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bugfix / pause + burst detection #554

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bugfix / pause + burst detection #554

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2149cd2
detect pauses update
mzabolocki Jan 11, 2023
cc93e60
Merge pull request #1 from mzabolocki/mzabolocki-patch-1
mzabolocki Jan 11, 2023
9fee29a
spfk rm for burst detect
mzabolocki Jan 11, 2023
0884c6d
pause_cost_weight --> pause_cost for pause
mzabolocki Jan 11, 2023
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2 changes: 1 addition & 1 deletion ipfx/feature_extractor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -284,7 +284,7 @@ def process(self, t, v, i, spikes_df, extra_features=None, exclude_clipped=False

if features["avg_rate"] > 0:
if 'pause' in extra_features:
features['pause'] = strf.pause(t, spikes_df, self.start, self.end, self.pause_cost_weight)
features['pause'] = strf.pause(t, spikes_df, self.start, self.end, self.pause_cost)
if 'burst' in extra_features:
features['burst'] = strf.burst(t, spikes_df, self.burst_tol, self.pause_cost)
if 'delay' in extra_features:
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4 changes: 2 additions & 2 deletions ipfx/spike_train_features.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ def pause(t, spikes_df, start, end, cost_weight=1.0):
isis = get_isis(t, thresholds)
isi_types = spikes_df["isi_type"][:-1].values

pause_list = spkf.detect_pauses(isis, isi_types, cost_weight)
pause_list = detect_pauses(isis, isi_types, cost_weight)

if len(pause_list) == 0:
return 0, 0.
Expand Down Expand Up @@ -84,7 +84,7 @@ def burst(t, spikes_df, tol=0.5, pause_cost=1.0):
slow_tr_t = spikes_df["slow_trough_t"].values
thr_v = spikes_df["threshold_v"].values

bursts = spkf.detect_bursts(isis, isi_types,
bursts = detect_bursts(isis, isi_types,
fast_tr_v, fast_tr_t,
slow_tr_v, slow_tr_t,
thr_v, tol, pause_cost)
Expand Down