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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.

KumoLiu and others added 20 commits April 12, 2024 14:37
@KumoLiu
Add kind property in MetaTensor (Project-MONAI#7488)
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
7928f32 
Signed-off-by: Ben Murray <[email protected]>
@atbenmurray atbenmurray changed the title Geometric all Geometric transform implementations Jul 26, 2024
@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

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@atbenmurray @vikashg @KumoLiu