junifer 0.0.5.dev145__py3-none-any.whl → 0.0.5.dev161__py3-none-any.whl

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/external/nilearn/__init__.py

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

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/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.dist-info → junifer-0.0.5.dev161.dist-info}/METADATA

@@ -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
@@ -53,14 +53,14 @@ 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'
 Provides-Extra: neurokit2
 Requires-Dist: neurokit2 >=0.1.7 ; extra == 'neurokit2'

{junifer-0.0.5.dev145.dist-info → junifer-0.0.5.dev161.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=-T9XmiCCL0j3YLx-0Pph15sPfL5FlcBDscajjJ-V4sU,604
-junifer/_version.py,sha256=LLX_zE2hwuXoJcCrJFHp63l96uwV1o-_baS2uJTkq4Y,428
+junifer/_version.py,sha256=UfXRLkQeUycPYOXVnbIPOq4a2hAaHq9EznoNGJMncyo,428
 junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
 junifer/api/__init__.py,sha256=lwyIF0hPc7fICuSoddJfay0LPqlTRxHJ_xbtizgFYZA,312
 junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
@@ -132,9 +132,9 @@ junifer/external/h5io/h5io/_h5io.py,sha256=8dWZDYegoPcBkH_fHPdl0eXNWTaRdk9hfIQo8
 junifer/external/h5io/h5io/_version.py,sha256=mFY0GwwuN-a3M8w93_mskS6GZIvv9SNdjLfJaWNsm-I,22
 junifer/external/h5io/h5io/chunked_array.py,sha256=K1HWf7R2Jc7gCzBqAoBjx0ZnMmUhTe3iAO6RF6PdUO4,3338
 junifer/external/h5io/h5io/chunked_list.py,sha256=1Y5BbuWzurJlEFQzJNuDdC3fNZ39ENEMba99X_4VeSM,1952
-junifer/external/nilearn/__init__.py,sha256=a2Umwm3_WeqIC7DqPUmnUonYfX3LUdQ0ScDGZrNP6y4,180
-junifer/external/nilearn/junifer_nifti_spheres_masker.py,sha256=sA8fbdaTHk2omYidApNO1hN0ObwDJR_h26P9i3MhbvM,16274
-junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py,sha256=qlMFWjo9y8mNLrdmN2qCEK6_nplASv2OlomSfTxDcuw,10370
+junifer/external/nilearn/__init__.py,sha256=Cx9SM-AHU2OmyC5n6YmRv2JMEYp3qoVnxl5bk4XYWjc,222
+junifer/external/nilearn/junifer_nifti_spheres_masker.py,sha256=DbSK2hKrgpHZ_vCRLbVv3YJpLZNkEAG0HFfQQpG6zdU,16546
+junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py,sha256=zpvBYIvaNjUj9fIUg5K78LRzJqbyMYlUo2UQYS9_lo4,12275
 junifer/markers/__init__.py,sha256=u4BFgS_3GXAwFN2HfqdAhlBkyenLw4IYlMlwXwnjkVQ,1235
 junifer/markers/base.py,sha256=7_TLrz8dZH_3t1zgSSW2yCnDO2DGGAxFMZLHDkvJ_NM,6985
 junifer/markers/brainprint.py,sha256=On1M8Hp14g-S-o-3TVVYTGfviJEz-xjuAVg0mRHyxFg,21793
@@ -263,10 +263,10 @@ junifer/utils/logging.py,sha256=b02qVTdE-WNVo6uxCYdIHVmNfM7An0NdCJNq_2Gte8o,9355
 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=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.5.dev145.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.5.dev145.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.5.dev145.dist-info/METADATA,sha256=wLNrUZogrVkFN8xbkxvaSa9uJys188Aq-NJ4OrWeUAU,8270
-junifer-0.0.5.dev145.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-junifer-0.0.5.dev145.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.5.dev145.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.5.dev145.dist-info/RECORD,,
+junifer-0.0.5.dev161.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.5.dev161.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.5.dev161.dist-info/METADATA,sha256=AFnrJ4D7WeYBR0_-Crevx4ezleXY3PX4hz5LR9VKvvo,8281
+junifer-0.0.5.dev161.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+junifer-0.0.5.dev161.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.5.dev161.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.5.dev161.dist-info/RECORD,,