kraken/backend/dataloaders/neo.py

import numpy as np
import os
import json
import mne
import glob
import pyedflib
from scipy import signal
from .utils import upsample_events
from settings.config import settings


FINGERMODEL_IDS = settings.FINGERMODEL_IDS

CONFIG_INFO = settings.CONFIG_INFO


def raw_preprocessing(data_root, session_paths:dict, 
                      do_rereference=True,
                      upsampled_epoch_length=1., 
                      ori_epoch_length=5, 
                      unify_label=True,
                      mov_trial_ind=[2, 3],
                      rest_trial_ind=[4]):
    """
    Params:
        subj_root: 
        session_paths: dict of lists
        do_rereference (bool): do common average rereference or not
        upsampled_epoch_length (None or float): None: do not do upsampling
        ori_epoch_length (int or 'varied'): original epoch length in second
        unify_label (True, original data didn't use unified event label, do unification (old pony format); False use original)
        mov_trial_ind: only used when unify_label == True, suggesting the raw file's annotations didn't use unified labels (old pony format)
        rest_trial_ind: only used when unify_label == True, 
    """
    raws_loaded = load_sessions(data_root, session_paths)
    # process event
    raws = []
    for (finger_model, raw) in raws_loaded:
        fs = raw.info['sfreq']
        events, _ = mne.events_from_annotations(raw)

        if not unify_label:
            mov_trial_ind = [FINGERMODEL_IDS[finger_model]]
            rest_trial_ind = [0]
        
        if isinstance(ori_epoch_length, int) or isinstance(ori_epoch_length, float):
            trial_duration = ori_epoch_length
        elif ori_epoch_length == 'varied':
            trial_duration = None
        else:
            raise ValueError(f'Unsupported epoch_length {ori_epoch_length}')
        events = reconstruct_events(events, fs, finger_model, 
                                    mov_trial_ind=mov_trial_ind,
                                    rest_trial_ind=rest_trial_ind,
                                    trial_duration=trial_duration, 
                                    use_original_label=not unify_label)
        if upsampled_epoch_length is not None:
            events = upsample_events(events, int(fs * upsampled_epoch_length))
        annotations = mne.annotations_from_events(events, fs, {FINGERMODEL_IDS[finger_model]: finger_model, FINGERMODEL_IDS['rest']: 'rest'})
        raw.set_annotations(annotations)
        raws.append(raw)

    raws = mne.concatenate_raws(raws)
    raws.load_data()

    if do_rereference:
        # common average
        raws.set_eeg_reference('average')
    # high pass
    raws = raws.filter(1, None)
    # filter 50Hz
    raws = raws.notch_filter([50, 100, 150], trans_bandwidth=3, verbose=False)

    return raws


def reconstruct_events(events, fs, finger_model, trial_duration=5, mov_trial_ind=[2, 3], rest_trial_ind=[4], use_original_label=False):
    """重构出事件序列中的单独运动事件
    Args:
        fs: int
        finger_model: 
    """
    # Trial duration are fixed to be ? seconds.
    # initialRest: 1, miFailed & miSuccess: 2 & 3, rest: 4
    # ignore initialRest
    # extract trials

    deduplicated_mov = np.diff(np.isin(events[:, 2], mov_trial_ind), prepend=0) == 1
    deduplicated_rest = np.diff(np.isin(events[:, 2], rest_trial_ind), prepend=0) == 1
    trials_ind_deduplicated = np.flatnonzero(np.logical_or(deduplicated_mov, deduplicated_rest))
    events_new = events[trials_ind_deduplicated]
    if trial_duration is None:
        events_new[:-1, 1] = np.diff(events_new[:, 0])
        events_new[-1, 1] = events[-1, 0] - events_new[-1, 0]
    else:
        events_new[:, 1] = int(trial_duration * fs)
    events_final = events_new.copy()
    if (not use_original_label) and (finger_model is not None):
        # process mov
        ind_mov = np.flatnonzero(np.isin(events_new[:, 2], mov_trial_ind))
        events_final[ind_mov, 2] = FINGERMODEL_IDS[finger_model] 
        # process rest
        ind_rest = np.flatnonzero(np.isin(events_new[:, 2], rest_trial_ind))
        events_final[ind_rest, 2] = 0
    return events_final


def load_sessions(data_root, session_names: dict):
    # return raws for different finger models on an interleaved manner
    raw_cnt = sum(len(session_names[k]) for k in session_names)
    raws = []
    i = 0
    while i < raw_cnt:
        for finger_model in session_names.keys():
            try:
                s = session_names[finger_model].pop(0)
                i += 1
            except IndexError:
                continue
            if glob.glob(os.path.join(data_root, s, 'evt.bdf')):
                # neo format
                raw = load_neuracle(os.path.join(data_root, s))
            else:
                # kraken format
                data_file = glob.glob(os.path.join(data_root, s, '*.bdf'))[0]
                raw = mne.io.read_raw_bdf(data_file)
            raws.append((finger_model, raw))
    return raws  


def load_neuracle(data_dir, data_type='ecog'):
    """
    neuracle file loader
    :param 
        data_dir: root data dir for the experiment
        sfreq: 
        data_type: 
    :return:
        raw: mne.io.RawArray
    """
    f = {
        'data': os.path.join(data_dir, 'data.bdf'),
        'evt': os.path.join(data_dir, 'evt.bdf'),
        'info': os.path.join(data_dir, 'recordInformation.json')
    }
    # read json
    with open(f['info'], 'r') as json_file:
        record_info = json.load(json_file)
    start_time_point = record_info['DataFileInformations'][0]['BeginTimeStamp']
    sfreq = record_info['SampleRate']

    # read data
    f_data = pyedflib.EdfReader(f['data'])
    ch_names = f_data.getSignalLabels()
    data = np.array([f_data.readSignal(i) for i in range(f_data.signals_in_file)]) * 1e-6  # to Volt

    info = mne.create_info(ch_names, sfreq, [data_type] * len(ch_names))
    raw = mne.io.RawArray(data, info)

    # read event
    try:
        f_evt = pyedflib.EdfReader(f['evt'])
        onset, duration, content = f_evt.readAnnotations()
        onset = np.array(onset) - start_time_point * 1e-3  # correct by start time point
        onset = (onset * sfreq).astype(np.int64)

        duration = (np.array(duration) * sfreq).astype(np.int64) 
        event_mapping = {c: i for i, c in enumerate(np.unique(content))}
        event_ids = [event_mapping[i] for i in content]
        events = np.stack((onset, duration, event_ids), axis=1)
        
        annotations = mne.annotations_from_events(events, sfreq)
        raw.set_annotations(annotations)
    except OSError:
        pass

    return raw