Add NeuroExplorerSortingExtractor

doc/api.rst

@@ -111,6 +111,7 @@ NEO-based
     .. autofunction:: read_neuralynx
     .. autofunction:: read_neuralynx_sorting
     .. autofunction:: read_neuroexplorer
+    .. autofunction:: read_neuroexplorer_sorting
     .. autofunction:: read_neuroscope
     .. autofunction:: read_nix
     .. autofunction:: read_openephys

doc/modules/extractors.rst

@@ -175,6 +175,7 @@ For sorted data formats, we currently support:
 * **Neurodata Without Borders** :py:func:`~spikeinterface.extractors.read_nwb_sorting()`
 * **Neuroscope** :py:func:`~spikeinterface.extractors.read_neuroscope_sorting()`
 * **Neuralynx spikes** :py:func:`~spikeinterface.extractors.read_neuralynx_sorting()`
+* **NeuroExplorer spikes** :py:func:`~spikeinterface.extractors.read_neuroexplorer_sorting()`
 * **NPZ (created by SpikeInterface)** :py:func:`~spikeinterface.core.read_npz_sorting()`
 * **Plexon spikes** :py:func:`~spikeinterface.extractors.read_plexon_sorting()`
 * **Plexon 2 spikes** :py:func:`~spikeinterface.extractors.read_plexon2_sorting()`

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -18,7 +18,12 @@
     read_neuroscope_sorting,
     read_neuroscope,
 )
-from .neuroexplorer import NeuroExplorerRecordingExtractor, read_neuroexplorer
+from .neuroexplorer import (
+    NeuroExplorerRecordingExtractor,
+    NeuroExplorerSortingExtractor,
+    read_neuroexplorer,
+    read_neuroexplorer_sorting,
+)
 from .nix import NixRecordingExtractor, read_nix
 from .openephys import (
     OpenEphysLegacyRecordingExtractor,
@@ -79,6 +84,9 @@
     PlexonSortingExtractor: dict(wrapper_string="read_plexon_sorting", wrapper_class=read_plexon_sorting),
     Plexon2SortingExtractor: dict(wrapper_string="read_plexon2_sorting", wrapper_class=read_plexon2_sorting),
     NeuroScopeSortingExtractor: dict(wrapper_string="read_neuroscope_sorting", wrapper_class=read_neuroscope_sorting),
+    NeuroExplorerSortingExtractor: dict(
+        wrapper_string="read_neuroexplorer_sorting", wrapper_class=read_neuroexplorer_sorting
+    ),
 }
 
 neo_event_extractors_dict = {

src/spikeinterface/extractors/neoextractors/neuroexplorer.py

@@ -1,8 +1,14 @@
 from pathlib import Path
 
+from spikeinterface.core import BaseSorting
 from spikeinterface.core.core_tools import define_function_from_class
 
-from .neobaseextractor import NeoBaseRecordingExtractor
+from .neobaseextractor import (
+    NeoBaseRecordingExtractor,
+    NeoBaseSortingExtractor,
+    NeoSortingSegment,
+    _NeoBaseExtractor,
+)
 
 
 class NeuroExplorerRecordingExtractor(NeoBaseRecordingExtractor):
@@ -72,3 +78,63 @@ def map_to_neo_kwargs(cls, file_path):
 
 
 read_neuroexplorer = define_function_from_class(source_class=NeuroExplorerRecordingExtractor, name="read_neuroexplorer")
+
+
+class NeuroExplorerSortingExtractor(NeoBaseSortingExtractor):
+    """
+    Class for reading the sorted units of NEX (NeuroExplorer data format) files.
+
+    Based on :py:class:`neo.rawio.NeuroExplorerRawIO`
+
+    Units are the neuron variables of the file and the unit ids are their names. Waveform variables
+    (for example the ``_wf`` and ``_template`` companions of each unit in Plexon exports) repeat
+    the spike times of a neuron variable or hold a mean waveform, so they are not units. They
+    remain available through ``neo_reader``.
+
+    Parameters
+    ----------
+    file_path : str | Path
+        The file path to load the sorting from.
+    """
+
+    NeoRawIOClass = "NeuroExplorerRawIO"
+    neo_returns_frames = True
+
+    def __init__(self, file_path):
+        neo_kwargs = self.map_to_neo_kwargs(file_path)
+        _NeoBaseExtractor.__init__(self, block_index=None, **neo_kwargs)
+
+        # Only neuron variables are units: they are the spike channels without waveforms
+        spike_channels = self.neo_reader.header["spike_channels"]
+        unit_ids = spike_channels["name"][spike_channels["wf_sampling_rate"] == 0]
+        # Spike timestamps are ticks of the file's global clock
+        sampling_frequency = self.neo_reader.global_header["freq"]
+        BaseSorting.__init__(self, sampling_frequency, unit_ids)
+
+        sorting_segment = NeuroExplorerSortingSegment(
+            neo_reader=self.neo_reader,
+            block_index=self.block_index,
+            segment_index=0,
+            t_start=None,
+            sampling_frequency=sampling_frequency,
+            neo_returns_frames=self.neo_returns_frames,
+        )
+        self.add_sorting_segment(sorting_segment)
+        self._kwargs = {"file_path": str(Path(file_path).absolute())}
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+        neo_kwargs = {"filename": str(file_path)}
+        return neo_kwargs
+
+
+class NeuroExplorerSortingSegment(NeoSortingSegment):
+    def map_from_unit_id_to_spike_channel_index(self, unit_id):
+        # Units are a subset of the spike channels, so the position of a unit id is not its spike channel index
+        spike_channel_names = list(self.neo_reader.header["spike_channels"]["name"])
+        return spike_channel_names.index(unit_id)
+
+
+read_neuroexplorer_sorting = define_function_from_class(
+    source_class=NeuroExplorerSortingExtractor, name="read_neuroexplorer_sorting"
+)

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -19,6 +19,7 @@
     IntanRecordingExtractor,
     NeuroScopeRecordingExtractor,
     NeuroExplorerRecordingExtractor,
+    NeuroExplorerSortingExtractor,
     NeuroScopeSortingExtractor,
     NeuroNexusRecordingExtractor,
     PlexonRecordingExtractor,
@@ -270,6 +271,15 @@ class NeuroExplorerRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class NeuroExplorerSortingTest(SortingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = NeuroExplorerSortingExtractor
+    downloads = ["neuroexplorer"]
+    entities = [
+        "neuroexplorer/File_neuroexplorer_1.nex",
+        "neuroexplorer/File_neuroexplorer_2.nex",
+    ]
+
+
 class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ExtractorClass = NeuroScopeSortingExtractor
     downloads = ["neuroscope"]