fix: extend tests and normalize error types

Author: oesteban

nitransforms/io/__init__.py

@@ -2,7 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Read and write transforms."""
 from nitransforms.io import afni, fsl, itk, lta
-from nitransforms.io.base import TransformFileError
+from nitransforms.io.base import TransformIOError, TransformFileError
 
 __all__ = [
     "afni",
@@ -11,6 +11,7 @@
     "lta",
     "get_linear_factory",
     "TransformFileError",
+    "TransformIOError",
 ]
 
 _IO_TYPES = {

nitransforms/io/afni.py

@@ -95,12 +95,16 @@ def from_string(cls, string):
         if not lines:
             raise TransformFileError
 
-        parameters = np.vstack(
-            (
-                np.genfromtxt([lines[0].encode()], dtype="f8").reshape((3, 4)),
-                (0.0, 0.0, 0.0, 1.0),
+        try:
+            parameters = np.vstack(
+                (
+                    np.genfromtxt([lines[0].encode()], dtype="f8").reshape((3, 4)),
+                    (0.0, 0.0, 0.0, 1.0),
+                )
             )
-        )
+        except ValueError as e:
+            raise TransformFileError from e
+
         sa["parameters"] = parameters
         return tf
 

nitransforms/io/base.py

@@ -6,8 +6,12 @@
 from ..patched import LabeledWrapStruct
 
 
-class TransformFileError(Exception):
-    """A custom exception for transform files."""
+class TransformIOError(IOError):
+    """General I/O exception while reading/writing transforms."""
+
+
+class TransformFileError(TransformIOError):
+    """Specific I/O exception when a file does not meet the expected format."""
 
 
 class StringBasedStruct(LabeledWrapStruct):

nitransforms/io/fsl.py

@@ -10,6 +10,7 @@
     BaseLinearTransformList,
     LinearParameters,
     DisplacementsField,
+    TransformIOError,
     TransformFileError,
     _ensure_image,
 )
@@ -40,7 +41,7 @@ def from_ras(cls, ras, moving=None, reference=None):
             moving = reference
 
         if reference is None:
-            raise ValueError("Cannot build FSL linear transform without a reference")
+            raise TransformIOError("Cannot build FSL linear transform without a reference")
 
         reference = _ensure_image(reference)
         moving = _ensure_image(moving)
@@ -77,7 +78,7 @@ def from_string(cls, string):
     def to_ras(self, moving=None, reference=None):
         """Return a nitransforms internal RAS+ matrix."""
         if reference is None:
-            raise ValueError("Cannot build FSL linear transform without a reference")
+            raise TransformIOError("Cannot build FSL linear transform without a reference")
 
         if moving is None:
             warnings.warn(

nitransforms/io/itk.py

@@ -8,6 +8,7 @@
     BaseLinearTransformList,
     DisplacementsField,
     LinearParameters,
+    TransformIOError,
     TransformFileError,
 )
 
@@ -306,7 +307,7 @@ def from_filename(cls, filename):
         from h5py import File as H5File
 
         if not str(filename).endswith(".h5"):
-            raise RuntimeError("Extension is not .h5")
+            raise TransformFileError("Extension is not .h5")
 
         with H5File(str(filename)) as f:
             return cls.from_h5obj(f)
@@ -355,7 +356,7 @@ def from_h5obj(cls, fileobj, check=True):
                 )
                 continue
 
-            raise NotImplementedError(
+            raise TransformIOError(
                 f"Unsupported transform type {xfm['TransformType'][0]}"
             )
 

nitransforms/linear.py

@@ -211,11 +211,11 @@ def from_filename(cls, filename, fmt=None, reference=None, moving=None):
                         raise TypeError("Cannot load transform array '%s'" % filename)
                     matrix = matrix[0]
                 return cls(matrix, reference=reference)
-            except TransformFileError:
+            except (TransformFileError, FileNotFoundError):
                 continue
 
         raise TransformFileError(
-            f"Could not open <{filename}> (formats tried: {', '.join(fmtlist)}."
+            f"Could not open <{filename}> (formats tried: {', '.join(fmtlist)})."
         )
 
     def __repr__(self):
@@ -468,11 +468,11 @@ def load(filename, fmt=None, reference=None, moving=None):
 
     Examples
     --------
-    >>> xfm = load(regress_dir / "affine-LAS.itk.tfm", fmt="itk")
+    >>> xfm = load(regress_dir / "affine-LAS.itk.tfm")
     >>> isinstance(xfm, Affine)
     True
 
-    >>> xfm = load(regress_dir / "itktflist.tfm", fmt="itk")
+    >>> xfm = load(regress_dir / "itktflist.tfm")
     >>> isinstance(xfm, LinearTransformsMapping)
     True
 

nitransforms/tests/test_io.py

@@ -24,7 +24,7 @@
     FSLinearTransform as LT,
     FSLinearTransformArray as LTA,
 )
-from ..io.base import LinearParameters, TransformFileError
+from ..io.base import LinearParameters, TransformIOError, TransformFileError
 
 LPS = np.diag([-1, -1, 1, 1])
 ITK_MAT = LPS.dot(np.ones((4, 4)).dot(LPS))
@@ -224,7 +224,7 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation, get_testdata):
 
     # Test without images
     if sw == "fsl":
-        with pytest.raises(ValueError):
+        with pytest.raises(TransformIOError):
             factory.from_ras(RAS)
     else:
         xfm = factory.from_ras(RAS)
@@ -422,7 +422,7 @@ def test_itk_h5(testdata_path):
         == 2
     )
 
-    with pytest.raises(RuntimeError):
+    with pytest.raises(TransformFileError):
         list(
             itk.ITKCompositeH5.from_filename(
                 testdata_path

nitransforms/tests/test_linear.py

@@ -54,6 +54,18 @@ def test_linear_valueerror():
         nitl.Affine(np.ones((4, 4)))
 
 
+def test_linear_load_unsupported(data_path):
+    """Exercise loading transform without I/O implementation."""
+    with pytest.raises(TypeError):
+        nitl.load(data_path / "itktflist2.tfm", fmt="X5")
+
+
+def test_linear_load_mistaken(data_path):
+    """Exercise loading transform without I/O implementation."""
+    with pytest.raises(io.TransformFileError):
+        nitl.load(data_path / "itktflist2.tfm", fmt="afni")
+
+
 def test_loadsave_itk(tmp_path, data_path, testdata_path):
     """Test idempotency."""
     ref_file = testdata_path / "someones_anatomy.nii.gz"
@@ -73,9 +85,13 @@ def test_loadsave_itk(tmp_path, data_path, testdata_path):
     )
 
 
+@pytest.mark.parametrize("autofmt", (False, True))
 @pytest.mark.parametrize("fmt", ["itk", "fsl", "afni", "lta"])
-def test_loadsave(tmp_path, data_path, testdata_path, fmt):
+def test_loadsave(tmp_path, data_path, testdata_path, autofmt, fmt):
     """Test idempotency."""
+    supplied_fmt = None if autofmt else fmt
+
+    # Load reference transform
     ref_file = testdata_path / "someones_anatomy.nii.gz"
     xfm = nitl.load(data_path / "itktflist2.tfm", fmt="itk")
     xfm.reference = ref_file
@@ -85,33 +101,33 @@ def test_loadsave(tmp_path, data_path, testdata_path, fmt):
 
     if fmt == "fsl":
         # FSL should not read a transform without reference
-        with pytest.raises(ValueError):
-            nitl.load(fname, fmt=fmt)
-            nitl.load(fname, fmt=fmt, moving=ref_file)
+        with pytest.raises(io.TransformIOError):
+            nitl.load(fname, fmt=supplied_fmt)
+            nitl.load(fname, fmt=supplied_fmt, moving=ref_file)
 
         with pytest.warns(UserWarning):
             assert np.allclose(
                 xfm.matrix,
-                nitl.load(fname, fmt=fmt, reference=ref_file).matrix,
+                nitl.load(fname, fmt=supplied_fmt, reference=ref_file).matrix,
             )
 
         assert np.allclose(
             xfm.matrix,
-            nitl.load(fname, fmt=fmt, reference=ref_file, moving=ref_file).matrix,
+            nitl.load(fname, fmt=supplied_fmt, reference=ref_file, moving=ref_file).matrix,
         )
     else:
-        assert xfm == nitl.load(fname, fmt=fmt, reference=ref_file)
+        assert xfm == nitl.load(fname, fmt=supplied_fmt, reference=ref_file)
 
     xfm.to_filename(fname, fmt=fmt, moving=ref_file)
 
     if fmt == "fsl":
         assert np.allclose(
             xfm.matrix,
-            nitl.load(fname, fmt=fmt, reference=ref_file, moving=ref_file).matrix,
+            nitl.load(fname, fmt=supplied_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)
+        assert xfm == nitl.load(fname, fmt=supplied_fmt, reference=ref_file)
 
     ref_file = testdata_path / "someones_anatomy.nii.gz"
     xfm = nitl.load(data_path / "affine-LAS.itk.tfm", fmt="itk")
@@ -121,21 +137,21 @@ def test_loadsave(tmp_path, data_path, testdata_path, fmt):
     if fmt == "fsl":
         assert np.allclose(
             xfm.matrix,
-            nitl.load(fname, fmt=fmt, reference=ref_file, moving=ref_file).matrix,
+            nitl.load(fname, fmt=supplied_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)
+        assert xfm == nitl.load(fname, fmt=supplied_fmt, reference=ref_file)
 
     xfm.to_filename(fname, fmt=fmt, moving=ref_file)
     if fmt == "fsl":
         assert np.allclose(
             xfm.matrix,
-            nitl.load(fname, fmt=fmt, reference=ref_file, moving=ref_file).matrix,
+            nitl.load(fname, fmt=supplied_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)
+        assert xfm == nitl.load(fname, fmt=supplied_fmt, reference=ref_file)
 
 
 @pytest.mark.parametrize("image_orientation", ["RAS", "LAS", "LPS", "oblique"])