junifer 0.0.6.dev175__py3-none-any.whl → 0.0.6.dev201__py3-none-any.whl

junifer/markers/falff/falff_parcels.py

@@ -24,8 +24,8 @@ class ALFFParcels(ALFFBase):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
-        :func:`.list_parcellations`.
+        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/markers/falff/falff_spheres.py

@@ -24,8 +24,8 @@ class ALFFSpheres(ALFFBase):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
-        :func:`.list_coordinates` for options.
+        The name of the coordinates list to use.
+        See :func:`.list_data` for options.
     using : {"junifer", "afni"}
         Implementation to use for computing ALFF:
 

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -23,7 +23,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
     ----------
     parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
-        See :func:`.list_parcellations` for options.
+        See :func:`.list_data` for options.
     agg_method : str, optional
         The method to perform aggregation using.
         See :func:`.get_aggfunc_by_name` for options

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -23,7 +23,7 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     ----------
     coords : str
         The name of the coordinates list to use.
-        See :func:`.list_coordinates` for options.
+        See :func:`.list_data` for options.
     radius : positive float, optional
         The radius of the sphere around each coordinates in millimetres.
         If None, the signal will be extracted from a single voxel.

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -23,7 +23,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
     ----------
     parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
-        See :func:`.list_parcellations` for options.
+        See :func:`.list_data` for options.
     agg_method : str, optional
         The method to perform aggregation using.
         See :func:`.get_aggfunc_by_name` for options

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -24,7 +24,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     ----------
     coords : str
         The name of the coordinates list to use.
-        See :func:`.list_coordinates` for options.
+        See :func:`.list_data` for options.
     radius : positive float, optional
         The radius of the sphere around each coordinates in millimetres.
         If None, the signal will be extracted from a single voxel.

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -14,7 +14,7 @@ from nilearn.maskers import NiftiLabelsMasker
 from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
-from junifer.data import get_parcellation
+from junifer.data import ParcellationRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivityParcels,
@@ -78,8 +78,8 @@ def test_FunctionalConnectivityParcels(
 
         # Compare with nilearn
         # Load testing parcellation for the target data
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Extract timeseries

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -15,7 +15,7 @@ from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
-from junifer.data import get_coordinates
+from junifer.data import CoordinatesRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivitySpheres,
@@ -80,7 +80,7 @@ def test_FunctionalConnectivitySpheres(
 
         # Compare with nilearn
         # Load testing coordinates for the target data
-        testing_coords, _ = get_coordinates(
+        testing_coords, _ = CoordinatesRegistry().get(
             coords="DMNBuckner", target_data=element_data["BOLD"]
         )
         # Extract timeseries

junifer/markers/parcel_aggregation.py

@@ -11,7 +11,7 @@ from nilearn.image import math_img
 from nilearn.maskers import NiftiMasker
 
 from ..api.decorators import register_marker
-from ..data import get_mask, get_parcellation
+from ..data import get_data
 from ..stats import get_aggfunc_by_name
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
@@ -27,8 +27,8 @@ class ParcelAggregation(BaseMarker):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
-        :func:`.list_parcellations`.
+        The name(s) of the parcellation(s) to use.
+        See :func:`.list_data` for options.
     method : str
         The method to perform aggregation using. Check valid options in
         :func:`.get_aggfunc_by_name`.
@@ -168,8 +168,9 @@ class ParcelAggregation(BaseMarker):
         )
 
         # Get parcellation tailored to target image
-        parcellation_img, labels = get_parcellation(
-            parcellation=self.parcellation,
+        parcellation_img, labels = get_data(
+            kind="parcellation",
+            names=self.parcellation,
             target_data=input,
             extra_input=extra_input,
         )
@@ -183,8 +184,11 @@ class ParcelAggregation(BaseMarker):
         if self.masks is not None:
             logger.debug(f"Masking with {self.masks}")
             # Get tailored mask
-            mask_img = get_mask(
-                masks=self.masks, target_data=input, extra_input=extra_input
+            mask_img = get_data(
+                kind="mask",
+                names=self.masks,
+                target_data=input,
+                extra_input=extra_input,
             )
             # Get "logical and" version of parcellation and mask
             parcellation_bin = math_img(

junifer/markers/reho/reho_parcels.py

@@ -24,8 +24,8 @@ class ReHoParcels(ReHoBase):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
-        :func:`.list_parcellations`.
+        The name(s) of the parcellation(s) to use.
+        See :func:`.list_data` for options.
     using : {"junifer", "afni"}
         Implementation to use for computing ReHo:
 

junifer/markers/reho/reho_spheres.py

@@ -24,8 +24,8 @@ class ReHoSpheres(ReHoBase):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
-        :func:`.list_coordinates` for options.
+        The name of the coordinates list to use.
+        See :func:`.list_data` for options.
     using : {"junifer", "afni"}
         Implementation to use for computing ReHo:
 

junifer/markers/sphere_aggregation.py

@@ -7,7 +7,7 @@
 from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 from ..api.decorators import register_marker
-from ..data import get_coordinates, get_mask
+from ..data import get_data
 from ..external.nilearn import JuniferNiftiSpheresMasker
 from ..stats import get_aggfunc_by_name
 from ..utils import logger, raise_error, warn_with_log
@@ -24,8 +24,8 @@ class SphereAggregation(BaseMarker):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
-        :func:`.list_coordinates` for options.
+        The name of the coordinates list to use.
+        See :func:`.list_data` for options.
     radius : float, optional
         The radius of the sphere in millimeters. If None, the signal will be
         extracted from a single voxel. See
@@ -177,8 +177,9 @@ class SphereAggregation(BaseMarker):
         )
 
         # Get seeds and labels tailored to target image
-        coords, labels = get_coordinates(
-            coords=self.coords,
+        coords, labels = get_data(
+            kind="coordinates",
+            names=self.coords,
             target_data=input,
             extra_input=extra_input,
         )
@@ -188,8 +189,11 @@ class SphereAggregation(BaseMarker):
         if self.masks is not None:
             logger.debug(f"Masking with {self.masks}")
             # Get tailored mask
-            mask_img = get_mask(
-                masks=self.masks, target_data=input, extra_input=extra_input
+            mask_img = get_data(
+                kind="mask",
+                names=self.masks,
+                target_data=input,
+                extra_input=extra_input,
             )
 
         # Initialize masker

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -20,8 +20,8 @@ class TemporalSNRParcels(TemporalSNRBase):
     Parameters
     ----------
     parcellation : str or list of str
-        The name(s) of the parcellation(s). Check valid options by calling
-        :func:`.list_parcellations`.
+        The name(s) of the parcellation(s) to use.
+        See :func:`.list_data` for options.
     agg_method : str, optional
         The method to perform aggregation using. Check valid options in
         :func:`.get_aggfunc_by_name` (default "mean").

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -21,8 +21,8 @@ class TemporalSNRSpheres(TemporalSNRBase):
     Parameters
     ----------
     coords : str
-        The name of the coordinates list to use. See
-        :func:`.list_coordinates` for options.
+        The name of the coordinates list to use.
+        See :func:`.list_data` for options.
     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`

junifer/markers/tests/test_ets_rss.py

@@ -10,7 +10,7 @@ from pathlib import Path
 
 from nilearn.maskers import NiftiLabelsMasker
 
-from junifer.data import get_parcellation
+from junifer.data import ParcellationRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.ets_rss import RSSETSMarker
 from junifer.storage import SQLiteFeatureStorage
@@ -32,8 +32,8 @@ def test_compute() -> None:
 
         # Compare with nilearn
         # Load testing parcellation
-        test_parcellation, _ = get_parcellation(
-            parcellation=[PARCELLATION],
+        test_parcellation, _ = ParcellationRegistry().get(
+            parcellations=[PARCELLATION],
             target_data=element_data["BOLD"],
         )
         # Extract timeseries

junifer/markers/tests/test_parcel_aggregation.py

@@ -16,7 +16,7 @@ from nilearn.masking import compute_brain_mask
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 from scipy.stats import trim_mean
 
-from junifer.data import get_mask, get_parcellation, register_parcellation
+from junifer.data import MaskRegistry, ParcellationRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.parcel_aggregation import ParcelAggregation
 from junifer.storage import SQLiteFeatureStorage
@@ -98,8 +98,8 @@ def test_ParcelAggregation_3D() -> None:
 
         # Compare with nilearn
         # Load testing parcellation
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Binarize parcellation
@@ -206,8 +206,8 @@ def test_ParcelAggregation_4D():
 
         # Compare with nilearn
         # Load testing parcellation
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Extract data
@@ -295,12 +295,12 @@ def test_ParcelAggregation_3D_mask() -> None:
 
         # Compare with nilearn
         # Load testing parcellation
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Load mask
-        mask_img = get_mask(
+        mask_img = MaskRegistry().get(
             "compute_brain_mask", target_data=element_data["BOLD"]
         )
         # Extract data
@@ -328,8 +328,8 @@ def test_ParcelAggregation_3D_mask_computed() -> None:
 
         # Compare with nilearn
         # Load testing parcellation
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Get a mask
@@ -396,8 +396,8 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
         ]
 
         # Load testing parcellation
-        testing_parcellation, labels = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, labels = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
 
@@ -424,14 +424,14 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
         nib.save(parcellation1_img, parcellation1_path)
         nib.save(parcellation2_img, parcellation2_path)
 
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_low",
             parcellation_path=parcellation1_path,
             parcels_labels=labels1,
             space="MNI152NLin2009cAsym",
             overwrite=True,
         )
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_high",
             parcellation_path=parcellation2_path,
             parcels_labels=labels2,
@@ -498,8 +498,8 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
         ]
 
         # Load testing parcellation
-        testing_parcellation, labels = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, labels = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
 
@@ -528,14 +528,14 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
         nib.save(parcellation1_img, parcellation1_path)
         nib.save(parcellation2_img, parcellation2_path)
 
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_low",
             parcellation_path=parcellation1_path,
             parcels_labels=labels1,
             space="MNI152NLin2009cAsym",
             overwrite=True,
         )
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_high",
             parcellation_path=parcellation2_path,
             parcels_labels=labels2,
@@ -609,8 +609,8 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
         ]
 
         # Load testing parcellation
-        testing_parcellation, labels = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, labels = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
 
@@ -637,14 +637,14 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
         nib.save(parcellation1_img, parcellation1_path)
         nib.save(parcellation2_img, parcellation2_path)
 
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_low",
             parcellation_path=parcellation1_path,
             parcels_labels=labels1,
             space="MNI152NLin2009cAsym",
             overwrite=True,
         )
-        register_parcellation(
+        ParcellationRegistry().register(
             name="TianxS1x3TxMNInonlinear2009cAsym_high",
             parcellation_path=parcellation2_path,
             parcels_labels=labels2,
@@ -719,8 +719,8 @@ def test_ParcelAggregation_4D_agg_time():
 
         # Compare with nilearn
         # Loading testing parcellation
-        testing_parcellation, _ = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        testing_parcellation, _ = ParcellationRegistry().get(
+            parcellations=["TianxS1x3TxMNInonlinear2009cAsym"],
             target_data=element_data["BOLD"],
         )
         # Extract data

junifer/markers/tests/test_sphere_aggregation.py

@@ -10,7 +10,7 @@ import pytest
 from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_equal
 
-from junifer.data import get_coordinates, get_mask
+from junifer.data import CoordinatesRegistry, MaskRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.sphere_aggregation import SphereAggregation
 from junifer.storage import SQLiteFeatureStorage
@@ -100,7 +100,7 @@ def test_SphereAggregation_3D() -> None:
 
         # Compare with nilearn
         # Load testing coordinates
-        testing_coords, _ = get_coordinates(
+        testing_coords, _ = CoordinatesRegistry().get(
             coords=COORDS, target_data=element_data["VBM_GM"]
         )
         # Extract data
@@ -132,7 +132,7 @@ def test_SphereAggregation_4D() -> None:
 
         # Compare with nilearn
         # Load testing coordinates
-        testing_coords, _ = get_coordinates(
+        testing_coords, _ = CoordinatesRegistry().get(
             coords=COORDS, target_data=element_data["BOLD"]
         )
         # Extract data
@@ -210,11 +210,11 @@ def test_SphereAggregation_3D_mask() -> None:
 
         # Compare with nilearn
         # Load testing coordinates
-        testing_coords, _ = get_coordinates(
+        testing_coords, _ = CoordinatesRegistry().get(
             coords=COORDS, target_data=element_data["VBM_GM"]
         )
         # Load mask
-        mask_img = get_mask(
+        mask_img = MaskRegistry().get(
             "compute_brain_mask", target_data=element_data["VBM_GM"]
         )
         # Extract data
@@ -253,7 +253,7 @@ def test_SphereAggregation_4D_agg_time() -> None:
 
         # Compare with nilearn
         # Load testing coordinates
-        testing_coords, _ = get_coordinates(
+        testing_coords, _ = CoordinatesRegistry().get(
             coords=COORDS, target_data=element_data["BOLD"]
         )
         # Extract data

junifer/pipeline/pipeline_component_registry.py

@@ -167,7 +167,7 @@ class PipelineComponentRegistry:
         """
         # Verify step
         self._check_valid_step(step)
-        # Log and register
+        # Log and de-register
         name = klass.__name__
         logger.info(f"De-registering {name} in {step}")
         _ = self._components[step].pop(name)

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -22,7 +22,7 @@ from nilearn import image as nimg
 from nilearn._utils.niimg_conversions import check_niimg_4d
 
 from ...api.decorators import register_preprocessor
-from ...data import get_mask
+from ...data import get_data
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 
@@ -546,8 +546,11 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         mask_img = None
         if self.masks is not None:
             logger.debug(f"Masking with {self.masks}")
-            mask_img = get_mask(
-                masks=self.masks, target_data=input, extra_input=extra_input
+            mask_img = get_data(
+                kind="mask",
+                names=self.masks,
+                target_data=input,
+                extra_input=extra_input,
             )
             # Return the BOLD mask and link it to the BOLD data type dict;
             # this allows to use "inherit" down the pipeline

{junifer-0.0.6.dev175.dist-info → junifer-0.0.6.dev201.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev175
+Version: 0.0.6.dev201
 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>