Add keypoints to 3d

[ternaus]

Summary by Sourcery

New Features:

• Added keypoint support to 3D augmentations such as Pad3D, PadIfNeeded3D, CenterCrop3D, RandomCrop3D, CoarseDropout3D, and CubicSymmetry. Keypoints are now correctly transformed along with volumes and masks, ensuring consistency after augmentation. Transforms now handle keypoints outside the volume boundaries correctly, filtering them out as needed. Improved handling of empty keypoint arrays and edge cases like points exactly on volume boundaries. Added tests to verify keypoint transformations match expected behavior and volume transformations.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request adds keypoint support to various 3D augmentations, ensuring keypoint positions are correctly updated after transformations like padding, cropping, and rotations. It also introduces a new function to filter keypoints located within specified 3D holes/bounding boxes.

Sequence diagram for keypoint filtering in CoarseDropout3D

sequenceDiagram
    participant T as Transform
    participant F as filter_keypoints_in_holes3d
    participant K as Keypoints
    T->>F: Pass keypoints and holes
    F->>K: Check keypoint positions
    Note over F,K: Compare each keypoint against hole boundaries
    F-->>T: Return filtered keypoints
    Note over T: Only keypoints outside
    Note over T: holes are preserved

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Class diagram showing updated Transform3D hierarchy with keypoint support

classDiagram
    class Transform3D {
        +apply_to_volume()
        +apply_to_mask3d()
        +apply_to_keypoints()
    }
    class BasePad3D {
        -_targets: (VOLUME, MASK3D, KEYPOINTS)
        +apply_to_keypoints()
    }
    class BaseCropAndPad3D {
        -_targets: (VOLUME, MASK3D, KEYPOINTS)
        +apply_to_keypoints()
    }
    class CoarseDropout3D {
        -_targets: (VOLUME, MASK3D, KEYPOINTS)
        +apply_to_keypoints()
    }
    class CubicSymmetry {
        -_targets: (VOLUME, MASK3D, KEYPOINTS)
        +apply_to_keypoints()
    }
    Transform3D <|-- BasePad3D
    Transform3D <|-- BaseCropAndPad3D
    Transform3D <|-- CoarseDropout3D
    Transform3D <|-- CubicSymmetry
    note for Transform3D "Added keypoints support"
    note for BasePad3D "Handles keypoint shifting during padding"
    note for BaseCropAndPad3D "Handles keypoint transformation during crop/pad"
    note for CoarseDropout3D "Filters keypoints in dropout regions"
    note for CubicSymmetry "Transforms keypoints during cube rotations"

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File-Level Changes

Change	Details	Files
Added keypoint transforms to 3D augmentations	Added apply_to_keypoints methods to Pad3D, PadIfNeeded3D, CenterCrop3D, RandomCrop3D, CoarseDropout3D, and CubicSymmetry to handle keypoint transformations. Updated _targets to include Targets.KEYPOINTS for these augmentations to indicate keypoint support	albumentations/augmentations/transforms3d/transforms.py
Implemented keypoint filtering within 3D holes	Added filter_keypoints_in_holes3d function to remove keypoints inside specified 3D bounding boxes (holes). Added tests for filter_keypoints_in_holes3d to verify its behavior with various inputs and edge cases	albumentations/augmentations/transforms3d/functional.py tests/transforms3d/test_functions.py
Added keypoint rotation utility function	Added keypoints_rot90 function to rotate keypoints by multiples of 90 degrees around specified axes. Added tests to verify keypoints_rot90 behavior and its consistency with np.rot90	albumentations/augmentations/transforms3d/functional.py tests/transforms3d/test_functions.py
Extended keypoint support for cubic symmetry transformations	Added transform_cube_keypoints function to transform keypoints according to cubic symmetry operations. Added tests to verify that transform_cube_keypoints correctly transforms keypoints and preserves extra columns in the keypoint array	albumentations/augmentations/transforms3d/functional.py tests/transforms3d/test_functions.py
Updated tests and documentation	Added tests for keypoint transformations in test_transforms.py. Updated serialization tests in test_serialization.py to include keypoints. Modified test_targets.py to reflect keypoint support. Updated documentation in README.md to include keypoints in the supported targets table. Modified make_transforms_docs.py to generate documentation for keypoint support. Added keypoints to targets in transforms_interface.py	tests/transforms3d/test_transforms.py tests/test_serialization.py tests/transforms3d/test_targets.py README.md tools/make_transforms_docs.py albumentations/core/transforms_interface.py

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[sourcery-ai]

Hey @ternaus - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 2 issues found
• 🟢 Security: all looks good
• 🟡 Testing: 2 issues found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[codecov]

Codecov Report

Attention: Patch coverage is 93.13725% with 7 lines in your changes missing coverage. Please review.

Project coverage is 89.81%. Comparing base (b1a79c2) to head (b39351a).
Report is 327 commits behind head on main.

Files with missing lines	Patch %	Lines
...entations/augmentations/transforms3d/transforms.py	76.92%	6 Missing ⚠️
...entations/augmentations/transforms3d/functional.py	98.68%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           main    #2217       +/-   ##
=========================================
+ Coverage      0   89.81%   +89.81%     
=========================================
  Files         0       50       +50     
  Lines         0     9095     +9095     
=========================================
+ Hits          0     8169     +8169     
- Misses        0      926      +926     

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