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#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];
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