct_grating_shift(self, cal_factor_x_axis, corr_factor_grating, field_of_view):
+    def correct_grating_shift(self, cal_factor_x_axis, corr_factor_grating, sem_magnification, **kwargs):
         """"
         Applies shift caused by the grating offset wrt the scanning centre.
         Authorship: Gunnar Kusch (gk419@cam.ac.uk)
 
         :param cal_factor_x_axis: The navigation correction factor.
         :param corr_factor_grating: The grating correction factor.
-        :param field_of_view: The SEM field of view (FOV).
+        :param sem_magnification: The SEM (real) magnification value.
+            For the Attolight original metadata, take the `SEM.Real_Magnification` value
+        :param kwargs: The parameters passed to `hyperspy.align1D()` function like:
+            interpolation_method ('linear', 'nearest', 'zero', 'slinear', 'quadratic, 'cubic')
+            parallel: Bool
+            crop, expand, fill_value ...
+
         """
 
         # Avoid correcting for this shift twice (first time it fails, so except
@@ -47,7 +53,7 @@ def correct_grating_shift(self, cal_factor_x_axis, corr_factor_grating, field_of
             # Get all relevant parameters
             nx = self.axes_manager.navigation_shape[0]
             ny = self.axes_manager.navigation_shape[1]
-            fov = field_of_view
+            fov = sem_magnification
 
             # Correction of the Wavelength Shift along the X-Axis
             calax = cal_factor_x_axis / (fov * nx)
@@ -57,7 +63,7 @@ def correct_grating_shift(self, cal_factor_x_axis, corr_factor_grating, field_of
                                 corr_factor_grating * calax * 1000)
             barray = np.full((ny, nx), garray)
 
-            self.shift1D(barray)
+            self.shift1D(barray, **kwargs)
 
             # Store modification in metadata
             self.metadata.set_item("Signal.grating_corrected", True)

lumispy/signals/cl_spectrum.py

@@ -24,6 +24,8 @@
 
 from hyperspy._signals.lazy import LazySignal
 from lumispy.signals.luminescence_spectrum import LumiSpectrum
+from hyperspy.signal_tools import SpikesRemoval
+import warnings
 
 
 class CLSpectrum(LumiSpectrum):
@@ -33,49 +35,91 @@ class CLSpectrum(LumiSpectrum):
     _signal_type = "CL"
     _signal_dimension = 1
 
-    def cosmic_rays_subtraction(self, extra_percent=50, inplace=False, **kwargs):
-        """
-        Masks the cosmic rays away
+    def _make_signal_mask(self, luminescence_roi):
+
+        ax = self.axes_manager.signal_axes[0].axis
+        signal_mask = np.ones(np.shape(ax))
+
+        if len(np.shape(luminescence_roi)) == 1:
+            luminescence_roi = np.array([luminescence_roi])
 
-        Parameters
-        -----------
-        extra_percent : float
-            Extra percent of intensity added to the maximum value of the mean spectrum, which is used to threshold. Default is an extra 500% (x5) to the maximum intensity value of the mean spectrum.
+        for p in luminescence_roi:
+            x, w = p
+            x_min = x - w / 2
+            x_max = x + w / 2
+            index_min = np.abs(ax - x_min).argmin()
+            index_max = np.abs(ax - x_max).argmin()
+            signal_mask[index_min:index_max + 1] *= 0
 
-        inplace : bool
+        return np.invert(signal_mask.astype('bool'))
+
+    def remove_spikes(self, threshold='auto', add_noise=True, noise_type='poisson',
+                      show_diagnosis_histogram=False, inplace=False, luminescence_roi=None, signal_mask=None,
+                      navigation_mask=None, default_spike_width=5, **kwargs):
+        """
+        Hyperspy-based spike removal function.
+        If a GUI interactive spike removal tool is desired, use `s.spikes_removal_tool()` instead.
+
+        :param threshold: 'auto' or int
+            The derivative magnitude threshold above which to find spikes.
+            If `int` set the threshold value use for the detecting the spikes.
+            If `auto`, determine the threshold value as being the first zero
+            value in the histogram obtained from the
+            :py:meth:`~hyperspy.signals._signal1d.Signal1D.spikes_diagnosis`
+            method.
+        :param add_noise: bool
+            Whether to add noise to the interpolated part of the spectrum.
+            The noise properties defined in the Signal metadata are used if present,
+             otherwise 'poisson' shot noise is used as a default.
+        :param noise_type: str
+            By default 'poission' shoot noise is used if `add_noise` is True.
+            Noise types: "white", "heteroscedastic" or "poisson".
+        :param show_diagnosis_histogram: bool
+            Plot or not the derivative histogram to show the magnitude of the spikes present.
+        :param inplace: bool
             If False, a new signal object is created and returned. If True, the original signal object is modified.
+        :param luminescence_roi: array
+            The peak position and peak widths of the peaks in the luminescence spectrum.
+            In the form of an array of pairwise elements [[peak1_x, peak1_width], [peak2_x, peak2_width],...]
+            in the units of the signal axis. It creates a signal_mask protecting the peak regions.
+            To be used instead of `signal_mask`.
+        :param signal_mask: boolean array
+            Restricts the operation to the signal locations not marked as True (masked).
+        :param navigation_mask: boolean array
+            Restricts the operation to the navigation locations not marked as True (masked).
+        :param default_spike_width: int
+            Width over which to do the interpolation when removing all spike.
+        :param kwargs: dict
+            Keyword arguments pass to `hyperspy.signal.signal.BaseSignal.get_histogram`.
+
+        :return: None or CLSpectrum
+            Depends on inplace, returns or overwrites the CLSpectrum after spike removal.
         """
+        if luminescence_roi is not None and signal_mask is None:
+            signal_mask = self._make_signal_mask(luminescence_roi)
+
+        if show_diagnosis_histogram:
+            self.spikes_diagnosis(navigation_mask=navigation_mask, signal_mask=signal_mask,
+                                  **kwargs)
+        if inplace:
+            signal = self
+        else:
+            signal = self.deepcopy()
+
+        spikes_removal = SpikesRemoval(signal=signal, navigation_mask=navigation_mask, signal_mask=signal_mask,
+                                       threshold=threshold, default_spike_width=default_spike_width,
+                                       add_noise=add_noise,)
+
+        setattr(spikes_removal, 'noise_type', noise_type)
+
+        if threshold == 'auto':
+            warnings.warn('Threshold value found: {:.2f}'.format(spikes_removal.threshold), UserWarning)
 
-        def get_threshold(self, extra_percent):
-            # Get the max threshold from the mean spectrum maximum
-            max_threshold = max(self.mean().data)
-            # Add an extra % of threshold
-            max_threshold = max_threshold * extra_percent
-            return max_threshold
-
-        def remove_cosmic_ray(spectrum, threshold, mean_spectrum):
-            # Remove cosmic ray leaving the spectrum pixel as normal noise
-            # TO DO: Modify noise creation to be relative to actual real noise.
-            if max(spectrum.data) > threshold:
-                import statistics
-                mean = statistics.mean(mean_spectrum.data)
-                stdev = statistics.stdev(mean_spectrum.data)
-                noise = np.random.normal(mean, stdev, spectrum.shape[0])
-                spectrum.data = noise
-            return spectrum
-
-        threshold = get_threshold(self, extra_percent)
-        mean_spectrum = self.mean()
-
-        if not inplace:
-            signal_filtered = self.map(remove_cosmic_ray, threshold=threshold, mean_spectrum=mean_spectrum,
-                                       show_progressbar=True, inplace=False)
-            signal_filtered.metadata.set_item("Signal.cosmic_rays_subtracted_extra_percent", extra_percent)
-            return signal_filtered
+        spikes_removal.remove_all_spikes()
+        if inplace:
+            return
         else:
-            self.metadata.set_item("Signal.cosmic_rays_subtracted_extra_percent", extra_percent)
-            return self.map(remove_cosmic_ray, threshold=threshold, mean_spectrum=mean_spectrum, show_progressbar=True,
-                            inplace=True)
+            return signal
 
 
 class LazyCLSpectrum(LazySignal, CLSpectrum):

lumispy/signals/common_luminescence.py

@@ -19,6 +19,7 @@
 """Signal class for Luminescence data (BaseSignal class).
 """
 
+
 class CommonLumi:
     """General Luminescence signal class (dimensionless).
     ----------
@@ -55,5 +56,3 @@ def crop_edges(self, crop_px):
             signal_cropped.metadata.set_item("Signal.cropped_edges", crop_px)
 
         return signal_cropped
-
-