Merge pull request #144 from effigies/fix/fsl_transforms

FIX: Increase FSL serialization precision

Author: oesteban

nitransforms/io/fsl.py

@@ -20,7 +20,7 @@ class FSLLinearTransform(LinearParameters):
     def __str__(self):
         """Generate a string representation."""
         lines = [
-            " ".join(["%g" % col for col in row])
+            " ".join("%.08f" % col for col in row)
             for row in self.structarr["parameters"]
         ]
         return "\n".join(lines + [""])
@@ -46,14 +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(inv(refspc).dot(inv(refswp)))
+        pre = reference.affine @ inv(refswp @ refspc)
 
         # Adjust for moving image offset and orientation
         movswp, movspc = _fsl_aff_adapt(moving)
-        post = inv(movswp).dot(movspc.dot(inv(moving.affine)))
+        post = movswp @ movspc @ inv(moving.affine)
 
         # Compose FSL transform
-        mat = inv(np.swapaxes(post.dot(ras.dot(pre)), 0, 1))
+        mat = inv(np.swapaxes(post @ ras @ pre, 0, 1))
 
         tf = cls()
         tf.structarr["parameters"] = mat.T
@@ -92,7 +92,7 @@ def to_ras(self, moving=None, reference=None):
         pre = refswp @ refspc @ inv(reference.affine)
         # Adjust for moving image offset and orientation
         movswp, movspc = _fsl_aff_adapt(moving)
-        post = moving.affine @ inv(movspc) @ inv(movswp)
+        post = moving.affine @ inv(movswp @ movspc)
         mat = self.structarr["parameters"].T
         return post @ np.swapaxes(inv(mat), 0, 1) @ pre
 

nitransforms/tests/data/affine-LPS.fsl

@@ -1,4 +1,4 @@
-0.999999 -0.00140494 0.000161717 -3.89014
-0.000999999 0.621609 -0.783327 105.905
-0.001 0.783327 0.62161 -34.3513
-0 0 0 1
+0.99999900 -0.00140494 0.00016172 -3.89014000
+0.00100000 0.62160900 -0.78332700 105.90500000
+0.00100000 0.78332700 0.62161000 -34.35130000
+0.00000000 0.00000000 0.00000000 1.00000000

nitransforms/tests/data/affine-RAS.fsl

@@ -1,4 +1,4 @@
-0.999999 -0.00140494 -0.000161717 4.14529
-0.000999999 0.621609 0.783327 -37.3811
--0.001 -0.783327 0.62161 107.976
-0 0 0 1
+0.99999900 -0.00140494 -0.00016172 4.14529000
+0.00100000 0.62160900 0.78332700 -37.38110000
+-0.00100000 -0.78332700 0.62161000 107.97600000
+0.00000000 0.00000000 0.00000000 1.00000000

nitransforms/tests/data/affine-oblique.fsl

@@ -1,4 +1,4 @@
-0.999998 -0.00181872 -0.0011965 4.26083
-0.00206779 0.621609 0.783325 -25.3129
--0.000680894 -0.783326 0.621611 101.967
-0 0 0 1
+0.99999800 -0.00181872 -0.00119650 4.26083000
+0.00206779 0.62160900 0.78332500 -25.31290000
+-0.00068089 -0.78332600 0.62161100 101.96700000
+0.00000000 0.00000000 0.00000000 1.00000000

nitransforms/tests/test_linear.py

@@ -92,13 +92,11 @@ def test_loadsave(tmp_path, data_path, testdata_path, fmt):
             assert np.allclose(
                 xfm.matrix,
                 nitl.load(fname, fmt=fmt, reference=ref_file).matrix,
-                rtol=1e-2,  # FSL incurs into large errors due to rounding
             )
 
         assert np.allclose(
             xfm.matrix,
             nitl.load(fname, fmt=fmt, reference=ref_file, moving=ref_file).matrix,
-            rtol=1e-2,  # FSL incurs into large errors due to rounding
         )
     else:
         assert xfm == nitl.load(fname, fmt=fmt, reference=ref_file)

nitransforms/tests/utils.py

@@ -24,4 +24,4 @@ def assert_affines_by_filename(affine1, affine2):
     else:
         xfm1 = np.loadtxt(str(affine1))
         xfm2 = np.loadtxt(str(affine2))
-        np.testing.assert_almost_equal(xfm1, xfm2)
+        np.allclose(xfm1, xfm2, atol=1e-04)