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← Revision 26 as of 2019-11-08 16:47:21 ⇥
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| This block batch registers images. | This block batch registers images. Each time you run a batch run of run_script.b (typically would have a different make_scriptR.seed), then run [[blockFinish]] to log the results. |
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| == Assumptions == * You have invoked a Bourne-Again Shell (bash) * 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 v2]] |
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| * 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. ---- |
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| === Set-up === | |
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| === 1. Initial inputs === | For script, set the ID |
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| imgListName=whatever-list.txt | ID=312 |
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| === 2. Set-up === | Ensure make_scriptR.seed is linked to the script you want to run. For starters, you can use one of the default ones. If needed, you can craft something specific and place it in lsupport. |
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| # Set-Up cd /SPC_Test/$testID/$dirID/ script date pwd ls -l |
relink.sh support/register-basic01.seed make_scriptR.seed relink.sh script/make_scriptR_02.seed make_scriptR.seed ls -l make_scriptR.seed | tee -a notes |
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| === 3. Set-up batch register files === | === Set-up batch register files === Replace [[make_script.in]] with a list of images that you want to use. It is important that the first character is blank and the file is terminated with an "END" |
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| # set-up batch register files ln -s lsupport/$imgListName make_script.in ln -s scripts/make_scriptR.SEED make_scriptR.seed make_scriptR ls -l |
# Create a list of images that need to be processed. echo working with dataset active.$ID | tee -a notes echo y | cp lsupport/active.$ID make_script.in echo END >> make_script.in wc -l make_script.in | tee -a notes |
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| === 4. Batch register images === | === Batch register images === Build the scripts. We use nohup to ensure that if the login window is lost, the process still runs. |
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| # Batch register images register -v nohup sh run_script.b & |
make_scriptR nohup sh run_script.b |
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| === 5. Monitor progress === | === Monitor progress === |
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| # Monitor progress ls -l *.INN *.OOT |
ls *.INN | wc ls *.OOT | wc |
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| === 6. Check results === | === Check results === This gives stats to help you see which things to work. |
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| # Check results ls *OOT > tmpList sh support/after.sh 0.5 tmpList cat goodList cat badList sh support/evalReg.sh badList |
registerEval.sh wc eval/evalGood.txt eval/evalBad.txt | tee -a notes |
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| === 7. Fix unregistered images === | If you so desire, especially early on, make R/B images to see the quality of the fit {{{ evalReg.sh make_script.in }}} === Fix unregistered images === |
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| === 8. Clean directory === {{{ # Clean directory sh rem_script.b rm TESTFILES/* rm nohup.out }}} |
=== Rerun === |
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| === 9. Complete procedure === | If evalBad.txt is large, then you can tweak [[make_scriptR.seed]] and rerun on the bad list |
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| # Block Complete exit # Save block log mv typescript step-reg |
cut -c 1-12 evalBad.txt | sed -e "s/^/ /" > make_script.in echo "END" >> make_script.in relink ________.seed make_scriptR.seed echo "Rerunning with evalBad.txt" >> notes ls -l make_scriptR.seed >> notes make_scriptR nohup sh run_script.b |
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=== Finish the Block === {{{ echo 2 | blockFinish ps$ID }}} |
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| ''(Compiled by DL)'' CategoryHowTos |
''(Compiled by EEP)'' |
Block 3 - Register V2
Description
This block batch registers images. Each time you run a batch run of run_script.b (typically would have a different make_scriptR.seed), then run blockFinish to log the results.
Procedure
Set-up
For script, set the ID
ID=312
Ensure make_scriptR.seed is linked to the script you want to run. For starters, you can use one of the default ones. If needed, you can craft something specific and place it in lsupport.
relink.sh support/register-basic01.seed make_scriptR.seed relink.sh script/make_scriptR_02.seed make_scriptR.seed ls -l make_scriptR.seed | tee -a notes
Set-up batch register files
Replace make_script.in with a list of images that you want to use. It is important that the first character is blank and the file is terminated with an "END"
# Create a list of images that need to be processed. echo working with dataset active.$ID | tee -a notes echo y | cp lsupport/active.$ID make_script.in echo END >> make_script.in wc -l make_script.in | tee -a notes
Batch register images
Build the scripts. We use nohup to ensure that if the login window is lost, the process still runs.
make_scriptR nohup sh run_script.b
Monitor progress
ls *.INN | wc ls *.OOT | wc
Check results
This gives stats to help you see which things to work.
registerEval.sh wc eval/evalGood.txt eval/evalBad.txt | tee -a notes
If you so desire, especially early on, make R/B images to see the quality of the fit
evalReg.sh make_script.in
Fix unregistered images
# Fix unregistered images .......
Rerun
If evalBad.txt is large, then you can tweak make_scriptR.seed and rerun on the bad list
cut -c 1-12 evalBad.txt | sed -e "s/^/ /" > make_script.in echo "END" >> make_script.in relink ________.seed make_scriptR.seed echo "Rerunning with evalBad.txt" >> notes ls -l make_scriptR.seed >> notes make_scriptR nohup sh run_script.b
Finish the Block
echo 2 | blockFinish ps$ID
(Compiled by EEP)