#!/usr/bin/perl
#
# Lisa Germany
# 16th June 2002
# Updated: 
#
####################################################################
#
# INPUT:
# Needs 3 files containing - list of bias images
#                          - list of flats with high counts
#                          - list of flats with low counts
#
# DESCRIPTION:
# - Processes raw images to make 8 badpix files - one for each chip
# - Gzips images ready for saving on tape
# - Tars and Gzips badpix files ready to go onto the web
#
#####################################################################


if ( $#ARGV <3 ) { die "\n\nUsage: mkBADPIX.pl biaslist lowflatlist highflatlist tarfilename\n\n"}

$biaslist = $ARGV[0];
$flatlowlist = $ARGV[1];
$flathighlist = $ARGV[2];
$tarfile = $ARGV[3];


##############################################################################
####                                                                      ####
####  (1) Run esowfi on all images                                        ####
####                                                                      ####
##############################################################################


unlink "login.cl" if -e "login.cl";
unlink "logfile" if -e "logfile";
unlink "loginuser.cl" if -e "loginuser.cl";
system( "cp source\/login.cl \.\/login.cl" );
system( "cp source\/loginuser.cl \.\/loginuser.cl" );
open ( F1, ">>login.cl" ) || die "Could not open login.cl\n";
print( F1 "esowfi\n");
print( F1 "unlearn esohdr\n");
print( F1 "esohdr \@$biaslist queryty=no obstype=zero\n");
print( F1 "esohdr \@$flathighlist queryty=no obstype=flat\n");
print( F1 "esohdr \@$flatlowlist queryty=no obstype=flat\n");
print( F1 "logout\n" ); 
close ( F1 );
system( "cl" );

##############################################################################
####                                                                      ####
####  (2) Overscan and Trim all images                                    ####
####      Make the master BIAS frame                                      ####
####      Bias subtract FLAT images                                       ####
####      Make FLATHIGH and FLATLOW combined images                       ####
####      Divide FLATLOW/FLATHIGH to make master frame                    ####
####                                                                      ####
##############################################################################

unlink "login.cl" if -e "login.cl";
unlink "loginuser.cl" if -e "loginuser.cl";
system( "cp source\/login.cl \.\/login.cl" );
system( "cp source\/loginuser.cl \.\/loginuser.cl" );
open ( F1, ">>login.cl" ) || die "Could not open login.cl\n";
print( F1 "mscred verbose=yes backup=once bkuproo=ORIG\n");

print( F1 "ccdproc *.fits output=\"\" ccdtype=\"\" noproc=no oversca=yes trim=yes fixpix=no zerocor=no darkcor=no flatcor=no sflatcor=no biassec=\!biassec trimsec=\!trimsec fixfile=badpix zero=BIAS flat=SKYFLAT minrepl=1. interac=no functio=legendre order=1 sample=* naverag=1 niterat=1 low_rej=3. high_re=3. grow=0. \n");

print( F1 "zerocombine \@$biaslist output=BIAS.fits ccdtype=\"\" process=no\n");

print( F1 "ccdproc \@$flathighlist output=\"\" ccdtype=\"\" noproc=no oversca=yes trim=yes fixpix=no zerocor=yes darkcor=no flatcor=no sflatcor=no biassec=\!biassec trimsec=\!trimsec fixfile=badpix zero=BIAS flat=SKYFLAT minrepl=1. interac=no functio=legendre order=1 sample=* naverag=1 niterat=1 low_rej=3. high_re=3. grow=0. \n");

print( F1 "ccdproc \@$flatlowlist output=\"\" ccdtype=\"\" noproc=no oversca=yes trim=yes fixpix=no zerocor=yes darkcor=no flatcor=no sflatcor=no biassec=\!biassec trimsec=\!trimsec fixfile=badpix zero=BIAS flat=SKYFLAT minrepl=1. interac=no functio=legendre order=1 sample=* naverag=1 niterat=1 low_rej=3. high_re=3. grow=0. \n");

print( F1 "flatcombine \@$flathighlist output=FLATHIGH ccdtype=\"\" process=no subsets=no \n");

print( F1 "flatcombine \@$flatlowlist output=FLATLOW ccdtype=\"\" process=no subsets=no \n");

print( F1 "mscarith FLATLOW.fits / FLATHIGH.fits FLATLHRATIO.fits \n");

print( F1 "mscsplit FLATLHRATIO.fits output=FLATLHRATIO verbose+ \n");

print( F1 "noao \n");
print( F1 "imred \n");
print( F1 "ccdred verbose=yes\n");
print( F1 "unlearn ccdmask \n");

for ($i=1;$i<=8;$i++) {
    print( F1 "ccdmask FLATLHRATIO\_$i.fits BADPIX5$i.pl lsigma=5 hsigma=5 \n");
}

print( F1 "logout\n" );
close ( F1 );
system( "cl" );


##############################################################################
####                                                                      ####
####  (3) Backup and Cleanup                                              ####
####                                                                      ####
##############################################################################

#unlink "login.cl" if -e "login.cl";
#unlink "loginuser.cl" if -e "loginuser.cl";
#unlink "logfile" if -e "logfile";
#unlink "WFI*.fits";

#print "Tarring up the BADPIX files...\n";
#system "tar cvf ${tarfile}.tar BADPIX*.pl\n";
#print "Gzipping ${tarfile}.tar...\n";
#system "gzip ${tarfile}.tar \n";

#print "\n Gzipping original images to save to tape.\n";
#print "This is going to take a while!!\n";
#system "gzip ORIG*.fits\n";
#system "gzip BIAS.fits\n";
#system "gzip FLATHIGH.fits\n";
#system "gzip FLATLOW.fits\n";