File: helpers.py

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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import os
from functools import partial

import numpy as np

import mne
from mne.utils import object_diff

info_ignored_fields = (
    "file_id",
    "hpi_results",
    "hpi_meas",
    "meas_id",
    "meas_date",
    "highpass",
    "lowpass",
    "subject_info",
    "hpi_subsystem",
    "experimenter",
    "description",
    "proj_id",
    "proj_name",
    "line_freq",
    "gantry_angle",
    "dev_head_t",
    "bads",
    "ctf_head_t",
    "dev_ctf_t",
    "dig",
)

ch_ignore_fields = (
    "logno",
    "cal",
    "range",
    "scanno",
    "coil_type",
    "kind",
    "loc",
    "coord_frame",
    "unit",
)

info_long_fields = ("hpi_meas", "projs")

system_to_reader_fn_dict = {
    "neuromag306": mne.io.read_raw_fif,
    "CNT": partial(mne.io.read_raw_cnt),
    "CTF": partial(mne.io.read_raw_ctf, clean_names=True),
    "BTI": partial(
        mne.io.read_raw_bti,
        head_shape_fname=None,
        rename_channels=False,
        sort_by_ch_name=False,
    ),
    "EGI": mne.io.read_raw_egi,
    "eximia": mne.io.read_raw_eximia,
}

ignore_channels_dict = {"BTI": ["MUz", "MLx", "MLy", "MUx", "MUy", "MLz"]}

drop_extra_chans_dict = {
    "EGI": ["STI 014", "DIN1", "DIN3", "DIN7", "DIN4", "DIN5", "DIN2"],
    "eximia": ["GateIn", "Trig1", "Trig2"],
}

system_decimal_accuracy_dict = {"CNT": 2}

pandas_not_found_warning_msg = (
    "The Pandas library is not installed. Not "
    "returning the original trialinfo matrix as "
    "metadata."
)

testing_path = mne.datasets.testing.data_path(download=False)


def _remove_ignored_ch_fields(info):
    if "chs" in info:
        for cur_ch in info["chs"]:
            for cur_field in ch_ignore_fields:
                if cur_field in cur_ch:
                    del cur_ch[cur_field]


def _remove_long_info_fields(info):
    for cur_field in info_long_fields:
        if cur_field in info:
            del info[cur_field]


def _remove_ignored_info_fields(info):
    for cur_field in info_ignored_fields:
        if cur_field in info:
            del info[cur_field]

    _remove_ignored_ch_fields(info)


def get_data_paths(system):
    """Return common paths for all tests."""
    return testing_path / "fieldtrip" / "ft_test_data" / system


def get_cfg_local(system):
    """Return cfg_local field for the system."""
    from pymatreader import read_mat

    cfg_local = read_mat(
        os.path.join(get_data_paths(system), "raw_v7.mat"), ["cfg_local"]
    )["cfg_local"]

    return cfg_local


def get_raw_info(system):
    """Return the info dict of the raw data."""
    cfg_local = get_cfg_local(system)

    raw_data_file = os.path.join(testing_path, cfg_local["file_name"])
    reader_function = system_to_reader_fn_dict[system]

    info = reader_function(raw_data_file, preload=False).info
    with info._unlock():
        info["comps"] = []
    return info


def get_raw_data(system, drop_extra_chs=False):
    """Find, load and process the raw data."""
    cfg_local = get_cfg_local(system)

    raw_data_file = os.path.join(testing_path, cfg_local["file_name"])
    reader_function = system_to_reader_fn_dict[system]

    raw_data = reader_function(raw_data_file, preload=True)
    crop = min(cfg_local["crop"], np.max(raw_data.times))
    if system == "eximia":
        crop -= 0.5 * (1.0 / raw_data.info["sfreq"])
    raw_data.crop(0, crop)
    raw_data.del_proj("all")
    with raw_data.info._unlock():
        raw_data.info["comps"] = []
    raw_data.drop_channels(cfg_local["removed_chan_names"])

    if system in ["EGI"]:
        raw_data._data[0:-1, :] = raw_data._data[0:-1, :] * 1e6

    if system in ["CNT"]:
        raw_data._data = raw_data._data * 1e6

    if system in ignore_channels_dict:
        raw_data.drop_channels(ignore_channels_dict[system])

    if system in drop_extra_chans_dict and drop_extra_chs:
        raw_data.drop_channels(drop_extra_chans_dict[system])

    return raw_data


def get_epochs(system):
    """Find, load and process the epoched data."""
    cfg_local = get_cfg_local(system)
    raw_data = get_raw_data(system)

    if cfg_local["eventtype"] in raw_data.ch_names:
        stim_channel = cfg_local["eventtype"]
    else:
        stim_channel = "STI 014"

    if system == "CNT":
        events, event_id = mne.events_from_annotations(raw_data)
        events[:, 0] = events[:, 0] + 1
    else:
        events = mne.find_events(raw_data, stim_channel=stim_channel, shortest_event=1)

        if isinstance(cfg_local["eventvalue"], np.ndarray):
            event_id = list(cfg_local["eventvalue"].astype("int"))
        else:
            event_id = [int(cfg_local["eventvalue"])]

        event_id = [id_ for id_ in event_id if id_ in events[:, 2]]

    epochs = mne.Epochs(
        raw_data,
        events=events,
        event_id=event_id,
        tmin=-cfg_local["prestim"],
        tmax=cfg_local["poststim"],
        baseline=None,
    )

    return epochs


def get_evoked(system):
    """Find, load and process the avg data."""
    epochs = get_epochs(system)
    return epochs.average(picks=np.arange(len(epochs.ch_names)))


def check_info_fields(expected, actual, has_raw_info):
    """
    Check if info fields are equal.

    Some fields are ignored.
    """
    expected = expected.info.copy()
    actual = actual.info.copy()

    if not has_raw_info:
        _remove_ignored_info_fields(expected)
        _remove_ignored_info_fields(actual)

    _remove_long_info_fields(expected)
    _remove_long_info_fields(actual)

    # we annoyingly have two ways of representing this, so just always use
    # an empty list here
    for obj in (expected, actual):
        if obj.get("dig", None) is None:
            with obj._unlock():
                obj["dig"] = []

    d = object_diff(actual, expected, allclose=True)
    assert d == "", d


def check_data(expected, actual, system):
    """Check data for equality."""
    decimal = 7
    if system in system_decimal_accuracy_dict:
        decimal = system_decimal_accuracy_dict[system]

    np.testing.assert_almost_equal(expected, actual, decimal=decimal)


def assert_warning_in_record(warning_message, warn_record):
    """Assert that a warning message is in the records."""
    all_messages = [str(w.message) for w in warn_record]
    assert warning_message in all_messages