[Mne_analysis] mne.viz.plot_topo behavior
Kambiz Tavabi
ktavabi at uw.edu
Thu Jun 27 17:38:35 EDT 2013
Hi all,
So I am not exactly sure about everything that has happened. I managed to
get things working by:
(1) Updating my EPD-CANOPY environment to version 1.0.3
(2) Update all my python packages via $ enpkg --update-all
(3) Nuked my mne-python directory and re-installed via (i) git clone git://
github.com/mne-tools/mne-python.git (ii) python setup.py install
It's not clear to me why there are so many alternative ways of installing
mne-python, but in trying to go from 0.6 to 0.7 I used pip install and
inadvertently ended up with both 0.6 & 0.7 recursively installed in my
/usr/local directory. I am assuming that to stay up to date with
developments the git approach is the way to go, correct?
I am now using mne 0.7.
@ Denis after upgrading python environment and packages I was still able to
reproduce the viz.plot_topo error in mne 0.6 using the sample data. The
command ipython --pylab qt generates yet another import error concerning
missing module sip. After updating to mne 0.7 I can now run the topo plots.
@Martin Yes, in hindsight it would've been better to go with EPD 7.3 or
perhaps even better Anaconda. This pylab back-end issue in Canopy has been
around for some time and was slated for a fix. It appears the new Canopy
update may have fixed it. Presently I find the entire Python environments
business very confusing and would like to just stick to one instead of flip
flopping around like a fish out of water; if I hit anymore snags I'll try
Anaconda.
Adios
Kambiz
On Thu, Jun 27, 2013 at 12:28 PM, Martin Luessi <mluessi at nmr.mgh.harvard.edu
> wrote:
> 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<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<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
>
--
------------------------------------------------------------
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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