Finally made things work as intended

outputDigitization.cc

 #include "TFile.h"
 #include "TH1F.h"
+#include "TGraph.h"
 #include "TF1.h"
 #include "TRandom.h"
 #include <TTree.h>
@@ -38,14 +39,14 @@ void cutZDCoutput(string fileName, string rod, double xOffset, double zOffset){
   inTree->SetBranchAddress("Py",&Pyf);
   inTree->SetBranchAddress("Pz",&Pzf);
   //inTree->SetBranchAddress("EventNo",&EventNf);
-  //intree->SetBranchAddress("NCherenkovs",&NCherenkovs);
+  // intree->SetBranchAddress("NCherenkovs",&NCherenkovs);
 
   //Output root file
-  TFile* outFile = new TFile( Form("output/Out_%s",fileName.c_str() ), "RECREATE");
+  TFile* outFile = new TFile( Form("output/%s_%s.root",fileName.substr(0,fileName.find_last_of(".")).c_str(), rod.c_str() ), "RECREATE");
   TTree* outTree = new TTree( "tree", "tree" );
 
-  outTree->Branch("X0",&x_0);
-  outTree->Branch("Z0",&z_0);
+  // outTree->Branch("X0",&x_0);
+  // outTree->Branch("Z0",&z_0);
   outTree->Branch("X",&x);
   outTree->Branch("Z",&z);
   outTree->Branch("Px",&px);
@@ -53,11 +54,12 @@ void cutZDCoutput(string fileName, string rod, double xOffset, double zOffset){
   outTree->Branch("Pz",&pz);
   outTree->Branch("Energy",&Energy);
   outTree->Branch("EventNo",&EventNo);
+	// outTree->SetBranchAddress("NCherenkovs",&NCherenkovs);
 
   // output txt file
-	ofstream outputFile( Form("output/Out_%s.txt",fileName.substr(0,fileName.find_last_of("," ) ).c_str() ) );
+	ofstream outputFile( Form("output/%s_%s.txt",fileName.substr(0,fileName.find_last_of("." ) ).c_str(), rod.c_str() ) );
 
-	//// Get the transmission data
+	//// Get the tr.ansmission data
 	////
 	vector< double > transData;
 	string str;
@@ -76,11 +78,14 @@ void cutZDCoutput(string fileName, string rod, double xOffset, double zOffset){
 
 	// Load that data into a histogram so we can use the GetBin function
 	TH1F* hTrans = new TH1F( "TransData", "TransData", nBins, 197.2888,  1027.23596);
+	TH1F* hTrans2 = new TH1F( "TransData2", "TransData2", nBins, 197.2888,  1027.23596);
 	float trans, rand;
 
 	for(int bin = 0; bin < nBins; bin++){
 		hTrans->SetBinContent( bin, transData[bin] );
 	}
+
+	// Apply a modified baseline to the fused quartz spectrum
 	if(rod == "fusedQuartz"){
 		TF1* bLine = new TF1("baseline","0.0883*log(0.013087*(x-156.8) ) + 0.802",197,1028);
 		hTrans->Multiply(bLine);
@@ -115,13 +120,14 @@ void cutZDCoutput(string fileName, string rod, double xOffset, double zOffset){
       // get the data from the appropriate bin.
       wl = 1240./energy;
       if(wl < 197.2888){
-        trans = hTrans->GetBinContent(1);
+      	trans = hTrans->GetBinContent(10);
       }else{
-			   trans = hTrans->GetBinContent( hTrans->GetBin( wl ) );
+			  trans = hTrans->GetBinContent( hTrans->FindBin( wl ) );
       }
 			// Give the photon a random chance to make it weighted
 			// by transmission %
-			if( rnd.Rndm() < trans ){
+			// if( rnd.Rndm() < trans ){
+			if( rnd.Rndm() < 1 ){
 
 				// If the photon is transmitted, add it to the vector
 				X = Xf->at(k) + xOffset;
@@ -214,17 +220,15 @@ void PMTcuts(string fileName, int PMTmodel = 6091){
 		}
 	}
 
-	// Load that data into a histogram so we can use the GetBin function
-	TH1F* hQE = new TH1F( "TransData", "TransData", wavelength.size(), wavelength.front(),  wavelength.back());
-	for(int bin = 0; bin < wavelength.size(); bin++){
-		hQE->SetBinContent(bin,efficiency[bin]);
-	}
+	TVectorD TvWL(wavelength.size(),&wavelength[0]);
+	TVectorD TvQE(efficiency.size(),&efficiency[0]);
+	TGraph* gQE = new TGraph(TvWL,TvQE);
 
 	//// begin loop over events
 	////
 	TRandom rnd;
   int nCut, nPhotons, totalCut=0, totalPhotons=0;
-  double X,Z,wl,trans;
+  double X,Z,wl,trans,rand;
 	int nEvents = inTree->GetEntries();
 	for (int ev = 0; ev < nEvents ; ev++){
 		inTree->GetEntry(ev);
@@ -243,9 +247,10 @@ void PMTcuts(string fileName, int PMTmodel = 6091){
         nCut++;
       } else{
         // Get transmission % from data
-        trans = hQE->GetBinContent( hQE->GetBin( wl ) );
+        trans = gQE->Eval( wl );
         // Give the photon a random chance to make it past the
         // Quantum Efficiency check
+				rand = 100*rnd.Rndm();
         if( 100*rnd.Rndm() > trans ){
           nCut++;
         }