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https://github.com/p2p-ld/nwb-linkml.git
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120 lines
3.6 KiB
Python
120 lines
3.6 KiB
Python
from typing import Tuple
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import numpy as np
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import pytest
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from nwb_linkml.models import (
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ElectricalSeries,
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ExtracellularEphysElectrodes,
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Device,
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ElectrodeGroup,
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DynamicTableRegion,
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Units,
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IntracellularElectrode,
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IntracellularElectrodesTable,
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IntracellularResponsesTable,
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IntracellularStimuliTable,
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IntracellularRecordingsTable,
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)
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@pytest.fixture()
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def electrical_series() -> Tuple["ElectricalSeries", "ExtracellularEphysElectrodes"]:
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"""
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Demo electrical series with adjoining electrodes
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"""
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n_electrodes = 5
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n_times = 100
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data = np.arange(0, n_electrodes * n_times).reshape(n_times, n_electrodes).astype(float)
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timestamps = np.linspace(0, 1, n_times)
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device = Device(name="my electrode")
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# electrode group is the physical description of the electrodes
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electrode_group = ElectrodeGroup(
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name="GroupA",
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device=device,
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description="an electrode group",
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location="you know where it is",
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)
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# make electrodes tables
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electrodes = ExtracellularEphysElectrodes(
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description="idk these are also electrodes",
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id=np.arange(0, n_electrodes),
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x=np.arange(0, n_electrodes).astype(float),
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y=np.arange(n_electrodes, n_electrodes * 2).astype(float),
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group=[electrode_group] * n_electrodes,
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group_name=[electrode_group.name] * n_electrodes,
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location=[str(i) for i in range(n_electrodes)],
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extra_column=["sup"] * n_electrodes,
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)
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electrical_series = ElectricalSeries(
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name="my recording!",
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electrodes=DynamicTableRegion(
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table=electrodes,
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value=np.arange(n_electrodes - 1, -1, step=-1),
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name="electrodes",
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description="hey",
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),
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timestamps=timestamps,
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data=data,
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)
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return electrical_series, electrodes
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def _ragged_array(n_units: int) -> tuple[list[np.ndarray], np.ndarray]:
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generator = np.random.default_rng()
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spike_times = [
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np.full(shape=generator.integers(10, 50), fill_value=i, dtype=float) for i in range(n_units)
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]
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spike_idx = []
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for i in range(n_units):
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if i == 0:
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spike_idx.append(len(spike_times[0]))
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else:
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spike_idx.append(len(spike_times[i]) + spike_idx[i - 1])
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spike_idx = np.array(spike_idx)
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return spike_times, spike_idx
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@pytest.fixture(params=[True, False])
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def units(request) -> Tuple[Units, list[np.ndarray], np.ndarray]:
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"""
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Test case for units
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Parameterized by extra_column because pandas likes to pivot dataframes
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to long when there is only one column and it's not len() == 1
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"""
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spike_times, spike_idx = _ragged_array(24)
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spike_times_flat = np.concatenate(spike_times)
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kwargs = {
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"description": "units!!!!",
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"spike_times": spike_times_flat,
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"spike_times_index": spike_idx,
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}
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if request.param:
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kwargs["extra_column"] = ["hey!"] * 24
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units = Units(**kwargs)
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return units, spike_times, spike_idx
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@pytest.fixture()
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def intracellular_recordings_table() -> IntracellularRecordingsTable:
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n_recordings = 10
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device = Device(name="my device")
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electrode = IntracellularElectrode(
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name="my_electrode", description="an electrode", device=device
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)
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electrodes = IntracellularElectrodesTable(
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name="intracellular_electrodes", electrode=[electrode] * n_recordings
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)
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stimuli = IntracellularStimuliTable(
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name="intracellular_stimuli",
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)
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responses = IntracellularResponsesTable()
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recordings_table = IntracellularRecordingsTable()
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