junifer 0.0.5__py3-none-any.whl → 0.0.5.dev11__py3-none-any.whl

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -1,1089 +0,0 @@
-"""Provide tests for JuniferConnectivityMeasure class."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import copy
-import warnings
-from math import cosh, exp, log, sinh, sqrt
-from typing import TYPE_CHECKING, List, Optional, Tuple, Type, Union
-
-import numpy as np
-import pytest
-from nilearn.connectome.connectivity_matrices import sym_matrix_to_vec
-from nilearn.tests.test_signal import generate_signals
-from numpy.testing import assert_array_almost_equal, assert_array_equal
-from pandas import DataFrame
-from scipy import linalg
-from sklearn.covariance import EmpiricalCovariance, LedoitWolf
-
-from junifer.external.nilearn import JuniferConnectivityMeasure
-from junifer.external.nilearn.junifer_connectivity_measure import (
-    _check_spd,
-    _check_square,
-    _form_symmetric,
-    _geometric_mean,
-    _map_eigenvalues,
-    is_spd,
-)
-
-
-if TYPE_CHECKING:
-    from numpy.typing import ArrayLike
-    from sklearn.base import BaseEstimator
-
-# New BSD License
-
-# Copyright (c) The nilearn developers.
-# All rights reserved.
-
-
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-
-#   a. Redistributions of source code must retain the above copyright notice,
-#      this list of conditions and the following disclaimer.
-#   b. Redistributions in binary form must reproduce the above copyright
-#      notice, this list of conditions and the following disclaimer in the
-#      documentation and/or other materials provided with the distribution.
-#   c. Neither the name of the nilearn developers nor the names of
-#      its contributors may be used to endorse or promote products
-#      derived from this software without specific prior written
-#      permission.
-
-
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-# DAMAGE.
-
-
-CONNECTIVITY_KINDS = (
-    "covariance",
-    "correlation",
-    "tangent",
-    "precision",
-    "partial correlation",
-)
-
-N_FEATURES = 49
-
-N_SUBJECTS = 5
-
-
-def random_diagonal(
-    p: int,
-    v_min: float = 1.0,
-    v_max: float = 2.0,
-    random_state: Union[int, np.random.RandomState] = 0,
-) -> np.ndarray:
-    """Generate a random diagonal matrix.
-
-    Parameters
-    ----------
-    p : int
-        The first dimension of the array.
-    v_min : float, optional
-        Minimal element (default 1.).
-    v_max : float, optional
-        Maximal element (default 2.).
-    random_state : int or numpy.random.RandomState instance, optional
-        random number generator, or seed (default 0).
-
-    Returns
-    -------
-    numpy.ndarray of shape (p, p)
-        A diagonal matrix with the given minimal and maximal elements.
-
-    """
-    random_state = np.random.default_rng(random_state)
-    diag = random_state.random(p) * (v_max - v_min) + v_min
-    diag[diag == np.amax(diag)] = v_max
-    diag[diag == np.amin(diag)] = v_min
-    return np.diag(diag)
-
-
-def random_spd(
-    p: int,
-    eig_min: float,
-    cond: float,
-    random_state: Union[int, np.random.RandomState] = 0,
-) -> np.ndarray:
-    """Generate a random symmetric positive definite matrix.
-
-    Parameters
-    ----------
-    p : int
-        The first dimension of the array.
-    eig_min : float
-        Minimal eigenvalue.
-    cond : float
-        Condition number, defined as the ratio of the maximum eigenvalue to the
-        minimum one.
-    random_state : int or numpy.random.RandomState instance, optional
-        random number generator, or seed (default 0).
-
-    Returns
-    -------
-    numpy.ndarray of shape (p, p)
-        A symmetric positive definite matrix with the given minimal eigenvalue
-        and condition number.
-
-    """
-    rand_gen = np.random.default_rng(random_state)
-    mat = rand_gen.standard_normal((p, p))
-    unitary, _ = linalg.qr(mat)
-    diag = random_diagonal(
-        p, v_min=eig_min, v_max=cond * eig_min, random_state=random_state
-    )
-    return unitary.dot(diag).dot(unitary.T)
-
-
-def _signals(
-    n_subjects: int = N_SUBJECTS,
-) -> Tuple[List[np.ndarray], np.ndarray]:
-    """Generate signals and compute covariances while applying confounds.
-
-    Parameters
-    ----------
-    n_subjects : int
-        Number of subjects.
-
-    Returns
-    -------
-    tuple of list of np.ndarray and np.ndarray.
-
-    """
-    n_features = N_FEATURES
-    signals = []
-    for k in range(n_subjects):
-        n_samples = 200 + k
-        signal, _, confounds = generate_signals(
-            n_features=n_features,
-            n_confounds=5,
-            length=n_samples,
-            same_variance=False,
-        )
-        signals.append(signal)
-        signal -= signal.mean(axis=0)
-    return signals, confounds
-
-
-@pytest.fixture
-def signals() -> List[np.ndarray]:
-    """Return signals as list of np.ndarray."""
-    return _signals(N_SUBJECTS)[0]
-
-
-@pytest.fixture
-def signals_and_covariances(
-    cov_estimator: Union[LedoitWolf, EmpiricalCovariance]
-) -> Tuple[List[np.ndarray], List[float]]:
-    """Return signals and covariances for a covariance estimator.
-
-    Parameters
-    ----------
-    cov_estimator : LedoitWolf instance or EmpiricalCovariance instance
-        The covariance estimator.
-
-    Returns
-    -------
-    tuple of list of np.ndarray and list of float
-
-    """
-    signals, _ = _signals()
-    emp_covs = []
-    ledoit_covs = []
-    ledoit_estimator = LedoitWolf()
-    for k, signal_ in enumerate(signals):
-        n_samples = 200 + k
-        signal_ -= signal_.mean(axis=0)
-        emp_covs.append((signal_.T).dot(signal_) / n_samples)
-        ledoit_covs.append(ledoit_estimator.fit(signal_).covariance_)
-
-    if isinstance(cov_estimator, LedoitWolf):
-        return signals, ledoit_covs
-    elif isinstance(cov_estimator, EmpiricalCovariance):
-        return signals, emp_covs
-
-
-def test_check_square() -> None:
-    """Test square matrix assertion."""
-    non_square = np.ones((2, 3))
-    with pytest.raises(ValueError, match="Expected a square matrix"):
-        _check_square(non_square)
-
-
-@pytest.mark.parametrize(
-    "invalid_input",
-    [
-        np.array([[0, 1], [0, 0]]),  # non symmetric
-        np.ones((3, 3)),  # non SPD
-    ],
-)
-def test_check_spd(invalid_input: np.ndarray) -> None:
-    """Test matrix is symmetric positive definite.
-
-    Parameters
-    ----------
-    invalid_input : numpy.ndarray
-        The parametrized invalid input array.
-
-    """
-    with pytest.raises(
-        ValueError, match="Expected a symmetric positive definite matrix."
-    ):
-        _check_spd(invalid_input)
-
-
-def test_map_eigenvalues_on_exp_map() -> None:
-    """Test exponential eigenvalues mapping."""
-    sym = np.ones((2, 2))
-    sym_exp = exp(1.0) * np.array(
-        [[cosh(1.0), sinh(1.0)], [sinh(1.0), cosh(1.0)]]
-    )
-    assert_array_almost_equal(_map_eigenvalues(np.exp, sym), sym_exp)
-
-
-def test_map_eigenvalues_on_sqrt_map() -> None:
-    """Test square-root eigenvalues mapping."""
-    spd_sqrt = np.array(
-        [[2.0, -1.0, 0.0], [-1.0, 2.0, -1.0], [0.0, -1.0, 2.0]]
-    )
-    spd = spd_sqrt.dot(spd_sqrt)
-    assert_array_almost_equal(_map_eigenvalues(np.sqrt, spd), spd_sqrt)
-
-
-def test_map_eigenvalues_on_log_map() -> None:
-    """Test logarithmic eigenvalues mapping."""
-    spd = np.array([[1.25, 0.75], [0.75, 1.25]])
-    spd_log = np.array([[0.0, log(2.0)], [log(2.0), 0.0]])
-    assert_array_almost_equal(_map_eigenvalues(np.log, spd), spd_log)
-
-
-def test_geometric_mean_couple() -> None:
-    """Test geometric mean."""
-    n_features = 7
-    spd1 = np.ones((n_features, n_features))
-    spd1 = spd1.dot(spd1) + n_features * np.eye(n_features)
-    spd2 = np.tril(np.ones((n_features, n_features)))
-    spd2 = spd2.dot(spd2.T)
-    vals_spd2, vecs_spd2 = np.linalg.eigh(spd2)
-    spd2_sqrt = _form_symmetric(np.sqrt, vals_spd2, vecs_spd2)
-    spd2_inv_sqrt = _form_symmetric(np.sqrt, 1.0 / vals_spd2, vecs_spd2)
-    geo = spd2_sqrt.dot(
-        _map_eigenvalues(np.sqrt, spd2_inv_sqrt.dot(spd1).dot(spd2_inv_sqrt))
-    ).dot(spd2_sqrt)
-
-    assert_array_almost_equal(_geometric_mean([spd1, spd2]), geo)
-
-
-def test_geometric_mean_diagonal() -> None:
-    """Test geometric mean along diagonal."""
-    n_matrices = 20
-    n_features = 5
-    diags = []
-    for k in range(n_matrices):
-        diag = np.eye(n_features)
-        diag[k % n_features, k % n_features] = 1e4 + k
-        diag[(n_features - 1) // (k + 1), (n_features - 1) // (k + 1)] = (
-            k + 1
-        ) * 1e-4
-        diags.append(diag)
-    geo = np.prod(np.array(diags), axis=0) ** (1 / float(len(diags)))
-
-    assert_array_almost_equal(_geometric_mean(diags), geo)
-
-
-def test_geometric_mean_geodesic() -> None:
-    """Test geometric mean along geodesic."""
-    n_matrices = 10
-    n_features = 6
-    sym = np.arange(n_features) / np.linalg.norm(np.arange(n_features))
-    sym = sym * sym[:, np.newaxis]
-    times = np.arange(n_matrices)
-    non_singular = np.eye(n_features)
-    non_singular[1:3, 1:3] = np.array([[-1, -0.5], [-0.5, -1]])
-    spds = [
-        non_singular.dot(_map_eigenvalues(np.exp, time * sym)).dot(
-            non_singular.T
-        )
-        for time in times
-    ]
-    gmean = non_singular.dot(_map_eigenvalues(np.exp, times.mean() * sym)).dot(
-        non_singular.T
-    )
-    assert_array_almost_equal(_geometric_mean(spds), gmean)
-
-
-def test_geometric_mean_properties() -> None:
-    """Test geometric mean properties."""
-    n_matrices = 40
-    n_features = 15
-    spds = [
-        random_spd(n_features, eig_min=1.0, cond=10.0, random_state=0)
-        for _ in range(n_matrices)
-    ]
-    input_spds = copy.copy(spds)
-
-    gmean = _geometric_mean(spds)
-
-    # Generic
-    assert isinstance(spds, list)
-    for spd, input_spd in zip(spds, input_spds):
-        assert_array_equal(spd, input_spd)
-    assert is_spd(gmean, decimal=7)
-
-
-def random_non_singular(
-    p: int,
-    sing_min: float = 1.0,
-    sing_max: float = 2.0,
-    random_state: Union[int, np.random.RandomState] = 0,
-) -> np.ndarray:
-    """Generate a random nonsingular matrix.
-
-    Parameters
-    ----------
-    p : int
-        The first dimension of the array.
-    sing_min : float, optional
-        Minimal singular value (default 1.).
-    sing_max : float, optional
-        Maximal singular value (default 2.).
-    random_state : int or numpy.random.RandomState instance, optional
-        random number generator, or seed (default 0).
-
-    Returns
-    -------
-    numpy.ndarray of shape (p, p)
-        A nonsingular matrix with the given minimal and maximal singular
-        values.
-
-    """
-    rand_gen = np.random.default_rng(random_state)
-    diag = random_diagonal(
-        p, v_min=sing_min, v_max=sing_max, random_state=random_state
-    )
-    mat1 = rand_gen.standard_normal((p, p))
-    mat2 = rand_gen.standard_normal((p, p))
-    unitary1, _ = linalg.qr(mat1)
-    unitary2, _ = linalg.qr(mat2)
-    return unitary1.dot(diag).dot(unitary2.T)
-
-
-def test_geometric_mean_properties_check_invariance() -> None:
-    """Test geometric mean properties' invariance."""
-    n_matrices = 40
-    n_features = 15
-    spds = [
-        random_spd(n_features, eig_min=1.0, cond=10.0, random_state=0)
-        for _ in range(n_matrices)
-    ]
-
-    gmean = _geometric_mean(spds)
-
-    # Invariance under reordering
-    spds.reverse()
-    spds.insert(0, spds[1])
-    spds.pop(2)
-    assert_array_almost_equal(_geometric_mean(spds), gmean)
-
-    # Invariance under congruent transformation
-    non_singular = random_non_singular(n_features, random_state=0)
-    spds_cong = [non_singular.dot(spd).dot(non_singular.T) for spd in spds]
-    assert_array_almost_equal(
-        _geometric_mean(spds_cong), non_singular.dot(gmean).dot(non_singular.T)
-    )
-
-    # Invariance under inversion
-    spds_inv = [linalg.inv(spd) for spd in spds]
-    init = linalg.inv(np.mean(spds, axis=0))
-    assert_array_almost_equal(
-        _geometric_mean(spds_inv, init=init), linalg.inv(gmean)
-    )
-
-
-def grad_geometric_mean(
-    mats: "ArrayLike",
-    init: Optional["ArrayLike"] = None,
-    max_iter: int = 10,
-    tol: float = 1e-7,
-) -> List[float]:
-    """Compute gradient of geometric mean.
-
-    Return the norm of the covariant derivative at each iteration step
-    of geometric_mean. See its docstring for details.
-
-    Norm is intrinsic norm on the tangent space of the manifold of symmetric
-    positive definite matrices.
-
-    Parameters
-    ----------
-    mats : array-like object
-        Object that can be converted to np.ndarray.
-    init : array-like object or None, optional
-        Initialization matrix (default None).
-    max_iter : int, optional
-        Maximum iteration for gradient descent (default 10).
-    tol : float, optional
-        Tolerance for norm (default 1e-7).
-
-    Returns
-    -------
-    grad_norm : list of float
-        Norm of the covariant derivative in the tangent space at each step.
-
-    """
-    mats = np.array(mats)
-
-    # Initialization
-    gmean = init or np.mean(mats, axis=0)
-
-    norm_old = np.inf
-    step = 1.0
-    grad_norm = []
-    for _ in range(max_iter):
-        # Computation of the gradient
-        vals_gmean, vecs_gmean = linalg.eigh(gmean)
-        gmean_inv_sqrt = _form_symmetric(np.sqrt, 1.0 / vals_gmean, vecs_gmean)
-        whitened_mats = [
-            gmean_inv_sqrt.dot(mat).dot(gmean_inv_sqrt) for mat in mats
-        ]
-        logs = [_map_eigenvalues(np.log, w_mat) for w_mat in whitened_mats]
-
-        # Covariant derivative is - gmean.dot(logs_mean)
-        logs_mean = np.mean(logs, axis=0)
-
-        # Norm of the covariant derivative on
-        # the tangent space at point gmean
-        norm = np.linalg.norm(logs_mean)
-
-        # Update of the minimizer
-        vals_log, vecs_log = linalg.eigh(logs_mean)
-        gmean_sqrt = _form_symmetric(np.sqrt, vals_gmean, vecs_gmean)
-        gmean = gmean_sqrt.dot(
-            _form_symmetric(np.exp, vals_log * step, vecs_log)
-        ).dot(gmean_sqrt)
-
-        # Update the norm and the step size
-        if norm < norm_old:
-            norm_old = norm
-        if norm > norm_old:
-            step = step / 2.0
-            norm = norm_old
-
-        grad_norm.append(norm / gmean.size)
-        if tol is not None and norm / gmean.size < tol:
-            break
-
-    return grad_norm
-
-
-def test_geometric_mean_properties_check_gradient() -> None:
-    """Test geometric mean properties' gradient."""
-    n_matrices = 40
-    n_features = 15
-    spds = [
-        random_spd(n_features, eig_min=1.0, cond=10.0, random_state=0)
-        for _ in range(n_matrices)
-    ]
-
-    grad_norm = grad_geometric_mean(spds, tol=1e-20)
-
-    # Gradient norm is decreasing
-    difference = np.diff(grad_norm)
-    assert np.amax(difference) <= 0.0
-
-    # Check warning if gradient norm in the last step is less than
-    # tolerance
-    max_iter = 1
-    tol = 1e-20
-    with warnings.catch_warnings(record=True) as w:
-        warnings.simplefilter("always")
-        _geometric_mean(spds, max_iter=max_iter, tol=tol)
-        assert len(w) == 1
-
-    grad_norm = grad_geometric_mean(spds, max_iter=max_iter, tol=tol)
-
-    assert len(grad_norm) == max_iter
-    assert grad_norm[-1] > tol
-
-
-# proportion of badly conditioned matrices
-@pytest.mark.parametrize("p", [0.5, 1.0])
-def test_geometric_mean_properties_evaluate_convergence(p: float) -> None:
-    """Test geometric mean properties' convergence.
-
-    Parameters
-    ----------
-    p : float
-        Convergence criteria.
-
-    """
-    n_matrices = 40
-    n_features = 15
-    # A warning is printed if tolerance is not reached
-    spds = [
-        random_spd(n_features, eig_min=1e-2, cond=1e6, random_state=0)
-        for _ in range(int(p * n_matrices))
-    ]
-    spds.extend(
-        random_spd(n_features, eig_min=1.0, cond=10.0, random_state=0)
-        for _ in range(int(p * n_matrices), n_matrices)
-    )
-    max_iter = 30 if p < 1 else 60
-
-    _geometric_mean(spds, max_iter=max_iter, tol=1e-5)
-
-
-def test_geometric_mean_error_non_square_matrix() -> None:
-    """Test geometric mean error for non-square matrix."""
-    n_features = 5
-    mat1 = np.ones((n_features, n_features + 1))
-
-    with pytest.raises(ValueError, match="Expected a square matrix"):
-        _geometric_mean([mat1])
-
-
-def test_geometric_mean_error_input_matrices_have_different_shapes() -> None:
-    """Test geometric mean error for different input matrices shape."""
-    n_features = 5
-    mat1 = np.eye(n_features)
-    mat2 = np.ones((n_features + 1, n_features + 1))
-
-    with pytest.raises(
-        ValueError, match="Matrices are not of the same shape."
-    ):
-        _geometric_mean([mat1, mat2])
-
-
-def test_geometric_mean_error_non_spd_input_matrix() -> None:
-    """Test geometric mean error for non SPD input matrix."""
-    n_features = 5
-    mat2 = np.ones((n_features + 1, n_features + 1))
-
-    with pytest.raises(
-        ValueError, match="Expected a symmetric positive definite matrix."
-    ):
-        _geometric_mean([mat2])
-
-
-def test_connectivity_measure_errors():
-    """Test errors."""
-    # Raising error for input subjects not iterable
-    conn_measure = JuniferConnectivityMeasure()
-
-    with pytest.raises(
-        ValueError, match="'subjects' input argument must be an iterable"
-    ):
-        conn_measure.fit(1.0)
-
-    # input subjects not 2D numpy.ndarrays
-    with pytest.raises(
-        ValueError, match="Each subject must be 2D numpy.ndarray."
-    ):
-        conn_measure.fit([np.ones((100, 40)), np.ones((10,))])
-
-    # input subjects with different number of features
-    with pytest.raises(
-        ValueError, match="All subjects must have the same number of features."
-    ):
-        conn_measure.fit([np.ones((100, 40)), np.ones((100, 41))])
-
-    # fit_transform with a single subject and kind=tangent
-    conn_measure = JuniferConnectivityMeasure(kind="tangent")
-
-    with pytest.raises(
-        ValueError,
-        match="Tangent space parametrization .* only be .* group of subjects",
-    ):
-        conn_measure.fit_transform([np.ones((100, 40))])
-
-
-@pytest.mark.parametrize(
-    "cov_estimator", [EmpiricalCovariance(), LedoitWolf()]
-)
-@pytest.mark.parametrize("kind", CONNECTIVITY_KINDS)
-def test_connectivity_measure_generic(
-    kind: str,
-    cov_estimator: Type["BaseEstimator"],
-    signals_and_covariances: Tuple[List[np.ndarray], List[float]],
-) -> None:
-    """Test generic JuniferConnectivityMeasure.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    cov_estimator : estimator object
-        The parametrized covariance estimator.
-    signals_and_covariances : tuple
-        The signals and covariances for a covariance estimator.
-
-    """
-    signals, covs = signals_and_covariances
-
-    # Check outputs properties
-    input_covs = copy.copy(covs)
-    conn_measure = JuniferConnectivityMeasure(
-        kind=kind, cov_estimator=cov_estimator
-    )
-    connectivities = conn_measure.fit_transform(signals)
-
-    # Generic
-    assert isinstance(connectivities, np.ndarray)
-    assert len(connectivities) == len(covs)
-
-    for k, _ in enumerate(connectivities):
-        assert_array_equal(input_covs[k], covs[k])
-
-        assert is_spd(covs[k], decimal=7)
-
-
-def _assert_connectivity_tangent(connectivities, conn_measure, covs) -> None:
-    """Assert tangent connectivity matrix.
-
-    Check output value properties for tangent connectivity measure
-    that they have the expected relationship
-    to the input covariance matrices.
-
-    - the geometric mean of the eigenvalues
-      of the mean covariance matrix is positive-definite
-    - the whitening matrix (used to transform the data
-        also produces a positive-definite matrix
-
-    """
-    for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
-    ):
-        assert_array_almost_equal(
-            estimated_covariance_matrix, estimated_covariance_matrix.T
-        )
-
-        assert is_spd(conn_measure.whitening_, decimal=7)
-
-        gmean_sqrt = _map_eigenvalues(np.sqrt, conn_measure.mean_)
-        assert is_spd(gmean_sqrt, decimal=7)
-        assert_array_almost_equal(
-            conn_measure.whitening_.dot(gmean_sqrt),
-            np.eye(N_FEATURES),
-        )
-        assert_array_almost_equal(
-            gmean_sqrt.dot(
-                _map_eigenvalues(np.exp, estimated_covariance_matrix)
-            ).dot(gmean_sqrt),
-            true_covariance_matrix,
-        )
-
-
-def _assert_connectivity_precision(connectivities, covs) -> None:
-    """Assert precision connectivity matrix.
-
-    Estimated precision matrix:
-    - is positive definite
-    - its product with the true covariance matrix
-      is close to the identity matrix
-
-    """
-    for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
-    ):
-        assert is_spd(estimated_covariance_matrix, decimal=7)
-        assert_array_almost_equal(
-            estimated_covariance_matrix.dot(true_covariance_matrix),
-            np.eye(N_FEATURES),
-        )
-
-
-def _assert_connectivity_correlation(
-    connectivities, cov_estimator, covs
-) -> None:
-    """Assert correlation connectivity matrix.
-
-    Verify that the estimated covariance matrix:
-       - is symmetric and positive definite
-       - has values close to 1 on its diagonal
-
-    If the covariance estimator is EmpiricalCovariance,
-    the product of:
-        - the square root of the diagonal of the true covariance matrix
-        - the estimated covariance matrix
-        - the square root of the diagonal of the true covariance matrix
-
-    should be close to the true covariance matrix.
-
-    """
-    for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
-    ):
-        assert is_spd(estimated_covariance_matrix, decimal=7)
-
-        assert_array_almost_equal(
-            np.diag(estimated_covariance_matrix), np.ones(N_FEATURES)
-        )
-
-        if cov_estimator == EmpiricalCovariance():
-            # square root of the diagonal of the true covariance matrix
-            d = np.sqrt(np.diag(np.diag(true_covariance_matrix)))
-
-            assert_array_almost_equal(
-                d.dot(estimated_covariance_matrix).dot(d),
-                true_covariance_matrix,
-            )
-
-
-def _assert_connectivity_partial_correlation(connectivities, covs) -> None:
-    """Assert partial correlation connectivity matrix."""
-    for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
-    ):
-        precision_matrix = linalg.inv(true_covariance_matrix)
-
-        # square root of the diagonal elements of the precision matrix
-        d = np.sqrt(np.diag(np.diag(precision_matrix)))
-
-        # normalize the computed partial correlation matrix
-        # necessary to ensure that the diagonal elements
-        # of the partial correlation matrix are equal to 1
-        normalized_partial_correlation_matrix = d.dot(
-            estimated_covariance_matrix
-        ).dot(d)
-
-        # expected value
-        partial_corrlelation_matrix = -precision_matrix + 2 * np.diag(
-            np.diag(precision_matrix)
-        )
-
-        assert_array_almost_equal(
-            normalized_partial_correlation_matrix,
-            partial_corrlelation_matrix,
-        )
-
-
-@pytest.mark.parametrize(
-    "kind",
-    ["tangent", "precision", "correlation", "partial correlation"],
-)
-@pytest.mark.parametrize(
-    "cov_estimator", [EmpiricalCovariance(), LedoitWolf()]
-)
-def test_connectivity_measure_specific_for_each_kind(
-    kind: str,
-    cov_estimator: Type["BaseEstimator"],
-    signals_and_covariances: Tuple[List[np.ndarray], List[float]],
-) -> None:
-    """Test connectivity matrix for each kind.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    cov_estimator : estimator object
-        The parametrized covariance estimator.
-    signals_and_covariances : tuple
-        The signals and covariances for a covariance estimator.
-
-    """
-    signals, covs = signals_and_covariances
-
-    conn_measure = JuniferConnectivityMeasure(
-        kind=kind, cov_estimator=cov_estimator
-    )
-    connectivities = conn_measure.fit_transform(signals)
-
-    if kind == "tangent":
-        _assert_connectivity_tangent(connectivities, conn_measure, covs)
-    elif kind == "precision":
-        _assert_connectivity_precision(connectivities, covs)
-    elif kind == "correlation":
-        _assert_connectivity_correlation(connectivities, cov_estimator, covs)
-    elif kind == "partial correlation":
-        _assert_connectivity_partial_correlation(connectivities, covs)
-
-
-@pytest.mark.parametrize("kind", CONNECTIVITY_KINDS)
-def test_connectivity_measure_check_mean(
-    kind: str, signals: List[np.ndarray]
-) -> None:
-    """Test mean of connectivity matrix for each kind.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    conn_measure = JuniferConnectivityMeasure(kind=kind)
-    conn_measure.fit_transform(signals)
-
-    assert (conn_measure.mean_).shape == (N_FEATURES, N_FEATURES)
-
-    if kind != "tangent":
-        assert_array_almost_equal(
-            conn_measure.mean_,
-            np.mean(conn_measure.transform(signals), axis=0),
-        )
-
-    # Check that the mean isn't modified in transform
-    conn_measure = JuniferConnectivityMeasure(kind="covariance")
-    conn_measure.fit(signals[:1])
-    mean = conn_measure.mean_
-    conn_measure.transform(signals[1:])
-
-    assert_array_equal(mean, conn_measure.mean_)
-
-
-@pytest.mark.parametrize("kind", CONNECTIVITY_KINDS)
-def test_connectivity_measure_check_vectorization_option(
-    kind: str, signals: List[np.ndarray]
-) -> None:
-    """Test vectorization of connectivity matrix for each kind.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    conn_measure = JuniferConnectivityMeasure(kind=kind)
-    connectivities = conn_measure.fit_transform(signals)
-    conn_measure = JuniferConnectivityMeasure(vectorize=True, kind=kind)
-    vectorized_connectivities = conn_measure.fit_transform(signals)
-
-    assert_array_almost_equal(
-        vectorized_connectivities, sym_matrix_to_vec(connectivities)
-    )
-
-    # Check not fitted error
-    with pytest.raises(ValueError, match="has not been fitted. "):
-        JuniferConnectivityMeasure().inverse_transform(
-            vectorized_connectivities
-        )
-
-
-@pytest.mark.parametrize(
-    "kind",
-    ["covariance", "correlation", "precision", "partial correlation"],
-)
-def test_connectivity_measure_check_inverse_transformation(
-    kind: str, signals: List[np.ndarray]
-) -> None:
-    """Test inverse transform.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    # without vectorization: input matrices are returned with no change
-    conn_measure = JuniferConnectivityMeasure(kind=kind)
-    connectivities = conn_measure.fit_transform(signals)
-
-    assert_array_almost_equal(
-        conn_measure.inverse_transform(connectivities), connectivities
-    )
-
-    # with vectorization: input vectors are reshaped into matrices
-    # if diagonal has not been discarded
-    conn_measure = JuniferConnectivityMeasure(kind=kind, vectorize=True)
-    vectorized_connectivities = conn_measure.fit_transform(signals)
-
-    assert_array_almost_equal(
-        conn_measure.inverse_transform(vectorized_connectivities),
-        connectivities,
-    )
-
-
-@pytest.mark.parametrize(
-    "kind",
-    ["covariance", "correlation", "precision", "partial correlation"],
-)
-def test_connectivity_measure_check_inverse_transformation_discard_diag(
-    kind: str, signals: List[np.ndarray]
-) -> None:
-    """Test diagonal for inverse transform.
-
-    Parameters
-    ----------
-    kind : str
-        The parametrized connectivity matrix kind.
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    # with vectorization
-    connectivities = JuniferConnectivityMeasure(kind=kind).fit_transform(
-        signals
-    )
-    conn_measure = JuniferConnectivityMeasure(
-        kind=kind, vectorize=True, discard_diagonal=True
-    )
-    vectorized_connectivities = conn_measure.fit_transform(signals)
-
-    if kind in ["correlation", "partial correlation"]:
-        assert_array_almost_equal(
-            conn_measure.inverse_transform(vectorized_connectivities),
-            connectivities,
-        )
-    elif kind in ["covariance", "precision"]:
-        diagonal = np.array(
-            [np.diagonal(conn) / sqrt(2) for conn in connectivities]
-        )
-        inverse_transformed = conn_measure.inverse_transform(
-            vectorized_connectivities, diagonal=diagonal
-        )
-
-        assert_array_almost_equal(inverse_transformed, connectivities)
-        with pytest.raises(
-            ValueError, match="cannot reconstruct connectivity matrices"
-        ):
-            conn_measure.inverse_transform(vectorized_connectivities)
-
-
-def test_connectivity_measure_inverse_transform_tangent(
-    signals: List[np.ndarray],
-) -> None:
-    """Test that for 'tangent' kind, covariance matrices are reconstructed.
-
-    Parameters
-    ----------
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    # Without vectorization
-    tangent_measure = JuniferConnectivityMeasure(kind="tangent")
-    displacements = tangent_measure.fit_transform(signals)
-    covariances = JuniferConnectivityMeasure(kind="covariance").fit_transform(
-        signals
-    )
-
-    assert_array_almost_equal(
-        tangent_measure.inverse_transform(displacements), covariances
-    )
-
-    # with vectorization
-    # when diagonal has not been discarded
-    tangent_measure = JuniferConnectivityMeasure(
-        kind="tangent", vectorize=True
-    )
-    vectorized_displacements = tangent_measure.fit_transform(signals)
-
-    assert_array_almost_equal(
-        tangent_measure.inverse_transform(vectorized_displacements),
-        covariances,
-    )
-
-    # When diagonal has been discarded
-    tangent_measure = JuniferConnectivityMeasure(
-        kind="tangent", vectorize=True, discard_diagonal=True
-    )
-    vectorized_displacements = tangent_measure.fit_transform(signals)
-
-    diagonal = np.array(
-        [np.diagonal(matrix) / sqrt(2) for matrix in displacements]
-    )
-    inverse_transformed = tangent_measure.inverse_transform(
-        vectorized_displacements, diagonal=diagonal
-    )
-
-    assert_array_almost_equal(inverse_transformed, covariances)
-    with pytest.raises(
-        ValueError, match="cannot reconstruct connectivity matrices"
-    ):
-        tangent_measure.inverse_transform(vectorized_displacements)
-
-
-def test_confounds_connectivity_measure() -> None:
-    """Test confounds."""
-    n_subjects = 10
-
-    signals, confounds = _signals(n_subjects)
-
-    correlation_measure = JuniferConnectivityMeasure(
-        kind="correlation", vectorize=True
-    )
-
-    # Clean confounds on 10 subjects with confounds filtered to 10 subjects in
-    # length
-    cleaned_vectors = correlation_measure.fit_transform(
-        signals, confounds=confounds[:10]
-    )
-
-    zero_matrix = np.zeros((confounds.shape[1], cleaned_vectors.shape[1]))
-    assert_array_almost_equal(
-        np.dot(confounds[:10].T, cleaned_vectors), zero_matrix
-    )
-    assert isinstance(cleaned_vectors, np.ndarray)
-
-    # Confounds as pandas DataFrame
-    confounds_df = DataFrame(confounds[:10])
-    correlation_measure.fit_transform(signals, confounds=confounds_df)
-
-
-def test_confounds_connectivity_measure_errors() -> None:
-    """Test errors for dealing with confounds."""
-    # Generate signals and compute covariances and apply confounds while
-    # computing covariances
-    signals, confounds = _signals()
-
-    # Raising error for input confounds are not iterable
-    conn_measure = JuniferConnectivityMeasure(vectorize=True)
-    msg = "'confounds' input argument must be an iterable"
-
-    with pytest.raises(ValueError, match=msg):
-        conn_measure._check_input(X=signals, confounds=1.0)
-
-    with pytest.raises(ValueError, match=msg):
-        conn_measure._fit_transform(
-            X=signals, do_fit=True, do_transform=True, confounds=1.0
-        )
-
-    with pytest.raises(ValueError, match=msg):
-        conn_measure.fit_transform(X=signals, y=None, confounds=1.0)
-
-    # Raising error for input confounds are given but not vectorize=True
-    conn_measure = JuniferConnectivityMeasure(vectorize=False)
-    with pytest.raises(
-        ValueError, match="'confounds' are provided but vectorize=False"
-    ):
-        conn_measure.fit_transform(signals, None, confounds[:10])
-
-
-def test_connectivity_measure_standardize(
-    signals: List[np.ndarray],
-) -> None:
-    """Check warning is raised and then suppressed with setting standardize.
-
-    Parameters
-    ----------
-    signals : list of np.ndarray
-        The input signals.
-
-    """
-    match = "default strategy for standardize"
-
-    with pytest.warns(DeprecationWarning, match=match):
-        JuniferConnectivityMeasure(kind="correlation").fit_transform(signals)
-
-    with warnings.catch_warnings(record=True) as record:
-        JuniferConnectivityMeasure(
-            kind="correlation", standardize="zscore_sample"
-        ).fit_transform(signals)
-        for m in record:
-            assert match not in m.message