Merge pull request #1520 from BoccaraLab/fix_axonarawio

Fix electrode selection in Axona raw recording

Author: zm711

doc/source/authors.rst

@@ -96,6 +96,7 @@ and may not be the current affiliation of a contributor.
 * Paul Adkisson [24]
 * Luiz Tauffer [24]
 * Akshaj Verma [46]
+* Letizia Signorelli [47]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -143,6 +144,7 @@ and may not be the current affiliation of a contributor.
 44. AquiNeuro, SAS
 45. Maxwell Biosystems AG
 46. Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands
+47. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
 
 
 

neo/rawio/axonarawio.py

@@ -377,8 +377,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
         if channel_indexes is None:
             channel_indexes = [i for i in range(bin_dict["num_channels"])]
         elif isinstance(channel_indexes, slice):
-            channel_indexes_all = [i for i in range(bin_dict["num_channels"])]
-            channel_indexes = channel_indexes_all[channel_indexes]
+            channel_indexes = self._get_active_channels()
 
         num_samples = i_stop - i_start
 
@@ -561,6 +560,20 @@ def get_active_tetrode(self):
                     tetrode_id = int(key.strip("collectMask_"))
                     active_tetrodes.append(tetrode_id)
         return active_tetrodes
+    
+    def _get_active_channels(self):
+        """
+        Returns the ID numbers of the active channels as a list.
+        E.g.: [20,21,22,23] for tetrode 6 active.
+        """
+        active_tetrodes = self.get_active_tetrode()
+        active_channels = []
+        
+        for tetrode in active_tetrodes:
+            chans = self._get_channel_from_tetrode(tetrode)
+            active_channels.append(chans)
+        
+        return np.concatenate(active_channels)
 
     def _get_channel_from_tetrode(self, tetrode):
         """
@@ -632,12 +645,13 @@ def _get_signal_chan_header(self):
         gain_list = self._get_channel_gain()
         offset = 0  # What is the offset?
 
+        first_channel = (active_tetrode_set[0] - 1)*elec_per_tetrode
         sig_channels = []
         for itetr in range(num_active_tetrode):
 
             for ielec in range(elec_per_tetrode):
-                cntr = (itetr * elec_per_tetrode) + ielec
-                ch_name = f"{itetr + 1}{letters[ielec]}"
+                cntr = (itetr * elec_per_tetrode) + ielec + first_channel
+                ch_name = f"{itetr + active_tetrode_set[0]}{letters[ielec]}"
                 chan_id = str(cntr)
                 gain = gain_list[cntr]
                 stream_id = "0"