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xrayutilities

Build Status

xrayutilities is a collection of scripts used to analyze and simulate x-ray diffraction data. It consists of a Python package and several routines coded in C. For analysis the package is especially useful for the reciprocal space conversion of diffraction data taken with linear and area detectors. For simulations code for X-ray reflectivity, kinematical and dynamical diffraction simulation of crystal truncation rods as well as fundamental parameters powder diffraction is included.

Copyright (C) 2009-2024 Dominik Kriegner [email protected]

Copyright (C) 2009-2013 Eugen Wintersberger [email protected]

Mailing list and issue tracker

To get in touch with us or report an issue please use the mailing list (https://sourceforge.net/p/xrayutilities/mailman/xrayutilities-users/) or the Github issue tracker (https://github.com/dkriegner/xrayutilities/issues). When you want to follow announcements of major changes or new releases its recommended to sign up for the mailing list

Contents

  • examples: directory with example scripts and configurations
  • lib/xrayutilities: directory with the sources for the Python package
  • tests: directory with the unittest scripts
  • setup.py: setuptools install script used for the package installation

Installation (pip)

Using the python package manager pip you can install xrayutilities by executing

pip install xrayutilities

or for a user installation (without admin access) use

pip install --user xrayutilities

Installation (source)

Installing xrayutilities from source is an easy process done by executing

pip install .

in the source folder of xrayutilities on the command line/terminal. Directly calling setup.py by

python setup.py install

or

python setup.py install --prefix=<install_path>

is possible but you have to manually ensure that the dependencies are all installed! The first command installs xrayutilities in the systems default directories, whereas in the second command you can manually specify the installation path.

By default the installation procedure tries to enable OpenMP support (recommended). It is disabled silently if OpenMP is not available. It can also be disabled by using the --without-openmp option for the installation:

python setup.py build_ext --without-openmp install

Requirements

The following requirements are needed for installing and using xrayutilities:

  • Python (>= 3.6)
  • h5py
  • scipy (version >= 0.18.0)
  • numpy (version >= 1.9, >2.0 since xrayutilities-1.7.8)
  • lmfit (>= 1.0.1)
  • matplotlib (optional, version >= 3.1.0)
  • mayavi (optional, only used optionally in Crystal.show_unitcell)

When building from source you also might need:

  • C-compiler (preferential with OpenMP support)
  • Python dev headers
  • setuptools
  • pytest (optional - only if you want to run the test environment)
  • sphinx (optional - only when you want to build the documentation)
  • numpydoc (optional - only when you want to build the documentation)
  • rst2pdf (optional - only when you want to build the documentation)
  • sphinx_rtd_theme (optional - only when you want to build the documentation)
  • svglib (optional - only when you want to build the pdf documentation)

refer to your operating system documentation to find out how to install those packages. On Microsoft Windows refer to the Documentation for the easiest way of the installation (Anaconda, Python(x,y), or WinPython).

Python-2.7 and Python-3.X compatibility

The current development is for Python3 (version >=3.6) only. xrayutilities up to version 1.5.x can be used with Python-2.7 as well. Python 3.3 to 3.5 was supported up to 1.6.0.

The Python package configuration

The following steps should only be necessary when using non-default installation locations to ensure the Python module is found by the Python interpreter. In this case the module is installed under /lib[64]/python?.?/site-packages on Unix systems and /Lib/site-packages on Windows systems.

If you have installed the Python package in a directory unknown to your Python distribution, you have to tell Python where to look for the Package. There are several ways how to do this:

  • add the directory where the package is installed to your PYTHONPATH environment variable.

  • add the path to sys.path in the .pythonrc file placed in your home directory

    import sys
sys.path.append("path to the xrayutilities package")

  • simply apply the previous method in every script where you want to use the xrayutilities package before importing the package

    import sys
sys.path.append("path to the xrayutilities package")
import xrayutilities

Obtaining the source code

The sources are hosted on sourceforge in git repository. Use

git clone https://github.com/dkriegner/xrayutilities.git

to clone the git repository. If you would like to have commit rights contact one of the administrators.

Update

if you already installed xrayutilities you can update it by navigating into its source folder and obtain the new sources by ::

git pull

or download the new tarball from sourceforge (https://sf.net/projects/xrayutilities) if any code changed during the update you need to reinstall the Python package. Thats easiest achieved by

pip install .

In case you are not certain about the installation location it can be determined by

python -c "import xrayutilities as xu; print xu.__file__"
  /usr/local/lib64/python3.6/site-packages/xrayutilities/__init__.pyc

if the output is e.g.: /usr/local/lib64/python3.6/site-packages/xrayutilities/init.py you previously installed xrayutilities in /usr/local, which should be used again as install path. Use ::

pip install --prefix=<path to install directory> .

to install the updated package.

Documentation

Documentation for xrayutilities is found on the webpage https://xrayutilities.sourceforge.io

The API-documentation can also be browsed by

pydoc -p PORT

in any web-browser, after the installation is finished.