Test F3F Procedures Block-6B - TILE - BIGMAP

##########################################################################
##                                                                      ##
##                               BLOCK 6B                               ##
##                            TILE - BIGMAP                             ##
##                                                                      ##
##########################################################################

## This block tiles a bigmap with a new suite of landmarks. Bigmap and maplet parameters
## are specified by the user, using the bigmap in files contained in 
## /SPC_Test/F3-base/base/support/ and the lithos options contained in the seed files in: 
## /SPC_Test/F3-base/base/scripts/

## Assumptions:
## User has invoked a Bourne-Again Shell (bash) on ormacsrv1.lpl.arizona.edu
## User is a member of the group OREX\spc
## User has set up a skeleton directory in the following format:
## /SPC_Test/F3G-Nav/
##                   base/
##                            IMAGEFILES/
##                            SHAPEFILES/
##                   lsupport/
##                            PICTLIST.TXT
##                   orig/
##                   results/
##                   test/
## User has completed the processing steps comprising Block 1A - TEST DIRECTORY
## SET-UP - ORIG
## User has set up the test sub-directory, as per Block 1B - TEST DIRECTORY 
## SET-UP - TEST
## User has ingested and registered test images as per Blocks 2A, 2B, and 3A

## User inputs:
## testID: Name of the F3 test directory (for example, F3E-Limbs)
## subTestID: (if required) Identifier for sub-test work (for example, F3G1)
## dirID: Name of sub-directory in which to work (e.g. orig, or test)
## bigmapInFileNm: Name of bigmap .in file located in /SPC_Test/F3-base/base/support/
## (for example, TILE20)
## tilingSeedFileNm: Name of tiling seeed file located in /SPC_Test/F3-base/base/scrits/
## (for example, XXX020)
## gSD: Maplet Ground Sample Distance in km (for example, 0.0002)
## blockID: User-specified identifier for typescript textfile name 
##          (for example, Block-6B-Tile-Bigmap-F3G1-20cmTiling)

# User inputs:
export testID=F3F-Photo
#export subTestID=NONE
export subTestID=F3F1
#export subTestID=F3F2
#export subTestID=F3F3
#export bigmapInFileNm=TILE20
#export bigmapInFileNm=TILE10
export bigmapInFileNm=TILE05
#export tilingSeedFileNm=XXX020
#export tilingSeedFileNm=XXX010
export tilingSeedFileNm=XXX005
#export gSD=0.0002
#export gSD=0.0001
export gSD=0.00005
export dirID=test${subTestID}
export blockID=Block-6B-Tile-Bigmap-${subTestID}-${bigmapInFileNm}

# Set-Up
cd /SPC_Test/$testID/$dirID/
script

# Display user inputs
echo $testID
echo $subTestID
echo $bigmapInFileNm
echo $tilingSeedFileNm
echo $gSD
echo $dirID
echo $blockID

date
pwd
ls -l

# Make tiling bigmap
echo "Bigmap .in file: support/${bigmapInFileNm}.in"
cat support/${bigmapInFileNm}.in
#ls -l /usr/local/bin/bigmap
bigmap -v
bigmap < support/${bigmapInFileNm}.in | tee log-${bigmapInFileNm}

# check resulting file
## Tiling bigmap has the same name as the .in file, 
## i.e. TILE20.in, produces the tiling bigmap: TILE20
echo ${bigmapInFileNm} | showmap

# Inspect showmap

## OPTION 1: Inspect showmap outputs on cloud
/opt/local/bin/display ${bigmapInFileNm}.pgm
## END OF OPTION 1

##OPTION 2: Inspect showmap output on a different machine
/opt/local/bin/convert ${bigmapInFileNm}.pgm ~/send/${bigmapInFileNm}.jpg
# showmap output inspected on different machine
## END OF OPTION 2

# Log showmap output
/opt/local/bin/convert ${bigmapInFileNm}.pgm ${bigmapInFileNm}-beforeTiling.jpg

# Set up tiling
cp MAPFILES/${bigmapInFileNm}.MAP MAPFILES/XXXXXX.MAP
ls -l /usr/local/bin/map_coverage
echo "XXXXXX" > map_coverage.in
echo 0 >> map_coverage.in
echo $gSD >> map_coverage.in
map_coverage < map_coverage.in

# Inspect map_coverage output

## OPTION 1: Inspect showmap outputs on cloud
/opt/local/bin/display coverage_m.pgm
## END OF OPTION 1

##OPTION 2: Inspect map_coverage output on a different machine
/opt/local/bin/convert coverage_m.pgm ~/send/coverage_m.jpg
# map_coverage output inspected on different machine
## END OF OPTION 2

# Log map_coverage output
/opt/local/bin/convert coverage_m.pgm coverage_m-${bigmapInFileNm}-beforeTiling.jpg

# Continue tiling set-up
echo "N" | make_tilefile | tee make_tilefile.out
sed 1d make_tilefile.out > temp.out
echo "XXXXXX" > make_scriptT.in
echo "scripts/${tilingSeedFileNm}.seed" >> make_scriptT.in
cat temp.out >> make_scriptT.in 
cat make_scriptT.in
cat scripts/${tilingSeedFileNm}.seed
make_scriptT
ls -l

## VARIANCE F3F: Edit INN files so that F3F-lithos is invoked
ls run_script* > listRUN
while read line; do
echo $line
sed 's/\/usr\/local\/bin/\./g' $line > TEMP
mv TEMP $line
done < listRUN
head run_script.b
## END OF VARIANCE

# Invoke tiling script
cat INIT_LITHOS.TXT
#lithos -v
./LITHOS -v
nohup sh run_script.b &

# Monitor progress
ls -l *.INN *.OOT
find_nofitT
sh support/logEvalP.sh

# Check results - correlation
find_nofitT | tee log-fitT-${bigmapInFileNm}
sh support/tileEval.sh
cat evalImg.txt 
cat evalLow.txt
cat evalOut.txt
cat evalRedo.txt

# Fix uncorrelated images
# Manually correlate as required

# Check results - tiling
map_coverage < map_coverage.in

# Inspect coverage_m:

## OPTION 1: Inspect display outputs on cloud
/opt/local/bin/display coverage_m.pgm
## END OF OPTION 1

##OPTION 2: Inspect display output on a different machine
cp coverage_m.pgm ~/send/
# images inspected on different machine
## END OF OPTION 2

# Log map_coverage output
/opt/local/bin/convert coverage_m.pgm coverage_m-${bigmapInFileNm}-afterTiling.jpg

# Fix tiling gaps
# Manually create maplets and correlate images as required

# Save tiling log files
mkdir -p /SPC_Test/$testID/$dirID/log/log-${blockID}
mv coverage_m-${bigmapInFileNm}-beforeTiling.jpg /SPC_Test/$testID/$dirID/log/log-${blockID}/
mv coverage_m-${bigmapInFileNm}-afterTiling.jpg /SPC_Test/$testID/$dirID/log/log-${blockID}/
mv *.INN *.OOT run* /SPC_Test/$testID/$dirID/log/log-${blockID}/
mv log-fitT-${bigmapInFileNm} eval* /SPC_Test/$testID/$dirID/log/log-${blockID}/

# Clean directory
sh rem_script.b
rm TESTFILES/*
rm TESTFILES1/*

# Generate and save evaluation files
bigmap < support/EVAL20.in
cp MAPFILES/EVAL20.MAP /SPC_Test/$testID/$dirID/log/log-${blockID}/EVAL20_${subTestID}_${bigmapInFileNm}.MAP
if [ ! -f MAPFILES/TVAL20.MAP ]; then
  ln -s /SPC_Test/truth/TVAL20.MAP MAPFILES/TVAL20.MAP
fi
bigMapRef < support/MREF20.in
cp MAPFILES/MREF20.MAP /SPC_Test/$testID/$dirID/log/log-${blockID}/MREF20_${subTestID}_${bigmapInFileNm}.MAP

# Block Complete
date
exit

# Save block log
if [ ! -d /SPC_Test/$testID/log ]; then
  mkdir /SPC_Test/$testID/log
fi

# OPTION 1: OVERWRITE TYPESCRIPT LOG
mv typescript /SPC_Test/$testID/log/log-typescript-${blockID}
# END OF OPTION 1

# OPTION 2: APPEND TYPESCRIPT LOG
cat typescript >> /SPC_Test/$testID/log/log-typescript-${blockID}
# END OF OPTION 2