MVAR connectivity and example by mbillingr · Pull Request #10 · mne-tools/mne-incubator

mbillingr · 2016-04-20T15:28:29Z

This PR implements connectivtiy based on MVAR using the SCoT toolbox. It was originally written during the June 2014 coding sprint. For details see mne-tools/mne-python#1356.

I have squashed the old commits and adjusted them to work correctly with mne-sandbox.

@cbrnr @agramfort @Eric89GXL @kingjr You may be interested in this :)

As a further step we could switch to a current version of SCoT. What do you think?

agramfort · 2016-04-20T20:45:58Z

for the sandbox I think we can leave with an install from scot/master or scot on pypi if released.

travis will complain if scot breaks API

mbillingr · 2016-04-21T08:19:19Z

I like that idea, because that means I can stop worrying about flake8 and scot :)

coveralls · 2016-04-21T08:49:49Z

Coverage decreased (-43.6%) to 56.379% when pulling 5a6b947 on mbillingr:mvar-connectivity into e60d9ab on mne-tools:master.

cbrnr · 2016-04-21T12:14:35Z

@mbillingr, don't stop worrying about coding style, we're gonna address this sooner or later in SCoT :-).

+1 for adapting to the latest SCoT version.

coveralls · 2016-04-21T13:06:23Z

Coverage decreased (-39.09%) to 60.905% when pulling c28e517 on mbillingr:mvar-connectivity into e60d9ab on mne-tools:master.

kingjr · 2016-04-23T08:56:00Z

ping me when travis' happy, I'll try to give it a try/review

coveralls · 2016-04-25T10:18:33Z

Coverage decreased (-6.5%) to 93.517% when pulling 147b774 on mbillingr:mvar-connectivity into e60d9ab on mne-tools:master.

coveralls · 2016-04-25T12:02:38Z

Coverage decreased (-6.3%) to 93.713% when pulling 2b426dd on mbillingr:mvar-connectivity into e60d9ab on mne-tools:master.

coveralls · 2016-04-26T15:33:08Z

Coverage decreased (-4.9%) to 94.617% when pulling bbece5a on mbillingr:mvar-connectivity into 9906704 on mne-tools:master.

mbillingr · 2016-04-26T18:36:47Z

@kingjr Travis is as happy as it will get at the moment. Feel free to review.

Is 100% coverage an imperative? I'd hate to test all the small branches in the visualization functions. 😄

kingjr · 2016-04-26T18:58:32Z

@mbillingr ok, can it wait until next week?

Is 100% coverage an imperative? I'd hate to test all the small branches in the visualization functions. 😄

No, we generally aim for >95%-97% I think. The more the better of course

coveralls · 2016-04-30T09:11:34Z

Coverage decreased (-2.7%) to 96.749% when pulling 3589751 on mbillingr:mvar-connectivity into 9906704 on mne-tools:master.

coveralls · 2016-04-30T10:48:43Z

Coverage decreased (-2.7%) to 96.749% when pulling 7baacab on mbillingr:mvar-connectivity into 9906704 on mne-tools:master.

cbrnr · 2016-05-02T08:55:38Z

mne_sandbox/connectivity/mvar.py

+
+
+# todo: I'm sure we can import generator from somewhere...
+def _generator():


Yes - types.GeneratorType.

coveralls · 2016-05-05T06:53:01Z

Coverage decreased (-2.6%) to 96.89% when pulling 910f7f7 on mbillingr:mvar-connectivity into 9906704 on mne-tools:master.

misc ENH: matrix-type connectivity visualization ENH: node colors moved plot_connectivity_matrix below plot_connectivity_circle ENH: improved MVAR interface rearranged function arguments Improved MVAR example fixed beta bandwidth added scot external improved documentation added new functions to documentation python 2 compatibility added externals.scot to setup.py updated scot package Adjusted MVAR interface to new scot structure updated scot tried to delete plotting scot: mne compatibility update added tests for MVAR connectivity fixed order of mean and abs ENH: model order selection (cross-validated) example cleanup no testin for model order eric's suggestions incorporated ENH: circle plot show node names in the status bar ENH: connectivity matrix shows node names and value in status bar ENH: function to plot in/out connectivity for one seed ENH: connectivity statistics! fixed string type checking mvar connectivity returns p_vals=None if no statistics done adjusted test to new mvar_connectivity return values updated scot (parallelization) joblib support for mvar_connectivity scot: fixed some parallelization issues misc added references misc adjusted default fig size to two circles merged examples fixed verbosity fixed verbosity mne-tools#2 misc fixed invalid ascii char deprecation warning in numpy (scot upstream fix) corrected newline at end of file fixed utf-8 character

coveralls · 2016-05-23T11:32:19Z

Coverage decreased (-2.6%) to 96.89% when pulling a038730 on mbillingr:mvar-connectivity into 91626fb on mne-tools:master.

mbillingr · 2016-05-23T11:38:05Z

I've rebased to current master, which made travis very happy.

Anyone care to review? :)

mbillingr force-pushed the mvar-connectivity branch from 63a8e08 to bbece5a Compare April 26, 2016 15:28

cbrnr reviewed May 2, 2016
View reviewed changes

Martin Billinger and others added 12 commits May 23, 2016 13:27

PEP 8

9bb5c69

Made scot a dependency rather than an external

b411693

Added test for surrogate connectivtiy

ef82549

No longer use assert_less, which is not available in Python 2.6

a43df07

Added tests for viz.connectivity

9a53592

Upgraded to recent SCoT

188aa7e

Fixed Yule-Walker fitting and added tests

a95ef08

Added tests for improved coverage of viz

91c4d76

Optimized autocorrelation computation.

5cb322d

Fixed Python 2.6 string formatting

cc7582b

Import GeneratorType

a038730

mbillingr force-pushed the mvar-connectivity branch from 910f7f7 to a038730 Compare May 23, 2016 11:28

mbillingr changed the title ~~WIP: MVAR connectivity and example~~ MVAR connectivity and example May 23, 2016

wmvanvliet changed the base branch from master to main September 2, 2022 11:09



		# todo: I'm sure we can import generator from somewhere...
		def _generator():

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