def test_get_subject(nwbfile, set_none):
sink = nwb2_sink.Nwb2Sink(None)
sink.nwbfile = nwbfile
if set_none:
nwbfile.subject = None
subject = sink._get_subject()
subject.subject_id = "foo"
assert nwbfile.subject.subject_id == "foo"
def test_roundtrip(tmpdir_factory, nwbfile):
tmpdir = str(tmpdir_factory.mktemp("test_serialize"))
first_path = os.path.join(tmpdir, "first.nwb")
second_path = os.path.join(tmpdir, "second.nwb")
with pynwb.NWBHDF5IO(first_path, "w") as writer:
writer.write(nwbfile)
sink = nwb2_sink.Nwb2Sink(first_path)
sink.register("institution", "AIBS")
sink.serialize({"output_path": second_path})
with pynwb.NWBHDF5IO(second_path, "r", load_namespaces=True) as reader:
obt = reader.read()
assert obt.institution == "AIBS"
def test_register(
tmpdir_factory, nwbfile, name, value, sweep_id, getter, expected
):
tmpdir = tmpdir_factory.mktemp("test_register")
path = os.path.join(str(tmpdir), "test.nwb")
sink = nwb2_sink.Nwb2Sink(None)
sink.nwbfile = nwbfile
sink.register(name, value, sweep_id)
with pynwb.NWBHDF5IO(path, "w") as writer:
writer.write(nwbfile)
with pynwb.NWBHDF5IO(path, "r") as reader:
obt_nwb = reader.read()
obtained = getter(obt_nwb)
assert obtained == expected
def test_serialize(tmpdir_factory, nwbfile):
out_path = os.path.join(
str(tmpdir_factory.mktemp("test_serialize")),
"out.nwb"
)
sink = nwb2_sink.Nwb2Sink(None)
sink._data = io.BytesIO()
sink._h5_file = h5py.File(sink._data, "w")
sink._nwb_io = pynwb.NWBHDF5IO(
path=sink._h5_file.filename,
mode="w",
file=sink._h5_file
)
sink.nwbfile = nwbfile
sink.serialize({"output_path": out_path})
with pynwb.NWBHDF5IO(out_path, "r", load_namespaces=True) as reader:
obt = reader.read()
assert obt.identifier == "test session"
def test_get_sweep_series(nwbfile):
sink = nwb2_sink.Nwb2Sink(None)
sink.nwbfile = nwbfile
obt = sink._get_sweep_series(12)[0]
assert np.allclose(obt.data[:], [1, 2, 3])
def test_get_single_ic_electrode(nwbfile):
sink = nwb2_sink.Nwb2Sink(None)
sink.nwbfile = nwbfile
obt = sink._get_single_ic_electrode()
assert obt.name == "my_electrode"