#include "TFile.h"

#include "TH1F.h"

#include <iostream>

#include <fstream>

using namespace std;

void analysis() {

Int_t nbins = 800;

Int_t j;

char name[20];

char title[100];

TH1F *HistoEvent[2214];

for (Int_t z=0;z<2214;z++) {

sprintf(name,"HistoEvent%d",z-1);

sprintf(title,"Event%d Histo", z-1);

HistoEvent[z] = new TH1F(name,title,nbins, -0.1, 159.9);

}

TH1F *NewHistoEvent[2214];

for (Int_t z=0;z<2214;z++) {

sprintf(name,"NewHistoEvent%d",z-1);

sprintf(title,"Event%d Histo", z-1);

NewHistoEvent[z] = new TH1F(name,title,nbins, -0.1, 159.9);

}

TH1F *NewHistoEventFFT[2214];

for (Int_t z=0;z<2214;z++) {

sprintf(name,"NewHistoEventFFT%d",z-1);

sprintf(title,"Event%d Histo", z-1);

NewHistoEventFFT[z] = new TH1F(name,title,nbins, 0, 5);

}

Double_t mean;

Double_t rms;

Double_t meansum = 0;

Double_t count = 0;

Double_t meanrms = 0;

TFile f("/home/marko/H4Analysis/ntuples/analysis_4443.root"); //ntuple generated by H4Analysis tool

TFile f1("/home/marko/H4Analysis/ntuples/analysis_3905.root");

TFile f2("/home/marko/Desktop/TB Timing Res/NormalizedSignalNoise.root", "read");

TH1F* BestSignal = (TH1F*) f2.Get("BetterSignal");

TFile outputfile("myoutput.root", "recreate");

TCanvas* TimeandFreq = new TCanvas("TimeandFreq","Time and Frequency",1500,900);

TCanvas* Freq = new TCanvas("Freq","Frequency",800,1200);

TCanvas* TimeSignal = new TCanvas("TimeSignal","Pure Signal",800,1200);

TimeandFreq->Divide(2,2);

TTree* h4 = (TTree*) f.Get("h4");

TTree* h4_2 = (TTree*) f1.Get("h4");

TString plot;

TString cut;

TH2F* WavePulse = new TH2F ("WavePulse", "Wave Pulse", nbins, -0.1, 159.9, 850, -50, 800);

TH2F* NoisePulse = new TH2F ("NoisePulse", "Noise", nbins, -0.1, 159.9, 100, -50, 50);

TH1F* PulseTime = new TH1F ("PulseTime", "Original Wave Pulse", nbins, -0.1, 159.9); //nanoseconds

TH2F* TempHisto = new TH2F ("TempHisto", "Temp Histo", nbins, -0.1, 159.9, 1000, -15, 15); //nanoseconds

h4->Draw("WF_val:WF_time>>WavePulse", "WF_ch==2 && event==1 && spill==1");

h4_2->Draw("WF_val:WF_time>>NoisePulse","WF_ch==APD1 && amp_max[APD3]<25 && b_rms[APD3]<5. && charge_tot[APD3]<20000 && amp_max[APD5]<25 && b_rms[APD5]<5. && amp_max[APD6]<25 && b_rms[APD6]<5. && amp_max[APD4]<25 && b_rms[APD4]<5. && amp_max[SiPM1]<20 && amp_max[SiPM2]<20 && amp_max[APD1]<40 && amp_max[APD2]<40 && b_rms[APD1]<5. && b_rms[APD2]<5. && WF_time<160");

for (Int_t i=0; i<nbins; i++) {

for (Int_t k=0; k<4096; k++) {

if (WavePulse->GetBinContent(i+1, k) != 0) {

PulseTime->SetBinContent(i+1,k-50);

}

}

}

TH1F *NoiseTime = new TH1F ("NoiseTime", "Noise", nbins, -0.1, 159.9);

for (Int_t i=0; i<nbins; i++) {

for (Int_t k=0; k<4096; k++) {

if (NoisePulse->GetBinContent(i+1, k) != 0) {

NoiseTime->SetBinContent(i+1,k-62.9087);

}

}

}

//TH1F* NormNoiseFFT = new TH1F ("NormNoiseFFT", "Normalized Noise FFT", nbins, 0, 5);

//TStopwatch t;

//t.Start(); //1 hour runtime

//for (j=10;j<20;j++) {

// plot = "WF_val:WF_time>>TempHisto";

// cut = "WF_ch==APD1 && amp_max[APD3]<25 && b_rms[APD3]<5. && charge_tot[APD3]<20000 && amp_max[APD5]<25 && b_rms[APD5]<5. && amp_max[APD6]<25 && b_rms[APD6]<5. && amp_max[APD4]<25 && b_rms[APD4]<5. && amp_max[SiPM1]<20 && amp_max[SiPM2]<20 && amp_max[APD1]<40 && amp_max[APD2]<40 && b_rms[APD1]<5. && b_rms[APD2]<5. && WF_time<160 && event==";

// cut += j;

// h4_2->Draw(plot, cut, "goff");

// if (TempHisto->GetMaximum() == 0) {

// delete HistoEvent[j+1];

// continue;

// }

// for (Int_t i=0; i<nbins; i++) {

// for (Int_t k=0; k<1000; k++) {

// if (TempHisto->GetBinContent(i+1, k) != 0) {

// HistoEvent[j+1]->SetBinContent(i+1,k*0.03-15);

// }

// }

// }

// mean = TempHisto->GetMean(2);

// rms = TempHisto->GetRMS(2);

// for (Int_t q=0;q<nbins;q++) {

// NewHistoEvent[j+1]->SetBinContent(q+1, HistoEvent[j+1]->GetBinContent(q+1)-mean);

// }

// NewHistoEvent[j+1]->Scale(1/rms);

// NewHistoEvent[j+1]->FFT(NewHistoEventFFT[j+1], "MAG");

// NormNoiseFFT->Add(NormNoiseFFT, NewHistoEventFFT[j+1]);

// TempHisto->Write();

// NewHistoEvent[j+1]->Write();

// NewHistoEventFFT[j+1]->Write();

// cout << "Event " << j << ", Mean = " << mean << ", RMS = " << rms << endl;

// count += 1;

//}

//NormNoiseFFT->Scale(1/count);

//NormNoiseFFT->Write();

//t.Stop();

//t.Print();

new TFile("/home/marko/H4Analysis/ntuples/analysis_4443.root"); // ignore this reloading of the same file, it is required or else the plots do not show up (when I tried)

TimeandFreq->cd(1);

PulseTime->GetXaxis()->SetTitle("Time (ns)");

PulseTime->GetYaxis()->SetTitle("Amplitude");

PulseTime->DrawClone(); //Wave Pulse in Time domain

TimeandFreq->cd(2);

TH1F* PulseFreq = new TH1F ("PulseFreq", "Pulse FFT", nbins, 0, 5);

TH1F* PulsePhase = new TH1F ("PulsePhase", "Pulse Phase", nbins, -0.1, 799.9);

PulseTime->FFT(PulseFreq, "MAG");

PulseTime->FFT(PulsePhase, "PH");

PulseFreq->SetLineColor(kRed);

PulseFreq->GetXaxis()->SetTitle("Frequency (GHz)");

PulseFreq->GetYaxis()->SetTitle("Amplitude");

PulseFreq->DrawClone(); //Wave Pulse in Frequency domain

gPad->SetLogy();

TimeandFreq->cd(3);

NoiseTime->GetXaxis()->SetTitle("Time (ns)");

NoiseTime->GetYaxis()->SetTitle("Amplitude");

NoiseTime->DrawClone(); // Noise from pedestal in Time domain

TimeandFreq->cd(4);

TH1F* NoiseFreq = new TH1F ("NoiseFreq", "Noise FFT", nbins, 0, 5);

NoiseTime->FFT(NoiseFreq, "MAG");

NoiseFreq->GetXaxis()->SetTitle("Frequency (GHz)");

NoiseFreq->GetYaxis()->SetTitle("Amplitude");

NoiseFreq->Draw(); // Noise from pedestal in Frequency domain

gPad->SetLogy();

Freq->Divide(1,3);

Freq->cd(1);

PulseFreq->DrawClone();

gPad->SetLogy();

Freq->cd(2);

NoiseFreq->DrawClone();

gPad->SetLogy();

Freq->cd(3);

PulseFreq->SetTitle("Pulse and Noise FFT Comparison");

PulseFreq->Draw();

NoiseFreq->Draw("same");

gPad->SetLogy();

TH1F* UnscaledSignalFreq = new TH1F ("UnscaledSignalFreq", "Unscaled Signal Frequency", nbins, -0.1, 799.9);

for (Int_t l=0; l<nbins; l++) {

UnscaledSignalFreq->SetBinContent(l+1, (PulseFreq->GetBinContent(l+1)-NoiseFreq->GetBinContent(l+1))/PulseFreq->GetBinContent(l+1));

}

TH1F* SignalFreq = new TH1F ("SignalFreq", "Signal Frequency", nbins, 0, 799.9);

for (Int_t m=0; m<nbins; m++) {

SignalFreq->SetBinContent(m+1, UnscaledSignalFreq->GetBinContent(m+1)*PulseFreq->GetBinContent(m+1));

}

Double_t *re_full = new Double_t[nbins];

Double_t *im_full = new Double_t[nbins];

for (Int_t n=0; n<nbins; n++) {

(re_full)[n]=(SignalFreq->GetBinContent(n+1)*cos(PulsePhase->GetBinContent(n+1)));

(im_full)[n]=(SignalFreq->GetBinContent(n+1)*sin(PulsePhase->GetBinContent(n+1)));

}

TVirtualFFT *invFFT = TVirtualFFT::FFT(1, &nbins, "C2R M K");

invFFT->SetPointsComplex(re_full, im_full);

invFFT->Transform();

TH1 *Signal = 0;

Signal = TH1::TransformHisto(invFFT,Signal,"Re");

Signal->SetTitle("Recovered Signal 'S'");

TH1F* BetterSignal = new TH1F ("BetterSignal", "Recovered Signal", nbins, -0.1, 159.9);

for (Int_t p=0; p<nbins; p++) {

BetterSignal->SetBinContent(p+1, Signal->GetBinContent(p+1)/nbins);

}

TimeSignal->Divide(1,2);

TimeSignal->cd(1);

PulseTime->DrawClone(); //Original Wave Pulse

TimeSignal->cd(2);

BetterSignal->GetXaxis()->SetTitle("Time (ns)");

BetterSignal->GetYaxis()->SetTitle("Amplitude");

BetterSignal->SetLineColor(kRed);

//BetterSignal->Draw(); // Recovered Wave Pulse with decreased contribution from background noise

BestSignal->SetLineColor(kGreen);

BestSignal->DrawClone("same");

PulseTime->DrawClone("same");

}

//for (Int_t k=0; k<PulseTime->GetNbinsX(); k++) {

// NoiseTime->SetBinContent(k+1, PulseTime->GetBinContent((k+1)%250));

//}

//h4->Draw("WF_val:WF_time"," WF_ch==APD1 && amp_max[APD3]<25 && b_rms[APD3]<5. && charge_tot[APD3]<20000 && amp_max[APD5]<25 && b_rms[APD5]<5. && amp_max[APD6]<25 && b_rms[APD6]<5. && amp_max[APD4]<25 && b_rms[APD4]<5. && amp_max[SiPM1]<20 && amp_max[SiPM2]<20 && amp_max[APD1]<40 && amp_max[APD2]<40 && b_rms[APD1]<5. && b_rms[APD2]<5.");

//gPad->SetGrid();

// Double_t binCenter = xaxis->GetBinCenter(bin); //where bin is a number corresponding to a bin

// Int_t BinSize = htemp->GetNBins();

// TAxis *xaxis = htemp->GetXaxis();

// TAxis *yaxis = htemp->GetYaxis();

//NoiseTime->GetXaxis()()->SetRangeUser(10,990);

//Freq->cd(4);

//UnscaledSignalFreq->DrawClone();

//NoiseTime->SetBinContent(k+1, sin(k/10.)/10.);

// TH2F* WavePulse=(TH2F*)gDirectory->Get("htemp");

// TTree *MyTree = new TTree("MyTree", "MyTree");

// MyTree->ReadFile("storage.txt", "x:y");

// MyTree->Draw("y:x","");

// TimeandFreq->cd(1);

// WavePulse->DrawClone("colz");

//NoiseTime->SetTitle("FFT");

//Double_t PulseFreqIntegral = PulseFreq->Integral();

//Double_t NoiseFreqIntegral = NoiseFreq->Integral();

//PulseFreq->Scale(1/PulseFreqIntegral);

//NoiseFreq->Scale(1/NoiseFreqIntegral);

//ofstream myfile;

//myfile.open ("storage.txt");

//myfile << "x" << "\t \t" << "y" << endl;

//myfile << i << "\t \t" << j-50 << endl; //subtract j by distance from lower limit of y to 0 (if negative)

//myfile.close();

//TGraph *MyGraph = new TGraph("storage.txt");