Merge branch 'main' into et

doc/changes/devel.rst

@@ -39,6 +39,7 @@ Enhancements
 - Refactored internals of :func:`mne.read_annotations` (:gh:`11964` by `Paul Roujansky`_)
 - Add support for drawing MEG sensors in :ref:`mne coreg` (:gh:`12098` by `Eric Larson`_)
 - Add ``check_version=True`` to :ref:`mne sys_info` to check for a new release on GitHub (:gh:`12146` by `Eric Larson`_)
+- Bad channels are now colored gray in addition to being dashed when spatial colors are used in :func:`mne.viz.plot_evoked` and related functions (:gh:`12142` by `Eric Larson`_)
 - By default MNE-Python creates matplotlib figures with ``layout='constrained'`` rather than the default ``layout='tight'`` (:gh:`12050`, :gh:`12103` by `Mathieu Scheltienne`_ and `Eric Larson`_)
 - Enhance :func:`~mne.viz.plot_evoked_field` with a GUI that has controls for time, colormap, and contour lines (:gh:`11942` by `Marijn van Vliet`_)
 - Add :class:`mne.viz.ui_events.UIEvent` linking for interactive colorbars, allowing users to link figures and change the colormap and limits interactively. This supports :func:`~mne.viz.plot_evoked_topomap`, :func:`~mne.viz.plot_ica_components`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_projs_topomap`, :meth:`~mne.Evoked.plot_image`, and :meth:`~mne.Epochs.plot_image` (:gh:`12057` by `Santeri Ruuskanen`_)
@@ -72,6 +73,7 @@ Bugs
 - Fix :func:`~mne.viz.plot_volume_source_estimates` with :class:`~mne.VolSourceEstimate` which include a list of vertices (:gh:`12025` by `Mathieu Scheltienne`_)
 - Add support for non-ASCII characters in Annotations, Evoked comments, etc when saving to FIFF format (:gh:`12080` by `Daniel McCloy`_)
 - Correctly handle passing ``"eyegaze"`` or ``"pupil"`` to :meth:`mne.io.Raw.pick` (:gh:`12019` by `Scott Huberty`_)
+- Fix bug with :func:`mne.time_frequency.Spectrum.plot` and related functions where bad channels were not marked (:gh:`12142` by `Eric Larson`_)
 - Fix bug with :func:`~mne.viz.plot_raw` where changing ``MNE_BROWSER_BACKEND`` via :func:`~mne.set_config` would have no effect within a Python session (:gh:`12078` by `Santeri Ruuskanen`_)
 - Improve handling of ``method`` argument in the channel interpolation function to support :class:`str` and raise helpful error messages (:gh:`12113` by `Mathieu Scheltienne`_)
 - Fix combination of ``DIN`` event channels into a single synthetic trigger channel ``STI 014`` by the MFF reader of :func:`mne.io.read_raw_egi` (:gh:`12122` by `Mathieu Scheltienne`_)

mne/time_frequency/tests/test_spectrum.py

@@ -1,9 +1,9 @@
 from contextlib import nullcontext
 from functools import partial
 
-import matplotlib.pyplot as plt
 import numpy as np
 import pytest
+from matplotlib.colors import same_color
 from numpy.testing import assert_allclose, assert_array_equal
 
 from mne import Annotations, create_info, make_fixed_length_epochs
@@ -449,8 +449,16 @@ def test_plot_spectrum(kind, array, request):
         data, freqs = spectrum.get_data(return_freqs=True)
         Klass = SpectrumArray if kind == "raw" else EpochsSpectrumArray
         spectrum = Klass(data=data, info=spectrum.info, freqs=freqs)
+    spectrum.info["bads"] = spectrum.ch_names[:1]  # one grad channel
     spectrum.plot(average=True, amplitude=True, spatial_colors=True)
-    spectrum.plot(average=False, amplitude=False, spatial_colors=False)
+    spectrum.plot(average=True, amplitude=False, spatial_colors=False)
+    n_grad = sum(ch_type == "grad" for ch_type in spectrum.get_channel_types())
+    for amp, sc in ((True, True), (False, False)):
+        fig = spectrum.plot(average=False, amplitude=amp, spatial_colors=sc, exclude=())
+        lines = fig.axes[0].lines[2:]  # grads, ignore two vlines
+        assert len(lines) == n_grad
+        bad_color = "0.5" if sc else "r"
+        n_bad = sum(same_color(line.get_color(), bad_color) for line in lines)
+        assert n_bad == 1
     spectrum.plot_topo()
     spectrum.plot_topomap()
-    plt.close("all")

mne/viz/evoked.py

@@ -679,15 +679,17 @@ def _plot_lines(
                     _handle_spatial_colors(
                         colors, info, idx, this_type, psd, ax, sphere
                     )
+                    bad_color = (0.5, 0.5, 0.5)
                 else:
                     if isinstance(_spat_col, (tuple, str)):
                         col = [_spat_col]
                     else:
                         col = ["k"]
+                    bad_color = "r"
                     colors = col * len(idx)
-                    for i in bad_ch_idx:
-                        if i in idx:
-                            colors[idx.index(i)] = "r"
+                for i in bad_ch_idx:
+                    if i in idx:
+                        colors[idx.index(i)] = bad_color
 
                 if zorder == "std":
                     # find the channels with the least activity

mne/viz/tests/test_evoked.py

@@ -16,6 +16,7 @@
 import pytest
 from matplotlib import gridspec
 from matplotlib.collections import PolyCollection
+from matplotlib.colors import same_color
 from mpl_toolkits.axes_grid1.parasite_axes import HostAxes  # spatial_colors
 from numpy.testing import assert_allclose
 
@@ -134,6 +135,12 @@ def test_plot_evoked():
     amplitudes = _get_amplitudes(fig)
     assert len(amplitudes) == len(default_picks)
     assert evoked.proj is False
+    assert evoked.info["bads"] == ["MEG 2641", "EEG 004"]
+    eeg_lines = fig.axes[2].lines
+    n_eeg = sum(ch_type == "eeg" for ch_type in evoked.get_channel_types())
+    assert len(eeg_lines) == n_eeg == 4
+    n_bad = sum(same_color(line.get_color(), "0.5") for line in eeg_lines)
+    assert n_bad == 1
     # Test a click
     ax = fig.get_axes()[0]
     line = ax.lines[0]

mne/viz/utils.py

@@ -2506,6 +2506,7 @@ def _plot_psd(
     if not average:
         picks = np.concatenate(picks_list)
         info = pick_info(inst.info, sel=picks, copy=True)
+        bad_ch_idx = [info["ch_names"].index(ch) for ch in info["bads"]]
         types = np.array(info.get_channel_types())
         ch_types_used = list()
         for this_type in _VALID_CHANNEL_TYPES:
@@ -2538,7 +2539,7 @@ def _plot_psd(
             xlim=(freqs[0], freqs[-1]),
             ylim=None,
             times=freqs,
-            bad_ch_idx=[],
+            bad_ch_idx=bad_ch_idx,
             titles=titles,
             ch_types_used=ch_types_used,
             selectable=True,

tutorials/intro/70_report.py

@@ -17,8 +17,7 @@
 HTML pages it generates are self-contained and do not require a running Python
 environment. However, it is less flexible as you can't change code and re-run
 something directly within the browser. This tutorial covers the basics of
-building a report. As usual, we will start by importing the modules and data we
-need:
+building a report. As usual, we will start by importing the modules and data we need:
 """
 
 # %%