test/test_ecephys.py

import unittest
from datetime import datetime

import ipywidgets as widgets
import numpy as np
import pytest
from dateutil.tz import tzlocal
from pynwb import NWBFile, TimeSeries
from pynwb.ecephys import LFP, ElectricalSeries, SpikeEventSeries
from pynwb.testing.mock.ecephys import mock_ElectrodeTable

from nwbwidgets import nwb2widget
from nwbwidgets.base import show_multi_container_interface
from nwbwidgets.ecephys import (
    show_ccf,
    show_electrodes,
    show_spectrogram,
    show_spike_event_series,
)
from nwbwidgets.view import default_neurodata_vis_spec


class ShowActivityTestCase(unittest.TestCase):
    def setUp(self):
        nwbfile = NWBFile(
            "my first synthetic recording",
            "EXAMPLE_ID",
            datetime.now(tzlocal()),
            experimenter="Dr. Matthew Douglass",
            lab="Vision Neuroscience Laboratory",
            institution="University of Middle Earth at the Shire",
            experiment_description="We recorded from macaque monkeys during memory-guided saccade task",
            session_id="LONELYMTL",
        )

        device = nwbfile.create_device(name="trodes_rig123")

        electrode_group = nwbfile.create_electrode_group(
            name="tetrode1",
            description="an example tetrode",
            location="somewhere in the hippocampus",
            device=device,
        )

        for idx in [1, 2, 3, 4]:
            nwbfile.add_electrode(
                id=idx,
                x=1.0,
                y=2.0,
                z=3.0,
                imp=float(-idx),
                location="CA1",
                filtering="none",
                group=electrode_group,
            )

        electrode_table_region = nwbfile.create_electrode_table_region([0, 2], "the first and third electrodes")

        self.electrodes = electrode_table_region

        rate = 10.0
        np.random.seed(1234)
        data_len = 1000
        ephys_data = np.random.rand(data_len * 2).reshape((data_len, 2))
        ephys_timestamps = np.arange(data_len) / rate

        self.ephys_ts = ElectricalSeries(
            "test_ephys_data",
            ephys_data,
            self.electrodes,
            timestamps=ephys_timestamps,
            resolution=0.001,
            description="Random numbers generated with numpy.random.rand",
        )

        self.lfp = LFP(electrical_series=self.ephys_ts, name="LFP data")

    def test_show_lfp(self):
        show_multi_container_interface(self.lfp, default_neurodata_vis_spec)

    def test_show_spike_event_series(self):
        rate = 10.0
        np.random.seed(1234)
        data_len = 1000
        ephys_data = np.random.rand(data_len * 6).reshape((data_len, 2, 3))
        ephys_timestamps = np.arange(data_len) / rate
        ses = SpikeEventSeries(
            name="test_ephys_data",
            data=ephys_data,
            timestamps=ephys_timestamps,
            electrodes=self.electrodes,
            resolution=0.001,
            comments="This data was randomly generated with numpy, using 1234 as the seed",
            description="Random numbers generated with numpy.random.rand",
        )

        assert isinstance(show_spike_event_series(ses), widgets.Widget)

    def test_show_ElectricalSeries(self):
        widget = nwb2widget(self.ephys_ts)
        widget.gas.range_controller.value = (0, 0)


def test_show_spectrogram():
    data = np.random.rand(160, 12)
    ts = TimeSeries(name="test_timeseries", data=data, unit="m", starting_time=0.0, rate=1.0)

    channel = 3
    show_spectrogram(ts, channel=channel)


def test_show_electrodes():
    electrode_table = mock_ElectrodeTable()
    show_electrodes(electrode_table)


@pytest.mark.skip(reason="Test broke somewhere around PR #219, but cause is unclear.")
def test_show_ccf():
    show_ccf()