Below is an example of a GrainSpotter loop for a multiphase sample. You can run it by typing
gsLoop-NPhases.sh > gsLoop-NPhases.log
The output of the loop will be saved in gsLoop-NPhases.log.
The options in this scripts are all in the top section of the file, which should be somewhat self-documented.
This script requires
The number of times to run GrainSpotter, number of parameters to try, etc, is not limited. In some cases, with have run GrainSpotter up to 100 times, with 100000 random trials at each run. This is a test for 10 million configurations.
What it will do
merge-XXX-grains.log for each phase,merge-XXX-grains-euler.txt so you can plot the orientations of the indexed grains,You wanted it?! Here is the source code for the loop above.
If you find that this script is useful for you, please cite one of the relevant TIMEleSS publications for which this script was slowly developped:
#!/bin/bash # # This is part of the TIMEleSS tools # http://timeless.texture.rocks/ # # Copyright (C) S. Merkel, Universite de Lille, France # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # Please cite one of the relevant TIMEleSS publications if you find that was of any use # # Number of phases nphases=2 # Name of phases (used for comments) phases=("Phase A" "Phase B") # Short name of phases (for generating file names, avoid spaces and funny characters please) # If your phase is BB, peaks will be in files peaks-BB.gve, grains in grains-BB.gve, and GrainSpotter input files in index-BB.in with additional numbers phasesShort=("phA" "phB") # Crystal symmetry codes, one per phase (used in merge grains) # Codes can be found here http://multigrain.texture.rocks/doku.php?id=processing:compare-grain-orientations crystalSymmetryCodes=(7 7) # Space groups, one per phase (used in grainspotter) spaceGroups=(245 212) # Starting GVE files, one per phase startGVEs=("phaseA.gve" "phaseB.gve") # Wavelength (in Angstrom) wavelength=0.34512 # Grain spotter parameters # For each line: # - How many times shall you run grainSpotter, parameters for phase 1, parameters for phase 2, parameters for phase 3 # - Parameter list for each phase: min_measuments min_completeness sigma_tth sigma_eta sigma_omega n_random # You can add as many lines as you want. The indexing will be longer but the script will handle it. gsPars=() gsPars+=("5, 10 0.4 0.02 1 2 10000, 10 0.4 0.02 1 2 100") # iterations 0 to 4 gsPars+=("10, 10 0.4 0.02 2 4 10000, 10 0.4 0.02 2 4 100") # iterations 5 to 14 # gsPars+=("5, 10 0.4 0.02 1 2 10000, 10 0.4 0.02 1 2 100") # iterations 15 to 19 # Example # gsPars+=("5, 10 0.4 0.02 1 2 10000, 10 0.4 0.02 1 2 100") # adds 5 iterations with # - for phase 1, 10 min_measuments, 0.4 min_completeness, 0.02 degrees sigma_tth, 1 degree sigma_eta and 2 degrees sigma_omega, 10000 random trials in GrainSpotter # - for phase 2, 10 min_measuments, 0.4 min_completeness, 0.02 degrees sigma_tth, 1 degree sigma_eta and 2 degrees sigma_omega, 100 random trials in GrainSpotter # # gsPars+=("10, 10 0.4 0.02 2 4 10000, 10 0.4 0.02 2 4 100") # adds 10 iterations with # - for phase 1, 10 min_measuments, 0.4 min_completeness, 0.02 degrees sigma_tth, 2 degrees sigma_eta and 4 degrees sigma_omega, 10000 random trials in GrainSpotter # - for phase 2, 10 min_measuments, 0.4 min_completeness, 0.02 degrees sigma_tth, 2 degrees sigma_eta and 4 degrees sigma_omega, 100 random trials in GrainSpotter # Number of indexings (number of time to repeat the full thing to test for results consistency) nIndexings=1 # Update parameters above as well as in # - create_GS_init # Location of executables GrainSpotter=/usr/local/bin/GrainSpotter.0.90 clearGVE=/usr/bin/timelessClearGVEGrains mergeGrains=/usr/bin/timelessGrainSpotterMerge extractEuler=/usr/bin/timelessExtractEulerAngles statistics=/usr/bin/timelessGSIndexingStatistics #----------------------------------------------------------------------------------------------- # # Call to create GrainSpotter input # 10 parameters # - 1: name of GrainSpotter output file # - 2: space group number # - 3: gve file # - 4: name of grain output file # - 5: min_measurments # - 6: min_completeness # - 7: sigma_tth # - 8: sigma_eta # - 9: sigma_omega # - 10: n_random # # Two theta ranges and other parameters for GrainSpotter are set by hand below. # They are identical for all phases and mostly depend on the experimental settings. # Please update according to your settings # # Other parameters are adjusted according to what was defined above in gsPars # #----------------------------------------------------------------------------------------------- create_GS_init () { cat > $1 <<- EOM spacegroup $2 ! spacegroup [space group nr] ! dsrange 0 0.34 ! dsrange [min max], d-spacing range, multiple ranges can be specified tthrange 3.5 6.95 ! tthrange [min max], multiple ranges can be specified tthrange 7.15 9.95 ! tthrange [min max], multiple ranges can be specified tthrange 10.1 12.2 ! tthrange [min max], multiple ranges can be specified tthrange 12.35 14.0 ! tthrange [min max], multiple ranges can be specified etarange 0 360 ! etarange [min max], multiple ranges can be specified domega 0.5 ! domega [stepsize] in omega, degrees omegarange -28 28 ! omegarange [min max] degrees, multiple ranges can be specified filespecs $3 $4 ! filespecs [gvecsfile grainsfile] cuts $5 $6 0.5 ! cuts [min_measuments min_completeness min_uniqueness] eulerstep 5 ! eulerstep [stepsize] : angle step size in Euler space uncertainties $7 $8 $9 ! 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 ${10} ! use randomly chosen orientation seeds #trials ! positionfit ! fit the position of the grain ! genhkl ! generate list of hkl's based on space group and cell parameters in gve file EOM } #----------------------------------------------------------------------------------------------- # # NOTHING SHOULD BE CHANGED BELOW # #----------------------------------------------------------------------------------------------- #----------------------------------------------------------------------------------------------- # # Actual indexing loop # Runs tens of GrainSpotter iterations with decreasing tolerances # Runs in the current folder # #----------------------------------------------------------------------------------------------- indexing_loop () { # Copy GVE file for each phase echo "#" echo "# Copy of starting GVE files into current working folder" echo "#" for (( i=0; i<$nphases; i++ )) do if [ ! -f "$home/${startGVEs[$i]}" ]; then echo "Error: starting GVE file ${startGVEs[$i]} does not exist in folder $home" echo "Can not go any further" exit fi cp -f $home/${startGVEs[$i]} peaks-${phasesShort[$i]}.gve cp -f $home/${startGVEs[$i]} peaks-ori-${phasesShort[$i]}.gve echo "Saved ${startGVEs[$i]} as peaks-${phasesShort[$i]}.gve and peaks-ori-${phasesShort[$i]}.gve" done echo "Done" # Loop on GrainSpotter indexings i=-1 for gsPar in "${gsPars[@]}" do # Set comma as delimiter IFS=',' # Split parameter information read -a pars <<< "$gsPar" # Number of GrainSpotter loops for this set of parameters nloops=${pars[0]} # Extracting GrainSpotter parameters for each phase parphases=() for (( j=0; j<$nphases; j++ )) do ((k = j + 1)) parphases[$j]=${pars[$k]} done # Run loop of GrainSpotter indexings for these parameters for (( loop=0; loop<$nloops; loop++ )) do ((i = i + 1)) echo "#" echo "# Running GS iteration $i. GS parameters in index-XXX-$i.ini, grains saved in grains-XXX-$i.log for each phase" echo "#" echo "#" for (( j=0; j<$nphases; j++ )) do echo "#" echo "# GS iteration $i. Parameters for ${phases[$j]}: ${parphases[$j]}" echo "#" # Splitting indexing parameters as array, otherwise it does not work IFS=' ' read -a pars <<< "${parphases[$j]}" # Creating GrainSpotter input file and running the indexing create_GS_init index-${phasesShort[$j]}-$i.ini ${spaceGroups[$j]} peaks-${phasesShort[$j]}.gve grains-${phasesShort[$j]}-$i.log ${pars[@]} $GrainSpotter index-${phasesShort[$j]}-$i.ini lastGSInput[$j]=index-${phasesShort[$j]}-$i.ini echo "#" echo "# Done with GS indexation on ${phases[$j]}." echo "# Indexing saved in grains-${phasesShort[$j]}-$i.log" echo "#" grainlists[$j]="${grainlists[$j]} grains-${phasesShort[$j]}-$i.log" echo "#" echo "# Clear indexed peaks from GVE lists" echo "#" # Removed used peaks from gve lists for (( k=0; k<$nphases; k++ )) do $clearGVE grains-${phasesShort[$j]}-$i.log peaks-${phasesShort[$k]}.gve tmp.gve mv -f tmp.gve peaks-${phasesShort[$k]}.gve echo "#" echo "# New peak list for ${phases[$k]} saved in peaks-${phasesShort[$k]}.gve" echo "#" done echo "#" echo "# Done with GS iteration $i on ${phases[$j]}" echo "#" done done done } #----------------------------------------------------------------------------------------------- # # Indexing loop, runs tens of GrainSpotter iterations with decreasing tolerances # Runs in the current folder # #----------------------------------------------------------------------------------------------- # Saving home directory home=`pwd` # Global parameter. Used to pass list of files between functions grainlists=() lastGSInput=() for (( i=0; i<$nphases; i++ )) do grainlists[$i]="" lastGSInput[$i]="" done # Make some tests to make sure all parameters have been set error=false for (( i=0; i<$nphases; i++ )) do if [ -z "${phases[$i]}" ]; then ((k = i + 1)) echo "Name of phase $k is blank. This should not happen. Check definition of \$phases variable."; error=true fi if [ -z "${phasesShort[$i]}" ]; then ((k = i + 1)) echo "Short name of phase $k is blank. This should not happen. Check definition of \$phasesShort variable."; error=true fi if [ -z "${crystalSymmetryCodes[$i]}" ]; then ((k = i + 1)) echo "Crystal symmetry code for phase $k is blank. This should not happen. Check definition of \$crystalSymmetryCodes variable."; error=true fi if [ -z "${spaceGroups[$i]}" ]; then ((k = i + 1)) echo "Space group for phase $k is blank. This should not happen. Check definition of \$spaceGroups variable."; error=true fi if [ -z "${startGVEs[$i]}" ]; then ((k = i + 1)) echo "Name of file for GVE vectors for phase $k is blank. This should not happen. Check definition of \$startGVEs variable."; error=true fi done ngs=-1 for gsPar in "${gsPars[@]}" do # Set comma as delimiter IFS=',' # Split parameter information read -a pars <<< "$gsPar" # Number of GrainSpotter loops for this set of parameters nloops=${pars[0]} ((ngs = ngs + nloops)) # Extracting GrainSpotter parameters for each phase for (( j=0; j<$nphases; j++ )) do ((k = j + 1)) if [ -z "${pars[$k]}" ]; then echo "No parameter for phase $k at line $gsPar" error=true fi done done if [ "$error" = true ]; then echo "" echo "There were errors while parsing the script parameters. See messages above." echo "" exit fi echo "# " echo "# " echo "# Multiphase multigrain indexing" echo "# " echo "# This script will run $nIndexings attemp(s) of an indexing with $nphases phases, with $ngs GrainSpotter iterations for each phase." echo "# Phase list: ${phases[@]}" echo "# Starting GVE-vectors saved in ${startGVEs[@]}" echo "# Parameters for GrainSpotter indexings" for gsPar in "${gsPars[@]}" do # Set comma as delimiter IFS=',' # Split parameter information read -a pars <<< "$gsPar" # Number of GrainSpotter loops for this set of parameters nloops=${pars[0]} echo "# - $nloops iteration(s) with" # Extracting GrainSpotter parameters for each phase for (( j=0; j<$nphases; j++ )) do ((k = j + 1)) echo "# * ${pars[$k]} for ${phases[$j]}" done done echo "#" echo "#" for (( loopIndexing=1; loopIndexing<=$nIndexings; loopIndexing++ )) do echo "#----------------------------------------------------------------------------------------" echo "#" echo "# Full indexing loop number $loopIndexing" echo "# Data saved in folder: Indexing-$loopIndexing" echo "#" echo "#----------------------------------------------------------------------------------------" echo "" folder="Indexing-$loopIndexing" \rm -rf $folder mkdir $folder cd $folder # Clear list of indexed grains for (( i=0; i<$nphases; i++ )) do grainlists[$i]="" done # Start indexing loop indexing_loop echo "" echo "#---------------------------------------" echo "# Indexing loop number $loopIndexing is finished" echo "#" # Merge grains for each phase mergeGrainFiles=() originalGVEFiles=() for (( i=0; i<$nphases; i++ )) do originalGVEFiles[$i]="peaks-ori-${phasesShort[$i]}.gve" echo "" echo "#---------------------------------------" echo "# Merging grain information for ${phases[$i]} into files starting with merge-${phasesShort[$i]}, i.e. merge-${phasesShort[$i]}-grains.log, etc" echo "#" $mergeGrains ${grainlists[$i]} -c "${crystalSymmetryCodes[$i]}" -o "merge-${phasesShort[$i]}" mergeGrainFiles[$i]="merge-${phasesShort[$i]}-grains.log" echo "" echo "#---------------------------------------" echo "# Extracting Euler angles for ${phases[$i]} into merge-${phasesShort[$i]}-grains-euler.txt" echo "#" $extractEuler -o "merge-${phasesShort[$i]}-grains-euler.txt" "merge-${phasesShort[$i]}-grains.log" echo "" echo "#---------------------------------------" echo "# Saving list of indexed g-vectors for ${phases[$i]} into gve-Indexed-${phasesShort[$i]}.gve" echo "# List of remaining g-vectors for ${phases[$i]} moved to gve-NotIndexed-${phasesShort[$i]}.gve" echo "#" $clearGVE -k gve-Indexed-${phasesShort[$i]}.gve merge-${phasesShort[$i]}-grains.log peaks-ori-${phasesShort[$i]}.gve tmp.gve rm tmp.gve mv peaks-${phasesShort[$i]}.gve gve-NotIndexed-${phasesShort[$i]}.gve done echo "" echo "#---------------------------------------" echo "# More indexing statistics" echo "#" $statistics -w $wavelength -i ${lastGSInput[@]} -l ${mergeGrainFiles[@]} -g ${originalGVEFiles[@]} cd $home echo "" echo "" echo "#----------------------------------------------------------------------------------------" echo "#" echo "# Done with indexing loop number $loopIndexing" echo "# Data saved in folder: Indexing-$loopIndexing" echo "#" echo "#----------------------------------------------------------------------------------------" echo "" echo "" done exit