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Table of Contents
Getting started with a Python environment
There is a whole suite of software required to run multigrain X-ray diffraction, and their installation procedure can be quite tricky if you are not comfortable with computing techniques.
The recommended method is to install a python dedicated environement. This has been tested on Linux, but should also work on mac and windows, if you have a working python installation (Instructions from a Windows user would be most welcome).
It is best to create and activate a virtual python environements dedicated to 3D-XRD. A virtual environment in Python is an isolated environment on your computer, where you can run and test your Python projects, without interfering with the main python installation or the rest of your computer system.
See instructions at https://www.w3schools.com/python/python_virtualenv.asp and many other places online.
Typically this is done by
Creating a dedicated folder
Move into this folder, and create a dedicated python environment for 3D-XRD work
python3 -m venv .venv
Activate the environment:
source .venv/bin/activate
Install ESRF data analysis tools, fabio, silx, and ImageD11
Within a terminal in which anaconda is activated
pip3 install fabio pip3 install silx pip3 install ImageD11
Install additional packages by hand
Fabian
Fabian is very handy to visualize diffraction images, figure out detector orientations, identify parameters for peak extraction, etc. It is an old piece of software, but there is not real replacement at this point.
Start by installing the Pmw libray, which is required by fabian
pip3 install Pmw
Create a folder for additional software somewhere on your hard disk, called Fable-3DXRD for instance. Move into this folder and create a clone of the repository at github
cd ~/Fable-3DXRD git clone https://github.com/FABLE-3DXRD/fabian.git cd fabian python3 setup.py build python3 setup.py install
Next time, if you want to update your installation of fabian with a new version, you will not need to clone the directory. You will move into your folder and update it:
cd ~/Fable-3DXRD/fabian/ git pull python3 setup.py build python3 setup.py install
We did have a problem while install fabian, which was calling some obscure functions with OpenGL. Move looked into the fabian source code to de-activate those functions. This should be documented somewhere but we did not do it yet.
PolyXSim
If you want to simulate data for training, you need will PolyXSim. The procedure is very similar to that we used for fabian. If you never installed PolyXSim:
cd ~/Fable-3DXRD git clone https://github.com/FABLE-3DXRD/PolyXSim.git cd PolyXSim python3 setup.py build python3 setup.py install
If you need to update PolyXSim:
cd ~/Fable-3DXRD/PolyXSim git pull python3 setup.py build python3 setup.py install
TIMEleSS-tools
The TIMEleSS-tools include many helpers, guis, etc that were developed along with this tutorial. You will probably need them.
If you never installed the TIMEleSS-tools:
cd ~/Fable-3DXRD git clone https://github.com/FABLE-3DXRD/TIMEleSS.git cd TIMEleSS python3 setup.py build python3 setup.py install
Otherwise, if you simply want to update your local copy:
cd ~/Fable-3DXRD/TIMEleSS git pull python3 setup.py build python3 setup.py install
Grainspotter
Grainspotter is often used to index grains. It is available on conda:
conda install -c fable grainspotter
Wrap-up
If you made it here, you are done! You can follow other pages of this wiki to get started. Good luck!
