bugfix in waveform extraction for OpenEphys

Author: Thinh Nguyen

elements_ephys/readers/openephys.py

@@ -144,20 +144,20 @@ def extract_spike_waveforms(self, spikes, channel, n_wf=500, wf_win=(-32, 32)):
         :param bit_volts: scalar required to convert int16 values into microvolts (default of 1)
         :return: waveforms (sample x channel x spike)
         """
-
+        data = self.ap_data.T  # (sample x channel)
         channel_ind = [np.where(self.ap_meta['channels_ids'] == chn)[0][0] for chn in channel]
 
         # ignore spikes at the beginning or end of raw data
         spikes = spikes[np.logical_and(spikes > (-wf_win[0] / self.ap_meta['sample_rate']),
-                                       spikes < (wf_win[-1] / self.ap_meta['sample_rate']))]
+                                       spikes < (self.ap_timestamps.max() - wf_win[-1] / self.ap_meta['sample_rate']))]
         # select a randomized set of "n_wf" spikes
         np.random.shuffle(spikes)
         spikes = spikes[:n_wf]
         # extract waveforms
         if len(spikes) > 0:
             spike_indices = np.searchsorted(self.ap_timestamps, spikes, side="left")
             # waveform at each spike: (sample x channel x spike)
-            spike_wfs = np.dstack([self.ap_data[int(spk + wf_win[0]):int(spk + wf_win[-1]), channel_ind]
+            spike_wfs = np.dstack([data[int(spk + wf_win[0]):int(spk + wf_win[-1]), channel_ind]
                                    for spk in spike_indices])
             return spike_wfs
         else:  # if no spike found, return NaN of size (sample x channel x 1)