Skip to content

Geometric transform implementations #7955

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Draft
wants to merge 31 commits into
base: dev
Choose a base branch
from
Draft

Geometric transform implementations #7955

wants to merge 31 commits into from

Conversation

atbenmurray
Copy link
Contributor

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 <55491388+KumoLiu@users.noreply.github.com>
@atbenmurray
Adding apply_to_geometry function
b2ab07e 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding load_geometry function
7c7ec30 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding missing import for apply_to_geometry
8077759 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding KindKeys to __all__ in monai.utils.enums.py
7edb44e 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding tests for apply_to_geometry
61cb5c3 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding apply_to_geometry to __all__ in lazy/functional.py
1e83ec8 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding flip functionality for geometric_tensors
e503d6a 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding KindKeys to utils/__init__
f345fc9 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding | None to meta_info for apply_to_geometry
edc4bb7 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding resize functionality for geometric tensors
b8baae9 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding rotate functionality for geometric tensors
e59b4a9 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Fixing line endings for monai/transforms/io/functional.py
a0b768e 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Fixed rotate to that output_shape is returned. Made resize consistent…
4e6ae70 
… with rotate

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

Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Bug fixes to make all related unit tests pass
aa83926 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Removed ndims (not ndim) from MetaTensor
55edf77 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding tests for rotate / flip
7928f32 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray atbenmurray changed the title Geometric all Geometric transform implementations Jul 26, 2024
@vikashg
Copy link

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
Copy link
Contributor Author

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
Copy link
Contributor Author

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 <ben.murray@gmail.com>
@atbenmurray
Resolving conflict
51d8d28 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
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 <ben.murray@gmail.com>
@atbenmurray
Zoom modified to use spatial_dims_from_tensorlike
2ff1d73 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Merge branch 'geometric_all' of github.com:atbenmurray/monai into geo…
c2d351f 
…metric_all
@atbenmurray
Added and tested point zoom functionality
645e0c6 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding traced_no_op function for use in transforms that no-op geometr…
f2e2426 
…y data (like Spacing)

Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding geometry support to Spacing transform
4898b88 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
@atbenmurray
Adding save_geometry function plus test
2cda79a 
Signed-off-by: Ben Murray <ben.murray@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@KumoLiu KumoLiu Awaiting requested review from KumoLiu KumoLiu will be requested when the pull request is marked ready for review KumoLiu is a code owner

@ericspod ericspod Awaiting requested review from ericspod ericspod will be requested when the pull request is marked ready for review ericspod is a code owner

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma Nic-Ma will be requested when the pull request is marked ready for review Nic-Ma is a code owner

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
Geometric Transforms
Status: In progress
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@atbenmurray @vikashg @KumoLiu