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amplitude cutoff should require amplitude scalings extension #4513

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amplitude cutoff should require amplitude scalings extension #4513

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3 changes: 2 additions & 1 deletion src/spikeinterface/metrics/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ def make_small_analyzer():
"waveforms": {},
"templates": {"operators": ["average", "median"]},
"spike_amplitudes": {},
"amplitude_scalings": {},
"spike_locations": {},
"principal_components": {},
}
Expand Down Expand Up @@ -80,6 +81,6 @@ def sorting_analyzer_simple():
sorting_analyzer.compute("noise_levels")
sorting_analyzer.compute("waveforms", **job_kwargs)
sorting_analyzer.compute("templates")
sorting_analyzer.compute(["spike_amplitudes", "spike_locations"], **job_kwargs)
sorting_analyzer.compute(["spike_amplitudes", "spike_locations", "amplitude_scalings"], **job_kwargs)

return sorting_analyzer
9 changes: 3 additions & 6 deletions src/spikeinterface/metrics/quality/misc_metrics.py
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Expand Up @@ -986,7 +986,7 @@ def compute_amplitude_cutoffs(
Notes
-----
This approach assumes the amplitude histogram is symmetric (not valid in the presence of drift).
If available, amplitudes are extracted from the "spike_amplitude" or "amplitude_scalings" extensions.
Amplitudes are extracted from the "amplitude_scalings" extension.

References
----------
Expand All @@ -1002,10 +1002,7 @@ def compute_amplitude_cutoffs(

all_fraction_missing = {}

available_extension = (
"spike_amplitudes" if sorting_analyzer.has_extension("spike_amplitudes") else "amplitude_scalings"
)
extension = sorting_analyzer.get_extension(available_extension)
extension = sorting_analyzer.get_extension("amplitude_scalings")
amplitudes_by_units = extension.get_data(outputs="by_unit", concatenated=True, periods=periods)

for unit_id in unit_ids:
Expand Down Expand Up @@ -1043,7 +1040,7 @@ class AmplitudeCutoff(BaseMetric):
"amplitude_cutoff": "Estimated fraction of missing spikes, based on the amplitude distribution."
}
supports_periods = True
depend_on = ["spike_amplitudes|amplitude_scalings"]
depend_on = ["amplitude_scalings"]


def compute_amplitude_medians(sorting_analyzer, unit_ids=None, periods=None):
Expand Down
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