Quickstart

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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.