clean-up and and comments

Author: zm711

neo/rawio/spikegadgetsrawio.py

@@ -81,14 +81,18 @@ 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
+        """Compute the channel ID labels for subset of spikegadgets recordings
         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
+
+        This doesn't work for all types of spikegadgets
+        see: https://github.com/NeuralEnsemble/python-neo/issues/1517
+
         """
         ephys_channel_ids_list = []
         for hw_channel in range(n_channels_per_chip):
@@ -120,6 +124,8 @@ def _parse_header(self):
         hconf = root.find("HardwareConfiguration")
         sconf = root.find("SpikeConfiguration")
 
+        # store trode version in case there are version changes in the future
+        self._trode_version = gconf["trodesVersion"]
         self._sampling_rate = float(hconf.attrib["samplingRate"])
         num_ephy_channels = int(hconf.attrib["numChannels"])
 
@@ -129,9 +135,11 @@ def _parse_header(self):
             num_ephy_channels = sconf_channels
         if sconf_channels > num_ephy_channels:
             raise NeoReadWriteError(
-                "SpikeGadgets: the number of channels in the spike configuration is larger than the number of channels in the hardware configuration"
+                "SpikeGadgets: the number of channels in the spike configuration is larger "
+                "than the number of channels in the hardware configuration"
             )
 
+        # as spikegadgets change we should follow this
         try:
             num_chan_per_chip = int(sconf.attrib["chanPerChip"])
         except KeyError:
@@ -207,9 +215,9 @@ def _parse_header(self):
             signal_streams.append((stream_name, stream_id))
             self._mask_channels_bytes[stream_id] = []
 
-            # we can only produce these channels for a subset of spikegadgets setup. If this criteria isn't 
+            # we can only produce these channels for a subset of spikegadgets setup. If this criteria isn't
             # true then we should just use the raw_channel_ids and let the end user sort everything out
-            if num_ephy_channels%num_chan_per_chip == 0:
+            if num_ephy_channels % num_chan_per_chip == 0:
                 channel_ids = self._produce_ephys_channel_ids(num_ephy_channels, num_chan_per_chip)
                 raw_channel_ids = False
             else:
@@ -231,6 +239,8 @@ def _parse_header(self):
                     units = ""
 
                 for schan in trode:
+                    # Here we use raw ids if necessary for parsing (for some neuropixel recordings)
+                    # otherwise we default back to the raw hwChan IDs
                     if raw_channel_ids:
                         name = "trode" + trode.attrib["id"] + "chan" + schan.attrib["hwChan"]
                         chan_id = schan.attrib["hwChan"]
@@ -261,7 +271,7 @@ def _parse_header(self):
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
-        # remove some stream if no wanted
+        # remove some stream if not wanted
         if self.selected_streams is not None:
             if isinstance(self.selected_streams, str):
                 self.selected_streams = [self.selected_streams]