====== Linux software kit installation ======

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 procedure below was tested with a recent Windows laptop. We proceed as follow:
  * Install a linux Ubuntu virtual machine
  * Set-up anaconda
  * Install the multigrain software suite within anaconda

You may be able to run this in windows only. This was not tested.

===== Install a linux Ubuntu virtual machine =====

There are many tutorials on how to do so on the internet. Here is a quick summary of how we proceeded
  * Download and install VirtualBox from [[https://www.virtualbox.org/]]
  * Download a recent Ubuntu Desktop linux from [[https://ubuntu.com/download/desktop]]
  * Install Ubuntu within a VirtualBox virtual machine

===== Anaconda =====

Anaconda is a distribution of the python and other programming languages for scientific computing. It makes it much easier to install and manage packages without messing up your environment or interfering with the operating system.  

Download Anaconda from [[https://www.anaconda.com/products/distribution]] 
Install anaconda
	sh Download/Anconda……. (change file name according to what was downloaded)
Keep note of where anaconda will be installed, typically ''/home/myhome/anaconda3''

Keep note of the instructions at the end of the anadonda installation as you may have to type those commands each time you start a new terminal. In our case
	eval “$(/home/myhome/anaconda3/bin/conda shell.bash hook)”
	conda init

===== 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!