PyXRD is a python implementation of the matrix algorithm developed for the X-ray diffraction analysis of disordered lamellar structures
Project description
PyXRD
PyXRD is a python implementation of the matrix algorithm for computer modeling of X-ray diffraction (XRD) patterns of disordered lamellar structures. It’s goals are to:
provide an easy user-interface for end-users
provide basic tools for displaying and manipulating XRD patterns
produce high-quality (publication-grade) figures
make modelling of XRD patterns for mixed-layer clay minerals ‘easy’
be free and open-source (open box instead of closed box model)
PyXRD was written with the multi-specimen full-profile fitting method in mind. A direct result is the ability to ‘share’ parameters among similar phases. This allows for instance to have an air-dry and a glycolated illite-smectite share their coherent scattering domain size, but still have different basal spacings and interlayer compositions for the smectite component.
Other features are (incomplete list):
Import/export several common XRD formats (.RD, .RAW, .CPI, ASCII)
Simple background subtraction/addition (linear or custom patterns)
Smoothing patterns and adding noise to patterns
Peak finding and annotating (markers)
Peak stripping and peak area calculation tools
Custom line colors, line widths, pattern positions, …
Goniometer settings (wavelengths, geometry settings, …)
Specimen settings (sample length, absorption, …)
- Automatic parameter refinement using several algorithms, e.g.:
L BFGS B
Brute Force
Covariation Matrix Adapation Evolutionary Strategy (CMA-ES; using DEAP 1.0)
Multiple Particle Swarm Optimization (MPSO; using DEAP 1.0)
Particle-swarm CMA-ES (PS-CMA-ES; using DEAP 1.0)
Scripting support
DISCLAIMER
PyXRD is still very much work in progress. Currently there is no strict development cycle as it is still a one-man project. This also means little time is going into testing and adding new tests for new features. Most of the codebase therefore remains untested at this point and Things May Break as a result.
If you encounter serious bugs please send me the output so we can improve! We’ll try to make a habit out of writing UnitTests for each bug we encounter.
INSTALLATION
As of version 0.5.0 PyXRD (finally) supports standard python packaging, meaning it is available from the [Python package index](https://pypi.python.org/pypi) and has become very easy to install for most Python users.
If you’re not used to (installing) Python software, see below for specific instructions.
DEPENDENCIES
This is what should be present on your system.
Python 2.7.11 (other version may also work, or may not)
Setuptools 1.4.1
PyGTK 2.24.2 or later
Numpy 1.11.0 or later
Scipy 0.17.0 or later
Matplotlib 1.2.1 or later
PyParsing 1.5.7 or later
Pyro4 4.41 or later
DEAP 1.0.0 or later
Additionally, to be able to run the unit tests, you’ll need to install pyton-mock (>= 1.3.0). To just run PyXRD, you won’t need it though.
Windows
There are numereous ways to install python ‘packages’ or software. If you’re a first-time Python user and don’t really care about what way it is installed, just download the most recent bundled installer (PyXRD-x.x.x-win32-bundle.exe) from the github page:
Linux
You’ll need a working version of Python 2.7 and then install all the other dependencies. PyGTK is currently not easily installable from the Python package index, as it needs to be compiled manually (it’s a binding to the GTK libs after all…).
So install these two packages from your systems package manager, terminal commands are given below to achieve that, but you can use your systems package manager if you like that better:
Debian/Ubuntu/…: `sudo apt-get install python python-gtk2`
- Fedora/Red Hat/… (not tested, gime some feedback if this works!):
`sudo yum install python python-gtk`
- OpenSuSE (not tested, gime some feedback if this works!):
`sudo zypper install python python-gtk`
Note: you could also add the Numpy, Scipy and Matplotlib libraries if these are provided by your OS’s package repositories. Sometimes these cause problems when installed using pip (see below).
Once this has been completed, keep the terminal open and issue these commands:
` sudo easy_install pip pip install --user 'pyxrd>=0.7.0' `
As this will install everyting under your ‘~/.local’ folder, you don’t need admin rights for these commands, and you will be able to run PyXRD as a regular user.
To run PyXRD type in the following:
` ~/.local/bin/PyXRD `
If you hate typing curly braces for this purpose, edit/create a .bashrc file in your home_directory and add a line like this: ` export PATH=$PATH:~/.local/bin/ `
Then all installed commands under that folder will be available, and you can start PyXRD by typing just that: PyXRD.
Mac OS X
Currently no support is given for Mac’s. The main problem is getting PyGTK to work under Mac. There has been some succes using MacPorts and the like (from what I can read & tell online), but your milage may vary, and I recommend novice users to switch to either a Windows or Linux PC. It should be possible to get the code running in script-mode, as it has been modified to run on headless (GTK-less) HPC infrastructure recently. Of course this is not a very easy way of working with PyXRD…
CREDITS
[xylib](http://github.com/wojdyr/xylib/) - Has been a great help at unravelling some common XRD formats
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