#include "hitutils.h"
#include <string>
#include <stdio.h>
#include <iostream>
#include <vector>
#include <utility>
#include <TH2.h>
#include <TF1.h>
#include <TStyle.h>
#include <TCanvas.h>
#include <TFile.h>
#include <TTree.h>
#include <TSystemDirectory.h>
#include <gsl/gsl_statistics.h>
#include <math.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_fft_complex.h>
#include <TF1.h>
#include <TGraphErrors.h>
#include <gsl/gsl_sort.h>
#include <TVector.h>
#include "TStopwatch.h"
#include "Math/MinimizerOptions.h"
#include "TVirtualFitter.h"
#include "TMatrixD.h"

//function declarations
int analyse(int argc, char **argv);
int opendatafiles(int argc, char ** argv);
void histograms(int argc, char ** argv);
void set_background_v1(int frames);
int closedatafiles();


//////global variables

//opendatafiles
long int  fileframesize;
BufferData* dataptr;
char * filename;
ifstream file;
TFile *rootFile; //output root file
TTree *rootTree; 
char * rootfilename;
char * ethercatfile;
TTree *tree2; //ethercat root tree
char * timestampfilename;
ifstream timestampfile;
char * offsetfilename;
ifstream offsetfile;
bool ethercat;

struct bpm_frame_v1 {
  double channel_amp[128];
  double avg_position;
  double avg_width;
  double integratedsignalamp;
  int maxchannel;
  double maxchannel_amp;
};

bpm_frame_v1 board_b[4];
bpm_frame_v1 board_b_bkg[4];

bpm_frame_v1 readboard(int frame, int boardnumber);
int framestart = 0;

struct beamRecon {
  double Position;
  double Focus;
  double Peak;
  double Rsqr;
  double Skew;
  double Kurtosis;
};

beamRecon beamreconstruction(bpm_frame_v1 frametoanalyse, double threshold);
beamRecon BPMbeamrecon[4];