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ENH: set color for bad channel with spatial_colors=True #12142

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merged 5 commits into from
Oct 27, 2023

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larsoner
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@larsoner larsoner commented Oct 26, 2023

Closes #12137

@hoechenberger can you try it with your data to see if it helps?

This will affect at least evoked.plot and spectrum.plot as spatial_colors=True by default.

  • See if it actually helps with reports
  • Add test
  • Add changelog entry

@larsoner larsoner added this to the 1.6 milestone Oct 26, 2023
@hoechenberger
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@larsoner i don't know when I'll will have time to test this, don't wait for me 🥹

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On main:

import mne
raw = mne.io.read_raw_fif(mne.datasets.sample.data_path() / "MEG" / "sample" / "sample_audvis_filt-0-40_raw.fif")
raw.pick("eeg", exclude=()).load_data()
raw.plot_psd(exclude=())

gives:

Screenshot from 2023-10-26 11-51-49

On this PR it's:

Screenshot from 2023-10-26 11-55-43

There is a bug on main where bad_ch_idx=[] so the dashed-ness was never applied. But I like that in this PR that is applied and it's gray -- I think it works well.

With the gray we could consider getting rid of the dashing which makes the bad one easier to resolve:

Screenshot from 2023-10-26 11-56-49

@hoechenberger
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I like the last figure you posted!

@larsoner
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Ready for review/merge from my end.

When I modified the Report tutorial with dashing turned off it looked like this. So I decided in the end to keep it to make it slightly more differentiable.

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👌

@larsoner larsoner merged commit cdad29d into mne-tools:main Oct 27, 2023
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@larsoner larsoner deleted the bads branch October 27, 2023 01:51
larsoner added a commit to larsoner/mne-python that referenced this pull request Nov 3, 2023
* upstream/main: (35 commits)
  [DOC] Add documentation for setting montage order (mne-tools#12160)
  Fix inferring fiducials from EEGLAB (mne-tools#12165)
  Try to fix ICA Report (mne-tools#12167)
  BUG: Fix bug with Report.add_ica component number (mne-tools#12156)
  MAINT: Add rstcheck to CIs and pre-commit (mne-tools#12163)
  DOC: fix sphinx style typos (mne-tools#12161)
  MAINT: Fix linkcheck (mne-tools#12162)
  ENH: Add multiple label support to source_band_induced_power, source_induced_power (mne-tools#12026)
  Allow automated metadata generation to be bounded by "row events" instead of explicit time windows (mne-tools#12118)
  ENH: Collapse only in doc gen (mne-tools#12145)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#12155)
  BUG: Fix bug with interior points not showing (mne-tools#12148)
  ENH: Warn about versions in sys_info (mne-tools#12146)
  Fix in conftest.py (mne-tools#12150)
  ENH: set color for bad channel with spatial_colors=True (mne-tools#12142)
  DOC: Better documentation of realign_raw (mne-tools#12135)
  Add mne-icalabel wildcard (mne-tools#12143)
  Remove LGTM.com configuration file (mne-tools#12139)
  DOC: Fix typo found by codespell (mne-tools#12140)
  DOC: Document governance updates (mne-tools#12133)
  ...
larsoner added a commit to JD-Zhu/mne-python that referenced this pull request Nov 3, 2023
* upstream/main: (26 commits)
  FIX: Fix bug with coreg scalars (mne-tools#12164)
  Changed casting rule in np.clip to allow reading of raw GDF files (mne-tools#12168)
  [DOC] Add documentation for setting montage order (mne-tools#12160)
  Fix inferring fiducials from EEGLAB (mne-tools#12165)
  Try to fix ICA Report (mne-tools#12167)
  BUG: Fix bug with Report.add_ica component number (mne-tools#12156)
  MAINT: Add rstcheck to CIs and pre-commit (mne-tools#12163)
  DOC: fix sphinx style typos (mne-tools#12161)
  MAINT: Fix linkcheck (mne-tools#12162)
  ENH: Add multiple label support to source_band_induced_power, source_induced_power (mne-tools#12026)
  Allow automated metadata generation to be bounded by "row events" instead of explicit time windows (mne-tools#12118)
  ENH: Collapse only in doc gen (mne-tools#12145)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#12155)
  BUG: Fix bug with interior points not showing (mne-tools#12148)
  ENH: Warn about versions in sys_info (mne-tools#12146)
  Fix in conftest.py (mne-tools#12150)
  ENH: set color for bad channel with spatial_colors=True (mne-tools#12142)
  DOC: Better documentation of realign_raw (mne-tools#12135)
  Add mne-icalabel wildcard (mne-tools#12143)
  Remove LGTM.com configuration file (mne-tools#12139)
  ...
snwnde pushed a commit to snwnde/mne-python that referenced this pull request Mar 20, 2024
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Should PSD plots in the report contain bad channels by default?
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