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

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
@@ -23,7 +23,7 @@ from nilearn import datasets, image
 from ...utils import logger, raise_error, warn_with_log
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
-from ..utils import closest_resolution
+from ..utils import closest_resolution, get_native_warper
 from ._ants_parcellation_warper import ANTsParcellationWarper
 from ._fsl_parcellation_warper import FSLParcellationWarper
 
@@ -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
@@ -394,16 +394,12 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         Raises
         ------
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
         ValueError
             If ``extra_input`` is None when ``target_data``'s space is native.
 
         """
         # 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
@@ -413,8 +409,16 @@ class ParcellationRegistry(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"]
@@ -428,12 +432,14 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         all_parcellations = []
         all_labels = []
         for name in parcellations:
+            # Load parcellation
             img, labels, _, space = self.load(
                 name=name,
                 resolution=resolution,
             )
 
-            # Convert parcellation spaces if required
+            # Convert parcellation spaces if required;
+            # cannot be "native" due to earlier check
             if space != target_std_space:
                 raw_img = ANTsParcellationWarper().warp(
                     parcellation_name=name,
@@ -441,7 +447,7 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     src=space,
                     dst=target_std_space,
                     target_data=target_data,
-                    extra_input=None,
+                    warp_data=None,
                 )
                 # Remove extra dimension added by ANTs
                 img = image.math_img("np.squeeze(img)", img=raw_img)
@@ -471,32 +477,22 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Warp parcellation if target space 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":
                 resampled_parcellation_img = FSLParcellationWarper().warp(
                     parcellation_name="native",
                     parcellation_img=resampled_parcellation_img,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
                 )
-            elif warp_file_ext == ".h5":
+            elif warper_spec["warper"] == "ants":
                 resampled_parcellation_img = ANTsParcellationWarper().warp(
                     parcellation_name="native",
                     parcellation_img=resampled_parcellation_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 resampled_parcellation_img, labels
@@ -507,7 +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
@@ -651,7 +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
@@ -753,7 +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
@@ -927,7 +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
@@ -1053,7 +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
@@ -1209,7 +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
@@ -1414,7 +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
@@ -1611,7 +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
@@ -1724,10 +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

@@ -4,19 +4,20 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from collections.abc import MutableMapping
+from typing import Optional, Union
 
 import numpy as np
 
-from ..utils.logging import logger
+from ..utils import logger, raise_error
 
 
-__all__ = ["closest_resolution"]
+__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.
 
@@ -49,3 +50,67 @@ def closest_resolution(
         closest = np.min(valid_resolution)
 
     return closest
+
+
+def get_native_warper(
+    target_data: MutableMapping,
+    other_data: MutableMapping,
+    inverse: bool = False,
+) -> dict:
+    """Get correct warping specification for native space.
+
+    Parameters
+    ----------
+    target_data : dict
+        The target data from the pipeline data object.
+    other_data : dict
+        The other data in the pipeline data object.
+    inverse : bool, optional
+        Whether to get the inverse warping specification (default False).
+
+    Returns
+    -------
+    dict
+        The correct warping specification.
+
+    Raises
+    ------
+    RuntimeError
+        If no warper or multiple possible warpers are found.
+
+    """
+    # Get possible warpers
+    possible_warpers = []
+    for entry in other_data["Warp"]:
+        if not inverse:
+            if (
+                entry["src"] == target_data["prewarp_space"]
+                and entry["dst"] == "native"
+            ):
+                possible_warpers.append(entry)
+        else:
+            if (
+                entry["dst"] == target_data["prewarp_space"]
+                and entry["src"] == "native"
+            ):
+                possible_warpers.append(entry)
+
+    # Check for no warper
+    if not possible_warpers:
+        raise_error(
+            klass=RuntimeError,
+            msg="Could not find correct warping specification",
+        )
+
+    # Check for multiple possible warpers
+    if len(possible_warpers) > 1:
+        raise_error(
+            klass=RuntimeError,
+            msg=(
+                "Cannot proceed as multiple warping specification found, "
+                "adjust either the DataGrabber or the working space: "
+                f"{possible_warpers}"
+            ),
+        )
+
+    return possible_warpers[0]

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
@@ -169,15 +169,28 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types

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
@@ -204,15 +204,28 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types
@@ -234,7 +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
@@ -266,7 +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
@@ -202,15 +202,28 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types
@@ -232,7 +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
@@ -248,7 +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

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -31,7 +31,7 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 )
 def test_DataladAOMICID1000(
     type_: str,
-    nested_types: Optional[List[str]],
+    nested_types: Optional[list[str]],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber.
 
@@ -87,7 +87,7 @@ def test_DataladAOMICID1000(
     ],
 )
 def test_DataladAOMICID1000_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -40,8 +40,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 )
 def test_DataladAOMICPIOP1(
     type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    tasks: Optional[list[str]],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
@@ -117,7 +117,7 @@ def test_DataladAOMICPIOP1(
     ],
 )
 def test_DataladAOMICPIOP1_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber partial data access.