pyvistaqt 3d backend - plot not interactive

  • MNE version: e.g. 1.1.0
  • pyvista version: e.g. 0.36.1
  • pyvistaqt version: e.g. 0.9.0
  • operating system: e.g. macOS 10.15

Hello,

I encountered an issue while trying to plot source localization.
Here is a snippet of the code I’m using.

import os
import mne
from mne import read_source_estimate
from mne.datasets import sample
print(__doc__)

# Paths to example data
sample_dir_raw = sample.data_path()
sample_dir = os.path.join(sample_dir_raw, 'MEG', 'sample')
subjects_dir = os.path.join(sample_dir_raw, 'subjects')
fname_stc = os.path.join(sample_dir, 'sample_audvis-meg')
stc = read_source_estimate(fname_stc, subject='sample')

# Define plotting parameters
surfer_kwargs = dict(
    hemi='lh', subjects_dir=subjects_dir,
    clim=dict(kind='value', lims=[8, 12, 15]), views='lateral',
    initial_time=0.09, time_unit='s', size=(800, 800),
    smoothing_steps=5)

# Plot surface
with mne.viz.use_3d_backend('pyvista'):
    brain=stc.plot(**surfer_kwargs, time_viewer=True)
brain.add_text(0.1, 0.9, 'SourceEstimate', 'title', font_size=16)

The pyvistaqt window does appear without any error, but I can’t interact with it, the Mac Spinning Wheel appearing.
Do you have any idea?

Hello @aalt, and welcome to the forum!

How did you run the code you shared with us? From the terminal, from a Juypyter Notebook, from the VS Code interactive window, …?

Also, could you please share the output of

import mne
mne.sys_info()

Thanks!

Richard

Dear @richard, thank you!
I am using PyCharm environment.

mne.sys_info() gives:

Platform:         macOS-10.15.7-x86_64-i386-64bit
Python:           3.10.2 (v3.10.2:a58ebcc701, Jan 13 2022, 14:50:16) [Clang 13.0.0 (clang-1300.0.29.30)]
Executable:       /Users/anaelle/PycharmProjects/main/venv/bin/python
CPU:              i386: 4 cores
Memory:           Unavailable (requires "psutil" package)
mne:              1.1.0
numpy:            1.23.1 {}
scipy:            1.9.0
matplotlib:       3.5.2 {backend=MacOSX}
sklearn:          1.1.1
numba:            Not found
nibabel:          4.0.1
nilearn:          0.9.1
dipy:             Not found
cupy:             Not found
pandas:           1.4.3
pyvista:          0.36.1 {OpenGL 4.1 NVIDIA-14.0.32 355.11.11.10.10.143 via NVIDIA GeForce GT 755M OpenGL Engine}
pyvistaqt:        0.9.0
ipyvtklink:       Not found
vtk:              9.2.0.rc2
qtpy:             2.1.0 {PyQt5=5.15.2}
ipympl:           Not found
pyqtgraph:        Not found
pooch:            v1.6.0
mne_bids:         Not found
mne_nirs:         Not found
mne_features:     Not found
mne_qt_browser:   Not found
mne_connectivity: 0.3
mne_icalabel:     0.2

Bests.

Thank you.

  • Can you try to run the script from the command line, outside of PyCharm, to see if this changes anything?
  • Getting MNE and all dependencies installed manually in a way that actually works well can be notoriously difficult. We therefore suggest you closely follow our installation instructions, which ask you to create a conda environment; or you could even try out our standalone installer if you want.

Best wishes,
Richard