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
def set_probe(self, probe, group_mode='by_probe', in_place=False):
"""
Wrapper on top on set_probes when there one unique probe.
"""
assert isinstance(probe, Probe), 'must give Probe'
probegroup = ProbeGroup()
probegroup.add_probe(probe)
return self.set_probes(probegroup, group_mode=group_mode, in_place=in_place)
def test_probegroup_3d():
probegroup = ProbeGroup()
for i in range(3):
probe = generate_dummy_probe().to_3d()
probe.move([i * 100, i * 80, i * 30])
probegroup.add_probe(probe)
assert probegroup.ndim == 3
def test_plot_probe_group():
probegroup = generate_dummy_probe_group()
plot_probe_group(probegroup, same_axe=True, with_channel_index=True)
plot_probe_group(probegroup, same_axe=False)
# 3d
probegroup_3d = ProbeGroup()
for probe in probegroup.probes:
probegroup_3d.add_probe(probe.to_3d())
probegroup_3d.probes[-1].move([0, 150, -50])
plot_probe_group(probegroup_3d, same_axe=True)
def test_probegroup():
probegroup = ProbeGroup()
for i in range(3):
probe = generate_dummy_probe()
probe.move([i * 100, i * 80])
probegroup.add_probe(probe)
indices = probegroup.get_global_device_channel_indices()
ids = probegroup.get_global_electrode_ids()
df = probegroup.to_dataframe()
def set_probes(self,
probe_or_probegroup,
group_mode='by_probe',
in_place=False):
"""
Attach a Probe to a recording.
For this Probe.device_channel_indices is used to link contacts to recording channels.
If some contacts of the Probe are not connected (device_channel_indices=-1)
then the recording is "sliced" and only connected channel are kept.
The probe order is not kept. Channel ids are re-ordered to match the channel_ids of the recording.
Parameters
----------
probe_or_probegroup: Probe, list of Probe, or ProbeGroup
The probe(s) to be attached to the recording
group_mode: str
'by_probe' or 'by_shank'. Adds grouping property to the recording based on the probes ('by_probe')
or shanks ('by_shanks')
in_place: bool
False by default.
Useful internally when extractor do self.set_probegroup(probe)
Returns
-------
sub_recording: BaseRecording
A view of the recording (ChannelSliceRecording or clone or itself)
"""
from spikeinterface import ChannelSliceRecording
assert group_mode in (
'by_probe',
'by_shank'), "'group_mode' can be 'by_probe' or 'by_shank'"
# handle several input possibilities
if isinstance(probe_or_probegroup, Probe):
probegroup = ProbeGroup()
probegroup.add_probe(probe_or_probegroup)
elif isinstance(probe_or_probegroup, ProbeGroup):
probegroup = probe_or_probegroup
elif isinstance(probe_or_probegroup, list):
assert all([isinstance(e, Probe) for e in probe_or_probegroup])
probegroup = ProbeGroup()
for probe in probe_or_probegroup:
probegroup.add_probe(probe)
else:
raise ValueError('must give Probe or ProbeGroup or list of Probe')
# handle not connected channels
assert all(probe.device_channel_indices is not None for probe in probegroup.probes), \
'Probe must have device_channel_indices'
# this is a vector with complex fileds (dataframe like) that handle all contact attr
arr = probegroup.to_numpy(complete=True)
# keep only connected contact ( != -1)
keep = arr['device_channel_indices'] >= 0
if np.any(~keep):
warn(
'The given probes have unconnected contacts: they are removed')
arr = arr[keep]
inds = arr['device_channel_indices']
order = np.argsort(inds)
inds = inds[order]
# check
if np.max(inds) >= self.get_num_channels():
raise ValueError(
'The given Probe have "device_channel_indices" that do not match channel count'
)
new_channel_ids = self.get_channel_ids()[inds]
arr = arr[order]
# create recording : channel slice or clone or self
if in_place:
if not np.array_equal(new_channel_ids, self.get_channel_ids()):
raise Exception(
'set_proce(inplace=True) must have all channel indices')
sub_recording = self
else:
if np.array_equal(new_channel_ids, self.get_channel_ids()):
sub_recording = self.clone()
else:
sub_recording = ChannelSliceRecording(self, new_channel_ids)
# create a vector that handle all conatcts in property
sub_recording.set_property('contact_vector', arr, ids=None)
# planar_contour is saved in annotations
for probe_index, probe in enumerate(probegroup.probes):
contour = probe.probe_planar_contour
if contour is not None:
sub_recording.set_annotation(
f'probe_{probe_index}_planar_contour',
contour,
overwrite=True)
# duplicate positions to "locations" property
ndim = probegroup.ndim
locations = np.zeros((arr.size, ndim), dtype='float64')
for i, dim in enumerate(['x', 'y', 'z'][:ndim]):
locations[:, i] = arr[dim]
sub_recording.set_property('location', locations, ids=None)
# handle groups
groups = np.zeros(arr.size, dtype='int64')
if group_mode == 'by_probe':
for group, probe_index in enumerate(np.unique(arr['probe_index'])):
mask = arr['probe_index'] == probe_index
groups[mask] = group
elif group_mode == 'by_shank':
assert all(probe.shank_ids is not None for probe in probegroup.probes), \
'shank_ids is None in probe, you cannot group by shank'
for group, a in enumerate(
np.unique(arr[['probe_index', 'shank_ids']])):
mask = (arr['probe_index'] == a['probe_index']) & (
arr['shank_ids'] == a['shank_ids'])
groups[mask] = group
sub_recording.set_property('group', groups, ids=None)
return sub_recording
from probeinterface.plotting import plot_probe_group
from probeinterface import generate_dummy_probe
##############################################################################
# Generate 2 dummy `Probe` objects with the utils function:
#
probe0 = generate_dummy_probe(elec_shapes='square')
probe1 = generate_dummy_probe(elec_shapes='circle')
probe1.move([250, -90])
##############################################################################
# Let's create a `ProbeGroup` and
# add the `Probe` objects into it:
probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)
print('probe0.get_electrode_count()', probe0.get_electrode_count())
print('probe1.get_electrode_count()', probe1.get_electrode_count())
print('probegroup.get_channel_count()', probegroup.get_channel_count())
##############################################################################
# We can now plot all probes in the same axis:
plot_probe_group(probegroup, same_axe=True)
##############################################################################
# or in separate axes:
##############################################################################
# Import
import numpy as np
import matplotlib.pyplot as plt
from probeinterface import Probe, ProbeGroup
from probeinterface.plotting import plot_probe, plot_probe_group
##############################################################################
# Generate 4 tetrodes:
#
from probeinterface import generate_tetrode
probegroup = ProbeGroup()
for i in range(4):
tetrode = generate_tetrode()
tetrode.move([i * 50, 0])
probegroup.add_probe(tetrode)
probegroup.set_global_device_channel_indices(np.arange(16))
df = probegroup.to_dataframe()
df
plot_probe_group(probegroup, with_channel_index=True, same_axes=True)
##############################################################################
# Generate a linear probe:
#
plot_probe(probe, with_channel_index=True)
##############################################################################
# Very often we have several probes on the device and this can lead to even
# more complex channel indices.
# `ProbeGroup.get_global_device_channel_indices()` gives an overview of the device wiring.
probe0 = 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})
probe1 = probe0.copy()
probe1.move([350, 200])
probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)
# wire probe0 0 to 31 and shuffle
channel_indices0 = np.arange(16)
np.random.shuffle(channel_indices0)
probe0.set_device_channel_indices(channel_indices0)
# wire probe0 32 to 63 and shuffle
channel_indices1 = np.arange(16, 32)
np.random.shuffle(channel_indices1)
probe1.set_device_channel_indices(channel_indices1)
print(probegroup.get_global_device_channel_indices())
from probeinterface import Probe, ProbeGroup
from probeinterface.plotting import plot_probe, plot_probe_group
from probeinterface import generate_dummy_probe
from probeinterface import write_probeinterface, read_probeinterface
from probeinterface import write_prb, read_prb
##############################################################################
# Let's first generate 2 dummy probes and combine them
# into a ProbeGroup
probe0 = generate_dummy_probe(elec_shapes='square')
probe1 = generate_dummy_probe(elec_shapes='circle')
probe1.move([250, -90])
probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)
##############################################################################
# With the `write_probeinterface` and `read_probeinterface` functions we can
# write to and read from the json-based probeinterface format:
write_probeinterface('my_two_probe_setup.json', probegroup)
probegroup2 = read_probeinterface('my_two_probe_setup.json')
plot_probe_group(probegroup2)
##############################################################################
# The format looks like this:
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
num_channels=16)
# make dumpable
recording = recording.save()
##############################################################################
# Initially all channel are in the same group.
print(recording.get_channel_groups())
##############################################################################
# Lets now change the probe mapping and assign a 4 tetrodes to this recording.
# for this we will use the `probeinterface` module and create a `ProbeGroup` containing for dummy tetrode.
from probeinterface import generate_tetrode, ProbeGroup
probegroup = ProbeGroup()
for i in range(4):
tetrode = generate_tetrode()
tetrode.set_device_channel_indices(np.arange(4) + i * 4)
probegroup.add_probe(tetrode)
##############################################################################
# now our new recording contain 4 groups
recording_4_tetrodes = recording.set_probegroup(probegroup,
group_mode='by_probe')
# get group
print(recording_4_tetrodes.get_channel_groups())
# similar to this
print(recording_4_tetrodes.get_property('group'))
