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
It is recommended to install ePDFpy via PyPI or Anaconda distribution. Users can establish the virtual environment (), then use following command line to install.
pip install epdfpy
Using source code
Users can either use pip or conda command to setup from the source code, downloaded from Github (https://github.com/GWlab-SKKU/ePDFpy).
pip install -p requirements.txt
pip install -e .
or
conda env create --file environmnts.yaml
conda install . (?)
ePDFpy GUI 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.
Using source code
Clone or download the source code and set up the Python environment with pre-required libraries:
- 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
For the convenience, 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 env create --file environment.yaml
GUI operation
ePDFpy GUI package
Simply open the executable file:
- Windows: ePDFpy.exe
- Mac: ePDFpy.app
With terminal:
Type:
epdfpy
which will automatically opens the GUI script (run_ui.py) in source folder.
Example
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.
