Add neuronexus allego recording Extractor (#3235)

* add neuronexus allego

* add tests

* fix neuronexus name

* Heberto feedback

* Fix capitalization

* oops

* add assert messaging

* Update src/spikeinterface/extractors/neoextractors/neuronexus.py

Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>

---------

Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>

Author: zm711

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -9,6 +9,7 @@
 from .mearec import MEArecRecordingExtractor, MEArecSortingExtractor, read_mearec
 from .mcsraw import MCSRawRecordingExtractor, read_mcsraw
 from .neuralynx import NeuralynxRecordingExtractor, NeuralynxSortingExtractor, read_neuralynx, read_neuralynx_sorting
+from .neuronexus import NeuroNexusRecordingExtractor, read_neuronexus
 from .neuroscope import (
     NeuroScopeRecordingExtractor,
     NeuroScopeSortingExtractor,
@@ -54,6 +55,7 @@
     MCSRawRecordingExtractor,
     NeuralynxRecordingExtractor,
     NeuroScopeRecordingExtractor,
+    NeuroNexusRecordingExtractor,
     NixRecordingExtractor,
     OpenEphysBinaryRecordingExtractor,
     OpenEphysLegacyRecordingExtractor,

src/spikeinterface/extractors/neoextractors/neuronexus.py

@@ -0,0 +1,66 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from spikeinterface.core.core_tools import define_function_from_class
+
+from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor
+
+
+class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading data from NeuroNexus Allego.
+
+    Based on :py:class:`neo.rawio.NeuronexusRawIO`
+
+    Parameters
+    ----------
+    file_path : str | Path
+        The file path to the metadata .xdat.json file of an Allego session
+    stream_id : str | None, default: None
+        If there are several streams, specify the stream id you want to load.
+    stream_name : str | None, default: None
+        If there are several streams, specify the stream name you want to load.
+    all_annotations : bool, default: False
+        Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
+
+        In Neuronexus the ids provided by NeoRawIO are the hardware channel ids stored as `ntv_chan_name` within
+        the metada and the names are the `chan_names`
+
+
+    """
+
+    NeoRawIOClass = "NeuroNexusRawIO"
+
+    def __init__(
+        self,
+        file_path: str | Path,
+        stream_id: str | None = None,
+        stream_name: str | None = None,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = 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,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
+        )
+
+        self._kwargs.update(dict(file_path=str(Path(file_path).resolve())))
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+
+        neo_kwargs = {"filename": str(file_path)}
+
+        return neo_kwargs
+
+
+read_neuronexus = define_function_from_class(source_class=NeuroNexusRecordingExtractor, name="read_neuronexus")

src/spikeinterface/extractors/tests/common_tests.py

@@ -52,8 +52,11 @@ def test_open(self):
                 num_samples = rec.get_num_samples(segment_index=segment_index)
 
                 full_traces = rec.get_traces(segment_index=segment_index)
-                assert full_traces.shape == (num_samples, num_chans)
-                assert full_traces.dtype == dtype
+                assert full_traces.shape == (
+                    num_samples,
+                    num_chans,
+                ), f"{full_traces.shape} != {(num_samples, num_chans)}"
+                assert full_traces.dtype == dtype, f"{full_traces.dtype} != {dtype=}"
 
                 traces_sample_first = rec.get_traces(segment_index=segment_index, start_frame=0, end_frame=1)
                 assert traces_sample_first.shape == (1, num_chans)

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -181,6 +181,14 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class NeuroNexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = NeuroNexusRecordingExtractor
+    downloads = ["neuronexus"]
+    entities = [
+        ("neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json", {"stream_id": "0"}),
+    ]
+
+
 class PlexonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = PlexonRecordingExtractor
     downloads = ["plexon"]