docs/builtin.rst

@@ -176,11 +176,11 @@ Available
      - Calculate regional homogeneity over spheres placed on coordinates
      - Done
      - 0.0.1
-   * - :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels`
+   * - :class:`junifer.markers.ALFFParcels`
      - Calculate (f)ALFF and aggregate using parcellations
      - Done
      - 0.0.1
-   * - :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres`
+   * - :class:`junifer.markers.ALFFSpheres`
      - Calculate (f)ALFF and aggregate using spheres placed on coordinates
      - Done
      - 0.0.1
@@ -541,13 +541,13 @@ Available
    * - Nilearn's MNI152 1mm-resolution mask
      - | ``compute_brain_mask``
      - 0.0.2
-     - | Compute the whole-brain mask. This mask is calculated using MNI152 1mm-resolution template mask onto the 
+     - | Compute the whole-brain mask. This mask is calculated using MNI152 1mm-resolution template mask onto the
        | target image. See :func:`nilearn.masking.compute_brain_mask`
    * - Nilearn's mask computed from FMRI data
      - | ``compute_epi_mask``
      - 0.0.2
-     - | Compute a brain mask from fMRI data. This is based on an heuristic proposed by T.Nichols: find the least 
+     - | Compute a brain mask from fMRI data. This is based on an heuristic proposed by T.Nichols: find the least
-       | dense point of the histogram, between fractions ``lower_cutoff`` and ``upper_cutoff`` of the total image 
+       | dense point of the histogram, between fractions ``lower_cutoff`` and ``upper_cutoff`` of the total image
        | histogram. See :func:`nilearn.masking.compute_epi_mask`
    * - Nilearn's background mask
      - | ``compute_background_mask``

docs/changes/newsfragments/187.bugfix

@@ -1 +1 @@
-Fix :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels`, :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres`, :class:`junifer.markers.ReHoSpheres` and :class:`junifer.markers.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
+Fix :class:`junifer.markers.ALFFParcels`, :class:`junifer.markers.ALFFSpheres`, :class:`junifer.markers.ReHoSpheres` and :class:`junifer.markers.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_

docs/changes/newsfragments/216.change

@@ -0,0 +1 @@
+``AmplitudeLowFrequencyFluctuationParcels`` and ``AmplitudeLowFrequencyFluctuationSpheres`` are renamed to :class:`junifer.markers.ALFFParcels` and :class:`junifer.markers.ALFFSpheres` by `Synchon Mandal`_

docs/whats_new.rst

@@ -150,9 +150,8 @@ Features
 - Implement :class:`junifer.markers.ReHoParcels` and
   :class:`junifer.markers.ReHoSpheres` markers by `Synchon Mandal`_ (:gh:`36`)
 
-- Implement :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels` and
+- Implement :class:`junifer.markers.ALFFParcels` and
-  :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres` markers by
+  :class:`junifer.markers.ALFFSpheres` markers by `Fede Raimondo`_ (:gh:`35`)
-  `Fede Raimondo`_ (:gh:`35`)
 
 Misc
 ^^^^

junifer/markers/__init__.py

@@ -18,10 +18,7 @@ from .functional_connectivity import (
     EdgeCentricFCSpheres,
 )
 from .reho import ReHoParcels, ReHoSpheres
-from .falff import (
+from .falff import ALFFParcels, ALFFSpheres
-    AmplitudeLowFrequencyFluctuationParcels,
-    AmplitudeLowFrequencyFluctuationSpheres,
-)
 from .temporal_snr import (
     TemporalSNRParcels,
     TemporalSNRSpheres,

junifer/markers/falff/__init__.py

@@ -3,5 +3,5 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from .falff_parcels import AmplitudeLowFrequencyFluctuationParcels
+from .falff_parcels import ALFFParcels
-from .falff_spheres import AmplitudeLowFrequencyFluctuationSpheres
+from .falff_spheres import ALFFSpheres

junifer/markers/falff/falff_base.py

@@ -10,10 +10,10 @@ from typing import Dict, List, Optional
 
 from ...utils.logging import raise_error
 from ..base import BaseMarker
-from .falff_estimator import AmplitudeLowFrequencyFluctuationEstimator
+from .falff_estimator import ALFFEstimator
 
 
-class AmplitudeLowFrequencyFluctuationBase(BaseMarker):
+class ALFFBase(BaseMarker):
     """Base class for (fractional) Amplitude Low Frequency Fluctuation.
 
     Parameters
@@ -144,7 +144,7 @@ class AmplitudeLowFrequencyFluctuationBase(BaseMarker):
                 "before calling the `compute` method."
             )
 
-        estimator = AmplitudeLowFrequencyFluctuationEstimator()
+        estimator = ALFFEstimator()
 
         alff, falff = estimator.fit_transform(
             use_afni=self.use_afni,

junifer/markers/falff/falff_estimator.py

@@ -26,16 +26,15 @@ if TYPE_CHECKING:
 
 
 @singleton
-class AmplitudeLowFrequencyFluctuationEstimator:
+class ALFFEstimator:
-    """Estimator class for AmplitudeLowFrequencyFluctuationBase.
+    """Estimator class for (fractional) Amplitude Low Frequency Fluctuation.
 
     This class is a singleton and is used for efficient computation of fALFF,
     by caching the voxel-wise ALFF map for a given set of file path and
     computation parameters.
 
     .. warning:: This class can only be used via
-    :class:`junifer.markers.falff.AmplitudeLowFrequencyFluctuationBase`
+    :class:`junifer.markers.falff.ALFFBase` as it serves a specific purpose.
-    as it serves a specific purpose.
 
     Parameters
     ----------

junifer/markers/falff/falff_parcels.py

@@ -9,13 +9,11 @@ from typing import Dict, List, Optional, Union
 
 from ...api.decorators import register_marker
 from .. import ParcelAggregation
-from .falff_base import AmplitudeLowFrequencyFluctuationBase
+from .falff_base import ALFFBase
 
 
 @register_marker
-class AmplitudeLowFrequencyFluctuationParcels(
+class ALFFParcels(ALFFBase):
-    AmplitudeLowFrequencyFluctuationBase
-):
     """Class for computing fALFF/ALFF on parcels.
 
     Parameters

junifer/markers/falff/falff_spheres.py

@@ -9,13 +9,11 @@ from typing import Dict, List, Optional, Union
 
 from ...api.decorators import register_marker
 from .. import SphereAggregation
-from .falff_base import AmplitudeLowFrequencyFluctuationBase
+from .falff_base import ALFFBase
 
 
 @register_marker
-class AmplitudeLowFrequencyFluctuationSpheres(
+class ALFFSpheres(ALFFBase):
-    AmplitudeLowFrequencyFluctuationBase
-):
     """Class for computing fALFF/ALFF on spheres.
 
     Parameters

junifer/markers/falff/tests/test_falff_estimator.py

@@ -10,22 +10,20 @@ from nibabel import Nifti1Image
 from scipy.stats import pearsonr
 
 from junifer.datareader import DefaultDataReader
-from junifer.markers.falff.falff_estimator import (
+from junifer.markers.falff.falff_estimator import ALFFEstimator
-    AmplitudeLowFrequencyFluctuationEstimator,
-)
 from junifer.pipeline.utils import _check_afni
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 from junifer.utils import logger
 
 
-def test_AmplitudeLowFrequencyFluctuationEstimator_cache_python() -> None:
+def test_ALFFEstimator_cache_python() -> None:
     """Test that the cache works properly when using python."""
     with PartlyCloudyTestingDataGrabber() as dg:
         input = dg["sub-01"]
 
     input = DefaultDataReader().fit_transform(input)
 
-    estimator = AmplitudeLowFrequencyFluctuationEstimator()
+    estimator = ALFFEstimator()
     start_time = time.time()
     alff, falff = estimator.fit_transform(
         use_afni=False,
@@ -111,14 +109,14 @@ def test_AmplitudeLowFrequencyFluctuationEstimator_cache_python() -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires afni to be in PATH"
 )
-def test_AmplitudeLowFrequencyFluctuationEstimator_cache_afni() -> None:
+def test_ALFFEstimator_cache_afni() -> None:
     """Test that the cache works properly when using afni."""
     with PartlyCloudyTestingDataGrabber() as dg:
         input = dg["sub-01"]
 
     input = DefaultDataReader().fit_transform(input)
 
-    estimator = AmplitudeLowFrequencyFluctuationEstimator()
+    estimator = ALFFEstimator()
     start_time = time.time()
     alff, falff = estimator.fit_transform(
         use_afni=True,
@@ -204,13 +202,13 @@ def test_AmplitudeLowFrequencyFluctuationEstimator_cache_afni() -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires afni to be in PATH"
 )
-def test_AmplitudeLowFrequencyFluctuationEstimator_afni_vs_python() -> None:
+def test_ALFFEstimator_afni_vs_python() -> None:
     """Test that the cache works properly when using afni."""
     with PartlyCloudyTestingDataGrabber() as dg:
         input = dg["sub-01"]
 
     input = DefaultDataReader().fit_transform(input)
-    estimator = AmplitudeLowFrequencyFluctuationEstimator()
+    estimator = ALFFEstimator()
 
     # Use an arbitrary TR to test the AFNI vs Python implementation
     afni_alff, afni_falff = estimator.fit_transform(

junifer/markers/falff/tests/test_falff_parcels.py

@@ -11,7 +11,7 @@ from numpy.testing import assert_array_equal
 from scipy.stats import pearsonr
 
 from junifer.datareader import DefaultDataReader
-from junifer.markers.falff import AmplitudeLowFrequencyFluctuationParcels
+from junifer.markers.falff import ALFFParcels
 from junifer.pipeline.utils import _check_afni
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
@@ -21,8 +21,8 @@ from junifer.utils import logger
 _PARCELLATION = "Schaefer100x7"
 
 
-def test_AmplitudeLowFrequencyFluctuationParcels_python() -> None:
+def test_ALFFParcels_python() -> None:
-    """Test AmplitudeLowFrequencyFluctuationParcels using python."""
+    """Test ALFFParcels using python."""
     # Get the SPM auditory data:
 
     with PartlyCloudyTestingDataGrabber() as dg:
@@ -30,7 +30,7 @@ def test_AmplitudeLowFrequencyFluctuationParcels_python() -> None:
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker = AmplitudeLowFrequencyFluctuationParcels(
+    marker = ALFFParcels(
         parcellation=_PARCELLATION,
         method="mean",
         use_afni=False,
@@ -46,15 +46,15 @@ def test_AmplitudeLowFrequencyFluctuationParcels_python() -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires afni to be in PATH"
 )
-def test_AmplitudeLowFrequencyFluctuationParcels_afni() -> None:
+def test_ALFFParcels_afni() -> None:
-    """Test AmplitudeLowFrequencyFluctuationParcels using afni."""
+    """Test ALFFParcels using afni."""
     # Get the SPM auditory data:
     with PartlyCloudyTestingDataGrabber() as dg:
         input = dg["sub-01"]
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker = AmplitudeLowFrequencyFluctuationParcels(
+    marker = ALFFParcels(
         parcellation=_PARCELLATION,
         method="mean",
         use_afni=True,
@@ -67,7 +67,7 @@ def test_AmplitudeLowFrequencyFluctuationParcels_afni() -> None:
     assert afni_values.shape == (1, 100)
 
     # Again, should be blazing fast
-    marker = AmplitudeLowFrequencyFluctuationParcels(
+    marker = ALFFParcels(
         parcellation=_PARCELLATION, method="mean", fractional=False
     )
     assert marker.use_afni is None
@@ -82,10 +82,10 @@ def test_AmplitudeLowFrequencyFluctuationParcels_afni() -> None:
 @pytest.mark.parametrize(
     "fractional", [True, False], ids=["fractional", "non-fractional"]
 )
-def test_AmplitudeLowFrequencyFluctuationParcels_python_vs_afni(
+def test_ALFFParcels_python_vs_afni(
     fractional: bool,
 ) -> None:
-    """Test AmplitudeLowFrequencyFluctuationParcels using python.
+    """Test ALFFParcels using python.
 
     Parameters
     ----------
@@ -98,7 +98,7 @@ def test_AmplitudeLowFrequencyFluctuationParcels_python_vs_afni(
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker_python = AmplitudeLowFrequencyFluctuationParcels(
+    marker_python = ALFFParcels(
         parcellation=_PARCELLATION,
         method="mean",
         use_afni=False,
@@ -110,7 +110,7 @@ def test_AmplitudeLowFrequencyFluctuationParcels_python_vs_afni(
     assert python_values.ndim == 2
     assert python_values.shape == (1, 100)
 
-    marker_afni = AmplitudeLowFrequencyFluctuationParcels(
+    marker_afni = ALFFParcels(
         parcellation=_PARCELLATION,
         method="mean",
         use_afni=True,
@@ -127,10 +127,10 @@ def test_AmplitudeLowFrequencyFluctuationParcels_python_vs_afni(
     assert r > 0.99
 
 
-def test_AmplitudeLowFrequencyFluctuationParcels_storage(
+def test_ALFFParcels_storage(
     tmp_path: Path,
 ) -> None:
-    """Test AmplitudeLowFrequencyFluctuationParcels storage.
+    """Test ALFFParcels storage.
 
     Parameters
     ----------
@@ -142,7 +142,7 @@ def test_AmplitudeLowFrequencyFluctuationParcels_storage(
         input = dg["sub-01"]
         input = DefaultDataReader().fit_transform(input)
         # Create ParcelAggregation object
-        marker = AmplitudeLowFrequencyFluctuationParcels(
+        marker = ALFFParcels(
             parcellation=_PARCELLATION,
             method="mean",
             use_afni=False,

junifer/markers/falff/tests/test_falff_spheres.py

@@ -11,7 +11,7 @@ from numpy.testing import assert_array_equal
 from scipy.stats import pearsonr
 
 from junifer.datareader import DefaultDataReader
-from junifer.markers.falff import AmplitudeLowFrequencyFluctuationSpheres
+from junifer.markers.falff import ALFFSpheres
 from junifer.pipeline.utils import _check_afni
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
@@ -21,8 +21,8 @@ from junifer.utils import logger
 _COORDINATES = "DMNBuckner"
 
 
-def test_AmplitudeLowFrequencyFluctuationSpheres_python() -> None:
+def test_ALFFSpheres_python() -> None:
-    """Test AmplitudeLowFrequencyFluctuationSpheres using python."""
+    """Test ALFFSpheres using python."""
     # Get the SPM auditory data:
 
     with PartlyCloudyTestingDataGrabber() as dg:
@@ -30,7 +30,7 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_python() -> None:
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker = AmplitudeLowFrequencyFluctuationSpheres(
+    marker = ALFFSpheres(
         coords=_COORDINATES,
         radius=5,
         method="mean",
@@ -47,15 +47,15 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_python() -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires afni to be in PATH"
 )
-def test_AmplitudeLowFrequencyFluctuationSpheres_afni() -> None:
+def test_ALFFSpheres_afni() -> None:
-    """Test AmplitudeLowFrequencyFluctuationSpheres using afni."""
+    """Test ALFFSpheres using afni."""
     # Get the SPM auditory data:
     with PartlyCloudyTestingDataGrabber() as dg:
         input = dg["sub-01"]
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker = AmplitudeLowFrequencyFluctuationSpheres(
+    marker = ALFFSpheres(
         coords=_COORDINATES,
         radius=5,
         method="mean",
@@ -69,7 +69,7 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_afni() -> None:
     assert afni_values.shape == (1, 6)
 
     # Again, should be blazing fast
-    marker = AmplitudeLowFrequencyFluctuationSpheres(
+    marker = ALFFSpheres(
         coords=_COORDINATES,
         radius=5,
         method="mean",
@@ -87,10 +87,10 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_afni() -> None:
 @pytest.mark.parametrize(
     "fractional", [True, False], ids=["fractional", "non-fractional"]
 )
-def test_AmplitudeLowFrequencyFluctuationSpheres_python_vs_afni(
+def test_ALFFSpheres_python_vs_afni(
     fractional: bool,
 ) -> None:
-    """Test AmplitudeLowFrequencyFluctuationSpheres python vs afni results.
+    """Test ALFFSpheres python vs afni results.
 
     Parameters
     ----------
@@ -102,7 +102,7 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_python_vs_afni(
 
     input = DefaultDataReader().fit_transform(input)
     # Create ParcelAggregation object
-    marker_python = AmplitudeLowFrequencyFluctuationSpheres(
+    marker_python = ALFFSpheres(
         coords=_COORDINATES,
         radius=5,
         method="mean",
@@ -115,7 +115,7 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_python_vs_afni(
     assert python_values.ndim == 2
     assert python_values.shape == (1, 6)
 
-    marker_afni = AmplitudeLowFrequencyFluctuationSpheres(
+    marker_afni = ALFFSpheres(
         coords=_COORDINATES,
         radius=5,
         method="mean",
@@ -133,10 +133,10 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_python_vs_afni(
     assert r > 0.99
 
 
-def test_AmplitudeLowFrequencyFluctuationSpheres_storage(
+def test_ALFFSpheres_storage(
     tmp_path: Path,
 ) -> None:
-    """Test AmplitudeLowFrequencyFluctuationSpheres storage.
+    """Test ALFFSpheres storage.
 
     Parameters
     ----------
@@ -148,7 +148,7 @@ def test_AmplitudeLowFrequencyFluctuationSpheres_storage(
         input = dg["sub-01"]
         input = DefaultDataReader().fit_transform(input)
         # Create ParcelAggregation object
-        marker = AmplitudeLowFrequencyFluctuationSpheres(
+        marker = ALFFSpheres(
             coords=_COORDINATES,
             radius=5,
             method="mean",

junifer/markers/parcel_aggregation.py

@@ -13,7 +13,7 @@ from nilearn.maskers import NiftiMasker
 from ..api.decorators import register_marker
 from ..data import get_mask, load_parcellation, merge_parcellations
 from ..stats import get_aggfunc_by_name
-from ..utils import logger, warn_with_log, raise_error
+from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker