#!/bin/bash

# Check command line arguments 
if [ -z "$1" ]
then
 printf "Usage: process_lrs2_images_step1 list.Qth Y N \n"
 printf "arg1 - Name of file with list of raw LRS2images (should be full path)\n"
 printf "arg2 - Use ds9 to set statistics box? (Y/N)\n"
 printf "arg3 - run in debug mode (Y/N)\n"
 exit
fi
if [ $1 = "--help" ]
then
 show_help process_lrs2_images_step1
 exit
fi
if [ -z "$2" ]
then
 printf "Usage: process_lrs2_images_step1 list.Qth Y N \n"
 printf "arg2 - Use ds9 to set statistics box? (Y/N)\n"
 exit
fi
if [ -z "$3" ]
then
 printf "Usage: process_lrs2_images_step1 list.10 N \n"
 printf "arg3 - run in debug mode (Y/N)\n"
 exit
fi

# assign useful names to input arguments 
fitslist="$1"
useds9="$2"
debug="$3"

if [ $debug = "Y" ] 
then 
 printf "\n"
 printf "The debug flag is ON in process_lrs2_images_step1.\n"
 printf "Name of input FITS file list of LRS2 images = $fitslist\n"
 printf "Use ds9_imstats to set the box = $useds9\n"
 message_and_read s
fi  

# Check that your basic file list is present 
if [ -e "$fitslist" ]
then 
 printf "input list is present\n" > /dev/null
else 
 printf "ERROR:  No file = $fitslist\n"
 exit 
fi 

# Find total number of images in the input list 
linecnt $fitslist > junk.number
read totalims < junk.number
\rm -f junk.number

#-----------------------------------------------------------------------------------------
# Read the box to be used for basic stats 
if [ $useds9 != "Y" ]
then 
 printf "\nFor basic box stats enter ixmin,ixmax,iymin,iymax (890 909 487 491): "
 read ixmin ixmax iymin iymax
fi 
#-----------------------------------------------------------------------------------------

#=========================================================================================
exec 3<$fitslist
i="0"
while read -u3 fullfits
do
 i=$[$i+1]

 printf "\nReady to process image $i of $totalims\n"

# Get the base image name
 just_fitsname.sh $fullfits > base.1
 read nchars fitsname < base.1
 locfits="${fitsname}.fits"

# subtract the bias (this make the local image named "lrs_bsub.fits"
lrs2_bias_sub.sh $fullfits
read  biaslev biaserr biascomm < lrs2_bias_sub.out
if [ $debug = "Y" ] 
then 
 printf "\n"
 printf "Bias and Bias_error = $biaslev $biaserr\n"
 message_and_read s
fi  

# Make a local version of the bias-subtracted image with the basename of the input image 
mv lrs_bsub.fits $locfits  

#----------------------------------------------------------
if [ $useds9 = "Y" ]
then 

# Handle the first image 
 if [ $i = "1" ]
 then 
  ds9_imstats $locfits N
  reg1="${fitsname}.reg"
  midodata.sh $locfits
  read inum regtype commo < midodata.1
  if [ $regtype != "box" ]
  then
   printf "ERROR:  You must set a single BOX region only. \n"
   exit
  fi 
  read p1 p2 p3 p4 p5 < midodata.5pars
  ixmin=`rounder.sh $p1 0`  
  ixmax=`rounder.sh $p2 0`  
  iymin=`rounder.sh $p3 0`  
  iymax=`rounder.sh $p4 0`  
 fi 
 if [ $debug = "Y" ]
 then
  printf "\nThe box limits (xmin,xmax,ymin,ymax) = $ixmin $ixmax $iymin $iymax\n"
  message_and_read s
 fi 

# Handle images after the firt image 
 if [ $i != "1" ]
 then 
  cp $reg1 ${fitsname}.reg
  ds9_imstats $locfits N
 fi 

fi 
#----------------------------------------------------------

# Run the basic box statistics routine 
clip_imstat.sh  $locfits $ixmin $ixmax $iymin $iymax
read fmean fme fsig NpixBox fmin fmax < clip_imstat.out
\rm -f clip_imstat.out

#----------------------------------------------------------
# If ds9_imstats was run, then collect some of those values 
fmeanDS9="none"
if [ $useds9 = "Y" ]
then 
  midodata.sh $locfits
  read xcen ycen fmeanDS9 fsigDS9 fmeDS9 NumDS9 < midodata.imstats
  midoclean 
fi 
#----------------------------------------------------------

# Grab a local version of the image
# Get a local version to work on
# mli_copy $fullfits
# locfits="${fitsname}.fits"
# locinfo="${fitsname}.info"
# locreg="${fitsname}.reg"

# Print the final answers 
 printf "$i $biaslev    $fmean $fmeanDS9    $fmax    $locfits \n" | tee -a process_lrs2_images_step1.out 

done 
#=========================================================================================

#------------------------------------------------------------------------------------------
# Make a table file 
printf "# data\n" > head 
cat head process_lrs2_images_step1.out > process_lrs2_images_step1.table

printf "ImNum     Image number \n" > process_lrs2_images_step1.parlab
printf "Bias      Mean image BIAS value \n" >> process_lrs2_images_step1.parlab
printf "Fmean     Average pixel value in box (ADU) \n" >> process_lrs2_images_step1.parlab
printf "FmeanDS9  Average pixel from ds9_imstats  \n" >> process_lrs2_images_step1.parlab
printf "Fmax      Maximum pixel value in box   \n" >> process_lrs2_images_step1.parlab
printf "Name      Bias-subtracted image name   \n" >> process_lrs2_images_step1.parlab
#------------------------------------------------------------------------------------------

if [ $debug = "Y" ] 
then 
 printf "\nYou are in debug mode, but you might want to clean up files anyway.\n"
 printf "Do you want to cleanup local files anyway? (Y/N): "
 read anso 
 if [ $anso != "Y" ] 
 then 
  exit 
 fi 
fi 

# make a last clean up
\rm -f pars.in fitsr2048.header_copy base.1 clip_imstat.explain 
\rm -f lrs2_bias_sub.out 
midoclean 
profclean