A Python interface to the electron microscopy simulation program QSTEM
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README.md

PyQSTEM

QSTEM is a program for quantitative image simulation in electron microscopy, including TEM, STEM and CBED image simulation.

This project interfaces the QSTEM code with Python and the Atomic Simulation Environment (ASE) to provide a single environment for building models, simulating and analysing images.

QSTEM webpage: http://qstem.org/

ASE webpage: http://wiki.fysik.dtu.dk/ase

Dependencies

Optional:

Building from Source

Linux

Install dependencies

FFTW is installed with apt-get, the rest with pip.

sudo apt-get install libfftw3-dev libfftw3-single3
pip install numpy scipy matplotlib ase
pip install cython jupyter scikit-image

Install PyQSTEM

When the dependencies are installed, download, compile and install PyQSTEM by writing.

git clone https://github.com/jacobjma/PyQSTEM.git
cd pyqstem
python setup.py install

You might get some warnings which can be ignored.

Mac OS X

Mac OS X comes with Python included, but installing packages into OS X's own Python is risky, as cleaning up a mess is almost impossible. For this reason, it is recommended to either install Python with Homebrew, or to install the Anaconda distribution. This guide uses homebrew's Python, as you will need to install a number of other packages with Homebrew anyway.

Install Homebrew

Install Homebrew following the instructions on the Homebrew website.

Install Python with homebrew.

Install Homebrew's python with the command

brew install python

or if you want Python 3 with

brew install python3

Please double-check that you get the version of python and pip installed in /usr/local/bin, and not the default one in /usr/bin.

Install dependencies

FFTW is installed with Homebrew, the rest with pip.

brew install fftw
pip install numpy scipy matplotlib ase
pip install cython jupyter scikit-image

Install PyQSTEM

When the dependencies are installed, download, compile and install PyQSTEM by writing.

git clone https://github.com/jacobjma/PyQSTEM.git
cd PyQSTEM
python setup.py install

You might get some warnings which can be ignored.

Windows

Install Python

If you are new to Python the easiest way to get started is downloading a bundle installer. We recommend Anaconda, this platform includes Python and makes it easier to install the dependencies. Download Anaconda here.

Install a C-compiler

Python 3.5 or later

Compiling C++-extensions for Python 3.5 on Windows requires Microsoft Visual C++ 14.0 or later. Download Visual C++ 2015 Build Tools from here, this requires 4 gb of free space and may take 20 minutes to install.

Python 2.7

If you are using Python 2.7 you can install TDM-GCC and in the Anaconda prompt write

conda install mingw libpython

FFTW

Precompiled libraries for FFTW 3.3.5 are included for both 32 and 64-bit Windows. You should not have to do anything.

Install dependencies

When Anaconda and a C++-compiler is installed, open the Anaconda prompt, and type the following commands to install ASE, cython and the rest of the dependencies:

pip install numpy matplotlib ase
conda install cython scipy

The other required dependencies should be included with Anaconda, otherwise install them using pip.

Install PyQSTEM

When the dependencies are installed, download, compile and install PyQSTEM by writing.

git clone https://github.com/jacobjma/PyQSTEM.git
cd pyqstem
python setup.py install

You might get some warnings which can be ignored.