diff --git a/Analysis/compareHisto.cpp b/Analysis/compareHisto.cpp
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+++ b/Analysis/compareHisto.cpp
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+/******************************************************************************
+ *
+ * This script contains three primary functions. The first, plotFromCSV, will take a
+ * .CSV file with data in the format:
+ *
+ * x,y,z
+ * x,y,z
+ *
+ * And create a 2D histogram with the values contained. The histogram will be
+ * saved to a root file with the name given by the second argument of the function.
+ *
+ * The second function, compareHistos, which takes the names of two root files
+ * as inputs, retrieves a histogram from within both, and can subtract or divide the two.
+ * REAL?? It then takes the subtracted histogram and fills another 1D
+ * histogram with the subtracted values, returning this histogram's RMS as the
+ * desired output
+ *
+ * The third function, averageHistos, takes 4 histograms as inputs and averages them,
+ * returning a new histogram called haverage.
+ *
+ * TO RUN:
+ * Open an interactive ROOT session
+ * $root -l
+ *
+ * Load the script
+ * [0].L plotFromCSV.cpp
+ *
+ * Run either of the functions (whatever is necessary at the time)
+ * [1]plotFromCSV("rawData.csv","outputRootFileName.root")
+ *
+ * or
+ * * TO RUN:
+ * Open an interactive ROOT session
+ * $root -l
+ *
+ * Load the script
+ * [0].L plotFromCSV.cpp
+ * [1]compareHistos("file1.root","file2.root")
+ *
+ * As written, file1 should be the real data, while file2 is the simulated data.
+ *
+ * or
+ * * TO RUN:
+ * Open an interactive ROOT session
+ * $root -l
+ *
+ * Load the script
+ * [0].L plotFromCSV.cpp
+ * [1]averageHistos("file1.root","file2.root","file3.root","file4.root")
+ *
+*******************************************************************************/
+
+
+#include <fstream>
+#include <string>
+#include "TVectorD.h"
+#include "TCanvas.h"
+#include "TGraph.h"
+#include "TFile.h"
+
+
+using namespace std;
+
+string getDataPoint( string &input, size_t spaces = 1, string delim = "," );
+
+void plotFromCSV(TString fileName, TString outFileName){
+
+ //Open the csv
+ ifstream file(fileName);
+ //Check if the file opened properly. Exit if not
+ if( !file.is_open() ){
+ cout << "File didn't open" << endl;
+ return;
+ }
+
+ //make sure the size of each histogram is the same && the bins are in the middle
+ float range = 54;
+ TH2F *h = new TH2F("lightguideintensity","Relative Intensity (Box experiment);X-plane (mm);Z-plane (mm)",18,-range/2.,range/2.,18,-range/2.,range/2.);
+
+ //While we still haven't reached the end of the file, get the next line, parse it, and fill the histogram
+ //with the value on that line
+ string buffer;
+ while( !file.eof() ){
+ getline(file,buffer);
+
+ float x = atof(getDataPoint(buffer,1).c_str() );
+ float y = atof(getDataPoint(buffer,1).c_str() );
+ float counts = atof(getDataPoint(buffer,1).c_str() );
+
+ h->Fill(x-range/2.,y-range/2.,counts);
+
+ }
+
+ //Create a new root file to save the histogram to. "recreate" will overwrite any file with the same name
+ TFile f(outFileName.Data(),"recreate");
+
+ // Scale it to make it relative like plothisto does
+ h->Scale(1.0/h->GetMaximum());
+ h->Write(); //Write the histogram to the file
+
+ //Create a new TCanvas to draw the histogram onto
+ TCanvas *c = new TCanvas("canv","canv",800,600);
+ //gStyle->SetPalette(55);
+ h->Draw("colz"); //Draw it. colz is "Colored Z axis"
+
+ f.Close(); //Close the file
+
+}
+
+void compareHistos( string file1, string file2){
+
+//----------------------RETIREVE THE HISTOGRAMS---------------------------------
+ //Open file 1 and retrieve the histogram from within
+ TFile f1(file1.c_str(),"read");
+ TH2F *hreal = (TH2F*)f1.Get("lightguideintensity");
+ // //normalize
+ // hreal->Scale(1./hreal->Integral());
+ //hreal->Scale(1.0/hreal->GetMaximum());
+
+ //Open file 2 and retrieve the histogram from within
+ TFile f2(file2.c_str(),"read");
+ TH2F *hsim = (TH2F*)f2.Get("eff");
+ // //normalize
+ // h2->Scale(1./h2->Integral());
+
+ //make some same-size hists to work with later, based on hreal
+ TH2F *hdiff = (TH2F*)hreal->Clone();
+ TH2F *hrat = (TH2F*)hreal->Clone();
+ TH2F *hcopy = (TH2F*)hreal->Clone();
+ hcopy->SetNameTitle("copy", "Difference;X-plane (mm);Z-plane (mm)");
+ hdiff->SetNameTitle("difference", "Difference;X-plane (mm);Z-plane (mm)");
+ hrat->SetNameTitle("divide", "Ratio;X-plane (mm);Z-plane (mm)");
+
+ //We want to subtract sim from real (add -1)
+ hdiff->Add(hsim, -1);
+
+ //Create a new histogram to hold the differences for each bin
+ // TH1F *hDev = new TH1F("stdDev","stdDev",100,-10,10);
+
+ // //For each bin in the original histogram, fill the new histogram
+ // //with the difference of the two
+ // int nBins = hcopy->GetNbinsX() * hdiff->GetNbinsY();
+ // for(int bin = 0; bin < nBins; bin++){
+ // float val = hdiff->GetBinContent(bin);
+ // hdiff->Fill(val);
+ // //h3->SetBinContent(bin,val);
+
+ //}
+
+ //make ratio histogram real/sim
+ hrat->Divide(hsim);
+
+ // make percent error histogram
+ TH2F *hpercer = (TH2F*)hdiff->Clone();
+ hpercer->SetNameTitle("percerror", "Percent Error;X-plane (mm);Z-plane (mm)");
+ hpercer->Divide(hreal);
+ hpercer->Scale(100.);
+ hpercer->Write();
+
+ // //Retrieve the RMS from this new histogram
+ // float RMS = hDev->GetRMS();
+ // cout << "RMS " << RMS << endl;
+ // //cout << "Percent error " << RMS << endl;
+
+ // //Create a canvas to view the histograms on
+ TCanvas *c = new TCanvas("canvas","canvas",4000,1600);
+ TFile f("comparison.root","recreate");
+ gStyle->SetOptStat(0);
+ c->Divide(3,2);
+ c->cd(1);
+ hreal->Draw("colz");
+ hreal->Write();
+
+ c->cd(2);
+ hsim->Draw("colz");
+ hsim->Write();
+
+ c->cd(3);
+ hdiff->Draw("colz");
+ hdiff->Write();
+
+ c->cd(4);
+ hrat->Draw("colz");
+ hrat->Write();
+
+ c->cd(5);
+ hpercer->Draw("cloz");
+ hpercer->Write();
+
+ c->Print("Comparison-plots.png");
+ // hDev->Write();
+
+ f.Close();
+ delete c;
+
+}
+
+///gernerate a similar series of histograms.
+//functionalize it. difference, ratio, relative error,
+// all for histograms normalized in different ways
+
+// outer fucntion --open each file, retrieve histograms,
+// loop --- for each normalization method
+/// ---- noramlize both histograms
+/// call anotehr function
+/// other function will make all the analysis whatevers (subtract, dev, divide, per erreor, etc)
+// write to file
+// give things good names
+//it would be nice to have a canvas for each normalization with all of the comparisons
+
+
+string getDataPoint( string &input, size_t spaces, string delim ){
+ size_t firstComma = input.find_first_of(delim.c_str());
+ string buffer = input.substr(0, firstComma );
+ input.erase(0,firstComma+spaces);
+ return buffer;
+}
+
+
+void averageHistos( string file1, string file2, string file3, string file4){
+
+// //----------------------RETIREVE THE HISTOGRAMS---------------------------------
+ //Open file 1 and retrieve the histogram from within
+ TFile f1(file1.c_str(),"read");
+ TH2F *h1 = (TH2F*)f1.Get("lightguideintensity");
+
+
+ //Open file 2 and retrieve the histogram from within
+ TFile f2(file2.c_str(),"read");
+ TH2F *h2 = (TH2F*)f2.Get("lightguideintensity");
+
+ //Open file 3 and retrieve the histogram from within
+ TFile f3(file3.c_str(),"read");
+ TH2F *h3 = (TH2F*)f3.Get("lightguideintensity");
+
+ //Open file 4 and retrieve the histogram from within
+ TFile f4(file4.c_str(),"read");
+ TH2F *h4 = (TH2F*)f4.Get("lightguideintensity");
+
+
+
+ //make some same-size hists to work with later, clone of h1
+ TH2F *htotal = (TH2F*)h1->Clone();
+
+ //add all the other histograms to it
+ htotal->Add(h2);
+ htotal->Add(h3);
+ htotal->Add(h4);
+
+ //divide total by 4?
+ TH2F *haverage = (TH2F*)htotal->Clone();
+ haverage->Scale(1./4); // this should take the average of the four files
+ haverage->SetNameTitle("average", "Average;X-plane (mm);Z-plane (mm)");
+ haverage->Write();
+
+
+}
+