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https://github.com/p2p-ld/nwb-linkml.git
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108 lines
3 KiB
Python
108 lines
3 KiB
Python
"""
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Placeholder test module to test reading from pynwb-generated NWB file
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"""
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import pytest
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from datetime import datetime
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from numpydantic.interface.hdf5 import H5Proxy
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from nwb_linkml.io.hdf5 import HDF5IO
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from nwb_models.models import NWBFile
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from pydantic import BaseModel
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import numpy as np
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import pandas as pd
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from pynwb import NWBHDF5IO, NWBFile as PyNWBFile
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def test_read_from_nwbfile(nwb_file):
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"""
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Read data from a pynwb HDF5 NWB file
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Placeholder that just ensures that reads work and all pydantic models validate,
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testing of correctness of read will happen elsewhere.
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"""
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res = HDF5IO(nwb_file).read()
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@pytest.fixture(scope="module")
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def read_nwbfile(nwb_file) -> NWBFile:
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res = HDF5IO(nwb_file).read()
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return res
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@pytest.fixture(scope="module")
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def read_pynwb(nwb_file) -> PyNWBFile:
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nwbf = NWBHDF5IO(nwb_file, "r")
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res = nwbf.read()
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yield res
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nwbf.close()
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def _compare_attrs(model: BaseModel, pymodel: object):
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for field, value in model.model_dump().items():
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if isinstance(value, (dict, H5Proxy)):
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continue
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if hasattr(pymodel, field):
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pynwb_val = getattr(pymodel, field)
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if isinstance(pynwb_val, list):
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if isinstance(pynwb_val[0], datetime):
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# need to normalize UTC numpy.datetime64 with datetime with tz
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continue
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assert all([val == pval for val, pval in zip(value, pynwb_val)])
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else:
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if not pynwb_val:
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# pynwb instantiates some stuff as empty dicts where we use ``None``
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assert bool(pynwb_val) == bool(value)
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else:
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assert value == pynwb_val
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def test_nwbfile_base(read_nwbfile, read_pynwb):
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"""
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Base attributes on top-level nwbfile are correct
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"""
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_compare_attrs(read_nwbfile, read_pynwb)
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def test_timeseries(read_nwbfile, read_pynwb):
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py_acq = read_pynwb.get_acquisition("test_timeseries")
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acq = read_nwbfile.acquisition["test_timeseries"]
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_compare_attrs(acq, py_acq)
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# data and timeseries should be equal
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assert np.array_equal(acq.data[:], py_acq.data[:])
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assert np.array_equal(acq.timestamps[:], py_acq.timestamps[:])
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def test_position(read_nwbfile, read_pynwb):
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trials = read_nwbfile.intervals.trials[:]
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py_trials = read_pynwb.trials.to_dataframe()
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pd.testing.assert_frame_equal(py_trials, trials)
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spatial = read_nwbfile.processing["behavior"].Position.SpatialSeries
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py_spatial = read_pynwb.processing["behavior"]["Position"]["SpatialSeries"]
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_compare_attrs(spatial, py_spatial)
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assert np.array_equal(spatial[:], py_spatial.data[:])
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assert np.array_equal(spatial.timestamps[:], py_spatial.timestamps[:])
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def test_ecephys(read_nwbfile, read_pynwb):
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pass
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def test_units(read_nwbfile, read_pynwb):
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pass
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def test_icephys(read_nwbfile, read_pynwb):
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pass
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def test_ca_imaging(read_nwbfile, read_pynwb):
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pass
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def test_read_from_yaml(nwb_file):
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"""
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Read data from a yaml-fied NWB file
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"""
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pass
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