def main():
import os,sys
import glob
import json
import numpy as np
import matplotlib
matplotlib.use('Agg')
import os
import json
import numpy as np
import nibabel as nib
os.environ['ETS_TOOLKIT'] = 'qt4'
os.environ['QT_API'] = 'pyqt5'
import pyvista
from pyvista.utilities import xvfb
pyvista.OFF_SCREEN=True
xvfb.start_xvfb()
from mne.viz import set_3d_backend
set_3d_backend('pyvista')
# grab config
with open('config.json','r') as config_f:
config = json.load(config_f)
# set up paths and variables
freesurfer='./output'
cortexmap='./cortexmap'
colormap = config['colormap']
min_percentile = config['min_percentile']
max_percentile = config['max_percentile']
threshold = np.float(config['threshold'])
measureFiles = np.unique([ f.split('h.')[1] for f in os.listdir('./'+cortexmap+'/func') if f.split('h.')[1] != 'goodvertex.func.gii' ])
surface = config['surface']
hemi=["lh","rh"]
#### set up other inputs ####
# set outdir
outdir = 'images'
# generate output directory if not already there
if os.path.isdir(outdir):
print("directory exits")
else:
print("making output directory")
os.mkdir(outdir)
for h in hemi:
for i in measureFiles:
print('generating image for %s.%s' %(h,i))
if surface == 'midthickness':
generateMeasureOverlayImage(freesurfer,h,'midthickness.very_inflated',i,colormap,min_percentile,max_percentile,threshold,outdir,'cortexmap')
else:
generateMeasureOverlayImage(freesurfer,h,surface,i,colormap,min_percentile,max_percentile,threshold,outdir,'cortexmap')
def test_set_3d_backend_bad(monkeypatch, tmp_path):
"""Test that the error emitted when a bad backend name is used."""
match = "Allowed values are 'pyvistaqt' and 'notebook'"
with pytest.raises(ValueError, match=match):
set_3d_backend('invalid')
# gh-9607
def fail(x):
raise ModuleNotFoundError(x)
monkeypatch.setattr('mne.viz.backends.renderer._reload_backend', fail)
monkeypatch.setattr('mne.viz.backends.renderer.MNE_3D_BACKEND', None)
match = 'Could not load any valid 3D.*\npyvistaqt: .*'
assert get_3d_backend() is None
with pytest.raises(RuntimeError, match=match):
_get_renderer()