Merge pull request #1524 from h-mayorquin/fix_plexon_streams

Fix-ate plexon signal streams

Author: zm711

neo/rawio/plexonrawio.py

@@ -24,6 +24,7 @@
 
 import datetime
 from collections import OrderedDict
+import re
 
 import numpy as np
 
@@ -146,7 +147,7 @@ def _parse_header(self):
 
             # Update tqdm with the number of bytes processed in this iteration
             if self.progress_bar:
-                progress_bar.update(length)
+                progress_bar.update(length)  # This was clever, Sam : )
 
         if self.progress_bar:
             progress_bar.close()
@@ -231,6 +232,7 @@ def _parse_header(self):
         # signals channels
         sig_channels = []
         all_sig_length = []
+        source_id = []
         if self.progress_bar:
             chan_loop = trange(nb_sig_chan, desc="Parsing signal channels", leave=True)
         else:
@@ -242,6 +244,7 @@ def _parse_header(self):
             length = self._data_blocks[5][chan_id]["size"].sum() // 2
             if length == 0:
                 continue  # channel not added
+            source_id.append(h["SrcId"])
             all_sig_length.append(length)
             sampling_rate = float(h["ADFreq"])
             sig_dtype = "int16"
@@ -255,7 +258,7 @@ def _parse_header(self):
                     0.5 * (2 ** global_header["BitsPerSpikeSample"]) * h["Gain"] * h["PreampGain"]
                 )
             offset = 0.0
-            stream_id = "0"
+            stream_id = "0"  # This is overwritten later
             sig_channels.append((name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id))
 
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
@@ -264,22 +267,49 @@ def _parse_header(self):
             signal_streams = np.array([], dtype=_signal_stream_dtype)
 
         else:
-            # detect groups (aka streams)
-            all_sig_length = all_sig_length = np.array(all_sig_length)
-            groups = set(zip(sig_channels["sampling_rate"], all_sig_length))
+            # Detect streams
+            all_sig_length = np.asarray(all_sig_length)
+
+            # names are WB{number}, FPX{number}, SPKCX{number}, AI{number}, etc
+            pattern = r"^\D+"  # Match any non-digit character at the beginning of the string
+            channels_prefixes = np.asarray([re.match(pattern, name).group(0) for name in sig_channels["name"]])
+            buffer_stream_groups = set(zip(channels_prefixes, sig_channels["sampling_rate"], all_sig_length))
+
+            # There are explanations of the streams based on channel names
+            # provided by a Plexon Engineer, see here:
+            # https://github.com/NeuralEnsemble/python-neo/pull/1495#issuecomment-2184256894
+            channel_prefix_to_stream_name = {
+                "WB": "WB-Wideband",
+                "FP": "FPl-Low Pass Filtered ",
+                "SP": "SPKC-High Pass Filtered",
+                "AI": "AI-Auxiliary Input",
+            }
+
+            # Using a mapping to ensure consistent order of stream_index
+            channel_prefix_to_stream_id = {
+                "WB": "0",
+                "FP": "1",
+                "SP": "2",
+                "AI": "3",
+            }
 
             signal_streams = []
             self._signal_length = {}
             self._sig_sampling_rate = {}
-            for stream_index, (sr, length) in enumerate(groups):
-                stream_id = str(stream_index)
+
+            for stream_index, (channel_prefix, sr, length) in enumerate(buffer_stream_groups):
+                # The users of plexon can modify the prefix of the channel names (e.g. `my_prefix` instead of `WB`). This is not common but in that case
+                # We assign the channel_prefix both as stream_name and stream_id
+                stream_name = channel_prefix_to_stream_name.get(channel_prefix, channel_prefix)
+                stream_id = channel_prefix_to_stream_id.get(channel_prefix, channel_prefix)
+
                 mask = (sig_channels["sampling_rate"] == sr) & (all_sig_length == length)
                 sig_channels["stream_id"][mask] = stream_id
 
                 self._sig_sampling_rate[stream_index] = sr
                 self._signal_length[stream_index] = length
 
-                signal_streams.append(("Signals " + stream_id, stream_id))
+                signal_streams.append((stream_name, stream_id))
 
             signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
 
@@ -363,8 +393,8 @@ def _segment_t_start(self, block_index, seg_index):
     def _segment_t_stop(self, block_index, seg_index):
         t_stop = float(self._last_timestamps) / self._global_ssampling_rate
         if hasattr(self, "_signal_length"):
-            for stream_id in self._signal_length:
-                t_stop_sig = self._signal_length[stream_id] / self._sig_sampling_rate[stream_id]
+            for stream_index in self._signal_length.keys():
+                t_stop_sig = self._signal_length[stream_index] / self._sig_sampling_rate[stream_index]
                 t_stop = max(t_stop, t_stop_sig)
         return t_stop
 

neo/test/iotest/test_plexonio.py

@@ -18,6 +18,7 @@ class TestPlexonIO(
         "plexon/File_plexon_1.plx",
         "plexon/File_plexon_2.plx",
         "plexon/File_plexon_3.plx",
+        "plexon/4chDemoPLX.plx"
     ]
 
 

neo/test/rawiotest/test_plexonrawio.py

@@ -15,6 +15,7 @@ class TestPlexonRawIO(
         "plexon/File_plexon_1.plx",
         "plexon/File_plexon_2.plx",
         "plexon/File_plexon_3.plx",
+        "plexon/4chDemoPLX.plx"
     ]