#!/bin/bash

#numer of events used for resolution study
SIMEVENTS=100000
#SIMEVENTS=100
#Declare array with elements for knoss stat. study
ARRAY=(100000 50000 20000 10000 5000 2000 1000 500 200 100)
# get number of elements in the array
ELEMENTS=${#ARRAY[@]}

#Declare array with elements for misalignment scale
#ARRAYD=(0 20 30 50 70 100 150 200 250 300 350 400 450 500) #mum
ARRAYD=(500) #mum
ELEMENTSD=${#ARRAYD[@]}
ARRAYA=(0 1 2 3 4 5 6 7 8 9 10 15 20 25 30 40 50 70 100) # 1e-3 rad
#ARRAYA=(1 5) # 1e-3 rad
# get number of elements in the array
ELEMENTSA=${#ARRAYA[@]}

# echo each element in array 
# for loop
 for (( j=0;j<$ELEMENTSD;j++)); do
     for (( ia=0;ia<$ELEMENTSA;ia++)); do
	 for (( i=0;i<$ELEMENTS;i++)); do
	 T="$(date)"
	echo ${T} ": Now we'll do test with "${ARRAY[${i}]} "events for misalignment ~ "${ARRAYD[${j}]} "mum and" ${ARRAYA[${ia}]} "*10e-3 rad">> logSTAT
# #----------------------------------------------------------------------
	rm /home/akaravdina/lmdMacro/tmpOutputAlign/*
##Full sim & rec
	time root -l -b -q runLumi0SimBox.C\(${SIMEVENTS},11.91,\"tmpOutputAlign\"\)
	time root -l -b -q runLumi1Digi.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
#	time root -l -b -q create_misalignment_lumi.C\(${ARRAYD[${j}]},0.\) #shift
#	time root -l -b -q create_misalignment_lumi.C\(0.,${ARRAYD[${j}]}\) #rotation
	    time root -l -b -q create_misalignment_lumi.C\(${ARRAYD[${j}]},${ARRAYA[${ia}]}\) #rotation and translation
	time root -l -b -q runLumi2Reco.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
#	time root -l -b -q runLumi3Finder.C\(${SIMEVENTS},0,\"tmpOutputAlign\",0,\"CA\",true\)>> logTrkFind
#	    time root -l -b -q runLumi3Finder.C\(${SIMEVENTS},0,\"tmpOutputAlign\",0,\"CA\",true\)
	    time root -l -b -q runLumi3Finder.C\(${SIMEVENTS},0,\"tmpOutputAlign\",0,\"CA\",false\)
	time root -l -b -q runLumi4Fitter.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
        time root -l -b -q runLumi5Geane.C\(${SIMEVENTS},11.91,0,\"tmpOutputAlign\"\)

	    cd /data/FAIRsorf/pandaroot/build/bin
##obtain information about resolution before alignment
	    ./rec_mc_match -s 0 -n ${SIMEVENTS} -mom 11.91 -path "/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign"

##obtain info about hits for alignment
	    ./hits_align -s 0 -n ${ARRAY[${i}]} -path "/home/akaravdina/lmdMacro/tmpOutputAlign" -out "/home/akaravdina/lmdMacro/tmpOutputAlign/TrackForAlign.txt" -outhist "/home/akaravdina/lmdMacro/tmpOutputAlign/ResidualsHist.root" -v 0

##do alignment
	    cd /data/FAIRsorf/pandaroot/karavdina/myKnossos
	    ./knossos -i "/home/akaravdina/lmdMacro/tmpOutputAlign/TrackForAlign.txt" -o "/home/akaravdina/lmdMacro/tmpOutputAlign/LumiAlignConst.txt" -n ${ARRAY[${i}]} -r 1

	    rm /home/akaravdina/lmdMacro/lumi.misalign_after.par
	    head -14 /home/akaravdina/lmdMacro/lumi.misalign.par >> /home/akaravdina/lmdMacro/lumi.misalign_after.par
#obtain results and write it in new *.par file
	    ./analyze -in '/home/akaravdina/lmdMacro/lumi.misalign.par' -out '/home/akaravdina/lmdMacro/tmpOutputAlign/LumiAlignConst.txt' -new '/home/akaravdina/lmdMacro/lumi.misalign_after.par' >> logAnalyze
## change old params for new params
	    mv  /home/akaravdina/lmdMacro/lumi.misalign.par  /home/akaravdina/lmdMacro/lumi.misalign_before.par
	    mv  /home/akaravdina/lmdMacro/lumi.misalign_after.par /home/akaravdina/lmdMacro/lumi.misalign.par

##save results in good storage place
	    cd /home/akaravdina/lmdMacro
	    #pathname=/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign/results/misalign${ARRAYD[${j}]}_10e-4radDOF000111_${ARRAY[${i}]}_events
	    pathname=/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign/results/misalign_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}_10e-3radDOF111111_${ARRAY[${i}]}_events
	  #  pathname=/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign/results/misalign_${ARRAYD[${j}]}mum_DOF111000_${ARRAY[${i}]}_events
	    mkdir ${pathname}
	    echo "dir " ${pathname} "is made!"
	    cp /home/akaravdina/lmdMacro/tmpOutputAlign/Lumi_out_MC_and_REC_trks_matches_with_IDs0.root ${pathname}/Lumi_out_MC_and_REC_trks_matches_with_IDs0_before.root
	    cp  /data/FAIRsorf/pandaroot/karavdina/myKnossos/Results.root ${pathname}/Results.root
	    cp /home/akaravdina/lmdMacro/lumi.misalign_before.par ${pathname}/.
	    cp /home/akaravdina/lmdMacro/lumi.misalign.par ${pathname}/lumi.misalign_after.par
	    cp /home/akaravdina/lmdMacro/tmpOutputAlign/ResidualsHist.root ${pathname}/ResidualsHist_before.root
	    rm /home/akaravdina/lmdMacro/tmpOutputAlign/*


##repeat rec with new params
	    time root -l -b -q runLumi0SimBox.C\(${SIMEVENTS},11.91,\"tmpOutputAlign\"\)
	    time root -l -b -q runLumi1Digi.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
	    time root -l -b -q runLumi2Reco.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
	    time root -l -b -q runLumi3Finder.C\(${SIMEVENTS},0,\"tmpOutputAlign\",0,\"CA\",true\)
	    time root -l -b -q runLumi4Fitter.C\(${SIMEVENTS},0,\"tmpOutputAlign\"\)
	    time root -l -b -q runLumi5Geane.C\(${SIMEVENTS},11.91,0,\"tmpOutputAlign\"\)
	    cd /data/FAIRsorf/pandaroot/build/bin
##obtain information about residuals and resolution before alignment
	    ./hits_align -s 0 -n ${ARRAY[${i}]} -path "/home/akaravdina/lmdMacro/tmpOutputAlign" -out "/home/akaravdina/lmdMacro/tmpOutputAlign/TrackForAlign.txt" -outhist "/home/akaravdina/lmdMacro/tmpOutputAlign/ResidualsHist.root" -v 0
	    ./rec_mc_match -s 0 -n ${SIMEVENTS} -mom 11.91 -path "/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign"
	    cp /home/akaravdina/lmdMacro/tmpOutputAlign/ResidualsHist.root ${pathname}/ResidualsHist_after.root
	    cp /home/akaravdina/lmdMacro/tmpOutputAlign/Lumi_out_MC_and_REC_trks_matches_with_IDs0.root  ${pathname}/Lumi_out_MC_and_REC_trks_matches_with_IDs0_after.root 
	    cd  /home/akaravdina/lmdMacro/
#	    time root -l -b -q GenAlignEffect.C\(\"${pathname}/\"\)
	    resfile=/data/FAIRsorf/pandaroot/trunk/macro/lmd/tmpOutputAlign/results/RotStudy
	    time root -l -b -q GenAlignEffect.C\(\"${pathname}/\",${ARRAYA[${ia}]},${ia},${ELEMENTSA},\"${resfile}\"\)
	    #time root -l -b -q GenAlignEffect.C\(\"${pathname}/\",${ARRAYD[${j}]},${j},${ELEMENTSD},\"${resfile}\"\)
# # #---------------------------------------------------------------------- 
	 done
     done
 done
echo "results saved in " ${pathname}
exit