fix: bug in oblique adjusting matrices computation

nipy · Nov 16, 2023 · 01cfcbc · 01cfcbc
1 parent 0a02bcf
commit 01cfcbc
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Showing 5 changed files with 16 additions and 8 deletions.
diff --git a/nitransforms/io/afni.py b/nitransforms/io/afni.py
@@ -135,10 +135,10 @@ def to_ras(self, moving=None, reference=None):
         if reference is not None and _is_oblique(ref_aff := _ensure_image(reference).affine):
             pre_rotation = _cardinal_rotation(ref_aff, True)
         if moving is not None and _is_oblique(mov_aff := _ensure_image(moving).affine):
-            post_rotation = _cardinal_rotation(mov_aff, True)
+            post_rotation = _cardinal_rotation(mov_aff, False)
 
         return np.stack([
-            post_rotation @ xfm.to_ras() @ pre_rotation
+            post_rotation @ (xfm.to_ras() @ pre_rotation)
             for xfm in self.xforms
         ])
 
@@ -152,14 +152,22 @@ def to_string(self):
                 if line.strip()
             ]
             strings += lines
-        return "\n".join(strings)
+        return "\n".join(strings + [""])
 
     @classmethod
     def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         _self = cls()
+
+        pre_rotation = post_rotation = np.eye(4)
+
+        if reference is not None and _is_oblique(ref_aff := _ensure_image(reference).affine):
+            pre_rotation = _cardinal_rotation(ref_aff, False)
+        if moving is not None and _is_oblique(mov_aff := _ensure_image(moving).affine):
+            post_rotation = _cardinal_rotation(mov_aff, True)
+
         _self.xforms = [
-            cls._inner_type.from_ras(ras[i, ...], moving=moving, reference=reference)
+            cls._inner_type.from_ras(post_rotation @ ras[i, ...] @ pre_rotation)
             for i in range(ras.shape[0])
         ]
         return _self

diff --git a/nitransforms/tests/data/affine-LAS.afni-array b/nitransforms/tests/data/affine-LAS.afni-array
@@ -0,0 +1 @@
+affine-RAS.afni-array
diff --git a/nitransforms/tests/data/affine-LPS.afni-array b/nitransforms/tests/data/affine-LPS.afni-array
@@ -0,0 +1 @@
+affine-RAS.afni-array
diff --git a/nitransforms/tests/data/affine-oblique.afni-array b/nitransforms/tests/data/affine-oblique.afni-array
@@ -0,0 +1 @@
+affine-RAS.afni-array
diff --git a/nitransforms/tests/test_io.py b/nitransforms/tests/test_io.py
@@ -208,9 +208,6 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation, get_testdata):
 
     fname = f"affine-{image_orientation}.{sw}{ext}"
 
-    if sw == "afni-array":
-        fname.replace(image_orientation, "RAS")
-
     # Test the transform loaders are implemented
     xfm = factory.from_filename(data_path / fname)
 
@@ -228,7 +225,7 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation, get_testdata):
     # Test from_ras
     RAS = from_matvec(euler2mat(x=0.9, y=0.001, z=0.001), [4.0, 2.0, -1.0])
     if sw == "afni-array":
-        RAS = [RAS, RAS]
+        RAS = np.array([RAS, RAS])
 
     xfm = factory.from_ras(RAS, reference=reference, moving=moving)
     assert np.allclose(xfm.to_ras(reference=reference, moving=moving), RAS)