= ISIS to Emission =

 * NOTE: We generate the emission data first since this shell script first initializes the LROC NAC EDR, which will be used by incidence and I/F.  The shell script here generates phoE.IMG.
{{{
# 4 Aug 2017 - Eric E. Palmer
# Script to do many of the steps required for building a photometric cube
# Requires a lot of directory setup.
#       Calibrated images in working/NEW_IMAGES
#  EDR images in img-<last4)[LR]
# Modified by JRW Oct 6 2017
# Modified by JRW Aug 28 2018
# Modified by JRW Nov 19 2018 to include last five digits.

# Usage
#                gen.sh <calibratedIMG> <last5[LR]>
file=$1
out=$2

if [ '$file' == '' ]
then
        echo "Usage $0 <calibratedIMG> <last5L>"
fi

if [ '$out' == '' ]
then
        echo "Usage $0 <calibratedIMG> <last5L>"
fi

echo "File: $file"
echo "Outfile: $out"

if [ 'two' == 'two' ]
then
        lronac2isis FROM=$file.IMG TO=$file.cub
        spiceinit FROM=$file.cub shape=ellipsoid
        caminfo FROM=$file.cub TO=info.txt

        # Generate emission data
        phocube FROM=$file.cub TO=phoE-$out.cub I=false PHASE=false LAT=false LON=false
        isis2pds FROM=phoE-$out.cub to=phoE-$out.img BITTYPE=u16bit STRETCH=linear MINPER=0 MAXPER=100
fi

calFile=`echo $file | tr E C`
echo "calFile: $calFile"

# Create an image that is really the image's phase
#ln -s ../working/NEW_IMAGES orig
#../bin/mergePhase $calFile emiss.img
#mv M*C.IMG orig


# Get the directory ready for dumpMapLRO.f
#ln -s ../working/MAPFILES .
}}}

 * Generating the IMG takes awhile, so we have a wrapper to run all the images at once. NOTE: This wrapper requires directory setup. Each image is placed in its own folder; the folder name is the last 5 digits of the NAC, plus the L or R for left/right. The wrapper should be placed in the directory containing all the image folders.
{{{
# 5 Aug 2018 - John Weiric2
# Wrapper for ISISe.sh to run multiple files
# Usage
#       sh wrapperISISe.sh <imageList>
# Modified Nov 19 2018 to include last 5 digits.

file=$1
list=`cat $file`


for i in $list
do

# need to determine the last five characters since
# that is how the directories are set up
  strLength=`echo $i | wc | cut -c23-24`
  if [ "$strLength" != "13" ]
  then
    if [ "$strLength" != "14" ]
    then
      echo "string length not supported"
      exit
    fi
  fi

  if [ "$strLength" == "13" ]
  then
    lastFive=`echo $i | cut -c6-11`
    echo $lastFive
  fi
  if [ "$strLength" == "14" ]
  then
    lastFive=`echo $i | cut -c7-12`
    echo $lastFive
  fi

#exit
# with last five character, can now get into folder

  cd img-$lastFive
  ../ISISe.sh $i $lastFive
  cd ..

done
}}}

 * With the emission IMG in hand, now attach the original image header. The source code is found here. [[attachment:mergeEmission.c]]
 * Below is a wrapper to run the "merge" software.
{{{
# 20 Nov 2018 - John Weirich
# Wrapper for t.mergeEmission to run multiple files
# Usage
#       sh wrapperMergeEmission.sh <imageList>

file=$1
list=`cat $file`

cd /Users/JW/LDAP16/IMG_RG2

for i in $list
do

# need to determine the last five characters since
# that is how the directories are set up
  strLength=`echo $i | wc | cut -c23-24`
  if [ "$strLength" != "13" ]
  then
    if [ "$strLength" != "14" ]
    then
      echo "string length not supported"
      exit
    fi
  fi

  if [ "$strLength" == "13" ]
  then
    lastFive=`echo $i | cut -c6-11`
    echo $lastFive
  fi
  if [ "$strLength" == "14" ]
  then
    lastFive=`echo $i | cut -c7-12`
    echo $lastFive
  fi

#exit
# with last five character, can now get into folder

echo "$i.IMG" > emmTmp
echo "/Users/JW/LDAP16/CubesReinerGamma2/img-$lastFive/phoE-$lastFive.img" >> emmTmp
~/Dropbox/Ingenii/src/t.mergeEmission < emmTmp

\mv -f ME* /Users/JW/LDAP16/CubesReinerGamma2/working/NEW_IMAGES/

done

rm emmTmp
}}}