# and make some alien probes
probe3 = Probe()
positions = [[0, 0], [0, 50], [25, 77], [45, 27]]
shapes = ['circle', 'square', 'rect', 'circle']
params = [{
'radius': 10
}, {
'width': 30
}, {
'width': 20,
'height': 12
}, {
'radius': 13
}]
probe3.set_electrodes(positions=positions, shapes=shapes, shape_params=params)
probe3.create_auto_shape(probe_type='rect')
probe3.rotate(theta=25)
probe3.move([600, 0])
plot_probe(probe3, ax=ax, electrode_colors=['b', 'c', 'g', 'y'])
ax.set_xlim(-100, 700)
ax.set_ylim(-200, 350)
ax.set_aspect('equal')
##############################################################################
# Some example in 3d for romantic who like flowers...
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1, projection='3d')
positions[i] = x, y
positions *= 20
positions[8:16, 1] -= 10
##############################################################################
# Now we can create a `Probe` object
# and set the position and shape of each electrode
#
# The `ndim` argument indicates that the electrode is 2d, so the positions have a (n_elec, 2) shape.
# We can also define 3d probe with `ndim=3` and positions will have a (n_elec, 3) shape.
#
# Note: `shapes` and `shape_params` could be arrays as well, indicating the shape for each electrode separately.
probe = Probe(ndim=2, si_units='um')
probe.set_electrodes(positions=positions,
shapes='circle',
shape_params={'radius': 5})
##############################################################################
# `Probe` objects have fancy prints!
print(probe)
##############################################################################
# In addition to electrodes, we can crate the planar contour (polygon) of the probe
polygon = [(-20, -30), (20, -110), (60, -30), (60, 190), (-20, 190)]
probe.set_planar_contour(polygon)
##############################################################################
# If `pandas` is installed, the `Probe` object can be exported as a dataframe for a simpler view:
##############################################################################
# The `plane_axes` argument handles the axis for each electrode.
# It can be used for electrode-wise rotations.
# `plane_axes` has a shape of (num_elec, 2, ndim)
plane_axes = [[[1 / np.sqrt(2), 1 / np.sqrt(2)],
[-1 / np.sqrt(2), 1 / np.sqrt(2)]]] * n
plane_axes = np.array(plane_axes)
##############################################################################
# Create the probe
probe = Probe(ndim=2, si_units='um')
probe.set_electrodes(positions=positions,
plane_axes=plane_axes,
shapes=shapes,
shape_params=shape_params)
probe.create_auto_shape()
##############################################################################
plot_probe(probe)
##############################################################################
# We can also use the `rotate_electrodes` to make electrode-wise rotations:
from probeinterface import generate_multi_columns_probe
probe = generate_multi_columns_probe(num_columns=3,
num_elec_per_column=8,
xpitch=20,
def test_probe():
positions = _dummy_posistion()
probe = Probe(ndim=2, si_units='um')
probe.set_electrodes(positions=positions,
shapes='circle',
shape_params={'radius': 5})
probe.set_electrodes(positions=positions,
shapes='square',
shape_params={'width': 5})
probe.set_electrodes(positions=positions,
shapes='rect',
shape_params={
'width': 8,
'height': 5
})
assert probe.get_electrode_count() == 24
# shape of the probe
vertices = [(-20, -30), (20, -110), (60, -30), (60, 190), (-20, 190)]
probe.set_planar_contour(vertices)
# auto shape
probe.create_auto_shape()
# device channel
chans = np.arange(0, 24, dtype='int')
np.random.shuffle(chans)
probe.set_device_channel_indices(chans)
# electrode_ids int or str
elec_ids = np.arange(24)
probe.set_electrode_ids(elec_ids)
elec_ids = [f'elec #{e}' for e in range(24)]
probe.set_electrode_ids(elec_ids)
# copy
probe2 = probe.copy()
# move rotate
probe.move([20, 50])
probe.rotate(theta=40, center=[0, 0], axis=None)
# make annimage
values = np.random.randn(24)
image, xlims, ylims = probe.to_image(values, method='cubic')
image2, xlims, ylims = probe.to_image(values, method='cubic', num_pixel=16)
#~ from probeinterface.plotting import plot_probe_group, plot_probe
#~ import matplotlib.pyplot as plt
#~ fig, ax = plt.subplots()
#~ plot_probe(probe, ax=ax)
#~ ax.imshow(image, extent=xlims+ylims, origin='lower')
#~ ax.imshow(image2, extent=xlims+ylims, origin='lower')
#~ plt.show()
# 3d
probe_3d = probe.to_3d()
probe_3d.rotate(theta=60, center=[0, 0, 0], axis=[0, 1, 0])
#~ from probeinterface.plotting import plot_probe_group, plot_probe
#~ import matplotlib.pyplot as plt
#~ plot_probe(probe_3d)
#~ plt.show()
# get shanks
for shank in probe.get_shanks():
print(shank)
print(shank.electrode_positions)
# get dict and df
d = probe.to_dict()
#~ print(d)
df = probe.to_dataframe()
print(df)