== 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=00000
Res=5

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

checkVar $ID $Res $logP
bigmap < nftConfig/nftBigmap-$ID-$Res.IN
}}}

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


{{{

checkVar $ID $Res $logP
echo "Getting ready for iteration $ID-$Res" >> notes
date >> notes
echo $ID$Res | tee -a notes
echo ${ID}A > tmpRun
cat nftConfig/nftBigmap-$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 1 > config/iterationCount
echo 3 > 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
 
{{{
     Deamon - Running
               F   L E
}}}

== Save iteration files ==
{{{
checkVar $ID $Res $logP

echo 2 | nftBlockFinish.sh nft.$ID
sh rem_script.b
}}}

== Run AUTOREGISTER before kicking off remaining iterations ==
A few iterations often allow us to pull in more images. Run AUTOREGISTER on the PG62 and P63 images, but NOT the P60 images. See below under the AUTOREGSITER heading.



{{{
checkVar $ID $Res $logP
bigmap < nftConfig/nftBigmap-$ID-$Res.IN
grep P62 USED_PICS.TXT > make_script.in
grep P63 USED_PICS.TXT >> make_script.in
grep P64 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; finished autoregister

autoEval.sh

checkVar  $ID $Res $logP
echo 3 | nftBlockFinish.sh nft.$ID
}}}

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

{{{
autoEval.sh
}}}

== Run NFTWeb to check stats, particularly stationEval.sh for landmarks with missing stations ==
{{{
nftWeb.sh $ID
}}}

== Complete remaining iterations. ==

{{{

checkVar $ID $Res $logP
echo "Getting ready for iteration $ID-$Res" >> notes
date >> notes
echo $ID$Res | tee -a notes
echo ${ID}A > tmpRun
cat nftConfig/nftBigmap-$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 3 > 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


When done, collect some statistics
{{{
checkVar $ID $Res $logP


mkdir -p log/${ID}A
grep SIGMAS.TXT notes > log/${ID}A/sigmas.txt
grep correlation notes > log/${ID}A/overlaps.txt
grep Errors notes > log/${ID}A/nocorr.txt
grep Ended notes > log/${ID}A/time.txt

grep "Average  " notes > log/${ID}A/corrAvg.txt
grep "Average Sig" notes > log/${ID}A/corrSigmaScore.txt
grep Above notes > log/${ID}A/corrAbove.txt


echo 2 | nftBlockFinish.sh nft.$ID
sh rem_script.b

}}}

== Tuck Log files into log  ==

{{{
mv log/out-* $logP
}}}




== Make sure you have 2 (preferably 3) BBD stations for each image ==

{{{

# Needs new maplets in MAPINFO.TXT; Run if RESIDUALS has not been run since tiling
echo "5 .001 .001" | RESIDUALS

bigmap < nftConfig/nftBigmap-$ID-A.IN
stationEval.sh USED_MAPS.TXT
head -1 eval/evalStation.txt
sort -k2,2 eval/evalStation.txt | more 

}}}