Added mask3d

[ternaus]

Summary by Sourcery

Add support for 3D masks and volumes in the transformation library, enabling operations on 3D data. Update the codebase to handle 3D data consistently alongside 2D data, and enhance documentation and tests to reflect these changes.

New Features:

• Introduce support for 3D masks and volumes in transformations, allowing operations on 3D data similar to 2D images.

Enhancements:

• Refactor transformation methods to handle both 2D and 3D data consistently, improving code maintainability and flexibility.

Documentation:

• Update documentation to reflect the addition of 3D mask and volume support in transformations, including changes in the README and docstrings.

Tests:

• Modify existing tests and add new ones to ensure the correct functionality of transformations with 3D masks and volumes.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR adds support for 3D data transformations by introducing new volume and mask3d targets, refactoring the Transform3D class, and updating all existing transforms to handle 3D data consistently. The implementation maintains backward compatibility while providing a cleaner API for working with volumetric data.

Class diagram for updated Transform3D and DualTransform classes

classDiagram
    class DualTransform {
        +apply_to_images(images: np.ndarray, **params: Any) np.ndarray
        +apply_to_mask(mask: np.ndarray, **params: Any) np.ndarray
        +apply_to_masks(masks: np.ndarray, **params: Any) np.ndarray
        +apply_to_volume(volume: np.ndarray, **params: Any) np.ndarray
        +apply_to_volumes(volumes: np.ndarray, **params: Any) np.ndarray
        +apply_to_mask3d(mask: np.ndarray, **params: Any) np.ndarray
        +apply_to_masks3d(masks: np.ndarray, **params: Any) np.ndarray
    }
    class Transform3D {
        +apply_to_volume(volume: np.ndarray, *args: Any, **params: Any) np.ndarray
        +apply_to_volumes(volumes: np.ndarray, *args: Any, **params: Any) np.ndarray
        +apply_to_mask3d(mask3d: np.ndarray, *args: Any, **params: Any) np.ndarray
        +apply_to_masks3d(masks3d: np.ndarray, *args: Any, **params: Any) np.ndarray
    }
    DualTransform <|-- Transform3D

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Class diagram for updated BasePad3D and BaseCropAndPad3D classes

classDiagram
    class BasePad3D {
        +apply_to_volume(volume: np.ndarray, padding: tuple[int, int, int, int, int, int], **params: Any) np.ndarray
        +apply_to_mask3d(mask3d: np.ndarray, padding: tuple[int, int, int, int, int, int], **params: Any) np.ndarray
    }
    class BaseCropAndPad3D {
        +apply_to_volume(volume: np.ndarray, crop_coords: tuple[int, int, int, int, int, int], pad_params: dict[str, int] | None, **params: Any) np.ndarray
        +apply_to_mask3d(mask3d: np.ndarray, crop_coords: tuple[int, int, int, int, int, int], pad_params: dict[str, int] | None, **params: Any) np.ndarray
    }

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File-Level Changes

Change	Details	Files
Added new volume and mask3d targets to support 3D data transformations	Added VOLUME and MASK3D to Targets enum Updated ALL_TARGETS to include new volume and mask3d targets Added volume and mask3d to AVAILABLE_KEYS Added new target checking methods for volume and mask3d data	albumentations/core/types.py albumentations/core/composition.py
Refactored Transform3D class to use consistent volume/mask3d terminology	Renamed images/masks methods to volume/mask3d for clarity Updated Transform3D to inherit from DualTransform Added apply_to_volume and apply_to_mask3d methods Removed deprecated 3D bboxes and keypoints support	albumentations/core/transforms_interface.py
Updated all transforms to support 3D data operations	Added volume and mask3d support to all existing transforms Updated transform docstrings to include new targets Modified shape handling to work with both 2D and 3D data Updated tests to use new volume/mask3d terminology	albumentations/augmentations/geometric/transforms.py albumentations/augmentations/transforms3d/transforms.py tests/transforms3d/test_transforms.py tests/test_targets.py
Improved parameter handling and shape validation	Added separate shape checks for 2D and 3D data Updated update_params_shape to handle volume dimensions Removed redundant rows/cols parameters in favor of shape Added validation for volume shapes consistency	albumentations/core/composition.py albumentations/core/transforms_interface.py

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[sourcery-ai]

Hey @ternaus - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider adding migration guide documentation to help users transition from the old 'images'/'masks' API to the new 'volume'/'mask3d' API for 3D data

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟡 Testing: 1 issue found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[codecov]

Codecov Report

Attention: Patch coverage is 73.33333% with 40 lines in your changes missing coverage. Please review.

Project coverage is 89.08%. Comparing base (b1a79c2) to head (e814ce0).
Report is 313 commits behind head on main.

Files with missing lines	Patch %	Lines
albumentations/core/transforms_interface.py	46.51%	23 Missing ⚠️
albumentations/core/composition.py	68.08%	15 Missing ⚠️
...entations/augmentations/transforms3d/functional.py	66.66%	1 Missing ⚠️
...entations/augmentations/transforms3d/transforms.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           main    #2200       +/-   ##
=========================================
+ Coverage      0   89.08%   +89.08%     
=========================================
  Files         0       50       +50     
  Lines         0     8834     +8834     
=========================================
+ Hits          0     7870     +7870     
- Misses        0      964      +964     

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