saving work again, refining and benchmarking energy loss and deposition

new file:   ELoss/Eloss_17F
	new file:   ELoss/Eloss_27Al
	new file:   ELoss/Eloss_alpha
	new file:   ELoss/Eloss_p
	modified:   MakeVertex.C
	deleted:    MakeVertex.C:Zone.Identifier
	deleted:    MakeVertex.h:Zone.Identifier

.gitignore

@@ -4,9 +4,28 @@ EventBuilder*
 *.pcm
 *.root
 *.exe
-
+*.txt
+*.err
+*.seq
+*.png
+*.pdf
 Mapper
 AnasenMS
+Armory/anasenMS
 
 data/
 data_proton/
+Sudarshan/
+Analyzer_C_ACLiC_dict0713aaa966_dictContent.h
+.gitignore
+Analyzer_C_ACLiC_dict5411fecd5c_dictUmbrella.h
+gainmatch.C
+gainmatch.h
+MakePlotsQQQ.C
+MakePlotsQQQ.h
+MakePlotsSX3.C
+MakePlotsSX3.h
+qqq_gains_det3.dat
+qqq_relative_gains.dat
+Armory/CorrelateQQQ.h
+QQQStage2.C

.vscode/c_cpp_properties.json

@@ -1,23 +1,24 @@
 {
     "configurations": [
         {
-            "name": "splitpole",
+            "name": "Linux",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/splitpole/cern/root/**"
+                "/opt/root-6.36.06/include",
+                "/home/jamesszalkie/anasen/Armory"
             ],
             "defines": [],
-            "compilerPath": "/usr/bin/gcc",
+            "compilerPath": "/usr/bin/g++",
-            "cStandard": "c17",
+            "cStandard": "c11",
-            "cppStandard": "gnu++17",
+            "cppStandard": "c++17",
-            "intelliSenseMode": "linux-gcc-x64"
+            "intelliSenseMode": "gcc-x64"
         },
         {
-            "name": "Ryan",
+            "name": "Hades",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/ryan/Downloads/root_build/**",
+                "/usr/include/x86_64-linux-gnu/qt6/**",
-                "/home/ryan/Downloads/root_build/include"
+                "/usr/local/cern/root_v6.26.06/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -29,7 +30,8 @@
             "name": "RyanUbuntu",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -38,10 +40,11 @@
             "intelliSenseMode": "linux-gcc-x64"
         },
         {
-            "name": "RyanHome",
+            "name": "Anasen",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/ryan/root_v6.30.06/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",
@@ -50,10 +53,38 @@
             "intelliSenseMode": "linux-gcc-x64"
         },
         {
-            "name": "Dirac",
+            "name": "Splitpole",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/usr/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/home/splitpole/cern/root/include/**",
+                "/usr/include/x86_64-linux-gnu/qt6/QtWidgets",
+                "/usr/include/x86_64-linux-gnu/qt6/QtCore"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "Penguin",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/usr/local/cern/root/include/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "VigneshROG",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/home/vsitaraman/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",

.vscode/settings.json

@@ -90,6 +90,42 @@
     "processRun.C": "cpp",
     "TrackRecon.C": "cpp",
     "processRuns.C": "cpp",
-    "Analysis.C": "cpp"
+    "Analysis.C": "cpp",
-  }
+    "datastructs.h": "c",
+    "ANASENPlotEdit.C": "cpp",
+    "GetMean_Q3_new.C": "cpp",
+    "AlphaCal_new.C": "cpp",
+    "f1.C": "cpp",
+    "GeoCal_Maria_new.C": "cpp",
+    "PCPulser_All_new.C": "cpp",
+    "PosCal_2.C": "cpp",
+    "AutoFit.C": "cpp",
+    "Fitting.C": "cpp",
+    "PCGainMatch.C": "cpp",
+    "Analyzer1.C": "cpp",
+    "FitHistogramsWithTSpectrum_Sequential_Improved.C": "cpp",
+    "PlotAndFitCentroids.C": "cpp",
+    "MatchAndPlotCentroids.C": "cpp",
+    "GainMatch.C": "cpp",
+    "GainMatchSX3.C": "cpp",
+    "RelBack_Fix_new.C": "cpp",
+    "SiRelativeGains_Step1_new.C": "cpp",
+    "charconv": "cpp",
+    "format": "cpp",
+    "GainMatchSX3Front.C": "cpp",
+    "GainMatchSX3Front1.C": "cpp",
+    "Calibration.C": "cpp",
+    "GainMatchQQQ.C": "cpp",
+    "UTF-8gainmatch.C": "cpp",
+    "MakePlotsQQQ.C": "cpp",
+    "MakePlotsSX3.C": "cpp",
+    "QQQ_Calibcheck.C": "cpp",
+    "QQQ_Calcheck.C": "cpp",
+    "makeplots.C": "cpp",
+    "GlobalMinimizeQQQ.C": "cpp",
+    "QQQStage2.C": "cpp",
+    "inspect.C": "cpp"
+  },
+  "github-enterprise.uri": "https://fsunuc.physics.fsu.edu",
+  "C_Cpp.default.compilerPath": "/usr/bin/gcc"
 }

Analyzer.h

@@ -18,6 +18,7 @@ public :
    Det sx3;
    Det qqq;
    Det pc ;
+   Det misc;
 
    ULong64_t       evID;
    UInt_t          run;
@@ -40,6 +41,13 @@ public :
    TBranch        *b_pcCh;   //!
    TBranch        *b_pcE;   //!
    TBranch        *b_pcT;   //!
+   TBranch        *b_miscMulti;   //!
+   TBranch        *b_miscID;   //!
+   TBranch        *b_miscCh;   //!
+   TBranch        *b_miscE;   //!
+   TBranch        *b_miscT;   //!
+   TBranch       *b_miscTf;   //!
+
 
    Analyzer(TTree * /*tree*/ =0) : fChain(0) { }
    virtual ~Analyzer() { }
@@ -92,6 +100,13 @@ void Analyzer::Init(TTree *tree){
    fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
    fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
    fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID",    &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh",    &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE",     &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT",     &misc.t, &b_miscT);
+   // fChain->SetBranchAddress("miscF",     &misc.tf, &b_miscTf);
+
 
 }
 

Analyzer1.C

@@ -0,0 +1,402 @@
+#define Analyzer1_cxx
+
+#include "Analyzer1.h"
+#include <TH2.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+
+#include <utility>
+#include <algorithm>
+
+#include "Armory/ClassSX3.h"
+#include "Armory/ClassPW.h"
+
+#include "TVector3.h"
+
+TH2F * hsx3IndexVE;
+TH2F * hqqqIndexVE;
+TH2F * hpcIndexVE;
+
+TH2F * hsx3Coin;
+TH2F * hqqqCoin;
+TH2F * hpcCoin;
+
+TH2F * hqqqPolar;
+TH2F * hsx3VpcIndex;
+TH2F * hqqqVpcIndex;
+TH2F * hqqqVpcE;
+TH2F * hsx3VpcE;
+TH2F * hanVScatsum;
+int padID = 0;
+
+SX3 sx3_contr;
+PW pw_contr;
+TVector3 hitPos;
+bool HitNonZero;
+
+TH1F * hZProj;
+
+void Analyzer1::Begin(TTree * /*tree*/){
+  TString option = GetOption();
+
+  hsx3IndexVE = new TH2F("hsx3IndexVE", "SX3 index vs Energy; sx3 index ; Energy",  24*12, 0,  24*12, 400, 0, 5000); hsx3IndexVE->SetNdivisions( -612, "x");
+  hqqqIndexVE = new TH2F("hqqqIndexVE", "QQQ index vs Energy; QQQ index ; Energy", 4*2*16, 0, 4*2*16, 400, 0, 5000); hqqqIndexVE->SetNdivisions( -1204, "x");
+  hpcIndexVE = new TH2F("hpcIndexVE",   "PC index vs Energy; PC index ; Energy",     2*24, 0,   2*24, 400, 0, 4000); hpcIndexVE->SetNdivisions( -1204, "x");
+
+
+  hsx3Coin = new TH2F("hsx3Coin", "SX3 Coincident",  24*12, 0,  24*12,  24*12, 0, 24*12);
+  hqqqCoin = new TH2F("hqqqCoin", "QQQ Coincident", 4*2*16, 0, 4*2*16, 4*2*16, 0, 4*2*16);
+  hpcCoin  = new TH2F("hpcCoin",  "PC Coincident",    2*24, 0,   2*24,   2*24, 0, 2*24);
+
+  hqqqPolar = new TH2F("hqqqPolar", "QQQ Polar ID", 16*4, -TMath::Pi(), TMath::Pi(),16, 10, 50);
+
+  hsx3VpcIndex = new TH2F("hsx3Vpcindex", "sx3 vs pc; sx3 index; pc index",  24*12, 0, 24*12, 48, 0, 48);
+  hsx3VpcIndex->SetNdivisions( -612, "x");
+  hsx3VpcIndex->SetNdivisions( -12, "y");
+  hqqqVpcIndex = new TH2F("hqqqVpcindex", "qqq vs pc; qqq index; pc index",  4*2*16, 0, 4*2*16, 48, 0, 48);
+  hqqqVpcIndex->SetNdivisions( -612, "x");
+  hqqqVpcIndex->SetNdivisions( -12, "y");
+
+  hqqqVpcE = new TH2F("hqqqVpcEnergy", "qqq vs pc; qqq energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hqqqVpcE->SetNdivisions( -612, "x");
+  hqqqVpcE->SetNdivisions( -12, "y");
+  
+  hsx3VpcE = new TH2F("hsx3VpcEnergy", "sx3 vs pc; sx3 energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hsx3VpcE->SetNdivisions( -612, "x");
+  hsx3VpcE->SetNdivisions( -12, "y");
+
+  hZProj = new TH1F("hZProj", "Z Projection", 1200, -600, 600);
+
+  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 10000, 400, 0 , 16000);
+
+  sx3_contr.ConstructGeo();
+  pw_contr.ConstructGeo();
+
+}
+
+
+
+
+Bool_t Analyzer1::Process(Long64_t entry){
+
+  // if ( entry > 100 ) return kTRUE;
+
+  hitPos.Clear();
+  HitNonZero = false;
+
+  // if( entry > 1) return kTRUE;
+  // printf("################### ev : %llu \n", entry);
+
+  b_sx3Multi->GetEntry(entry);
+  b_sx3ID->GetEntry(entry);
+  b_sx3Ch->GetEntry(entry);
+  b_sx3E->GetEntry(entry);
+  b_sx3T->GetEntry(entry);
+  b_qqqMulti->GetEntry(entry);
+  b_qqqID->GetEntry(entry);
+  b_qqqCh->GetEntry(entry);
+  b_qqqE->GetEntry(entry);
+  b_qqqT->GetEntry(entry);
+  b_pcMulti->GetEntry(entry);
+  b_pcID->GetEntry(entry);
+  b_pcCh->GetEntry(entry);
+  b_pcE->GetEntry(entry);
+  b_pcT->GetEntry(entry);
+
+  sx3.CalIndex();
+  qqq.CalIndex();
+  pc.CalIndex();
+
+  // sx3.Print();
+
+  //########################################################### Raw data
+  // //======================= SX3
+
+  std::vector<std::pair<int, int>> ID; // first = id, 2nd = index
+  for( int i = 0; i < sx3.multi; i ++){
+    ID.push_back(std::pair<int, int>(sx3.id[i], i));
+
+    hsx3IndexVE->Fill( sx3.index[i], sx3.e[i] );
+
+    for( int j = i+1; j < sx3.multi; j++){
+      hsx3Coin->Fill( sx3.index[i], sx3.index[j]);
+    }
+
+    for( int j = 0; j < pc.multi; j++){
+      hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+      //  if( sx3.ch[index] > 8 ){
+      //    hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+      //   }
+    }
+  }
+
+
+  if( ID.size() > 0 ){
+    std::sort(ID.begin(), ID.end(),  [](const std::pair<int, int> & a, const std::pair<int, int> & b) {
+      return a.first < b.first;
+    } );
+    // printf("##############################\n");
+    // for( size_t i = 0; i < ID.size(); i++) printf("%zu | %d %d \n", i, ID[i].first, ID[i].second );
+
+    std::vector<std::pair<int, int>> sx3ID; 
+    sx3ID.push_back(ID[0]);
+    bool found = false;
+    for( size_t i = 1; i < ID.size(); i++){
+      if( ID[i].first == sx3ID.back().first) {
+        sx3ID.push_back(ID[i]);
+        if( sx3ID.size() >= 3) {
+          found = true;
+        } 
+      }else{
+        if( !found ){
+          sx3ID.clear();
+          sx3ID.push_back(ID[i]);
+        }
+      }
+    }
+
+    // printf("---------- sx3ID Multi : %zu \n", sx3ID.size());
+
+    if( found ){
+      int sx3ChUp, sx3ChDn, sx3ChBk;
+      float sx3EUp, sx3EDn;
+      // printf("------ sx3 ID : %d, multi: %zu\n", sx3ID[0].first, sx3ID.size());
+      for( size_t i = 0; i < sx3ID.size(); i++ ){
+        int index = sx3ID[i].second;
+        // printf(" %zu | index %d | ch : %d, energy : %d \n", i, index, sx3.ch[index], sx3.e[index]);
+
+
+        if( sx3.ch[index] < 8 ){
+          if( sx3.ch[index] % 2 == 0) {
+            sx3ChDn = sx3.ch[index];
+            sx3EDn = sx3.e[index];
+          }else{
+            sx3ChUp = sx3.ch[index];
+            sx3EUp = sx3.e[index];
+          }
+        }else{
+          sx3ChBk = sx3.ch[index];
+        }
+         for( int j = 0; j < pc.multi; j++){
+      // hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+            if( sx3.ch[index] > 8 ){
+              hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+            }
+          }
+      }
+
+      sx3_contr.CalSX3Pos(sx3ID[0].first, sx3ChUp, sx3ChDn, sx3ChBk, sx3EUp, sx3EDn);
+      hitPos = sx3_contr.GetHitPos();
+      HitNonZero = true;
+      // hitPos.Print();
+    }
+
+  }
+  
+
+  // //======================= QQQ
+  for( int i = 0; i < qqq.multi; i ++){
+    // for( int j = 0; j < pc.multi; j++){
+        // if(pc.index[j]==4){
+          hqqqIndexVE->Fill( qqq.index[i], qqq.e[i] );
+        // }
+    // }
+    for( int j = 0; j < qqq.multi; j++){
+      if ( j == i ) continue;
+      hqqqCoin->Fill( qqq.index[i], qqq.index[j]);
+    }
+
+
+    for( int j = i + 1; j < qqq.multi; j++){
+      for( int k = 0; k < pc.multi; k++){
+        if(pc.index[k]<24 && pc.e[k]>50 ){
+          hqqqVpcE->Fill( qqq.e[i], pc.e[k] );
+          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+                hqqqVpcIndex->Fill( qqq.index[i], pc.index[j] );
+
+        }
+      // }
+      }
+      // if( qqq.used[i] == true ) continue;
+      
+      //if( qqq.id[i] == qqq.id[j] && (16 - qqq.ch[i]) * (16 - qqq.ch[j]) < 0  ){ // must be same detector and wedge and ring
+      if( qqq.id[i] == qqq.id[j]  ){ // must be same detector 
+        
+        int chWedge = -1;
+        int chRing  =  -1;
+        if( qqq.ch[i] < qqq.ch[j]){
+          chRing = qqq.ch[j] - 16;
+          chWedge = qqq.ch[i];
+        }else{
+          chRing = qqq.ch[i];
+          chWedge = qqq.ch[j] - 16;
+        }
+
+        // printf(" ID : %d , chWedge : %d, chRing : %d \n", qqq.id[i], chWedge, chRing);
+
+        double theta = -TMath::Pi()/2 + 2*TMath::Pi()/16/4.*(qqq.id[i]*16 + chWedge +0.5);
+        double rho   = 10.+40./16.*(chRing+0.5);
+        // if(qqq.e[i]>50){
+        hqqqPolar->Fill( theta, rho);
+        // }
+        // qqq.used[i] = true;
+        // qqq.used[j] = true;
+
+        if( !HitNonZero ){
+        double x = rho * TMath::Cos(theta);
+        double y = rho * TMath::Sin(theta);
+        hitPos.SetXYZ(x, y, 23 + 75 + 30);
+        HitNonZero = true;
+        }
+      }
+    }
+  
+   
+  }
+  // //======================= PC
+
+  ID.clear();
+  int counter=0;
+  std::vector<std::pair<int, double>> E; 
+  E.clear();
+  for( int i = 0; i < pc.multi; i ++){
+
+    if( pc.e[i] > 100 ) ID.push_back(std::pair<int, int>(pc.id[i], i));
+    if( pc.e[i] > 100 ) E.push_back(std::pair<int, double>(pc.index[i], pc.e[i]));
+
+    hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+
+    for( int j = i+1; j < pc.multi; j++){
+      hpcCoin->Fill( pc.index[i], pc.index[j]);
+    
+    }
+
+  }
+  //  for( size_t i = 0; i < E.size(); i++) printf("%zu | %d %d \n", i, E[i].first, E[i].second ); 
+
+  if( E.size()>=3 ){
+
+    int aID = 0;
+    int cID = 0;
+
+    float aE = 0;
+    float cE = 0;
+    bool multi_an =false;
+    // if( ID[0].first < 1 ) {
+    //   aID = pc.ch[ID[0].second];
+    //   cID = pc.ch[ID[1].second];
+    // }else{
+    //   cID = pc.ch[ID[0].second];
+    //   aID = pc.ch[ID[1].second];
+    // }
+    // printf("anode= %d, cathode = %d\n", aID, cID);
+
+  // for( int k = 0; k < qqq.multi; k++){
+  //   if(qqq.index[k]==75 && pc.index[k]==2 && pc.e[k]>100){
+      for(int l=0;l<E.size();l++){
+        if(E[l].first<24 ){
+          if(!multi_an){
+            aE = E[l].second;
+          }
+          multi_an=true;
+        }
+        else if (E[l].first>=24){
+          cE = E[l].second + cE;
+        }
+      }
+    // }
+  // }
+    hanVScatsum->Fill(aE,cE);
+      
+    if( ID[0].first < 1 ) {
+      aID = pc.ch[ID[0].second];
+      cID = pc.ch[ID[1].second];
+    }else{
+      cID = pc.ch[ID[0].second];
+      aID = pc.ch[ID[1].second];
+    }
+
+    if( HitNonZero){
+      pw_contr.CalTrack( hitPos, aID, cID);
+      hZProj->Fill(pw_contr.GetZ0());
+    }
+
+  
+  }
+  
+
+
+  //########################################################### Track constrcution
+
+
+  //############################## DO THE KINEMATICS
+
+
+  return kTRUE;
+}
+
+void Analyzer1::Terminate(){
+
+  gStyle->SetOptStat("neiou");
+  TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
+  canvas->Divide(3,3);
+
+  //hsx3VpcIndex->Draw("colz");
+
+  //=============================================== pad-1
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3IndexVE->Draw("colz");
+
+  //=============================================== pad-2
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hqqqIndexVE->Draw("colz");
+
+  //=============================================== pad-3
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcIndexVE->Draw("colz");
+
+  //=============================================== pad-4
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3Coin->Draw("colz");
+
+  //=============================================== pad-5
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  canvas->cd(padID)->SetLogz(true);
+
+  hqqqCoin->Draw("colz");
+
+  //=============================================== pad-6
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcCoin->Draw("colz");
+
+  //=============================================== pad-7
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hsx3VpcIndex ->Draw("colz"); 
+  hsx3VpcE->Draw("colz") ;
+
+  //=============================================== pad-8
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hqqqVpcIndex ->Draw("colz");  
+
+  hqqqVpcE ->Draw("colz");
+  //=============================================== pad-9
+  padID ++; 
+
+  // canvas->cd(padID)->DrawFrame(-50, -50, 50, 50);
+  // hqqqPolar->Draw("same colz pol");
+
+ canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+//  hZProj->Draw();
+  hanVScatsum->Draw("colz");
+
+}

Analyzer1.h

@@ -0,0 +1,114 @@
+#ifndef Analyzer1_h
+#define Analyzer1_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class Analyzer1 : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   Analyzer1(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~Analyzer1() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(Analyzer1,0);
+};
+
+#endif
+
+#ifdef Analyzer1_cxx
+void Analyzer1::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t Analyzer1::Notify(){
+
+   return kTRUE;
+}
+
+void Analyzer1::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void Analyzer1::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef Analyzer_cxx

Armory/ANASEN_model.C

@@ -26,23 +26,35 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
   TGeoVolume *worldBox = geom->MakeBox("ROOT", Vacuum, worldx, worldy, worldz);
   geom->SetTopVolume(worldBox);
 
-  //--- making axis
+  //--- making axis (X=red, Y=green, Z=blue)
-  TGeoVolume *axisX = geom->MakeTube("axisX", Al, 0, 0.1, 5.);
+  Double_t axisLen = 100.;
-  axisX->SetLineColor(1);
+  TGeoVolume *axisX = geom->MakeTube("axisX", Al, 0, 0.1, axisLen/2);
-  worldBox->AddNode(axisX, 1, new TGeoCombiTrans(5, 0, 0., new TGeoRotation("rotA", 90., 90., 0.)));
+  axisX->SetLineColor(kRed);
+  worldBox->AddNode(axisX, 1, new TGeoCombiTrans(axisLen/2, 0, 0., new TGeoRotation("rotA", 90., 90., 0.)));
 
-  TGeoVolume *axisY = geom->MakeTube("axisY", Al, 0, 0.1, 5.);
+  TGeoVolume *axisY = geom->MakeTube("axisY", Al, 0, 0.1, axisLen/2);
-  axisY->SetLineColor(1);
+  axisY->SetLineColor(kGreen);
-  worldBox->AddNode(axisY, 1, new TGeoCombiTrans(0, 5, 0., new TGeoRotation("rotB", 0., 90., 0.)));
+  worldBox->AddNode(axisY, 1, new TGeoCombiTrans(0, axisLen/2, 0., new TGeoRotation("rotB", 0., 90., 0.)));
 
-  TGeoVolume *axisZ = geom->MakeTube("axisZ", Al, 0, 0.1, 5.);
+  TGeoVolume *axisZ = geom->MakeTube("axisZ", Al, 0, 0.1, axisLen/2);
-  axisZ->SetLineColor(1);
+  axisZ->SetLineColor(kBlue);
-  worldBox->AddNode(axisZ, 1, new TGeoTranslation(0, 0,  5));
+  worldBox->AddNode(axisZ, 1, new TGeoTranslation(0, 0, axisLen/2));
+
+  //--- axis labels (draw as TPolyMarker3D + text because TGeo does not label directly)
+  TPolyMarker3D *marker = new TPolyMarker3D();
+  marker->SetMarkerSize(1.2);
+  marker->SetMarkerColor(kRed);
+  marker->SetPoint(0, axisLen, 0, 0); // X
+  marker->SetMarkerColor(kGreen);
+  marker->SetPoint(1, 0, axisLen, 0); // Y
+  marker->SetMarkerColor(kBlue);
+  marker->SetPoint(2, 0, 0, axisLen); // Z
+  marker->Draw();
 
   //--- making ANASEN
   const int nWire = 24;
   const int wireShift = 3;
-  const int zLen = 300; //mm
+  const int zLen = 350; //mm
   const int radiusA = 38;
   const int radiusC = 43;
 
@@ -103,8 +115,8 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
                                                        new TGeoRotation("rot1", 360/nSX3 * (i + 0.5), 0., 0.)));
   }
 
-  const int qqqR1 = 10;
+  const int qqqR1 = 50;
-  const int qqqR2 = 50;
+  const int qqqR2 = 100;
   TGeoVolume *qqq = geom->MakeTubs("qqq", Al, qqqR1, qqqR2, 0.5, 5, 85);
   qqq->SetLineColor(7);
   for( int i = 0; i < 4; i++){
@@ -119,3 +131,5 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
   geom->SetVisLevel(4);
   worldBox->Draw("ogle");
 }
+
+

Armory/AnasenMS.dSYM/Contents/Info.plist

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<key>CFBundleIdentifier</key>
+		<string>com.apple.xcode.dsym.AnasenMS</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundlePackageType</key>
+		<string>dSYM</string>
+		<key>CFBundleSignature</key>
+		<string>????</string>
+		<key>CFBundleShortVersionString</key>
+		<string>1.0</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+	</dict>
+</plist>

Armory/AnasenMS.dSYM/Contents/Resources/Relocations/aarch64/AnasenMS.yml

@@ -0,0 +1,5 @@
+---
+triple:          'arm64-apple-darwin'
+binary-path:     AnasenMS
+relocations:     []
+...

Armory/ClassAnasen.h

@@ -15,6 +15,9 @@
 
 #include "ClassSX3.h"
 #include "ClassPW.h"
+#include "ClassQQQ.h"
+
+//to not include certain wires in the simulation, pass the anode and cathode IDs to the constructor, e.g. for anode wires 5-10, pass anodeID1 = 5, anodeID2 = 10, and for cathode wires 20-25, pass cathodeID1 = 20, cathodeID2 = 25. To include all wires, pass -1 for all IDs.
 
 class ANASEN{
 public:
@@ -41,11 +44,15 @@ public:
 
   PW * GetPW() {return pw;}
   SX3 * GetSX3() {return sx3;}
+  QQQ * GetQQQ() {return qqq;}
+  TGeoManager * GetGeoManager() {return geom;}
+  TGeoVolume * GetWorldBox() {return worldBox;}
 
 private:
 
   PW * pw;
   SX3 * sx3;
+  QQQ * qqq;
 
   double sigmaA, sigmaC; // pw
   double sigmaW, sigmaL; // sx3
@@ -73,7 +80,7 @@ inline ANASEN::ANASEN(){
 
   pw = new PW();
   sx3 = new SX3();
-
+  qqq = new QQQ();
   CalGeometry();
 
   geom = nullptr;
@@ -106,17 +113,21 @@ inline void ANASEN::Construct3DModel(int anodeID1, int anodeID2, int cathodeID1,
   geom = new TGeoManager("Detector", "ANASEN");
 
   //--- define some materials
-  TGeoMaterial *matVacuum = new TGeoMaterial("Vacuum", 0,0,0);
+  //TGeoMaterial *matVacuum = new TGeoMaterial("Vacuum", 0,0,0); //name, A, Z, density 
+  TGeoMaterial *matHe = new TGeoMaterial("He", 4.0026, 2, 0.000861);
   TGeoMaterial *matAl = new TGeoMaterial("Al", 26.98,13,2.7);
+  TGeoMaterial *matSi = new TGeoMaterial("Si", 28.085,14,2.33);
   //--- define some media
-  TGeoMedium *Vacuum = new TGeoMedium("Vacuum",1, matVacuum);
+  //TGeoMedium *Vacuum = new TGeoMedium("Vacuum",1, matVacuum); //name, number of materials, material
+  TGeoMedium *He = new TGeoMedium("He",2, matHe);
   TGeoMedium *Al = new TGeoMedium("Root Material",2, matAl);
+  TGeoMedium *Si = new TGeoMedium("Si",3, matSi);
 
   //--- make the top container volume 
   Double_t worldx = 200.; //mm
   Double_t worldy = 200.; //mm
   Double_t worldz = 200.; //mm
-  worldBox = geom->MakeBox("ROOT", Vacuum, worldx, worldy, worldz);
+  worldBox = geom->MakeBox("ROOT", He, worldx, worldy, worldz); // name, medium, x half-length, y half-length, z half-length
   geom->SetTopVolume(worldBox);
 
   //--- making axis
@@ -181,7 +192,7 @@ inline void ANASEN::Construct3DModel(int anodeID1, int anodeID2, int cathodeID1,
                                                     new TGeoRotation("rot1", wirePhi , wireTheta, 0.)));
   }
 
-  TGeoVolume * sx3Det = geom->MakeBox("box", Al, 0.1, sx3->GetWidth()/2, sx3->GetLength()/2);
+  TGeoVolume * sx3Det = geom->MakeBox("box", Si, 0.1, sx3->GetWidth()/2, sx3->GetLength()/2);
   sx3Det->SetLineColor(kGreen+3);
 
   for( int i = 0; i < sx3->GetNumDet(); i++){
@@ -228,6 +239,7 @@ inline  void ANASEN::DrawTrack(TVector3 pos, TVector3 direction, bool drawEstima
 
   pw->FindWireID(pos, direction);
   sx3->FindSX3Pos(pos, direction);
+  qqq->FindQQQPos(pos, direction);
 
   std::pair<short, short> wireID = pw->GetNearestID();
   

Armory/ClassPW.h

@@ -2,17 +2,24 @@
 #define ClassPW_h
 
 #include <cstdio>
+#include <iostream>
 #include <TMath.h>
 #include <TVector3.h>
+#include <TRandom.h>
 
-struct PWHitInfo{
+std::vector<int> skipAnodes = {}; 
+std::vector<int> skipCathodes = {};
+
+struct PWHitInfo
+{
   std::pair<short, short> nearestWire;   // anode, cathode
   std::pair<double, double> nearestDist; // anode, cathode
 
   std::pair<short, short> nextNearestWire;   // anode, cathode
   std::pair<double, double> nextNearestDist; // anode, cathode
 
-  void Clear(){
+  void Clear()
+  {
     nearestWire.first = -1;
     nearestWire.second = -1;
     nearestDist.first = 999999999;
@@ -24,8 +31,21 @@ struct PWHitInfo{
   }
 };
 
+struct Coord
+{
+  float x, y, z;
+  Coord() : x(0), y(0), z(0) {}
+  Coord(const TVector3 &vec)
+  {
+    x = vec.X(); // TVector3's X() returns the x-coordinate
+    y = vec.Y(); // TVector3's Y() returns the y-coordinate
+    z = vec.Z(); // TVector3's Z() returns the z-coordinate
+  }
+};
+
 //! ########################################################
-class PW{ // proportional wire
+class PW
+{ // proportional wire
 public:
   PW() { ClearHitInfo(); };
   ~PW() {};
@@ -36,12 +56,23 @@ public:
   std::pair<short, short> Get2ndNearestID() const { return hitInfo.nextNearestWire; }
   std::pair<double, double> Get2ndNearestDistance() const { return hitInfo.nextNearestDist; }
 
+  std::vector<std::pair<TVector3, TVector3>> An; // the anode wire position vector in space
+  std::vector<std::pair<TVector3, TVector3>> Ca; // the cathode wire position vector in space
+
   TVector3 GetTrackPos() const { return trackPos; }
   TVector3 GetTrackVec() const { return trackVec; }
   double GetTrackTheta() const { return trackVec.Theta(); }
   double GetTrackPhi() const { return trackVec.Phi(); }
   double GetZ0();
 
+  inline std::tuple<std::pair<TVector3, TVector3>, double, double, double>  GetPseudoWire(const std::vector<std::tuple<int,double,double>>& cluster, std::string type);
+
+  inline std::tuple<TVector3,double,double,double,double,double,double,double> 
+  FindCrossoverProperties(const std::vector<std::tuple<int,double,double>>& a_cluster, const std::vector<std::tuple<int,double,double>>& c_cluster);
+
+  inline std::vector<std::vector<std::tuple<int,double,double>>>
+  Make_Clusters(std::unordered_map<int,std::tuple<int,double,double>> wireEvents);
+	
   int GetNumWire() const { return nWire; }
   double GetDeltaAngle() const { return dAngle; }
   double GetAnodeLength() const { return anodeLength; }
@@ -63,11 +94,11 @@ public:
   void ConstructGeo();
   void FindWireID(TVector3 pos, TVector3 direction, bool verbose = false);
   void CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose = false);
-  void CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA = 0, double sigmaC = 0, bool verbose = false);
+  //void CalTrack2(TVector3 sx3Pos, TVector3 anodeInt, bool verbose = false);
+  void CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose);
 
-  double CircularMean(std::vector<std::pair<int, double>> wireList);
+  void Print()
-
+  {
-  void Print(){
     printf("     The nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nearestWire.first,
            hitInfo.nearestDist.first,
            hitInfo.nearestWire.second,
@@ -80,7 +111,6 @@ public:
   }
 
 private:
-
   PWHitInfo hitInfo;
 
   TVector3 trackPos;
@@ -88,7 +118,8 @@ private:
 
   const int nWire = 24;
   const int wireShift = 3;
-  const float zLen = 380; //mm
+  //const float zLen = 380; // mm
+  const float zLen = 348.6; // mm
   const float radiusA = 37;
   const float radiusC = 43;
 
@@ -96,23 +127,25 @@ private:
   double anodeLength;
   double cathodeLength;
 
-  std::vector<std::pair<TVector3,TVector3>> An; // the anode wire position vector in space 
+  // std::vector<std::pair<TVector3, TVector3>> An; // the anode wire position vector in space
-  std::vector<std::pair<TVector3,TVector3>> Ca; // the cathode wire position vector in space 
+  // std::vector<std::pair<TVector3, TVector3>> Ca; // the cathode wire position vector in space
 
-  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2){
+  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2)
+  {
     TVector3 na = a1 - a2;
     TVector3 nb = b1 - b2;
     TVector3 nd = (na.Cross(nb)).Unit();
     return TMath::Abs(nd.Dot(a1 - b2));
   }
-
 };
 
-inline void PW::ClearHitInfo(){
+inline void PW::ClearHitInfo()
+{
   hitInfo.Clear();
 }
 
-inline void PW::ConstructGeo(){
+inline void PW::ConstructGeo()
+{
 
   An.clear();
   Ca.clear();
@@ -124,7 +157,8 @@ inline void PW::ConstructGeo(){
   // anode wire shift is right-hand.
   // cathode wire shift is left-hand.
 
-  for(int i = 0; i < nWire; i++ ){
+  for (int i = 0; i < nWire; i++)
+  {
     // Anode rotate right-hand
     p1.first.SetXYZ(radiusA * TMath::Cos(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
                     radiusA * TMath::Sin(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
@@ -134,38 +168,205 @@ inline void PW::ConstructGeo(){
                      -zLen / 2);
     An.push_back(p1);
 
-    // Cathod rotate left-hand
+    // Cathod rotate left-hand with the 3 wire offset accounted for (+1 from the calculated offset from the PC coincidence spectrum)
-    q1.first.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
+    q1.first.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i + wireShift + 1) + TMath::PiOver2()),
-                    radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
+                    radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i + wireShift + 1) + TMath::PiOver2()),
                     zLen / 2);
-    q1.second.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
+    q1.second.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i + 1) + TMath::PiOver2()),
-                      radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
+                     radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i + 1) + TMath::PiOver2()),
                      -zLen / 2);
     Ca.push_back(q1);
   }
+  // correcting for the fact that the order of the cathode wires is reversed
+  std::reverse(Ca.begin(), Ca.end());
+  // adjusting for the 3 wire offset, the rbegin and rend are used as the rotation of the wires is done in the opposite direction i.e. 1,2,3 -> 3,1,2
+  // NOT NECESSARY ANY MORE, HAS BEEN IMCORPORATED INTO THE WIREOFFSET IN THE BEGINNING
+  // std::rotate(Ca.rbegin(), Ca.rbegin() + 4, Ca.rend());
 
   dAngle = wireShift * TMath::TwoPi() / nWire;
   anodeLength = TMath::Sqrt(zLen * zLen + TMath::Power(2 * radiusA * TMath::Sin(dAngle / 2), 2));
-  cathodeLength = TMath::Sqrt( zLen*zLen + TMath::Power(2* radiusC * TMath::Sin(dAngle/2),2) );
+  cathodeLength = TMath::Sqrt(zLen * zLen + TMath::Power(2 * radiusC * TMath::Sin(dAngle / 2), 2)); //chord length subtending an angle alpha is 2rsin(alpha/2)
 }
 
-inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
+inline std::vector<std::vector<std::tuple<int,double,double>>>
+PW::Make_Clusters(std::unordered_map<int,std::tuple<int,double,double>> wireEvents) {
+   std::vector<std::vector<std::tuple<int,double,double>>> wireClusters;
+   std::vector<std::tuple<int,double,double>> wireCluster;
+	//TODO: Write a macro once, call it twice
+    int wirecount=0;
+	while(wirecount < 24) {
+		if(wireEvents.find(wirecount)==wireEvents.end()) {
+				wirecount++;
+				continue;
+		}
+		wireCluster.clear();
+		int ctr2=wirecount;
+		do {
+			wireCluster.emplace_back(wireEvents[ctr2]);
+			ctr2+=1;
+			if(ctr2==24 || ctr2-wirecount == 7) break; //loose logic, needs to be looked at.
+		} while(wireEvents.find(ctr2)!=wireEvents.end());
+		wireClusters.push_back(std::move(wireCluster));
+		wirecount = ctr2; //we already dealt with wires until the last value of ctr2
+	}
 
+	if(wireClusters.size() > 1) { //Deal with wraparound if required
+		auto first_cluster = wireClusters.front(); //front and back provide references to the elements themselves. less copy, can modify etc
+		auto last_cluster = wireClusters.back();
+		if(std::get<0>(last_cluster.back())==23 && std::get<0>(first_cluster.front())==0) {
+			last_cluster.insert(last_cluster.end(),first_cluster.begin(),first_cluster.end());
+		}
+		wireClusters.erase(wireClusters.begin()); //canonically, erase() needs an iterator, hence begin() not front()
+		//TODO: Can also deal with 'gaps' of missing wires similarly. end of one segment and beginning of another segment will be separated by missing wire --> combine the two
+		//TODO: Also needs some development regarding the time-correlation. Don't put wires in the same cluster if they aren't time coincident
+	}
+	return wireClusters;
+
+  /*if(aClusters.size()>1 || cClusters.size() > 1) {
+  	std::cout << " ============== " << std::endl;
+  }
+  if(aClusters.size()>1 && cClusters.size() >=1) {
+  	std::cout << aClusters.size() << " new anode clusters ----> " << std::endl;
+  	int cc=1;
+  	for(auto ac : aClusters) {
+  		std::cout << "  Cluster " << cc << std::endl;
+	  	double first_ts = std::get<2>(ac.at(0));
+  		for(auto item : ac) {
+	  		std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+  		}
+  		std::cout << "  ------" << std::endl;
+  		cc++;
+  	}
+  } 	
+
+  if(cClusters.size()>=1 ) {
+  	std::cout << cClusters.size() << " new cathode clusters ----> " << std::endl;
+  	int cc=1;
+  	for(auto ac : cClusters) {
+  		std::cout << "  Cluster " << cc << std::endl;
+	  	double first_ts = std::get<2>(ac.at(0));
+  		for(auto item : ac) {
+	  		std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+  		}
+  		std::cout << "  ------" << std::endl;
+  		cc++;
+  	}
+  } 	*/
+}
+
+inline std::tuple<std::pair<TVector3, TVector3>, double, double, double>
+PW::GetPseudoWire(const std::vector<std::tuple<int,double,double>>& cluster, std::string type) {
+	std::pair<TVector3,TVector3> avgvec = std::pair(TVector3(0,0,0),TVector3(0,0,0));
+	double sumEnergy = 0;
+	double maxEnergy = 0;
+	double tsMaxEnergy = 0;
+	if(type=="ANODE") {
+		//if(cluster.size()>1) std::cout << " -------anodes" << std::endl;
+		for( auto wire : cluster) {
+			avgvec.first += std::get<1>(wire)*TVector3(An.at(std::get<0>(wire)).first.X(), An.at(std::get<0>(wire)).first.Y(), 0) ;
+			avgvec.second += std::get<1>(wire)*TVector3(An.at(std::get<0>(wire)).second.X(), An.at(std::get<0>(wire)).second.Y(), 0);
+			sumEnergy += std::get<1>(wire);
+			if(std::get<1>(wire) > maxEnergy) {
+				maxEnergy = std::get<1>(wire);
+				tsMaxEnergy = std::get<2>(wire);
+			}
+			/*if(cluster.size()>1) {
+				std::cout << "\t\t ch:" << std::get<0>(wire) << " " << std::get<1>(wire) << " " << std::get<2>(wire) << std::endl;
+				std::cout << "\t\t w1(r,phi,z):" << An.at(std::get<0>(wire)).first.Perp() << " " << An.at(std::get<0>(wire)).first.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).first.Z() << std::endl;
+				std::cout << "\t\t w2(r,phi,z):" << An.at(std::get<0>(wire)).second.Perp() << " " << An.at(std::get<0>(wire)).second.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).second.Z() << std::endl;			
+			}*/
+		}
+		avgvec.first = avgvec.first*(1.0/sumEnergy);
+		avgvec.second = avgvec.second*(1.0/sumEnergy);
+		double phi1 = avgvec.first.Phi();
+		double phi2 = avgvec.second.Phi();
+		avgvec.first.SetXYZ(radiusA*TMath::Cos(phi1), radiusA*TMath::Sin(phi1), zLen/2);
+		avgvec.second.SetXYZ(radiusA*TMath::Cos(phi2), radiusA*TMath::Sin(phi2), -zLen/2);
+		/*if(cluster.size()>1) {
+			std::cout << "\t\t avg1(r,phi,z):" << avgvec.first.Perp() << " " << avgvec.first.Phi()*180/M_PI << " " << avgvec.first.Z() << std::endl;			
+			std::cout << "\t\t avg2(r,phi,z):" << avgvec.second.Perp() << " " << avgvec.second.Phi()*180/M_PI << " " << avgvec.second.Z() << std::endl;			
+		}*/	
+	} else if(type =="CATHODE") {
+		for( auto wire : cluster) {
+			avgvec.first += std::get<1>(wire)*TVector3(Ca.at(std::get<0>(wire)).first.X(), Ca.at(std::get<0>(wire)).first.Y(), 0) ;
+			avgvec.second += std::get<1>(wire)*TVector3(Ca.at(std::get<0>(wire)).second.X(), Ca.at(std::get<0>(wire)).second.Y(), 0);
+			sumEnergy += std::get<1>(wire);
+			if(std::get<1>(wire) > maxEnergy) {
+				maxEnergy = std::get<1>(wire);
+				tsMaxEnergy = std::get<2>(wire);
+			}
+		}
+		avgvec.first = avgvec.first*(1.0/sumEnergy);
+		avgvec.second = avgvec.second*(1.0/sumEnergy);
+		double phi1 = avgvec.first.Phi();
+		double phi2 = avgvec.second.Phi();
+		avgvec.first.SetXYZ(radiusC*TMath::Cos(phi1), radiusC*TMath::Sin(phi1), zLen/2);
+		avgvec.second.SetXYZ(radiusC*TMath::Cos(phi2), radiusC*TMath::Sin(phi2), -zLen/2);	
+	}
+	return std::tuple(avgvec, sumEnergy, maxEnergy, tsMaxEnergy); 
+}
+
+inline std::tuple<TVector3,double,double,double,double,double,double,double> PW::FindCrossoverProperties(const std::vector<std::tuple<int,double,double>>& a_cluster,
+																				 const std::vector<std::tuple<int,double,double>>& c_cluster) {
+	//std::pair<TVector3, TVector3> apwire = GetPseudoWire(a_cluster,"ANODE",anodeSumE);
+	//std::pair<TVector3, TVector3> cpwire = GetPseudoWire(c_cluster,"CATHODE",cathodeSumE);
+	auto [apwire, apSumE, apMaxE, apTSMaxE] = GetPseudoWire(a_cluster,"ANODE");
+	auto [cpwire, cpSumE, cpMaxE, cpTSMaxE] = GetPseudoWire(c_cluster,"CATHODE");
+
+	TVector3 crossover;
+	crossover.Clear();
+  	TVector3 a, c, diff;
+  	double a2, ac, c2, adiff, cdiff, denom, alpha=0;
+
+	if(apSumE && cpSumE) {
+    	a = apwire.first - apwire.second;
+		c = cpwire.first - cpwire.second;
+      	diff = apwire.first - cpwire.first;
+      	a2 = a.Dot(a);
+      	c2 = c.Dot(c);
+      	ac = a.Dot(c);
+      	adiff = a.Dot(diff);
+      	cdiff = c.Dot(diff);
+      	denom = a2 * c2 - ac * ac;
+      	alpha = (ac * cdiff - c2 * adiff) / denom;
+		crossover = apwire.first + alpha*a;		
+		if(crossover.z() < -190 || crossover.Z() > 190 ) {
+			alpha = 9999999;
+			apSumE=-1; cpSumE=-1;
+			apMaxE=-1; cpMaxE=-1;
+			apTSMaxE=-1; cpTSMaxE=-1;
+		}
+	}
+	//std::cout << apSumE << " " << cpSumE << " " << " " <<  crossover.Perp() << std::endl;
+	return std::tuple(crossover,alpha,apSumE,cpSumE,apMaxE,cpMaxE,apTSMaxE,cpTSMaxE);
+}
+
+inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose)
+{
+//to skip certain wires, add their IDs to the skipAnodes and skipCathodes vectors above, then in this function, add a check to set the distance to a large number if the wire ID is in the skip list, e.g. if(std::find(skipAnodes.begin(), skipAnodes.end(), i) != skipAnodes.end()) { disA = 99999999; } to skip anode wire i, and if(std::find(skipCathodes.begin(), skipCathodes.end(), i) != skipCathodes.end()) { disC = 99999999; } to skip cathode wire i.
+//do this on the line before the line "if (phiS < phi && phi < phiL)" in the anode and cathode loops below, respectively, so that the wires will be marked as invalid and not used in track reconstruction
   hitInfo.Clear();
   double phi = direction.Phi();
 
-  for( int i = 0; i < nWire; i++){
+  for (int i = 0; i < nWire; i++)
+  {
 
     double disA = 99999999;
     double phiS = An[i].first.Phi() - TMath::PiOver4();
     double phiL = An[i].second.Phi() + TMath::PiOver4();
     // printf("A%2d: %f %f | %f\n", i, phiS * TMath::RadToDeg(), phiL * TMath::RadToDeg(), phi * TMath::RadToDeg());
-    if( phi > 0 && phiS > phiL )  phiL = phiL + TMath::TwoPi();
+    if (phi > 0 && phiS > phiL)
-    if( phi < 0 && phiS > phiL )  phiS = phiS - TMath::TwoPi();
+      phiL = phiL + TMath::TwoPi();
-
+    if (phi < 0 && phiS > phiL)
-    if( phiS < phi && phi < phiL) {
+      phiS = phiS - TMath::TwoPi();
+    if(std::find(skipAnodes.begin(), skipAnodes.end(), i) != skipAnodes.end()) { // check if the current anode wire ID is in the skipAnodes vector
+      disA = 99999999;
+    }
+    if (phiS < phi && phi < phiL) // check if the track direction is within the angular range of the wire
+    {
       disA = Distance(pos, pos + direction, An[i].first, An[i].second);
-      if( disA < hitInfo.nearestDist.first ){
+      if (disA < hitInfo.nearestDist.first)
+      {
         hitInfo.nearestDist.first = disA;
         hitInfo.nearestWire.first = i;
       }
@@ -175,53 +376,73 @@ inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
     phiS = Ca[i].second.Phi() - TMath::PiOver4();
     phiL = Ca[i].first.Phi() + TMath::PiOver4();
     // printf("C%2d: %f %f\n", i, phiS * TMath::RadToDeg(), phiL * TMath::RadToDeg());
-    if( phi > 0 && phiS > phiL ) phiL = phiL + TMath::TwoPi();
+    if(std::find(skipCathodes.begin(), skipCathodes.end(), i) != skipCathodes.end()) { // check if the current cathode wire ID is in the skipCathodes vector
-    if( phi < 0 && phiS > phiL ) phiS = phiS - TMath::TwoPi();
+      disC = 99999999;
+    }
+    if (phi > 0 && phiS > phiL)
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();
 
-    if(phiS < phi && phi < phiL) {
+    if (phiS < phi && phi < phiL)
+    {
       disC = Distance(pos, pos + direction, Ca[i].first, Ca[i].second);
-      if( disC < hitInfo.nearestDist.second ){
+      if (disC < hitInfo.nearestDist.second)
+      {
         hitInfo.nearestDist.second = disC;
         hitInfo.nearestWire.second = i;
       }
     }
 
-    if(verbose) printf(" %2d | %8.2f, %8.2f\n", i, disA, disC);
+    if (verbose)
+      printf(" %2d | %8.2f, %8.2f\n", i, disA, disC);
   }
 
   //==== find the 2nd nearest wire
   short anode1 = hitInfo.nearestWire.first;
-  short aaa1 = anode1 - 1; if( aaa1 < 0 ) aaa1 += nWire;
+  short aaa1 = anode1 - 1;
+  if (aaa1 < 0)
+    aaa1 += nWire;
   short aaa2 = (anode1 + 1) % nWire;
 
   double haha1 = Distance(pos, pos + direction, An[aaa1].first, An[aaa1].second);
   double haha2 = Distance(pos, pos + direction, An[aaa2].first, An[aaa2].second);
-  if( haha1 < haha2){
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.first = aaa1;
     hitInfo.nextNearestDist.first = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.first = aaa2;
     hitInfo.nextNearestDist.first = haha2;
   }
 
   short cathode1 = hitInfo.nearestWire.second;
-  short ccc1 = cathode1 - 1; if( ccc1 < 0 ) ccc1 += nWire;
+  short ccc1 = cathode1 - 1;
+  if (ccc1 < 0)
+    ccc1 += nWire;
   short ccc2 = (cathode1 + 1) % nWire;
 
   haha1 = Distance(pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
   haha2 = Distance(pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
-  if( haha1 < haha2){
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.second = ccc1;
     hitInfo.nextNearestDist.second = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.second = ccc2;
     hitInfo.nextNearestDist.second = haha2;
   }
 
-  if( verbose ) Print();
+  if (verbose)
+    Print();
 }
 
-inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose){
+inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose)
+{
 
   trackPos = sx3Pos;
 
@@ -231,11 +452,13 @@ inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbo
   // if the handiness of anode and cathode revered, it should be n2 cross n1
   trackVec = (n2.Cross(n1)).Unit();
 
-  if( verbose ) printf("Theta, Phi = %f, %f \n", trackVec.Theta() *TMath::RadToDeg(), trackVec.Phi()*TMath::RadToDeg()); 
+  if (verbose)
-
+    printf("Theta, Phi = %f, %f \n", trackVec.Theta() * TMath::RadToDeg(), trackVec.Phi() * TMath::RadToDeg());
 }
 
-inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose){
+
+inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, double sigmaC, bool verbose)
+{
 
   trackPos = sx3Pos;
 
@@ -267,36 +490,31 @@ inline void PW::CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA, dou
   // if the handiness of anode and cathode revered, it should be n2 cross n1
   trackVec = (n2.Cross(n1)).Unit();
 
-  if( verbose ) printf("Theta, Phi = %f, %f \n", trackVec.Theta() *TMath::RadToDeg(), trackVec.Phi()*TMath::RadToDeg()); 
+  if (verbose)
-
+    printf("Theta, Phi = %f, %f \n", trackVec.Theta() * TMath::RadToDeg(), trackVec.Phi() * TMath::RadToDeg());
 }
 
-inline double PW::GetZ0(){
+/*inline TVector3 PW::CalTrack3(TVector3 siPos, TVector3 anodeInt, bool verbose)
+{
 
-  double x = trackPos.X();
+  TVector3 v = anodeInt-siPos;
-  double y = trackPos.Y();
+  double t_minimum = -1.0*(siPos.X()*v.X()+siPos.Y()*v.Y())/(v.X()*v.X()+v.Y()*v.Y());
-  double rho = TMath::Sqrt(x*x + y*y);
+  TVector3 vector_closest_to_z = siPos + t_minimum*v;
-  double theta = trackVec.Theta();
 
-  return trackPos.Z() - rho / TMath::Tan(theta);
+  return vector_closest_to_z;
+  if (verbose)
+    printf("X slope = %f and Y slope = %f \n", mx, my);
+}*/
 
-}
+inline double PW::GetZ0()
+{
 
-inline double PW::CircularMean(std::vector<std::pair<int, double>> wireList){
+  [[maybe_unused]]double x = trackPos.X();
-
+  [[maybe_unused]]double y = trackPos.Y();
-  //use unit vector, wireID start from Zero
+  [[maybe_unused]]double rho = TMath::Sqrt(x * x + y * y);
-  double xCom = 0, yCom = 0;
+  [[maybe_unused]]double theta = trackVec.Theta();
-  for( size_t i = 0; i < wireList.size() ; i++){
-    xCom += TMath::Cos(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
-    yCom += TMath::Sin(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
-  }
-
-  //calculate the angle of the summed unit vectors
-  double angle = TMath::ATan2(yCom, xCom);
-  if( angle < 0 ) angle += TMath::TwoPi(); // convert the angle from 0 to 2 pi
-
-  return angle/ TMath::TwoPi() * nWire;
 
+  return trackVec.Z();
 }
 
 #endif

Armory/ClassQQQ.h

@@ -0,0 +1,288 @@
+#ifndef ClassQQQ_h
+#define ClassQQQ_h
+
+#include <cstdio>
+#include <TMath.h>
+#include <TVector3.h>
+#include <TRandom.h>
+#include "TGeoManager.h"
+#include "TGeoVolume.h"
+#include "TGeoBBox.h"
+
+class QQQ{
+public:
+  QQQ(){Clear();};
+  ~QQQ(){}
+  
+  short GetID() const {return id;}
+  short GetChUp() const {return chUp;}
+  short GetChDn() const {return chDn;}
+  short GetChBk() const {return chBk;}
+
+  TVector3 GetHitPos() const {return hitPos;}
+  TVector3 GetHitPosWithSigma(double sigmaY_mm, double sigmaZ_mm);
+
+  double GetZFrac() const {return zFrac;} // range from -0.5 to 0.5
+
+  void Clear();
+  void ConstructGeo();
+  void FindQQQPos(TVector3 pos, TVector3 direction, bool verbose = false);
+  void CalQQQPos(unsigned short ID, unsigned short chUp, unsigned short chDown, unsigned short chBack, float eUp, float eDown);
+
+  double GetNumDet() const {return numDet;}
+
+  void Print(){ 
+    if( id == -1 ){
+      printf("Did not hit any QQQ.\n"); 
+    }else{
+      printf("ID: %d, U,D,B: %d %d %d| zFrac : %.2f\n", id, chUp, chDn, chBk, zFrac); 
+      printf("Hit Pos: %.2f, %.2f, %.2f\n", hitPos.X(), hitPos.Y(), hitPos.Z()); 
+    }
+  }
+
+  // void CalZFrac(){
+  //   zFrac = (eUp - eDn)/(eUp + eDn); 
+  // }
+
+private:
+
+  const int numDet = 4;
+  const float qqqR1 = 50;
+  const float qqqR2 = 100;
+  const float qqqZPos = 23 + 75 + 30;
+
+  short id; // -1 when no hit
+  short chUp;
+  short chDn;
+  short chBk;
+
+  double zFrac; // from +1 (downstream) to -1 (upstream)
+
+  double eUp;
+  double eDn;
+  double eBk;
+
+  TVector3 hitPos;
+
+  TGeoManager *geom;
+  TGeoVolume *worldBox;
+  TGeoMedium *Al;
+
+  // helper function to calculate intersection between line segments, return pair of (fraction along line1, fraction along line2) where the intersection occurs. If no intersection, return (0, -1).
+  std::pair<double, double> Intersect(TVector3 p1, TVector3 p2, TVector3 q1, TVector3 q2, bool verbose){ 
+
+    //see https://nukephysik101.wordpress.com/2023/12/30/intersect-between-2-line-segments/
+    //zero all z-component
+    TVector3 a0 = p1; a0.SetZ(0);
+    TVector3 a1 = p2; a1.SetZ(0);
+
+    TVector3 b0 = q1; b0.SetZ(0);
+    TVector3 b1 = q2; b1.SetZ(0);
+
+    double h = 0, k = 0; // placeholder values, implementation of intersection logic
+    if( verbose ) printf(" ----h, k : %f, %f\n", h, k);
+
+    return std::pair<double,double>(h,k);
+  }
+
+};
+
+inline void QQQ::Clear(){
+  id = -1;
+  chUp = -1;
+  chDn = -1;
+  chBk = -1;
+  zFrac = TMath::QuietNaN();
+
+  eUp = TMath::QuietNaN();
+  eDn = TMath::QuietNaN();
+  eBk = TMath::QuietNaN();
+}
+
+inline void QQQ::ConstructGeo(){
+  TGeoVolume *qqq = geom->MakeTubs("qqq", Al, qqqR1, qqqR2, 0.5, 5, 85);
+  qqq->SetLineColor(7);
+  for( int i = 0; i < 4; i++){
+    worldBox->AddNode(qqq, i+1, new TGeoCombiTrans( 0, 
+                                                    0, 
+                                                    qqqZPos, 
+                                                    new TGeoRotation("rot1", 360/4 * (i), 0., 0.)));
+  }
+}
+
+
+inline void QQQ::FindQQQPos(TVector3 pos,
+                            TVector3 direction,
+                            bool verbose){
+
+  id   = -1;
+  chUp = -1;
+  chDn = -1;
+  chBk = -1;
+
+  //--------------------------------------------
+  // Intersect trajectory with QQQ plane
+  //--------------------------------------------
+
+  if( TMath::Abs(direction.Z()) < 1e-10 ) return;
+
+  double t = (qqqZPos - pos.Z()) / direction.Z();
+
+  if( t <= 0 ) return;
+
+  hitPos = pos + t * direction;
+
+  //--------------------------------------------
+  // Cylindrical coordinates
+  //--------------------------------------------
+
+  double x = hitPos.X();
+  double y = hitPos.Y();
+
+  double r = TMath::Sqrt(x*x + y*y);
+
+  if( r < qqqR1 || r > qqqR2 ) return;
+
+  double phi = hitPos.Phi() * TMath::RadToDeg();
+
+  if( phi < 0 ) phi += 360.0;
+
+  //--------------------------------------------
+  // Determine detector ID
+  //--------------------------------------------
+
+  id = -1;
+
+  for(int det = 0; det < 4; det++){
+
+    double phiMin = det*90.0 + 5.0;
+    double phiMax = phiMin + 85.0;
+
+    if( phi >= phiMin && phi <= phiMax ){
+      id = det;
+      break;
+    }
+  }
+
+  if( id < 0 ) return;
+
+  //--------------------------------------------
+  // Ring number (32 strips)
+  //--------------------------------------------
+
+  const double ringWidth =
+      (qqqR2 - qqqR1)/32.0;
+
+  int ring =
+      (int)((r - qqqR1)/ringWidth);
+
+  if( ring < 0 ) ring = 0;
+  if( ring > 31 ) ring = 31;
+
+  //--------------------------------------------
+  // Sector number (4 strips)
+  //--------------------------------------------
+
+  double localPhi =
+      phi - (id*90.0 + 5.0);
+
+  int sector =
+      (int)(localPhi/(85.0/4.0));
+
+  if( sector < 0 ) sector = 0;
+  if( sector > 3 ) sector = 3;
+
+  chBk = ring;
+  chDn = sector;
+  chUp = sector;
+
+  zFrac = 0.0;
+
+  if(verbose){
+
+    printf("\nQQQ Hit\n");
+    printf(" ID     = %d\n", id);
+    printf(" Ring   = %d\n", ring);
+    printf(" Sector = %d\n", sector);
+    printf(" r      = %.2f mm\n", r);
+    printf(" phi    = %.2f deg\n", phi);
+
+    hitPos.Print();
+  }
+}
+/*s
+inline TVector3 QQQ::GetHitPosWithSigma(double sigmaY_mm, double sigmaZ_mm){
+
+  double phi = SNorml[id%numDet].Phi();
+
+  TVector3 haha = hitPos;
+  haha.RotateZ(-phi);
+
+  double y = haha.Y() + gRandom->Gaus(0, sigmaY_mm);
+  if( sigmaY_mm < 0 ){
+    double deltaW = width/4;
+    y = TMath::Floor((haha.Y()-deltaW)/deltaW)*deltaW + deltaW*1.5; // when ever land on each strip, set the position to be center of the strip.
+    if( y >= 25 ) y = 15;
+  }
+
+  double z = haha.Z() + gRandom->Gaus(0, sigmaZ_mm);
+  if( sigmaZ_mm < 0 ){
+    haha.Z();
+    double delta = length/4;
+    int sign = z > 0 ? 1 : -1;
+    z = TMath::Floor( (abs(z)-gap/2)/delta )*delta + 0.5 * delta + gap/2;
+    if( z >= 107.375 ) z = 88.625;
+    z = sign * z;
+  }
+
+  haha.SetY(y);
+  haha.SetZ(z);
+  haha.RotateZ(phi);
+
+  return haha;
+
+}*/
+
+
+inline void QQQ::CalQQQPos(unsigned short ID,
+                           unsigned short chUp,
+                           unsigned short chDown,
+                           unsigned short chBack,
+                           float eUp,
+                           float eDown){
+
+  hitPos.Clear();
+
+  if( ID > 3 ) return;
+  if( chBack > 31 ) return;
+  if( chDown > 3 ) return;
+
+  const double ringWidth =
+      (qqqR2 - qqqR1)/32.0;
+
+  double r =
+      qqqR1 + (chBack + 0.5)*ringWidth;
+
+  const double sectorWidth =
+      85.0/4.0;
+
+  double phiDeg =
+      ID*90.0 + 5.0 +
+      (chDown + 0.5)*sectorWidth;
+
+  double phi =
+      phiDeg * TMath::DegToRad();
+
+  hitPos.SetXYZ(
+      r*TMath::Cos(phi),
+      r*TMath::Sin(phi),
+      qqqZPos
+  );
+
+  id   = ID;
+  chBk = chBack;
+  chDn = chDown;
+  chUp = chUp;
+}
+
+#endif 

Armory/ClassSX3.h

@@ -57,8 +57,8 @@ private:
   const int numDet = 12;
   const float radius = 88;
   const float width = 40;
-  const float length = 75;
+  const float length = 75; // 75
-  const float gap = 46;
+  const float gap = 46; // 46
 
   short id; // -1 when no hit
   short chUp;

Armory/ClassTransfer.h

@@ -16,7 +16,6 @@
 #include "Isotope.h"
 
 class ReactionConfig{
-
 public:
 
   ReactionConfig(){}
@@ -47,9 +46,9 @@ public:
   std::vector<float> beamEx;        ///excitation_energy_of_A[MeV]
 
 
-  void SetReaction(int beamA, int beamZ,
+  void SetReaction(int beamA, int beamZ, // projectile
-                   int targetA, int targetZ,
+                   int targetA, int targetZ, // target
-                   int recoilA, int recoilZ, float beamEnergy_AMeV){
+                   int recoilA, int recoilZ, float beamEnergy_AMeV){ // light recoil, e.g. alpha
     this->beamA = beamA;
     this->beamZ = beamZ;
     this->targetA = targetA;
@@ -176,10 +175,10 @@ public:
   void SetA(int A, int Z, double Ex);
   void Seta(int A, int Z);
   void Setb(int A, int Z);
-  void SetB(int A, int Z);
+  void SetB(int A, int Z, double Ex);
   void SetIncidentEnergyAngle(double KEA, double theta, double phi);
-  void SetExA(double Ex);
+  void SetExA(double Ex); // excitation energy of A in MeV
-  void SetExB(double Ex);
+  void SetExB(double Ex); // excitation energy of B in MeV
   void SetReactionFromFile(string settingFile);
   
   TString GetReactionName();
@@ -246,8 +245,8 @@ TransferReaction::TransferReaction(){
    SetA(24, 12, 0);
    Seta(4,2);
    Setb(1,1);
-   SetB(27,13);
+   SetB(27,13, 0);
-   TA = 2.5;
+   TA = 2.5; // MeV/u
    T = TA * reaction.beamA;
    
    ExA = 0;
@@ -301,17 +300,19 @@ void TransferReaction::Setb(int A, int Z){
   isReady = false;
   isBSet = false;
 }
-void TransferReaction::SetB(int A, int Z){
+void TransferReaction::SetB(int A, int Z, double Ex = 0){
   Isotope temp (A, Z);
-  mB = temp.Mass;
+  double mB0 = temp.Mass;     // ground state mass
+  mB  = mB0;
   reaction.recoilHeavyA = A;
   reaction.recoilHeavyZ = Z;
   nameB = temp.Name;
+  ExB = Ex;
   isReady = false;
   isBSet = true;
 }
 
-void TransferReaction::SetIncidentEnergyAngle(double KEA, double theta, double phi){
+void TransferReaction::SetIncidentEnergyAngle(double KEA, double theta, double phi){ // KEA in MeV/u, theta and phi in degree
   this->TA = KEA;
   this->T = TA * reaction.beamA;
   this->thetaIN = theta;
@@ -390,7 +391,8 @@ void TransferReaction::CalReactionConstant(){
    beta = k / (mA + ExA + ma + T);
    gamma = 1 / TMath::Sqrt(1- beta * beta);   
    Etot = TMath::Sqrt(TMath::Power(mA + ExA + ma + T,2) - k * k);
-   p = TMath::Sqrt( (Etot*Etot - TMath::Power(mb + mB + ExB,2)) * (Etot*Etot - TMath::Power(mb - mB - ExB,2)) ) / 2 / Etot;
+   double mBtot = mB + ExB;
+   p = TMath::Sqrt( (Etot*Etot - TMath::Power(mb + mBtot,2)) * (Etot*Etot - TMath::Power(mb - mBtot,2)) ) / 2 / Etot;
    
    PA.SetXYZM(0, 0, k, mA + ExA);
    PA.RotateY(thetaIN);

Armory/HistPlotter.h

@@ -0,0 +1,414 @@
+#ifndef HISTPLOTTER_H
+#define HISTPLOTTER_H
+#include <TCanvas.h>
+#include <TROOT.h>
+#include <TSystem.h>
+#include <TStyle.h>
+#include <iostream>
+#include <TFile.h>
+#include <TMemFile.h>
+#include <TH1.h>
+#include <TH2.h>
+#include <TCutG.h>
+#include <signal.h>
+#include <cstdlib>
+#include <utility>
+#include <fstream>
+#include <sstream>
+#include <unordered_map>
+#include <set>
+#include <TGraphErrors.h>
+
+class HistPlotter {
+private:
+    long long barrier_count, barrier_limit; //meant to keep track of how often to call FillN() on histograms
+    enum {TFILE, TMEMFILE} filetype;
+    std::unordered_map<std::string,TObject*> oMap; //!< Maps std::string to all TH1, TH2 objects in the class
+    std::unordered_map<std::string,TObject*> cutsMap; //!< Maps std::string to TCutG objects held by the class
+    std::set<std::string> folderList; //!< List of all folder names used to nest objects
+    std::unordered_map<TObject*,std::string> foldersForObjects; //!< Map that returns the folder corresponding to the object whose pointer is specified
+    TFile *ofile=nullptr; //!< TFile pointer for the output file
+    TMemFile *omfile=nullptr; //!< TFile pointer for the output memfile
+
+    //Caches to permit FillN() calls
+    std::unordered_map<std::string, std::vector<double>> onedimcache;
+    std::unordered_map<std::string, std::pair<std::vector<double>, std::vector<double>>> twodimcache;
+    inline void FillN_All_Histograms();
+public:
+    HistPlotter(std::string outfile, std::string type);
+    inline void FlushToDisk(); //!< Writes all objects to file before closing, nesting objects in folders as is found necessary
+    inline void PrintObjects(); //!< Dump objects to std::cout for inspection
+    inline void ReadCuts(std::string); 
+    inline TCutG* FindCut(std::string cut) {
+        return static_cast<TCutG*>(cutsMap.at(cut));
+    }
+    inline void set_barrier_limit(long long limit) { barrier_limit = limit; }
+    inline void barrier_increment() {
+        barrier_count++;
+        if(barrier_count == barrier_limit) {
+            FillN_All_Histograms();
+            barrier_count=0;
+        }
+    }
+    /*! \fn void FindCut()
+        \brief        
+            - Searches for a cut by name 'cut' in the internal list of cuts 'cutsMap'. Ugly fails (via unresolved at()) if such a cut isn't found.            
+        \param filename - name of the plainxtext file containing the cut file locations and identifiers
+        \return Pointer to the TCutG object that matches the name. Very useful to use this as plotter.FindCut("protonbarrelpid")->IsInside(deltaE, E) for instance.
+    */
+
+    inline void SetNewTitle(std::string name, std::string title) {
+        auto result = oMap.find(name); //result is an iterator
+        if(result==oMap.end()) return; //no warnings, could be changed in future
+        else
+        	static_cast<TNamed*>(oMap.at(name))->SetTitle(title.c_str()); // set new title
+	}
+
+    //Smart functions that create a new histogram if it doesn't exist.
+    inline void FillGraph(const std::string &name, float valuex, float valuey, float errx=0, float erry=0);
+    inline void Fill1D(const std::string& name,int nbinsx, float xlow, float xhigh, float value);
+    inline void Fill2D(const std::string& name,int nbinsx, float xlow, float xhigh
+                ,int nbinsy, float ylow, float yhigh, float valuex, float valuey);
+    inline void Fill1D(const std::string& name,int nbinsx, float xlow, float xhigh, float value, const std::string& folder);
+    inline void Fill2D(const std::string& name,int nbinsx, float xlow, float xhigh
+                ,int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string& folder);
+    //TObject* findObject(std::string key);
+};
+
+HistPlotter::HistPlotter(std::string outfile, std::string type="") {
+    /*!
+        \brief Constructor. Opens a TFile instance with the specified filename
+        \param outfile : std::string that holds the desired output ROOT filename
+        \return None
+    */
+    if(type=="" || type == "TFILE") {
+        ofile = new TFile(outfile.c_str(),"recreate");
+        filetype = TFILE;
+    } else if(type =="TMEMFILE") {
+        omfile = new TMemFile(outfile.c_str(),"recreate");
+        filetype=TMEMFILE;
+    } else {
+        std::cout << "Unknown type "<< type << " specified for HistPlotter (use \"TFILE\" or \"TMEMFILE\"), using default \"TFILE\"  " << std::endl;
+        ofile = new TFile(outfile.c_str(),"recreate");
+        filetype = TFILE;
+    }
+    barrier_count=0;
+    barrier_limit=1000;
+}
+
+void HistPlotter::FillN_All_Histograms() {
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        //it->first is std::string 'name', it->second is the TObject
+        if(it->second->InheritsFrom("TH1F")) {
+            //FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size)
+            static_cast<TH1F*>(it->second)->FillN(onedimcache[it->first].size(), //size
+                                                  onedimcache[it->first].data(), //array
+                                                  std::vector<double>(onedimcache[it->first].size(),1.0).data()); //weight of ones
+            onedimcache[it->first].clear();
+        }  else if(it->second->InheritsFrom("TH2F")) {
+            //FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size))
+            static_cast<TH2F*>(it->second)->FillN(twodimcache[it->first].first.size(), //size
+                                                  twodimcache[it->first].first.data(), //x array
+                                                  twodimcache[it->first].second.data(), //y array
+                                                  std::vector<double>(twodimcache[it->first].first.size(),1.0).data()); //weight of ones
+           twodimcache[it->first].first.clear();
+           twodimcache[it->first].second.clear();
+        }
+    }
+    std::cout << "." << std::endl;
+}
+void HistPlotter::FlushToDisk() {
+    /*! \fn void FlushToDisk()
+        \brief         Function that can be used at any point to exit smoothly by saving all ROOT objects in memory
+        to the output file before closing it. Obeys the binding of histograms to separate folders, if so specified.
+        \return No return -- void
+    */
+    if(filetype==TMEMFILE && omfile) {
+        std::cout << "Not flushing a TMemfile .. exiting .." << std::endl;
+        delete omfile;
+        return;
+    }
+    if(ofile->IsZombie() || !ofile) {
+        std::cerr << "Output file is zombie, finishing up without writing to disk!" << std::endl;
+        return;
+    }
+    FillN_All_Histograms();
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        //omap maps: name(first) to object address(second).
+        // foldersForObjects maps: object address(first) to foldername(second)
+        auto result = foldersForObjects.find(it->second); //returns <TObject* histogram,std::string foldername> pair if found
+        if(result!=foldersForObjects.end()) { //we try to create folder if needed and cd to it
+            ofile->mkdir(result->second.c_str(),"",kTRUE); // args: name, title, returnExistingDirectory
+            ofile->cd(result->second.c_str());
+        } else {
+            ofile->cd(); //toplevel for all default histograms. Default setting
+        }
+        it->second->Write();
+    }
+
+    //Create a directory for all cuts, and save all cuts in them
+    ofile->mkdir("gCUTS","",kTRUE);
+    ofile->cd("gCUTS");
+    for(auto it=cutsMap.begin(); it!=cutsMap.end(); it++) {
+        (static_cast<TNamed*>(it->second))->SetName(it->first.c_str());
+        it->second->Write();
+    }
+    ofile->Close();
+    std::cout << "Wrote " << oMap.size() << " histograms to TFile " << std::string(ofile->GetName()) << std::endl;
+}
+
+void HistPlotter::FillGraph(const std::string& name, float valuex, float valuey, float errx, float erry) {
+    /*! \fn void FillGraph()
+        \brief
+        - Creates a TGraphError in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TGraph*
+
+        \param name name of the TGraph
+        \param valuex The xvalue
+        \param valuey The yvalue
+        \param errx The x error
+        \param erry The y error
+        \return No return void
+    */
+    auto result = oMap.find(name); 
+    if(result==oMap.end()) {
+        TGraphErrors *tempG = new TGraphErrors();
+        tempG->SetName(name.c_str());
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(tempG)));
+    }
+    if(!oMap.at(name)->InheritsFrom("TGraphErrors")) {
+        std::cerr << "Object " << name << " refers to something other than a TGraph*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    // static_cast<TGraphErrors*>(oMap.at(name))->AddPointError(valuex,valuey,errx,erry);
+}
+
+void HistPlotter::Fill1D(const std::string& name, int nbinsx, float xlow, float xhigh, float value) {
+    /*! \fn void Fill1D()
+        \brief  
+        - Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \return No return void
+    */
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH1F* temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+    } else if(foldersForObjects.find(oMap.at(name))!=foldersForObjects.end()) { //shouldn't have a folder associated with it
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH1F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    //static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill1D(const std::string& name, int nbinsx, float xlow, float xhigh, float value, const std::string& foldername) {
+    /*! \fn void Fill1D()
+        \brief        
+      -  Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not, defaults to toplevel.
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH1F* temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+        if(foldername!="") {
+            if(folderList.find(foldername)==folderList.end()) {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject*>(temp1D),foldername));
+        }
+    } else {
+        //object is present in map, but we enforce unique names
+        //it must already have a folder attached to it
+        if(foldersForObjects.find(oMap.at(name))==foldersForObjects.end()) {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        } else if(foldersForObjects[oMap[name]]!=foldername) {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH1F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    //static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill2D(const std::string& name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey) {
+    /*! \fn void Fill2D()
+        \brief        
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH2F* temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(),std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+    } else if(foldersForObjects.find(oMap.at(name))!=foldersForObjects.end()) { //shouldn't have a folder associated with it
+        std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH2F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    //static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::Fill2D(const std::string& name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string& foldername) {
+    /*! \fn void Fill2D()
+        \brief        
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not defaults to toplevel
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); //result is an iterator
+    if(result==oMap.end()) {
+        TH2F* temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name,static_cast<TObject*>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(),std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+        if(foldername!="") {
+            if(folderList.find(foldername)==folderList.end()) {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject*>(temp2D),foldername));
+        }
+    } else {
+        //object is present in map, but we enforce unique names
+        //it must already have a folder attached to it
+        if(foldersForObjects.find(oMap.at(name))==foldersForObjects.end()) {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        } else if(foldersForObjects[oMap.at(name)]!=foldername) {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] <<  ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+
+    //Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if(!oMap.at(name)->InheritsFrom("TH2F")) {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    //static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::ReadCuts(std::string filename) {
+    /*! \fn void ReadCuts()
+        \brief  Reads a list of cuts from a file. The file must have the format below, two columns
+                   - Column#1 - path to a file that contains a single TCutG object named "CUTG", the default name in ROOT.
+                   - Column#2 - The identifier name you plan to use in the code, like 'protonbarrelpid' or something, that will be searched by FindCut()
+        \param filename name of the plainxtext file containing the cut file locations and identifiers
+        \return No return -- void
+    */
+
+    std::ifstream infile;
+    infile.open(filename);
+    std::string cutfilename, cutname;
+    for(std::string line; std::getline(infile, line); ) {
+        if(line.size()!=0 && line[0]=='#')
+            ; //don't do anything with '#' lines
+        else {
+            std::stringstream ss(line);
+            ss>>cutfilename>>cutname;
+
+            TFile f(cutfilename.c_str());
+            if(f.IsZombie()) {
+                std::cerr << "Cannot open cutfile " << cutfilename << " .. skipping.." << std::endl;
+                continue;
+            }
+            TCutG *cut = (TCutG*)(f.Get("CUTG"));
+            cutsMap.insert(std::make_pair(cutname,static_cast<TObject*>(cut)));
+            f.Close();
+        } //else
+    }//for loop
+    infile.close();
+}
+
+void HistPlotter::PrintObjects() {
+    /*
+        void PrintObjects()
+        Prints the contents of the unordered_maps oMap and cutsMap to facilitate debugging
+
+    */
+    std::cout << "Type | Name " << std::endl;
+    std::cout << "---- | --------------------- " << std::endl;
+    for(auto it=oMap.begin(); it!=oMap.end(); it++ ) {
+        std::cout << it->second->ClassName() << " | "<< it->first << std::endl;
+    }
+    for(auto it=cutsMap.begin(); it!=cutsMap.end(); it++ ) {
+        std::cout << it->second->ClassName() << " | "<< it->first << std::endl;
+    }
+    std::cout << "---- | --------------------- " << std::endl;
+}
+
+#endif

Armory/Hit.h

@@ -0,0 +1,52 @@
+#ifndef Hit_H
+#define Hit_H
+
+#include <vector>
+
+class Hit{
+public:
+  unsigned short sn;
+  uint8_t ch;
+  unsigned short energy;
+  unsigned short energy2;
+  unsigned long long timestamp;
+  unsigned short fineTime;
+  bool pileUp;
+
+  unsigned short traceLength;
+  std::vector<short> trace;
+
+  Hit(){
+    Clear();
+  }
+
+  void Clear(){
+    sn = 0;
+    ch = 0;
+    energy = 0;
+    energy2 = 0;
+    timestamp = 0;
+    fineTime = 0;
+    traceLength = 0;
+    pileUp = false;
+    trace.clear();
+  }
+
+  void Print(){
+    printf("(%5d, %2d) %6d %16llu, %6d, %d, %5ld\n", sn, ch, energy, timestamp, fineTime, pileUp, trace.size());
+  }
+
+  void PrintTrace(){
+    for( unsigned short i = 0; i < traceLength; i++){
+      printf("%3u | %6d \n", i, trace[i]);
+    }
+  }
+
+  // Define operator< for sorting
+  bool operator<(const Hit& other) const {
+    return timestamp < other.timestamp;
+  }
+
+};
+
+#endif

Armory/LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
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+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

Armory/Makefile

@@ -1,28 +1,74 @@
 ########################################################################
-#
+# Cross-platform Makefile (macOS + Linux)
-#
+########################################################################
-#########################################################################
 
-CC	=	g++
+UNAME_S := $(shell uname -s)
 
-#COPTS	=	-fPIC -DLINUX -O2 -std=c++17 -lpthread
+########################################################################
-COPTS	=	-fPIC -DLINUX -g -O0 -Wall -std=c++17 -lpthread
+# Defaults
+########################################################################
 
-ROOTLIBS = `root-config --cflags --glibs`
+ifeq ($(UNAME_S),Darwin)
 
-ALL = Mapper AnasenMS
+########################################################################
+# macOS (Homebrew + Apple Clang)
+########################################################################
 
-#########################################################################
+SDKROOT := $(shell xcrun --show-sdk-path)
+
+CXX := clang++
+
+ROOTCFLAGS := $(shell root-config --cflags | sed 's/-stdlib=libc++//g')
+ROOTLIBS   := $(shell root-config --libs   | sed 's/-stdlib=libc++//g')
+
+CXXFLAGS := -g -O0 -Wall -std=c++17 -fPIC
+CXXFLAGS += $(ROOTCFLAGS)
+CXXFLAGS += -isysroot $(SDKROOT)
+CXXFLAGS += -I$(SDKROOT)/usr/include/c++/v1
+
+LDFLAGS := $(shell root-config --glibs) -lGeom -lEve -lGui
+
+else
+
+########################################################################
+# Linux (system g++)
+########################################################################
+
+CXX := g++
+
+COPTS := -fPIC -DLINUX -g -O0 -Wall -std=c++17 -pthread
+
+ROOTCFLAGS := $(shell root-config --cflags)
+ROOTLIBS   := $(shell root-config --libs)
+
+CXXFLAGS := $(COPTS) $(ROOTCFLAGS)
+LDFLAGS := $(ROOTLIBS) -lGeom -lEve -lGui
+
+endif
+
+########################################################################
+# Targets
+########################################################################
+
+ALL = Mapper EventBuilder AnasenMS
 
 all: $(ALL)
 
 clean:
-		/bin/rm -f $(OBJS) $(ALL)
+	/bin/rm -f $(ALL)
+
+########################################################################
+# Build rules
+########################################################################
 
 Mapper: Mapper.cpp ../mapping.h ClassDet.h
 	@echo "--------- making Mapper"
-		$(CC) $(COPTS) -o Mapper Mapper.cpp $(ROOTLIBS)
+	$(CXX) $(CXXFLAGS) Mapper.cpp -o Mapper $(LDFLAGS)
 
-AnasenMS : constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h anasenMS.cpp 
+EventBuilder: EventBuilder.cpp ClassData.h fsuReader.h Hit.h
+	@echo "--------- making EventBuilder"
+	$(CXX) $(CXXFLAGS) EventBuilder.cpp -o EventBuilder $(LDFLAGS)
+
+AnasenMS: anasenMS.cpp constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h
 	@echo "--------- making ANASEN Monte Carlo"
-		$(CC) $(COPTS) -o AnasenMS anasenMS.cpp $(ROOTLIBS)
+	$(CXX) $(CXXFLAGS) anasenMS.cpp -o AnasenMS $(LDFLAGS)

Armory/Mapper.dSYM/Contents/Info.plist

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<key>CFBundleIdentifier</key>
+		<string>com.apple.xcode.dsym.Mapper</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundlePackageType</key>
+		<string>dSYM</string>
+		<key>CFBundleSignature</key>
+		<string>????</string>
+		<key>CFBundleShortVersionString</key>
+		<string>1.0</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+	</dict>
+</plist>

Armory/Mapper.dSYM/Contents/Resources/Relocations/aarch64/Mapper.yml

@@ -0,0 +1,5 @@
+---
+triple:          'arm64-apple-darwin'
+binary-path:     Mapper
+relocations:     []
+...

Armory/README_anasenMS.md

@@ -0,0 +1,75 @@
+# ANASEN Monte Carlo (anasenMS.cpp)
+
+## Overview
+
+`anasenMS.cpp` is a standalone Monte Carlo simulation for an ANASEN-style detector setup. It generates transfer reaction kinematics, propagates products to a wire chamber (PW) and a silicon array (SX3), reconstructs tracks, and writes output to a ROOT tree.  
+
+## Requirements
+
+- ROOT (e.g. `root-config` for compile flags)
+- C++ compiler (gcc/g++)
+- Project includes: `ClassTransfer.h`, `ClassAnasen.h`, plus their dependent implementation files.
+
+## Build
+
+In `Armory` directory:
+
+the directory contains a make file
+
+Run `make AnasenMS` and it will automatically run
+
+```bash
+g++ -O2 -o anasenMS anasenMS.cpp ClassTransfer.cpp ClassAnasen.cpp ... `root-config --cflags --libs`
+```
+
+(Adjust source file list based on actual project layout.)
+
+## Run
+
+```bash
+./anasenMS [numEvents] vis(optional)
+```
+
+- `numEvents`: optional integer, default `1000000`
+- Outputs: `SimAnasen1.root` containing `tree1` and `tree2`
+tree1 contains pre-energy loss calculations
+tree2 contains post-energy loss calculations (subject to change)
+
+## What the code does
+
+- Detector geometry is built within ClassAnasen.h
+
+-To assign dead channels (anode/cathode/SX3), add ID's to IsDead<detector> boolean functions at top of simulation,
+  inside the set
+
+- Initializes reaction: `TransferReaction transfer`
+  - `SetA(24,12,0)` target
+  - `SetIncidentEnergyAngle(10,0,0)` beam energy and direction
+  - `Seta`, `Setb` reaction fragment indices
+- Sets excitation lists: `ExAList`, `ExList`
+- Vertex and resolution settings:
+  - `vertexX/Y/Z` ranges
+  - `sigmaSX3_W`, `sigmaSX3_L`, `sigmaPW_A`, `sigmaPW_C`
+- Loads energy loss tables from `../ELoss/` using `TGraph` for interpolation
+- Prepares ROOT output tree and branches for truth/reconstructed
+- Loop over events:
+  - Sample excitation and CM direction
+  - `transfer.Event(thetaCM, phiCM)` outputs `TLorentzVector` products
+  - Compute lab angles/energies
+  - Random vertex inside target volume
+  - Run detector response:
+    - `pw->FindWireID(...)`
+    - `sx3->FindSX3Pos(...)`
+  - Read out wire hits and SX3 channel + depth
+  - Apply position smearing for SX3
+  - **Apply energy loss** to light particle using interpolated dE/dx from table, based on path length from vertex to hit
+  - Reconstruct track via `pw->CalTrack` and `pw->CalTrack2`
+  - Fill ROOT tree
+- At end: write tree, close file, clean up
+
+## Notes
+
+- Important methods are from:
+  - `ClassTransfer` (`SetA`, `SetIncidentEnergyAngle`, `Seta`, `Setb`, `SetExA`, `SetExB`, `CalReactionConstant`, `Event`)
+  - `ClassAnasen` / `SX3` / `PW` (`FindWireID`, `FindSX3Pos`, `GetHitInfo`, `CalTrack`, `CalTrack2`, `GetTrackTheta`, `GetTrackPhi`, `GetZ0`, `GetHitPosWithSigma`, `GetID`, etc.)
+- Optional: change excitation lists, vertex spread, and sigma values to mimic different beam/target conditions.

Armory/SX3Geom.h

@@ -0,0 +1,183 @@
+#ifndef SX3Geom_h
+#define SX3Geom_h
+#include <vector>
+
+const double DEFAULT_NULL=-987654321.;
+
+class sx3_geometry_scalefactors {
+public:
+    //If sx3 has L, R being the left and right extremities, we choose add, stretch here such that
+    // x_mm = (x_raw+add)*stretch; so add=abs(L), stretch=75/(abs(L)+R)
+    float add[4];
+    float stretch[4];
+};
+
+class qqq5_finegains {
+public:
+    std::array<std::pair<float,float>,32> front;
+    //front.at(30).first = slope at clkpos 0, ring 30 for E front layer
+    //front.at(30).second = intercept for the same as above
+    std::array<std::pair<float,float>,4> back;
+};
+class sx3_fbgains {
+public:
+    //Order of indices is [pad][strip]
+    float padoffsets[4][4];
+    float padgains[4][4];
+
+    float stripLoffsets[4][4];
+    float stripLgains[4][4];
+
+    float stripRoffsets[4][4];
+    float stripRgains[4][4];
+};
+
+std::array<sx3_fbgains,24> sx3_xtalk_gains; //every sx3 needs to be gainmatched as a frontL-back, frontR-back pair (pad strip pair)
+std::array<sx3_geometry_scalefactors,24> sx3gs;
+
+class sx3 {
+public:
+    //TODO: Convert to std::array
+    //Holds all information in an event, including ped subtraction+scaling. back[2].at(0) will have the largest energy seen in ch2, if any
+    std::vector<float> back[4];
+    std::vector<float> frontL[4];
+    std::vector<float> frontR[4];
+
+    double ts = DEFAULT_NULL;
+    //Easy lookup of final calibrated event. Only filled for valid cases, assumed for now to be 1L, 1R, 1B
+    float frontX=DEFAULT_NULL;
+    float frontXmm=DEFAULT_NULL;
+    float frontE=DEFAULT_NULL;
+    float backE=DEFAULT_NULL;
+    int stripF=DEFAULT_NULL;
+    int stripB=DEFAULT_NULL;
+    float frontEL=DEFAULT_NULL;
+    float frontER=DEFAULT_NULL;
+
+    float phi=DEFAULT_NULL; //
+
+    std::set<int> valid_front_chans;
+    std::set<int> valid_back_chans;
+    std::set<int> unmatched_front_chans; //every front channel is unmatched and invalid at first. when it gets matched, it gets removed and sent to valid
+
+    bool foundevent=false;
+    bool valid=false;//valid will be set to false in all cases where we have ambiguity
+    int flags=-1;//flags settable to different types of values to indicate different invalid situations
+
+    void fillevent(const std::string& position, const int subchannel, const float value); //make 'const' what functions don't need to change, helps with performance
+    void validate(const sx3_fbgains&, const sx3_geometry_scalefactors&);
+    void validate();
+};
+
+
+void sx3::fillevent(const std::string& positionstring, const int subchannel, const float value) {
+    assert(subchannel>=0 && subchannel<4);
+    if(positionstring=="FRONT_L") {
+        frontL[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="FRONT_R") {
+        frontR[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="BACK") {
+        back[subchannel].push_back(value);
+        valid_back_chans.insert(subchannel);
+    } else {
+        std::cout << "Unknown string "+positionstring+" encountered in sx3::fillevent \n" << std::endl;
+    }
+    if(frontL[subchannel].size()!=0 && frontR[subchannel].size()!=0 ) {
+        unmatched_front_chans.erase(subchannel);
+        valid_front_chans.insert(subchannel); //std::set, so no duplication will happen
+    }
+}
+
+
+//void sx3::validate(const sx3_fbgains& fbgains, const sx3_geometry_scalefactors& sx3gs) {
+void sx3::validate() {
+    if(valid_front_chans.size()!=0 && valid_back_chans.size()!=0) {
+        valid=true;
+        float maxFE=0;
+        float maxBE=0;
+        //float zpos=0;
+        int bchan=-1;
+        int fchan=-1;
+/*            	for(auto cc: valid_front_chans) {
+            		std::cout << "fc" << cc << std::endl;// " " << frontL[cc].at(0) << " " << frontR[cc].at(0) << std::endl;
+            	}
+            	for(auto cc: valid_back_chans) {
+            		std::cout << "bc" << cc << std::endl; //" " << back[cc].at(0) << std::endl;
+            	}
+*/
+        for(auto chan: valid_front_chans) {
+            if(frontL[chan].size()>1) {
+                printf("\nmultihit sx3 at Lsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontL[chan]) printf("e: %f\t",e);
+                std::sort(frontL[chan].begin(), frontL[chan].end(), std::greater<float>());
+                flags += (-1000);
+            }
+            if(frontR[chan].size()>1) {
+                printf("\nmultihit sx3 at Rsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontR[chan]) printf("e: %f\t",e);
+                std::sort(frontR[chan].begin(), frontR[chan].end(), std::greater<float>());
+                flags += (-2000);
+            }
+            //assign position using max L+R value
+            /*printf("chan:%d sizeL: %d sizeR: %d\n",chan, frontL[chan].size(), frontR[chan].size()); fflush(stdout);
+			printf("foo\n");
+			std::cout << "\nL:" << std::endl;
+			for(auto thing: frontL[chan]) std::cout << thing << " " << std::flush;
+			std::cout << "\nR:" << std::endl;
+			for(auto thing: frontR[chan]) std::cout << thing << " " << std::flush;*/
+            if(frontL[chan].at(0) + frontR[chan].at(0)> maxFE) {
+                maxFE = frontL[chan].at(0) + frontR[chan].at(0);
+                //zpos = (frontL[chan].at(0)-frontR[chan].at(0))/maxFE;
+                fchan = chan;
+            }
+        }
+        for(auto chan: valid_back_chans) {
+            if(back[chan].size()>1) {
+                printf("\nmultihit sx3 at Bsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: back[chan]) printf("e: %f\t",e);
+                std::sort(back[chan].begin(), back[chan].end(), std::greater<float>());
+                flags += (-3000);
+            }
+            if(back[chan].size() ==0 ) {
+            	printf("foo\n");
+            	//continue;
+            }
+            if(back[chan].at(0) > maxBE) {
+                maxBE = back[chan].at(0);
+                bchan = chan;
+            }
+        }
+        /*
+        	Cross-talk corrections are important when evaluating 'energy' signals from strips/pads.
+        	They can cause unexpected behavior when used universally for all EL, ER cases, so we split scenarios in two.
+        		- Positions along each strip (frontX) *are not* corrected for crosstalk.
+        		- Total F and B energies (frontE, backE) *are*.
+        	Sudarsan B, 31 Oct 2024
+        */
+        float Eleft = frontL[fchan].at(0);
+        float Eright = frontR[fchan].at(0);
+        frontEL = Eleft;
+        frontER = Eright;
+        frontX = (Eleft-Eright)/(Eleft+Eright);
+        //frontXmm = (frontX+sx3gs.add[fchan])*sx3gs.stretch[fchan]; //convert to mm
+
+        //frontE = Eleft*fbgains.stripLgains[bchan][fchan] + fbgains.stripLoffsets[bchan][fchan]
+         //        + Eright*fbgains.stripRgains[bchan][fchan]  + fbgains.stripRoffsets[bchan][fchan];
+        //backE = back[bchan].at(0)*fbgains.padgains[bchan][fchan]+fbgains.padoffsets[bchan][fchan];
+        frontE = Eleft+Eright;
+        backE = maxBE;
+        stripF=fchan;
+        stripB=bchan;
+
+        flags = 0;
+    } else if(valid_front_chans.size()!=0 && valid_back_chans.size()==0) {
+        flags = -10;
+    } else if(valid_front_chans.size()==0 && valid_back_chans.size()!=0) {
+        flags = -20;
+    }
+}
+
+typedef sx3 sx3det;
+#endif

Armory/aarootscript.C

@@ -0,0 +1,134 @@
+#include "TFile.h"
+#include "TTree.h"
+#include "TGraph.h"
+#include "TLegend.h"
+#include "TCanvas.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
+
+void aarootscript(int argument = 0) {
+    std::cout << "\n\n\n";
+    std::cout << "=========================================\n";
+    std::cout << "=========   ANASEN Root Script  =========\n";
+    std::cout << "=========================================\n";
+
+    TFile *f = new TFile("SimAnasen1.root");
+    TTree *tree1 = (TTree*)f->Get("tree");
+    if (!tree1) {
+        std::cerr << "Error: tree1 not found in the file!" << std::endl;
+        return;
+    }
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    TTreeReader reader("tree");
+    TTreeReaderValue<double> Tb1(reader, "Tb"); // this line will read the "Tb" branch from the tree and save it as 
+    TTreeReaderValue<double> TB1(reader, "TB"); // this line will read the "TB" branch from the tree and save it as Tb1
+    //add Tb1 and TB1 together 
+
+    double totalSum = 0;
+    while (reader.Next()) {
+        totalSum += *Tb1;
+    }
+    std::cout << "Total Sum: " << totalSum << std::endl;
+
+    TTreeReader reader2("tree2");
+    TTreeReaderValue<double> Tb2(reader2, "Tb");
+    double totalSum2 = 0;
+    int zeroCount = 0;
+    while (reader2.Next()) {
+        totalSum2 += *Tb2;
+        if (*Tb2 == 0) {
+            zeroCount++;
+        }
+    }
+    std::cout << "Total Sum: " << totalSum2 << std::endl;
+
+    std::cout << "Difference: " << totalSum - totalSum2 << std::endl;
+
+    std::cout << "Zero Count: " << zeroCount << std::endl;
+
+
+
+    //std::cout << "Making histograms..." << std::endl;
+
+    gErrorIgnoreLevel = 2001;
+    gROOT->ProcessLine(".x histcomp.C"); 
+
+    std::cout << "=========================================\n";
+
+    if (argument == 1) {
+        if (tree1) {
+            gROOT->ProcessLine("tree->Print();");
+        } else {
+            std::cout << "Tree1 not found!" << std::endl;
+        }
+    }
+
+    if (argument == 2) {
+        if (tree2) {
+            gROOT->ProcessLine("tree2->Print();");
+        } else {
+            std::cout << "Tree2 not found!" << std::endl;
+        }
+    }
+
+    std::cout << "Creating Tb vs dEb plot..." << std::endl;
+
+    // Readers for both trees
+    TTreeReader r1(tree1);
+    TTreeReader r2(tree2);
+
+    TTreeReaderValue<double> Tb_val(r1, "Tb");
+    TTreeReaderValue<double> TB_val(r2, "TB");
+    TTreeReaderValue<double> dEb_val(r2, "dEb");
+
+    std::vector<double> x; // Tb (tree1)
+    std::vector<double> y; // dEb (tree2)
+
+
+    // Loop over both trees simultaneously
+    while (r1.Next() && r2.Next()) {
+        x.push_back(*Tb_val);
+        y.push_back(*dEb_val);
+    }
+    std::cout << "x length: " << x.size() << ", y length: " << y.size() << std::endl;
+
+    std::ofstream outfile("Tb_dEb_data.txt");
+
+    if (!outfile.is_open()) {
+        std::cerr << "Error: Could not open output file!" << std::endl;
+        return;
+    }
+
+    for (size_t i = 0; i < x.size(); i++) {
+        outfile << x[i] << " " << y[i] << "\n";
+    }
+
+    outfile.close();
+
+    std::cout << "Data written to Tb_dEb_data.txt" << std::endl;
+    /*
+    // Create graph
+    TGraph *gr = new TGraph(x.size(), &x[0], &y[0]);
+    gr->SetTitle("Tb (tree1) vs dEb (tree2);Tb;dEb");
+    gr->SetMarkerStyle(20);
+
+    // Draw
+    TCanvas *c1 = new TCanvas("c1", "Tb vs dEb", 800, 600);
+    gr->Draw("AP");
+    c1->Update();
+    c1->SaveAs("Tb_vs_dEb.png");
+    std::cout << "Plot saved as Tb_vs_dEb.pdf" << std::endl;
+    std::cout << "\n\n\n";
+
+    delete c1;
+    delete gr;*/
+
+
+
+
+}
+

Armory/analyze.C

@@ -0,0 +1,111 @@
+#include "TFile.h"
+#include "TTree.h"
+#include "TCanvas.h"
+#include "TH1D.h"
+#include "TLegend.h"
+#include "TString.h"
+#include "TStyle.h"
+#include <iostream>
+
+void analyze(const char* filename = "SimAnasen1.root")
+{
+    gStyle->SetOptStat(1);
+
+    TFile *f = TFile::Open(filename);
+    if (!f || f->IsZombie()) {
+        std::cerr << "ERROR: cannot open file " << filename << std::endl;
+        return;
+    }
+
+    TTree *tree = (TTree*)f->Get("tree");
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    if (!tree) {
+        std::cerr << "ERROR: tree not found\n";
+        return;
+    }
+
+    std::cout << "\n===== BASIC TREE INFO =====\n";
+    tree->Print();
+
+    // Event inspection tools
+    std::cout << "\n===== FIRST 10 EVENTS =====\n";
+    tree->Scan("Tb:TB:anodeID[0]:cathodeID[0]:sx3ID", "", "", 10);
+
+    std::cout << "\n===== SINGLE EVENT EXAMPLE (0) =====\n";
+    tree->Show(0);
+
+    // Quick detector gating examples
+    std::cout << "\n===== GATED STATS =====\n";
+    std::cout << "Events with anodeID[0]==5: "
+              << tree->GetEntries("anodeID[0]==5") << std::endl;
+
+    std::cout << "Events with sx3ID>=0: "
+              << tree->GetEntries("sx3ID>=0") << std::endl;
+
+    // Tb vs TB comparison histogram
+
+    TCanvas *c1 = new TCanvas("c1","Tb vs TB",800,600);
+    //set min and max from tree values
+    double min = tree->GetMinimum("Tb");
+    double max = tree->GetMaximum("TB");
+    min = min - max*0.1;
+    max = max * 1.1;
+    TH1D *hTb = new TH1D("hTb","Tb and TB;Energy (MeV);Counts",200,min,max); //arguments are name, title (with axis labels), number of bins, x-min, x-max
+    TH1D *hTB = new TH1D("hTB","",200,min,max);
+
+    tree->Draw("Tb>>hTb","","goff");
+    tree->Draw("TB>>hTB","","goff");
+
+    hTb->SetLineColor(kRed);
+    hTB->SetLineColor(kBlue);
+
+    hTb->Draw("HIST");
+    hTB->Draw("HIST SAME");
+
+    TLegend *leg = new TLegend(0.65,0.75,0.88,0.88);
+    leg->AddEntry(hTb,"Tb (light)","l");
+    leg->AddEntry(hTB,"TB (heavy)","l");
+    leg->Draw();
+
+    c1->SaveAs("Tb_TB_compare.png");
+
+    // 4. Detector-gated histogram
+
+    TCanvas *c2 = new TCanvas("c2","Anode gated Tb",800,600);
+    double min2 = tree->GetMinimum("Tb");
+    double max2 = tree->GetMaximum("Tb");
+    min2 = min2 - max2*0.1;
+    max2 = max2 * 1.1;
+    TH1D *hGate = new TH1D("hGate","Tb (anodeID[0]==5);Energy;Counts",200,min2,max2);
+
+    tree->Draw("Tb>>hGate","anodeID[0]==5","goff");
+
+    hGate->SetLineColor(kGreen+2);
+    hGate->Draw("HIST");
+
+    c2->SaveAs("Tb_anode5.png");
+
+    // Tb vs TB correlation (with gate)
+
+    TCanvas *c3 = new TCanvas("c3","dEb vs SX3z",800,600);
+
+    tree->Draw("TB:Tb>>h2(200,min,max,200,min,max)","","COLZ"); //arguments are "y:x>>histogram(bins,xmin,xmax,bins,ymin,ymax)", "selection", "options"
+
+    c3->SaveAs("Tb_vs_TB.png");
+
+    // Make gated trees 
+
+    TFile *out = new TFile("gated_output.root","RECREATE");
+
+    TTree *t_anode5 = tree->CopyTree("anodeID[0]==5");
+    t_anode5->Write("tree_anode5");
+
+    TTree *t_sx3valid = tree->CopyTree("sx3ID>=0");
+    t_sx3valid->Write("tree_sx3valid");
+
+    out->Close();
+
+    std::cout << "\n===== DONE =====\n";
+    std::cout << "Saved plots + gated trees in gated_output.root\n";
+}

Armory/anasenMS Decay Version.cpp

@@ -0,0 +1,632 @@
+#include "TRandom.h"      // ROOT random number generators, gRandom
+#include "TFile.h"        // ROOT file I/O
+#include "TTree.h"        // ROOT tree storage
+#include "TH1.h"          // 1D histograms
+#include "TH2.h"          // 2D histograms
+#include "TStyle.h"       // ROOT plotting style controls
+#include "TCanvas.h"      // ROOT canvas drawing
+#include "TBenchmark.h"   // timing measurement
+#include "TGraph.h"       // for energy loss interpolation
+#include <cstring>
+#include "TApplication.h" // ROOT app loop
+#include "ClassTransfer.h" // Reaction kinematics and MC event generation
+#include "ClassAnasen.h"   // ANASEN detector model classes (SX3, PW, etc.)
+#include <stdio.h>
+#include <stdlib.h>
+#include <set>
+#include "TLegend.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
+
+//======== Generate light particle based on reaction
+// calculate real and reconstructed tracks and Q-value uncertainty
+
+// Function to load energy loss table from file
+TGraph* LoadELoss(const char* filename) {
+  TGraph* g = new TGraph(filename, "%lg %lg");
+  return g;
+}
+
+bool IsDeadAnode(int id){
+    static std::set<int> dead = {}; // add dead anode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadCathode(int id){
+    static std::set<int> dead = {}; // add dead cathode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadSX3(int id){ 
+    static std::set<int> dead = {}; // add dead SX3 IDs here, 0-23 1,7,9,3
+    return dead.count(id);
+}
+
+// Simulate sequential two-body decay of an unstable parent in its rest frame.
+// The parent is boosted from the lab frame, the daughter (A1,Z1) is returned in lab frame,
+// and the emitted ejectile (A2,Z2) is written to ejectileOut.
+TLorentzVector SimulateSequentialDecay(const TLorentzVector &parent,
+                                       int daughterA, int daughterZ,
+                                       int ejectA, int ejectZ,
+                                       TLorentzVector &ejectileOut){
+  Isotope daughter(daughterA, daughterZ);
+  Isotope ejectile(ejectA, ejectZ);
+
+  double M = parent.M();
+  double mD = daughter.Mass;
+  double mE = ejectile.Mass;
+
+  double sqM = M * M;
+  double sum = mD + mE;
+  double diff = mD - mE;
+  double p2 = (sqM - sum*sum) * (sqM - diff*diff) / (4.0 * sqM);
+  if( p2 < 0 ) p2 = 0;
+  double p = TMath::Sqrt(p2);
+
+  double cosTheta = 2.0 * gRandom->Rndm() - 1.0;
+  double theta = TMath::ACos(cosTheta);
+  double phi = gRandom->Rndm() * TMath::TwoPi();
+
+  TVector3 v;
+  v.SetMagThetaPhi(p, theta, phi);
+
+  TLorentzVector daughterLab;
+  daughterLab.SetVectM(v, mD);
+
+  TLorentzVector ejectileLab;
+  ejectileLab.SetVectM(-v, mE);
+
+  TVector3 boost = parent.BoostVector();
+  daughterLab.Boost(boost);
+  ejectileLab.Boost(boost);
+
+  ejectileOut = ejectileLab;
+  return daughterLab;
+}
+
+int main(int argc, char **argv){
+
+  printf("=========================================\n");
+  printf("===       ANASEN Monte Carlo          ===\n");
+  printf("=========================================\n");
+
+  // number of events can be overridden from command line
+  int numEvent = 1000000;
+  if( argc >= 2 ) numEvent = atoi(argv[1]);
+
+  // Reaction setup for 18Ne + 4He -> p + 21Na*.
+  // The heavy product 21Na* is then decayed to 20Ne + p in the simulation.
+  TransferReaction transfer;
+
+  transfer.SetA(18, 10, 0);            // 18Ne
+  transfer.SetIncidentEnergyAngle(4.4, 0, 0); // KEA in MeV/u, theta and phi in degree
+  transfer.Seta(4, 2);                 // 4He target
+  transfer.Setb(1, 1);                 // outgoing proton from the primary transfer
+  transfer.SetB(21, 11);               // 21Na* heavy product
+
+  bool enableSequentialDecay = true;
+  const int decayDaughterA = 20;
+  const int decayDaughterZ = 10;
+  const int decayEjectA = 1;
+  const int decayEjectZ = 1;
+
+  // Excited state lists (projectile and heavy-product excitation states)
+  std::vector<float> ExAList = {0};              // 18Ne projectile excitations in MeV
+  std::vector<float> ExList = {2.5};             // 21Na* excitation in MeV (above proton separation threshold)
+
+  // define vertex position uniform distribution ranges (mm)
+  double vertexXRange[2] = {   -5,    5}; // mm
+  double vertexYRange[2] = {   -5,    5};
+  double vertexZRange[2] = { -100,  100};
+
+  // detector resolution / uncertainty parameters
+  double sigmaSX3_W = -1; // mm, if < 0 use mid-point (no spread in SX3 horizontal dimension)
+  double sigmaSX3_L = 3;  // mm, vertical spread for SX3
+  double sigmaPW_A  = 0;  // normalized anode uncertainty term (0-1)
+  double sigmaPW_C  = 0;  // normalized cathode uncertainty term (0-1)
+
+  // status printout
+  printf("------------ Vertex :\n");
+  printf("X : %7.2f - %7.2f mm\n", vertexXRange[0], vertexXRange[1]);
+  printf("Y : %7.2f - %7.2f mm\n", vertexYRange[0], vertexYRange[1]);
+  printf("Z : %7.2f - %7.2f mm\n", vertexZRange[0], vertexZRange[1]);
+  printf("------------ Uncertainty :\n");
+  printf(" SX3 horizontal : %.1f\n", sigmaSX3_W);
+  printf(" SX3   vertical : %.1f\n", sigmaSX3_L);
+  printf("          Anode : %.1f mm\n", sigmaPW_A);
+  printf("        Cathode : %.1f mm\n", sigmaPW_C);
+  printf("        num_eve : %d \n",numEvent);
+
+  // calculates energy/momentum/kinematics constants for transfer reaction
+  transfer.CalReactionConstant();
+  printf("Primary reaction: %s at %.2f MeV/u\n", transfer.GetReactionName().Data(), 4.4);
+  printf("Sequential decay enabled: %s\n", enableSequentialDecay ? "yes" : "no");
+
+  int nExA = ExAList.size();
+  int nEx  = ExList.size();
+
+  // optional visualization control: pass "vis" as 3rd arg
+  bool enableVis = (argc >= 3 && strcmp(argv[2], "vis") == 0);
+  TApplication *app = nullptr;
+  if(enableVis){
+    app = new TApplication("anasenVis", &argc, argv);
+  }
+
+  // storage for tracks during simulation (for visualization)
+  std::vector<TVector3> visTrackVertex, visTrackDir, visTrackHitPos;
+  std::vector<std::pair<int,int>> visTrackWires;  // {anodeID, cathodeID}
+
+  // create detector representation in memory
+  ANASEN * anasen = new ANASEN();       // top-level detector object
+  SX3 * sx3 = anasen->GetSX3();         // silicon array part
+  PW * pw = anasen->GetPW();            // proportional wire chamber part
+
+  // output file + trees
+  TString saveFileName = "SimAnasen1.root";
+  printf("\e[32m#################################### building Tree in %s\e[0m\n", saveFileName.Data());
+  TFile * saveFile = new TFile(saveFileName, "recreate");
+  TTree * tree1 = new TTree("tree1", "tree1");
+  TTree * tree2 = new TTree("tree2", "tree2");
+
+  // beam and CM variables saved in tree
+  double KEA;
+  double KEA2;
+  tree1->Branch("beamKEA",     &KEA, "beamKEA/D");
+  tree2->Branch("beamKEA",     &KEA2, "beamKEA/D");
+
+  double thetaCM, phiCM;
+  double thetaCM2, phiCM2;
+  tree1->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  tree1->Branch("phiCM",     &phiCM, "phiCM/D");
+  tree2->Branch("thetaCM", &thetaCM2, "thetaCM/D");
+  tree2->Branch("phiCM",     &phiCM2, "phiCM/D");
+
+  // outgoing particles in lab frame (light/heavy)
+  double thetab, phib;
+  double Tb;
+  double thetaB, phiB, TB;
+  std::array<double, 2> T;
+  tree1->Branch("thetab", &thetab, "thetab/D"); // polar angle of light particle in lab frame
+  tree1->Branch("phib",     &phib, "phib/D"); // azimuthal angle of light particle in lab frame
+  tree1->Branch("Tb",         &Tb, "Tb/D"); // kinetic energy of light particle at vertex (before energy loss)
+  tree1->Branch("thetaB", &thetaB, "thetaB/D");
+  tree1->Branch("phiB",     &phiB, "phiB/D");
+  tree1->Branch("TB",         &TB, "TB/D"); // kinetic energy of heavy particle at vertex
+  tree1->Branch("T",          &T, "T/D");   // placeholder for true Q-value, currently set to 0 for simplicity
+
+  double thetab2, phib2;
+  double Tb2;
+  double thetaB2, phiB2, TB2;
+  std::array<double, 2> T2;
+  tree2->Branch("thetab", &thetab2, "thetab/D");
+  tree2->Branch("phib",     &phib2, "phib/D");
+  tree2->Branch("Tb",         &Tb2, "Tb/D");
+  tree2->Branch("thetaB", &thetaB2, "thetaB/D");
+  tree2->Branch("phiB",     &phiB2, "phiB/D");
+  tree2->Branch("TB",         &TB2, "TB/D");
+  tree2->Branch("T",          &T2, "T/D");
+
+  // excitation state identifiers
+  int ExAID;
+  double ExA;
+  tree1->Branch("ExAID", &ExAID, "ExAID/I"); // projectile excitation state ID
+  tree1->Branch("ExA",     &ExA, "ExA/D"); // projectile excitation energy in MeV
+
+  int ExAID2;
+  double ExA2;
+  tree2->Branch("ExAID", &ExAID2, "ExAID/I");
+  tree2->Branch("ExA",     &ExA2, "ExA/D");
+
+  int ExID;
+  double Ex;
+  tree1->Branch("ExID", &ExID, "ExID/I"); // target excitation state ID
+  tree1->Branch("Ex",     &Ex, "Ex/D"); // target excitation energy in MeV
+
+  int ExID2;
+  double Ex2;
+  tree2->Branch("ExID", &ExID2, "ExID/I");
+  tree2->Branch("Ex",     &Ex2, "Ex/D");
+
+  // true vertex position in target volume
+  double vertexX, vertexY, vertexZ;
+  tree1->Branch("vX",     &vertexX, "VertexX/D"); // true vertex X position in mm
+  tree1->Branch("vY",     &vertexY, "VertexY/D"); // true vertex Y position in mm
+  tree1->Branch("vZ",     &vertexZ, "VertexZ/D"); // true vertex Z position in mm
+
+  double vertexX2, vertexY2, vertexZ2;
+  tree2->Branch("vX",     &vertexX2, "VertexX/D");
+  tree2->Branch("vY",     &vertexY2, "VertexY/D");
+  tree2->Branch("vZ",     &vertexZ2, "VertexZ/D");
+
+  // reconstructed SX3 hit position
+  double sx3X, sx3Y, sx3Z;
+  tree1->Branch("sx3X",     &sx3X, "sx3X/D"); // reconstructed X position from SX3 (with optional smearing)
+  tree1->Branch("sx3Y",     &sx3Y, "sx3Y/D"); // reconstructed Y position from SX3 (with optional smearing)
+  tree1->Branch("sx3Z",     &sx3Z, "sx3Z/D"); // reconstructed Z position from SX3 (with optional smearing)
+
+  double sx3X2, sx3Y2, sx3Z2;
+  tree2->Branch("sx3X",     &sx3X2, "sx3X/D");
+  tree2->Branch("sx3Y",     &sx3Y2, "sx3Y/D");
+  tree2->Branch("sx3Z",     &sx3Z2, "sx3Z/D");
+
+  // PW nearest and next nearest wires
+  int anodeID[2], cathodeID[2];
+  int anodeID2[2], cathodeID2[2];
+  tree1->Branch("aID", anodeID, "anodeID/I"); // anodeID[0] is nearest anode wire, anodeID[1] is next nearest anode wire
+  tree1->Branch("cID", cathodeID, "cathodeID/I"); // cathodeID[0] is nearest cathode wire, cathodeID[1] is next nearest cathode wire
+  tree2->Branch("aID", anodeID2, "anodeID/I");
+  tree2->Branch("cID", cathodeID2, "cathodeID/I");
+
+  // distances to nearest wires
+  double anodeDist[2], cathodeDist[2];
+  double anodeDist2[2], cathodeDist2[2];
+  tree1->Branch("aDist",   anodeDist, "anodeDist/D");
+  tree1->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  tree2->Branch("aDist",   anodeDist2, "anodeDist/D");
+  tree2->Branch("cDist",  cathodeDist2, "cathodeDist/D");
+
+  // SX3 channel assignment and Z fraction (depth) information
+  int sx3ID, sx3Up, sx3Dn, sx3Bk;
+  double sx3ZFrac;
+  int sx3ID2, sx3Up2, sx3Dn2, sx3Bk2;
+  double sx3ZFrac2;
+  tree1->Branch("sx3ID",   &sx3ID, "sx3ID/I");
+  tree1->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  tree1->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree1->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree1->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  tree2->Branch("sx3ID",   &sx3ID2, "sx3ID/I");
+  tree2->Branch("sx3Up",   &sx3Up2, "sx3Up/I");
+  tree2->Branch("sx3Dn",   &sx3Dn2, "sx3Dn/I");
+  tree2->Branch("sx3Bk",   &sx3Bk2, "sx3Bk/I");
+  tree2->Branch("sx3ZFrac", &sx3ZFrac2, "sx3ZFrac/D");
+
+  // reconstructed angles from PW track fit, method 1 and 2
+  double reTheta, rePhi;
+  double reTheta2, rePhi2;
+  tree1->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  tree1->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  tree2->Branch("reTheta", &reTheta2, "reconstucted_theta/D");
+  tree2->Branch("rePhi",     &rePhi2, "reconstucted_phi/D");
+
+  double reTheta1, rePhi1;
+  double reTheta12, rePhi12;
+  tree1->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  tree1->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  tree2->Branch("reTheta1", &reTheta12, "reconstucted_theta1/D");
+  tree2->Branch("rePhi1",     &rePhi12, "reconstucted_phi1/D");
+
+  // reconstructed vertex Z from PW fit
+  double z0;
+  double z02;
+  tree1->Branch("z0",     &z0, "reconstucted_Z/D");
+  tree2->Branch("z0",     &z02, "reconstucted_Z/D");
+
+  //========timer
+  TBenchmark clock;
+  bool shown ;
+  clock.Reset();
+  clock.Start("timer");
+  shown = false;
+
+  //================================= Calculate event loop
+  for( int i = 0; i < numEvent ; i++){
+
+    // randomly sample target/projectile excitations
+    ExAID = gRandom->Integer(nExA);
+    ExA = ExAList[ExAID];
+    transfer.SetExA(ExA);
+
+    ExID = gRandom->Integer(nEx);
+    Ex = ExList[ExID];
+    transfer.SetExB(Ex);
+
+    // recalc kinematic constants for chosen states
+    transfer.CalReactionConstant();
+
+    // isotropic CM direction
+    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ;
+    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
+
+    //==== Calculate reaction kinematics in lab frame for the primary transfer
+    TLorentzVector * output = transfer.Event(thetaCM, phiCM); // returns array of outputs
+    TLorentzVector Pb = output[2]; // primary proton from transfer
+    TLorentzVector PB = output[3]; // excited 21Na* heavy product
+
+    thetab = Pb.Theta() * TMath::RadToDeg();
+    Tb = (Pb.E() - Pb.M()); // kinetic energy of the light proton from the primary transfer
+    thetaB = PB.Theta() * TMath::RadToDeg();
+    TB = (PB.E() - PB.M());
+    phib = Pb.Phi() * TMath::RadToDeg();
+    phiB = PB.Phi() * TMath::RadToDeg();
+    T[0] = Tb;
+    T[1] = TB;
+
+    // prepare secondary proton from 21Na* sequential decay
+    TLorentzVector decayProton;
+    TLorentzVector heavy20;
+    if(enableSequentialDecay){
+      heavy20 = SimulateSequentialDecay(PB, decayDaughterA, decayDaughterZ,
+                                       decayEjectA, decayEjectZ, decayProton);
+      thetab2 = decayProton.Theta() * TMath::RadToDeg();
+      phib2 = decayProton.Phi() * TMath::RadToDeg();
+      Tb2 = decayProton.E() - decayProton.M();
+      thetaB2 = heavy20.Theta() * TMath::RadToDeg();
+      phiB2 = heavy20.Phi() * TMath::RadToDeg();
+      TB2 = heavy20.E() - heavy20.M();
+      T2[0] = Tb2;
+      T2[1] = TB2;
+    } else {
+      thetab2 = TMath::QuietNaN();
+      phib2  = TMath::QuietNaN();
+      Tb2    = TMath::QuietNaN();
+      thetaB2 = TMath::QuietNaN();
+      phiB2 = TMath::QuietNaN();
+      TB2 = TMath::QuietNaN();
+      T2[0] = TMath::QuietNaN();
+      T2[1] = TMath::QuietNaN();
+    }
+
+    delete [] output;
+
+    // vertex position in target volume
+    vertexX = (vertexXRange[1]- vertexXRange[0])*gRandom->Rndm() +  vertexXRange[0];
+    vertexY = (vertexYRange[1]- vertexYRange[0])*gRandom->Rndm() +  vertexYRange[0];
+    vertexZ = (vertexZRange[1]- vertexZRange[0])*gRandom->Rndm() +  vertexZRange[0];
+
+    TVector3 vertex(vertexX, vertexY, vertexZ);
+
+    // set direction vector from lab angle
+    TVector3 dir(1, 0, 0);
+    dir.SetTheta(thetab * TMath::DegToRad());
+    dir.SetPhi(phib * TMath::DegToRad());
+
+    // run detector response models for PW and SX3
+    pw->FindWireID(vertex, dir, false);
+    sx3->FindSX3Pos(vertex, dir, false);
+
+    PWHitInfo hitInfo = pw->GetHitInfo();
+
+    anodeID[0]   = hitInfo.nearestWire.first; // nearest anode wire ID
+    cathodeID[0] = hitInfo.nearestWire.second; // nearest cathode wire ID
+    anodeID[1]   = hitInfo.nextNearestWire.first; // next nearest anode wire ID
+    cathodeID[1] = hitInfo.nextNearestWire.second; // next nearest cathode wire ID
+
+    anodeDist[1]   = hitInfo.nextNearestDist.first; // distance to next nearest anode wire
+    cathodeDist[1] = hitInfo.nextNearestDist.second; // distance to next nearest cathode wire
+
+    if(IsDeadAnode(anodeID[0])) continue;
+    if(IsDeadCathode(cathodeID[0])) continue;
+
+    // SX3 hit channel info and depth fraction
+    sx3ID = sx3->GetID();
+
+    if(IsDeadSX3(sx3ID)) continue;
+
+    anodeDist[0]   = hitInfo.nearestDist.first; // distance to nearest anode wire
+    cathodeDist[0] = hitInfo.nearestDist.second; // distance to nearest cathode wire
+
+    if( sx3ID >= 0 ){
+      sx3Up    = sx3->GetChUp();
+      sx3Dn    = sx3->GetChDn();
+      sx3Bk    = sx3->GetChBk();
+      sx3ZFrac = sx3->GetZFrac();
+      
+      // apply intrinsic detector resolution to true SX3 hit position
+      // for no smearing comment out and use GetHitPos();
+      TVector3 hitPos = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+
+      sx3X = hitPos.X();
+      sx3Y = hitPos.Y();
+      sx3Z = hitPos.Z();
+
+      // store track data for visualization if enabled
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+      // reconstruct track from PW readings + SX3 hit
+      pw->CalTrack(hitPos, anodeID[0], cathodeID[0], false);
+      reTheta = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      // alternative track algorithm with uncertainty parameters
+      pw->CalTrack2(hitPos, hitInfo, sigmaPW_A, sigmaPW_C, false);
+      reTheta1 = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi1   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      z0 = pw->GetZ0();
+      tree1->Fill();
+
+      // fill tree2 using the secondary proton (proton 2) track
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      pw->FindWireID(vertex, dir2, false);
+      sx3->FindSX3Pos(vertex, dir2, false);
+      PWHitInfo hitInfo2 = pw->GetHitInfo();
+
+      anodeID2[0]   = hitInfo2.nearestWire.first;
+      cathodeID2[0] = hitInfo2.nearestWire.second;
+      anodeID2[1]   = hitInfo2.nextNearestWire.first;
+      cathodeID2[1] = hitInfo2.nextNearestWire.second;
+
+      anodeDist2[1]   = hitInfo2.nextNearestDist.first;
+      cathodeDist2[1] = hitInfo2.nextNearestDist.second;
+
+      if(IsDeadAnode(anodeID2[0]) || IsDeadCathode(cathodeID2[0])){
+        sx3ID2 = -1;
+      } else {
+        sx3ID2 = sx3->GetID();
+      }
+
+      if(sx3ID2 < 0 || IsDeadSX3(sx3ID2)){
+        sx3ID2 = -1;
+        sx3Up2 = -1;
+        sx3Dn2 = -1;
+        sx3Bk2 = -1;
+        sx3ZFrac2 = TMath::QuietNaN();
+        sx3X2 = TMath::QuietNaN();
+        sx3Y2 = TMath::QuietNaN();
+        sx3Z2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+      } else {
+        anodeDist2[0]   = hitInfo2.nearestDist.first;
+        cathodeDist2[0] = hitInfo2.nearestDist.second;
+        sx3Up2    = sx3->GetChUp();
+        sx3Dn2    = sx3->GetChDn();
+        sx3Bk2    = sx3->GetChBk();
+        sx3ZFrac2 = sx3->GetZFrac();
+        TVector3 hitPos2 = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+        sx3X2 = hitPos2.X();
+        sx3Y2 = hitPos2.Y();
+        sx3Z2 = hitPos2.Z();
+        pw->CalTrack(hitPos2, anodeID2[0], cathodeID2[0], false);
+        reTheta2 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi2   = pw->GetTrackPhi() * TMath::RadToDeg();
+        pw->CalTrack2(hitPos2, hitInfo2, sigmaPW_A, sigmaPW_C, false);
+        reTheta12 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi12   = pw->GetTrackPhi() * TMath::RadToDeg();
+        z02       = pw->GetZ0();
+      }
+
+      // copy common event info to tree2
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+
+      tree2->Fill();
+
+    }else{
+      // no valid SX3 hit: mark clearly invalid
+      sx3Up = -1;
+      sx3Dn = -1;
+      sx3Bk = -1;
+      sx3ZFrac = TMath::QuietNaN();
+
+      sx3X = TMath::QuietNaN();
+      sx3Y = TMath::QuietNaN();
+      sx3Z = TMath::QuietNaN();
+
+      reTheta  = TMath::QuietNaN();
+      rePhi    = TMath::QuietNaN();
+      reTheta1 = TMath::QuietNaN();
+      rePhi1   = TMath::QuietNaN();
+      z0       = TMath::QuietNaN();
+      //Tb = -12354567; // mark kinetic energy as invalid for no hit case
+      // fill tree with original data (no energy loss for these events)
+      //comment out tree fill for no hit case  
+      //tree->Fill();
+    }
+
+    //#################################################################### Timer
+    // measure elapsed real time and print progress roughly every 10 sec
+    clock.Stop("timer");
+    Double_t time = clock.GetRealTime("timer");
+    clock.Start("timer");
+
+    if ( !shown ) {
+      if (fmod(time, 10) < 1 ){
+        printf( "%10d[%2d%%]| %8.2f sec | expect: %5.1f min \n", i, TMath::Nint((i+1)*100./numEvent), time , numEvent*time/(i+1)/60);
+        shown = 1;
+      }
+    } else {
+      if (fmod(time, 10) > 9 ){
+        shown = 0;
+      }
+    }
+
+  }
+
+  // write results to ROOT file and close
+  tree1->Write("", TObject::kOverwrite);
+  tree2->Write("", TObject::kOverwrite);
+  int count1 = tree1->GetEntries();
+  int count2 = tree2->GetEntries();
+  saveFile->Close();
+
+  printf("=============== done. saved as %s. tree1 entries: %d, tree2 entries: %d\n", saveFileName.Data(), count1, count2);
+
+  if(enableVis){ // to enable visualization, run with 3rd argument "vis", e.g. "./anasenMC 1000 vis"
+    printf("Displaying geometry with %zu tracks from simulation\n", visTrackVertex.size());
+    
+    // Build full geometry with all wires
+    anasen->DrawAnasen(0, 23, 0, 23, -1, true);
+    
+    // Add all stored tracks to the geometry
+    TGeoManager *geom = anasen->GetGeoManager();
+    TGeoVolume *worldBox = anasen->GetWorldBox();
+    
+    if(geom && worldBox && visTrackVertex.size() > 0){
+      int trackNodeID = 500;  // start node IDs for tracks
+      
+      for(size_t iTrack = 0; iTrack < visTrackVertex.size(); ++iTrack){
+        TVector3 vertex = visTrackVertex[iTrack];
+        TVector3 dir = visTrackDir[iTrack];
+        TVector3 hitPos = visTrackHitPos[iTrack];
+        
+        double theta = dir.Theta() * TMath::RadToDeg();
+        double phi = dir.Phi() * TMath::RadToDeg();
+        
+        // Add a line marker at the vertex
+        TGeoVolume *startMarker = geom->MakeSphere("startMarker", 0, 0, 2.0);
+        startMarker->SetLineColor(kBlack);
+        worldBox->AddNode(startMarker, trackNodeID, 
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(), 
+                                          new TGeoRotation("rot", 0, 0, 0)));
+        trackNodeID++;
+        
+        // Add track line from vertex toward hit position
+        TGeoVolume *trackLine = geom->MakeTube("trackLine", 0, 0, 0.08, 150.0);
+        trackLine->SetLineColor(kBlue);
+        worldBox->AddNode(trackLine, trackNodeID,
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(),
+                                          new TGeoRotation("rotTrack", phi + 90, theta, 0)));
+        trackNodeID++;
+        
+        // Add hit position marker
+        TGeoVolume *hitMarker = geom->MakeSphere("hitMarker", 0, 0, 2.0);
+        hitMarker->SetLineColor(kRed);
+        worldBox->AddNode(hitMarker, trackNodeID,
+                         new TGeoCombiTrans(hitPos.X(), hitPos.Y(), hitPos.Z(),
+                                          new TGeoRotation("rotHit", 0, 0, 0)));
+        trackNodeID++;
+      }
+      
+      // Redraw geometry with all tracks
+      geom->CloseGeometry();
+      geom->SetVisLevel(4);
+      worldBox->Draw("ogle");
+    }
+    
+    if(app){
+      printf("Entering ROOT event loop\n");
+      app->Run();
+    }
+  }
+
+  delete anasen;
+
+
+  return 0;
+
+}

Armory/anasenMS.cpp

@@ -1,18 +1,90 @@
-#include "TRandom.h"
+#include "TRandom.h"      // ROOT random number generators, gRandom
-#include "TFile.h"
+#include "TFile.h"        // ROOT file I/O
-#include "TTree.h"
+#include "TTree.h"        // ROOT tree storage
-#include "TH1.h"
+#include "TH1.h"          // 1D histograms
-#include "TH2.h"
+#include "TH2.h"          // 2D histograms
-#include "TStyle.h"
+#include "TStyle.h"       // ROOT plotting style controls
-#include "TCanvas.h"
+#include "TCanvas.h"      // ROOT canvas drawing
-#include "TBenchmark.h"
+#include "TBenchmark.h"   // timing measurement
+#include "TGraph.h"       // for energy loss interpolation
+#include <cstring>
+#include "TApplication.h" // ROOT app loop
+#include "ClassTransfer.h" // Reaction kinematics and MC event generation
+#include "ClassAnasen.h"   // ANASEN detector model classes (SX3, PW, etc.)
+#include "ClassQQQ.h"      // QQQ detector model class
+#include <stdio.h>
+#include <stdlib.h>
+#include <set>
+#include "TLegend.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
 
-#include "ClassTransfer.h"
+//======== Generate light particle based on reaction
-#include "ClassAnasen.h"
+// calculate real and reconstructed tracks and Q-value uncertainty
 
-//======== Gerneate light particle based on reaction
+// Function to load energy loss table from file
-// find out the CalTrack and the real track
+TGraph* LoadELoss(const char* filename) {
-// find out the Q-value uncertaintly
+  TGraph* g = new TGraph(filename, "%lg %lg");
+  return g;
+}
+
+bool IsDeadAnode(int id){
+    static std::set<int> dead = {}; // add dead anode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadCathode(int id){
+    static std::set<int> dead = {}; // add dead cathode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadSX3(int id){ 
+    static std::set<int> dead = {}; // add dead SX3 IDs here, 0-23 1,7,9,3
+    return dead.count(id);
+}
+
+// Simulate sequential two-body decay of an unstable parent in its rest frame.
+TLorentzVector SimulateSequentialDecay(const TLorentzVector &parent,
+                                       int daughterA, int daughterZ,
+                                       int ejectA, int ejectZ,
+                                       TLorentzVector &ejectileOut){
+  Isotope daughter(daughterA, daughterZ);
+  Isotope ejectile(ejectA, ejectZ);
+
+  double M = parent.M();
+  double mD = daughter.Mass;
+  double mE = ejectile.Mass;
+
+  double sqM = M * M;
+  double sum = mD + mE;
+  double diff = mD - mE;
+  double p2 = (sqM - sum*sum) * (sqM - diff*diff) / (4.0 * sqM); // two-body decay momentum squared
+  if( p2 < 0 ) p2 = 0; // handle unphysical case where parent mass is less than sum of daughter and ejectile masses
+  double p = TMath::Sqrt(p2); // two-body decay momentum
+
+  double cosTheta = 2.0 * gRandom->Rndm() - 1.0; // isotropic decay in parent rest frame
+  double theta = TMath::ACos(cosTheta); // polar angle of daughter in parent rest frame
+  double phi = gRandom->Rndm() * TMath::TwoPi(); // azimuthal angle of daughter in parent rest frame
+
+  TVector3 v; // momentum vector of daughter in parent rest frame
+  v.SetMagThetaPhi(p, theta, phi); // daughter momentum in parent rest frame
+
+  TLorentzVector daughterLab; // daughter 4-vector in lab frame, initialized with momentum from decay and mass of daughter
+  daughterLab.SetVectM(v, mD); // set daughter 4-vector in parent rest frame, then boost to lab frame
+
+  TLorentzVector ejectileLab; // ejectile 4-vector in lab frame, initialized with momentum opposite to daughter and mass of ejectile
+  ejectileLab.SetVectM(-v, mE); //  set ejectile 4-vector in parent rest frame, then boost to lab frame
+
+  TVector3 boost = parent.BoostVector(); // boost vector to go from parent rest frame to lab frame
+  daughterLab.Boost(boost); // boost daughter to lab frame
+  ejectileLab.Boost(boost); // boost ejectile to lab frame
+
+  ejectileOut = ejectileLab; // return ejectile in lab frame
+  return daughterLab;
+}
 
 int main(int argc, char **argv){
 
@@ -20,33 +92,43 @@ int main(int argc, char **argv){
   printf("===       ANASEN Monte Carlo          ===\n");
   printf("=========================================\n");
 
+  // number of events can be overridden from command line
   int numEvent = 1000000;
   if( argc >= 2 ) numEvent = atoi(argv[1]);
-
-  //Reaction
   TransferReaction transfer;
 
-  transfer.SetA(24,12, 0);
+  //To set beam energy loss, use energy loss app, and create table with target isotope, set Initial beam energy as max energy 
-  transfer.SetIncidentEnergyAngle(10, 0, 0);
+  transfer.SetA(27, 13, 0);            // 18Ne projectile
-  transfer.Seta( 4, 2);
+  TGraph* elossBeam = LoadELoss("../ELoss/HeLoss/E_vs_x_Al-27.dat"); 
-  transfer.Setb( 1, 1);
+  transfer.Seta(4, 2);                 // 4He target
+  transfer.Setb(1, 1);                 // outgoing proton from the primary transfer
+  transfer.SetB(30, 14);               // 21Na* heavy product
+  const double beamA = 27;                   // mass number of 27Al beam
 
-  //TODO add alpha source
+  bool enableSequentialDecay = false; // turning to false to disable sequential decay for now, can be set to true to enable
+  const int decayDaughterA = 20;
+  const int decayDaughterZ = 10;
+  const int decayEjectA = 1;
+  const int decayEjectZ = 1;
 
-  std::vector<float> ExAList = {0};
+  // Excited state lists (projectile and heavy-product excitation states)
-  std::vector<float> ExList = {0, 1, 2};
+  std::vector<float> ExAList = {0};              // 18Ne projectile excitations in MeV
+  std::vector<float> ExList = {0};             // 21Na* excitation in MeV
 
-  double vertexXRange[2] = {   -5,    5}; // mm
+  // define vertex position uniform distribution ranges (mm)
-  double vertexYRange[2] = {   -5,    5}; 
+  double vertexXRange[2] = {   -5, 5}; // mm - 5, 5
-  double vertexZRange[2] = { -100,  100}; 
+  double vertexYRange[2] = {   -5, 5}; // -5, 5
+  double vertexZRange[2] = { -174.3, 174.3}; // -174.3, 174.3 (full length of gas volume, centered at 0)
+  const double beamEntranceZ = -280; //vertexZRange[0]; // mm, assumed beam entrance into the gas
 
-  double sigmaSX3_W = -1; // mm, < 0 use mid-point
-  double sigmaSX3_L = 3; // mm, < 0 use mid-point
-  double sigmaPW_A  = 0; // from 0 to 1.
-  double sigmaPW_C  = 0; // from 0 to 1.
 
-  //###################################################
+  // detector resolution / uncertainty parameters
+  double sigmaSX3_W = 0; // mm, if < 0 use mid-point (no spread in SX3 horizontal dimension)
+  double sigmaSX3_L = 0;  // mm, vertical spread for SX3
+  double sigmaPW_A  = 0;  // normalized anode uncertainty term (0-1)
+  double sigmaPW_C  = 0;  // normalized cathode uncertainty term (0-1)
 
+  // status printout
   printf("------------ Vertex :\n");
   printf("X : %7.2f - %7.2f mm\n", vertexXRange[0], vertexXRange[1]);
   printf("Y : %7.2f - %7.2f mm\n", vertexYRange[0], vertexYRange[1]);
@@ -57,83 +139,194 @@ int main(int argc, char **argv){
   printf("          Anode : %.1f mm\n", sigmaPW_A);
   printf("        Cathode : %.1f mm\n", sigmaPW_C);
   printf("        num_eve : %d \n",numEvent);
+
+  // calculates energy/momentum/kinematics constants for transfer reaction
   transfer.CalReactionConstant();
 
   int nExA = ExAList.size();
   int nEx  = ExList.size();
 
-  ANASEN * anasen = new ANASEN();
+  // optional visualization control: pass "vis" as 3rd arg
-  SX3 * sx3 = anasen->GetSX3();    
+  bool enableVis = (argc >= 3 && strcmp(argv[2], "vis") == 0);
-  PW * pw = anasen->GetPW(); 
+  TApplication *app = nullptr;
+  if(enableVis){
+    app = new TApplication("anasenVis", &argc, argv);
+  }
 
+  // storage for tracks during simulation (for visualization)
+  std::vector<TVector3> visTrackVertex, visTrackDir, visTrackHitPos;
+  std::vector<std::pair<int,int>> visTrackWires;  // {anodeID, cathodeID}
+
+  // create detector representation in memory
+  ANASEN * anasen = new ANASEN();       // top-level detector object
+  SX3 * sx3 = anasen->GetSX3();         // silicon array part
+  PW * pw = anasen->GetPW();            // proportional wire chamber part
+  QQQ * qqq = anasen->GetQQQ();         // optional QQQ detector part, not used in this simulation but can be enabled for visualization
+
+  // output file + trees
   TString saveFileName = "SimAnasen1.root";
   printf("\e[32m#################################### building Tree in %s\e[0m\n", saveFileName.Data());
   TFile * saveFile = new TFile(saveFileName, "recreate");
-  TTree * tree = new TTree("tree", "tree");
+  TTree * tree1 = new TTree("tree1", "tree1");
+  TTree * tree2 = new TTree("tree2", "tree2");
    
+
+  // beam and CM variables saved in tree
   double KEA;
-  tree->Branch("beamKEA",     &KEA, "beamKEA/D");
+  double KEA2;
+  double beamPath_cm;
+  double beamEnergy;
+  double beamEnergyLoss;
+  tree1->Branch("beamKEA",      &KEA, "beamKEA/D");
+  tree2->Branch("beamKEA",      &KEA2, "beamKEA/D");
+  tree1->Branch("beamPath_cm",  &beamPath_cm, "beamPath_cm/D");
+  tree2->Branch("beamPath_cm",  &beamPath_cm, "beamPath_cm/D");
+  tree1->Branch("beamEnergy",   &beamEnergy, "beamEnergy/D");
+  tree2->Branch("beamEnergy",   &beamEnergy, "beamEnergy/D");
+  tree1->Branch("beamEnergyLoss", &beamEnergyLoss, "beamEnergyLoss/D");
+  tree2->Branch("beamEnergyLoss", &beamEnergyLoss, "beamEnergyLoss/D");
 
   double thetaCM, phiCM;
-  tree->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  double thetaCM2, phiCM2;
-  tree->Branch("phiCM",     &phiCM, "phiCM/D");
+  tree1->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  tree1->Branch("phiCM",     &phiCM, "phiCM/D");
+  tree2->Branch("thetaCM", &thetaCM2, "thetaCM/D");
+  tree2->Branch("phiCM",     &phiCM2, "phiCM/D");
 
-  double thetab, phib, Tb;
+  // outgoing particles in lab frame (light/heavy)
-  double thetaB, phiB, TB;
+  double thetab, phib, Tb, qqqTb;
-  tree->Branch("thetab", &thetab, "thetab/D");
+  double thetaB, phiB, TB, qqqTB;
-  tree->Branch("phib",     &phib, "phib/D");
+  std::array<double, 2> T;
-  tree->Branch("Tb",         &Tb, "Tb/D");
+  tree1->Branch("thetab", &thetab, "thetab/D"); // polar angle of light particle in lab frame
-  tree->Branch("thetaB", &thetaB, "thetaB/D");
+  tree1->Branch("phib",     &phib, "phib/D"); // azimuthal angle of light particle in lab frame
-  tree->Branch("phiB",     &phiB, "phiB/D");
+  tree1->Branch("Tb",         &Tb, "Tb/D"); // kinetic energy of light particle at vertex (before energy loss)
-  tree->Branch("TB",         &TB, "TB/D");
+  tree1->Branch("thetaB", &thetaB, "thetaB/D");
+  tree1->Branch("phiB",     &phiB, "phiB/D");
+  tree1->Branch("TB",         &TB, "TB/D"); // kinetic energy of heavy particle at vertex (before energy loss)
+  tree1->Branch("T",          &T, "T/D");   // placeholder for true Q-value, currently set to 0 for simplicity
+  tree1->Branch("qqqTb", &qqqTb, "qqqTb/D"); // kinetic energy of light particle at vertex (before energy loss) for events where the light particle hits the QQQ, currently set to 0 for simplicity
+  tree1->Branch("qqqTB", &qqqTB, "qqqTB/D"); // kinetic energy of heavy particle at vertex (before energy loss) for events where the light
 
+  double thetab2, phib2, Tb2, qqqTb2;
+  double thetaB2, phiB2, TB2, qqqTB2;
+  std::array<double, 2> T2;
+  tree2->Branch("thetab", &thetab2, "thetab/D");
+  tree2->Branch("phib",     &phib2, "phib/D");
+  tree2->Branch("Tb",         &Tb2, "Tb/D");
+  tree2->Branch("thetaB", &thetaB2, "thetaB/D");
+  tree2->Branch("phiB",     &phiB2, "phiB/D");
+  tree2->Branch("TB",         &TB2, "TB/D");
+  tree2->Branch("T",          &T2, "T/D");
+  tree2->Branch("qqqTb", &qqqTb2, "qqqTb/D");
+  tree2->Branch("qqqTB", &qqqTB2, "qqqTB/D");
+
+  // excitation state identifiers
   int ExAID;
   double ExA;
-  tree->Branch("ExAID", &ExAID, "ExAID/I");
+  tree1->Branch("ExAID", &ExAID, "ExAID/I"); // projectile excitation state ID
-  tree->Branch("ExA",     &ExA, "ExA/D");
+  tree1->Branch("ExA",     &ExA, "ExA/D"); // projectile excitation energy in MeV
+
+  int ExAID2;
+  double ExA2;
+  tree2->Branch("ExAID", &ExAID2, "ExAID/I");
+  tree2->Branch("ExA",     &ExA2, "ExA/D");
 
   int ExID;
   double Ex;
-  tree->Branch("ExID", &ExID, "ExID/I");
+  tree1->Branch("ExID", &ExID, "ExID/I"); // target excitation state ID
-  tree->Branch("Ex",     &Ex, "Ex/D");
+  tree1->Branch("Ex",     &Ex, "Ex/D"); // target excitation energy in MeV
 
+  int ExID2;
+  double Ex2;
+  tree2->Branch("ExID", &ExID2, "ExID/I");
+  tree2->Branch("Ex",     &Ex2, "Ex/D");
+
+  // true vertex position in target volume
   double vertexX, vertexY, vertexZ;
-  tree->Branch("vX",     &vertexX, "VertexX/D");
+  tree1->Branch("vX",     &vertexX, "VertexX/D"); // true vertex X position in mm
-  tree->Branch("vY",     &vertexY, "VertexY/D");
+  tree1->Branch("vY",     &vertexY, "VertexY/D"); // true vertex Y position in mm
-  tree->Branch("vZ",     &vertexZ, "VertexZ/D");
+  tree1->Branch("vZ",     &vertexZ, "VertexZ/D"); // true vertex Z position in mm
 
+  double vertexX2, vertexY2, vertexZ2;
+  tree2->Branch("vX",     &vertexX2, "VertexX/D");
+  tree2->Branch("vY",     &vertexY2, "VertexY/D");
+  tree2->Branch("vZ",     &vertexZ2, "VertexZ/D");
+
+  // reconstructed SX3 hit position
   double sx3X, sx3Y, sx3Z;
-  tree->Branch("sx3X",     &sx3X, "sx3X/D");
+  tree1->Branch("sx3X",     &sx3X, "sx3X/D"); // reconstructed X position from SX3 (with optional smearing) in mm
-  tree->Branch("sx3Y",     &sx3Y, "sx3Y/D");
+  tree1->Branch("sx3Y",     &sx3Y, "sx3Y/D"); // reconstructed Y position from SX3 (with optional smearing)
-  tree->Branch("sx3Z",     &sx3Z, "sx3Z/D");
+  tree1->Branch("sx3Z",     &sx3Z, "sx3Z/D"); // reconstructed Z position from SX3 (with optional smearing)
 
+  double sx3X2, sx3Y2, sx3Z2;
+  tree2->Branch("sx3X",     &sx3X2, "sx3X/D");
+  tree2->Branch("sx3Y",     &sx3Y2, "sx3Y/D");
+  tree2->Branch("sx3Z",     &sx3Z2, "sx3Z/D");
+
+  double qqqX, qqqY, qqqZ;
+  tree1->Branch("qqqX",     &qqqX, "qqqX/D"); // reconstructed X position from QQQ (with optional smearing) in mm
+  tree1->Branch("qqqY",     &qqqY, "qqqY/D"); // reconstructed Y position from QQQ (with optional smearing)
+  tree1->Branch("qqqZ",     &qqqZ, "qqqZ/D"); // reconstructed Z position from QQQ (with optional smearing)
+
+  double qqqX2, qqqY2, qqqZ2;
+  tree2->Branch("qqqX",     &qqqX2, "qqqX/D");
+  tree2->Branch("qqqY",     &qqqY2, "qqqY/D");
+  tree2->Branch("qqqZ",     &qqqZ2, "qqqZ/D");
+
+  // PW nearest and next nearest wires
   int anodeID[2], cathodeID[2];
-  tree->Branch("aID", anodeID, "anodeID/I");
+  int anodeID2[2], cathodeID2[2];
-  tree->Branch("cID", cathodeID, "cathodeID/I");
+  tree1->Branch("aID", anodeID, "anodeID/I"); // anodeID[0] is nearest anode wire, anodeID[1] is next nearest anode wire
+  tree1->Branch("cID", cathodeID, "cathodeID/I"); // cathodeID[0] is nearest cathode wire, cathodeID[1] is next nearest cathode wire
+  tree2->Branch("aID", anodeID2, "anodeID/I");
+  tree2->Branch("cID", cathodeID2, "cathodeID/I");
 
+  // distances to nearest wires
   double anodeDist[2], cathodeDist[2];
-  tree->Branch("aDist",   anodeDist, "anodeDist/D");
+  double anodeDist2[2], cathodeDist2[2];
-  tree->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  tree1->Branch("aDist",   anodeDist, "anodeDist/D");
+  tree1->Branch("cDist",  cathodeDist, "cathodeDist/D");
+  tree2->Branch("aDist",   anodeDist2, "anodeDist/D");
+  tree2->Branch("cDist",  cathodeDist2, "cathodeDist/D");
 
-  int sx3ID, sx3Up, sx3Dn, sx3Bk;
+  // SX3 channel assignment and Z fraction (depth) information
+  int sx3ID, sx3Up, sx3Dn, sx3Bk, qqqID;
   double sx3ZFrac;
-  tree->Branch("sx3ID",   &sx3ID, "sx3ID/I");
+  int sx3ID2, sx3Up2, sx3Dn2, sx3Bk2, qqqID2;
-  tree->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  double sx3ZFrac2;
-  tree->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree1->Branch("sx3ID",   &sx3ID, "sx3ID/I");
-  tree->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree1->Branch("qqqID",   &qqqID, "qqqID/I");
-  tree->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  tree1->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  tree1->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree1->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree1->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+  tree2->Branch("sx3ID",   &sx3ID2, "sx3ID/I");
+  tree2->Branch("qqqID",   &qqqID2, "qqqID/I");
+  tree2->Branch("sx3Up",   &sx3Up2, "sx3Up/I");
+  tree2->Branch("sx3Dn",   &sx3Dn2, "sx3Dn/I");
+  tree2->Branch("sx3Bk",   &sx3Bk2, "sx3Bk/I");
+  tree2->Branch("sx3ZFrac", &sx3ZFrac2, "sx3ZFrac/D");
 
+  // reconstructed angles from PW track fit, method 1 and 2
   double reTheta, rePhi;
-  tree->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  double reTheta2, rePhi2;
-  tree->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  tree1->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  tree1->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+  tree2->Branch("reTheta", &reTheta2, "reconstucted_theta/D");
+  tree2->Branch("rePhi",     &rePhi2, "reconstucted_phi/D");
 
   double reTheta1, rePhi1;
-  tree->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  double reTheta12, rePhi12;
-  tree->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  tree1->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  tree1->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+  tree2->Branch("reTheta1", &reTheta12, "reconstucted_theta1/D");
+  tree2->Branch("rePhi1",     &rePhi12, "reconstucted_phi1/D");
 
+  // reconstructed vertex Z from PW fit
   double z0;
-  tree->Branch("z0",     &z0, "reconstucted_Z/D");
+  double z02;
-
+  tree1->Branch("z0",     &z0, "reconstucted_Z/D");
+  tree2->Branch("z0",     &z02, "reconstucted_Z/D");
 
   //========timer
   TBenchmark clock;
@@ -142,9 +335,10 @@ int main(int argc, char **argv){
   clock.Start("timer");
   shown = false;
 
-  //================================= Calculate event
+  //================================= Calculate event loop
   for( int i = 0; i < numEvent ; i++){
 
+    // randomly sample target/projectile excitations
     ExAID = gRandom->Integer(nExA);
     ExA = ExAList[ExAID];
     transfer.SetExA(ExA);
@@ -153,77 +347,214 @@ int main(int argc, char **argv){
     Ex = ExList[ExID];
     transfer.SetExB(Ex);
 
+    // recalc kinematic constants for chosen states
     transfer.CalReactionConstant();
 
-    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ; 
+    // vertex position in target volume
-    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
-
-    //==== Calculate reaction
-    TLorentzVector * output = transfer.Event(thetaCM, phiCM);
-    TLorentzVector Pb = output[2];
-    TLorentzVector PB = output[3];
-
-    thetab = Pb.Theta() * TMath::RadToDeg();
-    thetaB = PB.Theta() * TMath::RadToDeg();
-
-    Tb = Pb.E() - Pb.M();
-    TB = PB.E() - PB.M();
-
-    phib = Pb.Phi() * TMath::RadToDeg();
-    phiB = PB.Phi() * TMath::RadToDeg();
-
     vertexX = (vertexXRange[1]- vertexXRange[0])*gRandom->Rndm() +  vertexXRange[0];
     vertexY = (vertexYRange[1]- vertexYRange[0])*gRandom->Rndm() +  vertexYRange[0];
     vertexZ = (vertexZRange[1]- vertexZRange[0])*gRandom->Rndm() +  vertexZRange[0];
 
     TVector3 vertex(vertexX, vertexY, vertexZ);
 
+    // compute beam energy at the event vertex from the gas path length
+    beamPath_cm = TVector3(vertexZ - beamEntranceZ, vertexX, vertexY).Mag() * 0.1;
+    if( beamPath_cm < 0 ) beamPath_cm = 0;
+    beamEnergy = elossBeam->Eval(beamPath_cm); // MeV
+    beamEnergyLoss = elossBeam->Eval(0.0) - beamEnergy;
+    KEA = beamEnergy / beamA;
+    transfer.SetIncidentEnergyAngle(KEA, 0, 0);
+    transfer.CalReactionConstant();
+
+    // isotropic CM direction
+    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ; // polar angle in CM frame
+    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
+
+    //==== Calculate reaction kinematics in lab frame for the primary transfer
+    TLorentzVector * output = transfer.Event(thetaCM, phiCM); // returns array of outputs
+    TLorentzVector Pb = output[2]; // primary proton from transfer
+    TLorentzVector PB = output[3]; // excited 21Na* heavy product
+
+    thetab = Pb.Theta() * TMath::RadToDeg();
+    Tb = (Pb.E() - Pb.M()); // kinetic energy of the light proton from the primary transfer
+    thetaB = PB.Theta() * TMath::RadToDeg();
+    TB = (PB.E() - PB.M());
+    phib = Pb.Phi() * TMath::RadToDeg();
+    phiB = PB.Phi() * TMath::RadToDeg();
+    T[0] = Tb;
+    T[1] = TB;
+
+    //secondary decay
+    TLorentzVector decayProton;
+    TLorentzVector heavy20;
+    if(enableSequentialDecay){
+      heavy20 = SimulateSequentialDecay(PB, decayDaughterA, decayDaughterZ,
+                                       decayEjectA, decayEjectZ, decayProton);
+      thetab2 = decayProton.Theta() * TMath::RadToDeg();
+      phib2 = decayProton.Phi() * TMath::RadToDeg();
+      Tb2 = decayProton.E() - decayProton.M();
+      thetaB2 = heavy20.Theta() * TMath::RadToDeg();
+      phiB2 = heavy20.Phi() * TMath::RadToDeg();
+      TB2 = heavy20.E() - heavy20.M();
+      T2[0] = Tb2;
+      T2[1] = TB2;
+    } else {
+      thetab2 = TMath::QuietNaN();
+      phib2  = TMath::QuietNaN();
+      Tb2    = TMath::QuietNaN();
+      thetaB2 = TMath::QuietNaN();
+      phiB2 = TMath::QuietNaN();
+      TB2 = TMath::QuietNaN();
+      T2[0] = TMath::QuietNaN();
+      T2[1] = TMath::QuietNaN();
+    }
+
+    delete [] output;
+
+    // set direction vector from lab angle
     TVector3 dir(1, 0, 0);
     dir.SetTheta(thetab * TMath::DegToRad());
     dir.SetPhi(phib * TMath::DegToRad());
 
-   
+    // run detector response models for PW and SX3
     pw->FindWireID(vertex, dir, false);
     sx3->FindSX3Pos(vertex, dir, false);
+    qqq->FindQQQPos(vertex, dir, false);
 
     PWHitInfo hitInfo = pw->GetHitInfo();
 
-    anodeID[0]   = hitInfo.nearestWire.first;
+    anodeID[0]   = hitInfo.nearestWire.first; // nearest anode wire ID
-    cathodeID[0] = hitInfo.nearestWire.second;
+    cathodeID[0] = hitInfo.nearestWire.second; // nearest cathode wire ID
-    anodeID[1]   = hitInfo.nextNearestWire.first;
+    anodeID[1]   = hitInfo.nextNearestWire.first; // next nearest anode wire ID
-    cathodeID[1] = hitInfo.nextNearestWire.second;
+    cathodeID[1] = hitInfo.nextNearestWire.second; // next nearest cathode wire ID
 
-    anodeDist[0]   = hitInfo.nearestDist.first;
+    anodeDist[1]   = hitInfo.nextNearestDist.first; // distance to next nearest anode wire
-    cathodeDist[0] = hitInfo.nearestDist.second;
+    cathodeDist[1] = hitInfo.nextNearestDist.second; // distance to next nearest cathode wire
-    anodeDist[1]   = hitInfo.nextNearestDist.first;
-    cathodeDist[1] = hitInfo.nextNearestDist.second;
 
+    if(IsDeadAnode(anodeID[0])) continue;
+    if(IsDeadCathode(cathodeID[0])) continue;
+
+    // SX3 hit channel info and depth fraction
     sx3ID = sx3->GetID();
+    qqqID = qqq->GetID();
+
+    if(IsDeadSX3(sx3ID)) continue;
+
+    anodeDist[0]   = hitInfo.nearestDist.first; // distance to nearest anode wire
+    cathodeDist[0] = hitInfo.nearestDist.second; // distance to nearest cathode wire
+    
+    //start HERE
     if( sx3ID >= 0 ){
       sx3Up    = sx3->GetChUp();
       sx3Dn    = sx3->GetChDn();
       sx3Bk    = sx3->GetChBk();
       sx3ZFrac = sx3->GetZFrac();
       
-      //Introduce uncertaity
+      // apply intrinsic detector resolution to true SX3 hit position
-      // TVector3 hitPos = sx3->GetHitPos();
+      // for no smearing comment out and use GetHitPos();
       TVector3 hitPos = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
 
       sx3X = hitPos.X();
       sx3Y = hitPos.Y();
       sx3Z = hitPos.Z();
 
+      // store track data for visualization if enabled
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+      // reconstruct track from PW readings + SX3 hit
       pw->CalTrack(hitPos, anodeID[0], cathodeID[0], false);
       reTheta = pw->GetTrackTheta() * TMath::RadToDeg();
       rePhi   = pw->GetTrackPhi() * TMath::RadToDeg();
 
+      // alternative track algorithm with uncertainty parameters
       pw->CalTrack2(hitPos, hitInfo, sigmaPW_A, sigmaPW_C, false);
       reTheta1 = pw->GetTrackTheta() * TMath::RadToDeg();
       rePhi1   = pw->GetTrackPhi() * TMath::RadToDeg();
 
       z0 = pw->GetZ0();
+      tree1->Fill();
 
+      // fill tree2 using the secondary proton from 21Na* decay
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      pw->FindWireID(vertex, dir2, false);
+      sx3->FindSX3Pos(vertex, dir2, false);
+      PWHitInfo hitInfo2 = pw->GetHitInfo();
+
+      anodeID2[0]   = hitInfo2.nearestWire.first;
+      cathodeID2[0] = hitInfo2.nearestWire.second;
+      anodeID2[1]   = hitInfo2.nextNearestWire.first;
+      cathodeID2[1] = hitInfo2.nextNearestWire.second;
+
+      anodeDist2[1]   = hitInfo2.nextNearestDist.first;
+      cathodeDist2[1] = hitInfo2.nextNearestDist.second;
+
+      if(IsDeadAnode(anodeID2[0]) || IsDeadCathode(cathodeID2[0])){
+        sx3ID2 = -1;
       } else {
+        sx3ID2 = sx3->GetID();
+      }
+
+      if(sx3ID2 < 0 || IsDeadSX3(sx3ID2)){
+        sx3ID2 = -1;
+        sx3Up2 = -1;
+        sx3Dn2 = -1;
+        sx3Bk2 = -1;
+        sx3ZFrac2 = TMath::QuietNaN();
+        sx3X2 = TMath::QuietNaN();
+        sx3Y2 = TMath::QuietNaN();
+        sx3Z2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+      } else {
+        anodeDist2[0]   = hitInfo2.nearestDist.first;
+        cathodeDist2[0] = hitInfo2.nearestDist.second;
+        sx3Up2    = sx3->GetChUp();
+        sx3Dn2    = sx3->GetChDn();
+        sx3Bk2    = sx3->GetChBk();
+        sx3ZFrac2 = sx3->GetZFrac();
+        TVector3 hitPos2 = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+        sx3X2 = hitPos2.X();
+        sx3Y2 = hitPos2.Y();
+        sx3Z2 = hitPos2.Z();
+        pw->CalTrack(hitPos2, anodeID2[0], cathodeID2[0], false);
+        reTheta2 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi2   = pw->GetTrackPhi() * TMath::RadToDeg();
+        pw->CalTrack2(hitPos2, hitInfo2, sigmaPW_A, sigmaPW_C, false);
+        reTheta12 = pw->GetTrackTheta() * TMath::RadToDeg();
+        rePhi12   = pw->GetTrackPhi() * TMath::RadToDeg();
+        z02       = pw->GetZ0();
+      }
+
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+      qqqX = TMath::QuietNaN();
+      qqqY = TMath::QuietNaN();
+      qqqZ = TMath::QuietNaN();
+
+      tree2->Fill();
+
+    }else if (false){//(qqqID >= 0){
+      // handle QQQ hit case
       sx3Up = -1;
       sx3Dn = -1;
       sx3Bk = -1;
@@ -233,23 +564,96 @@ int main(int argc, char **argv){
       sx3Y = TMath::QuietNaN();
       sx3Z = TMath::QuietNaN();
 
-      // for( int i = 0; i < 12; i++){
+      reTheta  = TMath::QuietNaN();
-      //   sx3Index[i] = -1;
+      rePhi    = TMath::QuietNaN();
-      // }
+      reTheta1 = TMath::QuietNaN();
+      rePhi1   = TMath::QuietNaN();
+      z0       = TMath::QuietNaN();
+
+      qqqTb = Tb; // for simplicity, using the same kinetic energy for QQQ hit events, can be modified to simulate energy loss if desired
+      qqqTB = TB;
+
+      Tb = TMath::QuietNaN(); // mark kinetic energy as invalid for SX3 hit case
+      TB = TMath::QuietNaN();
+
+      TVector3 hitPos = qqq->GetHitPos();
+
+      qqqX = hitPos.X();
+      qqqY = hitPos.Y();
+      qqqZ = hitPos.Z();
+
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        //visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+
+      tree1->Fill();
+
+      TVector3 dir2(1, 0, 0);
+      dir2.SetTheta(thetab2 * TMath::DegToRad());
+      dir2.SetPhi(phib2 * TMath::DegToRad());
+
+      qqq->FindQQQPos(vertex, dir2, false);
+
+      if(qqqID2 < 0){
+        qqqID2 = -1;
+        qqqX2 = TMath::QuietNaN();
+        qqqY2 = TMath::QuietNaN();
+        qqqZ2 = TMath::QuietNaN();
+        anodeDist2[0] = TMath::QuietNaN();
+        cathodeDist2[0] = TMath::QuietNaN();
+        reTheta2 = TMath::QuietNaN();
+        rePhi2 = TMath::QuietNaN();
+        reTheta12 = TMath::QuietNaN();
+        rePhi12 = TMath::QuietNaN();
+        z02 = TMath::QuietNaN();
+        anodeID2[0]   = TMath::QuietNaN(); // no valid anode wire for QQQ hit case
+        cathodeID2[0] = TMath::QuietNaN(); // no valid cathode wire for QQQ hit case
+        anodeID2[1]   = TMath::QuietNaN(); // no valid next nearest anode wire for QQQ hit case
+        cathodeID2[1] = TMath::QuietNaN(); // no valid next nearest cathode wire for QQQ hit case
+        anodeDist2[1]   = TMath::QuietNaN();
+        cathodeDist2[1] = TMath::QuietNaN();
+      }
+
+      KEA2 = KEA;
+      thetaCM2 = thetaCM;
+      phiCM2 = phiCM;
+      ExAID2 = ExAID;
+      ExA2 = ExA;
+      ExID2 = ExID;
+      Ex2 = Ex;
+      vertexX2 = vertexX;
+      vertexY2 = vertexY;
+      vertexZ2 = vertexZ;
+
+      tree2->Fill();
+    }else{
+      // no valid SX3 hit: mark clearly invalid
+      sx3Up = -1;
+      sx3Dn = -1;
+      sx3Bk = -1;
+      sx3ZFrac = TMath::QuietNaN();
+
+      sx3X = TMath::QuietNaN();
+      sx3Y = TMath::QuietNaN();
+      sx3Z = TMath::QuietNaN();
 
       reTheta  = TMath::QuietNaN();
       rePhi    = TMath::QuietNaN();
-
       reTheta1 = TMath::QuietNaN();
       rePhi1   = TMath::QuietNaN();
-
       z0       = TMath::QuietNaN();
-
+      Tb       = TMath::QuietNaN(); // mark kinetic energy as invalid for no hit case
+      TB       = TMath::QuietNaN();
+      // fill tree with original data (no energy loss for these events)
+      //comment out tree fill for no hit case  
+      //tree1->Fill();
     }
 
-    tree->Fill();
-
     //#################################################################### Timer
+    // measure elapsed real time and print progress roughly every 10 sec
     clock.Stop("timer");
     Double_t time = clock.GetRealTime("timer");
     clock.Start("timer");
@@ -267,14 +671,76 @@ int main(int argc, char **argv){
 
   }
 
-  tree->Write();
+  // write results to ROOT file and close
-  int count = tree->GetEntries();
+  tree1->Write("", TObject::kOverwrite);
+  tree2->Write("", TObject::kOverwrite);
+  int count1 = tree1->GetEntries();
+  int count2 = tree2->GetEntries();
   saveFile->Close();
 
-  printf("=============== done. saved as %s. count(hit==1) : %d\n", saveFileName.Data(), count);
+  printf("=============== done. saved as %s. tree1 entries: %d, tree2 entries: %d\n", saveFileName.Data(), count1, count2);
+
+  if(enableVis){ // to enable visualization, run with 3rd argument "vis", e.g. "./anasenMC 1000 vis"
+    printf("Displaying geometry with %zu tracks from simulation\n", visTrackVertex.size());
+    
+    // Build full geometry with all wires
+    anasen->DrawAnasen(0, 23, 0, 23, -1, true);
+    
+    // Add all stored tracks to the geometry
+    TGeoManager *geom = anasen->GetGeoManager();
+    TGeoVolume *worldBox = anasen->GetWorldBox();
+    
+    if(geom && worldBox && visTrackVertex.size() > 0){
+      int trackNodeID = 500;  // start node IDs for tracks
+      
+      for(size_t iTrack = 0; iTrack < visTrackVertex.size(); ++iTrack){
+        TVector3 vertex = visTrackVertex[iTrack];
+        TVector3 dir = visTrackDir[iTrack];
+        TVector3 hitPos = visTrackHitPos[iTrack];
+        
+        double theta = dir.Theta() * TMath::RadToDeg();
+        double phi = dir.Phi() * TMath::RadToDeg();
+        
+        // Add a line marker at the vertex
+        TGeoVolume *startMarker = geom->MakeSphere("startMarker", 0, 0, 2.0);
+        startMarker->SetLineColor(kBlack);
+        worldBox->AddNode(startMarker, trackNodeID, 
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(), 
+                                          new TGeoRotation("rot", 0, 0, 0)));
+        trackNodeID++;
+        
+        // Add track line from vertex toward hit position
+        TGeoVolume *trackLine = geom->MakeTube("trackLine", 0, 0, 0.08, 150.0);
+        trackLine->SetLineColor(kBlue);
+        worldBox->AddNode(trackLine, trackNodeID,
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(),
+                                          new TGeoRotation("rotTrack", phi + 90, theta, 0)));
+        trackNodeID++;
+        
+        // Add hit position marker
+        TGeoVolume *hitMarker = geom->MakeSphere("hitMarker", 0, 0, 2.0);
+        hitMarker->SetLineColor(kRed);
+        worldBox->AddNode(hitMarker, trackNodeID,
+                         new TGeoCombiTrans(hitPos.X(), hitPos.Y(), hitPos.Z(),
+                                          new TGeoRotation("rotHit", 0, 0, 0)));
+        trackNodeID++;
+      }
+      
+      // Redraw geometry with all tracks
+      geom->CloseGeometry();
+      geom->SetVisLevel(4);
+      worldBox->Draw("ogle");
+    }
+    
+    if(app){
+      printf("Entering ROOT event loop\n");
+      app->Run();
+    }
+  }
 
   delete anasen;
 
+
   return 0;
 
 }

Armory/histcomp.C

@@ -0,0 +1,178 @@
+void histcomp() {
+    gROOT->SetBatch(kTRUE);
+
+    // Open file
+    TFile *f = new TFile("SimAnasen1.root");
+
+    // Get trees (MAKE SURE names are correct)
+    TTree *tree1 = (TTree*)f->Get("tree");
+    TTree *tree2 = (TTree*)f->Get("tree2");
+
+    if (!tree1 || !tree2) {
+    printf("Error: could not find trees. Check names!\n");
+    return;
+    }
+
+    // Create output directory (overwrite-safe)
+    gSystem->Exec("mkdir -p plots");
+
+    // Get list of branches
+    TObjArray *branches = tree1->GetListOfBranches();
+    int nBranches = branches->GetEntries();
+    //int nBranches = 1;
+
+    // Loop over branches
+    for (int i = 0; i < nBranches; i++) {
+        TBranch *br = (TBranch*)branches->At(i);
+        TString name = br->GetName();
+
+        //printf("Processing branch: %s\n", name.Data());
+
+        // Create histograms (auto-range using Draw first)
+        TString h1name = "h1_" + name;
+        TString h2name = "h2_" + name;
+
+        // Temporary draw to get range
+        double min, max;
+
+        if(name == "T"){
+            //Get minimum value of T[0] and use as min  
+            min = tree2->GetMinimum("Tb");
+            max = tree1->GetMaximum("TB");
+        }else{
+
+            tree1->Draw(name, "", "goff");
+
+            min = fmin(tree1->GetMinimum(name),
+                    tree2->GetMinimum(name));
+
+            max = fmax(tree1->GetMaximum(name),
+                    tree2->GetMaximum(name));
+        }
+
+        //if (min == max) continue; // skip constant branches
+
+        // Expand range slightly
+        double margin = 0.1 * (max - min);
+        min -= margin;
+        max += margin;
+
+        TH1D *h1 = new TH1D(h1name, name, 100, min, max);
+        TH1D *h2 = new TH1D(h2name, name, 100, min, max);
+
+        // Fill histograms
+        if(name == "T"){
+
+            // Fill both array elements into same histogram
+            tree1->Draw("Tb>>+" + h1name, "", "goff");
+            tree1->Draw("TB>>+" + h1name, "", "goff");
+
+            tree2->Draw("Tb>>+" + h2name, "", "goff");
+            tree2->Draw("TB>>+" + h2name, "", "goff");
+
+        }else{
+
+            tree1->Draw(name + ">>" + h1name, "", "goff");
+            tree2->Draw(name + ">>" + h2name, "", "goff");
+
+        }
+
+        // Style
+        h1->SetLineColor(kRed);
+        h1->SetLineWidth(2);
+
+        h2->SetLineColor(kBlue);
+        h2->SetLineWidth(2);
+
+        // Normalize (optional but useful)
+        //if (h1->GetEntries() > 0) h1->Scale(1.0 / h1->GetEntries());
+        //if (h2->GetEntries() > 0) h2->Scale(1.0 / h2->GetEntries());
+
+        // Canvas
+        TCanvas *c = new TCanvas("c", name, 900, 600); //arguments are (name, title, width, height)
+
+        c->SetRightMargin(0.18);
+        c->Modified(); 
+        c->Update();
+
+        h1->SetTitle(name + ";"+name+";Counts");
+        h1->Draw("HIST");
+        h2->Draw("HIST SAME");
+
+        gPad->Update();
+
+        TPaveStats *st = (TPaveStats*)h1->FindObject("stats");
+
+        st->SetX1NDC(0.85); // New X start (left)
+        st->SetY1NDC(0.5); // New Y start (bottom)
+        st->SetX2NDC(0.98); // New X end (right)
+        st->SetY2NDC(0.8); // New Y end (top)
+        st->Draw();
+        gPad->Modified();
+        gPad->Update();
+
+
+        // Legend
+        TLegend *leg = new TLegend(0.65 + .2,0.75 + .1,0.88 + .1,0.88 + .1);
+        leg->AddEntry(h1, "tree1", "l");
+        leg->AddEntry(h2, "tree2", "l");
+        leg->Draw();
+        //to plot both as one histogram in root, can use tree2->Draw("T(0)"); for light particle and tree2->Draw("T(1)") for heavy particle
+        // Save plot (overwrite each run)
+        TString filename = "plots/" + name + ".png";
+        c->SaveAs(filename);
+        // Optional: save log plots as well
+
+        if (false) { // set to True to also save log plots
+            c->SetLogy(1);
+            h1->SetTitle(name + " (log);"+name+";Counts");
+            c->SaveAs("plots/" + name + "_logy.png");
+
+            c->SetLogy(0);
+            c->SetLogx(1);
+            h1->SetTitle(name + " (log);"+name+";Counts");
+            c->SaveAs("plots/" + name + "_logx.png");
+
+            // Clean up
+            delete c;
+            delete h1;
+            delete h2;
+        }
+
+
+
+    }
+
+    // dEb on y, SX3z on x
+    TH2D *h2d = new TH2D("h2d", "dEb vs SX3z;SX3z (cm);dEb (MeV)", 500, tree2->GetMinimum("sx3Z"), tree2->GetMaximum("sx3Z"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb")); //arguments are (name, title, xbins, xlow, xup, ybins, ylow, yup)
+    tree2->Draw("dEb:sx3Z>>h2d", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2d = new TCanvas("c2d", "dEb vs SX3z", 900, 600);
+    h2d->Draw("COLZ");
+    c2d->SaveAs("plots/dEb_vs_SX3z.png");
+
+    TH2D *h2z = new TH2D("h2z", "dEb vs z0", 500, tree2->GetMinimum("z0"), tree2->GetMaximum("z0"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:z0>>h2z", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2z = new TCanvas("c2z", "dEb vs z0", 900, 600);
+    h2z->Draw("COLZ");
+    c2z->SaveAs("plots/dEb_vs_z0.png");
+
+    TH2D *h2theta = new TH2D("h2theta", "dEb vs reTheta", 500, tree2->GetMinimum("reTheta"), tree2->GetMaximum("reTheta"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:reTheta>>h2theta", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2theta = new TCanvas("c2theta", "dEb vs reTheta", 900, 600);
+    h2theta->Draw("COLZ");
+    c2theta->SaveAs("plots/dEb_vs_reTheta.png");
+
+    TH2D *h2phi = new TH2D("h2phi", "dEb vs rePhi", 500, tree2->GetMinimum("rePhi"), tree2->GetMaximum("rePhi"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:rePhi>>h2phi", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2phi = new TCanvas("c2phi", "dEb vs rePhi", 900, 600);
+    h2phi->Draw("COLZ");
+    c2phi->SaveAs("plots/dEb_vs_rePhi.png");
+
+    TH2D *h2dE = new TH2D("h2dE", "dEb vs Tb", 500, tree2->GetMinimum("Tb"), tree2->GetMaximum("Tb"), 500, tree2->GetMinimum("dEb"), tree2->GetMaximum("dEb"));
+    tree2->Draw("dEb:Tb>>h2dE", "", "goff"); // arguments are "y:x>>histogram", "selection", "options"
+    TCanvas *c2dE = new TCanvas("c2dE", "dEb vs Tb", 900, 600);
+    h2dE->Draw("COLZ");
+    c2dE->SaveAs("plots/dEb_vs_Tb.png");
+
+    printf("Done! Plots saved in ./plots/\n");
+}

Armory/macro.h

@@ -0,0 +1,56 @@
+#ifndef MACRO_H
+#define MACRO_H
+
+#define MaxNPorts 4   //for optical link
+#define MaxNBoards 4  //for both optical link and usb
+
+#define MaxNDigitizer MaxNPorts * MaxNBoards
+
+#define MaxRegChannel 16 
+#define MaxNChannels 64
+#define MaxRecordLength 0x3fff * 8 
+#define MaxSaveFileSize  1024 * 1024 * 1024 * 2
+
+#define MaxDisplayTraceTimeLength 20000 //ns
+#define ScopeUpdateMiliSec  200 // msec
+#define MaxNumberOfTrace  5   // in an event
+
+#define SETTINGSIZE 2048
+
+#define DAQLockFile "DAQLock.dat"
+#define PIDFile  "pid.dat"
+
+#include <sys/time.h> /** struct timeval, select() */
+
+inline unsigned int getTime_us(){
+  unsigned int time_us;
+  struct timeval t1;
+  struct timezone tz;
+  gettimeofday(&t1, &tz);
+  time_us = (t1.tv_sec) * 1000 * 1000 + t1.tv_usec;
+  return time_us;
+}
+
+#include <chrono>
+inline unsigned long long getTime_ns(){
+  std::chrono::high_resolution_clock::time_point currentTime = std::chrono::high_resolution_clock::now();
+  std::chrono::nanoseconds nanoseconds = std::chrono::duration_cast<std::chrono::nanoseconds>(currentTime.time_since_epoch());
+  return nanoseconds.count();
+}
+
+typedef unsigned short uShort;
+typedef unsigned int uInt;
+typedef unsigned long  uLong;
+typedef unsigned long long ullong;
+
+#define DebugMode 0 //process check, when 1, print out all function call
+
+// if DebugMode is 1, define DebugPrint() to be printf(), else, DebugPrint() define nothing
+#if DebugMode
+#define DebugPrint(fmt, ...) printf(fmt "::%s\n",##__VA_ARGS__, __func__);
+#else
+#define DebugPrint(fmt, ...)
+#endif
+
+
+#endif

Armory/run_script.C

@@ -0,0 +1,4 @@
+.L ANASEN_model.C
+.L anasenMS_root.cpp+
+ANASEN_model();
+Run(10);

Armory/vis_helpers.h

@@ -0,0 +1,61 @@
+#ifndef VIS_HELPERS_H
+#define VIS_HELPERS_H
+
+#include <TSystem.h>
+#include <TEvePointSet.h>
+#include <TTree.h>
+#include <vector>
+#include <mutex>
+
+static TEvePointSet* gVisPts = nullptr;
+static std::mutex gVisMutex;
+
+// Recommended: call once after opening TEve and adding a point set to gEve
+inline void SetVisPointSet(TEvePointSet* pts) { gVisPts = pts; }
+
+inline void UpdateVisPointSet(const std::vector<double>& x,
+                              const std::vector<double>& y,
+                              const std::vector<double>& z)
+{
+  if(!gVisPts) return;
+  std::lock_guard<std::mutex> lk(gVisMutex);
+  gVisPts->Reset();
+  size_t n = std::min({x.size(), y.size(), z.size()});
+  for(size_t i=0; i<n; ++i) gVisPts->SetNextPoint(x[i], y[i], z[i]);
+  if(gEve) {
+    gEve->Redraw3D();
+    gSystem->ProcessEvents();
+  }
+}
+
+// Fill a tree with pointlists (one entry per event); must have branches defined once by caller
+inline void RecordTreeXYZ(TTree* outTree,
+                           const std::vector<double>& x,
+                           const std::vector<double>& y,
+                           const std::vector<double>& z)
+{
+  if(!outTree) return;
+  static std::vector<double> tx, ty, tz;
+  tx = x;
+  ty = y;
+  tz = z;
+
+  if(outTree->GetBranch("x") == nullptr) outTree->Branch("x", &tx);
+  if(outTree->GetBranch("y") == nullptr) outTree->Branch("y", &ty);
+  if(outTree->GetBranch("z") == nullptr) outTree->Branch("z", &tz);
+
+  // Do NOT call SetBranchAddress() for the branch we are filling.
+  outTree->Fill();
+  outTree->GetCurrentFile()->Flush();
+}
+
+inline void PushEventAndRecord(const std::vector<double>& x,
+                               const std::vector<double>& y,
+                               const std::vector<double>& z,
+                               TTree* outTree = nullptr)
+{
+  if(outTree) RecordTreeXYZ(outTree, x, y, z);
+  UpdateVisPointSet(x,y,z);
+}
+
+#endif // VIS_HELPERS_H

Armory/vis_inproc.cpp

@@ -0,0 +1,65 @@
+//In-ROOT sim data
+
+// vis_inproc.cpp
+#include <TApplication.h>
+#include <TGeoManager.h>
+#include <TEveManager.h>
+#include <TEvePointSet.h>
+#include <TSystem.h>
+#include <TRandom3.h>
+#include <thread>
+#include <chrono>
+#include <vector>
+#include <iostream>
+
+void runSimulationAndUpdate(TEvePointSet* pts){
+  TRandom3 rnd(0);
+  for(int ev=0; ev<10000; ++ev){
+    pts->Reset();
+    int n = 100;
+    for(int i=0;i<n;++i){
+      double x = rnd.Uniform(-50,50);
+      double y = rnd.Uniform(-50,50);
+      double z = rnd.Uniform(-50,50);
+      pts->SetNextPoint(x,y,z);
+    }
+    gEve->Redraw3D();
+    gSystem->ProcessEvents();
+    std::this_thread::sleep_for(std::chrono::milliseconds(100));
+  }
+}
+
+void StartVis(const char* geomfile=nullptr){
+  int argc=0; char** argv=nullptr;
+  TApplication app("app",&argc,argv);
+  if(geomfile) TGeoManager::Import(geomfile);
+  TEveManager::Create();
+  TEvePointSet *pts = new TEvePointSet("hits");
+  gEve->AddElement(pts);
+  // runSimulationAndUpdate(pts);  // or leave update API to caller
+  app.Run();
+}
+
+int main(int argc, char** argv){
+  TApplication app("app",&argc,argv);
+
+  if(argc>1) TGeoManager::Import(argv[1]);
+
+  TEveManager::Create();
+
+  TEvePointSet *pts = new TEvePointSet("hits");
+  pts->SetMarkerStyle(20);
+  pts->SetMarkerSize(1.2);
+  pts->SetMarkerColor(kRed);
+  gEve->AddElement(pts);
+
+  // Option A: run simulation in same thread but yield to event loop inside the sim
+  runSimulationAndUpdate(pts);
+
+  // Option B: run sim in a separate thread (only if sim avoids ROOT globals)
+  // std::thread simThread(runSimulationAndUpdate, pts);
+  // simThread.detach();
+
+  app.Run();
+  return 0;
+}

BatchProcess.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+#parallel -j 6 echo ./ProcessRun.sh {1} 2000 0 ::: {020..400}
+
+#parallel --results log/log_{}.txt --ctag -j 6 ./ProcessRun.sh {1} 2000 0 ::: {020..400} # for 17F
+
+parallel --results log/log_{}.txt --ctag -j 6 ./ProcessRun.sh {1} 2000 0 ::: {001..021}  

Calibration.C

@@ -0,0 +1,270 @@
+
+#define Calibration_cxx
+
+#include <TH2.h>
+#include <TF1.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include "Armory/HistPlotter.h"
+#include "TVector3.h"
+#include "Calibration.h"
+
+TH2F *hQQQFVB;
+HistPlotter *plotter;
+int padID = 0;
+
+TCutG *cut;
+std::map<std::tuple<int, int, int>, std::vector<std::pair<double, double>>> dataPoints;
+
+bool qqqEcut = false;
+
+// Gain Arrays
+const int MAX_QQQ = 4;
+const int MAX_RING = 16;
+const int MAX_WEDGE = 16;
+double qqqwGain[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+// double qqqrGain[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+bool qqqwGainValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+// bool qqqrGainValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+
+void Calibration::Begin(TTree * /*tree*/)
+{
+    plotter = new HistPlotter("Calib.root", "TFILE");
+    // ----------------------- Load QQQ Gains
+    {
+        std::string filename = "qqq_GainMatch.txt";
+        std::ifstream infile(filename);
+        if (!infile.is_open())
+        {
+            std::cerr << "Error opening " << filename << "!" << std::endl;
+        }
+        else
+        {
+            int det, ring, wedge;
+            double gainw, gainr;
+            while (infile >> det >> ring >> wedge >> gainw >> gainr)
+            {
+                qqqwGain[det][ring][wedge] = gainw;
+                // qqqrGain[det][ring][wedge] = gainr;
+                qqqwGainValid[det][ring][wedge] = (gainw > 0);
+                // qqqrGainValid[det][ring][wedge] = (gainr > 0);
+            }
+            infile.close();
+            std::cout << "Loaded QQQ gains from " << filename << std::endl;
+        }
+    }
+    for (int det = 0; det < MAX_QQQ; det++)
+    {
+        for (int ring = 0; ring < MAX_RING; ring++)
+        {
+            for (int wedge = 0; wedge < MAX_WEDGE; wedge++)
+            {
+                TString hname = Form("hCal_qqq%d_ring%d_wedge%d", det, ring, wedge);
+                TString htitle = Form("QQQ det%d ring%d wedge%d; Energy (arb); Counts", det, ring, wedge);
+                // hQQQSpectra[det][ring][wedge] = new TH1F(hname, htitle, 4000, 0, 16000);
+            }
+        }
+    }
+}
+
+Bool_t Calibration::Process(Long64_t entry)
+{
+    b_qqqMulti->GetEntry(entry);
+    b_qqqID->GetEntry(entry);
+    b_qqqCh->GetEntry(entry);
+    b_qqqE->GetEntry(entry);
+    b_qqqT->GetEntry(entry);
+
+    qqq.CalIndex();
+
+    for (int i = 0; i < qqq.multi; i++)
+    {
+        for (int j = i + 1; j < qqq.multi; j++)
+        {
+            if (qqq.e[i] > 100)
+                qqqEcut = true;
+            if (qqq.id[i] == qqq.id[j])
+            {
+                int chWedge = -1;
+                int chRing = -1;
+                float eWedgeRaw = 0.0;
+                float eWedge = 0.0;
+                float eRingRaw = 0.0;
+                float eRing = 0.0;
+                if (qqq.ch[i] < 16 && qqq.ch[j] >= 16 && /*qqqrGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16] &&*/ qqqwGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16])
+                {
+                    chWedge = qqq.ch[i];
+                    eWedgeRaw = qqq.e[i];
+                    eWedge = qqq.e[i] * qqqwGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
+                    // printf("Wedge E: %.2f  Gain: %.4f \n", eWedge, qqqGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16]);
+                    chRing = qqq.ch[j] - 16;
+                    eRingRaw = qqq.e[j];
+                    eRing = qqq.e[j];// * qqqrGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16];
+                }
+                else if (qqq.ch[j] < 16 && qqq.ch[i] >= 16 && /*qqqrGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16] &&*/ qqqwGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16])
+                {
+                    chWedge = qqq.ch[j];
+                    eWedge = qqq.e[j] * qqqwGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16];
+                    eWedgeRaw = qqq.e[j];
+
+                    chRing = qqq.ch[i] - 16;
+                    eRing = qqq.e[i];// * qqqrGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
+                    eRingRaw = qqq.e[i];
+                }
+                else
+                    continue;
+
+                // hQQQFVB->Fill(eWedge, eRing);
+                plotter->Fill2D(Form("hRaw_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 16000, 400, 0, 16000, eWedgeRaw, eRingRaw, "ERaw");
+                plotter->Fill2D(Form("hGM_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 16000, 400, 0, 16000, eWedge, eRing, "EGM");
+                plotter->Fill2D("hRawQQQ", 4000, 0, 16000, 4000, 0, 16000, eWedgeRaw, eRingRaw);
+                plotter->Fill2D("hGMQQQ", 4000, 0, 16000, 4000, 0, 16000, eWedge, eRing);
+
+                TString histName = Form("hQQQFVB_id%d_r%d_w%d", qqq.id[i], chRing, chWedge);
+                // TH2F *hist2d = (TH2F *)gDirectory->Get(histName);
+                // if (!hist2d)
+                // {
+                //     hist2d = new TH2F(histName, Form("QQQ Det%d R%d W%d;Wedge E;Ring E", qqq.id[i], chRing, chWedge), 400, 0, 16000, 400, 0, 16000);
+                // }
+
+                // hist2d->Fill(eWedge, eRing);
+                // if (cut && cut->IsInside(eWedge, eRing))
+                const double MIN_ADC = 1500.0;
+                const double MAX_ADC = 3000.0;
+
+                // if (eWedge >= MIN_ADC && eWedge <= MAX_ADC &&
+                //     eRing >= MIN_ADC && eRing <= MAX_ADC)
+                double ratio = (eWedge > 0.0) ? (eRing / eWedge) : 0.0;
+
+                double maxslope = 1.5;
+
+                bool validPoint = false;
+                if (ratio < maxslope && ratio > 1. / maxslope)
+                {
+                    // Accumulate data for gain matching
+                    dataPoints[{qqq.id[i], chRing, chWedge}].emplace_back(eWedge, eRing);
+                }
+            }
+        }
+    }
+
+    return kTRUE;
+}
+
+void Calibration::Terminate()
+{
+    const double AM241_PEAK = 5485.56;
+    const double P_PEAK = 7000; // keV
+
+    double calibArray[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+    bool calibValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+
+    std::ofstream outFile("qqq_Calib.txt");
+    if (!outFile.is_open())
+    {
+        std::cerr << "Error opening qqq_Calib.txt!" << std::endl;
+        return;
+    }
+
+    //----------------------------------------------------------------------
+    // 1. Create per–channel 1D spectra in ADC from stored gain-matched data
+    //----------------------------------------------------------------------
+
+    std::map<std::tuple<int, int, int>, TH1F *> spectra;
+
+    for (auto &kv : dataPoints)
+    {
+        int det, ring, wedge;
+        std::tie(det, ring, wedge) = kv.first;
+
+        TString hname = Form("hSpec_d%d_r%d_w%d", det, ring, wedge);
+        TH1F *h = new TH1F(hname, hname, 4000, 0, 16000);
+
+        for (auto &p : kv.second)
+        {
+            double eWedge = p.first; // already gain-matched ADC
+            double eRing = p.second;
+
+            // Use ring ADC for calibration (cleaner alpha peak)
+            h->Fill(eRing);
+        }
+
+        spectra[kv.first] = h;
+    }
+
+    //----------------------------------------------------------------------
+    // 2. Fit Am-241 peak and extract keV/ADC calibration slope
+    //----------------------------------------------------------------------
+
+    for (auto &kv : spectra)
+    {
+        int det, ring, wedge;
+        std::tie(det, ring, wedge) = kv.first;
+        TH1F *h = kv.second;
+
+        if (!h || h->GetEntries() < 50)
+            continue;
+
+        int binMax = h->GetMaximumBin();
+        double adcPeak = h->GetXaxis()->GetBinCenter(binMax);
+
+        if (adcPeak <= 0)
+            continue;
+
+        // double slope_keV = AM241_PEAK / adcPeak; // keV per ADC
+        double slope_keV = P_PEAK / adcPeak; // keV per ADC
+
+        calibArray[det][ring][wedge] = slope_keV;
+        calibValid[det][ring][wedge] = true;
+
+        outFile << det << " " << wedge << " " << ring << " "
+                << slope_keV << "\n";
+
+        // printf("QQQ DET=%d R=%d W=%d  ADCpeak=%.1f  slope_keV=%.6f\n",det, ring, wedge, adcPeak, slope_keV);
+    }
+
+    outFile.close();
+    std::cout << "Wrote QQQ calibration file qqq_Calib.txt\n";
+
+    //----------------------------------------------------------------------
+    // 3. Build fully calibrated 2D combined histogram
+    //----------------------------------------------------------------------
+
+    TH2F *hCal = new TH2F("hCal",
+                          "All QQQ Calibrated;Wedge Energy (keV);Ring Energy (keV)",
+                          800, 0, 7000,
+                          800, 0, 7000);
+
+    for (auto &kv : dataPoints)
+    {
+        int det, ring, wedge;
+        std::tie(det, ring, wedge) = kv.first;
+
+        if (!calibValid[det][ring][wedge])
+            continue;
+
+        double slope = calibArray[det][ring][wedge];
+
+        for (auto &p : kv.second)
+        {
+            double eWGM = p.first; // gain matched ADC
+            double eRGM = p.second;
+
+            double eWkeV = eWGM * slope / 1000;
+            double eRkeV = eRGM * slope / 1000;
+
+            hCal->Fill(eWkeV, eRkeV);
+            plotter->Fill2D("hCalQQQ", 4000, 0, 10, 4000, 0, 10, eWkeV, eRkeV);
+            plotter->Fill2D(Form("hRCal_qqq%d", det), 16, 0, 15, 400, 0, 24, ring, eRkeV, "RingCal");
+            plotter->Fill2D(Form("hWCal_qqq%d", det), 16, 0, 15, 400, 0, 24, wedge, eWkeV, "WedgeCal");
+        }
+    }
+
+    plotter->FlushToDisk();
+    std::cout << "Calibrated 2D QQQ histogram saved.\n";
+}

Calibration.h

@@ -0,0 +1,114 @@
+#ifndef Calibration_h
+#define Calibration_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class Calibration : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   Calibration(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~Calibration() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(Calibration,0);
+};
+
+#endif
+
+#ifdef Calibration_cxx
+void Calibration::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t Calibration::Notify(){
+
+   return kTRUE;
+}
+
+void Calibration::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void Calibration::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef Calibration_cxx

DetectorConstruction.cc

@@ -0,0 +1,131 @@
+#include "DetectorConstruction.hh"
+
+#include "G4RunManager.hh"
+#include "G4NistManager.hh"
+#include "G4Box.hh"
+#include "G4Tubs.hh"
+#include "G4LogicalVolume.hh"
+#include "G4PVPlacement.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4RotationMatrix.hh"
+#include "G4ThreeVector.hh"
+
+DetectorConstruction::DetectorConstruction()
+: G4VUserDetectorConstruction(),
+  fScoringVolume(nullptr)
+{}
+
+DetectorConstruction::~DetectorConstruction()
+{}
+
+G4VPhysicalVolume* DetectorConstruction::Construct()
+{
+  // Get nist material manager
+  G4NistManager* nist = G4NistManager::Instance();
+
+  // Materials
+  G4Material* vacuum = nist->FindOrBuildMaterial("G4_Galactic");
+  G4Material* al = nist->FindOrBuildMaterial("G4_Al");
+
+  // World
+  G4double worldx = 200.*mm;
+  G4double worldy = 200.*mm;
+  G4double worldz = 200.*mm;
+  G4Box* solidWorld = new G4Box("World", worldx, worldy, worldz);
+  G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWorld, vacuum, "World");
+  G4VPhysicalVolume* physWorld = new G4PVPlacement(0, G4ThreeVector(), logicWorld, "World", 0, false, 0, true);
+
+  // Axes (optional, for visualization)
+  G4Tubs* solidAxis = new G4Tubs("Axis", 0, 0.1*mm, 5.*mm, 0, 360*deg);
+  G4LogicalVolume* logicAxisX = new G4LogicalVolume(solidAxis, al, "AxisX");
+  G4LogicalVolume* logicAxisY = new G4LogicalVolume(solidAxis, al, "AxisY");
+  G4LogicalVolume* logicAxisZ = new G4LogicalVolume(solidAxis, al, "AxisZ");
+
+  G4RotationMatrix* rotX = new G4RotationMatrix();
+  rotX->rotateY(90*deg);
+  rotX->rotateZ(90*deg);
+  new G4PVPlacement(rotX, G4ThreeVector(5*mm, 0, 0), logicAxisX, "AxisX", logicWorld, false, 0);
+
+  G4RotationMatrix* rotY = new G4RotationMatrix();
+  rotY->rotateX(90*deg);
+  new G4PVPlacement(rotY, G4ThreeVector(0, 5*mm, 0), logicAxisY, "AxisY", logicWorld, false, 0);
+
+  new G4PVPlacement(0, G4ThreeVector(0, 0, 5*mm), logicAxisZ, "AxisZ", logicWorld, false, 0);
+
+  // ANASEN geometry
+  const int nWire = 24;
+  const int wireShift = 3;
+  const G4double zLen = 350.*mm;
+  const G4double radiusA = 38.*mm;
+  const G4double radiusC = 43.*mm;
+
+  G4double dAngle = wireShift * 2 * CLHEP::pi / nWire;
+  G4double radiusAnew = radiusA * cos(dAngle / 2.);
+  G4double wireALength = sqrt(zLen*zLen + pow(2 * radiusA * sin(dAngle/2.), 2));
+  G4double wireATheta = atan2(2 * radiusA * sin(dAngle / 2.), zLen);
+
+  G4Tubs* solidPC_A = new G4Tubs("PC_A", 0, 0.01*mm, wireALength/2., 0, 360*deg);
+  G4LogicalVolume* logicPC_A = new G4LogicalVolume(solidPC_A, al, "PC_A");
+
+  for(int i = 0; i < nWire; i++){
+    G4double phi = 2 * CLHEP::pi / nWire * i + dAngle / 2.;
+    G4ThreeVector pos(radiusAnew * cos(phi), radiusAnew * sin(phi), 0);
+    G4RotationMatrix* rot = new G4RotationMatrix();
+    rot->rotateZ(360./nWire * (i + wireShift/2.) * deg);
+    rot->rotateY(wireATheta);
+    new G4PVPlacement(rot, pos, logicPC_A, "PC_A", logicWorld, false, i);
+  }
+
+  G4double radiusCnew = radiusC * cos(dAngle / 2.);
+  G4double wireCLength = sqrt(zLen*zLen + pow(2 * radiusC * sin(dAngle/2.), 2));
+  G4double wireCTheta = atan2(2 * radiusC * sin(dAngle / 2.), zLen);
+
+  G4Tubs* solidPC_C = new G4Tubs("PC_C", 0, 0.01*mm, wireCLength/2., 0, 360*deg);
+  G4LogicalVolume* logicPC_C = new G4LogicalVolume(solidPC_C, al, "PC_C");
+
+  for(int i = 0; i < nWire; i++){
+    G4double phi = 2 * CLHEP::pi / nWire * i - dAngle/2.;
+    G4ThreeVector pos(radiusCnew * cos(phi), radiusCnew * sin(phi), 0);
+    G4RotationMatrix* rot = new G4RotationMatrix();
+    rot->rotateZ(360./nWire * (i - wireShift/2.) * deg);
+    rot->rotateY(-wireCTheta);
+    new G4PVPlacement(rot, pos, logicPC_C, "PC_C", logicWorld, false, i);
+  }
+
+  const int nSX3 = 12;
+  const G4double sx3Radius = 88.*mm;
+  const G4double sx3Width = 40.*mm;
+  const G4double sx3Length = 75.*mm;
+  const G4double sx3Gap = 5.*mm;
+
+  G4Box* solidSX3 = new G4Box("SX3", 0.1*mm, sx3Width/2., sx3Length/2.);
+  G4LogicalVolume* logicSX3 = new G4LogicalVolume(solidSX3, al, "SX3");
+  fScoringVolume = logicSX3;
+
+  for(int i = 0; i < nSX3; i++){
+    G4double phi = 2 * CLHEP::pi / nSX3 * (i + 0.5);
+    G4ThreeVector pos1(sx3Radius * cos(phi), sx3Radius * sin(phi), sx3Length/2. + sx3Gap);
+    G4RotationMatrix* rot1 = new G4RotationMatrix();
+    rot1->rotateZ(360./nSX3 * (i + 0.5) * deg);
+    new G4PVPlacement(rot1, pos1, logicSX3, "SX3_front", logicWorld, false, 2*i);
+
+    G4ThreeVector pos2(sx3Radius * cos(phi), sx3Radius * sin(phi), -sx3Length/2. - sx3Gap);
+    G4RotationMatrix* rot2 = new G4RotationMatrix();
+    rot2->rotateZ(360./nSX3 * (i + 0.5) * deg);
+    new G4PVPlacement(rot2, pos2, logicSX3, "SX3_back", logicWorld, false, 2*i+1);
+  }
+
+  const G4double qqqR1 = 50.*mm;
+  const G4double qqqR2 = 100.*mm;
+  G4Tubs* solidQQQ = new G4Tubs("QQQ", qqqR1, qqqR2, 0.5*mm, 5*deg, 85*deg);
+  G4LogicalVolume* logicQQQ = new G4LogicalVolume(solidQQQ, al, "QQQ");
+
+  for(int i = 0; i < 4; i++){
+    G4ThreeVector pos(0, 0, 100.*mm);
+    G4RotationMatrix* rot = new G4RotationMatrix();
+    rot->rotateZ(360./4 * i * deg);
+    new G4PVPlacement(rot, pos, logicQQQ, "QQQ", logicWorld, false, i);
+  }
+
+  return physWorld;
+}

DetectorConstruction.hh

@@ -0,0 +1,20 @@
+#ifndef DetectorConstruction_h
+#define DetectorConstruction_h 1
+
+#include "G4VUserDetectorConstruction.hh"
+
+class DetectorConstruction : public G4VUserDetectorConstruction
+{
+  public:
+    DetectorConstruction();
+    virtual ~DetectorConstruction();
+
+    virtual G4VPhysicalVolume* Construct();
+
+    G4LogicalVolume* GetScoringVolume() const { return fScoringVolume; }
+
+  private:
+    G4LogicalVolume* fScoringVolume;
+};
+
+#endif

ELoss/EXtable.py

@@ -0,0 +1,131 @@
+import pycatima as catima
+import numpy as np
+import pandas as pd
+from scipy.interpolate import interp1d
+from scipy.integrate import cumulative_trapezoid
+import matplotlib.pyplot as plt
+
+# GAS SETUP
+
+P_TORR = 400
+TEMP_K = 293.15
+R = 8.3144
+
+# Gas density
+p_pa = P_TORR * 133.322
+molar_density = p_pa / (R * TEMP_K)
+
+m_he = 4.0026
+m_c  = 12.0000
+m_o  = 15.9949
+
+m_mix_avg = (0.96 * m_he) + (0.04 * (m_c + 2*m_o))
+
+rho_g_cm3 = (molar_density * m_mix_avg) / 1e6
+
+print(f"Gas density = {rho_g_cm3:.6e} g/cm^3")
+
+# MATERIAL
+material_def = [
+    (m_he, 2, 0.96),
+    (m_c,  6, 0.04),
+    (m_o,  8, 0.08)
+]
+
+gas_mix = catima.Material(material_def)
+gas_mix.density(rho_g_cm3)
+
+# FUNCTION
+
+def make_E_vs_x(
+    z,
+    mass_u,
+    emax_mev,
+    label,
+    npoints=500
+):
+
+    projectile = catima.Projectile(mass_u, z)
+
+    # Energy grid
+    E = np.linspace(0.01, emax_mev, npoints)
+
+    # Stopping power array
+    S_mass = np.zeros_like(E)
+
+    for i, energy in enumerate(E):
+
+        projectile.T(energy / mass_u)
+
+        # MeV / (g/cm^2)
+        S_mass[i] = catima.dedx(projectile, gas_mix)
+
+    # Convert to MeV/cm
+    S_linear = S_mass * rho_g_cm3
+
+    # Sort descending energy
+    sort_idx = np.argsort(E)[::-1]
+
+    E = E[sort_idx]
+    S_linear = S_linear[sort_idx]
+
+    # Integrate dx/dE = 1/S(E)
+    invS = 1.0 / S_linear
+
+    x = cumulative_trapezoid(
+        invS,
+        E,
+        initial=0
+    )
+
+    x = -x
+
+    # Output table
+    output = pd.DataFrame({
+        "Distance_cm": x,
+        "Energy_MeV": E
+    })
+
+    outfile = f"E_vs_x_{label}.dat"
+
+    output.to_csv(
+        outfile,
+        sep='\t',
+        index=False
+    )
+
+    print(f"Saved: {outfile}")
+
+    return x, E
+
+# RUN
+#proton parameters: z=1, mass_u=1.0078, emax_mev=20
+#alpha parameters: z=2, mass_u=4.0026, emax_mev=40
+x, E = make_E_vs_x(
+    z=1,
+    mass_u=1.0078,
+    emax_mev=20,
+    label="proton"
+)
+
+x, E = make_E_vs_x(
+    z=2,
+    mass_u=4.0026,
+    emax_mev=40,
+    label="alpha"
+)
+
+# PLOT
+
+plt.figure(figsize=(8,6))
+
+plt.plot(x, E)
+
+plt.xlabel("Distance in Gas (cm)")
+plt.ylabel("Energy (MeV)")
+plt.title("Energy Loss Curve")
+
+plt.grid(True)
+
+plt.show()
+#gives data in units of Energy (MeV) and Distance (cm). To convert to E(x), you can use the cumulative energy

ELoss/Eloss.cpp

@@ -0,0 +1,248 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <map>
+#include <cmath>
+#include <memory>
+#include <sstream>
+#include <algorithm>
+#include <filesystem>
+
+// ROOT
+#include "TFile.h"
+#include "TTree.h"
+#include "TH1D.h"
+#include "TH2D.h"
+#include "TCanvas.h"
+
+// Catima
+#include <catima/catima.h>
+
+using namespace std;
+
+/* =========================
+   GLOBAL STRUCTURES
+========================= */
+
+struct Particle {
+    int z;
+    double mass_u;
+    double emax;
+    string name;
+};
+
+map<string, Particle> particles = {
+    {"alpha",    {2, 4.0026, 40, "alpha"}},
+    {"proton",   {1, 1.0078, 20, "proton"}},
+    {"deuteron", {1, 2.0141, 30, "deuteron"}}
+};
+
+/* =========================
+   INTERPOLATION STORAGE
+========================= */
+
+struct EnergyTable {
+    vector<double> x;
+    vector<double> E;
+};
+
+map<string, EnergyTable> table_cache;
+
+/* Linear interpolation */
+double interp(const vector<double>& x, const vector<double>& y, double xi) {
+    if (xi <= x.front()) return y.front();
+    if (xi >= x.back()) return y.back();
+
+    auto it = upper_bound(x.begin(), x.end(), xi);
+    int i = distance(x.begin(), it) - 1;
+
+    double x0 = x[i], x1 = x[i+1];
+    double y0 = y[i], y1 = y[i+1];
+
+    return y0 + (y1 - y0) * (xi - x0) / (x1 - x0);
+}
+
+/* =========================
+   ENERGY TABLE GENERATION
+========================= */
+
+void make_E_vs_x(int z, double mass_u, double emax, string label, int npoints, double P_torr, double T) {
+
+    double R = 8.3144;
+
+    double p_pa = P_torr * 133.322;
+    double molar_density = p_pa / (R * T);
+
+    double m_he = 4.0026;
+    double m_c = 12.0;
+    double m_o = 15.9949;
+
+    double m_mix = 0.96*m_he + 0.04*(m_c + 2*m_o);
+
+    double rho = (molar_density * m_mix) / 1e6;
+
+    catima::Material gas({
+        {m_he, 2, 0.96},
+        {m_c,  6, 0.04},
+        {m_o,  8, 0.08}
+    });
+    gas.density(rho);
+
+    catima::Projectile proj(mass_u, z);
+
+    vector<double> E(npoints);
+    vector<double> S(npoints);
+
+    for (int i = 0; i < npoints; i++) {
+        E[i] = 0.01 + i * (emax / npoints);
+
+        proj.T(E[i] / mass_u);
+        S[i] = catima::dedx(proj, gas) * rho;
+    }
+
+    reverse(E.begin(), E.end());
+    reverse(S.begin(), S.end());
+
+    vector<double> x(npoints, 0.0);
+
+    for (int i = 1; i < npoints; i++) {
+        double invS = 1.0 / S[i];
+        x[i] = x[i-1] + 0.5 * (invS + 1.0/S[i-1]) * (E[i] - E[i-1]);
+    }
+
+    ofstream out("E_vs_x_" + label + ".dat");
+    for (int i = 0; i < npoints; i++) {
+        out << x[i] << "\t" << E[i] << "\n";
+    }
+
+    cout << "Saved E_vs_x_" << label << ".dat\n";
+}
+
+/* =========================
+   LOAD TABLE
+========================= */
+
+EnergyTable load_table(string fname) {
+    EnergyTable t;
+    ifstream in(fname);
+
+    double x, E;
+    while (in >> x >> E) {
+        t.x.push_back(x);
+        t.E.push_back(E);
+    }
+    return t;
+}
+
+/* =========================
+   GET TABLE
+========================= */
+
+EnergyTable& get_table(string particle) {
+    if (!table_cache.count(particle)) {
+        table_cache[particle] = load_table("E_vs_x_" + particle + ".dat");
+    }
+    return table_cache[particle];
+}
+
+/* =========================
+   ENERGY FUNCTIONS
+========================= */
+
+double energy_loss(string p, double Ei, double dx) {
+    auto &t = get_table(p);
+
+    double xi = interp(t.E, t.x, Ei);
+    double xf = xi + dx;
+
+    double Ef = interp(t.x, t.E, xf);
+    return max(Ef, 0.0);
+}
+
+double energy_reconstruction(string p, double Ef, double dx) {
+    auto &t = get_table(p);
+
+    double xf = interp(t.E, t.x, Ef);
+    double xi = xf - dx;
+
+    double Ei = interp(t.x, t.E, xi);
+    return max(Ei, 0.0);
+}
+
+double energy_distance(string p, double Ei, double Ef) {
+    auto &t = get_table(p);
+
+    double xi = interp(t.E, t.x, Ei);
+    double xf = interp(t.E, t.x, Ef);
+
+    return fabs(xf - xi);
+}
+
+/* =========================
+   ROOT FILE ANALYSIS
+========================= */
+
+void process_file(string filename) {
+
+    TFile f(filename.c_str());
+    TTree *tree = (TTree*)f.Get("tree");
+
+    double Tb, thetab, sx3Z;
+
+    tree->SetBranchAddress("Tb", &Tb);
+    tree->SetBranchAddress("thetab", &thetab);
+    tree->SetBranchAddress("sx3Z", &sx3Z);
+
+    vector<double> Ei, theta, sx3;
+
+    Long64_t n = tree->GetEntries();
+
+    for (Long64_t i = 0; i < n; i++) {
+        tree->GetEntry(i);
+
+        double th = thetab * M_PI / 180.0;
+        if (sin(th) == 0) continue;
+
+        Ei.push_back(Tb);
+        theta.push_back(th);
+        sx3.push_back(sx3Z);
+    }
+
+    cout << "Processed " << Ei.size() << " events\n";
+}
+
+/* =========================
+   MAIN CLI (simplified)
+========================= */
+
+int main() {
+
+    string cmd;
+
+    cout << "C++ PCEnergy Shell\n";
+
+    while (true) {
+        cout << ">> ";
+        getline(cin, cmd);
+
+        if (cmd == "exit") break;
+
+        if (cmd.rfind("make table", 0) == 0) {
+            string name = cmd.substr(11);
+            auto p = particles[name];
+
+            make_E_vs_x(p.z, p.mass_u, p.emax, p.name, 500, 400, 293.15);
+        }
+
+        else if (cmd.rfind("energy loss", 0) == 0) {
+            cout << "Use API call version in compiled mode\n";
+        }
+
+        else {
+            cout << "Unknown command\n";
+        }
+    }
+
+    return 0;
+}

ELoss/Eloss_HeAlpha

@@ -0,0 +1,121 @@
+1.00E-03	3.82E+02
+1.50E-03	3.68E+02
+2.00E-03	3.60E+02
+2.50E-03	3.57E+02
+3.00E-03	3.57E+02
+4.00E-03	3.62E+02
+5.00E-03	3.70E+02
+6.00E-03	3.81E+02
+7.00E-03	3.94E+02
+8.00E-03	4.07E+02
+9.00E-03	4.20E+02
+1.00E-02	4.34E+02
+1.25E-02	4.69E+02
+1.50E-02	5.03E+02
+1.75E-02	5.36E+02
+2.00E-02	5.69E+02
+2.25E-02	6.01E+02
+2.50E-02	6.32E+02
+2.75E-02	6.62E+02
+3.00E-02	6.91E+02
+3.50E-02	7.47E+02
+4.00E-02	8.01E+02
+4.50E-02	8.53E+02
+5.00E-02	9.02E+02
+5.50E-02	9.49E+02
+6.00E-02	9.95E+02
+6.50E-02	1.04E+03
+7.00E-02	1.08E+03
+7.50E-02	1.12E+03
+8.00E-02	1.16E+03
+8.50E-02	1.20E+03
+9.00E-02	1.24E+03
+9.50E-02	1.28E+03
+1.00E-01	1.31E+03
+1.25E-01	1.48E+03
+1.50E-01	1.63E+03
+1.75E-01	1.76E+03
+2.00E-01	1.88E+03
+2.25E-01	1.98E+03
+2.50E-01	2.08E+03
+2.75E-01	2.16E+03
+3.00E-01	2.24E+03
+3.50E-01	2.37E+03
+4.00E-01	2.47E+03
+4.50E-01	2.54E+03
+5.00E-01	2.59E+03
+5.50E-01	2.63E+03
+6.00E-01	2.65E+03
+6.50E-01	2.66E+03
+7.00E-01	2.65E+03
+7.50E-01	2.64E+03
+8.00E-01	2.62E+03
+8.50E-01	2.60E+03
+9.00E-01	2.57E+03
+9.50E-01	2.54E+03
+1.00E+00	2.51E+03
+1.25E+00	2.33E+03
+1.50E+00	2.14E+03
+1.75E+00	1.98E+03
+2.00E+00	1.83E+03
+2.25E+00	1.71E+03
+2.50E+00	1.59E+03
+2.75E+00	1.49E+03
+3.00E+00	1.40E+03
+3.50E+00	1.25E+03
+4.00E+00	1.13E+03
+4.50E+00	1.03E+03
+5.00E+00	9.54E+02
+5.50E+00	8.87E+02
+6.00E+00	8.30E+02
+6.50E+00	7.80E+02
+7.00E+00	7.37E+02
+7.50E+00	6.98E+02
+8.00E+00	6.64E+02
+8.50E+00	6.33E+02
+9.00E+00	6.06E+02
+9.50E+00	5.80E+02
+1.00E+01	5.57E+02
+1.25E+01	4.67E+02
+1.50E+01	4.04E+02
+1.75E+01	3.56E+02
+2.00E+01	3.20E+02
+2.50E+01	2.67E+02
+2.75E+01	2.47E+02
+3.00E+01	2.30E+02
+3.50E+01	2.02E+02
+4.00E+01	1.81E+02
+4.50E+01	1.65E+02
+5.00E+01	1.51E+02
+5.50E+01	1.39E+02
+6.00E+01	1.30E+02
+6.50E+01	1.21E+02
+7.00E+01	1.14E+02
+7.50E+01	1.08E+02
+8.00E+01	1.02E+02
+8.50E+01	9.72E+01
+9.00E+01	9.27E+01
+9.50E+01	8.86E+01
+1.00E+02	8.50E+01
+1.25E+02	7.07E+01
+1.50E+02	6.09E+01
+1.75E+02	5.37E+01
+2.00E+02	4.82E+01
+2.25E+02	4.39E+01
+2.50E+02	4.04E+01
+2.75E+02	3.74E+01
+3.00E+02	3.50E+01
+3.50E+02	3.11E+01
+4.00E+02	2.81E+01
+4.50E+02	2.57E+01
+5.00E+02	2.38E+01
+5.50E+02	2.22E+01
+6.00E+02	2.09E+01
+6.50E+02	1.98E+01
+7.00E+02	1.88E+01
+7.50E+02	1.80E+01
+8.00E+02	1.72E+01
+8.50E+02	1.66E+01
+9.00E+02	1.60E+01
+9.50E+02	1.55E+01
+1.00E+03	1.50E+01

ELoss/Graveyard/E_vs_x_heavy

@@ -0,0 +1,133 @@
+Distance_cm	Energy_MeV
+-0.0	10000.0
+5389774.75443511	9000.0
+10855647.976939568	8000.0
+16399799.429078534	7000.0
+22024503.893759202	6000.0
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ELoss/Graveyard/E_vs_x_light

@@ -0,0 +1,122 @@
+Distance_cm	Energy_MeV
+-0.0	1000.0
+38090.24265357861	950.0
+74970.65178025051	900.0
+110609.72374756227	850.0
+144982.69086113444	800.0
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+458143.67255874246	0.001

ELoss/Graveyard/Eloss_17F

@@ -0,0 +1,268 @@
+0.017002095	0.00676442
+0.03400419	0.0135288
+0.085010476	0.032227
+0.136016762	0.0489265
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+0.255031428	0.0823584
+0.340041904	0.102374
+0.42505238	0.120086
+0.510062856	0.135943
+0.595073332	0.150461
+0.680083808	0.164011
+0.765094284	0.176885
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+0.935115236	0.201176
+1.020125712	0.212518
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+1.360167616	0.254045
+1.530188568	0.27299
+1.70020952	0.291072
+2.040251424	0.325807
+2.380293328	0.359536
+2.720335232	0.392589
+3.060377136	0.425159
+3.40041904	0.457286
+4.2505238	0.536817
+5.10062856	0.615601
+5.95073332	0.693052
+6.80083808	0.769499
+7.65094284	0.845324
+8.5010476	0.920793
+10.20125712	1.07377
+11.90146664	1.23229
+13.60167616	1.39414
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+17.0020952	1.72459
+21.252619	2.15811
+25.5031428	2.61883
+29.7536666	3.10864
+34.0041904	3.62853
+38.2547142	4.17854
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+51.0062856	6.00863
+59.5073332	7.38089
+68.0083808	8.87668
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ELoss/Graveyard/Eloss_27Al

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ELoss/Graveyard/Eloss_alpha

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ELoss/Graveyard/Eloss_p

@@ -0,0 +1,268 @@
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ELoss/Graveyard/EvXconverter.py

@@ -0,0 +1,108 @@
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import sys
+
+from scipy.interpolate import interp1d
+from scipy.integrate import cumulative_trapezoid
+
+
+if len(sys.argv) > 1:
+    density = float(sys.argv[1])
+    print(f"Using user-provided density: {density} g/cm^3")
+else:
+    density = (2.1525e-7) * 400  # default density (g/cm^3)
+    print(f"No density provided, using default: {density} g/cm^3")
+
+filename = "/home/jamesszalkie/anasen/ELoss/Eloss_HeProton"
+delimiter = '\t'
+
+# Number of header lines to skip
+skiprows = 0
+
+data = pd.read_csv(
+    filename,
+    delimiter=delimiter,
+    skiprows=skiprows,
+    comment='#',
+    header=None
+)
+
+# Extract columns
+data = data.dropna()
+
+data[0] = pd.to_numeric(data[0], errors='coerce')
+data[1] = pd.to_numeric(data[1], errors='coerce')
+
+data = data.dropna()
+
+E = np.array(data[0], dtype=float)
+S_mass = np.array(data[1], dtype=float)
+
+# Convert:
+# (MeV cm^2/g) * (g/cm^3) = MeV/cm
+
+S_linear = S_mass * density
+
+sort_idx = np.argsort(E)[::-1]
+
+E = E[sort_idx]
+S_linear = S_linear[sort_idx]
+
+invS = 1.0 / S_linear
+
+x = cumulative_trapezoid(
+    invS,
+    E,
+    initial=0
+)
+
+x = -x
+
+E_of_x = interp1d(
+    x,
+    E,
+    bounds_error=False,
+    fill_value=0.0
+)
+
+x_of_E = interp1d(
+    E,
+    x,
+    bounds_error=False,
+    fill_value="extrapolate"
+)
+
+output = pd.DataFrame({
+    "Distance_cm": x,
+    "Energy_MeV": E
+})
+
+output.to_csv("/home/jamesszalkie/anasen/ELoss/E_vs_x_heavy", index=False, sep='\t')
+
+print("Saved E(x) dataset to:")
+print("/home/jamesszalkie/anasen/ELoss/E_vs_x_heavy")
+
+
+initial_energy = 10.0      # MeV
+distance = 5.0             # cm
+
+remaining_energy = E_of_x(distance)
+
+print("\nExample:")
+print(f"Initial Energy: {initial_energy:.3f} MeV")
+print(f"Distance traveled: {distance:.3f} cm")
+print(f"Remaining energy: {remaining_energy:.3f} MeV")
+
+
+plt.figure(figsize=(8,6))
+
+plt.plot(x, E)
+
+plt.xlabel("Distance in Helium (cm)")
+plt.ylabel("Proton Energy (MeV)")
+plt.title("Proton Energy Loss in Helium")
+
+plt.grid(True)
+
+plt.show()

ELoss/HeLoss/E_vs_x_Al-27.dat

@@ -0,0 +1,501 @@
+Distance_cm	Energy_MeV
+-0.0	56.0
+0.052815297998978813	55.88779559118236
+0.1055905973100307	55.77559118236473
+0.1583258903802704	55.663386773547096
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+3241.989400353421	0.05006012024048096
+3242.5361575547254	0.01

ELoss/anasenMS(ElossVersion).cpp

@@ -0,0 +1,518 @@
+#include "TRandom.h"      // ROOT random number generators, gRandom
+#include "TFile.h"        // ROOT file I/O
+#include "TTree.h"        // ROOT tree storage
+#include "TH1.h"          // 1D histograms
+#include "TH2.h"          // 2D histograms
+#include "TStyle.h"       // ROOT plotting style controls
+#include "TCanvas.h"      // ROOT canvas drawing
+#include "TBenchmark.h"   // timing measurement
+#include "TGraph.h"       // for energy loss interpolation
+#include <cstring>
+#include "TApplication.h" // ROOT app loop
+#include "ClassTransfer.h" // Reaction kinematics and MC event generation
+#include "ClassAnasen.h"   // ANASEN detector model classes (SX3, PW, etc.)
+#include <stdio.h>
+#include <stdlib.h>
+#include <set>
+#include "TLegend.h"
+#include "TH1D.h"
+#include "TObjArray.h"
+#include "TBranch.h"
+#include <iostream>
+#include <fstream>
+
+//======== Generate light particle based on reaction
+// calculate real and reconstructed tracks and Q-value uncertainty
+
+// Function to load energy loss table from file
+TGraph* LoadELoss(const char* filename) {
+  TGraph* g = new TGraph(filename, "%lg %lg");
+  return g;
+}
+
+bool IsDeadAnode(int id){
+    static std::set<int> dead = {}; // add dead anode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadCathode(int id){
+    static std::set<int> dead = {}; // add dead cathode IDs here, 0-23
+    return dead.count(id);
+}
+
+bool IsDeadSX3(int id){ 
+    static std::set<int> dead = {}; // add dead SX3 IDs here, 0-23 1,7,9,3
+    return dead.count(id);
+}
+
+static std::set<pair<int,int>> ReactionProductb = { {1,1} }; // add reaction product b (light particle) A,Z pairs here, e.g. {1,1} for proton, {4,2} for alpha 
+
+int main(int argc, char **argv){
+
+  printf("=========================================\n");
+  printf("===       ANASEN Monte Carlo          ===\n");
+  printf("=========================================\n");
+
+  // number of events can be overridden from command line
+  int numEvent = 1000000;
+  if( argc >= 2 ) numEvent = atoi(argv[1]);
+
+  // load energy loss tables (assume units: E in MeV, dE/dx in MeV/(mg/cm^2), density in mg/cm^3)
+  TGraph* elossAlpha = LoadELoss("../ELoss/E_vs_x_alpha.dat"); // for light particle (alpha)
+  TGraph* elossProton = LoadELoss("../ELoss/E_vs_x_proton.dat");     // for heavy particle (proton)
+  TGraph *invgAlpha = new TGraph(elossAlpha->GetN(), elossAlpha->GetY(), elossAlpha->GetX());
+  TGraph *invgProton = new TGraph(elossProton->GetN(), elossProton->GetY(), elossProton->GetX());
+
+  
+  //Plot energy loss tables (sanity check), vis will not work if this is ran without X11 display (e.g. on cluster), so comment out if running in headless mode
+  auto c1 = new TCanvas("c1", "Graph Example", 800, 600);
+  auto g = elossAlpha;
+  g->SetTitle("Energy Loss Table (Alpha);cm;Kinetic Energy (MeV)");
+  g->Draw("ALP");
+  g->SetLineColor(kRed);
+  //c1->SetLogy();
+  //c1->SetLogx();
+  c1->Print("eloss_alpha.png");
+
+  auto c2 = new TCanvas("c2", "Graph Example", 800, 600);
+  auto g2 = elossProton;
+  g2->SetTitle("Energy Loss Table (Proton);cm;Kinetic Energy (MeV)");
+  g2->Draw("ALP");
+  g2->SetLineColor(kBlue);
+  c2->Print("eloss_proton.png");
+
+  // Reaction setup: projectile + target configuration, energy, and product IDs
+  TransferReaction transfer;
+
+  transfer.SetA(18, 10, 0);           // e.g., 24Mg (Z=12) with 0 excitation
+  transfer.SetIncidentEnergyAngle((4.4), 0, 0); // arguments are KEA in MeV/u, theta and phi in degree
+  transfer.Seta( 4, 2);              // identify reaction product a in internal indexing e.g., 4He (alpha)
+  transfer.Setb(ReactionProductb.begin()->first, ReactionProductb.begin()->second);              // identify reaction product b e.g., 1H (proton)
+  transfer.SetB(21, 11);              // identify reaction product B e.g., 23Na (Z=11)
+
+  // TODO add alpha source or alternative reaction channel selection
+
+  // Excited state lists (target and projectile/excited products)
+  std::vector<float> ExAList = {0}; // projectile excitation states in MeV
+  std::vector<float> ExList = {0}; // target excitation states in MeV
+
+  // define vertex position uniform distribution ranges (mm)
+  double vertexXRange[2] = {   -5,    5}; // mm
+  double vertexYRange[2] = {   -5,    5};
+  double vertexZRange[2] = { -100,  100};
+
+  // detector resolution / uncertainty parameters
+  double sigmaSX3_W = -1; // mm, if < 0 use mid-point (no spread in SX3 horizontal dimension)
+  double sigmaSX3_L = 3;  // mm, vertical spread for SX3
+  double sigmaPW_A  = 0;  // normalized anode uncertainty term (0-1)
+  double sigmaPW_C  = 0;  // normalized cathode uncertainty term (0-1)
+
+  // status printout
+  printf("------------ Vertex :\n");
+  printf("X : %7.2f - %7.2f mm\n", vertexXRange[0], vertexXRange[1]);
+  printf("Y : %7.2f - %7.2f mm\n", vertexYRange[0], vertexYRange[1]);
+  printf("Z : %7.2f - %7.2f mm\n", vertexZRange[0], vertexZRange[1]);
+  printf("------------ Uncertainty :\n");
+  printf(" SX3 horizontal : %.1f\n", sigmaSX3_W);
+  printf(" SX3   vertical : %.1f\n", sigmaSX3_L);
+  printf("          Anode : %.1f mm\n", sigmaPW_A);
+  printf("        Cathode : %.1f mm\n", sigmaPW_C);
+  printf("        num_eve : %d \n",numEvent);
+
+  // calculates energy/momentum/kinematics constants for transfer reaction
+  transfer.CalReactionConstant();
+
+  int nExA = ExAList.size();
+  int nEx  = ExList.size();
+
+  // optional visualization control: pass "vis" as 3rd arg
+  bool enableVis = (argc >= 3 && strcmp(argv[2], "vis") == 0);
+  TApplication *app = nullptr;
+  if(enableVis){
+    app = new TApplication("anasenVis", &argc, argv);
+  }
+
+  // storage for tracks during simulation (for visualization)
+  std::vector<TVector3> visTrackVertex, visTrackDir, visTrackHitPos;
+  std::vector<std::pair<int,int>> visTrackWires;  // {anodeID, cathodeID}
+
+  // create detector representation in memory
+  ANASEN * anasen = new ANASEN();       // top-level detector object
+  SX3 * sx3 = anasen->GetSX3();         // silicon array part
+  PW * pw = anasen->GetPW();            // proportional wire chamber part
+
+  // output file + tree
+  TString saveFileName = "SimAnasen1.root";
+  printf("\e[32m#################################### building Tree in %s\e[0m\n", saveFileName.Data());
+  TFile * saveFile = new TFile(saveFileName, "recreate");
+  TTree * tree = new TTree("tree", "tree");
+   
+
+  // beam and CM variables saved in tree
+  double KEA;
+  tree->Branch("beamKEA",     &KEA, "beamKEA/D");
+
+  double thetaCM, phiCM;
+  tree->Branch("thetaCM", &thetaCM, "thetaCM/D");
+  tree->Branch("phiCM",     &phiCM, "phiCM/D");
+
+  // outgoing particles in lab frame (light/heavy)
+  double thetab, phib, Tb;
+  double thetaB, phiB, TB;
+  double dEb;
+  double dEB;
+  std::array<double, 2> T;
+  tree->Branch("thetab", &thetab, "thetab/D"); // polar angle of light particle in lab frame
+  tree->Branch("phib",     &phib, "phib/D"); // azimuthal angle of light particle in lab frame
+  tree->Branch("Tb",         &Tb, "Tb/D"); // kinetic energy of light particle at vertex (before energy loss)
+  tree->Branch("thetaB", &thetaB, "thetaB/D");
+  tree->Branch("phiB",     &phiB, "phiB/D");
+  tree->Branch("TB",         &TB, "TB/D"); // kinetic energy of heavy particle at vertex (before energy loss)
+  tree->Branch("dEb",        &dEb, "dEb/D");
+  tree->Branch("dEB",        &dEB, "dEB/D"); // placeholder for heavy particle energy loss, currently set equal to light particle loss for simplicity
+  tree->Branch("T",          &T, "T/D");   // placeholder for true Q-value, currently set to 0 for simplicity
+
+  // excitation state identifiers
+  int ExAID;
+  double ExA;
+  tree->Branch("ExAID", &ExAID, "ExAID/I"); // projectile excitation state ID
+  tree->Branch("ExA",     &ExA, "ExA/D"); // projectile excitation energy in MeV
+
+  int ExID;
+  double Ex;
+  tree->Branch("ExID", &ExID, "ExID/I"); // target excitation state ID
+  tree->Branch("Ex",     &Ex, "Ex/D"); // target excitation energy in MeV
+
+  // true vertex position in target volume
+  double vertexX, vertexY, vertexZ;
+  tree->Branch("vX",     &vertexX, "VertexX/D"); // true vertex X position in mm
+  tree->Branch("vY",     &vertexY, "VertexY/D"); // true vertex Y position in mm
+  tree->Branch("vZ",     &vertexZ, "VertexZ/D"); // true vertex Z position in mm
+
+  // reconstructed SX3 hit position
+  double sx3X, sx3Y, sx3Z;
+  tree->Branch("sx3X",     &sx3X, "sx3X/D"); // reconstructed X position from SX3 (with optional smearing)
+  tree->Branch("sx3Y",     &sx3Y, "sx3Y/D"); // reconstructed Y position from SX3 (with optional smearing)
+  tree->Branch("sx3Z",     &sx3Z, "sx3Z/D"); // reconstructed Z position from SX3 (with optional smearing)
+
+  // PW nearest and next nearest wires
+  int anodeID[2], cathodeID[2];
+  tree->Branch("aID", anodeID, "anodeID/I"); // anodeID[0] is nearest anode wire, anodeID[1] is next nearest anode wire
+  tree->Branch("cID", cathodeID, "cathodeID/I"); // cathodeID[0] is nearest cathode wire, cathodeID[1] is next nearest cathode wire
+
+  // distances to nearest wires
+  double anodeDist[2], cathodeDist[2];
+  tree->Branch("aDist",   anodeDist, "anodeDist/D");
+  tree->Branch("cDist",  cathodeDist, "cathodeDist/D");
+
+  // SX3 channel assignment and Z fraction (depth) information
+  int sx3ID, sx3Up, sx3Dn, sx3Bk;
+  double sx3ZFrac;
+  tree->Branch("sx3ID",   &sx3ID, "sx3ID/I");
+  tree->Branch("sx3Up",   &sx3Up, "sx3Up/I");
+  tree->Branch("sx3Dn",   &sx3Dn, "sx3Dn/I");
+  tree->Branch("sx3Bk",   &sx3Bk, "sx3Bk/I");
+  tree->Branch("sx3ZFrac", &sx3ZFrac, "sx3ZFrac/D");
+
+  // reconstructed angles from PW track fit, method 1 and 2
+  double reTheta, rePhi;
+  tree->Branch("reTheta", &reTheta, "reconstucted_theta/D");
+  tree->Branch("rePhi",     &rePhi, "reconstucted_phi/D");
+
+  double reTheta1, rePhi1;
+  tree->Branch("reTheta1", &reTheta1, "reconstucted_theta1/D");
+  tree->Branch("rePhi1",     &rePhi1, "reconstucted_phi1/D");
+
+  // reconstructed vertex Z from PW fit
+  double z0;
+  tree->Branch("z0",     &z0, "reconstucted_Z/D");
+
+  TTree* tree2 = tree->CloneTree(0);
+  tree2->SetName("tree2");
+
+  //========timer
+  TBenchmark clock;
+  bool shown ;
+  clock.Reset();
+  clock.Start("timer");
+  shown = false;
+  int ELossTotal = 0;
+
+  //================================= Calculate event loop
+  for( int i = 0; i < numEvent ; i++){
+
+    // randomly sample target/projectile excitations
+    ExAID = gRandom->Integer(nExA);
+    ExA = ExAList[ExAID];
+    transfer.SetExA(ExA);
+
+    ExID = gRandom->Integer(nEx);
+    Ex = ExList[ExID];
+    transfer.SetExB(Ex);
+
+    // recalc kinematic constants for chosen states
+    transfer.CalReactionConstant();
+
+    // isotropic CM direction
+    thetaCM = TMath::ACos(2 * gRandom->Rndm() - 1) ;
+    phiCM   = (gRandom->Rndm() - 0.5) * TMath::TwoPi();
+
+    //==== Calculate reaction kinematics in lab frame
+    TLorentzVector * output = transfer.Event(thetaCM, phiCM); // returns array of outputs
+    TLorentzVector Pb = output[2]; // light particle or product A
+    TLorentzVector PB = output[3]; // heavy particle or product B
+
+    thetab = Pb.Theta() * TMath::RadToDeg();
+    thetaB = PB.Theta() * TMath::RadToDeg();
+
+    Tb = (Pb.E() - Pb.M()); // kinetic energy of light particle at vertex (before energy loss) units of MeV
+    TB = (PB.E() - PB.M());
+    T[0] = Tb;
+    T[1] = TB;
+    //if (Tb < 1.5) {
+    //  //skip event if light particle energy after loss is below detection threshold of 1.5 MeV
+    //  continue;
+    //}
+
+    phib = Pb.Phi() * TMath::RadToDeg();
+    phiB = PB.Phi() * TMath::RadToDeg();
+
+    // vertex position in target volume
+    vertexX = (vertexXRange[1]- vertexXRange[0])*gRandom->Rndm() +  vertexXRange[0];
+    vertexY = (vertexYRange[1]- vertexYRange[0])*gRandom->Rndm() +  vertexYRange[0];
+    vertexZ = (vertexZRange[1]- vertexZRange[0])*gRandom->Rndm() +  vertexZRange[0];
+
+    TVector3 vertex(vertexX, vertexY, vertexZ);
+
+    // set direction vector from lab angle
+    TVector3 dir(1, 0, 0);
+    dir.SetTheta(thetab * TMath::DegToRad());
+    dir.SetPhi(phib * TMath::DegToRad());
+
+    // run detector response models for PW and SX3
+    pw->FindWireID(vertex, dir, false);
+    sx3->FindSX3Pos(vertex, dir, false);
+
+    PWHitInfo hitInfo = pw->GetHitInfo();
+
+    anodeID[0]   = hitInfo.nearestWire.first; // nearest anode wire ID
+    cathodeID[0] = hitInfo.nearestWire.second; // nearest cathode wire ID
+    anodeID[1]   = hitInfo.nextNearestWire.first; // next nearest anode wire ID
+    cathodeID[1] = hitInfo.nextNearestWire.second; // next nearest cathode wire ID
+
+    anodeDist[1]   = hitInfo.nextNearestDist.first; // distance to next nearest anode wire
+    cathodeDist[1] = hitInfo.nextNearestDist.second; // distance to next nearest cathode wire
+
+    if(IsDeadAnode(anodeID[0])) continue;
+    if(IsDeadCathode(cathodeID[0])) continue;
+
+    // SX3 hit channel info and depth fraction
+    sx3ID = sx3->GetID();
+
+    if(IsDeadSX3(sx3ID)) continue;
+
+    anodeDist[0]   = hitInfo.nearestDist.first; // distance to nearest anode wire
+    cathodeDist[0] = hitInfo.nearestDist.second; // distance to nearest cathode wire
+
+    if( sx3ID >= 0 ){
+      sx3Up    = sx3->GetChUp();
+      sx3Dn    = sx3->GetChDn();
+      sx3Bk    = sx3->GetChBk();
+      sx3ZFrac = sx3->GetZFrac();
+      
+      // apply intrinsic detector resolution to true SX3 hit position
+      // for no smearing comment out and use GetHitPos();
+      TVector3 hitPos = sx3->GetHitPosWithSigma(sigmaSX3_W, sigmaSX3_L);
+
+      sx3X = hitPos.X();
+      sx3Y = hitPos.Y();
+      sx3Z = hitPos.Z();
+
+      // store track data for visualization if enabled
+      if(enableVis){
+        visTrackVertex.push_back(vertex);
+        visTrackDir.push_back(dir);
+        visTrackHitPos.push_back(hitPos);
+        visTrackWires.push_back({anodeID[0], cathodeID[0]});
+      }
+      // reconstruct track from PW readings + SX3 hit
+      pw->CalTrack(hitPos, anodeID[0], cathodeID[0], false);
+      reTheta = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      // alternative track algorithm with uncertainty parameters
+      pw->CalTrack2(hitPos, hitInfo, sigmaPW_A, sigmaPW_C, false);
+      reTheta1 = pw->GetTrackTheta() * TMath::RadToDeg();
+      rePhi1   = pw->GetTrackPhi() * TMath::RadToDeg();
+
+      z0 = pw->GetZ0();
+      dEb = 0;
+      dEB = 0;
+      tree->Fill();
+
+      //Energy loss
+      double dl = (hitPos - vertex).Mag(); // path length in units of cm
+      if (numEvent <= 100){
+        //printf("Event %d: Ekin before loss = %f MeV, distance = %f cm\n", i, Tb, dl);
+        //printf("Total T before loss: %f MeV\n", T);
+      }
+      double tb_temp = Tb;
+
+      dEb = tb_temp - Tb; // total energy loss
+      if (ReactionProductb.count({4, 2})){ // if light particle is alpha, use alpha energy loss table
+        double x0b = invgAlpha->Eval(Tb);
+        x0b = x0b + dl;
+        Tb = elossAlpha->Eval(x0b);
+      } else if (ReactionProductb.count({1, 1})){ // if light particle is proton, use proton energy loss table
+        double x0b = invgProton->Eval(Tb);
+        x0b = x0b + dl;
+        Tb = elossProton->Eval(x0b);
+      } else {
+        // for other particle types, can add additional energy loss tables or use a generic approximation
+        // for now, we will just apply a simple linear energy loss as a placeholder
+        double dE_dx = 5; // MeV/cm, placeholder value for energy loss per unit length
+        Tb = Tb - dE_dx * dl;
+      }
+
+      //if (Tb < 0) {
+      //  Tb = TMath::QuietNaN();
+      //}
+
+      dEb = tb_temp - Tb; // total energy loss
+      
+      // fill tree2 with energy loss adjusted data
+      //Fill T so it can make a histogram of both Tb and TB in root script
+      T[0] = Tb;
+      T[1] = 0; 
+      //to plot both as one histogram in root, can use tree2->Draw("T(0)"); for light particle and tree2->Draw("T(1)") for heavy particle
+
+      tree2->Fill();
+      
+      if (numEvent <= 10){
+        //printf("Event %d: Tb after energy loss = %f MeV, energy loss = %f MeV\n", i, Tb, tb_temp - Tb);
+      } //to give in scientific notation, use %e instead of %f in the printf format string. For example: printf("Event %d: Tb after energy loss = %e MeV, energy loss = %e MeV\n", i, Tb, tb_temp - Tb);
+      ELossTotal += (tb_temp - Tb);
+
+    }else{
+      // no valid SX3 hit: mark clearly invalid
+      sx3Up = -1;
+      sx3Dn = -1;
+      sx3Bk = -1;
+      sx3ZFrac = TMath::QuietNaN();
+
+      sx3X = TMath::QuietNaN();
+      sx3Y = TMath::QuietNaN();
+      sx3Z = TMath::QuietNaN();
+
+      reTheta  = TMath::QuietNaN();
+      rePhi    = TMath::QuietNaN();
+      reTheta1 = TMath::QuietNaN();
+      rePhi1   = TMath::QuietNaN();
+      z0       = TMath::QuietNaN();
+      dEb      = TMath::QuietNaN();
+      dEB      = TMath::QuietNaN();
+      //Tb = -12354567; // mark kinetic energy as invalid for no hit case
+      // fill tree with original data (no energy loss for these events)
+      //comment out tree fill for no hit case  
+      //tree->Fill();
+      //tree2->Fill();
+    }
+
+    //#################################################################### Timer
+    // measure elapsed real time and print progress roughly every 10 sec
+    clock.Stop("timer");
+    Double_t time = clock.GetRealTime("timer");
+    clock.Start("timer");
+
+    if ( !shown ) {
+      if (fmod(time, 10) < 1 ){
+        printf( "%10d[%2d%%]| %8.2f sec | expect: %5.1f min \n", i, TMath::Nint((i+1)*100./numEvent), time , numEvent*time/(i+1)/60);
+        shown = 1;
+      }
+    } else {
+      if (fmod(time, 10) > 9 ){
+        shown = 0;
+      }
+    }
+
+  }
+
+  // write results to ROOT file and close
+  //tree->Write();
+  //tree2->Write();
+  tree->Write("", TObject::kOverwrite);
+  tree2->Write("", TObject::kOverwrite);
+  int count = tree->GetEntries();
+  int count2 = tree2->GetEntries();
+  saveFile->Close();
+
+  printf("=============== done. saved as %s. tree entries: %d, tree2 entries: %d\n", saveFileName.Data(), count, count2);
+  printf("Total energy loss across all events: %f MeV\n", (double)ELossTotal);
+  printf("Average energy loss across events: %f MeV\n", (double)ELossTotal / count);
+
+  if(enableVis){ // to enable visualization, run with 3rd argument "vis", e.g. "./anasenMC 1000 vis"
+    printf("Displaying geometry with %zu tracks from simulation\n", visTrackVertex.size());
+    
+    // Build full geometry with all wires
+    anasen->DrawAnasen(0, 23, 0, 23, -1, true);
+    
+    // Add all stored tracks to the geometry
+    TGeoManager *geom = anasen->GetGeoManager();
+    TGeoVolume *worldBox = anasen->GetWorldBox();
+    
+    if(geom && worldBox && visTrackVertex.size() > 0){
+      int trackNodeID = 500;  // start node IDs for tracks
+      
+      for(size_t iTrack = 0; iTrack < visTrackVertex.size(); ++iTrack){
+        TVector3 vertex = visTrackVertex[iTrack];
+        TVector3 dir = visTrackDir[iTrack];
+        TVector3 hitPos = visTrackHitPos[iTrack];
+        
+        double theta = dir.Theta() * TMath::RadToDeg();
+        double phi = dir.Phi() * TMath::RadToDeg();
+        
+        // Add a line marker at the vertex
+        TGeoVolume *startMarker = geom->MakeSphere("startMarker", 0, 0, 2.0);
+        startMarker->SetLineColor(kBlack);
+        worldBox->AddNode(startMarker, trackNodeID, 
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(), 
+                                          new TGeoRotation("rot", 0, 0, 0)));
+        trackNodeID++;
+        
+        // Add track line from vertex toward hit position
+        TGeoVolume *trackLine = geom->MakeTube("trackLine", 0, 0, 0.08, 150.0);
+        trackLine->SetLineColor(kBlue);
+        worldBox->AddNode(trackLine, trackNodeID,
+                         new TGeoCombiTrans(vertex.X(), vertex.Y(), vertex.Z(),
+                                          new TGeoRotation("rotTrack", phi + 90, theta, 0)));
+        trackNodeID++;
+        
+        // Add hit position marker
+        TGeoVolume *hitMarker = geom->MakeSphere("hitMarker", 0, 0, 2.0);
+        hitMarker->SetLineColor(kRed);
+        worldBox->AddNode(hitMarker, trackNodeID,
+                         new TGeoCombiTrans(hitPos.X(), hitPos.Y(), hitPos.Z(),
+                                          new TGeoRotation("rotHit", 0, 0, 0)));
+        trackNodeID++;
+      }
+      
+      // Redraw geometry with all tracks
+      geom->CloseGeometry();
+      geom->SetVisLevel(4);
+      worldBox->Draw("ogle");
+    }
+    
+    if(app){
+      printf("Entering ROOT event loop\n");
+      app->Run();
+    }
+  }
+
+  delete anasen;
+  delete elossAlpha;
+  delete elossProton;
+
+
+  return 0;
+
+}

ELoss/eloss.py

@@ -0,0 +1,179 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import pandas as pd
+from scipy.interpolate import interp1d
+import argparse
+
+#python3 eloss.py E_vs_X_table.txt --Ei <starting energy> --Ef <final energy>
+#python3 eloss.py E_vs_X_table.txt --Ei <starting energy> --dx <distance traveled>
+#python3 eloss.py E_vs_X_table.txt --Ef <final energy> --dx <distance traveled>
+
+def load_table(filename):
+    """
+    Load table with columns:
+        x(cm)   E(MeV)
+
+    Returns:
+        x_array, E_array
+    """
+
+    data = pd.read_csv(
+        filename,
+        sep='\s+',
+        comment="#",
+        header=None,
+        skiprows=1
+    )
+
+    x = data.iloc[:, 0].values
+    E = data.iloc[:, 1].values
+
+    return x, E
+
+
+def build_interpolators(x, E):
+
+    # E(x)
+    E_of_x = interp1d(
+        x,
+        E,
+        bounds_error=False,
+        fill_value=0.0
+    )
+
+    # x(E)
+    x_of_E = interp1d(
+        E[::-1],      # reverse so energy increases
+        x[::-1],
+        bounds_error=False,
+        fill_value="extrapolate"
+    )
+
+    return E_of_x, x_of_E
+
+def distance_traveled(Ei, Ef, x_of_E):
+
+    xi = float(x_of_E(Ei))
+    xf = float(x_of_E(Ef))
+
+    return abs(xf - xi)
+
+def final_energy(Ei, dx, x_of_E, E_of_x):
+
+    xi = float(x_of_E(Ei))
+
+    xf = xi + dx
+
+    Ef = float(E_of_x(xf))
+
+    return max(Ef, 0.0)
+
+
+def initial_energy(Ef, dx, x_of_E, E_of_x):
+
+    xf = float(x_of_E(Ef))
+
+    xi = xf - dx
+
+    Ei = float(E_of_x(xi))
+
+    return max(Ei, 0.0)
+
+
+def main():
+
+    parser = argparse.ArgumentParser(
+        description="Energy-distance calculator using E vs X tables"
+    )
+
+    parser.add_argument(
+        "table",
+        help="E vs X table file"
+    )
+
+    parser.add_argument(
+        "--Ei",
+        type=float,
+        help="Initial energy (MeV)"
+    )
+
+    parser.add_argument(
+        "--Ef",
+        type=float,
+        help="Final energy (MeV)"
+    )
+
+    parser.add_argument(
+        "--dx",
+        type=float,
+        help="Distance traveled (cm)"
+    )
+
+    args = parser.parse_args()
+
+    # Count supplied variables
+    supplied = [
+        args.Ei is not None,
+        args.Ef is not None,
+        args.dx is not None
+    ]
+
+    if sum(supplied) != 2:
+        print("\nERROR:")
+        print("Supply exactly TWO of: Ei, Ef, dx\n")
+        return
+
+    # Load table, skip the first row
+    x, E = load_table(args.table)
+
+    # Build interpolators
+    E_of_x, x_of_E = build_interpolators(x, E)
+
+    if args.Ei is not None and args.Ef is not None:
+
+        dx = distance_traveled(
+            args.Ei,
+            args.Ef,
+            x_of_E
+        )
+
+        print(f"\nDistance traveled: {dx:.6f} cm")
+
+    elif args.Ei is not None and args.dx is not None:
+
+        Ef = final_energy(
+            args.Ei,
+            args.dx,
+            x_of_E,
+            E_of_x
+        )
+
+        print(f"\nFinal energy: {Ef:.6f} MeV")
+
+    elif args.Ef is not None and args.dx is not None:
+
+        Ei = initial_energy(
+            args.Ef,
+            args.dx,
+            x_of_E,
+            E_of_x
+        )
+
+        print(f"\nInitial energy: {Ei:.6f} MeV")
+
+    elif args.Ei is not None and args.Ef is not None and args.dx is not None:
+        print("\nERROR: Supply exactly TWO of: Ei, Ef, dx\n")
+        return
+    
+    elif args.help:
+        parser.print_help()
+        return
+
+
+# ============================================================
+# Run
+# ============================================================
+
+if __name__ == "__main__":
+    main()

FitHistogramsWithTSpectrum_Sequential_Improved.C

@@ -0,0 +1,124 @@
+#include <TFile.h>
+#include <TH1.h>
+#include <TSpectrum.h>
+#include <TF1.h>
+#include <TCanvas.h>
+#include <vector>
+#include <iostream>
+#include <algorithm>
+#include <fstream>
+#include <TText.h>
+
+void FitHistogramsWithTSpectrum_Sequential_Improved() {
+    TFile *inputFile = new TFile("Histograms_anodes.root", "READ");
+    if (!inputFile || inputFile->IsZombie()) {
+        std::cerr << "Error opening the input file!" << std::endl;
+        return;
+    }
+
+    TCanvas *c1 = new TCanvas("c1", "Histogram Viewer", 800, 600);
+
+    // Open the output ASCII file to save the centroids
+    std::ofstream outFile("centroids.txt");
+    if (!outFile.is_open()) {
+        std::cerr << "Error opening output file!" << std::endl;
+        return;
+    }
+    outFile << "HistogramIndex\tPeakNumber\tCentroid\tAmplitude\tSigma" << std::endl;
+
+    for (int i = 0; i < 24; ++i) {
+        TH1 *histogram = dynamic_cast<TH1*>(inputFile->Get(Form("hCathode_%d", i)));
+        if (!histogram) {
+            std::cerr << "Failed to retrieve histogram_" << i << " from the file." << std::endl;
+            continue;
+        }
+
+        // Set range for peak search
+        double minX = 700;
+        double maxX = 25000;
+        histogram->GetXaxis()->SetRangeUser(minX, maxX);
+
+        // Draw the histogram
+        c1->cd();
+        histogram->Draw();
+
+        // Peak search using TSpectrum
+        const int maxPeaks = 5;
+        TSpectrum spectrumFinder(maxPeaks);
+        int nFound = spectrumFinder.Search(histogram, 2, "", 0.01);
+
+        if (nFound <= 0) {
+            std::cerr << "No peaks found for histogram " << i << std::endl;
+            continue;
+        }
+
+        Double_t *xPositions = spectrumFinder.GetPositionX();
+        Double_t *yPositions = spectrumFinder.GetPositionY();
+        std::vector<std::pair<Double_t, Double_t>> peaks;
+
+        // Collect and sort peaks by X position
+        for (int j = 0; j < nFound; ++j) {
+            peaks.emplace_back(xPositions[j], yPositions[j]);
+        }
+        std::sort(peaks.begin(), peaks.end());
+
+        // Fit each peak with a Gaussian
+        for (int j = 0; j < peaks.size(); ++j) {
+            Double_t peakX = peaks[j].first;
+            Double_t peakY = peaks[j].second;
+            Double_t initialAmplitude = peakY;  // Better initial guess
+            Double_t initialCentroid = peakX;   // Centroid based on peak position
+            Double_t initialSigma = 60.0;
+            // Define Gaussian with initial parameters
+            TF1 *gaussFit = new TF1(Form("gauss_%d", j), "gaus", peakX - 200, peakX + 200);
+            //gaussFit->SetParameters(peakY, peakX, 25.0); // Initial guesses for amplitude, mean, sigma
+            gaussFit->SetParameters(initialAmplitude, initialCentroid, initialSigma);
+            // Perform fit
+            int fitStatus = histogram->Fit(gaussFit, "RQ+");
+            if (fitStatus != 0) {
+                std::cerr << "Fit failed for peak " << j + 1 << " in histogram " << i << std::endl;
+                delete gaussFit;
+                continue;
+            }
+
+            // Retrieve fit parameters
+            double amplitude = gaussFit->GetParameter(0);
+            double centroid = gaussFit->GetParameter(1);
+            double sigma = gaussFit->GetParameter(2);
+            double amplitudeError = gaussFit->GetParError(0);
+            double centroidError = gaussFit->GetParError(1);
+            double sigmaError = gaussFit->GetParError(2);
+
+            // Chi-squared value
+            double chi2 = gaussFit->GetChisquare();
+            int ndf = gaussFit->GetNDF();
+            outFile << i << "\t" << j + 1 << "\t" << centroid << std::endl;
+            gaussFit->SetLineColor(kRed);
+            gaussFit->Draw("SAME");
+            TText *text = new TText();
+            text->SetNDC();
+            text->SetTextSize(0.03);
+            text->SetTextColor(kRed);
+            //text->DrawText(0.15, 0.8 - j * 0.05, Form("Peak %d: Amp=%.2f, Mean=%.2f, Sigma=%.2f", j + 1, amplitude, centroid, sigma));
+            text->DrawText(0.15, 0.8 - j * 0.05, 
+                Form("Peak %d: Amp=%.2f±%.2f, Mean=%.2f±%.2f, Sigma=%.2f±%.2f, Chi2/NDF=%.2f",
+                     j + 1, amplitude, amplitudeError, centroid, centroidError, sigma, sigmaError, chi2 / ndf));
+            // Save results
+            
+            
+            // Clean up
+            delete gaussFit;
+        }
+
+        // Update canvas for visualization
+        c1->Update();
+        std::cout << "Press Enter to view the next histogram..." << std::endl;
+        c1->WaitPrimitive(); // Wait until Enter is pressed in the ROOT console
+    }
+
+    // Close resources
+    inputFile->Close();
+    outFile.close();
+    delete c1;
+}
+

GainMatchQQQ.C

@@ -0,0 +1,309 @@
+#define GainMatchQQQ_cxx
+
+#include "GainMatchQQQ.h"
+#include <TH2.h>
+#include <TF1.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include <cmath>
+#include <numeric>
+#include "Armory/HistPlotter.h"
+#include "TVector3.h"
+#include "TGraphErrors.h"
+#include "TF1.h"
+#include <cmath>
+
+TH2F *hQQQFVB;
+HistPlotter *plotter;
+
+int padID = 0;
+
+TCutG *cut;
+std::map<std::tuple<int, int, int>, std::vector<std::pair<double, double>>> dataPoints;
+
+void GainMatchQQQ::Begin(TTree * /*tree*/)
+{
+    plotter = new HistPlotter("GainQQQ.root", "TFILE");
+    TString option = GetOption();
+
+    hQQQFVB = new TH2F("hQQQFVB", "QQQ Front vs Back; Front E; Back E", 800, 0, 16000, 800, 0, 16000);
+
+    // Load the TCutG object
+    TFile *cutFile = TFile::Open("qqqcorr.root");
+    if (!cutFile || cutFile->IsZombie())
+    {
+        std::cerr << "Error: Could not open qqqcorr.root" << std::endl;
+        return;
+    }
+    cut = dynamic_cast<TCutG *>(cutFile->Get("qqqcorr"));
+    if (!cut)
+    {
+        std::cerr << "Error: Could not find TCutG named 'qqqcorr' in qqqcorr.root" << std::endl;
+        return;
+    }
+    cut->SetName("qqqcorr"); // Ensure the cut has the correct name
+}
+
+Bool_t GainMatchQQQ::Process(Long64_t entry)
+{
+
+    int ringMults[16] = {0};
+    int wedgeMults[16] = {0};
+    std::vector<std::tuple<int, int, int, double, double>> events;
+
+    b_qqqMulti->GetEntry(entry);
+    b_qqqID->GetEntry(entry);
+    b_qqqCh->GetEntry(entry);
+    b_qqqE->GetEntry(entry);
+    b_qqqT->GetEntry(entry);
+
+    qqq.CalIndex();
+
+    for (int i = 0; i < qqq.multi; i++)
+    {
+        for (int j = i + 1; j < qqq.multi; j++)
+        {
+            if (qqq.id[i] == qqq.id[j])
+            {
+                int chWedge = -1;
+                int chRing = -1;
+                float eWedge = 0.0;
+                float eRing = 0.0;
+                if (qqq.ch[i] < 16 && qqq.ch[j] >= 16)
+                {
+                    chWedge = qqq.ch[i];
+                    eWedge = qqq.e[i];
+                    chRing = qqq.ch[j] - 16;
+                    eRing = qqq.e[j];
+                }
+                else if (qqq.ch[j] < 16 && qqq.ch[i] >= 16)
+                {
+                    chWedge = qqq.ch[j];
+                    eWedge = qqq.e[j];
+                    chRing = qqq.ch[i] - 16;
+                    eRing = qqq.e[i];
+                }
+                else
+                    continue;
+                ringMults[chRing]++;
+                wedgeMults[chWedge]++;
+                hQQQFVB->Fill(eWedge, eRing);
+                events.emplace_back(qqq.id[i], chRing, chWedge, eRing, eWedge);
+                plotter->Fill2D(Form("hRaw_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 800, 0, 3000, 800, 0, 3000, eWedge, eRing, "hRawQQQ");
+                // double ratio = (eWedge > 0.0) ? (eRing / eWedge) : 0.0;
+                // double maxslope = 1.5;
+
+                // bool validPoint = false;
+                // if (ratio < maxslope && ratio > 1. / maxslope)
+                // {
+                //     // Accumulate data for gain matching
+                //     dataPoints[{qqq.id[i], chRing, chWedge}].emplace_back(eWedge, eRing);
+                //     plotter->Fill2D("hAll_in", 4000, 0, 16000, 4000, 0, 16000, eWedge, eRing);
+                //     validPoint = true;
+                // }
+
+                // if (!validPoint)
+                // {
+                //     plotter->Fill2D("hAll_out", 4000, 0, 16000, 4000, 0, 16000, eWedge, eRing);
+                // }
+            }
+        }
+    }
+
+    for (auto tuple : events)
+    {
+        auto [id, chr, chw, er, ew] = tuple;
+        if (ringMults[chr] > 1 || wedgeMults[chw] > 1)
+            continue; // ignore multiplicity > 1 events
+        double ratio = (ew > 0.0) ? (er / ew) : 0.0;
+        double maxslope = 1.5;
+
+        bool validPoint = false;
+        if (ratio < maxslope && ratio > 1. / maxslope)
+        {
+                // Accumulate data for gain matching
+                dataPoints[{id, chr, chw}].emplace_back(ew, er);
+                plotter->Fill2D("hAll_in", 4000, 0, 16000, 4000, 0, 16000, ew, er);
+                validPoint = true;
+                    }
+        if (!validPoint)
+        {
+            plotter->Fill2D("hAll_out", 4000, 0, 16000, 4000, 0, 16000, ew, er);
+        }
+    }
+
+    return kTRUE;
+}
+
+
+void GainMatchQQQ::Terminate()
+{
+    const int MAX_DET = 4;
+    const int MAX_RING = 16;
+    const int MAX_WEDGE = 16;
+
+    // We store gains locally just for the "corrected" plot, 
+    // but the file will output Slopes for the global minimizer.
+    double gainW[MAX_DET][MAX_RING][MAX_WEDGE] = {{{0}}};
+    double gainR[MAX_DET][MAX_RING][MAX_WEDGE] = {{{0}}};
+    bool gainValid[MAX_DET][MAX_RING][MAX_WEDGE] = {{{false}}};
+
+    // Output file for the Minimizer
+    std::ofstream outFile("qqq_GainMatch.txt");
+    
+    // Benchmark/Debug file
+    std::ofstream benchFile("benchmark_diff.txt"); 
+    benchFile << "ID Wedge Ring Chi2NDF Slope SlopeErr" << std::endl;
+
+    if (!outFile.is_open()) { std::cerr << "Error opening output file!" << std::endl; return; }
+
+    const int MIN_POINTS = 50;
+    const int MAX_ITER = 3;        // Outlier rejection passes
+    const double CLIP_SIGMA = 2.5; // Sigma threshold for outliers
+
+    for (const auto &kv : dataPoints)
+    {
+        auto key = kv.first;
+        auto [id, ring, wedge] = key;
+        const auto &pts = kv.second;
+
+        if (pts.size() < (size_t)MIN_POINTS) continue;
+
+        std::vector<std::pair<double, double>> current_pts = pts;
+        
+        double finalSlope = 0.0;
+        double finalSlopeErr = 0.0;
+        bool converged = false;
+
+        // --- Iterative Fitting ---
+        for (int iter = 0; iter < MAX_ITER; ++iter)
+        {
+            if (current_pts.size() < (size_t)MIN_POINTS) break;
+
+            std::vector<double> x, y, ex, ey;
+
+            for (const auto &p : current_pts)
+            {
+                x.push_back(p.first);  // Wedge E
+                y.push_back(p.second); // Ring E
+                ex.push_back(std::sqrt(std::abs(p.first))); // Error in X (Poisson)
+                ey.push_back(std::sqrt(std::abs(p.second))); // Error in Y (Poisson)
+                
+                // Sanity check to avoid 0 error
+                if(ex.back() < 1.0) ex.back() = 1.0;
+                if(ey.back() < 1.0) ey.back() = 1.0;
+            }
+
+            // 2. Create Graph
+            TGraphErrors *gr = new TGraphErrors(current_pts.size(), x.data(), y.data(), ex.data(), ey.data());
+            
+            // 3. Fit Linear Function through Origin
+            TF1 *f1= new TF1("calibFit", "[0]*x", 0, 16000);
+            f1->SetParameter(0, 1.0);   
+
+            // "Q"=Quiet, "N"=NoDraw, "S"=ResultPtr
+            // We do NOT use "W" (Ignore weights), we want to use the errors we set.
+            int fitStatus = gr->Fit(f1, "QNS");
+
+            if (fitStatus != 0) {
+                delete gr; delete f1;
+                break; 
+            }
+
+            finalSlope = f1->GetParameter(0);
+            double chi2 = f1->GetChisquare();
+            double ndf = f1->GetNDF();
+            
+            // Get the statistical error on the slope
+            double rawErr = f1->GetParError(0);
+            
+            // SCALING ERROR:
+            // If Chi2/NDF > 1, the data scatters more than Poisson stats predict.
+            // // We inflate the error by sqrt(Chi2/NDF) to be conservative for the Minimizer.
+            // double redChi2 = (ndf > 0) ? (chi2 / ndf) : 1.0;
+            // double inflation = (redChi2 > 1.0) ? std::sqrt(redChi2) : 1.0;
+            
+            // finalSlopeErr = rawErr * inflation;
+
+            // 4. Outlier Rejection
+            if (iter == MAX_ITER - 1) {
+                converged = true;
+                delete gr; delete f1;
+                break;
+            }
+
+            // Calculate Residuals
+            std::vector<double> residuals;
+            double sumSqResid = 0.0;
+            for(size_t k=0; k<current_pts.size(); ++k) {
+                double val = f1->Eval(current_pts[k].first);
+                double res = current_pts[k].second - val;
+                residuals.push_back(res);
+                sumSqResid += res*res;
+            }
+        //     double sigma = std::sqrt(sumSqResid / current_pts.size());
+            
+        //     // Filter
+        //     std::vector<std::pair<double, double>> next_pts;
+        //     for(size_t k=0; k<current_pts.size(); ++k) {
+        //         if(std::abs(residuals[k]) < CLIP_SIGMA * sigma) {
+        //             next_pts.push_back(current_pts[k]);
+        //         }
+        //     }
+
+        //     if (next_pts.size() == current_pts.size()) {
+        //         converged = true; 
+        //         delete gr; delete f1;
+        //         break;
+        //     }
+        //     current_pts = next_pts;
+        //     delete gr; delete f1;
+        }
+
+        if (!converged || finalSlope <= 0) continue;
+
+        // --- Store/Output ---
+        
+        // 1. Save locally for the verification plot (hAll)
+        // Approximate local gain for plotting purposes only
+        double gW_local = std::sqrt(finalSlope);
+        double gR_local = 1.0 / gW_local;
+        gainW[id][ring][wedge] = gW_local;
+        gainR[id][ring][wedge] = gR_local;
+        gainValid[id][ring][wedge] = true;
+
+        // 2. Write to File for Minimizer
+        // Format: ID Wedge Ring Slope Error
+        outFile << id << " " << wedge << " " << ring << " " << finalSlope << " " << finalSlopeErr << std::endl;
+
+        // 3. Benchmark Info
+        benchFile << id << " " << wedge << " " << ring << " " 
+                  << finalSlope << " " << finalSlopeErr << std::endl;
+    }
+
+    outFile.close();
+    benchFile.close();
+    std::cout << "Gain matching with Errors complete." << std::endl;
+
+    // Plotting the corrected data (Visual check using local approx gains)
+    for (auto &kv : dataPoints)
+    {
+        int id, ring, wedge;
+        std::tie(id, ring, wedge) = kv.first;
+        if (!gainValid[id][ring][wedge]) continue;
+        auto &pts = kv.second;
+        for (auto &pr : pts)
+        {
+            double corrWedge = pr.first * gainW[id][ring][wedge];
+            double corrRing = pr.second * gainR[id][ring][wedge];
+            plotter->Fill2D("hAll", 4000, 0, 16000, 4000, 0, 16000, corrWedge, corrRing);
+        }
+    }
+
+    plotter->FlushToDisk();
+}

GainMatchQQQ.h

@@ -0,0 +1,114 @@
+#ifndef GainMatchQQQ_h
+#define GainMatchQQQ_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class GainMatchQQQ : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   GainMatchQQQ(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~GainMatchQQQ() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(GainMatchQQQ,0);
+};
+
+#endif
+
+#ifdef GainMatchQQQ_cxx
+void GainMatchQQQ::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t GainMatchQQQ::Notify(){
+
+   return kTRUE;
+}
+
+void GainMatchQQQ::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void GainMatchQQQ::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef GainMatchQQQ_cxx

GainMatchSX3.C

@@ -0,0 +1,432 @@
+#define GainMatchSX3_cxx
+
+#include "GainMatchSX3.h"
+#include <TH2.h>
+#include <TF1.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include <TProfile.h>
+#include "Armory/ClassSX3.h"
+#include "Armory/HistPlotter.h"
+#include <TGraphErrors.h>
+#include "TVector3.h"
+
+TH2F *hSX3FvsB;
+TH2F *hSX3FvsB_g;
+TH2F *hsx3IndexVE;
+TH2F *hsx3IndexVE_g;
+TH2F *hSX3;
+TH2F *hsx3Coin;
+
+int padID = 0;
+
+SX3 sx3_contr;
+TCutG *cut;
+TCutG *cut1;
+std::map<std::tuple<int, int, int, int>, std::vector<std::tuple<double, double, double>>> dataPoints;
+std::map<std::tuple<int, int, int, int>, int> comboCounts;
+
+const int MAX_DET = 24;
+const int MAX_UP = 4;
+const int MAX_DOWN = 4;
+const int MAX_BK = 4;
+
+double frontGainUp[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+double frontGainDown[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+bool frontGainValid[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{false}}}};
+TCanvas c("canvas", "canvas", 800, 600);
+
+// ==== Configuration Flags ====
+const bool interactiveMode = true; // If true: show canvas + wait for user
+const bool verboseFit = true;      // If true: print fit summary and chi²
+const bool drawCanvases = true;    // If false: canvases won't be drawn at all
+
+// HistPlotter plotter("SX3GainMatchBack.root");
+
+void GainMatchSX3::Begin(TTree * /*tree*/)
+{
+    TString option = GetOption();
+
+    hSX3FvsB = new TH2F("hSX3FvsB", "SX3 Front vs Back; Front E; Back E", 400, 0, 16000, 400, 0, 16000);
+    hSX3FvsB_g = new TH2F("hSX3FvsB_g", "SX3 Front vs Back; Front E; Back E", 400, 0, 16000, 400, 0, 16000);
+    hsx3IndexVE = new TH2F("hsx3IndexVE", "SX3 index vs Energy; sx3 index ; Energy", 24 * 12, 0, 24 * 12, 400, 0, 5000);
+    hsx3IndexVE_g = new TH2F("hsx3IndexVE_g", "SX3 index vs Energy; sx3 index ; Energy", 24 * 12, 0, 24 * 12, 400, 0, 5000);
+    hSX3 = new TH2F("hSX3", "SX3 Front v Back; Fronts; Backs", 8, 0, 8, 4, 0, 4);
+
+    hsx3Coin = new TH2F("hsx3Coin", "SX3 Coincident", 24 * 12, 0, 24 * 12, 24 * 12, 0, 24 * 12);
+
+    sx3_contr.ConstructGeo();
+
+    // Load the TCutG object
+    TFile *cutFile = TFile::Open("sx3cut.root");
+    if (!cutFile || cutFile->IsZombie())
+    {
+        std::cerr << "Error: Could not open sx3cut.root" << std::endl;
+        return;
+    }
+    cut = dynamic_cast<TCutG *>(cutFile->Get("sx3cut"));
+    if (!cut)
+    {
+        std::cerr << "Error: Could not find TCutG named 'sx3cut' in sx3cut.root" << std::endl;
+        return;
+    }
+    cut->SetName("sx3cut"); // Ensure the cut has the correct name
+
+    // Load the TCutG object
+    TFile *cutFile1 = TFile::Open("UvD.root");
+    bool cut1Loaded = (cut1 != nullptr);
+    cut1 = dynamic_cast<TCutG *>(cutFile1->Get("UvD"));
+    if (!cut1)
+    {
+        std::cerr << "Error: Could not find TCutG named 'UvD' in UvD.root" << std::endl;
+        return;
+    }
+    cut1->SetName("UvD");
+
+    // plotter.ReadCuts("cuts.txt");
+
+    std::string filename = "sx3_GainMatchfront.txt";
+    // std::string filename = "sx3_GainMatchfront.txt";
+
+    std::ifstream infile(filename);
+    if (!infile.is_open())
+    {
+        std::cerr << "Error opening " << filename << "!" << std::endl;
+        return;
+    }
+
+    int id, bk, u, d;
+    double gainup, gaindown;
+    while (infile >> id >> bk >> u >> d >> gainup >> gaindown)
+    {
+        frontGainUp[id][bk][u][d] = gainup;
+        frontGainDown[id][bk][u][d] = gaindown;
+        frontGainValid[id][bk][u][d] = true;
+        if(frontGainValid[id][bk][u][d]) {
+            // std::cout << "Loaded front gain for Det" << id << " Bk" << bk << " U" << u << " D" << d
+            //           << ": Up=" << gainup << ", Down=" << gaindown << std::endl;
+        }
+        else {
+            std::cout << "No valid front gain for Det" << id << " Bk" << bk << " U" << u << " D" << d << std::endl;
+        }
+    }
+}
+
+Bool_t GainMatchSX3::Process(Long64_t entry)
+{
+
+    b_sx3Multi->GetEntry(entry);
+    b_sx3ID->GetEntry(entry);
+    b_sx3Ch->GetEntry(entry);
+    b_sx3E->GetEntry(entry);
+    b_sx3T->GetEntry(entry);
+    b_qqqMulti->GetEntry(entry);
+    b_qqqID->GetEntry(entry);
+    b_qqqCh->GetEntry(entry);
+    b_qqqE->GetEntry(entry);
+    b_qqqT->GetEntry(entry);
+    b_pcMulti->GetEntry(entry);
+    b_pcID->GetEntry(entry);
+    b_pcCh->GetEntry(entry);
+    b_pcE->GetEntry(entry);
+    b_pcT->GetEntry(entry);
+
+    sx3.CalIndex();
+    qqq.CalIndex();
+    pc.CalIndex();
+
+    std::vector<std::pair<int, int>> ID;
+    for (int i = 0; i < sx3.multi; i++)
+    {
+
+        // for (int j = i + 1; j < sx3.multi; j++)
+        // {
+        //     if (sx3.id[i] == 3)
+        //         hsx3Coin->Fill(sx3.index[i], sx3.index[j]);
+        // }
+        if (sx3.e[i] > 100)
+        {
+            ID.push_back(std::pair<int, int>(sx3.id[i], i));
+            hsx3IndexVE->Fill(sx3.index[i], sx3.e[i]);
+        }
+    }
+
+    if (ID.size() > 0)
+    {
+        std::sort(ID.begin(), ID.end(), [](const std::pair<int, int> &a, const std::pair<int, int> &b)
+                  { return a.first < b.first; });
+
+        // start with the first entry in the sorted array: channels that belong to the same detector are together in sequenmce
+        std::vector<std::pair<int, int>> sx3ID;
+        sx3ID.push_back(ID[0]);
+        bool found = false;
+
+        for (size_t i = 1; i < ID.size(); i++)
+        { // Check if id of i belongs to the same detector and then add it to the detector ID vector
+            if (ID[i].first == sx3ID.back().first)
+            { // count the nunmber of hits that belong to the same detector
+                sx3ID.push_back(ID[i]);
+
+                if (sx3ID.size() >= 3)
+                {
+                    found = true;
+                }
+            }
+            else
+            { // the next event does not belong to the same detector, abandon the first event and continue with the next one
+                if (!found)
+                {
+                    sx3ID.clear();
+                    sx3ID.push_back(ID[i]);
+                }
+            }
+        }
+
+        if (found)
+        {
+            int sx3ChUp = -1, sx3ChDn = -1, sx3ChBk = -1;
+            float sx3EUp = 0.0, sx3EDn = 0.0, sx3EBk = 0.0;
+
+            // Build the correlated set once
+            for (size_t i = 0; i < sx3ID.size(); i++)
+            {
+                if (sx3.e[i] > 100)
+                {
+                    int index = sx3ID[i].second;
+                    if (sx3.ch[index] < 8)
+                    {
+                        if (sx3.ch[index] % 2 == 0)
+                        { 
+                            sx3ChDn = sx3.ch[index];
+                            sx3EDn = sx3.e[index];
+                            //
+                        }
+                        else
+                        {
+                            sx3ChUp = sx3.ch[index];
+                            sx3EUp = sx3.e[index];
+                        }
+                    }
+                    else
+                    {
+                        sx3ChBk = sx3.ch[index] - 8;
+                        sx3EBk = sx3.e[index];
+                    }
+                }
+                
+            }
+            // Only if we found all three channels do we proceed
+            if (sx3ChUp >= 0 && sx3ChDn >= 0 && sx3ChBk >= 0)
+            {
+                // Fill once per correlated set
+                hSX3->Fill(sx3ChDn + 4, sx3ChBk);
+                hSX3->Fill(sx3ChUp, sx3ChBk);
+                hSX3FvsB->Fill(sx3EUp + sx3EDn, sx3EBk);
+                
+                if (frontGainValid[sx3ID[0].first][sx3ChBk][sx3ChUp / 2][sx3ChDn / 2])
+                {
+                    sx3EUp *= frontGainUp[sx3ID[0].first][sx3ChBk][sx3ChUp / 2][sx3ChDn / 2];
+                    sx3EDn *= frontGainDown[sx3ID[0].first][sx3ChBk][sx3ChUp / 2][sx3ChDn / 2];
+                }
+                else
+                {
+                    // printf("No front gain for Det%d Bk%d U%d D%d\n", sx3ID[0].first, sx3ChBk, sx3ChUp / 2, sx3ChDn / 2);
+                    sx3EUp = sx3EDn = 0.;
+                }
+                // plotter.Fill2D("hSX3F", 400, 0, 16000, 400, 0, 16000, sx3EUp + sx3EDn, sx3EBk);
+
+                // Pick detector ID from one of the correlated hits (all same detector)
+                int detID = sx3ID[0].first;
+
+                TString histName = Form("hSX3FVB_id%d_U%d_D%d_B%d", detID, sx3ChUp, sx3ChDn, sx3ChBk);
+                TString histName1 = Form("UnCorr_id%d_U%d-D%dvsB%d", detID, sx3ChUp, sx3ChDn, sx3ChBk);
+
+                TH2F *hist2d = (TH2F *)gDirectory->Get(histName);
+                TH2F *hist2d1 = (TH2F *)gDirectory->Get(histName1);
+                if (!hist2d)
+                {
+                    hist2d = new TH2F(histName, histName,
+                                      400, 0, 16000, 400, 0, 16000);
+                }
+                if (!hist2d1)
+                {
+                    hist2d1 = new TH2F(histName1, histName1,
+                                       800, -1, 1, 800, 0, 4000);
+                }
+
+                if (sx3EBk > 100 || sx3EUp > 100 || sx3EDn > 100)
+                {
+                    hSX3FvsB_g->Fill(sx3EUp + sx3EDn, sx3EBk);
+
+                    // Use the correlated triplet directly
+                    dataPoints[{detID, sx3ChBk, sx3ChUp, sx3ChDn}]
+                        .emplace_back(sx3EBk, sx3EUp, sx3EDn);
+                }
+
+                hist2d->Fill(sx3EUp + sx3EDn, sx3EBk);
+                hist2d1->Fill((sx3EUp - sx3EDn) / (sx3EUp + sx3EDn), sx3EBk);
+            }
+        }
+    }
+
+    return kTRUE;
+}
+
+const double GAIN_ACCEPTANCE_THRESHOLD = 0.3;
+void GainMatchSX3::Terminate()
+{
+    double backSlope[MAX_DET][MAX_BK] = {{0}};
+    bool backSlopeValid[MAX_DET][MAX_BK] = {{false}};
+
+    std::ofstream outFile("sx3_BackGains0.txt");
+    if (!outFile.is_open())
+    {
+        std::cerr << "Error opening sx3_BackGains.txt for writing!" << std::endl;
+        return;
+    }
+
+    // === Gain fit: (Up+Dn) vs Back, grouped by [id][bk] ===
+    for (int id = 0; id < MAX_DET; id++)
+    {
+        for (int bk = 0; bk < MAX_BK; bk++)
+        {
+            std::vector<double> bkE, udE;
+
+            // Collect all (Up+Dn, Back) for this id,bk
+            for (const auto &kv : dataPoints)
+            {
+                auto [cid, cbk, u, d] = kv.first;
+                if (cid != id || cbk != bk)
+                    continue;
+
+                for (const auto &pr : kv.second)
+                {
+                    double eBk, eUp, eDn;
+                    std::tie(eBk, eUp, eDn) = pr;
+                    if ((eBk < 100) || (eUp < 100) || (eDn < 100))
+                        continue;
+
+                    bkE.push_back(eBk);
+                    udE.push_back(eUp + eDn);
+                }
+            }
+
+            if (bkE.size() < 5)
+                continue; // not enough statistics
+
+            // Build graph with errors
+            const double fixedError = 0.0;                      // ADC channels
+            std::vector<double> exVals(udE.size(), 0.0);        // no x error
+            std::vector<double> eyVals(udE.size(), fixedError); // constant y error
+
+            TGraphErrors g(udE.size(), udE.data(), bkE.data(),
+                           exVals.data(), eyVals.data());
+
+            TF1 f("f", "[0]*x", 0, 16000);
+            // f.SetParameter(0, 1.0); // initial slope
+
+            if (drawCanvases)
+            {
+                g.SetTitle(Form("Detector %d Back %d: (Up+Dn) vs Back", id, bk));
+                g.SetMarkerStyle(20);
+                g.SetMarkerColor(kBlue);
+                g.Draw("AP");
+
+                g.Fit(&f, interactiveMode ? "Q" : "QNR");
+
+                if (verboseFit)
+                {
+                    double chi2 = f.GetChisquare();
+                    int ndf = f.GetNDF();
+                    double reducedChi2 = (ndf != 0) ? chi2 / ndf : -1;
+
+                    std::cout << Form("Det%d Back%d → Slope: %.4f | χ²/ndf = %.2f/%d = %.2f",
+                                      id, bk, f.GetParameter(0), chi2, ndf, reducedChi2)
+                              << std::endl;
+                }
+
+                if (interactiveMode)
+                {
+                    c.Update();
+                    gPad->WaitPrimitive();
+                }
+                else
+                {
+                    c.Close();
+                }
+            }
+            else
+            {
+                g.Fit(&f, "QNR");
+            }
+
+            double slope = 1 / f.GetParameter(0);
+            if (std::abs(slope - 1.0) < 0.3) // sanity check
+            {
+                backSlope[id][bk] = slope;
+                backSlopeValid[id][bk] = true;
+                outFile << id << " " << bk << " " << slope << "\n";
+                printf("Back slope Det%d Bk%d → %.4f\n", id, bk, slope);
+            }
+            else
+            {
+                std::cerr << "Warning: Bad slope for Det" << id << " Bk" << bk
+                          << " slope=" << slope << std::endl;
+            }
+        }
+    }
+
+    outFile.close();
+    std::cout << "Back gain matching complete." << std::endl;
+
+    // === Create histograms ===
+    TH2F *hFVB = new TH2F("hFVB", "Corrected Up+Dn vs Corrected Back;Up+Dn E;Corrected Back E",
+                          600, 0, 16000, 600, 0, 16000);
+    TH2F *hAsym = new TH2F("hAsym", "Up vs Dn divide corrected back;Up/Back E;Dn/Back E",
+                           400, 0.0, 1.0, 400, 0.0, 1.0);
+    TH2F *hAsymUnorm = new TH2F("hAsymUnorm", "Up vs Dn;Up E;Dn E",
+                                800, 0.0, 4000.0, 800, 0.0, 4000.0);
+
+    // Fill histograms using corrected back energies
+    for (const auto &kv : dataPoints)
+    {
+        auto [id, bk, u, d] = kv.first;
+        if (!backSlopeValid[id][bk])
+            continue;
+
+        double slope = backSlope[id][bk];
+
+        for (const auto &pr : kv.second)
+        {
+            double eBk, eUp, eDn;
+            std::tie(eBk, eUp, eDn) = pr;
+
+            double updn = eUp + eDn;
+            if (updn == 0 || eBk == 0)
+                continue;
+
+            double correctedBack = eBk * slope;
+            double asym = (eUp - eDn) / updn;
+
+            hFVB->Fill(updn, correctedBack);
+            hAsym->Fill(eUp / correctedBack, eDn / correctedBack);
+            hAsymUnorm->Fill(eUp, eDn);
+            TString histNamex = Form("CorrBack_id%d_U%d-D%dvsB%d", id, u, d, bk);
+
+            TH2F *hist2dx = (TH2F *)gDirectory->Get(histNamex);
+            if (!hist2dx)
+            {
+                hist2dx = new TH2F(histNamex, histNamex,
+                                   800, -1, 1, 800, 0, 4000);
+            }
+
+            hist2dx->Fill((eUp - eDn) / (eUp + eDn), correctedBack);
+        }
+    }
+    // plotter.FlushToDisk();
+}

GainMatchSX3.h

@@ -0,0 +1,114 @@
+#ifndef GainMatchSX3_h
+#define GainMatchSX3_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class GainMatchSX3 : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   GainMatchSX3(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~GainMatchSX3() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(GainMatchSX3,0);
+};
+
+#endif
+
+#ifdef GainMatchSX3_cxx
+void GainMatchSX3::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t GainMatchSX3::Notify(){
+
+   return kTRUE;
+}
+
+void GainMatchSX3::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void GainMatchSX3::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef GainMatchSX3_cxx

GainMatchSX3Front.C

@@ -0,0 +1,420 @@
+#define GainMatchSX3Front_cxx
+
+#include "GainMatchSX3Front.h"
+#include <TH2.h>
+#include <TF1.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include <TProfile.h>
+#include "Armory/ClassSX3.h"
+#include "TGraphErrors.h"
+#include "TMultiDimFit.h"
+
+#include "TVector3.h"
+
+TH2F *hSX3FvsB;
+TH2F *hSX3FvsB_g;
+TH2F *hsx3IndexVE;
+TH2F *hsx3IndexVE_g;
+TH2F *hSX3;
+TH2F *hsx3Coin;
+
+int padID = 0;
+
+SX3 sx3_contr;
+TCutG *cut;
+TCutG *cut1;
+std::map<std::tuple<int, int, int, int>, std::vector<std::tuple<double, double, double>>> dataPoints;
+TCanvas c(Form("canvas"), "Fit", 800, 600);
+
+// Gain arrays
+
+const int MAX_DET = 24;
+const int MAX_UP = 4;
+const int MAX_DOWN = 4;
+const int MAX_BK = 4;
+double backGain[MAX_DET][MAX_BK] = {{0}};
+bool backGainValid[MAX_DET][MAX_BK] = {{false}};
+double frontGain[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+bool frontGainValid[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{false}}}};
+double uvdslope[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+// ==== Configuration Flags ====
+const bool interactiveMode = true; // If true: show canvas + wait for user
+const bool verboseFit = true;      // If true: print fit summary and chi²
+const bool drawCanvases = true;    // If false: canvases won't be drawn at all
+
+void GainMatchSX3Front::Begin(TTree * /*tree*/)
+{
+    TString option = GetOption();
+
+    hSX3FvsB = new TH2F("hSX3FvsB", "SX3 Front vs Back; Front E; Back E", 800, 0, 16000, 800, 0, 16000);
+    hSX3FvsB_g = new TH2F("hSX3FvsB_g", "SX3 Front vs Back; Front E; Back E", 800, 0, 16000, 800, 0, 16000);
+    hsx3IndexVE = new TH2F("hsx3IndexVE", "SX3 index vs Energy; sx3 index ; Energy", 24 * 12, 0, 24 * 12, 400, 0, 5000);
+    hsx3IndexVE_g = new TH2F("hsx3IndexVE_g", "SX3 index vs Energy; sx3 index ; Energy", 24 * 12, 0, 24 * 12, 400, 0, 5000);
+    hSX3 = new TH2F("hSX3", "SX3 Front v Back; Fronts; Backs", 8, 0, 8, 4, 0, 4);
+
+    hsx3Coin = new TH2F("hsx3Coin", "SX3 Coincident", 24 * 12, 0, 24 * 12, 24 * 12, 0, 24 * 12);
+
+    sx3_contr.ConstructGeo();
+
+    // Load the TCutG object
+    TFile *cutFile = TFile::Open("sx3cut.root");
+    bool cutLoaded = (cut != nullptr);
+    cut = dynamic_cast<TCutG *>(cutFile->Get("sx3cut"));
+    if (!cut)
+    {
+        std::cerr << "Error: Could not find TCutG named 'sx3cut' in sx3cut.root" << std::endl;
+        return;
+    }
+    cut->SetName("sx3cut"); // Ensure the cut has the correct name
+
+    // Load the TCutG object
+    TFile *cutFile1 = TFile::Open("UvD.root");
+    bool cut1Loaded = (cut1 != nullptr);
+    cut1 = dynamic_cast<TCutG *>(cutFile1->Get("UvD"));
+    if (!cut1)
+    {
+        std::cerr << "Error: Could not find TCutG named 'UvD' in UvD.root" << std::endl;
+        return;
+    }
+    cut1->SetName("UvD");
+
+    std::string filename = "sx3_BackGains.txt";
+
+    std::ifstream infile(filename);
+    if (!infile.is_open())
+    {
+        std::cerr << "Error opening " << filename << "!" << std::endl;
+        return;
+    }
+
+    int id, bk;
+    double gain;
+    while (infile >> id >> bk >> gain)
+    {
+        backGain[id][bk] = gain;
+        if (backGain[id][bk] > 0)
+            backGainValid[id][bk] = true;
+        else
+            backGainValid[id][bk] = false;
+    }
+
+    SX3 sx3_contr;
+}
+
+Bool_t GainMatchSX3Front::Process(Long64_t entry)
+{
+
+    b_sx3Multi->GetEntry(entry);
+    b_sx3ID->GetEntry(entry);
+    b_sx3Ch->GetEntry(entry);
+    b_sx3E->GetEntry(entry);
+    b_sx3T->GetEntry(entry);
+
+    sx3.CalIndex();
+
+    std::vector<std::pair<int, int>> ID;
+    for (int i = 0; i < sx3.multi; i++)
+    {
+
+        for (int j = i + 1; j < sx3.multi; j++)
+        {
+            // if (sx3.id[i] == 3)
+            hsx3Coin->Fill(sx3.index[i], sx3.index[j]);
+        }
+        if (sx3.e[i] > 100)
+        {
+            ID.push_back(std::pair<int, int>(sx3.id[i], i));
+            hsx3IndexVE->Fill(sx3.index[i], sx3.e[i]);
+        }
+    }
+
+    if (ID.size() > 0)
+    {
+        std::sort(ID.begin(), ID.end(), [](const std::pair<int, int> &a, const std::pair<int, int> &b)
+                  { return a.first < b.first; });
+
+        // start with the first entry in the sorted array: channels that belong to the same detector are together in sequenmce
+        std::vector<std::pair<int, int>> sx3ID;
+        sx3ID.push_back(ID[0]);
+        bool found = false;
+
+        for (size_t i = 1; i < ID.size(); i++)
+        { // Check if id of i belongs to the same detector and then add it to the detector ID vector
+            if (ID[i].first == sx3ID.back().first)
+            { // count the nunmber of hits that belong to the same detector
+                sx3ID.push_back(ID[i]);
+
+                if (sx3ID.size() >= 3)
+                {
+                    found = true;
+                }
+            }
+            else
+            { // the next event does not belong to the same detector, abandon the first event and continue with the next one
+                if (!found)
+                {
+                    sx3ID.clear();
+                    sx3ID.push_back(ID[i]);
+                }
+            }
+        }
+
+        if (found)
+        {
+            int sx3ChUp = -1, sx3ChDn = -1, sx3ChBk = -1;
+            float sx3EUp = 0.0, sx3EDn = 0.0, sx3EBk = 0.0;
+
+            for (size_t i = 0; i < sx3ID.size(); i++)
+            {
+                int index = sx3ID[i].second;
+                // Check the channel number and assign it to the appropriate channel type
+                if (sx3.ch[index] < 8)
+                {
+                    if (sx3.ch[index] % 2 == 0)
+                    {
+                        sx3ChDn = sx3.ch[index] / 2;
+                        sx3EDn = sx3.e[index];
+                    }
+                    else
+                    {
+                        sx3ChUp = sx3.ch[index] / 2;
+                        sx3EUp = sx3.e[index];
+                    }
+                }
+                else
+                {
+                    sx3ChBk = sx3.ch[index] - 8;
+                    // if (sx3ChBk == 2)
+                    //     printf("Found back channel Det %d Back %d \n", sx3.id[index], sx3ChBk);
+                    sx3EBk = sx3.e[index];
+                }
+            }
+
+            for (int i = 0; i < sx3.multi; i++)
+            {
+                // If we have a valid front and back channel, fill the histograms
+                hSX3->Fill(sx3ChDn + 4, sx3ChBk);
+                hSX3->Fill(sx3ChUp, sx3ChBk);
+
+                // Fill the histogram for the front vs back
+                hSX3FvsB->Fill(sx3EUp + sx3EDn, sx3EBk);
+
+                if (sx3.e[i] > 100 && sx3.id[i] == 3)
+                {
+                    // back gain correction
+
+                    // Fill the histogram for the front vs back with gain correction
+                    // hSX3FvsB_g->Fill(sx3EUp + sx3EDn, sx3EBk);
+                    // // Fill the index vs energy histogram
+                    // hsx3IndexVE_g->Fill(sx3.index[i], sx3.e[i]);
+                    // }
+                    // {
+                    TString histName = Form("hSX3FVB_id%d_U%d_D%d_B%d", sx3.id[i], sx3ChUp, sx3ChDn, sx3ChBk);
+                    TH2F *hist2d = (TH2F *)gDirectory->Get(histName);
+                    if (!hist2d)
+                    {
+                        hist2d = new TH2F(histName, Form("hSX3FVB_id%d_U%d_D%d_B%d", sx3.id[i], sx3ChUp, sx3ChDn, sx3ChBk), 400, 0, 16000, 400, 0, 16000);
+                    }
+
+                    // if (sx3ChBk == 2)
+                    //     printf("Found back channel Det %d Back %d \n", sx3.id[i], sx3ChBk);
+                    hsx3IndexVE_g->Fill(sx3.index[i], sx3.e[i]);
+                    hSX3FvsB_g->Fill(sx3EUp + sx3EDn, sx3EBk);
+
+                    hist2d->Fill(sx3EUp + sx3EDn, sx3EBk);
+
+                    if (cut && cut->IsInside(sx3EUp + sx3EDn, sx3EBk) && cut1 && cut1->IsInside(sx3EUp / sx3EBk, sx3EDn / sx3EBk))
+                    {
+
+                        if (backGainValid[sx3.id[i]][sx3ChBk])
+                        {
+                            sx3EBk *= backGain[sx3.id[i]][sx3ChBk];
+                        }
+                        // Accumulate data for gain matching
+                        dataPoints[{sx3.id[i], sx3ChBk, sx3ChUp, sx3ChDn}].emplace_back(sx3EBk, sx3EUp, sx3EDn);
+                    }
+                }
+            }
+        }
+    }
+
+    return kTRUE;
+}
+
+void GainMatchSX3Front::Terminate()
+{
+
+    std::map<std::tuple<int, int, int, int>, TVectorD> fitCoefficients;
+
+    // === Gain matching ===
+
+    std::ofstream outFile("sx3_GainMatchfront.txt");
+    if (!outFile.is_open())
+    {
+        std::cerr << "Error opening output file!" << std::endl;
+        return;
+    }
+
+    TH2F *hUvD = new TH2F("hUvD", " UvD; Up/CorrBack; Down/CorrBack", 600, 0, 1, 600, 0, 1);
+
+    for (const auto &kv : dataPoints)
+    {
+        auto [id, bk, u, d] = kv.first;
+        const auto &pts = kv.second;
+
+        if (pts.size() < 50)
+            continue;
+
+        std::vector<double> uE, dE, udE, corrBkE;
+
+        for (const auto &pr : pts)
+        {
+            double eBkCorr, eUp, eDn;
+            std::tie(eBkCorr, eUp, eDn) = pr;
+            if ((eBkCorr < 100) || (eUp < 100) || (eDn < 100))
+                continue; // Skip if any energy is zero
+            uE.push_back(eUp / eBkCorr);
+            dE.push_back(eDn / eBkCorr);
+            udE.push_back(eUp + eDn);
+            corrBkE.push_back(eBkCorr);
+            hUvD->Fill(eUp / eBkCorr, eDn / eBkCorr);
+        }
+        if (uE.size() < 5 || dE.size() < 5 || corrBkE.size() < 5)
+            continue; // Ensure we have enough points for fitting
+        // TGraph g(udE.size(), udE.data(), corrBkE.data());
+
+        // TF1 f("f", "[0]*x", 0, 20000);
+        // f.SetParameter(0, 1.0); // Initial guess for the gain
+        // g.Fit(&f, "R");
+
+        const double fixedError = 0.0; // in ADC channels
+
+        std::vector<double> xVals, yVals, exVals, eyVals;
+
+        // Build data with fixed error
+        for (size_t i = 0; i < udE.size(); ++i)
+        {
+            double x = uE[i]; // front energy
+            double y = dE[i]; // back energy
+
+            xVals.push_back(x);
+            yVals.push_back(y);
+            exVals.push_back(fixedError); // error in up energy
+            eyVals.push_back(0.);         // error in down energy
+        }
+
+        // Build TGraphErrors with errors
+        TGraphErrors g(xVals.size(), xVals.data(), yVals.data(), exVals.data(), eyVals.data());
+
+        TF1 f("f", "[0]*x+[1]", 0, 16000);
+        f.SetParameter(0, -1.0); // Initial guess
+
+        if (drawCanvases)
+        {
+            g.SetTitle(Form("Detector %d: U%d D%d B%d", id, u, d, bk));
+            g.SetMarkerStyle(20);
+            g.SetMarkerColor(kBlue);
+            g.Draw("AP");
+
+            g.Fit(&f, interactiveMode ? "Q" : "QNR"); // 'R' avoids refit, 'N' skips drawing
+
+            if (verboseFit)
+            {
+                double chi2 = f.GetChisquare();
+                int ndf = f.GetNDF();
+                double reducedChi2 = (ndf != 0) ? chi2 / ndf : -1;
+
+                std::cout << Form("Det%d U%d D%d B%d → Gain: %.4f | χ²/ndf = %.2f/%d = %.2f",
+                                  id, u, d, bk, f.GetParameter(0), chi2, ndf, reducedChi2)
+                          << std::endl;
+            }
+
+            if (interactiveMode)
+            {
+                c.Update();
+                gPad->WaitPrimitive();
+            }
+            else
+            {
+                c.Close(); // Optionally avoid clutter in batch
+            }
+        }
+        else
+        {
+            g.Fit(&f, "QNR");
+        }
+
+        double slope = f.GetParameter(0);
+        double intercept = f.GetParameter(1);   
+
+        // printf("Front gain Det%d Back%d Up%dDn%d → %.4f\n", id, bk, u, d, frontGain[id][bk][u][d]);
+        if (std::abs(slope + 1.0) < 0.3) // sanity check
+        {
+            frontGain[id][bk][u][d] = slope;
+
+            frontGainValid[id][bk][u][d] = true;
+            outFile << id << " " << bk << " " << u << " " << d << " " << TMath::Abs(slope)/intercept << " " << 1.0/intercept << std::endl;
+            printf("Back slope Det%d Bk%d → %.4f\n", id, bk, slope);
+        }
+        else
+        {
+            std::cerr << "Warning: Bad slope for Det" << id << " Bk" << bk
+                      << " slope=" << f.GetParameter(0) << std::endl;
+        }
+    }
+
+    outFile.close();
+    std::cout << "Gain matching complete." << std::endl;
+
+    // === Stage 3: Create corrected histogram ===
+    TH2F *hCorrectedFvB = new TH2F("hCorrectedFvB", "Corrected;Corrected Front Sum;Corrected Back", 800, 0, 8000, 800, 0, 8000);
+    TH2F *hCorrectedUvD = new TH2F("hCorrectedUvD", "Corrected UvD; UvD Up; UvD Down", 600, 0, 1, 600, 0, 1);
+
+    for (const auto &kv : dataPoints)
+    {
+
+        auto [id, bk, u, d] = kv.first;
+        double front;
+        if (frontGainValid[id][bk][u][d])
+            front = frontGain[id][bk][u][d];
+        else
+            continue;
+        for (const auto &pr : kv.second)
+        {
+            double eBk, eUp, eDn;
+            std::tie(eBk, eUp, eDn) = pr;
+            double corrUp = eUp * front;
+            // double corrDn = eDn * front;
+
+            hCorrectedFvB->Fill(corrUp + eDn, eBk);
+            hCorrectedUvD->Fill(corrUp / eBk, eDn / eBk);
+        }
+    }
+
+    // // === Final canvas ===
+    // gStyle->SetOptStat(1110);
+    // TCanvas *c1 = new TCanvas("c1", "Gain Correction Results", 1200, 600);
+    // c1->Divide(2, 1);
+
+    // c1->cd(1);
+    // hSX3FvsB_g->SetTitle("Before Correction (Gated)");
+    // hSX3FvsB_g->GetXaxis()->SetTitle("Measured Front Sum (E_Up + E_Dn)");
+    // hSX3FvsB_g->GetYaxis()->SetTitle("Measured Back E");
+    // hSX3FvsB_g->Draw("colz");
+
+    // c1->cd(2);
+    // hCorrectedFvB->SetTitle("After Correction");
+    // hCorrectedFvB->Draw("colz");
+    // TF1 *diag = new TF1("diag", "x", 0, 40000);
+    // diag->SetLineColor(kRed);
+    // diag->SetLineWidth(2);
+    // diag->Draw("same");
+
+    std::cout << "Terminate() completed successfully." << std::endl;
+}

GainMatchSX3Front.h

@@ -0,0 +1,104 @@
+#ifndef GainMatchSX3Front_h
+#define GainMatchSX3Front_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class GainMatchSX3Front : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   GainMatchSX3Front(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~GainMatchSX3Front() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(GainMatchSX3Front,0);
+};
+
+#endif
+
+#ifdef GainMatchSX3Front_cxx
+void GainMatchSX3Front::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+
+}
+
+Bool_t GainMatchSX3Front::Notify(){
+
+   return kTRUE;
+}
+
+void GainMatchSX3Front::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void GainMatchSX3Front::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef GainMatchSX3Front_cxx

GainMatchSX3Front1.C

@@ -0,0 +1,245 @@
+#define GainMatchSX3_cxx
+
+#include "GainMatchSX3.h"
+#include "Armory/ClassSX3.h"
+#include <TFile.h>
+#include <TTree.h>
+#include <TGraph.h>
+#include <TF1.h>
+#include <TH2F.h>
+#include <TCanvas.h>
+#include <TStyle.h>
+#include <TApplication.h>
+#include <map>
+#include <vector>
+#include <tuple>
+#include <fstream>
+#include <iostream>
+#include <algorithm>
+
+// Constants
+const int MAX_DET = 24;
+const int MAX_BK = 4;
+const int MAX_UP = 4;
+const int MAX_DOWN = 4;
+
+// Gain arrays
+double backGain[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+bool backGainValid[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{false}}}};
+
+double frontGain[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{0}}}};
+bool frontGainValid[MAX_DET][MAX_BK][MAX_UP][MAX_DOWN] = {{{{false}}}};
+
+// Data container
+std::map<std::tuple<int, int, int, int>, std::vector<std::tuple<double, double, double>>> dataPoints;
+
+// Load back gains
+void LoadBackGains(const std::string &filename)
+{
+    std::ifstream infile(filename);
+    if (!infile.is_open())
+    {
+        std::cerr << "Error opening " << filename << "!" << std::endl;
+        return;
+    }
+
+    int id, bk, u, d;
+    double gain;
+    while (infile >> id >> bk >> u >> d >> gain)
+    {
+        backGain[id][bk][u][d] = gain;
+        backGainValid[id][bk][u][d] = true;
+    }
+
+    infile.close();
+    std::cout << "Loaded back gains from " << filename << std::endl;
+    SX3 sx3_contr;
+}
+
+// Front gain matching function
+Bool_t GainMatchSX3::Process(Long64_t entry)
+{
+    // Link SX3 branches
+    
+    b_sx3Multi->GetEntry(entry);
+    b_sx3ID->GetEntry(entry);
+    b_sx3Ch->GetEntry(entry);
+    b_sx3E->GetEntry(entry);
+    b_sx3T->GetEntry(entry);
+
+    sx3.CalIndex();
+
+    Long64_t nentries = tree->GetEntries(Long64_t entry);
+    std::cout << "Total entries: " << nentries << std::endl;
+
+    TH2F *hBefore = new TH2F("hBefore", "Before Correction;E_Up+E_Dn;Back Energy", 400, 0, 40000, 400, 0, 40000);
+    TH2F *hAfter = new TH2F("hAfter", "After Correction;E_Up+E_Dn;Corrected Back Energy", 400, 0, 40000, 400, 0, 40000);
+
+    for (Long64_t entry = 0; entry < nentries; ++entry)
+    {
+        tree->GetEntry(entry);
+        sx3.CalIndex();
+
+        std::vector<std::pair<int, int>> ID;
+
+        for (int i = 0; i < sx3.multi; i++)
+        {
+            if (sx3.e[i] > 100)
+            {
+                ID.push_back({sx3.id[i], i});
+            }
+        }
+
+        if (ID.empty())
+            continue;
+
+        // Sort by id
+        std::sort(ID.begin(), ID.end(), [](auto &a, auto &b) { return a.first < b.first; });
+
+        std::vector<std::pair<int, int>> sx3ID;
+        sx3ID.push_back(ID[0]);
+        bool found = false;
+
+        for (size_t i = 1; i < ID.size(); i++)
+        {
+            if (ID[i].first == sx3ID.back().first)
+            {
+                sx3ID.push_back(ID[i]);
+                if (sx3ID.size() >= 3)
+                    found = true;
+            }
+            else if (!found)
+            {
+                sx3ID.clear();
+                sx3ID.push_back(ID[i]);
+            }
+        }
+
+        if (!found)
+            continue;
+
+        int sx3ChUp = -1, sx3ChDn = -1, sx3ChBk = -1;
+        float sx3EUp = 0.0, sx3EDn = 0.0, sx3EBk = 0.0;
+        int sx3id = sx3ID[0].first;
+
+        for (auto &[id, idx] : sx3ID)
+        {
+            if (sx3.ch[idx] < 8)
+            {
+                if (sx3.ch[idx] % 2 == 0)
+                {
+                    sx3ChDn = sx3.ch[idx] / 2;
+                    sx3EDn = sx3.e[idx];
+                }
+                else
+                {
+                    sx3ChUp = sx3.ch[idx] / 2;
+                    sx3EUp = sx3.e[idx];
+                }
+            }
+            else
+            {
+                sx3ChBk = sx3.ch[idx] - 8;
+                sx3EBk = sx3.e[idx];
+            }
+        }
+
+        if (sx3ChUp < 0 || sx3ChDn < 0 || sx3ChBk < 0)
+            continue;
+
+        if (!backGainValid[sx3id][sx3ChBk][sx3ChUp][sx3ChDn])
+            continue;
+
+        double corrBk = sx3EBk * backGain[sx3id][sx3ChBk][sx3ChUp][sx3ChDn];
+
+        hBefore->Fill(sx3EUp + sx3EDn, sx3EBk);
+        hAfter->Fill(sx3EUp + sx3EDn, corrBk);
+
+        dataPoints[{sx3id, sx3ChBk, sx3ChUp, sx3ChDn}].emplace_back(corrBk, sx3EUp, sx3EDn);
+    }
+
+    // === Fit front gains ===
+    std::ofstream outFile("sx3_GainMatchfront.txt");
+    if (!outFile.is_open())
+    {
+        std::cerr << "Error opening sx3_GainMatchfront.txt!" << std::endl;
+        return;
+    }
+
+    for (const auto &kv : dataPoints)
+    {
+        auto [id, bk, u, d] = kv.first;
+        const auto &pts = kv.second;
+
+        if (pts.size() < 5)
+            continue;
+
+        std::vector<double> udE, corrBkE;
+
+        for (const auto &pr : pts)
+        {
+            double eBkCorr, eUp, eDn;
+            std::tie(eBkCorr, eUp, eDn) = pr;
+            udE.push_back(eUp + eDn);
+            corrBkE.push_back(eBkCorr);
+        }
+
+        TGraph g(udE.size(), udE.data(), corrBkE.data());
+        TF1 f("f", "[0]*x", 0, 40000);
+        g.Fit(&f, "QNR");
+
+        frontGain[id][bk][u][d] = f.GetParameter(0);
+        frontGainValid[id][bk][u][d] = true;
+
+        outFile << id << " " << bk << " " << u << " " << d << " " << frontGain[id][bk][u][d] << std::endl;
+        printf("Front gain Det%d Back%d Up%dDn%d → %.4f\n", id, bk, u, d, frontGain[id][bk][u][d]);
+    }
+
+    outFile.close();
+    std::cout << "Front gain matching complete." << std::endl;
+
+    // === Draw diagnostic plots ===
+    gStyle->SetOptStat(1110);
+    TCanvas *c = new TCanvas("c", "Gain Matching Diagnostics", 1200, 600);
+    c->Divide(2, 1);
+
+    c->cd(1);
+    hBefore->Draw("colz");
+    TF1 *diag1 = new TF1("diag1", "x", 0, 40000);
+    diag1->SetLineColor(kRed);
+    diag1->Draw("same");
+
+    c->cd(2);
+    hAfter->Draw("colz");
+    TF1 *diag2 = new TF1("diag2", "x", 0, 40000);
+    diag2->SetLineColor(kRed);
+    diag2->Draw("same");
+}
+
+int main(int argc, char **argv)
+{
+    TApplication app("app", &argc, argv);
+
+    // Load back gains
+    LoadBackGains("sx3_GainMatchback.txt");
+
+    // Open tree
+    TFile *f = TFile::Open("input_tree.root"); // <<< Change file name
+    if (!f || f->IsZombie())
+    {
+        std::cerr << "Cannot open input_tree.root!" << std::endl;
+        return 1;
+    }
+    TTree *tree = (TTree *)f->Get("tree");
+    if (!tree)
+    {
+        std::cerr << "Tree not found!" << std::endl;
+        return 1;
+    }
+
+    // Run front gain matching
+    GainMatchSX3(tree);
+
+    app.Run();
+    return 0;
+}

MakeVertex.h

@@ -0,0 +1,132 @@
+#ifndef MakeVertex_h
+#define MakeVertex_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TApplication.h>
+#include <TFile.h>
+#include <TSelector.h>
+#include <iomanip>
+#include <vector>         // Required for vectors
+#include <utility>        // Required for std::pair
+
+#include "Armory/ClassDet.h"
+#include "Armory/ClassPW.h" // YOU ADDED THIS (Correct! Defines Coord)
+
+class MakeVertex : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+   Det misc;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+   TBranch        *b_miscMulti;   //!
+   TBranch        *b_miscID;   //!
+   TBranch        *b_miscCh;   //!
+   TBranch        *b_miscE;   //!
+   TBranch        *b_miscT;   //!
+   TBranch        *b_miscTf;   //!
+
+   // 1. Geometry Cache
+   Coord Crossover[24][24][2];
+
+   // 2. Persistent Vectors (REQUIRED for the optimized .cxx to work)
+   std::vector<std::pair<int, double>> anodeHits;
+   std::vector<std::pair<int, double>> cathodeHits;
+   std::vector<std::pair<int, double>> corrcatMax;
+   std::vector<std::pair<int, double>> corranoMax;
+   std::vector<double> cathodeTimes;
+   std::vector<double> anodeTimes;
+   
+   MakeVertex(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~MakeVertex() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(MakeVertex,0);
+};
+
+#endif
+
+#ifdef MakeVertex_cxx
+void MakeVertex::Init(TTree *tree){
+
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID",    &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh",    &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE",     &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT",     &misc.t, &b_miscT);
+}
+
+Bool_t MakeVertex::Notify(){
+   return kTRUE;
+}
+
+void MakeVertex::SlaveBegin(TTree * /*tree*/){
+   // TString option = GetOption();
+}
+
+void MakeVertex::SlaveTerminate(){
+}
+#endif // #ifdef MakeVertex_cxx

MatchAndPlotCentroids.C

@@ -0,0 +1,133 @@
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <map>
+#include <iostream>
+#include <TGraph.h>
+#include <TF1.h>
+#include <TCanvas.h>
+#include <TH1.h>
+
+
+
+void MatchAndPlotCentroids() {
+    // Open the centroid data file
+    std::ifstream inputFile("centroids.txt");
+    if (!inputFile.is_open()) {
+        std::cerr << "Error: Could not open Centroids.txt" << std::endl;
+        return;
+    }
+
+    // Data structure to store centroids by histogram and peak number
+    std::map<int, std::map<int, double>> centroidData;
+
+    // Read data from the file
+    std::string line;
+    while (std::getline(inputFile, line)) {
+        std::istringstream iss(line);
+        int histogramIndex, peakNumber;
+        double centroid;
+        if (iss >> histogramIndex >> peakNumber >> centroid) {
+            centroidData[histogramIndex][peakNumber] = centroid;
+        }
+    }
+
+    inputFile.close();
+
+    // Ensure histogram 24 exists and has data
+    if (centroidData.find(1) == centroidData.end()) {
+        std::cerr << "Error: Histogram 0 not found in the data!" << std::endl;
+        return;
+    }
+
+    // Reference centroids from histogram 24
+    const auto& referenceCentroids = centroidData[1];
+    std::ofstream outputFile("slope_intercept_results.txt");
+    if (!outputFile.is_open()) {
+        std::cerr << "Error: Could not open the output file for writing!" << std::endl;
+        return;
+    }
+    outputFile << "Histogram Number\tSlope\tIntercept\n";
+    // Loop through histograms 25 to 47
+    for (int targetHist = 0; targetHist <= 23; targetHist++) {
+        // Ensure the target histogram exists and matches in peak numbers
+        if (centroidData.find(targetHist) == centroidData.end() || centroidData[targetHist].size() != referenceCentroids.size()) {
+            //4th cnetroid data point for 19 was generated using the 3 datqa points for the slope of wires 0 and 19
+            std::cout << "Skipping Histogram " << targetHist << " due to mismatched or missing data." << std::endl;
+            continue;
+        }
+
+        // Prepare x and y values for TGraph
+        std::vector<double> xValues, yValues;
+        for (const auto& [peakNumber, refCentroid] : referenceCentroids) {
+            if (centroidData[targetHist].find(peakNumber) != centroidData[targetHist].end()) {
+                yValues.push_back(refCentroid);
+                xValues.push_back(centroidData[targetHist][peakNumber]);
+            } else {
+                std::cerr << "Warning: Peak " << peakNumber << " missing in histogram " << targetHist << std::endl;
+            }
+        }
+
+        if (xValues.size() < 3) {
+            std::cout << "Skipping Histogram " << targetHist << " as it has less than 3 matching centroids." << std::endl;
+            continue;
+        }
+
+        // Create a TGraph
+        TCanvas *c1 = new TCanvas(Form("c_centroid_1_vs_%d", targetHist), Form("Centroid 1 vs %d", targetHist), 800, 600);
+        TGraph *graph = new TGraph(xValues.size(), &xValues[0], &yValues[0]);
+        graph->SetTitle(Form("Centroid of Histogram  %d vs 1", targetHist));
+        graph->GetYaxis()->SetTitle("Centroid of Histogram 1");
+        graph->GetXaxis()->SetTitle(Form("Centroid of Histogram %d", targetHist));
+        graph->SetMarkerStyle(20); // Full circle marker
+        graph->SetMarkerSize(1.0);
+        graph->SetMarkerColor(kBlue);
+        // Draw the graph
+        graph->Draw("AP");
+        double minX = *std::min_element(xValues.begin(), xValues.end());
+        double maxX = *std::max_element(xValues.begin(), xValues.end());
+        // Fit the data with a linear function
+        TF1 *fitLine = new TF1("fitLine", "pol1", minX, maxX);  // Adjust range as needed
+	fitLine->SetLineColor(kRed); // Set the line color to distinguish it
+        fitLine->SetLineWidth(2);    // Thicker line for visibility
+        graph->Fit(fitLine, "M");
+        fitLine->Draw("same");
+        fitLine->SetParLimits(0, -10, 10); // Limit intercept between -10 and 10
+        fitLine->SetParLimits(1, 0, 2); 
+        // Extract slope and intercept
+        double slope = fitLine->GetParameter(1);
+        double intercept = fitLine->GetParameter(0);
+        outputFile << targetHist << "\t" << slope << "\t" << intercept << "\n";
+        std::cout << "Histogram 24 vs " << targetHist << ": Slope = " << slope << ", Intercept = " << intercept << std::endl;
+        std::vector<double> residuals;
+    for (size_t i = 0; i < xValues.size(); ++i) {
+        double fittedY = fitLine->Eval(xValues[i]); // Evaluate fitted function at x
+        double residual = yValues[i] - fittedY;    // Residual = observed - fitted
+        residuals.push_back(residual);
+    }
+
+    // Create a graph for the residuals
+    /*TGraph *residualGraph = new TGraph(residuals.size(), &xValues[0], &residuals[0]);
+    residualGraph->SetTitle(Form("Residuals for Histogram 24 vs %d", targetHist));
+    residualGraph->GetYaxis()->SetTitle("Residuals");
+    residualGraph->GetXaxis()->SetTitle(Form("Centroid of Histogram %d", targetHist));
+    residualGraph->SetMarkerStyle(20);
+    residualGraph->SetMarkerSize(1.0);
+    residualGraph->SetMarkerColor(kGreen);
+
+    // Draw the residuals plot below the original plot (can be on a new canvas if preferred)
+    TCanvas *c2 = new TCanvas(Form("c_residuals_24_vs_%d", targetHist), Form("Residuals for Centroid 24 vs %d", targetHist), 800, 400);
+    residualGraph->Draw("AP");*/
+        c1->Update();
+        //c2->Update();
+        std::cout << "Press Enter to continue..." << std::endl;
+        
+        //std::cin.get();
+        c1->WaitPrimitive();
+        //c2->WaitPrimitive();
+        //std::cin.get();
+        //std::cin.get();
+    }
+    outputFile.close();
+    std::cout << "Results written to slope_intercept_results.txt" << std::endl;
+}

PCGainMatch.C

@@ -0,0 +1,454 @@
+#define PCGainMatch_cxx
+
+#include "PCGainMatch.h"
+#include <TH2.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <utility>
+#include <algorithm>
+#include "Armory/ClassSX3.h"
+#include "Armory/ClassPW.h"
+
+#include "TVector3.h"
+
+TH2F * hsx3IndexVE;
+TH2F * hqqqIndexVE;
+TH2F * hpcIndexVE;
+
+TH2F * hsx3Coin;
+TH2F * hqqqCoin;
+TH2F * hpcCoin;
+
+TH2F * hqqqPolar;
+TH2F * hsx3VpcIndex;
+TH2F * hqqqVpcIndex;
+TH2F * hqqqVpcE;
+TH2F * hsx3VpcE;
+TH2F * hanVScatsum;
+TH2F * hanVScatsum_a[24];
+TH2F * hanVScatsum_hcut;
+TH2F * hanVScatsum_lcut;
+TH2F * hAnodeHits;
+TH1F * hAnodeMultiplicity;
+
+
+int padID = 0;
+
+SX3 sx3_contr;
+PW pw_contr;
+TVector3 hitPos;
+bool HitNonZero;
+
+TH1F * hZProj;
+TCutG *AnCatSum_high;
+TCutG *AnCatSum_low;
+TCutG *PCCoinc_cut1;
+TCutG *PCCoinc_cut2;
+bool inCuth;
+bool inCutl;
+bool inPCCut;
+
+void PCGainMatch::Begin(TTree * /*tree*/){
+  TString option = GetOption();
+
+  hsx3IndexVE = new TH2F("hsx3IndexVE", "SX3 index vs Energy; sx3 index ; Energy",  24*12, 0,  24*12, 400, 0, 5000); hsx3IndexVE->SetNdivisions( -612, "x");
+  hqqqIndexVE = new TH2F("hqqqIndexVE", "QQQ index vs Energy; QQQ index ; Energy", 4*2*16, 0, 4*2*16, 400, 0, 5000); hqqqIndexVE->SetNdivisions( -1204, "x");
+  hpcIndexVE = new TH2F("hpcIndexVE",   "PC index vs Energy; PC index ; Energy",     2*24, 0,   2*24, 800, 0, 16000); hpcIndexVE->SetNdivisions( -1204, "x");
+
+
+  hsx3Coin = new TH2F("hsx3Coin", "SX3 Coincident",  24*12, 0,  24*12,  24*12, 0, 24*12);
+  hqqqCoin = new TH2F("hqqqCoin", "QQQ Coincident", 4*2*16, 0, 4*2*16, 4*2*16, 0, 4*2*16);
+  hpcCoin  = new TH2F("hpcCoin",  "PC Coincident",    2*24, 0,   2*24,   2*24, 0, 2*24);
+
+  hqqqPolar = new TH2F("hqqqPolar", "QQQ Polar ID", 16*4, -TMath::Pi(), TMath::Pi(),16, 10, 50);
+
+  hsx3VpcIndex = new TH2F("hsx3Vpcindex", "sx3 vs pc; sx3 index; pc index",  24*12, 0, 24*12, 48, 0, 48);
+  hsx3VpcIndex->SetNdivisions( -612, "x");
+  hsx3VpcIndex->SetNdivisions( -12, "y");
+  hqqqVpcIndex = new TH2F("hqqqVpcindex", "qqq vs pc; qqq index; pc index",  4*2*16, 0, 4*2*16, 48, 0, 48);
+  hqqqVpcIndex->SetNdivisions( -612, "x");
+  hqqqVpcIndex->SetNdivisions( -12, "y");
+
+  hqqqVpcE = new TH2F("hqqqVpcEnergy", "qqq vs pc; qqq energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hqqqVpcE->SetNdivisions( -612, "x");
+  hqqqVpcE->SetNdivisions( -12, "y");
+  
+  hsx3VpcE = new TH2F("hsx3VpcEnergy", "sx3 vs pc; sx3 energy; pc energy", 400, 0, 5000, 400, 0, 5000);
+  hsx3VpcE->SetNdivisions( -612, "x");
+  hsx3VpcE->SetNdivisions( -12, "y");
+
+  hZProj = new TH1F("hZProj", "Nos of anodes", 20, 0, 19);
+  hAnodeHits = new TH2F("hAnodeHits", "Anode vs Anode Energy, Anode ID; Anode E", 24,0 , 23, 400, 0 , 20000);
+  hAnodeMultiplicity = new TH1F("hAnodeMultiplicity", "Number of Anodes/Event", 40, 0, 40); 
+  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 10000, 800, 0 , 16000);
+  for (int i = 0; i < 24; i++) {
+        TString histName = Form("hAnodeVsCathode_%d", i);
+        TString histTitle = Form("Anode %d vs Cathode Sum; Anode E; Cathode Sum E", i);
+        hanVScatsum_a[i] = new TH2F(histName, histTitle, 400, 0, 10000, 400, 0, 16000);
+    }
+  hanVScatsum_lcut = new TH2F("hanVScatsum_LCUT", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 16000, 400, 0 , 16000);
+  hanVScatsum_hcut = new TH2F("hanVScatsum_HCUT", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 16000, 400, 0 , 16000);
+
+  sx3_contr.ConstructGeo();
+  pw_contr.ConstructGeo();
+  // TFile *f1 = new TFile("AnCatSum_high.root");
+  // TFile *f2 = new TFile("AnCatSum_low.root");
+  // TFile *f3 = new TFile("PCCoinc_cut1.root");
+  // TFile *f4 = new TFile("PCCoinc_cut2.root");
+  // AnCatSum_high= (TCutG*)f1->Get("AnCatSum_high");
+  // AnCatSum_low= (TCutG*)f2->Get("AnCatSum_low");
+  // PCCoinc_cut1= (TCutG*)f3->Get("PCCoinc_cut1");
+  // PCCoinc_cut2= (TCutG*)f4->Get("PCCoinc_cut2");
+}
+
+
+
+
+Bool_t PCGainMatch::Process(Long64_t entry){
+// if (entry % 1000000 == 0) {
+//     std::cout << "Processing entry: " << entry << std::endl;
+// }
+  // if ( entry > 100 ) return kTRUE;
+
+  hitPos.Clear();
+  HitNonZero = false;
+
+  // if( entry > 1) return kTRUE;
+  // printf("################### ev : %llu \n", entry);
+
+  b_sx3Multi->GetEntry(entry);
+  b_sx3ID->GetEntry(entry);
+  b_sx3Ch->GetEntry(entry);
+  b_sx3E->GetEntry(entry);
+  b_sx3T->GetEntry(entry);
+  b_qqqMulti->GetEntry(entry);
+  b_qqqID->GetEntry(entry);
+  b_qqqCh->GetEntry(entry);
+  b_qqqE->GetEntry(entry);
+  b_qqqT->GetEntry(entry);
+  b_pcMulti->GetEntry(entry);
+  b_pcID->GetEntry(entry);
+  b_pcCh->GetEntry(entry);
+  b_pcE->GetEntry(entry);
+  b_pcT->GetEntry(entry);
+
+  sx3.CalIndex();
+  qqq.CalIndex();
+  pc.CalIndex();
+
+  // sx3.Print();
+
+  //########################################################### Raw data
+
+  // //======================= PC
+
+  std::vector<std::pair<int, double>> anodeHits={};
+  std::vector<std::pair<int, double>> cathodeHits={};  
+  int aID = 0;
+  int cID = 0;
+  float aE = 0;
+  float cE = 0;
+
+// Define the excluded SX3 and QQQ channels
+  // std::unordered_set<int> excludeSX3 = {34, 35, 36, 37, 61, 62, 67, 73, 74, 75, 76, 77, 78, 79, 80, 93, 97, 100, 103, 108, 109, 110, 111, 112};
+  // std::unordered_set<int> excludeQQQ = {0, 17, 109, 110, 111, 112, 113, 119, 127, 128};
+  // inCuth=false;
+  // inCutl=false;
+  // inPCCut=false;
+  for( int i = 0; i < pc.multi; i ++){
+    
+    if(pc.e[i]>50 && pc.multi<7){ 
+
+      float aESum = 0;
+      float cESum = 0;
+      if (pc.index[i] < 24 ) {
+            anodeHits.push_back(std::pair<int, double>(pc.index[i], pc.e[i]));
+        } else if (pc.index[i] >= 24) {
+            cathodeHits.push_back(std::pair<int, double>(pc.index[i], pc.e[i]));
+        }
+
+      for(int j=i+1;j<pc.multi;j++){
+        // if(PCCoinc_cut1->IsInside(pc.index[i], pc.index[j]) || PCCoinc_cut2->IsInside(pc.index[i], pc.index[j])){
+        //   // hpcCoin->Fill(pc.index[i], pc.index[j]);
+        //   inPCCut = true;
+        // }
+        hpcCoin->Fill(pc.index[i], pc.index[j]);
+      } 
+      if (anodeHits.size()==1 && cathodeHits.size() >= 1) {
+          
+          for (const auto& anode : anodeHits) {
+          // for(int l=0; l<sx3.multi; l++){
+          //   if (sx3.index[l]==80){
+
+              aID = anode.first;
+              aE = anode.second;
+              aESum += aE;
+              // printf("aID : %d, aE : %f\n", aID, aE);
+          }
+
+            // printf("aID : %d, aE : %f, cE : %f\n", aID, aE, cE);
+            for (const auto& cathode : cathodeHits) {
+              cID = cathode.first;
+              cE = cathode.second;
+              // if(cE>cEMax){
+              //   cEMax = cE;
+              //   cIDMax = cID;
+              // }
+              // if(cE>cEnextMax && cE<cEMax){
+              //   cEnextMax = cE;
+              //   cIDnextMax = cID;
+              // }
+
+              cESum += cE;
+              }
+          // }
+          
+          // inCuth = false;
+          // inCutl = false;
+          // inPCCut = false;
+          // for(int j=i+1;j<pc.multi;j++){
+          //   if(PCCoinc_cut1->IsInside(pc.index[i], pc.index[j]) || PCCoinc_cut2->IsInside(pc.index[i], pc.index[j])){
+          //     // hpcCoin->Fill(pc.index[i], pc.index[j]);
+          //     inPCCut = true;
+          //   }
+          //   hpcCoin->Fill(pc.index[i], pc.index[j]);
+          // } 
+
+          // Check if the accumulated energies are within the defined ranges
+          // if (AnCatSum_high && AnCatSum_high->IsInside(aESum, cESum)) {
+          //     inCuth = true;
+          // }
+          // if (AnCatSum_low && AnCatSum_low->IsInside(aESum, cESum)) {
+          //     inCutl = true;
+          // }
+          
+          // Fill histograms based on the cut conditions
+          // if (inCuth && inPCCut) {
+          //     hanVScatsum_hcut->Fill(aESum, cESum);
+          // }
+          // if (inCutl && inPCCut) {
+          //     hanVScatsum_lcut->Fill(aESum, cESum);
+          // }               
+            // for(auto anode : anodeHits){
+         
+              // float aE = anode.second;
+              // aESum += aE;
+              // if(inPCCut){
+            hanVScatsum->Fill(aESum, cESum);
+            // }
+            if (aID < 24 && aE > 50) {
+             hanVScatsum_a[aID]->Fill(aE, cESum);
+            }
+
+          
+            // }
+          // Fill histograms for the `pc` data
+          hpcIndexVE->Fill(pc.index[i], pc.e[i]);
+          // if(inPCCut){
+            hAnodeMultiplicity->Fill(anodeHits.size());
+          // }
+      }
+
+    }
+  }    
+  
+
+
+  // //======================= SX3
+
+  std::vector<std::pair<int, int>> ID; // first = id, 2nd = index
+  for( int i = 0; i < sx3.multi; i ++){
+    if(sx3.e[i]>50){
+      ID.push_back(std::pair<int, int>(sx3.id[i], i));
+      hsx3IndexVE->Fill( sx3.index[i], sx3.e[i] );
+
+      for( int j = i+1; j < sx3.multi; j++){
+        hsx3Coin->Fill( sx3.index[i], sx3.index[j]);
+      }
+
+      for( int j = 0; j < pc.multi; j++){
+        hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+        //  if( sx3.ch[index] > 8 ){
+        //    hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+        //   }
+      }
+    } 
+  }
+
+
+  if( ID.size() > 0 ){
+    std::sort(ID.begin(), ID.end(),  [](const std::pair<int, int> & a, const std::pair<int, int> & b) {
+      return a.first < b.first;
+    } );
+    // printf("##############################\n");
+    // for( size_t i = 0; i < ID.size(); i++) printf("%zu | %d %d \n", i, ID[i].first, ID[i].second );
+
+    std::vector<std::pair<int, int>> sx3ID; 
+    sx3ID.push_back(ID[0]);
+    bool found = false;
+    for( size_t i = 1; i < ID.size(); i++){
+      if( ID[i].first == sx3ID.back().first) {
+        sx3ID.push_back(ID[i]);
+        if( sx3ID.size() >= 3) {
+          found = true;
+        } 
+      }else{
+        if( !found ){
+          sx3ID.clear();
+          sx3ID.push_back(ID[i]);
+        }
+      }
+    }
+
+    // printf("---------- sx3ID Multi : %zu \n", sx3ID.size());
+
+    if( found ){
+      int sx3ChUp, sx3ChDn, sx3ChBk;
+      float sx3EUp, sx3EDn;
+      // printf("------ sx3 ID : %d, multi: %zu\n", sx3ID[0].first, sx3ID.size());
+      for( size_t i = 0; i < sx3ID.size(); i++ ){
+        int index = sx3ID[i].second;
+        // printf(" %zu | index %d | ch : %d, energy : %d \n", i, index, sx3.ch[index], sx3.e[index]);
+
+
+        if( sx3.ch[index] < 8 ){
+          if( sx3.ch[index] % 2 == 0) {
+            sx3ChDn = sx3.ch[index];
+            sx3EDn = sx3.e[index];
+          }else{
+            sx3ChUp = sx3.ch[index];
+            sx3EUp = sx3.e[index];
+          }
+        }else{
+          sx3ChBk = sx3.ch[index];
+        }
+         for( int j = 0; j < pc.multi; j++){
+
+      // hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+            if( sx3.ch[index] > 8 && pc.index[j]<24 && pc.e[j]>50 ){
+              hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
+          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+            }
+          }
+      }
+
+      sx3_contr.CalSX3Pos(sx3ID[0].first, sx3ChUp, sx3ChDn, sx3ChBk, sx3EUp, sx3EDn);
+      hitPos = sx3_contr.GetHitPos();
+      HitNonZero = true;
+      // hitPos.Print();
+    }
+
+  }
+  
+
+  // //======================= QQQ
+  for( int i = 0; i < qqq.multi; i ++){
+
+      // for( int j = 0; j < pc.multi; j++){
+        if(qqq.e[i]>50 ){
+          hqqqIndexVE->Fill( qqq.index[i], qqq.e[i] );
+          for( int j = 0; j < qqq.multi; j++){
+            if ( j == i ) continue;
+            hqqqCoin->Fill( qqq.index[i], qqq.index[j]);
+          }
+
+
+          for( int j = i + 1; j < qqq.multi; j++){
+            for( int k = 0; k < pc.multi; k++){
+              // if(qqq.e[i>50]){
+                hqqqVpcE->Fill( qqq.e[i], pc.e[k] );
+                hqqqVpcIndex->Fill( qqq.index[i], pc.index[j] );
+              }
+            // }
+          }
+        }  
+      // }
+  }
+
+    // hanVScatsum->Fill(aE,cE);
+    
+
+    if( HitNonZero){
+      pw_contr.CalTrack( hitPos, aID, cID);
+      hZProj->Fill(pw_contr.GetZ0());
+    }
+
+  
+  
+  
+
+
+  //########################################################### Track constrcution
+
+
+  //############################## DO THE KINEMATICS
+
+
+  return kTRUE;
+}
+
+void PCGainMatch::Terminate(){
+
+  gStyle->SetOptStat("neiou");
+  TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
+  canvas->Divide(3,3);
+
+  //hsx3VpcIndex->Draw("colz");
+
+  //=============================================== pad-1
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3IndexVE->Draw("colz");
+
+  //=============================================== pad-2
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hqqqIndexVE->Draw("colz");
+
+  //=============================================== pad-3
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcIndexVE->Draw("colz");
+
+  //=============================================== pad-4
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hsx3Coin->Draw("colz");
+
+  //=============================================== pad-5
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  canvas->cd(padID)->SetLogz(true);
+
+  hqqqCoin->Draw("colz");
+
+  //=============================================== pad-6
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  hpcCoin->Draw("colz");
+
+  //=============================================== pad-7
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hsx3VpcIndex ->Draw("colz"); 
+  hsx3VpcE->Draw("colz") ;
+
+  //=============================================== pad-8
+  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+
+  // hqqqVpcIndex ->Draw("colz");  
+
+  hqqqVpcE ->Draw("colz");
+  //=============================================== pad-9
+  padID ++; 
+
+  // canvas->cd(padID)->DrawFrame(-50, -50, 50, 50);
+  // hqqqPolar->Draw("same colz pol");
+
+ canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  hanVScatsum->Draw("colz");
+  // hAnodeHits->Draw("colz");
+  // hAnodeMultiplicity->Draw();
+}

PCGainMatch.h

@@ -0,0 +1,114 @@
+#ifndef PCGainMatch_h
+#define PCGainMatch_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class PCGainMatch : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   PCGainMatch(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~PCGainMatch() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(PCGainMatch,0);
+};
+
+#endif
+
+#ifdef PCGainMatch_cxx
+void PCGainMatch::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t PCGainMatch::Notify(){
+
+   return kTRUE;
+}
+
+void PCGainMatch::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void PCGainMatch::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef Analyzer_cxx

ProcessRun.sh

@@ -1,27 +1,34 @@
 #!/bin/bash
 
-if [ "$#" -ne 2 ]; then
+if [ "$#" -ne 3 ]; then
-    echo "Usage: $0 runID timeWindow_ns"
+    echo "Usage: $0 runID timeWindow_ns option"
+    echo "option: 0 - process raw data, 1 - process mapped data"
     echo "Exiting..."
     exit 1
 fi
 
-runID=$1
+runID=$(printf "%03d" $1)
 timeWindow=$2
 
-rawFolder=/home/tandem/Desktop/analysis/data
+option=$3
-rootFolder=/home/tandem/Desktop/analysis/data/root_data
 
-rsync -a splitpole@128.186.111.223:/media/nvmeData/ANASEN27Alap/*.fsu /home/tandem/Desktop/analysis/data
+# rawFolder=/home/tandem/data1/2024_09_17Fap/data
+rawFolder=/mnt/d/17F
+rootFolder=/mnt/d/Remapped_files/17F_data/root_data
 
-fileList=`\ls -1 ${rawFolder}/Run_${runID}_*.fsu`
+if [ $option -eq 0 ]; then
 
-./EventBuilder ${timeWindow} 0 0 10000000 ${fileList}
+    # rsync -auh --info=progress2 splitpole@128.186.111.223:/media/nvmeData/2024_09_17Fap/*.fsu /home/tandem/data1/2024_09_17Fap/data
+
+    fileList=`\ls -1 ${rawFolder}/*SourceRun_${runID}_*.fsu`
+
+    ./EventBuilder ${timeWindow} 0 0 100000000 ${fileList}
 
     outFile=${rawFolder}/*${runID}*${timeWindow}.root
 
     mv -vf ${outFile} ${rootFolder}/.
 
     ./Mapper ${rootFolder}/*${runID}*${timeWindow}.root
+fi
 
-root "processRun.C(\"${rootFolder}/Run_${runID}_mapped.root\")"
+# root "processRun.C(\"${rootFolder}/Run_${runID}_mapped.root\")"

QQQ_Calcheck.C

@@ -0,0 +1,167 @@
+
+#define QQQ_Calcheck_cxx
+
+#include <TH2.h>
+#include <TF1.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TMath.h>
+#include <TCutG.h>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include "Armory/HistPlotter.h"
+#include "TVector3.h"
+#include "QQQ_Calcheck.h"
+
+TH2F *hQQQFVB;
+HistPlotter *plotter;
+int padID = 0;
+
+TCutG *cut;
+std::map<std::tuple<int, int, int>, std::vector<std::pair<double, double>>> dataPoints;
+
+bool qqqEcut = false;
+
+// Gain Arrays
+const int MAX_QQQ = 4;
+const int MAX_RING = 16;
+const int MAX_WEDGE = 16;
+double qqqwGain[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+double qqqrGain[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+bool qqqwGainValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+bool qqqrGainValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+double qqqCalib[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+bool qqqCalibValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+
+void QQQ_Calcheck::Begin(TTree * /*tree*/)
+{
+    plotter = new HistPlotter("Cal_checkQQQ.root", "TFILE");
+    // ----------------------- Load QQQ Gains
+    {
+        std::string filename = "qqq_GainMatch.dat";
+        std::ifstream infile(filename);
+        if (!infile.is_open())
+        {
+            std::cerr << "Error opening " << filename << "!" << std::endl;
+        }
+        else
+        {
+            int det, ring, wedge;
+            double gainw,gainr;
+            while (infile >> det >> ring >> wedge >> gainw>> gainr)
+            {
+                qqqwGain[det][ring][wedge] = gainw;
+                // qqqrGain[det][ring][wedge] = gainr;
+                qqqwGainValid[det][ring][wedge] = (gainw > 0);
+                // qqqrGainValid[det][ring][wedge] = (gainr > 0);
+            }
+            infile.close();
+            std::cout << "Loaded QQQ gains from " << filename << std::endl;
+        }
+    }
+    // ----------------------- Load QQQ Calibrations
+    {
+        std::string filename = "qqq_Calib.dat";
+        std::ifstream infile(filename);
+        if (!infile.is_open())
+        {
+            std::cerr << "Error opening " << filename << "!" << std::endl;
+        }
+        else
+        {
+            int det, ring, wedge;
+            double slope;
+            while (infile >> det >> ring >> wedge >> slope)
+            {
+                qqqCalib[det][ring][wedge] = slope;
+                qqqCalibValid[det][ring][wedge] = (slope > 0);
+            }
+            infile.close();
+            std::cout << "Loaded QQQ calibrations from " << filename << std::endl;
+        }
+    }
+}
+
+Bool_t QQQ_Calcheck::Process(Long64_t entry)
+{
+    b_qqqMulti->GetEntry(entry);
+    b_qqqID->GetEntry(entry);
+    b_qqqCh->GetEntry(entry);
+    b_qqqE->GetEntry(entry);
+    b_qqqT->GetEntry(entry);
+
+    qqq.CalIndex();
+
+    for (int i = 0; i < qqq.multi; i++)
+    {
+        for (int j = i + 1; j < qqq.multi; j++)
+        {
+            if (qqq.e[i] > 100)
+                qqqEcut = true;
+            if (qqq.id[i] == qqq.id[j])
+            {
+                int chWedge = -1;
+                int chRing = -1;
+                float eWedgeRaw = 0.0;
+                float eWedge = 0.0;
+                float eWedgeMeV = 0.0;
+                float eRingRaw = 0.0;
+                float eRing = 0.0;
+                float eRingMeV = 0.0;
+                // plug in gains
+                if (qqq.ch[i] < 16 && qqq.ch[j] >= 16 && /*qqqrGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16] &&*/ qqqwGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16])
+                {
+                    chWedge = qqq.ch[i];
+                    eWedgeRaw = qqq.e[i];
+                    eWedge = qqq.e[i] * qqqwGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
+                    // printf("Wedge E: %.2f  Gain: %.4f \n", eWedge, qqqGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16]);
+                    chRing = qqq.ch[j] - 16;
+                    eRingRaw = qqq.e[j];
+                    eRing = qqq.e[j];//* qqqrGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i]-16];
+                }
+                else if (qqq.ch[j] < 16 && qqq.ch[i] >= 16/* && qqqrGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16] */&& qqqwGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16])
+                {
+                    chWedge = qqq.ch[j];
+                    eWedge = qqq.e[j] * qqqwGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16];
+                    eWedgeRaw = qqq.e[j];
+
+                    chRing = qqq.ch[i] - 16;
+                    eRing = qqq.e[i];// * qqqrGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
+                    eRingRaw = qqq.e[i];
+                }
+                else
+                    continue;
+                // plug in calibrations
+                if (qqqCalibValid[qqq.id[i]][chWedge][chRing])
+                {
+                    eWedgeMeV = eWedge * qqqCalib[qqq.id[i]][chWedge][chRing] / 1000;
+                    eRingMeV = eRing * qqqCalib[qqq.id[i]][chWedge][chRing] / 1000;
+                }
+                else
+                    continue;
+
+                // hQQQFVB->Fill(eWedge, eRing);
+                plotter->Fill2D(Form("hRaw_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 8000, 400, 0, 8000, eWedgeRaw, eRingRaw, "ERaw");
+                plotter->Fill2D(Form("hGM_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 16000, 400, 0, 16000, eWedge, eRing, "EGM");
+                plotter->Fill2D(Form("hCal_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 10, 400, 0, 10, eWedgeMeV, eRingMeV, "ECal");
+                if(eWedgeRaw >1500 && eRingRaw>1500 )
+                plotter->Fill2D(Form("hCal_cut_qqq%d_ring%d_wedge%d", qqq.id[i], chRing, chWedge), 400, 0, 10, 400, 0, 10, eWedgeMeV, eRingMeV, "ECal_cut");
+                
+                plotter->Fill2D(Form("hRCal_qqq%d", qqq.id[i]), 16, 0, 15, 1000, 0, 30, chRing, eRingMeV, "RingCal");
+                plotter->Fill2D(Form("hWCal_qqq%d", qqq.id[i]), 16, 0, 15, 1000, 0, 30, chWedge, eWedgeMeV, "WedgeCal");
+                plotter->Fill2D("hRawQQQ", 4000, 0, 8000, 4000, 0, 8000, eWedgeRaw, eRingRaw);
+                plotter->Fill2D("hGMQQQ", 4000, 0, 8000, 4000, 0, 8000, eWedge, eRing);
+                plotter->Fill2D("hCalQQQ", 4000, 0, 10, 4000, 0, 10, eWedgeMeV, eRingMeV);
+            }
+        }
+    }
+
+    return kTRUE;
+}
+
+void QQQ_Calcheck::Terminate()
+{
+    plotter->FlushToDisk();
+    std::cout << "Calibration check file for 2D QQQ histogram saved.\n";
+}

QQQ_Calcheck.h

@@ -0,0 +1,114 @@
+#ifndef QQQ_Calcheck_h
+#define QQQ_Calcheck_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class QQQ_Calcheck : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+
+   QQQ_Calcheck(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~QQQ_Calcheck() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(QQQ_Calcheck,0);
+};
+
+#endif
+
+#ifdef QQQ_Calcheck_cxx
+void QQQ_Calcheck::Init(TTree *tree){
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+
+}
+
+Bool_t QQQ_Calcheck::Notify(){
+
+   return kTRUE;
+}
+
+void QQQ_Calcheck::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void QQQ_Calcheck::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef QQQ_Calcheck_cxx

RunTimeSummary.C

@@ -0,0 +1,140 @@
+#include <TFile.h>
+#include <TH1.h>
+#include <TH2.h>
+#include <TString.h>
+#include <TSystem.h>
+#include <TCanvas.h>
+#include <iostream>
+
+void RunTimeSummary(int startRun, int endRun)
+{
+    TString fileDir = "/mnt/d/Remapped_files/17F_data/root_data/";
+    TString histName = "AnodeQQQ_Time";
+    TString filePattern = "Run_%03d_mapped_histograms.root";
+    TString filePatternAlt = "ProtonRun_%d_mapped_histograms.root";
+    TString filePatternAlt2 = "Source_%d_mapped_histograms.root";
+
+    int nBinsTime = 0;
+    double timeMin = 0, timeMax = 0;
+    bool foundRef = false;
+
+    for (int r = startRun; r <= endRun; r++)
+    {
+        TString tempName;
+
+        // 1. Try Pattern 1: Run_XXX...
+        tempName = fileDir + Form(filePattern, r);
+        if (gSystem->AccessPathName(tempName))
+        { // Returns true if MISSING
+
+            // 2. Try Pattern 2: ProtonRun_X...
+            tempName = fileDir + Form(filePatternAlt, r);
+            if (gSystem->AccessPathName(tempName))
+            {
+
+                // 3. Try Pattern 3: Source_X...
+                tempName = fileDir + Form(filePatternAlt2, r);
+                if (gSystem->AccessPathName(tempName))
+                {
+                    // All 3 patterns failed. Skip this run.
+                    continue;
+                }
+            }
+        }
+
+        // If we get here, 'tempName' holds the valid filename that was found
+        TFile *fTemp = TFile::Open(tempName);
+        if (!fTemp || fTemp->IsZombie())
+        {
+            if (fTemp)
+                delete fTemp;
+            continue;
+        }
+
+        TH1F *hRef = (TH1F *)fTemp->Get(histName);
+        if (hRef)
+        {
+
+            nBinsTime = hRef->GetNbinsX();
+            timeMin = hRef->GetXaxis()->GetXmin();
+            timeMax = hRef->GetXaxis()->GetXmax();
+            foundRef = true;
+
+            delete hRef;
+            fTemp->Close();
+            delete fTemp;
+            printf("Reference found in Run %d: %d bins, Range [%.1f, %.1f]\n", r, nBinsTime, timeMin, timeMax);
+            break;
+        }
+        fTemp->Close();
+        delete fTemp;
+    }
+
+    if (!foundRef)
+    {
+        printf("Error: No valid histograms found in the entire range. Exiting.\n");
+        return;
+    }
+
+    int nRuns = endRun - startRun + 1;
+    TH2F *hSummary = new TH2F("hSummary",
+                              Form("Timing Summary (Runs %d-%d);Timing;Run Number", startRun, endRun),
+                              nBinsTime, timeMin, timeMax,
+                              nRuns, startRun, endRun + 1);
+
+    for (int run = startRun; run <= endRun; run++)
+    {
+
+        TString filename = fileDir + Form(filePattern, run);
+
+        if (gSystem->AccessPathName(filename))
+            continue;
+
+        TFile *fin = TFile::Open(filename);
+        if (!fin || fin->IsZombie())
+        {
+            if (fin)
+                delete fin;
+            continue;
+        }
+
+        TH1F *hin = (TH1F *)fin->Get(histName);
+
+        if (hin)
+        {
+            // Determine which ROW (Y-bin) corresponds to this Run
+            // Note: ROOT bins start at 1.
+            // If startRun=10 and run=10 -> binY=1.
+            int binY_Run = run - startRun + 1;
+
+            // Loop through the Time bins (X-bins in the 1D hist)
+            for (int binX_Time = 1; binX_Time <= hin->GetNbinsX(); binX_Time++)
+            {
+
+                double content = hin->GetBinContent(binX_Time);
+
+                // Copy content to: (Time, Run)
+                if (content > 0)
+                {
+                    hSummary->SetBinContent(binX_Time, binY_Run, content);
+                }
+            }
+            delete hin;
+        }
+
+        fin->Close();
+        delete fin;
+
+        if ((run - startRun) % 10 == 0)
+            printf("Stitched Run %d...\n", run);
+    }
+
+    TFile *fOut = new TFile("SummaryPlot.root", "RECREATE");
+    hSummary->Write();
+
+    TCanvas *c1 = new TCanvas("c1", "Time Summary Plot", 1000, 800);
+    hSummary->SetStats(0);
+    hSummary->Draw("COLZ");
+
+    printf("Done! Saved to SummaryPlot.root\n");
+}

TrackRecon.C

@@ -1,65 +1,188 @@
-#define Analyzer_cxx
+#define TrackRecon_cxx
+
+#include "TrackRecon.h"
+#include "Armory/ClassPW.h"
+#include "Armory/HistPlotter.h"
 
-#include "Analyzer.h"
 #include <TH2.h>
 #include <TStyle.h>
 #include <TCanvas.h>
 #include <TMath.h>
+#include "TVector3.h"
 
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <map>
 #include <utility>
 #include <algorithm>
 
-#include "Armory/ClassSX3.h"
+// Global instances
-#include "Armory/ClassPC1An.h"
+PW pw_contr;
-
+PW pwinstance;
-#include "TVector3.h"
-
-TH2F * hsx3IndexVE;
-TH2F * hqqqIndexVE;
-TH2F * hpcIndexVE;
-
-TH2F * hsx3Coin;
-TH2F * hqqqCoin;
-TH2F * hpcCoin;
-
-TH2F * hqqqPolar;
-TH2F * hsx3VpcIndex;
-TH2F * hqqqVpcIndex;
-TH2F * hqqqVpcE;
-TH2F * hsx3VpcE;
-TH2F * hanVScatsum;
-int padID = 0;
-
-SX3 sx3_contr;
-PC pw_contr;
 TVector3 hitPos;
+double qqqenergy,qqqtime;
+
+// Calibration globals
+const int MAX_QQQ = 4;
+const int MAX_RING = 16;
+const int MAX_WEDGE = 16;
+double qqqGain[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+bool qqqGainValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+double qqqCalib[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{0}}};
+bool qqqCalibValid[MAX_QQQ][MAX_RING][MAX_WEDGE] = {{{false}}};
+// TCutg *cutQQQ;
+
+// PC Arrays
+double pcSlope[48];
+double pcIntercept[48];
+
+HistPlotter *plotter;
+
 bool HitNonZero;
+bool sx3ecut;
+bool qqqEcut;
 
-TH1F * hZProj;
+void TrackRecon::Begin(TTree *tree)
+{ // get file name
+  std::cout << tree->GetCurrentFile()->GetName() << std::endl;
+  // get substring from file name to identify run number
 
-void Analyzer::Begin(TTree * /*tree*/){
   TString option = GetOption();
+  std::string treefilename(tree->GetCurrentFile()->GetName());
 
-  hZProj = new TH1F("hZProj", "Z Projection", 200, -600, 600);
+  plotter = new HistPlotter(treefilename.substr(0, treefilename.length() - std::string(".root").length()) + "_histograms.root", "TFILE");
+  // plotter = new HistPlotter("Analyzer.root", "TFILE");
 
-  sx3_contr.ConstructGeo();
   pw_contr.ConstructGeo();
+  pwinstance.ConstructGeo();
 
+  // ---------------------------------------------------------
+  // 1. CRITICAL FIX: Initialize PC Arrays to Default (Raw)
+  // ---------------------------------------------------------
+  for (int i = 0; i < 48; i++)
+  {
+    pcSlope[i] = 1.0;     // Default slope = 1 (preserves Raw energy)
+    pcIntercept[i] = 0.0; // Default intercept = 0
   }
 
+  // Calculate Crossover Geometry ONCE
+  TVector3 a, c, diff;
+  double a2, ac, c2, adiff, cdiff, denom, alpha;
 
+  for (size_t i = 0; i < pwinstance.An.size(); i++)
+  {
+    a = pwinstance.An[i].first - pwinstance.An[i].second;
 
+    for (size_t j = 0; j < pwinstance.Ca.size(); j++)
+    {
+      c = pwinstance.Ca[j].first - pwinstance.Ca[j].second;
+      diff = pwinstance.An[i].first - pwinstance.Ca[j].first;
+      a2 = a.Dot(a);
+      c2 = c.Dot(c);
+      ac = a.Dot(c);
+      adiff = a.Dot(diff);
+      cdiff = c.Dot(diff);
+      denom = a2 * c2 - ac * ac;
+      alpha = (ac * cdiff - c2 * adiff) / denom;
 
-Bool_t Analyzer::Process(Long64_t entry){
+      Crossover[i][j][0].x = pwinstance.An[i].first.X() + alpha * a.X();
+      Crossover[i][j][0].y = pwinstance.An[i].first.Y() + alpha * a.Y();
+      Crossover[i][j][0].z = pwinstance.An[i].first.Z() + alpha * a.Z();
 
-  // if ( entry > 100 ) return kTRUE;
+      if (Crossover[i][j][0].z < -190 || Crossover[i][j][0].z > 190 || (i + j) % 24 == 12)
+      {
+        Crossover[i][j][0].z = 9999999;
+      }
 
+      Crossover[i][j][1].x = alpha;
+      Crossover[i][j][1].y = 0;
+    }
+  }
+
+  // Load PC Calibrations
+  std::ifstream inputFile("slope_intercept_results.dat");
+  if (inputFile.is_open())
+  {
+    std::string line;
+    int index;
+    double slope, intercept;
+    while (std::getline(inputFile, line))
+    {
+      std::stringstream ss(line);
+      ss >> index >> slope >> intercept;
+      if (index >= 0 && index <= 47)
+      {
+        pcSlope[index] = slope;
+        pcIntercept[index] = intercept;
+      }
+    }
+    inputFile.close();
+  }
+  else
+  {
+    std::cerr << "Error opening slope_intercept.txt" << std::endl;
+  }
+
+  // Load QQQ Cuts from file
+  //   {
+  //     std::string filename = "QQQ_PCCut.root";
+  //     TFile *cutFile = TFile::Open(filename.c_str(), "READ");
+  //     if (cutFile && !cutFile->IsZombie())
+  //     {
+  //       cutQQQ = (TCutg *)cutFile->Get("cutQQQPC");
+  //       if (cutQQQ)
+  //       {
+  //         std::cout << "Loaded QQQ PC cut from " << filename << std::endl;
+  //       }
+  //       else
+  //       {
+  //         std::cerr << "Error: cutQQQPC not found in " << filename << std::endl;
+  //       }
+  //       cutFile->Close();
+  //   }
+  // }
+
+  // ... (Load QQQ Gains and Calibs - same as before) ...
+  {
+    std::string filename = "qqq_GainMatch.dat";
+    std::ifstream infile(filename);
+    if (infile.is_open())
+    {
+      int det, ring, wedge;
+      double gainw, gainr;
+      while (infile >> det >> wedge >> ring >> gainw >> gainr)
+      {
+        qqqGain[det][wedge][ring] = gainw;
+        qqqGainValid[det][wedge][ring] = (gainw > 0);
+        // std::cout << "QQQ Gain Loaded: Det " << det << " Ring " << ring << " Wedge " << wedge << " GainW " << gainw << " GainR " << gainr << std::endl;
+      }
+      infile.close();
+    }
+  }
+  {
+    std::string filename = "qqq_Calib.dat";
+    std::ifstream infile(filename);
+    if (infile.is_open())
+    {
+      int det, ring, wedge;
+      double slope;
+      while (infile >> det >> wedge >> ring >> slope)
+      {
+        qqqCalib[det][wedge][ring] = slope;
+        qqqCalibValid[det][wedge][ring] = (slope > 0);
+        // std::cout << "QQQ Calib Loaded: Det " << det << " Ring " << ring << " Wedge " << wedge << " Slope " << slope << std::endl;
+      }
+      infile.close();
+    }
+  }
+}
+
+Bool_t TrackRecon::Process(Long64_t entry)
+{
   hitPos.Clear();
   HitNonZero = false;
-
+  bool qqq1000cut = false;
-  // if( entry > 1) return kTRUE;
-  // printf("################### ev : %llu \n", entry);
-
   b_sx3Multi->GetEntry(entry);
   b_sx3ID->GetEntry(entry);
   b_sx3Ch->GetEntry(entry);
@@ -80,224 +203,558 @@ Bool_t Analyzer::Process(Long64_t entry){
   qqq.CalIndex();
   pc.CalIndex();
 
-  // sx3.Print();
+  // QQQ Processing
 
-  //########################################################### Raw data
+  int qqqCount = 0;
-  // //======================= SX3
+  int qqqAdjCh = 0;
+  qqqenergy=-1;
+  qqqtime=-1;
 
-  std::vector<std::pair<int, int>> ID; // first = id, 2nd = index
+  // REMOVE WHEN RERUNNING USING THE NEW CALIBRATION FILE
+  // for (int i = 0; i < qqq.multi; i++)
+  // {
+  //   if ((qqq.id[i] == 3 || qqq.id[i] == 1) && qqq.ch[i] < 16)
+  //   {
+  //     qqq.ch[i] = 16 - qqq.ch[i];
+  //   }
+  // }
+  // for (int i = 0; i < qqq.multi; i++)
+  // {
+  //   if (qqq.id[i] == 0 && qqq.ch[i] >= 16)
+  //   {
+  //     qqq.ch[i] = 31 - qqq.ch[i] + 16;
+  //   }
+  // }
 
-  if( ID.size() > 0 ){
+  bool PCQQQTimeCut = false;
-    std::sort(ID.begin(), ID.end(),  [](const std::pair<int, int> & a, const std::pair<int, int> & b) {
+  for (int i = 0; i < qqq.multi; i++)
-      return a.first < b.first;
+  {
-    } );
-    // printf("##############################\n");
-    // for( size_t i = 0; i < ID.size(); i++) printf("%zu | %d %d \n", i, ID[i].first, ID[i].second );
 
-    std::vector<std::pair<int, int>> sx3ID; 
+    plotter->Fill2D("QQQ_Index_Vs_Energy", 16 * 8, 0, 16 * 8, 2000, 0, 16000, qqq.index[i], qqq.e[i], "hRawQQQ");
-    sx3ID.push_back(ID[0]);
+
-    bool found = false;
+    for (int j = 0; j < qqq.multi; j++)
-    for( size_t i = 1; i < ID.size(); i++){
+    {
-      if( ID[i].first == sx3ID.back().first) {
+      if (j == i)
-        sx3ID.push_back(ID[i]);
+        continue;
-        if( sx3ID.size() >= 3) {
+      plotter->Fill2D("QQQ_Coincidence_Matrix", 16 * 8, 0, 16 * 8, 16 * 8, 0, 16 * 8, qqq.index[i], qqq.index[j], "hRawQQQ");
-          found = true;
-        } 
-      }else{
-        if( !found ){
-          sx3ID.clear();
-          sx3ID.push_back(ID[i]);
-        }
-      }
     }
 
-    // printf("---------- sx3ID Multi : %zu \n", sx3ID.size());
+    for (int k = 0; k < pc.multi; k++)
-
+    {
-    if( found ){
+      if (pc.index[k] < 24 && pc.e[k] > 50)
-      int sx3ChUp, sx3ChDn, sx3ChBk;
+      {
-      float sx3EUp, sx3EDn;
+        plotter->Fill2D("QQQ_Vs_Anode_Energy", 400, 0, 4000, 1000, 0, 16000, qqq.e[i], pc.e[k], "hRawQQQ");
-      // printf("------ sx3 ID : %d, multi: %zu\n", sx3ID[0].first, sx3ID.size());
+        plotter->Fill2D("QQQ_Vs_PC_Index", 16 * 8, 0, 16 * 8, 24, 0, 24, qqq.index[i], pc.index[k], "hRawQQQ");
-      for( size_t i = 0; i < sx3ID.size(); i++ ){
-        int index = sx3ID[i].second;
-        // printf(" %zu | index %d | ch : %d, energy : %d \n", i, index, sx3.ch[index], sx3.e[index]);
-
-
-        if( sx3.ch[index] < 8 ){
-          if( sx3.ch[index] % 2 == 0) {
-            sx3ChDn = sx3.ch[index];
-            sx3EDn = sx3.e[index];
-          }else{
-            sx3ChUp = sx3.ch[index];
-            sx3EUp = sx3.e[index];
-          }
-        }else{
-          sx3ChBk = sx3.ch[index];
-        }
-         for( int j = 0; j < pc.multi; j++){
-      // hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
-            if( sx3.ch[index] > 8 ){
-              hsx3VpcE->Fill( sx3.e[i], pc.e[j] );
-          //  hpcIndexVE->Fill( pc.index[i], pc.e[i] );
       }
+      else if (pc.index[k] >= 24 && pc.e[k] > 50)
+      {
+        plotter->Fill2D("QQQ_Vs_Cathode_Energy", 400, 0, 4000, 1000, 0, 16000, qqq.e[i], pc.e[k], "hRawQQQ");
       }
     }
 
-      sx3_contr.CalSX3Pos(sx3ID[0].first, sx3ChUp, sx3ChDn, sx3ChBk, sx3EUp, sx3EDn);
+    for (int j = i + 1; j < qqq.multi; j++)
-      hitPos = sx3_contr.GetHitPos();
+    {
-      HitNonZero = true;
+      if (qqq.id[i] == qqq.id[j])
-      // hitPos.Print();
+      {
-    }
+        qqqCount++;
 
-  }
-  
-
-  // //======================= QQQ
-  for( int i = 0; i < qqq.multi; i ++){
-    for( int j = i + 1; j < qqq.multi; j++){
-      if( qqq.id[i] == qqq.id[j]  ){ // must be same detector 
         int chWedge = -1;
         int chRing = -1;
-        if( qqq.ch[i] < qqq.ch[j]){
+        double eWedge = 0.0;
-          chRing = qqq.ch[j] - 16;
+        double eWedgeMeV = 0.0;
+        double eRing = 0.0;
+        double eRingMeV = 0.0;
+        double tRing = 0.0;
+        double tWedge = 0.0;
+
+        if (qqq.ch[i] < 16 && qqq.ch[j] >= 16 && qqqGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16])
+        {
           chWedge = qqq.ch[i];
-        }else{
+          eWedge = qqq.e[i] * qqqGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
-          chRing = qqq.ch[i];
+          chRing = qqq.ch[j] - 16;
-          chWedge = qqq.ch[j] - 16;
+          eRing = qqq.e[j];
+          tRing = static_cast<double>(qqq.t[j]);
+          tWedge = static_cast<double>(qqq.t[i]);
+        }
+        else if (qqq.ch[j] < 16 && qqq.ch[i] >= 16 && qqqGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16])
+        {
+          chWedge = qqq.ch[j];
+          eWedge = qqq.e[j] * qqqGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16];
+          chRing = qqq.ch[i] - 16;
+          eRing = qqq.e[i];
+          tRing = static_cast<double>(qqq.t[i]);
+          tWedge = static_cast<double>(qqq.t[j]);
+        }
+        else
+          continue;
+
+        plotter->Fill1D("Wedgetime_Vs_Ringtime", 100, -1000, 1000, tWedge - tRing, "hTiming");
+        plotter->Fill2D("RingE_vs_Index", 16 * 4, 0, 16 * 4, 1000, 0, 16000, chRing + qqq.id[i] * 16, eRing, "hRawQQQ");
+        plotter->Fill2D("WedgeE_vs_Index", 16 * 4, 0, 16 * 4, 1000, 0, 16000, chWedge + qqq.id[i] * 16, eWedge, "hRawQQQ");
+
+        if (qqqCalibValid[qqq.id[i]][chWedge][chRing])
+        {
+          eWedgeMeV = eWedge * qqqCalib[qqq.id[i]][chWedge][chRing] / 1000;
+          eRingMeV = eRing * qqqCalib[qqq.id[i]][chWedge][chRing] / 1000;
+        }
+        else
+          continue;
+
+        plotter->Fill2D("WedgeE_Vs_RingECal", 1000, 0, 10, 1000, 0, 10, eWedgeMeV, eRingMeV, "hCalQQQ");
+         if(qqq.multi>2 )       plotter->Fill2D("WedgeE_Vs_RingECal_mulit>2", 1000, 0, 10, 1000, 0, 10, eWedgeMeV, eRingMeV, "hCalQQQ");
+         if(qqq.multi==2 )       plotter->Fill2D("WedgeE_Vs_RingECal_mulit=2", 1000, 0, 10, 1000, 0, 10, eWedgeMeV, eRingMeV, "hCalQQQ");
+
+        for (int k = 0; k < pc.multi; k++)
+        {
+          plotter->Fill2D("RingCh_vs_Anode_Index", 16 * 4, 0, 16 * 4, 24, 0, 24, chRing + qqq.id[i] * 16, pc.index[k], "hRawQQQ");
+          plotter->Fill2D("WedgeCh_vs_Anode_Index", 16 * 4, 0, 16 * 4, 24, 0, 24, chWedge + qqq.id[i] * 16, pc.index[k], "hRawQQQ");
+          plotter->Fill2D("WedgeCh_vs_Anode_Index" + std::to_string(qqq.id[i]), 16 * 4, 0, 16 * 4, 24, 0, 24, chWedge + qqq.id[i] * 16, pc.index[k]);
+          plotter->Fill2D("RingCh_vs_Cathode_Index", 16 * 4, 0, 16 * 4, 24, 24, 48, chRing + qqq.id[i] * 16, pc.index[k], "hRawQQQ");
+          plotter->Fill2D("WedgeCh_vs_Cathode_Index", 16 * 4, 0, 16 * 4, 24, 24, 48, chWedge + qqq.id[i] * 16, pc.index[k], "hRawQQQ");
+
+          if (pc.index[k] < 24 && pc.e[k] > 50)
+          {
+            // plotter->Fill2D("QQQ_CalibW_Vs_PC_Energy", 1000, 0, 16, 2000, 0, 30000, eWedgeMeV, pc.e[k], "hCalQQQ");
+            // plotter->Fill2D("QQQ_CalibR_Vs_PC_Energy", 1000, 0, 16, 2000, 0, 30000, eRingMeV, pc.e[k], "hCalQQQ");
+
+            // if (tRing - static_cast<double>(pc.t[k]) < 0 && tRing - static_cast<double>(pc.t[k]) > -600)
+            // // {
+            // //   plotter->Fill2D("QQQ_CalibW_Vs_PC_Energy_Tight", 1000, 0, 16, 2000, 0, 30000, eWedgeMeV, pc.e[k], "hCalQQQ");
+            // //   plotter->Fill2D("QQQ_CalibR_Vs_PC_Energy_Tight", 1000, 0, 16, 2000, 0, 30000, eRingMeV, pc.e[k], "hCalQQQ");
+            // // }
+            // // else
+            // // {
+            // //   plotter->Fill2D("QQQ_CalibW_Vs_PC_Energy_OffTime", 1000, 0, 16, 2000, 0, 30000, eWedgeMeV, pc.e[k], "hCalQQQ");
+            // //   plotter->Fill2D("QQQ_CalibR_Vs_PC_Energy_OffTime", 1000, 0, 16, 2000, 0, 30000, eRingMeV, pc.e[k], "hCalQQQ");
+            // // }
+            plotter->Fill2D("Timing_Difference_QQQR_Anode_vRing", 1250, -2500, 2500, 16, 0, 16, tRing - static_cast<double>(pc.t[k]), chRing, "hTiming");
+            plotter->Fill2D("DelT_Vs_QQQRingECal", 500, -2500, 2500, 1000, 0, 10, tRing - static_cast<double>(pc.t[k]), eRingMeV, "hTiming");
+            plotter->Fill2D("CalibratedQQQEvsAnodeE_R", 1000, 0, 10, 2000, 0, 30000, eRingMeV, pc.e[k], "hPCQQQ");
+            plotter->Fill2D("CalibratedQQQEvsAnodeE_W", 1000, 0, 10, 2000, 0, 30000, eWedgeMeV, pc.e[k], "hPCQQQ");
+            if (tRing - static_cast<double>(pc.t[k]) < -150) // 27Al
+            // if (tRing - static_cast<double>(pc.t[k]) < -75 && tRing - static_cast<double>(pc.t[k]) > -145) // 17F
+            {
+              PCQQQTimeCut = true;
+            }
           }
 
-        // printf(" ID : %d , chWedge : %d, chRing : %d \n", qqq.id[i], chWedge, chRing);
+          if (pc.index[k] >= 24 && pc.e[k] > 50)
+          {
+            plotter->Fill2D("Timing_Difference_QQQR_Cathode_vRing", 1250, -2500, 2500, 16, 0, 16, tRing - static_cast<double>(pc.t[k]), chRing, "hTiming");
+          }
+        }
 
         double theta = -TMath::Pi() / 2 + 2 * TMath::Pi() / 16 / 4. * (qqq.id[i] * 16 + chWedge + 0.5);
-        double rho   = 10.+40./16.*(chRing+0.5);
+        double rho = 50. + 50. / 16. * (chRing + 0.5);
-        // if(qqq.e[i]>50){
-        hqqqPolar->Fill( theta, rho);
-        // }
-        // qqq.used[i] = true;
-        // qqq.used[j] = true;
 
-        if( !HitNonZero ){
+        plotter->Fill2D("QQQPolarPlot", 16 * 4, -TMath::Pi(), TMath::Pi(), 32, 40, 100, theta, rho, "hCalQQQ");
+        plotter->Fill2D("QQQCartesianPlot", 200, -100, 100, 200, -100, 100, rho * TMath::Cos(theta), rho * TMath::Sin(theta), "hCalQQQ");
+        plotter->Fill2D("QQQCartesianPlot" + std::to_string(qqq.id[i]), 200, -100, 100, 200, -100, 100, rho * TMath::Cos(theta), rho * TMath::Sin(theta), "hCalQQQ");
+        if (PCQQQTimeCut)
+        {
+          plotter->Fill2D("PC_XY_Projection_QQQ_TimeCut" + std::to_string(qqq.id[i]), 400, -100, 100, 400, -100, 100, rho * TMath::Cos(theta), rho * TMath::Sin(theta), "hPCQQQ");
+        }
+        plotter->Fill2D("PC_XY_Projection_QQQ" + std::to_string(qqq.id[i]), 400, -100, 100, 400, -100, 100, rho * TMath::Cos(theta), rho * TMath::Sin(theta), "hPCQQQ");
+
+        if (!HitNonZero)
+        {
           double x = rho * TMath::Cos(theta);
           double y = rho * TMath::Sin(theta);
           hitPos.SetXYZ(x, y, 23 + 75 + 30);
+          qqqenergy = eRingMeV;
+          qqqtime = tRing;
           HitNonZero = true;
         }
       }
     }
-  
-   
-  }
-  // //======================= PC
- PCHit_1An hitInfo;
-
-  ID.clear();
-  int counter=0;
-  std::vector<std::pair<int, double>> E; 
-  E.clear();
-
-  if( E.size()==3 ){
-    float aE = 0;
-    float cE = 0;
-    bool multi_an =false;
-      for(int l=0;l<E.size();l++){
-        if(E[l].first<24 && E[l].first!=20 && E[l].first!=12){
-          if(!multi_an){
-            aE = E[l].second;
-          }
-          multi_an=true;
-        }
-        else {
-          cE = E[l].second + cE;
-        }
-      }
-    // printf("anode= %d, cathode = %d\n", aID, cID);
-  // }
-    if( ID[0].first < 1 ) {
-      aID = pc.ch[ID[0].second];
-      cID = pc.ch[ID[1].second];
-    }else{
-      cID = pc.ch[ID[0].second];
-      aID = pc.ch[ID[1].second];
   }
 
-    hanVScatsum->Fill(aE,cE);
+  plotter->Fill1D("QQQ_Multiplicity", 10, 0, 10, qqqCount, "hRawQQQ");
 
-    if( HitNonZero){
+  // PC Gain Matching and Filling
-      pw_contr.CalTrack3( hitPos, hitinfo, cID);
+  double anodeT = -99999;
-      hZProj->Fill(pw_contr.GetZ0());
+  double cathodeT = 99999;
+  int anodeIndex = -1;
+  int cathodeIndex = -1;
+  for (int i = 0; i < pc.multi; i++)
+  {
+    if (pc.e[i] > 10)
+    {
+      plotter->Fill2D("PC_Index_Vs_Energy", 48, 0, 48, 2000, 0, 30000, pc.index[i], static_cast<double>(pc.e[i]), "hRawPC");
     }
 
-  // }
+    if (pc.index[i] < 48)
+    {
+      pc.e[i] = pcSlope[pc.index[i]] * pc.e[i] + pcIntercept[pc.index[i]];
+      plotter->Fill2D("PC_Index_VS_GainMatched_Energy", 48, 0, 48, 2000, 0, 30000, pc.index[i], pc.e[i], "hGMPC");
     }
 
+    if (pc.index[i] < 24)
+    {
+      anodeT = static_cast<double>(pc.t[i]);
+      anodeIndex = pc.index[i];
+    }
+    else
+    {
+      cathodeT = static_cast<double>(pc.t[i]);
+      cathodeIndex = pc.index[i] - 24;
+    }
 
+    if (anodeT != -99999 && cathodeT != 99999)
+    {
+      for (int j = 0; j < qqq.multi; j++)
+      {
+        plotter->Fill1D("AC_Time_qqq_coin", 500, -2500, 2500, anodeT - cathodeT, "hTiming");
+        // plotter->Fill2D("AC_Time_Vs_QQQ_ch", 500, -2500, 2500, 16 * 8, 0, 16 * 8, anodeT - cathodeT, qqq.ch[j], "hTiming");
+        plotter->Fill2D("AC_Time_vs_AIndex", 500, -2500, 2500, 24, 0, 24, anodeT - cathodeT, anodeIndex, "hTiming");
+        plotter->Fill2D("AC_Time_vs_CIndex", 500, -2500, 2500, 24, 0, 24, anodeT - cathodeT, cathodeIndex, "hTiming");
+        // plotter->Fill1D("AC_Time_A" + std::to_string(anodeIndex) + "_C" + std::to_string(cathodeIndex), 200, -1000, 1000, anodeT - cathodeT, "TimingPC");
+      }
 
-  //########################################################### Track constrcution
+      for (int j = 0; j < sx3.multi; j++)
+      {
+        plotter->Fill1D("AC_Time_sx3_coinc", 500, -2500, 2500, anodeT - cathodeT, "hTiming");
+      }
 
+      plotter->Fill1D("AC_Time", 500, -2500, 2500, anodeT - cathodeT, "hTiming");
+    }
 
-  //############################## DO THE KINEMATICS
+    for (int j = i + 1; j < pc.multi; j++)
+    {
+      // plotter->Fill2D("PC_Coincidence_Matrix_anodeMinusCathode_lt_-200_" + std::to_string(anodeT - cathodeT < -200), 48, 0, 48, 48, 0, 48, pc.index[i], pc.index[j], "hRawPC");
+      if(pc.e[i]>50 && pc.e[j]>50)
+      plotter->Fill2D("Anode_V_Anode", 24, 0, 24, 24, 0, 24, pc.index[i], pc.index[j], "hRawPC");
+    }
+  }
 
+  anodeHits.clear();
+  cathodeHits.clear();
+  corrcatMax.clear();
+
+  int aID = 0;
+  int cID = 0;
+  double aE = 0;
+  double cE = 0;
+  double aESum = 0;
+  double cESum = 0;
+  double aEMax = 0;
+  int aIDMax = 0;
+
+  for (int i = 0; i < pc.multi; i++)
+  {
+    // if (pc.e[i] > 100)
+    {
+      if (pc.index[i] < 24)
+        anodeHits.push_back(std::pair<int, double>(pc.index[i], pc.e[i]));
+      else if (pc.index[i] >= 24)
+        cathodeHits.push_back(std::pair<int, double>(pc.index[i] - 24, pc.e[i]));
+    }
+  }
+
+  // std::sort(anodeHits.begin(), anodeHits.end(), [](const std::pair<int, double> &a, const std::pair<int, double> &b)
+  //           { return a.second > b.second; });
+  // std::sort(cathodeHits.begin(), cathodeHits.end(), [](const std::pair<int, double> &a, const std::pair<int, double> &b)
+  //           { return a.second > b.second; });
+
+  if (anodeHits.size() >= 1 && cathodeHits.size() >= 1)
+  {
+    // 2. CRITICAL FIX: Define reference vector 'a'
+    // In Analyzer.cxx, 'a' was left over from the loop. We use the first anode wire as reference here.
+    // (Assuming pwinstance.An is populated and wires are generally parallel).
+    TVector3 refAnode = pwinstance.An[0].first - pwinstance.An[0].second;
+
+    {
+      for (const auto &anode : anodeHits)
+      {
+        aID = anode.first;
+        aE = anode.second;
+        aESum += aE;
+        if (aE > aEMax)
+        {
+          aEMax = aE;
+          aIDMax = aID;
+        }
+      }
+
+      for (const auto &cathode : cathodeHits)
+      {
+        cID = cathode.first;
+        cE = cathode.second;
+        plotter->Fill2D("AnodeMax_Vs_Cathode_Coincidence_Matrix", 24, 0, 24, 24, 0, 24, aIDMax, cID, "hRawPC");
+        plotter->Fill2D("Anode_Vs_Cathode_Coincidence_Matrix", 24, 0, 24, 24, 0, 24, aID, cID, "hRawPC");
+        plotter->Fill2D("Anode_vs_CathodeE", 2000, 0, 30000, 2000, 0, 30000, aE, cE, "hGMPC");
+        // plotter->Fill2D("CathodeMult_V_CathodeE", 6, 0, 6, 2000, 0, 30000, cathodeHits.size(), cE, "hGMPC");
+        for (int j = -4; j < 3; j++)
+        {
+          if ((aIDMax + 24 + j) % 24 == 23 - cID)
+          {
+            corrcatMax.push_back(std::pair<int, double>(cID, cE));
+            cESum += cE;
+          }
+        }
+      }
+    }
+  }
+
+  TVector3 anodeIntersection;
+  anodeIntersection.Clear();
+  if (corrcatMax.size() > 0)
+  {
+    double x = 0, y = 0, z = 0;
+    for (const auto &corr : corrcatMax)
+    {
+      if (Crossover[aIDMax][corr.first][0].z > 9000000)
+        continue;
+      if (cESum > 0)
+      {
+        x += (corr.second) / cESum * Crossover[aIDMax][corr.first][0].x;
+        y += (corr.second) / cESum * Crossover[aIDMax][corr.first][0].y;
+        z += (corr.second) / cESum * Crossover[aIDMax][corr.first][0].z;
+      }
+    }
+    if (x == 0 && y == 0 && z == 0)
+      ;
+    // to ignore events with no valid crossover points
+    else
+      anodeIntersection = TVector3(x, y, z);
+    // std::cout << "Anode Intersection: " << anodeIntersection.X() << ", " << anodeIntersection.Y() << ", " << anodeIntersection.Z() << std::endl;
+  }
+  bool PCQQQPhiCut = false;
+  // flip the algorithm for cathode 1 multi anode events
+  if ((hitPos.Phi() > (anodeIntersection.Phi() - TMath::PiOver4())) && (hitPos.Phi() < (anodeIntersection.Phi() + TMath::PiOver4())))
+  {
+    PCQQQPhiCut = true;
+  }
+
+  for (double AIz = 20; AIz <= 100; AIz += 5.0)
+  {
+    TVector3 TargetPos(0, 0, AIz);
+    if (PCQQQPhiCut && anodeIntersection.Perp() != 0 && cathodeHits.size() >= 2)
+      // TVector3 anodePosAtZ(anodeIntersection.X() * (AIz / anodeIntersection.Z()), anodeIntersection.Y() * (AIz / anodeIntersection.Z()), AIz);
+      // TVector3 anodePosAtZ(anodeIntersection.X(), anodeIntersection.Y(),anodeIntersection.Z() + AIz);
+      plotter->Fill2D("Inttheta_vs_QQQtheta_TC" + std::to_string(PCQQQTimeCut) + "_TZ" + std::to_string(AIz), 180, 0, 180, 90, 0, 90, (anodeIntersection - TargetPos).Theta() * 180. / TMath::Pi(),
+                      (hitPos - TargetPos).Theta() * 180. / TMath::Pi(), "TPosVariation");
+  }
+
+  if (anodeIntersection.Perp() != 0)
+  {
+    plotter->Fill1D("PC_Z_Projection", 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+    plotter->Fill2D("Z_Proj_VsDelTime", 600, -300, 300, 200, -2000, 2000, anodeIntersection.Z(), anodeT - cathodeT, "hPCzQQQ");
+    plotter->Fill2D("IntPhi_vs_QQQphi", 100, -200, 200, 80, -200, 200, anodeIntersection.Phi() * 180. / TMath::Pi(), hitPos.Phi() * 180. / TMath::Pi(), "hPCQQQ");
+    plotter->Fill1D("IntRho", 200, 0, 100, anodeIntersection.Perp(), "hRawPC");
+    plotter->Fill2D("Inttheta_vs_QQQtheta", 90, 0, 180, 20, 0, 45, anodeIntersection.Theta() * 180. / TMath::Pi(), hitPos.Theta() * 180. / TMath::Pi(), "hPCQQQ");
+    plotter->Fill2D("Inttheta_vs_QQQtheta_TC" + std::to_string(PCQQQTimeCut), 90, 0, 180, 20, 0, 45, anodeIntersection.Theta() * 180. / TMath::Pi(), hitPos.Theta() * 180. / TMath::Pi(), "hPCQQQ");
+    plotter->Fill2D("IntPhi_vs_QQQphi_TC" + std::to_string(PCQQQTimeCut) + "PhiC" + std::to_string(PCQQQPhiCut), 100, -200, 200, 80, -200, 200, anodeIntersection.Phi() * 180. / TMath::Pi(), hitPos.Phi() * 180. / TMath::Pi(), "hPCQQQ");
+  }
+  if (anodeIntersection.Perp() != 0 && cathodeHits.size() >= 2)
+    plotter->Fill1D("PC_Z_Projection_TC" + std::to_string(PCQQQTimeCut) + "PhiC" + std::to_string(PCQQQPhiCut), 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+
+  if (anodeIntersection.Perp() != 0 && cathodeHits.size() == 1)
+  {
+    plotter->Fill1D("PC_Z_proj_1C", 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+    plotter->Fill2D("IntersectionPhi_vs_AnodeZ_1C", 400, -200, 200, 600, -300, 300, anodeIntersection.Phi() * 180. / TMath::Pi(), anodeIntersection.Z(), "hPCzQQQ");
+  }
+
+  if (anodeIntersection.Perp() != 0 && cathodeHits.size() == 2)
+  {
+    plotter->Fill1D("PC_Z_proj_2C", 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+    plotter->Fill2D("IntersectionPhi_vs_AnodeZ_2C", 400, -200, 200, 600, -300, 300, anodeIntersection.Phi() * 180. / TMath::Pi(), anodeIntersection.Z(), "hPCzQQQ");
+  }
+  if (anodeIntersection.Perp() != 0 && cathodeHits.size() > 2)
+  {
+    plotter->Fill1D("PC_Z_proj_nC", 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+    plotter->Fill2D("IntersectionPhi_vs_AnodeZ_nC", 400, -200, 200, 600, -300, 300, anodeIntersection.Phi() * 180. / TMath::Pi(), anodeIntersection.Z(), "hPCzQQQ");
+  }
+  if (anodeHits.size() > 0 && cathodeHits.size() > 0)
+    plotter->Fill2D("AHits_vs_CHits", 12, 0, 11, 6, 0, 5, anodeHits.size(), cathodeHits.size(), "hRawPC");
+
+  // make another plot with nearest neighbour constraint
+  bool hasNeighbourAnodes = false;
+  bool hasNeighbourCathodes = false;
+
+  // 1. Check Anodes for neighbours (including wrap-around 0-23)
+  for (size_t i = 0; i < anodeHits.size(); i++)
+  {
+    for (size_t j = i + 1; j < anodeHits.size(); j++)
+    {
+      int diff = std::abs(anodeHits[i].first - anodeHits[j].first);
+      if (diff == 1 || diff == 23)
+      { // 23 handles the cylindrical wrap
+        hasNeighbourAnodes = true;
+        break;
+      }
+    }
+    if (hasNeighbourAnodes)
+      break;
+  }
+
+  // 2. Check Cathodes for neighbours (including wrap-around 0-23)
+  for (size_t i = 0; i < cathodeHits.size(); i++)
+  {
+    for (size_t j = i + 1; j < cathodeHits.size(); j++)
+    {
+      int diff = std::abs(cathodeHits[i].first - cathodeHits[j].first);
+      if (diff == 1 || diff == 23)
+      {
+        hasNeighbourCathodes = true;
+        break;
+      }
+    }
+    if (hasNeighbourCathodes)
+      break;
+  }
+
+  // ---------------------------------------------------------
+  // FILL PLOTS
+  // ---------------------------------------------------------
+  if (anodeHits.size() > 0 && cathodeHits.size() > 0)
+  {
+    // plotter->Fill2D("AHits_vs_CHits_NA" + std::to_string(hasNeighbourAnodes), 12, 0, 11, 6, 0, 5, anodeHits.size(), cathodeHits.size(), "hRawPC");
+    // plotter->Fill2D("AHits_vs_CHits_NC" + std::to_string(hasNeighbourCathodes), 12, 0, 11, 6, 0, 5, anodeHits.size(), cathodeHits.size(), "hRawPC");
+
+    // Constraint Plot: Only fill if BOTH planes have adjacent hits
+    // This effectively removes events with only isolated single-wire hits (noise)
+    if (hasNeighbourAnodes && hasNeighbourCathodes)
+    {
+      plotter->Fill2D("AHits_vs_CHits_NN", 12, 0, 11, 6, 0, 5, anodeHits.size(), cathodeHits.size(), "hRawPC");
+    }
+  }
+
+  if (HitNonZero && anodeIntersection.Z() != 0)
+  {
+    pw_contr.CalTrack2(hitPos, anodeIntersection);
+    plotter->Fill1D("VertexRecon", 600, -300, 300, pw_contr.GetZ0());
+
+    if (PCQQQPhiCut && PCQQQTimeCut)
+    {
+      if (cathodeHits.size() == 2)
+        plotter->Fill1D("VertexRecon_TC_PhiC_2C", 600, -300, 300, pw_contr.GetZ0());
+    }
+    plotter->Fill1D("VertexRecon_TC" + std::to_string(PCQQQTimeCut) + "_PhiC" + std::to_string(PCQQQPhiCut), 600, -300, 300, pw_contr.GetZ0());
+  }
+
+  for (int i = 0; i < qqq.multi; i++)
+  {
+    if (PCQQQTimeCut)
+    {
+      plotter->Fill2D("PC_XY_Projection_QQQ_TimeCut" + std::to_string(qqq.id[i]), 400, -100, 100, 400, -100, 100, anodeIntersection.X(), anodeIntersection.Y(), "hPCQQQ");
+    }
+    plotter->Fill2D("PC_XY_Projection_QQQ" + std::to_string(qqq.id[i]), 400, -100, 100, 400, -100, 100, anodeIntersection.X(), anodeIntersection.Y(), "hPCQQQ");
+
+    for (int j = i + 1; j < qqq.multi; j++)
+    {
+      if (qqq.id[i] == qqq.id[j])
+      {
+        int chWedge = -1;
+        int chRing = -1;
+        double eWedge = 0.0;
+        double eWedgeMeV = 0.0;
+        double eRing = 0.0;
+        double eRingMeV = 0.0;
+        double tRing = 0.0;
+        int qqqID = -1;
+        if (qqq.ch[i] < 16 && qqq.ch[j] >= 16 && qqqGainValid[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16])
+        {
+          chWedge = qqq.ch[i];
+          eWedge = qqq.e[i] * qqqGain[qqq.id[i]][qqq.ch[i]][qqq.ch[j] - 16];
+          chRing = qqq.ch[j] - 16;
+          eRing = qqq.e[j];
+          tRing = static_cast<double>(qqq.t[j]);
+          qqqID = qqq.id[i];
+        }
+        else if (qqq.ch[j] < 16 && qqq.ch[i] >= 16 && qqqGainValid[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16])
+        {
+          chWedge = qqq.ch[j];
+          eWedge = qqq.e[j] * qqqGain[qqq.id[j]][qqq.ch[j]][qqq.ch[i] - 16];
+          chRing = qqq.ch[i] - 16;
+          tRing = static_cast<double>(qqq.t[i]);
+          eRing = qqq.e[i];
+          qqqID = qqq.id[i];
+        }
+        else
+          continue;
+
+        if (qqqCalibValid[qqq.id[i]][chRing][chWedge])
+        {
+          eWedgeMeV = eWedge * qqqCalib[qqq.id[i]][chRing][chWedge] / 1000;
+          eRingMeV = eRing * qqqCalib[qqq.id[i]][chRing][chWedge] / 1000;
+        }
+        else
+          continue;
+
+        // if (anodeIntersection.Z() != 0)
+        {
+          plotter->Fill2D("PC_Z_vs_QQQRing", 600, -300, 300, 16, 0, 16, anodeIntersection.Z(), chRing, "hPCzQQQ");
+        }
+
+        if (anodeIntersection.Z() != 0 && cathodeHits.size() == 2)
+        {
+          plotter->Fill2D("PC_Z_vs_QQQRing_2C", 600, -300, 300, 16, 0, 16, anodeIntersection.Z(), chRing, "hPCzQQQ");
+          plotter->Fill2D("PC_Z_vs_QQQRing_2C" + std::to_string(qqq.id[i]), 600, -300, 300, 16, 0, 16, anodeIntersection.Z(), chRing, "hPCzQQQ");
+          plotter->Fill2D("PC_Z_vs_QQQWedge_2C", 600, -300, 300, 16, 0, 16, anodeIntersection.Z(), chWedge, "hPCzQQQ");
+        }
+        plotter->Fill2D("Vertex_V_QQQRing", 600, -300, 300, 16, 0, 16, pw_contr.GetZ0(), chRing, "hPCQQQ");
+        double phi = TMath::ATan2(anodeIntersection.Y(), anodeIntersection.X()) * 180. / TMath::Pi();
+        // while (phi > 180)
+        //   phi -= 180;
+        // while (phi < -180)
+        //   phi += 180;
+        plotter->Fill2D("PolarAngle_Vs_QQQWedge" + std::to_string(qqqID), 360, -360, 360, 16, 0, 16, phi, chWedge, "hPCQQQ");
+        // plotter->Fill2D("EdE_PC_vs_QQQ_timegate_ls1000"+std::to_string())
+
+        plotter->Fill2D("PC_Z_vs_QQQRing_Det" + std::to_string(qqqID), 600, -300, 300, 16, 0, 16, anodeIntersection.Z(), chRing, "hPCQQQ");
+        for (int k = 0; k < pc.multi; k++)
+        {
+          if (pc.index[k] >= 24)
+            continue;
+          plotter->Fill2D("CalibratedQQQE_RvsAnodeE_TC" + std::to_string(PCQQQTimeCut) + "PhiC" + std::to_string(PCQQQPhiCut), 1000, 0, 10, 2000, 0, 30000, eRingMeV, pc.e[k], "hPCQQQ");
+          plotter->Fill2D("CalibratedQQQE_WvsAnodeE_TC" + std::to_string(PCQQQTimeCut) + "PhiC" + std::to_string(PCQQQPhiCut), 1000, 0, 10, 2000, 0, 30000, eWedgeMeV, pc.e[k], "hPCQQQ");
+          plotter->Fill2D("AnodeQQQ_dTimevsdPhi", 200, -2000, 2000, 80, -200, 200, tRing - static_cast<double>(pc.t[k]), (hitPos.Phi() - anodeIntersection.Phi()) * 180. / TMath::Pi(), "hTiming");
+          plotter->Fill1D("AnodeQQQ_Time", 200, -2000, 2000, tRing - static_cast<double>(pc.t[k]));
+        }
+      }
+    }
+  }
+
+  TVector3 guessVertex(0, 0, 90.);
+  // rho=40.0 mm is halfway between the cathodes(rho=42) and anodes(rho=37)
+  double pcz_guess = 42.0 / TMath::Tan((hitPos - guessVertex).Theta()) + guessVertex.Z(); // this is ideally kept to be all QQQ+userinput for calibration of pcz
+  if (PCQQQTimeCut && PCQQQPhiCut && hitPos.Perp() > 0 && anodeIntersection.Perp() > 0 && cathodeHits.size() >= 2)
+  {
+    plotter->Fill2D("pczguess_vs_qqqE", 100, 0, 200, 800, 0, 20, pcz_guess, qqqenergy, "pczguess");
+    // plotter->Fill2D("pczguess_vs_pcz_rad="+std::to_string(hitPos.Perp()),100,0,200,150,0,200,pcz_guess,anodeIntersection.Z(),"pczguess"); //entirely qqq-derived position vs entirely PC derived position
+    plotter->Fill2D("pczguess_vs_pcz_phi=" + std::to_string(hitPos.Phi() * 180. / M_PI), 100, 0, 200, 150, 0, 200, pcz_guess, anodeIntersection.Z() / 0.8, "pczguess"); // entirely qqq-derived position vs entirely PC derived position
+    plotter->Fill2D("pczguess_vs_pcz", 100, 0, 200, 150, 0, 200, pcz_guess, anodeIntersection.Z() / 0.8);
+    plotter->Fill2D("pcz_vs_pcPhi_rad=" + std::to_string(hitPos.Perp()), 360, 0, 360, 150, 0, 200, anodeIntersection.Phi() * 180. / M_PI, anodeIntersection.Z() / 0.8, "pczguess");
+  }
+
+  for (int i = 0; i < sx3.multi; i++)
+  {
+    // plotting sx3 strip hits vs anode phi
+    if (sx3.ch[i] < 8)
+      plotter->Fill2D("AnodePhi_vs_SX3Strip", 100, -200, 200, 8 * 24, 0, 8 * 24, anodeIntersection.Phi() * 180. / TMath::Pi(), sx3.id[i] * 8 + sx3.ch[i]);
+  }
+
+  if (anodeIntersection.Z() != 0 && cathodeHits.size() == 3)
+  {
+    plotter->Fill1D("PC_Z_proj_3C", 600, -300, 300, anodeIntersection.Z(), "hPCzQQQ");
+  }
+
+  plotter->Fill2D("AnodeMaxE_Vs_Cathode_Sum_Energy", 2000, 0, 30000, 2000, 0, 30000, aEMax, cESum, "hGMPC");
+  plotter->Fill1D("Correlated_Cathode_MaxAnode", 6, 0, 5, corrcatMax.size(), "hGMPC");
+  plotter->Fill2D("Correlated_Cathode_VS_MaxAnodeEnergy", 6, 0, 5, 2000, 0, 30000, corrcatMax.size(), aEMax, "hGMPC");
+  plotter->Fill1D("AnodeHits", 12, 0, 11, anodeHits.size(), "hGMPC");
+  plotter->Fill2D("AnodeMaxE_vs_AnodeHits", 12, 0, 11, 2000, 0, 30000, anodeHits.size(), aEMax, "hGMPC");
+
+  if (anodeHits.size() < 1)
+  {
+    plotter->Fill1D("NoAnodeHits_CathodeHits", 6, 0, 5, cathodeHits.size(), "hGMPC");
+  }
 
   return kTRUE;
 }
 
-void Analyzer::Terminate(){
+void TrackRecon::Terminate()
-
+{
-  gStyle->SetOptStat("neiou");
+  plotter->FlushToDisk();
-  TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
-  canvas->Divide(3,3);
-
-  //hsx3VpcIndex->Draw("colz");
-
-  //=============================================== pad-1
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hsx3IndexVE->Draw("colz");
-
-  //=============================================== pad-2
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hqqqIndexVE->Draw("colz");
-
-  //=============================================== pad-3
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hpcIndexVE->Draw("colz");
-
-  //=============================================== pad-4
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hsx3Coin->Draw("colz");
-
-  //=============================================== pad-5
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hqqqCoin->Draw("colz");
-
-  //=============================================== pad-6
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hpcCoin->Draw("colz");
-
-  //=============================================== pad-7
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hsx3VpcIndex ->Draw("colz"); 
-  // hsx3VpcE->Draw("colz") ;
-
-  //=============================================== pad-8
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-
-  hqqqVpcIndex ->Draw("colz");  
-
-  // hqqqVpcE ->Draw("colz");
-  //=============================================== pad-9
-  padID ++; 
-
-  // canvas->cd(padID)->DrawFrame(-50, -50, 50, 50);
-  // hqqqPolar->Draw("same colz pol");
-
- canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
- hZProj->Draw();
-  // hanVScatsum->Draw("colz");
-
 }

TrackRecon.h

@@ -0,0 +1,127 @@
+#ifndef TrackRecon_h
+#define TrackRecon_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+#include <vector>         // Required for vectors
+#include <utility>        // Required for std::pair
+
+#include "Armory/ClassDet.h"
+#include "Armory/ClassPW.h" // YOU ADDED THIS (Correct! Defines Coord)
+
+class TrackRecon : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+   Det misc;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+   TBranch        *b_miscMulti;   //!
+   TBranch        *b_miscID;   //!
+   TBranch        *b_miscCh;   //!
+   TBranch        *b_miscE;   //!
+   TBranch        *b_miscT;   //!
+   TBranch        *b_miscTf;   //!
+
+   // 1. Geometry Cache
+   Coord Crossover[24][24][2];
+
+   // 2. Persistent Vectors (REQUIRED for the optimized .cxx to work)
+   std::vector<std::pair<int, double>> anodeHits;
+   std::vector<std::pair<int, double>> cathodeHits;
+   std::vector<std::pair<int, double>> corrcatMax;
+
+   TrackRecon(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~TrackRecon() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(TrackRecon,0);
+};
+
+#endif
+
+#ifdef TrackRecon_cxx
+void TrackRecon::Init(TTree *tree){
+
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID",    &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh",    &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE",     &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT",     &misc.t, &b_miscT);
+}
+
+Bool_t TrackRecon::Notify(){
+   return kTRUE;
+}
+
+void TrackRecon::SlaveBegin(TTree * /*tree*/){
+   // TString option = GetOption();
+}
+
+void TrackRecon::SlaveTerminate(){
+}
+#endif // #ifdef TrackRecon_cxx

centroids.txt

@@ -0,0 +1,97 @@
+HistogramIndex	PeakNumber	Centroid	Amplitude	Sigma
+0	1	991.118
+0	2	2026.83
+0	3	3060.26
+0	4	4092.45
+1	1	922.213
+1	2	1885.55
+1	3	2845.53
+1	4	3810.32
+2	1	955.591
+2	2	1953.17
+2	3	2949.37
+2	4	3950.79
+3	1	995.787
+3	2	2036.58
+3	3	3076.91
+3	4	4112.05
+4	1	1017.48
+4	2	2080.19
+4	3	3142.24
+4	4	4206.1
+5	1	1022.78
+5	2	2091.21
+5	3	3158.28
+5	4	4226.97
+6	1	1076.22
+6	2	2203.37
+6	3	3329.53
+6	4	4457.69
+7	1	977.46
+7	2	1998.02
+7	3	3017.36
+7	4	4040.47
+8	1	1049.74
+8	2	2144.38
+8	3	3238.2
+8	4	4335.25
+9	1	1000.59
+9	2	2046.42
+9	3	3090.29
+9	4	4129.63
+10	1	1014.92
+10	2	2076.16
+10	3	3134.59
+10	4	4213.42
+11	1	1004.85
+11	2	2052.88
+11	3	3100.3
+11	4	4164.75
+12	1	945.861
+12	2	1932.49
+12	3	2917.95
+12	4	3955.15
+13	1	998.307
+13	2	2040.38
+13	3	3078.76
+13	4	4135.51
+14	1	966.429
+14	2	1972.15
+14	3	2974.84
+14	4	4056.41
+15	1	958.352
+15	2	1958.64
+15	3	2957.7
+15	4	3970.41
+16	1	970.732
+16	2	1977.63
+16	3	2984.97
+16	4	4002.56
+17	1	1013.65
+17	2	2064.9
+17	3	3114.19
+17	4	4190.98
+18	1	975.538
+18	2	1990.64
+18	3	3005.46
+18	4	4048.99
+19	1	1082.91
+19	2	2194.08
+19	3	3303.65
+19	4	4411.32
+20	1	912.778
+20	2	1866.83
+20	3	2819.21
+20	4	3781.63
+21	1	1002.36
+21	2	1989.95
+21	3	2975.53
+21	4	3986.71
+22	1	1075.38
+22	2	2144.25
+22	3	3210.17
+22	4	4312.84
+23	1	988.828
+23	2	2016.35
+23	3	3044.19
+23	4	4082.41

centroids_edited.txt

@@ -0,0 +1,89 @@
+HistogramIndex	PeakNumber	Centroid	Amplitude	Sigma
+1	1	922.213
+1	2	1885.55
+1	3	2845.53
+1	4	3810.32
+2	1	955.591
+2	2	1953.17
+2	3	2949.37
+2	4	3950.79
+3	1	995.787
+3	2	2036.58
+3	3	3076.91
+3	4	4112.05
+4	1	1017.48
+4	2	2080.19
+4	3	3142.24
+4	4	4206.1
+5	1	1022.78
+5	2	2091.21
+5	3	3158.28
+5	4	4226.97
+6	1	1076.22
+6	2	2203.37
+6	3	3329.53
+6	4	4457.69
+7	1	977.46
+7	2	1998.02
+7	3	3017.36
+7	4	4040.47
+8	1	1049.74
+8	2	2144.38
+8	3	3238.2
+8	4	4335.25
+9	1	1000.59
+9	2	2046.42
+9	3	3090.29
+9	4	4129.63
+10	1	1014.92
+10	2	2076.16
+10	3	3134.59
+10	4	4213.42
+11	1	1004.85
+11	2	2052.88
+11	3	3100.3
+11	4	4164.75
+12	1	945.861
+12	2	1932.49
+12	3	2917.95
+12	4	3955.15
+13	1	998.307
+13	2	2040.38
+13	3	3078.76
+13	4	4135.51
+14	1	966.429
+14	2	1972.15
+14	3	2974.84
+14	4	4056.41
+15	1	958.352
+15	2	1958.64
+15	3	2957.7
+15	4	3970.41
+16	1	970.732
+16	2	1977.63
+16	3	2984.97
+16	4	4002.56
+17	1	1013.65
+17	2	2064.9
+17	3	3114.19
+17	4	4190.98
+18	1	975.538
+18	2	1990.64
+18	3	3005.46
+18	4	4048.99
+20	1	912.778
+20	2	1866.83
+20	3	2819.21
+20	4	3781.63
+21	1	1002.36
+21	2	1989.95
+21	3	2975.53
+21	4	3986.71
+22	1	1075.38
+22	2	2144.25
+22	3	3210.17
+22	4	4312.84
+23	1	988.828
+23	2	2016.35
+23	3	3044.19
+23	4	4082.41