#!/bin/bash
# HIMster script ----------------------------------------------------------------------
# part3: run simulation with new alignment constants
# each misalignment consts combination used in ${nDataSamp} diff. data samples
# each data sample used in a sum from 1 to ${nDataSamp} samples
# each sample contains $numEv events (2e4)
# ver 1.0 [16/07/2014] 
# author: A.Karavdina
# ---------------------------------------------------------------------------------------
nDataSamp=100
#nConsSamp=5
nConsSamp=3
numEv=50000 #number of events in one sample
#TRANS=(0 50 100 200 300 400 500 600) #mkm
#TRANS=(0 10 50 100 200 300 400 500 600 800 1000) #mkm
#ROT=(0 0.2 1 3 5) #mrad
TRANS=(0 10) #mkm
ROT=(0 0.2) #mrad
TRANSN=${#TRANS[@]}
ROTN=${#ROT[@]}
#-----------------------------------------------------------------------------------------

verbose=0
PANDAROOT=/home/karavdin/pandaroot13
PANDAROOTmy=/home/karavdin/develop/karavdina/
# #----------------------------------------------------------------------
#pbeam=1.5
echo Enter momentum from "1.5, 4.06, 8.9, 11.91, 15 [GeV/c]":
read pbeam
echo "Beam mometum is: $pbeam!"
momStr=`echo $pbeam | sed -e '{ s/\./_/g; }'`
#pathG=/home/karavdin/datastorage/AlignmentLMDpixel/100data_10consts_SamplesStudyOct2013/BOX/mom_${momStr}
pathG=/home/karavdin/datastorage/AlignmentLMDpixel/RECdataAUG2014/BOX/mom_${momStr}
pathMC=/home/karavdin/datastorage/AlignmentLMDpixel/MCdataJuly2014/BOX/mom_${momStr}
mkdir -p ${pathG}
# if [ ! -r  ${pathG}/MCsamples ]; then
# mkdir ${pathG}/MCsamples
# fi
if [ ! -r  ${pathG}/misalignConsts ]; then
    mkdir ${pathG}/misalignConsts
fi
numTrks=1
mergedHits=true
#switch on "missing plane" search algorithm
	 misspl=true
#use cuts during trk seacrh with "CA". Should be 'false' if sensors missaligned!
	 trkcut=false
useMSerr=false
doalign=true
##Skip kinematic filter (before back-propagation)
SkipFilt=false
### if SkipFilt=false (XThetaCut or YPhiCut) or BoxCut should be true:
### X-Theta kinematic cut before back-propagation, add constant shift dX[cm] if beam is shifted
XThetaCut=true
dX=0.
### Y-Phi kinematic cut before back-propagation, add constant shift dY[cm] if beam is shifted
YPhiCut=true
dY=0.
### BOX cut before back-propagation
BoxCut=false

## Clean after back-propagation (M-cut: momentum or MVA cut)
CleanSig=true

## Combined filter (X&Y and M-cut)
CombFilt=false

## Write all MC info in TrkQA array
WrAllMC=false
##############

##ITTER=(1)
##ITTERN=${#ITTER[@]}
### pick up half solenoid maps for 1.5 GeV/c [tmp, should be removed one day!] ###
source /home/karavdin/pandaroot13/buildPanda/config.sh
# solsw=3 #GeV, switch between half and full solenoid: below half of solenoid
# if [[ $(echo "if (${pbeam} > ${solsw}) 1 else 0" | bc) -eq 1 ]]; then
#     echo "FULL solenoid field maps"
#     ln -sf ${VMCWORKDIR}/input/solenoid_fc/* ${VMCWORKDIR}/input/.
# else
#     echo "HALF solenoid field maps"
#     ln -sf ${VMCWORKDIR}/input/solenoid_hc/* ${VMCWORKDIR}/input/.
# fi
# ######################################################

for (( jr=0;jr<$ROTN;jr++)); do
    for (( jt=0;jt<$TRANSN;jt++)); do
	dr=${TRANS[${jt}]}
	da=${ROT[${jr}]}
	daStr=`echo $da | sed -e '{ s/\./_/g; }'`
	for(( js=0;js<${nConsSamp};js++));do #samples with diff Delta_x, Delta_al in the same scale
	    pathDxDa=${pathG}/${dr}mkm_${daStr}mrad/ConstSample${js}
	    if [ ! -r ${pathDxDa} ]; then
		echo "Beam path ${pathDxDa} doesn't exist!"
	    fi
	    for jsn in `seq 0 ${step} $(( ${nDataSamp} - 1))`; do
		
		path_res=${pathDxDa}/RECsum$((${jsn}+1))DataSamples/
		if [ ! -r ${path_res} ]; then
		    echo "Beam path ${path_res} doesn't exist!"
		fi
		for jn in `seq 0 ${step} $(( ${nDataSamp} - 1))`; do
		    path=${path_res}/RECalignDataSample${jn}/
		    mkdir -p ${path}
		    pathMC_sample=${pathMC}/Sample${jn}/
		    path_loc=/local/scratch/karavdina/${dr}mkm_${daStr}mrad/${js}Sum$((${jsn}+1))Samples_Sample${jn}/
		    if [ ! -d jobs/align/mom_${momStr}/ ]; then 
			mkdir -p jobs/align/mom_${momStr}/
		    fi
		    cat >jobs/align/mom_${momStr}/job_${dr}mkm_${daStr}mrad_${js}Sum${jsn}_samp${jn}.sh <<EOF
#!/bin/bash
#
#PBS -j oe 
#PBS -N Align${dr}_${daStr}.${js}_$((${jsn}+1))sum.${jn}
#PBS -o ${path}/LOGhimsterFile_part3
#PBS -V
#PBS -l nodes=1:ppn=1,walltime=04:59:00
export PATH=\$PBS_O_PATH
cd \$PBS_O_WORKDIR
echo "Start Simulation for Alignment study"
echo "Time of start: `date` "
       if [ ! -r ${path_loc} ]; then 
        mkdir -p ${path_loc}
       fi

     cd ${PANDAROOT}/macro/lmd
     source ${PANDAROOT}/buildPanda/config.sh
     cp  ${path_res}/lumi.misalign_pixel_after.par ${path_loc}/lumi.misalign_pixel.par

     cp ${VMCWORKDIR}/geometry/trafo_matrices_lmd.dat  ${path_loc}/trafo_matrices_lmd.dat
     cp ${pathMC_sample}/* ${path_loc}/.


#digi
    root -l -b -q runLumiPixel1Digi.C\(${numEv},0,"\"${path_loc}\""\)
#hit reconstruction with misaligned consts
    root -l -b -q runLumiPixel2Reco.C\(${numEv},0,"\"${path_loc}\"",0,$doalign\)
# ##merge hits
     root -l -b -q runLumiPixel2bHitMerge.C\(${numEv},0,"\"${path_loc}\"",0,$doalign\)

#switch on "missing plane" search algorithm
	 misspl=true
#use cuts during trk seacrh with "CA". Should be 'false' if sensors missaligned!
	 trkcut=false
### change "CA" --> "Follow" if you want to use Trk-Following as trk-search algorithm
### NB: CA can use merged or single(not merged) hits, Trk-Following can't
     root -l -b -q runLumiPixel3Finder.C\(${numEv},0,"\"${path_loc}\"",0,"\"CA\"",${misspl},${mergedHits},${trkcut},${pbeam}\)

#track fit: 
### Possible options: "Minuit", "KalmanGeane", "KalmanRK"
       root -l -b -q runLumiPixel4Fitter.C\(${numEv},0,"\"${path_loc}\"",0,"\"Minuit\"",${mergedHits}\)

#track filter (on number of hits and chi2)
     root -l -b -q runLumiPixel4aFilter.C\(${numEv},0,"\"${path_loc}\"",0,${mergedHits},${SkipFilt},${XThetaCut},${YPhiCut},${BoxCut},${dX},${dY}\) 
#save filtered results as standart Track array
     mv ${path_loc}/Lumi_Track_0.root ${path_loc}/Lumi_TrackNotFiltered_0.root 
     cp ${path_loc}/Lumi_TrackFiltered_0.root ${path_loc}/Lumi_Track_0.root
#back-propgation GEANE
### Possible options: "Geane", "RK"
     root -l -b -q runLumiPixel5BackProp.C\(${numEv},0,"\"${path_loc}\"",0,"\"Geane\"",${mergedHits},${pbeam}\)

#clean signal from background (momentum cut or MVA cut)
	 if [ $CleanSig == "true" ]; then 
	     root -l -b -q runLumiPixel5bCleanSig.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${dX},${dY}\)
	 fi
	 #combined filter (X&Y and M cuts)
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel5cCombFilt.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${dX},${dY}\)
	 fi

# # Quality assurance task(s)
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7QA.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7QA.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${CleanSig}\)
	 fi
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${WrAllMC},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEv},0,"\"${path_loc}\"",0,${pbeam},${WrAllMC},${CleanSig}\)
	 fi
	  mv ${path_loc}/Lumi_QA_0.root  ${path_loc}/Lumi_QA_after.root 
### And now give some work to Millipede
	  cd ${VMCWORKDIR}/buildPanda/bin
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 0 -out ${path_loc}/hits_trk_for_alignment_sector0.txt -outhist ${path_loc}/hitsRes_after_alignment_sector0.root &> ${path_loc}/logCreatAlignSampl0
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 1 -out ${path_loc}/hits_trk_for_alignment_sector1.txt -outhist ${path_loc}/hitsRes_after_alignment_sector1.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 2 -out ${path_loc}/hits_trk_for_alignment_sector2.txt -outhist ${path_loc}/hitsRes_after_alignment_sector2.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 3 -out ${path_loc}/hits_trk_for_alignment_sector3.txt -outhist ${path_loc}/hitsRes_after_alignment_sector3.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 4 -out ${path_loc}/hits_trk_for_alignment_sector4.txt -outhist ${path_loc}/hitsRes_after_alignment_sector4.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 5 -out ${path_loc}/hits_trk_for_alignment_sector5.txt -outhist ${path_loc}/hitsRes_after_alignment_sector5.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 6 -out ${path_loc}/hits_trk_for_alignment_sector6.txt -outhist ${path_loc}/hitsRes_after_alignment_sector6.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 7 -out ${path_loc}/hits_trk_for_alignment_sector7.txt -outhist ${path_loc}/hitsRes_after_alignment_sector7.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 8 -out ${path_loc}/hits_trk_for_alignment_sector8.txt -outhist ${path_loc}/hitsRes_after_alignment_sector8.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path_loc} -m 9 -out ${path_loc}/hits_trk_for_alignment_sector9.txt -outhist ${path_loc}/hitsRes_after_alignment_sector9.root

##cp ${path_loc}/* ${path}/.
mv  ${path_loc}/hitsRes_after* ${path}/.
mv ${path_loc}/Lumi_QA_after.root ${path}/.
rm -r ${path_loc}

echo "Time of end: `date` "
exit 0
EOF
		 
	#	  echo "Output files will be saved in $path_res"
### submit job to batch system
    		iter=0
		while [ $iter -lt 1 ];do 
		    qsub jobs/align/mom_${momStr}/job_${dr}mkm_${daStr}mrad_${js}Sum${jsn}_samp${jn}.sh
		    done_test=$(echo $?)
		    if [ "$done_test" -eq "0" ];then
			echo "Output files will be saved in $path"
			iter=1
		    else
			echo "qsub did not work sleep for 60 seconds and then try again." 
			sleep 60
		    fi
		done
   		done
	    done
	done
    done
done