Find all the lines positions in a spectrum Sergio Sousa This is the README file for the LINESEARCHER code variation from ARES code This package can be found in http://www.astro.up.pt/~sousasag/ares/
If you got this package from another place, please report to sousasag@astro.up.pt or go to http://www.astro.up.pt/~sousasag/ares/ to fill the form to download the latest version of this code.
linesearcher.c - source code for LINESEARCHER input.search - input parameters for ARES README - this file sun_harps_ganymede.lines - example of a output file logsearch.txt - log file from ARES sun_harps_ganymede.fits - Spectrum from the Sun via Ganymede corrected from the radial velocity, taken from: http://www.ls.eso.org/lasilla/sciops/3p6/harps/monitoring/sun.html
cfitsio - CFITSIO - http://heasarc.nasa.gov/fitsio/fitsio.html gcc - GNU Compiler Colection - http://gcc.gnu.org/ gsl - GNU Scientific Library - http://www.gnu.org/software/gsl/
You can see the webpages for each packadge enumerated before.
I have the code running in two different machines. In a PC Desktop with the Fedora Core 5, and in my laptop with the Ubuntu dapper.
In both this cases it was very easy to install the packages required to compile/run ARES C++ code.
For CFITSIO packadge i followed the instruction in the website and installations files of CFITSIO. Careful: Remember where do you set the installation directory...
For the GCC, GSL and plotutils:
In the Fedora Core 5 you can use the YUM to find these packages, or use the graphical interface Package Manager (Add and Remove software) and use the search button to find the packages.
Same in Ubuntu, you can use the APP-GET command, or use the graphical interface Synaptic Package Manager (Add/Remove... in advance mode) and use it to search the packages.
In my computer u use this command to compile ARES, You can try it, but careful with the CFITSIO installation directories...
$gcc -o runsearch linesearcher.c -L/usr/local/cfitsio/lib/ -I/usr/local/cfitsio/include/ -lcfitsio -lgsl -lgslcblas -lm
Note: -L and -I is the location of the libraries and the include files of the cfitsio package.
In case of having problems finding the libraries, you can add the path of the files missed to find (e.g. error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory) to $LD_LIBRARY_PATH.
After the compilation is completed you can create a link into your favorite link directories (e.g. ~/bin)
symbolic link directory.
$ln -s compiledfile ~/bin/runsearch (it is better to use the full paths of both files)
If you have the ~/bin/ in the $PATH system variable then you can run the program easily by typing:
$runsearch
make sure that you have the mine.opt file in the running directory.
specfits : 1D fits spectrum for the analysis fileout : output file for the results lambdai : initial wavelength for the search of the lines lambdaf : final wavelength for the search of the lines smoothder : parameter for the calibration of the search of the lines. Noise smoother for the derivatives. rejt : parameter for the calibration of the continuum position. lineresol : this parameter sets the line resolution of the input spectra. If the code finds two lines closer than the value set for this parameters, then we take the two lines as one line alone.
Detailed description:
To run the code it is necessary to have a file in the system running directory named mine.opt that contains the input parameters with a specified format. The format of this file can be seen below. The input parameters required to run are the following:
-specfits : is the location of the spectra in the FITS format. The header of this file must contain the CRVAL1 and CDELT1 keywords. The spectra should be reduced and calibrated in wavelength. It is supposed that the spectra should have a preliminary normalization to avoid abnormal features in the 1D spectra such the ones that can appear when using reduced echelle spectra. -fileout : the output file. The results for the identified lines are prompted in this file with the following order: the central line wavelength, the depth of the line respectively. -lambdai : initial wavelength of the interval to search the lines. -lambdaf : final wavelength of the interval to search the lines. -smoothder : value of the smooth \textit{boxcar} to use in the numerical derivatives. Value 1 implies no smoothing. -rejt : parameter required to calibrate the local continuum determination. -lineresol : minimum distance in Angstroms between lines in the spectra.
specfits='sun_harps_ganymede.fits' fileout='sun_harps_ganymede.lines' lambdai=6000. lambdaf=6500. smoothder=4 rejt=0.995 lineresol=0.07
6-OUTPUT RESULT('sun_harps_ganymede.lines'):
6012.23 0.82531 6012.45 0.97689 6013.16 0.96213 6013.50 0.49826 6013.91 0.97736 6014.76 0.97985 6014.85 0.97235 6015.25 0.96125 6016.65 0.45574 6018.31 0.93221 6019.38 0.95885 6020.02 0.61637 6020.19 0.45431
Output report: 1st column: wavelength spectra of the line 2nd column: estimated the depth of the line