Source code for mne_nirs.io.snirf._aux

# Author: Robert Luke <code@robertluke.net>
#
# License: BSD (3-clause)

import logging

import h5py
import numpy as np
from mne.io import Raw
from pandas import DataFrame
from scipy import interpolate




def read_snirf_aux_data(fname: str, raw: Raw):
    """Read auxiliary data from SNIRF file.

    Reads the auxiliary channel data (e.g. heart rate data,
    accelerometer, etc). The auxiliary data will be resampled
    to match the raw data.

    Parameters
    ----------
    fname : str
        Path to the SNIRF data file.
    raw : Raw
        Instance of raw snirf data as created by read_raw_snirf.

    Returns
    -------
    fname : str
        Path to the SNIRF data file.
    """
    with h5py.File(fname, "r") as dat:
        if "nirs" in dat:
            basename = "nirs"
        elif "nirs1" in dat:
            basename = "nirs1"
        else:
            raise RuntimeError("Data does not contain nirs field")

        all_keys = list(dat.get(basename).keys())
        aux_keys = [i for i in all_keys if i.startswith("aux")]
        aux_names = [_decode_name(dat.get(f"{basename}/{k}/name")) for k in aux_keys]
        logging.debug(f"Found auxiliary channels {aux_names}")

        d = {"times": raw.times}
        for idx, aux in enumerate(aux_keys):
            aux_data = np.array(dat.get(f"{basename}/{aux}/dataTimeSeries"))
            aux_time = np.array(dat.get(f"{basename}/{aux}/time"))
            aux_data_interp = interpolate.interp1d(
                aux_time, aux_data, axis=0, bounds_error=False, fill_value="extrapolate"
            )
            aux_data_matched_to_raw = aux_data_interp(raw.times)
            d[aux_names[idx]] = aux_data_matched_to_raw

        df = DataFrame(data=d)
        df = df.set_index("times")

    return df



def _decode_name(key):
    return np.array(key)[0].decode()