junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev252__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],
-        extra_input: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class ANTsCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of coordinates
-            (default None).
+        warp_data : dict or None
+            The warp data item of the data object.
 
         Returns
         -------
@@ -79,7 +77,7 @@ class ANTsCoordinatesWarper:
             "-f 0",
             f"-i {pretransform_coordinates_path.resolve()}",
             f"-o {transformed_coords_path.resolve()}",
-            f"-t {extra_input['Warp']['path'].resolve()};",
+            f"-t {warp_data['path'].resolve()}",
         ]
         # Call antsApplyTransformsToPoints
         run_ext_cmd(

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
@@ -14,6 +14,7 @@ from numpy.typing import ArrayLike
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
+from ..utils import get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
@@ -134,7 +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:
@@ -235,7 +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
@@ -284,9 +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
@@ -311,7 +312,8 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         Raises
         ------
         RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
+            If warping specification required for warping using ANTs, is not
+            found.
         ValueError
             If ``extra_input`` is None when ``target_data``'s space is native.
 
@@ -329,27 +331,38 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     f"{target_data['space']} space for further computation."
                 )
 
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
+            # Conditional for warping tool implementation
+            if warper_spec["warper"] == "fsl":
                 seeds = FSLCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
+                )
+            elif warper_spec["warper"] == "ants":
+                # Requires the inverse warp
+                inverse_warper_spec = get_native_warper(
+                    target_data=target_data,
+                    other_data=extra_input,
+                    inverse=True,
                 )
-            elif warp_file_ext == ".h5":
+                # Check warper
+                if inverse_warper_spec["warper"] != "ants":
+                    raise_error(
+                        klass=RuntimeError,
+                        msg=(
+                            "Warping specification mismatch for native space "
+                            "warping of coordinates using ANTs."
+                        ),
+                    )
                 seeds = ANTsCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=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],
-        extra_input: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class FSLCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of coordinates
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -72,7 +70,7 @@ class FSLCoordinatesWarper:
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
             f"-dest {target_data['reference_path'].resolve()}",
-            f"-warp {extra_input['Warp']['path'].resolve()}",
+            f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",
         ]

junifer/data/masks/_ants_mask_warper.py

@@ -4,12 +4,12 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -33,8 +33,8 @@ class ANTsMaskWarper:
         mask_img: "Nifti1Image",
         src: str,
         dst: str,
-        target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -55,17 +55,20 @@ class ANTsMaskWarper:
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of mask
-            (default None).
-
+        warp_data : dict or None
+            The warp data item of the data object. The value is unused if
+            ``dst!="T1w"``.
 
         Returns
         -------
         nibabel.nifti1.Nifti1Image
             The transformed mask image.
 
+        Raises
+        ------
+        RuntimeError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
         """
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
@@ -80,7 +83,11 @@ class ANTsMaskWarper:
         )
 
         # Native space warping
-        if dst == "T1w":
+        if dst == "native":
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+
             logger.debug("Using ANTs for mask transformation")
 
             # Save existing mask image to a tempfile
@@ -98,7 +105,7 @@ class ANTsMaskWarper:
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
                 f"-r {target_data['reference_path'].resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]
             # Call antsApplyTransforms

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],
-        extra_input: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -44,10 +44,8 @@ class FSLMaskWarper:
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of mask
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -77,7 +75,7 @@ class FSLMaskWarper:
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference_path'].resolve()}",
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]
         # Call applywarp

junifer/data/masks/_masks.py

@@ -9,10 +9,7 @@ from typing import (
     TYPE_CHECKING,
     Any,
     Callable,
-    Dict,
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -29,7 +26,7 @@ from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
-from ..utils import closest_resolution
+from ..utils import closest_resolution, get_native_warper
 from ._ants_mask_warper import ANTsMaskWarper
 from ._fsl_mask_warper import FSLMaskWarper
 
@@ -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":
@@ -105,14 +102,16 @@ def compute_brain_mask(
                 "data type to infer target template space."
             )
         # Set target standard space to warp file space source
-        target_std_space = extra_input["Warp"]["src"]
+        for entry in extra_input["Warp"]:
+            if entry["dst"] == "native":
+                target_std_space = entry["src"]
 
     # Fetch template in closest resolution
     template = get_template(
         space=target_std_space,
         target_data=target_data,
         extra_input=extra_input,
-        template_type=mask_type if mask_type in ["gm", "wm"] else "T1w",
+        template_type=mask_type,
     )
     # Resample template to target image
     target_img = target_data["data"]
@@ -264,7 +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
@@ -330,9 +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.
 
@@ -357,8 +356,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         Raises
         ------
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
         ValueError
             If extra key is provided in addition to mask name in ``masks`` or
             if no mask is provided or
@@ -372,8 +369,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         """
         # Check pre-requirements for space manipulation
         target_space = target_data["space"]
-        # Set target standard space to target space
-        target_std_space = target_space
         # Extra data type requirement check if target space is native
         if target_space == "native":
             # Check for extra inputs
@@ -383,8 +378,16 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     "data types in particular for transformation to "
                     f"{target_data['space']} space for further computation."
                 )
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
             # Set target standard space to warp file space source
-            target_std_space = extra_input["Warp"]["src"]
+            target_std_space = warper_spec["src"]
+        else:
+            # Set target standard space to target space
+            target_std_space = target_space
 
         # Get the min of the voxels sizes and use it as the resolution
         target_img = target_data["data"]
@@ -489,7 +492,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                         src=mask_space,
                         dst=target_std_space,
                         target_data=target_data,
-                        extra_input=None,
+                        warp_data=None,
                     )
 
             all_masks.append(mask_img)
@@ -510,32 +513,22 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Warp mask if target data is native
         if target_space == "native":
-            # extra_input check done earlier
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # extra_input check done earlier and warper_spec exists
+            if warper_spec["warper"] == "fsl":
                 mask_img = FSLMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
                 )
-            elif warp_file_ext == ".h5":
+            elif warper_spec["warper"] == "ants":
                 mask_img = ANTsMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     src="",
-                    dst="T1w",
+                    dst="native",
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return mask_img

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

@@ -4,12 +4,12 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -33,8 +33,8 @@ class ANTsParcellationWarper:
         parcellation_img: "Nifti1Image",
         src: str,
         dst: str,
-        target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 
@@ -55,17 +55,20 @@ class ANTsParcellationWarper:
         target_data : dict
             The corresponding item of the data object to which the parcellation
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of parcellation
-            (default None).
-
+        warp_data : dict or None
+            The warp data item of the data object. The value is unused if
+            ``dst!="T1w"``.
 
         Returns
         -------
         nibabel.nifti1.Nifti1Image
             The transformed parcellation image.
 
+        Raises
+        ------
+        ValueError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
         """
         # Create element-scoped tempdir so that warped parcellation is
         # available later as nibabel stores file path reference for
@@ -80,7 +83,11 @@ class ANTsParcellationWarper:
         )
 
         # Native space warping
-        if dst == "T1w":
+        if dst == "native":
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+
             logger.debug("Using ANTs for parcellation transformation")
 
             # Save existing parcellation image to a tempfile
@@ -102,7 +109,7 @@ class ANTsParcellationWarper:
                 f"-i {prewarp_parcellation_path.resolve()}",
                 # use resampled reference
                 f"-r {target_data['reference_path'].resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_parcellation_path.resolve()}",
             ]
             # Call antsApplyTransforms

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],
-        extra_input: Dict[str, Any],
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 
@@ -44,10 +44,8 @@ class FSLParcellationWarper:
         target_data : dict
             The corresponding item of the data object to which the parcellation
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of parcellation
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -81,7 +79,7 @@ class FSLParcellationWarper:
             f"-i {prewarp_parcellation_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference_path'].resolve()}",
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
             f"-o {warped_parcellation_path.resolve()}",
         ]
         # Call applywarp