Add ignore_timestamps_errors to OpenEphys interfaces

CHANGELOG.md

@@ -2,7 +2,8 @@
 
 ### Fixes
 
-* Changed the date parsing in `OpenEphysLegacyRecordingInterface` to `datetime.strptime` with the expected date format explicitly set to `"%d-%b-%Y %H%M%S"`.
+* Changed the date parsing in `OpenEphysLegacyRecordingInterface` to `datetime.strptime` with the expected date format explicitly set to `"%d-%b-%Y %H%M%S"`. [PR #577](https://github.com/catalystneuro/neuroconv/pull/577)
+* Added `ignore_timestamps_errors` keyword argument to `OpenEphysRecordingInterface` and `OpenEphysLegacyRecordingInterface` to have the possibility of ignoring discontinuous timestamps errors in neo. [PR #579](https://github.com/catalystneuro/neuroconv/pull/579)
 
 # v0.4.4
 

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

@@ -18,6 +18,7 @@ def __new__(
         stream_name: Optional[str] = None,
         verbose: bool = True,
         es_key: str = "ElectricalSeries",
+        ignore_timestamps_errors: bool = False,
     ):
         """
         Abstract class that defines which interface class to use for a given Open Ephys recording.
@@ -34,13 +35,19 @@ def __new__(
             When channel stream is not available the name of the stream must be specified.
         verbose : bool, default: True
         es_key : str, default: "ElectricalSeries"
+        ignore_timestamps_errors : bool, default: False
+            Ignore the discontinuous timestamps error in neo. Only relevant for the "legacy" format (.continuous) files.
         """
         super().__new__(cls)
 
         folder_path = Path(folder_path)
         if any(folder_path.rglob("*.continuous")):
             return OpenEphysLegacyRecordingInterface(
-                folder_path=folder_path, stream_name=stream_name, verbose=verbose, es_key=es_key
+                folder_path=folder_path,
+                stream_name=stream_name,
+                verbose=verbose,
+                es_key=es_key,
+                ignore_timestamps_errors=ignore_timestamps_errors,
             )
 
         elif any(folder_path.rglob("*.dat")):

src/neuroconv/datainterfaces/ecephys/openephys/openephyslegacydatainterface.py

@@ -11,10 +11,13 @@ class OpenEphysLegacyRecordingInterface(BaseRecordingExtractorInterface):
     Uses :py:class:`~spikeinterface.extractors.OpenEphysLegacyRecordingExtractor`."""
 
     @classmethod
-    def get_stream_names(cls, folder_path: FolderPathType) -> List[str]:
+    def get_stream_names(cls, folder_path: FolderPathType, ignore_timestamps_errors: bool = False) -> List[str]:
         from spikeinterface.extractors import OpenEphysLegacyRecordingExtractor
 
-        stream_names, _ = OpenEphysLegacyRecordingExtractor.get_streams(folder_path=folder_path)
+        stream_names, _ = OpenEphysLegacyRecordingExtractor.get_streams(
+            folder_path=folder_path,
+            ignore_timestamps_errors=ignore_timestamps_errors,
+        )
         return stream_names
 
     @classmethod
@@ -33,6 +36,7 @@ def __init__(
         stream_name: Optional[str] = None,
         verbose: bool = True,
         es_key: str = "ElectricalSeries",
+        ignore_timestamps_errors: bool = False,
     ):
         """
         Initialize reading of OpenEphys legacy recording (.continuous files).
@@ -46,8 +50,12 @@ def __init__(
             The name of the recording stream.
         verbose : bool, default: True
         es_key : str, default: "ElectricalSeries"
+        ignore_timestamps_errors : bool, default: False
+            Ignore the discontinuous timestamps error in neo.
         """
-        available_streams = self.get_stream_names(folder_path=folder_path)
+        available_streams = self.get_stream_names(
+            folder_path=folder_path, ignore_timestamps_errors=ignore_timestamps_errors
+        )
         if len(available_streams) > 1 and stream_name is None:
             raise ValueError(
                 "More than one stream is detected! Please specify which stream you wish to load with the `stream_name` argument. "
@@ -58,7 +66,21 @@ def __init__(
                 f"The selected stream '{stream_name}' is not in the available streams '{available_streams}'!"
             )
 
-        super().__init__(folder_path=folder_path, stream_name=stream_name, verbose=verbose, es_key=es_key)
+        super().__init__(
+            folder_path=folder_path,
+            stream_name=stream_name,
+            ignore_timestamps_errors=ignore_timestamps_errors,
+            verbose=verbose,
+            es_key=es_key,
+        )
+
+        if ignore_timestamps_errors and self.recording_extractor.has_time_vector():
+            for segment_index in range(self.recording_extractor.get_num_segments()):
+                self.recording_extractor._recording_segments[segment_index].time_vector = None
+            warn(
+                "The recording has a time vector but the timestamps might be discontinuous. "
+                "The time vector was reset to None to avoid writing these timestamps with the electrical series."
+            )
 
     def get_metadata(self):
         metadata = super().get_metadata()

src/neuroconv/datainterfaces/ecephys/requirements.txt

@@ -1,2 +1,2 @@
-spikeinterface>=0.98.2
+spikeinterface @ git+https://github.com/SpikeInterface/spikeinterface.git@main
 packaging<22.0