#!/bin/bash

# Starting GVE file
startGVE=../HTC_04_02_3D_03_merge.gve
# Starting GVE file
crystalSymmetryCode=3
# Number of indexings
nLoops=3
# Threshold for considering 2 grains are the same (in degrees)
matchgrainThreshold=1
# Step in omega, in degrees
omegastep=0.25
# 2 theta range
min2theta=4.0
max2theta=17.0
# Wavelength
wave=0.3738

# 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=/usr/bin/timelessExtractEulerAngles
indexingStatistics=/usr/bin/timelessGSIndexingStatistics

# 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 63					! spacegroup [space group nr]
etarange 0 360					! etarange [min max]
! dsrange 0.0 2.0				! dsrange [min max], reciprocal d-spacing range, multiple ranges can be specified
tthrange $min2theta $max2theta	! tthrange [min max], multiple ranges can be specified
domega $omegastep				! domega [stepsize] in omega, degrees
omegarange -29.0 30.0 			! omegarange [min max] degrees, multiple ranges can be specified
filespecs $2 $3					! [gvecsfile grainsfile]
cuts $4 $5 1.0 					! cuts [min_measuments min_completeness min_uniqueness]
eulerstep 3                		! 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
!Nhkls_in_indexing 31        	! Nhkls_in_indexing [Nfamilies] : use first Nfamilies in indexing
random $9               		! random sampling of orientation space trying 10000 sample points
minfracg 0.99					! stop search when minfracg (0..1) of the gvectors have been assigned to grains
! 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 () {
local grainlist="" # Declaring this variable as local to be able to run multiple indexings in parallel

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 25 0.5 0.05 1.2 1.2 10000
$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..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 25 0.5 0.05 1.2 1.2 10000
	$GrainSpotter index-$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"
	rm peaks_after_step-$j.gve
done

for i in {21..40}
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 25 0.5 0.07 2.0 2.0 10000
	$GrainSpotter index-$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"
	rm peaks_after_step-$j.gve
done

for i in {41..60}
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 15 0.3 0.05 1.2 1.2 10000
	$GrainSpotter index-$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"
	rm peaks_after_step-$j.gve
done


for i in {61..80}
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 15 0.3 0.07 2.0 2.0 10000
	$GrainSpotter index-$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"
	rm peaks_after_step-$j.gve
done

rm peaks_after_step-80.gve
$mergeGrains -c $crystalSymmetryCode -m $matchgrainThreshold -o merge $grainlist
$extractEuler -o merge-grains-euler.txt merge-grains.log
$indexingStatistics -i index-80.ini -l merge-grains.log -g ../$startGVE -w $wave 

}

#-----------------------------------------------------------------------------------------------
#
# 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
	cd $folder
	indexing_loop > "../indexing-$loop.log" &
	cd ..

	echo ""
	echo ""
	echo "#"
	echo "# Done starting the indexing loop number $loop"
	echo "# Data saved in folder: Indexing-$loop"
	echo "# Log file is indexing-$loop.log"
	echo "#"
	echo "#----------------------------------------------------------------------------------------"
	echo ""
	echo ""
done

exit