adding basic auto-scaling functionality for raw and epochs classes #3198

choldgraf · 2016-04-29T23:24:54Z

This is a first-pass PR at adding auto-scaling functionality for plotting raw / epoched data. The basic change is to include a "compute_scalings" function in the viz.utils module. This takes a scalings dictionary, and for any value that is 'auto', it will use the data instance provided to auto-calculate the scaling. Alternatively you can supply only the string "auto" and it'll auto-compute for all channel types in the data. Then it goes on to plotting as normal.

There are some weird things that I did to make iterating through channel types easier (e.g., I've got a hard-coded list of channel types but maybe that exists elsewhere, I also wrote a function to return a list of the channel type for all channels, as well as a dictionary of channel type: ixs, but maybe that's already been done elsewhere?)

Suggestions etc are welcome! Here's the basic idea of what this does:

scalings_def = dict(eeg='auto', grad='auto')
scalings_raw = mne.viz.utils.compute_scalings(scalings_def, raw)
scalings_ep = mne.viz.utils.compute_scalings(scalings_def, epochs)
scalings_all = mne.viz.utils.compute_scalings('auto', raw)
print('{}\n\n{}\n\n{}\n\n{}'.format(scalings_def, scalings_raw, scalings_ep, scalings_all))

{'eeg': 'auto', 'grad': 'auto'}

{'eeg': 7.1589975858543653e-05, 'grad': 1.928710961556987e-11}

{'eeg': 3.6195661505710243e-05, 'grad': 3.506747202830885e-11}

{'ecg': None, 'bio': None, 'emg': None, 'stim': 0.0, 'eog': 1.7976379496076333e-05, 'ref_meg': None, 'resp': None, 'misc': None, 'seeg': None, 'chpi': None, 'mag': 1.3265991686001318e-12, 'syst': None, 'eeg': 7.1589975858543653e-05, 'grad': 1.928710961556987e-11, 'ias': None, 'exci': None}

originally comes from #2253

kingjr · 2016-04-30T01:51:50Z

mne/viz/utils.py


+_channel_types = ['eeg', 'seeg', 'eog', 'ecg', 'emg', 'ref_meg', 'stim',
+                  'resp', 'misc', 'chpi', 'syst', 'ias', 'exci', 'bio']
+_meg_types = ['mag', 'grad']


shouldn't this be (already?) in mne.channels?

agramfort · 2016-04-30T11:39:59Z

have a look at the _picks_by_type function in pick.py and maybe _PICK_TYPES_DATA_DICT, _PICK_TYPES_KEYS and _DATA_CH_TYPES_SPLIT in pick.py

coveralls · 2016-04-30T17:58:38Z

Coverage decreased (-0.1%) to 90.704% when pulling 31b68c0 on choldgraf:add_plot_auto_scale into 199c8e9 on mne-tools:master.

choldgraf · 2016-04-30T21:34:10Z

Think I addressed people's comments. Using percentile now instead of absolute median deviation, also updated dictionaries to be 2.6 compatible

choldgraf · 2016-04-30T21:36:19Z

Also hanging participle has been fixed @kingjr, I'll make sure to bring my copy of Strunk and White for my next PR :)

coveralls · 2016-04-30T21:46:52Z

Coverage decreased (-0.1%) to 90.698% when pulling 9ceb761 on choldgraf:add_plot_auto_scale into 199c8e9 on mne-tools:master.

coveralls · 2016-04-30T22:05:33Z

Coverage increased (+0.0004%) to 90.808% when pulling 9ceb761 on choldgraf:add_plot_auto_scale into 199c8e9 on mne-tools:master.

coveralls · 2016-04-30T22:28:38Z

Coverage increased (+0.006%) to 90.814% when pulling 9ceb761 on choldgraf:add_plot_auto_scale into 199c8e9 on mne-tools:master.

coveralls · 2016-04-30T22:32:12Z

Coverage increased (+0.005%) to 90.812% when pulling 9ceb761 on choldgraf:add_plot_auto_scale into 199c8e9 on mne-tools:master.

choldgraf · 2016-05-03T17:30:53Z

(LMK if there's anything else you'd like me to change here)

kingjr · 2016-05-03T17:33:32Z

+1 to merge on my side

larsoner · 2016-05-03T18:06:50Z

mne/viz/utils.py

    return fig
+
+
+def compute_scalings(scalings, inst):


make private

larsoner · 2016-05-03T18:10:49Z

Otherwise LGTM

choldgraf · 2016-05-04T20:42:57Z

just made edits from above and included the 100mb size max etc, let me know if that looks OK. I'll try to find an example to show this now, and will create a change to whatsnew etc next

choldgraf · 2016-05-04T20:55:53Z

ok - also rebased onto master, updated whats new / a doc, and push that. There was an example showing plotting from raw array data, which is a good use case for this PR. That said, I think it'd be great to have an actual "visualization tutorial", maybe a project for the summer? Once these PRs are taken care of (including the CFC one), I'd like to help build some documentation along those lines.

coveralls · 2016-05-04T21:08:33Z

Coverage increased (+0.01%) to 90.837% when pulling 77c68f4 on choldgraf:add_plot_auto_scale into 767d84b on mne-tools:master.

coveralls · 2016-05-04T21:27:01Z

Coverage increased (+0.004%) to 90.839% when pulling 9297b5a on choldgraf:add_plot_auto_scale into 0271393 on mne-tools:master.

coveralls · 2016-05-04T21:45:58Z

Coverage increased (+0.002%) to 90.837% when pulling 9297b5a on choldgraf:add_plot_auto_scale into 0271393 on mne-tools:master.

agramfort · 2016-05-05T06:35:59Z

there is now tutorials for viz see: http://martinos.org/mne/dev/tutorials.html and for Raw http://martinos.org/mne/dev/auto_tutorials/plot_visualize_raw.html can you add a note there?

choldgraf · 2016-05-05T06:55:28Z

ah that's great - I'll add tomorrow

On Wed, May 4, 2016 at 11:36 PM, Alexandre Gramfort <
notifications@github.com> wrote:

there is now tutorials for viz see:

http://martinos.org/mne/dev/tutorials.html

and for Raw

http://martinos.org/mne/dev/auto_tutorials/plot_visualize_raw.html

can you add a note there?

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#3198 (comment)

choldgraf · 2016-05-06T00:18:42Z

looking at this now - I realized that I didn't see it before because there are two tutorials folders...one in doc, and the other in the main mne_python folder. I added in a sentence about it in the raw plotting tutorial. Is that enough? (also rebased onto master)

larsoner · 2016-05-06T00:20:13Z

Argh, it does seem like the ones in doc/tutorials should be moved to tutorials. @agramfort is that right?

coveralls · 2016-05-06T01:09:12Z

Coverage increased (+0.007%) to 90.841% when pulling 9241afb on choldgraf:add_plot_auto_scale into 2134e8e on mne-tools:master.

choldgraf · 2016-05-06T02:19:01Z

Is that something you'd like me to take care of in this PR?

larsoner · 2016-05-06T02:24:44Z

No, that should probably be separate

choldgraf · 2016-05-06T03:21:10Z

ok cool, will hold off on doing anything else in this PR until somebody
tells me to :)

On Thu, May 5, 2016 at 7:24 PM, Eric Larson notifications@github.com
wrote:

No, that should probably be separate

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#3198 (comment)

larsoner · 2016-05-06T12:41:25Z

doc/whats_new.rst


    - Add option for ``first_samp`` in :func:`mne.make_fixed_length_events` by `Jon Houck`_

+    - Add ability to auto-scale channel types for `mne.viz.plot_raw` and `mne.viz.plot_epochs` and corresponding object plotting methods by `Chris Holdgraf`_


:func: in front (see other lines above for examples)

+1 then +1 for merge

agramfort · 2016-05-06T13:53:45Z

Argh, it does seem like the ones in doc/tutorials should be moved to
tutorials. @agramfort https://github.com/agramfort is that right?

the files in doc/tutorials are in rst format.

the files in tutorials are python files that are rendered with sphinx
gallery.

it's on purpose.

larsoner · 2016-05-06T13:57:40Z

it's on purpose.

Why not have one or the other? I don't see any reason why these couldn't be made into proper Python tutorials:

https://github.com/mne-tools/mne-python/blob/master/doc/tutorials/report.rst
https://github.com/mne-tools/mne-python/blob/master/doc/tutorials/seven_stories_about_mne.rst

The only one that seems like it can't is the MNE command-line tools one, and we can move that elsewhere.

larsoner · 2016-05-06T13:59:00Z

At the very least I think we should just move those files to the root doc directory, and get rid of the doc/tutorials directory -- it's confusing to have that, and one at the repo root.

larsoner · 2016-05-06T14:00:12Z

I'll fix the :func: in master -- thanks @choldgraf!

larsoner · 2016-05-06T14:03:09Z

Merged by rebase with minor fix

larsoner · 2016-05-06T14:05:42Z

After going to edit the doc, I see what you're saying @agramfort, I'm going to leave it alone :)

choldgraf · 2016-05-06T16:09:31Z

wahoo! thanks all

kingjr reviewed Apr 30, 2016
View reviewed changes

choldgraf force-pushed the add_plot_auto_scale branch from 22e9f42 to 31b68c0 Compare April 30, 2016 17:25

choldgraf force-pushed the add_plot_auto_scale branch 4 times, most recently from 5538cd7 to 9ceb761 Compare April 30, 2016 21:32

larsoner reviewed May 3, 2016
View reviewed changes

choldgraf force-pushed the add_plot_auto_scale branch from f8eeeda to 9297b5a Compare May 4, 2016 20:54

choldgraf added 5 commits May 5, 2016 17:11

adding basic auto-scaling functionality for raw and epochs classes

bcd7d1b

removing unnecessary function and cleaning things up a bit

799d2e5

turning compute_scalings to a private function and updating tests

eaaaeca

adding auto_scaling size limit when loading data

8624f09

updating whats new and modifying example to show this functionality

9241afb

choldgraf force-pushed the add_plot_auto_scale branch from 9297b5a to 9241afb Compare May 6, 2016 00:18

larsoner reviewed May 6, 2016
View reviewed changes

larsoner closed this May 6, 2016

choldgraf mentioned this pull request May 8, 2016

adding support for other channel types with auto-scale #3216

Merged


		- Add option for ``first_samp`` in :func:`mne.make_fixed_length_events` by `Jon Houck`_

		- Add ability to auto-scale channel types for `mne.viz.plot_raw` and `mne.viz.plot_epochs` and corresponding object plotting methods by `Chris Holdgraf`_

Uh oh!

adding basic auto-scaling functionality for raw and epochs classes #3198

adding basic auto-scaling functionality for raw and epochs classes #3198

Uh oh!

Conversation

choldgraf commented Apr 29, 2016

Uh oh!

kingjr Apr 30, 2016

Choose a reason for hiding this comment

Uh oh!

agramfort commented Apr 30, 2016

Uh oh!

coveralls commented Apr 30, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

choldgraf commented Apr 30, 2016

Uh oh!

choldgraf commented Apr 30, 2016

Uh oh!

coveralls commented Apr 30, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coveralls commented Apr 30, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coveralls commented Apr 30, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coveralls commented Apr 30, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

choldgraf commented May 3, 2016

Uh oh!

kingjr commented May 3, 2016

Uh oh!

larsoner May 3, 2016

Choose a reason for hiding this comment

Uh oh!

choldgraf May 3, 2016

Choose a reason for hiding this comment

Uh oh!

larsoner commented May 3, 2016

Uh oh!

choldgraf commented May 4, 2016

Uh oh!

choldgraf commented May 4, 2016

Uh oh!

coveralls commented May 4, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coveralls commented May 4, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coveralls commented May 4, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

agramfort commented May 5, 2016 via email

Uh oh!

choldgraf commented May 5, 2016

Uh oh!

choldgraf commented May 6, 2016

Uh oh!

larsoner commented May 6, 2016

Uh oh!

coveralls commented May 6, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

choldgraf commented May 6, 2016

Uh oh!

larsoner commented May 6, 2016 via email

Uh oh!

choldgraf commented May 6, 2016

Uh oh!

larsoner May 6, 2016

Choose a reason for hiding this comment

Uh oh!

agramfort May 6, 2016

Choose a reason for hiding this comment

Uh oh!

agramfort commented May 6, 2016

coveralls commented Apr 30, 2016 •

edited

Loading

coveralls commented Apr 30, 2016 •

edited

Loading

coveralls commented Apr 30, 2016 •

edited

Loading

coveralls commented Apr 30, 2016 •

edited

Loading

coveralls commented Apr 30, 2016 •

edited

Loading

coveralls commented May 4, 2016 •

edited

Loading

coveralls commented May 4, 2016 •

edited

Loading

coveralls commented May 4, 2016 •

edited

Loading

coveralls commented May 6, 2016 •

edited

Loading