#!/bin/bash 
################################################################
## script for running sim&rec and sim&rec for LMD alignment with current LMD reconstruction
## 28/11/2013 1st version
## A.Karavdina
################################################################
echo Enter momentum from "1.5, 4.06, 8.9, 11.91, 15 [GeV/c]":
read mom
echo "Beam mometum is: $mom!"
echo Enter sample number:
read sNum
cd ${VMCWORKDIR}/macro/lmd/
PANDAROOTmy=/panda/karavdina/
pbeam=$mom
momStr=`echo $pbeam | sed -e '{ s/\./_/g; }'`
#path=${VMCWORKDIR}/macro/lmd/testPixelAlignChallenge/mom_${momStr}/
# # create misalignment consts
TRANS=(0 50 100 200 300 400 500 600 800 1000) #mkm
#TRANS=(0) #mkm
TRANSN=${#TRANS[@]}
ROT=(0 1 3 5) #mrad
#ROT=(0) #mrad
ROTN=${#ROT[@]}
  for (( jt=0;jt<$TRANSN;jt++)); do
	for (( jr=0;jr<$ROTN;jr++)); do
	    cd ${VMCWORKDIR}/macro/lmd/
	    dr=${TRANS[${jt}]}
	    da=${ROT[${jr}]}
	    #number of events
	    #for alignment
	    #numEvB=3000000
	    numEvB=5000000
	    #for results test
	    numEvA=10000
	#    numEvA=1000	   
	    numEv=${numEvB}
	    pathMC=${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/MCfilesBOX${sNum}/mom_${momStr}
	    path=${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/mom_${momStr}/${dr}mkm_${da}mrad/
	    mkdir -p ${path}
	    #number of trks per event
	    numTrks=1
	    #merge hits on sensors from different sides. true=yes
	    mergedHits=true
	    
	    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
	    ##############
	    
	    #
	    # #generate misalignment consts
	    if [ ! -r  ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/misalignConsts/${dr}mkm_${da}mrad/lumi.misalign_pixel.par ]; then
		root -l -b -q LMD_alignment/create_misalignment_lmd_pixel.C\(${dr},${da},"\"${path}/lumi.misalign_pixel.par\""\)
		mkdir -p ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/misalignConsts/${dr}mkm_${da}mrad/
		mv ${path}/lumi.misalign_pixel.par ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/misalignConsts/${dr}mkm_${da}mrad/.
	    fi
	    cp  ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_${numEvB}/misalignConsts/${dr}mkm_${da}mrad/lumi.misalign_pixel.par ${path}/.
		cp ${VMCWORKDIR}/geometry/trafo_matrices_lmd.dat ${path}/.
		
		# #use externally generated geometry
		#  cp /panda/nov2013pandaroot/macro/lmd/LMD_alignment/challenge/trafo_matrices_lmd.dat ${path}/.
		# cp /panda/nov2013pandaroot/macro/lmd/LMD_alignment/challenge/Luminosity-Detector.root ${VMCWORKDIR}/input/.
		# cp ${VMCWORKDIR}/macro/lmd/LMD_alignment/lumi.align_pixel_ideal.par ${path}/lumi.misalign_pixel.par
		
		# #simulation with Box generator
		if [ ! -r ${pathMC}/Lumi_MC_0.root ]; then
		    mkdir -p ${pathMC}
		    root -l -b -q runLumiPixel0SimBox.C\(${numEv},0,"\"${pathMC}\"",0,-2212,${pbeam},${numTrks},0\)
		fi
		#copy data from MC data storage 
		cp ${pathMC}/Lumi_MC_0.root ${path}/.
		cp ${pathMC}/Lumi_Params_0.root ${path}/.
		### #simulation with DPM
		## #modeDPM=1 #el+inel
		##   root -l -b -q runLumiPixel0SimDPMDirect.C\(${numEv},0,${pbeam},"\"${path}\"",0,3562,$modeDPM,0.12\)
		
		#digi
		root -l -b -q runLumiPixel1Digi.C\(${numEv},0,"\"${path}\""\)
		    #hit reconstruction with misaligned consts
		    root -l -b -q runLumiPixel2Reco.C\(${numEv},0,"\"${path}\"",0,$doalign\)
			# ##merge hits
			root -l -b -q runLumiPixel2bHitMerge.C\(${numEv},0,"\"${path}\"",0,$doalign\)
			    
#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\(${numEv},0,"\"${path}\"",0,"\"CA\"",${misspl},${mergedHits},${trkcut},${pbeam}\)

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

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

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

# # Quality assurance task(s)
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7QA.C\(${numEvA},0,"\"${path}\"",0,${pbeam},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7QA.C\(${numEvA},0,"\"${path}\"",0,${pbeam},${CleanSig}\)
	 fi
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEvA},0,"\"${path}\"",0,${pbeam},${WrAllMC},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEvA},0,"\"${path}\"",0,${pbeam},${WrAllMC},${CleanSig}\)
	 fi
	  mv ${path}/Lumi_QA_0.root  ${path}/Lumi_QA_before.root 
### And now give some work to Millipede
#	  cd ${VMCWORKDIR}/buildPanda/bin

	  cp ${PANDAROOTmy}/myKnossos/constantsLMD.h ${path}/.
	  rm ${path}/logKnossos*
	  rm ${path}/LumiAlignConst.txt
	  rm ${path}/ModulesStat.txt
	  for (( jm=0;jm<10;jm++)); do
	      cd ${VMCWORKDIR}/buildPanda/bin
	      ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m ${jm} -out ${path}/hits_trk_for_alignment_sector${jm}.txt -outhist ${path}/hitsRes_before_alignment_sector${jm}.root 
	      cd ${PANDAROOTmy}/myKnossos
	      /usr/bin/time -v ./knossos -i ${path}/hits_trk_for_alignment_sector${jm}.txt -o ${path}/LumiAlignConst_sector${jm}.txt -n ${numEv} -r 1 &> ${path}/logKnossos${jm}
	      cat ${path}/LumiAlignConst_sector${jm}.txt >> ${path}/LumiAlignConst.txt
	      echo "Module #${jm}:" >> ${path}/ModulesStat.txt
	      grep "Alignment based on" ${path}/logKnossos${jm} >> ${path}/ModulesStat.txt
	      grep "Last iteration used" ${path}/logKnossos${jm} >> ${path}/ModulesStat.txt
	  done

   #obtain results and write it in new *.par file
   rm ${path}/lumi.misalign_pixel_after.par
   head -16 ${path}/lumi.misalign_pixel.par &> ${path}/lumi.misalign_pixel_after.par

     cd ${VMCWORKDIR}/buildPanda/bin
   ./analyze_alignment -stat ${path}/ModulesStat.txt -in ${path}/lumi.misalign_pixel.par -out ${path}/LumiAlignConst.txt -new ${path}/lumi.misalign_pixel_after.par -outroot ${path}/KnossosResults.root &> ${path}/logAnaKnossos

   cd ${VMCWORKDIR}/macro/lmd/
   mv ${path}/Lumi_TrksQA_0.root ${path}/Lumi_TrksQA_before.root
   rm ${path}/Lumi_MC_0.root 
   rm ${path}/Lumi_Params_0.root
   rm ${path}/Lumi_digi_0.root
   rm ${path}/Lumi_reco_0.root
   rm ${path}/Lumi_recoMerged_0.root
   rm ${path}/Lumi_TCand_0.root
   rm ${path}/Lumi_Track_0.root
   rm ${path}/Lumi_TrackFiltered_0.root
   rm ${path}/Lumi_TrackNotFiltered_0.root
   rm ${path}/Lumi_Geane_0.root
   rm ${path}/Lumi_GeaneFiltered_0.root
   rm ${path}/Lumi_IGNORE_0.root

# TODO: apply all cuts (XY and M)
# ## change old params for new params
mv  ${path}/lumi.misalign_pixel.par  ${path}/lumi.misalign_pixel_before.par
cp  ${path}/lumi.misalign_pixel_after.par ${path}/lumi.misalign_pixel.par

  numEv=$numEvA
##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


# #simulation with Box generator
#   root -l -b -q runLumiPixel0SimBox.C\(${numEv},0,"\"${path}\"",0,-2212,${pbeam},${numTrks},3562\)
	#copy data from MC data storage 
		cp ${pathMC}/Lumi_MC_0.root ${path}/.
		cp ${pathMC}/Lumi_Params_0.root ${path}/.
# #simulation with DPM
 #modeDPM=1 #el+inel
 #   root -l -b -q runLumiPixel0SimDPMDirect.C\(${numEv},0,${pbeam},"\"${path}\"",0,3562,$modeDPM,0.12\)

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

#switch on "missing plane" search algorithm
	 misspl=true
#use cuts during trk seacrh with "CA".
	 trkcut=true
### 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\(${numEv},0,"\"${path}\"",0,"\"CA\"",${misspl},${mergedHits},${trkcut},${pbeam}\)

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

#track filter (on number of hits and chi2)
    root -l -b -q runLumiPixel4aFilter.C\(${numEv},0,"\"${path}\"",0,${mergedHits},${SkipFilt},${XThetaCut},${YPhiCut},${BoxCut},${dX},${dY}\) 
#save filtered results as standart Track array
     mv ${path}/Lumi_Track_0.root ${path}/Lumi_TrackNotFiltered_0.root 
     cp ${path}/Lumi_TrackFiltered_0.root ${path}/Lumi_Track_0.root


#back-propgation GEANE
### Possible options: "Geane", "RK"
     root -l -b -q runLumiPixel5BackProp.C\(${numEv},0,"\"${path}\"",0,"\"Geane\"",${mergedHits},${pbeam}\)

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

# # Quality assurance task(s)
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7QA.C\(${numEv},0,"\"${path}\"",0,${pbeam},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7QA.C\(${numEv},0,"\"${path}\"",0,${pbeam},${CleanSig}\)
	 fi
	 if [ $CombFilt == "true" ]; then 
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEv},0,"\"${path}\"",0,${pbeam},${WrAllMC},${CombFilt}\)
	 else
	     root -l -b -q runLumiPixel7TrksQA.C\(${numEv},0,"\"${path}\"",0,${pbeam},${WrAllMC},${CleanSig}\)
	 fi

	  mv ${path}/Lumi_QA_0.root  ${path}/Lumi_QA_after.root 

	  cd ${VMCWORKDIR}/buildPanda/bin
	  for (( jm=0;jm<10;jm++)); do
	      ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m ${jm} -out ${path}/hits_trk_for_alignment_sector${jm}_after.txt -outhist ${path}/hitsRes_after_alignment_sector${jm}.root
	  done
mv ${path}/Lumi_TrksQA_0.root ${path}/Lumi_TrksQA_after.root
rm ${path}/Lumi_MC_0.root 
rm ${path}/Lumi_Params_0.root
rm ${path}/Lumi_digi_0.root
rm ${path}/Lumi_reco_0.root
rm ${path}/Lumi_recoMerged_0.root
rm ${path}/Lumi_TCand_0.root
rm ${path}/Lumi_Track_0.root
rm ${path}/Lumi_TrackFiltered_0.root
rm ${path}/Lumi_TrackNotFiltered_0.root
rm ${path}/Lumi_Geane_0.root
rm ${path}/Lumi_GeaneFiltered_0.root
rm ${path}/Lumi_IGNORE_0.root
## ##clean tmp storage place
#rm ${path}/FairRunInfo*
#rm ${path}/hits_trk_for_alignment*
#rm ${path}/Lumi_*
	done
  done
  exit