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ImageD11

Installing ImageD11

Necessary Hardware and Software

First of all, you will need Linux, either as a separate harddrive (with lots of memory space) or as a virtual machine on your Windows/Apple computer. In case you are not familiar with Linux, ask your administrator for help and maybe do an online crash course to learn basic navigation and so on.

Having Linux is a good start, but not enough. You will also need a couple of other programs. When you click on the Fabian homepage and scroll down, there is a list of all the stuff you need in order to run Fabian properly. Most of the computers, which were working with Linux before, usually have installed most of these software/libraries already. But if you got a brandnew Linux from your IT guys, there is usually only the very basic stuff on it.

Now you have two options:

  1. Download and install all these packages one by one or
  2. Download and install Anaconda.

The benefit of Anaconda is that it contains most of the necessary libraries and you are done with installations within 5 minutes. There are also several other advantages coming with Anaconda (for example the installation assistant for GrainSpotter).

Installation

Go to the homepage and click on the green button “clone or download”. Click on “Download ZIP”. After the download is finished, navigate to the “Downloads” folder and unpack the ZIP folder to a directory of your choice.

Open the Konsole and navigate to the unpacked Fabian directory. There should be a folder called “setup.py”. Type the following to the Konsole:

  python setup.py build

If you get an error, there might be some of the additional libraries still missing.

Be aware that the Konsole is now occupied with running Fabian. You have to open a second Konsole window if you want to do something else with the Konsole.

Starting the software

Open the program by going to the folder where the processed data is stored. Now open the program by typing the following to the Konsole:

  ImageD11_gui.py

ImageD11 is written and maintained by John Wright from ESRF and has an extensive manual available here https://pythonhosted.org/ImageD11/.

When you try to open the program for the first time there is usually an error: “cannot find module FitAllB.conversion”. This error occurs due to a bug in FitAllB, which you have to fix manually. This is how to to it (AFTER you installed FitAllB, of course):
Go to the FitAllB directory and try to find the missing file conversion.py. It should be in a directory like this:

  ../FitAllB-master/FitAllB/

Look again at the error message in the Konsole which tells you the exact path of where

Basic instructions

The program should open. In ImageD11 go to Transformation, then Load filtered peaks and choose the .flt file you would like to see (You automatically should be in the right folder.).

Then go to Transformation and plot y/z. You should see a 2D diffraction image of all the spots which passed the threshold. From now on, we call this image diffraction plot. You should remember, which file you opened, because ImageD11 doesn't show this anywhere.

ImageD11 can show only one diffraction plot at once. If you want to compare two (or more) diffraction plots, you can either save the plots (as .png file) or open a new ImageD11 in a new tab of the Konsole.

software/imaged11.1530871094.txt.gz · Last modified: 2019/02/18 10:11 (external edit)