import pathlib
import typing
import numpy
import pydantic
import pynwb
import pynwb.testing.mock.ecephys
import pynwb.testing.mock.file
import pynwb.testing.mock.icephys
[docs]
def get_tutorial_directory() -> pathlib.Path:
tutorial_dir = pathlib.Path.home() / "nwb2bids_tutorials"
tutorial_dir.mkdir(exist_ok=True)
return tutorial_dir
def _generate_ecephys_file(*, nwbfile_path: pathlib.Path, subject_id: str = "001", session_id: str = "A") -> None:
nwbfile = pynwb.testing.mock.file.mock_NWBFile(
session_id=session_id,
session_description=(
"An example NWB file containing ecephys neurodata types - for use in the nwb2bids tutorials."
),
)
subject = pynwb.file.Subject(
subject_id=subject_id,
species="Mus musculus",
sex="M",
)
nwbfile.subject = subject
probe = pynwb.testing.mock.ecephys.mock_Device(
name="ExampleProbe",
description="This is an example ecephys probe used for demonstration purposes.",
manufacturer="`nwb2bids` test suite",
nwbfile=nwbfile,
)
shank = pynwb.testing.mock.ecephys.mock_ElectrodeGroup(
name="ExampleShank",
description="This is an example electrode group (shank) used for demonstration purposes.",
location="hippocampus",
device=probe,
nwbfile=nwbfile,
)
number_of_electrodes = 8
for index in range(number_of_electrodes):
nwbfile.add_electrode(imp=150_000.0, location="hippocampus", group=shank, filtering="HighpassFilter")
electrodes = nwbfile.create_electrode_table_region(
region=list(range(number_of_electrodes)),
description="A `DynamicTableRegion` referring to all electrodes in this file.",
)
pynwb.testing.mock.ecephys.mock_ElectricalSeries(
name="ExampleElectricalSeries",
description=(
"An example electrical series that represents data which could have been "
"read off of the channels of an ecephys probe."
),
data=numpy.ones(shape=(10, number_of_electrodes)),
electrodes=electrodes,
rate=30_000.0,
nwbfile=nwbfile,
conversion=0.00000302734375,
)
with pynwb.NWBHDF5IO(path=nwbfile_path, mode="w") as file_stream:
file_stream.write(nwbfile)
def _generate_icephys_file(*, nwbfile_path: pathlib.Path, subject_id: str = "001", session_id: str = "A") -> None:
nwbfile = pynwb.testing.mock.file.mock_NWBFile(
session_id=session_id,
session_description=(
"An example NWB file containing icephys neurodata types - for use in the nwb2bids tutorials."
),
)
subject = pynwb.file.Subject(
subject_id=subject_id,
species="Mus musculus",
sex="M",
)
nwbfile.subject = subject
# Icephys 'probes'
probe1 = pynwb.testing.mock.icephys.mock_Device(
name="pipette01",
description="This is an example icephys probe used for demonstration purposes.",
manufacturer="Sutter",
nwbfile=nwbfile,
)
probe2 = pynwb.testing.mock.icephys.mock_Device(
name="pipette02",
description="This is an example icephys probe used for demonstration purposes.",
manufacturer="Sutter",
nwbfile=nwbfile,
)
probe3 = pynwb.testing.mock.icephys.mock_Device(
name="pipette03",
description="This is an example icephys probe used for demonstration purposes.",
manufacturer="WPI",
nwbfile=nwbfile,
)
# Icephys electrodes
electrode1 = nwbfile.create_icephys_electrode(
name="patch01",
description="This is an example icephys electrode used for demonstration purposes.",
device=probe1,
location="VISp2/3",
)
electrode2 = nwbfile.create_icephys_electrode(
name="patch02",
description="This is an example icephys electrode used for demonstration purposes.",
device=probe2,
location="VISp2/3",
)
electrode3 = nwbfile.create_icephys_electrode(
name="sharp01",
description="This is an example icephys electrode used for demonstration purposes.",
device=probe3,
location="PL5",
)
# Icephys series
series1 = pynwb.testing.mock.icephys.mock_CurrentClampSeries(
name="ExampleCurrentClampSeries1",
data=[-70, -60, -50, -40, -30],
conversion=1e-3,
resolution=numpy.nan,
rate=20e3,
electrode=electrode1,
gain=0.01,
bias_current=1e-12,
bridge_balance=70e6,
capacitance_compensation=1e-12,
)
series2 = pynwb.testing.mock.icephys.mock_CurrentClampSeries(
name="ExampleCurrentClampSeries2",
data=[-10, 0, 10, 20, 30],
conversion=1e-3,
resolution=numpy.nan,
rate=20e3,
electrode=electrode2,
gain=0.01,
bias_current=1e-12,
bridge_balance=70e6,
capacitance_compensation=1e-12,
)
nwbfile.add_intracellular_recording(electrode=electrode1, response=series1)
nwbfile.add_intracellular_recording(electrode=electrode2, response=series2)
pynwb.testing.mock.icephys.mock_VoltageClampSeries(
name="ExampleVoltageClampSeries1",
data=[1.0, 2.0, 3.0, 4.0, 5.0],
conversion=1e-12,
resolution=numpy.nan,
rate=20e3,
electrode=electrode3,
gain=5e-12,
capacitance_slow=100e-12,
resistance_comp_correction=70.0,
nwbfile=nwbfile,
)
with pynwb.NWBHDF5IO(path=nwbfile_path, mode="w") as file_stream:
file_stream.write(nwbfile)
[docs]
@pydantic.validate_call
def generate_ephys_tutorial(
*,
mode=typing.Literal["file", "dataset"],
output_directory: pydantic.DirectoryPath | None = None,
modality: typing.Literal["ecephys", "icephys"] = "ecephys",
) -> pathlib.Path:
if output_directory is None:
tutorial_dir = get_tutorial_directory()
output_directory = tutorial_dir / f"{modality}_tutorial_{mode}"
output_directory.mkdir(exist_ok=True)
if mode == "file":
nwbfile_path = output_directory / f"{modality}.nwb"
if modality == "ecephys":
_generate_ecephys_file(nwbfile_path=nwbfile_path)
else:
_generate_icephys_file(nwbfile_path=nwbfile_path)
return nwbfile_path
subdir = output_directory / "some_sessions"
subdir.mkdir(exist_ok=True)
index_to_paths = {
0: subdir / f"{modality}_session_1.nwb",
1: subdir / f"{modality}_session_2.nwb",
2: output_directory / f"{modality}_session_3.nwb",
3: output_directory / "DO_NOT_CONVERT.nwb",
}
index_to_subject_id = {
0: "001",
1: "001",
2: "002",
3: "003",
}
index_to_session_id = {
0: "A",
1: "B",
2: "C",
3: "D",
}
for index in range(4):
nwbfile_path = index_to_paths[index]
if modality == "ecephys":
_generate_ecephys_file(
nwbfile_path=nwbfile_path, subject_id=index_to_subject_id[index], session_id=index_to_session_id[index]
)
else:
_generate_icephys_file(
nwbfile_path=nwbfile_path, subject_id=index_to_subject_id[index], session_id=index_to_session_id[index]
)
return output_directory
