Inconsistent writing of Metadata. Loading + Saving results in different metadata.

[phcerdan]

Describe the bug
Using SaveImage after LoadImage results in image saved with different metadata.

To Reproduce
Steps to reproduce the behavior:

    original2 = LoadImage(image_only=True)(original_file)
    SaveImage(output_dir=output_folder + "/monai_modified_meta",
              output_ext = ".nrrd",
              writer= "ITKWriter",
              resample=False,
              separate_folder= False,
              squeeze_end_dims = False,
              output_dtype=itk.SI)(original2)

Where original_file points to the attached image (a dcm 2D slice):
CT.X.1.2.276.0.7230010.3.1.4.0.6.1667732449.1809819.zip

Expected behavior
The metadata should be the same of the original image after save.

Screenshots
The original dcm loaded in Slicer:

The result after loading + saving with the above code:

Environment

Ensuring you use the relevant python executable, please paste the output of:

python -c 'import monai; monai.config.print_debug_info()'

MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: a2ec3752f54bfc3b40e7952234fbeb5452ed63e3

Additional context
I have tested using itk:

original_itk = itk.imread(original_file)
itk.imwrite(original_itk, output_folder + "/monai_modified_meta/original_after_itk_save.nrrd")

and the metadata is conserved (afer opening it in Slicer).
There must be some internal Monai logic messing this up.

The data is a bit odd, but correct, the spacing is negative. ITK corrects this at the moment of reading, flipping the sign in the direction matrix for those indices with negative spacing (and flipping the signs in spacing).

[wyli]

thanks for reporting, original2 = LoadImage(image_only=True, affine_lps_to_ras=False)(original_file) when loading with give the itk result.

I think there's a separate bug for the default image writing, will look into it soon.

[phcerdan]

Thanks @wyli.
How can I provide that afine_lps_to_ras = False option to SaveImage instead of LoadImage? I see the option is there for the ITKWriter, but SaveImage doesn't seem to accept it.

[wyli]

yes, I also tried that, currently the usage is

save = SaveImage(
    output_dir=output_folder + "/monai_modified_meta",
    output_ext=".nrrd",
    writer="ITKWriter",
    resample=False,
    separate_folder=False,
    squeeze_end_dims=False,
    output_dtype=itk.SI,
)
save.set_options(init_kwargs={"affine_lps_to_ras": False})
save(original2)

but this logic doesn't look right at the moment...

MONAI/monai/data/image_writer.py

Lines 501 to 502 in a8302ec

	if isinstance(data_array, MetaTensor) and data_array.meta.get(MetaKeys.SPACE, SpaceKeys.LPS) != SpaceKeys.LPS:
	affine_lps_to_ras = False # do the converting from LPS to RAS only if the space type is currently LPS.

(another workaround is to set output_ext=".nii.gz", this works because nifti's affine is in RAS)

[KumoLiu]

I find another bug when taking a look at this issue.
When using PydicomReader to read a dcm slice(2d), we didn't correctly record the spacing. Maybe using (0028, 0030) Pixel Spacing this tag can be safer.

MONAI/monai/data/image_reader.py

Line 687 in 678b512

dr, dc = metadata.get("spacing", (1.0, 1.0))[:2]

[phcerdan]

I would recommend to have only one source of truth for geometrical metadata (Origin, Spacing, Orientation), and that to be the affine attribute (the matrix) of the Metatensor.
Having spacing in metadata makes no sense, you can get the spacing from the affine matrix.