#!/bin/bash
# HIMster script ----------------------------------------------------------------------
# part2: run an alignment 
# 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 $numEv events (2e4)
# ver 1.0 [16/07/2014] 
# author: A.Karavdina
# ---------------------------------------------------------------------------------------
nDataSamp=100
#nConsSamp=10
nConsSamp=5
numEv=50000 #number of events in one sample
#TRANS=(0 10 50 100 200 300 400 500 600 700 800 1000) #mkm
#TRANS=(0 10 50 100 200 300 400 500 600 700 800) #mkm
#TRANS=(10 50 100 200 300 400 500 0) #mkm
#TRANS=(50 100 200 300 400 500 600 700 10 0) #mkm
TRANS=(0) #mkm
#ROT=(0 0.2 1 3 5) #mrad
#ROT=(3 1 5 0) #mrad
ROT=(0) #mrad
TRANSN=${#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=true
### 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=false
dX=0.
### Y-Phi kinematic cut before back-propagation, add constant shift dY[cm] if beam is shifted
YPhiCut=false
dY=0.
### BOX cut before back-propagation
BoxCut=false

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

## 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
#	for(( js=5;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} $(( ${nDataSamp} - 1))`; do
		path=${pathDxDa}/RECrawDataSample${jn}/
		path_res=${pathDxDa}/RECsum$((${jsn}+1))DataSamples/
		if [ ! -r ${path_res} ]; then
		    mkdir -p ${path_res}
		fi

		cat > ${path_res}/QA_hitsSamples.log  <<EOF
EOF
		for (( jm=0;jm<10;jm++)); do
		    cat > ${path_res}/names_hits_sec${jm}.log <<EOF
EOF
		done
		
		
		for jn in `seq 0 1 ${jsn}`; do
		    path=${pathDxDa}/RECrawDataSample${jn}/
		    for (( jm=0;jm<10;jm++)); do
			if [ ! -r  ${path}/hits_trk_for_alignment_sector${jm}.txt ]; then
			    echo "Sample${js}${jn}: ouput doesn't exist"  >> ${path_res}/QA_hitsSamples.log 
			fi
			if [ -r ${path}/hits_trk_for_alignment_sector${jm}.txt ]; then
			    echo -n "${path}/hits_trk_for_alignment_sector${jm}.txt " >> ${path_res}/names_hits_sec${jm}.log
			fi
		    done
		done
	    done
	    for jsn in `seq 0 ${step} $(( ${nDataSamp} - 1))`; do
		path_res=${pathDxDa}/RECsum$((${jsn}+1))DataSamples/
		path_resLOC=/local/scratch/karavdina/${dr}mkm_${daStr}mrad_${momStr}/${js}Sum$((${jsn}+1))Samples/
		if [ ! -d jobs/align/mom_${momStr}/ ]; then 
		    mkdir -p jobs/align/mom_${momStr}/
		fi
		numEvKnossos=$(expr  $(expr ${jsn} + 1) \* $numEv)
		#echo "current number of events is $numEvKnossos"
#		numEvKnossos = expr ((${jsn}+1)) \* $numEv
		cat >jobs/align/mom_${momStr}/job_${dr}mkm_${daStr}mrad_${js}Sum${jsn}.sh <<EOF
#!/bin/bash
#
#PBS -N Align.${dr}.${daStr}_$js.$((${jsn}+1))sum
#PBS -j oe
#PBS -o ${path_res}/LOGhimsterFile_part2
#PBS -V
#PBS -l nodes=1:ppn=1,walltime=03:59:00
export PATH=\$PBS_O_PATH
cd \$PBS_O_WORKDIR
echo "Start Sum sample simulations for Alignment study"
echo "Time of start: `date` "
   if [ ! -r  ${path_resLOC} ]; then
   mkdir -p ${path_resLOC}
  fi

    cat ${filenames0} `cat ${path_res}/names_hits_sec0.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector0.txt
    cat ${filenames1} `cat ${path_res}/names_hits_sec1.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector1.txt
    cat ${filenames2} `cat ${path_res}/names_hits_sec2.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector2.txt
    cat ${filenames3} `cat ${path_res}/names_hits_sec3.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector3.txt
    cat ${filenames4} `cat ${path_res}/names_hits_sec4.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector4.txt
    cat ${filenames5} `cat ${path_res}/names_hits_sec5.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector5.txt
    cat ${filenames6} `cat ${path_res}/names_hits_sec6.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector6.txt
    cat ${filenames7} `cat ${path_res}/names_hits_sec7.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector7.txt
    cat ${filenames8} `cat ${path_res}/names_hits_sec8.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector8.txt
    cat ${filenames9} `cat ${path_res}/names_hits_sec9.log` >>  ${path_resLOC}/hits_trk_for_alignment_sector9.txt
PANDAROOT=/home/karavdin/pandaroot13
     cd ${PANDAROOT}/macro/lmd
     source ${PANDAROOT}/buildPanda/config.sh

     cd ${PANDAROOTmy}/myKnossos
   ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector0.txt -o  ${path_resLOC}/LumiAlignConst_sector0.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos0
   ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector1.txt -o  ${path_resLOC}/LumiAlignConst_sector1.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos1
  ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector2.txt -o  ${path_resLOC}/LumiAlignConst_sector2.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos2
   ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector3.txt -o  ${path_resLOC}/LumiAlignConst_sector3.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos3
  ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector4.txt -o  ${path_resLOC}/LumiAlignConst_sector4.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos4
  ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector5.txt -o  ${path_resLOC}/LumiAlignConst_sector5.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos5
./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector6.txt -o  ${path_resLOC}/LumiAlignConst_sector6.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos6
  ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector7.txt -o  ${path_resLOC}/LumiAlignConst_sector7.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos7
  ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector8.txt -o  ${path_resLOC}/LumiAlignConst_sector8.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos8
 ./knossos -i  ${path_resLOC}/hits_trk_for_alignment_sector9.txt -o  ${path_resLOC}/LumiAlignConst_sector9.txt -n ${numEvKnossos} -r 1 &>  ${path_resLOC}/logKnossos9

if [ -r  ${path_resLOC}/LumiAlignConst.txt ]; then
   rm   ${path_resLOC}/LumiAlignConst.txt
fi
	   cat   ${path_resLOC}/LumiAlignConst_sector0.txt   ${path_resLOC}/LumiAlignConst_sector1.txt   ${path_resLOC}/LumiAlignConst_sector2.txt   ${path_resLOC}/LumiAlignConst_sector3.txt   ${path_resLOC}/LumiAlignConst_sector4.txt   ${path_resLOC}/LumiAlignConst_sector5.txt   ${path_resLOC}/LumiAlignConst_sector6.txt   ${path_resLOC}/LumiAlignConst_sector7.txt   ${path_resLOC}/LumiAlignConst_sector8.txt   ${path_resLOC}/LumiAlignConst_sector9.txt >   ${path_resLOC}/LumiAlignConst.txt
if [ -r ${path_resLOC}/ModulesStat.txt ]; then
 rm ${path_resLOC}/ModulesStat.txt
fi
echo "Module #0:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos0 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos0 >> ${path_resLOC}/ModulesStat.txt
echo "Module #1:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos1 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos1 >> ${path_resLOC}/ModulesStat.txt
echo "Module #2:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos2 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos2 >> ${path_resLOC}/ModulesStat.txt
echo "Module #3:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos3 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos3 >> ${path_resLOC}/ModulesStat.txt
echo "Module #4:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos4 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos4 >> ${path_resLOC}/ModulesStat.txt
echo "Module #5:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos5 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos5 >> ${path_resLOC}/ModulesStat.txt
echo "Module #6:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos6 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos6 >> ${path_resLOC}/ModulesStat.txt
echo "Module #7:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos7 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos7 >> ${path_resLOC}/ModulesStat.txt
echo "Module #8:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos8 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos8 >> ${path_resLOC}/ModulesStat.txt
echo "Module #9:" >> ${path_resLOC}/ModulesStat.txt
	      grep "Alignment based on" ${path_resLOC}/logKnossos9 >> ${path_resLOC}/ModulesStat.txt
	      grep "Last iteration used" ${path_resLOC}/logKnossos9 >> ${path_resLOC}/ModulesStat.txt


if [ -r ${path_res}/lumi.misalign_pixel_after.par ]; then
 rm   ${path_res}/lumi.misalign_pixel_after.par
fi
   cp ${pathG}/misalignConsts/lumi.misalign_pixel_${dr}mkm_${daStr}mrad_${js}.par ${path_resLOC}/lumi.misalign_pixel.par
   head -16 ${path_resLOC}/lumi.misalign_pixel.par >>  ${path_resLOC}/lumi.misalign_pixel_after.par
     cd ${PANDAROOT}//buildPanda/bin
   ./analyze_alignment -stat ${path_resLOC}/ModulesStat.txt -in ${path_resLOC}/lumi.misalign_pixel.par -out  ${path_resLOC}/LumiAlignConst.txt -new  ${path_resLOC}/lumi.misalign_pixel_after.par -outroot ${path_resLOC}/KnossosResults.root
## mv ${path_resLOC}/logKnossos* ${path_res}/.
mv ${path_resLOC}/logKnossos0 ${path_res}/.
mv ${path_resLOC}/hits_trk_for_alignment_sector0.txt ${path_res}/.
mv ${path_resLOC}/LumiAlignConst.txt ${path_res}/.
mv ${path_resLOC}/lumi.misalign_pixel_after.par ${path_res}/.
mv ${path_resLOC}/KnossosResults.root ${path_res}/.
rm -r ${path_resLOC}
rm ${path_res}/names_*
echo "Time: `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}.sh
		    done_test=$(echo $?)
		    if [ "$done_test" -eq "0" ];then
			echo "Output files will be saved in $path_res"
			iter=1
		    else
			echo "qsub did not work sleep for 60 seconds and then try again." 
			sleep 60
		    fi
		done

   	      done
	done
  done
done