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| * '''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') |
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| 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-${subTestID}-Post05cmTiling |
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| cd /SPC_Test/$testID/$dirID/ | cd /SPC_Test/workingDirectory |
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| (./) How to handle the different scenarios? Perhaps needs sub headings? | ==== Full list of landmarks ==== |
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| ## DECISION | |
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| cp LMRKLIST.TXT make_script.in | cp LMRKLIST.TXT LIST.TXT duplicates |
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| ## SCENARIO 2: Iterate landmarks which overlap a region-of-interest defined via a bigmap .in file | }}} ==== Recently Tiled ==== {{{ ## SCENARIO 2: Iterate landmarks that were just created by tiling cp LMRKLIST1.TXT LIST.TXT duplicates ## END OF SCENARIO 2 }}} ==== List of landmarks from a region (BIGMAP) ==== {{{ ## SCENARIO 3: Iterate landmarks which overlap a region-of-interest defined via a bigmap .in file |
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| cat support/TAG100.in | cat lsupport/TAG100.in |
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| bigmap < support/TAG100.in | bigmap < lsupport/TAG100.in |
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| ## END OF SCENARIO 2 | ## END OF SCENARIO 3 }}} |
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| ==== Finish Setup ==== {{{ |
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| === 7. Fix uncorrelated images === {{{ # Fix uncorrelated images ......... }}} |
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| if [ ! -d /SPC_Test/$testID/log ]; then mkdir /SPC_Test/$testID/log fi mv typescript /SPC_Test/$testID/log/log-typescript-${blockID} |
mv typescript <newname> |
Block 5 - Iterate V0
copied from working--needs revision
Description
This block iterates a set of landmarks specified 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 Block 1 - Setup Directory
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
Procedure
1. Initial Inputs
# User inputs:
2. Set-up
# Set-Up cd /SPC_Test/workingDirectory script date pwd ls -l
3. Set-up batch iteration files
Full list of landmarks
# Set-up batch iteration files ## SCENARIO 1: Iterate all landmarks lised in LMRKLIST.TXT cp LMRKLIST.TXT LIST.TXT duplicates ## END OF SCENARIO 1
Recently Tiled
## SCENARIO 2: Iterate landmarks that were just created by tiling cp LMRKLIST1.TXT LIST.TXT duplicates ## END OF SCENARIO 2
List of landmarks from a region (BIGMAP)
## SCENARIO 3: 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 lsupport/TAG100.in ls -l /usr/local/bin/bigmap bigmap < lsupport/TAG100.in cp USED_MAPS.TXT LIST.TXT duplicates ## END OF SCENARIO 3
Finish Setup
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
8. Clean directory
# Clean directory sh rem_script.b rm TESTFILES/* rm TESTFILES1/*
9. Complete procedure
# Block Complete exit # Save block log mv typescript <newname>
(Compiled by DL)