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https://github.com/bhklab/readii

Radiomic Extraction and Analysis for DICOM Images (READII)

https://github.com/bhklab/readii

Science Score: 13.0%

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    Scientific vocabulary similarity
    Low similarity (16.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Radiomic Extraction and Analysis for DICOM Images (READII)

Basic Info
Statistics
  • Stars: 5
  • Watchers: 9
  • Forks: 0
  • Open Issues: 30
  • Releases: 68
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License

README.md

READII

codecov CI-CD CodeFactor

GitHub Release pixi-badge

PyPI - Python Version PyPI - Version PyPI - Format Downloads Docker Pulls

Radiomic Extraction and Analysis for DICOM Images

A package to extract radiomic features from DICOM CT images.

Installation

bash $ pip install readii

(recommended) Create new pixi environment for a project

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

(recommended) Create new conda virtual environment

bash 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.

bash $ 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:

```text (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.

Serve Documentation Locally

bash pixi run -e docs doc-serve

License

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

GitHub Events

Total
  • Create event: 90
  • Release event: 31
  • Issues event: 62
  • Watch event: 3
  • Delete event: 49
  • Member event: 1
  • Issue comment event: 100
  • Push event: 254
  • Pull request review comment event: 275
  • Pull request review event: 243
  • Pull request event: 77
Last Year
  • Create event: 90
  • Release event: 31
  • Issues event: 62
  • Watch event: 3
  • Delete event: 49
  • Member event: 1
  • Issue comment event: 100
  • Push event: 254
  • Pull request review comment event: 275
  • Pull request review event: 243
  • Pull request event: 77

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 51
  • Total pull requests: 91
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.43
  • Average comments per pull request: 1.21
  • Merged pull requests: 74
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 46
  • Pull requests: 62
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.41
  • Average comments per pull request: 1.69
  • Merged pull requests: 45
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • strixy16 (41)
  • jjjermiah (11)
  • nirelias (1)
Pull Request Authors
  • strixy16 (87)
  • jjjermiah (45)
  • Mogtaba-Alim (8)
Top Labels
Issue Labels
enhancement (11) bug (5) feature (5) refactor (3) documentation (2) help wanted (1) good first issue (1) question (1)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 236 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 65
  • Total maintainers: 1
pypi.org: readii

A package to extract radiomic features!

  • Versions: 65
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 236 Last month
Rankings
Dependent packages count: 10.0%
Average: 37.8%
Dependent repos count: 65.7%
Maintainers (1)
bhaibeka
Last synced: 6 months ago