junifer 0.0.6.dev536__py3-none-any.whl → 0.0.7.dev18__py3-none-any.whl

junifer/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev536'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev536')
+__version__ = version = '0.0.7.dev18'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev18')

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,6 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import sys
+from itertools import product
 from typing import Callable, Optional
 
 import numpy as np
@@ -322,11 +324,13 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         The covariance estimator
         (default ``EmpiricalCovariance(store_precision=False)``).
     kind : {"covariance", "correlation", "spearman correlation", \
-            "partial correlation", "tangent", "precision"}, optional
+            "partial correlation", "xi correlation", "tangent", \
+            "precision"}, optional
         The matrix kind. The default value uses Pearson's correlation.
         If ``"spearman correlation"`` is used, the data will be ranked before
-        estimating the covariance. For the use of ``"tangent"`` see [1]_
-        (default "correlation").
+        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").
     vectorize : bool, optional
         If True, connectivity matrices are reshaped into 1D arrays and only
         their flattened lower triangular parts are returned (default False).
@@ -372,6 +376,12 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
            Springer.
            doi:10/cn2h9c.
 
+    .. [2] Chatterjee, S.
+           A new coefficient of correlation.
+           Journal of the American Statistical Association 116.536 (2021):
+           2009-2022.
+           doi:10.1080/01621459.2020.1758115.
+
     """
 
     def __init__(
@@ -420,6 +430,25 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
                 covariances_std.append(self.cov_estimator_.fit(x).covariance_)
 
             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]
+                connectivity = np.ones((n_rois, n_rois))
+                for i, j in product(range(n_rois), range(n_rois)):
+                    if i != j:
+                        connectivity[i, j] = stats.chatterjeexi(
+                            x[:, i], x[:, j], y_continuous=True
+                        ).statistic
+                connectivities.append(connectivity)
         else:
             covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
             if self.kind in ("covariance", "tangent"):

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import copy
+import sys
 import warnings
 from math import cosh, exp, log, sinh, sqrt
 from typing import TYPE_CHECKING, Optional, Union
@@ -12,7 +13,11 @@ 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 numpy.testing import (
+    assert_allclose,
+    assert_array_almost_equal,
+    assert_array_equal,
+)
 from pandas import DataFrame
 from scipy import linalg
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
@@ -1088,3 +1093,42 @@ def test_connectivity_measure_standardize(
         ).fit_transform(signals)
         for m in record:
             assert match not in m.message
+
+
+@pytest.mark.skipif(
+    sys.version_info > (3, 9),
+    reason="will have correct scipy version so no error",
+)
+def test_xi_correlation_error() -> None:
+    """Check xi correlation according to paper."""
+    with pytest.raises(RuntimeError, match="scipy.stats.chatterjeexi"):
+        JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+            np.zeros((2, 2))
+        )
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 10),
+    reason=(
+        "needs scipy 1.15.0 and above which in turn requires "
+        "python 3.10 and above"
+    ),
+)
+def test_xi_correlation() -> None:
+    """Check xi correlation according to paper."""
+    rng = np.random.default_rng(25982435982346983)
+    x = rng.random(size=10)
+    y = rng.random(size=10)
+    arr = np.column_stack((x, y))
+    expected = np.array(
+        [
+            [
+                [1.0, -0.3030303],
+                [-0.18181818, 1.0],
+            ]
+        ]
+    )
+    got = JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+        [arr]
+    )
+    assert_allclose(expected, got)

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -143,14 +143,17 @@ class FunctionalConnectivityBase(BaseMarker):
             },
         )
         # Create dictionary for output
+        labels = aggregation["aggregation"]["col_names"]
         return {
             "functional_connectivity": {
                 "data": connectivity.fit_transform(
                     [aggregation["aggregation"]["data"]]
                 )[0],
-                # Create column names
-                "row_names": aggregation["aggregation"]["col_names"],
-                "col_names": aggregation["aggregation"]["col_names"],
-                "matrix_kind": "tril",
+                "row_names": labels,
+                "col_names": labels,
+                # xi correlation coefficient is not symmetric
+                "matrix_kind": (
+                    "full" if self.conn_method == "xi correlation" else "tril"
+                ),
             },
         }

{junifer-0.0.6.dev536.dist-info → junifer-0.0.7.dev18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.6.dev536
+Version: 0.0.7.dev18
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev536.dist-info → junifer-0.0.7.dev18.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=1MngmE54O_4DFiyuN6qI5ONmhjA8aVCEk7aPZdjJ1hY,528
+junifer/_version.py,sha256=GyAsN4t__QNl7uIDhLy7GlyhnLiTFiaNd9nlKJfEFik,526
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -173,10 +173,10 @@ junifer/external/h5io/h5io/chunked_array.py,sha256=K1HWf7R2Jc7gCzBqAoBjx0ZnMmUhT
 junifer/external/h5io/h5io/chunked_list.py,sha256=1Y5BbuWzurJlEFQzJNuDdC3fNZ39ENEMba99X_4VeSM,1952
 junifer/external/nilearn/__init__.py,sha256=pvDmJMwOBki2oaEw-bsniMQ9UXvzecwu6EwJvbVxD50,210
 junifer/external/nilearn/__init__.pyi,sha256=bcCz7O02UameBxbtPjhUal-Z9rI01pv3iktPs_Nq7Ts,208
-junifer/external/nilearn/junifer_connectivity_measure.py,sha256=R868Z6ltm2OiMgEVEBBtqTTtWkwhU5O7yhNSQDYudDA,17316
+junifer/external/nilearn/junifer_connectivity_measure.py,sha256=oP7JyggH0w4V9FlEXSn0wCApXYy9zBj-XSawOBmMniY,18588
 junifer/external/nilearn/junifer_nifti_spheres_masker.py,sha256=1CqtGFpfgVR2sK_pDYsBlgAEg-fIG5CkKzXzTTXG7EY,16533
 junifer/external/nilearn/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/external/nilearn/tests/test_junifer_connectivity_measure.py,sha256=wOk8BOK_MZWJ0cdvN1lBRAVf8CHIlOi2A3-ZRqG894k,33928
+junifer/external/nilearn/tests/test_junifer_connectivity_measure.py,sha256=CVUA1AV4syIMWq3S-cqXYvuBPzHZHiZLeTi_sAkuI6g,35042
 junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py,sha256=9UvBAVO-uo0nMIHYfAQ85kJMrwpBxpVRsN1-mHLk7ik,12244
 junifer/markers/__init__.py,sha256=wHAxljlZppxgXimSJw21mp9oUYYyaID4LYfeBolva30,310
 junifer/markers/__init__.pyi,sha256=9a72D9k6esTzLvmvULXHOeaQtIchjtN7VELpCeaddsM,957
@@ -221,7 +221,7 @@ junifer/markers/functional_connectivity/__init__.pyi,sha256=qfw6WVyE65u-5NZNi0xP
 junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py,sha256=uLdVGywmL7qrzloh1YBL4g4tPiamA47MgHF2DQH0JTU,5733
 junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py,sha256=pMKGRdhjs_KXMonmQxI71v6-w93DFTzgTlrvouY9kIg,4724
 junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py,sha256=TnwG1uF1PH2mN6n6ZhEvYsn9mEnhKVshRLHuI36kwqI,5393
-junifer/markers/functional_connectivity/functional_connectivity_base.py,sha256=6M7iVPNSbQ1D0O8-1onCbgsLGWri1egyAIQvo9yfgnI,5676
+junifer/markers/functional_connectivity/functional_connectivity_base.py,sha256=4bE95pHSZ2Ju0q2pXjHyPqBYwEpoba2YPBGkF4f_QPY,5783
 junifer/markers/functional_connectivity/functional_connectivity_parcels.py,sha256=yjXPcpXmleHWlwxNEEL_1EuW_clsjq1qCcnCCLa576c,4192
 junifer/markers/functional_connectivity/functional_connectivity_spheres.py,sha256=2JczueAU31fh6sW0Ecn8ap2lZhEG19oUvuR7w2mFDuE,4927
 junifer/markers/functional_connectivity/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -341,10 +341,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev536.dist-info/licenses/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev536.dist-info/licenses/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev536.dist-info/METADATA,sha256=AzQT3btyWGNgZ2dvjq42ZlYrQmaKwdUPVwpkky2NeH4,8442
-junifer-0.0.6.dev536.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-junifer-0.0.6.dev536.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev536.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev536.dist-info/RECORD,,
+junifer-0.0.7.dev18.dist-info/licenses/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.7.dev18.dist-info/licenses/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.7.dev18.dist-info/METADATA,sha256=CUXcvLUz6uv5RXTxeF45miX5qqdHSnOrbqHu1h9luRY,8441
+junifer-0.0.7.dev18.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+junifer-0.0.7.dev18.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.7.dev18.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.7.dev18.dist-info/RECORD,,

{junifer-0.0.6.dev536.dist-info → junifer-0.0.7.dev18.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any