Metadata-Version: 2.1
Name: dcmrtstruct2nii
Version: 1.0.19
Summary: Convert DICOM RT-Struct to nii
Home-page: https://github.com/Sikerdebaard/dcmrtstruct2nii
Author: Thomas Phil
Author-email: thomas@tphil.nl
License: UNKNOWN
Description: [![DOI](https://zenodo.org/badge/166835376.svg)](https://zenodo.org/badge/latestdoi/166835376)
        
        # dcmrtstruct2nii
        DICOM RT-Struct to nii-mask. This is a naïve 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.
        
        # Rasterization
        Currently 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.
        
        # Interpolation
        Interpolation of the mask between slices is currently unsupported. Send us an algorithm or a pull requests and we'll happly add it.
        
        # Input file format
        The DICOM and RT-Struct inputs need to be unzipped in a directory. Currently this is the only way to read the input files.
        
        # CLI Tool
        ```
        # install using pip and show tool help
        pip install dcmrtstruct2nii
        dcmrtstruct2nii --help
        
        # list structures in DICOM RT Struct
        dcmrtstruct2nii list -r /path/to/rtstruct/file
        
        # convert help output
        dcmrtstruct2nii convert --help
        
        # convert DICOM RT Structs to .nii.gz masks
        dcmrtstruct2nii convert -r /path/to/rtstruct/file.dcm -d /path/to/original/extracted/dicom -o /output/path
        ```
        
        # Python API
        ```
        # install using pip and show tool help
        pip install dcmrtstruct2nii
        ```
        
        ```
        # lets test it
        from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
        
        print(list_rt_structs('/path/to/dicom/rtstruct/file.dcm'))
        
        dcmrtstruct2nii('/path/to/dicom/rtstruct/file.dcm', '/path/to/original/extracted/dicom/files', '/output/path')
        ```
        
        # License and academic use
        
        The program is licensed [Apache license 2.0](https://github.com/Sikerdebaard/dcmrtstruct2nii/blob/master/LICENSE).
        
        For 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). 
        
        Please cite:
        
        ```Phil, T. (2020). Sikerdebaard/dcmrtstruct2nii: v1.0.19 (v1.0.19) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.4037865```
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
