Block-3B - AUTOREGISTER IMAGES - BATCH

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##                                                                      ##
##                               BLOCK 3B                               ##
##                         AUTOREGISTER - BATCH                         ##
##                                                                      ##
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## This block batch autoregisters images contained in lsupport/listImagesForRegistering

## 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 additionally populated the orig/ dircteory with test-specific images as per 
## Block 2A / 2B
## User has populated lsupport/listImagesForRegistering with the correct subset of 
## images to register 
## User has registered images listed in lsupport/listImagesForRegistering as per 
## Block 3A 

## User inputs:
## testID: Name of the F3 test directory (for example, F3E-Limbs)
## 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-3B-Autoregister-Images-F3G-GenericImages)

# User inputs:
testID=F3G-Nav
dirID=orig
blockID=Block-3B-Autoregister-Images-F3G-GenericImages

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

date
pwd
ls -l

# set-up batch autoregister files
cp lsupport/listImagesForRegistering make_script.in
cat make_script.in
cp scripts/make_scriptA.seed .
cat make_scriptA.seed
make_scriptA
ls -l

# Batch autoregister images
ls -l /usr/local/bin/autoregister
nohup sh run_script.b &

# Monitor progress
ls -l *.INN *.OOT

# Check results
# Since early iterations are not masked - logEval picks up NO CORRS which are later eliminated
sh support/logEvalP.sh
cat logResults.txt 
cat lowImg.txt
cat redo.txt

# Inspect display outputs
## DECISION:

## OPTION 1: Inspect display outputs on ormacsrv1
ls TESTFILES > listTemp
while read line; do
echo "Displaying $line"
done < listTemp 
rm listTemp
## END OF OPTION 1

##OPTION 2: Inspect disaply output on a different machine
convert TESTFILES/*.pgm TESTFILES/*.jpg
cp TESTFILES/*.jpg ~/send
# images inspected on different machine
## END OF OPTION2

# Fix uncorrelated images
# Manually autoregister images and inspect output displays as required

# Clean directory
sh rem_script.b
rm TESTFILES/*
rm nohup.out

# 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}