Fix ephys channel ids in spikegadgetsrawio

Fix NeuralEnsemble#1215
rly · Jul 6, 2023 · 3a9caae · 3a9caae
1 parent 6ce00dc
commit 3a9caae
Showing 1 changed file with 22 additions and 3 deletions.
diff --git a/neo/rawio/spikegadgetsrawio.py b/neo/rawio/spikegadgetsrawio.py
@@ -54,6 +54,21 @@ def __init__(self, filename='', selected_streams=None):
     def _source_name(self):
         return self.filename
 
+    def _produce_ephys_channel_ids(self, n_total_channels, n_channels_per_chip):
+      """Compute the channel ID labels
+      The ephys channels in the .rec file are stored in the following order: 
+      hwChan ID of channel 0 of first chip, hwChan ID of channel 0 of second chip, ..., hwChan ID of channel 0 of Nth chip, 
+      hwChan ID of channel 1 of first chip, hwChan ID of channel 1 of second chip, ..., hwChan ID of channel 1 of Nth chip,
+      ...
+      So if there are 32 channels per chip and 128 channels (4 chips), then the channel IDs are:
+      0, 32, 64, 96, 1, 33, 65, 97, ..., 128
+      See also: https://github.com/NeuralEnsemble/python-neo/issues/1215
+      """
+      x = []
+      for k in range(n_channels_per_chip):
+          x.append([k+i*n_channels_per_chip for i in range(int(n_total_channels/n_channels_per_chip))])
+      return [item for sublist in x for item in sublist]
+
     def _parse_header(self):
         # parse file until "</Configuration>"
         header_size = None
@@ -77,7 +92,8 @@ def _parse_header(self):
         sconf = root.find('SpikeConfiguration')
 
         self._sampling_rate = float(hconf.attrib['samplingRate'])
-        num_ephy_channels = int(hconf .attrib['numChannels'])
+        num_ephy_channels = int(hconf.attrib['numChannels'])
+        num_chan_per_chip = int(sconf.attrib['chanPerChip'])
 
         # explore sub stream and count packet size
         # first bytes is 0x55
@@ -147,11 +163,14 @@ def _parse_header(self):
             signal_streams.append((stream_name, stream_id))
             self._mask_channels_bytes[stream_id] = []
 
+            channel_ids = self._produce_channel_ids(num_ephy_channels, num_chan_per_chip)
+
             chan_ind = 0
             for trode in sconf:
                 for schan in trode:
-                    name = 'trode' + trode.attrib['id'] + 'chan' + schan.attrib['hwChan']
-                    chan_id = schan.attrib['hwChan']
+                    chan_id = str(channel_ids[chan_ind])
+                    name = 'chan' + chan_id
+
                     # TODO LATER : handle gain correctly according the file version
                     units = ''
                     gain = 1.