MVAR connectivity and example #10
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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 |
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I like that idea, because that means I can stop worrying about flake8 and scot :) |
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@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. |
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ping me when travis' happy, I'll try to give it a try/review |
mbillingr
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@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. 😄 |
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@mbillingr ok, can it wait until next week?
No, we generally aim for >95%-97% I think. The more the better of course |
mne_sandbox/connectivity/mvar.py
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| # todo: I'm sure we can import generator from somewhere... | ||
| def _generator(): |
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
mbillingr
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I've rebased to current master, which made travis very happy. Anyone care to review? :) |
mbillingr
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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?