riCOM

This repository contains the C++ implementation of the riCOM (Real Time Centre Of Mass) algorithm for 4D Scanning electron microscopy as described in this publication. At this point it is compatible with .mib files (Quantum Detectors Merlin) and .t3p (Timepix camera) data and can be run in live mode with the Merlin camera.

Installation

Binaries

• Just download the precompiled executable for your system from Releases or for the latest development version the artefacts of the automated compilation run from the Repositories "Actions" Tab, for example here!
• The Windows version includes additional libraries, which need to be kept in the same folder as the executable. Linux requires SDL2 and FFTW3 libraries on your system (see below).
• Alternatively build from source as outlined below. Make sure you clone the repository including submodules: git clone --recurse-submodules -j2 git@github.com:ThFriedrich/riCOM_cpp.git
• The project uses features of C++ standard 17. You may need appropriate compilers and libraries.
• Generally the performance/speed may not be ideal using precompiled binaries. For best results compile on the machine you want to run the software on, using the "native" option for the "ARCH" variable in the CMakeLists.txt file

Generally build instructions can be followed step by step from the automated build setup from command line

Build instructions Linux

Dependencies

• g++/gcc compiler version >=9
  • sudo apt-get install gcc-9 g++-9
• make & cmake
• SDL2
  • sudo apt-get install libsdl2-dev libsdl2-image-dev
• FFTW3
  • sudo apt-get install libfftw3-dev

Building from Command Line

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
cmake --build .

Build instructions Windows

Dependencies

• Visual Studio Community with C++ Desktop Development Kit or msbuild tools
  • including the msvc compiler, cmake and msbuild
• SDL2
  • Download 'SDL2-devel-2.0.xx-VC.zip' (Visual C++ 32/64-bit) from http://www.libsdl.org/download-2.0.php#source and SDL2-image
  • Both zip folder share a common sub-structure. Extract contents of the zips to 'C:/SDL2_VC', merging the contents of both zips into the same folder structure.
• FFTW
  • Download and extract FFTW3 library
  • run lib /machine:x64 /def:libfftw3f-3.def

Building from Command Line (Use Developer Powershell for VS)

mkdir build
cd build
cmake ..
msbuild .\RICOM.vcxproj /p:configuration=Release

The executable RICOM.exe will be in the folder 'build\Release'. Make sure the files 'SDL2.dll', 'SDL2_image.dll', 'libfftw3f-3.dll' and 'libfftw3f-3.lib' are in the same location as the executable. When using oneAPI icx compiler from Intel, also the libraries: the files 'svml_dispmd.dll', 'libmmdd.dll' and 'libmmd.dll' must be in this directory.

Running the program

Running in Live mode with Quantum Detector MerlinEM camera

To send instructions to the camera a python scipt is executed internally, which relies on the Merlin Interface package. It is a submodule of this repository, but it can also be manually downloaded. The file merlin_interface.py should be placed in the same directory as the RICOM executable.

Running example files

A set of compatible example datasets are provided in an open data repository on Zenodo.

Command Line Interface

The program can be run from command line without opening a GUI. The input file path and other parameters are being specified by additional parameters as listed here.
Example usage:

./RICOM -filename default1.mib -nx 64 -ny 64

This functionality was originally intended for dubugging purposes. It is therefore not fully developed yet, but may be useful for some users nevertheless.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You may contact the University of Antwerp for alternative licensing options if necessary.

Cite

If you use this software in your research please cite:

@article{
  ricom_2022, 
  title={Real-Time Integration Center of Mass (riCOM) Reconstruction for 4D STEM}, 
  DOI={10.1017/S1431927622000617}, 
  journal={Microscopy and Microanalysis}, 
  publisher={Cambridge University Press}, 
  author={Yu, Chu-Ping and Friedrich, Thomas and Jannis, Daen and Van Aert, Sandra and Verbeeck, Johan}, 
  year={2022}, 
  pages={1–12}}