Merge pull request #1926 from cboulay/nev-22-spikes-above-255

Blackrock: read NEV 2.2 spikes on electrodes above 255

Author: h-mayorquin

neo/rawio/blackrockrawio.py

@@ -2744,14 +2744,25 @@ def _is_set(self, flag, pos):
 # Used to create masks that filter raw data packets by their packet ID field.
 # Single values indicate equality check, tuples (min, max) indicate range check.
 # According to NEV spec: packet IDs < 32768 identify channels, IDs >= 32768 are system events.
+# Packets whose ID is not listed for a spec are not read. Known cases, ignored on purpose:
+# - 0x8000 + channel (e.g. 32769): preview packets of the live protocol (cbproto's "Preview Data Packet
+#   Definitions"), found in 3.0 files written by Central. They carry no neural data.
+# - 0xFFF9: recording events of 3.0 files written by Central (header type 0 start, 1 stop, 2 pause,
+#   3 resume; Central's CNevFile30::AddRecordingEvent). Not used to split segments, which come from
+#   resets and gaps.
 NEV_PACKET_IDENTIFIERS_BY_SPEC = {
     "2.1": {
         "NonNeural": 0,
         "Spikes": (1, 255),  # Packet IDs in this range identify spike events on electrodes
     },
     "2.2": {
         "NonNeural": 0,
-        "Spikes": (1, 255),  # Packet IDs in this range identify spike events on electrodes
+        # Packet IDs in this range identify spike events on electrodes. Wider than 2.1's range:
+        # Ripple Trellis writes 2.2 files with electrode IDs above 255 (its front-end ports are
+        # numbered 1-128, 129-256, 257-384...), and every spike on them was dropped without a
+        # warning (NeuralEnsemble/python-neo#1918). The bound is 5120 because Trellis writes
+        # stimulation packets on 5120 plus the electrode ID.
+        "Spikes": (1, 5120),
     },
     "2.3": {
         "NonNeural": 0,

neo/test/rawiotest/test_blackrockrawio.py

@@ -651,6 +651,23 @@ def test_nev_segments_ignore_order_between_packet_types(self):
             )
             self.assertEqual(returned, 960)
 
+    def test_nev_22_reads_spikes_on_electrodes_above_255(self):
+        """
+        A FileSpec 2.2 NEV written by Ripple Trellis keeps its spikes on electrodes above 255, as 2.3
+        does (NeuralEnsemble/python-neo#1918). Trellis numbers its front-end ports 1-128, 129-256,
+        257-384..., and this file has one spike on each of 28 electrodes between 257 and 306.
+        """
+        filename = self.get_local_path("blackrock/version_2_2/spikes/electrode_ids_above_255/electrode_ids_above_255")
+        reader = BlackrockRawIO(filename=filename)
+        reader.parse_header()
+        electrodes = [channel for channel, _ in reader.internal_unit_ids]
+        self.assertEqual(len(electrodes), 28)
+        self.assertTrue(all(257 <= electrode <= 306 for electrode in electrodes))
+        spikes = [
+            reader.get_spike_timestamps(0, 0, unit_index, None, None).size for unit_index in range(len(electrodes))
+        ]
+        self.assertEqual(spikes, [1] * 28)
+
 
 if __name__ == "__main__":
     unittest.main()