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[Doc] improve spike_train_generation.spike_extraction parameter documentation #641

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[Doc] improve spike_train_generation.spike_extraction parameter documentation #641

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f9d58df
add notes section and more details for interval parameter
Moritz-Alexander-Kern Sep 23, 2024
be21820
pep8
Moritz-Alexander-Kern Sep 23, 2024
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17 changes: 15 additions & 2 deletions elephant/spike_train_generation.py
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Expand Up @@ -186,21 +186,34 @@ def spike_extraction(
Default: None
interval : tuple of :class:`pq.Quantity`
Specifies the time interval around the `time_stamps` where the waveform
is extracted.
is extracted. The default values [-2ms, 4ms] are based on experience,
and many spike sorting tools choose values in this range:
Spikes are typically about 1-2 ms in length. This is to include a small interval before
the spike peak and a slightly larger interval after the spike peak to capture the dynamics following
the spike. Adjusting this interval will modify the waveforms stored in the neo :class:`neo.core.SpikeTrain`,
but it will not affect the spike times.
Default: (-2 * pq.ms, 4 * pq.ms)
always_as_list: bool, optional
If True, :class:`neo.core.spiketrainslist.SpikeTrainList` is returned.
Default: False

Returns
------- # noqa
-------
result_st : :class:`neo.core.SpikeTrain`, :class:`neo.core.spiketrainslist.SpikeTrainList`.
Contains the time_stamps of each of the spikes and the waveforms in
`result_st.waveforms`.

See Also
--------
:func:`elephant.spike_train_generation.peak_detection`

Notes
-----
If `time_stamps` is set to None, peaks are extracted using numpy's peak finder. Therefore, the spike times will
not be affected by the `interval` parameter. However, the waveforms stored in the neo :class:`neo.core.SpikeTrain`
object (in `result_st.waveforms`, an NxM matrix for the N spikes, each row containing a waveform) should be
different depending on the `interval` parameter. For example, if the sampling frequency is 10KHz, and 123 spikes
were detected, then `result_st.waveforms` should be size 123x200 for an interval of [-10ms, 10ms].
"""
if isinstance(signal, neo.core.AnalogSignal):
if signal.shape[1] == 1:
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