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5. Data analysis with spectra
Spectra is a beamline control and data analysis program written by
Thorsten Kracht from Hamburger Synchrotronstrahlungslabor at Deutsches Elektronensynchrotron. It is widely used at Institute for Scattering Methods for data
analysis because it uses the fio standart for data files defined at
Hamburger Synchrotronstrahlungslabor. Therefore, to keep the compatibility with data taken at
Hamburger Synchrotronstrahlungslabor it was decided to implement Spectra as the standart data
analysis program at the 6ID-D Side Station.
Spectra is installed on all unix mashines belonging to the sidestation.
It is not recommended to use it directly on the beamline computer.
For use together with data created at the 6ID-D Side Station there are the
idduser accounts at idefix.mu.aps.anl.govand mar.mu.aps.anl.gov. For use together with data created
at the 6ID-B Main Station there are the useraccounts user at idefix.mu.aps.anl.govand
idbuser at mar.mu.aps.anl.gov.
Spectra is only running when a X-connection is available for graphics
output. To start spectra enter the command spectra in any
5.1 Getting spectra to run properly
Example for a typical spectra picture of
a data set. Here scan align04_856.fio is shown, a
of a Si powder sample measured at 100 keV. The detector signal
is shown in the lower left corner, the monitor signal and the ring current
in the upper left corner and the sample temperature and for example a fluorescence
measurement on the right. In addition information about the scan in general,
the peak in the detector window and averages of the other for data sets displayed
When Spectra is invoked it automatically reads the file
spectra_ini.gra from the actual directory. If this
file is not present it tries to read the spectra_ini.gra
file from the home directory of the user. In all of the above mentioned
accounts a spectra_ini.gra file is present in
the home directory. Normally no changes to the spectra_ini.gra
file are necessary.
spectra_ini.gra calls a file named set_names.gra
which has to be present in the directory from which Spectra was started.
In this file it is defined which information of the scans is plotted and what
the filenames to look for are.
To get spectra running this file has to be adopted to your setup of
spec. The first block in this file contains definitions which enables
the macro to access the data files created during the beamtime.
In addition five more symbols have to be defined:
= [[ .data]] Gives the directory where the fio files are
copied from the beamline computer. Please use exactly this notation, marks
the home directory of the user so in this example it links to /home/idduser/data/
if idduser is the username. Relative links are not permitted.
- filename = "align04_"
- A filename is assigned. Thus files named
align04_xxx.fio will be analysed where xxx is replaced by scan_number which is
only initialised in set_names.gra and can hold any integer
- get_zone = "firstname.lastname@example.org:/export/home/spec/hp/data/"
a fio file is not present in the directory given by store_zone Spectra tries
to copy it from the directory given in get_zone. Here the format is
user@computer:directory/, the usual format for the scp command.
This way the user can chose wich information is displayed in which window. The symbols
have to have the exact names given in this example, than the name of a column out of
the spec data sets is assigned, for example det. If the symbol is not defined nothing
will be displayed except a column with the same name exists in the spec data sets.
Once these definitions are made at the beginning of a beamtime normally no changes
are necessary any more.
- detector = det
- monitor = mon
- current = cur
- countera = coa
- temperature = DegK_sample
5.2 Commands usefull for data analysis
Spectra is a very powerfull programm with lots of possibilities to treat
data. But it takes some time to get used to its commands. This short manual
is in no way intended to replace the Spectra manual which can be found
on the Hamburger Synchrotronstrahlungslabor web pages. In this section four commands will be explained
which allow even users without any experience to display and print their data
to be able to check the progress of their measurements during the experiment.
All these commands are symbols which are defined in spectra_ini.gra. You can
not make changes directly to these programs because on the computers for data analysis they are stored
in the directory /home/hupfeld/common/. You have to copy these macros to a directory of your choice
and modify them there. All you have to do afterwords is to change the symbol definitions in
spectra_ini.gra so that they are now pointing to your directory. Please do not
change the spectra_ini.gra file in the home directory. Copy it to your directory
and make the changes there. If you start Spectra from your own directory with a
spectra_ini.gra file present the one in the home directory will not be read.
Same rule applies for the set_names.gra file.
- single xxx
- displays the scan with number xxx as seen in figure 5.1.
If no number is given the scan following the last scan displayed will be shown
- multi xxx
- multi searches the hard disk for the highest scan number and than waits
for the next arriving scan. Once this scan arrives it is displayed and multi waits
for the next scan. The program can be aborted by hitting the space key. It is only necessary
to supply a number xxx if there are already several thousand scans on the hard disk and
you do not want the program wasting time with finding the last number. If xxx is supplied the
search starts with xxx (auto_plot_6idb.gra).
- the actual content of the graphic window of Spectra is send to the beamline
- Shows the actual configuration which was done in set_names.gra
as described in section 5.1. This command also shows the status of two more
variables: yeslaser and nolaser. The choice of names has historical reasons. If the variable
yeslaser is defined (just assign any number at the commandline, for example yeslaser=42) every
scan displayed by single or multi will automatically be printed on the beamline printer.
If nolaser is not defined (to revoke a definition type nolaser= at the command line), a
postscript file will be created for each scan with the same name and in the same directory of
the fio files with extension ``.ps'' (settings_spec.gra).
- This gives a short help and shows some variables (hilfe_spec.gra).
- This command should not be called by users. This is the macro which displays the
scans and it is called by single and multi (after_spec.gra).
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Previous: 4. spec