pyradise 0.2.3

PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion

PyRaDiSe

PyRaDiSe is an open-source Python (Py) package for developing deployable, radiotherapy-oriented (Ra), DICOM-based (Di) auto-segmentation (Se) solutions. PyRaDiSe is DL framework-independent but can easily integrate most DL frameworks, such as PyTorch or TensorFlow. The package addresses the following challenges for building radiotherapy-oriented auto-segmentation solutions: handling DICOM data, managing and converting DICOM-RTSS data (incl. a 2D-based and a 3D-based conversion algorithm), invertible pre-processing, and post-processing. In addition to building auto-segmentation solutions, PyRaDiSe allows for converting and curating DICOM image series and DICOM-RTSS data to simplify segmentation training dataset construction. Therefore, PyRaDiSe is highly flexible, allows for fast prototyping, and facilitates a fast transition of data science research results into clinical radiotherapy research.

Main Features

The main features of PyRaDiSe are data handling, conversion from and to DICOM-RTSS, and data processing, including deep learning model inference. The intended use of PyRaDiSe in the radiotherapy environment is depicted below. The DICOM and other discrete medical image file formats, such as NIfTI, are imported into the provided data model using the fileio package. In contrast to the standard way of loading DICOM data, this package provides comprehensive and flexible import routines that consider data relation details and automate import steps, such as registering DICOM images if DICOM registration files are available. However, in some cases, the DICOM standard does not provide sufficient information for automation, requiring minimal human interaction for resolution. In addition, discrete medical images also suffer from the lack of identification data needed for automation. However, the fileio package package offers the necessary methods to address these issues with flexible approaches and prototypes. Furthermore, the fileio package provides routines to select specific entities from the available data before loading by generating filterable pre-loading information (so-called SeriesInfo) so that the computation time and memory usage for loading is minimal. Finally, after the data is loaded, it is represented using the data model implemented in the data package. All downstream tasks are performed using the simple and extensible radiotherapy-oriented data model from this step on.

After loading, the data is either converted and written to a file or processed using routines from the process package. This package includes functionality and prototypes for pre-processing, deep learning model inference, and post-processing with a similar mode of operations as well-known medical image libraries, such as SimpleITK or ITK. However, in contrast to other libraries, the process package offers a mechanism for guaranteeing reproducibility and limited invertibility.

After processing or loading, the altered data can be written to disk using a versatile writer from the fileio package to save the data as either a discrete image file or as DICOM-RTSS. In addition, specific writers provide the additional functionality to copy the input data from the source to the target directory. This feature is handy if the developed auto-segmentation solution will be deployed to the clinical environment or the cloud, where the original input data should remain unmodified.

Getting Started

If you are new to PyRaDiSe, here are a few guides to get you up to speed right away:

• Installation for installation instructions - or simply run pip install pyradise
• Examples give you an overview of PyRaDiSe's intended use. Jupyter notebooks are available in the directory ./examples.
• Change history
• Acknowledgments

Citation

If you use PyRaDiSe for your research, please acknowledge it accordingly by citing our paper:

BibTeX entry:

@article{Ruefenacht2023,
author = {Rüfenacht, Elias and Kamath, Amith and Suter, Yannick and Poel, Robert and Ermis, Ekin and Scheib, Stefan and Reyes, Mauricio},
title = {{PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion}},
journal = {Computer Methods and Programs in Biomedicine},
doi = {10.1016/j.cmpb.2023.107374},
issn = {0169-2607},
year = {2023}
}