Hello everyone!
I’m having problem using functions which use pyvistaqt for plotting. When I run the example script from the MNE-Python webiste:
from pathlib import Path
import mne
from mne.datasets import sample, spm_face, testing
from mne.io import (
read_raw_artemis123,
read_raw_bti,
read_raw_ctf,
read_raw_fif,
read_raw_kit,
)
from mne.viz import plot_alignment, set_3d_title
print(__doc__)
root_path = Path(mne.__file__).parent.absolute()
kwargs = dict(eeg=False, coord_frame="meg", show_axes=True, verbose=True)
raw = read_raw_fif(sample.data_path() / "MEG" / "sample" / "sample_audvis_raw.fif")
fig = plot_alignment(raw.info, meg=("helmet", "sensors"), **kwargs)
set_3d_title(figure=fig, title="Neuromag")
I get the following Segmentation fault
(mne)$ python MNE-plot-aligment-test.py
None
Opening raw data file /home/workma/mne_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.
Using pyvistaqt 3d backend.
qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""
Segmentation fault (core dumped)
If I add to the code
import os
os.environ["QT_API"] = "PyQT6"
I get rid of the message qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in "", but the Segmentation fault (core dumped) stays. A blank black window pops up for 1 second, which previously does not occur.
My clean install on Fedora 38 (used conda create --override-channels --channel=conda-forge --name=mne mne):
>>> mne.sys_info()
Platform Linux-6.2.14-300.fc38.x86_64-x86_64-with-glibc2.37
Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 18:58:44) [GCC 11.3.0]
Executable /home/workma/.var/miniconda3/envs/mne/bin/python
CPU (12 cores)
Memory 30.5 GB
Core
├☑ mne 1.4.0
├☑ numpy 1.23.5 (OpenBLAS 0.3.21 with 12 threads)
├☑ scipy 1.10.1
├☑ matplotlib 3.7.1 (backend=QtAgg)
├☑ pooch 1.7.0
└☑ jinja2 3.1.2
Numerical (optional)
├☑ sklearn 1.2.2
├☑ numba 0.56.4
├☑ nibabel 5.1.0
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
├☑ openmeeg 2.5.6
├☑ pandas 2.0.1
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.39.0 (OpenGL 4.6 (Core Profile) Mesa 23.0.3 via AMD Radeon RX 6650 XT (navi23, LLVM 16.0.1, DRM 3.49, 6.2.14-300.fc38.x86_64))
├☑ pyvistaqt 0.0.0
├☑ ipyvtklink 0.2.2
├☑ vtk 9.2.6
qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""
├☑ qtpy 2.3.1 (PyQt5=5.15.6)
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.0.0
└☐ unavailable ipympl
Ecosystem (optional)
└☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline
Then I tried to install the pip version of MNE and pyvistaqt. I created a new conda env and installed pyvista and pyvistaqt etc. with pip. This is the mne.sys_info():
mne.sys_info()
Platform: Linux-6.2.14-300.fc38.x86_64-x86_64-with-glibc2.37
Python: 3.11.3 (main, Apr 19 2023, 23:54:32) [GCC 11.2.0]
Executable: /home/workma/.var/miniconda3/envs/mne-pip/bin/python
CPU: : 12 cores
Memory: 30.5 GB
mne: 1.3.1
numpy: 1.24.3 {unknown linalg bindings (threadpoolctl module not found: No module named 'threadpoolctl')}
scipy: 1.10.1
matplotlib: 3.7.1 {backend=QtAgg}
sklearn: Not found
numba: Not found
nibabel: Not found
nilearn: Not found
dipy: Not found
openmeeg: Not found
cupy: Not found
pandas: Not found
pyvista: 0.38.5 {OpenGL 4.6 (Core Profile) Mesa 23.0.3 via AMD Radeon RX 6650 XT (navi23, LLVM 16.0.1, DRM 3.49, 6.2.14-300.fc38.x86_64)}
pyvistaqt: 0.10.0
ipyvtklink: 0.2.3
vtk: 9.2.6
qtpy: 2.3.1 {PyQt5=5.15.2}
ipympl: Not found
pyqtgraph: Not found
pooch: v1.7.0
mne_bids: Not found
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: Not found
mne_connectivity: Not found
mne_icalabel: Not found
If I add to the code
import os
os.environ["QT_API"] = "PyQT6"
I get the window
but when I close I get the error
HBox(children=(Text(value='', layout=Layout(margin='2px 0px 2px 0px', min_width='0px'), placeholder='Type a file name'), Button(icon='camera', layout=Layout(margin='2px 0px 2px 0px', min_width='0px'), style=ButtonStyle(), tooltip='Take a screenshot')))
/home/workma/.local/lib/python3.11/site-packages/pyvista/plotting/plotting.py:6510: UserWarning: Not within a jupyter notebook environment.
Ignoring ``jupyter_backend``.
warnings.warn(
Traceback (most recent call last):
File "/home/workma/DevExamples/MNEExample/MNE-plot-aligment-test.py", line 26, in <module>
fig = plot_alignment(raw.info, meg=("helmet", "sensors"), **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-122>", line 10, in plot_alignment
File "/home/workma/.local/lib/python3.11/site-packages/mne/viz/_3d.py", line 833, in plot_alignment
renderer.show()
File "/home/workma/.local/lib/python3.11/site-packages/mne/viz/backends/_notebook.py", line 1460, in show
viewer.layout.width = None # unlock the fixed layout
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'layout'
If I add to the code
import os
os.environ["QT_QPA_PLATFORM"] = "xcb"
I get no error, but the pplot hides in 1 s.
I apologize for my long post. Does someone know what could be the issue?
