= How to Iterate Landmarks V0 =

== Description ==

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 ==
 * You have invoked a Bourne-Again Shell (bash) on ormacsrv1.lpl.arizona.edu
 * You are a member of the group OREX\spc
 * You have set up a skeleton directory in the following format:
{{{
 /SPC_Test/F3G-Nav/
                   ORex/
                            DATA/
                   base/
                            IMAGEFILES/
                            SHAPEFILES/
                   lsupport/
                   orig/
                   results/
                   test/
}}}
 * You have completed the processing steps in How to Test Directory Set-Up - ORIG
 * If you are working in the '''test/''' sub-directory, you have set up the test sub-directory following the steps in How to 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-04-01-Iterate-Landmarks-01stInvocation-PostRegistrationOfDSNavCamImages')


== Procedure ==

=== 1. Initial Inputs ===

{{{
# 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-04-01-Iterate-Landmarks-PostRegistrationOfDSNavCamImages
#blockID=Block-04-01-Iterate-Landmarks-${subTestID}-Post20cmTiling
#blockID=Block-04-01-Iterate-Landmarks-${subTestID}-Post10cmTiling
blockID=Block-04-01-Iterate-Landmarks-${subTestID}-Post05cmTiling
}}}

=== 2. Set-up ===
{{{
# Set-Up
cd /SPC_Test/$testID/$dirID/
script
date
pwd
ls -l
}}}

=== 3. Set-up batch iteration files ===
 (./) How to handle the different scenarios?  Perhaps needs sub headings?

{{{
# 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
}}}

=== 4. Invoke batch iteration ===
{{{

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

=== 5. Monitor progress ===
{{{
# Monitor progress
ls
ls -l *.INN *.OOT
find_nofitP
sh support/logEvalP.sh
}}}

=== 6. Check results ===

{{{

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

=== 7. Fix uncorrelated images ===
{{{
# Fix uncorrelated images
.........
}}}

=== 8. Clean directory ===
{{{
# Clean directory
sh rem_script.b
rm TESTFILES/*
rm TESTFILES1/*
}}}

=== 9. Complete procedure ===
{{{
# Block Complete
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}

}}}

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''(Compiled by DL)''

CategoryHowTos