"""Test the mask-extracting utilities."""

import re
import warnings

import numpy as np
import pytest
from nibabel import Nifti1Image
from numpy.testing import assert_array_equal, assert_equal
from sklearn.preprocessing import StandardScaler

from nilearn._utils import data_gen
from nilearn._utils.testing import write_imgs_to_path
from nilearn.conftest import _affine_eye, _rng
from nilearn.exceptions import DimensionError, MaskWarning
from nilearn.image import get_data, high_variance_confounds
from nilearn.maskers import NiftiMasker
from nilearn.masking import (
    _unmask_3d,
    _unmask_4d,
    apply_mask,
    compute_background_mask,
    compute_brain_mask,
    compute_epi_mask,
    compute_multi_brain_mask,
    compute_multi_epi_mask,
    extrapolate_out_mask,
    intersect_masks,
    load_mask_img,
    unmask,
    unmask_from_to_3d_array,
)
from nilearn.surface.surface import SurfaceImage

_TEST_DIM_ERROR_MSG = (
    "Input data has incompatible dimensionality: "
    "Expected dimension is 3D and you provided "
    "a %s image"
)


def _simu_img():
    # Random confounds
    rng = _rng()
    conf = 2 + rng.standard_normal((100, 6))
    # Random 4D volume
    vol = 100 + 10 * rng.standard_normal((5, 5, 2, 100))
    img = Nifti1Image(vol, np.eye(4))
    # Create an nifti image with the data, and corresponding mask
    mask = Nifti1Image(np.ones([5, 5, 2]), np.eye(4))
    return img, mask, conf


def _cov_conf(tseries, conf):
    conf_n = StandardScaler().fit_transform(conf)
    _ = StandardScaler().fit_transform(tseries)
    cov_mat = np.dot(tseries.T, conf_n)
    return cov_mat


@pytest.mark.thread_unsafe
def test_load_mask_img_error_inputs(surf_img_2d, img_4d_ones_eye):
    """Check input validation of load_mask_img."""
    with pytest.raises(
        TypeError, match="a 3D/4D Niimg-like object or a SurfaceImage"
    ):
        load_mask_img(1)

    with pytest.raises(
        TypeError,
        match=r"Expected dimension is 3D and you provided a 4D image.",
    ):
        load_mask_img(img_4d_ones_eye)

    with pytest.raises(
        ValueError, match=r"Data for each part of .* should be 1D."
    ):
        load_mask_img(surf_img_2d())


@pytest.mark.thread_unsafe
def test_load_mask_img_surface(surf_mask_1d):
    """Check load_mask_img returns a boolean surface image \
    when SurfaceImage is used as input.
    """
    mask, _ = load_mask_img(surf_mask_1d)
    assert isinstance(mask, SurfaceImage)
    for hemi in mask.data.parts.values():
        assert hemi.dtype == "bool"


@pytest.mark.slow
def test_high_variance_confounds():
    """Test high_variance_confounds."""
    img, mask, conf = _simu_img()

    hv_confounds = high_variance_confounds(img)

    masker1 = NiftiMasker(
        standardize="zscore_sample",
        detrend=False,
        high_variance_confounds=False,
        mask_img=mask,
    ).fit()
    tseries1 = masker1.transform(img, confounds=[hv_confounds, conf])

    masker2 = NiftiMasker(
        standardize="zscore_sample",
        detrend=False,
        high_variance_confounds=True,
        mask_img=mask,
    ).fit()
    tseries2 = masker2.transform(img, confounds=conf)

    assert_array_equal(tseries1, tseries2)


def _confounds_regression(
    standardize_signal="zscore_sample", standardize_confounds=True
):
    img, mask, conf = _simu_img()

    masker = NiftiMasker(
        standardize=standardize_signal,
        standardize_confounds=standardize_confounds,
        detrend=False,
        mask_img=mask,
    ).fit()

    tseries = masker.transform(img, confounds=conf)

    if standardize_confounds:
        conf = StandardScaler(with_std=False).fit_transform(conf)

    cov_mat = _cov_conf(tseries, conf)

    return np.sum(np.abs(cov_mat))


@pytest.mark.parametrize(
    "standardize_signal, standardize_confounds, expected",
    [
        # Signal is not standardized
        (False, True, 10.0 * 10e-10),
        # Signal is z-scored with string arg
        ("zscore_sample", True, 10e-10),
        # Signal is psc standardized
        ("psc", True, 10.0 * 10e-10),
    ],
)
def test_confounds_standardization(
    standardize_signal, standardize_confounds, expected
):
    """Tests for confounds standardization.

    Explicit standardization of confounds

    See Issue #2584
    Code from @pbellec
    """
    assert (
        _confounds_regression(
            standardize_signal=standardize_signal,
            standardize_confounds=standardize_confounds,
        )
        < expected
    )


@pytest.mark.parametrize(
    "standardize_signal",
    [
        # Signal is not standardized
        False,
        # Signal is z-scored with string arg
        "zscore_sample",
        # Signal is psc standardized
        "psc",
    ],
)
def test_confounds_not_standardized(standardize_signal):
    """Tests for confounds standardization.

    Confounds are not standardized
    In this case, the regression should fail...

    See Issue #2584
    Code from @pbellec
    """
    # Signal is not standardized
    assert (
        _confounds_regression(
            standardize_signal=standardize_signal,
            standardize_confounds=False,
        )
        > 100
    )


@pytest.mark.parametrize(
    "fn",
    [
        compute_background_mask,
        compute_brain_mask,
        compute_epi_mask,
    ],
)
def test_compute_mask_error(fn):
    """Check that an empty list of images creates a meaningful error."""
    with pytest.raises(TypeError, match="Cannot concatenate empty objects"):
        fn([])


def test_compute_epi_mask(affine_eye):
    """Test compute_epi_mask."""
    mean_image = np.ones((9, 9, 3))
    mean_image[3:-2, 3:-2, :] = 10
    mean_image[5, 5, :] = 11
    mean_image = Nifti1Image(mean_image, affine_eye)

    mask1 = compute_epi_mask(mean_image, opening=False, verbose=1)
    mask2 = compute_epi_mask(mean_image, exclude_zeros=True, opening=False)

    # With an array with no zeros, exclude_zeros should not make
    # any difference
    assert_array_equal(get_data(mask1), get_data(mask2))

    # Check that padding with zeros does not change the extracted mask
    mean_image2 = np.zeros((30, 30, 3))
    mean_image2[3:12, 3:12, :] = get_data(mean_image)
    mean_image2 = Nifti1Image(mean_image2, affine_eye)

    mask3 = compute_epi_mask(mean_image2, exclude_zeros=True, opening=False)

    assert_array_equal(get_data(mask1), get_data(mask3)[3:12, 3:12])

    # However, without exclude_zeros, it does
    mask3 = compute_epi_mask(mean_image2, opening=False)
    assert not np.allclose(get_data(mask1), get_data(mask3)[3:12, 3:12])


def test_compute_epi_mask_errors_warnings(affine_eye):
    """Check that we get a ValueError for incorrect shape."""
    mean_image = np.ones((9, 9))
    mean_image[3:-3, 3:-3] = 10
    mean_image[5, 5] = 100
    mean_image = Nifti1Image(mean_image, affine_eye)

    with pytest.raises(
        ValueError,
        match=(
            "Computation expects 3D or 4D images, but 2 dimensions were given"
        ),
    ):
        compute_epi_mask(mean_image)

    # Check that we get a useful warning for empty masks
    mean_image = np.zeros((9, 9, 9))
    mean_image[0, 0, 1] = -1
    mean_image[0, 0, 0] = 1.2
    mean_image[0, 0, 2] = 1.1
    mean_image = Nifti1Image(mean_image, affine_eye)

    with pytest.warns(MaskWarning, match="Computed an empty mask"):
        compute_epi_mask(mean_image, exclude_zeros=True)


@pytest.mark.parametrize("value", (0, np.nan))
def test_compute_background_mask(affine_eye, value):
    """Test compute_background_mask."""
    mean_image = value * np.ones((9, 9, 9))
    mean_image[3:-3, 3:-3, 3:-3] = 1
    mask = mean_image == 1
    mean_image = Nifti1Image(mean_image, affine_eye)

    mask1 = compute_background_mask(mean_image, opening=False, verbose=1)

    assert_array_equal(get_data(mask1), mask.astype(np.int8))


def test_compute_background_mask_errors_warnings(affine_eye):
    """Check that we get a ValueError for incorrect shape."""
    mean_image = np.ones((9, 9))
    mean_image[3:-3, 3:-3] = 10
    mean_image[5, 5] = 100
    mean_image = Nifti1Image(mean_image, affine_eye)

    with pytest.raises(ValueError):
        compute_background_mask(mean_image)

    # Check that we get a useful warning for empty masks
    mean_image = np.zeros((9, 9, 9))
    mean_image = Nifti1Image(mean_image, affine_eye)

    with pytest.warns(MaskWarning, match="Computed an empty mask"):
        compute_background_mask(mean_image)


def test_compute_brain_mask():
    """Test compute_brain_mask."""
    img, _ = data_gen.generate_mni_space_img(res=8, random_state=0)

    brain_mask = compute_brain_mask(img, threshold=0.2, verbose=1)
    gm_mask = compute_brain_mask(img, threshold=0.2, mask_type="gm")
    wm_mask = compute_brain_mask(img, threshold=0.2, mask_type="wm")

    brain_data, gm_data, wm_data = map(
        get_data, (brain_mask, gm_mask, wm_mask)
    )

    # Check that whole-brain mask is non-empty
    assert (brain_data != 0).any()
    for subset in gm_data, wm_data:
        # Test that gm and wm masks are included in the whole-brain mask
        assert (
            np.logical_and(brain_data, subset) == subset.astype(bool)
        ).all()
        # Test that gm and wm masks are non-empty
        assert (subset != 0).any()

    # Test that gm and wm masks have empty intersection
    assert (np.logical_and(gm_data, wm_data) == 0).all()

    # Check that we get a useful warning for empty masks
    with pytest.warns(MaskWarning):
        compute_brain_mask(img, threshold=1)

    # Check that masks obtained from same FOV are the same
    img1, _ = data_gen.generate_mni_space_img(res=8, random_state=1)
    mask_img1 = compute_brain_mask(img1, verbose=1, threshold=0.2)

    assert (brain_data == get_data(mask_img1)).all()

    # Check that error is raised if mask type is unknown
    with pytest.raises(ValueError, match=r"Unknown mask type foo."):
        compute_brain_mask(img, verbose=1, mask_type="foo")


@pytest.mark.parametrize(
    "affine",
    [_affine_eye(), np.diag((1, 1, -1, 1)), np.diag((0.5, 1, 0.5, 1))],
)
@pytest.mark.parametrize("create_files", (False, True))
def test_apply_mask(tmp_path, create_files, affine):
    """Test smoothing of timeseries extraction."""
    # A delta in 3D
    # Standard masking
    data = np.zeros((40, 40, 40, 2))
    data[20, 20, 20] = 1
    data_img = Nifti1Image(data, affine)

    mask = np.ones((40, 40, 40))
    mask_img = Nifti1Image(mask, affine)

    filenames = write_imgs_to_path(
        data_img,
        mask_img,
        file_path=tmp_path,
        create_files=create_files,
    )

    series = apply_mask(filenames[0], filenames[1], smoothing_fwhm=9)

    series = np.reshape(series[0, :], (40, 40, 40))
    vmax = series.max()
    # We are expecting a full-width at half maximum of
    # 9mm/voxel_size:
    above_half_max = series > 0.5 * vmax
    for axis in (0, 1, 2):
        proj = np.any(
            np.any(np.rollaxis(above_half_max, axis=axis), axis=-1),
            axis=-1,
        )

        assert_equal(proj.sum(), 9 / np.abs(affine[axis, axis]))


def test_apply_mask_surface(surf_img_2d, surf_mask_1d):
    """Test apply_mask on surface."""
    length = 5
    series = apply_mask(surf_img_2d(length), surf_mask_1d)

    assert isinstance(series, np.ndarray)
    assert series.shape[0] == length


def test_apply_mask_nan(affine_eye):
    """Check that NaNs in the data do not propagate."""
    data = np.zeros((40, 40, 40, 2))
    data[20, 20, 20] = 1
    data[10, 10, 10] = np.nan
    data_img = Nifti1Image(data, affine_eye)

    mask = np.ones((40, 40, 40))
    mask_img = Nifti1Image(mask, affine_eye)

    series = apply_mask(data_img, mask_img, smoothing_fwhm=9)

    assert np.all(np.isfinite(series))


def test_apply_mask_errors(affine_eye, shape_3d_default):
    """Check errors for dimension."""
    data = np.zeros((40, 40, 40, 2))
    data[20, 20, 20] = 1
    data_img = Nifti1Image(data, affine_eye)

    mask = np.ones((40, 40, 40))
    mask_img = Nifti1Image(mask, affine_eye)

    full_mask = np.zeros((40, 40, 40))
    full_mask_img = Nifti1Image(full_mask, affine_eye)

    # veriy that 4D masks are rejected
    mask_img_4d = Nifti1Image(np.ones((40, 40, 40, 2)), affine_eye)

    with pytest.raises(DimensionError, match=_TEST_DIM_ERROR_MSG % "4D"):
        apply_mask(data_img, mask_img_4d)

    # Check that 3D data is accepted
    data_3d = Nifti1Image(
        np.arange(27, dtype="int32").reshape((3, 3, 3)), affine_eye
    )
    mask_data_3d = np.zeros((3, 3, 3))
    mask_data_3d[1, 1, 0] = True
    mask_data_3d[0, 1, 0] = True
    mask_data_3d[0, 1, 1] = True

    data_3d = apply_mask(data_3d, Nifti1Image(mask_data_3d, affine_eye))

    assert sorted(data_3d.tolist()) == [3.0, 4.0, 12.0]

    # Check data shape and affine
    with pytest.raises(DimensionError, match=_TEST_DIM_ERROR_MSG % "2D"):
        apply_mask(data_img, Nifti1Image(mask[20, ...], affine_eye))

    with pytest.raises(
        ValueError, match=r"5\]\]\n is different from img affine:\n\[\[1"
    ):
        apply_mask(data_img, Nifti1Image(mask, affine_eye / 2.0))

    wrong_shape_mask_data = np.zeros(shape_3d_default)
    wrong_shape_mask_data[1, 1, 0] = True
    wrong_shape_mask_data[0, 1, 0] = True
    wrong_shape_mask_data[0, 1, 1] = True

    with pytest.raises(
        ValueError,
        match=re.escape(
            "Mask shape: (7, 8, 9)\n is different from img shape:(40, 40, 40)"
        ),
    ):
        apply_mask(data_img, Nifti1Image(wrong_shape_mask_data, affine_eye))

    # Check that full masking raises error
    with pytest.raises(
        ValueError,
        match=r"The mask is invalid as it is empty: it masks all data.",
    ):
        apply_mask(data_img, full_mask_img)

    # Check weird values in data
    mask[10, 10, 10] = 2
    with pytest.raises(
        ValueError,
        match=r"Background of the mask must be represented with 0.",
    ):
        apply_mask(data_img, Nifti1Image(mask, affine_eye))

    mask[15, 15, 15] = 3
    with pytest.raises(
        ValueError, match=r"Given mask is not made of 2 values.*"
    ):
        apply_mask(Nifti1Image(data, affine_eye), mask_img)


def test_unmask_4d(rng, affine_eye, shape_4d_default):
    """Test unmask on 4D images."""
    data4D = rng.uniform(size=shape_4d_default)
    mask = rng.integers(2, size=shape_4d_default[:3], dtype="int32")
    mask_img = Nifti1Image(mask, affine_eye)
    mask = mask.astype(bool)

    masked4D = data4D[mask, :].T
    unmasked4D = data4D.copy()
    unmasked4D[np.logical_not(mask), :] = 0

    # 4D Test, test value ordering at the same time.
    t = get_data(unmask(masked4D, mask_img, order="C"))

    assert t.ndim == 4
    assert t.flags["C_CONTIGUOUS"]
    assert not t.flags["F_CONTIGUOUS"]
    assert_array_equal(t, unmasked4D)

    t = unmask([masked4D], mask_img, order="F")
    t = [get_data(t_) for t_ in t]

    assert isinstance(t, list)
    assert t[0].ndim == 4
    assert not t[0].flags["C_CONTIGUOUS"]
    assert t[0].flags["F_CONTIGUOUS"]
    assert_array_equal(t[0], unmasked4D)


@pytest.mark.parametrize("create_files", [False, True])
def test_unmask_3d_with_files(
    rng, affine_eye, tmp_path, create_files, shape_3d_default
):
    """Test unmask on 3D images.

    Check both with Nifti1Image and file.
    """
    data3D = rng.uniform(size=shape_3d_default)
    mask = rng.integers(2, size=shape_3d_default, dtype="int32")
    mask_img = Nifti1Image(mask, affine_eye)
    mask = mask.astype(bool)

    masked3D = data3D[mask]
    unmasked3D = data3D.copy()
    unmasked3D[np.logical_not(mask)] = 0

    filename = write_imgs_to_path(
        mask_img,
        file_path=tmp_path,
        create_files=create_files,
    )
    t = get_data(unmask(masked3D, filename, order="C"))

    assert t.ndim == 3
    assert t.flags["C_CONTIGUOUS"]
    assert not t.flags["F_CONTIGUOUS"]
    assert_array_equal(t, unmasked3D)

    t = unmask([masked3D], filename, order="F")
    t = [get_data(t_) for t_ in t]

    assert isinstance(t, list)
    assert t[0].ndim == 3
    assert not t[0].flags["C_CONTIGUOUS"]
    assert t[0].flags["F_CONTIGUOUS"]
    assert_array_equal(t[0], unmasked3D)


def test_unmask_errors(rng, affine_eye, shape_3d_default):
    """Test unmask errors."""
    # A delta in 3D
    mask = rng.integers(2, size=shape_3d_default, dtype="int32")
    mask_img = Nifti1Image(mask, affine_eye)
    mask = mask.astype(bool)

    # Error test: shape
    vec_1D = np.empty((500,), dtype=int)

    msg = "X must be of shape"
    with pytest.raises(TypeError, match=msg):
        unmask(vec_1D, mask_img)
    with pytest.raises(TypeError, match=msg):
        unmask([vec_1D], mask_img)

    vec_2D = np.empty((500, 500), dtype=np.float64)

    with pytest.raises(TypeError, match=msg):
        unmask(vec_2D, mask_img)

    with pytest.raises(TypeError, match=msg):
        unmask([vec_2D], mask_img)

    # Error test: mask type
    msg = "mask must be a boolean array"
    with pytest.raises(TypeError, match=msg):
        _unmask_3d(vec_1D, mask.astype(int))

    with pytest.raises(TypeError, match=msg):
        _unmask_4d(vec_2D, mask.astype(np.float64))

    # Transposed vector
    transposed_vector = np.ones((np.sum(mask), 1), dtype=bool)
    with pytest.raises(TypeError, match="X must be of shape"):
        unmask(transposed_vector, mask_img)


def test_unmask_error_shape(rng, affine_eye, shape_4d_default):
    """Test unmask errors shape between mask and image."""
    X = rng.standard_normal()
    mask_img = np.zeros(shape_4d_default, dtype=np.uint8)
    mask_img[rng.standard_normal(size=shape_4d_default) > 0.4] = 1
    n_features = (mask_img > 0).sum()
    mask_img = Nifti1Image(mask_img, affine_eye)
    n_samples = shape_4d_default[0]

    X = rng.standard_normal(size=(n_samples, n_features, 2))

    # 3D X (unmask should raise a DimensionError)
    with pytest.raises(DimensionError, match=_TEST_DIM_ERROR_MSG % "4D"):
        unmask(X, mask_img)

    X = rng.standard_normal(size=(n_samples, n_features))

    # Raises an error because the mask is 4D
    with pytest.raises(DimensionError, match=_TEST_DIM_ERROR_MSG % "4D"):
        unmask(X, mask_img)


@pytest.fixture
def img_2d_mask_bottom_right(affine_eye):
    """Return 3D nifti binary mask image with bottom right filled.

    +---+---+---+---+
    |   |   |   |   |
    +---+---+---+---+
    |   |   |   |   |
    +---+---+---+---+
    |   |   | X | X |
    +---+---+---+---+
    |   |   | X | X |
    +---+---+---+---+

    """
    mask_a = np.zeros((4, 4, 1), dtype=bool)
    mask_a[2:4, 2:4] = 1
    return Nifti1Image(mask_a.astype("int32"), affine_eye)


@pytest.fixture
def img_2d_mask_center(affine_eye):
    """Return 3D nifti binary mask image with center filled.

    +---+---+---+---+
    |   |   |   |   |
    +---+---+---+---+
    |   | X | X |   |
    +---+---+---+---+
    |   | X | X |   |
    +---+---+---+---+
    |   |   |   |   |
    +---+---+---+---+

    """
    mask_b = np.zeros((4, 4, 1), dtype=bool)
    mask_b[1:3, 1:3] = 1
    return Nifti1Image(mask_b.astype("int32"), affine_eye)


@pytest.mark.thread_unsafe
@pytest.mark.parametrize("create_files", (False, True))
def test_intersect_masks_filename(
    tmp_path, img_2d_mask_bottom_right, img_2d_mask_center, create_files
):
    """Test the intersect_masks function on files."""
    filenames = write_imgs_to_path(
        img_2d_mask_bottom_right,
        img_2d_mask_center,
        file_path=tmp_path,
        create_files=create_files,
    )
    mask_ab = np.zeros((4, 4, 1), dtype=bool)
    mask_ab[2, 2] = 1
    mask_ab_ = intersect_masks(filenames, threshold=1.0)

    assert_array_equal(mask_ab, get_data(mask_ab_))


def test_intersect_masks_f8(img_2d_mask_bottom_right, img_2d_mask_center):
    """Test intersect mask images with '>f8'.

    This function uses largest_connected_component
    to check if intersect_masks passes
    with connected=True (which is by default)
    """
    mask_a_img_change_dtype = Nifti1Image(
        get_data(img_2d_mask_bottom_right).astype(">f8"),
        affine=img_2d_mask_bottom_right.affine,
    )
    mask_b_img_change_dtype = Nifti1Image(
        get_data(img_2d_mask_center).astype(">f8"),
        affine=img_2d_mask_center.affine,
    )
    mask_ab_change_type = intersect_masks(
        [mask_a_img_change_dtype, mask_b_img_change_dtype], threshold=1.0
    )

    mask_ab = np.zeros((4, 4, 1), dtype=bool)
    mask_ab[2, 2] = 1
    assert_array_equal(mask_ab, get_data(mask_ab_change_type))


@pytest.mark.slow
def test_intersect_masks(
    affine_eye, img_2d_mask_bottom_right, img_2d_mask_center
):
    """Test the intersect_masks function."""
    mask_c = np.zeros((4, 4, 1), dtype=bool)
    mask_c[:, 2] = 1
    mask_c[0, 0] = 1
    mask_c_img = Nifti1Image(mask_c.astype("int32"), affine_eye)

    # +---+---+---+---+
    # | X |   | X |   |
    # +---+---+---+---+
    # |   |   | X |   |
    # +---+---+---+---+
    # |   |   | X |   |
    # +---+---+---+---+
    # |   |   | X |   |
    # +---+---+---+---+

    mask_a = np.zeros((4, 4, 1), dtype=bool)
    mask_a[2:4, 2:4] = 1

    mask_b = np.zeros((4, 4, 1), dtype=bool)
    mask_b[1:3, 1:3] = 1

    mask_abc = mask_a + mask_b + mask_c
    mask_abc_ = intersect_masks(
        [img_2d_mask_bottom_right, img_2d_mask_center, mask_c_img],
        threshold=0.0,
        connected=False,
    )

    assert_array_equal(mask_abc, get_data(mask_abc_))

    mask_abc[0, 0] = 0
    mask_abc_ = intersect_masks(
        [img_2d_mask_bottom_right, img_2d_mask_center, mask_c_img],
        threshold=0.0,
    )

    assert_array_equal(mask_abc, get_data(mask_abc_))

    mask_abc = np.zeros((4, 4, 1), dtype=bool)
    mask_abc[2, 2] = 1
    mask_abc_ = intersect_masks(
        [img_2d_mask_bottom_right, img_2d_mask_center, mask_c_img],
        threshold=1.0,
    )

    assert_array_equal(mask_abc, get_data(mask_abc_))

    mask_abc[1, 2] = 1
    mask_abc[3, 2] = 1
    mask_abc_ = intersect_masks(
        [img_2d_mask_bottom_right, img_2d_mask_center, mask_c_img]
    )

    assert_array_equal(mask_abc, get_data(mask_abc_))


def test_intersect_masks_errors(affine_eye, surf_img_1d):
    """Test errors of intersect_masks."""
    affine_b = affine_eye * 2

    shape_a = (2, 2, 2)
    shape_b = (3, 3, 3)

    shape_a_affine_a = Nifti1Image(np.ones(shape_a), affine_eye)
    shape_a_affine_b = Nifti1Image(np.ones(shape_a), affine_b)
    shape_b_affine_a = Nifti1Image(np.ones(shape_b), affine_eye)
    shape_b_affine_b = Nifti1Image(np.ones(shape_b), affine_b)

    with pytest.raises(ValueError, match="No mask provided for intersection"):
        intersect_masks([])
    with pytest.raises(
        ValueError, match="The threshold should be greater than 0"
    ):
        intersect_masks([shape_a_affine_a, shape_a_affine_a], threshold=-1)
    with pytest.raises(
        ValueError, match="The threshold should be smaller than 1"
    ):
        intersect_masks([shape_a_affine_a, shape_a_affine_a], threshold=2)
    with pytest.raises(
        TypeError, match=r"All masks must be a 3D Niimg-like object."
    ):
        intersect_masks([shape_a_affine_a, surf_img_1d])
    with pytest.raises(
        ValueError, match="Following field of view errors were detected"
    ):
        intersect_masks(
            [
                shape_a_affine_a,
                shape_a_affine_b,
                shape_b_affine_a,
                shape_b_affine_b,
            ]
        )


def test_compute_multi_epi_mask(affine_eye):
    """Test resampling done with compute_multi_epi_mask."""
    mask_a = np.zeros((4, 4, 1), dtype=bool)
    mask_a[2:4, 2:4] = 1
    mask_a_img = Nifti1Image(mask_a.astype("uint8"), affine_eye)

    mask_b = np.zeros((8, 8, 1), dtype=bool)
    mask_b[2:6, 2:6] = 1
    mask_b_img = Nifti1Image(mask_b.astype("uint8"), affine_eye / 2.0)

    with warnings.catch_warnings():
        warnings.simplefilter("ignore", MaskWarning)
        with pytest.raises(
            ValueError, match="cannot convert float NaN to integer"
        ):
            compute_multi_epi_mask([mask_a_img, mask_b_img])

    mask_ab = np.zeros((4, 4, 1), dtype=bool)
    mask_ab[2, 2] = 1
    mask_ab_ = compute_multi_epi_mask(
        [mask_a_img, mask_b_img],
        threshold=1.0,
        opening=0,
        target_affine=affine_eye,
        target_shape=(4, 4, 1),
        verbose=1,
    )

    assert_array_equal(mask_ab, get_data(mask_ab_))


@pytest.mark.slow
def test_compute_multi_brain_mask_error():
    """Check error raised if images with different shapes given as input."""
    imgs = [
        data_gen.generate_mni_space_img(res=8)[0],
        data_gen.generate_mni_space_img(res=12)[0],
    ]
    with pytest.raises(
        ValueError,
        match=r"Field of view of image #1 is different from reference FOV.",
    ):
        compute_multi_brain_mask(imgs)


@pytest.mark.slow
def test_compute_multi_brain_mask():
    """Check results are the same if affine is the same."""
    imgs1 = [
        data_gen.generate_mni_space_img(res=9, random_state=0)[0],
        data_gen.generate_mni_space_img(res=9, random_state=1)[0],
    ]
    imgs2 = [
        data_gen.generate_mni_space_img(res=9, random_state=2)[0],
        data_gen.generate_mni_space_img(res=9, random_state=3)[0],
    ]
    mask1 = compute_multi_brain_mask(imgs1, threshold=0.2, verbose=1)
    mask2 = compute_multi_brain_mask(imgs2, threshold=0.2)

    assert_array_equal(get_data(mask1), get_data(mask2))


def test_nifti_masker_empty_mask_warning(affine_eye):
    """Check error is raised when mask_strategy="epi" masks all data."""
    X = Nifti1Image(np.ones((2, 2, 2, 5)), affine_eye)
    with pytest.raises(
        ValueError,
        match="The mask is invalid as it is empty: it masks all data",
    ):
        NiftiMasker(mask_strategy="epi").fit_transform(X)


def test_unmask_list(rng, shape_3d_default, affine_eye):
    """Test unmask on list input.

    Results should be equivalent to array input.
    """
    mask_data = rng.uniform(size=shape_3d_default) < 0.5
    mask_img = Nifti1Image(mask_data.astype(np.uint8), affine_eye)

    a = unmask(mask_data[mask_data], mask_img)
    b = unmask(mask_data[mask_data].tolist(), mask_img)  # shouldn't crash

    assert_array_equal(get_data(a), get_data(b))


def test_extrapolate_out_mask():
    """Test extrapolate_out_mask."""
    # Input data:
    initial_data = np.zeros((5, 5, 5))
    initial_data[1, 2, 2] = 1
    initial_data[2, 1, 2] = 2
    initial_data[2, 2, 1] = 3
    initial_data[3, 2, 2] = 4
    initial_data[2, 3, 2] = 5
    initial_data[2, 2, 3] = 6
    initial_mask = initial_data.copy() != 0

    # Expected result
    target_data = np.array(
        [
            [
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 1.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
            ],
            [
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 1.5, 0.0, 0.0],
                [0.0, 2.0, 1.0, 3.5, 0.0],
                [0.0, 0.0, 3.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
            ],
            [
                [0.0, 0.0, 2.0, 0.0, 0.0],
                [0.0, 2.5, 2.0, 4.0, 0.0],
                [3.0, 3.0, 3.5, 6.0, 6.0],
                [0.0, 4.0, 5.0, 5.5, 0.0],
                [0.0, 0.0, 5.0, 0.0, 0.0],
            ],
            [
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 3.0, 0.0, 0.0],
                [0.0, 3.5, 4.0, 5.0, 0.0],
                [0.0, 0.0, 4.5, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
            ],
            [
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 4.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
                [0.0, 0.0, 0.0, 0.0, 0.0],
            ],
        ]
    )
    target_mask = np.array(
        [
            [
                [False, False, False, False, False],
                [False, False, False, False, False],
                [False, False, True, False, False],
                [False, False, False, False, False],
                [False, False, False, False, False],
            ],
            [
                [False, False, False, False, False],
                [False, False, True, False, False],
                [False, True, True, True, False],
                [False, False, True, False, False],
                [False, False, False, False, False],
            ],
            [
                [False, False, True, False, False],
                [False, True, True, True, False],
                [True, True, True, True, True],
                [False, True, True, True, False],
                [False, False, True, False, False],
            ],
            [
                [False, False, False, False, False],
                [False, False, True, False, False],
                [False, True, True, True, False],
                [False, False, True, False, False],
                [False, False, False, False, False],
            ],
            [
                [False, False, False, False, False],
                [False, False, False, False, False],
                [False, False, True, False, False],
                [False, False, False, False, False],
                [False, False, False, False, False],
            ],
        ]
    )

    # Test:
    extrapolated_data, extrapolated_mask = extrapolate_out_mask(
        initial_data, initial_mask, iterations=1
    )

    assert_array_equal(extrapolated_data, target_data)
    assert_array_equal(extrapolated_mask, target_mask)


@pytest.mark.parametrize("ndim", range(4))
def test_unmask_from_to_3d_array(rng, ndim):
    """Test unmask_from_to_3d_array."""
    size = 5
    shape = [size] * ndim
    mask = np.zeros(shape).astype(bool)
    mask[rng.uniform(size=shape) > 0.8] = 1
    support = rng.standard_normal(size=mask.sum())

    full = unmask_from_to_3d_array(support, mask)

    assert_array_equal(full.shape, shape)
    assert_array_equal(full[mask], support)
