= How to Autoregister Images - Batch V0 =

== Description ==

This block batch autoregisters images contained in lsupport/PICTLIST.TXT.

== 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/
}}}
 (./) Need to figure out how we will refer to these (block number? name?) and if they should be links. 
 * You have completed the processing steps in Block 01-01 [[How to Test Directory Set-Up - ORIG]]
 * You have populated the orig/ directory with test-specific images following the steps in:
  * Block 02-01 How to
  * Block 02-02 How to
 * You have populated lsupport/PICTLIST-forRegistering.TXT with the correct subset of images to register 
 * You have registered images listed in lsupport/PICTLIST.TXT-forRegistering.TXT following these steps in Block 03-01 How to


== 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-03-02-Autoregister-Images-01stInvocation-F3G-GenericImages')

== Procedure ==

Copy and paste the following lines in the Unix terminal, only changing for your inputs and variances. Comment lines (# or ##) will appear in the typescript output.

{{{
# User inputs:
testID=F3G-Nav
dirID=orig
blockID=Block-03-02-Autoregister-Images-01stInvocation-F3G-GenericImages

# Set-Up
cd /SPC_Test/$testID/$dirID/
script
date
pwd
ls -l

# set-up batch autoregister files
cp lsupport/PICTLIST-forRegistering.TXT 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
convert TESTFILES/*.pgm TESTFILES/*.jpg
open TESTFILES/*.jpg
## VARIANCE-dlambert@ORMACSRV1.lpl.arizona.edu:
cp TESTFILES/*.jpg ~/send
# images inspected on home-machine
## END OF VARIANCE

# Fix uncorrelated images
.......

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

# 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