|R3D, a package for reducing IFS data|
R3D is a package for reducing fiber based integral field spectroscopy data. The purpose of this package is to unify the reduction techniques for the different IFS instruments to a single one, in order to allow the general public to reduce different instruments data in an homogeneus, consistent and simple way.
Although still in its prototyping phase, it has been proved to be useful to reduce PMAS (both in the Larr and the PPAK modes), VIMOS and INTEGRAL data. The current version has been coded in Perl, using PDL, in order to speed-up the algorithm testing phase.
We have translated to C most of the time critical algorithms, and it is our intention to translate all of them. However, even in this phase R3D is fast enough to produce valuable science frames in reasonable time.
Download, Requirements and Installation (Perl Version)
The last stable Perl version of R3D can be download here.
R3D Perl version requires the following perl modules to be installed in your computer:
All this modules can be found at CPAN.
It is recomended the lastest possible version of PDL.
./change_line.pl /home/sanchez/sda1/perl/MY/my.pl DIR/my.plYou can test the scripts by running:
./test_r3d.plIf you do not get any error or warning message you have suscessfully installed R3D. Then, add the directory DIR to your PATH. If you find any problem, please send an email to S.F.Sanchez
Download, Requirements and Installation (C Version)
The last stable C version of R3D can be download here.
It required the Lyon-C library, and PGPLOT with Tcl/tk (basically the same requirements than E3D. To install it:
For binary releases:
1. Download the binary release for your platform into a directory of your choice: (a) Linux 64bits available
(b)Linux 32bits available
2. Unpack the distribution using e.g. tar xvzf R3D_c_linux.gz, this will create a directory R3D containing the R3D programs.
3. Add the new directory to your PATH.
For source code tarballs:
1. Download the last stable version of the R3D distribution (e.g. r3d-0.1.tar.gz) from the list of Downloads and copy it into the Euro3D directory (given by the environment variable IFU_PATH, read the preinstalation requeriments).
2. Extracting the archive via tar xvfz r3d-0.1.tar.gz under the $IFU_PATH path will create the directory e3d-1.3a or a newer version number respectively.
3. Change into the created directory and execute the configure and make scripts:
The make can fail due to a different definition of certain libraries. We have tested the procedure under the two main Linux distributions, RedHat (7.1 and 8.0) and Suse (8.2). They differ in the definition of TCL/TK libraries. You should edit the file add_defs/makedefs.local to select the proper definition of V3D_LIBS for your distribution and add your E3D path to the declaration of the chosen (#HOME) V3D_LIBS as well as to V3D_INC.
4. Add the directory user/bin of r3d to your PATH, e.g. for csh add in .login or .cshrc:
NOTE The command line programs require similar inputs and produce similar outputs in both versions.
R3D C version requires to have installed PGPLOT with Tcl/TK
To reduce fiber-based IFS data it is needed to follow a basic sequence (assuming a bias-subtracted frame and possibly corrected for pixel-to-pixel response variation*):
Typical reduction of PMAS data
Assuming that gbias.fits is the BIAS file, TRACE.fits a continuum illuminated file, and WAVE.fits an ARC frame, the following scripts will reduce the WAVE.fits file (appart from fiber-flat correction) and derive the distortion and dispersion corrrections:
# BIAS subtraction: imarith.pl WAVE.fits - gbias.fits wjunk.fits # BIAS subtraction: imarith.pl TRACE.fits - gbias.fits tjunk.fits # PEAK finding peak_find.pl tjunk.fits 0 5 1 5 2 3.5 0.1 tjunk.peaks # TRACING THE PEAKS trace_peaks_recursive.pl tjunk.fits 0 tjunk.peaks 1 3 0 5 2 tjunk.trc.fits 0 5 # EXTRACTING extract_aper.pl wjunk.fits 0 tjunk.trc.fits 5 wjunk.ms.fits 0 # DISTORTION CORRECTION dist_cor.pl wjunk.ms.fits wjunk.dc0.fits wjunk.dist.txt 0 675 50 2 0 3 1 675 mdist_cor_sp.pl wjunk.dc0.fits 6 30 4 wjunk.dc1.fits wjunk.dist.fits 1 1050 1 # DISPERSION CORRECTION disp_cor.pl wjunk.dc1.fits 3700 3 5 128 5 3 wjunk.disp_cor.fits wjunk.disp.txt 1 mv wjunk.disp_cor.fits WAVE.disp_cor.fitsThese scripts assume that there is an emission line near the pixel 675, and that the final dispersion solution is CRVAL1=3700AA and CDELT1=3AA.
Once reduced the ARC frame it is possible to reduce a science frame (PREFIX.fits), using the scripts:
# BIAS subtraction: imarith.pl PREFIX.fits - gbias.fits junk.fits # EXTRACTING extract_aper.pl junk.fits 0 tjunk.trc.fits 5 junk.ms.fits 0 # DISTORTION CORRECTION mdist_cor_external.pl junk.dc0.fits wjunk.dist.txt wjunk.dist.fits junk.dc1.fits 0 # DISPERSION CORRECTION disp_cor_external.pl junk.dc1.fits 3700 3 junk.disp_cor.fits wjunk.disp.txt 0
We are working on a publication on R3D, and an "User Guide". By now you can quote:
Publications about R3D
Publicatons using R3D
S.F.Sanchez et al.