/**
 * \file TrkCore.cpp
 * \author Elena Vannuccini
 */
// .........................................................
// ROOT header files
// .........................................................
#include <TTree.h>
#include <TClassEdit.h>
#include <TObject.h>
#include <TList.h>
#include <TSystem.h>
#include <TSystemDirectory.h>
#include <TString.h>
#include <TFile.h>
#include <TClass.h>
#include <TCanvas.h>
#include <TH1.h>
#include <TH1F.h>
#include <TH2D.h>
#include <TLatex.h>
#include <TPad.h>
#include <TSQLServer.h>
#include <TSQLRow.h>
#include <TSQLResult.h>
// .........................................................
// other general header files
// .........................................................
#include <fstream>
#include <iostream>
// .........................................................
// files in the inc directory
// .........................................................
#include <RunInfo.h>
#include <GLTables.h>
#include <TrkVerl2.h>
#include <TrkProcess.h>
//#include <TrkStruct.h>
#include <TrkLevel2.h> 
//#include <TrkLevel1.h> 
#include <TrkLevel0.h> 
// .........................................................
// YODA header files 
// .........................................................
#include <PamelaRun.h>
#include <RegistryEvent.h>
#include <physics/tracker/TrackerEvent.h>
#include <CalibTrk1Event.h>
#include <CalibTrk2Event.h>

// .........................................................
// namespaces
// .........................................................
using namespace std;
using namespace pamela;
//  ================================================================================
//
//
//  ================================================================================
/**
 * \brief Tracker data reduction routine. 
 *
 * It performs data reduction LEVEL0->LEVEL1->LEVEL2, producing LEVEL1 and or LEVEL2 output, in ROOT or HBOOK format.
 * Input parameters:
 * @param run id of the run to be processed (if run=0 a whole file is reprocessed)
 * @param dbc pointer to BD server
 * @param file1 output LEVEL1 file name (null if no LEVEL1 output is required)
 * @param file2 output LEVEL2 file name (null if no LEVEL2 output is required)
 * @param standalone (flag to run the program in standalone mode, that is without reading RunInfo)
 */
//short int TrkCore(Int_t run, TSQLServer *dbc, TString file1, TString file2, Bool_t standalone)
int TrkCore(ULong64_t run, TFile *f2, TSQLServer *dbc, int ncustom, char*vcustom[])   
{
    // ---------------------------
    // Define some basic variables
    // ---------------------------

    TString  filename     = 0; 
    TString  trkcalibfile = 0;
    Int_t    last_trk_calib_used = 0;
    Long64_t nevents = 0LL;
    
    // LEVEL0 input 
    TFile         *f0 = 0;
    TFile         *f0_c = 0;
    TTree         *physicsTree = 0;
    TBranch       *b_registry  = 0;
    TBranch       *b_trk       = 0;
    TBranch       *b_header    = 0;
    RegistryEvent *reg     = 0;  
    EventHeader   *header  = 0;
    PscuHeader    *pscu    = 0;
    TrkLevel0     *l0_event = 0;
    // RunInfo 
    ItoRunInfo *runinfo = 0;
    TArrayL    *runlist = 0;
    ULong64_t      from_run;
    ULong64_t      to_run;
    Bool_t      reprocessing = false;
    //LEVEL1 output - ROOT
//    TFile   *f1;
//    TTree   *t_level1;
//    TrkLevel1 *l1_event;
    //LEVEL2 output - ROOT
    TTree     *t_level2 = 0; 
    TTree     *t_clone = 0; 
    TrkLevel2 *l2_event = new TrkLevel2();
    TrkLevel2 *l2_clone = new TrkLevel2();
// -----------------------
// -----------------------
// Handle input parameters
// (data)
//
// - open/create output files, determining the environment root/hbook from the estension
// - create the level1/level2 tree+branch/nt-uple
// -----------------------
// -----------------------	
    TrkProcess *p = new TrkProcess(run,f2);
    p->HandleCustomPar(ncustom,vcustom);
    if( p->DebugMode() )p->Dump();

    
    
// ===================================
// Open/Create level1 output file
// (NB output files other than LEVEL2 are 
// created in a separate folder)
// ===================================
    if(p->get1){
	if(p->ifroot1){
	    throw -299;
	}else{
	    throw -299;
	};
    };    
// ===================================
// Open/Create level2 output file
// ===================================
    if(p->get2){
//	if(p->ifroot2){ // root
        //-------------------------------------------
	// read RunInfo
	//-------------------------------------------
	if(!(p->standalone)){
	    // Open "RunInfo" tree and get list of run
	    runinfo = new ItoRunInfo(f2);
	    char *trkversion = TrkInfo(false);
	    int runinfo_error = runinfo->Update(run,"TRK",trkversion);
	    if( runinfo_error ) throw runinfo_error;
	    runlist = runinfo->GetRunList();
	    reprocessing = runinfo->IsReprocessing();//????				
	    if(p->VerboseMode()){
		cout << "#events       "<< runinfo->GetFileEntries() << endl;// #events in the file 
		cout << "#runs         "<< runinfo->GetRunEntries()  << endl;// #runs in the file
		cout << "1-st run      "<< runlist->At(0)            << endl;
		cout << "last run      "<< runlist->At(runinfo->GetRunEntries()-1) << endl;
		cout << "1-st event    "<< runinfo->GetFirstEntry()  << endl;// first event of our run
		cout << "last event+1  "<< runinfo->GetLastEntry()   << endl;// first event AFTER the last event of our run
		cout << "reprocessing  "<< runinfo->IsReprocessing() << endl << endl;
	    };
	};
	//-------------------------------------------
	//
	//-------------------------------------------
	// Take (if present) the old Tracker tree
	t_clone = (TTree*)f2->Get("Tracker");
	if( t_clone != NULL ) t_clone->SetBranchAddress("TrkLevel2",&l2_clone);
	// Create NEW Tracker tree			
	t_level2 = new TTree("Tracker","PAMELA tracker level2 data ");
	t_level2->Branch("TrkLevel2","TrkLevel2",&l2_event);	  	
//    }else{       // hbook
//	throw -299;
//    }
    };
	

// -------------------------------------------
// define runs to be processed/reprocessed
// -------------------------------------------
    if(run == 0){
	// reprocessing ALL runs
	if(p->standalone)throw -298; // reprocessing not implemented
	from_run = runlist->At(0);
	to_run   = runlist->At(runinfo->GetRunEntries()-1);
    }else{
	// processing/reprocessing ONE single run
	from_run = run;
	to_run   = run;
    };
    
    //
    // init "expiration date" of calibrations and parameters
    //
    ULong64_t pedsig_time =0ULL;
    ULong64_t B_time      =0ULL;
    ULong64_t mip_time    =0ULL;
    ULong64_t charge_time =0ULL;
    ULong64_t eta_time    =0ULL;
    ULong64_t align_time  =0ULL;
    ULong64_t mask_time   =0ULL;
    //
    // init event counter
    //
    Int_t ev_count =0;
    //
    // create query-results objects
    //
    GL_RUN q1       = GL_RUN();
    GL_TRK_CALIB q2 = GL_TRK_CALIB();
    GL_ROOT      q3 = GL_ROOT();
    GL_PARAM     q4 = GL_PARAM();
	
// ------------------------------------------------------------
//  if reprocessing one run, copy all the events BEFORE the run
// ------------------------------------------------------------
    if( !(p->standalone) ){
	for(UInt_t i=0; i<runinfo->GetFirstEntry(); i++){
	    t_clone->GetEntry(i);
	    *l2_event = *l2_clone;
	    t_level2->Fill();
	    l2_event->Clear();
	    // COPY COPY COPY
	};
    };
// ------------------------------------------------------------
// ------------------------------------------------------------
//  START LOOP OVER RUNS TO PROCESSED/REPROCESSED
// ------------------------------------------------------------
// ------------------------------------------------------------
    for(ULong64_t idRun=from_run; idRun <= to_run; idRun++){
	
	if(p->VerboseMode()) cout << endl<<" ========================= Run: "<< idRun << endl;
	ULong64_t runheadtime    = 0ULL;
	ULong64_t runtrailtime   = 0ULL;
	UInt_t    evfrom         = 0;
	UInt_t    evto           = 0;
	Int_t     id_reg_run     =-1;
	Int_t     trk_calib_used = 0;
	
	if(p->standalone){
	    // ==============================
	    // first query: retrieve run info
	    // ==============================
	    if (q1.Query_GL_RUN(idRun,dbc) )throw -50;   
	    id_reg_run     = q1.ID_REG_RUN;
	    runheadtime    = q1.RUNHEADER_TIME;
	    runtrailtime   = q1.RUNTRAILER_TIME;
	    evfrom         = q1.EV_REG_PHYS_FROM;
	    evto           = q1.EV_REG_PHYS_TO;
	    trk_calib_used = q1.TRK_CALIB_USED;
	}else{
	    // ==============================
	    // get run info from RunInfo tree
	    // ==============================
	    int runinfo_error = runinfo->GetRunInfo(idRun);
	    if( runinfo_error ) throw runinfo_error;		
	    id_reg_run     = runinfo->ID_REG_RUN;
	    runheadtime    = runinfo->RUNHEADER_TIME;
	    runtrailtime   = runinfo->RUNTRAILER_TIME;
	    evfrom         = runinfo->EV_REG_PHYS_FROM;
	    evto           = runinfo->EV_REG_PHYS_TO;
	    trk_calib_used = runinfo->TRK_CALIB_USED;
	};
	//
	if(p->VerboseMode()){
	    cout << "ROOT file ID    "<< id_reg_run     << endl;
	    cout << "RunHeader time  "<< runheadtime    << endl;
	    cout << "RunTrailer time "<< runtrailtime   << endl;
	    cout << " from event "<< evfrom         << endl;
	    cout << " to event   "<< evto           << endl;
	    cout << "trk-calibration used "<< trk_calib_used << endl;
	};
	// ========================================================
	// second query: search the LEVEL0 file that contains idRun
	// ========================================================
	TString lastfilename = filename;
	if( q3.Query_GL_ROOT(id_reg_run,dbc) )throw -51;
	filename = q3.PATH + q3.NAME;	
	// ========================================================
	// Open the input LEVEL0 data file
	// ========================================================
	if(filename.CompareTo(lastfilename)){
	    if(!lastfilename.IsNull())f0->Close();
	    //if( debug ) cout << "Opening LEVEL0 file: "<< filename << endl;
	    if(p->VerboseMode()) cout << "Opening LEVEL0 file: "<< filename << endl;
	    FileStat_t t;
	    if( gSystem->GetPathInfo(filename.Data(),t) )throw -6;
	    f0 = new TFile(filename);
	    if ( !f0 ) throw -6;
	    physicsTree = (TTree*)f0->Get("Physics");          if(!physicsTree) throw -7;
	    b_header    = physicsTree ->GetBranch("Header");   if(!b_header   ) throw -8;
	    b_registry  = physicsTree ->GetBranch("Registry"); if(!b_registry ) throw -9;
	    b_trk       = physicsTree ->GetBranch("Tracker");  if(!b_trk      ) throw -203;
	    physicsTree->SetBranchAddress("Tracker" ,&l0_event);
	    physicsTree->SetBranchAddress("Registry",&reg);
	    physicsTree->SetBranchAddress("Header",&header);
	    
	    nevents = physicsTree->GetEntries(); 
	    if ( nevents < 1 ) throw -11;
	    if ( nevents < (evto+1)) throw -12;
	};
	
	// =============================================================
	// retrieve calibration file needed to reduce data 
	// =============================================================
	// if run OBT is > last calibration "expiration date"
	//  - search for new calibration packet
	//  - load calibration parameters (full + truncated)
	if(p->VerboseMode() )cout << "Full pedestals for cluster finding:" << endl;
	if(runheadtime > pedsig_time){
	    if( q2.Query_GL_TRK_CALIB(runheadtime,dbc) )throw -53;
	    pedsig_time = q2.TO_TIME;
	    if(q2.EV_REG_CALIBTRK1 != q2.EV_REG_CALIBTRK2) 
		printf("WARNING!! ---> EV_REG_CALIBTRK1=%d it's different from EV_REG_CALIBTRK2=%d \n\n",q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	    if( q3.Query_GL_ROOT(q2.ID_REG_CALIBTRK,dbc) )throw -51;
	    trkcalibfile = q3.PATH + q3.NAME;
	    if(trkcalibfile.CompareTo(filename)){
//                if( f0_c->IsOpen() )f0_c->Close();
		if(p->VerboseMode()) cout << "Opening LEVEL0 file: "<< trkcalibfile << endl;
		FileStat_t t;
		if( gSystem->GetPathInfo(trkcalibfile.Data(),t) )throw -6;
		f0_c=new TFile(trkcalibfile);
		if ( !f0_c ) throw -6;
	    }else{
		f0_c = f0;
	    };
	    if(p->VerboseMode()) {
                cout << "Loading calibration entries "<< q2.EV_REG_CALIBTRK1 << " " << q2.EV_REG_CALIBTRK2; 
		cout << " (from time "<< q2.FROM_TIME <<" to time "<< q2.TO_TIME <<")"<<endl;
	    };
	    pedsigbad_.FillACalibFrom(f0_c,q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	};
	if( p->DebugMode() ) for(int i=0; i<12; i++) cout << " DSP "<< i << " "<< pedsigbad_.pedestal[64][12][i] << endl;
	// =============================================================
	// retrieve calibration file needed to uncompress data
	// =============================================================
	// if the run was compressed using default calib
	// load truncated pedestals from default
	// otherwise reload them from on-line calibration
	if(p->VerboseMode() )cout << "Truncated pedestals for uncompression:";
	if(trk_calib_used==104 && last_trk_calib_used!=104){
	    
	    if(p->VerboseMode() )cout << ">> Loading default calibration " << endl; 
	    if (q4.Query_GL_PARAM(runheadtime,"default calibration",dbc) )throw -52;	    
	    pedsigbad_.FillTCalibFrom(q4.PATH+q4.NAME);
	    
	}else if( (trk_calib_used==1 | trk_calib_used==2) &&  last_trk_calib_used==104  ){

	    if(p->VerboseMode()) cout << ">> Re-loading on-line calibration " << endl;
	    pedsigbad_.FillTCalibFrom(f0_c,q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	}else{
	    if(p->VerboseMode()) cout << ">> Using on-line calibration " << endl;
	};
	if( p->DebugMode() ) for(int i=0; i<12; i++) cout << " DSP "<< i << " "<< pedsigbad_.pedestal_t[64][12][i] << endl;
	last_trk_calib_used = trk_calib_used;
	
/*	// =============================================================
	// retrieve calibration file needed to uncompress data
	// =============================================================
	if(trk_calib_used==104 && last_trk_calib_used!=104){
	    
	    if(p->VerboseMode() )cout << "** Using default calibration **" << endl; 
	    
	    if (q4.Query_GL_PARAM(runheadtime,"default calibration",dbc) )throw -52;	    
	    path_.FillWith(q4.PATH+q4.NAME);	      
	    fillpedsigfromdefault_();
	    if(path_.error) throw -216;
	    
	}else if( (trk_calib_used==1 | trk_calib_used==2) && runheadtime > pedsig_time){
	    
	    if( q2.Query_GL_TRK_CALIB(runheadtime,dbc) )throw -53;
	    pedsig_time = q2.TO_TIME;
	    if(q2.EV_REG_CALIBTRK1 != q2.EV_REG_CALIBTRK2) 
		printf("WARNING!! ---> EV_REG_CALIBTRK1=%d it's different from EV_REG_CALIBTRK2=%d \n\n",q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	    
	    if( q3.Query_GL_ROOT(q2.ID_REG_CALIBTRK,dbc) )throw -51;
	    
	    trkcalibfile = q3.PATH + q3.NAME;
	    // store calibration informations
	    if(p->VerboseMode()) cout << "Online calibration: "<< trkcalibfile << endl;
//			pedsigbad_ = TrkFlightPede(trkcalibfile,q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	    TFile* f0_c= f0;
	    if(trkcalibfile.CompareTo(filename))f0_c = new TFile(trkcalibfile);
	    
	    pedsigbad_.FillAllFrom(f0_c,q2.EV_REG_CALIBTRK1,q2.EV_REG_CALIBTRK2);
	    
	    if(trkcalibfile.CompareTo(filename))f0_c->Close();
	};
	last_trk_calib_used = trk_calib_used;*/
	// =============================================================
	// retrieve information about parameters to process LEVEL2
	// =============================================================  
	//
	// magnetic field
	//
	if(p->VerboseMode()) cout << "Loading parameter files : "<< endl;
	
	if(runheadtime > B_time){
	    if( q4.Query_GL_PARAM(runheadtime,"field",dbc) )throw -52;
	    B_time = q4.TO_TIME;
	    l2_event->LoadField(q4.PATH+q4.NAME);
//	    l2_event->LoadField(q4.PATH+q4.NAME);
	    if(path_.error) throw -215;
	};
	//
	// mip conversion parameters
	//
	if(runheadtime > mip_time){
	    if( q4.Query_GL_PARAM(runheadtime,"trk mip",dbc) )throw -52;
	    mip_time = q4.TO_TIME;
	    path_.FillWith(q4.PATH+q4.NAME);
	    readmipparam_();
	    if(path_.error) throw -212;
	};
	//
	// charge correlation parameters
	//
	if(runheadtime > charge_time){
	    if( q4.Query_GL_PARAM(runheadtime,"trk charge",dbc) )throw -52;
	    charge_time = q4.TO_TIME;
	    path_.FillWith(q4.PATH+q4.NAME);
	    readchargeparam_();
	    if(path_.error) throw -213;
	};
	//
	// eta p.f.a. parameters
	//
	if(runheadtime > eta_time){
	    if( q4.Query_GL_PARAM(runheadtime,"trk pfa",dbc) )throw -52;
	    eta_time = q4.TO_TIME;
	    path_.FillWith(q4.PATH+q4.NAME);
	    readetaparam_();
	    if(path_.error) throw -214;
	};
	//
	// alignment parameters
	//
	if(runheadtime > align_time){
	    if( q4.Query_GL_PARAM(runheadtime,"trk alignment",dbc) )throw -52;
	    align_time = q4.TO_TIME;
	    path_.FillWith(q4.PATH+q4.NAME);
	    readalignparam_();
	    if(path_.error) throw -211;
	};
	//
	// viking mask 
	//
	if(runheadtime > mask_time){
	    if( q4.Query_GL_PARAM(runheadtime,"trk mask",dbc) )throw -52;
	    mask_time = q4.TO_TIME; 
	    path_.FillWith(q4.PATH+q4.NAME);
	    readvkmask_();
	    if(path_.error) throw -210;
	};

	//
	// ====================================================
	// start looping on events cointained in the data file  
	// ====================================================		
	for (UInt_t re = evfrom; re <= evto; re++){
	    
	    ev_count++;
//	    if ( p->DEBUG && re%100 == 0 && re > 0 ) printf(" %iK \n",re/1000);
	    if ( p->DebugMode() && re%100 == 0 && re > 0 ) cout << ".";
	    
	    b_registry->GetEntry(re);
	    b_trk->GetEntry(reg->event);
	    b_header->GetEntry(reg->event);
	    pscu = header->GetPscuHeader();
	    //    pscu->Print();
	    //	    cout <<endl<< " *************** Pkt ID "<< (UINT32)pscu->Counter << endl;
	    
	    p->ProcessEvent(l0_event);
	    
	    // ----------------
	    //  LEVEL1 output
	    // ----------------
	    if(p->get1){
		if(p->ifroot1){ // root
		}else{       // hbook
		};
	    };
	    // ----------------
	    //  LEVEL2 output
	    // ----------------
	    if(p->get2){
//		if(p->ifroot2){ // root
		    l2_event->FillCommonVar(&level2event_);
		    //		    l2_event->Dump();	      
		    t_level2->Fill();
		    l2_event->Clear();
//		}else{       // hbook
//		}
	    };
	    
	}; // end loop on events
	if(p->VerboseMode())cout << " >>> processed "<< ev_count <<" events"<< endl;
    }; // end loop on runs
// ------------------------------------------------------------
//  if reprocessing one run, copy all the events AFTER the run
// ------------------------------------------------------------
    if( !(p->standalone) ){
	for(UInt_t i=runinfo->GetLastEntry()+1; i<runinfo->GetFileEntries(); i++){
	    t_clone->GetEntry(i);
	    *l2_event = *l2_clone;
	    t_level2->Fill();
	    l2_event->Clear();
	    // COPY COPY COPY
	};
    };
    // ---------------
    // close the files
    // ---------------
    if(p->get1){
	if(p->ifroot1){ // root
	}else{       // hbook
	}
    };
    if(p->get2){
//	if(p->ifroot2){ // root			
	    if( t_clone )t_clone->Delete("all");//delete old tree from file
	    if( !(p->standalone) )runinfo->Close();
	    f2->Write("Tracker");
	    if( t_level2 )t_level2->Delete();  //delete new tree from memory
	    
//	}else{       // hbook
//	}
    };
    if( f0->IsOpen() )  f0->Close();
    if( f0_c->IsOpen() )f0_c->Close();
    
    return(p->ostatus);
}