Merge pull request #4021 from h-mayorquin/add_axon

Add Axon recording

Author: alejoe91

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -1,4 +1,5 @@
 from .alphaomega import AlphaOmegaRecordingExtractor, AlphaOmegaEventExtractor, read_alphaomega, read_alphaomega_event
+from .axon import AxonRecordingExtractor, read_axon
 from .axona import AxonaRecordingExtractor, read_axona
 from .biocam import BiocamRecordingExtractor, read_biocam
 from .blackrock import BlackrockRecordingExtractor, BlackrockSortingExtractor, read_blackrock, read_blackrock_sorting
@@ -44,6 +45,7 @@
 
 neo_recording_extractors_dict = {
     AlphaOmegaRecordingExtractor: dict(wrapper_string="read_alphaomega", wrapper_class=read_alphaomega),
+    AxonRecordingExtractor: dict(wrapper_string="read_axon", wrapper_class=read_axon),
     AxonaRecordingExtractor: dict(wrapper_string="read_axona", wrapper_class=read_axona),
     BiocamRecordingExtractor: dict(wrapper_string="read_biocam", wrapper_class=read_biocam),
     BlackrockRecordingExtractor: dict(wrapper_string="read_blackrock", wrapper_class=read_blackrock),

src/spikeinterface/extractors/neoextractors/axon.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
+
+
+class AxonRecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading Axon Binary Format (ABF) files.
+
+    Based on :py:class:`neo.rawio.AxonRawIO`
+
+    Supports both ABF1 (pClamp ≤9) and ABF2 (pClamp ≥10) formats.
+    Can read data from pCLAMP and AxoScope software.
+
+    Parameters
+    ----------
+    file_path : str or Path
+        The ABF file path to load the recordings from.
+    stream_id : str or None, default: None
+        If there are several streams, specify the stream id you want to load.
+    stream_name : str or 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.
+
+    Examples
+    --------
+    >>> from spikeinterface.extractors import read_axon
+    >>> recording = read_axon(file_path='path/to/file.abf')
+    """
+
+    NeoRawIOClass = "AxonRawIO"
+
+    def __init__(
+        self,
+        file_path,
+        stream_id=None,
+        stream_name=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).absolute())))
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+        neo_kwargs = {"filename": str(file_path)}
+        return neo_kwargs
+
+
+read_axon = define_function_from_class(source_class=AxonRecordingExtractor, name="read_axon")

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -40,6 +40,7 @@
     Spike2RecordingExtractor,
     EDFRecordingExtractor,
     Plexon2RecordingExtractor,
+    AxonRecordingExtractor,
 )
 
 from spikeinterface.extractors.extractor_classes import KiloSortSortingExtractor
@@ -294,6 +295,12 @@ class TdTRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     entities = [("tdt/aep_05", {"stream_id": "1"})]
 
 
+class AxonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = AxonRecordingExtractor
+    downloads = ["axon"]
+    entities = ["axon/extracellular_data/four_electrodes/24606005_SampleData.abf"]
+
+
 class AxonaRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = AxonaRecordingExtractor
     downloads = ["axona"]