Add plexon2 recording, sorting and event support

.github/actions/build-test-environment/action.yml

@@ -40,3 +40,10 @@ runs:
         tar xvzf git-annex-standalone-amd64.tar.gz
         echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
       shell: bash
+    - name: Install wine (needed for Plexon2)
+      run: |
+        sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+        sudo dpkg --add-architecture i386
+        sudo apt-get update -qq
+        sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
+      shell: bash

pyproject.toml

@@ -68,6 +68,7 @@ extractors = [
     "ONE-api>=1.19.1",
     "ibllib>=2.21.0",
     "pymatreader>=0.0.32", # For cell explorer matlab files
+    "zugbruecke", # For plexon2
 ]
 
 streaming_extractors = [

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -25,6 +25,14 @@
     read_openephys_event,
 )
 from .plexon import PlexonRecordingExtractor, PlexonSortingExtractor, read_plexon, read_plexon_sorting
+from .plexon2 import (
+    Plexon2SortingExtractor,
+    Plexon2RecordingExtractor,
+    Plexon2EventExtractor,
+    read_plexon2,
+    read_plexon2_sorting,
+    read_plexon2_event,
+)
 from .spike2 import Spike2RecordingExtractor, read_spike2
 from .spikegadgets import SpikeGadgetsRecordingExtractor, read_spikegadgets
 from .spikeglx import SpikeGLXRecordingExtractor, read_spikeglx
@@ -49,12 +57,18 @@
     OpenEphysBinaryRecordingExtractor,
     OpenEphysLegacyRecordingExtractor,
     PlexonRecordingExtractor,
+    Plexon2RecordingExtractor,
     Spike2RecordingExtractor,
     SpikeGadgetsRecordingExtractor,
     SpikeGLXRecordingExtractor,
     TdtRecordingExtractor,
 ]
 
-neo_sorting_extractors_list = [BlackrockSortingExtractor, MEArecSortingExtractor, NeuralynxSortingExtractor]
+neo_sorting_extractors_list = [
+    BlackrockSortingExtractor,
+    MEArecSortingExtractor,
+    NeuralynxSortingExtractor,
+    Plexon2SortingExtractor,
+]
 
-neo_event_extractors_list = [AlphaOmegaEventExtractor, OpenEphysBinaryEventExtractor]
+neo_event_extractors_list = [AlphaOmegaEventExtractor, OpenEphysBinaryEventExtractor, Plexon2EventExtractor]

src/spikeinterface/extractors/neoextractors/plexon2.py

@@ -0,0 +1,103 @@
+from spikeinterface.core.core_tools import define_function_from_class
+
+from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor, NeoBaseEventExtractor
+
+
+class Plexon2RecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading plexon pl2 files.
+
+    Based on :py:class:`neo.rawio.Plexon2RawIO`
+
+    Parameters
+    ----------
+    file_path: str
+        The file path to load the recordings from.
+    stream_id: str, optional
+        If there are several streams, specify the stream id you want to load.
+    stream_name: str, optional
+        If there are several streams, specify the stream name you want to load.
+    all_annotations: bool, default: False
+        Load exhaustively all annotations from neo.
+    """
+
+    mode = "file"
+    NeoRawIOClass = "Plexon2RawIO"
+    name = "plexon2"
+
+    def __init__(self, file_path, stream_id=None, stream_name=None, all_annotations=False):
+        neo_kwargs = self.map_to_neo_kwargs(file_path)
+        NeoBaseRecordingExtractor.__init__(
+            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+        )
+        self._kwargs.update({"file_path": str(file_path)})
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+        neo_kwargs = {"filename": str(file_path)}
+        return neo_kwargs
+
+
+class Plexon2SortingExtractor(NeoBaseSortingExtractor):
+    """
+    Class for reading plexon spiking data from .pl2 files.
+
+    Based on :py:class:`neo.rawio.Plexon2RawIO`
+
+    Parameters
+    ----------
+    file_path: str
+        The file path to load the recordings from.
+    sampling_frequency: float, default: None
+        The sampling frequency of the sorting (required for multiple streams with different sampling frequencies).
+    """
+
+    mode = "file"
+    NeoRawIOClass = "Plexon2RawIO"
+    neo_returns_frames = True
+    name = "plexon2"
+
+    def __init__(self, file_path, sampling_frequency=None):
+        from neo.rawio import Plexon2RawIO
+
+        neo_kwargs = self.map_to_neo_kwargs(file_path)
+        neo_reader = Plexon2RawIO(**neo_kwargs)
+        neo_reader.parse_header()
+        NeoBaseSortingExtractor.__init__(self, sampling_frequency=sampling_frequency, **neo_kwargs)
+        self._kwargs.update({"file_path": str(file_path), "sampling_frequency": sampling_frequency})
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+        neo_kwargs = {"filename": str(file_path)}
+        return neo_kwargs
+
+
+class Plexon2EventExtractor(NeoBaseEventExtractor):
+    """
+    Class for reading plexon spiking data from .pl2 files.
+
+    Based on :py:class:`neo.rawio.Plexon2RawIO`
+
+    Parameters
+    ----------
+    folder_path: str
+
+    """
+
+    mode = "file"
+    NeoRawIOClass = "Plexon2RawIO"
+    name = "plexon2"
+
+    def __init__(self, folder_path, block_index=None):
+        neo_kwargs = self.map_to_neo_kwargs(folder_path)
+        NeoBaseEventExtractor.__init__(self, block_index=block_index, **neo_kwargs)
+
+    @classmethod
+    def map_to_neo_kwargs(cls, folder_path):
+        neo_kwargs = {"filename": str(folder_path)}
+        return neo_kwargs
+
+
+read_plexon2 = define_function_from_class(source_class=Plexon2RecordingExtractor, name="read_plexon2")
+read_plexon2_sorting = define_function_from_class(source_class=Plexon2SortingExtractor, name="read_plexon2_sorting")
+read_plexon2_event = define_function_from_class(source_class=Plexon2EventExtractor, name="read_plexon2_event")

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -121,6 +121,14 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class Plexon2EventTest(EventCommonTestSuite, unittest.TestCase):
+    ExtractorClass = Plexon2EventExtractor
+    downloads = ["plexon"]
+    entities = [
+        ("plexon/4chDemoPL2.pl2"),
+    ]
+
+
 class PlexonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = PlexonRecordingExtractor
     downloads = ["plexon"]
@@ -129,6 +137,14 @@ class PlexonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class Plexon2RecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = Plexon2RecordingExtractor
+    downloads = ["plexon"]
+    entities = [
+        ("plexon/4chDemoPL2.pl2", {"stream_id": "3"}),
+    ]
+
+
 class PlexonSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ExtractorClass = PlexonSortingExtractor
     downloads = ["plexon"]
@@ -137,6 +153,12 @@ class PlexonSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class Plexon2SortingTest(SortingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = Plexon2SortingExtractor
+    downloads = ["plexon"]
+    entities = [("plexon/4chDemoPL2.pl2", {"sampling_frequency": 40000})]
+
+
 class NeuralynxRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = NeuralynxRecordingExtractor
     downloads = ["neuralynx"]
@@ -304,7 +326,7 @@ def test_pickling(self):
     # test = PlexonRecordingTest()
     # test = PlexonSortingTest()
     # test = NeuralynxRecordingTest()
-    test = BlackrockRecordingTest()
+    test = Plexon2RecordingTest()
     # test = MCSRawRecordingTest()
     # test = KiloSortSortingTest()
     # test = Spike2RecordingTest()