bugfix - openephys waveform extraction

Author: Thinh Nguyen

elements_ephys/readers/openephys.py

@@ -148,16 +148,15 @@ def lfp_timestamps(self):
             self._lfp_timestamps = np.hstack([s.times for s in self.lfp_analog_signals])
         return self._lfp_timestamps
 
-    def extract_spike_waveforms(self, spikes, channel, n_wf=500, wf_win=(-32, 32)):
+    def extract_spike_waveforms(self, spikes, channel_ind, n_wf=500, wf_win=(-32, 32)):
         """
         :param spikes: spike times (in second) to extract waveforms
-        :param channel: channel (name, not indices) to extract waveforms
+        :param channel_ind: channel indices (of meta['channels_ids']) to extract waveforms
         :param n_wf: number of spikes per unit to extract the waveforms
         :param wf_win: number of sample pre and post a spike
         :return: waveforms (sample x channel x spike)
         """
-        channel_ind = [np.where(self.ap_meta['channels_ids'] == chn)[0][0] for chn in channel]
-        channel_bit_volts = self.ap_meta['channels_gains'][channel_ind]
+        channel_bit_volts = np.array(self.ap_meta['channels_gains'])[channel_ind]
 
         # ignore spikes at the beginning or end of raw data
         spikes = spikes[np.logical_and(spikes > (-wf_win[0] / self.ap_meta['sample_rate']),
@@ -174,4 +173,4 @@ def extract_spike_waveforms(self, spikes, channel, n_wf=500, wf_win=(-32, 32)):
                                    for spk in spike_indices])
             return spike_wfs
         else:  # if no spike found, return NaN of size (sample x channel x 1)
-            return np.full((len(range(*wf_win)), len(channel), 1), np.nan)
+            return np.full((len(range(*wf_win)), len(channel_ind), 1), np.nan)