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--- examples:gs_loop_olivine [2019/12/05 10:19]
smerkel
+++ examples:gs_loop_olivine [2023/12/09 22:21] (current)
smerkel ↷ Page moved from restricted:gs_loop_olivine to examples:gs_loop_olivine
@@ Line 10: / Line 10: @@
 The loop can run //nLoops// indexings (typically 3). For each, the loop runs
-  * 6 iterations of 100000 GrainSpotter orientation searches with the following thresholds (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)
+  * 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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