neuralynxio.py

"""
Class for reading data from Neuralynx files.
This IO supports NCS, NEV and NSE file formats.

Depends on: numpy

Supported: Read

Author: Julia Sprenger, Carlos Canova
"""

from neo.io.basefromrawio import BaseFromRaw
from neo.rawio.neuralynxrawio.neuralynxrawio import NeuralynxRawIO


class NeuralynxIO(NeuralynxRawIO, BaseFromRaw):
    """
    Class for reading data from Neuralynx files.
    This IO supports NCS, NEV, NSE, NTT and NVT file formats.

    NCS contains signals for one channel
    NEV contains events
    NSE contains spikes and waveforms for mono electrodes
    NTT contains spikes and waveforms for tetrodes
    NVT contains coordinates and head angles for video tracking
    """

    _prefered_signal_group_mode = "group-by-same-units"
    mode = "dir"

    def __init__(
        self,
        dirname="",
        filename="",
        use_cache=False,
        cache_path="same_as_resource",
        exclude_filename=None,
        keep_original_times=False,
        ignore_nvt=False,
    ):
        """
        Initialise IO instance

        Parameters
        ----------
        dirname : str
            Directory containing data files
        filename : str
            Name of a single ncs, nse, nev, or ntt file to include in dataset. Will be ignored,
            if dirname is provided.
        use_cache : bool, optional
            Cache results of initial file scans for faster loading in subsequent runs.
            Default: False
        cache_path : str, optional
            Folder path to use for cache files.
            Default: 'same_as_resource'
        exclude_filename: str or list
            Filename or list of filenames to be excluded. Expects base filenames without
            directory path.
        keep_original_times : bool
            Preserve original time stamps as in data files. By default datasets are
            shifted to begin at t_start = 0*pq.second.
            Default: False
        ignore_nvt : bool
            Ignore NVT files when loading data. This is only a temporary argument before
            support for multiple NVT files are added. Turn it on if there are multiple NVT 
            files in the directory.
            Default: False
        """
        NeuralynxRawIO.__init__(
            self,
            dirname=dirname,
            filename=filename,
            use_cache=use_cache,
            cache_path=cache_path,
            exclude_filename=exclude_filename,
            keep_original_times=keep_original_times,
            ignore_nvt=ignore_nvt,
        )
        if self.rawmode == "one-file":
            BaseFromRaw.__init__(self, filename)
        elif self.rawmode == "one-dir":
            BaseFromRaw.__init__(self, dirname)