ePDFpy

ePDFpy is a standalone tool for reduced electron pair distribution function (ePDF) analysis. Users can do ePDF analysis with the diffraction images obtained by transmission electron microscope (TEM), and use the outputs to deduce the atomic structures.

This software is Python-based software with an interactive graphical user interface (GUI) environment built with PyQt5. Currently, built with the python3.8 version but confirmed that still compatible with python3.10.

Installation

First, users must install pre-requiste libralies, which are listed in below:

• numpy >= 1.22.4
• scipy >= 1.9.1
• opencv (cv2) >= 4.6.0
• pandas >= 1.4.4
• pyqt5 >= 5.15.7
• pyqtgraph >= 0.12.4
• hyperspy >= 1.7.1
• mrcfile >= 1.4.2
• pyqtdarktheme == 2.1.0

Users can install all dependencies manually using pip install.

pip install -r requirements.txt
pip install epdfpy

It is recommended to use Anaconda (www.anaconda.com/download) or Miniconda ( https://docs.conda.io/en/latest/miniconda.html) to set up a virtual environment. All dependencies can easily installed by using 'environment.yaml' file in the conda terminal:

conda create -n epdfpy python=3.8
conda activate epdfpy
pip install epdfpy

Using source code

If users want to install ePDFpy directly from the source code, download the source code, and moved into the directory path. Using terminal type:

python setup.py install

ePDFpy GUI standalone package

For those who are not familiar with Python, users can simply download executable files for each OS (Windows, Mac, Linux), which are compiled with PyInstaller. Simply open the executable file:

• Windows: ePDFpy.exe
• Mac: ePDFpy.app

Running GUI

After installation, users can open ePDFpy simply typing command line in the terminal:

epdfpy

which will automatically opens the GUI script (run_ui.py) in source folder.

Those who are not accustomed to Python, just open executable files from distributed package.

Source codes

Separated by folders, each folders contains:

• assets: Requisite data files, such as calculated scattering factor values for each atoms.
• calculate: Calculation modules for image process (profile extraction), I(q) and G(r) calculation based on the input variable (pdf analysis) and advance fitting.
• datacube: Moldules to assign and save every parameters and variable for each data files.
• file: Modules to related to loading data files (diffraction pattern image) and saving output files.
• settings: Pre-saved default settings and presets.
• ui: Each GUI panels and windows made by PyQt5.

Example

User guide

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License

GNU GPLv3

ePDFpy is open-source software distributed under a GPLv3 license. It is free to use, alter, or build on, provided that any work derived from ePDFpy is also kept free and open under a GPLv3 license.