example_spike_amplitudes.py

# 8/31/22
# https://figurl.org/f?v=gs://figurl/spikesortingview-8&d=sha1://1e667e92ee3be76c8e4a85af4a94784329c710d2&label=test_spike_amplitudes

import numpy as np
from typing import List
import sortingview.views as vv
import spikeinterface as si
import spikeinterface.extractors as se
import kachery as ka


def main():
    ka.use_sandbox()
    recording, sorting = se.toy_example(num_units=12, duration=300, seed=0, num_segments=1)
    assert isinstance(recording, si.BaseRecording)

    view = example_spike_amplitudes(recording=recording, sorting=sorting)

    url = view.url(label="Spike amplitudes example")
    print(url)


def example_spike_amplitudes(*, recording: si.BaseRecording, sorting: si.BaseSorting, hide_unit_selector: bool = False, height=500):
    rng = np.random.default_rng(2022)
    plot_items: List[vv.SpikeAmplitudesItem] = []
    for unit_id in sorting.get_unit_ids():
        spike_times_sec = np.array(sorting.get_unit_spike_train(segment_index=0, unit_id=unit_id)) / sorting.get_sampling_frequency()
        plot_items.append(
            vv.SpikeAmplitudesItem(
                unit_id=unit_id,
                spike_times_sec=spike_times_sec.astype(np.float32),
                spike_amplitudes=rng.uniform(0, 5) + rng.normal(0, 0.2, spike_times_sec.shape).astype(np.float32),  # fake amplitudes
            )
        )

    view = vv.SpikeAmplitudes(
        start_time_sec=0,
        end_time_sec=recording.get_num_frames(segment_index=0) / recording.get_sampling_frequency(),
        plots=plot_items,
        hide_unit_selector=hide_unit_selector,
        height=height,
    )
    return view


if __name__ == "__main__":
    main()