def generate_CN_probe(probe_info, probeIdx):
"""
Generate a mono shank CN probe
"""
if probe_info['part'] == 'Fb' or probe_info['part'] == 'F':
probe = generate_multi_columns_probe(
num_columns=probe_info['electrode_cols_n'],
num_contact_per_column=[
int(x) for x in convert_probe_shape(
probe_info['electrode_rows_n'])[probeIdx]
],
xpitch=float(probe_info['electrodeSpacingWidth_um']),
ypitch=probe_info['electrodeSpacingHeight_um'],
y_shift_per_column=convert_probe_shape(
probe_info['electrode_yShiftCol'])[probeIdx],
contact_shapes=probe_info['ElectrodeShape'],
contact_shape_params={
'width': probe_info['electrodeWidth_um'],
'height': probe_info['electrodeHeight_um']
})
probe.set_planar_contour(convert_probe_shape(probe_info['probeShape']))
else:
probe = generate_multi_columns_probe(
num_columns=probe_info['electrode_cols_n'],
num_contact_per_column=int(probe_info['electrode_rows_n']),
xpitch=float(probe_info['electrodeSpacingWidth_um']),
ypitch=probe_info['electrodeSpacingHeight_um'],
y_shift_per_column=convert_contact_shape(
probe_info['electrode_yShiftCol']),
contact_shapes=probe_info['ElectrodeShape'],
contact_shape_params={
'width': probe_info['electrodeWidth_um'],
'height': probe_info['electrodeHeight_um']
})
probe.set_planar_contour(convert_probe_shape(probe_info['probeShape']))
if type(probe_info['electrodesCustomPosition']) == str:
probe._contact_positions = np.array(
convert_probe_shape(probe_info['electrodesCustomPosition']))
return probe
def test_generate():
probe = generate_dummy_probe()
probegroup = generate_dummy_probe_group()
tetrode = generate_tetrode()
multi_columns = generate_multi_columns_probe(num_columns=3,
num_elec_per_column=[10, 12, 10],
xpitch=22, ypitch=20,
y_shift_per_column=[0, -10, 0])
linear = generate_linear_probe(num_elec=16, ypitch=20,
electrode_shapes='square', electrode_shape_params={'width': 15})
multi_shank = generate_multi_shank()
#
from probeinterface import generate_linear_probe
linear_probe = generate_linear_probe(num_elec=16, ypitch=20)
plot_probe(linear_probe, with_channel_index=True)
##############################################################################
# Generate a multi-column probe:
#
from probeinterface import generate_multi_columns_probe
multi_columns = generate_multi_columns_probe(num_columns=3,
num_contact_per_column=[10, 12, 10],
xpitch=22, ypitch=20,
y_shift_per_column=[0, -10, 0],
contact_shapes='square', contact_shape_params={'width': 12})
plot_probe(multi_columns, with_channel_index=True, )
##############################################################################
# Generate a square probe:
#
square_probe = generate_multi_columns_probe(num_columns=12,
num_contact_per_column=12,
xpitch=10, ypitch=10,
contact_shapes='square', contact_shape_params={'width': 8})
square_probe.create_auto_shape('rect')
plot_probe(square_probe)
##############################################################################
# Import
import numpy as np
import matplotlib.pyplot as plt
from probeinterface import Probe, ProbeGroup
from probeinterface.plotting import plot_probe, plot_probe_group
from probeinterface import generate_multi_columns_probe
##############################################################################
# Let's first generate a probe. By default, the wiring is not complicated:
# each column increments the electrode index from the bottom to the top of the probe:
probe = generate_multi_columns_probe(num_columns=3,
num_elec_per_column=[5, 6, 5],
xpitch=75, ypitch=75, y_shift_per_column=[0, -37.5, 0],
electrode_shapes='circle', electrode_shape_params={'radius': 12})
plot_probe(probe, with_channel_index=True)
##############################################################################
# The Probe is not connected to any device yet:
print(probe.device_channel_indices)
##############################################################################
# Let's imagine we have a headstage with the following wiring: the first half
# of the channels have natural indices, but the order of other half is reversed:
channel_indices = np.arange(16)
channel_indices[8:16] = channel_indices[8:16][::-1]
shapes=shapes,
shape_params=shape_params)
probe.create_auto_shape()
##############################################################################
plot_probe(probe)
##############################################################################
# We can also use the `rotate_contacts` to make contact-wise rotations:
from probeinterface import generate_multi_columns_probe
probe = generate_multi_columns_probe(num_columns=3,
num_contact_per_column=8,
xpitch=20,
ypitch=20,
contact_shapes='square',
contact_shape_params={'width': 12})
probe.rotate_contacts(45)
plot_probe(probe)
##############################################################################
probe = generate_multi_columns_probe(num_columns=5,
num_contact_per_column=5,
xpitch=20,
ypitch=20,
contact_shapes='square',
contact_shape_params={'width': 12})
thetas = np.arange(25) * 360 / 25
probe.rotate_contacts(thetas)
############################################################################## # Import import numpy as np import matplotlib.pyplot as plt from probeinterface import Probe, ProbeGroup from probeinterface.plotting import plot_probe, plot_probe_group from probeinterface import generate_multi_columns_probe, generate_linear_probe ############################################################################## # Some examples in 2d fig, ax = plt.subplots() probe0 = generate_multi_columns_probe() plot_probe(probe0, ax=ax) # make some colors for each probe probe1 = generate_linear_probe(num_elec=9) probe1.rotate(theta=15) probe1.move([200, 0]) plot_probe(probe1, ax=ax, electrode_colors=['red', 'cyan', 'yellow'] * 3) # prepare yourself for carnival! probe2 = generate_linear_probe() probe2.rotate(theta=-35) probe2.move([400, 0]) n = probe2.get_electrode_count() rand_colors = np.random.rand(n, 3) plot_probe(probe2,
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,
ypitch=20,
electrode_shapes='square',
electrode_shape_params={'width': 12})
probe.rotate_electrodes(45)
plot_probe(probe)
##############################################################################
probe = generate_multi_columns_probe(num_columns=5,
num_elec_per_column=5,
xpitch=20,
ypitch=20,
electrode_shapes='square',
electrode_shape_params={'width': 12})
thetas = np.arange(25) * 360 / 25
probe.rotate_electrodes(thetas)