#include <iostream>
#include <TFile.h>
#include <TTree.h>
#include <TChain.h>
#include <TH1.h>
#include <TH2.h>
#include <TF1.h>
#include <TString.h>
#include "analysis.h"
#include <string>
#include "decoding.h"
using namespace std;

char input[200];

// Develop all functions


TChain *read_pedestal_XY(Int_t startrun, Int_t endrun, Int_t check_MS,  Char_t *inputdir)
{
 // cout << inputdir <<endl;
  TChain *ch = new TChain("DataTree","DATA");
  for(int i=startrun; i<=endrun; i++)
    {

    for(int k=1; k<=check_MS; k++)
     {
      sprintf(input,"%s/Pedestal_%d_%d.root",inputdir,i,k);
      cout << input << endl;
      // ------ check for file existence
      TFile *ftemp = new TFile(input,"READ");
      TTree *temp = (TTree*)ftemp->Get("DataTree");
      if(!temp)
        {
          ftemp->Close();
          cout << "Segment " << k << " of run " << i << " is not present " << endl;
          continue;
        }
      ch->Add(input,0);
      cout << "Added segment " << k << " of run " << i <<  endl;

     }
    }
  return ch;


}

Double_t **pedestal_calc(char* inputdir,char* outputdir,int pederun, int check_max_subrun, Option_t *direction)
 {
  cout << " HELLO bis" << endl;
  Double_t **pedestal_value = new Double_t*[32];
  for(int i=0;i<XYSTRIPS;i++) pedestal_value[i] = new Double_t[4];    // 4 variable for every strip

  cout << " pederun " << pederun<< endl;
  cout << " max_subrun " << check_max_subrun<< endl;
  cout << " input dir " << inputdir << endl;
  TChain *t_p = read_pedestal_XY(pederun, pederun, check_max_subrun, inputdir);


  double          time_ns_p;                                // Variable to read the time stamp
  int             card_nb_p;                                // Variable to read the card number
  vector<double>  *q_p;                                      // Create a vector to contain the 32 signals for each one of the 32 strips
  vector<double>  *sat_p;                                    // Create a vector to contain the 32 indexes saying, for each of the 32 strips, if the signal is saturated


  TBranch *charge_p     = 0;                                           // Create pointers to the branches of the TTree
  TBranch *saturation_p = 0;
  TBranch *card_p       = 0;
  TBranch *time_p       = 0;

  t_p->SetBranchAddress("time",&time_ns_p);                           // Get the branches
  t_p->SetBranchAddress("card",&card_nb_p);
  t_p->SetBranchAddress("Q",   &q_p,       &charge_p);
  t_p->SetBranchAddress("S",   &sat_p,     &saturation_p);



  // The next operation is performed just to set the single channel histogram range and binning;
  int nEntries_p=t_p->GetEntries();
  double temp_mean_card1 = 0;
  double temp_mean_card2 = 0;
  double flag_card1 = 0;
  double flag_card2 = 0;

  Int_t ii = 0;
  while(flag_card1==0 ||flag_card2 ==0)
      {
  
       if(ii>=nEntries_p) {cout << "You have data only from one card or no card at all " << endl;
                         exit(0);}
      else{                   
      cout << ii << endl;
      Long64_t tentry_p = t_p->LoadTree(ii);
      charge_p->GetEntry(tentry_p);
      saturation_p->GetEntry(tentry_p);

     ii++;}
                       
   }



 return pedestal_value;


 }