# "@(#) $Id: README 2844 2015-11-17 13:46:05Z jpritcha $" README file for J.Pritchard's ESO-MIDAS FEROS Data Reduction System Environment This archive (jFEROS-DRS.tgz) contains the J.Pritchard's *personal* version of the FEROS Data Reduction System MIDAS scripts plus various helper scripts and c code. It is derived from version v1.61 of the official FEROS-DRS.tgz available from: http://www.ls.eso.org/lasilla/sciops/2p2/E2p2M/FEROS/DRS/index.html I develope this personal version of the FEROS-DRS (jFEROS-DRS) for my own benefit. I make it available to the public via my web site: http://www.hq.eso.org/~jpritcha/jFEROS-DRS/index.html Of course I give no guarantee of its suitability for your needs or its scientific efficacy and neither I nor ESO accepts any responsibility for data loss, hardware loss, or loss of any otherkind resulting from its use in any way, shape or form. None the less, if you use my version, I of course expect suitable recognition in any resulting publication. If you ask for my help and/or advise and any such help and/or advise is useful, then I expect to be included as a co-author in any resulting scientific publication. Table of contents ================= 0.0 Requirements 1.0 Installation 1.1 Shell configuration 1.2 Screen Colour Depth 1.3 Graphic and display windows 2.0 Use 2.1 Prepare the data directory 2.2 Extract the data from the Archive CDs 2.3 Run the DRS 2.4 General Controlling Environmental and/or MIDAS variables 2.4.1 Pack Reduced files 2.4.1.1 Sorting Packed Red files by Target 2.4.1.2 Cleaning Up after packing 2.4.2 Make HTML summary pages 2.4.2.1 Submit convert commands into background 2.4.3 Choice of filenames for FITS versions of DRS products 2.4.4 Creation of RAW image PS/PNG files 2.4.5 AutoInit 2.4.6 Extract Non-Flatfielded spectra 2.4.7 Merge DRS Product FITS into EXTENDED FITS 2.4.8 Use MODIFY/COLUMN instead of @@ colmean 2.4.9 Expected Number of orders in Initialisation 2.4.10 Reduce All Images 2.4.11 Background Subtraction 2.4.12 Input FITS file extensions 2.5 Observatory Specific Controlling Environmental and/or MIDAS variables 2.5.1 Make Quality Control Plots 2.5.2 Inclusion of FFHV TCCD images in DRS tar files 2.5.3 Concatenate tar files 2.5.4 Process DRS Products for QC 2.5.5 Archive DRS tar files in ESO Science Archive 2.5.6 Display QC web pages after init... 2.5.7 Keep Intermediate MT files 2.6 Multiple Extension FITS files 2.7 Timezone 2.8 Cross Correlation Functions 2.9 Running in an esorex environment Appendix 1: DRS Product filename conventions Appendix 2: Shell Variables Appendix 3: Installation on w2p2off Appendix 4: MIDAS variables Appendix 5: Dependant software ================================================================================ ================================================================================ 0.0 Requirements ================ The scripts have been prepared originally under Linux, and more recently under Mac OS X with a view to portability. They are tested regularly within these two environments. Several scripts rely the WCS-Tools package, CFITSIO and PGPlot which are all incldued in SciSoft. http://www.eso.org/science/scisoft/ If you do not have and/or do not wish to install SciSoft then they should be installed independantly (See Appendix 5). The wget tool is used by in the Makefile in the src directory. wget is a standard part of most Linux distributions. For Mac OS X it is available as a standalone Cocoa Applet from: http://e.cocoawget.nobody.jp/ or as part of Fink or MacPorts/DarwinPorts. Alternatively you can download the required packages manaully. A complete list of packages to be downloaded is given in Appendix 5. Please report any problems you experience with the MIDAS scripts or the other files in the archive to: j.pritchard@eso.org ================================================================================ 1.0 Installation ================ Normally this archive should be extracted into the user's home directory, though you may want to extract to a dedicated subdirectory to avoid the possibility of overwriting already existing files. In the following it will be assumed the user creates a directory FEROS-DRS in their Home directory in which to extract the file: mkdir $HOME/FEROS-DRS cd $HOME/FEROS-DRS tar -zxvf /jFEROS-DRS.tgz or alternatively... gzip -dc /jFEROS-DRS.tgz | tar -xvf - This should produce eight directories and this README file... README bin dat fmt html lib midwork saved_session src Assuming you have and use SciSoft, then: Build src code: *) For tcsh: setenv FEROS_DRS `pwd` cd src setenv PERL5LIB ${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl setenv CFITSIO /scisoft setenv PERL `which perl` setenv PGPLOT /scisoft You may also need to set the folowing vaiables to appropriate values for your system: MIDASHOME, MIDVERS. make PMs make all install If you wish to use the new PERL script for cross-correlation you will also need to do: make XPMs *) For Bash: export FEROS_DRS=`pwd` cd src export PERL5LIB=${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl export CFITSIO=/scisoft export PGPLOT=/scisoft export PERL=`which perl` You may also need to set the folowing vaiables to appropriate values for your system: MIDASHOME, MIDVERS. make PMs make all install If you wish to use the new PERL script for cross-correlation you will also need to do: make XPMs 1.1 Shell configuration ======================= Once the software is installed, you will need to set several environment variables. The following are the basic minimum. Others are detailed in the sections that follow, and the complete lists are sumarised in Appendix 2. *) For tcsh, add the following lines to .cshrc (or .tcshrc): setenv FEROS_DRS "${HOME}/FEROS-DRS" setenv FEROS_MIDWORK "${FEROS_DRS}/midwork" alias inmidas.feros "inmidas -m ${FEROS_MIDWORK}" setenv PATH ${PATH}:${FEROS_DRS}/bin if ( $?PERL5LIB ) then setenv PERL5LIB ${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl else setenv PERL5LIB ${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl endif *) For Bash, add the following lines to .bashrc export FEROS_DRS="${HOME}/FEROS-DRS" export FEROS_MIDWORK="${FEROS_DRS}/midwork" alias inmidas.feros="inmidas -m ${FEROS_MIDWORK}" export PATH=${PATH}:${FEROS_DRS}/bin export PERL5LIB=${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl To get MIDAS running in a nice blue separate xterminal just like at the telescope use the following for you inmidas.feros alias: *) For tcsh, add the following lines to .cshrc (or .tcshrc): alias inmidas.feros "xterm -ls -bg blue -fg white -geometry 80x34+0-6 -fn 8x16 -sb -e inmidas -m ${FEROS_MIDWORK}" *) For Bash, add the following lines to .bashrc alias inmidas.feros="xterm -ls -bg blue -fg white -geometry 80x34+0-6 -fn 8x16 -sb -e inmidas -m ${FEROS_MIDWORK:-$HOME/FEROS-DRS/midwork}" 1.2 Screen Colour Depth ----------------------- In the file midwork/login.prg it is assumed the X11 Screen Colour Depth will be 24-bit. If you do not have this you will need to comment out the line: init/displ p5=RGBQ 1.3 Graphic and display windows ------------------------------- Several of the integral MIDAS prg files now require FIVE MIDAS graphic windows (with IDs 0, 1, 2, 3, 4) to exist before running. By default these are created in a rather simple fashion by the login.prg file, however several other more sophisticated examples are provided in the files midwork/creaDandG.prg.alt*. To use one of these examples you can simply make a softlink pointing at the relevant one, e.g.: cd $HOME/FEROS-DRS/midwork ln -s creaDandG.prg.alt0 creaDandG.prg If you want to customise one of the alternatives, then (for example): cd $HOME/FEROS-DRS/midwork cp creaDandG.prg.alt0 creaDandG.prg $EDITOR creaDandG.prg or if you use the same midwork directory from different computers with different Video capabilities you may want to create a HOST specific creaDandG.prg: cd $HOME/FEROS-DRS/midwork cp creaDandG.prg.alt0 creaDandG.prg.${HOST} $EDITOR creaDandG.prg.${HOST} In either of the two above cases the files creaDandG.prg, creaDandG.prg.${HOST} will survive an installation to a new version of the jFEROS-DRS.tgz package. If you make a link but then edit the original file, these modifications will be overwritten when a new version of the jFEROS-DRS.tgz package is installed. ================================================================================ 2.0 Use ======= As an example, assume we want to reduce the data from the night of 2003-01-21... 2.1 Prepare the data directory ------------------------------ cd ~/FEROS-DRS ferosPrepDateDir 2003-01-21 This will create a directory 2003-01-21 and then make softlinks pointing to the initial guess files. With no -g option to ferosPrepDateDir, the default initial guess (9001) will be used. If the initial guess files do not already exist they will be created in the separate directory guess9001. 2.2 Extract the data from the Archive CDs ----------------------------------------- ferosPrepRawData 2003-01-21 -r /2003-01-21 This will uncompress the files on the FEROS Archive CD and rename them with their original name (i.e. in fero.mt format for BIAS images or FEROS_ech_... for FIERA images). The script will automatically detect if the image was created with FIERA and if so then attempt to make softlinks of the form fero.mt using the ferosMkferoNNNNLink script. You may need to do the above command several times if the data from one night is on more than one CD. In addition to the Image files, the LOG files will be copied to. If there are images you are not interested in they can be easily removed using the log file and the ferosCleanByLog script. Simple edit the log file and remove the entries for images you do NOT want to reduce and then run the ferosCleanByLog script: cd 2003-01-21 FEROS.2003-01-21.log ferosCleanByLog FEROS.2003-01-21.log 2.3 Run the DRS --------------- inmidas.feros -P And then follow the instructions in ~/FEROS-DRS/midwork/README... 2.4 General Controlling Environmental and/or MIDAS variables ------------------------------------------------------------ A number of features have been implemented which are controlled by the existance and/or value of Operating System Environment variables and/or MIDAS keywords. They are detailed below. 2.4.1 Pack Reduced files ------------------------ In order to package the reduced files for each reduction as well as the Guess and Session archives, you need to set the FEROSPackRedFiles environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFiles "Y" *) For Bash, add the following line to .bashrc export FEROSPackRedFiles="Y" To include bias straightened images (e.g. back_str_C1.bdf etc) and pre-flatfield extracted images (e.g. bfext1) in the tarballs then set the FEROSPackRedFilesIncAll environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFilesIncAll "Y" *) For Bash, add the following line to .bashrc export FEROSPackRedFilesIncAll="Y" 2.4.1.1 Sorting Packed Red files by Target ------------------------------------------ In order to create softlinks pointing to the PackRedFiles sorted into directories on a target by target basis, you need set the FEROSPackRedFilesTargetsDir environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFilesTargetsDir "$FEROS_DRS/targets" *) For Bash, add the following line to .bashrc export FEROSPackRedFilesTargetsDir="$FEROS_DRS/targets" Above $FEROS_DRS/targets is given as an example, but it can be anything. 2.4.1.2 Cleaning Up after packing --------------------------------- To cleanup the reduction directory after packing set the FEROSPackRedFilesCleanUp environment variables. The BDF, FITS and PS ones allow to turn off cleanup of these specific items. *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFilesCleanUp "Y" *) For Bash, add the following line to .bashrc export FEROSPackRedFilesCleanUp="Y" If FEROSPackRedFilesCleanUp=Y then the following can be set to turn off cleanup of these specific items: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFilesCleanUpBDF "N" setenv FEROSPackRedFilesCleanUpFITS "N" setenv FEROSPackRedFilesCleanUpPS "N" *) For Bash, add the following line to .bashrc export FEROSPackRedFilesCleanUpBDF="N" export FEROSPackRedFilesCleanUpFITS="N" export FEROSPackRedFilesCleanUpPS="N" 2.4.2 Make HTML summary pages ----------------------------- In order create HTML summary pages, you need to set the FEROSmkHTML environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSmkHTML "Y" *) For Bash, add the following line to .bashrc export FEROSmkHTML="Y" or at the MIDAS prompt: write/keyword symMkHTML/c/1/1 "Y" You can also turn on debugging in the ferosMkHTML.pl script using the FEROSmkHTMLdebug environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSmkHTMLdebug "-d" *) For Bash, add the following line to .bashrc export FEROSmkHTMLdebug="-d" or at the MIDAS prompt: write/keyword symMkHTMLdebug/c/1/2 "-d" 2.4.2.1 Run convert commands into background ------------------------------------------------ To run the commands to convert PS files into PNGs in the background, you need to set the FEROSmkHTMLbgConv environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSmkHTMLbgConv "Y" *) For Bash, add the following line to .bashrc export FEROSmkHTMLbgConv="Y" 2.4.3 Choice of filenames for FITS versions of DRS products ----------------------------------------------------------- To have VLT compliant name format for output DRS files, i.e. r..nnnn.fits (See Appendix 1 below for naming conventions), you need to set the FEROSUseAFDRSFITS environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSUseAFDRSFITS "Y" *) For Bash, add the following line to .bashrc export FEROSUseAFDRSFITS="Y" or at the MIDAS prompt: write/keyword UseAFDRSFITS/c/1/1 "Y" 2.4.4 Creation of RAW image PS/PNG files ---------------------------------------- To create PS and/or PNG files (PNGs will then be included in the html pages set the following environment variables: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSDRSDS9mkPS "Y" setenv FEROSDRSDS9mkPNG "Y" *) For Bash, add the following line to .bashrc export FEROSDRSDS9mkPS="Y" export FEROSDRSDS9mkPNG="Y" You must have the ds9 software installed (preferably the latest version, 4.0b7 at this writing) and there must exist a softlink ferosDRSds9 which points to the ds9 binary (though the software will try to create this if it does not already exist if the ds9 binary can be found using the which command, see ferosDRSds9cmd) PNG files are created from the PS files so PNG creation implies PS creation also. If these variables do not exist nothing happens. Furthermore the name of the output PS/PNG files can be controlled using the FEROSDRSDS9useVLTFN environment variable: If set as follows: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSDRSDS9useVLTFN "Y" *) For Bash, add the following line to .bashrc export FEROSDRSDS9useVLTFN="Y" output files will have the filesname FEROS.yyyy-mm-ddThh:mm:ss.sss.ps/png, otherwise they will be fero.ps/png. The resulting PNG files will be included in the html files whichever filename format is used. 2.4.5 AutoInit -------------- At the telescope the the daily health check allows initialisation of both 1x1 and 2x2 binning modes. In order to use the correct initialisation during the night it is necessary to enable AutoInit detection. To do so set the following environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSAutoInit "Y" *) For Bash, add the following line to .bashrc export FEROSAutoInit="Y" This will override any manual setting of the FEROS configuration, e.g. to make a Optimum extraction. Therefore to be able to control the reduction in Visitor mode, in the MIDAS DRS session set the following MIDAS variable as follows: write/key symAutoInit/c/1/1 "N" The the extraction mode (for example) can be set to OPTIMUM as follows: set/feros EXT_MODE=O This functionality is implemented in autoreduce.prg. 2.4.6 Extract Non-Flatfielded spectra ------------------------------------- To extract Non-Flatfielded spectra AS WELL AS flatfielded spectra set following environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSExtractNonFFSpec "Y" *) For Bash, add the following line to .bashrc export FEROSExtractNonFFSpec="Y" or at the MIDAS prompt: write/keyword ExtrNonFFSpec/c/1/1 "Y" Non-Flatfielded spectra are useful when there is VERY little flux in the flatfield, as was the case for the first few bluest orders prior to 2004-Sep-09. For these spectra what signal there was in the SCIENCE spectra were completely dominated by the noise in the zero signal flatfields. 2.4.7 Merge DRS Product FITS into EXTENDED FITS ----------------------------------------------- By default the DRS produces one BDF for the merged spectrum and one BDF image for each unmerged individual order, i.e. 39 files for each fibre. Since by default the pipeline generates flatfielded and NON-flatfielded reductions in the end this is 2 x (1+39) x 2 = 120 files. If one also does all this for Optimum as well as Standard extraction you get 240 files! By default each these is converted to one FITS file. This option allows to merge these individual FITS files into 4 FITS files each with 40 Header Data Units (HDUs) thus keeping things a little tidier. As of MIDAS 06FEB it will be possible to create the 40 HDU FITS files directly from MIDAS with outdisk/sfits but MIDAS versions before 06FEB can not cope with so many input files. Therefore this in the meantime this is achieved with a simple C program (ferosMkMEFs) based on the FITSIO library. *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSMkMEFs "Y" *) For Bash, add the following line to .bashrc export FEROSMkMEFs="Y" or at the MIDAS prompt: write/keyword symMkExtdFITS/c/1/1 "Y" In the resulting Multi-HDU FITS or Multi Extension FITS (MEF) files the merged spectrum is in the zero-index HDU and the non-merged orders are in index 1-39 HDUs. 2.4.8 Use MODIFY/COLUMN instead of @@ colmean --------------------------------------------- To use the MIDAS generic MODIFY/COLUMN command instead of the FEROS DRS @@ colmean command to deal with bad columns set following environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSUseModColumn "Y" *) For Bash, add the following line to .bashrc export FEROSUseModColumn="Y" or at the MIDAS prompt: write/keyword symUseModColumn/c/1/1 "Y" At least one of the "bad columns" (at column 1350 in raw frames, column 1300 in prered processed frames) actually affects two consequetive columns. The MIDAS MODIFY/COLUMN command which can deal with consequective columns therefore does a better job than @@ colmean which can only deal with one column at a time. 2.4.9 Expected Number of orders in Initialisation ------------------------------------------------- By default the FEROS DRS currently expects to locate 39 orders when performing the order location step in the DRS initialisation. This can be controlled by the environment variable FEROSInitExpectNOrders: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSInitExpectNOrders "" *) For Bash, add the following line to .bashrc export FEROSInitExpectNOrders="" or at the MIDAS prompt: write/keyword FEROSInitExpNo/I/1/1 where is an integer, e.g. 38 or 40... 2.4.10 Reduce All Images ------------------------ By default the FEROS DRS only reduces spectra with EXPTYPE = SCIENCE. To force a reduction of all EXPTYPES set the MIDAS variable RedAllIms: at the MIDAS prompt: write/keyword RedAllIms/C/1/1 "Y" to disable: delete/keyword RedAllIms or write/keyword RedAllIms/C/1/1 "N" 2.4.11 Background Subtraction ----------------------------- By default the FEROS DRS the 1st step of the autoreduce procedure is background subtration (BACKGROUND/FEROS). To disable this set the MIDAS variable ARBkgSub: at the MIDAS prompt: write/keyword ARBkgSub/C/1/1 "N" to disable: delete/keyword ARBkgSub or write/keyword ARBkgSub/C/1/1 "Y" 2.4.12 Input FITS file extensions --------------------------------- By default, due to historical reasons, input files are expected with filenames like fero.mt (.mt is a MIDAS and/or ESO file extension for "Magnetic Tape", but in this case also implies fits files). Alternatively .fits can be used (i.e. input files with filenames like fero.fits). This can be controlled by the environment variable FEROSferoNNNNsuf: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSferoNNNNsuf "fits" *) For Bash, add the following line to .bashrc export FEROSferoNNNNsuf="fits" 2.5 Observatory Specific Controlling Environmental and/or MIDAS variables ------------------------------------------------------------------------- A number of futher features have been implemented which are controlled by the existance and/or value of Operating System Environment variables and/or MIDAS keywords but are generally only relevant to operations at the telescope. They are detailed below. 2.5.1 Make Quality Control Plots -------------------------------- In order to create Quality Control plots, you need to set the FEROSQCPlots environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSQCPlots "Y" *) For Bash, add the following line to .bashrc export FEROSQCPlots="Y" This is done automatically at the telescope by detection of the hostname being equal to w2p2off. 2.5.2 Inclusion of FFHV TCCD images in DRS tar files ---------------------------------------------------- To include FFHV TCCD images in the DRS product tar files, you need to set the FEROSFFHVImFitsFile environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSFFHVImFitsFile "" *) For Bash, add the following line to .bashrc export FEROSFFHVImFitsFile="" 2.5.3 Concatenate tar files --------------------------- To concatenate files to already existing DRS product tar files set the FEROSConcatTarFiles environment variable as follows: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSConcatTarFiles "Y" *) For Bash, add the following line to .bashrc export FEROSConcatTarFiles="Y" 2.5.4 Process DRS Products for QC --------------------------------- To Process the DRS Products for QC trending, you need to set the FEROSProcImage environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSProcImage "Y" *) For Bash, add the following line to .bashrc export FEROSProcImage="Y" 2.5.5 Archive DRS tar files in ESO Science Archive -------------------------------------------------- To copy the the DRS product tar files (including TCCD images) into the ESO Science Archive via the DFS, you need to set the FEROSDRStars2DFS environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSDRStars2DFS "Y" *) For Bash, add the following line to .bashrc export FEROSDRStars2DFS="Y" You will probably also want to force the inclusion of README files for the Archive tarballs: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSPackRedFilesSpecialIncludes " [file2...]" *) For Bash, add the following line to .bashrc export FEROSPackRedFilesSpecialIncludes=" [file2...]" 2.5.6 Display QC web pages after init... ---------------------------------------- To display QC web pages after an initialisation set the following environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSQCURLroot "" *) For Bash, add the following line to .bashrc export FEROSQCURLroot="" or at the MIDAS prompt: write/keyword FEROSQCURLroot/c/1/100 "" 2.5.7 Keep Intermediate MT files --------------------------------- By default when MEFs and/or VLT filenames are used for output files the intermediate f1.mt, f0001.mt etc files are deleted. This can be switched off by setting the following environment variable: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROSKeepIntMTs "Y" *) For Bash, add the following line to .bashrc export FEROSKeepIntMTs="Y" or at the MIDAS prompt: write/keyword symKeepIntMTs/c/1/1 "Y" 2.6 Multiple Extension FITS files --------------------------------- Creation of Multiple Extension FITS (MEF) files for FEROS will be supported by MIDAS natively as of version 06SEP. To obtain MEFs under pre 06SEP versions of MIDAS do: cd $HOME/FEROS-DRS/src make all install to create ferosMkMEFs, a simple tool based on cfitsio. 2.7 Timezone ------------ Since files are sorted in the web pages according to date and time of OB start and grouped together according to local midday before the night till local midday the day after the night it can be useful to set the timezone to "Chile/Continental" or the equivalent on your system for use by ferosMJD2DSofN.pl, the script used to compute the date of the start of the night i.e.: *) For tcsh, add the following line to .cshrc (or .tcshrc): setenv FEROS_TZ "Chile/Continental" *) For Bash, add the following line to .bashrc export FEROS_TZ="Chile/Continental" 2.8 Cross Correlation Functions ------------------------------- The MIDAS xcorall.prg script allows crosscorrelation between two FEROS spectra as well as allowing to make a correction based on simultaneous WLC spectra taken. This is useful to (for example) build the radial velocity curve for an object for which you have multiple spectra observed in Simultaneous Calibration (OBJCAL) mode. A new perl script, ferosXcor.pl, has been implemented and allows the crosscorrelation of FEROS spectra both with other FEROS spectra but also with (almost) any other kind of spectrum, e.g. a theoretical template. If the -p or -P command line options are given (see ferosXcor.pl -h) plots will be made to the /XWIN and /CPS devices by default. These two options can be overridden by the Environment variables PGPLOT_DEV and PGPLOT_PSPNG. The -G command line option will also force plotting to the /PNG device rather than the /CPS device. 2.9 Running in an esorex environment ------------------------------------ export FEROSesorex="Y" export FEROSferoNNNNsuf="fits" export FEROSusePROCATGnames="Y" export FEROSnoDisplay="Y" export FEROSUseAFDRSFITS="N" export FEROSMkMEFs="Y" export FEROSmkHTML="N" export FEROSPackRedFiles="N" Note: in all of the below, optional handling of the MASTER_BIAS is not yet implemented. 2.9.1 I/O for DRS_INIT ====================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+BIAS DPR.CATG+DPR.TYPE=CALIB+FLAT DPR.CATG+DPR.TYPE=CALIB+WAVE CALIB ...from calibDB: PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL PRO.CATG=DRS_SETUP_TBL PRO.CATG=LINE_TBL_1 PRO.CATG=LINE_TBL_2 PRO.CATG=ORDER_GUESS_TBL PRO.CATG=ORDER_TBL PRO.CATG=PROF_TEMPLATE PRO.CATG=COEFF_TBL_1 PRO.CATG=COEFF_TBL_2 Output PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=COEFF_TBL_1 coeff_tbl_1.fits PRO.CATG=COEFF_TBL_2 coeff_tbl_2.fits PRO.CATG=DRS_SETUP_TBL drs_setup_tbl.fits PRO.CATG=EXTR_FF_1 extr_ff1.fits PRO.CATG=EXTR_FF_2 extr_ff2.fits PRO.CATG=EXTR_WLC_1 extr_wlc1.fits PRO.CATG=EXTR_WLC_2 extr_wlc2.fits PRO.CATG=LINE_REF_TBL line_ref_tbl.fits PRO.CATG=LINE_TBL_1 line_tbl_1.fits PRO.CATG=LINE_TBL_2 line_tbl_2.fits PRO.CATG=MASTER_BIAS master_bias.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=MASTER_WAVE master_wave.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATE prof_template.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits 2.9.2 I/O for BIAS ================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+BIAS CALIB: None required Output PRO.CATG=MASTER_BIAS master_bias.fits master-bias-0001.paf 2.9.3 I/O for DARK ================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+DARK CALIB: ...from localDB PRO.CATG=MASTER_BIAS master_bias.fits Output PRO.CATG=MASTER_DARK master_dark.fits master_dark-0001.paf 2.9.4 I/O for FLAT ================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+FLAT CALIB: ...from calibDB PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL PRO.CATG=DRS_SETUP_TBL PRO.CATG=LINE_TBL_1 PRO.CATG=LINE_TBL_2 PRO.CATG=ORDER_GUESS_TBL PRO.CATG=ORDER_TBL PRO.CATG=PROF_TEMPLATE PRO.CATG=COEFF_TBL_1 PRO.CATG=COEFF_TBL_2 ...from localDB PRO.CATG=MASTER_BIAS master_bias.fits Output PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=EXTR_FF_1 extr_ff_1.fits PRO.CATG=EXTR_FF_2 extr_ff_2.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits master_flat-0001.paf 2.9.5 I/O for WAVE ================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+WAVE CALIB: ...from calibDB PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL PRO.CATG=DRS_SETUP_TBL PRO.CATG=LINE_TBL_1 PRO.CATG=LINE_TBL_2 PRO.CATG=PROF_TEMPLATE PRO.CATG=COEFF_TBL_1 PRO.CATG=COEFF_TBL_2 ...from localDB PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=EXTR_FF_1 extr_ff_1.fits PRO.CATG=EXTR_FF_2 extr_ff_2.fits PRO.CATG=MASTER_BIAS master_bias.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits Output PRO.CATG=COEFF_TBL_1 coeff_tbl_1.fits PRO.CATG=COEFF_TBL_2 coeff_tbl_2.fits PRO.CATG=DRS_SETUP_TBL drs_setup_tbl.fits PRO.CATG=EXTR_WLC_1 extr_wlc_1.fits PRO.CATG=EXTR_WLC_2 extr_wlc_2.fits PRO.CATG=LINE_TBL_1 line_tbl_1.fits PRO.CATG=LINE_TBL_2 line_tbl_2.fits PRO.CATG=MASTER_WAVE master_wave.fits master_wave-0001.paf 2.9.6 I/O for SCIENCE ===================== Input: RAW: DPR.CATG=SCIENCE CALIB: ...from calibDB PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL ...from localDB PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=COEFF_TBL_1 coeff_tbl_1.fits PRO.CATG=COEFF_TBL_2 coeff_tbl_2.fits PRO.CATG=DRS_SETUP_TBL drs_setup_tbl.fits PRO.CATG=EXTR_FF_1 extr_ff1.fits PRO.CATG=EXTR_FF_2 extr_ff2.fits PRO.CATG=EXTR_WLC_1 extr_wlc1.fits PRO.CATG=EXTR_WLC_2 extr_wlc2.fits PRO.CATG=LINE_REF_TBL line_ref_tbl.fits PRO.CATG=LINE_TBL_1 line_tbl_1.fits PRO.CATG=LINE_TBL_2 line_tbl_2.fits PRO.CATG=MASTER_BIAS master_bias.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=MASTER_WAVE master_wave.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATE prof_template.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits Output PRO.CATG=EXTR_SCI_1 extr_sci_1.fits PRO.CATG=EXTR_SCI_2 extr_sci_2.fits PRO.CATG=RED_SCI_1 red_sci_1.fits PRO.CATG=RED_SCI_2 red_sci_2.fits 2.9.7 I/O for SKY,SKY ===================== Input: RAW: DPR.CATG+DPR.TYPE=CALIB+SKY,SKY CALIB: ...from calibDB PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL ...from localDB PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=COEFF_TBL_1 coeff_tbl_1.fits PRO.CATG=COEFF_TBL_2 coeff_tbl_2.fits PRO.CATG=DRS_SETUP_TBL drs_setup_tbl.fits PRO.CATG=EXTR_FF_1 extr_ff1.fits PRO.CATG=EXTR_FF_2 extr_ff2.fits PRO.CATG=EXTR_WLC_1 extr_wlc1.fits PRO.CATG=EXTR_WLC_2 extr_wlc2.fits PRO.CATG=LINE_REF_TBL line_ref_tbl.fits PRO.CATG=LINE_TBL_1 line_tbl_1.fits PRO.CATG=LINE_TBL_2 line_tbl_2.fits PRO.CATG=MASTER_BIAS master_bias.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=MASTER_WAVE master_wave.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATE prof_template.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits Output PRO.CATG=EXTR_SOL_1 extr_sol_1.fits PRO.CATG=EXTR_SOL_2 extr_sol_2.fits PRO.CATG=RED_SOL_1 red_sol_1.fits PRO.CATG=RED_SOL_2 red_sol_2.fits PRO.CATG=FIBRATIO_TBL fibratio_tbl.fits fibratio_tbl-0001.paf 2.9.8 I/O for Standard stars ============================ Input: RAW: DPR.CATG+DPR.TYPE=CALIB+... CALIB: ...from calibDB PRO.CATG=BLAZE_TBL PRO.CATG=LINE_REF_TBL ...from localDB PRO.CATG=COEF_COP_1 coef_cop_1.fits PRO.CATG=COEF_COP_2 coef_cop_2.fits PRO.CATG=COEFF_TBL_1 coeff_tbl_1.fits PRO.CATG=COEFF_TBL_2 coeff_tbl_2.fits PRO.CATG=DRS_SETUP_TBL drs_setup_tbl.fits PRO.CATG=EXTR_FF_1 extr_ff1.fits PRO.CATG=EXTR_FF_2 extr_ff2.fits PRO.CATG=EXTR_WLC_1 extr_wlc1.fits PRO.CATG=EXTR_WLC_2 extr_wlc2.fits PRO.CATG=LINE_REF_TBL line_ref_tbl.fits PRO.CATG=LINE_TBL_1 line_tbl_1.fits PRO.CATG=LINE_TBL_2 line_tbl_2.fits PRO.CATG=MASTER_BIAS master_bias.fits PRO.CATG=MASTER_FLAT master_flat.fits PRO.CATG=MASTER_WAVE master_wave.fits PRO.CATG=ORDER_GUESS_TBL order_guess_tbl.fits PRO.CATG=ORDER_TBL order_tbl.fits PRO.CATG=PROF_TEMPLATE prof_template.fits PRO.CATG=PROF_TEMPLATET prof_templatet.fits PRO.CATG=FLUX_STD_TABLE .fits PRO.CATG=EXTCOEFF_TABLE atmoextn.fits Output PRO.CATG=EXTR_STD_1 extr_std_1.fits PRO.CATG=EXTR_STD_2 extr_std_2.fits PRO.CATG=RED_STD_1 red_std_1.fits PRO.CATG=RED_STD_2 red_std_2.fits PRO.CATG=EFFICIENCY_TBL efficiency_tbl.fits PRO.CATG=RESPONSE_TBL response_tbl.fits PRO.CATG=RESPONSE_IMG response_img.fits efficiency_tbl-0001.paf 2.10 Using the Herman Hensberge algorithm ========================================= Prof. Herman Hensberge and his group have provided updates to the ferso software, including both bug-fixes and an alternative approach to the ordertracing algorithm. By default the alternative approach is DISABLED. So to use the alternative apporach, set the following environment variable: *) For tcsh: setenv FEROSUseHH Y *) For Bash: export FEROSUseHH=Y Details concerning the alternative approcah are given in <>. John Pritchard 2007-03-18 ================================================================================ ============================================================================ Appendix 1: DRS Product filename conventions ============================================ If FEROSUseAFDRSFITS="Y" then DRS products converted to FITS files according to the following convention: mDPID = modified DPID = FEROS.YYYY-MM-DDTHH:MM:ss.sss i.e. without the .fits extension The one dimensional extracted frames are: MEF FITS files (if FEROSMkMEFs="Y") ----------------------------------- If both Merged and Non-Merged products are produced: Standard extraction... r..1081.fits <==> f1.bdf,f10001.bdf,...,f10039.bdf r..1082.fits <==> f2.bdf,f20001.bdf,...,f20039.bdf Optimum extraction... r..2081.fits <==> o1.bdf,o10001.bdf,...,o10039.bdf r..2082.fits <==> o2.bdf,o20001.bdf,...,o20039.bdf If only Non-Merged products are produced: Standard extraction... r..1091.fits <==> f10001.bdf,...,f10039.bdf r..1092.fits <==> f20001.bdf,...,f20039.bdf Optimum extraction... r..2091.fits <==> o10001.bdf,...,o10039.bdf r..2092.fits <==> o20001.bdf,...,o20039.bdf If only Merged products are produced: Standard extraction... r..1101.fits <==> f1.bdf r..1102.fits <==> f2.bdf Optimum extraction... r..2101.fits <==> o1.bdf r..2102.fits <==> o2.bdf i.e. the same as in the case of Single HDU FITS files... Single HDU FITS files (if FEROSMkMEFs=/="Y") -------------------------------------------- Standard extraction... Merged... r..1101.fits <==> f1.bdf r..1102.fits <==> f2.bdf Non-Merged, order-by-order... r..1251.fits <==> f10039.bdf r..1252.fits <==> f20039.bdf .. r..1631.fits <==> f10001.bdf r..1632.fits <==> f20001.bdf Optimum extraction... Merged... r..2101.fits <==> o1.bdf r..2102.fits <==> o2.bdf Non-Merged, order-by-order... r..2251.fits <==> o10039.bdf r..2252.fits <==> o20039.bdf .. r..2631.fits <==> o10001.bdf r..2632.fits <==> o20001.bdf The complete list: Pre-Extraction products... ========================== MEF files (if FEROSMkMEFs="Y") ------------------------------ r..0001.fits <==> back_str_C1.bdf, back_str_D1.bdf, back_str_X1.bdf r..0002.fits <==> back_str_C2.bdf, back_str_D2.bdf, back_str_X2.bdf Single HDU FITS files (if FEROSMkMEFs=/="Y") -------------------------------------------- r..0011.fits <==> back_str_C1.bdf r..0021.fits <==> back_str_D1.bdf r..0031.fits <==> back_str_X1.bdf r..0011.fits <==> back_str_C2.bdf r..0022.fits <==> back_str_D2.bdf r..0032.fits <==> back_str_X2.bdf Standard extraction: ==================== r..1041.fits <==> bfext1.bdf r..1042.fits <==> bfext2.bdf r..1051.fits <==> fext1.bdf r..1052.fits <==> fext2.bdf r..1061.fits <==> rebinned1.bdf r..1062.fits <==> rebinned2.bdf r..1063.fits or r..1071.fits <==> rebinnedNoFF1.bdf r..1064.fits or r..1072.fits <==> rebinnedNoFF2.bdf MEF files (if FEROSMkMEFs="Y") ------------------------------ r..1081.fits <==> f1.bdf,f10001.bdf,...,f10039.bdf r..1082.fits <==> f2.bdf,f20001.bdf,...,f20039.bdf r..1083.fits <==> noFFf1.bdf,noFFf10001.bdf,...,noFFf10039.bdf r..1084.fits <==> noFFf2.bdf,noFFf20001.bdf,...,noFFf20039.bdf r..1091.fits <==> f10001.bdf,...,f10039.bdf r..1092.fits <==> f20001.bdf,...,f20039.bdf r..1093.fits <==> noFFf10001.bdf,...,noFFf10039.bdf r..1094.fits <==> noFFf20001.bdf,...,noFFf20039.bdf If FEROSMkMEFs="Y" but MERGE_MTD="S" or "A" then the products will be as for Single HDU FITS file (see below). r..1111.tfits <==> efficiencyf1.tbl r..1112.tfits <==> efficiencyf2.tbl r..1121.tfits <==> responsef1.bdf,responsef1.tbl r..1122.tfits <==> responsef2.bdf,responsef2.tbl r..1130.tfits <==> fiberratiof.tbl Single HDU FITS files (if FEROSMkMEFs=/="Y") -------------------------------------------- Merged: r..1101.fits <==> f1.bdf r..1102.fits <==> f2.bdf r..1103.fits <==> noFFf1.bdf r..1104.fits <==> noFFf2.bdf Non-Merged, order-by-order... r..1251.fits <==> f10039.bdf r..1252.fits <==> f20039.bdf r..1253.fits <==> noFFf10039.bdf r..1254.fits <==> noFFf20039.bdf .. r..1631.fits <==> f10001.bdf r..1632.fits <==> f20001.bdf r..1633.fits <==> noFFf10001.bdf r..1634.fits <==> noFFf20001.bdf Optimum extraction: =================== r..2041.fits <==> boext1.bdf r..2042.fits <==> boext2.bdf r..2051.fits <==> oext1.bdf r..2052.fits <==> oext2.bdf r..2061.fits <==> rebinned1.bdf r..2062.fits <==> rebinned2.bdf r..2063.fits or r..2071.fits <==> rebinnedNoFF1.bdf r..2064.fits or r..2072.fits <==> rebinnedNoFF2.bdf MEF files (if FEROSMkMEFs="Y") ------------------------------ r..2081.fits <==> o1.bdf,o10001.bdf,...,o10039.bdf r..2082.fits <==> o2.bdf,o20001.bdf,...,o20039.bdf r..2083.fits <==> noFFo1.bdf,noFFo10001.bdf,...,noFFo10039.bdf r..2084.fits <==> noFFo2.bdf,noFFo20001.bdf,...,noFFo20039.bdf r..2091.fits <==> o10001.bdf,...,o10039.bdf r..2092.fits <==> o20001.bdf,...,o20039.bdf r..2093.fits <==> noFFo10001.bdf,...,noFFo10039.bdf r..2094.fits <==> noFFo20001.bdf,...,noFFo20039.bdf If FEROSMkMEFs="Y" but MERGE_MTD="S" or "A" then the products will be as for Single HDU FITS file (see below). r..2111.tfits <==> efficiencyo1.tbl r..2112.tfits <==> efficiencyo2.tbl r..2121.tfits <==> responseo1.bdf,responseo1.tbl r..2122.tfits <==> responseo2.bdf,responseo2.tbl Single HDU FITS files (if FEROSMkMEFs=/="Y") -------------------------------------------- Merged: r..2101.fits <==> o1.bdf r..2102.fits <==> o2.bdf r..2103.fits <==> noFFo1.bdf r..2104.fits <==> noFFo2.bdf Non-Merged, order-by-order... r..2251.fits <==> o10039.bdf r..2252.fits <==> o20039.bdf r..2253.fits <==> noFFo10039.bdf r..2254.fits <==> noFFo20039.bdf .. r..2631.fits <==> o10001.bdf r..2632.fits <==> o20001.bdf r..2633.fits <==> noFFo10001.bdf r..2634.fits <==> noFFo20001.bdf Appendix 2: Shell Variables =========================== All the environment variable options in one place... tcsh ---- setenv FEROS_DRS "${HOME}/FEROS-DRS" setenv FEROS_MIDWORK "${FEROS_DRS}/midwork" setenv PATH ${PATH}:${FEROS_DRS}/bin if ( $?PERL5LIB ) then setenv PERL5LIB ${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl else setenv PERL5LIB ${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl endif setenv FEROSferoNNNNsuf "fits" setenv FEROSPackRedFiles "Y" #setenv FEROSPackRedFilesIncAll "Y" #setenv FEROSPackRedFilesTargetsDir "$FEROS_DRS/targets" setenv FEROSPackRedFilesCleanUp "Y" #setenv FEROSPackRedFilesCleanUpBDF "N" #setenv FEROSPackRedFilesCleanUpFITS "N" #setenv FEROSPackRedFilesCleanUpPS "N" setenv FEROSmkHTML "Y" setenv FEROSmkHTMLbgConv "Y" #setenv FEROS_HTML "" setenv FEROSUseAFDRSFITS "Y" setenv FEROSDRSDS9mkPS "Y" setenv FEROSDRSDS9mkPNG "Y" setenv FEROSDRSDS9useVLTFN "Y" setenv FEROSAutoInit "Y" setenv FEROSExtractNonFFSpec "Y" setenv FEROSMkMEFs "Y" setenv FEROSUseModColumn "Y" setenv FEROSInitExpectNOrders "" setenv FEROS_TZ "Chile/Continental" #setenv FEROSUseHH Y # On Mac OS X if ( `uname -s` == "Darwin" ) then ## tar from Mac OS X does not support the --force-local command line option, ## Please install gnutar from MacPorts, or Fink or... setenv FEROS_TAR "gnutar" endif ## The following are normally only relevant at the telescope... #setenv FEROSQCPlots "Y" #setenv FEROSFFHVImFitsFile "" #setenv FEROSConcatTarFiles "Y" #setenv FEROSDRStars2DFS "Y" #setenv FEROSPackRedFilesSpecialIncludes " [file2...]" #setenv FEROSQCURLroot "" #setenv FEROSProcImage "Y" #setenv FEROSKeepIntMTs "Y" bash ---- export FEROS_DRS="${HOME}/FEROS-DRS" export FEROS_MIDWORK="${FEROS_DRS}/midwork" export PATH=${PATH}:${FEROS_DRS}/bin export PERL5LIB=${PERL5LIB}:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl export FEROSferoNNNNsuf="fits" export FEROSPackRedFiles="Y" #export FEROSPackRedFilesIncAll="Y" #export FEROSPackRedFilesTargetsDir="$FEROS_DRS/targets" export FEROSPackRedFilesCleanUp="Y" #export FEROSPackRedFilesCleanUpBDF="N" #export FEROSPackRedFilesCleanUpFITS="N" #export FEROSPackRedFilesCleanUpPS="N" export FEROSmkHTML="Y" export FEROSmkHTMLbgConv="Y" #export FEROS_HTML="" export FEROSUseAFDRSFITS="Y" export FEROSDRSDS9mkPS="Y" export FEROSDRSDS9mkPNG="Y" export FEROSDRSDS9useVLTFN="Y" export FEROSAutoInit="Y" export FEROSExtractNonFFSpec="Y" export FEROSMkMEFs="Y" export FEROSUseModColumn="Y" export FEROSInitExpectNOrders="" export FEROS_TZ="Chile/Continental" #export FEROSUseHH=Y # On Mac OS X if `uname -s` == "Darwin" ; then ## tar from Mac OS X does not support the --force-local command line option, ## Please install gnutar from MacPorts, or Fink or... export FEROS_TAR="gnutar" fi ## The following are normally only relevant at the telescope... #export FEROSQCPlots="Y" #export FEROSFFHVImFitsFile="" #export FEROSConcatTarFiles="Y" #export FEROSDRStars2DFS="Y" #export FEROSPackRedFilesSpecialIncludes=" [file2...]" #export FEROSQCURLroot="" #export FEROSProcImage="Y" #export FEROSKeepIntMTs="Y" Appendix 3: Installation on w2p2off =================================== For installation on w2p2off, i.e. at the 2.20m telescope, the following environment variables must be set (normally in .pecs/misc-all.env) for the account running the pipeline (normally user astro): ###################################################################### ## For the FEROS Pipeline... #### Paths export FEROS_DRS="${HOME}/FEROS-DRS" export FEROS_MIDWORK="${FEROS_DRS}/midwork" export PATH=${PATH}:${FEROS_DRS}/bin:/data/E2P2OPS/FEROS-DRS/bin export PERL5LIB=${PERL5LIB}:/vlt/INTROOT/E2P2OPS/lib/perl5:${FEROS_DRS}/lib/perl5:${FEROS_DRS}/lib/perl5/site_perl ### Controlling environment variables export FEROSPackRedFiles="Y" #export FEROSPackRedFilesIncAll="Y" export FEROSmkHTML="Y" export FEROSmkHTMLbgConv="Y" export FEROSUseAFDRSFITS="Y" export FEROSDRSDS9mkPS="Y" #export FEROSDRSDS9mkPNG="Y" export FEROSDRSDS9useVLTFN="Y" export FEROSAutoInit="Y" #export FEROSExtractNonFFSpec="Y" export FEROSMkMEFs="Y" export FEROSUseModColumn="Y" ## The following are normally only relevant at the telescope... export FEROSQCPlots="Y" export FEROSFFHVImFitsFile="/data/E2P2OPS/FEROS-Archive/FFHV" #export FEROSConcatTarFiles="Y" export FEROSQCURLroot="file:///data/E2P2OPS/FEROS-QC/html/QC" export FEROSDRStars2DFS="Y" export FEROSPackRedFilesSpecialIncludes="README README.DRS" export FEROSProcImage="Y" #export FEROSKeepIntMTs="Y" ###################################################################### Normally these are set in the ~/astro/.pecs/misc-all.env file. Appendix 4: MIDAS variables =========================== All the MIDAS control keywords in one place: write/keyword UseAFDRSFITS/c/1/1 "Y" write/keyword symAutoInit/c/1/1 "N" write/keyword ExtrNonFFSpec/c/1/1 "Y" write/keyword symMkExtdFITS/c/1/1 "Y" write/keyword symUseModColumn/c/1/1 "Y" write/keyword FEROSInitExpNo/I/1/1 write/keyword FEROSQCURLroot/c/1/1 "" write/keyword RedAllIms/C/1/1 "Y" write/keyword ARBkgSub/C/1/1 "N" write/keyword symKeepIntMTs/c/1/1 "Y" Appendix 5: Dependant software ============================== SciSoft: will provide WCS-Tools, CFITSIO and PGPLOT. Alterantively you can install the individual packages. Install in your path: WCS-Tools http://tdc-www.harvard.edu/software/wcstools.html http://tdc-www.harvard.edu/software/wcstools/wcstools-3.6.8.tar.gz CFITSIO http://heasarc.nasa.gov/lheasoft/fitsio/fitsio.html ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3100.tar.gz PGPLOT http://www.astro.caltech.edu/~tjp/pgplot/ ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz