enh: load ITK's .mat files with Affine's loaders

Author: oesteban

nitransforms/io/itk.py

@@ -204,7 +204,14 @@ def from_string(cls, string):
         parameters[:3, :3] = vals[:-3].reshape((3, 3))
         parameters[:3, 3] = vals[-3:]
         sa["parameters"] = parameters
-        return tf
+
+        # Try to double-dip and see if there are more transforms
+        try:
+            cls.from_string("\n".join(lines[4:8]))
+        except TransformFileError:
+            return tf
+        else:
+            raise TransformFileError("More than one linear transform found.")
 
 
 class ITKLinearTransformArray(BaseLinearTransformList):

nitransforms/linear.py

@@ -203,18 +203,33 @@ def from_filename(cls, filename, fmt=None, reference=None, moving=None):
         """Create an affine from a transform file."""
         fmtlist = [fmt] if fmt is not None else ("itk", "lta", "afni", "fsl")
 
+        is_array = cls != Affine
+
+        errors = []
         for potential_fmt in fmtlist:
+            if (potential_fmt == "itk" and Path(filename).suffix == ".mat"):
+                is_array = False
+                cls = Affine
+
             try:
-                struct = get_linear_factory(potential_fmt).from_filename(filename)
-                matrix = struct.to_ras(reference=reference, moving=moving)
-                if cls == Affine:
-                    if np.shape(matrix)[0] != 1:
-                        raise TypeError("Cannot load transform array '%s'" % filename)
-                    matrix = matrix[0]
-                return cls(matrix, reference=reference)
-            except (TransformFileError, FileNotFoundError):
+                struct = get_linear_factory(
+                    potential_fmt,
+                    is_array=is_array
+                ).from_filename(filename)
+            except (TransformFileError, FileNotFoundError) as err:
+                errors.append((potential_fmt, err))
                 continue
 
+            matrix = struct.to_ras(reference=reference, moving=moving)
+
+            # Process matrix
+            if not is_array and np.ndim(matrix) == 3:
+                if np.shape(matrix)[0] != 1:
+                    raise TypeError("Cannot load transform array '%s'" % filename)
+                matrix = matrix[0]
+
+            return cls(matrix, reference=reference)
+
         raise TransformFileError(
             f"Could not open <{filename}> (formats tried: {', '.join(fmtlist)})."
         )
@@ -499,6 +514,8 @@ def load(filename, fmt=None, reference=None, moving=None):
     xfm = LinearTransformsMapping.from_filename(
         filename, fmt=fmt, reference=reference, moving=moving
     )
-    if len(xfm) == 1:
-        return xfm[0]
+
+    if isinstance(xfm, LinearTransformsMapping) and len(xfm) == 1:
+        xfm = xfm[0]
+
     return xfm

nitransforms/tests/test_linear.py

@@ -44,7 +44,7 @@ def test_linear_typeerrors1(matrix):
 
 def test_linear_typeerrors2(data_path):
     """Exercise errors in Affine creation."""
-    with pytest.raises(TypeError):
+    with pytest.raises(io.TransformFileError):
         nitl.Affine.from_filename(data_path / "itktflist.tfm", fmt="itk")