#!/usr/bin/perl -w
# Files needed:
# the only file needed is the output from hedit.  For example, type the 
# following line at the iraf prompt:
# hedit @filenames fields=exptime value="." add- delete- verify- >hedit_out

# Make sure "filenames" contains only files that you want to use.  For example,
# if you took one test exposures to check exposure times, and the exp time
# is not the same as the rest, and you don't want to use these files, DON'T
# include them in "filenames".

# The script reads in hedit_out and extracts filenames, exposure times and
# prefixes.  

# Then I create an iraf
# batch file that initializes iraf, combines darks of the same exposure time
# (assumes that darks start with dk), runs ccdproc for dark subtraction
# using dark=dk$exptime on all images with this same exptime.
# Then, files are grouped according to prefix, and batch file then 
# runs ccdproc for
# masking, flattens images, combines, makes object masks, makes 
# masklets, reflattens, corrects for distortion, realigns and recombines.  
# And that's it!
# 
#
# Make sure the following tasks are loaded before starting batch file
#    stsdas
#    toolbox
#    imgtools
#    phiirs
#    phat
#    task getshifts=home$scripts/getshifts.cl
#    task domanygeotran=home$scripts/domanygeotran.cl

# RAF 6/3/99
open (BATCH,">batch.cl") || die "cannot open file";

get_name_exptime(); # reads output of hedit file that contains file 
                  # names and exp times.  Groups files with same exp time.


initialize_iraf(); #initializes iraf

group_prefixes(); #subroutine to sort prefixes and write all files with 
                  #same prefix into a file called $prefix

# comment next three commands if you don't want to do dark subtraction.
# comment next command if you are using darks from another night but still
# want to run dark subtraction on images.
combine_darks(); #write to batch file to combine darks, assumes darks start with dk

group_exptimes(); #groups files with same exptime and writes filenames 
                  #to FILE$exptime

dark_subtract(); #write out commands to batch file to dark-subtract files 
                 #with same exptime



image_process(); #subroutine that writes the rest of the image-processsing 
                 #commands to BATCH


close (BATCH) || die "couldn't close batch.cl: $!";



#############################################################################
##################          subroutines       #############################
###########################################################################


#subroutine to read in output from hedit and get filenames and exptimes.
#this also stores a prefix for each file, which is the filename, minus .*,
#minus the last 3 characters which are presumably the 3 numbers assigned
#by wfirc data acquisition software 
sub get_name_exptime {
    $nfiles=0;
    open (HEDIT, "hedit_out") || die "can't open hedit_out: $!";
    while (defined ($temp = <HEDIT>)) {
	chomp($temp); #removes \n from line
	($name{$nfiles},$t1)=split(/,/,$temp);
	#print "$name{$nfiles}\n";
	($t2,$time[$nfiles])=split(/=/,$t1);
	#print "$time[$nfiles]\n";
	$exptime{$nfiles}=$time[$nfiles];
	($allprefix{$nfiles},$t3) = split(/\./,$name{$nfiles});
	#print "$allprefix{$nfiles}\n";
	$length = length($allprefix{$nfiles});
	#print "$length\n";
	$noextention[$nfiles]=$allprefix{$nfiles};
	$end=$length-3;
	$allprefix[$nfiles] = substr($noextention[$nfiles],0,$end);
	#print "$allprefix[$nfiles]\n";
	$nfiles++;
    }
}


#####################################################################

#initializes iraf
sub initialize_iraf {
    print BATCH "images\n";
    print BATCH "imred\n";
    print BATCH "ccdred\n";
    print BATCH "unlearn imcombine\n";

}

###################################################################

#subroutine to sort prefixes and write all files with same prefix into
#a file called $prefix
sub group_prefixes {
    $i=0;
    $j=0;
    $k=0;
    $t1=0;
    $temp="none";
    #print "@allprefix\n";
	
    @sorted_prefix = sort @allprefix; #sorts names in alphabetical order
    #print "@allprefix\n";
    #print "@sorted_prefix\n";
    while ($k < $nfiles) {
	$t1 = $sorted_prefix[$k];
	#print "$t1\n";
	if ($t1 ne $temp) {
	    $f = join "",("FILE",$t1); #reference for file = FILEprefix
	    #$times{$j}=$t1; #saves an array of exposure times
	    open ($f, ">$t1") || die "can't open $t1: $!";
	    $i=0;
	    while ($i < $nfiles) {
		
		if ($allprefix[$i] eq $t1) {
		    print $f "$noextention[$i]\n";
		    #print "$i $name{$i}\n";
		}
		$i++;
	    }
	    $temp=$t1;
	    $prefix{$j}=$temp;
	    #print "$prefix{$j}\n";
	    #print "help\n";

	    $j++;
	    $nprefix=$j;
	    close ($f) || die "can't close $f: $!";
	}
	$k++;
    }


    $i=0;
    while  ($i < $nprefix) {
	$dummy[$i]=0;
	$i++;
    }
    $i=0;
    while ($i < $nprefix) {
	$j=0;
	while ($j < $nfiles) {
	    #print "$name{$j} $prefix{$i}\n";
	    if ($noextention[$j] =~ /^$prefix{$i}/){
		    if ($dummy[$i] == 0) {
			$ref[$i]=$noextention[$j];
			#print "reference = $ref[$i]\n";
			$dummy[$i]++;
		    }
		}
	    $j++;
	}
	$i++;
    }
		

}

#######################################################################

# writes to BATCH file to combine darks, assumes darks start with dk.
# combined dark is called for example, dk10 for 10 sec darks.
sub combine_darks {
    #print "combining darks\n";
    $index=0;
    while ($index < $nprefix) {     # combines darks first
	if ( $prefix{$index} =~ /^dk/ ){
	    #print "file starting with dk";
	    print BATCH "chpixtype \@$prefix{$index} \@$prefix{$index} newpixtype=short\n";
	    print BATCH "imcombine \@$prefix{$index} $prefix{$index} combine=ave reject=minmax lsigma=3 hsigma=3\n";
	}
	$index++;
    }
}

##################################################################

# groups filenames according to exposure times and writes filenames to files
# called FILE$exptime for dark subtraction.  Filenames starting with dk are
# ignored
sub group_exptimes {
    $temp=0;
    $i=0;
    $j=0;
    $k=0;
    @sorted_times= sort {$a <=> $b} @time;
    while ($k < $nfiles) {
	$t1=$sorted_times[$k];
	if ($t1 != $temp) {
	    $f = join "" ,("FILE",$t1);
	    $times{$j}=$t1; #saves an array of exposure times
	    $t2="FILE".(1*$t1);
	    #print "filename = $t2\n";
	    open ($f, ">$t2") || die "can't open $t2: $!";
	    $i=0;
	    while ($i < $nfiles) {
		if (!($name{$i} =~ /^dk/)){
		    
		    if ($exptime{$i} == $t1) {
			print $f "$name{$i}\n";
		    }
		}
		$i++;
	    }
	    $temp=$t1;
	    $j++;
	    $ntimes=$j; # keeps track of number of different exposure times
	    close ($f) || die "can't close $f: $!";
	}
	$k++;
    }
}


#########################################################################

#write out commands to batch files to change pixtype to ushort for object
#frames and dark-subtract files with same exptime
sub dark_subtract {
    $i=0;
    while ( $i < $ntimes ) {
	$darkname="dk".(1*$times{$i}); #assumes darks are named dk##
	#print "$darkname\n";
	$f="FILE".(1*$times{$i}); #file containing files w/same exptime
	print BATCH "chpixtype \@$f \@$f newpixtype=ushort\n";
	print BATCH "ccdproc \@$f fixpix- overscan- trim- zerocor- darkcor=yes flatcor- dark+ dark=$darkname\n";
	$i++;
    }
}

##########################################################################

#subroutine that writes the rest of the image-processsing commands to BATCH
sub image_process{ 

    $index=0;
    while ($index < $nprefix) {
	#print "$prefix{$index}\n";
	if ( !($prefix{$index} =~ /^dk/)) {

	    print BATCH "mask files=\@$prefix{$index} mask=invmaskj.imh invmask=maskj.pl\n"; # mask has good values=1, invmask has good value=0
	    print BATCH "flush\n";
	    print BATCH "irflat $prefix{$index} flatstring=f number=8 log=log objmask- stdpars+\n";
	    print BATCH "irshiftrf flatlist=$prefix{$index}f refimage=$ref[$index]f prefix=$prefix{$index} suffix=shift\n";
	    print BATCH "imcopy $ref[$index] qem$index\n";
	    print BATCH "imarith qem$index / qem$index qem$index\n";
	    print BATCH "ircoadd comblist=$prefix{$index}f outimage=$prefix{$index}f expmap=qem$index shiftlist=$prefix{$index}.roundoff.shift scaling=none weighting=none zeroing=mode unzero+ stdpars+ magfac=1 stack- logfile=ircoad\n";
	    print BATCH "imcopy $prefix{$index}f $prefix{$index}em\n";
	    print BATCH "imarith $prefix{$index}em / $prefix{$index}em $prefix{$index}em\n";
	    print BATCH "mkobjmask image=$prefix{$index}f  expname=$prefix{$index}em i_nsmooth=3 i_subsample=1 i_filtsize=15 i_ngrow=1 suffix=mask prefix=norm nsmooth=3 subsample=1 filtsize=15 ngrow=1 interact- echog+ mode=ql\n";
	    print BATCH "masklet image=$prefix{$index}f  objmask=$prefix{$index}fmask.pl suffix=om shiftfile=$prefix{$index}f.imshifts  flip- update+ echog+\n";
	    print BATCH "imdel \@$prefix{$index}f\n";
	    print BATCH "irflat imagelist=$prefix{$index} flatstring=fm number=8 log=log objmask+ stdpars+\n";
	    print BATCH "domanygeotran $prefix{$index} $prefix{$index} H_9904_geomapout geo.dat\n";  
	    print BATCH "irshiftrf flatlist=$prefix{$index}fm refimage=$ref[$index]fm prefix=$prefix{$index}fm suffix=shift\n";
	    print BATCH "ircoadd comblist=$prefix{$index}fm outimage=$prefix{$index}fm expmap=qem$index shiftlist=$prefix{$index}fm.roundoff.shift scaling=none weighting=none zeroing=mode unzero+ stdpars+ magfac=1 stack- logfile=ircoad\n";
	}
	$index++;

    }
}