parallel_DEM-SMG.sh

#!/bin/bash

set -ue
set -xv

# ------------------------------------------------------------------------------------------------
# This script receives a input file with a list of two files names for the DEM (left and right)
# ------------------------------------------------------------------------------------------------

INPUT_FILE="$1"
declare -a FILES=()
declare -a NAMES=()
declare -a FILESL1=()
declare -a FILESL2=()

OLDIFS="$IFS"
IFS=$'\n' FILES=($(cat $INPUT_FILE))
IFS="$OLDIFS"
NUMLINES=${#FILES[@]}

for ((i=0;i<$NUMLINES;i++)); do
    FILE=${FILES[$i]}

    NAME=${FILE:0:26}
    #NAME=${LINE%.IMG}
    #NAME=${NAME%.img}
    NAMES[$i]=${NAME}

    FILE_L2="${NAME}_L1.map.cub"
    FILESL2[$i]="$FILE_L2"
    FILE_L1="${NAME}_L1.cub"
    FILESL1[$i]="$FILE_L1"

done

parallel mroctx2isis from={}.IMG to={.}_L0.cub ::: ${NAMES[@]}

parallel spiceinit from={.}_L0.cub ::: ${NAMES[@]}

parallel ctxcal from={.}_L0.cub to={.}_L1cal.cub ::: ${NAMES[@]}

parallel ctxevenodd from={.}_L1cal.cub to={.}_L1.cub ::: ${NAMES[@]}

cam2map4stereo.py ${FILESL1[*]} 

RES_STEREO=$(printf "_%s" "${NAMES[@]}")
RES_STEREO="${RES_STEREO:1}"

bundle_adjust ${FILESL2[*]} \
  -o ba/ba

parallel_stereo ${FILESL2[*]} \
  results_stereo/$RES_STEREO \
  --bundle-adjust-prefix ba/ba

pc_align --max-displacement 7000 --datum MOLA   \
  --highest-accuracy    \
  --save-transformed-source-points           \
  --save-inv-transformed-reference-points    \
  results_stereo/${RES_STEREO}-PC.tif crop-mola.tif -o align/align   

point2dem --t_srs "+proj=eqc +lat_0=0 +lon_0=0 +k=1 +a=3396190 +b=3396190 +units=m +no_defs" \
   --nodata -32767 --dem-hole-fill-len 1000 --orthoimage-hole-fill-len 1000 --remove-outliers-params 75.0 3.0 \
   --orthoimage results_stereo/${RES_STEREO}-L.tif align/align-trans_reference.tif \
    -o ASP-adjusted-${RES_STEREO}


# Cleaning

rm *_L0.cub

rm *_L1cal.cub

rm *_L1.cub


# The end.