Source code for neuroconv.datainterfaces.ecephys.axon.axondatainterface

from datetime import datetime, timedelta
from pathlib import Path
from warnings import warn

from pydantic import FilePath
from pynwb.ecephys import ElectricalSeries

from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
from ....utils import DeepDict, get_schema_from_hdmf_class




class AxonRecordingInterface(BaseRecordingExtractorInterface):
    """
    Data interface class for converting extracellular data recorded in Axon Binary Format (ABF) data.

    Uses the :py:func:`~spikeinterface.extractors.read_axon` reader from SpikeInterface.
    """

    display_name = "Axon Recording"
    keywords = BaseRecordingExtractorInterface.keywords + ("axon", "abf")
    associated_suffixes = (".abf",)
    info = "Interface for extracellular data recorded in Axon Binary Format (ABF) recordings."



    @classmethod
    def get_source_schema(cls) -> dict:
        source_schema = super().get_source_schema()
        source_schema["properties"]["file_path"]["description"] = "Path to an Axon Binary Format (.abf) file"
        return source_schema




    @classmethod
    def get_extractor_class(cls):
        from spikeinterface.extractors.extractor_classes import AxonRecordingExtractor

        return AxonRecordingExtractor


    def __init__(
        self,
        file_path: FilePath,
        verbose: bool = False,
        es_key: str = "ElectricalSeries",
    ):
        """
        Load and prepare raw data and corresponding metadata from the Axon Binary Format (.abf files).

        Parameters
        ----------
        file_path : FilePath
            Path to an Axon Binary Format (.abf) file
        verbose : bool, default: False
            Verbose
        es_key : str, default: "ElectricalSeries"
            The key for the ElectricalSeries in the metadata
        """

        self.file_path = Path(file_path)

        super().__init__(file_path=file_path, verbose=verbose, es_key=es_key)

    def _get_start_datetime(self, neo_reader):
        """
        Get start datetime for ABF file.

        Parameters
        ----------
        neo_reader : neo.io.AxonIO
            The Neo reader object for the ABF file.

        Returns
        -------
        datetime
            The start date and time of the recording.
        """
        if all(k in neo_reader._axon_info for k in ["uFileStartDate", "uFileStartTimeMS"]):
            startDate = str(neo_reader._axon_info["uFileStartDate"])
            startTime = round(neo_reader._axon_info["uFileStartTimeMS"] / 1000)
            startDate = datetime.strptime(startDate, "%Y%m%d")
            startTime = timedelta(seconds=startTime)
            return startDate + startTime
        else:
            warn(
                f"uFileStartDate or uFileStartTimeMS not found in {neo_reader.filename.split('/')[-1]}, datetime for "
                "recordings might be wrongly stored."
            )
            return neo_reader._axon_info["rec_datetime"]



    def get_metadata_schema(self) -> dict:
        metadata_schema = super().get_metadata_schema()
        metadata_schema["properties"]["Ecephys"]["properties"].update(
            ElectricalSeriesRaw=get_schema_from_hdmf_class(ElectricalSeries)
        )
        return metadata_schema




    def get_metadata(self) -> DeepDict:
        metadata = super().get_metadata()
        ecephys_metadata = metadata["Ecephys"]

        # Extract session start time from ABF file using the existing neo_reader
        neo_reader = self.recording_extractor.neo_reader
        session_start_time = self._get_start_datetime(neo_reader)
        session_start_time_str = session_start_time.strftime("%Y-%m-%dT%H:%M:%S%z")
        metadata["NWBFile"].update(session_start_time=session_start_time_str)

        # Add device information
        axon_device = dict(
            name="Axon Instruments",
            description="Axon Instruments data acquisition system (pCLAMP/AxoScope)",
            manufacturer="Molecular Devices",
        )
        device_list = [axon_device]
        ecephys_metadata.update(Device=device_list)

        # Update electrode groups with device information
        electrode_group_metadata = ecephys_metadata["ElectrodeGroup"]
        for electrode_group in electrode_group_metadata:
            electrode_group["device"] = axon_device["name"]

        # Add electrical series metadata
        ecephys_metadata.update(
            ElectricalSeriesRaw=dict(
                name="ElectricalSeriesRaw", description="Raw acquisition traces from Axon Binary Format file."
            ),
        )

        return metadata