#!/bin/ksh

#	200711 7 311 16:40:38UT :
#	- added radius of earth to fitone.inp
#	- then sed into	 fasc.tmplt

# 10 March 2005
#	- big re-edit diffed with current scripts on yampa and pave

# 6 Jan2002
# edit for SFIT2 change name to fit2.k

# 14 November 2000
#	Added filename_line to input
#	rearrange (rewrite) short file for header on plot

# 11 Oct 2000
# updates to solve changes
# new sed patterns
# add linepos to inp file

# 03 May 1999
# Some changes to work only in one directory

# input files
#	fitone.inp
#	fasc0
#	fasc1
#	fasc0.prf
#	binput
#	temp.bnr


# This is a modified version of the fitscript script used to process the SESAME
# data along with DOLIST

# This script automates many (but unfortunately, not all) of
# the operations necessary to run sfit, once the files have
# been set up for the initial case.
# Uses input file: fitone.inp
# USAGE:  fitone

umask 111

exec 7<fitone.inp
	read -u7 autodir
	read -u7 sza
	read -u7 alt
	read -u7 mpd
	read -u7 fov
	read -u7 apd
	read -u7 fastcode_sw
	read -u7 result_fname
	read -u7 linepos
	read -u7 filename_line
	read -u7 nscan
	read -u7 Sver
	read -u7 bin
	read -u7 UTdatetime
	read -u7 latlon
	read -u7 ratioflag
	read -u7 azm
	read -u7 radofearth
	read -u7 daydir
	read -u7 ftmplt
	read -u7 ratiodir
	read -u7 savedir
	read -u7 thisfltr
	read -u7 outputpath
	read -u7 dur
exec 7<&-

fastdir="$autodir/fast"
sfitdir="$autodir/sfit"
plotdir="$autodir/plot"

print -R "  fitn.k : SZA : ${sza#*00}, Alt : ${alt##*00}, Fastc Switch: $fastcode_sw"

# sza		   - astronomical solar zenith angle calculated from time in
#		OPUS file
# alt		   - observation altitude defined in fitbatch
# mpd		   - maximum path difference from OPUS file
# fov		   - field of view in mrad form OPUS file
# apd		   - apodization function from OPUS file in OPUS nemonic
#		This must be converted to SFIT integer index number
#		currently supported BX -> 0
# fastcode_sw  - 0-don't run fastcode, 1- run fastcode
# result_fname - an output file to put results for an entire run into
#				 not used yet
# linepos	   - wavenumber of line to fitted, used for refractive index calc
#		in fastcode. Sed(ed) into input file

# 1. FASTCODE

# Use stream editor to put zenith angle and obs alt into the fastcode input
# files in $fastdir.
# Check fastcode_sw, if we are fitting a new region of the previously fitted
# spectrum we don't have to run fastcode again.
# 2 Aug 2000 made changes to accommmodate new fastcode - now only one input file

# these typeset cmds don't work in linux as they did in AIX
# alt is set to 9 char in fitbatch (OPUS) & ?? for OTA OTM
# sza is set to 9 char in o2bq

set -A Asza
integer iscan=0
set $sza
while (( ${iscan} < ${nscan} ))
do
	Asza[iscan]=$1
	#print ${Asza[iscan]}
	shift
	let iscan=${iscan}+1
done

#print $alt $sza
if [[ ${#alt} != 9 ]]
then
	typeset -Z9 alt=$alt
fi
#if [[ ${#sza} != 9 ]]
#then
#	typeset -Z9 sza=$sza
#fi
#print $alt $sza
#exit

typeset -Z9 lnp=$linepos.0
((ln1=$linepos+1))
typeset -Z9 ln1=$ln1.0

if ((fastcode_sw == 1))
then

	# now we are going to read and write fasc.inp
	# each block will be written nscan times
	set -A fscline
	let nfln=0
	exec 7< ${ftmplt}
	while read -u7 fscline[nfln]
	do
		((nfln=${nfln}+1))
	done
	exec 7<&-
   #print "  Lines in fasc.tmplt : " $nfln

	# now that we have the lines change to fastdir to do the work
	cd ${fastdir}

	# print out the header block
	print -R "${fscline[0]}" > fasc.0
	print -R "${fscline[1]}" >> fasc.0

	# change the nscan variable add 1 for 0 zenith angle calculation
	typeset -Z2 nsc
	((nsc=${nscan}+1))
	sed -e s/NN/${nsc}/g fasc.0 >fasc.inp

	# now print out a block for each of nscan sza's  / 49 layers in FH TAB
	let iscan=0
	while (( ${iscan} <= ${nscan} ))
	do
	   i=2
	   rm -f fasc.inp.tmp
	   while (( $i < $nfln ))
	   do
   		print -R "${fscline[$i]}" >> fasc.inp.tmp
         ((i=$i+1))
         #print $i
      done
      SZA=${Asza[iscan]}
      if (( ${iscan} == ${nscan} ))
      then
         SZA=0000000.0
      fi
      #print $SZA
		sed -e s/FIRSTLAYR/$alt/g \
			 -e s/SOLARZENA/${SZA}/g \
			 -e s/LOREFRACI/$lnp/g \
			 -e s/HIREFRACI/$ln1/g \
			 -e s/RADISEARTH/$radofearth/g \
			  fasc.inp.tmp >>fasc.inp
		((iscan=${iscan}+1))
   done

	cp ../fasc41.prf fasc.prf
   if [[ $? -ne 0 ]]
   then
      print "!!! cp fas41.prf returned not ok !!!"
      exit 7
   fi

	# now run the fastcode program

	print "  fitn.k : Running fastc.k..."

	#${bin}fastc.k fasc 1
	${bin}fast2.k -ffasc -v${Sver}
	fOK=$?
	if [ $fOK -ne 0 ]
   then
      print "!!! fastc.k returned not ok !!!"
      exit 7
   fi

	# copy the output files back here
	cd $autodir
	cp $fastdir/fasc\.* ${sfitdir}
else
	print -R "	Skipping FASTCODE..." >>$result_fname
	print -R "" >>$result_fname
fi

# 2. SFIT

# setup the spectra

	cd $sfitdir

   print -R $ratiodir >ratio.dir

	print ""
	print "  fitn.k : Setting up spectra..."
	integer iscan=0
	while (( ${iscan} < ${nscan} ))
	do
		typeset -Z2 isc=${iscan}
		cp ../temp.bnr.${isc} temp.bnr.${isc}
		let iscan=${iscan}+1
	done

	# now create the fitting parameter file cinput
	# get the id number for this scan from the z file

	print "  fitn.k : Editing cinput..."
	set -A id
	exec 7<fasc.z
	read -u7 nscn nlev

	integer iscan=0
	while (( ${iscan} < ${nscan} ))
	do
		read -u7 id[iscan] junk
		#print ${id[iscan]}
		let iscan=${iscan}+1
	done
	exec 7<&-

	# use the stream editor to put the id number, field of view, apodization index,
	# and maximum path difference into the binput file

	#typeset -R4 id=$id
	#typeset -R5 fov=$fov
	#typeset -Z9 mpd=$mpd
	typeset -Z3 apd=$apd
	typeset -Z4 nlev=$nlev

	sed -e s/IIII/$id/g -e s/MAXPATHDF/$mpd/g  \
		 -e s/APD/$apd/g   -e s/FFFFF/$fov/g  -e s/NNNNN/${nscan}/g \
		 -e s/NLEV/${nlev}/g \
		  ${autodir}/cinput > ${sfitdir}/cinput.tmp

	# now add the 0 at the end of the file or the snr regions to be
	# updated we are only allowing 1 region!!!

	# note in bbedit an extra blank line is needed at end of file

	lline=$(tail -1 cinput.tmp)
	count=$(wc -l cinput.tmp)
	integer Nlln="${count% *}"
	#print ""
	#print "  Fixing up tail end of cinput..."
	#print "   lastline in cinput.tmp	: " $lline
	#print "   # of lines in cinput.tmp : " $Nlln
	#print "   first part of last line	: " "${lline%%.*}"
	#print ""
	#print "  testing for end of file <0> or snr lines on : " "${lline%.*}"

	if [ "${lline%.*}" != 0 ]
	then
		# has snr lines
		# grab the last 2 lines or N lines later...
		#l2line=$(tail -2 cinput.tmp)
		let svln=${Nlln}-2
		#print "	  # lines - snr region lines : " $svln
		#print "	  last 1 lines ${lline}"
		head -${svln} cinput.tmp > cinput
	else
		let svln=${Nlln}-1
		#print "	  # lines - <0 line> " $svln
		head -${svln} cinput.tmp > cinput
	fi

	#print "first part of last line: " "${lline%%.*}"
	#print ""
	#print "  Adding in spectrum code and bnr lines..."

	# tack on the last lines containing bnr zenith angle code:
	# 1 block for each scan
	# add filter to temp.bnr filename to get it into specasc5 from cinput

	integer iscan=0
	while (( ${iscan} < ${nscan} ))
	do
		print -R "${id[iscan]}   1" >>cinput
		# used to be Z2 but this ksh goes to 2 w/ just -Z !!!
		#typeset -Z2 isc=${iscan}         # on acd
		typeset -Z isc=${iscan}         # on mac
		#print 1 $isc 2 $iscan 3 temp.bnr.${isc}
		#print $isc $iscan
		fprefix=${thisfltr}
		if [ ${ratioflag} == 0 ]
		then
			fprefix=0
		fi
		print "  fitn.k : filter = ${thisfltr}, prefix = ${fprefix}"
		print -R "${fprefix}temp.bnr.${isc}" >>cinput
		let iscan=${iscan}+1
	done

	#print "first part of last line: " "${lline%%.*}"
	#print ""
	#print "  replace 0 or snr lines..."

	if [ "${lline%%.*}" != 0 ]
	then
		# only accounting for changing the snr in one region for now!!!
		print 1 >>cinput
		#print "	  added line : "  "${lline}"
		print "${lline}" >>cinput
	else
		# this says no update of snr by region
		print 0 >>cinput
	fi

#exit

	# now we are ready to call the fitting program
	# note sfitinpx is not run from sfit.k binput assumed to be correct
	# use argument "nointerp" to call specasc4
	# use argument "interp" or nothing to call specasc5
	print "  fitn.k : Running sfit.k... ${Sver}"

		${bin}sfit2.k -s 6 -v ${Sver}
	   if [[ $? -ne 0 ]]
      then
         print "!!! sfit2.k returned not ok !!!"
         exit 7
      fi
#	fi

	# 3. RESULTS
	# get the data from the short output for the results file

	set -A sline
	short="summary.st"

	if [[ -s ${short} ]]
	then
		count=$(wc -l ${short})
		integer nlines="${count% *}"
		integer n=0
		exec 7< ${short}
		while ((n < nlines))
		do
			read -u7 sline[n]
			if [[ ${sline[n]} == "Itr"* ]]
			then
				itrline=${sline[n]}
				#print $itrline
				set $itrline
				#print $1
				#itr="${1%%:??}"
				q=${1#*:}
				#print $q
				itr=${q%/*}
				#print 'itr : ' $itr
			fi
			let n=${n}+1
		done
		exec 7<&-
	else
		integer nlines=1
		sline[0]="!short output file: empty"
	fi
	#print $nlines

	# put the short output file to the results file
	# add filename_line
	print -R "$filename_line"  >> ${result_fname}

   soutfile='specasc.out'
	if [[ -s ${soutfile} ]]
	then
	   exec 7<${soutfile}
     read -u7 tag zro junk
	   exec 7<&-
	else
	   zro=0.00000
	fi

	# Make list file
	set ${sline[1]}					#this is 80char bnr header
	dte=$1
	tme="${2%%UT*}"
	#print $dte $tme

	let n=${nlines}-1
	set ${sline[n]}
	# this line looks like:
	#pcol CHF2CL  0.394	 1.150	  4.2	77.5   2.3294E+15  9.2688E+14  7.4581E+13  3.5740E+15  1.9749E+25

	mymol=$2
	pcol="$zro $3 $4 $5 $6 ${10} ${11}"	  # params + partial columns
	pc2="$3 $4 $5 $6 ${10}"				# params and total column, air column
	#print $9 ${10}
	#print $pcol
	#print $pc2

	aircol=${11}
	print -R "${outputpath} ${savedir} ${daydir} ${tme} ${dur} ${sza} ${azm} ${radofearth} ${itr} ${thisfltr} ${pcol}" >> ${result_fname}.l

	# make profile listing from PRFS.out file
	pline=''
	pclin=''

	click=0
	while read line
	do
		#print ${line}
		set ${line}
		if [ $click == 0 ]
		then
			click=1
		else
			 pline="$4 ${pline}"
			 pclin="$7 ${pclin}"
		fi
	done <PRFS.out

	print "${mymol} ${daydir} ${tme} ${sza} ${azm} ${thisfltr} $pc2 ${pline}" >> ${result_fname}.q
	print "${mymol} ${daydir} ${tme} ${sza} ${azm} ${thisfltr} $pc2 ${pclin}" >> ${result_fname}.qc

	# rearrange the short output file for plotting in IDL sfitplt.pro
	# save as zsum
# 	print -R "[filenames]"			>  zsum
# 	print -R "rdrv.ctl"				>> zsum
# 	print -R "[titles]"				>> zsum
# 	print -R "${sline[0]}"			>> zsum
# 	print -R "$filename_line"		>> zsum

	# also print run summary info to screen
	print " "
	print "Run summary:"
	print -R "${sline[0]}"
	print -R "$filename_line"

	print -R "$filename_line" >>summary.st

	# one loop does it all
	let n=1
	while(( ${n} < ${nlines} ))
	do
		print -R "${sline[n]}"	  >> ${result_fname}
#		print -R "${sline[n]}"	  >> zsum
		print -R "${sline[n]}"
		let n=${n}+1
	done
	# let n=1
	# while(( ${n} < ${nlines} ))
	# do
	#	 if [[ ${sline[n]} == "Itr"* ]]
	#	 then
	#		 print -R "${sline[n]}"	   >> zsum
	#		 let n=${nlines}-1
	#	 else
	#		 print -R "${sline[n]}"	   >> zsum
	#		 let n=${n}+1
	#	 fi
	# done

	print " "  >> $result_fname
	print "*****************************************************************************************"

# we are all done (if everything worked!)

exit 0