Differences between revisions 1 and 9 (spanning 8 versions)
⇤ ← Revision 1 as of 2016-02-18 11:24:46 →
Size: 3708
Editor: BMittan
Comment:
← Revision 9 as of 2016-08-10 01:01:11 → ⇥
Size: 2384
Editor: EricPalmer
Comment:
Deletions are marked like this. Additions are marked like this.
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= Block 4 - Iterate V0 = ## page was renamed from Block 5 - Iterate V0
## page was renamed from Block 4 - Iterate V0
= Block 5 - Iterate V0 =
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 (./) copied from working--needs revision
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 * 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/
}}}
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 * 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
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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 workingDirectory
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 (./) How to handle the different scenarios? Perhaps needs sub headings?
==== Scenario - 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 }}}

==== Scenario - Recently Tiled ====
{{{
## SCENARIO 2: Iterate landmarks that were just created by tiling
cp LMRKLIST1.TXT LIST.TXT
duplicates
## END OF SCENARIO 2
}}}


==== Scenario - 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

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 have completed the processing steps in Block 1 - Setup Directory

User inputs

Procedure

1. Initial Inputs

# User inputs:

2. Set-up

# Set-Up
cd workingDirectory
script
date
pwd
ls -l

3. Set-up batch iteration files

Scenario - 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

Scenario - Recently Tiled

## SCENARIO 2: Iterate landmarks that were just created by tiling 
cp LMRKLIST1.TXT LIST.TXT
duplicates 
## END OF SCENARIO 2

Scenario - 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)

CategoryHowTos

Block 5 - Iterate (last edited 2016-08-10 01:01:11 by EricPalmer)