BSSN STEM data, atomic image quantification and vPCF analysis codes
softwareposted on 22.10.2021, 17:20 by Stephen FunniStephen Funni, Elizabeth DickeyElizabeth Dickey
This data includes the atomic column position finding code, vector pair correlation function (vPCF) and STEM image data used in our APL Materials paper: "Theory and application of the vector pair correlation function for real-space crystallographic analysis of order/disorder correlations from STEM images. (https://aip.scitation.org/doi/10.1063/5.0058928)
SingleOrigin: Python code module for locating and indexing atomic columns in STEM lattice images using a reference lattice generated from a .cif file.
SO_script: calls SingleOrigin classes, methods, and functions to quantify STEM images; implements the vPCF method to calculate and analyze local structural order/disorder.
To use SingleOrigin: place all files with lowercase filenames and the README file into a folder entitled "SingleOrigin". Open the SO_script.py in Spyder and run cell-by-cell. You will need to make sure the .cif, image file, and SingleOrigin folder are in the working directory or provide in the script correct paths to their locations on your computer.
You will need to install all dependencies not included in your Python environment. These are typically: scikit-image, joblib, psutil, pyCifRW, imageio, matplotlib-scalebar, and OpenCV.