LANE=1
CYCLES=5
YPIXELS=10000
XPIXELS=2048
SWATHNUM=1
SURFACE=top
FWD=1
REV=2
SEQRUN=$FWD
TOPDIR=BLESS_SN870_LANE_${LANE}_SWATH${SWATHNUM}_SURFACE_${SURFACE}_YPIXELS_${YPIXELS}
OUTPUTPREFIX=s_${LANE}_${SEQRUN}
if [[ $1 == "clean" ]]
then
    echo "clean all, press return"
    read
    rm -rf ${TOPDIR}
    exit
fi

SOURCE=$1/Images/L00${LANE}

if [ ! -d $SOURCE ]
then
  echo 'sorry' $SOURCE 'not found'
  exit
fi
echo 'using images from ' $SOURCE

    
if [ -d $TOPDIR ]
then
  echo 'oops' $TOPDIR 'exists'
  exit
fi

mkdir $TOPDIR
cd $TOPDIR
mkdir Images
cd Images
mkdir L00${LANE}
cd L00${LANE}
for((c=1;c<=$CYCLES;c++));
do
  IMAGEFILE_A=${SOURCE}/C${c}.${SEQRUN}/*_${SURFACE}_s${SWATHNUM}_a.tif
  echo $IMAGEFILE_A
  if [ ! -d C${c}.${SEQRUN} ]
  then
    mkdir C${c}.${SEQRUN}
  fi
  tiffsplit $IMAGEFILE_A ./C${c}.${SEQRUN}/A 2>/dev/null
  mogrify -crop ${XPIXELS}x${YPIXELS} ./C${c}.${SEQRUN}/Aaaa.tif
  tiffsplit ./C${c}.${SEQRUN}/Aaaa.tif ./C${c}.${SEQRUN}/
  rm ./C${c}.${SEQRUN}/Aaaa.tif
  mv ./C${c}.${SEQRUN}/aaa.tif ./C${c}.${SEQRUN}/${OUTPUTPREFIX}_a.tif
  rm ./C${c}.${SEQRUN}/a*.tif
done

for((c=1;c<=$CYCLES;c++));
do
  IMAGEFILE_C=${SOURCE}/C${c}.${SEQRUN}/*_${SURFACE}_s${SWATHNUM}_c.tif
  echo $IMAGEFILE_C
  if [ ! -d C${c}.${SEQRUN} ]
  then
    mkdir C${c}.${SEQRUN}
  fi
  tiffsplit $IMAGEFILE_C ./C${c}.${SEQRUN}/C 2>/dev/null
  mogrify -crop ${XPIXELS}x${YPIXELS} ./C${c}.${SEQRUN}/Caaa.tif
  tiffsplit ./C${c}.${SEQRUN}/Caaa.tif ./C${c}.${SEQRUN}/
  rm ./C${c}.${SEQRUN}/Caaa.tif
  mv ./C${c}.${SEQRUN}/aaa.tif ./C${c}.${SEQRUN}/${OUTPUTPREFIX}_c.tif
  rm ./C${c}.${SEQRUN}/a*.tif
done

for((c=1;c<=$CYCLES;c++));
do
  IMAGEFILE_G=${SOURCE}/C${c}.${SEQRUN}/*_${SURFACE}_s${SWATHNUM}_g.tif
  echo $IMAGEFILE_G
  if [ ! -d C${c}.${SEQRUN} ]
  then
    mkdir C${c}.${SEQRUN}
  fi
  tiffsplit $IMAGEFILE_G ./C${c}.${SEQRUN}/G 2>/dev/null
  mogrify -crop ${XPIXELS}x${YPIXELS} ./C${c}.${SEQRUN}/Gaaa.tif
  tiffsplit ./C${c}.${SEQRUN}/Gaaa.tif ./C${c}.${SEQRUN}/
  rm ./C${c}.${SEQRUN}/Gaaa.tif
  mv ./C${c}.${SEQRUN}/aaa.tif ./C${c}.${SEQRUN}/${OUTPUTPREFIX}_g.tif
  rm ./C${c}.${SEQRUN}/a*.tif
done


for((c=1;c<=$CYCLES;c++));
do
  IMAGEFILE_T=${SOURCE}/C${c}.${SEQRUN}/*_${SURFACE}_s${SWATHNUM}_t.tif
  echo $IMAGEFILE_T
  if [ ! -d C${c}.${SEQRUN} ]
  then
    mkdir C${c}.${SEQRUN}
  fi
  tiffsplit $IMAGEFILE_T ./C${c}.${SEQRUN}/T 2>/dev/null
  mogrify -crop ${XPIXELS}x${YPIXELS} ./C${c}.${SEQRUN}/Taaa.tif
  tiffsplit ./C${c}.${SEQRUN}/Taaa.tif ./C${c}.${SEQRUN}/
  rm ./C${c}.${SEQRUN}/Taaa.tif
  mv ./C${c}.${SEQRUN}/aaa.tif ./C${c}.${SEQRUN}/${OUTPUTPREFIX}_t.tif
  rm ./C${c}.${SEQRUN}/a*.tif
done