handles extraction of connected channels for NP_PROBE format in OpenEphys

Author: Thinh Nguyen

element_array_ephys/ephys_no_curation.py

@@ -971,9 +971,8 @@ def get_recording_channels_details(ephys_recording_key):
     elif acq_software == 'Open Ephys':
         oe_probe = get_openephys_probe_data(ephys_recording_key)
         channels_details['uVPerBit'] = oe_probe.ap_meta['channels_gains'][0]
-        channels_details['connected'] = np.array([int(v == 1)
-                                                  for c, v in
-                                                  oe_probe.channel_status.items()
-                                                  if c in channels_details['channel_ind']])
+        channels_details['connected'] = np.array([
+            int(v == 1) for c, v in oe_probe.channels_connected.items()
+            if c in channels_details['channel_ind']])
 
     return channels_details

element_array_ephys/readers/openephys.py

@@ -134,7 +134,9 @@ def __init__(self, processor, probe_index=0):
             self.probe_model = {
                 "Neuropix-PXI": "neuropixels 1.0 - 3B",
                 "Neuropix-3a": "neuropixels 1.0 - 3A"}[processor['@pluginName']]
-            channel_status_str = 'CHANNELSTATUS'
+            self._channels_connected = {int(re.search(r'\d+$', k).group()): int(v)
+                                        for k, v in self.probe_info.pop('CHANNELSTATUS').items()}
+
         else:
             self.probe_info = processor['EDITOR']['NP_PROBE'][probe_index]
             self.probe_SN = self.probe_info['@probe_serial_number']
@@ -143,10 +145,8 @@ def __init__(self, processor, probe_index=0):
                 "Neuropixels Ultra": "neuropixels UHD",
                 "Neuropixels 21": "neuropixels 2.0 - SS",
                 "Neuropixels 24": "neuropixels 2.0 - MS"}[self.probe_info['@probe_name']]
-            channel_status_str = 'CHANNELS'
-
-        self.channel_status = {int(re.search(r'\d+$', k).group()): int(v)
-                               for k, v in self.probe_info.pop(channel_status_str).items()}
+            self._channels_connected = {int(re.search(r'\d+$', k).group()): 1
+                                        for k in self.probe_info.pop('CHANNELS')}
 
         self.ap_meta = {}
         self.lfp_meta = {}
@@ -164,6 +164,11 @@ def __init__(self, processor, probe_index=0):
         self._lfp_timeseries = None
         self._lfp_timestamps = None
 
+    @property
+    def channels_connected(self):
+        return {chn_idx: self._channels_connected.get(chn_idx, 0)
+                for chn_idx in self.ap_meta['channels_indices']}
+
     @property
     def ap_timeseries(self):
         """