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

import hashlib
from copy import deepcopy
from functools import partial
from pathlib import Path

import numpy as np
import pytest
from numpy.testing import assert_allclose, assert_array_equal, assert_equal
from scipy.io import savemat

from mne import (
    Epochs,
    EpochsArray,
    EvokedArray,
    create_info,
    make_ad_hoc_cov,
    pick_channels,
    pick_types,
    read_events,
)
from mne._fiff.constants import FIFF, _ch_unit_mul_named
from mne.channels import (
    combine_channels,
    equalize_channels,
    find_ch_adjacency,
    get_builtin_ch_adjacencies,
    make_1020_channel_selections,
    read_ch_adjacency,
    read_custom_montage,
    rename_channels,
)
from mne.channels.channels import (
    _BUILTIN_CHANNEL_ADJACENCIES,
    _BuiltinChannelAdjacency,
    _ch_neighbor_adjacency,
    _compute_ch_adjacency,
)
from mne.datasets import testing
from mne.io import (
    RawArray,
    read_info,
    read_raw_bti,
    read_raw_ctf,
    read_raw_eeglab,
    read_raw_fif,
    read_raw_kit,
)
from mne.parallel import parallel_func
from mne.utils import requires_good_network

io_dir = Path(__file__).parents[2] / "io"
base_dir = io_dir / "tests" / "data"
raw_fname = base_dir / "test_raw.fif"
eve_fname = base_dir / "test-eve.fif"
fname_kit_157 = io_dir / "kit" / "tests" / "data" / "test.sqd"
testing_path = testing.data_path(download=False)


@pytest.mark.parametrize("preload", (True, False))
@pytest.mark.parametrize("proj", (True, False))
def test_reorder_channels(preload, proj):
    """Test reordering of channels."""
    raw = read_raw_fif(raw_fname).crop(0, 0.1).del_proj()
    if proj:  # a no-op but should test it
        raw._projector = np.eye(len(raw.ch_names))
    if preload:
        raw.load_data()
    # with .reorder_channels
    if proj and not preload:
        with pytest.raises(RuntimeError, match="load data"):
            raw.copy().reorder_channels(raw.ch_names[::-1])
        return
    raw_new = raw.copy().reorder_channels(raw.ch_names[::-1])
    assert raw_new.ch_names == raw.ch_names[::-1]
    if proj:
        assert_allclose(raw_new._projector, raw._projector, atol=1e-12)
    else:
        assert raw._projector is None
        assert raw_new._projector is None
    assert_array_equal(raw[:][0], raw_new[:][0][::-1])
    raw_new.reorder_channels(raw_new.ch_names[::-1][1:-1])
    raw.drop_channels(raw.ch_names[:1] + raw.ch_names[-1:])
    assert_array_equal(raw[:][0], raw_new[:][0])
    with pytest.raises(ValueError, match="repeated"):
        raw.reorder_channels(raw.ch_names[:1] + raw.ch_names[:1])
    # and with .pick
    reord = [1, 0] + list(range(2, len(raw.ch_names)))
    rev = np.argsort(reord)
    raw_new = raw.copy().pick(reord)
    assert_array_equal(raw[:][0], raw_new[rev][0])


def test_rename_channels():
    """Test rename channels."""
    info = read_info(raw_fname)
    # Error Tests
    # Test channel name exists in ch_names
    mapping = {"EEG 160": "EEG060"}
    pytest.raises(ValueError, rename_channels, info, mapping)
    # Test improper mapping configuration
    mapping = {"MEG 2641": 1.0}
    pytest.raises(TypeError, rename_channels, info, mapping)
    # Test non-unique mapping configuration
    mapping = {"MEG 2641": "MEG 2642"}
    pytest.raises(ValueError, rename_channels, info, mapping)
    # Test bad input
    pytest.raises(ValueError, rename_channels, info, 1.0)
    pytest.raises(ValueError, rename_channels, info, 1.0)

    # Test successful changes
    # Test ch_name and ch_names are changed
    info2 = deepcopy(info)  # for consistency at the start of each test
    info2["bads"] = ["EEG 060", "EOG 061"]
    mapping = {"EEG 060": "EEG060", "EOG 061": "EOG061"}
    rename_channels(info2, mapping)
    assert info2["chs"][374]["ch_name"] == "EEG060"
    assert info2["ch_names"][374] == "EEG060"
    assert info2["chs"][375]["ch_name"] == "EOG061"
    assert info2["ch_names"][375] == "EOG061"
    assert_array_equal(["EEG060", "EOG061"], info2["bads"])
    info2 = deepcopy(info)
    rename_channels(info2, lambda x: x.replace(" ", ""))
    assert info2["chs"][373]["ch_name"] == "EEG059"
    info2 = deepcopy(info)
    info2["bads"] = ["EEG 060", "EEG 060"]
    rename_channels(info2, mapping)
    assert_array_equal(["EEG060", "EEG060"], info2["bads"])

    # test that keys in Raw._orig_units will be renamed, too
    raw = read_raw_fif(raw_fname).crop(0, 0.1)
    old, new = "EEG 060", "New"
    raw._orig_units = {old: "V"}

    raw.rename_channels({old: new})
    assert old not in raw._orig_units
    assert new in raw._orig_units


def test_set_channel_types():
    """Test set_channel_types."""
    raw = read_raw_fif(raw_fname)
    # Error Tests
    # Test channel name exists in ch_names
    mapping = {"EEG 160": "EEG060"}
    with pytest.raises(ValueError, match=r"name \(EEG 160\) doesn't exist"):
        raw.set_channel_types(mapping)
    # Test change to illegal channel type
    mapping = {"EOG 061": "xxx"}
    with pytest.raises(ValueError, match="cannot change to this channel type"):
        raw.set_channel_types(mapping)
    # Test changing type if in proj
    mapping = {
        "EEG 057": "dbs",
        "EEG 058": "ecog",
        "EEG 059": "ecg",
        "EEG 060": "eog",
        "EOG 061": "seeg",
        "MEG 2441": "eeg",
        "MEG 2443": "eeg",
        "MEG 2442": "hbo",
        "EEG 001": "resp",
    }
    raw2 = read_raw_fif(raw_fname)
    raw2.info["bads"] = ["EEG 059", "EEG 060", "EOG 061"]
    with pytest.raises(RuntimeError, match='type .* in projector "PCA-v1"'):
        raw2.set_channel_types(mapping)  # has prj
    raw2.add_proj([], remove_existing=True)

    # Should raise
    with pytest.raises(ValueError, match="unit for channel.* has changed"):
        raw2.copy().set_channel_types(mapping, on_unit_change="raise")

    # Should warn
    with pytest.warns(RuntimeWarning, match="unit for channel.* has changed"):
        raw2.copy().set_channel_types(mapping)

    # Shouldn't warn
    raw2.set_channel_types(mapping, on_unit_change="ignore")

    info = raw2.info
    assert info["chs"][371]["ch_name"] == "EEG 057"
    assert info["chs"][371]["kind"] == FIFF.FIFFV_DBS_CH
    assert info["chs"][371]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][371]["coil_type"] == FIFF.FIFFV_COIL_EEG
    assert info["chs"][372]["ch_name"] == "EEG 058"
    assert info["chs"][372]["kind"] == FIFF.FIFFV_ECOG_CH
    assert info["chs"][372]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][372]["coil_type"] == FIFF.FIFFV_COIL_EEG
    assert info["chs"][373]["ch_name"] == "EEG 059"
    assert info["chs"][373]["kind"] == FIFF.FIFFV_ECG_CH
    assert info["chs"][373]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][373]["coil_type"] == FIFF.FIFFV_COIL_NONE
    assert info["chs"][374]["ch_name"] == "EEG 060"
    assert info["chs"][374]["kind"] == FIFF.FIFFV_EOG_CH
    assert info["chs"][374]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][374]["coil_type"] == FIFF.FIFFV_COIL_NONE
    assert info["chs"][375]["ch_name"] == "EOG 061"
    assert info["chs"][375]["kind"] == FIFF.FIFFV_SEEG_CH
    assert info["chs"][375]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][375]["coil_type"] == FIFF.FIFFV_COIL_EEG
    for idx in pick_channels(raw.ch_names, ["MEG 2441", "MEG 2443"], ordered=False):
        assert info["chs"][idx]["kind"] == FIFF.FIFFV_EEG_CH
        assert info["chs"][idx]["unit"] == FIFF.FIFF_UNIT_V
        assert info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_EEG
    idx = pick_channels(raw.ch_names, ["MEG 2442"])[0]
    assert info["chs"][idx]["kind"] == FIFF.FIFFV_FNIRS_CH
    assert info["chs"][idx]["unit"] == FIFF.FIFF_UNIT_MOL
    assert info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_FNIRS_HBO

    # resp channel type
    idx = pick_channels(raw.ch_names, ["EEG 001"])[0]
    assert info["chs"][idx]["kind"] == FIFF.FIFFV_RESP_CH
    assert info["chs"][idx]["unit"] == FIFF.FIFF_UNIT_V
    assert info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_NONE

    # Test meaningful error when setting channel type with unknown unit
    raw.info["chs"][0]["unit"] = 0.0
    ch_types = {raw.ch_names[0]: "misc"}
    pytest.raises(ValueError, raw.set_channel_types, ch_types)

    # test reset of channel units on unit change
    idx = raw.ch_names.index("EEG 003")
    raw.info["chs"][idx]["unit_mul"] = _ch_unit_mul_named[-6]
    assert raw.info["chs"][idx]["unit_mul"] == -6
    raw.set_channel_types({"EEG 003": "misc"}, on_unit_change="ignore")
    assert raw.info["chs"][idx]["unit_mul"] == 0


def test_get_builtin_ch_adjacencies():
    """Test retrieving the names of all built-in FieldTrip neighbors."""
    names = get_builtin_ch_adjacencies()
    assert names
    assert len(names) == len(set(names))  # no duplicates
    assert len(names) == len(_BUILTIN_CHANNEL_ADJACENCIES)

    names_and_descriptions = get_builtin_ch_adjacencies(descriptions=True)
    for name_and_description in names_and_descriptions:
        assert len(name_and_description) == 2


@pytest.mark.parametrize("name", get_builtin_ch_adjacencies())
@pytest.mark.parametrize("picks", ["pick-slice", "pick-arange", "pick-names"])
def test_read_builtin_ch_adjacency_picks(name, picks):
    """Test picking channel subsets when reading builtin adjacency matrices."""
    ch_adjacency, ch_names = read_ch_adjacency(name)
    assert_equal(ch_adjacency.shape[0], len(ch_names))
    subset_names = ch_names[::2]
    if picks == "pick-slice":
        subset = slice(None, None, 2)
    elif picks == "pick-arange":
        subset = np.arange(0, len(ch_names), 2)
    else:
        assert picks == "pick-names"
        subset = subset_names

    ch_subset_adjacency, ch_subset_names = read_ch_adjacency(name, subset)
    assert_array_equal(ch_subset_names, subset_names)


def test_read_ch_adjacency(tmp_path):
    """Test reading channel adjacency templates."""
    a = partial(np.array, dtype="<U7")
    # no pep8
    nbh = np.array(
        [
            [
                (["MEG0111"], [[a(["MEG0131"])]]),
                (["MEG0121"], [[a(["MEG0111"])], [a(["MEG0131"])]]),
                (["MEG0131"], [[a(["MEG0111"])], [a(["MEG0121"])]]),
            ]
        ],
        dtype=[("label", "O"), ("neighblabel", "O")],
    )
    mat = dict(neighbours=nbh)
    mat_fname = tmp_path / "test_mat.mat"
    savemat(mat_fname, mat, oned_as="row")

    ch_adjacency, ch_names = read_ch_adjacency(mat_fname)

    x = ch_adjacency
    assert_equal(x.shape[0], len(ch_names))
    assert_equal(x.shape, (3, 3))
    assert_equal(x[0, 1], False)
    assert_equal(x[0, 2], True)
    assert np.all(x.diagonal())
    pytest.raises(IndexError, read_ch_adjacency, mat_fname, [0, 3])
    ch_adjacency, ch_names = read_ch_adjacency(mat_fname, picks=[0, 2])
    assert_equal(ch_adjacency.shape[0], 2)
    assert_equal(len(ch_names), 2)

    ch_names = ["EEG01", "EEG02", "EEG03"]
    neighbors = [["EEG02"], ["EEG04"], ["EEG02"]]
    pytest.raises(ValueError, _ch_neighbor_adjacency, ch_names, neighbors)
    neighbors = [["EEG02"], ["EEG01", "EEG03"], ["EEG 02"]]
    pytest.raises(ValueError, _ch_neighbor_adjacency, ch_names[:2], neighbors)
    neighbors = [["EEG02"], "EEG01", ["EEG 02"]]
    pytest.raises(ValueError, _ch_neighbor_adjacency, ch_names, neighbors)
    adjacency, ch_names = read_ch_adjacency("neuromag306mag")
    assert_equal(adjacency.shape, (102, 102))
    assert_equal(len(ch_names), 102)
    pytest.raises(ValueError, read_ch_adjacency, "bananas!")

    # In EGI 256, E31 sensor has no neighbour
    a = partial(np.array)
    nbh = np.array(
        [
            [
                (["E31"], []),
                (["E1"], [[a(["E2"])], [a(["E3"])]]),
                (["E2"], [[a(["E1"])], [a(["E3"])]]),
                (["E3"], [[a(["E1"])], [a(["E2"])]]),
            ]
        ],
        dtype=[("label", "O"), ("neighblabel", "O")],
    )
    mat = dict(neighbours=nbh)
    mat_fname = tmp_path / "test_isolated_mat.mat"
    savemat(mat_fname, mat, oned_as="row")
    ch_adjacency, ch_names = read_ch_adjacency(mat_fname)
    x = ch_adjacency.todense()
    assert_equal(x.shape[0], len(ch_names))
    assert_equal(x.shape, (4, 4))
    assert np.all(x.diagonal())
    assert not np.any(x[0, 1:])
    assert not np.any(x[1:, 0])

    # Check for neighbours consistency. If a sensor is marked as a neighbour,
    # then it should also have its neighbours defined.
    a = partial(np.array)
    nbh = np.array(
        [
            [
                (["E31"], []),
                (["E1"], [[a(["E8"])], [a(["E3"])]]),
                (["E2"], [[a(["E1"])], [a(["E3"])]]),
                (["E3"], [[a(["E1"])], [a(["E2"])]]),
            ]
        ],
        dtype=[("label", "O"), ("neighblabel", "O")],
    )
    mat = dict(neighbours=nbh)
    mat_fname = tmp_path / "test_error_mat.mat"
    savemat(mat_fname, mat, oned_as="row")
    pytest.raises(ValueError, read_ch_adjacency, mat_fname)


def _download_ft_neighbors(target_dir):
    """Download the known neighbors from FieldTrip."""

    # The entire FT repository is larger than a GB, so we'll just download
    # the few files we need.
    def _download_one_ft_neighbor(neighbor: _BuiltinChannelAdjacency):
        # Log level setting must happen inside the job to work properly
        import pooch

        pooch.get_logger().setLevel("ERROR")  # reduce verbosity
        fname = neighbor.fname
        url = neighbor.source_url

        pooch.retrieve(
            url=url,
            known_hash=None,
            fname=fname,
            path=target_dir,
        )

    parallel, p_fun, _ = parallel_func(func=_download_one_ft_neighbor, n_jobs=-1)
    parallel(
        p_fun(neighbor)
        for neighbor in _BUILTIN_CHANNEL_ADJACENCIES
        if neighbor.source_url is not None
    )


@pytest.mark.slowtest
@requires_good_network
def test_adjacency_matches_ft(tmp_path):
    """Test correspondence of built-in adjacency matrices with FT repo."""
    builtin_neighbors_dir = Path(__file__).parents[1] / "data" / "neighbors"
    ft_neighbors_dir = tmp_path
    del tmp_path

    _download_ft_neighbors(target_dir=ft_neighbors_dir)

    for adj in _BUILTIN_CHANNEL_ADJACENCIES:
        fname = adj.fname
        if not (ft_neighbors_dir / fname).exists():
            continue  # only exists in MNE, not FT

        hash_mne = hashlib.sha256()
        hash_ft = hashlib.sha256()

        with open(builtin_neighbors_dir / fname, "rb") as f:
            data = f.read()
            hash_mne.update(data)

        with open(ft_neighbors_dir / fname, "rb") as f:
            data = f.read()
            hash_ft.update(data)

        if hash_mne.hexdigest() != hash_ft.hexdigest():
            raise ValueError(
                f"Hash mismatch between built-in and FieldTrip neighbors "
                f"for {fname}"
            )


def test_get_set_sensor_positions():
    """Test get/set functions for sensor positions."""
    raw1 = read_raw_fif(raw_fname)
    picks = pick_types(raw1.info, meg=False, eeg=True)
    pos = np.array([ch["loc"][:3] for ch in raw1.info["chs"]])[picks]
    raw_pos = raw1._get_channel_positions(picks=picks)
    assert_array_equal(raw_pos, pos)

    ch_name = raw1.info["ch_names"][13]
    pytest.raises(ValueError, raw1._set_channel_positions, [1, 2], ["name"])
    raw2 = read_raw_fif(raw_fname)
    raw2.info["chs"][13]["loc"][:3] = np.array([1, 2, 3])
    raw1._set_channel_positions([[1, 2, 3]], [ch_name])
    assert_array_equal(raw1.info["chs"][13]["loc"], raw2.info["chs"][13]["loc"])


@testing.requires_testing_data
def test_1020_selection():
    """Test making a 10/20 selection dict."""
    pytest.importorskip("pymatreader")
    raw_fname = testing_path / "EEGLAB" / "test_raw.set"
    loc_fname = testing_path / "EEGLAB" / "test_chans.locs"
    raw = read_raw_eeglab(raw_fname, preload=True)
    montage = read_custom_montage(loc_fname)
    raw = raw.rename_channels(dict(zip(raw.ch_names, montage.ch_names)))
    raw.set_montage(montage)

    for input_ in ("a_string", 100, raw, [1, 2]):
        pytest.raises(TypeError, make_1020_channel_selections, input_)

    sels = make_1020_channel_selections(raw.info)
    # are all frontal channels placed before all occipital channels?
    for name, picks in sels.items():
        fs = min(
            [ii for ii, pick in enumerate(picks) if raw.ch_names[pick].startswith("F")]
        )
        ps = max(
            [ii for ii, pick in enumerate(picks) if raw.ch_names[pick].startswith("O")]
        )
        assert fs > ps

    # are channels in the correct selection?
    fz_c3_c4 = [raw.ch_names.index(ch) for ch in ("Fz", "C3", "C4")]
    for channel, roi in zip(fz_c3_c4, ("Midline", "Left", "Right")):
        assert channel in sels[roi]

    # ensure returning channel names works as expected
    sels_names = make_1020_channel_selections(raw.info, return_ch_names=True)
    for selection, ch_names in sels_names.items():
        assert ch_names == [raw.ch_names[idx] for idx in sels[selection]]


@testing.requires_testing_data
def test_find_ch_adjacency():
    """Test computing the adjacency matrix."""
    raw = read_raw_fif(raw_fname)
    sizes = {"mag": 828, "grad": 1700, "eeg": 384}
    nchans = {"mag": 102, "grad": 204, "eeg": 60}
    for ch_type in ["mag", "grad", "eeg"]:
        conn, ch_names = find_ch_adjacency(raw.info, ch_type)
        # Silly test for checking the number of neighbors.
        assert_equal(conn.astype(bool).sum(), sizes[ch_type])
        assert_equal(len(ch_names), nchans[ch_type])
        kwargs = dict(exclude=())
        if ch_type in ("mag", "grad"):
            kwargs["meg"] = ch_type
        else:
            kwargs[ch_type] = True
        want_names = [raw.ch_names[pick] for pick in pick_types(raw.info, **kwargs)]
        assert ch_names == want_names
    pytest.raises(ValueError, find_ch_adjacency, raw.info, None)

    # Test computing the conn matrix with gradiometers.
    conn, ch_names = _compute_ch_adjacency(raw.info, "grad")
    assert_equal(conn.astype(bool).sum(), 2680)

    # Test ch_type=None.
    raw.pick(picks="mag")
    find_ch_adjacency(raw.info, None)

    bti_fname = testing_path / "BTi" / "erm_HFH" / "c,rfDC"
    bti_config_name = testing_path / "BTi" / "erm_HFH" / "config"
    raw = read_raw_bti(bti_fname, bti_config_name, None)
    _, ch_names = find_ch_adjacency(raw.info, "mag")
    assert "A1" in ch_names

    ctf_fname = testing_path / "CTF" / "testdata_ctf_short.ds"
    raw = read_raw_ctf(ctf_fname)
    _, ch_names = find_ch_adjacency(raw.info, "mag")
    assert "MLC11" in ch_names

    pytest.raises(ValueError, find_ch_adjacency, raw.info, "eog")

    raw_kit = read_raw_kit(fname_kit_157)
    neighb, ch_names = find_ch_adjacency(raw_kit.info, "mag")
    assert neighb.data.size == 1329
    assert ch_names[0] == "MEG 001"


@testing.requires_testing_data
def test_neuromag122_adjacency():
    """Test computing the adjacency matrix of Neuromag122-Data."""
    nm122_fname = testing_path / "misc" / "neuromag122_test_file-raw.fif"
    raw = read_raw_fif(nm122_fname)
    conn, ch_names = find_ch_adjacency(raw.info, "grad")
    assert conn.astype(bool).sum() == 1564
    assert len(ch_names) == 122
    assert conn.shape == (122, 122)


def test_drop_channels():
    """Test if dropping channels works with various arguments."""
    raw = read_raw_fif(raw_fname).crop(0, 0.1)
    raw.drop_channels(["MEG 0111"])  # list argument
    raw.drop_channels("MEG 0112")  # str argument
    raw.drop_channels({"MEG 0132", "MEG 0133"})  # set argument
    pytest.raises(ValueError, raw.drop_channels, ["MEG 0111", 5])
    pytest.raises(ValueError, raw.drop_channels, 5)  # must be list or str

    # by default, drop channels raises a ValueError if a channel can't be found
    m_chs = ["MEG 0111", "MEG blahblah"]
    with pytest.raises(ValueError, match="not found, nothing dropped"):
        raw.drop_channels(m_chs)
    # ...but this can be turned to a warning
    with pytest.warns(RuntimeWarning, match="not found, nothing dropped"):
        raw.drop_channels(m_chs, on_missing="warn")
    # ...or ignored altogether
    raw.drop_channels(m_chs, on_missing="ignore")
    with pytest.raises(ValueError, match="All channels"):
        raw.drop_channels(raw.ch_names)


def test_pick_channels():
    """Test if picking channels works with various arguments."""
    raw = read_raw_fif(raw_fname).crop(0, 0.1)

    # selected correctly 3 channels
    raw.pick(["MEG 0113", "MEG 0112", "MEG 0111"])
    assert len(raw.ch_names) == 3

    # selected correctly 3 channels and ignored 'meg', and emit warning
    with pytest.raises(ValueError, match="not present in the info"):
        raw.pick(["MEG 0113", "meg", "MEG 0112", "MEG 0111"])

    names_len = len(raw.ch_names)
    raw.pick(["all"])  # selected correctly all channels
    assert len(raw.ch_names) == names_len
    raw.pick("all")  # selected correctly all channels
    assert len(raw.ch_names) == names_len


def test_add_reference_channels():
    """Test if there is a new reference channel that consist of all zeros."""
    raw = read_raw_fif(raw_fname, preload=True)
    n_raw_original_channels = len(raw.ch_names)
    epochs = Epochs(raw, read_events(eve_fname))
    epochs.load_data()
    epochs_original_shape = epochs._data.shape[1]
    evoked = epochs.average()
    n_evoked_original_channels = len(evoked.ch_names)

    # Raw object
    raw.add_reference_channels(["REF 123"])
    assert len(raw.ch_names) == n_raw_original_channels + 1
    assert np.all(raw.get_data()[-1] == 0)

    # Epochs object
    epochs.add_reference_channels(["REF 123"])
    assert epochs._data.shape[1] == epochs_original_shape + 1

    # Evoked object
    evoked.add_reference_channels(["REF 123"])
    assert len(evoked.ch_names) == n_evoked_original_channels + 1
    assert np.all(evoked._data[-1] == 0)


def test_equalize_channels():
    """Test equalizing channels and their ordering."""
    # This function only tests the generic functionality of equalize_channels.
    # Additional tests for each instance type are included in the accompanying
    # test suite for each type.
    pytest.raises(
        TypeError,
        equalize_channels,
        ["foo", "bar"],
        match="Instances to be modified must be an instance of",
    )

    raw = RawArray(
        [[1.0], [2.0], [3.0], [4.0]],
        create_info(["CH1", "CH2", "CH3", "CH4"], sfreq=1.0),
    )
    epochs = EpochsArray(
        [[[1.0], [2.0], [3.0]]], create_info(["CH5", "CH2", "CH1"], sfreq=1.0)
    )
    cov = make_ad_hoc_cov(create_info(["CH2", "CH1", "CH8"], sfreq=1.0, ch_types="eeg"))
    cov["bads"] = ["CH1"]
    ave = EvokedArray([[1.0], [2.0]], create_info(["CH1", "CH2"], sfreq=1.0))

    raw2, epochs2, cov2, ave2 = equalize_channels([raw, epochs, cov, ave], copy=True)

    # The Raw object was the first in the list, so should have been used as
    # template for the ordering of the channels. No bad channels should have
    # been dropped.
    assert raw2.ch_names == ["CH1", "CH2"]
    assert_array_equal(raw2.get_data(), [[1.0], [2.0]])
    assert epochs2.ch_names == ["CH1", "CH2"]
    assert_array_equal(epochs2.get_data(copy=False), [[[3.0], [2.0]]])
    assert cov2.ch_names == ["CH1", "CH2"]
    assert cov2["bads"] == cov["bads"]
    assert ave2.ch_names == ave.ch_names
    assert_array_equal(ave2.data, ave.data)

    # All objects should have been copied, except for the Evoked object which
    # did not have to be touched.
    assert raw is not raw2
    assert epochs is not epochs2
    assert cov is not cov2
    assert ave is ave2

    # Test in-place operation
    raw2, epochs2 = equalize_channels([raw, epochs], copy=False)
    assert raw is raw2
    assert epochs is epochs2


def test_combine_channels():
    """Test channel combination on Raw, Epochs, and Evoked."""
    raw = read_raw_fif(raw_fname, preload=True)
    raw_ch_bad = read_raw_fif(raw_fname, preload=True)
    raw_ch_bad.info["bads"] = ["MEG 0113", "MEG 0112"]
    epochs = Epochs(raw, read_events(eve_fname))
    evoked = epochs.average()
    good = dict(foo=[0, 1, 3, 4], bar=[5, 2])  # good grad and mag

    # Test good cases
    combine_channels(raw, good)
    combined_epochs = combine_channels(epochs, good)
    assert_array_equal(combined_epochs.events, epochs.events)
    assert epochs.baseline == combined_epochs.baseline
    combined_evoked = combine_channels(evoked, good)
    assert evoked.baseline == combined_evoked.baseline
    combine_channels(raw, good, drop_bad=True)
    combine_channels(raw_ch_bad, good, drop_bad=True)

    # Test with stimulus channels
    combine_stim = combine_channels(raw, good, keep_stim=True)
    target_nchan = len(good) + len(pick_types(raw.info, meg=False, stim=True))
    assert combine_stim.info["nchan"] == target_nchan

    # Test results with one ROI
    good_single = dict(foo=[0, 1, 3, 4])  # good grad
    combined_mean = combine_channels(raw, good_single, method="mean")
    combined_median = combine_channels(raw, good_single, method="median")
    combined_std = combine_channels(raw, good_single, method="std")
    foo_mean = np.mean(raw.get_data()[good_single["foo"]], axis=0)
    foo_median = np.median(raw.get_data()[good_single["foo"]], axis=0)
    foo_std = np.std(raw.get_data()[good_single["foo"]], axis=0)
    assert_array_equal(combined_mean.get_data(), np.expand_dims(foo_mean, axis=0))
    assert_array_equal(combined_median.get_data(), np.expand_dims(foo_median, axis=0))
    assert_array_equal(combined_std.get_data(), np.expand_dims(foo_std, axis=0))

    # Test bad cases
    bad1 = dict(foo=[0, 376], bar=[5, 2])  # out of bounds
    bad2 = dict(foo=[0, 2], bar=[5, 2])  # type mix in same group
    with pytest.raises(ValueError, match='"method" must be a callable, or'):
        combine_channels(raw, good, method="bad_method")
    with pytest.raises(TypeError, match='"keep_stim" must be of type bool'):
        combine_channels(raw, good, keep_stim="bad_type")
    with pytest.raises(TypeError, match='"drop_bad" must be of type bool'):
        combine_channels(raw, good, drop_bad="bad_type")
    with pytest.raises(ValueError, match="Some channel indices are out of"):
        combine_channels(raw, bad1)
    with pytest.raises(ValueError, match="Cannot combine sensors of diff"):
        combine_channels(raw, bad2)

    # Test warnings
    raw_no_stim = read_raw_fif(raw_fname, preload=True)
    raw_no_stim.pick(picks="meg")
    warn1 = dict(foo=[375, 375], bar=[5, 2])  # same channel in same group
    warn2 = dict(foo=[375], bar=[5, 2])  # one channel (last channel)
    warn3 = dict(foo=[0, 4], bar=[5, 2])  # one good channel left
    with pytest.warns(RuntimeWarning, match="Could not find stimulus"):
        combine_channels(raw_no_stim, good, keep_stim=True)
    with pytest.warns(RuntimeWarning, match="Less than 2 channels") as record:
        combine_channels(raw, warn1)
        combine_channels(raw, warn2)
        combine_channels(raw_ch_bad, warn3, drop_bad=True)
    assert len(record) == 3


def test_combine_channels_metadata():
    """Test if metadata is correctly retained in combined object."""
    pd = pytest.importorskip("pandas")
    raw = read_raw_fif(raw_fname, preload=True)
    epochs = Epochs(raw, read_events(eve_fname), preload=True)

    metadata = pd.DataFrame({"A": np.arange(len(epochs)), "B": np.ones(len(epochs))})
    epochs.metadata = metadata

    good = dict(foo=[0, 1, 3, 4], bar=[5, 2])  # good grad and mag
    combined_epochs = combine_channels(epochs, good)
    pd.testing.assert_frame_equal(epochs.metadata, combined_epochs.metadata)