Release Notes

2.2.0_3.1.0 [2025-12-18]

Maintenance:

Migrated from poetry to uv for dependency management
Updated CI configuration to use new qa-ci repository structure
Upgraded python from 3.9.20 to 3.9.25
Updated flywheel-gear-toolkit from 0.5.1 to >=0.6.22
Updated pillow from 8.2.0 to >=11.3.0 to address security vulnerabilities
Updated pynrrd from 0.4.2 to >=1.1.3
Updated fw-file from 1.1.2 to <3
Upgraded upstream pyradiomics package to latest version for improved compatibility
Refactored Dockerfile to use multi-stage builds with uv for virtual environment management
Added non-root flywheel user (UID 31337) to container
Updated .pre-commit-config.yaml hooks to use latest qa-ci configurations
Added pyproject_export, eolfix, jsonlint, and linkcheck pre-commit hooks
Migrated build system from poetry.core.masonry.api to hatchling.build
Updated pyproject.toml to use PEP 621 format
Removed deprecated development dependencies (isort, pylint, pycodestyle, pydocstyle, mypy, black)

Documentation:

Enhancements:

Improved error handling with dedicated read_image() function that catches and logs exceptions during image loading

Fixes:

Fixed typo in conditional check (image_sitk in None changed to image_sitk is None)

Maintenance:

Updated PYTHON_VERSION from 3.9.19 to 3.9.20
Corrected source and url fields in manifest to point to correct GitLab repository

Enhancements:

Added support for custom parameter configuration files via params_file input
Added parameter file validation to ensure configuration integrity
Enhanced README with comprehensive usage examples and custom configuration guide
Added README figures, including schema diagram and configuration screenshots
Improved error handling and logging throughout the codebase

Fixes:

Fixed mask creation for empty mask scenarios to handle edge cases properly
Fixed type validation in radiomic feature calculations to prevent runtime errors
Corrected feature extraction to properly handle 2D/3D images without redundant iterations

Maintenance:

Documentation:

Maintenance:

Migrated CI configuration from flywheel-apps/utils/ci-templates to scientific-solutions/etc/sse-qa-ci
Updated pre-commit hooks to use versioned references instead of main/master branches
Updated poetry version requirement from 1.1.2 to 1.1.12 in Dockerfile
Moved black back to dev dependency and upgraded to ^22.3.0
Updated isort to ^5.11.5
Added missing newline at end of file for .env and .gitignore
Removed blank lines before class definitions per Python style conventions

Documentation:

Fixed trailing whitespace issues across multiple files
Corrected Unicode character encoding in manifest.json citation (dash character)

Enhancements:

Added support for 3D images including zipped DICOM series and numpy arrays
Added convert_numpy_to_single_channel config option to convert 3-channel numpy arrays to single-channel for radiomic feature calculation
Added voxel_based config option placeholder for future voxel-based feature calculations
Added factory pattern for image readers to handle multiple image formats (SimpleITK, numpy arrays, zipped DICOM)
Added factory pattern for image preparers to handle image preprocessing based on file type
Added modular calculator system (PyradCalc) to separate feature extraction logic
Added writer system for outputting features to CSV and Flywheel metadata
Added image dimension and channel validation to ensure proper input format
Added automatic mask generation from input image when no mask is provided
Added support for calculating 2D features for each slice in 3D images
Enhanced CSV output to support multiple image slices with one row per slice

Fixes:

Fixed handling of 3-channel (RGB) images by extracting only the first channel for radiomic calculations
Fixed mask geometry parameters to match input image metadata
Fixed image dimension checks to properly handle both 2D and 3D inputs

Maintenance:

Documentation:

Updated README with link to pyradiomics documentation
Expanded input documentation to specify support for both 2D and 3D images
Added Outputs section documenting the CSV file suffix
Added documentation for new config options (convert_numpy_to_single_channel, voxel_based)
Added Acknowledgements section with pyradiomics citation and test data attribution
Updated manifest description to explain segment-based feature extraction and mask requirements
Updated manifest with proper citation for van Griethuysen et al. 2017
Swapped manifest source and url fields to correctly reference GitLab repo and documentation
Changed manifest label from "pyradiomics" to "PyRadiomics"
Changed manifest license from "MIT" to "BSD-3-Clause"

Enhancements:

Added support for extracting radiomic features from 2D images using pyradiomics library
Added optional mask input for feature extraction; auto-generates mask if not provided
Added shape2D feature extraction for 2D images with user-provided masks
Added CSV output of computed radiomic features

Documentation:

Maintenance:

Added CI/CD pipeline configuration using poetry-pre-commit.yml template
Added pre-commit hooks for code quality (isort, black, pytest, manifest validation)
Added development dependencies (pytest, pytest-cov, pytest-mock, black, isort)
Added project dependencies (flywheel-gear-toolkit, numpy, Pillow, pynrrd, pyradiomics)
Added python 3.7 base Docker image with poetry 1.1.2
Added .gitignore for Python artifacts, coverage reports, and editor files