Iterate

Loop as required. Do nftBlockFinish when done with iterations.

Log the following. localLoop.sh will handle this

• sigma after each iteration
• nofit "no correlation" flags
  • Stop on a real flag and email
• Number of nofits
• corrEval results

Batch Run

Check the following

• Daemon is running
• Terminate is unset (if you want more than one)

• localLoop.sh is set (map=<ID><Res>)

• interationCount is a useful number. Whatever number is set in "iterationCount" when monitor is start will be increment and used as the $id variable in localLoop.sh. Thus, it is useful to set it to something new if you are doing a different suite of iterations.

For the first 2 full iterations (i.e. over ALL maplets), make sure there are no images with a correlation <0.1 before starting a full iteration. If there are images that are getting a correlation <0.1 even after several iterations, delete if emission angle is >50, illumination coverage (after x-0.025) < 0.5, or phase less than 8 or 9. They are weak images and will not contribute much anyway.

After you have done 2 full iterations, clean according to the criteria for a correlation <0.1, but apply it to correlations <0.3. Again, if after many iterations they still are <0.3, they are not strong anyway.

The final check for an MLN is to use bigEval.sh <Feature Name>A

• If the resulting bigmap has SigmaScore >2, you are done. Make sure you've run at least 2 full iterations (all maplets) to make sure everything has stabilized.

• More iterations may help (stop if the avg sigmaScore is going down) or you may need more images, a fill, or some other technique.

Note: Consider changing USRMX to something other than 12. If there are < 24 landmarks, then using N as user max will be faster. While each process takes longer to run, it is faster than doing two maplets in succession.

Setup ROI Iterate

NOTE - Be sure you have made the bigmap before pasting below.

Because bigmap provides sigmas in km, it lacks the resolution needed for good statistics. Thus, we need to use bigmapRef, which outputs SIGMA.TXT in units of meters. However, bigmapRef needs an additional bigmap name as the first line of the file to define the normal plane. Thus, we have to run normal bigmap before we run bigmapRef

ID=RDL09
Res=5

logP=log/$ID$Res
mkdir -p $logP

bigmap < nftConfig/nftBigmap-$ID-$Res.in

ROI Iterate over new maplets (Note: Uses LMRKLIST1.TXT)

echo "Getting ready for iteration $ID-$Res" >> notes
date >> notes
echo $ID$Res | tee -a notes
echo ${ID}$Res > tmpRun
cat nftConfig/nftBigmap-${ID}-$Res.in >> tmpRun
cat tmpRun >> notes
bigMapRef < tmpRun
tail -2 SIGMAS.TXT | head -1 | tee -a notes
echo y | cp -v LMRKLIST1.TXT LIST.TXT
duplicates

relink.sh scripts/Piterate1St.seed make_scriptP.seed | tee -a notes
ls -l make_scriptP.seed >> notes
MAKE_LMRKLISTX 


make_scriptP | tee run.sh
echo "Running iteration at " `date` >> notes
sh run.sh
monitor

bigMapRef < tmpRun
echo "Post run Sigma" >> notes
tail -2 SIGMAS.TXT | head -1 | tee -a notes

nftBlockFinish.sh nft.$ID

Run AUTOREGISTER before kicking off remaining iterations

grep P6 USED_PICS.TXT > make_script.in
echo END >> make_script.in
echo "Running AUTOREGISTER" > notes

relink.sh support/make_scriptA_jrwLowerC2.seed make_scriptA.seed
make_scriptA
nohup sh run_script.b

autoEval.sh

nftBlockFinish.sh nft.$ID

If AUTOREGISTER excludes many images, do another iterate over the new maplets

autoEval.sh

Make sure you have 3 BBD stations for each image

# Run if RESIDUALS has not been run since tiling
echo "5 .001 .001" | RESIDUALS

getImagesInLandmarks2.sh LMRKLIST1.TXT

sort -k16,16

Setup Batch Iterate NFT Feature (Note: Uses USED_MAPS.TXT)

ID=RDL09
Res=5

echo "Getting ready for iteration $ID-$Res" >> notes
date >> notes
echo $ID$Res | tee -a notes
echo ${ID}$Res > tmpRun
cat nftConfig/nftBigmap-${ID}-$Res.in >> tmpRun
cat tmpRun >> notes
bigMapRef < tmpRun
tail -2 SIGMAS.TXT | head -1 | tee -a notes
echo y | cp -v USED_MAPS.TXT LIST.TXT
duplicates

relink.sh scripts/Piterate1St.seed make_scriptP.seed | tee -a notes
ls -l make_scriptP.seed >> notes
MAKE_LMRKLISTX 

echo nft=$ID > config/nftID
echo res=$Res >> config/nftID
echo 0 > config/iterationCount
echo 10 > config/stopCount

relink.sh /opt/local/spc/bin/nftLoop.sh localLoop.sh

make_scriptP | tee run.sh
echo "Running iteration at " `date` >> notes
sh run.sh
monitor

Run the normal NFT iterate steps to start the running.

Remember to:

• Turn off terminate
• Run localLoop
• Start the deamon

nftBlockFinish.sh nft.$ID

Tuck Log files into logNFT

mkdir -p logNFT
mkdir -p logNFT/$ID
mv log/* logNFT/$ID/