Merge pull request #69 from thewtex/to-zarr-mode

BUG: Pass mode to to_zarr superclass method
spatial-image · Jul 22, 2024 · eb0968f · eb0968f
2 parents f89b18e + 3e31f85
commit eb0968f
Show file tree

Hide file tree

Showing 6 changed files with 187 additions and 50 deletions.
diff --git a/multiscale_spatial_image/multiscale_spatial_image.py b/multiscale_spatial_image/multiscale_spatial_image.py
@@ -124,4 +124,4 @@ def to_zarr(
         ngff_metadata = {"multiscales": multiscales, "multiscaleSpatialImageVersion": 1}
         self._dt.ds = self._dt.ds.assign_attrs(**ngff_metadata)
 
-        self._dt.to_zarr(store, **kwargs)
+        self._dt.to_zarr(store, mode=mode, **kwargs)
diff --git a/multiscale_spatial_image/to_multiscale/itk_image_to_multiscale.py b/multiscale_spatial_image/to_multiscale/itk_image_to_multiscale.py
@@ -39,14 +39,15 @@ def itk_image_to_multiscale(
     # Orient 3D image so that direction is identity wrt RAI coordinates
     image_dimension = image.GetImageDimension()
     input_direction = np.array(image.GetDirection())
+    oriented_image = image
     if anatomical_axes and image_dimension == 3 and not (np.eye(image_dimension) == input_direction).all():
         desired_orientation = itk.SpatialOrientationEnums.ValidCoordinateOrientations_ITK_COORDINATE_ORIENTATION_RAI
         oriented_image = itk.orient_image_filter(image, use_image_direction=True, desired_coordinate_orientation=desired_orientation)
 
     elif anatomical_axes and image_dimension != 3:
         raise ValueError(f'Cannot use anatomical axes for input image of size {image_dimension}')
 
-    image_da = itk.xarray_from_image(image)
+    image_da = itk.xarray_from_image(oriented_image)
     image_da.name = name
 
     image_dims: Tuple[str, str, str, str] = ("x", "y", "z", "t") # ITK dims are in xyzt order