READII

Radiomic Extraction and Analysis for DICOM Images

A package to extract radiomic features from DICOM CT images.

Installation

$ pip install readii

(recommended) Create new pixi environment for a project

mkdir my_project
cd my_project
pixi init
pixi add --pypi readii

(recommended) Create new conda virtual environment

conda create -n readii python=3.9
conda activate readii
pip install readii

Usage

readii is a tool to perform radiomic feature extraction on DICOM CT images with region of interest (ROI) segmentations as either DICOM SEG or RTSTRUCT.

$ readii [INPUT DIRECTORY] [OUTPUT DIRECTORY] \
  --roi_names [str] \
  --pyradiomics_setting [str] \
  --negative_controls [str: shuffled_full,shuffled_roi,shuffled_non_roi,randomized_full,randomized_roi,randomized_non_roi,randomized_sampled_full,randomized_sampled_roi, randomized_sampled_non_roi] \
  --parallel [flag]
  --update [flag]

Negative control options

Negative controls are applied to one of three masks:

1. full = voxels in the entire image
2. roi = just voxels within the specified region of interest (ROI) in the segmentation
3. non_roi = all voxels except the ROI.

The three transformations are:

1. shuffle = shuffle all voxels in the specified mask
2. randomized = randomly generate new values within the original range within the specified mask
3. randomized_sampled = randomly sample original values with replacement to get new values within the specified mask

Contributing

Please use the following angular commit message format:

<type>(optional scope): short summary in present tense

(optional body: explains motivation for the change)

(optional footer: note BREAKING CHANGES here, and issues to be closed)

<type> refers to the kind of change made and is usually one of:

• feat: A new feature.
• fix: A bug fix.
• docs: Documentation changes.
• style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc).
• refactor: A code change that neither fixes a bug nor adds a feature.
• perf: A code change that improves performance.
• test: Changes to the test framework.
• build: Changes to the build process or tools.

scope is an optional keyword that provides context for where the change was made. It can be anything relevant to your package or development workflow (e.g., it could be the module or function - name affected by the change).

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

readii was created by Katy Scott. It is licensed under the terms of the MIT license.

Credits

readii was created with cookiecutter and the py-pkgs-cookiecutter template.