def test_write_probe_lfp_file_roundtrip(tmpdir_factory, roundtrip, lfp_data, probe_data, csd_data):
expected_csd = xr.DataArray(
name="CSD",
data=csd_data["csd"],
dims=["virtual_channel_index", "time"],
coords={
"virtual_channel_index": np.arange(csd_data["csd"].shape[0]),
"time": csd_data["relative_window"],
"vertical_position": (("virtual_channel_index",), csd_data["csd_locations"][:, 1]),
"horizontal_position": (("virtual_channel_index",), csd_data["csd_locations"][:, 0]),
}
)
expected_lfp = xr.DataArray(
name="LFP",
data=lfp_data["data"],
dims=["time", "channel"],
coords=[lfp_data["timestamps"], [2, 1]]
)
tmpdir = Path(tmpdir_factory.mktemp("probe_lfp_nwb"))
input_data_path = tmpdir / Path("lfp_data.dat")
input_timestamps_path = tmpdir / Path("lfp_timestamps.npy")
input_channels_path = tmpdir / Path("lfp_channels.npy")
input_csd_path = tmpdir / Path("csd.h5")
output_path = str(tmpdir / Path("lfp.nwb")) # pynwb.NWBHDF5IO chokes on Path
test_lfp_paths = {
"input_data_path": input_data_path,
"input_timestamps_path": input_timestamps_path,
"input_channels_path": input_channels_path,
"output_path": output_path
}
probe_data.update({"lfp": test_lfp_paths})
probe_data.update({"csd_path": input_csd_path})
write_csd_to_h5(path=input_csd_path, **csd_data)
np.save(input_timestamps_path, lfp_data["timestamps"], allow_pickle=False)
np.save(input_channels_path, lfp_data["subsample_channels"], allow_pickle=False)
with open(input_data_path, "wb") as input_data_file:
input_data_file.write(lfp_data["data"].tobytes())
write_nwb.write_probe_lfp_file(4242, None, datetime.now(), logging.INFO, probe_data)
obt = EcephysNwbSessionApi(path=None, probe_lfp_paths={12345: NWBHDF5IO(output_path, "r").read})
obtained_lfp = obt.get_lfp(12345)
obtained_csd = obt.get_current_source_density(12345)
xr.testing.assert_equal(obtained_lfp, expected_lfp)
xr.testing.assert_equal(obtained_csd, expected_csd)
def test_add_raw_running_data_to_nwbfile(nwbfile, raw_running_data, roundtripper, roundtrip):
nwbfile = write_nwb.add_raw_running_data_to_nwbfile(nwbfile, raw_running_data)
if roundtrip:
api_obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
api_obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
obtained = api_obt.get_raw_running_data()
expected = raw_running_data.rename(columns={"dx": "net_rotation", "vsig": "signal_voltage", "vin": "supply_voltage"})
pd.testing.assert_frame_equal(expected, obtained, check_like=True)
def test_add_probe_to_nwbfile(nwbfile, roundtripper, roundtrip, pid, name, srate, lfp_srate, has_lfp, expected):
nwbfile, _, _ = write_nwb.add_probe_to_nwbfile(nwbfile, pid,
name=name,
sampling_rate=srate,
lfp_sampling_rate=lfp_srate,
has_lfp_data=has_lfp)
if roundtrip:
obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(expected, obt.get_probes(), check_like=True)
def test_add_running_speed_to_nwbfile(nwbfile, running_speed, roundtripper, roundtrip, include_rotation):
nwbfile = write_nwb.add_running_speed_to_nwbfile(nwbfile, running_speed)
if roundtrip:
api_obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
api_obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
obtained = api_obt.get_running_speed(include_rotation=include_rotation)
expected = running_speed
if not include_rotation:
expected = expected.drop(columns="net_rotation")
pd.testing.assert_frame_equal(expected, obtained, check_like=True)
def test_add_eye_tracking_rig_geometry_data_to_nwbfile(nwbfile, roundtripper,
roundtrip,
eye_tracking_rig_geometry,
expected):
nwbfile = write_nwb.add_eye_tracking_rig_geometry_data_to_nwbfile(nwbfile,
eye_tracking_rig_geometry)
if roundtrip:
obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
obtained_metadata = obt.get_rig_metadata()
pd.testing.assert_frame_equal(obtained_metadata["geometry"], expected["geometry"], check_like=True)
assert obtained_metadata["equipment"] == expected["equipment"]
def test_add_probewise_data_to_nwbfile(monkeypatch, nwbfile, roundtripper,
roundtrip, probes, parsed_probe_data,
expected_units_table):
def mock_parse_probes_data(probes):
return parsed_probe_data
monkeypatch.setattr(write_nwb, "parse_probes_data", mock_parse_probes_data)
nwbfile = write_nwb.add_probewise_data_to_nwbfile(nwbfile, probes)
if roundtrip:
obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(obt.nwbfile.units.to_dataframe(),
expected_units_table)
def _build_nwb_api_for_session(self, path, session_id, filter_by_validity, **unit_filter_kwargs):
get_analysis_metrics = partial(
self.get_unit_analysis_metrics_for_session,
session_id=session_id,
annotate=False,
filter_by_validity=True,
**unit_filter_kwargs
)
return EcephysNwbSessionApi(
path=path,
probe_lfp_paths=self._setup_probe_promises(session_id),
additional_unit_metrics=get_analysis_metrics,
external_channel_columns=partial(self._get_substitute_channel_columns, session_id),
filter_by_validity=filter_by_validity,
**unit_filter_kwargs
)
def test_add_eye_tracking_data_to_nwbfile(nwbfile, roundtripper, roundtrip,
eye_tracking_frame_times,
eye_dlc_tracking_data,
eye_gaze_data,
expected_pupil_data, expected_gaze_data):
nwbfile = write_nwb.add_eye_tracking_data_to_nwbfile(nwbfile,
eye_tracking_frame_times,
eye_dlc_tracking_data,
eye_gaze_data)
if roundtrip:
obt = roundtripper(nwbfile, EcephysNwbSessionApi)
else:
obt = EcephysNwbSessionApi.from_nwbfile(nwbfile)
obtained_pupil_data = obt.get_pupil_data()
obtained_screen_gaze_data = obt.get_screen_gaze_data(include_filtered_data=True)
pd.testing.assert_frame_equal(obtained_pupil_data,
expected_pupil_data, check_like=True)
pd.testing.assert_frame_equal(obtained_screen_gaze_data,
expected_gaze_data, check_like=True)