Minimum working example

Author: guptadivyansh

neo/rawio/spikeglxrawio.py

@@ -297,7 +297,7 @@ def _get_event_timestamps(self, block_index, seg_index, event_channel_index, t_s
         dig_ch = info["digital_channels"]
         if len(dig_ch) > 0:
             event_data = self._events_memmap
-            channel = dig_ch[event_channel_index]
+            channel = dig_ch[event_channel_index] # 'XD0', 'XD1', etc.
             ch_idx = 7 - int(channel[2:])  # They are in the reverse order
             this_stream = event_data[:, ch_idx]
             timestamps, durations, labels = self._find_events_in_channel(this_stream, channel)
@@ -309,18 +309,59 @@ def _get_event_timestamps(self, block_index, seg_index, event_channel_index, t_s
 
         return timestamps, durations, labels
 
-    def _get_sync_events(self, stream_index):
-        #find sync events in the 'SY0' channel of imec streams
-        channel = 'SY0'
-        sync_data = self.get_analogsignal_chunk(channel_names = [channel], stream_index = stream_index)
-        #uint16 word to uint8 bytes to bits
-        sync_data_uint8 = sync_data.view(np.uint8)
-        unpacked_sync_data = np.unpackbits(sync_data_uint8, axis=1)
-        #sync line is the 6th bit (so 1st bit because reversed order)
-        #https://billkarsh.github.io/SpikeGLX/Sgl_help/Metadata_30.html
-        sync_line = unpacked_sync_data[:,1]
-        raise NotImplementedError("Work in progress")
-        return self._find_events_in_channel(sync_line, "SY0")
+    def _get_sync_events(self, stream_index, seg_index = 0):
+        '''
+        Find sync events in the stream.
+        For imec streams, the sync events are found in the 'SY0' channel, 
+        which should be the 6th bit in the last 'analog' channel in the stream.
+        For nidq streams, the sync events are found in the channel specified by the metadata fields
+        'syncNiChanType' and 'syncNiChan'.
+
+        Meta file descriptions taken from:
+        https://billkarsh.github.io/SpikeGLX/Sgl_help/Metadata_30.html
+
+        Returns timestamps, durations, labels of rising or falling edges in these channels
+        '''
+
+        stream_name = self.header["signal_streams"][stream_index]["name"]
+        info = self.signals_info_dict[seg_index, stream_name] 
+
+        if 'imec' in stream_name:
+            if not self.load_sync_channel:
+                raise ValueError("SYNC channel was not loaded. Try setting load_sync_channel=True")
+            if not info["has_sync_trace"]:
+                raise ValueError("SYNC channel is not present in the recording."
+                " Cannot find sync events based on metadata field 'snsApLfSy'")
+            
+            #find sync events in the 'SY0' channel of imec streams
+            channel = 'SY0'
+            sync_data = self.get_analogsignal_chunk(channel_names = [channel], 
+                                                    stream_index = stream_index, 
+                                                    seg_index = seg_index)
+            #uint16 word to uint8 bytes to bits
+            sync_data_uint8 = sync_data.view(np.uint8)
+            unpacked_sync_data = np.unpackbits(sync_data_uint8, axis=1)
+            sync_line = unpacked_sync_data[:,1]
+            return self._find_events_in_channel(sync_line, channel)
+        elif 'nidq' in self.header['signal_streams'][stream_index]['name']:
+            #find channel from metafile
+            meta = info['meta']
+            niChanType = int(meta['syncNiChanType'])
+            niChan = int(meta['syncNiChan'])
+            if niChanType == 0: #digital channel
+                return self._get_event_timestamps(0, seg_index, niChan)
+            elif niChanType == 1: #analog channel
+                niThresh = float(meta['syncNiThresh']) #volts
+                sync_line = self.get_analogsignal_chunk(channel_names = [f'XA{niChan}'],
+                                                        stream_index = stream_index, 
+                                                        seg_index = seg_index)
+                #Does this need to be scaled by channel gain before threshold?
+                sync_line = sync_line > niThresh
+                raise NotImplementedError("Analog sync events not yet implemented")
+                return self._find_events_in_channel(sync_line, f'XA{niChan}')
+        else:
+            raise ValueError("Unknown stream type, cannot find sync events")
+
 
     def _find_events_in_channel(self, channel_data, channel_name):
 
@@ -343,8 +384,10 @@ def _find_events_in_channel(self, channel_data, channel_name):
             labels = np.asarray(labels) 
         return timestamps, durations, labels
 
-    def _rescale_event_timestamp(self, event_timestamps, dtype, event_channel_index):
-        info = self.signals_info_dict[0, "nidq"]  # There are no events that are not in the nidq stream
+    def _rescale_event_timestamp(self, event_timestamps, dtype=np.float64, event_channel_index=0, 
+                                 stream_index = 0):
+        stream_name = self.header["signal_streams"][stream_index]["name"]
+        info = self.signals_info_dict[0, stream_name]  # get sampling rate from first segment
         event_times = event_timestamps.astype(dtype) / float(info["sampling_rate"])
         return event_times