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restricted:gs_loop_olivine [2019/12/05 11:18] – created smerkelexamples:gs_loop_olivine [2023/12/09 23:21] (current) – ↷ Page moved from restricted:gs_loop_olivine to examples:gs_loop_olivine smerkel
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 The loop can run //nLoops// indexings (typically 3). For each, the loop runs The loop can run //nLoops// indexings (typically 3). For each, the loop runs
-  * 6 iterations of 100000 GrainSpotter orientation searches with the following thresholds (minNPeaks: 20, minCompleteness: 0.5, Δ(2θ)=0.06°, Δ(η)=1°, Δ(ω)=1°, and a maximum deviation n<sub>σ</sub>=2+  * 6 iterations of 100000 GrainSpotter orientation searches with the following threshold 
 +<WRAP center indent 60%> 
 +  * min<sub>NPeaks</sub> = 20 
 +  * min<sub>Completeness</sub> = 0.5 
 +  * Δ<sub>2θ</sub> = 0.06° 
 +  * Δ<sub>η</sub> = 1° 
 +  * Δ<sub>ω</sub> = 1° 
 +  * maximum deviation n<sub>σ</sub> = 2 
 +</WRAP> 
 +  * 5 iterations of 100000 GrainSpotter orientation searches with 
 +<WRAP center indent 60%> 
 +  * min<sub>NPeaks</sub> = 20 
 +  * min<sub>Completeness</sub> = 0.5 
 +  * Δ<sub>2θ</sub> = 0.06° 
 +  * Δ<sub>η</sub> = 2° 
 +  * Δ<sub>ω</sub> = 2° 
 +  * maximum deviation n<sub>σ</sub> = 2 
 +</WRAP> 
 +  * 5 iterations of 100000 GrainSpotter orientation searches with 
 +<WRAP center indent 60%> 
 +  * min<sub>NPeaks</sub> = 20 
 +  * min<sub>Completeness</sub> = 0.3 
 +  * Δ<sub>2θ</sub> = 0.06° 
 +  * Δ<sub>η</sub> = 2° 
 +  * Δ<sub>ω</sub> = 2° 
 +  * maximum deviation n<sub>σ</sub> = 2 
 +</WRAP> 
 +  * 5 iterations of 100000 GrainSpotter orientation searches with 
 +<WRAP center indent 60%> 
 +  * min<sub>NPeaks</sub> = 20 
 +  * min<sub>Completeness</sub> = 0.3 
 +  * Δ<sub>2θ</sub> = 0.06° 
 +  * Δ<sub>η</sub> = 3° 
 +  * Δ<sub>ω</sub> = 3° 
 +  * maximum deviation n<sub>σ</sub> = 2 
 +</WRAP> 
 +  * 5 iterations of 100000 GrainSpotter orientation searches with 
 +<WRAP center indent 60%> 
 +  * min<sub>NPeaks</sub> = 20 
 +  * min<sub>Completeness</sub> = 0.3 
 +  * Δ<sub>2θ</sub> = 0.10° 
 +  * Δ<sub>η</sub> = 3° 
 +  * Δ<sub>ω</sub> = 3° 
 +  * maximum deviation n<sub>σ</sub> = 2 
 +</WRAP> 
 + 
 +At the end of the loop, all results for the corresponding loop number are saved in a folder called ''Indexing-$loop'', where ''$loop'' is the loop number. Merged grains are in a file called ''merge-grains.log'' and their Euler angles in ''merge-grains-euler.txt''. 
 + 
 +===== Getting some idea on indexing capabilities ===== 
 + 
 +There is now a dedicated TIMEleSS tool to [[evaluation:evaluate_indexing_statistics|evaluate your indexing performance]]. 
 + 
 +===== The loop ===== 
 + 
 +You wanted it?! Here is the source code for the loop above 
 + 
 +<code bash gsLoop.sh> 
 +#!/bin/bash 
 + 
 +# Starting GVE file 
 +startGVE=../LTC_05_01_s26_t50_ol-seb-edit.gve 
 +# Starting GVE file 
 +crystalSymmetryCode=3 
 +# Number of indexings 
 +nLoops=3 
 + 
 +# Update parameters above as well as in  
 +#    - create_GS_init 
 +#    - fine details in indexing_loop 
 + 
 +# Location of executables 
 +GrainSpotter=/usr/local/bin/GrainSpotter.0.90 
 +clearGVE=/usr/bin/timelessClearGVEGrains 
 +mergeGrains=/usr/bin/timelessGrainSpotterMerge 
 +extractEuler=timelessExtractEulerAngles 
 + 
 +# Global parameter. Used to pass list of files between functions 
 +grainlist="" 
 + 
 +#----------------------------------------------------------------------------------------------- 
 +# 
 +# Call to create GrainSpotter input 
 +# 3 parameters 
 +# - first: name of GrainSpotter output file 
 +# - second: name gve file 
 +# - third: name of grain output file 
 +# - forth : min_measurments 
 +# - fifth : min_completeness 
 +# - sixth : sigma_tth 
 +# - seventh : sigma_eta 
 +# - eighth : sigma_omega 
 +# 
 +#----------------------------------------------------------------------------------------------- 
 +create_GS_init () { 
 +cat > $1 <<- EOM 
 +spacegroup 62                ! spacegroup [space group nr] 
 +! dsrange 0 0.34                         ! dsrange [min max], d-spacing range, multiple ranges can be specified 
 +tthrange 2 10.2                          ! tthrange [min max], multiple ranges can be specified 
 +! tthrange 2 8.8                          ! tthrange [min max], multiple ranges can be specified 
 +! tthrange 9 10.2                          ! tthrange [min max], multiple ranges can be specified 
 +tthrange 10.5 14.4                          ! tthrange [min max], multiple ranges can be specified 
 +! tthrange 14.6 17                          ! tthrange [min max], multiple ranges can be specifie 
 +etarange 0 360                ! etarange [min max], multiple ranges can be specified 
 +domega 0.5                        ! domega [stepsize] in omega, degrees  
 +omegarange -21 13 ! omegarange [min max] degrees, multiple ranges can be specified 
 +filespecs $2 $3 ! filespecs [gvecsfile grainsfile]  
 +cuts $4 $5 0.5                ! cuts [min_measuments min_completeness min_uniqueness] 
 +eulerstep 5                ! eulerstep [stepsize] : angle step size in Euler space 
 +uncertainties $6 $7 $8    ! uncertainties [sigma_tth sigma_eta sigma_omega] in degrees 
 +nsigmas 2                    ! nsigmas [Nsig] : maximal deviation in sigmas 
 +! minfracg 1                            ! stop search when minfracg (0..1) of the gvectors have been assigned to grains  
 +! Nhkls_in_indexing 15 ! Nhkls_in_indexing [Nfamilies] : use first Nfamilies in indexing 
 +random 100000                           ! use randomly chosen orientation seeds #trials 
 +! positionfit                            ! fit the position of the grain 
 +! genhkl                                  ! generate list of hkl's based on space group and cell parameters in gve file 
 +EOM 
 +} 
 + 
 + 
 +#----------------------------------------------------------------------------------------------- 
 +# 
 +# Actual indexing loop 
 +# Runs tens of GrainSpotter iterations with decreasing tolerances 
 +# Runs in the current folder 
 +# 
 +#----------------------------------------------------------------------------------------------- 
 + 
 +indexing_loop () { 
 + 
 +echo "#" 
 +echo "#" 
 +echo "# Running first GS iteration. Starting from $startGVE, GS parameters in index-0.ini, grains saved in grains0.log" 
 +echo "#" 
 +echo "#" 
 +create_GS_init index-0.ini $startGVE grains-0.log 20 0.5 0.06 1 1 
 +$GrainSpotter index-0.ini 
 +echo "#" 
 +echo "#" 
 +echo "# Done with iteration 0. New list of GVE will be peaks_after_step-0.gve" 
 +echo "#" 
 +echo "#" 
 +$clearGVE grains-0.log $startGVE peaks_after_step-0.gve  
 +grainlist="grains-0.log" 
 + 
 +for i in {1..5} 
 +do 
 + j="$((i - 1))" 
 + echo "#" 
 + echo "#" 
 + echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" 
 + echo "#" 
 + echo "#" 
 + # Use from previous step and create grains$i.log 
 + create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.5 0.06 1 1 
 + $GrainSpotter index-$i.ini  
 + echo "#" 
 + echo "#" 
 + echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" 
 + echo "#" 
 + echo "#" 
 + $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve 
 + grainlist="$grainlist grains-$i.log" 
 +done 
 + 
 +for i in {6..10} 
 +do 
 + j="$((i - 1))" 
 + echo "#" 
 + echo "#" 
 + echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grain-$i.log" 
 + echo "#" 
 + echo "#" 
 + create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.5 0.06 2 2 
 + $GrainSpotter index-$i.ini  
 + echo "#" 
 + echo "#" 
 + echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" 
 + echo "#" 
 + echo "#" 
 + # Remove peaks that have been indexed 
 + $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve 
 + grainlist="$grainlist grains-$i.log" 
 +done 
 + 
 +for i in {11..15} 
 +do 
 + j="$((i - 1))" 
 + echo "#" 
 + echo "#" 
 + echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" 
 + echo "#" 
 + echo "#" 
 + create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.06 2 2 
 + $GrainSpotter index-$i.ini  
 + echo "#" 
 + echo "#" 
 + echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" 
 + echo "#" 
 + echo "#" 
 + # Remove peaks that have been indexed 
 + $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve 
 + grainlist="$grainlist grains-$i.log" 
 +done 
 + 
 + 
 +for i in {16..20} 
 +do 
 + j="$((i - 1))" 
 + echo "#" 
 + echo "#" 
 + echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" 
 + echo "#" 
 + echo "#" 
 + # Use from previous step and create grains$i.log 
 + create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.06 3 3 
 + $GrainSpotter index-$i.ini  
 + # Remove peaks that have been indexed 
 + echo "#" 
 + echo "#" 
 + echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" 
 + echo "#" 
 + echo "#" 
 + $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve 
 + grainlist="$grainlist grains-$i.log" 
 +done 
 + 
 +for i in {21..25} 
 +do 
 + j="$((i - 1))" 
 + echo "#" 
 + echo "#" 
 + echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" 
 + echo "#" 
 + echo "#" 
 + # Use from previous step and create grains$i.log 
 + create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.1 3 3 
 + $GrainSpotter index-$i.ini  
 + # Remove peaks that have been indexed 
 + echo "#" 
 + echo "#" 
 + echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" 
 + echo "#" 
 + echo "#" 
 + $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve 
 + grainlist="$grainlist grains-$i.log" 
 +done 
 + 
 +} 
 + 
 +#----------------------------------------------------------------------------------------------- 
 +# 
 +# Indexing loop, runs tens of GrainSpotter iterations with decreasing tolerances 
 +# Runs in the current folder 
 +# 
 +#----------------------------------------------------------------------------------------------- 
 + 
 +for (( loop=1; loop<=$nLoops; loop++ )) 
 +do 
 + echo "#----------------------------------------------------------------------------------------" 
 + echo "#" 
 + echo "# Full indexing loop number $loop" 
 + echo "# Data saved in folder: Indexing-$loop" 
 + echo "#" 
 + echo "#----------------------------------------------------------------------------------------" 
 + echo "" 
 + folder="Indexing-$loop" 
 + \rm -rf $folder 
 + mkdir $folder 
 +  
 + grainlist="" 
 + indexing_loop 
 + $mergeGrains -c $crystalSymmetryCode -o merge $grainlist 
 + $extractEuler -o merge-grains-euler.txt merge-grains.log 
 + mv grains-* $folder 
 + mv peaks_after_step* $folder 
 + mv merge-*  $folder 
 + mv index-*.ini  $folder 
 +  
 + echo "" 
 + echo "" 
 + echo "#----------------------------------------------------------------------------------------" 
 + echo "#" 
 + echo "# Done with indexing loop number $loop" 
 + echo "# Data saved in folder: Indexing-$loop" 
 + echo "#" 
 + echo "#----------------------------------------------------------------------------------------" 
 + echo "" 
 + echo "" 
 +done 
 + 
 +exit 
 +</code>
examples/gs_loop_olivine.1575541112.txt.gz · Last modified: by smerkel