From 2149cd23cd61a2b52731dc82885e1d4b92866752 Mon Sep 17 00:00:00 2001 From: Michael Zabolocki <89680425+mzabolocki@users.noreply.github.com> Date: Wed, 11 Jan 2023 15:41:47 +1030 Subject: [PATCH 1/3] detect pauses update module not in spfk --- ipfx/spike_train_features.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ipfx/spike_train_features.py b/ipfx/spike_train_features.py index ac18ec0a..954b6fbd 100644 --- a/ipfx/spike_train_features.py +++ b/ipfx/spike_train_features.py @@ -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. From 9fee29a533e78e1baf7b43f36e9f6c7a3f267203 Mon Sep 17 00:00:00 2001 From: Michael Zabolocki <89680425+mzabolocki@users.noreply.github.com> Date: Wed, 11 Jan 2023 15:54:58 +1030 Subject: [PATCH 2/3] spfk rm for burst detect --- ipfx/spike_train_features.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ipfx/spike_train_features.py b/ipfx/spike_train_features.py index 954b6fbd..737741cd 100644 --- a/ipfx/spike_train_features.py +++ b/ipfx/spike_train_features.py @@ -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) From 0884c6d199d73201aa3ca2621ec8349b8f6b6264 Mon Sep 17 00:00:00 2001 From: Michael Zabolocki <89680425+mzabolocki@users.noreply.github.com> Date: Wed, 11 Jan 2023 15:58:06 +1030 Subject: [PATCH 3/3] pause_cost_weight --> pause_cost for pause --- ipfx/feature_extractor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ipfx/feature_extractor.py b/ipfx/feature_extractor.py index 08d4061c..7df8e9f8 100644 --- a/ipfx/feature_extractor.py +++ b/ipfx/feature_extractor.py @@ -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: