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Set num_histogram_bins in amplitude_cutoff (back) to 100 (#4415)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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src/spikeinterface/metrics/quality/misc_metrics.py

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1021,8 +1021,12 @@ def compute_amplitude_cutoffs(
10211021
amplitudes_bins_min_ratio,
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)
10231023

1024-
if np.any(np.isnan(list(all_fraction_missing.values()))):
1025-
warnings.warn(f"Some units have too few spikes : amplitude_cutoff is set to NaN")
1024+
units_with_few_spikes = [unit_id for unit_id, amp_cutoff in all_fraction_missing.items() if np.isnan(amp_cutoff)]
1025+
if len(units_with_few_spikes) > 0:
1026+
min_num_spikes = amplitudes_bins_min_ratio * num_histogram_bins
1027+
warnings.warn(
1028+
f"Amplitude cutoff set to NaN for units {units_with_few_spikes}: too few spikes (< {min_num_spikes})."
1029+
)
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10271031
return all_fraction_missing
10281032

@@ -1031,7 +1035,7 @@ class AmplitudeCutoff(BaseMetric):
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metric_name = "amplitude_cutoff"
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metric_function = compute_amplitude_cutoffs
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metric_params = {
1034-
"num_histogram_bins": 200,
1038+
"num_histogram_bins": 100,
10351039
"histogram_smoothing_value": 3,
10361040
"amplitudes_bins_min_ratio": 5,
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}
@@ -1634,7 +1638,7 @@ def isi_violations(spike_trains, total_duration_s, isi_threshold_s=0.0015, min_i
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16351639
def amplitude_cutoff(
16361640
amplitudes,
1637-
num_histogram_bins=500,
1641+
num_histogram_bins=100,
16381642
histogram_smoothing_value=3,
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amplitudes_bins_min_ratio=5,
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):

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