junifer 0.0.6.dev248__py3-none-any.whl → 0.0.6.dev258__py3-none-any.whl

junifer/data/_dispatch.py

@@ -8,10 +8,7 @@ from typing import (
     TYPE_CHECKING,
     Any,
     Callable,
-    Dict,
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -40,15 +37,15 @@ def get_data(
     kind: str,
     names: Union[
         str,  # coordinates, parcellation, mask
-        List[str],  # parcellation, mask
-        Dict,  # mask
-        List[Dict],  # mask
+        list[str],  # parcellation, mask
+        dict,  # mask
+        list[dict],  # mask
     ],
-    target_data: Dict[str, Any],
-    extra_input: Optional[Dict[str, Any]] = None,
+    target_data: dict[str, Any],
+    extra_input: Optional[dict[str, Any]] = None,
 ) -> Union[
-    Tuple[ArrayLike, List[str]],  # coordinates
-    Tuple["Nifti1Image", List[str]],  # parcellation
+    tuple[ArrayLike, list[str]],  # coordinates
+    tuple["Nifti1Image", list[str]],  # parcellation
     "Nifti1Image",  # mask
 ]:
     """Get tailored ``kind`` for ``target_data``.
@@ -102,7 +99,7 @@ def get_data(
         raise_error(f"Unknown data kind: {kind}")
 
 
-def list_data(kind: str) -> List[str]:
+def list_data(kind: str) -> list[str]:
     """List available data for ``kind``.
 
     Parameters
@@ -137,9 +134,9 @@ def load_data(
     name: str,
     **kwargs,
 ) -> Union[
-    Tuple[ArrayLike, List[str], str],  # coordinates
-    Tuple[Optional["Nifti1Image"], List[str], Path, str],  # parcellation
-    Tuple[
+    tuple[ArrayLike, list[str], str],  # coordinates
+    tuple[Optional["Nifti1Image"], list[str], Path, str],  # parcellation
+    tuple[
         Optional[Union["Nifti1Image", Callable]], Optional[Path], str
     ],  # mask
 ]:

junifer/data/coordinates/_ants_coordinates_warper.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -25,8 +25,8 @@ class ANTsCoordinatesWarper:
     def warp(
         self,
         seeds: ArrayLike,
-        target_data: Dict[str, Any],
-        warp_data: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -55,19 +55,24 @@ class ANTsCoordinatesWarper:
 
         # Save existing coordinates to a tempfile
         pretransform_coordinates_path = (
-            element_tempdir / "pretransform_coordinates.txt"
+            element_tempdir / "pretransform_coordinates.csv"
         )
+        # Convert LPS to RAS
+        seeds[:, 0] *= -1
+        seeds[:, 1] *= -1
         np.savetxt(
             pretransform_coordinates_path,
             seeds,
             delimiter=",",
             # Add header while saving to make ANTs work
             header="x,y,z",
+            # Remove comment tag for header
+            comments="",
         )
 
         # Create a tempfile for transformed coordinates output
         transformed_coords_path = (
-            element_tempdir / "coordinates_transformed.txt"
+            element_tempdir / "coordinates_transformed.csv"
         )
         # Set antsApplyTransformsToPoints command
         apply_transforms_to_points_cmd = [
@@ -86,9 +91,14 @@ class ANTsCoordinatesWarper:
         )
 
         # Load coordinates
-        return np.loadtxt(
+        transformed_seeds = np.loadtxt(
             # Skip header when reading
             transformed_coords_path,
             delimiter=",",
             skiprows=1,
         )
+        # Convert RAS to LPS
+        transformed_seeds[:, 0] *= -1
+        transformed_seeds[:, 1] *= -1
+
+        return transformed_seeds

junifer/data/coordinates/_coordinates.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple
+from typing import Any, Optional
 
 import numpy as np
 import pandas as pd
@@ -135,7 +135,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         self,
         name: str,
         coordinates: ArrayLike,
-        voi_names: List[str],
+        voi_names: list[str],
         space: str,
         overwrite: Optional[bool] = False,
     ) -> None:
@@ -236,7 +236,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         # Update registry
         _ = self._registry.pop(name)
 
-    def load(self, name: str) -> Tuple[ArrayLike, List[str], str]:
+    def load(self, name: str) -> tuple[ArrayLike, list[str], str]:
         """Load coordinates.
 
         Parameters
@@ -285,9 +285,9 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
     def get(
         self,
         coords: str,
-        target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[ArrayLike, List[str]]:
+        target_data: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[ArrayLike, list[str]]:
         """Get coordinates, tailored for the target data.
 
         Parameters
@@ -362,7 +362,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                 seeds = ANTsCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    warp_data=warper_spec,
+                    warp_data=inverse_warper_spec,
                 )
 
         return seeds, labels

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -25,8 +25,8 @@ class FSLCoordinatesWarper:
     def warp(
         self,
         seeds: ArrayLike,
-        target_data: Dict[str, Any],
-        warp_data: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 

junifer/data/masks/_ants_mask_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 
@@ -33,8 +33,8 @@ class ANTsMaskWarper:
         mask_img: "Nifti1Image",
         src: str,
         dst: str,
-        target_data: Dict[str, Any],
-        warp_data: Optional[Dict[str, Any]],
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 

junifer/data/masks/_fsl_mask_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 
@@ -30,8 +30,8 @@ class FSLMaskWarper:
         self,
         mask_name: str,
         mask_img: "Nifti1Image",
-        target_data: Dict[str, Any],
-        warp_data: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 

junifer/data/masks/_masks.py

@@ -9,10 +9,7 @@ from typing import (
     TYPE_CHECKING,
     Any,
     Callable,
-    Dict,
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -46,8 +43,8 @@ _masks_path = Path(__file__).parent
 
 
 def compute_brain_mask(
-    target_data: Dict[str, Any],
-    extra_input: Optional[Dict[str, Any]] = None,
+    target_data: dict[str, Any],
+    extra_input: Optional[dict[str, Any]] = None,
     mask_type: str = "brain",
     threshold: float = 0.5,
 ) -> "Nifti1Image":
@@ -266,7 +263,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         name: str,
         resolution: Optional[float] = None,
         path_only: bool = False,
-    ) -> Tuple[Optional[Union["Nifti1Image", Callable]], Optional[Path], str]:
+    ) -> tuple[Optional[Union["Nifti1Image", Callable]], Optional[Path], str]:
         """Load mask.
 
         Parameters
@@ -332,9 +329,9 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
     def get(  # noqa: C901
         self,
-        masks: Union[str, Dict, List[Union[Dict, str]]],
-        target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        masks: Union[str, dict, list[Union[dict, str]]],
+        target_data: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
     ) -> "Nifti1Image":
         """Get mask, tailored for the target image.
 

junifer/data/masks/tests/test_masks.py

@@ -7,7 +7,7 @@
 
 import socket
 from pathlib import Path
-from typing import Callable, Dict, List, Optional, Union
+from typing import Callable, Optional, Union
 
 import nibabel as nib
 import numpy as np
@@ -254,7 +254,7 @@ def test_load_incorrect() -> None:
 def test_vickery_patil(
     name: str,
     resolution: Optional[float],
-    pixdim: List[float],
+    pixdim: list[float],
     fname: str,
 ) -> None:
     """Test Vickery-Patil mask.
@@ -396,7 +396,7 @@ def test_get_errors() -> None:
 def test_nilearn_compute_masks(
     mask_name: str,
     function: Callable,
-    params: Union[Dict, None],
+    params: Union[dict, None],
     resample: bool,
 ) -> None:
     """Test using nilearn compute mask functions.
@@ -479,7 +479,7 @@ def test_get_inherit() -> None:
     ],
 )
 def test_get_multiple(
-    masks: Union[str, Dict, List[Union[Dict, str]]], params: Dict
+    masks: Union[str, dict, list[Union[dict, str]]], params: dict
 ) -> None:
     """Test getting multiple masks.
 

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 
@@ -33,8 +33,8 @@ class ANTsParcellationWarper:
         parcellation_img: "Nifti1Image",
         src: str,
         dst: str,
-        target_data: Dict[str, Any],
-        warp_data: Optional[Dict[str, Any]],
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 
@@ -30,8 +30,8 @@ class FSLParcellationWarper:
         self,
         parcellation_name: str,
         parcellation_img: "Nifti1Image",
-        target_data: Dict[str, Any],
-        warp_data: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 

junifer/data/parcellations/_parcellations.py

@@ -12,7 +12,7 @@ import tempfile
 import zipfile
 from itertools import product
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
+from typing import TYPE_CHECKING, Any, Optional, Union
 
 import httpx
 import nibabel as nib
@@ -190,7 +190,7 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         self,
         name: str,
         parcellation_path: Union[str, Path],
-        parcels_labels: List[str],
+        parcels_labels: list[str],
         space: str,
         overwrite: bool = False,
     ) -> None:
@@ -272,7 +272,7 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         parcellations_dir: Union[str, Path, None] = None,
         resolution: Optional[float] = None,
         path_only: bool = False,
-    ) -> Tuple[Optional["Nifti1Image"], List[str], Path, str]:
+    ) -> tuple[Optional["Nifti1Image"], list[str], Path, str]:
         """Load parcellation and labels.
 
         If it is a built-in parcellation and the file is not present in the
@@ -367,10 +367,10 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
     def get(
         self,
-        parcellations: Union[str, List[str]],
-        target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple["Nifti1Image", List[str]]:
+        parcellations: Union[str, list[str]],
+        target_data: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple["Nifti1Image", list[str]]:
         """Get parcellation, tailored for the target image.
 
         Parameters
@@ -503,7 +503,7 @@ def _retrieve_parcellation(
     parcellations_dir: Union[str, Path, None] = None,
     resolution: Optional[float] = None,
     **kwargs,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve a brain parcellation object from nilearn or online source.
 
     Only returns one parcellation per call. Call function multiple times for
@@ -647,7 +647,7 @@ def _retrieve_schaefer(
     resolution: Optional[float] = None,
     n_rois: Optional[int] = None,
     yeo_networks: int = 7,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve Schaefer parcellation.
 
     Parameters
@@ -749,7 +749,7 @@ def _retrieve_tian(
     scale: Optional[int] = None,
     space: str = "MNI152NLin6Asym",
     magneticfield: str = "3T",
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve Tian parcellation.
 
     Parameters
@@ -923,7 +923,7 @@ def _retrieve_suit(
     parcellations_dir: Path,
     resolution: Optional[float],
     space: str = "MNI152NLin6Asym",
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve SUIT parcellation.
 
     Parameters
@@ -1049,7 +1049,7 @@ def _retrieve_aicha(
     parcellations_dir: Path,
     resolution: Optional[float] = None,
     version: int = 2,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve AICHA parcellation.
 
     Parameters
@@ -1205,7 +1205,7 @@ def _retrieve_shen(  # noqa: C901
     resolution: Optional[float] = None,
     year: int = 2015,
     n_rois: int = 268,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve Shen parcellation.
 
     Parameters
@@ -1410,7 +1410,7 @@ def _retrieve_yan(
     n_rois: Optional[int] = None,
     yeo_networks: Optional[int] = None,
     kong_networks: Optional[int] = None,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve Yan parcellation.
 
     Parameters
@@ -1607,7 +1607,7 @@ def _retrieve_brainnetome(
     parcellations_dir: Path,
     resolution: Optional[float] = None,
     threshold: Optional[int] = None,
-) -> Tuple[Path, List[str]]:
+) -> tuple[Path, list[str]]:
     """Retrieve Brainnetome parcellation.
 
     Parameters
@@ -1720,10 +1720,10 @@ def _retrieve_brainnetome(
 
 
 def merge_parcellations(
-    parcellations_list: List["Nifti1Image"],
-    parcellations_names: List[str],
-    labels_lists: List[List[str]],
-) -> Tuple["Nifti1Image", List[str]]:
+    parcellations_list: list["Nifti1Image"],
+    parcellations_names: list[str],
+    labels_lists: list[list[str]],
+) -> tuple["Nifti1Image", list[str]]:
     """Merge all parcellations from a list into one parcellation.
 
     Parameters

junifer/data/parcellations/tests/test_parcellations.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List
 
 import nibabel as nib
 import numpy as np
@@ -171,7 +170,7 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
 def test_register(
     name: str,
     parcellation_path: str,
-    parcels_labels: List[str],
+    parcels_labels: list[str],
     space: str,
     overwrite: bool,
 ) -> None:

junifer/data/pipeline_data_registry_base.py

@@ -4,7 +4,8 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
-from typing import Any, List, Mapping
+from collections.abc import Mapping
+from typing import Any
 
 from ..utils import raise_error
 from ..utils.singleton import ABCSingleton
@@ -38,7 +39,7 @@ class BasePipelineDataRegistry(ABC, metaclass=ABCSingleton):
         return self._registry
 
     @property
-    def list(self) -> List[str]:
+    def list(self) -> list[str]:
         """List available pipeline data keys."""
         return sorted(self._registry.keys())
 

junifer/data/template_spaces.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Any, Dict, Optional, Union
+from typing import Any, Optional, Union
 
 import datalad.api as dl
 import nibabel as nib
@@ -122,8 +122,8 @@ def get_xfm(
 
 def get_template(
     space: str,
-    target_data: Dict[str, Any],
-    extra_input: Optional[Dict[str, Any]] = None,
+    target_data: dict[str, Any],
+    extra_input: Optional[dict[str, Any]] = None,
     template_type: str = "T1w",
 ) -> nib.Nifti1Image:
     """Get template for the space, tailored for the target image.

junifer/data/tests/test_data_utils.py

@@ -3,7 +3,6 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from typing import List
 
 import numpy as np
 import pytest
@@ -24,7 +23,7 @@ from junifer.data.utils import closest_resolution
     ],
 )
 def test_closest_resolution(
-    resolution: float, valid_resolutions: List[float], expected: float
+    resolution: float, valid_resolutions: list[float], expected: float
 ):
     """Test closest_resolution.
 

junifer/data/utils.py

@@ -4,7 +4,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, MutableMapping, Optional, Union
+from collections.abc import MutableMapping
+from typing import Optional, Union
 
 import numpy as np
 
@@ -16,7 +17,7 @@ __all__ = ["closest_resolution", "get_native_warper"]
 
 def closest_resolution(
     resolution: Optional[Union[float, int]],
-    valid_resolution: Union[List[float], List[int], np.ndarray],
+    valid_resolution: Union[list[float], list[int], np.ndarray],
 ) -> Union[float, int]:
     """Find the closest resolution.
 
@@ -55,7 +56,7 @@ def get_native_warper(
     target_data: MutableMapping,
     other_data: MutableMapping,
     inverse: bool = False,
-) -> Dict:
+) -> dict:
     """Get correct warping specification for native space.
 
     Parameters

junifer/datagrabber/aomic/id1000.py

@@ -8,7 +8,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ..pattern_datalad import PatternDataladDataGrabber
@@ -39,7 +39,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        types: Union[str, List[str], None] = None,
+        types: Union[str, list[str], None] = None,
         native_t1w: bool = False,
     ) -> None:
         # The patterns

junifer/datagrabber/aomic/piop1.py

@@ -9,7 +9,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -50,8 +50,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        types: Union[str, List[str], None] = None,
-        tasks: Union[str, List[str], None] = None,
+        types: Union[str, list[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
         native_t1w: bool = False,
     ) -> None:
         # Declare all tasks
@@ -247,7 +247,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             confounds_format="fmriprep",
         )
 
-    def get_item(self, subject: str, task: str) -> Dict:
+    def get_item(self, subject: str, task: str) -> dict:
         """Index one element in the dataset.
 
         Parameters
@@ -279,7 +279,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
 
         return super().get_item(subject=subject, task=new_task)
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of subjects in the dataset.
 
         Returns

junifer/datagrabber/aomic/piop2.py

@@ -9,7 +9,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -50,8 +50,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        types: Union[str, List[str], None] = None,
-        tasks: Union[str, List[str], None] = None,
+        types: Union[str, list[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
         native_t1w: bool = False,
     ) -> None:
         # Declare all tasks
@@ -245,7 +245,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             confounds_format="fmriprep",
         )
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of elements in the dataset.
 
         Returns
@@ -261,7 +261,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             elems.append((subject, task))
         return elems
 
-    def get_item(self, subject: str, task: str) -> Dict:
+    def get_item(self, subject: str, task: str) -> dict:
         """Index one element in the dataset.
 
         Parameters