multielectrode_grasp/code/python-neo/doc/source/scripts/multi_tetrode_example.py

"""
Example for usecases.rst
"""

from itertools import cycle
import numpy as np
from quantities import ms, mV, kHz
import matplotlib.pyplot as plt
from neo import Block, Segment, ChannelView, Group, SpikeTrain, AnalogSignal

store_signals = False

block = Block(name="probe data", tetrode_ids=["Tetrode #1", "Tetrode #2"])
block.segments = [Segment(name="trial #1", index=0),
                  Segment(name="trial #2", index=1),
                  Segment(name="trial #3", index=2)]

n_units = {
    "Tetrode #1": 2,
    "Tetrode #2": 5
}

# Create a group for each neuron, annotate each group with the tetrode from which it was recorded
groups = []
counter = 0
for tetrode_id, n in n_units.items():
    groups.extend(
        [Group(name=f"neuron #{counter + i + 1}", tetrode_id=tetrode_id)
         for i in range(n)]
    )
    counter += n
block.groups.extend(groups)

iter_group = cycle(groups)

# Create dummy data, one segment at a time
for segment in block.segments:
    segment.block = block

    # create two 4-channel AnalogSignals with dummy data
    signals = {
        "Tetrode #1": AnalogSignal(np.random.rand(1000, 4) * mV,
                                   sampling_rate=10 * kHz, tetrode_id="Tetrode #1"),
        "Tetrode #2": AnalogSignal(np.random.rand(1000, 4) * mV,
                                   sampling_rate=10 * kHz, tetrode_id="Tetrode #2")
    }
    if store_signals:
        segment.analogsignals.extend(signals.values())
        for signal in signals:
            signal.segment = segment

    # create spike trains with dummy data
    # we will pretend the spikes have been extracted from the dummy signal
    for tetrode_id in ("Tetrode #1", "Tetrode #2"):
        for i in range(n_units[tetrode_id]):
            spiketrain = SpikeTrain(np.random.uniform(0, 100, size=30) * ms, t_stop=100 * ms)
            # assign each spiketrain to the appropriate segment
            segment.spiketrains.append(spiketrain)
            spiketrain.segment = segment
            # assign each spiketrain to a given neuron
            current_group = next(iter_group)
            current_group.add(spiketrain)
            if store_signals:
                # add to the group a reference to the signal from which the spikes were obtained
                # this does not give a 1:1 correspondance between spike trains and signals,
                # for that we could use additional groups (and have groups of groups)
                current_group.add(signals[tetrode_id])


# Now plot the data

# .. by trial
plt.figure()
for seg in block.segments:
    print(f"Analyzing segment {seg.index}")
    stlist = [st - st.t_start for st in seg.spiketrains]
    plt.subplot(len(block.segments), 1, seg.index + 1)
    count, bins = np.histogram(stlist)
    plt.bar(bins[:-1], count, width=bins[1] - bins[0])
    plt.title(f"PSTH in segment {seg.index}")
plt.show()

# ..by neuron

plt.figure()
for i, group in enumerate(block.groups):
    stlist = [st - st.t_start for st in group.spiketrains]
    plt.subplot(len(block.groups), 1, i + 1)
    count, bins = np.histogram(stlist)
    plt.bar(bins[:-1], count, width=bins[1] - bins[0])
    plt.title(f"PSTH of unit {group.name}")
plt.show()

# ..by tetrode

plt.figure()
for i, tetrode_id in enumerate(block.annotations["tetrode_ids"]):
    stlist = []
    for unit in block.filter(objects=Group, tetrode_id=tetrode_id):
        stlist.extend([st - st.t_start for st in unit.spiketrains])
    plt.subplot(2, 1, i + 1)
    count, bins = np.histogram(stlist)
    plt.bar(bins[:-1], count, width=bins[1] - bins[0])
    plt.title(f"PSTH blend of tetrode {tetrode_id}")
plt.show()