Spacing transform does not update pixdim

[KumoLiu]

Discussed in #6831

^{Originally posted by agaldran August 7, 2023}
Hello,

Sorry about the naive question, I am trying to wrap my head around transforms and meta_dicts. Right now I have the following operations:

import monai.transforms as t

data_dict = {'image': 'data/ct/images/.whatever.nii.gz'}
loader = t.LoadImaged(keys=('image'), image_only=False)
loaded_data_dict = loader(data_dict)
print(loaded_data_dict['image'].shape, loaded_data_dict['image_meta_dict']['pixdim'][1:4])

which returns a shape and voxel sizes of [281, 313, 182] and (0.50,0.50,0.75) respectively. Now, if I run:

spacing = t.Spacingd(keys=['image'], pixdim=(0.50, 0.50, 1.5), mode=('bilinear')) 
spaced_data_dict = spacing(loaded_data_dict)
print(spaced_data_dict['image'].shape, spaced_data_dict['image_meta_dict']['pixdim'][1:4])

I am expecting to see approx half the voxels in the Z direction, as the original spacing was 0.75 and I am asking for twice that spacing. For the other directions, nothing should be changed^* . This is what I get:

[281, 313, 92], (0.50,0.50,0.75)

So, although the number of voxels are as expected, the spacing remains the same. I cannot find any other key in the meta data dictionary that tells me what is the current spacing for this volume. Am I doing something wrong here?

[wyli]

yes, the image's original 'pixdim' is not modified, the current pixdim is a property: spaced_data_dict["image"].pixdim

[KumoLiu]

yes, the image's original 'pixdim' is not modified, the current pixdim is a property: spaced_data_dict["image"].pixdim

Does it mean we don't need to modify it or we may enhance it in the future?

[wyli]

We don't have a good reason to modify it at the moment, a single source of truth for the original and current pixdim seems to be consistent and easy to maintain..