Hands-on training: Simulating X-ray images on GPU with

Content of this file

• Installation
  • Using Conda
  • Using pip
• Content of this repository
  • Cheat sheet
  • Test installation
  • First X-ray simulation
  • Multi-material anatomical example
• How to find help
• How to report bugs/request a new feature
• Q&A
• How to cite
• Research excellence
• User contributions

Installation

Using Conda

conda env create -f environment.yml
conda activate gvxr-tutorials

Using pip

pip install gvxr
pip install matplotlib viewscad xpecgen spekpy SimpleITK

Content of this repository

• Cheat sheet: This document list all gVXR's functions used in the tutorial notebooks. It also includes the help messages to describe the purpose of each function.
• Test installation: Run the quick test script provided with gVirtualXray's Python package to make sure the installation is working well on your system.
• First X-ray simulation: Explore the step-by-step notebook to create our first X-ray radiograph. A mono-material object is imaged with a monochromatic source and an ideal detector. We show how to visualise the X-ray radiograph and take a screenshot of the 3D visualisation of the simulation environment.
• Multi-material anatomical example: Using the knowledge learnt in First X-ray simulation, initialise your own simulation to create a radiograph of the Lungman phantom.

How to find help

• Email me (Franck P. Vidal, STFC);
• Raise an issue on GitHub: https://github.com/TomographicImaging/gVXR-Tutorials/issues
• Open a ticket on SourceForge: https://sourceforge.net/p/gvirtualxray/tickets;
• Use the forum on SourceForge: https://sourceforge.net/p/gvirtualxray/discussion/;
• Subscribe to the mailing list: https://sourceforge.net/projects/gvirtualxray/lists/gvirtualxray-discuss
• Check the technical documentation, e.g. calling help(gvxr) for help on the Python package or something like help(gvxr.createNewContext) for a specific function.
• Look at the cheat sheet that lists all the gVXR's functions used in the tutorial notebooks. It also includes the help messages to describe the purpose of each function.

How to report bugs or request a new feature

• Email me (Franck P. Vidal, STFC);
• Raise an issue on GitHub: https://github.com/TomographicImaging/gVXR-Tutorials/issues
• Open a ticket on SourceForge: https://sourceforge.net/p/gvirtualxray/tickets;
• Use the forum on SourceForge: https://sourceforge.net/p/gvirtualxray/discussion/;

Q&A

See Q&A.

How to cite

If you use gVXR in your own applications, particularly for research & development, I will be grateful if you could cite the articles as follows:

• Seminal paper: Vidal, F. P., Garnier, M., Freud, N., Létang, J. M., and John, N. W., “Simulation of x-ray attenuation on the GPU,” in Proceedings of Theory and Practice of Computer Graphics 2009, 25–32, Eurographics Association, Cardiff, UK (June 2009). DOI: 10.2312/LocalChapterEvents/TPCG/TPCG09/025-032
• First reference to gVXR as an opensource software: Vidal, F. P. and Villard, P.-F., “Development and validation of real-time simulation of x-ray imaging with respiratory motion,” Computerized Medical Imaging and Graphics 49, 1–15 (2016). DOI: 10.1016/j.compmedimag.2015.12.002
• Clinical validation study: Pointon, J. L., Wen, T., Tugwell-Allsup, J., Sújar, A., Létang, J. M., and Vidal, F. P., “Simulation of x-ray projections on gpu: Benchmarking gvirtualxray with clinically realistic phantoms,” Computer Methods and Programs in Biomedicine 234, 107500 (2023). DOI: 10.1016/j.cmpb.2023.107500
• Review paper on CT applications: Vidal, F. P., Afshari, S., Ahmed, S., Atkins, C. Béchet, E., Bellot, A., Bosse, S., Chahid, Y., Chou, C.-Y., Culver, R., Dixon, L., Friemann, J., Garbout, A., Hatton, C., Henry, A., Leblanc, C., Leonardi, A., Létang, J. M., Lipscomb, H., Manchester, T., Meere, B., Middleburgh, S., Mitchell, I., Perera, L., Puig, M., and Tugwell-Allsup, J., “X-ray simulations with gVXR as a useful tool for education, data analysis, set-up of CT scans, and scanner development,” in Developments in X-Ray Tomography XV, SPIE Optics & Photonics, Volume 13152, SPIE, San Diego, California, United States (Aug 2024). DOI: 10.1117/12.3025315

User contributions on our website

We'd like to share user contributions in a new section of gVXR's website https://gvirtualxray.sourceforge.io/. If you'd like to showcase your work, please contact me by email (Franck P. Vidal, STFC) or raise an issue on GitHub (https://github.com/TomographicImaging/gVXR-Tutorials/issues).