junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev252__py3-none-any.whl

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@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
@@ -61,12 +61,12 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, List[str]],
+        parcellation: Union[str, list[str]],
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
+        agg_method_params: Optional[dict] = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        conn_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
@@ -80,8 +80,8 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
         )
 
     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 and ETS computation.
 
         Parameters

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@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
@@ -73,10 +73,10 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         radius: Optional[float] = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
+        agg_method_params: Optional[dict] = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        conn_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -94,8 +94,8 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         )
 
     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 and ETS computation.
 
         Parameters

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -5,7 +5,7 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from typing import Any, ClassVar, Optional, Union
 
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
@@ -63,10 +63,10 @@ class FunctionalConnectivityBase(BaseMarker):
     def __init__(
         self,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
+        agg_method_params: Optional[dict] = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        conn_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
@@ -83,9 +83,9 @@ class FunctionalConnectivityBase(BaseMarker):
     @abstractmethod
     def aggregate(
         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]:
         """Perform aggregation."""
         raise_error(
             msg="Concrete classes need to implement aggregate().",
@@ -94,9 +94,9 @@ class FunctionalConnectivityBase(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/functional_connectivity/functional_connectivity_parcels.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@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
@@ -55,12 +55,12 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, List[str]],
+        parcellation: Union[str, list[str]],
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
+        agg_method_params: Optional[dict] = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        conn_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
@@ -74,8 +74,8 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         )
 
     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/functional_connectivity/functional_connectivity_spheres.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@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
@@ -68,10 +68,10 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         radius: Optional[float] = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[Dict] = None,
+        agg_method_params: Optional[dict] = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[Dict] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        conn_method_params: Optional[dict] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -89,8 +89,8 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         )
 
     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/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Dict
 
 import pytest
 
@@ -24,7 +23,7 @@ from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 )
 def test_EdgeCentricFCParcels(
     tmp_path: Path,
-    conn_method_params: Dict[str, bool],
+    conn_method_params: dict[str, bool],
 ) -> None:
     """Test EdgeCentricFCParcels.
 

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Dict
 
 import pytest
 
@@ -24,7 +23,7 @@ from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 )
 def test_EdgeCentricFCSpheres(
     tmp_path: Path,
-    conn_method_params: Dict[str, bool],
+    conn_method_params: dict[str, bool],
 ) -> None:
     """Test EdgeCentricFCSpheres.
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -6,7 +6,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Dict, Type
+from typing import TYPE_CHECKING
 
 import pytest
 from nilearn.connectome import ConnectivityMeasure
@@ -36,8 +36,8 @@ if TYPE_CHECKING:
 )
 def test_FunctionalConnectivityParcels(
     tmp_path: Path,
-    conn_method_params: Dict[str, bool],
-    cov_estimator: Type["BaseEstimator"],
+    conn_method_params: dict[str, bool],
+    cov_estimator: type["BaseEstimator"],
 ) -> None:
     """Test FunctionalConnectivityParcels.
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -7,7 +7,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Dict, Type
+from typing import TYPE_CHECKING
 
 import pytest
 from nilearn.connectome import ConnectivityMeasure
@@ -37,8 +37,8 @@ if TYPE_CHECKING:
 )
 def test_FunctionalConnectivitySpheres(
     tmp_path: Path,
-    conn_method_params: Dict[str, bool],
-    cov_estimator: Type["BaseEstimator"],
+    conn_method_params: dict[str, bool],
+    cov_estimator: type["BaseEstimator"],
 ) -> None:
     """Test FunctionalConnectivitySpheres.
 

junifer/markers/parcel_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from typing import Any, ClassVar, Optional, Union
 
 import numpy as np
 from nilearn.image import math_img
@@ -96,13 +96,13 @@ class ParcelAggregation(BaseMarker):
 
     def __init__(
         self,
-        parcellation: Union[str, List[str]],
+        parcellation: Union[str, list[str]],
         method: str,
-        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:
         if not isinstance(parcellation, list):
@@ -128,8 +128,8 @@ class ParcelAggregation(BaseMarker):
         self.time_method_params = time_method_params or {}
 
     def compute(
-        self, input: Dict[str, Any], extra_input: Optional[Dict] = None
-    ) -> Dict:
+        self, input: dict[str, Any], extra_input: Optional[dict] = None
+    ) -> dict:
         """Compute.
 
         Parameters

junifer/markers/reho/_afni_reho.py

@@ -9,7 +9,6 @@ from typing import (
     TYPE_CHECKING,
     ClassVar,
     Optional,
-    Tuple,
 )
 
 import nibabel as nib
@@ -61,7 +60,7 @@ class AFNIReHo(metaclass=Singleton):
         box_x: Optional[int] = None,
         box_y: Optional[int] = None,
         box_z: Optional[int] = None,
-    ) -> Tuple["Nifti1Image", Path]:
+    ) -> tuple["Nifti1Image", Path]:
         """Compute ReHo map.
 
         Parameters

junifer/markers/reho/_junifer_reho.py

@@ -9,7 +9,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Tuple,
 )
 
 import nibabel as nib
@@ -51,7 +50,7 @@ class JuniferReHo(metaclass=Singleton):
         self,
         data: "Nifti1Image",
         nneigh: int = 27,
-    ) -> Tuple["Nifti1Image", Path]:
+    ) -> tuple["Nifti1Image", Path]:
         """Compute ReHo map.
 
         Parameters

junifer/markers/reho/reho_base.py

@@ -9,9 +9,7 @@ from typing import (
     TYPE_CHECKING,
     Any,
     ClassVar,
-    Dict,
     Optional,
-    Tuple,
 )
 
 from ...typing import ConditionalDependencies, MarkerInOutMappings
@@ -82,9 +80,9 @@ class ReHoBase(BaseMarker):
 
     def _compute(
         self,
-        input_data: Dict[str, Any],
+        input_data: dict[str, Any],
         **reho_params: Any,
-    ) -> Tuple["Nifti1Image", Path]:
+    ) -> tuple["Nifti1Image", Path]:
         """Compute voxel-wise ReHo.
 
         Calculates Kendall's W per voxel using neighborhood voxels.

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
 
@@ -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
 
@@ -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

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from typing import Any, ClassVar, Optional, Union
 
 from ..api.decorators import register_marker
 from ..data import get_data
@@ -105,11 +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
@@ -136,9 +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

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -5,7 +5,7 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from typing import Any, ClassVar, Optional, Union
 
 from nilearn import image as nimg
 
@@ -49,8 +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
@@ -60,8 +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().",
@@ -70,9 +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
@@ -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
@@ -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/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/_brainprint.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, Optional
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -17,7 +17,7 @@ __all__ = ["normalize", "reweight"]
 
 def normalize(
     storage: StorageLike,
-    features: Dict[str, Dict[str, Optional[str]]],
+    features: dict[str, dict[str, Optional[str]]],
     kind: str,
 ) -> pd.DataFrame:
     """Read stored brainprint data and normalize either surfaces or volumes.

junifer/onthefly/read_transform.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Dict, Optional, Tuple
+from typing import Optional
 
 import pandas as pd
 
@@ -20,8 +20,8 @@ def read_transform(
     transform: str,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
-    transform_args: Optional[Tuple] = None,
-    transform_kw_args: Optional[Dict] = None,
+    transform_args: Optional[tuple] = None,
+    transform_kw_args: Optional[dict] = None,
 ) -> pd.DataFrame:
     """Read stored feature and transform to specific statistical output.