[Mne_analysis] Questions with regard to replicate tutorial examples

Christopher Bailey cjb at cfin.au.dk
Tue Feb 2 02:56:53 EST 2016
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Dear Foucault,

In addition to checking your Mayavi-installation as Mainak suggests, try the notebook inline-magic

%gui qt

If pyqt is indeed set up, this should allow you to run the example.

Note that you cannot both have the cake and eat it: using %matplotlib inline forces rendering to bitmaps (that can be embedded into HTML and displayed in the browser). To get access to interactive OpenGL-rendering, you need another (GUI) backend, such as qt.

For completeness, I’d like to mention that on my OS X system, despite having wxpython installed, I am unable to run %gui wx. I get an error complaining about access to the screen on a non-“framework” python build. I’d be curious to hear if anyone out there has a fix for this?

/Chris
/Aarhus, DK

On 30 Jan 2016, at 00:14, Mainak Jas <mainakjas at gmail.com<mailto:mainakjas at gmail.com>> wrote:

Dear Foucault,

What you see in the tutorial is not an ipython notebook. It is in fact an restructured text document rendered in the style of ipython notebook using the sphinx gallery (http://sphinx-gallery.readthedocs.org/en/latest/tutorials/plot_notebook.html#sphx-glr-tutorials-plot-notebook-py).

That said, I am able to run the example smoothly on an ipython notebook. It seems to me that there is something wrong with your mayavi installation. Are you able to run the example as a regular python script? I suspect you would need to install mayavi correctly.

Best regards,
Mainak

On Mon, Jan 25, 2016 at 10:51 AM, zuxfoucault Wong <zuxfoucault at gmail.com<mailto:zuxfoucault at gmail.com>> wrote:
Dear all,

I try to replicate the example in http://martinos.org/mne/stable/auto_tutorials/plot_source_localization_basics.html.

However, there's some problem with PySurfer.
I use Jupyter notebook to run the code. In PySurfer document, it use PyQT ( export QT_API=pyqt ). I'm wondering if I use %matplotlib inline magic, should I still have to use PyQT. From the tutorial, it seems the results were shown in notebook environment.

I'm trying to find the TraitsBackendWX backend connector to install (as the error message complained). But I can't find the proper TraitsBackendWX package to install.

Any advice would be appreciated!

The following is the traceback.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-12-c34103ae717e> in <module>()
      2
      3 subjects_dir = data_path + '/subjects'
----> 4 brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir)

/mne-python/mne/source_estimate.pyc in plot(self, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, config_opts, subjects_dir, figure, views, colorbar, clim)
   1364                                       subjects_dir=subjects_dir, figure=figure,
   1365                                       views=views, colorbar=colorbar,
-> 1366                                       clim=clim)
   1367         return brain
   1368

/Volumes/SSD/Space/utility/mne-python/mne/viz/_3d.pyc 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)
    638         kwargs['views'] = views
    639     with warnings.catch_warnings(record=True):  # traits warnings
--> 640         brain = Brain(subject, hemi, surface, **kwargs)
    641     for hemi in hemis:
    642         hemi_idx = 0 if hemi == 'lh' else 1

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/surfer/viz.pyc in __init__(self, subject_id, hemi, surf, curv, title, cortex, size, background, foreground, figure, subjects_dir, views, show_toolbar, offscreen, config_opts)
    393         self._set_window_properties(size, background, foreground)
    394         figures, _v = _make_viewer(figure, n_row, n_col, title,
--> 395                                    self._scene_size, offscreen)
    396         self._figures = figures
    397         self._v = _v

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/surfer/viz.pyc in _make_viewer(figure, n_row, n_col, title, scene_size, offscreen)
    210             # Triage: don't make TraitsUI if we don't have to
    211             if n_row == 1 and n_col == 1:
--> 212                 figure = mlab.figure(title, size=(w, h))
    213                 mlab.clf(figure)
    214                 figures = [[figure]]

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-macosx-10.11-x86_64.egg/mayavi/tools/figure.pyc in figure(figure, bgcolor, fgcolor, engine, size)
     62     else:
     63         if engine is None:
---> 64             engine = get_engine()
     65         if figure is None:
     66             name = max(__scene_number_list) + 1

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-macosx-10.11-x86_64.egg/mayavi/tools/engine_manager.pyc in get_engine(self)
     95                                 if e.__class__.__name__ == 'Engine']
     96         if len(suitable) == 0:
---> 97             return self.new_engine()
     98         else:
     99             # Return the most engine add to the list most recently.

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-macosx-10.11-x86_64.egg/mayavi/tools/engine_manager.pyc in new_engine(self)
    140             options.
    141         """
--> 142         check_backend()
    143         if options.backend == 'envisage':
    144             from mayavi.plugins.app import Mayavi

/Volumes/SSD/Space/vEnvs2/ipy2/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-macosx-10.11-x86_64.egg/mayavi/tools/engine_manager.pyc in check_backend()
     47 wxPython: http://www.wxpython.org/
     48 PyQT: http://www.riverbankcomputing.co.uk/software/pyqt/intro
---> 49 ''')
     50
     51

ImportError: Could not import backend for traits
_______________________________________________________________________________
Make sure that you have either the TraitsBackendWx or the TraitsBackendQt
projects installed. If you installed Mayavi with easy_install, try
easy_install <pkg_name>. easy_install Mayavi[app] will also work.

If you performed a source checkout, be sure to run 'python setup.py install'
in Traits, TraitsGUI, and the Traits backend of your choice.

Also make sure that either wxPython or PyQT is installed.
wxPython: http://www.wxpython.org/
PyQT: http://www.riverbankcomputing.co.uk/software/pyqt/intro




Foucault

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