Update ['pixdim'] after Spacing transform in meta dict. #8269

slicepaste · 2024-12-23T08:40:29Z

Description

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 #6832.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

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 <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

monai/data/meta_tensor.py

monai/transforms/spatial/array.py

KumoLiu

Thanks for the contribution! Leave several comments inline.

monai/transforms/spatial/dictionary.py

monai/transforms/spatial/array.py

atbenmurray · 2025-01-17T15:26:33Z

Hi folks. I had a look through the code and the PR, but I need to do a deeper evaluation of how this intersects with lazy resampling and the consistency of behaviour between MetaTensor and _meta_dict modes

atbenmurray · 2025-01-24T14:08:07Z

In the middle of extending test scenarios. Please bear with me.

slicepaste · 2025-02-14T09:54:36Z

@einsyang723 @IamTingTing The current PR is not our final version, and it has remained unchanged for a while.
We should continue working on this issue and update the final version ASAP so we can move forward with this PR.
Let me know if you need any help. Thanks!

Previously, a method was defined in `meta_tensor`, and using `data_array.clone()` introduced additional costs. After reevaluating the code, modifying the `TraceableTransform.track_transform_meta()` method executed by `SpatialResample` makes it much cleaner and more maintainable. Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Previously, a method was defined in `meta_tensor`, and using `data_array.clone()` introduced additional costs. After reevaluating the code, modifying the `TraceableTransform.track_transform_meta()` method executed by `SpatialResample` makes it much cleaner and more maintainable. Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

…ix-6840

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

atbenmurray · 2025-02-19T09:23:23Z

Picking this up again. Will have a review for you all today.

monai/transforms/spatial/dictionary.py

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 <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

Previously, a method was defined in `meta_tensor`, and using `data_array.clone()` introduced additional costs. After reevaluating the code, modifying the `TraceableTransform.track_transform_meta()` method executed by `SpatialResample` makes it much cleaner and more maintainable. Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Checking all dictionary keys that start with `{key}_` to support custom settings of `meta_keys` and `meta_key_postfix`. This ensures that no matter how users configure the naming conventions in `LoadImaged`, we can correctly synchronize metadata from the MetaTensor to the corresponding meta dictionary. Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

atbenmurray · 2025-04-04T14:12:34Z

@einsyang723 @slicepaste @ericspod @KumoLiu @IamTingTing
Hi folks. Sorry it has been a while but I have a candidate PR #8411 that I think is important to address as a prerequisite to this PR. It is still in draft phase but take a look when you have a moment

atbenmurray

The change made in monai/transforms/spatial/dictionary.py means the issue that I raised is much less relevant now

slicepaste · 2025-05-12T09:33:31Z

The change made in monai/transforms/spatial/dictionary.py means the issue that I raised is much less relevant now

@atbenmurray Thank you for the approval. Just to confirm our understanding — this PR can be merged first, and the remaining concerns regarding meta_keys, meta_key_postfix, and the additional metadata dictionary changes will be addressed in PR #8411 , right?

atbenmurray · 2025-05-12T10:15:21Z

The change made in monai/transforms/spatial/dictionary.py means the issue that I raised is much less relevant now

@atbenmurray Thank you for the approval. Just to confirm our understanding — this PR can be merged first, and the remaining concerns regarding meta_keys, meta_key_postfix, and the additional metadata dictionary changes will be addressed in PR #8411 , right?

Exactly. Yes. This PR is decoupled from PR #8411 now.

slicepaste · 2025-05-13T06:09:54Z

Exactly. Yes. This PR is decoupled from PR #8411 now.

Thanks for the confirmation. Looking forward to the merge!

ericspod

I think everything has been addressed here, @KumoLiu please trigger blossom and we'll integrate this soon. Thanks!

slicepaste changed the title ~~Fixes #6840~~ Update ['pixdim'] after Spacing transform in meta dict. Dec 23, 2024

slicepaste added 5 commits December 23, 2024 17:19

fix issue 6840

8cc6175

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix issue 6840 format

501bc45

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix casting

c5ebb0d

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix image_only flag issue

1aabdae

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix format issue

fe05f59

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

ericspod reviewed Dec 24, 2024

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ericspod reviewed Dec 24, 2024

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monai/transforms/spatial/array.py Outdated Show resolved Hide resolved

ericspod requested review from atbenmurray and KumoLiu December 24, 2024 04:01

KumoLiu reviewed Jan 3, 2025

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monai/transforms/spatial/dictionary.py Outdated Show resolved Hide resolved

monai/transforms/spatial/array.py Outdated Show resolved Hide resolved

KumoLiu requested a review from ericspod January 17, 2025 15:28

Merge branch 'dev' into fix-6840

14b4942

slicepaste and others added 11 commits February 17, 2025 16:22

Merge branch 'Project-MONAI:dev' into fix-6840

3935ff5

fix format issue

b73e733

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Merge branch 'fix-6840' of https://github.com/slicepaste/MONAI into f…

c593d01

…ix-6840

fix dependency issue

6f217d1

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Add constraint for pixdim

2d703c4

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix format

b6dd460

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix constraint for pixdim in track_transform_meta() function

a34a656

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Merge branch 'Project-MONAI:dev' into fix-6840

e4e089f

Merge branch 'dev' into fix-6840

8b7463d

atbenmurray requested changes Feb 21, 2025

View reviewed changes

monai/transforms/spatial/dictionary.py Outdated Show resolved Hide resolved

slicepaste and others added 15 commits March 6, 2025 17:25

Merge branch 'Project-MONAI:dev' into fix-6840

5da7c66

fix issue 6840

173c6c1

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix issue 6840 format

5250d15

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix casting

f8fcae3

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix image_only flag issue

5639313

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix format issue

8c73c69

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com>

fix format issue

707e102

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix dependency issue

7bee286

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

Add constraint for pixdim

651eac5

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix format

ae086d0

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix constraint for pixdim in track_transform_meta() function

9e51576

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

fix the issue of naming rule of key_meta_dict

e6b289b

Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Co-authored-by: einsyang723 <tina910723@gmail.com> Co-authored-by: IamTingTing <6121smile@gmail.com>

atbenmurray approved these changes May 9, 2025

View reviewed changes

Merge branch 'dev' into fix-6840

98e7b68

ericspod approved these changes May 13, 2025

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Update ['pixdim'] after Spacing transform in meta dict. #8269

Update ['pixdim'] after Spacing transform in meta dict. #8269

slicepaste commented Dec 23, 2024 •

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Update ['pixdim'] after Spacing transform in meta dict. #8269

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Update ['pixdim'] after Spacing transform in meta dict. #8269

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