Merge pull request #37 from zm711/ref-dur-refactor

calculate refractory period violations with samples
zm711 · Aug 25, 2023 · 721355f · 721355f
2 parents 1104ebe + 8c5b95d
commit 721355f
Showing 1 changed file with 3 additions and 7 deletions.
diff --git a/src/spikeanalysis/spike_data.py b/src/spikeanalysis/spike_data.py
@@ -224,23 +224,19 @@ def refractory_violation(self, ref_dur_ms: float):
         """
         print("calculating refractory period violation fraction")
         self._goto_file_path()
-        ref_dur = ref_dur_ms / 1000
+        ref_dur_samples = ref_dur_ms / 1000 * self._sampling_rate
         spike_clusters = np.squeeze(np.load("spike_clusters.npy"))
         violations = np.zeros((len(set(spike_clusters))))
         violations[:] = np.nan
-
-        try:
-            spike_times = self.spike_times
-        except AttributeError:
-            spike_times = self.raw_spike_times / self._sampling_rate
+        spike_times = self.raw_spike_times
 
         for idx, cluster in enumerate(tqdm(set(spike_clusters))):
             spikes = spike_times[self.spike_clusters == cluster]
             # print(len(spikes))
             if len(spikes) < 10:
                 continue
             else:
-                num_violations = float(len(np.where(np.diff(spikes) <= ref_dur)[0]))
+                num_violations = float(len(np.where(np.diff(spikes) <= ref_dur_samples)[0]))
                 total_spikes = len(spikes)
                 violations[idx] = num_violations / total_spikes