[Mne_analysis] mne.viz.plot_source_estimates generates a blank window

Gladia Hotan gladiach at gmail.com
Tue Apr 26 14:00:51 EDT 2016
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Hi,

This is on Linux.

Sure, should I post the error on github?

I'm quite new to python so I don't know how to check if my packages are up
to date. I'm using the python package installed on the cluster at the
Martinos center. I'll check with the IT folks, thanks!

Best,
Gladia

On Tuesday, April 26, 2016, Eric Larson <larson.eric.d at gmail.com> wrote:

> Is this on Windows? That looks like a Unix directory structure to me.
>
> In any case, it looks like a bug with Anaconda to me. It will probably be
> tough to debug. If you can make an mne-python issue, we can try to isolate
> it to some minimal example that only uses Mayavi. Then the Anaconda folks
> can fix it hopefully.
>
> In the meantime, do you know if your packages are up to date? You can
> normally do e.g. `conda update mayavi` but it looks like you're on a site
> install, so you'll have to ask your IT folks (and maybe see if they can
> replicate it, too).
>
> Eric
>
>
> On Tue, Apr 26, 2016 at 1:35 PM, Denis-Alexander Engemann <
> denis.engemann at gmail.com
> <javascript:_e(%7B%7D,'cvml','denis.engemann at gmail.com');>> wrote:
>
>> Oh, this does not look nice. Does anybody have experience with Mayavi on
>> Windows? Eric?
>>
>>
>> On Tue, Apr 26, 2016 at 7:30 PM Gladia Hotan <gladiach at gmail.com
>> <javascript:_e(%7B%7D,'cvml','gladiach at gmail.com');>> wrote:
>>
>>> Hi, I ran mne.viz.plot_source_estimates(stc,subject=<subject_name>,...)
>>> but I got a blank window and this error:
>>>
>>> (<unknown>:39799): Gtk-WARNING **: gtk_disable_setlocale() must be
>>> called before gtk_init()
>>> Traceback (most recent call last):
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
>>> line 3035, in run_code
>>>     exec(code_obj, self.user_global_ns, self.user_ns)
>>>   File "<ipython-input-1-16aa827441a7>", line 1, in <module>
>>>
>>> mne.viz.plot_source_estimates(stc,subject='eeganes03',surface='inflated',hemi='lh',colormap='auto',time_label='time=%0.2fms',smoothing_steps=10,transparent=None,alpha=1.0,time_viewer=False,config_opts=None,subjects_dir=None,figure=None,views='lat',colorbar=True,clim='auto')
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mne/viz/_3d.py",
>>> line 593, in plot_source_estimates
>>>     brain = Brain(subject, hemi, surface, **kwargs)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/surfer/viz.py",
>>> line 395, in __init__
>>>     self._scene_size, offscreen)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/surfer/viz.py",
>>> line 212, in _make_viewer
>>>     figure = mlab.figure(title, size=(w, h))
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/tools/figure.py",
>>> line 86, in figure
>>>     engine.new_scene(name=name, size=size)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/apptools/scripting/recordable.py",
>>> line 45, in _wrapper
>>>     result = func(*args, **kw)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/engine.py",
>>> line 434, in new_scene
>>>     viewer = self.scene_factory(**factory_kwargs)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/ui/mayavi_scene.py",
>>> line 89, in viewer_factory
>>>     viewer.open()
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/pyface/i_window.py",
>>> line 145, in open
>>>     self._create()
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/pyface/ui/wx/application_window.py",
>>> line 151, in _create
>>>     contents = self._create_contents(body)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/tools/ivtk.py",
>>> line 392, in _create_contents
>>>     self.scene = self._scene_factory(parent)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/ui/mayavi_scene.py",
>>> line 68, in mayavi_scene_factory
>>>     s = MayaviScene(parent, stereo=p['stereo'])
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/decorated_scene.py",
>>> line 69, in __init__
>>>     super(DecoratedScene, self).__init__(parent, **traits)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/scene.py",
>>> line 302, in __init__
>>>     super(Scene, self).__init__(parent, **traits)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/tvtk_scene.py",
>>> line 201, in __init__
>>>     self.control = self._create_control(parent)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/decorated_scene.py",
>>> line 103, in _create_control
>>>     self._panel)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/scene.py",
>>> line 575, in _create_control
>>>     stereo=self.stereo)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/wxVTKRenderWindowInteractor.py",
>>> line 186, in __init__
>>>     attribList=attribList)
>>>   File
>>> "/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/wx-3.0-gtk2/wx/glcanvas.py",
>>> line 106, in __init__
>>>     _glcanvas.GLCanvas_swiginit(self,_glcanvas.new_GLCanvas(*args,
>>> **kwargs))
>>> TypeError: Argument given by name ('attribList') and position (3)
>>>
>>> I get the same error whether or not I set the 'SUBJECT' environment
>>> variable (using os.environ['SUBJECT']=<subject_name>. Could anyone tell me
>>> how to get around this?
>>>
>>> Best,
>>> Gladia
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