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BUG: Pass mode to to_zarr superclass method #69

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merged 3 commits into from
Jul 22, 2024
Merged

BUG: Pass mode to to_zarr superclass method #69

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a6f0d80
BUG: Pass mode to to_zarr superclass method
thewtex Sep 26, 2022
7149340
BUG: Output oriented image
thewtex Sep 29, 2022
3e31f85
ENH: Add pixi data feature for updating the data tarball
thewtex Jul 22, 2024
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2 changes: 1 addition & 1 deletion multiscale_spatial_image/multiscale_spatial_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
3 changes: 2 additions & 1 deletion multiscale_spatial_image/to_multiscale/itk_image_to_multiscale.py
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Expand Up @@ -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
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