enh: review comments

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Author: oesteban

Diff for: nitransforms/io/base.py

@@ -1,4 +1,5 @@
 """Read/write linear transforms."""
+from pathlib import Path
 import numpy as np
 from nibabel import load as loadimg
 from scipy.io.matlab.miobase import get_matfile_version
@@ -174,3 +175,9 @@ def _read_mat(byte_stream):
     else:
         raise TransformFileError("Not a Matlab file.")
     return reader.get_variables()
+
+
+def _ensure_image(img):
+    if isinstance(img, (str, Path)):
+        return loadimg(img)
+    return img

Diff for: nitransforms/io/fsl.py

@@ -2,11 +2,16 @@
 import os
 import warnings
 import numpy as np
+from numpy.linalg import inv
 from pathlib import Path
-from nibabel import load as _nbload
 from nibabel.affines import voxel_sizes
 
-from .base import BaseLinearTransformList, LinearParameters, TransformFileError
+from .base import (
+    BaseLinearTransformList,
+    LinearParameters,
+    TransformFileError,
+    _ensure_image,
+)
 
 
 class FSLLinearTransform(LinearParameters):
@@ -41,14 +46,14 @@ def from_ras(cls, ras, moving=None, reference=None):
 
         # Adjust for reference image offset and orientation
         refswp, refspc = _fsl_aff_adapt(reference)
-        pre = reference.affine.dot(np.linalg.inv(refspc).dot(np.linalg.inv(refswp)))
+        pre = reference.affine.dot(inv(refspc).dot(inv(refswp)))
 
         # Adjust for moving image offset and orientation
         movswp, movspc = _fsl_aff_adapt(moving)
-        post = np.linalg.inv(movswp).dot(movspc.dot(np.linalg.inv(moving.affine)))
+        post = inv(movswp).dot(movspc.dot(inv(moving.affine)))
 
         # Compose FSL transform
-        mat = np.linalg.inv(np.swapaxes(post.dot(ras.dot(pre)), 0, 1))
+        mat = inv(np.swapaxes(post.dot(ras.dot(pre)), 0, 1))
 
         tf = cls()
         tf.structarr["parameters"] = mat.T
@@ -84,19 +89,13 @@ def to_ras(self, moving=None, reference=None):
         moving = _ensure_image(moving)
 
         refswp, refspc = _fsl_aff_adapt(reference)
-        pre = reference.affine.dot(np.linalg.inv(refspc).dot(np.linalg.inv(refswp)))
 
+        pre = refswp @ refspc @ inv(reference.affine)
         # Adjust for moving image offset and orientation
         movswp, movspc = _fsl_aff_adapt(moving)
-        post = np.linalg.inv(movswp).dot(movspc.dot(np.linalg.inv(moving.affine)))
-
+        post = moving.affine @ inv(movspc) @ inv(movswp)
         mat = self.structarr["parameters"].T
-
-        return (
-            np.linalg.inv(post)
-            @ np.swapaxes(np.linalg.inv(mat), 0, 1)
-            @ np.linalg.inv(pre)
-        )
+        return post @ np.swapaxes(inv(mat), 0, 1) @ pre
 
 
 class FSLLinearTransformArray(BaseLinearTransformList):
@@ -187,9 +186,3 @@ def _fsl_aff_adapt(space):
         swp[0, 0] = -1.0
         swp[0, 3] = (space.shape[0] - 1) * zooms[0]
     return swp, np.diag(zooms)
-
-
-def _ensure_image(img):
-    if isinstance(img, (str, Path)):
-        return _nbload(img)
-    return img

Diff for: nitransforms/tests/test_linear.py

@@ -72,7 +72,7 @@ def test_loadsave_itk(tmp_path, data_path, testdata_path):
     )
 
 
-@pytest.mark.xfail(reason="Not fully implemented")
+# @pytest.mark.xfail(reason="Not fully implemented")
 @pytest.mark.parametrize("fmt", ["itk", "fsl", "afni", "lta"])
 def test_loadsave(tmp_path, data_path, testdata_path, fmt):
     """Test idempotency."""