[Mne_analysis] stc.plot() Error: raise ValueError('time is not the same length as array.shape[1]')
Eric Larson
larson.eric.d at gmail.com
Fri May 13 21:53:27 EDT 2016
PySurfer will need to be updated to be Python3 compatible. Can you open a
GitHub issue on the PySurfer repo?
Eric
On May 13, 2016 21:27, "Nakagawa Tristan T" <nakagawa-t at ifrec.osaka-u.ac.jp>
wrote:
> 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> 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 2B6-2http://seymourlab.com
>
>
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> Mne_analysis mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
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