nwb-linkml/nwb_linkml/tests/test_includes/test_hdmf.py

from typing import Tuple, TYPE_CHECKING
from types import ModuleType

import numpy as np
import pytest

# FIXME: Make this just be the output of the provider by patching into import machinery
from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
    ElectricalSeries,
    ElectrodeGroup,
    NWBFileGeneralExtracellularEphysElectrodes,
)


@pytest.fixture()
def electrical_series() -> Tuple["ElectricalSeries", "NWBFileGeneralExtracellularEphysElectrodes"]:
    """
    Demo electrical series with adjoining electrodes
    """
    n_electrodes = 5
    n_times = 100
    data = np.arange(0, n_electrodes * n_times).reshape(n_times, n_electrodes)
    timestamps = np.linspace(0, 1, n_times)

    # electrode group is the physical description of the electrodes
    electrode_group = ElectrodeGroup(
        name="GroupA",
    )

    # make electrodes tables
    electrodes = NWBFileGeneralExtracellularEphysElectrodes(
        id=np.arange(0, n_electrodes),
        x=np.arange(0, n_electrodes),
        y=np.arange(n_electrodes, n_electrodes * 2),
        group=[electrode_group] * n_electrodes,
    )