Enhance RegionBox with flexible padding options and module updates

[jjjermiah]

Introduce the BoxPadMethod enum for padding flexibility in RegionBox. Update import paths and remove deprecated modules to streamline the codebase.

Summary by CodeRabbit

• New Features

  • Introduced enhanced region adjustments with customizable padding options, allowing users to choose between symmetric and alternative padding behaviors.

• Refactor

  • Removed legacy 3D boundary manipulation functionality and streamlined internal type references for a more consistent and maintainable experience.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request introduces two new public entities, BoxPadMethod and RegionBox, into the module interfaces while updating several import statements from .helper_types to .spatial_types. In addition, the RegionBox.pad method in the box module is enhanced with an optional method parameter using a match statement and error handling for different padding behaviors. Furthermore, a deprecated file containing old 3D bounding box utilities has been removed, streamlining the overall code structure.

Changes

File(s)	Change Summary
src/imgtools/__init__.py src/imgtools/coretypes/__init__.py src/imgtools/coretypes/imagetypes.py	Updated module public interfaces by adding BoxPadMethod and RegionBox to the __all__ exports and adjusting import statements to load Coordinate3D, Size3D, and Spacing3D from .spatial_types instead of .helper_types.
src/imgtools/coretypes/box.py	Introduced the BoxPadMethod enum and updated the RegionBox.pad method signature to accept an optional method parameter (defaulting to BoxPadMethod.SYMMETRIC). The method logic now uses a match statement for conditional padding and raises a ValueError for invalid methods, alongside updating its imports.
src/imgtools/coretypes/deprecated_bbox.py	Deleted the deprecated module that contained older implementations of 3D bounding box classes and helper functions.

Feedback

The changes are organized in a way that improves code clarity and modularity. Maintaining explicit public interfaces through updated __all__ declarations and consolidating import paths helps future maintainability. The enhanced RegionBox.pad method employs a clear match-based control flow and proper error handling, contributing to readability. Removing deprecated code further streamlines the codebase; however, ensuring inline comments explain the padding logic in detail may be beneficial for ongoing maintenance.

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📜 Recent review details

Configuration used: .coderabbit.yaml
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 2a45a5a and 13ff5f7.

⛔ Files ignored due to path filters (9)

• docs/notebooks/functional.ipynb is excluded by none and included by none
• docs/usage/.pages is excluded by none and included by none
• docs/usage/CoreTypes/index.md is excluded by none and included by none
• docs/usage/CoreTypes/regionbox.ipynb is excluded by none and included by none
• docs/usage/Functional/functional.ipynb is excluded by none and included by none
• mkdocs.yml is excluded by none and included by none
• pixi.lock is excluded by !**/*.lock and included by none
• pixi.toml is excluded by none and included by none
• src/imgtools/datasets/data/merged_duck_with_star.nii.gz is excluded by !**/*.gz and included by src/**

📒 Files selected for processing (5)

• src/imgtools/__init__.py (2 hunks)
• src/imgtools/coretypes/__init__.py (1 hunks)
• src/imgtools/coretypes/box.py (3 hunks)
• src/imgtools/coretypes/deprecated_bbox.py (0 hunks)
• src/imgtools/coretypes/imagetypes.py (1 hunks)

💤 Files with no reviewable changes (1)

• src/imgtools/coretypes/deprecated_bbox.py

✅ Files skipped from review due to trivial changes (1)

• src/imgtools/coretypes/imagetypes.py

🧰 Additional context used

📓 Path-based instructions (1)

`src/**/*.py`: Review the Python code for compliance with PE...

src/**/*.py: Review the Python code for compliance with PEP 8 and PEP 257 (docstring conventions). Ensure the following: - Variables and functions follow meaningful naming conventions. - Docstrings are present, accurate, and align with the implementation. - Code is efficient and avoids redundancy while adhering to DRY principles. - Consider suggestions to enhance readability and maintainability. - Highlight any potential performance issues, edge cases, or logical errors. - Ensure all imported libraries are used and necessary.

• src/imgtools/__init__.py
• src/imgtools/coretypes/__init__.py
• src/imgtools/coretypes/box.py

🪛 GitHub Check: codecov/patch

src/imgtools/coretypes/box.py

[warning] 211-221: src/imgtools/coretypes/box.py#L211-L221
Added lines #L211 - L221 were not covered by tests

🔇 Additional comments (5)

src/imgtools/coretypes/__init__.py (1)

1-4: LGTM! Clean import organization.

The import statements are well-organized, with the new entities properly imported and the path updated from helper_types to spatial_types.

src/imgtools/__init__.py (1)

3-3: LGTM! Well-organized exports.

The new entities are properly imported and exported, maintaining alphabetical order in both the import statement and all list.

Also applies to: 15-16

src/imgtools/coretypes/box.py (3)

65-70: LGTM! Well-defined enum for padding methods.

The BoxPadMethod enum is well-documented and provides clear options for padding behavior.

---

165-207: Excellent docstring with clear examples!

The docstring is comprehensive, including:

• Clear description of functionality
• Well-documented parameters
• Illustrative examples showing both padding methods

---

211-221: Add test coverage for the match statement.

The match statement handling different padding methods lacks test coverage.

Would you like me to help generate test cases for the different padding methods? The test cases should cover:

1. BoxPadMethod.SYMMETRIC
2. BoxPadMethod.END
3. Invalid padding method

def test_pad_methods(self):
    box = RegionBox(
        Coordinate3D(5, 5, 5),
        Coordinate3D(10, 10, 10)
    )
    
    # Test SYMMETRIC padding
    padded_symmetric = box.pad(5, BoxPadMethod.SYMMETRIC)
    self.assertEqual(padded_symmetric.min, Coordinate3D(0, 0, 0))
    self.assertEqual(padded_symmetric.max, Coordinate3D(15, 15, 15))
    
    # Test END padding
    padded_end = box.pad(5, BoxPadMethod.END)
    self.assertEqual(padded_end.min, Coordinate3D(5, 5, 5))
    self.assertEqual(padded_end.max, Coordinate3D(15, 15, 15))
    
    # Test invalid method
    with self.assertRaises(ValueError):
        box.pad(5, "invalid")

✅ Verification successful

Test Coverage Enhancement for BoxPadMethod in pad()

The tests you proposed correctly validate all branches of the match statement by ensuring that:

• BoxPadMethod.SYMMETRIC adjusts both min and max as expected.
• BoxPadMethod.END leaves the lower bound unchanged while modifying the upper bound.
• An invalid method causes a proper exception with a clear error message.

Incorporating these tests into your test suite will improve maintainability and readability by directly verifying the intended outcome for each branch. Here's an example unit test snippet that you can include in your tests:

import unittest

from src.imgtools.coretypes.box import RegionBox, BoxPadMethod
from src.imgtools.coretypes.coordinate import Coordinate3D

class TestRegionBoxPadMethods(unittest.TestCase):
    def test_pad_symmetric(self):
        box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10))
        # Expect padding to apply symmetrically
        padded_box = box.pad(5, BoxPadMethod.SYMMETRIC)
        self.assertEqual(padded_box.min, Coordinate3D(0, 0, 0))
        self.assertEqual(padded_box.max, Coordinate3D(15, 15, 15))
    
    def test_pad_end(self):
        box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10))
        # Expect only the max to be extended
        padded_box = box.pad(5, BoxPadMethod.END)
        self.assertEqual(padded_box.min, Coordinate3D(5, 5, 5))
        self.assertEqual(padded_box.max, Coordinate3D(15, 15, 15))

    def test_pad_invalid_method(self):
        box = RegionBox(Coordinate3D(5, 5, 5), Coordinate3D(10, 10, 10))
        # Expect a ValueError when an invalid method is passed
        with self.assertRaises(ValueError):
            box.pad(5, "invalid")

if __name__ == '__main__':
    unittest.main()

These tests not only verify correctness but also serve as clear documentation for the functionality in the future, aiding maintainability. Let me know if you need further refinements or if there's any additional behavior you'd like to cover.

🧰 Tools

🪛 GitHub Check: codecov/patch

[warning] 211-221: src/imgtools/coretypes/box.py#L211-L221
Added lines #L211 - L221 were not covered by tests

✨ Finishing Touches

• 📝 Generate Docstrings (Beta)

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[codecov]

Codecov Report

Attention: Patch coverage is 47.61905% with 11 lines in your changes missing coverage. Please review.

Project coverage is 61.28%. Comparing base (e147629) to head (13ff5f7).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/imgtools/coretypes/box.py	35.29%	11 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #215      +/-   ##
==========================================
- Coverage   62.09%   61.28%   -0.81%     
==========================================
  Files          49       50       +1     
  Lines        3659     3761     +102     
==========================================
+ Hits         2272     2305      +33     
- Misses       1387     1456      +69     

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