Block-4A - ITERATE LANDMARKS

##########################################################################
##                                                                      ##
##                               BLOCK 4A                               ##
##                          ITERATE LANDMARKS                           ##
##                                                                      ##
##########################################################################

## This block iterates a set of landmarks sepcified by the user, using the lithosP
## options contained in the file: /SPC_Test/F3-base/base/scripts.make_scriptP.seed

## 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
## If working in the test/ sub-directory, user has set up the test sub-directory, as per
## Block 1B - TEST DIRECTORY SET-UP - TEST

## 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)
## blockID: User-specified identifier for typescript textfile name 
##          (for example, Block-4A-Iterate-Landmarks-PostRegistrationOfDSNavCamImages)

# User inputs:
testID=F3G-Nav
subTestID=F3G1
#subTestID=F3G2
#subTestID=F3G3
#subTestID=F3G4
#subTestID=F3G5
#subTestID=F3G6
#subTestID=F3G7
dirID=orig
#dirID=test
blockID=Block-4A-Iterate-Landmarks-PostRegistrationOfDSNavCamImages
#blockID=Block-4A-Iterate-Landmarks-${subTestID}-Post20cmTiling
#blockID=Block-4A-Iterate-Landmarks-${subTestID}-Post10cmTiling
#blockID=Block-4A-Iterate-Landmarks-${subTestID}-Post05cmTiling

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

date
pwd
ls -l

# Set-up batch iteration files

## DECISION

## SCENARIO 1: Iterate all landmarks lised in LMRKLIST.TXT
cp LMRKLIST.TXT make_script.in 
## END OF SCENARIO 1

## SCENARIO 2: Iterate landmarks which overlap a region-of-interest defined via a bigmap .in file
## TAG100.in is a 100m x 100m region around the center of TAG site 1
cat support/TAG100.in
ls -l /usr/local/bin/bigmap
bigmap < support/TAG100.in
cp USED_MAPS.TXT LIST.TXT 
duplicates
## END OF SCENARIO 2

cat make_script.in
ls -l /usr/local/bin/MAKE_LMRKLISTX
MAKE_LMRKLISTX 
cp scripts/make_scriptP.seed .
cat make_scriptP.seed
make_scriptP | tee run.sh
ls -l

# Invoke batch iteration
cat INIT_LITHOS.TXT
lithosP -v
nohup sh run.sh &

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

# Check results
find_nofitP | tee log-fitP
sh support/logEvalP.sh
cat logResults.txt 
cat lowImg.txt
cat redo.txt

# Fix uncorrelated images
# Manual correlation as required

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

# Block Complete
date
exit

# Save block log
if [ ! -d /SPC_Test/$testID/log ]; then
  mkdir /SPC_Test/$testID/log
fi
mv typescript /SPC_Test/$testID/log/log-typescript-${blockID}