#!/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!"
cd ${VMCWORKDIR}/macro/lmd/
PANDAROOTmy=/home/karavdina/soft/develop/
pbeam=$mom
### pick up half solenoid maps for 1.5 GeV/c [tmp, should be removed one day!] ###
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
######################################################

momStr=`echo $pbeam | sed -e '{ s/\./_/g; }'`
#path=${VMCWORKDIR}/macro/lmd/testPixelAlignChallenge/mom_${momStr}/
# # create misalignment consts
dr=200
da=3
path=${VMCWORKDIR}/macro/lmd/testPixelAlignSIM_DPM/mom_${momStr}/${dr}mkm_${da}mrad/
mkdir -p ${path}
#number of trks per event
numTrks=1
#merge hits on sensors from different sides. true=yes
mergedHits=true
#number of events
numEvB=1000
numEvA=1000
numEv=$numEvB
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
root -l -b -q LMD_alignment/create_misalignment_lmd_pixel.C\(${dr},${da},"\"${path}/lumi.misalign_pixel.par\""\)
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
#root -l -b -q runLumiPixel0SimBox.C\(${numEv},0,"\"${path}\"",0,-2212,${pbeam},${numTrks},3562\)

# #copy MC data for ideal case
# cp ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM/mom_${momStr}/0mkm_0mrad/Lumi_MC_0.root ${path}/.
# cp ${VMCWORKDIR}/macro/lmd/testPixelAlignSIM/mom_${momStr}/0mkm_0mrad/Lumi_Params_0.root ${path}/.

### #simulation with DPM
#modeDPM=1 #el+inel
modeDPM=2 #el
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\(${numEv},0,"\"${path}\"",0,"\"Geane\"",${mergedHits},${pbeam}\)

#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_before.root 
### And now give some work to Millipede
	  cd ${VMCWORKDIR}/build/bin
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 0 -out ${path}/hits_trk_for_alignment_sector0.txt -outhist ${path}/hitsRes_before_alignment_sector0.root &> ${path}/logCreatAlignSampl0
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 1 -out ${path}/hits_trk_for_alignment_sector1.txt -outhist ${path}/hitsRes_before_alignment_sector1.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 2 -out ${path}/hits_trk_for_alignment_sector2.txt -outhist ${path}/hitsRes_before_alignment_sector2.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 3 -out ${path}/hits_trk_for_alignment_sector3.txt -outhist ${path}/hitsRes_before_alignment_sector3.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 4 -out ${path}/hits_trk_for_alignment_sector4.txt -outhist ${path}/hitsRes_before_alignment_sector4.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 5 -out ${path}/hits_trk_for_alignment_sector5.txt -outhist ${path}/hitsRes_before_alignment_sector5.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 6 -out ${path}/hits_trk_for_alignment_sector6.txt -outhist ${path}/hitsRes_before_alignment_sector6.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 7 -out ${path}/hits_trk_for_alignment_sector7.txt -outhist ${path}/hitsRes_before_alignment_sector7.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 8 -out ${path}/hits_trk_for_alignment_sector8.txt -outhist ${path}/hitsRes_before_alignment_sector8.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 9 -out ${path}/hits_trk_for_alignment_sector9.txt -outhist ${path}/hitsRes_before_alignment_sector9.root

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

   rm  ${path}/LumiAlignConst.txt
   cat ${path}/LumiAlignConst_sector0.txt ${path}/LumiAlignConst_sector1.txt ${path}/LumiAlignConst_sector2.txt ${path}/LumiAlignConst_sector3.txt ${path}/LumiAlignConst_sector4.txt ${path}/LumiAlignConst_sector5.txt ${path}/LumiAlignConst_sector6.txt ${path}/LumiAlignConst_sector7.txt ${path}/LumiAlignConst_sector8.txt ${path}/LumiAlignConst_sector9.txt > ${path}/LumiAlignConst.txt

   # cp ${path}/LumiAlignConst_sector0.txt ${path}/LumiAlignConst.txt
   # head -28 ${path}/LumiAlignConst_sector1.txt &> ${path}/LumiAlignConst.txt
   # head -28 ${path}/LumiAlignConst_sector2.txt &> ${path}/LumiAlignConst.txt
   # head -28 ${path}/LumiAlignConst_sector3.txt &> ${path}/LumiAlignConst.txt
   # head -28 ${path}/LumiAlignConst_sector4.txt &> ${path}/LumiAlignConst.txt

   #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}/build/bin
   ./analyze_alignment -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/
# 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\(${numEv},0,"\"${path}\"",0,-2212,${pbeam},${numTrks},3562\)

# #simulation with DPM
 #modeDPM=1 #el+inel
modeDPM=2 #el
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}/build/bin
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 0 -out ${path}/hits_trk_for_alignment_sector0_after.txt -outhist ${path}/hitsRes_after_alignment_sector0.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 1 -out ${path}/hits_trk_for_alignment_sector1_after.txt -outhist ${path}/hitsRes_after_alignment_sector1.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 2 -out ${path}/hits_trk_for_alignment_sector2_after.txt -outhist ${path}/hitsRes_after_alignment_sector2.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 3 -out ${path}/hits_trk_for_alignment_sector3_after.txt -outhist ${path}/hitsRes_after_alignment_sector3.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 4 -out ${path}/hits_trk_for_alignment_sector4_after.txt -outhist ${path}/hitsRes_after_alignment_sector4.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 5 -out ${path}/hits_trk_for_alignment_sector5_after.txt -outhist ${path}/hitsRes_after_alignment_sector5.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 6 -out ${path}/hits_trk_for_alignment_sector6_after.txt -outhist ${path}/hitsRes_after_alignment_sector6.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 7 -out ${path}/hits_trk_for_alignment_sector7_after.txt -outhist ${path}/hitsRes_after_alignment_sector7.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 8 -out ${path}/hits_trk_for_alignment_sector8_after.txt -outhist ${path}/hitsRes_after_alignment_sector8.root
	  ./hits_align_pixel -s 0 -n ${numEv} -path ${path} -m 9 -out ${path}/hits_trk_for_alignment_sector9_after.txt -outhist ${path}/hitsRes_after_alignment_sector9.root
## ##clean tmp storage place
#rm ${path}/FairRunInfo*
#rm ${path}/hits_trk_for_alignment*
#rm ${path}/Lumi_*