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

Denis-Alexander Engemann denis.engemann at gmail.com
Fri May 13 08:02:38 EDT 2016
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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> 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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