v1.19.0

v1.19.0 (2024-12-11)

Features

• Add abstract and concrete classes for negative controls and regions (#81, c10a568)

4D-Lung

Order of operations

1. negative_control_strategy(image, mask=mask, region=region_strategy) 2. runs the __call__ on the negative_control_strategy 3. which runs the __call__ of region(image_array, mask_array) 4. the result of which is used to figure out what indices of the original image to apply the transform method of the NegativeControlStrategy concrete classes to 5. only replace the region indices image_array[mask_indices] = transformed_values

Resource on Strategy Pattern: https://refactoring.guru/design-patterns/strategy/python/example

---

Co-authored-by: Katy Scott [email protected]

Refactoring

• Update Ruff configuration and refactor codebase (#68, e88e704)

Enhance the Ruff configuration to include additional files and ignore specific PEP-8 naming conventions. Refactor the codebase by replacing os.path with pathlib, improving logging verbosity, adding type annotations, and organizing imports.

• Bug Fixes

• Improved error handling for image cropping and feature extraction processes, ensuring robustness and clearer logging.

• Chores

• Updated configuration settings to refine linting rules and file inclusions, optimizing code quality checks.

• Incremented Pixi version across CI-CD jobs for improved performance.

• feature-extraction: Extract-method refactor to simplify workflow, prepare for class-based feature extraction (#69, 3bcaa28)

summary: Refactor code to improve readability, logging, and type annotations while addressing various bugs and updating dependencies.

mostly extract-method refactoring to make following code flow a bit easier. - setting up to create a class for the module to save from passing around all the parameters

updates to code quality control tasks - for the most part will follow suit with med-imagetools configuration for qc - pixi run qc will run ruff format and lint on files included in ruff.toml - Enhance ruff configuration to include additional files and ignore specific PEP-8 naming conventions.

• New Features - Introduced new functions for enhanced radiomic feature extraction: generateNegativeControl, cropImageAndMask, and featureExtraction.

• Improvements - Enhanced error handling and logging for the feature extraction process. - Improved documentation and formatting in loaders for better readability.

• Configuration Updates - Updated linting configuration to include specific files for checks and clarified linting rules with detailed comments. - Updated project version to "1.18.0" and added new dependencies for Jupyter-related packages. - Streamlined CI-CD workflow by modifying linting commands and removing unnecessary jobs.

---

Detailed Changes: v1.18.0...v1.19.0

v1.18.0

v1.18.0 (2024-11-28)

Features

• Add slicedim to displayimageslice (#67, c018de5)

• feat: add slice dimension variable for displayImageSlice

Allows user to indicate whether the slice index is first or last

• build: add libraries to run jupyter notebooks

• docs: fix variable type for sliceDim in displayImageSlice docstring

v1.17.0

v1.17.0 (2024-11-22)

Features

• Replace get_logger with imgtools inherited logging instance across modules (01bd13f)

v1.16.0

v1.16.0

v1.14.1

v1.14.1 (2024-11-07)

Bug Fixes

• fix: add readii cli entry point to pyproject (#58) (1710b72)

v1.14.0

v1.14.0 (2024-11-01)

Features

• feat: remove dicom-parser, update mit, deprecate padSeg (#51)

• fix: Update med-imagetools dependency and handle deprecated padSegToMatchCT function in feature_extraction.py with error logging

• chore: Update .gitignore to exclude .old, data, and trash directories for working dir

• Update src/readii/feature_extraction.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

• fix: change gitignore data

• better handling of data ignore

---

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> (a6658e7)

v1.13.2

v1.13.2 (2024-10-22)

Bug Fixes

• fix: Remove hatch config and streamline build settings in pyproject.toml for better package management and deployment (0cf184c)

v1.13.1

v1.13.1 (2024-10-22)

Bug Fixes

• fix: Update CI/CD workflow for PyPI publishing; enhance publish step, remove TestPyPI, and configure pixi.lock sha256 (743ea52)

v1.13.0

v1.13.0 (2024-10-22)

Bug Fixes

• fix: update CI/CD workflow to trigger only on pushes to main branch (2cc686f)

• fix: correct version location in pyproject.toml configuration (bdb49ea)

• fix: improve modality handling in loadSegmentation by reinforcing RTSTRUCT validation and simplifying modality checks (5d1fef6)

• fix: update ruff configuration and linting rules, switch docstring style to numpy, and enhance loader type annotations (0142860)

Chores

• chore: refine CI-CD workflow for Publish-To-PyPi and update pixi.lock SHA for dependency consistency (3c904e1)

• chore: add Ruff linter to CI-CD workflow and update project config for linting and formatting tasks (ecebe9a)

• chore: adjust CI-CD workflow to trigger on any branch for pull requests and comment out previous push configuration (3c77975)

• chore: add Codecov badge to README for improved visibility of test coverage (9472ab6)

• chore: add Codecov step in CI/CD workflow to track coverage and report using coverage.xml (fcbe561)

Continuous Integration

• ci: clean up .github/workflows/ci-cd.yml by removing unnecessary whitespace and ensuring proper formatting at end of file (a6298ab)

• ci: update CI-CD workflow to include Ruff as a dependency for the Unit-Tests job before deployment to PyPI (5d6a7f3)

Documentation

• docs: update README with installation + badges (7bdf5d3)

Features

• feat: enhance segmentation loading by adding validation for unsupported modalities in loadSegmentation function (9ee6931)

• feat: rename job to Publish-To-Test-PyPi and add Test-TestPypi-Installation steps for verifying package deployment (336185f)

• feat: update CI-CD workflow to include publishing to TestPyPI with new environment variables for authentication (d645af1)

• feat: expand pyproject.toml with publish-test command for deploying to test PyPI and add description for build task (f309346)

Unknown

• Merge pull request #42 from bhklab/jjjermiah/refactor/main

feat: Enhance CI/CD Workflow with TestPyPI Publishing, Linting Improvements, and minor docs update (376b414)

• doc: enhance docstrings in loaders.py, providing clearer descriptions and improving module documentation for DICOM and RTSTRUCT functions (249238c)

v1.12.0

v1.12.0 (2024-10-22)

Chores

• chore: update CI/CD workflow to use actions/checkout@v3, fix semantic-release task, and update pixi.lock (790ae04)

• chore: refactor CI/CD workflow with enhanced job structure and add basic config files for coverage and linting (994fd75)

Features

• feat: add semantic-release workflow for automated versioning and update readii version to 1.11.0 with new author email (92bc4d4)

• feat: update to use pixi and pyradiomics-bhklab (6a67be4)

Unknown

• Merge pull request #40 from bhklab/jjjermiah/add-pixi

feat: Use Pixi, pyradiomics fork (fd582a5)