Add example showing all the eeg helmets by massich · Pull Request #6158 · mne-tools/mne-python

massich · 2019-04-16T16:14:30Z

This PR mimics the first step of #6146 for all the montage files. And fix whatever is needed to have a convenient user code like:

for current_montage in get_builtin_montages():
    montage = mne.channels.read_montage(current_montage)
    info = mne.create_info(ch_names=montage.ch_names,
                           sfreq=1,
                           ch_types='eeg',
                           montage=montage)

    plot_alignment(info, trans=None, subject='fsaverage',
                   subjects_dir=subjects_dir,
                   eeg=['original', 'projected'])

What I've used to see if the results are more or less ok

agramfort · 2019-04-16T17:09:11Z

here is the rendered doc: https://12266-1301584-gh.circle-artifacts.com/0/dev/auto_examples/visualization/plot_montage.html

to should see montage file by montage file what option is needed to make it correct.
I expect some adhoc options that we should make superfluous with a future release
so it jsut works out of the box for any of these files

@massich can you report which should be fixed to move forward here?

codecov · 2019-04-16T19:51:52Z

Codecov Report

Merging #6158 into master will increase coverage by 1.77%.
The diff coverage is 50%.

@@            Coverage Diff             @@
##           master    #6158      +/-   ##
==========================================
+ Coverage   87.21%   88.98%   +1.77%     
==========================================
  Files         412      412              
  Lines       73985    74004      +19     
  Branches    12270    12273       +3     
==========================================
+ Hits        64525    65853    +1328     
+ Misses       6588     5249    -1339     
- Partials     2872     2902      +30

massich · 2019-04-18T14:17:36Z

the easycap_m10 seems a bit off in pitch, based on this

And so does M1

massich · 2019-04-19T11:07:49Z

https://12328-1301584-gh.circle-artifacts.com/0/dev/auto_examples/visualization/plot_montage.html?highlight=plot_montage

agramfort

what do we do with this PR? I am now lost.

agramfort · 2019-04-20T09:03:53Z

mne/channels/montage.py

-        Unit of the input file. If not 'm' (default), coordinates will be
-        rescaled to 'm'.
+    unit : 'm' | 'cm' | 'mm' | 'auto'
+        Unit of the input file. Defaults to 'auto'.


'auto' is not documented

agramfort · 2019-04-20T09:04:07Z

examples/visualization/plot_montage.py

+Plotting sensor layouts of EEG Systems
+======================================
+
+Show sensor layouts of different EEG systems.


too short. please explain more what you did.

massich · 2019-04-20T09:15:10Z

This pr was adding a short example. Shame as the example we have with MEG helmet. But rather than showing the default Meg helmets shows the eeg default montages. In other words, a place to point people.

…

On Sat, Apr 20, 2019, 11:05 Alexandre Gramfort ***@***.***> wrote: ***@***.**** commented on this pull request. what do we do with this PR? I am now lost. ------------------------------ In mne/channels/montage.py <#6158 (comment)>: > @@ -132,9 +132,8 @@ def read_montage(kind, ch_names=None, path=None, unit='m', transform=False): path : str | None The path of the folder containing the montage file. Defaults to the mne/channels/data/montages folder in your mne-python installation. - unit : 'm' | 'cm' | 'mm' - Unit of the input file. If not 'm' (default), coordinates will be - rescaled to 'm'. + unit : 'm' | 'cm' | 'mm' | 'auto' + Unit of the input file. Defaults to 'auto'. 'auto' is not documented ------------------------------ In examples/visualization/plot_montage.py <#6158 (comment)>: > @@ -0,0 +1,45 @@ +# -*- coding: utf-8 -*- +""" +Plotting sensor layouts of EEG Systems +====================================== + +Show sensor layouts of different EEG systems. too short. please explain more what you did. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6158 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVX5Y743CECD4VVAKRXJ4TPRLMEBANCNFSM4HGLFQOA> .

agramfort · 2019-04-20T10:27:19Z

yes I understand the purpose but it contains the fsaverage fetcher so I cannot merge this.

* FIX: Fix inconsistencies with compute_proj_raw * BUG: SciPy req

…ne-tools#6143)

* Added import _freq_mask Enable import the function _freq_mask from .numerics * Added _freq_mask function Added _freq_mask function equivalent to _time_mask function, but for frequency * Added tests for _freq_mask Added tests for _freq_mask * Added frequency cropping args to BaseTFR class Enables frequency cropping with tfr.crop(fmin, fmax) for TFR objects * Enhanced test_crop Enhanced test_crop to also test for frequency cropping. * updated documentation for BaseTFR.crop function, fixed floating point issues in utils.numerics._freq_mask * Updated docstring for BaseTFR.crop Updated docstring for BaseTFR.crop to show fmin/fmax params * Fixed _freq_mask fixed floating point error in _freq_mask * Adapted test_freq_mask to function changes Adapted test_freq_mask to error fix in freq_mask * Adapted docstring BaseTFR.crop Adapted docstring for version in BaseTFR.crop * Removed Debugging notes Removed Debugging notes from test_crop * correct spacing correct spacing * Fixed code format Fixed some code for flake8 * Updated whats_new.rst Added changes to whats_new.rst * Updated whats_new.rst Fixed update to whats_new.rst * Eliminated Conflicts with master eliminated merge conflicts in mne.utils.__init__.py Also edited test_freq_mask and test_time_mask mne.utils.tests.test_numerics to find errors more explicitely. * fixed flake8 probs * changed _time/_freq_mask code style changed code format and error message. * Removed sfreq=None from _freq_mask -Removed sfreq=None argument default from mne/utils/numerics.py::_freq_mask -Adapted relevant tests and methods accordingly * Removed support for sfreq=None from _freq_mask -Introduced raise(ValueError) When sfreq=None -Introduced tests for sfreq=None case * Made _BaseTFR.crop omit mask if not defined. - _time_mask or _freq_mask are only called, if they were defined in crop() - _time_mask, _freq_mask were changed back to save time & mem * corrected new merge conflicts once again corrected merge conflicts with mne/utils/__init__.py * corrected conditions in _BaseTFR.crop corrected ```_time_mask``` and ```_freq_mask``` conditions in ```_BaseTFR.crop()``` * Make TFR raise value error for freqs <= 0 Make multitaper and morlet raise a value error if freqs include a frequency <= 0. Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at> * convert freqs in morlet and _make_dpss to np.array convert freqs in morlet and _make_dpss to np.array for faster computation Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at> * changed error statements changed error statements for invalid frequencies passed in mne/time_frequency/tfr.py ::morlet and ::_make_dpss Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>

…ne-tools#6173) * better title in plot_compare_evokeds (closes mne-tools#6165) * use logger.info instead of warn * fix stupidity * simplify

…ne-tools#6182)

…mestamps (mne-tools#6184) * DOC: make sure you get a warning when reading onsets which are not timestamps in .csv * non-empty match

* Add an example using the LSLClient n_chan --> n_channels * Refactor FTClient; Add MockLSLStream, refactor test to use mock stream * update reference and whats new * fixing some errors * update style * temp * improvements to the realtime module currently the test is breaking when it comes to using the RtEpochs object. * minor fix * move the RtEpochs testing to separate PR * cleanup * fix the way super is called * updated the MockLSLStream to take raw instance * add time dilation factor, cleanup * add more info on lsl identifier * address ci * skip running test with multiprocessing on windows Windows runs into a problem with multiprocessing: 'https://stackoverflow.com/questions/50079165/' * cleaned up the windows check * update the pylsl requirement to 1.12 this is compatible across platforms

* Keep eric's fsaverage * make set_montage_coreg_path as private * stip check manifest out from fsaverage * ENH: better parameter name * move the fsaverage info to fsaverage * FIX: docstring * [skip ci] move fsaverage files * rename * update the fsaverage manifests * FIX: use the new zip files * FIX: Fix test * FIX: manifests * FIX: Manifest again * FIX: Doc * FIX: call montage setter * ENH: Simplify * FIX: string * fix * Skip the test for 3.5, since zipfiles cannot be written

larsoner · 2019-04-23T22:28:09Z

Thanks @massich

Add plot_montage (that uses the same code as plot_eeg_no_mri)

8be92ab

massich force-pushed the plot_eeg_helmets branch from 14e4c60 to b128ec9 Compare April 16, 2019 19:51

massich force-pushed the plot_eeg_helmets branch from b128ec9 to 8be92ab Compare April 16, 2019 20:33

massich added the Digitization label Apr 17, 2019

agramfort changed the title ~~Add example showing all the eeg helmets~~ [WIP] Add example showing all the eeg helmets Apr 20, 2019

agramfort reviewed Apr 20, 2019

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massich self-assigned this Apr 23, 2019

Joan Massich and others added 15 commits April 23, 2019 15:01

MAINT: Use version-based permalink for download (mne-tools#6161)

22c2b41

use unit='auto'

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use auto and transform=False

9b01b71

fix

fac9c01

MRG: Fix inconsistencies with compute_proj_raw (mne-tools#6160)

96d1070

* FIX: Fix inconsistencies with compute_proj_raw * BUG: SciPy req

ENH: Add the ids='all' as an option for mne.event.shift_time_events (m…

cce5cec

…ne-tools#6143)

nilearn was updated

1690d14

init (mne-tools#6181)

8dc00bf

MRG+1: better title in plot_compare_evokeds (closes mne-tools#6165) (m…

fd1d227

…ne-tools#6173) * better title in plot_compare_evokeds (closes mne-tools#6165) * use logger.info instead of warn * fix stupidity * simplify

This commit adds additional explanation to the contributing guide. (m…

09eeb1e

…ne-tools#6182)

DOC: make sure you get a warning when reading onsets which are not ti…

2e0d870

…mestamps (mne-tools#6184) * DOC: make sure you get a warning when reading onsets which are not timestamps in .csv * non-empty match

update example to use fetch_fsaverage

79ccebc

massich force-pushed the plot_eeg_helmets branch from 27b251b to 79ccebc Compare April 23, 2019 13:59

Merge branch 'master' into plot_eeg_helmets

c88bf12

Joan Massich added 4 commits April 23, 2019 17:59

whats new + couple words

c9f75ae

Merge branch 'master' into plot_eeg_helmets

2226da4

document 'auto'

72c12e0

Cross reference the example

d4613b8

massich changed the title ~~[WIP] Add example showing all the eeg helmets~~ Add example showing all the eeg helmets Apr 23, 2019

Joan Massich and others added 3 commits April 23, 2019 18:44

fix cross references

f5553d4

I forgot one

8f16135

FIX: Spelling [ci skip]

f0044f3

larsoner merged commit 0b637d8 into mne-tools:master Apr 23, 2019

jeythekey pushed a commit to jeythekey/mne-python that referenced this pull request Apr 27, 2019

Add example showing all the eeg helmets (mne-tools#6158)

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massich deleted the plot_eeg_helmets branch May 27, 2019 12:09

massich mentioned this pull request Jun 17, 2019

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Add example showing all the eeg helmets#6158

Add example showing all the eeg helmets#6158
larsoner merged 24 commits intomne-tools:masterfrom
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