#!/usr/bin/perl
use strict;
use warnings;

#
# Repipelines the data assuming default parameter values. 
# 
# Requirements:
#    0) Must be run from ODF/odf directory. 
#    1) Assumes that SAS has been initialized.
#

# Verify we're in the right directory. 


my @res1;
my $baseDir;
my $currDir;
chomp ($currDir = `pwd`);

if ($currDir =~ m/ODF/) {
   print "In the ODF directory, continuing. \n";
   @res1 = split(/ODF/, $currDir);
   $baseDir = $res1[0];
}
if ($currDir =~ m/odf/) {
   print "In the ODF directory, continuing. \n";
   @res1 = split(/odf/, $currDir);
   $baseDir = $res1[0];
}
if ($currDir !~ m/ODF/i) {
   print "Not in the ODF directory, stopping now. \n";
   exit;
}


#
# I assume SAS has been initialized. Continue merrily on.
#

# Let's get all the information we need at the start.

my $specbinchoice;
my $lcchoice;
my $imagechoice;
my $specbin = 'lambda';
my $lcbin = 0 ;
my $lcflag = 0;
my $imageflag = 0;

print "You can process the data in one of these ways: \n";
print "1) with the option to combine 1st order spectra from RGS1 and RGS2 later on, or  \n" ;
print "2) with the option to combine 1st and 2nd order spectra from one RGS instrument later on. \n";
print "\n";
print "Which would you like? (1/2) ";

chomp ($specbinchoice = <> );

if ($specbinchoice eq '2') {
   $specbin = 'beta';
   print "Ok, setting the appropriate parameter value. \n"
}
if ($specbinchoice eq '1') {
   print "Ok, setting the appropriate parameter value. \n"
} 
if (($specbinchoice ne '1') and ($specbinchoice ne '2')) {
   print "I don't know what that means; going with the default value (1). \n"
}
print "\n"; 
print "Would you like to make light curves? Y/N: "; 
chomp ($lcchoice = <>) ;
if (($lcchoice eq 'Y') or ($lcchoice eq 'y')) { 
   $lcflag = 1 ; 
} 
if (($lcchoice eq 'N') or ($lcchoice eq 'n')) { 
   $lcflag = 0 ; 
}
if (($lcchoice ne 'Y') and ($lcchoice ne 'y') and ($lcchoice ne 'N') and ($lcchoice ne 'n'))  {
   print "I don't know what that means; I will assume it's a no. \n" ; 
}
if ($lcflag eq 1) { 
   print "Please enter the size of the time bins, in seconds, for the light curves.\n ";
   chomp ($lcbin = <>) ;
   if (($lcbin =~ m/\D+/) or ($lcbin =~ m/\s/)) { 
      print "I don't know what that means; going with 10s.\n";
      $lcbin = 10;
   } 
}
print "\n";
print "Would you like to make images of PI, XDSP_CORR, and BETA_CORR? Y/N: ";
chomp ($imagechoice = <>) ;
if (($imagechoice eq 'Y') or ($imagechoice eq 'y')) {
   $imageflag = 1 ;
}           
if (($imagechoice eq 'N') or ($imagechoice eq 'n')) {
   $imageflag = 0 ; 
}
if (($imagechoice ne 'Y') and ($imagechoice ne 'y') and ($imagechoice ne 'N') and ($imagechoice ne 'n'))  {
   print "I don't know what that means; assuming it's a no. \n" ;
   $imageflag = 0 ;
}
print "\n";


$ENV{SAS_ODF} = $currDir; 
$ENV{SAS_ODFPATH} = $currDir;
print "Making the ccf.cif... \n";
`cifbuild`;
$ENV{SAS_CCF} = $currDir.'/ccf.cif'; 
print "Extending the ODF summary file... \n";
`odfingest`; 
my $sumsas = glob ("*SUM.SAS"); 
$ENV{SAS_ODF} = $currDir.'/'.$sumsas; 

print "$ENV{SAS_ODF}\n";
print "$ENV{SAS_ODFPATH}\n";
print "$ENV{SAS_CCF}\n";

chdir $baseDir; 
if (! -d $baseDir.'proc') { 
   `mkdir proc`; 
}
chdir $baseDir.'proc';

print "Reprocessing the data.\n";
`rgsproc spectrumbinning=$specbin` ; 

my $r1_evt1 = glob ("*R1*EVENLI*.FIT");  
my $r2_evt1 = glob ("*R2*EVENLI*.FIT");

`cp $r1_evt1 'r1_evt1.fits'`; 
`cp $r2_evt1 'r2_evt1.fits'`;

if ($imageflag eq 1) {
   print "Making the images. \n" ;
   if (! -d $baseDir.'proc/image') { 
   `mkdir image`; 
   }
   chdir $baseDir.'proc/image';
   `cp ../r1_evt1.fits .`;
   `cp ../r2_evt1.fits .`;

   `evselect table=r1_evt1.fits withimageset=yes imageset=r1_pi_bc_image.fits xcolumn=BETA_CORR ycolumn=PI imagebinning=imageSize ximagesize=600 yimagesize=600`;
   `evselect table=r2_evt1.fits withimageset=yes imageset=r2_pi_bc_image.fits xcolumn=BETA_CORR ycolumn=PI imagebinning=imageSize ximagesize=600 yimagesize=600`; 

   `evselect table=r1_evt1.fits withimageset=yes imageset=r1_xd_bc_image.fits xcolumn=BETA_CORR ycolumn=XDSP_CORR imagebinning=imageSize ximagesize=600 yimagesize=600`;
   `evselect table=r2_evt1.fits withimageset=yes imageset=r2_xd_bc_image.fits xcolumn=BETA_CORR ycolumn=XDSP_CORR imagebinning=imageSize ximagesize=600 yimagesize=600`;

   `rm r1_evt1.fits`; 
   `rm r2_evt1.fits`;
   }

if ($lcflag eq 1) {
   print "Making light curves. \n" ; 
   chdir $baseDir.'proc'; 
   if (! -d $baseDir.'proc/lightcurve') {
   `mkdir lightcurve`;
   }
   my $r1_srcli = glob ("*R1*SRCLI*.FIT");
   my $r2_srcli = glob ("*R2*SRCLI*.FIT");

   `cp $r1_srcli 'r1_srcli.fits'`;
   `cp $r2_srcli 'r2_srcli.fits'`;

   chdir $baseDir.'proc/lightcurve';

   `cp ../r1_evt1.fits .`;
   `cp ../r2_evt1.fits .`;
   `cp ../r1_srcli.fits .`;
   `cp ../r2_srcli.fits .`;

   `evselect table=r1_evt1.fits withrateset=yes rateset='r1_ltcrv_bin$lcbin.fits' maketimecolumn=yes timebinsize=$lcbin makeratecolumn=yes expression='(CCDNR==9)&&(REGION(r1_srcli.fits:RGS1_BACKGROUND,M_LAMBDA,XDSP_CORR))'`;

   `evselect table=r2_evt1.fits withrateset=yes rateset='r2_ltcrv_bin$lcbin.fits' maketimecolumn=yes timebinsize=$lcbin makeratecolumn=yes expression='(CCDNR==9)&&(REGION(r2_srcli.fits:RGS2_BACKGROUND,M_LAMBDA,XDSP_CORR))'`;

   `rm r1_evt1.fits`;
   `rm r2_evt1.fits`;
   `rm r1_srcli.fits`;
   `rm r2_srcli.fits`;

   chdir $baseDir.'proc';
}

chdir $baseDir.'proc';
print "Done. \n";