junifer 0.0.8.dev202__tar.gz → 0.0.8.dev206__tar.gz

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev202
+Version: 0.0.8.dev206
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.8.dev206/docs/changes/newsfragments/510.bugfix

@@ -0,0 +1 @@
+Normalise enum-based spaces such as ``AOMICSpace`` to strings before being passed to :func:`.get_xfm` or :func:`.get_template` by `Synchon Mandal`_

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev202'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev202')
+__version__ = version = '0.0.8.dev206'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev206')
 
-__commit_id__ = commit_id = 'gceb29ce8e'
+__commit_id__ = commit_id = 'g381832862'

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/data/maps/_ants_maps_warper.py

@@ -9,6 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import SpaceLike
 from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
@@ -31,8 +32,8 @@ class ANTsMapsWarper:
         self,
         maps_name: str,
         maps_img: "Nifti1Image",
-        src: str,
-        dst: str,
+        src: SpaceLike,
+        dst: SpaceLike,
         target_data: dict[str, Any],
         warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":
@@ -44,10 +45,10 @@ class ANTsMapsWarper:
             The name of the maps.
         maps_img : nibabel.nifti1.Nifti1Image
             The maps image to transform.
-        src : str
+        src : str or Enum
             The data type or template space to warp from.
             It should be empty string if ``dst="T1w"``.
-        dst : str
+        dst : str or Enum
             The data type or template space to warp to.
             `"T1w"` is the only allowed data type and it uses the resampled T1w
             found in ``target_data.reference``. The ``"reference"``

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/data/masks/_ants_mask_warper.py

@@ -10,6 +10,7 @@ import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
+from ...typing import SpaceLike
 from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
@@ -52,8 +53,8 @@ class ANTsMaskWarper:
         self,
         mask_name: str,
         mask_img: "Nifti1Image",
-        src: str,
-        dst: str,
+        src: SpaceLike,
+        dst: SpaceLike,
         target_data: dict[str, Any],
         warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":  # pragma: no cover
@@ -65,10 +66,10 @@ class ANTsMaskWarper:
             The name of the mask.
         mask_img : nibabel.nifti1.Nifti1Image
             The mask image to transform.
-        src : str
+        src : str or Enum
             The data type or template space to warp from.
             It should be empty string if ``dst="native"``.
-        dst : str
+        dst : str or Enum
             The data type or template space to warp to.
             `"native"` is the only allowed data type and it uses the resampled
             T1w found in ``target_data.reference``. The

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/data/parcellations/_ants_parcellation_warper.py

@@ -9,6 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import SpaceLike
 from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
@@ -31,8 +32,8 @@ class ANTsParcellationWarper:
         self,
         parcellation_name: str,
         parcellation_img: "Nifti1Image",
-        src: str,
-        dst: str,
+        src: SpaceLike,
+        dst: SpaceLike,
         target_data: dict[str, Any],
         warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":
@@ -44,10 +45,10 @@ class ANTsParcellationWarper:
             The name of the parcellation.
         parcellation_img : nibabel.nifti1.Nifti1Image
             The parcellation image to transform.
-        src : str
+        src : str or Enum
             The data type or template space to warp from.
             It should be empty string if ``dst="T1w"``.
-        dst : str
+        dst : str or Enum
             The data type or template space to warp to.
             `"T1w"` is the only allowed data type and it uses the resampled T1w
             found in ``target_data.reference``. The ``"reference"``

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/data/template_spaces.py

@@ -12,6 +12,7 @@ import structlog
 from junifer_data import get
 from templateflow import api as tflow
 
+from ..typing import SpaceLike
 from ..utils import raise_error
 from .utils import JUNIFER_DATA_PARAMS, closest_resolution, get_dataset_path
 
@@ -22,14 +23,14 @@ _log = structlog.get_logger("junifer")
 logger = _log.bind(pkg="data")
 
 
-def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
+def get_xfm(src: SpaceLike, dst: SpaceLike) -> Path:  # pragma: no cover
     """Fetch warp files to convert from ``src`` to ``dst``.
 
     Parameters
     ----------
-    src : str
+    src : str or Enum
         The template space to transform from.
-    dst : str
+    dst : str or Enum
         The template space to transform to.
 
     Returns
@@ -38,6 +39,9 @@ def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
         The path to the transformation file.
 
     """
+    # Normalise enum-based spaces (e.g. `AOMICSpace`) to their values
+    src = getattr(src, "value", src)
+    dst = getattr(dst, "value", dst)
     # Set file path to retrieve
     xfm_file_path = Path(f"xfms/{src}_to_{dst}/{src}_to_{dst}_Composite.h5")
     # Retrieve file
@@ -49,7 +53,7 @@ def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
 
 
 def get_template(
-    space: str,
+    space: SpaceLike,
     target_img: nib.Nifti1Image,
     extra_input: dict[str, Any] | None = None,
     template_type: str = "T1w",
@@ -59,7 +63,7 @@ def get_template(
 
     Parameters
     ----------
-    space : str
+    space : str or Enum
         The name of the template space.
     target_img : Nifti1Image
         The corresponding image for which the template space will be loaded.
@@ -88,6 +92,8 @@ def get_template(
         If required template is not found.
 
     """
+    # Normalise enum-based spaces (e.g. `AOMICSpace`) to their values
+    space = getattr(space, "value", space)
     # Check for invalid space; early check to raise proper error
     if space not in tflow.templates():
         raise_error(f"Unknown template space: {space}")

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/markers/utils.py

@@ -19,7 +19,7 @@ from ..utils import raise_error
 
 def _ets(
     bold_ts: np.ndarray,
-    roi_names: None | list[str] = None,
+    roi_names: list[str] | None = None,
 ) -> tuple[np.ndarray, list[str] | None]:
     """Compute the edge-wise time series based on BOLD time series.
 

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/preprocess/warping/_ants_warper.py

@@ -13,7 +13,7 @@ import numpy as np
 
 from ...data import get_template, get_xfm
 from ...pipeline import ExtDep, WorkDirManager
-from ...typing import Dependencies, ExternalDependencies
+from ...typing import Dependencies, ExternalDependencies, SpaceLike
 from ...utils import raise_error, run_ext_cmd
 from ..base import logger
 
@@ -42,7 +42,7 @@ class ANTsWarper:
         self,
         input: dict[str, Any],
         extra_input: dict[str, Any],
-        reference: str,
+        reference: SpaceLike,
     ) -> dict[str, Any]:
         """Preprocess using ANTs.
 
@@ -53,7 +53,7 @@ class ANTsWarper:
         extra_input : dict
             The other fields in the Junifer Data object. Should have ``T1w``
             and ``Warp`` data types.
-        reference : str
+        reference : str or Enum
             The data type or template space to use as reference for warping.
 
         Returns

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/typing/__init__.pyi

@@ -12,6 +12,7 @@ __all__ = [
     "MarkerInOutMappings",
     "DataGrabberPatterns",
     "ConfigVal",
+    "SpaceLike",
     "Element",
     "Elements",
 ]
@@ -30,6 +31,7 @@ from ._typing import (
     MarkerInOutMappings,
     DataGrabberPatterns,
     ConfigVal,
+    SpaceLike,
     Element,
     Elements,
 )

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer/typing/_typing.py

@@ -12,6 +12,7 @@ else:
     from typing import TypedDict
 
 from collections.abc import Sequence
+from enum import Enum
 from typing import (
     TYPE_CHECKING,
     Union,
@@ -43,6 +44,7 @@ __all__ = [
     "MarkerLike",
     "PipelineComponent",
     "PreprocessorLike",
+    "SpaceLike",
     "StorageLike",
 ]
 
@@ -79,5 +81,6 @@ DataGrabberPatterns = dict[
     dict[str, dict[str, str] | str] | dict[str, str] | list[dict[str, str]],
 ]
 ConfigVal = bool | int | float | str
+SpaceLike = str | Enum
 Element = str | tuple[str, ...]
 Elements = Sequence[Element]

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev202
+Version: 0.0.8.dev206
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer.egg-info/SOURCES.txt

@@ -79,6 +79,7 @@ docs/changes/newsfragments/492.bugfix
 docs/changes/newsfragments/499.enh
 docs/changes/newsfragments/502.bugfix
 docs/changes/newsfragments/503.enh
+docs/changes/newsfragments/510.bugfix
 docs/extending/confounds_format.rst
 docs/extending/coordinates.rst
 docs/extending/data_dump_asset.rst

{junifer-0.0.8.dev202 → junifer-0.0.8.dev206}/junifer.egg-info/scm_file_list.json

@@ -64,6 +64,7 @@
     "docs/changes/newsfragments/499.enh",
     "docs/changes/newsfragments/502.bugfix",
     "docs/changes/newsfragments/503.enh",
+    "docs/changes/newsfragments/510.bugfix",
     "docs/conf.py",
     "docs/contribution.rst",
     "docs/extending/confounds_format.rst",

junifer-0.0.8.dev206/junifer.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.0.7",
+  "distance": 206,
+  "node": "g3818328623d281e9cdd80366b974f4decdd44ece",
+  "dirty": false,
+  "branch": "main",
+  "node_date": "2026-09-30"
+}

junifer-0.0.8.dev202/junifer.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "0.0.7",
-  "distance": 202,
-  "node": "gceb29ce8e3661513719c790075259928eb4fd890",
-  "dirty": false,
-  "branch": "main",
-  "node_date": "2026-08-25"
-}