├── .coveragerc ├── .devcontainer ├── devcontainer.json ├── docker-compose.yml └── install-dev-tools.sh ├── .github └── workflows │ ├── docs.yml │ └── pull-request.yml ├── .gitignore ├── .pylintrc ├── .vscode └── settings.json ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── assets └── pydicer-working-directory-structure.png ├── docker-compose.yml ├── docs ├── Makefile ├── _static │ └── custom.css ├── analyse.rst ├── code_of_conduct.rst ├── conf.py ├── config.rst ├── contributing.rst ├── convert.rst ├── dataset.rst ├── generate.rst ├── index.rst ├── input.rst ├── make.bat ├── nnunet.rst ├── preprocess.rst ├── tool.rst ├── utils.rst └── visualise.rst ├── examples ├── ASMIRTWorkshop │ ├── 1_Python_Intro.ipynb │ ├── 2_DICOM.ipynb │ ├── 3_RT_Data_Analysis.ipynb │ └── README.md ├── AutoSegmentation.ipynb ├── Configuration.ipynb ├── ConvertingData.ipynb ├── DatasetPreparation.ipynb ├── DoseMetrics.ipynb ├── GettingStarted.ipynb ├── ObjectGeneration.ipynb ├── Radiomics.ipynb ├── VisualiseData.ipynb ├── WorkingWithData.ipynb ├── WorkingWithStructures.ipynb └── nnUNet.ipynb ├── poetry.lock ├── pydicer ├── __init__.py ├── analyse │ ├── __init__.py │ ├── compare.py │ └── data.py ├── cli │ ├── __init__.py │ ├── contants.py │ ├── input.py │ └── run.py ├── config.py ├── constants.py ├── convert │ ├── __init__.py │ ├── data.py │ ├── headers.py │ ├── pt.py │ └── rtstruct.py ├── dataset │ ├── __init__.py │ ├── functions.py │ ├── nnunet.py │ ├── preparation.py │ └── structureset.py ├── generate │ ├── __init__.py │ ├── mhubconfigs │ │ ├── casust.yml │ │ ├── lungmask.yml │ │ ├── nnunet_liver.yml │ │ ├── nnunet_pancreas.yml │ │ ├── platipy.yml │ │ └── totalsegmentator.yml │ ├── models.py │ ├── object.py │ └── segmentation.py ├── input │ ├── __init__.py │ ├── base.py │ ├── filesystem.py │ ├── orthanc.py │ ├── pacs.py │ ├── tcia.py │ ├── test.py │ └── web.py ├── logger.py ├── preprocess │ ├── __init__.py │ └── data.py ├── quarantine.py ├── tool.py ├── utils.py └── visualise │ ├── __init__.py │ └── data.py ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt └── tests ├── __init__.py ├── conftest.py ├── test_compare.py ├── test_config.py ├── test_convert.py ├── test_generate.py ├── test_input.py ├── test_nnunet.py ├── test_pipeline.py ├── test_quarantine.py ├── test_segmentation.py ├── test_structure_set.py └── test_utils.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AustralianCancerDataNetwork/pydicer/HEAD/.coveragerc -------------------------------------------------------------------------------- /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AustralianCancerDataNetwork/pydicer/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- 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