junifer 0.0.5.dev145__tar.gz → 0.0.5.dev161__tar.gz

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev145
+Version: 0.0.5.dev161
 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>
@@ -29,13 +29,13 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<1.27,>=1.24
-Requires-Dist: scipy<=1.11.4,>=1.9.0
-Requires-Dist: datalad<0.20,>=0.15.4
-Requires-Dist: pandas<2.2,>=1.4.0
-Requires-Dist: nibabel<5.11,>=3.2.0
-Requires-Dist: nilearn<=0.10.2,>=0.9.0
-Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+Requires-Dist: numpy<2.0.0,>=1.24.0
+Requires-Dist: scipy<=1.14.0,>=1.10.0
+Requires-Dist: datalad<1.2.0,>=1.0.0
+Requires-Dist: pandas<2.3.0,>=2.0.0
+Requires-Dist: nibabel<5.3.0,>=5.2.0
+Requires-Dist: nilearn<=0.10.4,>=0.10.3
+Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.18,>=0.17
 Requires-Dist: h5py>=3.10
 Requires-Dist: httpx[http2]==0.26.0
@@ -57,14 +57,14 @@ Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
-Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
-Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
-Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
-Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
+Requires-Dist: sphinx<7.4.0,>=7.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.17.0,>=0.15.0; extra == "docs"
+Requires-Dist: furo<2024.6.0,>=2024.4.27; extra == "docs"
+Requires-Dist: numpydoc<1.8.0,>=1.6.0; extra == "docs"
+Requires-Dist: julearn==0.3.3; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")

junifer-0.0.5.dev161/docs/changes/newsfragments/136.enh

@@ -0,0 +1 @@
+Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean aggregation function behaves exactly as :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_

junifer-0.0.5.dev161/docs/changes/newsfragments/347.misc

@@ -0,0 +1 @@
+Update core and docs dependencies by `Synchon Mandal`_

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev145'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev145')
+__version__ = version = '0.0.5.dev161'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev161')

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer/external/nilearn/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .junifer_nifti_spheres_masker import JuniferNiftiSpheresMasker
+
+
+__all__ = ["JuniferNiftiSpheresMasker"]

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -10,9 +10,9 @@ from nilearn import image, masking
 from nilearn._utils.class_inspect import get_params
 from nilearn._utils.niimg import img_data_dtype
 from nilearn._utils.niimg_conversions import (
-    _safe_get_data,
     check_niimg_3d,
     check_niimg_4d,
+    safe_get_data,
 )
 from nilearn.maskers import NiftiSpheresMasker
 from nilearn.maskers.base_masker import _filter_and_extract
@@ -29,9 +29,12 @@ if TYPE_CHECKING:
     from pandas import DataFrame
 
 
+__all__ = ["JuniferNiftiSpheresMasker"]
+
+
 # New BSD License
 
-# Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) The nilearn developers.
 # All rights reserved.
 
 
@@ -99,12 +102,23 @@ def _apply_mask_and_get_affinity(
         Contains the boolean indices for each sphere.
         shape: (number of seeds, number of voxels)
 
+    Raises
+    ------
+    ValueError
+        If ``niimg`` and ``mask_img`` are both provided or
+        if overlap is detected between spheres.
+
+    Warns
+    -----
+    RuntimeWarning
+        If the provided images contain NaN, they will be converted to zeroes.
+
     """
     seeds = list(seeds)
 
     # Compute world coordinates of all in-mask voxels.
     if niimg is None:
-        mask, affine = masking._load_mask_img(mask_img)
+        mask, affine = masking.load_mask_img(mask_img)
         # Get coordinate for all voxels inside of mask
         mask_coords = np.asarray(np.nonzero(mask)).T.tolist()
         X = None
@@ -118,21 +132,21 @@ def _apply_mask_and_get_affinity(
             target_shape=niimg.shape[:3],
             interpolation="nearest",
         )
-        mask, _ = masking._load_mask_img(mask_img)
+        mask, _ = masking.load_mask_img(mask_img)
         mask_coords = list(zip(*np.where(mask != 0)))
 
-        X = masking._apply_mask_fmri(niimg, mask_img)
+        X = masking.apply_mask_fmri(niimg, mask_img)
 
     elif niimg is not None:
         affine = niimg.affine
-        if np.isnan(np.sum(_safe_get_data(niimg))):
+        if np.isnan(np.sum(safe_get_data(niimg))):
             warn_with_log(
                 "The imgs you have fed into fit_transform() contains NaN "
                 "values which will be converted to zeroes."
             )
-            X = _safe_get_data(niimg, True).reshape([-1, niimg.shape[3]]).T
+            X = safe_get_data(niimg, True).reshape([-1, niimg.shape[3]]).T
         else:
-            X = _safe_get_data(niimg).reshape([-1, niimg.shape[3]]).T
+            X = safe_get_data(niimg).reshape([-1, niimg.shape[3]]).T
 
         mask_coords = list(np.ndindex(niimg.shape[:3]))
 
@@ -210,7 +224,7 @@ def _iter_signals_from_spheres(
     X, A = _apply_mask_and_get_affinity(
         seeds, niimg, radius, allow_overlap, mask_img=mask_img
     )
-    for _, row in enumerate(A.rows):
+    for row in A.rows:
         yield X[:, row]
 
 

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py

@@ -4,12 +4,14 @@
 # License: AGPL
 
 import warnings
+from typing import List, Tuple
 
 import nibabel
 import numpy as np
 import pytest
 from nilearn._utils import data_gen
 from nilearn.image import get_data
+from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_equal
 
 from junifer.external.nilearn import JuniferNiftiSpheresMasker
@@ -17,7 +19,7 @@ from junifer.external.nilearn import JuniferNiftiSpheresMasker
 
 # New BSD License
 
-# Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) The nilearn developers.
 # All rights reserved.
 
 
@@ -331,3 +333,76 @@ def test_nifti_spheres_masker_io_shapes() -> None:
         )
         test_data = masker.transform(img_4d)
         assert test_data.shape == (n_volumes, n_regions)
+
+
+@pytest.mark.parametrize(
+    "shape",
+    [
+        (10, 11, 12),
+        (10, 11, 12, 5),
+    ],
+)
+@pytest.mark.parametrize(
+    "radius, allow_overlap",
+    [
+        (2.0, True),
+        (2.0, False),
+        (3.0, True),
+        (4.0, True),
+        (5.0, True),
+    ],
+)
+@pytest.mark.parametrize(
+    "coords",
+    [
+        [(1, 1, 1)],
+        [(1, 1, 1), (4, 4, 4)],
+        [(1, 1, 1), (4, 4, 4), (10, 10, 10)],
+    ],
+)
+def test_junifer_and_nilearn_mean_agg_are_equal(
+    shape: Tuple[int, ...],
+    radius: float,
+    allow_overlap: bool,
+    coords: List[Tuple[int, int, int]],
+) -> None:
+    """Test junifer's masker behaves same as nilearn's when agg is mean.
+
+    Parameters
+    ----------
+    shape : tuple of int
+        The parametrized shape of the input image.
+    radius : float
+        The parametrized radius of the spheres.
+    allow_overlap : bool
+        The parametrized option to overlap spheres or not.
+    coords : list of tuple of int, int and int
+        The parametrized seeds.
+
+    """
+    # Set affine
+    affine = np.eye(4)
+    # Generate random image
+    input_img, mask_img = data_gen.generate_random_img(
+        shape=shape,
+        affine=affine,
+    )
+    # Compute junifer's version
+    junifer_masker = JuniferNiftiSpheresMasker(
+        seeds=coords,
+        radius=radius,
+        allow_overlap=allow_overlap,
+        mask_img=mask_img,
+    )
+    junifer_output = junifer_masker.fit_transform(input_img)
+    # Compute nilearn's version
+    nilearn_masker = NiftiSpheresMasker(
+        seeds=coords,
+        radius=radius,
+        allow_overlap=allow_overlap,
+        mask_img=mask_img,
+    )
+    nilearn_output = nilearn_masker.fit_transform(input_img)
+    # Checks
+    assert junifer_output.shape == nilearn_output.shape
+    np.testing.assert_almost_equal(junifer_output, nilearn_output)

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev145
+Version: 0.0.5.dev161
 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>
@@ -29,13 +29,13 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<1.27,>=1.24
-Requires-Dist: scipy<=1.11.4,>=1.9.0
-Requires-Dist: datalad<0.20,>=0.15.4
-Requires-Dist: pandas<2.2,>=1.4.0
-Requires-Dist: nibabel<5.11,>=3.2.0
-Requires-Dist: nilearn<=0.10.2,>=0.9.0
-Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+Requires-Dist: numpy<2.0.0,>=1.24.0
+Requires-Dist: scipy<=1.14.0,>=1.10.0
+Requires-Dist: datalad<1.2.0,>=1.0.0
+Requires-Dist: pandas<2.3.0,>=2.0.0
+Requires-Dist: nibabel<5.3.0,>=5.2.0
+Requires-Dist: nilearn<=0.10.4,>=0.10.3
+Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.18,>=0.17
 Requires-Dist: h5py>=3.10
 Requires-Dist: httpx[http2]==0.26.0
@@ -57,14 +57,14 @@ Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
-Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
-Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
-Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
-Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
+Requires-Dist: sphinx<7.4.0,>=7.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.17.0,>=0.15.0; extra == "docs"
+Requires-Dist: furo<2024.6.0,>=2024.4.27; extra == "docs"
+Requires-Dist: numpydoc<1.8.0,>=1.6.0; extra == "docs"
+Requires-Dist: julearn==0.3.3; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer.egg-info/SOURCES.txt

@@ -58,6 +58,7 @@ docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/115.doc
+docs/changes/newsfragments/136.enh
 docs/changes/newsfragments/161.feature
 docs/changes/newsfragments/273.feature
 docs/changes/newsfragments/323.feature
@@ -76,6 +77,7 @@ docs/changes/newsfragments/344.feature
 docs/changes/newsfragments/345.feature
 docs/changes/newsfragments/346.enh
 docs/changes/newsfragments/346.feature
+docs/changes/newsfragments/347.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/junifer.egg-info/requires.txt

@@ -1,11 +1,11 @@
 click<8.2,>=8.1.3
-numpy<1.27,>=1.24
-scipy<=1.11.4,>=1.9.0
-datalad<0.20,>=0.15.4
-pandas<2.2,>=1.4.0
-nibabel<5.11,>=3.2.0
-nilearn<=0.10.2,>=0.9.0
-sqlalchemy<=2.1.0,>=1.4.27
+numpy<2.0.0,>=1.24.0
+scipy<=1.14.0,>=1.10.0
+datalad<1.2.0,>=1.0.0
+pandas<2.3.0,>=2.0.0
+nibabel<5.3.0,>=5.2.0
+nilearn<=0.10.4,>=0.10.3
+sqlalchemy<=2.1.0,>=2.0.25
 ruamel.yaml<0.18,>=0.17
 h5py>=3.10
 httpx[http2]==0.26.0
@@ -31,14 +31,14 @@ tox
 pre-commit
 
 [docs]
-seaborn<0.13,>=0.11.2
-sphinx<7.3,>=5.3.0
-sphinx-gallery<0.15.0,>=0.11.0
-furo<2023.10.0,>=2022.9.29
-numpydoc<1.6,>=1.5.0
-julearn<0.4,>=0.3.0
+seaborn<0.14.0,>=0.13.0
+sphinx<7.4.0,>=7.3.0
+sphinx-gallery<0.17.0,>=0.15.0
+furo<2024.6.0,>=2024.4.27
+numpydoc<1.8.0,>=1.6.0
+julearn==0.3.3
 sphinx-copybutton<0.5.3,>=0.5.1
-towncrier<23.7,>=22.12.0
+towncrier<23.12.0,>=23.10.0
 sphinxcontrib-mermaid<0.10,>=0.8.1
 
 [neurokit2]

{junifer-0.0.5.dev145 → junifer-0.0.5.dev161}/pyproject.toml

@@ -37,13 +37,13 @@ classifiers = [
 ]
 dependencies = [
     "click>=8.1.3,<8.2",
-    "numpy>=1.24,<1.27",
-    "scipy>=1.9.0,<=1.11.4",
-    "datalad>=0.15.4,<0.20",
-    "pandas>=1.4.0,<2.2",
-    "nibabel>=3.2.0,<5.11",
-    "nilearn>=0.9.0,<=0.10.2",
-    "sqlalchemy>=1.4.27,<=2.1.0",
+    "numpy>=1.24.0,<2.0.0",
+    "scipy>=1.10.0,<=1.14.0",
+    "datalad>=1.0.0,<1.2.0",
+    "pandas>=2.0.0,<2.3.0",
+    "nibabel>=5.2.0,<5.3.0",
+    "nilearn>=0.10.3,<=0.10.4",
+    "sqlalchemy>=2.0.25,<=2.1.0",
     "ruamel.yaml>=0.17,<0.18",
     "h5py>=3.10",
     "httpx[http2]==0.26.0",
@@ -76,14 +76,14 @@ onthefly = [
 neurokit2 = ["neurokit2>=0.1.7"]
 dev = ["tox", "pre-commit"]
 docs = [
-    "seaborn>=0.11.2,<0.13",
-    "sphinx>=5.3.0,<7.3",
-    "sphinx-gallery>=0.11.0,<0.15.0",
-    "furo>=2022.9.29,<2023.10.0",
-    "numpydoc>=1.5.0,<1.6",
-    "julearn>=0.3.0,<0.4",
+    "seaborn>=0.13.0,<0.14.0",
+    "sphinx>=7.3.0,<7.4.0",
+    "sphinx-gallery>=0.15.0,<0.17.0",
+    "furo>=2024.4.27,<2024.6.0",
+    "numpydoc>=1.6.0,<1.8.0",
+    "julearn==0.3.3",
     "sphinx-copybutton>=0.5.1,<0.5.3",
-    "towncrier>=22.12.0,<23.7",
+    "towncrier>=23.10.0,<23.12.0",
     "sphinxcontrib-mermaid>=0.8.1,<0.10",
 ]