Merge branch 'main' into doc-updates

.github/workflows/black.yml

@@ -6,6 +6,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.3.0
+      - uses: actions/checkout@v3.5.3
       - uses: actions/setup-python@v4
       - uses: psf/black@stable

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.3
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2

.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
       VERSION: ${{ env.VERSION }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.3
       - name: Create Release
         id: create_release
         uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
@@ -47,7 +47,7 @@ jobs:
     needs: create_release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.3.0
+      - uses: actions/checkout@v3.5.3
 
       - name: Set up Python
         uses: actions/setup-python@v4

.github/workflows/tests.yml

@@ -23,7 +23,7 @@ jobs:
             PYTEST_ARGS_COVERAGE: --cov=lumispy --cov-report=xml
             LABEL: /coverage
     steps:
-      - uses: actions/checkout@v3.3.0
+      - uses: actions/checkout@v3.5.3
 
       - uses: actions/setup-python@v4
         name: Install Python

doc/source/user_guide/signal_tools.rst

@@ -199,3 +199,19 @@ The default operational mode is ``inplace=False`` (a new signal object is return
 
     >>> s.remove_negative(0.1)
 
+
+.. _crop_edges:
+
+Crop edges
+==========
+
+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>`.
+
+.. code-block:: python
+
+    >>> s.crop_edges(crop_px=2)
+
+*[TODO: add possibility to crop different amounts of pixels on different sides]*

doc/source/user_guide/utilities.rst

@@ -5,7 +5,6 @@ Utility functions
 
 This section summarizes various useful functions implemented in LumiSpy.
 
-
 .. _join_spectra:
 
 Join spectra
@@ -27,27 +26,53 @@ signals in the range of +/- 50 pixels around the centre of the overlapping regio
     >>> s = lum.join_spectra([s1,s2])
 
 
-.. _spectral_map_utils:
+.. _exporting_text_files:
 
-Utilities for spectral maps
-===========================
+Exporting text files
+====================
 
-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>`.
+LumiSpy includes a function :py:meth:`~.signals.luminescence_spectrum.LumiSpectrum.savetxt`
+that exports the data of a signal object
+(with not more than two axes) to a simple `.txt` (or `.csv`) file. Can facilitate
+data transfer to other programs, but no metadata is included. By default,
+the axes are saved as first column (and row in 2d case). Set ``axes=False`` to
+save the data object only. The function can also ``transpose`` (default ``False``)
+the dataset or take a custom ``fmt`` (default ``%.5f``) or delimiter (default
+``\t``) string.
 
 .. code-block:: python
 
-    >>> s.crop_edges(crop_px=2)
-
-*[TODO: add possibility to crop different amounts of pixels on different sides]*
-
+    >>> import lumispy as lum
+    >>> import numpy as np
+    ...
+    >>> # Spectrum:
+    >>> S = lum.signals.LumiSpectrum(np.arange(5))
+    >>> lum.savetxt(S, 'spectrum.txt')
+    0.00000	0.00000
+    1.00000	1.00000
+    2.00000	2.00000
+    3.00000	3.00000
+    4.00000	4.00000
+    ...
+    >>> # Linescan:
+    >>> L = lum.signals.LumiSpectrum(np.arange(25).reshape((5,5)))
+    >>> lum.savetxt(L, 'linescan.txt')
+    0.00000	0.00000	1.00000	2.00000	3.00000	4.00000
+    0.00000	0.00000	5.00000	10.00000	15.00000	20.00000
+    1.00000	1.00000	6.00000	11.00000	16.00000	21.00000
+    2.00000	2.00000	7.00000	12.00000	17.00000	22.00000
+    3.00000	3.00000	8.00000	13.00000	18.00000	23.00000
+    4.00000	4.00000	9.00000	14.00000	19.00000	24.00000
+
+.. _mathematical_utilities:
+
+Mathematical routines
+=====================
 
 .. _unit_conversion:
 
 Unit conversion
-===============
+---------------
 
 For convenience, LumiSpy provides functions that convert between different
 units commonly used for the signal axis. Namely,
@@ -64,8 +89,10 @@ index of air.
 .. _grating_equation:
 
 Solving the grating equation
-============================
+----------------------------
+
+The function :py:func:`~.utils.axes.solve_grating_equation` (relationship between
+wavelength and pixel position in the detector plane) follows the conventions
+described in the tutorial from  `Horiba Scientific
+<https://horiba.com/uk/scientific/products/optics-tutorial/wavelength-pixel-position>`_.
 
-The function :py:func:`~.utils.axes.solve_grating_equation` follows the
-conventions described in the tutorial from 
-`Horiba Scientific <https://horiba.com/uk/scientific/products/optics-tutorial/wavelength-pixel-position>`_.

lumispy/tests/signals/test_cl_spectrum.py

@@ -48,11 +48,10 @@ def test__make_signal_mask(self):
 
     def test_remove_spikes(self):
         s = CLSpectrum(np.ones((2, 3, 30)))
-        np.random.seed(1)
         s.add_gaussian_noise(1e-5)
         # Add three spikes
         s.data[1, 0, 1] += 2
-        s.data[0, 2, 29] += 1
+        s.data[0, 2, 29] += 1.001
 
         if not "threshold" in getfullargspec(s.spikes_removal_tool)[0]:
             try:
@@ -67,7 +66,7 @@ def test_remove_spikes(self):
             s1 = s.remove_spikes()
 
         np.testing.assert_almost_equal(s1.data[1, 0, 1], 1, decimal=4)
-        # np.testing.assert_almost_equal(s1.data[0, 2, 29], 1, decimal=4)
+        np.testing.assert_almost_equal(s1.data[0, 2, 29], 1, decimal=4)
 
         s3 = s.remove_spikes(show_diagnosis_histogram=True)
         hist_data = s._spikes_diagnosis(
@@ -82,7 +81,7 @@ def test_remove_spikes(self):
         expected_data[-1] = 1
         np.testing.assert_allclose(hist_data.data, expected_data)
         np.testing.assert_almost_equal(s3.data[1, 0, 1], 1, decimal=4)
-        # np.testing.assert_almost_equal(s3.data[0, 2, 29], 1, decimal=5)
+        np.testing.assert_almost_equal(s3.data[0, 2, 29], 1, decimal=4)
 
         lum_roi = [1, 1]
         s4 = s.remove_spikes(luminescence_roi=lum_roi, threshold=0.5)