#! /bin/sh
# This is the LHEA perl script: /cvmfs/extras-fp7.egi.eu/extras/heasoft/ftools/x86_64-unknown-linux-gnu-libc2.19-0/bin/seplot
# The purpose of this special block is to make this script work with
# the user's local perl, regardless of where that perl is installed.
# The variable LHEAPERL is set by the initialization script to
# point to the local perl installation.
#-------------------------------------------------------------------------------
eval '
if [ "x$LHEAPERL" = x ]; then
  echo "Please run standard LHEA initialization before attempting to run /cvmfs/extras-fp7.egi.eu/extras/heasoft/ftools/x86_64-unknown-linux-gnu-libc2.19-0/bin/seplot."
  exit 3
elif [ "$LHEAPERL" = noperl ]; then
  echo "During LHEA initialization, no acceptable version of Perl was found."
  echo "Cannot execute script /cvmfs/extras-fp7.egi.eu/extras/heasoft/ftools/x86_64-unknown-linux-gnu-libc2.19-0/bin/seplot."
  exit 3
elif [ `$LHEAPERL -v < /dev/null 2> /dev/null | grep -ic "perl"` -eq 0 ]; then
  echo "LHEAPERL variable does not point to a usable perl."
  exit 3
else
  # Force Perl into 32-bit mode (to match the binaries) if necessary:
  if [ "x$HD_BUILD_ARCH_32_BIT" = xyes ]; then
    if [ `$LHEAPERL -V 2> /dev/null | grep -ic "USE_64_BIT"` -ne 0 ]; then
      VERSIONER_PERL_PREFER_32_BIT=yes
      export VERSIONER_PERL_PREFER_32_BIT
    fi
  fi
  exec $LHEAPERL -x $0 ${1+"$@"}
fi
'
if(0);
# Do not delete anything above this comment from an installed LHEA script!
#-------------------------------------------------------------------------------
#!/usr1/local/bin/perl
#
# Script to run sebitmask and fselect one after the other and create
# an output file
#
# Brian K. Elza 3/7/95
# XTE GSFC/NASA
#
# A C-shell script performing similar operations will also exist.
# version 1.0.0 3/7/95

use Getopt::Std;

#============================================================#
#
# See if there are any flags:
#

getopts('h');			
if (defined $opt_h) {
    print <<EOHELP1;

NAME
    seplot -- a script that queries the user for  all  required  input
    and runs in sucession SEEXTRCT and FPLOT. 
    
    
USAGE
    seplot 
    
    
DESCRIPTION
    This script file is meant to allow the user to add files for filtering on 
    the fly and then plot the results. In this way the user can add files to
    be processed on the fly and see the results of each additional file added.
    After the first run all previous answers are carried through for each 
    subsequent iteration. 

    This script file will ask the user if he wants full filtering capability.
If the user answers YES than ALL of the required parameters for SEEXTRCT will
be asked for. If the user answers NO than only the absolutely necessary 
parameters will be asked for. 
    The script will (if there is more than one possiblity) ask the user if 
the lightcurve or the spectra is to be plotted. The user will be able to 
interact with FPLOT interactively at the PLT> command option. 
    
PARAMETERS
    
EXAMPLES
    1. seplot
    
    
NOTES:
    
    
BUGS
    
        Please report problems to xtehelp\@athena.gsfc.nasa.gov. Provide a
        detailed  description  of  the  problem and an e-mail address at
        which you can be reached if  further  information  is  required.
        Before  reporting  a  bug  please  check  your .PAR file. At the
        moment all comparisons are CASE SENSITIVE.
    
    
SEE ALSO
    SEEXTRCT and FSELECT for more information

EOHELP1
exit;
    }

# now onto the program ...

require "utils.pl";

print "Do you want full filtering capability (Yes/No)?";
chop($answer = <STDIN>);

@infile2=&runcom('pget seextrct infile');
chop($infile2[0]);
print "Input file name or \@file-of-filenames:[$infile2[0]]";
($infile = <STDIN>);
if($infile =~ /^./ ){
    chop($infile);
}
else{
    $infile = $infile2[0];
}

$origfile = $infile;

# Now we will test to see if the input file is a LIST of files. If it is
# then we will copy all of the files contained within this file to a
# unique filename
if($infile =~ /^@/ ){

    $infile =~ s/^@//;	# Remove the @ symbol
    $origfile = $infile;	# Store the filename in origfile
    open(INPUT_FILE,"$infile") || die "Sorry can't find $infile\n"; # Open the input file
    open(OUTPUT_FILE,">outfile_${$}") || die "Sorry can't open outfile_${$}\n"; # Open a unique output file
    while(<INPUT_FILE>) {
	print OUTPUT_FILE $_; # Copy files from INFILE to OUTPUT
    }
    close(INPUT_FILE);	# We are finished with the input file.
    close(OUTPUT_FILE);	# Close up the output file too.
    print "output file created was outfile_${$}\n";
}
else {
    open(OUTPUT_FILE,">outfile_${$}") || die "Sorry can't open outfile_${$}\n"; # open a unique output file
    print OUTPUT_FILE "$infile \n"; # Copy the filename to output file
    close(OUTPUT_FILE);	# Close the output file.
}

if($answer =~ /^[yY]/){
    @infile2=&runcom('pget seextrct gtiorfile');
    chop($infile2[0]);
    print "Input GTI files to be OR'd with INFILE:[$infile2[0]]";
    ($gtiorfile = <STDIN>);
    if($gtiorfile =~ /^./){
	chop($gtiorfile);}
    else{
	$gtiorfile = $infile2[0];
    }

    @infile2=&runcom('pget seextrct gtiandfile');
    chop($infile2[0]);
    print "Input GTI files to be AND'd with INFILE:[$infile2[0]]";
    ($gtiandfile = <STDIN>);
    if($gtiandfile =~ /^./){
	chop($gtiandfile);}
    else{
	$gtiandfile = $infile2[0];
    }
}

@infile2=&runcom('pget seextrct outroot');
chop($infile2[0]);
print "Root name for output file:[$infile2[0]]";
($outroot = <STDIN>);
if($outroot =~ /^./){
    chop($outroot);}
else{
    $outroot = $infile2[0];
}

@infile2=&runcom('pget seextrct timecol');
chop($infile2[0]);
print "Name of TIME column:[$infile2[0]]";
($timecol = <STDIN>);
if($timecol =~ /^./){
    chop($timecol);}
else{
    $timecol = $infile2[0];
}

@infile2=&runcom('pget seextrct columns');
chop($infile2[0]);
print "Name of COLUMN to be accumulated:[$infile2[0]]";
($columns = <STDIN>);
if($columns =~ /^./){
    chop($columns);}
else{
    $columns = $infile2[0];
}

@infile2=&runcom('pget seextrct binsz');
chop($infile2[0]);
print "Input the binsize in seconds, use 0.1 etc. if nec (INDEF):[$infile2[0]]"; 
($binsz = <STDIN>); 
if($binsz =~ /^./){
    chop($binsz);}
else{
    $binsz = $infile2[0];
}

if($answer =~ /^[yY]/){
    @infile2=&runcom('pget seextrct mfracexp');
    chop($infile2[0]);
    print "Minimum acceptable fractional exposure (INDEF):[$infile2[0]]";
    ($mfracexp = <STDIN>);
    if($mfracexp =~ /^./){
	chop($mfracexp);}
    else{
	$mfracexp = $infile2[0];
    }
}

@infile2=&runcom('pget seextrct printmode');
chop($infile2[0]);
print "Chose print option, LIGHTCURVE, SPECTRUM, or BOTH:[$infile2[0]]";
($printmode = <STDIN>);
if($printmode =~ /^./){
    chop($printmode);}
else{
    $printmode = $infile2[0];
}
			      
@infile2=&runcom('pget seextrct lcmode');
chop($infile2[0]);
print "Type of binning for LIGHTCURVE: (SUM, RATE, MEAN):[$infile2[0]]";
($lcmode = <STDIN>);
if($lcmode =~ /^./){
    chop($lcmode);}
else{
    $lcmode = $infile2[0];
}

    @infile2=&runcom('pget seextrct spmode');
    chop($infile2[0]);
    print "Type of binning for SPECTRUM (SUM, RATE, MEAN):[$infile2[0]]";
    ($spmode = <STDIN>);
    if($spmode =~ /^./){
	chop($spmode);}
    else{
	$spmode = $infile2[0];
    }

if($answer =~ /^[yY]/){
    @infile2=&runcom('pget seextrct mlcinten');
    chop($infile2[0]);
    print "Maximum acceptable intensity for Light Curve (INDEF):[$infile2[0]]";
    ($mlcinten = <STDIN>);
    if($mlcinten =~ /^./){
	chop($mlcinten);}
    else{
	$mlcinten = $infile2[0];
    }

    @infile2=&runcom('pget seextrct mspinten');
    chop($infile2[0]);
    print "Maximum acceptable intensity for Spectrum (INDEF):[$infile2[0]]";
    ($mspinten = <STDIN>);
    if($mspinten =~ /^./){
	chop($mspinten);}
    else{
	$mspinten = $infile2[0];
    }

    @infile2=&runcom('pget seextrct timemin');
    chop($infile2[0]);
    print "Starting time for summation in seconds (INDEF):[$infile2[0]]";
    ($timemin = <STDIN>);
    if($timemin =~ /^./){
	chop($timemin);}
    else{
	$timemin = $infile2[0];
    }

    @infile2=&runcom('pget seextrct timemax');
    chop($infile2[0]);
    print "Ending time for summation in seconds (INDEF):[$infile2[0]]";
    ($timemax = <STDIN>);
    if($timemax =~ /^./){
	chop($timemax);}
    else{
	$timemax = $infile2[0];
    }

    @infile2=&runcom('pget seextrct timeint');
    chop($infile2[0]);
    print "Input time intervals t1-t2,t3-t4 in seconds (INDEF):[$infile2[0]]";
    ($timeint = <STDIN>);
    if($timeint =~ /^./){
	chop($timeint);}
    else{
	$timeint = $infile2[0];
    }

    @infile2=&runcom('pget seextrct chmin');
    chop($infile2[0]);
    print "Minimum energy bin to include in Spectra (INDEF) or 0-255:[$infile2[0]]";
    ($chmin = <STDIN>);
    if($chmin =~ /^./){
	chop($chmin);}
    else{
	$chmin = $infile2[0];
    }

    @infile2=&runcom('pget seextrct chmax');
    chop($infile2[0]);
    print "Maximum energy bin to include in Spectra (INDEF) or 0-255:[$infile2[0]]";
    ($chmax = <STDIN>);
    if($chmax =~ /^./){
	chop($chmax);}
    else{
	$chmax = $infile2[0];
    }
    
    @infile2=&runcom('pget seextrct chint');
    chop($infile2[0]);
    print "Input energy intervals to be retained 0-1,2-255 (INDEF):[$infile2[0]]";
    ($chint = <STDIN>);
    if($chint =~ /^./){
	chop($chint);}
    else{
	$chint = $infile2[0];
    }
    
    @infile2=&runcom('pget seextrct chbin');
    chop($infile2[0]);
    print "Input channels for each bin 0-5,6-255 (INDEF):[$infile2[0]]";
    ($chbin = <STDIN>);
    if($chbin =~ /^./){
	chop($chbin);}
    else{
	$chbin = $infile2[0];
    }
 
    @infile2=&runcom('pget seextrct ephem');
    chop($infile2[0]);
    print "Input the ephemeris of the phase in seconds (INDEF):[$infile2[0]]";
    ($ephem = <STDIN>);
    if($ephem =~ /^./){
	chop($ephem);}
    else{
	$ephem = $infile2[0];
    }
    
    @infile2=&runcom('pget seextrct period');
    chop($infile2[0]);
    print "Input the period in seconds, use 0.1 etc. if nec (INDEF):[$infile2[0]]";
    ($period = <STDIN>);
    if($period =~ /^./){
	chop($period);}
    else{
	$period = $infile2[0];
    }

    @infile2=&runcom('pget seextrct phaseint');
    chop($infile2[0]);
    print "Input phase interval 0.0-0.5,0.75-1.0 (INDEF):[$infile2[0]]";
    ($phaseint = <STDIN>);
    if($phaseint =~ /^./){
	chop($phaseint);}
    else{
	$phaseint = $infile2[0];
    }
}
    print "\n";
    print "Running seextrct:\n";

# Here we set up seextrct_string to get ready to call seextrct.

if($answer =~ /^[yY]/){
    $tmp_file='@'."outfile_${$}";
    $seextrct_string = "seextrct infile='".$tmp_file."' gtiorfile=$gtiorfile " ; 
    $seextrct_string .= "gtiandfile=$gtiandfile outroot=$outroot extenpha='.pha' extenlc='.lc' ";  
    $seextrct_string .= "phasefile=' ' bitfile=' ' timecol=$timecol ";
    $seextrct_string .= "columns='".$columns."' multiple='no' "; 
    $seextrct_string .= "binsz=$binsz mfracexp=$mfracexp tnull=0.0 printmode=$printmode "; 
    $seextrct_string .= "lcmode=$lcmode spmode=$spmode mlcinten=$mlcinten ";
    $seextrct_string .= "mspinten=$mspinten timemin=$timemin timemax=$timemax "; 
    $seextrct_string .= "timeint='".$timeint."' gticols='START STOP' "; 
    $seextrct_string .= "chmin=$chmin chmax=$chmax "; 
    $seextrct_string .= "chint=$chint chbin=$chbin ephem=$ephem period=$period "; 
    $seextrct_string .= "phaseint=$phaseint obsdate='MJDREF' obstime='TSTART TSTOP' " ;   
    $seextrct_string .= "sensecase=no ";
    $seextrct_string .= "chkit=no clobber=yes negative=IGNORE bailout=no mode='h' ";

} 
else {
    $tmp_file='@'."outfile_${$}";
    $seextrct_string = " seextrct infile='".$tmp_file."' gtiorfile='-' " ; 
    $seextrct_string .= "gtiandfile='-' outroot=$outroot extenpha='.pha' extenlc='.lc' ";  
    $seextrct_string .= "phasefile=' ' bitfile=' ' timecol=$timecol ";
    $seextrct_string .= "columns='".$columns."' multiple='no' "; 
    $seextrct_string .= "binsz=$binsz mfracexp='INDEF' tnull=0.0 printmode=$printmode "; 
    $seextrct_string .= "lcmode=$lcmode spmode=$spmode mlcinten='INDEF' ";
    $seextrct_string .= "mspinten='INDEF' timemin='INDEF' timemax='INDEF' "; 
    $seextrct_string .= "timeint='INDEF' gticols='START STOP' "; 
    $seextrct_string .= "chmin='INDEF' chmax='INDEF' "; 
    $seextrct_string .= "chint='INDEF' chbin='INDEF' ephem='INDEF' period='INDEF' "; 
    $seextrct_string .= "phaseint='INDEF' obsdate='MJDREF' obstime='TSTART TSTOP' " ;   
    $seextrct_string .= "sensecase=no ";
    $seextrct_string .= "chkit='no' clobber='yes' negative='IGNORE' bailout='no' mode='h' ";
}

$extenpha = '.pha';
$extenlc = '.lc';

print "Running seextrct - be patient!\n";
print "$seextrct_string\n";

system($seextrct_string);

#@result=&runcom($seextrct_string);
#print "@result";

print "\n";
print "###########################################################\n";
print "Completed running seextrct\n";

print "Calling FPLOT\n\n";


# This is where we have to get ready for plotting the light-curve,
# spectra, or both. We allow the user to change the output and select
# the rows to be applied for each call...

if($printmode =~ /^both/i){
    print "Do you want to plot the light-curve (l), spectra (s), or both (b): [l,s,b]";
    $answer2 = <STDIN>;
    if($answer2 =~ /^./){
	chop($answer2);}
    else{
	print "Defaulting to plotting both files...\n";
	$answer2 = 'b'
    }

    if($answer2 =~ /^[Bb]/){
	print "Since you have selected both, lets deal with the LIGHT-CURVE first.\n";
    }
}

if($printmode =~ /^lightcurve/i){
    $pltfilelc = "$outroot" . "$extenlc";
    $xparmlc = "TIME";
    if($lcmode =~ /^sum/i){
	$yparmlc = "COUNTS";
    }elsif($lcmode =~ /^rate/i){
	$yparmlc = "RATE";
    }elsif($lcmode =~ /^mean/i){
	$yparmlc = "MEAN";
    }else {
	print "ERROR LCMODE can only be SUM, RATE, or MEAN\n";
    }

} elsif($printmode =~ /^spectrum/i){
    $pltfilesp = "$outroot" . "$extenpha";
    $xparmsp = "CHANNEL";
    if($spmode =~ /^sum/i){
	$yparmso = "COUNTS";
    }elsif($spmode =~ /^rate/i){
	$yparmsp = "RATE";
    }elsif($spmode =~ /^mean/i){
	$yparmsp = "MEAN";
    }else {
	print "ERROR SPMODE can only be SUM, RATE, or MEAN\n";
    }
} elsif($printmode =~ /^both/i){
    if($answer2 =~ /^[Ll]/ || $answer2 =~ /^[Bb]/){
	$pltfilelc = "$outroot" . "$extenlc";
	$xparmlc = "TIME";
	if($lcmode =~ /^sum/i){
	    $yparmlc = "COUNTS";
	}elsif($lcmode =~ /^rate/i){
	    $yparmlc = "RATE";
	}elsif($lcmode =~ /^mean/i){
	    $yparmlc = "MEAN";
	}else {
	    print "ERROR LCMODE can only be SUM, RATE, or MEAN\n";
	}
    } 
    
    if($answer2 =~ /^[Ss]/ || $answer2 =~ /^[Bb]/){
	$pltfilesp = "$outroot" . "$extenpha";
	$xparmsp = "CHANNEL";
	if($spmode =~ /^sum/i){
	    $yparmsp = "COUNTS";
	}elsif($spmode =~ /^rate/i){
	    $yparmsp = "RATE";
	}elsif($spmode =~ /^mean/i){
	    $yparmsp = "MEAN";
	}else {
	    print "ERROR SPMODE can only be SUM, RATE, or MEAN\n";
	}
    }
}

if($answer2 =~ /^[Ll]/ || $answer2 =~ /^[Bb]/){
    print"\nPlotting Light-curve with FPLOT\n";

    @infile2=&runcom('pget fplot rows');
    chop($infile2[0]);
    print "Lists of rows:[$infile2[0]]";
    ($rows = <STDIN>);
    if($rows =~ /^./){
	chop($rows);}
    else{
	$rows = $infile2[0];
    }

    @infile2=&runcom('pget fplot device');
    chop($infile2[0]);
    print "Device: /XWindow, /XTerm, /TK, /PS, etc:[$infile2[0]]";
    ($device = <STDIN>);
    if($device =~ /^./){
	chop($device);}
    else{
	$device = $infile2[0];
    }

    @infile2=&runcom('pget fplot pltcmd');
    chop($infile2[0]);
    print "Any legal PLT command:[$infile2[0]]";
    ($pltcmd = <STDIN>);
    if($pltcmd =~ /^./){
	chop($pltcmd);}
    else{
	$pltcmd = $infile2[0];
    }

    $fplot_stringlc = "fplot infile=$pltfilelc xparm=$xparmlc yparm=$yparmlc rows='".$rows."' device='".$device."' pltcmd='".$pltcmd." ' offset=no maxpts=10000 binmode=DEFAULT mode=h";

    print "$fplot_stringlc\n";
    system($fplot_stringlc);
} 

if($answer2 =~ /^[Ss]/ || $answer2 =~ /^[Bb]/){
    print "\nPlotting Spectra with FPLOT\n";
    
    @infile2=&runcom('pget fplot rows');
    chop($infile2[0]);
    print "Lists of rows:[$infile2[0]]";
    ($rows = <STDIN>);		
    if($rows =~ /^./){		
	chop($rows);}
    else{
	$rows = $infile2[0];
    }

    @infile2=&runcom('pget fplot device');
    chop($infile2[0]);
    print "Device: /XWindow, /XTerm, /TK, /PS, etc:[$infile2[0]]";
    ($device = <STDIN>);
    if($device =~ /^./){
	chop($device);}
    else{
	$device = $infile2[0];
    }

    @infile2=&runcom('pget fplot pltcmd');
    chop($infile2[0]);
    print "Any legal PLT command:[$infile2[0]]";
    ($pltcmd = <STDIN>);
    if($pltcmd =~ /^./){
	chop($pltcmd);}
    else{
	$pltcmd = $infile2[0];
    }

    $fplot_stringsp = "fplot infile=$pltfilesp xparm=$xparmsp yparm='".$yparmsp."' rows='".$rows."' device='".$device."' pltcmd='".$pltcmd." ' offset=no maxpts=10000 binmode=DEFAULT mode=h";

    print "$fplot_stringsp\n";
    system($fplot_stringsp);
}

print "\n";
print "###########################################################\n";

print "Next file or list of files to be processed? (RETURN to end)\n";
$infile = <STDIN>;
if($infile =~ /^./){
    chop($infile);
    $terminate=0;}
else{
    print "Terminating.... a list of all files processed is in outfile_${$}\n";
    $terminate=1;
}

until($terminate){
    if($infile =~ /^@/ ){

	$infile =~ s/^@//;	# Remove the @ symbol
	$origfile = $infile;	# Store the filename in origfile
	open(INPUT_FILE,"$infile") || die "Sorry can't find $infile\n"; # Open the input file
	open(OUTPUT_FILE,">>outfile_${$}") || die "Sorry can't open outfile_${$}\n"; # Open a unique output file
	while(<INPUT_FILE>) {
	    print OUTPUT_FILE $_; # Copy files from INFILE to OUTPUT
	}
	close(INPUT_FILE);	# We are finished with the input file.
	close(OUTPUT_FILE);	# Close up the output file too.
	print "output file created was outfile_${$}\n";
    }
    else {
	$origfile = $infile;
	open(OUTPUT_FILE,">>outfile_${$}") || die "Sorry can't open outfile_${$}\n"; # open a unique output file
	print OUTPUT_FILE "$infile \n"; # Copy the filename to output file
	close(OUTPUT_FILE);	# Close the output file.
    }

    print "Calling seextrct\n";   
    system($seextrct_string);

    print "Calling fplot\n";
    if($answer2 =~ /^[Lc]/ || $answer2 =~ /^[Bb]/){
	print "Plotting Light-curve\n";
	system($fplot_stringlc);
    } 
    
    if($answer2 =~ /^[Ss]/ || $answer2 =~ /^[Bb]/){
	print "Plotting Spectra\n";
	system($fplot_stringsp);
    }


    print "Next file or list of files to be processed? (RETURN to end)\n";
    $infile = <STDIN>;
    if($infile =~ /^./){
	chop($infile);
	$terminate=0;}
    else{
	print "Terminating.... a list of all files processed is in outfile_${$}\n";
	$terminate=1;
    }
}

print "File stored is $origfile\n";
@result=&runcom("pset seextrct infile='".$origfile."' ");
print "Do you want to save this file? [Yes,No]";
chop($answer10 = <STDIN>);
if($answer10 =~ /^[Yy]/){
}
else{
    print "Deleting outfile_${$}\n";
    unlink("outfile_${$}") || print "Having trouble deleting outfile_${$}\n"; # Remove the output file if not told to save it.
}