Update ['pixdim'] after Spacing transform in meta dict. #8269
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According to the issue, this PR addresses on the meta dictionary `data['pixdim']` of NIfTI images does not update after applying the `spacing` or `spacingd`.
To align with `affine`, we update `data['pixdim']` and keep the original metainfo in `data['original_pixdim']`.
Additionally, this PR also update the metainfo `key_{meta_key_postfix}['pixdim']` in NIfTI images, consistent with `spaced_data_dict['image_meta_dict']['pixdim']` in issue Project-MONAI#6832.
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Co-authored-by: einsyang723 <[email protected]>
Co-authored-by: IamTingTing <[email protected]>
slicepaste
changed the title
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Signed-off-by: Wei_Chuan, Chiang <[email protected]>
ericspod
reviewed
Dec 24, 2024
| @@ -477,6 +477,10 @@ def pixdim(self): | |||
| return [affine_to_spacing(a) for a in self.affine] | |||
| return affine_to_spacing(self.affine) | |||
|
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| def set_pixdim(self) -> None: | |||
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Does it make sense for this to be a method? If it's only going to be called in one place it's simple code could just be put there. If there's anticipation that this would be called by other things then that's fine.
ericspod
reviewed
Dec 24, 2024
| @@ -535,6 +535,9 @@ def __call__( | |||
| dtype=dtype, | |||
| lazy=lazy_, | |||
| ) | |||
| if isinstance(data_array, MetaTensor) and "pixdim" in data_array.meta: | |||
| data_array = cast(MetaTensor, data_array.clone()) | |||
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Why is it necessary to clone the data array here? This is going to have a cost and I think isn't compatible with lazy resampling. Perhaps this is code that should be SpactialResample instead? @atbenmurray If you could please check if this is going to interact with laziness, thanks.
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Fixes #6840
Description
According to the issue, this PR addresses on the meta dictionary
data['pixdim']of NIfTI images does not update after applying thespacingorspacingd. To align withaffine, we updatedata['pixdim']and keep the original metainfo indata['original_pixdim']. Additionally, this PR also update the metainfokey_{meta_key_postfix}['pixdim']in NIfTI images, consistent withspaced_data_dict['image_meta_dict']['pixdim']in issue #6832.Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.