Merge pull request #7 from HanHsuanWu/main

align_zero_loss_peak should take left and right arguments for low loss spectra

CHANGES.rst

@@ -7,6 +7,7 @@ https://holospy.readthedocs.io/en/latest/changes.html
 0.1.dev0 (UNRELEASED)
 =====================
 
+- Enable ``signal_range`` arguments when using ``subpixel=True`` in :py:meth:`~.signals.EELSSpectrum.align_zero_loss_peak` (`#7 <https://github.com/hyperspy/exspy/pull/7>`_)
 - Support for tabulated :ref:`Generalised Oscillator Strengths (GOS) <eels.GOS>` using the
   `GOSH <https://gitlab.com/gguzzina/gosh>`_ open file format. By default, a freely
   usable dataset is downloaded from `doi:10.5281/zenodo.7645765 <https://zenodo.org/record/6599071>`_

exspy/signals/eels.py

@@ -335,7 +335,8 @@ def align_zero_loss_peak(
         """Align the zero-loss peak.
 
         This function first aligns the spectra using the result of
-        `estimate_zero_loss_peak_centre` and afterward, if subpixel is True,
+        `estimate_zero_loss_peak_centre` which finds the maximum in the
+        given energy range, then if subpixel is True,
         proceeds to align with subpixel accuracy using `align1D`. The offset
         is automatically correct if `calibrate` is True.
 
@@ -450,26 +451,28 @@ def estimate_zero_loss_peak_centre(s, mask, signal_range):
 
         if subpixel is False:
             return
-        left, right = -3.0, 3.0
+
+        start, end = signal_range or (-3.0, 3.0)
+
         if calibrate is False:
-            left += mean_
-            right += mean_
+            start += mean_
+            end += mean_
 
-        left = (
-            left
-            if left > self.axes_manager[-1].axis[0]
+        start = (
+            start
+            if start > self.axes_manager[-1].axis[0]
             else self.axes_manager[-1].axis[0]
         )
-        right = (
-            right
-            if right < self.axes_manager[-1].axis[-1]
+        end = (
+            end
+            if end < self.axes_manager[-1].axis[-1]
             else self.axes_manager[-1].axis[-1]
         )
 
         if self.axes_manager.navigation_size > 1:
             self.align1D(
-                left,
-                right,
+                start,
+                end,
                 also_align=also_align,
                 show_progressbar=show_progressbar,
                 mask=mask,

exspy/tests/signals/test_eels.py

@@ -193,6 +193,18 @@ def test_align_zero_loss_peak_crop_false(self):
         s.align_zero_loss_peak(crop=False, print_stats=False)
         assert original_size == s.axes_manager.signal_axes[0].size
 
+    @pytest.mark.parametrize("signal_range", ((-2.0, 2.0), (0, 40), "roi"))
+    def test_align_zero_loss_peak_start_end_float(self, signal_range):
+        s = self.signal
+        if signal_range == "roi":
+            signal_range = hs.roi.SpanROI(-3, 3)
+        s.axes_manager[-1].offset = -2
+        s.align_zero_loss_peak(subpixel=True, signal_range=signal_range)
+        zlpc = s.estimate_zero_loss_peak_centre()
+        # Check if start and end arguments work
+        assert zlpc.data.mean() == 0
+        assert zlpc.data.std() == 0
+
 
 @lazifyTestClass
 class TestSpikesRemovalToolZLP:

pyproject.toml

@@ -93,6 +93,14 @@ force-exclude = '''
   | exspy/misc/elements.py
 '''
 
+[tool.coverage.run]
+branch = true
+source = ["hyperspy"]
+omit = ["hyperspy/tests/*"]
+
+[tool.coverage.report]
+precision = 2
+
 [tool.pytest.ini_options]
 addopts = "-ra -n auto --dist loadfile"
 testpaths = ["exspy/tests", ]