feat: add test reading a real h5 generated by ANTs

Author: oesteban

nitransforms/io/itk.py

@@ -30,7 +30,9 @@ def __init__(self, parameters=None, offset=None):
         """Initialize with default offset and index."""
         super().__init__()
         self.structarr['index'] = 0
-        self.structarr['offset'] = offset or [0, 0, 0]
+        if offset is None:
+            offset = np.zeros((3,), dtype='float')
+        self.structarr['offset'] = offset
         self.structarr['parameters'] = np.eye(4)
         if parameters is not None:
             self.structarr['parameters'] = parameters
@@ -307,24 +309,25 @@ def from_h5obj(cls, fileobj, check=True):
         except KeyError:
             typo_fallback = "Tranform"
 
-        for xfm in reversed(h5group.keys())[:-1]:
-            if h5group[xfm]["TransformType"][0].startswith(b"AffineTransform"):
+        for xfm in reversed(list(h5group.values())[1:]):
+            if xfm["TransformType"][0].startswith(b"AffineTransform"):
+                _params = np.asanyarray(xfm[f"{typo_fallback}Parameters"])
                 xfm_list.append(
                     ITKLinearTransform(
-                        parameters=np.asanyarray(h5group[xfm][f"{typo_fallback}Parameters"]),
-                        offset=np.asanyarray(h5group[xfm][f"{typo_fallback}FixedParameters"])
+                        parameters=from_matvec(_params[:-3].reshape(3, 3), _params[-3:]),
+                        offset=np.asanyarray(xfm[f"{typo_fallback}FixedParameters"])
                     )
                 )
                 continue
-            if h5group[xfm]["TransformType"][0].startswith(b"DisplacementFieldTransform"):
-                _fixed = np.asanyarray(h5group[xfm][f"{typo_fallback}FixedParameters"])
+            if xfm["TransformType"][0].startswith(b"DisplacementFieldTransform"):
+                _fixed = np.asanyarray(xfm[f"{typo_fallback}FixedParameters"])
                 shape = _fixed[:3].astype('uint16').tolist()
                 offset = _fixed[3:6].astype('uint16')
                 zooms = _fixed[6:9].astype('float')
                 directions = _fixed[9:].astype('float').reshape((3, 3))
                 affine = from_matvec(directions * zooms, offset)
-                field = np.asanyarray(h5group[xfm][f"{typo_fallback}Parameters"]).reshape(
-                    tuple(shape + [-1])
+                field = np.asanyarray(xfm[f"{typo_fallback}Parameters"]).reshape(
+                    tuple(shape + [1, -1])
                 )
                 hdr = Nifti1Header()
                 hdr.set_intent("vector")
@@ -338,7 +341,7 @@ def from_h5obj(cls, fileobj, check=True):
                 continue
 
             raise NotImplementedError(
-                f"Unsupported transform type {h5group[xfm]['TransformType'][0]}"
+                f"Unsupported transform type {xfm['TransformType'][0]}"
             )
 
         return xfm_list

nitransforms/tests/data/ds-005_sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5

@@ -324,22 +324,26 @@ def _mockreturn(arg):
                 _read_mat(f)
 
 
-@pytest.mark.parametrize('sw_tool', ['afni'])
-def test_Displacements(sw_tool):
+def test_afni_Displacements():
     """Test displacements fields."""
+    field = nb.Nifti1Image(np.zeros((10, 10, 10)), None, None)
+    with pytest.raises(TransformFileError):
+        afni.AFNIDisplacementsField.from_image(field)
 
-    if sw_tool == 'afni':
-        field = nb.Nifti1Image(np.zeros((10, 10, 10)), None, None)
-        with pytest.raises(TransformFileError):
-            afni.AFNIDisplacementsField.from_image(field)
+    field = nb.Nifti1Image(np.zeros((10, 10, 10, 2, 3)), None, None)
+    with pytest.raises(TransformFileError):
+        afni.AFNIDisplacementsField.from_image(field)
 
-        field = nb.Nifti1Image(np.zeros((10, 10, 10, 2, 3)), None, None)
-        with pytest.raises(TransformFileError):
-            afni.AFNIDisplacementsField.from_image(field)
+    field = nb.Nifti1Image(np.zeros((10, 10, 10, 1, 4)), None, None)
+    with pytest.raises(TransformFileError):
+        afni.AFNIDisplacementsField.from_image(field)
 
-        field = nb.Nifti1Image(np.zeros((10, 10, 10, 1, 4)), None, None)
-        with pytest.raises(TransformFileError):
-            afni.AFNIDisplacementsField.from_image(field)
+
+def test_itk_h5(data_path):
+    """Test displacements fields."""
+    itk.ITKCompositeH5.from_filename(
+        data_path / 'ds-005_sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5'
+    )
 
 
 @pytest.mark.parametrize('file_type, test_file', [