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adds data and unit arguments to spiketimes TimeSeries object #405

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merged 2 commits into from
Apr 24, 2020
Merged

adds data and unit arguments to spiketimes TimeSeries object #405

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b90d359
adds data and unit arguments to spiketimes TimeSeries object
MatthewAitken Apr 23, 2020
c390774
stores data as np.array to avoid errors when spike times is []
MatthewAitken Apr 23, 2020
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5 changes: 4 additions & 1 deletion ipfx/nwb_append.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from hdmf.backends.hdf5.h5_utils import H5DataIO
from pynwb import TimeSeries
from pynwb import ProcessingModule
import numpy as np


PathLike = Union[
Expand Down Expand Up @@ -50,9 +51,11 @@ def append_spike_times(input_nwb_path: PathLike,
spike_module = ProcessingModule(name='spikes',
description='detected spikes')
for sweep_num, spike_times in sweep_spike_times.items():
wrapped_spike_times = H5DataIO(data=spike_times,
wrapped_spike_times = H5DataIO(data=np.asarray(spike_times),
compression=True)
ts = TimeSeries(timestamps=wrapped_spike_times,
unit='seconds',
data=wrapped_spike_times,
name=f"Sweep_{sweep_num}")
spike_module.add_data_interface(ts)

Expand Down