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

junifer/markers/falff/falff_parcels.py

@@ -6,10 +6,14 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Annotated, Any
+
+from pydantic import BeforeValidator
 
 from ...api.decorators import register_marker
-from ...utils import logger
+from ...datagrabber import DataType
+from ...utils import ensure_list
+from ..base import logger
 from ..parcel_aggregation import ParcelAggregation
 from .falff_base import ALFFBase
 
@@ -26,33 +30,27 @@ class ALFFParcels(ALFFBase):
     parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
-    using : {"junifer", "afni"}
-        Implementation to use for computing ALFF:
-
-        * "junifer" : Use ``junifer``'s own ALFF implementation
-        * "afni" : Use AFNI's ``3dRSFC``
-
+    using : :enum:`.ALFFImpl`
+    agg_method : str, optional
+        The aggregation function to use.
+        See :func:`.get_aggfunc_by_name` for options (default "mean").
+    agg_method_params : dict or None, optional
+        The parameters to pass to the aggregation function.
+        See :func:`.get_aggfunc_by_name` for valid options (default None).
     highpass : positive float, optional
-        The highpass cutoff frequency for the bandpass filter. If 0,
-        it will not apply a highpass filter (default 0.01).
+        Highpass cutoff frequency (default 0.01).
     lowpass : positive float, optional
-        The lowpass cutoff frequency for the bandpass filter (default 0.1).
+        Lowpass cutoff frequency (default 0.1).
     tr : positive float, optional
-        The Repetition Time of the BOLD data. If None, will extract
-        the TR from NIfTI header (default None).
-    agg_method : str, optional
-        The method to perform aggregation using. 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
-        :func:`.get_aggfunc_by_name` (default None).
-    masks : str, dict or list of dict or str, optional
+        The repetition time of the BOLD data.
+        If None, will extract the TR from NIfTI header (default None).
+    masks : str, dict, list of them or None, 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
-        None).
+    name : str or None, optional
+        The name of the marker.
+        If None, will use the class name (default None).
 
     Notes
     -----
@@ -68,35 +66,12 @@ class ALFFParcels(ALFFBase):
 
     """
 
-    def __init__(
-        self,
-        parcellation: Union[str, list[str]],
-        using: str,
-        highpass: float = 0.01,
-        lowpass: float = 0.1,
-        tr: Optional[float] = None,
-        agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
-        name: Optional[str] = None,
-    ) -> None:
-        # Superclass init first to validate `using` parameter
-        super().__init__(
-            highpass=highpass,
-            lowpass=lowpass,
-            using=using,
-            tr=tr,
-            name=name,
-        )
-        self.parcellation = parcellation
-        self.agg_method = agg_method
-        self.agg_method_params = agg_method_params
-        self.masks = masks
+    parcellation: Annotated[str | list[str], BeforeValidator(ensure_list)]
 
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 
@@ -129,7 +104,7 @@ class ALFFParcels(ALFFBase):
 
         # Compute ALFF + fALFF
         alff_output, falff_output, alff_output_path, falff_output_path = (
-            self._compute(input_data=input)
+            self._compute(input_data=input, extra_input=extra_input)
         )
 
         # Perform aggregation on ALFF + fALFF
@@ -147,7 +122,7 @@ class ALFFParcels(ALFFBase):
                     method=self.agg_method,
                     method_params=self.agg_method_params,
                     masks=self.masks,
-                    on="BOLD",
+                    on=DataType.BOLD,
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
@@ -159,7 +134,7 @@ class ALFFParcels(ALFFBase):
                     method=self.agg_method,
                     method_params=self.agg_method_params,
                     masks=self.masks,
-                    on="BOLD",
+                    on=DataType.BOLD,
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,

junifer/markers/falff/falff_spheres.py

@@ -6,10 +6,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any, Literal
+
+from pydantic import PositiveFloat
 
 from ...api.decorators import register_marker
-from ...utils import logger
+from ...datagrabber import DataType
+from ..base import logger
 from ..sphere_aggregation import SphereAggregation
 from .falff_base import ALFFBase
 
@@ -26,40 +29,35 @@ class ALFFSpheres(ALFFBase):
     coords : str
         The name of the coordinates list to use.
         See :func:`.list_data` for options.
-    using : {"junifer", "afni"}
-        Implementation to use for computing ALFF:
-
-        * "junifer" : Use ``junifer``'s own ALFF implementation
-        * "afni" : Use AFNI's ``3dRSFC``
-
-    radius : float, optional
-        The radius of the sphere in mm. If None, the signal will be extracted
-        from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker`
-        for more information (default None).
+    using : :enum:`.ALFFImpl`
+    radius : ``zero`` or positive float or None, optional
+        The radius of the sphere in millimetres.
+        If None, the signal will be extracted from a single voxel.
+        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).
+        Whether to allow overlapping spheres.
+        If False, an error is raised if the spheres overlap (default False).
+    agg_method : str, optional
+        The aggregation function to use.
+        See :func:`.get_aggfunc_by_name` for options (default "mean").
+    agg_method_params : dict or None, optional
+        The parameters to pass to the aggregation function.
+        See :func:`.get_aggfunc_by_name` for valid options (default None).
     highpass : positive float, optional
-        The highpass cutoff frequency for the bandpass filter. If 0,
-        it will not apply a highpass filter (default 0.01).
+        Highpass cutoff frequency (default 0.01).
     lowpass : positive float, optional
-        The lowpass cutoff frequency for the bandpass filter (default 0.1).
+        Lowpass cutoff frequency (default 0.1).
     tr : positive float, optional
-        The Repetition Time of the BOLD data. If None, will extract
-        the TR from NIfTI header (default None).
-    agg_method : str, optional
-        The method to perform aggregation using. 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
-        :func:`.get_aggfunc_by_name`.
-    masks : str, dict or list of dict or str, optional
+        The repetition time of the BOLD data.
+        If None, will extract the TR from NIfTI header (default None).
+    masks : str, dict, list of them or None, 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
-        None).
+    name : str or None, optional
+        The name of the marker.
+        If None, will use the class name (default None).
 
     Notes
     -----
@@ -75,39 +73,14 @@ class ALFFSpheres(ALFFBase):
 
     """
 
-    def __init__(
-        self,
-        coords: str,
-        using: str,
-        radius: Optional[float] = None,
-        allow_overlap: bool = False,
-        highpass: float = 0.01,
-        lowpass: float = 0.1,
-        tr: Optional[float] = None,
-        agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
-        name: Optional[str] = None,
-    ) -> None:
-        # Superclass init first to validate `using` parameter
-        super().__init__(
-            highpass=highpass,
-            lowpass=lowpass,
-            using=using,
-            tr=tr,
-            name=name,
-        )
-        self.coords = coords
-        self.radius = radius
-        self.allow_overlap = allow_overlap
-        self.agg_method = agg_method
-        self.agg_method_params = agg_method_params
-        self.masks = masks
+    coords: str
+    radius: Literal[0] | PositiveFloat | None = None
+    allow_overlap: bool = False
 
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 
@@ -140,7 +113,7 @@ class ALFFSpheres(ALFFBase):
 
         # Compute ALFF + fALFF
         alff_output, falff_output, alff_output_path, falff_output_path = (
-            self._compute(input_data=input)
+            self._compute(input_data=input, extra_input=extra_input)
         )
 
         # Perform aggregation on ALFF / fALFF
@@ -160,7 +133,7 @@ class ALFFSpheres(ALFFBase):
                     method=self.agg_method,
                     method_params=self.agg_method_params,
                     masks=self.masks,
-                    on="BOLD",
+                    on=DataType.BOLD,
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
@@ -174,7 +147,7 @@ class ALFFSpheres(ALFFBase):
                     method=self.agg_method,
                     method_params=self.agg_method_params,
                     masks=self.masks,
-                    on="BOLD",
+                    on=DataType.BOLD,
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,

junifer/markers/falff/tests/test_falff_maps.py

@@ -7,14 +7,18 @@ import logging
 from pathlib import Path
 
 import pytest
-import scipy as sp
+import scipy.stats as sps
 
-from junifer.datagrabber import PatternDataladDataGrabber
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
-from junifer.markers import ALFFMaps
+from junifer.markers import ALFFImpl, ALFFMaps
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
 from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import ADHDTestingDataGrabber
+
+
+pytestmark = pytest.mark.external
 
 
 MAPS = "Smith_rsn_10"
@@ -38,14 +42,13 @@ def test_ALFFMaps_storage_type(feature: str) -> None:
     """
     assert "vector" == ALFFMaps(
         maps=MAPS,
-        using="junifer",
-    ).storage_type(input_type="BOLD", output_feature=feature)
+        using=ALFFImpl.junifer,
+    ).storage_type(input_type=DataType.BOLD, output_feature=feature)
 
 
 def test_ALFFMaps(
     caplog: pytest.LogCaptureFixture,
     tmp_path: Path,
-    maps_datagrabber: PatternDataladDataGrabber,
 ) -> None:
     """Test ALFFMaps.
 
@@ -55,27 +58,25 @@ def test_ALFFMaps(
         The pytest.LogCaptureFixture object.
     tmp_path : pathlib.Path
         The path to the test directory.
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
 
     """
     # Update workdir to current test's tmp_path
     WorkDirManager().workdir = tmp_path
 
     with caplog.at_level(logging.DEBUG):
-        with maps_datagrabber as dg:
-            element = dg[("sub-01", "sub-001", "rest", "1")]
+        with ADHDTestingDataGrabber() as dg:
+            element = dg["sub-01"]
             element_data = DefaultDataReader().fit_transform(element)
 
             # Initialize marker
             marker = ALFFMaps(
                 maps=MAPS,
-                using="junifer",
+                using=ALFFImpl.junifer,
             )
             # Check correct output
             for name in ["alff", "falff"]:
                 assert "vector" == marker.storage_type(
-                    input_type="BOLD", output_feature=name
+                    input_type=DataType.BOLD, output_feature=name
                 )
 
             # Fit transform marker on data
@@ -99,7 +100,7 @@ def test_ALFFMaps(
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = HDF5FeatureStorage(tmp_path / "falff_maps.hdf5")
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_maps.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,
@@ -118,30 +119,26 @@ def test_ALFFMaps(
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires AFNI to be in PATH"
 )
-def test_ALFFMaps_comparison(
-    tmp_path: Path, maps_datagrabber: PatternDataladDataGrabber
-) -> None:
+def test_ALFFMaps_comparison(tmp_path: Path) -> None:
     """Test ALFFMaps implementation comparison.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
 
     """
     # Update workdir to current test's tmp_path
     WorkDirManager().workdir = tmp_path
 
-    with maps_datagrabber as dg:
-        element = dg[("sub-01", "sub-001", "rest", "1")]
+    with ADHDTestingDataGrabber() as dg:
+        element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
 
         # Initialize marker
         junifer_marker = ALFFMaps(
             maps=MAPS,
-            using="junifer",
+            using=ALFFImpl.junifer,
         )
         # Fit transform marker on data
         junifer_output = junifer_marker.fit_transform(element_data)
@@ -151,7 +148,7 @@ def test_ALFFMaps_comparison(
         # Initialize marker
         afni_marker = ALFFMaps(
             maps=MAPS,
-            using="afni",
+            using=ALFFImpl.afni,
         )
         # Fit transform marker on data
         afni_output = afni_marker.fit_transform(element_data)
@@ -160,7 +157,7 @@ def test_ALFFMaps_comparison(
 
         for feature in afni_output_bold.keys():
             # Check for Pearson correlation coefficient
-            r, _ = sp.stats.pearsonr(
+            r, _ = sps.pearsonr(
                 junifer_output_bold[feature]["data"][0],
                 afni_output_bold[feature]["data"][0],
             )

junifer/markers/falff/tests/test_falff_mask.py

@@ -0,0 +1,99 @@
+"""Provide tests for the ALFF and fALFF computation with masks."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+
+import nibabel as nib
+import numpy as np
+import pytest
+from numpy.testing import assert_allclose, assert_array_equal
+
+from junifer.markers.falff._afni_falff import AFNIALFF
+from junifer.markers.falff._junifer_falff import JuniferALFF
+from junifer.pipeline import WorkDirManager
+from junifer.pipeline.utils import _check_afni
+
+
+def _save(data: np.ndarray, path: Path, tr: float = 2.0) -> Path:
+    """Save data as NIfTI, with the TR in the header for 4D data."""
+    img = nib.Nifti1Image(data, np.eye(4))
+    if data.ndim == 4:
+        img.header.set_zooms((1.0, 1.0, 1.0, tr))
+    nib.save(img, path)
+    return path
+
+
+def _data(tmp_path: Path) -> tuple[Path, Path, np.ndarray]:
+    """Create BOLD data and a mask of half of the voxels."""
+    data = np.random.default_rng(0).normal(size=(6, 6, 6, 100)) + 100
+    bold_path = _save(data.astype(np.float32), tmp_path / "bold.nii")
+    mask = np.zeros((6, 6, 6), dtype=np.uint8)
+    mask[3:] = 1
+    mask_path = _save(mask, tmp_path / "mask.nii")
+    return bold_path, mask_path, mask.astype(bool)
+
+
+@pytest.mark.parametrize(
+    "estimator",
+    [
+        JuniferALFF,
+        pytest.param(
+            AFNIALFF,
+            marks=pytest.mark.skipif(
+                _check_afni() is False, reason="requires AFNI to be in PATH"
+            ),
+        ),
+    ],
+)
+def test_ALFF_mask(
+    estimator: type[JuniferALFF | AFNIALFF], tmp_path: Path
+) -> None:
+    """Test the ALFF and fALFF computation is restricted to the mask.
+
+    The values are computed for each voxel, so inside the mask they are the
+    same as without mask, and outside the mask they are 0.
+
+    Parameters
+    ----------
+    estimator : JuniferALFF or AFNIALFF
+        The ALFF estimator to test.
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    WorkDirManager().workdir = tmp_path
+    bold_path, mask_path, mask = _data(tmp_path)
+    kwargs = {"highpass": 0.01, "lowpass": 0.1, "tr": 2.0}
+    masked = estimator().compute(bold_path, mask_path=mask_path, **kwargs)
+    unmasked = estimator().compute(bold_path, **kwargs)
+    for i_map in range(2):  # ALFF and fALFF
+        t_masked = masked[i_map].get_fdata()
+        t_unmasked = unmasked[i_map].get_fdata()
+        assert_array_equal(t_masked[~mask], 0)
+        assert (t_masked[mask] > 0).all()
+        assert_allclose(t_masked[mask], t_unmasked[mask], rtol=1e-6)
+
+
+@pytest.mark.skipif(
+    _check_afni() is False, reason="requires AFNI to be in PATH"
+)
+def test_AFNIALFF_no_time_series(tmp_path: Path) -> None:
+    """Test 3dRSFC does not output the bandpassed time series.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    WorkDirManager().workdir = tmp_path
+    bold_path, mask_path, _ = _data(tmp_path)
+    alff_path = AFNIALFF().compute(
+        bold_path, highpass=0.01, lowpass=0.1, tr=2.0, mask_path=mask_path
+    )[2]
+    # Only the parameters (ALFF, fALFF and mALFF) are in the output directory
+    outputs = {x.name for x in alff_path.parent.iterdir()}
+    assert not any("_LFF+" in x for x in outputs)
+    assert any("_ALFF+" in x for x in outputs)

junifer/markers/falff/tests/test_falff_parcels.py

@@ -8,16 +8,20 @@ import logging
 from pathlib import Path
 
 import pytest
-import scipy as sp
+import scipy.stats as sps
 
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
-from junifer.markers.falff import ALFFParcels
+from junifer.markers import ALFFImpl, ALFFParcels
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
 
@@ -39,8 +43,8 @@ def test_ALFFParcels_storage_type(feature: str) -> None:
     """
     assert "vector" == ALFFParcels(
         parcellation=PARCELLATION,
-        using="junifer",
-    ).storage_type(input_type="BOLD", output_feature=feature)
+        using=ALFFImpl.junifer,
+    ).storage_type(input_type=DataType.BOLD, output_feature=feature)
 
 
 def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
@@ -63,7 +67,7 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Initialize marker
             marker = ALFFParcels(
                 parcellation=PARCELLATION,
-                using="junifer",
+                using=ALFFImpl.junifer,
             )
             # Fit transform marker on data
             output = marker.fit_transform(element_data)
@@ -86,7 +90,7 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(tmp_path / "falff_parcels.sqlite")
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_parcels.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,
@@ -116,7 +120,7 @@ def test_ALFFParcels_comparison(tmp_path: Path) -> None:
         # Initialize marker
         junifer_marker = ALFFParcels(
             parcellation=PARCELLATION,
-            using="junifer",
+            using=ALFFImpl.junifer,
         )
         # Fit transform marker on data
         junifer_output = junifer_marker.fit_transform(element_data)
@@ -126,7 +130,7 @@ def test_ALFFParcels_comparison(tmp_path: Path) -> None:
         # Initialize marker
         afni_marker = ALFFParcels(
             parcellation=PARCELLATION,
-            using="afni",
+            using=ALFFImpl.afni,
         )
         # Fit transform marker on data
         afni_output = afni_marker.fit_transform(element_data)
@@ -135,7 +139,7 @@ def test_ALFFParcels_comparison(tmp_path: Path) -> None:
 
         for feature in afni_output_bold.keys():
             # Check for Pearson correlation coefficient
-            r, _ = sp.stats.pearsonr(
+            r, _ = sps.pearsonr(
                 junifer_output_bold[feature]["data"][0],
                 afni_output_bold[feature]["data"][0],
             )

junifer/markers/falff/tests/test_falff_spheres.py

@@ -8,16 +8,20 @@ import logging
 from pathlib import Path
 
 import pytest
-import scipy as sp
+import scipy.stats as sps
 
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
-from junifer.markers.falff import ALFFSpheres
+from junifer.markers import ALFFImpl, ALFFSpheres
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 COORDINATES = "DMNBuckner"
 
 
@@ -39,8 +43,8 @@ def test_ALFFSpheres_storage_type(feature: str) -> None:
     """
     assert "vector" == ALFFSpheres(
         coords=COORDINATES,
-        using="junifer",
-    ).storage_type(input_type="BOLD", output_feature=feature)
+        using=ALFFImpl.junifer,
+    ).storage_type(input_type=DataType.BOLD, output_feature=feature)
 
 
 def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
@@ -63,7 +67,7 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Initialize marker
             marker = ALFFSpheres(
                 coords=COORDINATES,
-                using="junifer",
+                using=ALFFImpl.junifer,
                 radius=5.0,
             )
             # Fit transform marker on data
@@ -89,7 +93,7 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(tmp_path / "falff_spheres.sqlite")
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_spheres.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,
@@ -119,7 +123,7 @@ def test_ALFFSpheres_comparison(tmp_path: Path) -> None:
         # Initialize marker
         junifer_marker = ALFFSpheres(
             coords=COORDINATES,
-            using="junifer",
+            using=ALFFImpl.junifer,
             radius=5.0,
         )
         # Fit transform marker on data
@@ -130,7 +134,7 @@ def test_ALFFSpheres_comparison(tmp_path: Path) -> None:
         # Initialize marker
         afni_marker = ALFFSpheres(
             coords=COORDINATES,
-            using="afni",
+            using=ALFFImpl.afni,
             radius=5.0,
         )
         # Fit transform marker on data
@@ -140,7 +144,7 @@ def test_ALFFSpheres_comparison(tmp_path: Path) -> None:
 
         for feature in afni_output_bold.keys():
             # Check for Pearson correlation coefficient
-            r, _ = sp.stats.pearsonr(
+            r, _ = sps.pearsonr(
                 junifer_output_bold[feature]["data"][0],
                 afni_output_bold[feature]["data"][0],
             )