Merge pull request #208 from nipy/fix/remaining-apply-on-object

FIX: Forgotten test using ``xfm.apply()``

Author: oesteban

Dockerfile

@@ -28,10 +28,14 @@ RUN apt-get update && \
                     unzip && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+RUN update-ca-certificates -f
+
 # FreeSurfer 7.3.2
 FROM downloader as freesurfer
 COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
+COPY docker/files/fs-cert.pem /usr/local/etc/fs-cert.pem
+RUN curl --cacert /usr/local/etc/fs-cert.pem \
+     -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
      | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt
 
 # AFNI

docker/files/fs-cert.pem

@@ -0,0 +1,44 @@
+-----BEGIN CERTIFICATE-----
+MIIHuDCCBiCgAwIBAgIRAMa1FS9MSn5TXKMgD8OXtoswDQYJKoZIhvcNAQEMBQAw
+RDELMAkGA1UEBhMCVVMxEjAQBgNVBAoTCUludGVybmV0MjEhMB8GA1UEAxMYSW5D
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+QXaR+CbnTBx1PeB4nf+yHg2VBvKk6m7E9lnyymENmbeaLC67CJQgr+ne1rpOuEIs
+fVbKUP437fyEvPuZCZ+3gxFsKgOerk2J95+AdLKB01pQFh/ITS/2zHHeMeD118sR
+mUO+RXiPX5ZUqu/M
+-----END CERTIFICATE-----

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

@@ -67,6 +67,11 @@ def __len__(self):
         """Enable using len()."""
         return len(self.transforms)
 
+    @property
+    def ndim(self):
+        """Get the number of dimensions."""
+        return max(x.ndim for x in self._transforms)
+
     @property
     def transforms(self):
         """Get the internal list of transforms."""

nitransforms/manip.py

@@ -317,11 +317,11 @@ def map(self, x, inverse=False):
         --------
         >>> xfm = BSplineFieldTransform(test_dir / "someones_bspline_coefficients.nii.gz")
         >>> xfm.reference = test_dir / "someones_anatomy.nii.gz"
-        >>> xfm.map([-6.5, -36., -19.5]).tolist()
-        [[-6.5, -31.476097418406784, -19.5]]
+        >>> xfm.map([-6.5, -36., -19.5]).tolist()  # doctest: +ELLIPSIS
+        [[-6.5, -31.476097418406..., -19.5]]
 
-        >>> xfm.map([[-6.5, -36., -19.5], [-1., -41.5, -11.25]]).tolist()
-        [[-6.5, -31.476097418406784, -19.5], [-1.0, -3.8072675377121996, -11.25]]
+        >>> xfm.map([[-6.5, -36., -19.5], [-1., -41.5, -11.25]]).tolist()  # doctest: +ELLIPSIS
+        [[-6.5, -31.4760974184..., -19.5], [-1.0, -3.807267537712..., -11.25]]
 
         """
         vfunc = partial(

nitransforms/nonlinear.py

@@ -14,6 +14,7 @@
     RMSE_TOL,
     APPLY_NONLINEAR_CMD,
 )
+from nitransforms.resampling import apply
 
 FMT = {"lta": "fs", "tfm": "itk"}
 
@@ -54,7 +55,7 @@ def test_itk_h5(tmp_path, testdata_path):
     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")
     diff = sw_moved.get_fdata() - nt_moved.get_fdata()
     # A certain tolerance is necessary because of resampling at borders

nitransforms/tests/test_manip.py

@@ -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(