[Mne_analysis] stc.plot() Error: raise ValueError('time is not the same length as array.shape[1]')

Nakagawa Tristan T nakagawa-t at ifrec.osaka-u.ac.jp
Fri May 13 21:26:39 EDT 2016
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Actually, as I mention below, vtk7 (main release) is compatible with Python3

https://blog.kitware.com/vtk-7-0-0/

and with this and mayavi 4.4.4, after fixing the viz.py script, I could
plot meg activity onto the cortical surface without any apparent
problems so far, all in python 3.

Cheers
Tristan

On 2016年05月13日 21:02, Denis-Alexander Engemann wrote:
> Mayavi does not yet work with Python3 unfortunately. Rumors have been
> existing that there is some unmerged experimental dev branch of VTK
> that supports mayavi 3, but I'm not sure if mayavi can already be used.
>
> Btw. anyone who wants to help writing an API for plotting freesurfer
> outputs using matplotlib without extra dependencies deserves many
> beers {insert favourite drink}. Look also here for the first attempts:
> https://github.com/nilearn/nilearn/pull/1016
>
> Denis
>
> On Fri, May 13, 2016 at 8:01 AM Nakagawa Tristan T
> <nakagawa-t at ifrec.osaka-u.ac.jp
> <mailto:nakagawa-t at ifrec.osaka-u.ac.jp>> wrote:
>
>     I figured it out, it seems the code is still not compatible with
>     python3.
>
>     adding to viz.py :
>
>     try:
>         basestring
>     except NameError:
>         basestring = str
>
>     fixes this error and makes the plot possible.
>
>     I never worked with python2 (and didn't know basestring was a type);
>     do I have to expect silent wrong results using the
>     python3/mayavi4.4.4/vtk7 combination?
>
>
>     ---
>     If anybody is interested (unless this isn't advised), The install
>     procedure gave me some trouble but finally worked in this combination
>     (with anaconda python):
>     conda install -c menpo vtk=7.0.0
>     pip install mayavi
>     pip install pysurfer
>
>     cheers
>     Tristan
>
>
>     On 2016年05月13日 13:39, Nakagawa Tristan T wrote:
>     > I was confused, sorry. the actual error is:
>     >
>     > --> 876             if isinstance(time_label, basestring):
>     >
>     > as in:
>     > In [96]: stc.plot()
>     > Updating smoothing matrix, be patient..
>     > Smoothing matrix creation, step 1
>     > Smoothing matrix creation, step 2
>     > Smoothing matrix creation, step 3
>     > Smoothing matrix creation, step 4
>     > Smoothing matrix creation, step 5
>     > Smoothing matrix creation, step 6
>     > Smoothing matrix creation, step 7
>     > Smoothing matrix creation, step 8
>     > Smoothing matrix creation, step 9
>     > Smoothing matrix creation, step 10
>     >
>     ---------------------------------------------------------------------------
>     > NameError                                 Traceback (most recent
>     call last)
>     > <ipython-input-96-2a3e72fcca14> in <module>()
>     > ----> 1 stc.plot()
>     >
>     >
>     /home/tristan/anaconda3/lib/python3.5/site-packages/mne-0.12.dev0-py3.5.egg/mne/source_estimate.py
>     > in plot(self, subject, surface, hemi, colormap, time_label,
>     > smoothing_steps, transparent, alpha, time_viewer, config_opts,
>     > subjects_dir, figure, views, colorbar, clim)
>     >    1376                                     
>      subjects_dir=subjects_dir,
>     > figure=figure,
>     >    1377                                       views=views,
>     > colorbar=colorbar,
>     > -> 1378                                       clim=clim)
>     >    1379         return brain
>     >    1380
>     >
>     >
>     /home/tristan/anaconda3/lib/python3.5/site-packages/mne-0.12.dev0-py3.5.egg/mne/viz/_3d.py
>     > in plot_source_estimates(stc, subject, surface, hemi, colormap,
>     > time_label, smoothing_steps, transparent, alpha, time_viewer,
>     > config_opts, subjects_dir, figure, views, colorbar, clim)
>     >     747                            smoothing_steps=smoothing_steps,
>     > time=time,
>     >     748                            time_label=time_label,
>     alpha=alpha,
>     > hemi=hemi,
>     > --> 749                            colorbar=colorbar)
>     >     750
>     >     751         # scale colormap and set time (index) to display
>     >
>     > /home/tristan/anaconda3/lib/python3.5/site-packages/surfer/viz.py in
>     > add_data(self, array, min, max, thresh, colormap, alpha, vertices,
>     > smoothing_steps, time, time_label, colorbar, hemi, remove_existing,
>     > time_label_size)
>     >     874                 raise ValueError('time is not the same
>     length as '
>     >     875                                  'array.shape[1]')
>     > --> 876             if isinstance(time_label, basestring):
>     >     877                 time_label_fmt = time_label
>     >     878                 time_label = lambda x: time_label_fmt % x
>     >
>     > NameError: name 'basestring' is not defined
>     >
>     > In [97]: stc.time_label
>     >
>     ---------------------------------------------------------------------------
>     > AttributeError                            Traceback (most recent
>     call last)
>     > <ipython-input-97-3f447cdfe95d> in <module>()
>     > ----> 1 stc.time_label
>     >
>     > AttributeError: 'SourceEstimate' object has no attribute
>     'time_label'
>     >
>     >
>     >
>     >
>     >
>     > On 2016年05月13日 11:54, Nakagawa Tristan T wrote:
>     >> Hi,
>     >>
>     >> I get this error when trying to plot my source estimates:
>     >> stc.plot()  Error: raise ValueError('time is not the same length as
>     >> array.shape[1]')
>     >>
>     >> however,
>     >> stc: <SourceEstimate  |  10629 vertices, subject : S23, tmin :
>     -1100.0
>     >> (ms), tmax : 1000.0 (ms), tstep : 1.0 (ms), data size : 10629 x
>     2101>
>     >>
>     >> In [93]:   stc.times.shape
>     >> Out[93]: (2101,)
>     >>
>     >> In [94]:   stc.shape
>     >> Out[94]: (10629, 2101)
>     >>
>     >> Here is one of the hemispheres stc:
>     >> https://www.dropbox.com/s/d3vvmy79gddvuev/grad_CS-lh.stc?dl=0
>     >>
>     >> Any ideas?
>     >> I just installed mayavi 4.4.4 with vtk 7.0 on python3, not sure
>     if that
>     >> might cause problems, but the error doesn't look like it.
>     >>
>     >> Thanks,
>     >> Tristan
>     >>
>
>     --
>     Tristan T. Nakagawa, Ph.D.
>     Laboratory for Brain-Immune Interaction,
>     iFReC, Osaka University
>     3-1 Yamadaoka, Suita, Osaka, Japan
>     Tel: 0668789710
>     Office: CiNet R 2B6-2
>     http://seymourlab.com
>
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-- 
Tristan T. Nakagawa, Ph.D.
Laboratory for Brain-Immune Interaction,
iFReC, Osaka University 
3-1 Yamadaoka, Suita, Osaka, Japan
Tel: 0668789710
Office: CiNet R 2B6-2
http://seymourlab.com

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