Updates CLI conversion with explicit spatial axis labels

Configures the conversion utility to explicitly label axes as "spatial_x", "spatial_y", and "spatial_z" for 2D and 3D images. This ensures that MLArray correctly interprets the XYZ axis convention provided by MedVol, preventing the default ZYX permutation and ensuring the affine matrix is applied correctly to the underlying array.

Author: Karol-G

mlarray/cli.py

@@ -130,10 +130,22 @@ def convert_to_mlarray(load_filepath: Union[str, Path], save_filepath: Union[str
     # Let MedVol auto-detect the backend (nibabel for NIfTI, pynrrd for NRRD).
     # The default canonicalize=True reorients the array+affine to RAS+.
     image_medvol = MedVol(load_filepath)
+    # MedVol canonical output uses nibabel's XYZ axis convention: axis 0 ≈ X, axis 1 ≈ Y,
+    # axis 2 ≈ Z, with affine column i = direction of array axis i.
+    # SlicerMLArray assumes ZYX order when axis_labels is None. Supply explicit XYZ labels so
+    # Slicer uses an identity permutation and the stored affine is used as-is.
+    ndim = image_medvol.array.ndim
+    if ndim == 3:
+        axis_labels = ["spatial_x", "spatial_y", "spatial_z"]
+    elif ndim == 2:
+        axis_labels = ["spatial_x", "spatial_y"]
+    else:
+        axis_labels = None  # 4D: non-spatial axis ambiguous; leave unlabeled
     image_mlarray = MLArray(
         image_medvol.array,
         affine=image_medvol.affine,
         meta=_header_to_source_meta(image_medvol.header),
+        axis_labels=axis_labels,
     )
     coord_system = _coord_system_alias(image_medvol.coordinate_system)
     if coord_system is not None:

tests/test_cli.py

@@ -134,6 +134,8 @@ def test_convert_to_mlarray_from_nifti_copies_medvol_header_and_spatial(self):
             )
             self.assertEqual(loaded.meta._image_meta_format.to_plain(), "nifti")
             self.assertEqual(loaded.meta.spatial.coord_system, "RAS+")
+            # XYZ axis labels are set so Slicer uses the affine as-is (identity permutation).
+            self.assertEqual(loaded.meta.spatial.axis_labels, ["spatial_x", "spatial_y", "spatial_z"])
 
     def test_convert_to_mlarray_from_nrrd_uses_medvol_coord_system(self):
         with tempfile.TemporaryDirectory() as tmpdir: