docs/changes/newsfragments/348.change

@@ -0,0 +1 @@
+For :class:`.CrossParcellationFC`, ``aggregation_method`` and ``correlation_method`` have been renamed to ``agg_method`` and ``corr_method`` respectively and ``agg_method_params`` has been added; for ``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`, :class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon Mandal`_

docs/changes/newsfragments/348.enh

@@ -0,0 +1 @@
+``FunctionalConnectivity``-family Markers now use :class:`sklearn.covariance.EmpiricalCovariance` as the default covariance estimator and ``correlation`` as the default connecivity matrix kind by `Synchon Mandal`_

docs/changes/newsfragments/348.feature

@@ -0,0 +1 @@
+Introduce :class:`.JuniferConnectivityMeasure` for customising functional connectivity matrix kinds and measurements by `Synchon Mandal`_

docs/conf.py

@@ -170,6 +170,7 @@ numpydoc_xref_ignore = {
     "Engine",
     "positive",
     "negative",
+    "estimator",
 }
 # numpydoc_validation_checks = {
 #     "all",

ignore_words.txt

@@ -5,3 +5,4 @@ sepulcre
 arange
 sinc
 whit
+amin

junifer/external/nilearn/__init__.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 from .junifer_nifti_spheres_masker import JuniferNiftiSpheresMasker
+from .junifer_connectivity_measure import JuniferConnectivityMeasure
 
 
-__all__ = ["JuniferNiftiSpheresMasker"]
+__all__ = ["JuniferNiftiSpheresMasker", "JuniferConnectivityMeasure"]

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -0,0 +1,483 @@
+"""Provide JuniferConnectivityMeasure class."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import Callable, List, Optional
+
+import numpy as np
+from nilearn import signal
+from nilearn.connectome import (
+    ConnectivityMeasure,
+    cov_to_corr,
+    prec_to_partial,
+    sym_matrix_to_vec,
+)
+from scipy import linalg
+from sklearn.base import clone
+from sklearn.covariance import EmpiricalCovariance
+
+from ...utils import logger, raise_error, warn_with_log
+
+
+__all__ = ["JuniferConnectivityMeasure"]
+
+
+DEFAULT_COV_ESTIMATOR = EmpiricalCovariance(store_precision=False)
+
+
+# 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.
+
+
+def _check_square(matrix: np.ndarray) -> None:
+    """Raise a ValueError if the input matrix is square.
+
+    Parameters
+    ----------
+    matrix : numpy.ndarray
+        Input array.
+
+    Raises
+    ------
+    ValueError
+        If ``matrix`` is not a square matrix.
+
+    """
+    if matrix.ndim != 2 or (matrix.shape[0] != matrix.shape[-1]):
+        raise_error(
+            f"Expected a square matrix, got array of shape {matrix.shape}."
+        )
+
+
+def is_spd(M: np.ndarray, decimal: int = 15) -> bool:  # noqa: N803
+    """Check that input matrix is symmetric positive definite.
+
+    ``M`` must be symmetric down to specified ``decimal`` places.
+    The check is performed by checking that all eigenvalues are positive.
+
+    Parameters
+    ----------
+    M : numpy.ndarray
+        Input matrix to check for symmetric positive definite.
+    decimal : int, optional
+        Decimal places to check (default 15).
+
+    Returns
+    -------
+    bool
+        True if matrix is symmetric positive definite, False otherwise.
+
+    """
+    if not np.allclose(M, M.T, atol=0, rtol=10**-decimal):
+        logger.debug(f"matrix not symmetric to {decimal:d} decimals")
+        return False
+    eigvalsh = np.linalg.eigvalsh(M)
+    ispd = eigvalsh.min() > 0
+    if not ispd:
+        logger.debug(f"matrix has a negative eigenvalue: {eigvalsh.min():.3f}")
+    return ispd
+
+
+def _check_spd(matrix: np.ndarray) -> None:
+    """Check ``matrix`` is symmetric positive definite.
+
+    Parameters
+    ----------
+    matrix : numpy.ndarray
+        Input array.
+
+    Raises
+    ------
+    ValueError
+        If the input matrix is not symmetric positive definite.
+
+    """
+    if not is_spd(matrix, decimal=7):
+        raise_error("Expected a symmetric positive definite matrix.")
+
+
+def _form_symmetric(
+    function: Callable[[np.ndarray], np.ndarray],
+    eigenvalues: np.ndarray,
+    eigenvectors: np.ndarray,
+) -> np.ndarray:
+    """Return the symmetric matrix.
+
+    Apply ``function`` to ``eigenvalues``, construct symmetric matrix with it
+    and ``eigenvectors`` and return the constructed symmetric matrix.
+
+    Parameters
+    ----------
+    function : callable (function numpy.ndarray -> numpy.ndarray)
+        The transform to apply to the eigenvalues.
+    eigenvalues : numpy.ndarray of shape (n_features, )
+        Input argument of the function.
+    eigenvectors : numpy.ndarray of shape (n_features, n_features)
+        Unitary matrix.
+
+    Returns
+    -------
+    numpy.ndarray of shape (n_features, n_features)
+        The symmetric matrix obtained after transforming the eigenvalues, while
+        keeping the same eigenvectors.
+
+    """
+    return np.dot(eigenvectors * function(eigenvalues), eigenvectors.T)
+
+
+def _map_eigenvalues(
+    function: Callable[[np.ndarray], np.ndarray], symmetric: np.ndarray
+) -> np.ndarray:
+    """Matrix function, for real symmetric matrices.
+
+    The function is applied to the eigenvalues of ``symmetric``.
+
+    Parameters
+    ----------
+    function : callable (function numpy.ndarray -> numpy.ndarray)
+        The transform to apply to the eigenvalues.
+    symmetric : numpy.ndarray of shape (n_features, n_features)
+        The input symmetric matrix.
+
+    Returns
+    -------
+    numpy.ndarray of shape (n_features, n_features)
+        The new symmetric matrix obtained after transforming the eigenvalues,
+        while keeping the same eigenvectors.
+
+    Notes
+    -----
+    If input matrix is not real symmetric, no error is reported but result will
+    be wrong.
+
+    """
+    eigenvalues, eigenvectors = linalg.eigh(symmetric)
+    return _form_symmetric(function, eigenvalues, eigenvectors)
+
+
+def _geometric_mean(
+    matrices: List[np.ndarray],
+    init: Optional[np.ndarray] = None,
+    max_iter: int = 10,
+    tol: Optional[float] = 1e-7,
+) -> np.ndarray:
+    """Compute the geometric mean of symmetric positive definite matrices.
+
+    The geometric mean of ``n`` positive definite matrices
+    ``M_1, ..., M_n`` is the minimizer of the sum of squared distances from an
+    arbitrary matrix to each input matrix ``M_k``
+
+    .. math:: gmean(M_1, ..., M_n) = argmin_X sum_{k=1}^N dist(X, M_k)^2
+
+    where the used distance is related to matrices logarithm
+
+    .. math:: dist(X, M_k) = ||log(X^{-1/2} M_k X^{-1/2)}||
+
+    In case of positive numbers, this mean is the usual geometric mean.
+
+    See Algorithm 3 of [1]_ .
+
+    Parameters
+    ----------
+    matrices : list of numpy.ndarray, all of shape (n_features, n_features)
+        List of matrices whose geometric mean to compute. Raise an error if the
+        matrices are not all symmetric positive definite of the same shape.
+    init : numpy.ndarray of shape (n_features, n_features), optional
+        Initialization matrix, default to the arithmetic mean of matrices.
+        Raise an error if the matrix is not symmetric positive definite of the
+        same shape as the elements of matrices (default None).
+    max_iter : int, optional
+        Maximal number of iterations (default 10).
+    tol : positive float or None, optional
+        The tolerance to declare convergence: if the gradient norm goes below
+        this value, the gradient descent is stopped. If None, no check is
+        performed (default 1e-7).
+
+    Returns
+    -------
+    gmean : numpy.ndarray of shape (n_features, n_features)
+        Geometric mean of the matrices.
+
+    References
+    ----------
+    .. [1] Fletcher, T., P., Joshi, S.
+           Riemannian geometry for the statistical analysis of diffusion tensor
+           data.
+           Signal Processing, Volume 87, Issue 2, 2007, Pages 250-262
+           https://doi.org/10.1016/j.sigpro.2005.12.018.
+
+    """
+    # Shape and symmetry positive definiteness checks
+    n_features = matrices[0].shape[0]
+    for matrix in matrices:
+        _check_square(matrix)
+        if matrix.shape[0] != n_features:
+            raise_error("Matrices are not of the same shape.")
+        _check_spd(matrix)
+
+    # Initialization
+    matrices = np.array(matrices)
+    if init is None:
+        gmean = np.mean(matrices, axis=0)
+    else:
+        _check_square(init)
+        if init.shape[0] != n_features:
+            raise_error("Initialization has incorrect shape.")
+        _check_spd(init)
+        gmean = init
+
+    norm_old = np.inf
+    step = 1.0
+
+    # Gradient descent
+    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_matrices = [
+            gmean_inv_sqrt.dot(matrix).dot(gmean_inv_sqrt)
+            for matrix in matrices
+        ]
+        logs = [_map_eigenvalues(np.log, w_mat) for w_mat in whitened_matrices]
+        # Covariant derivative is - gmean.dot(logms_mean)
+        logs_mean = np.mean(logs, axis=0)
+        if np.any(np.isnan(logs_mean)):
+            raise_error(
+                klass=FloatingPointError,
+                msg="Nan value after logarithm operation.",
+            )
+
+        # 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)
+        # Move along the geodesic
+        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
+        elif norm > norm_old:
+            step = step / 2.0
+            norm = norm_old
+        if tol is not None and norm / gmean.size < tol:
+            break
+    if tol is not None and norm / gmean.size >= tol:
+        warn_with_log(
+            f"Maximum number of iterations {max_iter} reached without "
+            f"getting to the requested tolerance level {tol}."
+        )
+
+    return gmean
+
+
+class JuniferConnectivityMeasure(ConnectivityMeasure):
+    """Class for custom ConnectivityMeasure.
+
+    Differs from :class:`nilearn.connectome.ConnectivityMeasure` in the
+    following ways:
+
+    * default ``cov_estimator`` is
+      :class:`sklearn.covariance.EmpiricalCovariance`
+    * default ``kind`` is ``"correlation"``
+
+    Parameters
+    ----------
+    cov_estimator : estimator object, optional
+        The covariance estimator
+        (default ``EmpiricalCovariance(store_precision=False)``).
+    kind : {"covariance", "correlation", "partial correlation", \
+            "tangent", "precision"}, optional
+        The matrix kind. For the use of ``"tangent"`` see [1]_
+        (default "correlation").
+    vectorize : bool, optional
+        If True, connectivity matrices are reshaped into 1D arrays and only
+        their flattened lower triangular parts are returned (default False).
+    discard_diagonal : bool, optional
+        If True, vectorized connectivity coefficients do not include the
+        matrices diagonal elements. Used only when vectorize is set to True
+        (default False).
+    standardize : bool, optional
+        If standardize is True, the data are centered and normed: their mean
+        is put to 0 and their variance is put to 1 in the time dimension
+        (default True).
+
+        .. note::
+
+            Added to control passing value to ``standardize`` of
+            ``signal.clean`` to call new behavior since passing ``"zscore"`` or
+            True (default) is deprecated. This parameter will be deprecated in
+            version 0.13 and removed in version 0.15.
+
+    Attributes
+    ----------
+    cov_estimator_ : estimator object
+        A new covariance estimator with the same parameters as
+        ``cov_estimator``.
+    mean_ : numpy.ndarray
+        The mean connectivity matrix across subjects. For ``"tangent"`` kind,
+        it is the geometric mean of covariances (a group covariance
+        matrix that captures information from both correlation and partial
+        correlation matrices). For other values for ``kind``, it is the
+        mean of the corresponding matrices.
+    whitening_ : numpy.ndarray
+        The inverted square-rooted geometric mean of the covariance matrices.
+
+    References
+    ----------
+    .. [1] Varoquaux, G., Baronnet, F., Kleinschmidt, A. et al.
+           Detection of brain functional-connectivity difference in
+           post-stroke patients using group-level covariance modeling.
+           In Tianzi Jiang, Nassir Navab, Josien P. W. Pluim, and
+           Max A. Viergever, editors, Medical image computing and
+           computer-assisted intervention - MICCAI 2010, Lecture notes
+           in computer science, Pages 200-208. Berlin, Heidelberg, 2010.
+           Springer.
+           doi:10/cn2h9c.
+
+    """
+
+    def __init__(
+        self,
+        cov_estimator=DEFAULT_COV_ESTIMATOR,
+        kind="correlation",
+        vectorize=False,
+        discard_diagonal=False,
+        standardize=True,
+    ):
+        super().__init__(
+            cov_estimator=cov_estimator,
+            kind=kind,
+            vectorize=vectorize,
+            discard_diagonal=discard_diagonal,
+            standardize=standardize,
+        )
+
+    def _fit_transform(
+        self,
+        X,  # noqa: N803
+        do_transform=False,
+        do_fit=False,
+        confounds=None,
+    ):
+        """Avoid duplication of computation."""
+        self._check_input(X, confounds=confounds)
+        if do_fit:
+            self.cov_estimator_ = clone(self.cov_estimator)
+
+        # Compute all the matrices, stored in "connectivities"
+        if self.kind == "correlation":
+            covariances_std = [
+                self.cov_estimator_.fit(
+                    signal.standardize_signal(
+                        x,
+                        detrend=False,
+                        standardize=self.standardize,
+                    )
+                ).covariance_
+                for x in X
+            ]
+            connectivities = [cov_to_corr(cov) for cov in covariances_std]
+        else:
+            covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
+            if self.kind in ("covariance", "tangent"):
+                connectivities = covariances
+            elif self.kind == "precision":
+                connectivities = [linalg.inv(cov) for cov in covariances]
+            elif self.kind == "partial correlation":
+                connectivities = [
+                    prec_to_partial(linalg.inv(cov)) for cov in covariances
+                ]
+            else:
+                allowed_kinds = (
+                    "correlation",
+                    "partial correlation",
+                    "tangent",
+                    "covariance",
+                    "precision",
+                )
+                raise_error(
+                    f"Allowed connectivity kinds are {allowed_kinds}. "
+                    f"Got kind {self.kind}."
+                )
+
+        # Store the mean
+        if do_fit:
+            if self.kind == "tangent":
+                self.mean_ = _geometric_mean(
+                    covariances, max_iter=30, tol=1e-7
+                )
+                self.whitening_ = _map_eigenvalues(
+                    lambda x: 1.0 / np.sqrt(x), self.mean_
+                )
+            else:
+                self.mean_ = np.mean(connectivities, axis=0)
+                # Fight numerical instabilities: make symmetric
+                self.mean_ = self.mean_ + self.mean_.T
+                self.mean_ *= 0.5
+
+        # Compute the vector we return on transform
+        if do_transform:
+            if self.kind == "tangent":
+                connectivities = [
+                    _map_eigenvalues(
+                        np.log, self.whitening_.dot(cov).dot(self.whitening_)
+                    )
+                    for cov in connectivities
+                ]
+
+            connectivities = np.array(connectivities)
+
+            if confounds is not None and not self.vectorize:
+                error_message = (
+                    "'confounds' are provided but vectorize=False. "
+                    "Confounds are only cleaned on vectorized matrices "
+                    "as second level connectome regression "
+                    "but not on symmetric matrices."
+                )
+                raise_error(error_message)
+
+            if self.vectorize:
+                connectivities = sym_matrix_to_vec(
+                    connectivities, discard_diagonal=self.discard_diagonal
+                )
+                if confounds is not None:
+                    connectivities = signal.clean(
+                        connectivities, confounds=confounds
+                    )
+
+        return connectivities

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -28,18 +28,24 @@ class CrossParcellationFC(BaseMarker):
         The name of the first parcellation.
     parcellation_two : str
         The name of the second parcellation.
-    aggregation_method : str, optional
+    agg_method : str, optional
-        The aggregation method (default "mean").
+        The method to perform aggregation using.
-    correlation_method : str, optional
+        See :func:`.get_aggfunc_by_name` for options
+        (default "mean").
+    agg_method_params : dict, optional
+        Parameters to pass to the aggregation function.
+        See :func:`.get_aggfunc_by_name` for options
+        (default None).
+    corr_method : str, optional
         Any method that can be passed to
-        :any:`pandas.DataFrame.corr` (default "pearson").
+        :meth:`pandas.DataFrame.corr` (default "pearson").
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. If None, will use the class name
+        The name of the marker. If None, will use
-        (default None).
+        ``BOLD_CrossParcellationFC`` (default None).
 
     """
 
@@ -55,8 +61,9 @@ class CrossParcellationFC(BaseMarker):
         self,
         parcellation_one: str,
         parcellation_two: str,
-        aggregation_method: str = "mean",
+        agg_method: str = "mean",
-        correlation_method: str = "pearson",
+        agg_method_params: Optional[Dict] = None,
+        corr_method: str = "pearson",
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -66,8 +73,9 @@ class CrossParcellationFC(BaseMarker):
             )
         self.parcellation_one = parcellation_one
         self.parcellation_two = parcellation_two
-        self.aggregation_method = aggregation_method
+        self.agg_method = agg_method
-        self.correlation_method = correlation_method
+        self.agg_method_params = agg_method_params
+        self.corr_method = corr_method
         self.masks = masks
         super().__init__(on=["BOLD"], name=name)
 
@@ -115,13 +123,17 @@ class CrossParcellationFC(BaseMarker):
         # Perform aggregation using two parcellations
         aggregation_parcellation_one = ParcelAggregation(
             parcellation=self.parcellation_one,
-            method=self.aggregation_method,
+            method=self.agg_method,
+            method_params=self.agg_method_params,
             masks=self.masks,
+            on="BOLD",
         ).compute(input, extra_input=extra_input)
         aggregation_parcellation_two = ParcelAggregation(
             parcellation=self.parcellation_two,
-            method=self.aggregation_method,
+            method=self.agg_method,
+            method_params=self.agg_method_params,
             masks=self.masks,
+            on="BOLD",
         ).compute(input, extra_input=extra_input)
 
         return {
@@ -133,7 +145,7 @@ class CrossParcellationFC(BaseMarker):
                     pd.DataFrame(
                         aggregation_parcellation_two["aggregation"]["data"]
                     ),
-                    method=self.correlation_method,
+                    method=self.corr_method,
                 ).values,
                 # Columns should be named after parcellation 1
                 "col_names": aggregation_parcellation_one["aggregation"][

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -22,36 +22,40 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
+        The name(s) of the parcellation(s) to use.
-        :func:`.list_parcellations`.
+        See :func:`.list_parcellations` for options.
     agg_method : str, optional
-        The method to perform aggregation of BOLD time series.
+        The method to perform aggregation using.
-        Check valid options in :func:`.get_aggfunc_by_name`
+        See :func:`.get_aggfunc_by_name` for options
         (default "mean").
     agg_method_params : dict, optional
-        Parameters to pass to the aggregation function. Check valid options in
+        Parameters to pass to the aggregation function.
-        :func:`.get_aggfunc_by_name` (default None).
+        See :func:`.get_aggfunc_by_name` for options
-    cor_method : str, optional
+        (default None).
-        The method to perform correlation. Check valid options in
+    conn_method : str, optional
-        :class:`nilearn.connectome.ConnectivityMeasure`
+        The method to perform connectivity measure using.
-        (default "covariance").
+        See :class:`.JuniferConnectivityMeasure` for options
-    cor_method_params : dict, optional
+        (default "correlation").
-        Parameters to pass to the correlation function. Check valid options in
+    conn_method_params : dict, optional
-        :class:`nilearn.connectome.ConnectivityMeasure` (default None).
+        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+        If None, ``{"empirical": True}`` will be used, which would mean
+        :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
+        covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
+        desired, ``{"empirical": False}`` should be passed
+        (default None).
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. If None, will use the class name (default
+        The name of the marker. If None, will use
-        None).
+        ``BOLD_EdgeCentricFCParcels`` (default None).
 
     References
     ----------
     .. [1] Jo et al. (2021)
-            Subject identification using
+           Subject identification using edge-centric functional connectivity.
-            edge-centric functional connectivity
+           https://doi.org/10.1016/j.neuroimage.2021.118204
-            doi: https://doi.org/10.1016/j.neuroimage.2021.118204
 
     """
 
@@ -60,8 +64,8 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
         parcellation: Union[str, List[str]],
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        cor_method: str = "covariance",
+        conn_method: str = "correlation",
-        cor_method_params: Optional[Dict] = None,
+        conn_method_params: Optional[Dict] = None,
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -69,8 +73,8 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
         super().__init__(
             agg_method=agg_method,
             agg_method_params=agg_method_params,
-            cor_method=cor_method,
+            conn_method=conn_method,
-            cor_method_params=cor_method_params,
+            conn_method_params=conn_method_params,
             masks=masks,
             name=name,
         )

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -22,42 +22,48 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
+        The name of the coordinates list to use.
-        :func:`.list_coordinates` for options.
+        See :func:`.list_coordinates` for options.
-    radius : float, optional
+    radius : positive float, optional
-        The radius of the sphere in mm. If None, the signal will be extracted
+        The radius of the sphere around each coordinates in millimetres.
-        from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker`
+        If None, the signal will be extracted from a single voxel.
-        for more information (default None).
+        See :class:`.JuniferNiftiSpheresMasker` for more information
+        (default None).
     allow_overlap : bool, optional
         Whether to allow overlapping spheres. If False, an error is raised if
-        the spheres overlap (default is False).
+        the spheres overlap (default False).
     agg_method : str, optional
-        The aggregation method to use.
+        The method to perform aggregation using.
-        See :func:`.get_aggfunc_by_name` for more information
+        See :func:`.get_aggfunc_by_name` for options
-        (default None).
+        (default "mean").
     agg_method_params : dict, optional
-        The parameters to pass to the aggregation method (default None).
+        Parameters to pass to the aggregation function.
-    cor_method : str, optional
+        See :func:`.get_aggfunc_by_name` for options
-        The method to perform correlation using. Check valid options in
+        (default None).
-        :class:`nilearn.connectome.ConnectivityMeasure` (default "covariance").
+    conn_method : str, optional
-    cor_method_params : dict, optional
+        The method to perform connectivity measure using.
-        Parameters to pass to the correlation function. Check valid options in
+        See :class:`.JuniferConnectivityMeasure` for options
-        :class:`nilearn.connectome.ConnectivityMeasure` (default None).
+        (default "correlation").
+    conn_method_params : dict, optional
+        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+        If None, ``{"empirical": True}`` will be used, which would mean
+        :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
+        covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
+        desired, ``{"empirical": False}`` should be passed
+        (default None).
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. By default, it will use
+        The name of the marker. If None, will use
-        KIND_EdgeCentricFCSpheres where KIND is the kind of data it
+        ``BOLD_EdgeCentricFCSpheres`` (default None).
-        was applied to (default None).
 
     References
     ----------
     .. [1] Jo et al. (2021)
-            Subject identification using
+           Subject identification using edge-centric functional connectivity.
-            edge-centric functional connectivity
+           https://doi.org/10.1016/j.neuroimage.2021.118204
-            doi: https://doi.org/10.1016/j.neuroimage.2021.118204
 
     """
 
@@ -68,8 +74,8 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         allow_overlap: bool = False,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        cor_method: str = "covariance",
+        conn_method: str = "correlation",
-        cor_method_params: Optional[Dict] = None,
+        conn_method_params: Optional[Dict] = None,
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -81,8 +87,8 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         super().__init__(
             agg_method=agg_method,
             agg_method_params=agg_method_params,
-            cor_method=cor_method,
+            conn_method=conn_method,
-            cor_method_params=cor_method_params,
+            conn_method_params=conn_method_params,
             masks=masks,
             name=name,
         )

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -7,9 +7,9 @@
 from abc import abstractmethod
 from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
-from nilearn.connectome import ConnectivityMeasure
+from sklearn.covariance import EmpiricalCovariance, LedoitWolf
-from sklearn.covariance import EmpiricalCovariance
 
+from ...external.nilearn import JuniferConnectivityMeasure
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -23,25 +23,31 @@ class FunctionalConnectivityBase(BaseMarker):
     Parameters
     ----------
     agg_method : str, optional
-        The method to perform aggregation using. Check valid options in
+        The method to perform aggregation using.
-        :func:`.get_aggfunc_by_name` (default "mean").
+        Check valid options in :func:`.get_aggfunc_by_name`
+        (default "mean").
     agg_method_params : dict, optional
-        Parameters to pass to the aggregation function. Check valid options in
+        Parameters to pass to the aggregation function.
-        :func:`.get_aggfunc_by_name` (default None).
+        Check valid options in :func:`.get_aggfunc_by_name`
-    cor_method : str, optional
+        (default None).
-        The method to perform correlation using. Check valid options in
+    conn_method : str, optional
-        :class:`nilearn.connectome.ConnectivityMeasure`
+        The method to perform connectivity measure using.
-        (default "covariance").
+        Check valid options in :class:`.JuniferConnectivityMeasure`
-    cor_method_params : dict, optional
+        (default "correlation").
-        Parameters to pass to the correlation function. Check valid options in
+    conn_method_params : dict, optional
-        :class:`nilearn.connectome.ConnectivityMeasure` (default None).
+        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+        If None, ``{"empirical": True}`` will be used, which would mean
+        :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
+        covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
+        desired, ``{"empirical": False}`` should be passed
+        (default None).
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. If None, will use the class name (default
+        The name of the marker. If None, will use ``BOLD_<class_name>``
-        None).
+        (default None).
 
     """
 
@@ -57,19 +63,18 @@ class FunctionalConnectivityBase(BaseMarker):
         self,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        cor_method: str = "covariance",
+        conn_method: str = "correlation",
-        cor_method_params: Optional[Dict] = None,
+        conn_method_params: Optional[Dict] = None,
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
-        self.cor_method = cor_method
+        self.conn_method = conn_method
-        self.cor_method_params = cor_method_params or {}
+        self.conn_method_params = conn_method_params or {}
-
+        # Reverse of nilearn behavior
-        # default to nilearn behavior
+        self.conn_method_params["empirical"] = self.conn_method_params.get(
-        self.cor_method_params["empirical"] = self.cor_method_params.get(
+            "empirical", True
-            "empirical", False
         )
         self.masks = masks
         super().__init__(on="BOLD", name=name)
@@ -121,14 +126,21 @@ class FunctionalConnectivityBase(BaseMarker):
         """
         # Perform necessary aggregation
         aggregation = self.aggregate(input, extra_input=extra_input)
-        # Compute correlation
+        # Set covariance estimator
-        if self.cor_method_params["empirical"]:
+        if self.conn_method_params["empirical"]:
-            connectivity = ConnectivityMeasure(
+            cov_estimator = EmpiricalCovariance(store_precision=False)
-                cov_estimator=EmpiricalCovariance(),  # type: ignore
-                kind=self.cor_method,
-            )
         else:
-            connectivity = ConnectivityMeasure(kind=self.cor_method)
+            cov_estimator = LedoitWolf(store_precision=False)
+        # Compute correlation
+        connectivity = JuniferConnectivityMeasure(
+            cov_estimator=cov_estimator,
+            kind=self.conn_method,
+            **{
+                k: v
+                for k, v in self.conn_method_params.items()
+                if k != "empirical"
+            },
+        )
         # Create dictionary for output
         return {
             "functional_connectivity": {

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -22,28 +22,34 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
+        The name(s) of the parcellation(s) to use.
-        :func:`.list_parcellations`.
+        See :func:`.list_parcellations` for options.
     agg_method : str, optional
-        The method to perform aggregation using. Check valid options in
+        The method to perform aggregation using.
-        :func:`.get_aggfunc_by_name` (default "mean").
+        See :func:`.get_aggfunc_by_name` for options
+        (default "mean").
     agg_method_params : dict, optional
-        Parameters to pass to the aggregation function. Check valid options in
+        Parameters to pass to the aggregation function.
-        :func:`.get_aggfunc_by_name` (default None).
+        See :func:`.get_aggfunc_by_name` for options
-    cor_method : str, optional
+        (default None).
-        The method to perform correlation using. Check valid options in
+    conn_method : str, optional
-        :class:`nilearn.connectome.ConnectivityMeasure`
+        The method to perform connectivity measure using.
-        (default "covariance").
+        See :class:`.JuniferConnectivityMeasure` for options
-    cor_method_params : dict, optional
+        (default "correlation").
-        Parameters to pass to the correlation function. Check valid options in
+    conn_method_params : dict, optional
-        :class:`nilearn.connectome.ConnectivityMeasure` (default None).
+        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+        If None, ``{"empirical": True}`` will be used, which would mean
+        :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
+        covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
+        desired, ``{"empirical": False}`` should be passed
+        (default None).
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. If None, will use the class name (default
+        The name of the marker. If None, will use
-        None).
+        ``BOLD_FunctionalConnectivityParcels`` (default None).
 
     """
 
@@ -52,8 +58,8 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         parcellation: Union[str, List[str]],
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        cor_method: str = "covariance",
+        conn_method: str = "correlation",
-        cor_method_params: Optional[Dict] = None,
+        conn_method_params: Optional[Dict] = None,
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -61,8 +67,8 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         super().__init__(
             agg_method=agg_method,
             agg_method_params=agg_method_params,
-            cor_method=cor_method,
+            conn_method=conn_method,
-            cor_method_params=cor_method_params,
+            conn_method_params=conn_method_params,
             masks=masks,
             name=name,
         )

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -23,35 +23,42 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
+        The name of the coordinates list to use.
-        :func:`.list_coordinates` for options.
+        See :func:`.list_coordinates` for options.
-    radius : float, optional
+    radius : positive float, optional
-        The radius of the sphere in mm. If None, the signal will be extracted
+        The radius of the sphere around each coordinates in millimetres.
-        from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker`
+        If None, the signal will be extracted from a single voxel.
-        for more information (default None).
+        See :class:`.JuniferNiftiSpheresMasker` for more information
+        (default None).
     allow_overlap : bool, optional
         Whether to allow overlapping spheres. If False, an error is raised if
-        the spheres overlap (default is False).
+        the spheres overlap (default False).
     agg_method : str, optional
-        The aggregation method to use.
+        The method to perform aggregation using.
-        See :func:`.get_aggfunc_by_name` for more information
+        See :func:`.get_aggfunc_by_name` for options
-        (default None).
+        (default "mean").
     agg_method_params : dict, optional
-        The parameters to pass to the aggregation method (default None).
+        Parameters to pass to the aggregation function.
-    cor_method : str, optional
+        See :func:`.get_aggfunc_by_name` for options
-        The method to perform correlation using. Check valid options in
+        (default None).
-        :class:`nilearn.connectome.ConnectivityMeasure` (default "covariance").
+    conn_method : str, optional
-    cor_method_params : dict, optional
+        The method to perform connectivity measure using.
-        Parameters to pass to the correlation function. Check valid options in
+        See :class:`.JuniferConnectivityMeasure` for options
-        :class:`nilearn.connectome.ConnectivityMeasure` (default None).
+        (default "correlation").
+    conn_method_params : dict, optional
+        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+        If None, ``{"empirical": True}`` will be used, which would mean
+        :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
+        covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
+        desired, ``{"empirical": False}`` should be passed
+        (default None).
     masks : str, dict or list of dict or str, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
     name : str, optional
-        The name of the marker. By default, it will use
+        The name of the marker. If None, will use
-        KIND_FunctionalConnectivitySpheres where KIND is the kind of data it
+        ``BOLD_FunctionalConnectivitySpheres`` (default None).
-        was applied to (default None).
 
     """
 
@@ -62,8 +69,8 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         allow_overlap: bool = False,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        cor_method: str = "covariance",
+        conn_method: str = "correlation",
-        cor_method_params: Optional[Dict] = None,
+        conn_method_params: Optional[Dict] = None,
         masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -75,8 +82,8 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         super().__init__(
             agg_method=agg_method,
             agg_method_params=agg_method_params,
-            cor_method=cor_method,
+            conn_method=conn_method,
-            cor_method_params=cor_method_params,
+            conn_method_params=conn_method_params,
             masks=masks,
             name=name,
         )

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -27,7 +27,7 @@ def test_init() -> None:
         CrossParcellationFC(
             parcellation_one="a",
             parcellation_two="a",
-            correlation_method="pearson",
+            corr_method="pearson",
         )
 
 
@@ -58,7 +58,7 @@ def test_compute(tmp_path: Path) -> None:
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
-            correlation_method="spearman",
+            corr_method="spearman",
         )
         out = crossparcellation.compute(element_data["BOLD"])[
             "functional_connectivity"
@@ -86,7 +86,7 @@ def test_store(tmp_path: Path) -> None:
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
-            correlation_method="spearman",
+            corr_method="spearman",
         )
         storage = SQLiteFeatureStorage(
             uri=tmp_path / "test_crossparcellation.sqlite", upsert="ignore"

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -5,6 +5,9 @@
 # License: AGPL
 
 from pathlib import Path
+from typing import Dict
+
+import pytest
 
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCParcels
@@ -12,20 +15,35 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
+@pytest.mark.parametrize(
+    "conn_method_params",
+    [
+        {"empirical": False},
+        {"empirical": True},
+    ],
+)
+def test_EdgeCentricFCParcels(
+    tmp_path: Path,
+    conn_method_params: Dict[str, bool],
+) -> None:
     """Test EdgeCentricFCParcels.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    conn_method_params : dict
+        The parametrized parameters to connectivity measure method.
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:
+        # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Setup marker
         marker = EdgeCentricFCParcels(
             parcellation="TianxS1x3TxMNInonlinear2009cAsym",
-            cor_method_params={"empirical": True},
+            conn_method="correlation",
+            conn_method_params=conn_method_params,
         )
         # Check correct output
         assert "matrix" == marker.get_output_type(
@@ -41,8 +59,7 @@ def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
         assert "data" in edge_fc_bold
         assert "row_names" in edge_fc_bold
         assert "col_names" in edge_fc_bold
-        assert edge_fc_bold["data"].shape[0] == n_edges
+        assert edge_fc_bold["data"].shape == (n_edges, n_edges)
-        assert edge_fc_bold["data"].shape[1] == n_edges
         assert len(set(edge_fc_bold["row_names"])) == n_edges
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -5,6 +5,9 @@
 # License: AGPL
 
 from pathlib import Path
+from typing import Dict
+
+import pytest
 
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCSpheres
@@ -12,19 +15,36 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
-def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
+@pytest.mark.parametrize(
+    "conn_method_params",
+    [
+        {"empirical": False},
+        {"empirical": True},
+    ],
+)
+def test_EdgeCentricFCSpheres(
+    tmp_path: Path,
+    conn_method_params: Dict[str, bool],
+) -> None:
     """Test EdgeCentricFCSpheres.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    conn_method_params : dict
+        The parametrized parameters to connectivity measure method.
 
     """
     with SPMAuditoryTestingDataGrabber() as dg:
+        # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        # Setup marker
         marker = EdgeCentricFCSpheres(
-            coords="DMNBuckner", radius=5.0, cor_method="correlation"
+            coords="DMNBuckner",
+            radius=5.0,
+            conn_method="correlation",
+            conn_method_params=conn_method_params,
         )
         # Check correct output
         assert "matrix" == marker.get_output_type(
@@ -45,13 +65,6 @@ def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
         assert len(set(edge_fc_bold["row_names"])) == n_edges
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
-        # Check empirical correlation method parameters
-        marker = EdgeCentricFCSpheres(
-            coords="DMNBuckner",
-            radius=5.0,
-            cor_method="correlation",
-            cor_method_params={"empirical": True},
-        )
         # Store
         storage = SQLiteFeatureStorage(
             uri=tmp_path / "test_edge_fc_spheres.sqlite", upsert="ignore"

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -6,10 +6,13 @@
 # License: AGPL
 
 from pathlib import Path
+from typing import TYPE_CHECKING, Dict, Type
 
+import pytest
 from nilearn.connectome import ConnectivityMeasure
 from nilearn.maskers import NiftiLabelsMasker
 from numpy.testing import assert_array_almost_equal
+from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from junifer.data import get_parcellation
 from junifer.datareader import DefaultDataReader
@@ -20,19 +23,42 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
+if TYPE_CHECKING:
+    from sklearn.base import BaseEstimator
+
+
+@pytest.mark.parametrize(
+    "conn_method_params, cov_estimator",
+    [
+        ({"empirical": False}, LedoitWolf(store_precision=False)),
+        ({"empirical": True}, EmpiricalCovariance(store_precision=False)),
+    ],
+)
+def test_FunctionalConnectivityParcels(
+    tmp_path: Path,
+    conn_method_params: Dict[str, bool],
+    cov_estimator: Type["BaseEstimator"],
+) -> None:
     """Test FunctionalConnectivityParcels.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    conn_method_params : dict
+        The parametrized parameters to connectivity measure method.
+    cov_estimator : estimator object
+        The parametrized covariance estimator.
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:
+        # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Setup marker
         marker = FunctionalConnectivityParcels(
-            parcellation="TianxS1x3TxMNInonlinear2009cAsym"
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            conn_method="correlation",
+            conn_method_params=conn_method_params,
         )
         # Check correct output
         assert "matrix" == marker.get_output_type(
@@ -65,7 +91,7 @@ def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            kind="covariance"
+            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal
@@ -73,11 +99,6 @@ def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
             connectivity_measure, fc_bold["data"], decimal=3
         )
 
-        # Check empirical correlation method parameters
-        marker = FunctionalConnectivityParcels(
-            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
-            cor_method_params={"empirical": True},
-        )
         # Store
         storage = SQLiteFeatureStorage(
             uri=tmp_path / "test_fc_parcels.sqlite", upsert="ignore"

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -7,12 +7,13 @@
 # License: AGPL
 
 from pathlib import Path
+from typing import TYPE_CHECKING, Dict, Type
 
 import pytest
 from nilearn.connectome import ConnectivityMeasure
 from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_almost_equal
-from sklearn.covariance import EmpiricalCovariance
+from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from junifer.data import get_coordinates
 from junifer.datareader import DefaultDataReader
@@ -23,19 +24,43 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
-def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
+if TYPE_CHECKING:
+    from sklearn.base import BaseEstimator
+
+
+@pytest.mark.parametrize(
+    "conn_method_params, cov_estimator",
+    [
+        ({"empirical": False}, LedoitWolf(store_precision=False)),
+        ({"empirical": True}, EmpiricalCovariance(store_precision=False)),
+    ],
+)
+def test_FunctionalConnectivitySpheres(
+    tmp_path: Path,
+    conn_method_params: Dict[str, bool],
+    cov_estimator: Type["BaseEstimator"],
+) -> None:
     """Test FunctionalConnectivitySpheres.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    conn_method_params : dict
+        The parametrized parameters to connectivity measure method.
+    cov_estimator : estimator object
+        The parametrized covariance estimator.
 
     """
     with SPMAuditoryTestingDataGrabber() as dg:
+        # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        # Setup marker
         marker = FunctionalConnectivitySpheres(
-            coords="DMNBuckner", radius=5.0, cor_method="correlation"
+            coords="DMNBuckner",
+            radius=5.0,
+            conn_method="correlation",
+            conn_method_params=conn_method_params,
         )
         # Check correct output
         assert "matrix" == marker.get_output_type(
@@ -67,7 +92,7 @@ def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            kind="correlation"
+            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal
@@ -88,65 +113,9 @@ def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
         )
 
 
-def test_FunctionalConnectivitySpheres_empirical(tmp_path: Path) -> None:
-    """Test FunctionalConnectivitySpheres with empirical covariance.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
-    with SPMAuditoryTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        marker = FunctionalConnectivitySpheres(
-            coords="DMNBuckner",
-            radius=5.0,
-            cor_method="correlation",
-            cor_method_params={"empirical": True},
-        )
-        # Check correct output
-        assert "matrix" == marker.get_output_type(
-            input_type="BOLD", output_feature="functional_connectivity"
-        )
-
-        # Fit-transform the data
-        fc = marker.fit_transform(element_data)
-        fc_bold = fc["BOLD"]["functional_connectivity"]
-
-        assert "data" in fc_bold
-        assert "row_names" in fc_bold
-        assert "col_names" in fc_bold
-        assert fc_bold["data"].shape == (6, 6)
-        assert len(set(fc_bold["row_names"])) == 6
-        assert len(set(fc_bold["col_names"])) == 6
-
-        # Compare with nilearn
-        # Load testing coordinates for the target data
-        testing_coords, _ = get_coordinates(
-            coords="DMNBuckner", target_data=element_data["BOLD"]
-        )
-        # Extract timeseries
-        nifti_spheres_masker = NiftiSpheresMasker(
-            seeds=testing_coords, radius=5.0
-        )
-        extracted_timeseries = nifti_spheres_masker.fit_transform(
-            element_data["BOLD"]["data"]
-        )
-        # Compute the connectivity measure
-        connectivity_measure = ConnectivityMeasure(
-            cov_estimator=EmpiricalCovariance(), kind="correlation"  # type: ignore
-        ).fit_transform([extracted_timeseries])[0]
-
-        # Check that FC are almost equal
-        assert_array_almost_equal(
-            connectivity_measure, fc_bold["data"], decimal=3
-        )
-
-
 def test_FunctionalConnectivitySpheres_error() -> None:
     """Test FunctionalConnectivitySpheres errors."""
     with pytest.raises(ValueError, match="radius should be > 0"):
         FunctionalConnectivitySpheres(
-            coords="DMNBuckner", radius=-0.1, cor_method="correlation"
+            coords="DMNBuckner", radius=-0.1, conn_method="correlation"
         )