Welcome to SimEx-Lite’s documentation!

Quickstart

https://img.shields.io/pypi/v/SimEx-Lite.svg https://travis-ci.com/PaNOSC-ViNYL/SimEx-Lite.svg?branch=main Documentation Status

SimEx-Lite is the core package of the SIMEX platform providing the calculator interfaces and data APIs.

Installing

SimEx-Lite can be installed with Python 3.6 or later:

$ pip install SimEx-Lite

To test the latest updates, install from sources as shown below.

Developing

We encourage everyone to contribute to SimEx. For a detailed guide, please visit https://simex-lite.readthedocs.io/en/latest/contributing.html

  1. Clone this Github repository:

$ git clone --recursive git@github.com:PaNOSC-ViNYL/SimEx-Lite.git

  1. Install the package locally:

$ cd SimEx-Lite
$ pip install -e .

Tests

  1. Enable the testFiles submodule.

$ git submodule init
$ git submodule update

  1. Run the test

$ pytest .

Features

SimEx-Lite provides

  • python interfaces for SIMEX backengines (aka “Calculators”)

    • SourceCalculators

    • PropagationCalculators

    • PMICalculators (PhotonMattterInteractionCalculators)

    • DiffractionCalculators

    • DetectorCalculators

  • data APIs for different data formats.

    • PMI (Photon matter interaction) data

    • Wavefront data

    • Diffraction data

Citation

Please cite the following paper if you use SimEx-Lite for your research:

E, J. et al. SimEx-Lite: easy access to start-to-end simulation for experiments at advanced light sources. in Advances in Computational Methods for X-Ray Optics VI (eds. Chubar, O. & Tanaka, T.) 22 (SPIE, San Diego, United States, 2023). doi.org/10.1117/12.2677299

Publications using SIMEX platform

  1. E, J. et al. SimEx-Lite: easy access to start-to-end simulation for experiments at advanced light sources. in Advances in Computational Methods for X-Ray Optics VI (eds. Chubar, O. & Tanaka, T.) 22 (SPIE, San Diego, United States, 2023). doi:10.1117/12.2677299.

  2. E, J. et al. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Sci Rep 13, 16359 (2023).

  3. E, J. et al. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. Structural Dynamics 9, 064101 (2022).

  4. E, J. et al. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser. Sci Rep 11, 17976 (2021).

  5. E, J. et al. VINYL: The VIrtual Neutron and x-raY Laboratory and its applications. in Advances in Computational Methods for X-Ray Optics V (eds. Sawhney, K. & Chubar, O.) 33 (SPIE, Online Only, United States, 2020). doi:10.1117/12.2570378.

  6. Fortmann-Grote, C. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. IUCrJ 4, 560–568 (2017).

  7. Fortmann-Grote, C. et al. Simulations of ultrafast x–ray laser experiments. in Advances in X-ray Free-Electron Lasers Instrumentation IV (eds. Tschentscher, T. & Patthey, L.) 102370S (Prague, Czech Republic, 2017). doi:10.1117/12.2270552.

  8. Fortmann-Grote, C. et al. SIMEX: Simulation of Experiments at Advanced Light Sources. arXiv:1610.05980 [physics] (2016).

  9. Yoon, C. H. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. Scientific Reports 6, 24791 (2016).

Acknowledgement

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 823852.

Introduction

Users

Developers

Indices and tables