[MRG] ENH/DOC: demo custom spectrum creation by dengemann · Pull Request #11493 · mne-tools/mne-python

dengemann · 2023-02-17T21:25:04Z

What does this implement/fix?

Explain your changes.

A simple example of how to put custom power spectral data into an average Spectrum class.
A proper SpectrumArray class could follow if there is interest.

Additional information

Any additional information you think is important.

Discussed with @drammock @hoechenberger in past 2 office hours.

tutorials/simulation/10_array_objs.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

dengemann · 2023-02-17T22:17:35Z

tutorials/simulation/10_array_objs.py

+        dims=('channel', 'freq'),
+        freqs=freqs,
+        inst_type_str='Raw',
+        data_type='simulated signals',


@drammock I put this for illustration purposes. Are there any expectations in the Spectrum code regarding this field? It was 'Averaged EEG' in my concrete case on which this example is based.

right now it is only used in the repr of the object. I don't have any concrete plans to use it in any other way (and I would actively avoid using it in if clauses to triage different flavors of spectrum, it's probably not reliable to do so)

native values for this are Fourier Coefficients, Power Spectrum, and Averaged Power Spectrum. Averaged Fourier Coefficients is not supported, see

mne-python/mne/time_frequency/spectrum.py

Lines 1109 to 1118 in 18474b1

# averaging unaggregated spectral estimates are not supported

if hasattr(self, '_mt_weights'):

raise NotImplementedError(

'Averaging complex spectra is not supported. Consider '

'averaging the signals before computing the complex spectrum.')

elif 'segment' in self._dims:

raise NotImplementedError(

'Averaging individual Welch segments across epochs is not '

'supported. Consider averaging the signals before computing '

'the Welch spectrum estimates.')

drammock · 2023-02-17T23:32:34Z

CircleCI failure is this:

Traceback (most recent call last):
  File "/home/circleci/project/tutorials/simulation/10_array_objs.py", line 243, in <module>
    spectrum.plot(picks=[0, 1])
  File "/home/circleci/project/mne/time_frequency/spectrum.py", line 606, in plot
    _plot_psd(self, fig, self.freqs, psd_list, picks_list, titles_list,
  File "/home/circleci/project/mne/viz/utils.py", line 2297, in _plot_psd
    _plot_lines(psd_array, info, picks, fig, ax_list, spatial_colors,
  File "/home/circleci/project/mne/viz/evoked.py", line 472, in _plot_lines
    warn('Channel locations not available. Disabling spatial '
  File "/home/circleci/project/mne/utils/_logging.py", line 400, in warn
    warnings.warn_explicit(
RuntimeWarning: Channel locations not available. Disabling spatial colors.

it's just a warning, but it's annoying when this breaks our CIs. Makes me wonder if we should either (1) make it a logger.info or (2) make spatial_colors='auto' somehow.

drammock

changes LGTM. +1 for merge when CIs are green.

My one hesitation is about data_type: I might be more comfortable sticking with Power Spectrum here, since our tutorials are implicitly supposed to demonstrate best practices and Power Spectrum would be the most consistent description of what the data are.

dengemann · 2023-02-18T22:43:50Z

Comments addressed, CIs green. Good to go from my side.

hoechenberger · 2023-02-19T09:19:05Z

The only thing I'd change is the indentation of the custom function header; I would blackify it

tutorials/simulation/10_array_objs.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

* upstream/main: (46 commits) Fix docstrings by replacing str with path-like and fix double backticks for formatting (mne-tools#11499) Use pathlib.Path instead of os.path to handle files and folders [circle deploy] (mne-tools#11473) MAINT: Fix Circle [circle deploy] (mne-tools#11497) MAINT: Use mamba in CIs (mne-tools#11471) Updating documentation to clarify full vs half-bandwidth and defaults in time_frequency.multitaper.py (mne-tools#11479) Fix typo in tutorial (mne-tools#11498) Typo fix and added colons before code (mne-tools#11496) [MRG] ENH/DOC: demo custom spectrum creation (mne-tools#11493) Accept only left-clicks for adding annotations (mne-tools#11491) [BUG, MRG] Fix pial surface loading, logging in locate_ieeg (mne-tools#11489) [ENH] Added unit_role to add non-breaking space between magnitude and units (mne-tools#11469) MAINT: Fix CircleCI build (mne-tools#11488) [DOC] Updated decoding.SSD documentation and internal variable naming (mne-tools#11475) Typo fix (mne-tools#11485) [MRG] Forward argument axes from plot_sensors to DigMontage.plot (mne-tools#11470) [MRG] Improve error message raised on channels missing from DigMontage (mne-tools#11472) MAINT: Deal with pkg_resources usage bugs (mne-tools#11478) Add object array support and docstring (mne-tools#11465) [ENH] Adjusted SSD algorithm to support non-full rank data (mne-tools#11458) [BUG] fix nibabel reference (mne-tools#11467) ...

* upstream/main: (264 commits) BUG: Fix deprecated API usage in example (mne-tools#11512) Deprecate 'kind' and 'path' in favor of 'fname' in the layout reader (mne-tools#11500) EGI/MFF events outside EEG recording should not break the code (mne-tools#11505) fixed annotations error on export (mne-tools#11435) DOC: Update installer links [skip azp] [skip actions] [skip cirrus] (mne-tools#11506) BUG: updates for MPL 3.7 compatibility (mne-tools#11409) Fix docstrings by replacing str with path-like and fix double backticks for formatting (mne-tools#11499) Use pathlib.Path instead of os.path to handle files and folders [circle deploy] (mne-tools#11473) MAINT: Fix Circle [circle deploy] (mne-tools#11497) MAINT: Use mamba in CIs (mne-tools#11471) Updating documentation to clarify full vs half-bandwidth and defaults in time_frequency.multitaper.py (mne-tools#11479) Fix typo in tutorial (mne-tools#11498) Typo fix and added colons before code (mne-tools#11496) [MRG] ENH/DOC: demo custom spectrum creation (mne-tools#11493) Accept only left-clicks for adding annotations (mne-tools#11491) [BUG, MRG] Fix pial surface loading, logging in locate_ieeg (mne-tools#11489) [ENH] Added unit_role to add non-breaking space between magnitude and units (mne-tools#11469) MAINT: Fix CircleCI build (mne-tools#11488) [DOC] Updated decoding.SSD documentation and internal variable naming (mne-tools#11475) Typo fix (mne-tools#11485) ...

demo custom spectrum creation

4ea147d

dengemann requested a review from drammock February 17, 2023 21:25

dengemann added 2 commits February 17, 2023 22:27

cosmit

21ce1c2

Merge branch 'main' into SpectrumArray

dd86e96

hoechenberger reviewed Feb 17, 2023

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dengemann and others added 2 commits February 17, 2023 23:14

Update tutorials/simulation/10_array_objs.py

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Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

Update tutorials/simulation/10_array_objs.py

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Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

dengemann commented Feb 17, 2023

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drammock approved these changes Feb 17, 2023

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address comments by @drammock

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dengemann changed the title ~~ENH/DOC: demo custom spectrum creation~~ [MRG] ENH/DOC: demo custom spectrum creation Feb 18, 2023

hoechenberger approved these changes Feb 19, 2023

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Update tutorials/simulation/10_array_objs.py

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Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

hoechenberger approved these changes Feb 19, 2023

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hoechenberger enabled auto-merge (squash) February 19, 2023 21:13

hoechenberger merged commit 0cafb67 into mne-tools:main Feb 19, 2023

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[MRG] ENH/DOC: demo custom spectrum creation#11493

[MRG] ENH/DOC: demo custom spectrum creation#11493
hoechenberger merged 7 commits intomne-tools:mainfrom
dengemann:SpectrumArray

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	# averaging unaggregated spectral estimates are not supported
	if hasattr(self, '_mt_weights'):
	raise NotImplementedError(
	'Averaging complex spectra is not supported. Consider '
	'averaging the signals before computing the complex spectrum.')
	elif 'segment' in self._dims:
	raise NotImplementedError(
	'Averaging individual Welch segments across epochs is not '
	'supported. Consider averaging the signals before computing '
	'the Welch spectrum estimates.')

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dengemann commented Feb 17, 2023

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hoechenberger commented Feb 19, 2023 •

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