#!/usr/local/bin/perl
############################
# DEFINE DEFF HIT CLEANING #
############################

# no deff hit cleaning in template ....

#################
# BEGIN PROGRAM #
#################

# INPUT AND OUTPUT FILE HANDLING: CHANGE ACCORDING TO YOUR NEEDS (JC)

$recoos = "/group/amanda/bin.OSF1/recoos";
$infile = $ARGV[0];
@filetoks = split /\//, $infile;
$filename = pop @filetoks;
$filepath = join '/', @filetoks;
open(ERR,">>errorFile");
$l = rindex($infile,".gz");
$m = rindex($infile,".bz2");
if ($l > 0) {   # gzipped
  $outfile = substr($infile,0,$l);
  $cat = " gunzip -c ";
} elsif ($m > 0) {   # bzipped
  $outfile = substr($infile,0,$m);
  $cat = " bunzip2 -c ";
} else {   # uncompressed
  $outfile = $infile;
  $cat = " cat ";
}
if ($outfile =~ /f2k/) {
  $outfile =~ s/f2k/mrec.f2k.gz/;
} else {
  die "Can't find f2k token to replace in input filename.\n";
}


# CHANGE HERE FOR WHAT YOU NEED
# Process as data if matches pattern ....

if ( $infile =~ /(\d+)_U?_?(\d+)-97-/ ) { # real 1997 data
  
  ($run, $yday) = ($1, $2);
  $tshift= $tshift_data;
  
  #	print "Processing data from run $run, day $yday\n";

# subroutine performs run based OM cuts and BAD RUNs

  $omcut= hitclean($run,$yday);
  
  if ($omcut =~ /^badrun/) {
    warn "Skipping bad run $infile\n"; next FILE;
  }


# SAME SCRIPT CAN BE USED FOR MONTE CARLO

# Process as Monte Carlo if matches pattern *ama*...etc
} elsif ( $infile =~ /ama/ || $infile =~ /atmos/ || $infile =~ /atm/ ||
	$infile =~ /mass/ || $infile =~ /nusim/ || $infile =~ /^bg/ ) {
  $omcut= hitclean("mc",1)
  
  # File not recognized as data or monte carlo...
} else {
  print " Could not recognize type of file as MC or data.\n"
    . " Please update the script template.pl\n";

} # end of if data or MC


# OM which are allways cut (and String 11-13): 

$chncuts = " -y S=11 -y S=12 -y S=13 " 
  . " -y N=3  -y N=28 -y N=32 "  
  . " -y N=36 -y N=39 -y N=40 -y N=41 -y N=42 "
  . " -y N=44 -y N=47 -y N=50 -y N=57 -y N=61 -y N=62 -y N=78" 
  . " -y N=81 -y N=82 -y N=83 -y N=84 -y N=85 -y N=86 -y N=94 -y N=96" 
  . " -y N=117 -y N=143 -y N=169 -y N=172 -y N=186 -y N=189 -y N= 190"
  . " -y N=195 -y N=197 -y N=199 -y N=215 -y N=227 -y N=229 -y N=231" 
  . " -y N=232 -y N=235 -y N=243 -y N=244 -y N=265 -y N=267"; 



$cln_flags  = " $omcut $chncuts ";

$ example reconstruction with cuts:

$exe= "$cat $infile "

  . " | $recoos "
  . " -r n -i m -p w=0. -X g=f "
  . " -x x,y,z,zenith,azimuth "
  . " -p n=1000:4500 -p j=15 -p a=96. -p t=1:5 -X o=2 "
  . " $cln_flags "

print $exe."\n";

`$exe`;


close(ERR);

# end of script; subroutines follow

######################################################################
# This routine returns the recoos flags to hit-clean given the 
# run number and day of the year.  
######################################################################

sub hitclean {
 
########################
# BEGIN RUN-BASED CUTS #
########################

# Put here your favourite MC selection criterion ....

    if ($run =~ /^mc/) {
	$reco_flag .= "";
	return $reco_flag;
    }

#OM(RUN) selection

    if ($run=11) {$reco_flag .= " -y N=254 -y =264";}
    if ($run=97) {$reco_flag .= " -y N=16 ;}
    if ($run=112 || $run=477) {$reco_flag .= " -y N=263";}
    if (($run>=160) && ($run<=162)) {$reco_flag .= " -y N=234 -y N=249 -y N=258";}
    if (($run>=215) && ($run<=224)) {$reco_flag .= " -y N=302";}
    if ($run=217) {$reco_flag .= " -y N=263 -y N=302";}
    if ($run=308) {$reco_flag .= " -y N=263";}
    if (run= 450) {$reco_flag .= " -y N=198 -y N=263";}     
    if (($run>=667) && ($run<=670)) {$reco_flag .= " -y N=302";} 
    if (($run=661 || run= 664 ) {$reco_flag .= " -y N=302";}
    if (($run>=674) && ($run<=676)) {$reco_flag .= " -y N=277 -y N= 289";}
    if (($run =678) {$reco_flag .= " -y N=302;}
    if (($run>=682) && ($run<=683)) {$reco_flag .= " -y N=302";} 
   
#################
# BAD RUN CHECK #
#################

if (($run <= 7) || (($run>=16)&&($run<=17)) || (($run>=21)&&($run<=31))){
   return "badrun";
}
if (($run = 33) || ($run = 35) ||(($run>=39)&&($run<=47))){
   return "badrun";
}
if (($run = 67) || ($run = 69) || ($run = 71) ||(($run>=73)&&($run<=91))){
   return "badrun";
}
if (($run = 102) || ($run = 106)){
   return "badrun";
} 
if (($run = 108) || ($run = 109) || ($run = 111) || ($run = 112)){
   return "badrun";
}
if (($run = 116) ||(($run>=149)&&($run<=157))){
   return "badrun";
}
if (($run = 243) ||(($run>=345)&&($run<=346))){
   return "badrun";
}
if (($run = 251) || ($run = 276) || ($run = 291) || ($run = 326) || ($run = 379|| ($run = 389) )){
   return "badrun";
}
if (($run = 428) ||(($run>=412)&&($run<=426))){
   return "badrun";
}
if (($run = 549) ||(($run>=500)&&($run<=511))){
   return "badrun";
}

if (($run = 518) ||(($run = 531) {
   return "badrun"
}
if (($run = 685) ||(($run>=686)&&($run<=700))){
   return "badrun";
}


    return $reco_flag;

} # end of sub hitclean