Crop edges update simplified

CHANGELOG.rst

@@ -15,6 +15,7 @@ Changed
   for integrity check as `it replaces LGTM
   <https://github.blog/2022-08-15-the-next-step-for-lgtm-com-github-code-scanning/>`_
 - Added a centroid/center of mass functionality to analyse peak position of a spectrum (both in `utils`` and in `LumiSpectrum``)
+- `s.crop_edges` moved to utils. It also now can take 1,2 or 4 values as input (can crop each axis independently) and also accepts percentages. The use of it under the `CommonLumiSpectrum` class is deprecated.
 
 Maintenance
 -----------

doc/source/user_guide/utilities.rst

@@ -29,19 +29,34 @@ signals in the range of +/- 50 pixels around the centre of the overlapping regio
 
 .. _spectral_map_utils:
 
-Utilities for spectral maps
-===========================
-
-The function :py:meth:`~.signals.common_luminescence.CommonLumi.crop_edges`
-removes the specified number of pixels from all four edges of a spectral map.
-It is a convenience wrapper for the ``inav`` :external+hyperspy:ref:`method in
-HyperSpy <signal.indexing>`.
+Cropping multiple signals in the navigation axis 
+================================================
+
+The function :py:meth:`~.utils.axes.crop_edges`
+removes the specified number of pixels or % from the four edges of a spectral map,
+from the edges inwards. It takes a list of `Signals` and cropping can happen
+uniformly on all sides or by specifying the cropping range for each axis or each
+side. If the navigation axes shape across the list of signals is different, all
+signals can be rebinned to match the shape of the first signal in the list.
+It is a convenience wrapper for the ``inav`` `method in HyperSpy
+<https://hyperspy.org/hyperspy-doc/current/user_guide/signal.html#indexing>`_.
 
 .. code-block:: python
+    >>> signals = [cl_map, sem_image]
+    >>> signals
+    [CLSpectrum <256,256|1024>, Signal2D <128,128|1>]
+    >>> signals_cropped = lum.utils.crop_edges(signals, crop_range=5, crop_units="%", rebin_nav=True)
+    >>> signals_cropped
+    [CLSpectrum <243,243|1024>, Signal2D <243,243|1>]
+.. Note::
+
+    Many scanning luminescence techniques result in edge defects at the edges of the scanned region.
+    This function enables the same cropping of the navigation axis for a list of signals in the same
+    region to correct for such defect.
 
-    >>> s.crop_edges(crop_px=2)
+.. Note::
 
-*[TODO: add possibility to crop different amounts of pixels on different sides]*
+    Before version `0.2.2` this function belonged to the class `CommonLumi` as :py:meth:`~.signals.common_luminescence.CommonLumi.crop_edges`. This use is now deprecated.
 
 
 .. _unit_conversion:

lumispy/__init__.py

@@ -23,6 +23,7 @@
 
 from lumispy.utils.axes import nm2eV, eV2nm, nm2invcm, invcm2nm, join_spectra
 from lumispy.utils.io import to_array, savetxt
+from lumispy.utils import crop_edges
 
 from lumispy import signals
 from lumispy import components

lumispy/signals/common_luminescence.py

@@ -23,47 +23,18 @@
 
 from numpy import isnan
 from warnings import warn
+from lumispy.utils.signals import crop_edges
 
 
 class CommonLumi:
     """**General luminescence signal class (dimensionless)**"""
 
     def crop_edges(self, crop_px):
-        """Crop the amount of pixels from the four edges of the scanning
-        region, from out the edges inwards.
-
-        Parameters
-        ----------
-        crop_px : int
-            Amount of pixels to be cropped on each side individually.
-
-        Returns
-        -------
-        signal_cropped : CommonLuminescence
-            A smaller cropped CL signal object. If inplace is True, the original
-            object is modified and no LumiSpectrum is returned.
-        """
-
-        width = self.axes_manager.shape[0]
-        height = self.axes_manager.shape[1]
-
-        if crop_px * 2 > width or crop_px * 2 > height:
-            raise ValueError(
-                "The pixels to be cropped cannot be larger than half the width or the length!"
-            )
-        else:
-            signal_cropped = self.inav[
-                crop_px + 1 : width - crop_px + 1, crop_px + 1 : height - crop_px + 1
-            ]
-
-        # Store transformation in metadata (or update the value if already previously transformed)
-
-        try:
-            signal_cropped.metadata.Signal.cropped_edges += crop_px
-        except AttributeError:
-            signal_cropped.metadata.set_item("Signal.cropped_edges", crop_px)
-
-        return signal_cropped
+        warn(
+            "This function is deprecated and will be deleted in v1.0. Please use ``sc = lum.utils.crop_edges(s)`` instead with the ``crop_range`` parameter instead.",
+            DeprecationWarning,
+        )
+        return crop_edges(self, crop_px=crop_px)
 
     def remove_negative(self, basevalue=1, inplace=False):
         """Sets all negative values to 'basevalue', e.g. for logarithmic scale

lumispy/tests/signals/test_common_luminescence.py

@@ -23,18 +23,12 @@
 
 
 class TestCommonLumi:
-    def test_crop_edges(self):
+    def test_crop_edges_deprecated(self):
         s1 = LumiSpectrum(np.ones((10, 10, 10)))
-        s2 = LumiTransientSpectrum(np.ones((10, 10, 10, 10)))
-        s3 = LumiSpectrum(np.ones((3, 3, 10)))
-        s1 = s1.crop_edges(crop_px=2)
-        s2 = s2.crop_edges(crop_px=2)
-        assert s1.axes_manager.navigation_shape[0] == 6
-        assert s1.axes_manager.navigation_shape[1] == 6
-        assert s2.axes_manager.navigation_shape[0] == 6
-        assert s2.axes_manager.navigation_shape[1] == 6
-        with pytest.raises(ValueError):
-            s3.crop_edges(crop_px=2)
+        with pytest.warns(DeprecationWarning, match="This function is deprecated"):
+            s2 = s1.crop_edges(crop_px=1)
+        assert s2.axes_manager.navigation_shape[0] == 8
+        assert s2.axes_manager.navigation_shape[1] == 8
 
     def test_remove_negative(self):
         s1 = LumiSpectrum(np.random.random((10, 10, 10))) - 0.3