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====== GrainSpotter loop for olivine  ======

Below is an example of a GrainSpotter loop for olivine. You can run it by typing
<code>
gsLoop.sh > gsLoop.log
</code>
The output of the loop will be saved in ''gsLoop.log''.

===== Main idea =====

The loop can run //nLoops// indexings (typically 3). For each, the loop runs
  * 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>
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