Differences between revisions 4 and 6 (spanning 2 versions)

Block 3 - Register V0

Description

This block batch registers images contained in newImageList.txt. That file is created by the user, typically by hand. It requires the SPC standards of an "END" at the end of the file and each image should be preceded by a space.

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
You have populated the working directory with new images following the steps in:
- Block 2 - Ingest
You have populated lsupport/newImageList.txt with the correct subset of images to register

User inputs

The filename of a list of images to register.

Procedure

1. Initial inputs

imgListName=whatever-list.txt

2. Set-up

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

3. Set-up batch register files

# set-up batch register files
ln -s lsupport/$imgListName make_script.in
ln -s scripts/make_scriptR.SEED make_scriptR.seed
make_scriptR
ls -l

4. Batch register images

# Batch register images
register -v
nohup sh run_script.b &

5. Monitor progress

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

6. Check results

# Check results
ls *OOT > tmpList
sh support/after.sh 0.5 tmpList
cat goodList 
cat badList
sh support/evalReg.sh badList

7. Fix unregistered images

# Fix unregistered images
.......

8. Clean directory

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

9. Complete procedure

# Block Complete
exit
# Save block log
mv typescript step-reg

(Compiled by DL)

CategoryHowTos

-  ⇤ ← Revision 4 as of 2016-02-23 23:55:51 → 
  Size: 3281
  Editor: EricPalmer
  Comment:
+   ← Revision 6 as of 2016-02-24 00:23:54 → ⇥
  Size: 1889
  Editor: EricPalmer
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
- (./) copied from working--needs revision
-Line 8:
+Line 7:
-This block batch registers images contained in lsupport/PICTLIST.TXT.
+This block batch registers images contained in newImageList.txt.  That file is created by the user, typically by hand. It requires the SPC standards of an "END" at the end of the file and each image should be preceded by a space.
-Line 12:
+Line 11:
- * 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.
-Line 28:
+Line 13:
- * You have populated the orig/ directory with test-specific images following the steps in:
  * Block 2 - Ingest
  * Block ?????????
 * You have populated lsupport/PICTLIST-forRegistering.TXT with the correct subset of images to register
+ * You have populated the working directory with new images following the steps in:
  * [[Block 2 - Ingest]]
-Line 33:
+Line 16:
+ * You have populated lsupport/newImageList.txt with the correct subset of images to register
-Line 34:
+Line 18:
+----
-Line 35:
+Line 20:
- * '''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-03-01-Register-Images-F3G-GenericImages')
+The filename of a list of images to register.
-Line 40:
+Line 22:
+----
-Line 44:
+Line 27:
-{{{
# User inputs:
testID=F3G-Nav
#subTestID=F3G1
#subTestID=F3G2
#subTestID=F3G3
#subTestID=F3G4
#subTestID=F3G5
#subTestID=F3G6
subTestID=F3G7
dirID=test
#blockID=Block-03-01-Register-Images-F3G-GenericImages
blockID=Block-03-01-Register-Images-${subTestID}-Images
}}}
+imgListName=whatever-list.txt
-Line 73:
+Line 42:
-cp lsupport/PICTLIST-forRegistering.TXT make_script.in
cat make_script.in
cp scripts/make_scriptR.SEED make_scriptR.seed
cat make_scriptR.seed
+ln -s lsupport/$imgListName make_script.in
ln -s scripts/make_scriptR.SEED make_scriptR.seed
-Line 97:
+Line 64:
- (./) how to handle variance within?  Needed?
-Line 100:
+Line 66:
-sh support/after.sh 0.5 make_script.in
+ls *OOT > tmpList
sh support/after.sh 0.5 tmpList
-Line 103:
+Line 70:
-convert TESTFILES/*.pgm TESTFILES/*.jpg
open TESTFILES/*.jpg

## [email protected]:
cp TESTFILES/*.jpg ~/send
# images inspected on home-machine
## END OF VARIANCE
+sh support/evalReg.sh badList
-Line 133:
+Line 93:
-if [ ! -d /SPC_Test/$testID/log ]; then
  mkdir /SPC_Test/$testID/log
fi
mv typescript /SPC_Test/$testID/log/log-typescript-${blockID}
+mv typescript step-reg