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Geometric transform implementations #7955

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Geometric transform implementations #7955

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atbenmurray
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Implementations for unified spatial raster / geometry operations along with unit tests. More to be added later

Description

A few sentences describing the changes proposed in this pull request.

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.

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KumoLiu and others added 20 commits April 12, 2024 14:37
@KumoLiu
Add kind property in MetaTensor (Project-MONAI#7488)

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00436d0 
Part of Project-MONAI#7486


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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.

---------

Signed-off-by: YunLiu <[email protected]>
@atbenmurray
Adding apply_to_geometry function
b2ab07e 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding load_geometry function
7c7ec30 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding missing import for apply_to_geometry
8077759 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding KindKeys to __all__ in monai.utils.enums.py
7edb44e 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding tests for apply_to_geometry
61cb5c3 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding apply_to_geometry to __all__ in lazy/functional.py
1e83ec8 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding flip functionality for geometric_tensors
e503d6a 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding KindKeys to utils/__init__
f345fc9 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding | None to meta_info for apply_to_geometry
edc4bb7 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding resize functionality for geometric tensors
b8baae9 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding rotate functionality for geometric tensors
e59b4a9 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Fixing line endings for monai/transforms/io/functional.py
a0b768e 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Fixed rotate to that output_shape is returned. Made resize consistent…
4e6ae70 
… with rotate

Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Work towards geometry tests for rotate
f763c8f 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Fixed KindKey types for flip functionality
fc8e0b8 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Fix to handle 2d data being multiplied by a 3d transform from the met…
0857ac7 
…atensor api

Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Bug fixes to make all related unit tests pass
aa83926 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Removed ndims (not ndim) from MetaTensor
55edf77 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding tests for rotate / flip
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7928f32 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray atbenmurray changed the title Geometric all Geometric transform implementations Jul 26, 2024
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
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1a216e9 
for more information, see https://pre-commit.ci
@vikashg
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vikashg commented Jul 31, 2024

Hello Ben,
Can you also add a jupyter-notebook with some real images and geometric points (annotations). It will be much easier for to play around with the code without breaking anything.
Thanks

@atbenmurray
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Hi @vikashg. I will. As soon as I've finished my camera ready presentation I'll finish this PR. Should all be ready for thursday

@atbenmurray atbenmurray mentioned this pull request Aug 2, 2024
Merged
7 tasks
@atbenmurray
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Hello Ben, Can you also add a jupyter-notebook with some real images and geometric points (annotations). It will be much easier for to play around with the code without breaking anything. Thanks

Yes, I'll provide one

atbenmurray and others added 4 commits August 2, 2024 10:43
@atbenmurray
load_geometry functionality and tests
7004598 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Resolving conflict
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51d8d28 
Signed-off-by: Ben Murray <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
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62f506b 
for more information, see https://pre-commit.ci
@atbenmurray
Adding spatial_dims_from_tensorlike function to handle point tensors
4740533 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Zoom modified to use spatial_dims_from_tensorlike
2ff1d73 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Merge branch 'geometric_all' of github.com:atbenmurray/monai into geo…
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c2d351f 
…metric_all
@atbenmurray
Added and tested point zoom functionality
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645e0c6 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding traced_no_op function for use in transforms that no-op geometr…
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f2e2426 
…y data (like Spacing)

Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding geometry support to Spacing transform
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4898b88 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray
Adding save_geometry function plus test
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2cda79a 
Signed-off-by: Ben Murray <[email protected]>
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@atbenmurray @vikashg @KumoLiu