/*****************************************************************************
 *                                                                           *
 *         lst2roor                                                          *
 *   Program used to read lst files from the PTB experiment and              *
 *   store them in a TTree.                                                  *
 *   The TTre is then read and histograms are created out of that            *
 *   Based on the c version written by LCM, updated by AN (Nov. 2007) +      *
 *   Changes by CR (March 2010): noted with ##                               *            
 *   Modified by FB (July 2014)                                              *
 *                                                                           *
 *****************************************************************************/
// Compile with: make
// Launch with: lst2root /home/thomas/Fra_temp/PTB/Analysis/2013/Pu/3.5MeV lst lst2root/file.txt

// CPP includes
#include <cstdlib>
#include <cstdio>
#include <iostream>
#include <cmath>
#include <vector>
#include <string>
#include <iostream>
#include <sstream>

// C includes
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>

// ROOT includes
// ROOT includes
#include <TSystem.h>
#include <TROOT.h>
//#include <TApplication.h>
#include <TRint.h>
#include <TDirectory.h>
#include <TFile.h>
#include <TChain.h>
#include <TTree.h>
#include <TNtuple.h>
#include <TBranch.h>
#include <TH1.h>
#include <TAxis.h>
#include <TCanvas.h>
#include <TColor.h>
#include <TPad.h>
#include <TStyle.h>
#include <TKey.h>
#include <TLegend.h>
#include <TText.h>
#include <TPaveText.h>
#include <TLine.h>
#include <TMarker.h>
#include <TLatex.h>
#include <TMath.h>
#include <TH1.h>
#include <TH2.h>
#include <TF1.h>
#include <TF2.h>
#include <TSystem.h>
using namespace std;



#define VERSION "v1.0_20140714";

#define EVENTSIZE 4L              // It should mean that for every number written on the binary file, 4 words are allocated
#define ADCSIZE 8192              // 8192 is it internal setting?
//#define ADCSIZE 2048              // 8192 is it internal setting?
//TF1 *fa2 = new TF1("fa1","0.135*(x-358)*(x-358)+340",270,500)



//## Event format=	4 U16 words 1st=anode 2nd=grid  3rd=time
void swapbytes(unsigned short *buf,int size)
{
  int i;
  unsigned char t;
  union { unsigned short w; unsigned char b[2]; } v;
  for(i=0;i<size;i++) {
    v.w   =buf[i];
    t     =v.b[0];
    v.b[0]=v.b[1];
    v.b[1]=t;
    buf[i]=v.w;
  }
}

void clearnmsb(unsigned short *rec,short n){
  if(n==3) *rec = (*rec) & 0X1FFF;
  if(n==4) *rec = (*rec) & 0X0FFF;
}


typedef struct {
  int adc1;
  int adc2;
  int adc3;
  int adc4;
}
data;





void process_TTree(TFile *f){
  // Prepare the Canvases for drawing
  TCanvas*c1= new TCanvas("c1","c1",500,500);
  TCanvas*c2= new TCanvas("c2","c2",500,500);
  TCanvas*c3= new TCanvas("c3","c3",500,500);
  TCanvas*c4= new TCanvas("c4","c4",500,500);
  
  printf("Starting processing the TTree \n");
  TTree*t =(TTree*)f->Get("t");
  data data_tree_read;
  t->SetBranchAddress("adc1",&data_tree_read.adc1);
  t->SetBranchAddress("adc2",&data_tree_read.adc2);
  t->SetBranchAddress("adc3",&data_tree_read.adc3);
  t->SetBranchAddress("adc4",&data_tree_read.adc4);
  int nEntries=t->GetEntries();
  
  
  TH1D*h1=new TH1D("h1","adc1",8192,0.,8192.);
  TH1D*h2=new TH1D("h2","adc2",8192,0.,8192.);
  TH1D*h3=new TH1D("h3","adc3",8192,0.,8192.);
  TH1D*h4=new TH1D("h4","adc4",8192,0.,8192.);

  h1->SetXTitle("Amplitude (ch)");
  h1->SetYTitle("Counts");
  h2->SetXTitle("Amplitude (ch)");
  h2->SetYTitle("Counts");
  h3->SetXTitle("Amplitude (ch)");
  h3->SetYTitle("Counts");
  h4->SetXTitle("Amplitude (ch)");
  h4->SetYTitle("Counts");
 
  for(int i=0;i<nEntries;i++){
    t->GetEntry(i);
    
    /// histogram
    h1->Fill(data_tree_read.adc1);
    h2->Fill(data_tree_read.adc2);
    h3->Fill(data_tree_read.adc3);
    h4->Fill(data_tree_read.adc4);
  }
  c1->cd();
  h1->Draw("");

  c2->cd();
  h2->Draw("");

  c3->cd();
  h3->Draw("");

  c4->cd();
  h4->Draw("");


  h1->Write("",TObject::kOverwrite);
  h2->Write("",TObject::kOverwrite);
  h3->Write("",TObject::kOverwrite);
  h4->Write("",TObject::kOverwrite);
}




























int run(const char* path, const char* lstdirectory,const char* lstfilename)
{

  // gSystem->Load("libTree.so"); 
  // Open a TFile (it is the equivalent of a folder) where you are going to store 
  // the info retrieved from the lst data and some histograms
   TFile*f=new TFile("Foreground2.root","recreate");   //<----------------
  // Associate a structure to the TTree that you are going to create
  data data_tree;
  // Some variables
  FILE *inp, *out, *list;
  char cycle[80], listname[80], outname[80], inpName[80];
  unsigned short nread, event[EVENTSIZE];
  int i,k;
  int *adc1, *adc2, *adc3, *adc4;

  // Open the txt file containing a list of *.lst files to analyze
  printf("\n    Open the file containing the *lst file names to treat\n\n");
  sprintf(inpName, "%s/%s", path, lstfilename);
  printf("   Cycles' file: %s\n", inpName);
  if((inp=fopen(inpName,"r"))==NULL){
    printf("   ERROR: Cannot open cycles file.\n");
    return 1;
  }
  // Create an outup file where you are going to write the content of the 
  //*.lst files processed in such a way to be equivalent to the *.his files
  sprintf(outname,"%s", "Comp.dat"); 
  if((out=fopen(outname,"w"))==NULL){
    printf("   ERROR: Cannot open cycles file.\n");
    return 1;
  }
  // Create 3 arrays where you will store the info retrieved from the *.lst files for 3 ADCs.
  // ADCSIZE/4 is used because you know that every ADC is configured to store data in 2048 ch.
  //(you know this by looking at how many rows the *.his files have)
  adc1      = (int*)malloc(sizeof(int)*ADCSIZE);
  adc2      = (int*)malloc(sizeof(int)*ADCSIZE);  
  adc3      = (int*)malloc(sizeof(int)*ADCSIZE);
  adc4      = (int*)malloc(sizeof(int)*ADCSIZE);
  
  // Initialize the arrays and a counter
  k=-1;
  for(i=0; i<ADCSIZE; i++) adc1[i] = adc2[i] = adc3[i] = adc4[i] = 0;



  // Create the TTree and its branches ("/I"=means that you are going to store inteher numbers in the branches. You have one branch for ADC)
  TTree*t= new TTree("t","Foreground2 data");
  t->Branch("adc1",&data_tree.adc1,"adc1/I");
  t->Branch("adc2",&data_tree.adc2,"adc2/I");
  t->Branch("adc3",&data_tree.adc3,"adc3/I");
  t->Branch("adc4",&data_tree.adc4,"adc4/I");    
 
  
  while((fscanf(inp, "%s", cycle))>0){// Loop on the *.lst files to open (=lines in the file containing the *.lst filenames)
    k++;
    sprintf(listname, "%s/%s/%s", path, lstdirectory, cycle);
    printf("=== %s \n",listname);
    if((list=fopen(listname,"rb"))==NULL){
      printf("   ERROR: Cannot open list file %s\n", listname);
      return 1;
    }
    while((nread=fread(event,sizeof(unsigned short), EVENTSIZE, list))>0){ // While over events in a listfile; read one event after the other
      swapbytes(event, EVENTSIZE);
      for(i=2; i<EVENTSIZE; i++)        // ## was  for(i=3; i<EVENTSIZE; i++) : No idea  of why 2 should be better than 1...
      clearnmsb(event+i,3);
      // Fill the TTree 
      data_tree.adc1= (unsigned int)event[0];
      data_tree.adc2=(unsigned int)event[1];
      data_tree.adc3=(unsigned int)event[2];
      data_tree.adc4=(unsigned int)event[2];
      
      t->Fill();
      // Process the content of the *.lst files to obtain the *.his files
      if((unsigned int)event[0]!=0) adc1[(unsigned int)event[0]]++;
      if((unsigned int)event[1]!=0) adc2[(unsigned int)event[1]]++;
      if((unsigned int)event[2]!=0) adc3[(unsigned int)event[2]]++;
      if((unsigned int)event[2]!=0) adc4[(unsigned int)event[3]]++;

    }  // End of while for events in a *.lst file
    printf("   Cycle %s sorted.\n", listname);
    for(i=0;i<ADCSIZE;i++) fprintf(out,"%d %d %d  %d %d\n", i, adc1[i],adc2[i],adc3[i], adc4[i] );
    // Reset the content of the arrays to 0
    for(i=0; i<ADCSIZE; i++)  adc1[i] = adc2[i] = adc3[i] = adc4[i] = 0;
    i=0;
    fclose(list);
   
  } // End of loop on the *.lst files to open (=lines in the file containing the *.lst filenames)

  f->cd();
  t->Write("",TObject::kOverwrite);
  process_TTree(f);
  f->Close();
  fclose(inp);
  fclose(out);
  printf("Bye \n");
  
}