junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl

junifer/markers/reho/reho_parcels.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 
@@ -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:
 
@@ -92,12 +92,12 @@ class ReHoParcels(ReHoBase):
 
     def __init__(
         self,
-        parcellation: Union[str, List[str]],
+        parcellation: Union[str, list[str]],
         using: str,
-        reho_params: Optional[Dict] = None,
+        reho_params: Optional[dict] = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        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
@@ -110,9 +110,9 @@ class ReHoParcels(ReHoBase):
 
     def compute(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Dict[str, Any]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> dict[str, Any]:
         """Compute.
 
         Parameters

junifer/markers/reho/reho_spheres.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 
@@ -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:
 
@@ -107,10 +107,10 @@ class ReHoSpheres(ReHoBase):
         using: str,
         radius: Optional[float] = None,
         allow_overlap: bool = False,
-        reho_params: Optional[Dict] = None,
+        reho_params: Optional[dict] = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        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
@@ -125,9 +125,9 @@ class ReHoSpheres(ReHoBase):
 
     def compute(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Dict[str, Any]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> dict[str, Any]:
         """Compute.
 
         Parameters

junifer/markers/sphere_aggregation.py

@@ -4,12 +4,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Optional, 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 ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
@@ -24,8 +25,8 @@ 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
@@ -66,9 +67,9 @@ class SphereAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "T1w": {
             "aggregation": "vector",
         },
@@ -104,11 +105,11 @@ class SphereAggregation(BaseMarker):
         radius: Optional[float] = None,
         allow_overlap: bool = False,
         method: str = "mean",
-        method_params: Optional[Dict[str, Any]] = None,
+        method_params: Optional[dict[str, Any]] = None,
         time_method: Optional[str] = None,
-        time_method_params: Optional[Dict[str, Any]] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
-        on: Union[List[str], str, None] = None,
+        time_method_params: Optional[dict[str, Any]] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        on: Union[list[str], str, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -135,9 +136,9 @@ class SphereAggregation(BaseMarker):
 
     def compute(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict] = None,
-    ) -> Dict:
+        input: dict[str, Any],
+        extra_input: Optional[dict] = None,
+    ) -> dict:
         """Compute.
 
         Parameters
@@ -177,8 +178,9 @@ 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 +190,11 @@ 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/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from .temporal_snr_parcels import TemporalSNRParcels
-from .temporal_snr_spheres import TemporalSNRSpheres
+import lazy_loader as lazy
 
 
-__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/markers/temporal_snr/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]
+
+from .temporal_snr_parcels import TemporalSNRParcels
+from .temporal_snr_spheres import TemporalSNRSpheres

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -5,10 +5,11 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Optional, Union
 
 from nilearn import image as nimg
 
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -37,9 +38,9 @@ class TemporalSNRBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "tsnr": "vector",
         },
@@ -48,8 +49,8 @@ class TemporalSNRBase(BaseMarker):
     def __init__(
         self,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        agg_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.agg_method = agg_method
@@ -59,8 +60,8 @@ class TemporalSNRBase(BaseMarker):
 
     @abstractmethod
     def aggregate(
-        self, input: Dict[str, Any], extra_input: Optional[Dict] = None
-    ) -> Dict[str, Any]:
+        self, input: dict[str, Any], extra_input: Optional[dict] = None
+    ) -> dict[str, Any]:
         """Perform aggregation."""
         raise_error(
             msg="Concrete classes need to implement aggregate().",
@@ -69,9 +70,9 @@ class TemporalSNRBase(BaseMarker):
 
     def compute(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict] = None,
-    ) -> Dict:
+        input: dict[str, Any],
+        extra_input: Optional[dict] = None,
+    ) -> dict:
         """Compute.
 
         Parameters

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -3,7 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Optional, Union
 
 from ...api.decorators import register_marker
 from ..parcel_aggregation import ParcelAggregation
@@ -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").
@@ -40,10 +40,10 @@ class TemporalSNRParcels(TemporalSNRBase):
 
     def __init__(
         self,
-        parcellation: Union[str, List[str]],
+        parcellation: Union[str, list[str]],
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        agg_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
@@ -55,8 +55,8 @@ class TemporalSNRParcels(TemporalSNRBase):
         )
 
     def aggregate(
-        self, input: Dict[str, Any], extra_input: Optional[Dict] = None
-    ) -> Dict:
+        self, input: dict[str, Any], extra_input: Optional[dict] = None
+    ) -> dict:
         """Perform parcel aggregation.
 
         Parameters

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -3,7 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Optional, Union
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -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`
@@ -53,8 +53,8 @@ class TemporalSNRSpheres(TemporalSNRBase):
         radius: Optional[float] = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        agg_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -70,8 +70,8 @@ class TemporalSNRSpheres(TemporalSNRBase):
         )
 
     def aggregate(
-        self, input: Dict[str, Any], extra_input: Optional[Dict] = None
-    ) -> Dict:
+        self, input: dict[str, Any], extra_input: Optional[dict] = None
+    ) -> dict:
         """Perform sphere aggregation.
 
         Parameters

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/markers/utils.py

@@ -8,7 +8,7 @@
 #          Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
 # License: AGPL
 
-from typing import Callable, List, Optional, Tuple, Union
+from typing import Callable, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -19,8 +19,8 @@ from ..utils import raise_error
 
 def _ets(
     bold_ts: np.ndarray,
-    roi_names: Union[None, List[str]] = None,
-) -> Tuple[np.ndarray, Optional[List[str]]]:
+    roi_names: Union[None, list[str]] = None,
+) -> tuple[np.ndarray, Optional[list[str]]]:
     """Compute the edge-wise time series based on BOLD time series.
 
     Take a timeseries of brain areas, and calculate timeseries for each

junifer/onthefly/__init__.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 from .read_transform import read_transform
+from . import _brainprint as brainprint
 
 
-__all__ = ["read_transform"]
+__all__ = ["read_transform", "brainprint"]