Merge pull request #564 from catalystneuro/add_spikeinterface_support…

…_to_openephys

Add spikeinterface support to `OpenEphysRecordingExtractorInterface`

docs/conversion_examples_gallery/recording/openephys.rst

@@ -14,11 +14,11 @@ Convert OpenEphys data to NWB using :py:class:`~nwb_conversion_tools.datainterfa
     >>> folder_path = f"{ECEPHY_DATA_PATH}/openephysbinary/v0.4.4.1_with_video_tracking"
     >>> # Change the folder_path to the appropiate location in your system
     >>> interface = OpenEphysRecordingExtractorInterface(folder_path=folder_path, verbose=False)
+    >>> # Extract what metadata we can from the source files
+    >>> metadata = interface.get_metadata()
     Loading Open-Ephys: reading settings...
     Decoding data from  binary  format
     Reading oebin file
-    >>> # Extract what metadata we can from the source files
-    >>> metadata = interface.get_metadata()
     >>> # session_start_time is required for conversion. If it cannot be inferred
     >>> # automatically from the source files you must supply one.
     >>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=tz.gettz("US/Pacific")).isoformat()

requirements-full.txt

@@ -23,3 +23,4 @@ sonpy>=1.7.1
 tiffile==2018.10.18
 ndx-dandi-icephys>=0.4.0
 pillow==9.1.1
+pyopenephys==1.1.2

requirements-minimal.txt

@@ -15,3 +15,4 @@ roiextractors @ git+https://github.com/catalystneuro/roiextractors.git@1d50cbeb1
 lxml>=4.6.5
 scipy>=1.4.1
 click  # must be unspecified version to handle platform/pyVersion
+pyopenephys>=1.1.2

src/nwb_conversion_tools/datainterfaces/ecephys/openephys/openephysdatainterface.py

@@ -1,8 +1,10 @@
-"""Authors: Luiz Tauffer."""
-import pytz
-import spikeextractors as se
+"""Authors: Heberto Mayorquin, Luiz Tauffer."""
 from typing import Optional
 
+import pyopenephys
+import spikeextractors as se
+from spikeinterface.extractors import OpenEphysBinaryRecordingExtractor
+
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
 from ..basesortingextractorinterface import BaseSortingExtractorInterface
 from ....utils import get_schema_from_method_signature, FolderPathType
@@ -11,7 +13,7 @@
 class OpenEphysRecordingExtractorInterface(BaseRecordingExtractorInterface):
     """Primary data interface class for converting a OpenEphysRecordingExtractor."""
 
-    RX = se.OpenEphysRecordingExtractor
+    RX = OpenEphysBinaryRecordingExtractor
 
     @classmethod
     def get_source_schema(cls):
@@ -27,27 +29,36 @@ def __init__(
         folder_path: FolderPathType,
         experiment_id: Optional[int] = 0,
         recording_id: Optional[int] = 0,
-        stub_test: Optional[bool] = False,
+        stub_test: bool = False,
         verbose: bool = True,
+        spikeextractors_backend: bool = False,
     ):
-        super().__init__(
-            folder_path=folder_path, experiment_id=experiment_id, recording_id=recording_id, verbose=verbose
-        )
+        self.spikeextractors_backend = spikeextractors_backend
+        if spikeextractors_backend:
+            self.RX = se.OpenEphysRecordingExtractor
+
+            super().__init__(
+                folder_path=folder_path, experiment_id=experiment_id, recording_id=recording_id, verbose=verbose
+            )
+
+        else:
+            super().__init__(folder_path=folder_path, verbose=verbose)
+
         if stub_test:
             self.subset_channels = [0, 1]
 
     def get_metadata(self):
         """Auto-fill as much of the metadata as possible. Must comply with metadata schema."""
         metadata = super().get_metadata()
 
-        # Open file and extract info
-        session_start_time = self.recording_extractor._fileobj.experiments[0].datetime
-        session_start_time_tzaware = pytz.timezone("EST").localize(session_start_time)
-
-        metadata["NWBFile"] = dict(
-            session_start_time=session_start_time_tzaware.strftime("%Y-%m-%dT%H:%M:%S"),
-        )
+        if self.spikeextractors_backend:
+            session_start_time = self.recording_extractor._fileobj.experiments[0].datetime
+        else:
+            folder_path = self.source_data["folder_path"]
+            fileobj = pyopenephys.File(folder_path)
+            session_start_time = fileobj.experiments[0].datetime
 
+        metadata["NWBFile"] = dict(session_start_time=session_start_time)
         return metadata
 
 

tests/test_on_data/test_gin_ecephys.py

@@ -42,9 +42,12 @@
 
 
 def custom_name_func(testcase_func, param_num, param):
+    interface_name = param.kwargs["data_interface"].__name__
+    reduced_interface_name = interface_name.replace("Recording", "").replace("Interface", "").replace("Sorting", "")
+
     return (
         f"{testcase_func.__name__}_{param_num}_"
-        f"{parameterized.to_safe_name(param.kwargs['data_interface'].__name__)}"
+        f"{parameterized.to_safe_name(reduced_interface_name)}"
         f"_{param.kwargs.get('case_name', '')}"
     )
 
@@ -98,16 +101,24 @@ class TestConverter(NWBConverter):
             data_interface=NeuralynxRecordingInterface,
             interface_kwargs=dict(folder_path=str(DATA_PATH / "neuralynx" / "Cheetah_v5.7.4" / "original_data")),
         ),
-        param(
-            data_interface=OpenEphysRecordingExtractorInterface,
-            interface_kwargs=dict(folder_path=str(DATA_PATH / "openephysbinary" / "v0.4.4.1_with_video_tracking")),
-        ),
         param(
             data_interface=AxonaRecordingExtractorInterface,
             interface_kwargs=dict(file_path=str(DATA_PATH / "axona" / "axona_raw.bin")),
         ),
     ]
 
+    for spikeextractors_backend in [True, False]:
+        parameterized_recording_list.append(
+            param(
+                data_interface=OpenEphysRecordingExtractorInterface,
+                interface_kwargs=dict(
+                    folder_path=str(DATA_PATH / "openephysbinary" / "v0.4.4.1_with_video_tracking"),
+                    spikeextractors_backend=spikeextractors_backend,
+                ),
+                case_name=f"spikeextractors_backend={spikeextractors_backend}",
+            )
+        )
+
     for spikeextractors_backend in [True, False]:
         parameterized_recording_list.append(
             param(