Merge branch 'main' into basemodel

README.rst

@@ -2,29 +2,35 @@
 Spectral Parameterization
 =========================
 
-|ProjectStatus|_ |Version|_ |BuildStatus|_ |Coverage|_ |License|_ |PythonVersions|_ |Paper|_
+|ProjectStatus| |Version| |BuildStatus| |Coverage| |License| |PythonVersions| |Publication|
 
 .. |ProjectStatus| image:: http://www.repostatus.org/badges/latest/active.svg
-.. _ProjectStatus: https://www.repostatus.org/#active
+   :target: https://www.repostatus.org/#active
+   :alt: project status
 
 .. |Version| image:: https://img.shields.io/pypi/v/fooof.svg
-.. _Version: https://pypi.python.org/pypi/fooof/
+   :target: https://pypi.python.org/pypi/fooof/
+   :alt: version
 
 .. |BuildStatus| image:: https://github.com/fooof-tools/fooof/actions/workflows/build.yml/badge.svg
-.. _BuildStatus: https://github.com/fooof-tools/fooof/actions/workflows/build.yml
+   :target: https://github.com/fooof-tools/fooof/actions/workflows/build.yml
+   :alt: build status
 
 .. |Coverage| image:: https://codecov.io/gh/fooof-tools/fooof/branch/main/graph/badge.svg
-.. _Coverage: https://codecov.io/gh/fooof-tools/fooof
+   :target: https://codecov.io/gh/fooof-tools/fooof
+   :alt: coverage
 
 .. |License| image:: https://img.shields.io/pypi/l/fooof.svg
-.. _License: https://opensource.org/licenses/Apache-2.0
+   :target: https://opensource.org/licenses/Apache-2.0
+   :alt: license
 
 .. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/fooof.svg
-.. _PythonVersions: https://pypi.python.org/pypi/fooof/
-
-.. |Paper| image:: https://img.shields.io/badge/paper-nn10.1038-informational.svg
-.. _Paper: https://doi.org/10.1038/s41593-020-00744-x
+   :target: https://pypi.python.org/pypi/fooof/
+   :alt: python versions
 
+.. |Publication| image:: https://img.shields.io/badge/paper-nn10.1038-informational.svg
+   :target: https://doi.org/10.1038/s41593-020-00744-x
+   :alt: publication
 
 Spectral parameterization (`specparam`, formerly `fooof`) is a fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
 

specparam/plts/utils.py

@@ -65,7 +65,8 @@ def set_alpha(n_points):
     return alpha
 
 
-def add_shades(ax, shades, colors='r', add_center=False, logged=False):
+def add_shades(ax, shades, colors='r', alpha=0.2,
+               add_center=False, center_alpha=0.6, logged=False):
     """Add shaded regions to a plot.
 
     Parameters
@@ -76,8 +77,13 @@ def add_shades(ax, shades, colors='r', add_center=False, logged=False):
         Shaded region(s) to add to plot, defined as [lower_bound, upper_bound].
     colors : str or list of string
         Color(s) to plot shades.
+    alpha : float or list of float, optional, default: 0.2
+        The alpha level to add the shade regions with.
+        If a list, can specify a separate alpha level per shade.
     add_center : boolean, default: False
         Whether to add a line at the center point of the shaded regions.
+    center_alpha : float, optional, default: 0.6
+        The alpha level for the center line, if added.
     logged : boolean, default: False
         Whether the shade values should be logged before applying to plot axes.
     """
@@ -87,16 +93,17 @@ def add_shades(ax, shades, colors='r', add_center=False, logged=False):
         shades = [shades]
 
     colors = repeat(colors) if not isinstance(colors, list) else colors
+    alphas = repeat(alpha) if not isinstance(alpha, list) else alpha
 
-    for shade, color in zip(shades, colors):
+    for shade, color, alpha in zip(shades, colors, alphas):
 
         shade = np.log10(shade) if logged else shade
 
-        ax.axvspan(shade[0], shade[1], color=color, alpha=0.2, lw=0)
+        ax.axvspan(shade[0], shade[1], color=color, alpha=alpha, lw=0)
 
         if add_center:
             center = sum(shade) / 2
-            ax.axvspan(center, center, color='k', alpha=0.6)
+            ax.axvspan(center, center, color='k', alpha=center_alpha)
 
 
 def recursive_plot(data, plot_function, ax, **kwargs):

specparam/tests/plts/test_utils.py

@@ -33,6 +33,10 @@ def test_add_shades(skip_if_no_mpl):
 
     add_shades(check_ax(None), [4, 8])
 
+@plot_test
+def test_add_shades_multi(skip_if_no_mpl):
+    add_shades(check_ax(None), [[4, 8], [8, 12], [12, 25]], colors=['b', 'c', 'y'], alpha=0.3)
+
 @plot_test
 def test_recursive_plot(skip_if_no_mpl):