def test_channels_grid():
grid_chan = chan(lambda x: x.label.startswith('grid'))
assert grid_chan.n_chan == 16
grid_chan.export(exported_chan_path)
imported = Channels(exported_chan_path)
assert imported.n_chan == grid_chan.n_chan
def plot_electrodes(elec, freesurfer, labels=None, values=None):
if labels is None:
labels = [x['name'] for x in elec.electrodes.tsv]
xyz = array(elec.get_xyz(labels))
# convert from RAS to tkRAS
xyz -= freesurfer.surface_ras_shift
chan = Channels(labels, xyz)
if median(chan.return_xyz()[:, 0]) > 0:
surf = freesurfer.read_brain().rh
else:
surf = freesurfer.read_brain().lh
v = Viz3()
v.add_chan(chan, values=values)
v.add_surf(surf, alpha=0.5)
return v
def test_plot3d_surf_chan_color_one_alpha():
surf = Surf(surf_path)
channels = Channels(chan_path)
v = Viz3()
v.add_chan(channels, color=(1, 0, 0), alpha=0.5)
v.add_surf(surf, alpha=.5)
v.save(VIZ_PATH / 'viz3_07_surf_chan_color_one_alpha.png')
v.close()
def test_plot3d_surf_chan():
surf = Surf(surf_path)
channels = Channels(chan_path)
v = Viz3()
v.add_chan(channels)
v.add_surf(surf, alpha=.8)
v.save(VIZ_PATH / 'viz3_05_surf_chan.png')
v.close()
def test_plot3d_surf_chan_color_everyother():
from numpy import tile
surf = Surf(surf_path)
channels = Channels(chan_path)
color_everyother = tile([[1, 0, 0], [0, 0, 1]], (14, 1))
v = Viz3()
v.add_chan(channels, color=color_everyother)
v.add_surf(surf, alpha=.5)
v.save(VIZ_PATH / 'viz3_08_surf_chan_color_everyother.png')
v.close()
def test_plot3d_surf_chan_values():
from numpy import arange
surf = Surf(surf_path)
channels = Channels(chan_path)
v = Viz3()
v.add_chan(channels, values=arange(channels.n_chan), colorbar=True)
v.add_surf(surf, alpha=.5)
v.save(VIZ_PATH / 'viz3_09_surf_chan_values.png')
v.close()
# reuse the limits_c
v.add_chan(channels, values=arange(channels.n_chan))
from nibabel import load as nload
from wonambi.attr import Channels, Freesurfer
from wonambi.attr.chan import (
find_channel_groups,
create_sphere_around_elec,
)
from .paths import (
chan_path,
fs_path,
template_mri_path,
exported_chan_path,
)
chan = Channels(chan_path)
def test_channels():
assert chan.n_chan == 28
xyz = chan.return_xyz()
assert xyz.shape == (28, 3)
labels = chan.return_label()
assert len(labels) == 28
def test_channels_grid():
grid_chan = chan(lambda x: x.label.startswith('grid'))
assert grid_chan.n_chan == 16
def test_source_linear():
surf = Surf(surf_path)
channels = Channels(chan_path)
Linear(surf, channels)