def test_probegroup():
probegroup = ProbeGroup()
nchan = 0
for i in range(3):
probe = generate_dummy_probe()
probe.move([i * 100, i * 80])
n = probe.get_contact_count()
probe.set_device_channel_indices(np.arange(n)[::-1] + nchan)
shank_ids = np.ones(n)
shank_ids[:n // 2] *= i * 2
shank_ids[n // 2:] *= i * 2 + 1
probe.set_shank_ids(shank_ids)
probegroup.add_probe(probe)
nchan += n
indices = probegroup.get_global_device_channel_indices()
ids = probegroup.get_global_contact_ids()
df = probegroup.to_dataframe()
#~ print(df['global_contact_ids'])
arr = probegroup.to_numpy(complete=False)
other = ProbeGroup.from_numpy(arr)
arr = probegroup.to_numpy(complete=True)
other = ProbeGroup.from_numpy(arr)
d = probegroup.to_dict()
other = ProbeGroup.from_dict(d)
#~ from probeinterface.plotting import plot_probe_group, plot_probe
#~ import matplotlib.pyplot as plt
#~ plot_probe_group(probegroup)
#~ plot_probe_group(other)
#~ plt.show()
# checking automatic generation of ids with new dummy probes
probegroup.probes = []
for i in range(3):
probegroup.add_probe(generate_dummy_probe())
probegroup.auto_generate_contact_ids()
probegroup.auto_generate_probe_ids()
for p in probegroup.probes:
assert p.contact_ids is not None
assert 'probe_id' in p.annotations
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