docs/changes/newsfragments/413.change

@@ -0,0 +1 @@
+``target_data`` parameter of :func:`.get_template` has been replaced with ``target_img`` by `Fede Raimondo`_

junifer/data/masks/_ants_mask_warper.py

@@ -125,7 +125,7 @@ class ANTsMaskWarper:
             # Get template space image
             template_space_img = get_template(
                 space=dst,
-                target_data=target_data,
+                target_img=mask_img,
                 extra_input=None,
             )
             # Save template to a tempfile

junifer/data/masks/_masks.py

@@ -106,15 +106,15 @@ def compute_brain_mask(
             if entry["dst"] == "native":
                 target_std_space = entry["src"]
 
+    target_img = target_data["data"]
     # Fetch template in closest resolution
     template = get_template(
         space=target_std_space,
-        target_data=target_data,
+        target_img=target_img,
         extra_input=extra_input,
         template_type=mask_type,
     )
     # Resample template to target image
-    target_img = target_data["data"]
     resampled_template = resample_to_img(
         source_img=template, target_img=target_img
     )

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -131,7 +131,7 @@ class ANTsParcellationWarper:
             # Get template space image
             template_space_img = get_template(
                 space=dst,
-                target_data=target_data,
+                target_img=parcellation_img,
                 extra_input=None,
             )
             # Save template to a tempfile

junifer/data/template_spaces.py

@@ -122,7 +122,7 @@ def get_xfm(
 
 def get_template(
     space: str,
-    target_data: dict[str, Any],
+    target_img: nib.Nifti1Image,
     extra_input: Optional[dict[str, Any]] = None,
     template_type: str = "T1w",
 ) -> nib.Nifti1Image:
@@ -132,9 +132,9 @@ def get_template(
     ----------
     space : str
         The name of the template space.
-    target_data : dict
+    target_img : Nifti1Image
-        The corresponding item of the data object for which the template space
+        The corresponding image for which the template space will be loaded.
-        will be loaded.
+        This is used to obtain the best matching resolution.
     extra_input : dict, optional
         The other fields in the data object. Useful for accessing other data
         types (default None).
@@ -163,7 +163,6 @@ def get_template(
         raise_error(f"Unknown template type: {template_type}")
 
     # Get the min of the voxels sizes and use it as the resolution
-    target_img = target_data["data"]
     resolution = np.min(target_img.header.get_zooms()[:3]).astype(int)
 
     # Fetch available resolutions for the template

junifer/data/tests/test_template_spaces.py

@@ -61,7 +61,9 @@ def test_get_template(template_type: str) -> None:
         bold = element_data["BOLD"]
         # Get tailored parcellation
         tailored_template = get_template(
-            space=bold["space"], target_data=bold, template_type=template_type
+            space=bold["space"],
+            target_img=bold["data"],
+            template_type=template_type,
         )
         assert isinstance(tailored_template, nib.Nifti1Image)
 
@@ -74,7 +76,7 @@ def test_get_template_invalid_space() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Get tailored parcellation
         with pytest.raises(ValueError, match="Unknown template space:"):
-            get_template(space="andromeda", target_data=vbm_gm)
+            get_template(space="andromeda", target_img=vbm_gm["data"])
 
 
 def test_get_template_invalid_template_type() -> None:
@@ -87,7 +89,7 @@ def test_get_template_invalid_template_type() -> None:
         with pytest.raises(ValueError, match="Unknown template type:"):
             get_template(
                 space=vbm_gm["space"],
-                target_data=vbm_gm,
+                target_img=vbm_gm["data"],
                 template_type="xenon",
             )
 
@@ -100,5 +102,7 @@ def test_get_template_closest_resolution() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Change header resolution to fetch closest resolution
         element_data["VBM_GM"]["data"].header.set_zooms((3, 3, 3))
-        template = get_template(space=vbm_gm["space"], target_data=vbm_gm)
+        template = get_template(
+            space=vbm_gm["space"], target_img=vbm_gm["data"]
+        )
         assert isinstance(template, nib.Nifti1Image)

junifer/preprocess/warping/_ants_warper.py

@@ -189,7 +189,7 @@ class ANTsWarper:
             # Get template space image
             template_space_img = get_template(
                 space=reference,
-                target_data=input,
+                target_img=input["data"],
                 extra_input=None,
             )
             # Save template