fabian

Introduction

Fabian (Fable image analysis) has been developed in order to make a program for analysing, which allows for easy browsing through a series of diffraction images, without having to load a full images series into memory before being able to do so. Furthermore we wanted to make a program which could be used free of charge. Fabian is written in python using various python modules. At this stage fabian only has limited set of Tools available as seen below.
We kindly ask users to submit bug reports and/or feature requests to the fable sourceforge fabian tracker, under the categories Bugs and Feature Requests respectively. We do check it and someone will do something about your particular issue in a not too distant future.

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 fabian-0.7.0.tar.gz
or
unzip fabian-0.7.0.zip

a files are unpacked into the directory fabian-0.7.0. To install these do

cd fabian-0.7.0

and install fabian with (most likely you will need to be done with root privileges)

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/fabian

If all needed python modules have been installed in should be possible to say e.g.:

fabian.py my_image0001.edf

Python and python modules needed

The installation of modules is easiest if Python 2.4 or later (Python 2.5 and 2.6 ) is installed. Since precompiled and installation ready versions are available of all the needed python modules.
For full functionality of fabian the following modules need to be installed.

• FabIO? (FABle Input Output library)
• PIL (python imaging library) - http://www.pythonware.com
• numpy - http://www.numpy.org (Fabian 0.5 and onwards)
• Pmw - Python Mega Widgets - http://pmw.sourceforge.net
• pyopengl (2.0.0.44) - http://pyopengl.sourceforge.net
• Matplotlib - http://matplotlib.sourceforge.net

The first five modules are mandatory and the latter two are optional, but if left out some of the tools will not work. SVN branch of FabIO is available at

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

Ubuntu specific installation details

To run fabian (and ImageD11) 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-matplotlib
• python-numpy
• python-pmw
• python-opengl

using apt-get these can be installed as:

sudo apt-get install python-imaging python-imaging-tk python-matplotlib python-numpy python-pmw python-opengl

using Synaptic Package Manager:

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

unfortunately a small part, opengl tk interface togl, of the python-opengl is broken in Ubuntu 7.04 (Feisty Fawn) and Ubuntu 7.10 (Gutsy Gibbon), In Ubuntu 6.06 LTS (Dapper Drake) this problem does not exist. Fortunately thereis a way around this.

Install Togl

Jon Wright made this recipe for version 7.04:
Obtain and build Togl, e.g.:

$ cd
$ wget http://downloads.sourceforge.net/togl/Togl-1.7.tar.gz?modtime=1136507319&big_mirror=0
$ tar -zxf Togl-1.7.tar.gz
$ cd Togl-1.7
$ ./configure -with-tclconfig=/usr/lib/tcl8.4/tclConfig.sh --with-tkconfig=/usr/lib/tk8.4/tkConfig.sh
$ make

... you need a variety of "dev" packages for this to work.

• tk8.4-dev
• tcl8.4-dev
• libxmu-dev
• maybe more (e.g. GL header files) need a new clean dist to test, please send a mail if you of packages missing in the list.

Install these packages with apt-get or Synaptic Package Manager as described above.
When the Togl library has been succesfully compiled you just need to replace:

/usr/lib/python2.5/site-packages/OpenGL/Tk/linux2-tk8.4/Togl.so

with:

~/Togl-1.7/libTogl1.7.so

by:

$ sudo cp ~/Togl-1.7/libTogl1.7.so /usr/lib/python2.5/site-packages/OpenGL/Tk/linux2-tk8.4/Togl.so

On Ubuntu 7.10 the last part is not working. Since there is no such file already. Instead one should do the installation using make:

sudo make install

Easy or what ?

Main window

Menu bar

The menu bar is fairly simple. At present (release 0.5) it has six main items - File, Tools, Image, CrystTools, History and Help.

File

• Open... [short cut: o] - Open a new image
• Auto file update [short cut key: f]- if chosen fabian will automatically continue to load the next image in the directory. This can be used to look through a series of images as a "movie" and to let fabian show newly collected images as theay saved by the device server. The speed of update can be altered by Arrow up(faster)/down(slower).
• Quit [short cut: q]

Tools?

Tools

is the most important item. Four different tools can be chosen and their functions are all (well one at the time) bound to mouse button 1 for choosing an area-of-interest (AOI). All the tools below, can also be used in the zoom windows. The zoom function is always possible using mouse button 3.

• Zoom (default tool) [short cut: F1]- a zoom (4 times) of the AOI is shown in a new window.
  • z (mouse scroll up) will rezoom by a factor of 2
  • x (mouse scroll down) will rezoom by 0.5.
• Line profile [short cut: F2] - a line profile is plottet
• Integr. profile [short cut: F3]- projection of the intensity in the box on the horizontal and vertical border
• 
• Relief [short cut: F4] - a 3D relief map of the chosen AOI is shown.
  • Mouse button 1: translate plot
  • Mouse button 2: rotate plot
  • Mouse button 3: scale plot
• Rocking curve [short cut: F5] - The intensity of pixels in the AOI is integrated for a series of files. The series can either be chosen as +/-X frames, or by giving a specific start and end frame number
• 

Image

The image menu is intended to be for various image operations.

• Tranform - Possibility to make the following image transformations
  • Flip horizontal
  • Flip vertical
  • Rotate 90
  • Rotate 180
  • Rotate 270
  • Reset - will deselect all tranformations and show the image in the original setting

The transformations are implemented such that if a transformation is selected a second time it means deselect the operation. The transformations will be applied to newly loaded images as well until reset is chosen.

CrystTools

• Peaks...
  • Show [short cut: p]- show peaks overlaid found with peaksearch from ImageD11. If you wish load another peak file clean the memory for knowledge of the old by pressing "c" for clean. p toggles the between peaks overlaid or not.
  • Options - a few options for showing the peaks - color of outline, radius of outline circle, and a minimum peak size (in pixels).

History

Image history - easy way to open formerly analyzed images. The list shows the 20 last loaded images.

Help

• Help [short cut: h] - Link to this page
• About [short cut: a] - well not much to say

Image canvas/Image information

Notebook pages are used for easy access to both the diffraction image and the header information.

On this page it is possible to change scale and diffraction image shown above the diffraction image itself. fabian will update all zoom, line profile and relief plot windows upon changing scale or diffraction image. In the bottom of the this page the minimum, maximum and mean pixel values are shown to the left and to the right the zoom factor of the canvas is shown together with the pointer position and intensity of the pixel at this pointer position.
[
The image header information notebook page ordered alphabetically
As mentioned above, this notebook page shows all header information. Choosing a header item will make the item and its value appear just under the diffraction image, in the Image tab, such that it can be followed when browsing through a file series.

Key short cuts

o - open new file
q - quit application
a - see "help - about"
h - see "help - help"
z - zoom in
x - zoom out
p - show/hide peaks found by ImageD11 peaksearch
c - clear peaks from memory
f - activate/deactivate "File - auto file update"
up-arrow - add 0.5 sec. to time delay between loading files in auto file update mode
down-arrow - subtract 0.5 sec. from the time delay between loading files in auto file update mode
F1 - activate zoom tool
F2 - activate line profile tool
F3 - activate intensity projections on vertical/horizontal box sides
F4 - activate relief plot tool
F5 - activate rocking curve tool
right arrow - next image
left arrow - previous image