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Set amplitude scalings equal zero for zero template units #4455

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Merged
alejoe91 merged 2 commits into from
Mar 18, 2026
Merged

Set amplitude scalings equal zero for zero template units #4455

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274a08c
set amplitude scalings equal zero for zero template units
chrishalcrow Mar 17, 2026
b72a948
oups
chrishalcrow Mar 18, 2026
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13 changes: 13 additions & 0 deletions src/spikeinterface/postprocessing/amplitude_scalings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,9 @@ def __init__(
max_margin_collisions = delta_collision_samples + margin_waveforms
self._margin = max_margin_collisions

# for some edge cases a template can be zero, leading to problems later
template_is_zero = [np.all(template == 0) for template in all_templates]

self._all_templates = all_templates
self._sparsity_mask = sparsity_mask
self._nbefore = nbefore
Expand All @@ -209,6 +212,7 @@ def __init__(
self._cut_out_after = cut_out_after
self._handle_collisions = handle_collisions
self._delta_collision_samples = delta_collision_samples
self._template_is_zero = template_is_zero

self._kwargs.update(
all_templates=all_templates,
Expand All @@ -220,6 +224,7 @@ def __init__(
return_in_uV=return_in_uV,
handle_collisions=handle_collisions,
delta_collision_samples=delta_collision_samples,
template_is_zero=template_is_zero,
)

def get_dtype(self):
Expand All @@ -239,6 +244,7 @@ def compute(self, traces, peaks):
cut_out_after = self._cut_out_after
handle_collisions = self._handle_collisions
delta_collision_samples = self._delta_collision_samples
template_is_zero = self._template_is_zero

# local_spikes_within_margin = peaks
# i0 = np.searchsorted(local_spikes_within_margin["sample_index"], left_margin)
Expand All @@ -265,7 +271,14 @@ def compute(self, traces, peaks):
if spike_index in collisions.keys():
# we deal with overlapping spikes later
continue

unit_index = spike["unit_index"]

if template_is_zero[unit_index]:
# if template is zero, linregress will fail so we intervene
scalings[spike_index] = 0
continue

sample_centered = spike["sample_index"]
(sparse_indices,) = np.nonzero(sparsity_mask[unit_index])
template = all_templates[unit_index][:, sparse_indices]
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