Merge branch 'master' into ebrains

Author: h-mayorquin

neo/io/kwikio.py

@@ -25,7 +25,8 @@
 import importlib.metadata
 from packaging.version import Version, parse
 
-numpy_version = parse(importlib.metadata.version('numpy'))
+numpy_version = parse(importlib.metadata.version("numpy"))
+
 
 class KwikIO(BaseIO):
     """
@@ -64,10 +65,12 @@ def __init__(self, filename):
         """
 
         if numpy_version >= Version("2.3.0"):
-            deprecation_msg = ("As the kwik package is no longer actively maintained it only works with NumPy < 2.3.0 and your environment "
-            f"has {numpy_version}. Downgrade your NumPy version to use this IO")
+            deprecation_msg = (
+                "As the kwik package is no longer actively maintained it only works with NumPy < 2.3.0 and your environment "
+                f"has {numpy_version}. Downgrade your NumPy version to use this IO"
+            )
             raise NeoReadWriteError(deprecation_msg)
-        
+
         from klusta import kwik
 
         BaseIO.__init__(self)

neo/rawio/openephysbinaryrawio.py

@@ -159,11 +159,14 @@ def _parse_header(self):
                     # We then set the stream_id to the sync stream id
                     channel_stream_id = sync_stream_id
 
-                if "ADC" in chan_id:
-                    # These are non-neural channels and their stream should be separated
-                    # We defined their stream_id as the stream_index of neural data plus the number of neural streams
-                    # This is to not break backwards compatbility with the stream_id numbering
-                    channel_stream_id = str(stream_index + len(sig_stream_names))
+                if "OneBox" not in stream_name:
+                    # If recording system is not OneBox, which has already a separate stream for ADC channels,
+                    # we need to separate ADC channels from neural channels.
+                    if "ADC" in chan_id:
+                        # These are non-neural channels and their stream should be separated
+                        # We defined their stream_id as the stream_index of neural data plus the number of neural streams
+                        # This is to not break backwards compatbility with the stream_id numbering
+                        channel_stream_id = str(stream_index + len(sig_stream_names))
 
                 gain = float(chan_info["bit_volts"])
                 sampling_rate = float(info["sample_rate"])
@@ -271,10 +274,22 @@ def _parse_header(self):
                             "SYNC channel must be the last channel in the buffer. Open an issue in python-neo to request this feature."
                         )
 
-                    neural_channels = [ch for ch in info["channels"] if "ADC" not in ch["channel_name"]]
-                    adc_channels = [ch for ch in info["channels"] if "ADC" in ch["channel_name"]]
-                    num_neural_channels = len(neural_channels)
-                    num_adc_channels = len(adc_channels)
+                    if "OneBox" not in info["stream_name"]:
+                        # If recording system is not OneBox, which has already a separate stream for ADC channels,
+                        # we need to separate ADC channels from neural channels.
+                        # We do this by defining different stream_ids for ADC and non-ADC channels
+                        # (see above when creating signal_channels and signal_streams)
+
+                        # Split neural and ADC channels
+                        # SYNC channel is handled separately below
+                        neural_channels = [ch for ch in info["channels"] if "ADC" not in ch["channel_name"]]
+                        adc_channels = [ch for ch in info["channels"] if "ADC" in ch["channel_name"]]
+                        num_neural_channels = len(neural_channels)
+                        num_adc_channels = len(adc_channels) if "OneBox" not in info["stream_name"] else 0
+                    else:
+                        # OneBox already has a separate stream for ADC channels, so no need to split them here
+                        num_neural_channels = num_channels - 1 if has_sync_trace else num_channels
+                        num_adc_channels = 0
 
                     if num_adc_channels == 0:
                         if has_sync_trace and not self.load_sync_channel:
@@ -498,12 +513,17 @@ def _parse_header(self):
                             if has_sync_trace:
                                 values = values[:-1]
 
-                            neural_channels = [ch for ch in info["channels"] if "ADC" not in ch["channel_name"]]
-                            num_neural_channels = len(neural_channels)
-                            if is_neural_stream:
-                                values = values[:num_neural_channels]
-                            else:
-                                values = values[num_neural_channels:]
+                            if "SYNC" in stream_name and not self.load_sync_channel:
+                                # This is the sync stream, we only keep the last value
+                                values = values[-1:]
+
+                            if "OneBox" not in info["stream_name"]:
+                                neural_channels = [ch for ch in info["channels"] if "ADC" not in ch["channel_name"]]
+                                num_neural_channels = len(neural_channels)
+                                if is_neural_stream:
+                                    values = values[:num_neural_channels]
+                                else:
+                                    values = values[num_neural_channels:]
 
                             sig_ann["__array_annotations__"][key] = values
 

neo/test/iotest/test_kwikio.py

@@ -7,10 +7,10 @@
 import importlib.metadata
 from packaging.version import Version, parse
 
-kwik_spec = importlib.util.find_spec('klusta')
+kwik_spec = importlib.util.find_spec("klusta")
 # kwik no longer works with recent versions of numpy
-numpy_version = parse(importlib.metadata.version('numpy'))
-numpy_okay = numpy_version < Version('2.3.0')
+numpy_version = parse(importlib.metadata.version("numpy"))
+numpy_okay = numpy_version < Version("2.3.0")
 if kwik_spec is not None and numpy_okay:
     HAVE_KWIK = True
 else:

neo/test/rawiotest/test_openephysbinaryrawio.py

@@ -16,14 +16,16 @@ class TestOpenEphysBinaryRawIO(BaseTestRawIO, unittest.TestCase):
         "openephysbinary/v0.6.x_neuropixels_multiexp_multistream",
         "openephysbinary/v0.6.x_neuropixels_with_sync",
         "openephysbinary/v0.6.x_neuropixels_missing_folders",
+        "openephysbinary/v0.6.x_onebox_neuropixels",
         "openephysbinary/neural_and_non_neural_data_mixed",
     ]
 
     def test_sync(self):
-        rawio_with_sync = OpenEphysBinaryRawIO(
-            self.get_local_path("openephysbinary/v0.6.x_neuropixels_with_sync"), load_sync_channel=True
-        )
-        rawio_with_sync.parse_header()
+        with self.assertWarns(DeprecationWarning):
+            rawio_with_sync = OpenEphysBinaryRawIO(
+                self.get_local_path("openephysbinary/v0.6.x_neuropixels_with_sync"), load_sync_channel=True
+            )
+            rawio_with_sync.parse_header()
         stream_name = [s_name for s_name in rawio_with_sync.header["signal_streams"]["name"] if "AP" in s_name][0]
         stream_index = list(rawio_with_sync.header["signal_streams"]["name"]).index(stream_name)
 
@@ -69,10 +71,12 @@ def test_sync_channel_access(self):
     def test_no_sync(self):
         # requesting sync channel when there is none raises an error
         with self.assertRaises(ValueError):
-            rawio_no_sync = OpenEphysBinaryRawIO(
-                self.get_local_path("openephysbinary/v0.6.x_neuropixels_multiexp_multistream"), load_sync_channel=True
-            )
-            rawio_no_sync.parse_header()
+            with self.assertWarns(DeprecationWarning):
+                rawio_no_sync = OpenEphysBinaryRawIO(
+                    self.get_local_path("openephysbinary/v0.6.x_neuropixels_multiexp_multistream"),
+                    load_sync_channel=True,
+                )
+                rawio_no_sync.parse_header()
 
     def test_missing_folders(self):
         # missing folders should raise an error