############################################################################## # `Probe` objects have fancy prints! print(probe) ############################################################################## # In addition to contacts, 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: df = probe.to_dataframe() df ############################################################################## # If `matplotlib` is installed, the `Probe` can also be easily plotted: plot_probe(probe) ############################################################################## # A 2d `Probe` can be transformed to a 3d `Probe` by indicating the `axes` # on which contacts will lie (Here the 'y' coordinate will be 0 for all contacts): probe_3d = probe.to_3d(axes='xz') plot_probe(probe_3d) plt.show()
positions *= 20
positions[8:16, 1] -= 10
probe_2d = Probe(ndim=2, si_units='um')
probe_2d.set_contacts(positions=positions,
shapes='circle',
shape_params={'radius': 5})
probe_2d.create_auto_shape(probe_type='tip')
##############################################################################
# Let's transform it into a 3d probe.
#
# Here the axes are 'xz' so y will be 0 for all contacts.
# The shape of probe_3d.contact_positions is now (n_elec, 3)
probe_3d = probe_2d.to_3d(axes='xz')
print(probe_2d.contact_positions.shape)
print(probe_3d.contact_positions.shape)
##############################################################################
# Note that all **"y"** coordinates are 0
df = probe_3d.to_dataframe()
df[['x', 'y', 'z']].head()
##############################################################################
# The plotting function autiomatically displays the `Probe` in 3d:
plot_probe(probe_3d)
##############################################################################
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)
############################################################################## # `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: df = probe.to_dataframe() df ############################################################################## # If `matplotlib` is installed, the `Probe` can also be easily plotted: plot_probe(probe) ############################################################################## # A 2d `Probe` can be transformed to a 3d `Probe` by indicating the `plane` # on which electrodes will lie (Here the 'y' coordinate will be 0 for all electrodes): probe_3d = probe.to_3d(plane='xz') plot_probe(probe_3d) plt.show()
positions *= 20
positions[8:16, 1] -= 10
probe_2d = Probe(ndim=2, si_units='um')
probe_2d.set_electrodes(positions=positions,
shapes='circle',
shape_params={'radius': 5})
probe_2d.create_auto_shape(probe_type='tip')
##############################################################################
# Let's transform it into a 3d probe.
#
# Here the plane is 'xz' so y will be 0 for all electrodes.
# The shape of probe_3d.electrode_positions is now (n_elec, 3)
probe_3d = probe_2d.to_3d(plane='xz')
print(probe_2d.electrode_positions.shape)
print(probe_3d.electrode_positions.shape)
##############################################################################
# Note that all **"y"** coordinates are 0
df = probe_3d.to_dataframe()
df[['x', 'y', 'z']].head()
##############################################################################
# The plotting function autiomatically displays the `Probe` in 3d:
plot_probe(probe_3d)
##############################################################################