fix: process exceptions when trying to open X5

Author: oesteban

nitransforms/io/x5.py

@@ -140,15 +140,21 @@ def to_filename(fname: str | Path, x5_list: List[X5Transform]):
 
 def from_filename(fname: str | Path) -> List[X5Transform]:
     """Read a list of :class:`X5Transform` objects from an X5 HDF5 file."""
-    with h5py.File(str(fname), "r") as in_file:
-        if in_file.attrs.get("Format") != "X5":
-            raise ValueError("Input file is not in X5 format")
-
-        tg = in_file["TransformGroup"]
-        return [
-            _read_x5_group(node)
-            for _, node in sorted(tg.items(), key=lambda kv: int(kv[0]))
-        ]
+    try:
+        with h5py.File(str(fname), "r") as in_file:
+            if in_file.attrs.get("Format") != "X5":
+                raise TypeError("Input file is not in X5 format")
+
+            tg = in_file["TransformGroup"]
+            return [
+                _read_x5_group(node)
+                for _, node in sorted(tg.items(), key=lambda kv: int(kv[0]))
+            ]
+    except OSError as err:
+        if "file signature not found" in err.args[0]:
+            raise TypeError("Input file is not HDF5.")
+
+        raise  # pragma: no cover
 
 
 def _read_x5_group(node) -> X5Transform:

nitransforms/linear.py

@@ -9,6 +9,7 @@
 """Linear transforms."""
 
 import warnings
+from collections import namedtuple
 import numpy as np
 from pathlib import Path
 
@@ -187,9 +188,18 @@ def from_filename(
         if fmt and fmt.upper() == "X5":
             x5_xfm = load_x5(filename)[x5_position]
             Transform = cls if x5_xfm.array_length == 1 else LinearTransformsMapping
-            if x5_xfm.domain:
-                # override reference
-                raise NotImplementedError
+            if (
+                x5_xfm.domain
+                and not x5_xfm.domain.grid
+                and len(x5_xfm.domain.size) == 3
+            ):  # pragma: no cover
+                raise NotImplementedError(
+                    "Only 3D regularly gridded domains are supported"
+                )
+            elif x5_xfm.domain:
+                # Override reference
+                Domain = namedtuple("Domain", "affine shape")
+                reference = Domain(x5_xfm.domain.mapping, x5_xfm.domain.size)
 
             return Transform(x5_xfm.transform, reference=reference)
 

nitransforms/tests/test_linear.py

@@ -265,6 +265,9 @@ def test_linear_to_x5(tmpdir, store_inverse):
 
     aff.to_filename("export1.x5", x5_inverse=store_inverse)
 
+    # Test round trip
+    assert aff == nitl.Affine.from_filename("export1.x5", fmt="X5")
+
     # Test with Domain
     img = nb.Nifti1Image(np.zeros((2, 2, 2), dtype="float32"), np.eye(4))
     img_path = Path(tmpdir) / "ref.nii.gz"
@@ -275,6 +278,9 @@ def test_linear_to_x5(tmpdir, store_inverse):
     assert node.domain.size == aff.reference.shape
     aff.to_filename("export2.x5", x5_inverse=store_inverse)
 
+    # Test round trip
+    assert aff == nitl.Affine.from_filename("export2.x5", fmt="X5")
+
     # Test with Jacobian
     node.jacobian = np.zeros((2, 2, 2), dtype="float32")
     io.x5.to_filename("export3.x5", [node])

nitransforms/tests/test_x5.py

@@ -73,5 +73,5 @@ def test_from_filename_invalid(tmp_path):
     with H5File(fname, "w") as f:
         f.attrs["Format"] = "NOTX5"
 
-    with pytest.raises(ValueError):
+    with pytest.raises(TypeError):
         from_filename(fname)