ENH: add reading montages #1390

dengemann · 2014-06-25T16:03:07Z

self-explanatory, I think

dengemann · 2014-06-25T16:07:39Z

cc @deep-introspection

dengemann · 2014-06-25T16:08:32Z

@deep-introspection we could actually also add support for your polhemus files here. please share

dengemann · 2014-06-25T17:34:00Z

examples/plot_from_raw_to_epochs_to_evoked.py

unfortunately the wrong montage ....

dengemann · 2014-06-25T17:35:03Z

cc @t3on @christianbrodbeck this might also be interesting for you. Feedback welcome.

deep-introspection · 2014-06-26T14:08:51Z

@dengemann Seems cool! Shall I send you a sample file? How can I help?

dengemann · 2014-06-26T14:12:37Z

@deep-introspection are you around? We could try to find some time to move on with things. Today is open night at La Paillasse. If you have data for which you know how things are supposed to look like we could try and play with the montages. Adding polhemus is also a good idea.

coveralls · 2014-06-26T14:27:00Z

Coverage increased (+0.0%) when pulling 18ba184 on dengemann:montage into f4c6245 on mne-tools:master.

coveralls · 2014-06-26T14:42:44Z

Coverage increased (+0.0%) when pulling 18ba184 on dengemann:montage into f4c6245 on mne-tools:master.

deep-introspection · 2014-06-26T17:13:54Z

@dengemann I am not available tonight... There is a brainy event Sunday late afternoon at La Generale (http://www.lagenerale.fr/?p=4674), want to meet before in the corner(~2pm)?

agramfort · 2014-07-23T11:47:08Z

@t3on can you give @dengemann a hand on this?

wmvanvliet · 2014-09-25T06:35:18Z

What more is needed to complete this PR? Can I help?

dengemann · 2014-09-25T11:53:09Z

@wmvanvliet @t3on let me review and see where we are. I think this PR is actually almost ready.

dengemann · 2014-09-25T12:23:37Z

I rebased this branch. If I remember correctly a rotation of the coordinates is missing for one of the montages. Thanks to our new interpolation + topomap plots this should be easy to figure out.

wmvanvliet · 2014-10-01T05:42:42Z

A few things that needed doing before I could merge it in my own fork:

moving your edits to viz.py to viz/montages.py
match against full montage name instead of part of it to remove ambiguity between M1 and M10 montages
use os.path.splitext instead of relying on filename[:4] to deal with file extensions

You can find these changes at my montage branch, pull from there if you like them.

dengemann · 2014-10-01T10:25:03Z

@wmvanvliet you can send me a PR into this branch, how about that? Visit my fork and open a PR, I'm happy to review and incorporate your changes.

wmvanvliet · 2014-10-01T20:55:44Z

took me a while how to make a PR from a specific fork/branch to a specific fork/branch, but I got it working now.

Marijn.

On 1 okt. 2014, at 12:25, Denis A. Engemann notifications@github.com wrote:

@wmvanvliet you can send me a PR into this branch, how about that? Visit my fork and open a PR, I'm happy to review and incorporate your changes.

—
Reply to this email directly or view it on GitHub.

Marijn van Vliet
w.m.vanvliet@gmail.com

larsoner · 2014-10-02T21:13:54Z

Files should go in mne/data/montages instead of creating a new root directory mne/montages

larsoner · 2014-10-02T21:14:05Z

Also needs a rebase

wmvanvliet · 2014-10-17T12:50:39Z

the easycaps coordinates are wrong. They are rotated 90 degrees along the x-axis.

dengemann · 2014-10-19T15:34:55Z

@wmvanvliet yo, it turns out the montage was correct all the time (before the last commits). It's just that the sample dataset uses M11 not M10 as I seem to have figured. We need to rethink the example. M11 coordinates are not available as far as I know. Using standard 10-5 system we could have a mapping if we knew the standard channel names and the order but we don't. I'm now taking a look at the other EEG dataset that we have.

coveralls · 2014-10-31T09:34:08Z

Coverage increased (+0.0%) when pulling c8a7c65 on dengemann:montage into 9bc5e41 on mne-tools:master.

When some sensors are defined in the montage file, but not present in the info structure, they are silently skipped.

Also don't use try/catch

update manifest.in some cleanup (s/layout/montage etc.)

coveralls · 2014-10-31T10:31:48Z

Coverage decreased (-0.01%) when pulling e7a5907 on dengemann:montage into 5997ec8 on mne-tools:master.

coveralls · 2014-10-31T10:56:46Z

Coverage decreased (-0.01%) when pulling e7a5907 on dengemann:montage into 5997ec8 on mne-tools:master.

coveralls · 2014-10-31T12:36:15Z

Coverage decreased (-0.01%) when pulling c72ecc6 on dengemann:montage into 5997ec8 on mne-tools:master.

agramfort · 2014-10-31T13:06:28Z

I am done here (i think)

let's wait for travis to be happy and let's merge !

coveralls · 2014-10-31T13:13:59Z

Coverage decreased (-0.01%) when pulling 217e1f4 on dengemann:montage into 5997ec8 on mne-tools:master.

coveralls · 2014-10-31T13:31:13Z

Coverage decreased (-0.01%) when pulling 0d0879b on dengemann:montage into 5997ec8 on mne-tools:master.

ENH: add reading montages

dengemann · 2014-10-31T13:34:07Z

@wmvanvliet @agramfort thanks for your participation. One more EEG feature merged :)

dengemann reviewed Jun 25, 2014
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unfortunately the wrong montage ....

dengemann force-pushed the montage branch from 18ba184 to a3b85c7 Compare September 25, 2014 12:19

dengemann mentioned this pull request Sep 29, 2014

ENH add biosemi layout #1581

Merged

dengemann force-pushed the montage branch 2 times, most recently from 4bc1efc to 42621a4 Compare October 15, 2014 16:25

wmvanvliet mentioned this pull request Oct 21, 2014

Topo plots for EEG data, even when no digitization points are present #1619

Merged

dengemann added 4 commits October 31, 2014 10:46

ENH: add montage reading support

5e419c4

add files

ada6762

cosmits

8db275e

ENH: add apply montage function

4ebddd5

wmvanvliet and others added 14 commits October 31, 2014 10:46

Skip missing sensors

0cc2ff1

When some sensors are defined in the montage file, but not present in the info structure, they are silently skipped.

Throw exception when no sensors match

1a987c3

Also don't use try/catch

Added montages to setup

3488cb2

fixed mayavi check

7b20fca

fix mayavi import

b1e0194

example fixes

1751e40

topop xy fix attempt

8894a7c

Added flag to plot electrode names

1c1b32f

small fix

4826354

draw_names -> show_names

ab3f1fb

revert transformation and show names

9a186b4

rename names to ch_names

d1e322d

update manifest.in some cleanup (s/layout/montage etc.)

add csd reading support

472672a

ENH : plot montage with matplotlib (not mayavi)

e7a5907

agramfort force-pushed the montage branch from c5a32ca to e7a5907 Compare October 31, 2014 09:46

remove montage from examples until we have a good demo dataset

4bc6380

update what's new + python reference

217e1f4

agramfort force-pushed the montage branch from c72ecc6 to 217e1f4 Compare October 31, 2014 12:38

agramfort added 2 commits October 31, 2014 13:40

fix docstring

7356c19

fix py3k

0d0879b

dengemann added a commit that referenced this pull request Oct 31, 2014

Merge pull request #1390 from dengemann/montage

7e5b90e

ENH: add reading montages

dengemann merged commit 7e5b90e into mne-tools:master Oct 31, 2014

massich mentioned this pull request Feb 15, 2019

[wip] [I will rewrite hist] work-on montage #5836

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ENH: add reading montages #1390

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