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mne-tools / mne-python

MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
https://mne.tools
BSD 3-Clause "New" or "Revised" License
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report won't add plot_alignment figure #5476

Closed dnacombo closed 6 years ago

dnacombo commented 6 years ago

Running the code below should open a plot_alignment figure, add it to a report, save the report and close. It only works line by line (in spyder, F9 runs current line of the editor), but not when running the whole file, be it with "play" button at the top of my editor (spyder again), or with python test.py in a linux terminal.

from mne.io import read_raw_fif
from mne.datasets import sample
from mne.report import Report
from mne.viz import plot_alignment

raw = read_raw_fif(sample.data_path() +
                             '/MEG/sample/sample_audvis_raw.fif')

report = Report(title='Checking brain-MEG coregistration')

meg = ['helmet', 'sensors', 'ref']
fig = plot_alignment(raw.info, trans=None, dig=False, eeg=False,
                     surfaces=[], meg=meg, coord_frame='meg',
                     verbose=True)

report.add_figs_to_section(fig,captions='test')

report.save('report_test.html', overwrite=True, open_browser=True)

Actual results

in a terminal, outside of spyder:

python test.py
Opening raw data file //MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Current compensation grade : 0
Embedding : jquery-1.10.2.min.js
Embedding : jquery-ui.min.js
Embedding : bootstrap.min.js
Embedding : jquery-ui.min.css
Embedding : bootstrap.min.css
Getting helmet for system 306m
Segmentation fault (core dumped)

in spyder's ipython console:

Opening raw data file /network/lustre/iss01/cenir/analyse/meeg/CAUSALITY_JUELICH/Collab_Juelich_CTPS+Causality_Data/Analysis_Max/MNE_analysis/data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Current compensation grade : 0
Embedding : jquery-1.10.2.min.js
Embedding : jquery-ui.min.js
Embedding : bootstrap.min.js
Embedding : jquery-ui.min.css
Embedding : bootstrap.min.css
Getting helmet for system 306m
Traceback (most recent call last):

  File "<ipython-input-98-d30dad6db3c2>", line 1, in <module>
    runfile('/home/maximilien.chaumon/owncloud/Lab/Projects/CTPS/code/test.py', wdir='/home/maximilien.chaumon/owncloud/Lab/Projects/CTPS/code')

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/spyder_kernels/customize/spydercustomize.py", line 678, in runfile
    execfile(filename, namespace)

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/spyder_kernels/customize/spydercustomize.py", line 106, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "/home/maximilien.chaumon/owncloud/Lab/Projects/CTPS/code/test.py", line 26, in <module>
    report.add_figs_to_section(fig,captions='test')

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 967, in add_figs_to_section
    comments=comments)

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 922, in _add_figs_to_section
    img = _fig_to_img(fig, image_format, scale)

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 77, in _fig_to_img
    img = mlab.screenshot(figure=fig)

  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 352, in screenshot
    out.shape = shape

ValueError: cannot reshape array of size 12 into shape (0,0,3)

Additional information

Paste the output of mne.sys_info() here.

Platform:      Linux-4.15.0-32-generic-x86_64-with-debian-buster-sid
Python:        3.6.6 |Anaconda, Inc.| (default, Jun 28 2018, 17:14:51)  [GCC 7.2.0]
Executable:    /home/maximilien.chaumon/anaconda3/envs/mne/bin/python
CPU:           x86_64: 8 cores
Memory:        31.3 GB

mne:           0.17.dev0
numpy:         1.14.5 {blas=mkl_rt, lapack=mkl_rt}
scipy:         1.1.0
matplotlib:    2.2.2 {backend=Qt5Agg}

sklearn:       0.19.1
nibabel:       2.3.0
mayavi:        4.6.1 {qt_api=pyqt5}
pycuda:        Not found
skcuda:        Not found
pandas:        0.23.2
larsoner commented 6 years ago

Sometimes Spyder does not get along so well with Mayavi when re-running scripts. Do you get this error even if you close the terminal, then run with IT (which should open a fresh terminal)?

dnacombo commented 6 years ago

Don't know what IT stands for here. Running the script completely outside of spyder in a terminal returns what is shown in the second code block above (segmentation fault).

larsoner commented 6 years ago

Sorry "IT" was an autocorrect typo. I meant F5 :)

Also Spyder has a backend option for MPL -- you could try setting this to PyQt5 and it might work better.

I'm not sure why you would get a seg fault when running. Can you try enabling faulthandler in your script with:

import faulthandler
faulthandler.enable()
dnacombo commented 6 years ago

with faulthandler enabled:

Fatal Python error: Segmentation fault

Current thread 0x00007efed80fb740 (most recent call first):
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 569 in _wrap_call
  File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 77 in _fig_to_img
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 922 in _add_figs_to_section
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 967 in add_figs_to_section
  File "test.py", line 27 in <module>
Segmentation fault (core dumped)

Also changing graphics backend of spyder's ipython console to PyQt5 does not solve the issue.

larsoner commented 6 years ago

Argh. This seems like a VTK bug :( Some ideas for how to proceed (sorry for the hassle but debugging these things is a pain):

  1. Just for completeness, what are the outputs of: 
    $ glxinfo | grep renderer
$ glxinfo | grep version
  2. To try to make a minimal example to open for Mayavi, does this also error/work/segfault for Spyder-F5/Spyder-line-by-line/console, respectively: 
    from mayavi import mlab
mlab.test_plot3d()
mlab.screenshot()
  3. Can you try adding import matplotlib.pyplot as plt; assert plt.get_backend() == 'Qt5Agg' at the top of your file and try running it again and see if it still errors/works/segfaults, respectively? It might help forcing some library loads.
dnacombo commented 6 years ago

1.

$ glxinfo | grep renderer
OpenGL renderer string: Quadro K2200/PCIe/SSE2
$ glxinfo | grep version
server glx version string: 1.4
client glx version string: 1.4
GLX version: 1.4
OpenGL core profile version string: 4.6.0 NVIDIA 390.48
OpenGL core profile shading language version string: 4.60 NVIDIA
OpenGL version string: 4.6.0 NVIDIA 390.48
OpenGL shading language version string: 4.60 NVIDIA
OpenGL ES profile version string: OpenGL ES 3.2 NVIDIA 390.48
OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20
    GL_EXT_shader_implicit_conversions, GL_EXT_shader_integer_mix,

2. the 3 lines run fine line by line in spyder. (notice warning about Qt4)

In [1]: from mayavi import mlab
Changing backend to Qt4 for Mayavi

In [2]: mlab.test_plot3d()
Out[2]: <mayavi.modules.surface.Surface at 0x7fefa0446570>

In [3]: mlab.screenshot()
Out[3]: 
array([[[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]],

       [[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]],

       [[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]],

       ...,

       [[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]],

       [[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]],

       [[127, 127, 127],
        [127, 127, 127],
        [127, 127, 127],
        ...,
        [127, 127, 127],
        [127, 127, 127],
        [127, 127, 127]]], dtype=uint8)

In [4]:

with F5 too (no output) from the terminal (faulthandler enabled):

$ python untitled0.py 
Fatal Python error: Segmentation fault

Current thread 0x00007f6b1feaa740 (most recent call first):
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 569 in _wrap_call
  File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot
  File "untitled0.py", line 13 in <module>
Segmentation fault (core dumped)
  1. adding import matplotlib.pyplot as plt; assert plt.get_backend() == 'Qt5Agg' in this test script 
    
$ python untitled0.py 
Fatal Python error: Segmentation fault

Current thread 0x00007f3af28fa740 (most recent call first): File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 569 in _wrap_call File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot File "untitled0.py", line 13 in Segmentation fault (core dumped)


in my script

Fatal Python error: Segmentation fault

Current thread 0x00007fbc11807740 (most recent call first): File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 569 in _wrap_call File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 77 in _fig_to_img File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 922 in _add_figs_to_section File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 967 in add_figs_to_section File "test.py", line 29 in Segmentation fault (core dumped)

larsoner commented 6 years ago

Okay one more idea. From Spyder and terminal, do:

>>> import vtk
>>> vtk

To tell us where vtk is being imported. Then finally:

$ conda list

To get your environment. If two vtk libraries are listed, do:

$ conda uninstall vtk
$ pip uninstall mayavi vtk
$ pip install vtk
$ pip install mayavi

Then see if anything works better. We might as well test the minimal example code with test_plot3d because it's simplest.

dnacombo commented 6 years ago

in spyder:

<module 'vtk' from '/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/vtk/__init__.py'>

indeed two vtk listed in conda list

vtk                       8.1.0           py36h9686630_201  
vtk                       8.1.1                     <pip>

Then I get the following:


$ pip install vtk
Requirement already satisfied: vtk in /home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages (8.1.1)
mkl-random 1.0.1 requires cython, which is not installed.
mkl-fft 1.0.2 requires cython, which is not installed.
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

however, cython is installed

$ which cython
/usr/bin/cython
larsoner commented 6 years ago

If you got that message at the pip install step, you must have skipped the conda uninstall (maybe remove) and/or pip uninstall steps because these should ensure that vtk is no longer installed

dnacombo commented 6 years ago

my bad. Now reinstalled. Running my test with F5:

An error ocurred while starting the kernel
Qt WebEngine seems to be initialized from a plugin. Please set Qt::AA_ShareOpenGLContexts using QCoreApplication::setAttribute before constructing QGuiApplication.
Fatal Python error: Segmentation fault

Thread 0x00007f2ae774b700 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/zmq/utils/garbage.py", line 47 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x00007f2aee1e9700 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/parentpoller.py", line 39 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x00007f2b067fc700 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 295 in wait
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 551 in wait
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/history.py", line 829 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/history.py", line 58 in needs_sqlite
File "", line 2 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x00007f2b07fff700 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/heartbeat.py", line 61 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x00007f2b0cd84700 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/selectors.py", line 445 in select
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/asyncio/base_events.py", line 1398 in _run_once
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/asyncio/base_events.py", line 422 in run_forever
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/tornado/platform/asyncio.py", line 127 in start
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/iostream.py", line 78 in _thread_main
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 864 in run
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x00007f2b2bf34740 (most recent call first):
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/tvtk/tvtk_base.py", line 568 in _wrap_call
File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/mayavi/tools/figure.py", line 348 in screenshot
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/mne/mne/report.py", line 77 in _fig_to_img
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/mne/mne/report.py", line 922 in _add_figs_to_section
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/mne/mne/report.py", line 967 in add_figs_to_section
File "/home/maximilien.chaumon/owncloud/Lab/Projects/CTPS/code/test.py", line 29 in 
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/spyder_kernels/customize/spydercustomize.py", line 106 in execfile
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/spyder_kernels/customize/spydercustomize.py", line 678 in runfile
File "", line 1 in 
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/interactiveshell.py", line 2963 in run_code
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/interactiveshell.py", line 2909 in run_ast_nodes
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/interactiveshell.py", line 2785 in _run_cell
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/IPython/core/interactiveshell.py", line 2662 in run_cell
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/zmqshell.py", line 537 in run_cell
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/ipkernel.py", line 208 in do_execute
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/kernelbase.py", line 399 in execute_request
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/kernelbase.py", line 233 in dispatch_shell
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/kernelbase.py", line 283 in dispatcher
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/tornado/stack_context.py", line 276 in null_wrapper
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/zmq/eventloop/zmqstream.py", line 432 in _run_callback
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/zmq/eventloop/zmqstream.py", line 480 in _handle_recv
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/zmq/eventloop/zmqstream.py", line 357 in flush
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/kernelbase.py", line 298 in do_one_iteration
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/eventloops.py", line 39 in process_stream_events
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/eventloops.py", line 106 in _loop_qt
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/eventloops.py", line 122 in loop_qt4
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/eventloops.py", line 134 in loop_qt5
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/ipykernel/kernelbase.py", line 263 in enter_eventloop
File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site‑packages/tornad

From the terminal:

$ python test.py 
Opening raw data file /network/lustre/iss01/cenir/analyse/meeg/CAUSALITY_JUELICH/Collab_Juelich_CTPS+Causality_Data/Analysis_Max/MNE_analysis/data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Current compensation grade : 0
Embedding : jquery-1.10.2.min.js
Embedding : jquery-ui.min.js
Embedding : bootstrap.min.js
Embedding : jquery-ui.min.css
Embedding : bootstrap.min.css
Getting helmet for system 306m
Fatal Python error: Segmentation fault

Current thread 0x00007f7def61d740 (most recent call first):
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 568 in _wrap_call
  File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 77 in _fig_to_img
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 922 in _add_figs_to_section
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mne/mne/report.py", line 967 in add_figs_to_section
  File "test.py", line 29 in <module>
Segmentation fault (core dumped)
larsoner commented 6 years ago

You get these same errors with the minimal example I had above, right? Let's call that 3-line script minimal_example_fail.py.

If so, the next steps might be to create a clean env with:

$ conda deactivate
$ conda create -n test python=3.6 numpy "pyqt>=5" matplotlib traits pyface traitsui
$ conda activate test
$ pip install vtk
$ pip install mayavi
$ python minimal_example_fail.py

If this dies, then we can open a Mayavi issue about it. If it does not fail, then we perhaps you can do some testing to figure out what package difference exists between the mne and test envs.

One other thing to try is to change ENABLE_USER_SITE = None to False in anaconda3/envs/mne/lib/python3.6/site.py to see if it makes anything better.

dnacombo commented 6 years ago

minimal_example_fail.py:

import faulthandler
faulthandler.enable()

#import matplotlib.pyplot as plt; assert plt.get_backend() == 'Qt5Agg'

from mayavi import mlab
mlab.test_plot3d()
mlab.screenshot()

$ python minimal_example_fail.py 
Fatal Python error: Segmentation fault

Current thread 0x00007f2c3107e740 (most recent call first):
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 568 in _wrap_call
  File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
  File "/home/maximilien.chaumon/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot
  File "minimal_example_fail.py", line 15 in <module>
Segmentation fault (core dumped)

After creating test environment, activating it, successfully installing vtk 8.1.1 and mayavi 4.6.2 (warning about cython not being installed, though it is)...

$ python minimal_example_fail.py
Fatal Python error: Segmentation fault

Current thread 0x00007f8575b66740 (most recent call first):
  File "/home/maximilien.chaumon/anaconda3/envs/test/lib/python3.6/site-packages/tvtk/tvtk_base.py", line 568 in _wrap_call
  File "tvtk_classes/open_gl_render_window.py", line 79 in get_pixel_data
  File "/home/maximilien.chaumon/anaconda3/envs/test/lib/python3.6/site-packages/mayavi/tools/figure.py", line 348 in screenshot
  File "minimal_example_fail.py", line 15 in <module>
Segmentation fault (core dumped)
agramfort commented 6 years ago

open an issue on mayavi tracker with the necessary info to replicate.

cc @larsoner and myself on this.

larsoner commented 6 years ago

Closing this because it's an upstream bug, but please let us know what the solution is if/when it's sorted out