fix: replace all remaining xfm.apply() calls

Author: oesteban

docs/notebooks/Reading and Writing transforms.ipynb

@@ -46,6 +46,7 @@
     "import numpy as np\n",
     "import nibabel as nb\n",
     "import nitransforms as nt\n",
+    "from nitransforms.resampling import apply\n",
     "\n",
     "cwd = TemporaryDirectory()\n",
     "os.chdir(cwd.name)\n",
@@ -263,7 +264,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "moved = xfm.apply(nii, order=0)\n",
+    "moved = apply(xfm, nii, order=0)\n",
     "moved.to_filename('moved-nb.nii.gz')"
    ]
   },
@@ -741,7 +742,7 @@
    "outputs": [],
    "source": [
     "xfm.reference = oblique\n",
-    "moved_oblique = xfm.apply(las_anatomy)"
+    "moved_oblique = apply(xfm, las_anatomy)"
    ]
   },
   {
@@ -895,7 +896,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -909,9 +910,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docs/notebooks/isbi2020.ipynb

@@ -169,7 +169,7 @@ def test_displacements_field1(
     exit_code = check_call([cmd], shell=True)
     assert exit_code == 0
     sw_moved_mask = nb.load("resampled_brainmask.nii.gz")
-    nt_moved_mask = xfm.apply(msk, order=0)
+    nt_moved_mask = apply(xfm, msk, order=0)
     nt_moved_mask.set_data_dtype(msk.get_data_dtype())
     diff = np.asanyarray(sw_moved_mask.dataobj) - np.asanyarray(nt_moved_mask.dataobj)
 
@@ -189,7 +189,7 @@ def test_displacements_field1(
     assert exit_code == 0
     sw_moved = nb.load("resampled.nii.gz")
 
-    nt_moved = xfm.apply(nii, order=0)
+    nt_moved = apply(xfm, nii, order=0)
     nt_moved.set_data_dtype(nii.get_data_dtype())
     nt_moved.to_filename("nt_resampled.nii.gz")
     sw_moved.set_data_dtype(nt_moved.get_data_dtype())
@@ -229,7 +229,7 @@ def test_displacements_field2(tmp_path, testdata_path, sw_tool):
     assert exit_code == 0
     sw_moved = nb.load("resampled.nii.gz")
 
-    nt_moved = xfm.apply(img_fname, order=0)
+    nt_moved = apply(xfm, img_fname, order=0)
     nt_moved.to_filename("nt_resampled.nii.gz")
     sw_moved.set_data_dtype(nt_moved.get_data_dtype())
     diff = np.asanyarray(