├── .codacy.yml ├── .codebeatignore ├── .coveragerc ├── .github ├── CODE_OF_CONDUCT.md ├── ISSUE_TEMPLATE │ └── ISSUE_TEMPLATE.md ├── PULL_REQUEST_TEMPLATE │ └── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── docs.yml │ ├── python.yml │ ├── ubuntu.yaml │ └── windows.yaml ├── .gitignore ├── .readthedocs.yml ├── AUTHORS.md ├── CTLungSeg ├── __init__.py ├── __main__.py ├── __version__.py ├── evaluate.py ├── labeling.py ├── lung_extraction.py ├── method.py ├── metrics.py ├── segmentation.py ├── train.py └── utils.py ├── LICENSE ├── MANIFEST.in ├── README.md ├── SOURCES.txt ├── Snakefile ├── centroids.pkl.npy ├── config.yaml ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── examples │ ├── body_segmentation.ipynb │ ├── examples.rst │ └── pipeline_workflow.ipynb │ ├── images │ └── Multi_Channel.png │ ├── index.rst │ ├── installation.rst │ ├── modules.rst │ ├── references.rst │ ├── script.rst │ ├── snakemake.rst │ └── theory.rst ├── images └── results.png ├── labeling.ps1 ├── labeling.sh ├── lung_extraction.ps1 ├── lung_extraction.sh ├── paper ├── paper.bib └── paper.md ├── requirements.txt ├── setup.cfg ├── setup.py ├── testing ├── __init__.py ├── images │ └── .gitkeep ├── test_method.py ├── test_metrics.py ├── test_segmentation.py └── test_utils.py ├── train.ps1 └── train.sh /.codacy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiccardoBiondi/segmentation/HEAD/.codacy.yml -------------------------------------------------------------------------------- /.codebeatignore: -------------------------------------------------------------------------------- 1 | *.md 2 | testing/* 3 | -------------------------------------------------------------------------------- /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiccardoBiondi/segmentation/HEAD/.coveragerc 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