def get_probegroup(self):
arr = self.get_property('contact_vector')
if arr is None:
positions = self.get_property('location')
if positions is None:
raise ValueError(
'There is not Probe attached to recording. use set_probe(...)'
)
else:
warn(
'There is no Probe attached to this recording. Creating a dummy one with contact positions'
)
ndim = positions.shape[1]
probe = Probe(ndim=ndim)
probe.set_contacts(positions=positions,
shapes='circle',
shape_params={'radius': 5})
probe.set_device_channel_indices(
np.arange(self.get_num_channels(), dtype='int64'))
# probe.create_auto_shape()
probegroup = ProbeGroup()
probegroup.add_probe(probe)
else:
probegroup = ProbeGroup.from_numpy(arr)
for probe_index, probe in enumerate(probegroup.probes):
contour = self.get_annotation(
f'probe_{probe_index}_planar_contour')
if contour is not None:
probe.set_planar_contour(contour)
return probegroup
#
# Note: `shapes` and `shape_params` could be arrays as well, indicating the shape for each contact separately.
probe = Probe(ndim=2, si_units='um')
probe.set_contacts(positions=positions, shapes='circle', shape_params={'radius': 5})
##############################################################################
# `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):
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)