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Speed up select_periods and get_data(periods=...) by finding each period's spikes with searchsorted #4940

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Speed up select_periods and get_data(periods=...) by finding each period's spikes with searchsorted #4940

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13 changes: 8 additions & 5 deletions src/spikeinterface/core/sorting_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -491,12 +491,15 @@ def select_sorting_periods_mask(sorting: BaseSorting, periods):
for unit_index, unit_id in enumerate(sorting.unit_ids):
# filter by unit index
periods_for_unit = periods_in_segment[periods_in_segment["unit_index"] == unit_index]
if len(periods_for_unit) == 0:
continue
global_indices = global_indices_segment[unit_id]
spiketrains = spike_vector[global_indices]["sample_index"]
if len(periods_for_unit) > 0:
for period in periods_for_unit:
mask = (spiketrains >= period["start_sample_index"]) & (spiketrains < period["end_sample_index"])
keep_mask[global_indices[mask]] = True
spiketrain = spike_vector["sample_index"][global_indices]
# the spike train is sorted, so the spikes in [start, end) of each period are one slice of it
starts = np.searchsorted(spiketrain, periods_for_unit["start_sample_index"])
ends = np.searchsorted(spiketrain, periods_for_unit["end_sample_index"])
for start, end in zip(starts, ends):
keep_mask[global_indices[start:end]] = True
return keep_mask


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