nwb-linkml/nwb_linkml/tests/test_io/test_io_nwb.py

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"""
Placeholder test module to test reading from pynwb-generated NWB file
"""
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import pytest
from datetime import datetime
from numpydantic.interface.hdf5 import H5Proxy
from nwb_linkml.io.hdf5 import HDF5IO
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from nwb_models.models import NWBFile
from pydantic import BaseModel
import numpy as np
import pandas as pd
from pynwb import NWBHDF5IO, NWBFile as PyNWBFile
def test_read_from_nwbfile(nwb_file):
"""
Read data from a pynwb HDF5 NWB file
Placeholder that just ensures that reads work and all pydantic models validate,
testing of correctness of read will happen elsewhere.
"""
res = HDF5IO(nwb_file).read()
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@pytest.fixture(scope="module")
def read_nwbfile(nwb_file) -> NWBFile:
res = HDF5IO(nwb_file).read()
return res
@pytest.fixture(scope="module")
def read_pynwb(nwb_file) -> PyNWBFile:
nwbf = NWBHDF5IO(nwb_file, "r")
res = nwbf.read()
yield res
nwbf.close()
def _compare_attrs(model: BaseModel, pymodel: object):
for field, value in model.model_dump().items():
if isinstance(value, (dict, H5Proxy)):
continue
if hasattr(pymodel, field):
pynwb_val = getattr(pymodel, field)
if isinstance(pynwb_val, list):
if isinstance(pynwb_val[0], datetime):
# need to normalize UTC numpy.datetime64 with datetime with tz
continue
assert all([val == pval for val, pval in zip(value, pynwb_val)])
else:
if not pynwb_val:
# pynwb instantiates some stuff as empty dicts where we use ``None``
assert bool(pynwb_val) == bool(value)
else:
assert value == pynwb_val
def test_nwbfile_base(read_nwbfile, read_pynwb):
"""
Base attributes on top-level nwbfile are correct
"""
_compare_attrs(read_nwbfile, read_pynwb)
def test_timeseries(read_nwbfile, read_pynwb):
py_acq = read_pynwb.get_acquisition("test_timeseries")
acq = read_nwbfile.acquisition["test_timeseries"]
_compare_attrs(acq, py_acq)
# data and timeseries should be equal
assert np.array_equal(acq.data[:], py_acq.data[:])
assert np.array_equal(acq.timestamps[:], py_acq.timestamps[:])
def test_position(read_nwbfile, read_pynwb):
trials = read_nwbfile.intervals.trials[:]
py_trials = read_pynwb.trials.to_dataframe()
pd.testing.assert_frame_equal(py_trials, trials)
spatial = read_nwbfile.processing["behavior"].Position.SpatialSeries
py_spatial = read_pynwb.processing["behavior"]["Position"]["SpatialSeries"]
_compare_attrs(spatial, py_spatial)
assert np.array_equal(spatial[:], py_spatial.data[:])
assert np.array_equal(spatial.timestamps[:], py_spatial.timestamps[:])
def test_ecephys(read_nwbfile, read_pynwb):
pass
def test_units(read_nwbfile, read_pynwb):
pass
def test_icephys(read_nwbfile, read_pynwb):
pass
def test_ca_imaging(read_nwbfile, read_pynwb):
pass
def test_read_from_yaml(nwb_file):
"""
Read data from a yaml-fied NWB file
"""
pass