Software useful for synchrotron users (ESRF, ...)

Contents:

 

unspec: parser of spec files

This program is being written (updated, fixed, extended, ...) since our first experiment at the ESRF in 1993 (?) until nowadays. The text below is a copy from my freeware page.

unspec

Unspec decomposes (splits) data files created by the program spec (by Certified Software; hm, they have no such a command-line drive convertor) and it extracts scans from these data files. I think that unspec has more options than the specex program by ESRF; moreover, unspec comes with the source code thus it is available for any platform. Further, unspec supports also PSD/MCA scans inside or outside the spec file.

You may know that spec is a program to driver diffractometers and other staff at beamlines, used e.g. in the ESRF.
[Version 18. 1. 2017]    [What is new: select scan types for output; support for multiple MCA's during measurement.]

spec macros

The following are my favourite macros, developed over time measuring at the ESRF. You can "install" them yourself via e.g. qdo stepscan.mac, but it is a good idea that these macros become loaded automatically on spec startup (ask your beamline local contact).

File stepscan.mac contains these commands:

File dtp_cen.mac contains these commands:

File stepscan.mac was written by me, file dtp_cen.mac by Daniel Luebbert and updated by me. You can use them as you like, but don't change their names please.

Readers and workers for ESRF Data Files (EDF, EHF)

EDF/EHF files mean ESRF Data (Header) Files; currently they are used at the ESRF for storing and dealing with data from two-dimensional detectors (cameras). They contain a text header (multiple of 512 bytes, usually 1024 bytes), followed by the binary data (EDF) or with the binary data in another file (EHF).

The official documentation for this format from the ESRF.

The following summarizes my contributions to the EDF reading/analyzing/writing open-source software.

 

Applications: gnuplot

Gnuplot 4.2 and higher contains two new features which enable reading and displaying edf files: See gnuplot 4.2 image demos for a screenshot. What are the advantages of using gnuplot for displaying edf files? Axes and annotations: you can use all the other well-known gnuplot commands to annotate your graph or to print it to many output formats (postscript, png, epslatex, fig, ...).
What are the disadvantages? Gnuplot is not a typical bitmap-image drawing program, and thus it is a bit slower in displaying very large images on screen.

You can draw edf files with this command: 

plot "data.edf" binary filetype=edf with image
plot "data.edf" binary filetype=auto with image
or 
set datafile binary filetype=auto
plot "data.edf" binary with image

It is useful to have a script file plotedf.gp in your path which contains commands 

set autoscale fix
set tics out
set grid front lt 6
set datafile binary filetype=auto
plot "$0" binary with image
then you can easily 
call "plotedf.gp" "data.edf"

Hint: you can also put line 

set datafile binary filetype=auto
into your $HOME/.gnuplot (gnuplot start-up file).

You can have a look into breaders.c how I coded gnuplot reader of .edf files in C.

 

Applications: zimg

Program zimg by Johannes Zellner generates bitmap images (gif, png, jpeg, ppm, pgm) from arbitrary formatted two-dimensional ascii or binary data. It can also read EDF/EHF files.

I have added a possibility to use for generating movies from a series of edf files. See what man zimg says: 

  zimg -P -o- --scale=0.25 --gray *.edf | convert -delay 100 - movie.mng
        read all edf files, scale them down and convert them into a gray scale movie
        (mng is an animated png). Note that not using --crange makes color scaling
        (z-range) individually autoscaled in each image instead of using the same
        z-range for all images as in the previous example.
Some other similar commands are: 
  zimg -P -o- --scale=0.25 --gray *.edf | animate
  zimg -P -o- --scale=0.25 --crange=100,2000 *.edf | convert -delay 333 - movie.gif

 

Hints for *.edf and *.ehf files associations

Often you use some kind of a file commander to browse your filesystem. Here are some hints for file associations of *.edf and *.ehf by means of zimg:

Midnight Commander (any OS): Go to menu Edit extension file or to file $HOME/.mc/bindings and add there:
# edf, ehf
regex/\.e[dh]f$
        Open=zimg --gray %f | xv -
        View=zimg %f | xv -
Note that you can add --cbox and --statistics options, if you like to see more information on your screen.

File Commander (OS/2, Windows): Go to menu File associations or to file fc2.ini / fcw.ini and add there:
*.{edf,ehf}: (zimg -o c:/tmp/zimg$.png !) && (start C:\Apps\Graphics\IrfanView\i_view32.exe c:\\tmp\\zimg$.png)

 Under OS/2, use path to PMView instead of Irfan View.

Under file managers which honor MIME types (e.g. Konqueror), I recommend to add new MIME type image/x-edf associated to *.edf and *.ehf  files with commands like in the Midnight Commander above.

 

Applications: ImageJ plug-in

ImageJ is an open-source application for image data analysis. Being written in Java, it is portable to numerous platforms. It is very efficiently written and it is very fast.

Plug-in ESRF Reader for reading EDF files was originally written by Olof Svensson, then recoded by me. Download the ESRF_reader from here. (The source code is in Java, of course.)

How to use it: copy the class file into ImageJ's plugin directory. Then you can read EDF files when going into menus Plugins / Input-Output / ESRF Reader.

Hmm, I wonder the plugin is not on ESRF web page?

Note: there is an ImageJ plugins repository, maybe this plugin could be contributed there?

 

Source codes: pmedf package for GNU Octave and Matlab

Note: GNU Octave is an open source GPL variant to the commercial Matlab. They are cca 99 % compatible; mainly (if you miss something, then get an Octave-forge package.

Package pmedf (version: February 28, 2017) is a package for dealing with ESRF Data and Header Files .edf / .ehf (and .edf.gz/.ehf.gz).

Note: here is the previous version (version: August 11, 2010).

Advantages of pmedf:

Features:

See here some examples.

Last change: January 2017