Merge branch 'master' into master

Author: philipp-mxw

neo/rawio/blackrockrawio.py

@@ -597,10 +597,17 @@ def _parse_header(self):
             for c in range(spike_channels.size):
                 st_ann = seg_ann["spikes"][c]
                 channel_id, unit_id = self.internal_unit_ids[c]
-                unit_tag = {0: "unclassified", 255: "noise"}.get(unit_id, str(unit_id))
                 st_ann["channel_id"] = channel_id
                 st_ann["unit_id"] = unit_id
-                st_ann["unit_tag"] = unit_tag
+                if unit_id == 0:
+                    st_ann["unit_classification"] = "unclassified"
+                elif 1 <= unit_id <= 16:
+                    st_ann["unit_classification"] = "sorted"
+                elif unit_id == 255:
+                    st_ann["unit_classification"] = "noise"
+                else:  # 17-254 are reserved
+                    st_ann["unit_classification"] = "reserved"
+                st_ann['unit_tag'] = st_ann['unit_classification']
                 st_ann["description"] = f"SpikeTrain channel_id: {channel_id}, unit_id: {unit_id}"
                 st_ann["file_origin"] = self._filenames["nev"] + ".nev"
 

neo/rawio/spikeglxrawio.py

@@ -78,7 +78,7 @@ class SpikeGLXRawIO(BaseRawWithBufferApiIO):
         The spikeglx folder containing meta/bin files
     load_sync_channel: bool, default: False
         Can be used to load the synch stream as the last channel of the neural data.
-        This option is deprecated and will be removed in version 0.15. 
+        This option is deprecated and will be removed in version 0.15.
         From versions higher than 0.14.1 the sync channel is always loaded as a separate stream.
     load_channel_location: bool, default: False
         If True probeinterface is used to load the channel locations from the directory
@@ -116,7 +116,8 @@ def __init__(self, dirname="", load_sync_channel=False, load_channel_location=Fa
             warn(
                 "The load_sync_channel=True option is deprecated and will be removed in version 0.15 \n"
                 "The sync channel is now loaded as a separate stream by default and should be accessed as such. ",
-                DeprecationWarning, stacklevel=2
+                DeprecationWarning,
+                stacklevel=2,
             )
         self.load_channel_location = load_channel_location
 
@@ -162,7 +163,7 @@ def _parse_header(self):
         signal_streams = []
         signal_channels = []
         sync_stream_id_to_buffer_id = {}
-        
+
         for stream_name in stream_names:
             # take first segment
             info = self.signals_info_dict[0, stream_name]
@@ -179,16 +180,21 @@ def _parse_header(self):
             for local_chan in range(info["num_chan"]):
                 chan_name = info["channel_names"][local_chan]
                 chan_id = f"{stream_name}#{chan_name}"
-                
+
                 # Sync channel
-                if "nidq" not in stream_name and "SY0" in chan_name and not self.load_sync_channel and local_chan == info["num_chan"] - 1:
+                if (
+                    "nidq" not in stream_name
+                    and "SY0" in chan_name
+                    and not self.load_sync_channel
+                    and local_chan == info["num_chan"] - 1
+                ):
                     # This is a sync channel and should be added as its own stream
                     sync_stream_id = f"{stream_name}-SYNC"
                     sync_stream_id_to_buffer_id[sync_stream_id] = buffer_id
                     stream_id_for_chan = sync_stream_id
                 else:
                     stream_id_for_chan = stream_id
-                
+
                 signal_channels.append(
                     (
                         chan_name,
@@ -205,26 +211,26 @@ def _parse_header(self):
 
             # all channel by default unless load_sync_channel=False
             self._stream_buffer_slice[stream_id] = None
-            
+
             # check sync channel validity
             if "nidq" not in stream_name:
                 if not self.load_sync_channel and info["has_sync_trace"]:
                     # the last channel is removed from the stream but not from the buffer
                     self._stream_buffer_slice[stream_id] = slice(0, -1)
-                    
+
                     # Add a buffer slice for the sync channel
                     sync_stream_id = f"{stream_name}-SYNC"
                     self._stream_buffer_slice[sync_stream_id] = slice(-1, None)
-                    
+
                 if self.load_sync_channel and not info["has_sync_trace"]:
                     raise ValueError("SYNC channel is not present in the recording. " "Set load_sync_channel to False")
 
         signal_buffers = np.array(signal_buffers, dtype=_signal_buffer_dtype)
-        
+
         # Add sync channels as their own streams
         for sync_stream_id, buffer_id in sync_stream_id_to_buffer_id.items():
             signal_streams.append((sync_stream_id, sync_stream_id, buffer_id))
-            
+
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
@@ -266,14 +272,14 @@ def _parse_header(self):
                 t_start = frame_start / sampling_frequency
 
                 self._t_starts[stream_name][seg_index] = t_start
-                
+
                 # This need special logic because sync not present in stream_names
                 if f"{stream_name}-SYNC" in signal_streams["name"]:
                     sync_stream_name = f"{stream_name}-SYNC"
                     if sync_stream_name not in self._t_starts:
                         self._t_starts[sync_stream_name] = {}
                     self._t_starts[sync_stream_name][seg_index] = t_start
-                
+
                 t_stop = info["sample_length"] / info["sampling_rate"]
                 self._t_stops[seg_index] = max(self._t_stops[seg_index], t_stop)
 
@@ -302,11 +308,11 @@ def _parse_header(self):
                 if self.load_channel_location:
                     # need probeinterface to be installed
                     import probeinterface
-                    
+
                     # Skip for sync streams
                     if "SYNC" in stream_name:
                         continue
-                    
+
                     info = self.signals_info_dict[seg_index, stream_name]
                     if "imroTbl" in info["meta"] and info["stream_kind"] == "ap":
                         # only for ap channel

neo/test/rawiotest/test_spikeglxrawio.py

@@ -137,22 +137,26 @@ def test_sync_channel_as_separate_stream(self):
         # Test with load_sync_channel=False (default)
         rawio_no_sync = SpikeGLXRawIO(self.get_local_path("spikeglx/NP2_with_sync"), load_sync_channel=False)
         rawio_no_sync.parse_header()
-        
+
         # Get stream names
         stream_names = rawio_no_sync.header["signal_streams"]["name"].tolist()
-        
+
         # Check if there's a sync channel stream (should contain "SY0" or "SYNC" in the name)
         sync_streams = [name for name in stream_names if "SY0" in name or "SYNC" in name]
         assert len(sync_streams) > 0, "No sync channel stream found when load_sync_channel=False"
-        
+
         # Test deprecation warning when load_sync_channel=True
         with warnings.catch_warnings(record=True) as w:
             warnings.simplefilter("always")
             rawio_with_sync = SpikeGLXRawIO(self.get_local_path("spikeglx/NP2_with_sync"), load_sync_channel=True)
-            
+
             # Check if deprecation warning was raised
-            assert any(issubclass(warning.category, DeprecationWarning) for warning in w), "No deprecation warning raised"
-            assert any("will be removed in version 0.15" in str(warning.message) for warning in w), "Deprecation warning message is incorrect"
+            assert any(
+                issubclass(warning.category, DeprecationWarning) for warning in w
+            ), "No deprecation warning raised"
+            assert any(
+                "will be removed in version 0.15" in str(warning.message) for warning in w
+            ), "Deprecation warning message is incorrect"
 
     def test_t_start_reading(self):
         """Test that t_start values are correctly read for all streams and segments."""