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processing:minimal_software_intallation

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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!

processing/minimal_software_intallation.1786349446.txt.gz · Last modified: by smerkel