[Mne_analysis] mne.viz.plot_topo behavior

Martin Luessi mluessi at nmr.mgh.harvard.edu
Thu Jun 27 15:28:25 EDT 2013
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Hi Kambiz,

It seems to me that Canopy has some problems. I tried using it myself a 
few months ago and it didn't work at all (I got errors like "os has no 
module path"). So I switched back to EPD 7.3.1. I also just heard from 
someone else about the "wxagg require > wxPython >=2.8" error. This 
error is quite strange, as Canopy is supposed to include wxPython 2.8.10.1.

I recommend trying EPD or Anaconda from Continuum (I haven't tried it 
yet, but it's on my list).

Best,

Martin

On 06/27/13 15:13, Kambiz Tavabi wrote:
> Hi Denis,
> At the moment I am experiencing this issue with the master 0.6 branch
> (FYI I also expect to be working with the christianmbrodbeck branch). On
> my machine (Ubuntu 13.04 64bit running canopy-1.0.0.1160.rh5-x86_64 &
> python2.7) the topo plot example does not work using IPython notebook or
> Enthough console.
>
> In a last ditch effort to dig into this issue further I tried running
> the tutorial example in an ipython --pylab terminal and noticed a pylab
> issue (ImportError: Matplotlib backend_wx and backend_wxagg require
> wxPython >=2.8); So I just updated my enthought package as per web forum
> advice and now I cannot import MNE because of these NEW errors:
>
> ---------------------------------------------------------------------------
> RuntimeError                               Traceback (most recent call last)
> RuntimeError: module compiled against API version 7 but this version of numpy is 6
> ...
>
> ImportError: numpy.core.multiarray failed to import
>
> ---------------------------------------------------------------------------
>
>
>
> Needless to say, I am royally confused.
>
> Kambiz
>
>
>
> On Wed, Jun 26, 2013 at 4:25 PM, Denis-Alexander Engemann
> <denis.engemann at gmail.com <mailto:denis.engemann at gmail.com>> wrote:
>
>     Hi Kambiz,
>
>     which version of mne-python are you running? Does the example you
>     refer to work on your machine?
>     And, yes, using plot_topo, theoretically any number of conditions
>     can be visualized.
>
>     Cheers,
>     Denis
>
>
>
>     On Thu, Jun 27, 2013 at 1:12 AM, Kambiz Tavabi <ktavabi at uw.edu
>     <mailto:ktavabi at uw.edu>> wrote:
>
>         Hi all,
>         A little quirky behavior I can't make sense of; I am trying to
>         show topography for different conditions using mne.viz.plot_topo
>         however I keep getting a type error regarding the number of
>         input arguments i.e., plot_topo() takes at least X arguments (Y
>         given) that I can't make sense of. By the way, I assume I can
>         plot any number of conditions using this function, right?
>
>         Here is my code snippet:
>         # Generate list of evoked objects from conditions names
>         evokeds = [epochs[name].average() for name in
>         'retroflex_standard', 'dental_deviant']
>
>         *print* evokeds
>         [<Evoked  |  comment : 'retroflex_standard', time : [-0.100000,
>         0.500000], n_epochs : 79, n_channels x n_times : 204 x 601>,
>         <Evoked  |  comment : 'dental_deviant', time : [-0.100000,
>         0.500000], n_epochs : 80, n_channels x n_times : 204 x 601>]
>
>          From the tutorial
>         <http://martinos.org/mne/auto_examples/plot_topo_compare_conditions.html>
>
>         from mne.viz import plot_topo
>         # Show topography for different conditions
>         colors = 'yellow', 'green'
>         title = 'Evoked responses'
>         plot_topo(evokeds, color=colors, title=title)
>         conditions = [e.comment for e in evokeds]
>         for cond, col, pos in zip(conditions, colors, (0.025, 0.07)):
>              pl.figtext(0.775, pos, cond, color=col, fontsize=12)
>         pl.show()
>
>         ---------------------------------------------------------------------------
>         TypeError                                 Traceback (most recent
>         call last)
>         <ipython-input-120-5809c3f526e8> in <module>()
>                5 title = 'Evoked responses'
>                6
>         ----> 7 plot_topo(evokeds, color=colors, title=title)
>                8
>                9 conditions = [e.comment for e in evokeds]
>
>         TypeError: plot_topo() takes at least 2 arguments (3 given)
>
>         Thanks in advance
>         Kambiz
>         --
>         ------------------------------------------------------------
>         Kambiz Tavabi PhD
>         Institute for Learning & Brain Sciences
>         1715 Columbia Road N
>         Portage Bay Building
>         Box 357988
>         University of Washington
>         Seattle, WA 98195-7988
>         Tel: 206-221-6415 <tel:206-221-6415>
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> --
> ------------------------------------------------------------
> Kambiz Tavabi PhD
> Institute for Learning & Brain Sciences
> 1715 Columbia Road N
> Portage Bay Building
> Box 357988
> University of Washington
> Seattle, WA 98195-7988
> Tel: 206-221-6415
> ------------------------------------------------------------
>
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-- 
Martin Luessi, Ph.D.

Research Fellow

Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129

Fax: +1 617 726-7422



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