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        "description": "[![DOI](https://zenodo.org/badge/166835376.svg)](https://zenodo.org/badge/latestdoi/166835376)\n![unit tests](https://github.com/Sikerdebaard/dcmrtstruct2nii/workflows/Unit%20Tests/badge.svg)\n  \n\n# dcmrtstruct2nii\nDICOM RT-Struct to nii-mask. This is a na\u00efve approach to rasterizing rt-struct to masks in nii format. If there's holes in your RT-Struct then this approach will most likely not work. The RT-Struct needs to be within the bounds of the slices of the original DICOM. Rasterization is done on a slice-by-slice basis, interpolation between slices is currently unsupported.\n\n# Rasterization\nCurrently the RT-Struct is treated as a polygon and is rasterized trough [this function](https://github.com/Sikerdebaard/dcmrtstruct2nii/blob/master/dcmrtstruct2nii/adapters/convert/rtstructcontour2mask.py#L10) on a slice-by-slice basis. We'll hapilly add other rasterization algorithms (e.g. ones that can deal with holes in the polygon) if you point us to some code to do that or if you send in a pull request.\n\n# Interpolation\nInterpolation of the mask between slices is currently unsupported. Send us an algorithm or a pull requests and we'll happly add it.\n\n# Input file format\nThe DICOM and RT-Struct inputs need to be unzipped in a directory. Currently this is the only way to read the input files.\n\n# CLI Tool\n```\n# install using pip and show tool help\npip install dcmrtstruct2nii\ndcmrtstruct2nii --help\n\n# list structures in DICOM RT Struct\ndcmrtstruct2nii list -r /path/to/rtstruct/file\n\n# convert help output\ndcmrtstruct2nii convert --help\n\n# convert DICOM RT Structs to .nii.gz masks\ndcmrtstruct2nii convert -r /path/to/rtstruct/file.dcm -d /path/to/original/extracted/dicom -o /output/path\n```\n\n# Python API\n```\n# install using pip and show tool help\npip install dcmrtstruct2nii\n```\n\n```\n# lets test it\nfrom dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs\n\nprint(list_rt_structs('/path/to/dicom/rtstruct/file.dcm'))\n\ndcmrtstruct2nii('/path/to/dicom/rtstruct/file.dcm', '/path/to/original/extracted/dicom/files', '/output/path')\n```\n\n# License and academic use\n\nThe program is licensed [Apache license 2.0](https://github.com/Sikerdebaard/dcmrtstruct2nii/blob/master/LICENSE).\n\nFor academic use, use a presistent copy from [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037865.svg)](https://doi.org/10.5281/zenodo.4037865). \n\nPlease cite:\n\n```Phil, T. (2020). Sikerdebaard/dcmrtstruct2nii: v1.0.19 (v1.0.19) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.4037865```",
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