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[MRG] Do not exclude bads if channel indices are supplied#6678

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agramfort merged 1 commit intomne-tools:masterfrom
cbrnr:plot_psd_bads
Aug 20, 2019
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[MRG] Do not exclude bads if channel indices are supplied#6678
agramfort merged 1 commit intomne-tools:masterfrom
cbrnr:plot_psd_bads

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@cbrnr cbrnr commented Aug 20, 2019

Fixes #6637. The following example correctly produces the PSD for all channels supplied in picks:

import mne
from mne.datasets import sample


data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(raw_fname, preload=True)

raw.drop_channels(raw.info["ch_names"][:315])
raw.drop_channels(raw.info["ch_names"][4:])
raw.info["bads"] = ['EEG 003', 'EEG 004']

raw.plot_psd(spatial_colors=False, picks=range(4))  # plot all 4 channels

The default behavior is still to exclude bad channels, that is

raw.plot_psd(spatial_colors=False)
raw.plot_psd(spatial_colors=False, picks="all")

generate PSDs only for the 2 good channels just like before.

However, I don't know what's the deal with spatial_colors=True, which only plots 3 channels ("EEG 001", "EEG 002", and "EEG 004"). But maybe this should be fixed in a different PR.

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codecov bot commented Aug 20, 2019 •
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Codecov Report

Merging #6678 into master will not change coverage.
The diff coverage is n/a.

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  Coverage   89.39%   89.39%           
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  Files         415      415           
  Lines       75230    75230           
  Branches    12366    12366           
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  Hits        67249    67249           
  Misses       5149     5149           
  Partials     2832     2832

@cbrnr cbrnr changed the title Do not exclude bads if channel indices are supplied [MRG] Do not exclude bads if channel indices are supplied Aug 20, 2019
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cbrnr commented Aug 20, 2019

Regarding spatial_colors=True, actually all 4 channels are plotted, but one of them in light light almost white gray so that I was not able to see it.
Figure_1
Not sure if this is intended or should be changed, but not in this PR. So I guess the original issue has been resolved and this is ready for merge.

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agramfort commented Aug 20, 2019

it's because colors are coming from relative position on the topo (not absolute)

can you open a dedicated issue?

@agramfort agramfort merged commit 86ab291 into mne-tools:master Aug 20, 2019
@cbrnr cbrnr deleted the plot_psd_bads branch August 21, 2019 06:43
@cbrnr cbrnr mentioned this pull request Aug 21, 2019
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alexrockhill pushed a commit to alexrockhill/mne-python that referenced this pull request Oct 1, 2019
@cbrnr
Do not exclude bads if channel indices are supplied (mne-tools#6678)
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@cbrnr cbrnr mentioned this pull request Jun 2, 2021
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Ignoring bads in raw.plot_psd doesn't work

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@cbrnr @agramfort @larsoner