bugfix

Author: Thinh Nguyen

elements_ephys/ephys.py

@@ -228,7 +228,7 @@ def make(self, key):
             spikeglx_rec_dir = (root_dir / spikeglx_meta_fp).parent
             spikeglx_recording = spikeglx.SpikeGLX(spikeglx_rec_dir)
 
-            lfp_chn_ind = spikeglx_recording.lfmeta.recording_channels[-1::-self.skip_chn_counts]
+            lfp_chn_ind = spikeglx_recording.lfmeta.recording_channels[-1::-self._skip_chn_counts]
 
             # Extract LFP data at specified channels and convert to uV
             lfp = spikeglx_recording.lf_timeseries[:, lfp_chn_ind]  # (sample x channel)
@@ -258,10 +258,10 @@ def make(self, key):
             loaded_oe = openephys.OpenEphys(sess_dir)
             oe_probe = loaded_oe.probes[probe_sn]
 
-            lfp_chn_ind = np.arange(len(oe_probe.lfp_meta['channels_ids']))[-1::-self.skip_chn_counts]
+            lfp_chn_ind = np.arange(len(oe_probe.lfp_meta['channels_ids']))[-1::-self._skip_chn_counts]
 
             lfp = oe_probe.lfp_timeseries[:, lfp_chn_ind]  # (sample x channel)
-            lfp = (lfp * oe_probe.lfp_meta['channels_gains'][lfp_chn_ind]).T  # (channel x sample)
+            lfp = (lfp * np.array(oe_probe.lfp_meta['channels_gains'])[lfp_chn_ind]).T  # (channel x sample)
             lfp_timestamps = oe_probe.lfp_timestamps
 
             self.insert1(dict(key,
@@ -271,7 +271,7 @@ def make(self, key):
 
             q_electrodes = probe.ProbeType.Electrode * probe.ElectrodeConfig.Electrode * EphysRecording & key
             electrodes = []
-            for chn_idx in oe_probe.lfp_meta['channels_ids'][lfp_chn_ind]:
+            for chn_idx in np.array(oe_probe.lfp_meta['channels_ids'])[lfp_chn_ind]:
                 electrodes.append((q_electrodes & {'electrode': chn_idx}).fetch1('KEY'))
 
             chn_lfp = list(zip(electrodes, lfp))

elements_ephys/readers/spikeglx.py

@@ -41,7 +41,7 @@ def __init__(self, root_dir):
             meta_filepath = next(pathlib.Path(root_dir).glob('*.ap.meta'))
         except StopIteration:
             raise FileNotFoundError(f'No SpikeGLX file (.ap.meta) found at: {root_dir}')
-            
+
         self.root_name = meta_filepath.name.replace('.ap.meta', '')
 
     @property
@@ -187,8 +187,7 @@ def __init__(self, meta_filepath):
         self.imroTbl = self._parse_imrotbl(self.meta['~imroTbl']) if '~imroTbl' in self.meta else None
 
         # Channels being recorded, exclude Sync channels - basically a 1-1 mapping to shankmap
-        self.recording_channels = [int(v[0]) for k, v in self.chanmap.items()
-                                   if k != 'shape' and not k.startswith('SY')]
+        self.recording_channels = np.arange(len(self.imroTbl['data']))[self.get_recording_channels_indices(exclude_sync=True)]
 
     @staticmethod
     def _parse_chanmap(raw):