[ENH] add exclude kw to psd_plot

doc/changes/latest.inc

@@ -23,6 +23,8 @@ Enhancements
 ~~~~~~~~~~~~
 .. - Add something cool (:gh:`9192` **by new contributor** |New Contributor|_)
 
+- Add the "exclude" keyword to the psd_plot in :func:`mne.time_frequency.psd.py` (:gh:`9379` by `Eduard ort`_)
+
 - New function :func:`mne.chpi.get_chpi_info` to retrieve basic information about the cHPI system used when recording MEG data (:gh:`9369` by `Richard Höchenberger`_)
 
 

mne/epochs.py

@@ -1116,16 +1116,17 @@ def plot(self, picks=None, scalings=None, n_epochs=20, n_channels=20,
     @copy_function_doc_to_method_doc(plot_epochs_psd)
     def plot_psd(self, fmin=0, fmax=np.inf, tmin=None, tmax=None,
                  proj=False, bandwidth=None, adaptive=False, low_bias=True,
-                 normalization='length', picks=None, ax=None, color='black',
-                 xscale='linear', area_mode='std', area_alpha=0.33,
-                 dB=True, estimate='auto', show=True, n_jobs=1,
-                 average=False, line_alpha=None, spatial_colors=True,
+                 normalization='length', picks=None, exclude='bads', ax=None,
+                 color='black', xscale='linear', area_mode='std',
+                 area_alpha=0.33, dB=True, estimate='auto', show=True,
+                 n_jobs=1, average=False, line_alpha=None, spatial_colors=True,
                  sphere=None, verbose=None):
         return plot_epochs_psd(self, fmin=fmin, fmax=fmax, tmin=tmin,
                                tmax=tmax, proj=proj, bandwidth=bandwidth,
                                adaptive=adaptive, low_bias=low_bias,
-                               normalization=normalization, picks=picks, ax=ax,
-                               color=color, xscale=xscale, area_mode=area_mode,
+                               normalization=normalization, picks=picks,
+                               exclude=exclude, ax=ax, color=color,
+                               xscale=xscale, area_mode=area_mode,
                                area_alpha=area_alpha, dB=dB, estimate=estimate,
                                show=show, n_jobs=n_jobs, average=average,
                                line_alpha=line_alpha,

mne/io/base.py

@@ -1540,18 +1540,19 @@ def plot(self, events=None, duration=10.0, start=0.0, n_channels=20,
     @copy_function_doc_to_method_doc(plot_raw_psd)
     def plot_psd(self, fmin=0, fmax=np.inf, tmin=None, tmax=None, proj=False,
                  n_fft=None, n_overlap=0, reject_by_annotation=True,
-                 picks=None, ax=None, color='black', xscale='linear',
-                 area_mode='std', area_alpha=0.33, dB=True, estimate='auto',
-                 show=True, n_jobs=1, average=False, line_alpha=None,
-                 spatial_colors=True, sphere=None, window='hamming',
-                 verbose=None):
+                 picks=None, exclude='bads', ax=None, color='black',
+                 xscale='linear', area_mode='std', area_alpha=0.33, dB=True,
+                 estimate='auto', show=True, n_jobs=1, average=False,
+                 line_alpha=None, spatial_colors=True, sphere=None,
+                 window='hamming', verbose=None):
         return plot_raw_psd(self, fmin=fmin, fmax=fmax, tmin=tmin, tmax=tmax,
                             proj=proj, n_fft=n_fft, n_overlap=n_overlap,
                             reject_by_annotation=reject_by_annotation,
-                            picks=picks, ax=ax, color=color, xscale=xscale,
-                            area_mode=area_mode, area_alpha=area_alpha,
-                            dB=dB, estimate=estimate, show=show, n_jobs=n_jobs,
-                            average=average, line_alpha=line_alpha,
+                            picks=picks, exclude=exclude, ax=ax, color=color,
+                            xscale=xscale, area_mode=area_mode,
+                            area_alpha=area_alpha, dB=dB, estimate=estimate,
+                            show=show, n_jobs=n_jobs, average=average,
+                            line_alpha=line_alpha,
                             spatial_colors=spatial_colors, sphere=sphere,
                             window=window, verbose=verbose)
 

mne/viz/_figure.py

@@ -52,7 +52,8 @@
                     _get_color_list, logger, _validate_if_list_of_axes,
                     _plot_psd)
 from ..defaults import _handle_default
-from ..utils import set_config, _check_option, _check_sphere, Bunch
+from ..utils import (set_config, _check_option, _check_sphere, _validate_type,
+                     Bunch)
 from ..annotations import _sync_onset
 from ..time_frequency import psd_welch, psd_multitaper
 from ..io.pick import (pick_types, _picks_to_idx, channel_indices_by_type,
@@ -2313,8 +2314,8 @@ def _line_figure(inst, axes=None, picks=None, **kwargs):
     return fig, axes
 
 
-def _psd_figure(inst, proj, picks, axes, area_mode, tmin, tmax, fmin, fmax,
-                n_jobs, color, area_alpha, dB, estimate, average,
+def _psd_figure(inst, proj, picks, exclude, axes, area_mode, tmin, tmax, fmin,
+                fmax, n_jobs, color, area_alpha, dB, estimate, average,
                 spatial_colors, xscale, line_alpha, sphere, window, **kwargs):
     """Instantiate a new power spectral density figure."""
     from .. import BaseEpochs
@@ -2351,6 +2352,20 @@ def _psd_figure(inst, proj, picks, axes, area_mode, tmin, tmax, fmin, fmax,
     titles_list = list()
     scalings_list = list()
     psd_list = list()
+    # exclude channels
+    inst.info._check_consistency()
+    _validate_type(exclude, (list, tuple, str), 'exclude')
+    if isinstance(exclude, str):
+        _check_option('exclude', exclude, 'bads', extra='when str')
+        exclude = inst.info['bads']
+    for ei, ex in enumerate(exclude):
+        if not isinstance(ex, str) or ex not in inst.info['ch_names']:
+            raise ValueError(f'exclude[{ei}] ({repr(ex)}) '
+                             'not found in info["ch_names"]')
+    if len(exclude) > 0:
+        picks = np.array([pick for pick in picks if
+                          inst.info['ch_names'][pick] not in exclude], int)
+
     # initialize figure
     fig, axes = _line_figure(inst, axes, picks, **kwargs)
     # split picks, units, etc, for each subplot

mne/viz/epochs.py

@@ -899,11 +899,11 @@ def plot_epochs(epochs, picks=None, scalings=None, n_epochs=20, n_channels=20,
 @verbose
 def plot_epochs_psd(epochs, fmin=0, fmax=np.inf, tmin=None, tmax=None,
                     proj=False, bandwidth=None, adaptive=False, low_bias=True,
-                    normalization='length', picks=None, ax=None, color='black',
-                    xscale='linear', area_mode='std', area_alpha=0.33,
-                    dB=True, estimate='auto', show=True, n_jobs=1,
-                    average=False, line_alpha=None, spatial_colors=True,
-                    sphere=None, verbose=None):
+                    normalization='length', picks=None, exclude='bads',
+                    ax=None, color='black', xscale='linear', area_mode='std',
+                    area_alpha=0.33, dB=True, estimate='auto', show=True,
+                    n_jobs=1, average=False, line_alpha=None,
+                    spatial_colors=True, sphere=None, verbose=None):
     """%(plot_psd_doc)s.
 
     Parameters
@@ -934,6 +934,9 @@ def plot_epochs_psd(epochs, fmin=0, fmax=np.inf, tmin=None, tmax=None,
         be normalized by the sampling rate as well as the length of
         the signal (as in nitime).
     %(plot_psd_picks_good_data)s
+    exclude : list of str | 'bads'
+        Channels names to exclude from being shown. If 'bads', the
+        bad channels are excluded.
     ax : instance of Axes | None
         Axes to plot into. If None, axes will be created.
     %(plot_psd_color)s
@@ -961,12 +964,12 @@ def plot_epochs_psd(epochs, fmin=0, fmax=np.inf, tmin=None, tmax=None,
     # epochs always use multitaper, not Welch, so no need to allow "window"
     # param above
     fig = _psd_figure(
-        inst=epochs, proj=proj, picks=picks, axes=ax, tmin=tmin, tmax=tmax,
-        fmin=fmin, fmax=fmax, sphere=sphere, xscale=xscale, dB=dB,
-        average=average, estimate=estimate, area_mode=area_mode,
-        line_alpha=line_alpha, area_alpha=area_alpha, color=color,
-        spatial_colors=spatial_colors, n_jobs=n_jobs, bandwidth=bandwidth,
-        adaptive=adaptive, low_bias=low_bias, normalization=normalization,
-        window='hamming')
+        inst=epochs, proj=proj, picks=picks, exclude=exclude, axes=ax,
+        tmin=tmin, tmax=tmax, fmin=fmin, fmax=fmax, sphere=sphere,
+        xscale=xscale, dB=dB, average=average, estimate=estimate,
+        area_mode=area_mode, line_alpha=line_alpha, area_alpha=area_alpha,
+        color=color, spatial_colors=spatial_colors, n_jobs=n_jobs,
+        bandwidth=bandwidth, adaptive=adaptive, low_bias=low_bias,
+        normalization=normalization, window='hamming')
     plt_show(show)
     return fig

mne/viz/raw.py

@@ -367,11 +367,11 @@ def plot_raw(raw, events=None, duration=10.0, start=0.0, n_channels=20,
 @verbose
 def plot_raw_psd(raw, fmin=0, fmax=np.inf, tmin=None, tmax=None, proj=False,
                  n_fft=None, n_overlap=0, reject_by_annotation=True,
-                 picks=None, ax=None, color='black', xscale='linear',
-                 area_mode='std', area_alpha=0.33, dB=True, estimate='auto',
-                 show=True, n_jobs=1, average=False, line_alpha=None,
-                 spatial_colors=True, sphere=None, window='hamming',
-                 verbose=None):
+                 picks=None, exclude='bads', ax=None, color='black',
+                 xscale='linear', area_mode='std', area_alpha=0.33, dB=True,
+                 estimate='auto', show=True, n_jobs=1, average=False,
+                 line_alpha=None, spatial_colors=True, sphere=None,
+                 window='hamming', verbose=None):
     """%(plot_psd_doc)s.
 
     Parameters
@@ -397,6 +397,9 @@ def plot_raw_psd(raw, fmin=0, fmax=np.inf, tmin=None, tmax=None, proj=False,
         is 0 (no overlap).
     %(reject_by_annotation_raw)s
     %(plot_psd_picks_good_data)s
+    exclude : list of str | 'bads'
+        Channels names to exclude from being shown. If 'bads', the
+        bad channels are excluded.
     ax : instance of Axes | None
         Axes to plot into. If None, axes will be created.
     %(plot_psd_color)s
@@ -430,8 +433,8 @@ def plot_raw_psd(raw, fmin=0, fmax=np.inf, tmin=None, tmax=None, proj=False,
         n_fft = min(np.diff(raw.time_as_index([tmin, tmax]))[0] + 1, 2048)
     # generate figure
     fig = _psd_figure(
-        inst=raw, proj=proj, picks=picks, axes=ax, tmin=tmin, tmax=tmax,
-        fmin=fmin, fmax=fmax, sphere=sphere, xscale=xscale, dB=dB,
+        inst=raw, proj=proj, picks=picks, exclude=exclude, axes=ax, tmin=tmin,
+        tmax=tmax, fmin=fmin, fmax=fmax, sphere=sphere, xscale=xscale, dB=dB,
         average=average, estimate=estimate, area_mode=area_mode,
         line_alpha=line_alpha, area_alpha=area_alpha, color=color,
         spatial_colors=spatial_colors, n_jobs=n_jobs, n_fft=n_fft,

mne/viz/tests/test_epochs.py

@@ -349,6 +349,8 @@ def test_plot_psd_epochs(epochs):
     epochs.plot_psd(average=True, spatial_colors=False)
     epochs.plot_psd(average=False, spatial_colors=True)
     epochs.plot_psd(average=False, spatial_colors=False)
+    epochs.plot_psd(average=True, exclude='bads')
+
     # test plot_psd_topomap errors
     with pytest.raises(RuntimeError, match='No frequencies in band'):
         epochs.plot_psd_topomap(bands=[(0, 0.01, 'foo')])

mne/viz/tests/test_figure.py

@@ -15,4 +15,4 @@ def test_browse_figure_constructor():
 def test_psd_figure_constructor():
     """Test error handling in MNELineFigure constructor."""
     with pytest.raises(TypeError, match='an instance of Raw or Epochs, got'):
-        _psd_figure('foo', *((None,) * 19))
+        _psd_figure('foo', *((None,) * 20))

mne/viz/tests/test_raw.py

@@ -588,6 +588,8 @@ def test_plot_raw_psd(raw):
     picks = pick_types(raw.info, meg='mag', eeg=False)[:4]
     raw.plot_psd(tmax=None, picks=picks, area_mode='range', average=False,
                  spatial_colors=True)
+    raw.plot_psd(tmax=None, picks=picks, exclude='bads', area_mode='range',
+                 average=False, spatial_colors=True)
     raw.plot_psd(tmax=20., color='yellow', dB=False, line_alpha=0.4,
                  n_overlap=0.1, average=False)
     plt.close('all')
@@ -663,6 +665,9 @@ def test_plot_raw_psd(raw):
                           verbose='error')
     fig = raw.plot_psd()
     assert len(fig.axes) == 10
+    # test excludeing one channel
+    fig = raw.plot_psd(exclude=['MEG 0113'])
+    assert len(fig.axes) == 9
     plt.close('all')
 
     # gh-7631