#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<int>    *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;
  
  
  /*

 for (Int_t i = 0; i < nEntries_p; i++) {                             // This loop is used to read the TTree data and fill the histograms. 
      
      t_p->GetEntry(i);

      //cout << "time " << time_ns_p << endl;
      //cout << "card_nb " << card_nb_p << endl;


      Long64_t tentry_p = t_p->LoadTree(i);
      charge_p->GetEntry(tentry_p);
      saturation_p->GetEntry(tentry_p);
      //for (UInt_t j = 0; j < q->size(); ++j) {
      // printf("%lf   %d \n",  q->at(j) , sat->at(j));}
      if(card_nb_p==1)   {
                          for (UInt_t j = 0; j < q_p->size(); ++j) { cout <<  q_p->at(j) << endl;
                                              
                                                                   }
                        }
 
      if(card_nb_p==2)   {
                          for (UInt_t j = 0; j < q_p->size(); ++j) {   cout <<  q_p->at(j) << endl;
                                              }   
                                              
                       }

   }


*/
 
 
 
  
  
  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);}
      if(ii<nEntries_p){                   
      cout << ii << endl;
  //    t_p->GetEntry(ii);   
      Long64_t tentry_p = t_p->LoadTree(ii);
      charge_p->GetEntry(tentry_p);
      saturation_p->GetEntry(tentry_p);
  
  
     /* if(card_nb_p==1 && flag_card1==0 )   {
                                      flag_card1 = 1;
                                      for (UInt_t j = 0; j < q_p->size(); ++j) {
                                      temp_mean_card1 += q_p->at(j);
                                                                   }
                        }
 
      if(card_nb_p==2 && flag_card2==0)   {
                                        flag_card2 = 1;
                                        for (UInt_t j = 0; j < q_p->size(); ++j) {
                                        temp_mean_card2+=q_p->at(j);
                                                                    }                                                 
                       }
                       
      */
     ii++;}
                       
   }
   
  /* cout << temp_mean_card1/XYSTRIPS << endl;
   cout << temp_mean_card2/XYSTRIPS << endl;
*//*   
   
 
 TFile *fpede = new TFile(TString::Format("%spedestal_histo_%s_run%d.root",outputdir, direction, pederun),"RECREATE");
 TH1F *pedestal_histo[XYSTRIPS];
 int nbins = sqrt(nEntries_p/2)/2;
 
 for(Int_t i=0; i<XYSTRIPS; i++)
  {
    pedestal_histo[i] = new TH1F(TString::Format("pedestal_histo_%s_strip_%d",direction, i),TString::Format("pedestal_histo_%s_strip_%d",direction,i),nbins,0,temp_mean_card1); // metterei 257 da 0 a 257
    pedestal_histo[i]->GetXaxis()->SetTitle("Q (pC)");
    pedestal_histo[i]->GetYaxis()->SetTitle("Occurrence");
    for(int j=1;j<=nbins;j++) pedestal_histo[i]->SetBinContent(j,0);
  }  
 
 */
 
 /*
  for(Int_t i=0; i<nEntries_p; i++)
    {
      t_p->GetEntry(i);
      for (int j=0;j<XYSTRIPS;j++){ if (strcmp(direction,"X")==0) {if(data_tree_p.card_nb_p==1)  
                                                                     for (UInt_t j = 0; j < data_tree_p.q_p->size(); ++j) pedestal_histo[j]->Fill(data_tree_p.q_p->at(j));}
                                                                     
                                    if (strcmp(direction,"Y")==0)  {if(data_tree_p.card_nb_p==2)  
                                                                     for (UInt_t j = 0; j < data_tree_p.q_p->size(); ++j) pedestal_histo[j]->Fill(data_tree_p.q_p->at(j));}}
    }
    
    */
 //t_p->ResetBranchAddresses();
/* delete t_p;  
 for(Int_t i=0; i<XYSTRIPS; i++) pedestal_histo[i]->Write();

 for(Int_t i=0; i<XYSTRIPS; i++)
   {
    TF1 *ffit = new TF1("ffit","gaus",pedestal_histo[i]->GetMean()-20,pedestal_histo[i]->GetMean()+20);
    pedestal_histo[i]->Fit("ffit","RQ0+");
    Float_t p_mean = ffit->GetParameter(1);
    Float_t p_errmean = ffit->GetParError(1);
    Float_t p_sigma = ffit->GetParameter(2);
    Float_t p_errsigma = ffit->GetParError(2);
    pedestal_value[i][0]=p_mean;
    pedestal_value[i][1]=p_errmean;
    pedestal_value[i][2]=p_sigma;
    pedestal_value[i][3]=p_errsigma;
   }
// cout << pedestal_value[0][0] << " " << pedestal_value[0][1] << " " << pedestal_value[0][2] << " " << pedestal_value[0][3]<<endl;
  fpede->Close();
  for(Int_t i=0; i<XYSTRIPS; i++) delete pedestal_histo[i];
  delete fpede;


  // function must return a vector for X with 96 channels showing the mean value of the amplitude of the strips. The same for Y
 */ return pedestal_value;  
 
 
 }