SimEx-Lite 1.0.1

The core package of the SIMEX platform providing the calculator interfaces.

Quickstart

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

• Free software: GNU General Public License v3

• Documentation: https://SimEx-Lite.readthedocs.io

• GitHub: https://github.com/PaNOSC-ViNYL/SimEx-Lite

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 [e-mail]:PaNOSC-ViNYL/SimEx-Lite.git

2. Install the package locally:

$ cd SimEx-Lite
$ pip install -e .

Tests

1. Enable the testFiles submodule.

$ git submodule init
$ git submodule update

2. Run the test

$ git clone https://github.com/PaNOSC-ViNYL/SimEx-Lite-testFiles testFiles
$ pytest tests

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.

History

1.1.0

• Add EMC format

• Add the function to write multiple files into one file in EMC format

• Add CXI format

• Add Condor format

1.0.0 (2022-09-27)

• Refactor based on libpyvinyl.

• Support instrument class.

• Updated documents for backengines installation.

0.3.4 - 0.3.7 (2022-09-19)

• Support for the legacy DiffractionData class.

0.3.3 (2022-08-05)

• Fixed reading singfel rewrited data.

• Add chunk functions to GaussianNoiseCalculator.

0.3.2 (2021-10-20)

• Included utils as a subpackage.

0.3.1 (2021-09-29)

• Updated the interface of data APIs. Details at this PR link.

• Updated the deployment guide for PyPI in CONTRIBUTING.

0.2.1 (2021-04-19)

• Deploy PyPI with Travis

0.2.0 (2021-04-17)

• Data API:

  • Added: PhotonBeamData.py

  • Added: SampleData.py

  • Added: DiffractionData.py

  • Added Singfel Diffraction data API

  • Added EMC photon data API

• Calculator:

  • Detector calculators:

    • Added Gaussian noise calculator

• Examples:

  • Added singfel2EMC data analysis example

0.1.0 (2021-02-24)

• First release on PyPI.