#!/bin/sh

# Create a specpr file for collecting the average spectra in the
#     directory where a mappign runs has completed
#          - R Clark 04/24/2023

echo " "
echo "##########   get average spectra for each mapped material  ###########"

err=0
if [ -z "$2" ]
then
	err=1
fi
if [ "$1" != "box" -o "$1" != "dirs" ]
then
	err=1
fi

b1=0  # bounting box x,y upper left, lower right
b2=0
b3=0
b4=0

if [ "$1" = "box" -a "$5" -gt "0" ]
then
	b1=$2
	b2=$3
	b3=$4
	b4=$5
	shift
	shift
	shift
	shift
	shift
else
        echo "$0  box error: our of range"
	err=1
fi
if [ "$1" = "dirs" ]
then
	shift
	dirlist=$*
	echo "dirlist= $dirlist"
else
        echo "$0   dirs error: dirs flag not found"
	err=1
fi

if [ -z "$1" ]
then
	echo "ERROR: directory variable is null"
	echo " "
	echo "Usage:"
	echo "       cmd.get.average.spectra.of.mapped.materials  dirs dirlist|all"
	echo "   or"
	echo "       cmd.get.average.spectra.of.mapped.materials  box a b c d  dirs dirlist|all"
	echo " "
	echo "           where:  a= upper left x,  b=upper left y,  c= lower right x, d= lower right y"
	echo "exit 1"
	exit 1
fi



echo " "
echo "start: " `date`
echo " "

# check that all needed files exist

ierr=0
for ifile in AAA.info/cubefilename.txt  \
             AAA.info/image-xpixels.txt \
             AAA.info/image-ypixels.txt \
             AAA.info/shortcubeid.txt   \
             AAA.info/cube-scale-factor \
             AAA.info/shortcubeid.txt   \
             AAA.info/cube-scale-factor
do
	if [ ! -f "$ifile" ]
	then
		echo "ERROR:  "$ifile"  not found"
		ierr=1
	fi
done

if [ "$ierr" -ne "0" ]
then
	echo "exit 1"
	exit 1
fi

cubepath=`cat AAA.info/cubefilename.txt`
cube=`basename $cubepath | cut -c 1-70`

if [ ! -f "$cubepath" ]
then
	echo "ERROR:  $cubepath  not found"
	echo "exit 1"
	exit 1
fi

if [ -f "$cubepath" ]
then
	# if envi, start of first line of *.hdr = ENVI
	# if vicar, start of first line of      = LBLSIZE=

	cubtest1=`dd if=$cubepath ibs=4 count=1 | cat -v`
	if [ "$cubtest1" = "ENVI" ]
	then
		echo "ENVI header found: $cubepath"

	elif [ "$cubtest1" = "LBLS" ]
	then
		echo "VICAR header found: $cubepath"

	elif [ -f ${cubepath}.hdr ]
	then
		cubepath2=${cubepath}.hdr

		cubtest2=`dd if=$cubepath2 ibs=4 count=1 | cat -v`

		if [ "$cubtest2" = "ENVI" ]
		then

			cube=${cubepath}.hdr
			cubepath=${cubepath}.hdr
		fi

	fi

fi

echo "cube= $cube"

splib=`grep iyfl= r1 | sed -e 's/iyfl=//'`
spdir=`dirname $splib`
spfile=`basename $splib`

spstart=${spdir}/startfiles/${spfile}.start

     # example:    cp /sl1/usgs/library06.conv/startfiles/s06emitc.start spreslt1

if [ -f "$spstart" ]
then
	if [ -f "spreslt1" ]
	then
		echo "NOTE: file  spreslt1  already exists, appending"
	else
		echo "creating spreslt1 specpr file"
		cp $spstart spreslt1
    		sp_stamp spreslt1
		spsettitle  spreslt1 1 '*************  spreslt1  ****************' -force
		spsettitle  spreslt1 2 '**** extracted spectra from cube:   *****' -force
		spsettitle  spreslt1 3 "$cube                                   " -force
	fi
else
	echo "ERROR:  $spstart  not found"
	echo "exit 1"
	exit 1
fi

# cube isze:
xpx=`cat AAA.info/image-xpixels.txt`
ypx=`cat AAA.info/image-ypixels.txt`

if [ $b1 -gt "0" -a $b2 -gt "0" -a $b3 -le $xpx -a $b4 -le $ypx ]
then
	echo "box $b1 $b2 $b3 $b4 is withing range"
else
	b1=1
	b2=1
	b3=$xpx
	b4=$ypx
fi

echo "cube size:  $xpx  $ypx  pixels"

# get average spectra for all mapped materials:
avspec='cmds.all.support/cmd.get.mapped.material.spectral.averages-v5'
shortid=`cat AAA.info/shortcubeid.txt`   # short cube ID  up to 10 characters
cscale=`cat AAA.info/cube-scale-factor`

if [ "$1" = "all" ]
then
	dirlist='all'
else
	dirlist=$*
fi

echo " working,  short ID= $shortid   Cube scale facotor= $cscale"

echo "$avspec  $shortid  $cubepath  $cscale  spreslt1 box $b1 $b2 $b3 $b4 dirs $dirlist"

      $avspec  $shortid  $cubepath  $cscale  spreslt1 box $b1 $b2 $b3 $b4 dirs $dirlist

echo "now add spreslt1 to restart file"

cp -a r1 r1.bak

# get size in specpr records

spfilebytes=`ls -l spreslt1 | awk '{ print $5}'`
sprecs=`expr $spfilebytes / 1536 - 1`

ex - r1 <<EOI
/^ivfl=/ s,ivfl=.dev.null,ivfl=spreslt1 ,
/^isavt=/ s/.unasnd./spreslt1/
/^iprtv=/ s/   0/$sprecs /
w
q
EOI


echo " "
echo "finished getting average spectra " `date`
echo " "