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/

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
If you are working in the test/ sub-directory, you have set up the test sub-directory following the steps in Block 01-02 - 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

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
#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

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

# 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

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

# Monitor progress
ls
ls -l *.INN *.OOT
find_nofitP
sh support/logEvalP.sh

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

# Fix uncorrelated images
.........

# Clean directory
sh rem_script.b
rm TESTFILES/*
rm TESTFILES1/*

# 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}

(Compiled by DL)

CategoryHowTos

Choose style		book: Create a structured PDF document with headings, chapters, etc. webpage: Specifies that the HTML sources are unstructured (plain web pages.) A page break is inserted between each file or URL in the output. continuous: Specifies that the HTML sources are unstructured (plain web pages.) No page breaks are inserted between each file or URL in the output.
Title		Title of the document for the front page.
Heading 1 as title		Extract the first heading of the document and use it as title. If checked the title field has no effect.
Title file/image		The title image or HTML page. These file has to be an attachments!
Version		Specify document version to be displayed on the title page.
Author		Intellectual property owner of this document.
Copyright		Copyright notice for this document.
Apply page information		Information about who and when modified the document are applied at the end.

Output format		Specifies the output format.
Output options	Grayscale document Title page Compression : JPEG big images

Body color		Enter the HTML color for the body (background).
Body image		Enter the image file for the body (background). These file has to be an attachments!
Text color		Enter the HTML color for the text.
HTTP links color		Sets the color of links.
Style of HTTP links
Create HTTP links		Enables generation of links in PDF files.

Base font size		Set the default size of text.
Line spacing		Set the spacing between lines of text.
Body typeface		Choose the default typeface (font) of text.
Heading typeface		Choose the default typeface (font) of headings.
Header/Footer size		Set the size of header and footer text.
Header/Footer font		Choose the font for header and footer text.
Charset set		Change the encoding of the text in document.
Embed fonts		Check to embed font in the output file.

Page mode		Controls the initial viewing mode for the document. Document: Displays only the docuemnt pages. Outline: Display the table-of-contents outline as well as the document pages. Full-screen: Displays pages on the whole screen; this mode is used primarily for presentations.
Page layout		Controls the initial layout of document pages on the screen. Single: Displays a single page at a time. One column: Displays a single column of pages at a time. Two column left/right: Display two columns of pages at a time; the first page is displayed in the left or right column as selected.
First page		Choose the initial page that will be shown.

Input

Output

Page

Contents

Colors

Fonts

PDF

Security

Expert

About

How to Iterate Landmarks V0

Description

Assumptions

User inputs

Procedure

Encryption		Check to number all of the headings in the document.
Permissions	Print Modify Copy Annotate	Specifies the document permissions.
User password		Specifies the user password to restrict viewing permissions on this PDF document. Empty for no encryption.
Owner password		Specifies the owner password to control who can change document permissions etc. If this field is left blank, a random 32-character password is generated so that no one can change the document.

Language translation		Specify language to use for date and time format.
Dynamic code block		Shrink code blocks on page.
Lines in code block		Show line numbers for code blocks.
Use dots instead of spaces in code blocks		Make spaces visable by dots (·) instead of white spaces.
Use a para character for line breaks		Make line breaks visable by a extra character (¶) at the end.
Enable debugging information		Enable this feature if you searching for problems or intent to report a bug report