fabric

Fabric

is a program for data reduction of multigrain diffraction data. This program is presently under heavy development. There are two different versions of the program a Matlab version, which can perform analysis of the orientation distribution of the grain and reconstruct this distribution. Eventually the idea is to calculate reflection profiles and integrate the reflections by a fitting procedure. The Matlab version has a number of limitations e.g. only two detector file formats are supported and no correction for detector imperfections.

The python program determines the spot positions with crystalline grains with known orientation and unit cell dimensions. Checks for possible overlaps between spots and harvesting the intensity in the area around the calculated reflection position. Finally the intensity is integrated and an file is written with Miller indices, reflection intensities and an estimated uncertainty, Presently the integration method is quite crude - just summation of the pixels inside the user defined shoebox area.

All detector formats implemented in FabIO are supported.

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Installation

The program can be downloaded from the Fable page on sourceforge.net. Presently the code has been distributed as a zip package or a compressed tarball of the source code. Download either one and unpack it.

e.g.
tar xvzf fabric-0.0.1.tar.gz
or
unzip fabric-0.0.1.zip

a files are unpacked into the directory fabric-0.0.1. To install these do

cd fabric-0.0.1

and install fabric with (most likely you will need to be done with root privileges, e.g. put sudo in front of command)

python setup.py install

The newest development version can be obtained by checking it out from the subversion (SVN) repository. Do

svn co https://fable.svn.sourceforge.net/svnroot/fable/fabric

Python and python modules needed

The installation of modules is easiest if Python 2.4 or later is installed. Since precompiled and installation ready versions are available of all the needed python modules.
For full functionality of fabric the following modules need to be installed.

• FabIO? (FABle Input Output library) - OBS You have to use the numpy version of FabIO - found presently only on subversion. Do the checkout shown below and go to the directory fabio/branch/numpy and run python setyp.py install.
• ImageD11
• PIL (python imaging library) - http://www.pythonware.com
• numpy - http://www.numpy.org

SVN branch of FabIO is available at

svn co https://fable.svn.sourceforge.net/svnroot/fable/fabio

Ubuntu specific installation details

To run fabric (if you already have a running version of ImageD11 or fabian you have probably installed all the needed packages) on Ubuntu (a linux distribution based on Debian) most of the python modules can be installed either through the Synaptic Package Manager (found in System -> Administration) or using apt-get on from the command line in a terminal.
The extra ubuntu packages needed are:

• python-imaging
• python-imaging-tk
• python-numpy

using apt-get these can be installed as:

sudo apt-get install python-imaging python-imaging-tk python-numpy

using Synaptic Package Manager:

**search** to find the specific ubuntu packages instead
**mark** them for installation
**Apply** to install

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Running fabric

Create an input file with your favorite editor and run fabric.

fabric.py -i name.inp

In version 0.0.1 this command read the input, check whether all needed input has been provided before determination of
reflection positions. These are saved in files with extension .ref.

• filestem_gr0000_set0000.ref
• filestem_gr0001_set0000.ref
• etc

The shoebox information is saved in .hst files

• filestem_gr0000_set0000.hst
• filestem_gr0001_set0000.hst
• etc

The shoeboxes can be analysed with plothst.py

plothst.py -n <filestem> -D <directory of hst files> -g <grain no> -r <refl no>

before doing the integration with

integrate.py -n <filestem> -D <directory of hst files> -g <grain no> -r <refl no>

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Input file

In the input file all parameters needed to perform the integration is given. Here the different parameters shown and explained.

Java GUI

The Fabric program may now be launched from the Fable GUI. A basic version with most of the above functionality has been implemented (May 2009) and will continue to be developed in the near future.

Status

Essentially the complete functionality of the fabric.py and plothst.py scripts is available in the Fable GUI (via the fable.fabric plug-in). The integrate.py script remains to be included, but should pose no great difficulty as its implementation is expected to be simpler than the other two.

Usage

Firstly one should open the Fabric perspective from the GUI drop-down menu. One should see a Navigator pane on the left and the Fable output console on the bottom-right. Add a project directory to Navigator. The directory should either already contain a Fabric input file, <filename>.inp, or one should be created there from scratch (right click > New > Other > File ...). Open the file (if not already opened at its creation) by double clicking on it. The editor highlights keywords and comments in different colours. Complete as necessary and save via the right-click menu. (Make sure that the relevant image files and directories referred to in the input file are all present and correct.) When an input file is open in the editor the Run button for the fabric.py script appears on the GUI's toolbar. Push the button to run the script and note the informational output in the console.
To run the plothst.py script open the Plothst view (Window > Show View > Other > Fabric > Plothst). This will first show some controls corresponding roughly to the command-line arguments and the Tk GUI above, underneath which is a space for informational text and statistics relating to the shoebox to be displayed. Enter (or browse to find) the directory containing the .hst files, and enter (or browse for) an example file from which the file-name stem is obtained. Choose desired grain and reflection numbers and push the Display button. An ImageViewer will open up with the shoebox images as in the Tk GUI, but with extra functionality. It is useful to move the Plothst and ImageViewer panes to convenient places within the Fabric perspective for comfortable viewing.

To do

Fabric:

• Connect remaining dummy Fabric menu and tool-bar buttons to their respective functions. (The functionality itself is already available as per the instructions above.)

Plothst:

• Connect dummy Plothst menu and tool-bar buttons. (Functionality is already available.)
• Tweak the shoebox display image (?).

Integrate:

• Implement the integrate.py script.