import ROOT, glob, math, sys, os
from ROOT import std

#void runRecoFOPI_batch_standalone_mb(TString filename, TString outpath, 
#				     int field, TString gas, int bfield,
#				     unsigned int smoothing = 0, unsigned int nEvents = 0, 
#				     unsigned int nEvStart = 0,unsigned int outnum=0) {
# ========================================================================
# Verbosity level (0=quiet, 1=event level, 2=track level, 3=debug)
iVerbose = 1;

#  TStopwatch timer;
#  timer.Start();
  
  
basedir = ROOT.TString(gSystem->Getenv("VMCWORKDIR"))
fRun = ROOT.FairRunAna();

jobdir = ROOT.TString(outpath)
jobname=(filename.Data());
last = jobname.rfind("/");
if(last>0):
    jobname = jobname.jobname[last+1,jobname.size()+1]  
  
outName=ROOT.TString(jobname);
if(outName.Contains("repaired.")):
    outName.ReplaceAll(".lmd_decoded_repaired.root",".reco.root")
if(outName.Contains("decoded.")):
    outName.ReplaceAll(".lmd_decoded.root",".reco.root");
if(smoothing):
    outName.ReplaceAll("reco.root", "smoothed_reco.root");
if(outnum>0):
    outName.ReplaceAll(".root",Form("%i.root",outnum));
outFile = ROOT.TString(outpath+"/")
outFile += outName; 
    
  TString PROutFile = outFile;
  PROutFile.ReplaceAll(".reco.root",".patternReco.root");
  TFile test(PROutFile, "recreate");
  if(!test.IsZombie()) { //delete file
    gSystem->Setenv("PROUTFILENAME", PROutFile.Data());
    gROOT->ProcessLine(".! rm $PROUTFILENAME");
    gSystem->Unsetenv("PROUTFILENAME");
  }
  
  fRun->SetOutputFile(outFile);
 
  FairRuntimeDb* rtdb = fRun->GetRuntimeDb();
  FairParAsciiFileIo* parInput1 = new FairParAsciiFileIo();
  TString tpcDigiFile = basedir;
  tpcDigiFile += "/tpc/FOPI/par/tpc.TBtestChamber.";
  tpcDigiFile += field;
  tpcDigiFile += gas;
  tpcDigiFile +=".par";
  parInput1->open(tpcDigiFile.Data(),"in"); 
  
  rtdb->setFirstInput(parInput1);
  
  rtdb->Print();
  
  TString geoFile = basedir;
  geoFile+="/tpc/TestBench/FOPIGeo.root";
  fRun->SetGeomFile(geoFile);
  
  PndConstField *fMagField=new PndConstField();
  if (bfield == 1)
    fMagField->SetField(0., 0. , 6. ); // values are in kG
  if (bfield == 0)
    fMagField->SetField(0., 0. , 0. ); // values are in kG
  // values are in cm
  fMagField->SetFieldRegion(-50, 50,-50, 50, -2000, 2000);
      
  fRun->SetField(fMagField);
  
  //extract number of entries in external data tree
  TFile testFile(filename);
  unsigned int numEvents = ((TTree*)testFile.Get("tpcEvent"))->GetEntries();
  std::cout<<"Found "<<nEvents<<" events in input data file"<<std::endl;
  if(nEvents==0 || nEvents>numEvents) nEvents=numEvents;


  TpcAlignmentManager * align = TpcAlignmentManager::getInstance("/nfs/hicran/project/panda/SIM/bergerm/fopiroot/tpc/FOPI/par/dummy_alignment.txt");
  //--------------------SET UP TASKS ------------------------------

  FairGeane *Geane = new FairGeane();
  fRun->AddTask(Geane);
    
  TpcDataReaderTask* read = new TpcDataReaderTask();
  //read->SetPersistence();
  read->SetDatafile(filename);
  read->SetClusterBranchName("TpcSample");
  read->SetStartEvent(nEvStart);
  //read->SetCutSmallPad();
  //read->SetMinSamples(1000);
  fRun->AddTask(read);
  

  TpcPSATask* tpsa = new  TpcPSATask();
  tpsa->SetPersistence();
  tpsa->SetSamplePersistence();
  tpsa->SetSampleBranchName("TpcSample"); // Input of PSA
  fRun->AddTask(tpsa);


  TpcClusterFinderTask* tpcCF = new TpcClusterFinderTask();
  tpcCF->SetDigiPersistence(); // keep Digis copys in clusters
  tpcCF->SetPersistence(); // keep Clusters
  tpcCF->timeslice(6); //in samples
  tpcCF->SetSingleDigiClusterAmpCut(20);
  tpcCF->SetClusterAmpCut(9.1); // cut on mean digi amplitude
  tpcCF->SetErrorPars(600.,400.);
  tpcCF->SetSimpleClustering(); // use TpcClusterFinderSimple
  fRun->AddTask(tpcCF);
  
  TpcClusterAlignmentTask *tpcAlign = new TpcClusterAlignmentTask();
  tpcAlign->SetPersistence();
  tpcAlign->SetClusterInBranchName("TpcClusterRaw");
  tpcAlign->SetClusterOutBranchName("TpcCluster");
  fRun->AddTask(tpcAlign);    

  //find TpcRiemannTracks in the TPC alone
  TpcRiemannTrackingTask* tpcSPR = new TpcRiemannTrackingTask();
  tpcSPR->SetClusterBranchName("TpcCluster");
  tpcSPR->SetPersistence();
  tpcSPR->SetSortingParameters(true,1,0);
  fRun->AddTask(tpcSPR);

  //build GFTracks from TpcRiemannTracks
  TpcTrackInitTask* trackInit=new TpcTrackInitTask();
  trackInit->SetClusterBranchName("TpcCluster");
  trackInit->SetOutBranchName("TpcTrackPreFit");
  trackInit->SetPersistence();
  //trackInit->SetVerbose(1);
  //trackInit->SetMCPid(); // use ideal particle identification
  trackInit->SetPDG(211);
  //trackInit->useGeane(); // uses RKTrackrep and GeaneTrackrep
  if (smoothing==1)
    trackInit->SetSmoothing(true);
  fRun->AddTask(trackInit);

  TpcSLPatternRecoTask* tpcSLPR = new TpcSLPatternRecoTask();
  tpcSLPR->SetPersistence(true);
  tpcSLPR->SetStoreHistograms(PROutFile);
  tpcSLPR->SetClusterAmpCut(20.);
  tpcSLPR->SetCutTracksParallelZ(5);
  //tpcSLPR->SetXSorting(true);
  double parMins[4] = {-TMath::Pi(),0.,-TMath::Pi(),0.};
  double parMaxs[4] = {TMath::Pi(),10.,TMath::Pi(),20.};
  tpcSLPR->SetParameterSpace(parMins, parMaxs);
  tpcSLPR->SetDepth(8);
  tpcSLPR->SetThresh(15);
  tpcSLPR->SetMinCandHits(15);
  //tpcSLPR->SetClusterBranchName("TpcCluster_cut");
  tpcSLPR->SetAbsMomentum(1000);
  //fRun->AddTask(tpcSLPR);


  KalmanTask* kalman =new KalmanTask();
  kalman->SetTpcClusterBranchName("TpcCluster");
  kalman->SetTrackBranchName("TpcTrackPreFit");
  kalman->SetOutBranchName("TrackPostFit");
  kalman->SetPersistence();
  //kalman->SetClusterBranchName("TpcCluster_cut");
  kalman->SetNumIterations(3); // number of fitting iterations (back and forth)
  fRun->AddTask(kalman);


  TpcResidualTask* Res = new TpcResidualTask();
  Res->SetPersistence();
  Res->SetNumberOfTrackReps(1); // set to 2 if you use GeaneTrackrep (tpcSPR->useGeane();)
  if (smoothing==1)
    Res->SetUnbiased();
  //SLres->SetClusterBranchName("TpcCluster_cut");
  fRun->AddTask(Res);
  
  //  TpcSLResidualTask* SLres = new TpcSLResidualTask();
  // SLres->SetPersistence();
  //SLres->SetClusterBranchName("TpcCluster_cut");
  //  SLres->SetSecondarySuppression(true);
  //fRun->AddTask(SLres);
  

  // -----   Intialise and run   --------------------------------------------
 
  fRun->Init();
  std::cout<<"start:"<<nEvStart<<" end:"<<nEvents<<std::endl;
  fRun->Run(nEvStart,nEvents);

  timer.Stop();
  Double_t rtime = timer.RealTime();
  Double_t ctime = timer.CpuTime();
  printf("RealTime=%f seconds, CpuTime=%f seconds\n",rtime,ctime);
  
  std::cout<<"OutputFile: "<<outFile<<std::endl;
  testFile.Close();

  //return 0;
}