import numpy
import pynwb
import pynwb.testing.mock.base
[docs]
def mock_trials_table(nwbfile: pynwb.NWBFile | None = None) -> pynwb.epoch.TimeIntervals:
"""
Generate a mock trials table.
These are shorter than epochs and fit neatly within them in a qualitative manner.
If a NWBFile is provided, a TimeSeriesReference to a mock TimeSeries will be added to each trial.
"""
trials = pynwb.epoch.TimeIntervals(name="trials", description="A mock trials table.")
trials.add_column(name="trial_condition", description="Extra information per trial.")
trials.add_column(
name="indexed_column",
description="A more complicated type of column that contains structured data.",
index=True,
)
kwargs_per_row = [
{"start_time": 0.0, "stop_time": 1.0, "trial_condition": "A", "indexed_column": [0, 1]},
{"start_time": 2.0, "stop_time": 3.0, "trial_condition": "B", "indexed_column": [2, 3]},
{"start_time": 5.0, "stop_time": 5.5, "trial_condition": "C", "indexed_column": [4, 5]},
{"start_time": 5.5, "stop_time": 6.0, "trial_condition": "D", "indexed_column": [6, 7]},
]
if nwbfile is not None:
timeseries = pynwb.testing.mock.base.mock_TimeSeries(nwbfile=nwbfile)
timeseries_ref = pynwb.base.TimeSeriesReference(
idx_start=0, count=timeseries.data.shape[0], timeseries=timeseries
)
for kwargs in kwargs_per_row:
kwargs["timeseries"] = [timeseries_ref]
for kwargs in kwargs_per_row:
trials.add_row(**kwargs)
return trials
[docs]
def mock_epochs_table() -> pynwb.epoch.TimeIntervals:
"""
Generate a mock epochs table.
These are longer than trials and encompass several of them in a qualitative manner.
"""
epochs = pynwb.epoch.TimeIntervals(name="epochs", description="A mock epochs table.")
epochs.add_column(name="epoch_condition", description="Extra information per epoch.")
epochs.add_row(start_time=0.0, stop_time=3.5, epoch_condition="AB")
epochs.add_row(start_time=4.5, stop_time=6.0, epoch_condition="CD")
return epochs
[docs]
def mock_time_intervals() -> pynwb.epoch.TimeIntervals:
"""Generate a mock time intervals table."""
time_intervals = pynwb.epoch.TimeIntervals(name="mock_time_intervals", description="A mock time intervals table.")
time_intervals.add_column(name="tag", description="A tag assigned to each interval.")
time_intervals.add_row(start_time=0.5, stop_time=0.75, tag="tag1")
time_intervals.add_row(start_time=5.1, stop_time=5.23, tag="tag2")
return time_intervals
[docs]
def mock_trials_table_with_numpy_column() -> pynwb.epoch.TimeIntervals:
"""
Generate a mock trials table with a numpy array-valued column.
Reproduces the scenario from https://github.com/con/nwb2bids/issues/338,
where a column stores a fixed-size array per trial (e.g. multi-pulse optogenetics data).
Without serialization, numpy's ``__str__`` inserts line-breaks into wide arrays, breaking TSV rows.
"""
trials = pynwb.epoch.TimeIntervals(name="trials", description="A mock trials table.")
trials.add_column(name="trial_condition", description="Extra information per trial.")
trials.add_column(name="pulse_times", description="Array of pulse timestamps per trial.")
trials.add_row(
start_time=0.0,
stop_time=1.0,
trial_condition="A",
pulse_times=numpy.array([float("nan")] * 20),
)
trials.add_row(
start_time=1.0,
stop_time=2.0,
trial_condition="B",
pulse_times=numpy.array([0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0] * 2),
)
return trials
