junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/external/BrainPrint/doc/index.rst

@@ -0,0 +1,140 @@
+.. include:: ./links.inc
+
+.. .. literalinclude:: ../README.md
+..    :language: markdown
+
+.. image:: https://badge.fury.io/py/brainprint.svg
+   :target: https://pypi.org/project/brainprint/
+
+BrainPrint
+==========
+
+This is the `brainprint` python package, a derivative of the original `BrainPrint-legacy <https://github.com/Deep-MI/BrainPrint-legacy>`_ scripts, 
+with the primary goal to provide a Python-only version, to integrate the `LaPy <https://github.com/Deep-MI/LaPy>`_ package, 
+and to remove dependencies on third-party software (shapeDNA-* binaries, gmsh, meshfix). 
+As a result, some functionality of the original BrainPrint-legacy scripts is no longer maintained (currently no support of tetrahedral meshes and no support of cortical parcellations or label files).
+
+Installation
+------------
+
+Use the following code to install the latest release of LaPy into your local Python package directory:
+
+.. code-block:: bash
+
+   python3 -m pip install brainprint
+
+This will also install the necessary dependencies, e.g. the `LaPy <https://github.com/Deep-MI/LaPy>`_ package. 
+You may need to add your local Python package directory to your $PATH in order to run the scripts.
+
+Usage
+-----
+
+Command Line Interface (CLI)
+----------------------------
+
+Once installed, the package provides a `brainprint` executable which can be run from the command line.
+
+The `brainprint` CLI enables per-subject computation of the individual brainprint descriptors. Its usage and options are summarized below; detailed info is available by calling the script without any arguments from the command line.
+
+brainprint Command-Line Interface
+'''''''''''''''''''''''''''''''''
+
+.. code-block:: sh
+
+    brainprint 
+    --sdir <directory> 
+    --sid <SubjectID>  
+    [--num <num>] [--evec] [--skipcortex] 
+    [--norm <surface|volume|geometry|none> ] 
+    [--reweight] [--asymmetry] [--outdir <directory>] 
+    [--help] [--more-help]
+
+Options
+'''''''
+
+``--help`` Show this help message and exit.
+
+``--more-help`` Show extensive help message and exit.
+
+Required options
+''''''''''''''''
+
+``--sid <SubjectID>`` Subject ID (FreeSurfer-processed directory inside the subjects directory).
+
+``--sdir <directory>`` FreeSurfer subjects directory.
+
+Processing directives
+'''''''''''''''''''''
+
+``--num <num>`` Number of eigenvalues/vectors to compute (default: 50).
+
+``--evec`` Switch on eigenvector computation (default: off).
+
+``--skipcortex`` Skip cortical surfaces (default: off).
+
+``--norm <surface|volume|geometry|none>`` Switch on eigenvalue normalization; will be either surface, volume, or determined by the geometry of the object. Use "none" or leave out entirely to skip normalization.
+
+``--reweight`` Switch on eigenvalue reweighting (default: off).
+
+``--asymmetry`` Perform left-right asymmetry calculation (default: off).
+
+``--cholmod`` Switch on use of (faster) Cholesky decomposition instead of (slower) LU decomposition (default: off). May require manual install of scikit-sparse package.
+
+Output parameters
+'''''''''''''''''
+
+``--outdir=OUTDIR`` Output directory (default: <sdir>/<sid>/brainprint).
+
+``--keep-temp`` Whether to keep the temporary files directory or not (default: False).
+
+
+Python Package
+--------------
+
+`brainprint` can also be run within a pure Python environment, i.e. installed and imported as a Python package. E.g.:
+
+.. code-block:: python
+
+   from brainprint import Brainprint
+
+   subjects_dir = "/path/to/freesurfer/subjects_dir/"
+   subject_id = "42"
+
+   bp = Brainprint(subjects_dir=subjects_dir, asymmetry=True, keep_eigenvectors=True)
+   results = bp.run(subject_id=subject_id)
+   results
+   {"eigenvalues": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.csv"), 
+   "eigenvectors": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/eigenvectors"), 
+   "distances": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.asymmetry.csv")}
+
+
+Output
+------
+The script will create an output directory that contains a CSV table with
+values (in that order) for the area, volume, and first n eigenvalues per each
+FreeSurfer structure. An additional output file will be created if the
+asymmetry calculation is performed and/or for the eigenvectors (CLI `--evecs` flag or `keep_eigenvectors` on class initialization).
+
+Changes
+-------
+
+There are some changes in functionality in comparison to the original `BrainPrint <https://github.com/Deep-MI/BrainPrint-legacy>`_ scripts:
+
+- Currently, there is no support for tetrahedral meshes.
+- Currently, there is no support for analyses of cortical parcellation or label files.
+- No more Python 2.x compatibility.
+
+References
+----------
+
+If you use this software for a publication, please cite:
+
+[1] BrainPrint: a discriminative characterization of brain morphology. Wachinger C, Golland P, Kremen W, Fischl B, Reuter M. Neuroimage. 2015;109:232-48. `http://dx.doi.org/10.1016/j.neuroimage.2015.01.032 <http://dx.doi.org/10.1016/j.neuroimage.2015.01.032>`_ `PubMed <http://www.ncbi.nlm.nih.gov/pubmed/25613439>`_
+
+[2] Laplace-Beltrami spectra as 'Shape-DNA' of surfaces and solids. Reuter M, Wolter F-E, Peinecke N. Computer-Aided Design. 2006;38:342-366. `http://dx.doi.org/10.1016/j.cad.2005.10.011 <http://dx.doi.org/10.1016/j.cad.2005.10.011>`_
+
+
+.. toctree::
+   :hidden:
+
+   api/index

junifer/external/BrainPrint/doc/links.inc

@@ -0,0 +1,36 @@
+.. This (-*- rst -*-) format file contains commonly used link targets and name
+   substitutions.  It may be included in many files, therefore it should only
+   contain link targets and name substitutions. Try grepping for "^\.\. _" to
+   find plausible candidates for this list.
+
+.. NOTE: reST targets are
+   __not_case_sensitive__, so only one target definition is needed for:
+   nipy, NIPY, Nipy, etc...
+
+
+.. project
+
+.. _project pypi: https://pypi.org/project/lapy/
+.. _project conda: https://anaconda.org/conda-forge/lapy
+.. _project github: https://github.com/Deep-MI/BrainPrint
+.. _project license: https://github.com/Deep-MI/BrainPrint/blob/main/LICENSE
+.. _project brainprint: https://pypi.org/project/brainprint/
+
+.. license
+
+.. _MIT license: https://opensource.org/licenses/MIT
+
+
+.. numpy
+
+.. _numpy: https://numpy.org/
+
+
+.. sklearn
+
+.. _scikit-learn: https://scikit-learn.org/stable/
+
+
+.. scipy
+
+.. _scipy: https://scipy.org/

junifer/external/BrainPrint/doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

junifer/external/BrainPrint/doc/references.bib

@@ -0,0 +1,23 @@
+@article{numpy_2020,
+ author = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
+ doi = {10.1038/s41586-020-2649-2},
+ journal = {Nature},
+ month = {September},
+ number = {7825},
+ pages = {357--362},
+ title = {Array programming with {NumPy}},
+ volume = {585},
+ year = {2020}
+}
+
+@article{scipy_2020,
+ author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll, Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee, Antony and Rokem, Ariel and Woods, C. Nathan and Fulton, Chad and Masson, Charles and Häggström, Christian and Fitzgerald, Clark and Nicholson, David A. and Hagen, David R. and Pasechnik, Dmitrii V. and Olivetti, Emanuele and Martin, Eric and Wieser, Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian and Young, G. and Price, Gavin A. and Ingold, Gert-Ludwig and Allen, Gregory E. and Lee, Gregory R. and Audren, Hervé and Probst, Irvin and Dietrich, Jörg P. and Silterra, Jacob and Webber, James T and Slavič, Janko and Nothman, Joel and Buchner, Johannes and Kulick, Johannes and Schönberger, Johannes L. and de Miranda Cardoso, José Vinícius and Reimer, Joscha and Harrington, Joseph and Rodríguez, Juan Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and Tritz, Kevin and Thoma, Martin and Newville, Matthew and Kümmerer, Matthias and Bolingbroke, Maximilian and Tartre, Michael and Pak, Mikhail and Smith, Nathaniel J. and Nowaczyk, Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and Brodtkorb, Per A. and Lee, Perry and McGibbon, Robert T. and Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert, Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J. and Robitaille, Thomas P. and Spura, Thomas and Jones, Thouis R. and Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and Upadhyay, Utkarsh and Halchenko, Yaroslav O. and Vázquez-Baeza, Yoshiki},
+ doi = {10.1038/s41592-019-0686-2},
+ journal = {Nature Methods},
+ month = {March},
+ number = {3},
+ pages = {261--272},
+ title = {{SciPy} 1.0: fundamental algorithms for scientific computing in {Python}},
+ volume = {17},
+ year = {2020}
+}

junifer/external/BrainPrint/pyproject.toml

@@ -0,0 +1,170 @@
+[build-system]
+requires = ['setuptools >= 61.0.0']
+build-backend = 'setuptools.build_meta'
+
+[project]
+name = 'brainprint'
+version = '0.4.0'
+description = 'A package to compute BrainPrint (shape descriptors) from FastSurfer/FreeSurfer MRI segmentations'
+readme = 'README.md'
+license = {file = 'LICENSE'}
+requires-python = '>=3.8'
+authors = [
+    {name = 'Martin Reuter', email = 'martin.reuter@dzne.de'},
+    {name = 'Kersten Diers', email = 'kersten.diers@dzne.de'},
+]
+maintainers = [
+    {name = 'Martin Reuter', email = 'martin.reuter@dzne.de'},
+]
+keywords = [
+    'neuroscience', 
+    'sMRI', 
+    'FreeSurfer'
+]
+classifiers = [
+    'Operating System :: Microsoft :: Windows',
+    'Operating System :: Unix',
+    'Operating System :: MacOS',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Natural Language :: English',
+    'License :: OSI Approved :: MIT License',
+    'Intended Audience :: Science/Research',
+]
+dependencies = [
+    'numpy',
+    'scipy',
+    'pandas',
+    'lapy >= 1.0.0, <2',
+    'psutil'
+]
+
+[project.optional-dependencies]
+build = [
+    'build',
+    'twine',
+]
+doc = [
+    'furo!=2023.8.17',
+    'matplotlib',
+    'memory-profiler',
+    'numpydoc',
+    'sphinx!=7.2.*',
+    'sphinxcontrib-bibtex',
+    'sphinx-copybutton',
+    'sphinx-design',
+    'sphinx-gallery',
+    'sphinx-issues',
+    'pypandoc',
+    'nbsphinx',
+    'IPython', # For syntax highlighting in notebooks
+    'ipykernel',
+]
+style = [
+    'bibclean',
+    'black',
+    'codespell',
+    'isort',
+    'pydocstyle[toml]',
+    'ruff',
+]
+test = [
+    'pytest',
+    'pytest-cov',
+    'pytest-timeout',
+]
+all = [
+    'brainprint[build]',
+    'brainprint[doc]',
+    'brainprint[style]',
+    'brainprint[test]',
+]
+full = [
+    'brainprint[all]',
+]
+
+[project.urls]
+homepage = 'https://github.com/Deep-MI/BrainPrint'
+documentation = 'https://github.com/Deep-MI/BrainPrint'
+source = 'https://github.com/Deep-MI/BrainPrint'
+tracker = 'https://github.com/Deep-MI/BrainPrint/issues'
+
+[project.scripts]
+brainprint = 'brainprint.cli:main'
+brainprint-sys_info = 'brainprint.commands.sys_info:run'
+
+[tool.setuptools]
+include-package-data = false
+
+[tool.setuptools.packages.find]
+include = ['brainprint*']
+exclude = ['brainprint*tests']
+
+[tool.black]
+line-length = 88
+target-version = ['py38']
+include = '\.pyi?$'
+extend-exclude = '''
+(
+      __pycache__
+    | .github
+    | setup.py
+    | data/
+    | doc/
+    | examples/
+)
+'''
+
+[tool.isort]
+profile = 'black'
+multi_line_output = 3
+line_length = 88
+py_version = 38
+extend_skip_glob = [
+    'setup.py',
+    'data/*',
+    'doc/*',
+    'examples/*',
+]
+
+[tool.pydocstyle]
+convention = 'numpy'
+ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
+match = '^(?!setup|__init__|test_).*\.py'
+match-dir = '^brainprint.*'
+add_ignore = 'D100,D104,D107'
+
+[tool.ruff]
+line-length = 88
+extend-exclude = [
+    "doc",
+    "setup.py",
+]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
+
+[tool.pytest.ini_options]
+minversion = '6.0'
+addopts = '--durations 20 --junit-xml=junit-results.xml --verbose'
+filterwarnings = []
+
+[tool.coverage.run]
+branch = true
+cover_pylib = false
+omit = [
+    '**/__init__.py',
+    '**/brainprint/_version.py',
+    '**/brainprint/commands/*',
+    '**/tests/**',
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    'pragma: no cover',
+    'if __name__ == .__main__.:',
+]
+precision = 2

junifer/external/BrainPrint/setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

junifer/external/__init__.py

@@ -2,3 +2,8 @@
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,9 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
+from collections.abc import Callable
 from itertools import product
-from typing import Callable, Optional
 
 import numpy as np
 from nilearn import signal
@@ -19,7 +18,7 @@ from scipy import linalg, stats
 from sklearn.base import clone
 from sklearn.covariance import EmpiricalCovariance
 
-from ...utils import logger, raise_error, warn_with_log
+from ...utils import check_standardize, logger, raise_error, warn_with_log
 
 
 __all__ = ["JuniferConnectivityMeasure"]
@@ -189,9 +188,9 @@ def _map_eigenvalues(
 
 def _geometric_mean(
     matrices: list[np.ndarray],
-    init: Optional[np.ndarray] = None,
+    init: np.ndarray | None = None,
     max_iter: int = 10,
-    tol: Optional[float] = 1e-7,
+    tol: float | None = 1e-7,
 ) -> np.ndarray:
     """Compute the geometric mean of symmetric positive definite matrices.
 
@@ -314,9 +313,19 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
     following ways:
 
     * default ``cov_estimator`` is
-      :class:`sklearn.covariance.EmpiricalCovariance`
-    * default ``kind`` is ``"correlation"``
+      :class:`sklearn.covariance.EmpiricalCovariance` instead of
+      :class:`sklearn.covariance.LedoitWolf`, and ``cov_estimator=None`` is
+      not supported
+    * default ``kind`` is ``"correlation"`` instead of ``"covariance"``
     * supports Spearman's correlation via ``kind="spearman correlation"``
+    * supports Chatterjee's xi correlation via ``kind="xi correlation"``
+    * ``kind`` is validated when computing the matrices instead of when
+      fitting
+    * no ``verbose`` parameter, so nothing is logged while fitting
+    * ``inverse_transform()`` only knows the diagonal of
+      ``"correlation"`` and ``"partial correlation"`` matrices, so with
+      ``discard_diagonal=True`` the other kinds (including
+      ``"spearman correlation"``) need the ``diagonal`` to be passed
 
     Parameters
     ----------
@@ -330,7 +339,10 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         If ``"spearman correlation"`` is used, the data will be ranked before
         estimating the covariance. For ``"xi correlation"``, the coefficient
         is not symmetric and should be interpreted as a measure of dependence
-        [2]_ . For the use of ``"tangent"`` see [1]_ (default "correlation").
+        [2]_ ; ``cov_estimator`` and ``standardize`` are not used, ``mean_``
+        is symmetrized and, if ``vectorize=True``, only the lower triangular
+        part is kept. 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).
@@ -338,17 +350,13 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         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.
+    standardize : {"zscore_sample", "psc"} or None, optional
+        The strategy to standardize the signals before estimating the
+        covariance. ``"zscore_sample"`` sets them to zero mean and unit
+        variance (using the sample standard deviation), ``"psc"`` converts
+        them to percent signal change and None does not standardize them.
+        Only used for ``"correlation"`` and ``"spearman correlation"``
+        (default "zscore_sample").
 
     Attributes
     ----------
@@ -390,7 +398,7 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         kind="correlation",
         vectorize=False,
         discard_diagonal=False,
-        standardize=True,
+        standardize="zscore_sample",
     ):
         super().__init__(
             cov_estimator=cov_estimator,
@@ -400,6 +408,59 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
             standardize=standardize,
         )
 
+    def _validate_input(
+        self,
+        X,  # noqa: N803
+        do_transform=False,
+        confounds=None,
+    ):
+        """Validate the input of ``_fit_transform``.
+
+        Parameters
+        ----------
+        X : iterable of numpy.ndarray
+            The time series of each subject.
+        do_transform : bool, optional
+            Whether the input will be transformed (default False).
+        confounds : numpy.ndarray, optional
+            The confounds (default None).
+
+        Returns
+        -------
+        list of numpy.ndarray
+            The time series of each subject.
+
+        Raises
+        ------
+        TypeError
+            If ``X`` is not iterable.
+        ValueError
+            If ``standardize`` is a boolean or
+            if ``X`` is a single subject and ``kind="tangent"``.
+
+        """
+        check_standardize(self.standardize)
+        if not hasattr(X, "__iter__"):
+            raise_error(
+                "Input must be an iterable of numpy arrays. "
+                f"Got {X.__class__.__name__}",
+                klass=TypeError,
+            )
+        # A single subject can be passed as a 2D array
+        if isinstance(X, np.ndarray) and X.ndim == 2:
+            X = [X]
+        self._check_input(X, confounds=confounds)
+        if do_transform and self.kind == "tangent" and len(X) <= 1:
+            # Check that people are applying transform to a group of subjects
+            # We can only impose this in transform,
+            # as it is legit to fit only on a single given reference point
+            raise_error(
+                "Tangent space parametrization can only be applied to a "
+                "group of subjects, as it returns deviations to the mean. "
+                f"You provided {X!r}"
+            )
+        return X
+
     def _fit_transform(
         self,
         X,  # noqa: N803
@@ -408,9 +469,19 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         confounds=None,
     ):
         """Avoid duplication of computation."""
-        self._check_input(X, confounds=confounds)
+        X = self._validate_input(
+            X, do_transform=do_transform, confounds=confounds
+        )
         if do_fit:
+            if not hasattr(self.cov_estimator, "fit"):
+                raise_error(
+                    "'cov_estimator' must be an estimator with '.fit()' and "
+                    "'.covariance_' (e.g., from `sklearn.covariance` or a "
+                    "custom estimator constructed similarly). Got: "
+                    f"`{type(self.cov_estimator).__name__}`."
+                )
             self.cov_estimator_ = clone(self.cov_estimator)
+            self.n_features_in_ = next(iter(s.shape[1] for s in X))
 
         # Compute all the matrices, stored in "connectivities"
         if self.kind in ["correlation", "spearman correlation"]:
@@ -431,14 +502,6 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
 
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
         elif self.kind == "xi correlation":
-            if sys.version_info < (3, 10):  # pragma: no cover
-                raise_error(
-                    klass=RuntimeError,
-                    msg=(
-                        "scipy.stats.chatterjeexi is available from "
-                        "scipy 1.15.0 and that requires Python 3.10 and above."
-                    ),
-                )
             connectivities = []
             for x in X:
                 n_rois = x.shape[1]
@@ -461,10 +524,12 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
                 ]
             else:
                 allowed_kinds = (
+                    "covariance",
                     "correlation",
+                    "spearman correlation",
                     "partial correlation",
+                    "xi correlation",
                     "tangent",
-                    "covariance",
                     "precision",
                 )
                 raise_error(
@@ -499,15 +564,6 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
 
             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