//This macro is coincidence analysis, subtracting background spectra from a gated spectrum and analyzing the remaining peaks. 

#include <TH2.h>
#include <TStyle.h>
#include <TCanvas.h>
#include <TGraph.h>
#include <TCutG.h>
#include <TFile.h>
#include "TH2.h"
#include "TH1.h"
#include "TRandom.h"
#include "iostream"
#include <TMath.h>
#include "TObjArray.h"
#include "TF1.h"
#include "TSpectrum.h"
#include "TVirtualFitter.h"
#include "Riostream.h"

TObjArray List1;
TObjArray List2;
TObjArray List3;

void bgs(){

// func = Gate - 0.5(background_gate + background_gate_2) -> function used to subtract out the gated peak of interest (POI).

// Retrieve the histogram:
TFile *file = new TFile("out_gate_2270_2570_2070_2170_2670_2770.root");

// Create a new canvas:
TCanvas * c0 = new TCanvas("c0", "64Ni 8.7MeV Coincidence Analysis", 10,10, 800, 800);

// Create a THStack object to hold the histograms:
THStack * stack = new THStack("stack", "Stacked Histograms");

// Placing multiple histograms on the same canvas:
TH1D * gate_hist=new TH1D("gatehist","gatehist",4096,-2.0,16382.0);
TH1D * avg_bg=new TH1D("avg_bg","avg_bg",4096,-2.0,16382.0);
TH1D * gated_bgs=new TH1D("gated_bgs","gate_bgs",4096,-2.0,16382.0);
TH1D * gated_cal=new TH1D("gated_cal","gate_Cal",4096,-2.0,16382.0);//calibrated spectrum

// Placing in the gated spectra:    
c0->Divide(2,3);
c0->cd(1);   
gPad->SetLogy(0);//Linear(0), Log(1)
gate_hist->Add(gate,1);
gate_hist->Draw();

// Placing the background regions into the canvas then subtract the gated_spectrum from the avg_bg (scale factor determined in hdtv). Adding the background spectra (pad2):

c0->cd(2);
gPad->SetLogy(0);//Linear(0), Log(1)
avg_bg->Add(background_gate,0.5);
avg_bg->Add(background_gate_2,0.5);
avg_bg->Draw();

// Subtracting gate from avg_bg into pad3:
// Scaling factors to normalize the avg_bg:
// projx scaling: 1345 -> 1.693 , 2276 -> 1.7, 2610 -> 1.25, 2867 -> 1.453, 3025 -> 1.792, 3463 -> 1.406

//Log and Linear histograms:
TH1D * log_cal = new TH1D("log_cal","log_cal",4096,-2.0,16382.0);//log spectrum
TH1D * linear_cal = new TH1D("linear_cal","linear_cal",4096,-2.0,16382.0);//linear spectrum

// Base and Transparent pad to place a log and linear graph on the same plot:
TPad * Blog_pad = new TPad("log","LogHist",0,0,1,1);//log spectrum
Blog_pad->SetFillColor(0);
Blog_pad->SetFillStyle(0);
TH1D * linear_padT = new TH1D("lin","LinHist",4096,-2.0,16382.0);//linear spectrum

// Linear pad:
    c0->cd(3);
    //linear_cal->GetYaxis()->SetRangeUser(0, linear_cal->GetMaximum() * 1.1);
    gPad->SetLogy(0);//Linear(0), setting the y-axis scale
    linear_cal->Add(gate_hist,1);
    linear_cal->Add(avg_bg,-1);
    linear_cal->Add(avg_bg,-1.7);
    linear_cal->SetLineColor(kBlack);
    linear_cal->GetYaxis()->SetTitle("Hist 1 axis label");
    linear_cal->GetXaxis()->SetTitle("x axis label");
    linear_cal->GetYaxis()->SetTitle("Left y axis label");
    linear_cal->SetMarkerStyle(kFullCircle);
    linear_cal->Draw();

// Log pad:
    c0->cd(4);
    //log_cal->GetYaxis()->SetRangeUser(0, linear_cal->GetMaximum() * 1.1);
    gPad->SetLogy(1);//Log(1)
    log_cal->Add(gate_hist,1);
    log_cal->Add(avg_bg,-1);
    log_cal->Add(avg_bg,-1.7);
    log_cal->GetYaxis()->SetTitle("Right y axis label");
    log_cal->GetYaxis()->SetTitleOffset(1.3);
    log_cal->SetLineColor(kBlue);
    log_cal->SetMarkerColor(kBlue);
    log_cal->SetMarkerStyle(kOpenCircle);
    log_cal->Draw();
    
// Create a TMultiGraph to hold the log and linear graphs:
    //TMultiGraph * mg = new TMultiGraph();
    //TGraph * linear_graph = new TGraph(linear_cal);
    //linear_graph->SetLineColor(kBlack);
    //mg->Add(linear_graph);

    //TGraph * log_graph = new TGraph(log_cal);
    //log_graph->SetLineColor(kBlue);
    //mg->Add(log_graph);

    // Draw the TMultiGraph on the canvas:
    //c0->cd(3);
    //gPad->SetLogy(0);
    //mg->Draw("a");


// Add the first histogram to the pad -linear:
//c0->cd(5);

    linear_cal->Add(gate_hist,1);
    linear_cal->Add(avg_bg,-1);
    linear_cal->Add(avg_bg,-1.7);
    linear_cal->SetLineColor(kBlack);
    linear_cal->GetYaxis()->SetTitle("Hist 1 axis label");
    linear_cal->GetXaxis()->SetTitle("x axis label");
    linear_cal->GetYaxis()->SetTitle("Left y axis label");
    linear_cal->GetYaxis()->SetRangeUser(1e-16, 1.4);
    linear_cal->SetMarkerStyle(kFullCircle);
    linear_cal->Draw();

//linear_padT->SetFillColor(0);
//linear_padT->SetFillStyle(0);
//gPad->SetLogy(0);//Linear(0)
//linear_cal->Add(gate_hist,1);
//linear_cal->Add(avg_bg,-1);
//linear_cal->Add(avg_bg,-1.7);
//linear_padT->GetYaxis()->SetTitle("Hist 1 axis label");
//linear_padT->GetXaxis()->SetTitle("x axis label");
//linear_padT->GetYaxis()->SetTitle("Left y axis label");
//linear_padT->SetLineColor(kGreen);
//stack->Add(linear_cal);

// Add the second histogram to the pad-log:
//gPad->SetLogy(1);// Log(1)

Blog_pad->Draw();
Blog_pad->cd();
Blog_pad->SetTicks(0,0);
Blog_pad->SetLogy(0);

log_cal->GetYaxis()->SetTitle("Right y axis label");
log_cal->GetYaxis()->SetTitleOffset(1.3);
log_cal->GetYaxis()->SetRangeUser( 1e-2, 20);
log_cal->SetLineColor(kBlue);
log_cal->Draw("Y+");
//stack->Add(log_cal);

// Draw the stacked histograms:
//stack->Draw("stack");

// Add a legend:
//TLegend* legend = new TLegend(0.1, 0.7, 0.3, 0.9);
//legend->SetHeader("Legend Title","C");//"C" options centers the header
//legend->AddEntry(log_cal, "Log", "l");
//legend->AddEntry(linear_cal, "Linear", "l");
//legend->Draw();

// Update the canvas
c0->Update();

}