fix: missing copy method

Author: clementpoiret

roiloc/registration.py

@@ -1,3 +1,4 @@
+from copy import deepcopy
 from pathlib import PosixPath
 from typing import Optional
 
@@ -6,12 +7,14 @@
 from rich import print
 
 
-def register(fixed: ANTsImage,
-             moving: ANTsImage,
-             type_of_transform: list,
-             outprefix: str = "",
-             path: Optional[PosixPath] = None,
-             mask: Optional[str] = None) -> dict:
+def register(
+    fixed: ANTsImage,
+    moving: ANTsImage,
+    type_of_transform: list,
+    outprefix: str = "",
+    path: Optional[PosixPath] = None,
+    mask: Optional[str] = None,
+) -> dict:
     """Registration wrapper around ANTs
 
     Args:
@@ -28,27 +31,29 @@ def register(fixed: ANTsImage,
     if mask:
         mask_path = list(path.glob(mask))
         if mask_path:
-            mask = ants.image_read(str(mask_path[0]),
-                                   pixeltype="unsigned int",
-                                   reorient="LPI")
+            mask = ants.image_read(
+                str(mask_path[0]), pixeltype="unsigned int", reorient="LPI"
+            )
             print(f"\tUsing mask {str(mask_path[0])}")
         else:
-            print(
-                "\t[bold red]Warning: no mask found. Registering without mask..."
-            )
+            print("\t[bold red]Warning: no mask found. Registering without mask...")
 
-    return ants.registration(fixed=fixed,
-                             moving=moving,
-                             type_of_transform=type_of_transform,
-                             mask=mask,
-                             outprefix=outprefix)
+    return ants.registration(
+        fixed=fixed,
+        moving=moving,
+        type_of_transform=type_of_transform,
+        mask=mask,
+        outprefix=outprefix,
+    )
 
 
-def get_roi(registered_atlas: ANTsImage,
-            idx: int,
-            output_dir: Optional[str] = None,
-            output_file: Optional[str] = None,
-            save: bool = True) -> ANTsImage:
+def get_roi(
+    registered_atlas: ANTsImage,
+    idx: int,
+    output_dir: Optional[str] = None,
+    output_file: Optional[str] = None,
+    save: bool = True,
+) -> ANTsImage:
     """Get the registered ROI from CerebrA atlas, into a
     subject's native space.
 
@@ -64,7 +69,7 @@ def get_roi(registered_atlas: ANTsImage,
     Returns:
         ANTsImage: ROI in native space
     """
-    roi = registered_atlas.copy()
+    roi = deepcopy(registered_atlas)
     roi[roi != idx] = 0
     # roi[~np.isin(roi, idx)] = 0