#!/bin/csh -f

source /star/etc/login  >& /dev/null
source /star/etc/cshrc  >& /dev/null
kappa >& /dev/null

if (`alias kappa` == "") then
  echo ""
  echo "Fatal: Initialization error of kappa environment"
  echo ""
  exit
endif

set kap = $KAPPA_DIR

set argv = `echo "$argv" | sed s/":"/" "/g`

if ($#argv < 4) set argv = "help"

if ($argv[1] =~ *"help"* || $argv[1] == "-h") then
  echo ""
  echo "Use: sp_bsl  file  order  v1:v2  [[v3:v4] ...]"
  echo "     e.g. 'sp_bsl myfile 1 -300:-100 100:300 ...'"
  echo ""
  echo "Note: the boundaries must be in increasing order!"
  echo ""
  exit
endif

set infile = $argv[1]
set infile = `echo "$infile" | cut -d\. -f1`
set infile = "${infile}.sdf"
shift argv
if !(-e "$infile") then
  echo ""
  echo "Fatal: file $infile not found"
  echo ""
  exit
endif

echo ""
echo "Remove baseline from file ${infile}:"

# ----------------------------------------------------------------------
# Remove Polynomial Baseline
#

 FIT_BSL:

    set order = $argv[1]
    shift argv

    if ( `echo "$#argv%2" | bc` == 1 ) then
      echo "Use: sp_bsl file order v1:v2 [[v3:v4] ...]"
      exit
    endif

    set parts = `echo "$argv" | sed s/":"/" "/g`
    set regions = ""
    @ ii = 1
    while ($ii <= $#parts)
      if ($ii > 1) set regions = "${regions},"
      if ("${parts[$ii]}" =~ *'.'*) then
        set regions = "${regions}${parts[$ii]}"
      else
        set regions = "${regions}${parts[$ii]}."
      endif
      @ ii ++
    end
    unset parts

    set regions = `echo "$regions" | sed s/" "/","/g`
    set fpb_par = "${order} ${regions}"

    set base = `echo $infile | sed s/.sdf//`
    set basefile = ${base}_bsl.sdf
    set outfile = ${base}_rembsl.sdf

#
# Use mfittrend twice because the 'sub' option apparently looses the
# variance (at the moment)
#
    echo "Regions: '${regions}'"
    ${kap}/mfittrend in=$infile axis=3 order=${order} out=$basefile \
                     ranges='"'${regions}'"' variance=false subtract=false
    ${kap}/mfittrend in=$infile axis=3 order=${order} out=$outfile \
                     ranges='"'${regions}'"' variance=false subtract=true

    if (-e "${basefile}") then
       echo "The fitted baseline has been saved in file:"
         echo "   '${basefile}'"
#       ${kap}/sub ${infile} ${basefile} ${outfile}
       if (-e "${outfile}") then
         echo "The baselines subtracted cube has been saved in:"
         echo "   '${outfile}'"
       else
           echo "ERROR: subtraction of the baseline failed"
         endif
       else
         echo "ERROR: the baseline fit failed"
       endif
    endif

    echo ""