Restored transform doesn't restore orientation

[AHarouni]

Describe the bug
I use Restored transform to invert the space resolution, however it fails to restore the orientation changed with any of the Orientationd(keys="image", axcodes="RAS"),

To Reproduce
add this transform to spleen model
in the pretranforms
Orientationd(keys="image", axcodes="RAS"),

and in the post transform
Restored(keys="pred", ref_image="image"),

you would see that the segmentation is wrong

[tangy5]

Do we need to support re-orientation for the Restored? The Inverted can do inverse orientation. Restored is a flexible choice for resampling for MONAI Label to my understanding. Thanks!

[diazandr3s]

Do we need to support re-orientation for the Restored? The Inverted can do inverse orientation. Restored is a flexible choice for resampling for MONAI Label to my understanding. Thanks!

Very good point @tangy5.
I think the idea here is to avoid the inverted transforms method when running inference. For this, I've proposed a transform to restore orientation here: https://github.com/Project-MONAI/MONAILabel/blob/fullCTSegmentation/sample-apps/radiology/lib/transforms/transforms.py#L511

[AHarouni]

The issue with invert transforms is that they are very very slow. We usually only need to invert the spacing and the orientation.
@diazandr3s I have tried the code you pointed to with some dicoms and they didn't invert correctly vs the invert transform which did the job.
So I ended up using the restore and do a running the invert over a single transform.

[diazandr3s]

Yes, I've found the same issue but discovered that it is related to wrong image headers. In any case, applying the invert to only Orientationd transform will facilitate things.

[SachidanandAlle]

is it possible to add the orientation option in the Restored transform... by default flag can be in disabled.. can someone prepare the PR?

[diazandr3s]

Happy to start that PR :)

[diazandr3s]

#1365

[diazandr3s]

Please use flag invert_orient in Restored transform to invert Orientation

#1365

[AHarouni]

Thanks for the fix, I did get an error
https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/transform/post.py#L140
as this is a numpy, error asking to use np.any
simple change to the line as if orig_affine is not None: fixed it for me.

A bigger ask now is to move this transformation to a new separate transform RestoreOrientation for multiple reasons:

• I needed the code in restorelabeld which is in the deepedit and also in monai.apps transforms.
• order matters specially in the restorelabeld so user should be able to restore the orientation before or after resample depending on the pre transforms

Separating this logic into a new transform is a better solution in my opinion.