modified: .gitignore

modified: Analyzer.C
modified: Analyzer.C modfied the algorithm for selection of valid cathodes, the section is now based on geometry
2025-02-17 17:06:33 -05:00 · 2025-02-17 17:03:58 -05:00 · 2025-02-17 16:59:08 -05:00 · 2025-02-05 14:59:02 -05:00 · 2025-02-05 08:23:23 -05:00 · 2025-02-03 10:32:07 -05:00
19 changed files with 2432 additions and 361 deletions
--- a/.gitignore
+++ b/.gitignore
@ -4,7 +4,7 @@ EventBuilder*
 *.pcm
 *.root
 *.exe
-
+*.txt
 Mapper
 AnasenMS

--- a/.vscode/c_cpp_properties.json
+++ b/.vscode/c_cpp_properties.json
@ -1,23 +1,11 @@
 {
    "configurations": [
        {
-            "name": "splitpole",
+            "name": "Hades",
            "includePath": [
                "${workspaceFolder}/**",
-                "/home/splitpole/cern/root/**"
-            ],
-            "defines": [],
-            "compilerPath": "/usr/bin/gcc",
-            "cStandard": "c17",
-            "cppStandard": "gnu++17",
-            "intelliSenseMode": "linux-gcc-x64"
-        },
-        {
-            "name": "Ryan",
-            "includePath": [
-                "${workspaceFolder}/**",
-                "/home/ryan/Downloads/root_build/**",
-                "/home/ryan/Downloads/root_build/include"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/usr/local/cern/root_v6.26.06/include/**"
            ],
            "defines": [],
            "compilerPath": "/usr/bin/gcc",
@ -29,7 +17,8 @@
            "name": "RyanUbuntu",
            "includePath": [
                "${workspaceFolder}/**",
-                "/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
            ],
            "defines": [],
            "compilerPath": "/usr/bin/gcc",
@ -38,10 +27,11 @@
            "intelliSenseMode": "linux-gcc-x64"
        },
        {
-            "name": "RyanHome",
+            "name": "Anasen",
            "includePath": [
                "${workspaceFolder}/**",
-                "/home/ryan/root_v6.30.06/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/opt/root/include/**"
            ],
            "defines": [],
            "compilerPath": "/usr/bin/gcc",
@ -50,10 +40,26 @@
            "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",
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@ -90,6 +90,22 @@
    "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"
+  },
+  "github-enterprise.uri": "https://fsunuc.physics.fsu.edu"
 }
--- a/Analyzer.C
+++ b/Analyzer.C
@ -1,84 +1,149 @@
 #define Analyzer_cxx

 #include "Analyzer.h"
+#include "Armory/ClassSX3.h"
+#include "Armory/ClassPW.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"
-#include "Armory/ClassPW.h"
+TH2F *hsx3IndexVE;
+TH2F *hqqqIndexVE;
+TH2F *hpcIndexVE;

-#include "TVector3.h"
+TH2F *hpcIndexVE_GM;
+TH2F *hsx3Coin;
+TH2F *hqqqCoin;
+TH2F *hpcCoin;
+TH2F *hAVCcoin;

-TH2F * hsx3IndexVE;
-TH2F * hqqqIndexVE;
-TH2F * hpcIndexVE;
+TH2F *hqqqPolar;
+TH2F *hsx3VpcIndex;
+TH2F *hqqqVpcIndex;
+TH2F *hqqqVpcE;
+TH2F *hsx3VpcE;
+TH2F *hanVScatsum;
+TH2F *hanVScatsum_a[24];
+TH1F *hPC_E[48];
+TH1F *hCat4An;
+TH1F *hCat0An;
+TH1F *hAnodehits;
+TH2F *hNosvAe;
+TH2F *hUncorrCAN;

-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;
+PW pwinstance;
 TVector3 hitPos;
+// TVector3 anodeIntersection;
+std::map<int, std::pair<double, double>> slopeInterceptMap;
+
 bool HitNonZero;
+bool sx3ecut;
+bool qqqEcut;

-TH1F * hZProj;
+TH1F *hZProj;
+TH1F *hPCZProj;

-void Analyzer::Begin(TTree * /*tree*/){
+void Analyzer::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");
+  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, 16000);
+  hpcIndexVE->SetNdivisions(-1204, "x");
+  hpcIndexVE_GM = new TH2F("hpcIndexVE_GM", "PC index vs Energy; PC index ; Energy", 2 * 24, 0, 2 * 24, 400, 0, 16000);
+  hpcIndexVE_GM->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);
+  hAVCcoin = new TH2F("hAVCcoin", "Anode vs Cathode Coincident", 24, 0, 24, 24, 0, 24);

-  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);

-  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");

-  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, 800, 0, 16000);
+  hqqqVpcE->SetNdivisions(-612, "x");
+  hqqqVpcE->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");
+  hsx3VpcE = new TH2F("hsx3VpcEnergy", "sx3 vs pc; sx3 energy; pc energy", 400, 0, 5000, 800, 0, 16000);
+  hsx3VpcE->SetNdivisions(-612, "x");
+  hsx3VpcE->SetNdivisions(-12, "y");

-  hZProj = new TH1F("hZProj", "Z Projection", 200, -600, 600);
-
-  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 10000, 400, 0 , 16000);
+  // hZProj = new TH1F("hZProj", "Z Projection", 1200, -600, 600);
+  hPCZProj = new TH1F("hPCZProj", "PC Z Projection", 600, -300, 300);

+  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400, 0, 16000, 400, 0, 20000);
+  hCat4An = new TH1F("hCat4An", "Number of Cathodes/Anode", 24, 0, 24);
+  hCat0An = new TH1F("hCat0An", "Number of Cathodes without Anode", 24, 0, 24);
+  hAnodehits = new TH1F("hAnodehits", "Number of Anode hits", 24, 0, 24);
+  hNosvAe = new TH2F("hnosvAe", "Number of Cathodes/Anode vs Anode Energy", 20, 0, 20, 400, 0, 16000);
+  hUncorrCAN = new TH2F("hUncorrCAn", "Uncorrelated Cathodes/Anode", 24, 0, 24, 24, 0, 24);
+  // 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, 16000, 400, 0, 20000);
+  // }
+  // for (int i = 0; i < 48; i++)
+  // {
+  //   TString histName = Form("hCathode_%d", i);
+  //   TString histTitle = Form("Cathode_E_%d;", i);
+  //   hPC_E[i] = new TH1F(histName, histTitle, 3200, 0, 32000);
+  // }
  sx3_contr.ConstructGeo();
  pw_contr.ConstructGeo();

+  std::ifstream inputFile("slope_intercept_results.txt");
+
+  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;
+      // wires 37, 39, 44 have fit data that is incorrect or not present, they have thus been set to 1,0 (slope, intercept) for convenience
+      // wire 19 the 4th point was genereated using the slope of the line produced uising the other 3 points from the wire 1 vs wire 19 plot
+      if (index >= 0 && index <= 47)
+      {
+        slopeInterceptMap[index] = std::make_pair(slope, intercept);
+      }
+    }
+    inputFile.close();
+  }
+  else
+  {
+    std::cerr << "Error opening slope_intercept.txt" << std::endl;
+  }
 }

-
-
-
-Bool_t Analyzer::Process(Long64_t entry){
+Bool_t Analyzer::Process(Long64_t entry)
+{

  // if ( entry > 100 ) return kTRUE;

@ -110,46 +175,58 @@ Bool_t Analyzer::Process(Long64_t entry){

  // sx3.Print();

-  //########################################################### Raw data
-  // //======================= SX3
-
+  // ########################################################### Raw data
+  //  //======================= SX3
+  sx3ecut = false;
  std::vector<std::pair<int, int>> ID; // first = id, 2nd = index
-  for( int i = 0; i < sx3.multi; i ++){
+  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]);
+    hsx3IndexVE->Fill(sx3.index[i], sx3.e[i]);
+    if (sx3.e[i] > 1000 && sx3.e[i] < 2200)
+    {
+      sx3ecut = true;
    }

-    for( int j = 0; j < pc.multi; j++){
-      hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
+    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;
-    } );
+  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; 
+    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) {
+    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) {
+        if (sx3ID.size() >= 3)
+        {
          found = true;
-        } 
-      }else{
-        if( !found ){
+        }
+      }
+      else
+      {
+        if (!found)
+        {
          sx3ID.clear();
          sx3ID.push_back(ID[i]);
        }
@ -158,33 +235,42 @@ Bool_t Analyzer::Process(Long64_t entry){

    // printf("---------- sx3ID Multi : %zu \n", sx3ID.size());

-    if( found ){
+    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++ ){
+      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) {
+        if (sx3.ch[index] < 8)
+        {
+          if (sx3.ch[index] % 2 == 0)
+          {
            sx3ChDn = sx3.ch[index];
            sx3EDn = sx3.e[index];
-          }else{
+          }
+          else
+          {
            sx3ChUp = sx3.ch[index];
            sx3EUp = sx3.e[index];
          }
-        }else{
+        }
+        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] );
-            }
+        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);
@ -192,211 +278,494 @@ Bool_t Analyzer::Process(Long64_t entry){
      HitNonZero = true;
      // hitPos.Print();
    }
-
  }
-  
-
+  qqqEcut = false;
  // //======================= QQQ
-  for( int i = 0; i < qqq.multi; i ++){
+  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] );
-        // }
+    // 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]);
+    if (qqq.e[i] > 1600 && qqq.e[i] < 2600)
+    {
+      qqqEcut = true;
+    }
+    // }
+    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] );
+    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] );
-
+          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 
-        
+
+      // 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]){
+        int chRing = -1;
+        if (qqq.ch[i] < qqq.ch[j])
+        {
          chRing = qqq.ch[j] - 16;
          chWedge = qqq.ch[i];
-        }else{
+        }
+        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);
+        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);
+        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;
+        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 ++){
+  // Calculate the crossover points and put them into an array

-    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]));
+  pwinstance.ConstructGeo();
+  Coord Crossover[24][24][2];
+  TVector3 a, c, diff, an, cn;
+  double a2, an2, ac, c2, cn2, adiff, cdiff, denom, alpha, beta;
+  int index = 0;
+  for (int i = 0; i < pwinstance.An.size(); i++)
+  {
+    a = pwinstance.An[i].first - pwinstance.An[i].second;

-    hpcIndexVE->Fill( pc.index[i], pc.e[i] );
+    for (int j = 0; j < pwinstance.Ca.size(); j++)
+    {
+      // Ok so this method uses what is essentially the solution of 2 equations to find the point of intersection between the anode and cathode wires
+      // here a and c are the vectors of the anode and cathode wires respectively
+      // diff is the perpendicular vector between the anode and cathode wires
+      // The idea behind this is to then find the scalars alpha and beta that give a ratio between 0 and -1,

-    for( int j = i+1; j < pc.multi; j++){
-      hpcCoin->Fill( pc.index[i], pc.index[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);
+      an2 = an.Dot(an);
+      cn2 = cn.Dot(cn);
+      denom = a2 * c2 - ac * ac;
+      alpha = (ac * cdiff - c2 * adiff) / denom;
+      beta = (a2 * cdiff - ac * adiff) / denom;
+
+      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(Crossover[i][j][0].z <-190 || Crossover[i][j][0].z > 190) Crossover[i][j][0].z = 9999999;
+
+      // placeholder variable Crossover[i][j][2].x has nothing to do with the geometry of the crossover and is being used to store the alpha value-
+      //-so that it can be used to sort "good" hits later
+      Crossover[i][j][1].x = alpha;
+      Crossover[i][j][1].y = 0;
+      // printf("AID, CID, Crossover z and alpha are :  %d %d %f %f \n", i, j, Crossover[i][j][0].z, Crossover[i][j][1].x /*this is alpha*/);
+    }
+  }
+
+  // if (i == 4)
+  {
+    // for (int k = -4; k < 3; k++)
+    // {
+    //   if ((i + 24 + k) % 24 == 23 - j) // the 23-j is used to accomodate for the fact that the order of the cathodes was reversed
+    //   {
+    //     Crossover[i][j][1].y = 1;
+    //   }
+    // }
+    // for (int k = -4; k < 3; k++)
+    // {
+    //   if (Crossover[i][j][k].y != 1)
+    //   // if (alpha < 1 && alpha >= -1)
+    //   {
+    //     // printf("i an: %d %f %f %f \n", i, an.X(), an.Y(), an.Z());
+    //     Crossover[i][j][0].z = 9999999; // this is a placeholder value to indicate that the anode and cathode wires do not intersect
+    //   }
+    // }
+  }
+  // printf("Anode and cathode indices, alpha, denom, andiff, cndiff : %d %d %f %f %f %f\n", i, j, alpha, denom, adiff, cdiff);
+
+  // anodeIntersection.Clear();
+  for (int i = 0; i < pc.multi; i++)
+  {
+
+    if (pc.e[i] > 100)
+    {
+      hpcIndexVE->Fill(pc.index[i], pc.e[i]); // non gain matched energy
    }

+    // Gain Matching of PC wires
+    if (pc.index[i] >= 0 && pc.index[i] < 48)
+    {
+      // printf("index: %d, Old cathode energy: %d \n", pc.index[i],pc.e[i]);
+      auto it = slopeInterceptMap.find(pc.index[i]);
+      if (it != slopeInterceptMap.end())
+      {
+        double slope = it->second.first;
+        double intercept = it->second.second;
+        // printf("slope: %f, intercept:%f\n" ,slope, intercept);
+        pc.e[i] = slope * pc.e[i] + intercept;
+        // printf("index: %d, New cathode energy: %d \n",pc.index[i], pc.e[i]);
+      }
+      hpcIndexVE_GM->Fill(pc.index[i], pc.e[i]);
+      // hPC_E[pc.index[i]]->Fill(pc.e[i]); // gain matched energy per channel
+    }
  }
-  //  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 ){
+  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>> corrcatnextMax = {};
+  std::vector<std::pair<int, double>> commcat = {};
+  int aID = 0;
+  int cID = 0;
+  float aE = 0;
+  float cE = 0;
+  float aESum = 0;
+  float cESum = 0;
+  float aEMax = 0;
+  float cEMax = 0;
+  float aEnextMax = 0;
+  float cEnextMax = 0;
+  int aIDMax = 0;
+  int cIDMax = 0;
+  int aIDnextMax = 0;
+  int cIDnextMax = 0;

-    int aID = 0;
-    int cID = 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] > 100 /*&& pc.multi < 7*/)
+    {
+      // creating a vector of pairs of anode and cathode hits
+      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]));
+      }

-    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 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]);
+      }
+    }
+  }
+  // sorting the anode and cathode hits in descending order of energy
+  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; });

-  // 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 && E[l].first!=20 && E[l].first!=12){
-          if(!multi_an){
-            aE = E[l].second;
-          }
-          multi_an=true;
+  if (anodeHits.size() >= 1 && cathodeHits.size() >=1)
+  {
+
+    for (const auto &anode : anodeHits)
+    {
+      aID = anode.first;
+      aE = anode.second;
+      aESum += aE;
+      if (aE > aEMax)
+      {
+        aEMax = aE;
+        aIDMax = aID;
+      }
+      if (aE > aEnextMax && aE < aEMax)
+      {
+        aEnextMax = aE;
+        aIDnextMax = aID;
+      }
+      // for(const auto &cat : cathodeHits){
+      //   hAVCcoin->Fill(aID, cat.first);
+      // }
+    }
+
+    // std::cout << " Anode iD : " << aIDMax << " Energy : " << aEMax << std::endl;
+
+    // printf("aID : %d, aE : %f, cE : %f\n", aID, aE, cE);
+    corrcatMax.clear();
+    for (const auto &cathode : cathodeHits)
+    {
+      cID = cathode.first;
+      cE = cathode.second;
+      // std::cout << "Cathode ID : " << cID << " Energy : " << cE << std::endl;
+      // if (cE > cEMax)
+      // {
+      //   cIDnextMax = cIDMax;
+      //   cEnextMax = cEMax;
+      //   cEMax = cE;
+      //   cIDMax = cID;
+      // }
+      // if (cE > cEnextMax && cE < cEMax)
+      // {
+      //   cEnextMax = cE;
+      //   cIDnextMax = cID;
+      // }
+
+      // This section of code is used to find the cathodes are correlated with the max and next max anodes, as well as to figure out if there are any common cathodes
+      // the anodes are correlated with the cathodes +/-3 from the anode number in the reverse order
+      // bool corr = false;
+          hAVCcoin->Fill(aIDMax, cID);
+      for (int j = -4; j < 3; j++)
+      {
+        if ((aIDMax + 24 + j) % 24 == 23 - cID) /* the 23-cID is used to accomodate for the fact that the order of the cathodes was reversed relative top the physical geometry */
+        {
+          corrcatMax.push_back(std::pair<int, double>(cID, cE));
+          // printf("Max Anode : %d Correlated Cathode : %d Anode Energy : %f z value : %f \n", aIDMax, cID, cESum, Crossover[aIDMax][cID][1].z /*prints alpha*/);
+          // std::cout << " Cathode iD : " << cID << " Energy : " << cE << std::endl;
+          cESum += cE;
+          // corr = true;
        }
-        else {
-          cE = E[l].second + cE;
+        // if ((aIDnextMax + 24 + j) % 24 == cID)
+        // {
+        //   corrcatnextMax.push_back(std::pair<int, double>(cathode.first, cathode.second));
+        //   std::sort(corrcatMax.begin(), corrcatMax.end(), [](const std::pair<int, double> &a, const std::pair<int, double> &b)S
+        //             { return a.second > b.second; });
+        // }
+        // for (int k = 0; k < 5; k++)
+        // {
+        //   if ((aIDMax + 24 + j) % 24 == (aIDnextMax + 24 + k) % 24)
+        //   {
+        //     commcat.push_back(std::pair<int, double>(cathode.first, cathode.second));
+        //   }
+        // }
+      }
+      // if (!corr)
+      // {
+      //   hUncorrCAN->Fill(aIDMax, cID);
+      // }
+    }
+
+    TVector3 anodeIntersection;
+    anodeIntersection.Clear();
+    // Implementing a method for PC reconstruction using a single Anode event
+    // if (anodeHits.size() == 1)
+    {
+      float x, y, z = 0;
+      for (const auto &corr : corrcatMax)
+      {
+        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;
+          // printf("Max Anode : %d Correlated Cathode : %d cathode Energy : %f cESum Energy : %f z value : %f \n", aIDMax, corr.first, corr.second, cESum, Crossover[aIDMax][corr.first][1].z /*prints alpha*/);
+        }
+        else
+        {
+          printf("Warning: No valid cathode hits to correlate with anode %d! \n", aIDMax);
        }
      }
+      anodeIntersection = TVector3(x, y, z);
+      // std::cout << "Anode Intersection " << anodeIntersection.Z() << " " << x << " " << y << " " << z << std::endl;
+    }
+
+    // Filling the PC Z projection histogram
+    // std::cout << anodeIntersection.Z() << std::endl;
+    hPCZProj->Fill(anodeIntersection.Z());
+
    // }
-  // }
-    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];
+
+    // 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(aEMax, cESum);
+    // }
+
+    // if (sx3ecut)
+    // {
+    hCat4An->Fill(corrcatMax.size());
+    hNosvAe->Fill(corrcatMax.size(), aEMax);
+    hAnodehits->Fill(anodeHits.size());
+    // }
+
+    // }
+    if (anodeHits.size() < 1)
+    {
+      hCat0An->Fill(cathodeHits.size());
    }

-    if( HitNonZero){
-      pw_contr.CalTrack( hitPos, aID, cID);
-      hZProj->Fill(pw_contr.GetZ0());
-    }
-
-  
+    // if (HitNonZero)
+    // {
+    //   pw_contr.CalTrack(hitPos, aID, cID);
+    //   hZProj->Fill(pw_contr.GetZ0());
+    // }
  }
-  

+  // ########################################################### Track constrcution

-  //########################################################### Track constrcution
-
-
-  //############################## DO THE KINEMATICS
-
+  // ############################## DO THE KINEMATICS

  return kTRUE;
 }

-void Analyzer::Terminate(){
+void Analyzer::Terminate()
+{

  gStyle->SetOptStat("neiou");
-  TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
-  canvas->Divide(3,3);
+  TCanvas *canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000);
+  canvas->Divide(3, 3);

-  //hsx3VpcIndex->Draw("colz");
+  // hsx3VpcIndex->Draw("colz");

  //=============================================== pad-1
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

  hsx3IndexVE->Draw("colz");

  //=============================================== pad-2
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

  hqqqIndexVE->Draw("colz");

  //=============================================== pad-3
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

  hpcIndexVE->Draw("colz");

  //=============================================== pad-4
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

  hsx3Coin->Draw("colz");

  //=============================================== pad-5
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  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);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

  hpcCoin->Draw("colz");

  //=============================================== pad-7
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

-  // hsx3VpcIndex ->Draw("colz"); 
-  hsx3VpcE->Draw("colz") ;
+  // hsx3VpcIndex ->Draw("colz");
+  hsx3VpcE->Draw("colz");

  //=============================================== pad-8
-  padID ++; canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
+  padID++;
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);

-  // hqqqVpcIndex ->Draw("colz");  
+  // hqqqVpcIndex ->Draw("colz");

-  hqqqVpcE ->Draw("colz");
+  hqqqVpcE->Draw("colz");
  //=============================================== pad-9
-  padID ++; 
+  padID++;

  // canvas->cd(padID)->DrawFrame(-50, -50, 50, 50);
  // hqqqPolar->Draw("same colz pol");

- canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-//  hZProj->Draw();
+  canvas->cd(padID);
+  canvas->cd(padID)->SetGrid(1);
+  //  hZProj->Draw();
  hanVScatsum->Draw("colz");

+  // TFile *outRoot = new TFile("Histograms.root", "RECREATE");
+
+  // if (!outRoot->IsOpen())
+  // {
+  //   std::cerr << "Error opening file for writing!" << std::endl;
+  //   return;
+  // }
+
+  // // Loop through histograms and write them to the ROOT file
+  // for (int i = 0; i < 48; i++)
+  // {
+  //   if (hPC_E[i] != nullptr)
+  //   {
+  //     hPC_E[i]->Write(); // Write histogram to file
+  //   }
+  // }
+
+  // outRoot->Close();
 }
--- a/Analyzer.h
+++ b/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);
+

 }

--- a/Analyzer1.C
+++ b/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");
+
+}
--- a/Analyzer1.h
+++ b/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
--- a/Armory/ClassPW.h
+++ b/Armory/ClassPW.h
@ -4,15 +4,18 @@
 #include <cstdio>
 #include <TMath.h>
 #include <TVector3.h>
+#include <TRandom.h>

-struct PWHitInfo{
-  std::pair<short, short>   nearestWire; // anode, cathode
+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<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;
@ -24,40 +27,56 @@ struct PWHitInfo{
  }
 };

-//!########################################################
-class PW{ // proportional wire
-public: 
-  PW(){ ClearHitInfo();};
-  ~PW(){};
+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
+  }
+};

-  PWHitInfo GetHitInfo() const {return hitInfo;}
-  std::pair<short, short>   GetNearestID()          const {return hitInfo.nearestWire;}
-  std::pair<double, double> GetNearestDistance()    const {return hitInfo.nearestDist;}
-  std::pair<short, short>   Get2ndNearestID()       const {return hitInfo.nextNearestWire;}
-  std::pair<double, double> Get2ndNearestDistance() const {return hitInfo.nextNearestDist;}
+//! ########################################################
+class PW
+{ // proportional wire
+public:
+  PW() { ClearHitInfo(); };
+  ~PW() {};

-  TVector3 GetTrackPos() const {return trackPos;}
-  TVector3 GetTrackVec() const {return trackVec;}
-  double GetTrackTheta() const {return trackVec.Theta();}
-  double GetTrackPhi()   const {return trackVec.Phi();}
+  PWHitInfo GetHitInfo() const { return hitInfo; }
+  std::pair<short, short> GetNearestID() const { return hitInfo.nearestWire; }
+  std::pair<double, double> GetNearestDistance() const { return hitInfo.nearestDist; }
+  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();

-  int GetNumWire() const {return nWire;}
-  double GetDeltaAngle() const {return dAngle;}
-  double GetAnodeLength() const {return anodeLength;}
-  double GetCathodeLength() const {return cathodeLength;}
-  TVector3 GetAnodeDn(short id) const {return An[id].first;}
-  TVector3 GetAnodeUp(short id) const {return An[id].second;}
-  TVector3 GetCathodeDn(short id) const {return Ca[id].first;}
-  TVector3 GetCathodeUp(short id) const {return Ca[id].second;}
+  int GetNumWire() const { return nWire; }
+  double GetDeltaAngle() const { return dAngle; }
+  double GetAnodeLength() const { return anodeLength; }
+  double GetCathodeLength() const { return cathodeLength; }
+  TVector3 GetAnodeDn(short id) const { return An[id].first; }
+  TVector3 GetAnodeUp(short id) const { return An[id].second; }
+  TVector3 GetCathodeDn(short id) const { return Ca[id].first; }
+  TVector3 GetCathodeUp(short id) const { return Ca[id].second; }

-  TVector3 GetAnodneMid(short id)  const {return (An[id].first + An[id].second) * 0.5; }
-  double   GetAnodeTheta(short id) const {return (An[id].first - An[id].second).Theta();}
-  double   GetAnodePhi(short id)   const {return (An[id].first - An[id].second).Phi();}
+  TVector3 GetAnodneMid(short id) const { return (An[id].first + An[id].second) * 0.5; }
+  double GetAnodeTheta(short id) const { return (An[id].first - An[id].second).Theta(); }
+  double GetAnodePhi(short id) const { return (An[id].first - An[id].second).Phi(); }

-  TVector3 GetCathodneMid(short id)  const {return (Ca[id].first + Ca[id].second) * 0.5; }
-  double   GetCathodeTheta(short id) const {return (Ca[id].first - Ca[id].second).Theta();}
-  double   GetCathodePhi(short id)   const {return (Ca[id].first - Ca[id].second).Phi();}
+  TVector3 GetCathodneMid(short id) const { return (Ca[id].first + Ca[id].second) * 0.5; }
+  double GetCathodeTheta(short id) const { return (Ca[id].first - Ca[id].second).Theta(); }
+  double GetCathodePhi(short id) const { return (Ca[id].first - Ca[id].second).Phi(); }

  void ClearHitInfo();
  void ConstructGeo();
@ -65,22 +84,20 @@ public:
  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);

-  double CircularMean(std::vector<std::pair<int, double>> wireList);
+  void Print()
+  {
+    printf("     The nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nearestWire.first,
+           hitInfo.nearestDist.first,
+           hitInfo.nearestWire.second,
+           hitInfo.nearestDist.second);

-  void Print(){
-    printf("     The nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nearestWire.first, 
-                                                                         hitInfo.nearestDist.first, 
-                                                                         hitInfo.nearestWire.second, 
-                                                                         hitInfo.nearestDist.second);
-
-    printf(" The 2nd nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nextNearestWire.first, 
-                                                                         hitInfo.nextNearestDist.first, 
-                                                                         hitInfo.nextNearestWire.second, 
-                                                                         hitInfo.nextNearestDist.second);
+    printf(" The 2nd nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nextNearestWire.first,
+           hitInfo.nextNearestDist.first,
+           hitInfo.nextNearestWire.second,
+           hitInfo.nextNearestDist.second);
  }

 private:
-
  PWHitInfo hitInfo;

  TVector3 trackPos;
@ -88,7 +105,7 @@ private:

  const int nWire = 24;
  const int wireShift = 3;
-  const float zLen = 380; //mm
+  const float zLen = 380; // mm
  const float radiusA = 37;
  const float radiusC = 43;

@ -96,23 +113,25 @@ 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>> Ca; // the cathode 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

-  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));
-  } 
-
+    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();
@ -120,108 +139,136 @@ inline void PW::ConstructGeo(){
  std::pair<TVector3, TVector3> p1; // anode
  std::pair<TVector3, TVector3> q1; // cathode

-  //anode and cathode start at pos-Y axis and count in right-Hand
-  //anode wire shift is right-hand.
-  //cathode wire shift is left-hand.
+  // anode and cathode start at pos-Y axis and count in right-Hand
+  // 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()),
-                    zLen/2);
-    p1.second.SetXYZ( radiusA * TMath::Cos( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
-                      radiusA * TMath::Sin( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
-                    -zLen/2);
+    p1.first.SetXYZ(radiusA * TMath::Cos(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    radiusA * TMath::Sin(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    zLen / 2);
+    p1.second.SetXYZ(radiusA * TMath::Cos(TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+                     radiusA * TMath::Sin(TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+                     -zLen / 2);
    An.push_back(p1);

    // Cathod rotate left-hand
-    q1.first.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
-                    zLen/2);
-    q1.second.SetXYZ( radiusC * TMath::Cos( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
-                      radiusC * TMath::Sin( TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
-                      -zLen/2);
+    q1.first.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i) + TMath::PiOver2()),
+                    zLen / 2);
+    q1.second.SetXYZ(radiusC * TMath::Cos(TMath::TwoPi() / nWire * (i - wireShift) + TMath::PiOver2()),
+                     radiusC * TMath::Sin(TMath::TwoPi() / nWire * (i - wireShift) + 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
+  std::rotate(Ca.rbegin(), Ca.rbegin() + 3, 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) );
+  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));
 }

-inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
+inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose)
+{

  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 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 )  phiS = phiS - TMath::TwoPi();
+    if (phi > 0 && phiS > phiL)
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();

-    if( phiS < phi && phi < phiL) {
-      disA = Distance( pos, pos + direction, An[i].first, An[i].second);
-      if( disA < hitInfo.nearestDist.first ){
+    if (phiS < phi && phi < phiL)
+    {
+      disA = Distance(pos, pos + direction, An[i].first, An[i].second);
+      if (disA < hitInfo.nearestDist.first)
+      {
        hitInfo.nearestDist.first = disA;
        hitInfo.nearestWire.first = i;
      }
    }

    double disC = 99999999;
-    phiS = Ca[i].second.Phi()- TMath::PiOver4();
+    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( phi < 0 && phiS > phiL ) phiS = phiS - TMath::TwoPi();
+    if (phi > 0 && phiS > phiL)
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();

-    if(phiS < phi && phi < phiL) {
-      disC = Distance( pos, pos + direction, Ca[i].first, Ca[i].second);
-      if( disC < hitInfo.nearestDist.second ){
+    if (phiS < phi && phi < phiL)
+    {
+      disC = Distance(pos, pos + direction, Ca[i].first, Ca[i].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 aaa2 = (anode1 + 1) % 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){
+  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)
+  {
    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 ccc2 = (cathode1 + 1) % 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){
+  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)
+  {
    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 +278,12 @@ 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 +315,19 @@ 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 double PW::GetZ0()
+{

  double x = trackPos.X();
  double y = trackPos.Y();
-  double rho = TMath::Sqrt(x*x + y*y);
+  double rho = TMath::Sqrt(x * x + y * y);
  double theta = trackVec.Theta();
-  
+
  return trackPos.Z() - rho / TMath::Tan(theta);
-
 }

-inline double PW::CircularMean(std::vector<std::pair<int, double>> wireList){
-
-  //use unit vector, wireID start from Zero
-  double xCom = 0, yCom = 0;
-  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;
-
-}
-
-#endif 
+#endif
--- a/FitHistogramsWithTSpectrum_Sequential_Improved.C
+++ b/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;
+}
+
--- a/MatchAndPlotCentroids.C
+++ b/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;
+}
--- a/PCGainMatch.C
+++ b/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();
+}
--- a/PCGainMatch.h
+++ b/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
--- a/ProcessRun.sh
+++ b/ProcessRun.sh
@ -1,7 +1,8 @@
 #!/bin/bash

-if [ "$#" -ne 2 ]; then
-    echo "Usage: $0 runID timeWindow_ns"
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 runID timeWindow_ns option"
+    echo "option: 0 - process raw data, 1 - process mapped data"
    echo "Exiting..."
    exit 1
 fi
@ -9,19 +10,24 @@ fi
 runID=$1
 timeWindow=$2

-rawFolder=/home/tandem/Desktop/analysis/data
-rootFolder=/home/tandem/Desktop/analysis/data/root_data
+option=$3

-rsync -a splitpole@128.186.111.223:/media/nvmeData/ANASEN27Alap/*.fsu /home/tandem/Desktop/analysis/data
+rawFolder=/home/tandem/data1/2024_09_17Fap/data
+rootFolder=../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

-outFile=${rawFolder}/*${runID}*${timeWindow}.root
+    fileList=`\ls -1 ${rawFolder}/*Run_${runID}_*.fsu`

-mv -vf ${outFile} ${rootFolder}/.
+    ./EventBuilder ${timeWindow} 0 0 100000000 ${fileList}

-./Mapper ${rootFolder}/*${runID}*${timeWindow}.root
+    outFile=${rawFolder}/*${runID}*${timeWindow}.root

-root "processRun.C(\"${rootFolder}/Run_${runID}_mapped.root\")"
+    mv -vf ${outFile} ${rootFolder}/.
+
+    ./Mapper ${rootFolder}/*${runID}*${timeWindow}.root
+fi
+
+root "processRun.C(\"${rootFolder}/ProtonRun_${runID}_mapped.root\")"
--- a/centroids.txt
+++ b/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
--- a/centroids_edited.txt
+++ b/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
--- a/mapping.h
+++ b/mapping.h
@ -19,21 +19,23 @@ const std::map<int, unsigned short> board = {
   {4, 22129},
   {5, 15529},
   {6, 15528},
+  //  {7,89},
   {7,   334},
   {8,   379},
   {9,   325},
-   {10,  405}
+   {10,  405} 
 };
 const int nBd = board.size();

 const int nV1740 = 7;
-const int nV1725 = 3;
+const int nV1725 = 4;

 //+++++++++++++++++++ detID;
 // The detectors are seperated into 2 type: SuperX3, QQQ, and PC
 // the SuperX3 has 24 detectors for each kind, wach detector has 12 channels
 // the QQQ has 4 detectors for each kind, each detector has 32 channels
 // the PC has 2 types, anode and cathode, each has 24 channels
+// the MISC has 6 channels, the lollipop IC and siliscon followed by the hotneedle IC, as well as the Rf and MCP
 // The detID = Type * 10000 + index * 100 + channel
 // fro example, detID(superX3-8, ch-7) = 00807

@ -76,17 +78,23 @@ const std::vector<int> mapping = {
    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
+ //================== 89
+  //  0     1      2      3      4      5      6      7      8      9     10     11     12     13     14     15
+//  30004,    -1, 30003,    -1,    -1,    -1,    -1,    -1,     -1,   -1,    -1,    -1,    -1,    -1,    -1,    -1,
  //================== 334
- 20116, 20117, 20118, 20119, 20120, 20121, 20122, 20123, 20016, 20017, 20018, 20019, 20020, 20021, 20022, 20023,
+ 20116, 20117, 20118, 20119,    -1, 20121, 20122, 20123, 20016, 20017, 20018,    -1, 20020, 20021, 20022, 20023,
  //================== 379
- 20000, 20001, 20002, 20003, 20004, 20005,    -1, 20007, 20008,    -1, 20010, 20011, 20012, 20013, 20014, 20015,
+  -1  , 20001, 20002, 20003, 20004, 20005,    -1, 20007, 20008,    -1, 20010, 20011, 20012, 20013, 20014, 20015,
  //================== 325
- 20100, 20101, 20102, 20103, 20104, 20105, 20106, 20107, 20108, 20109, 20110, 20111, 20112, 20113, 20114, 20115,
+ 20100, 20101, 20102, 20103, 20104, 20105, 20106, 20107, 20108, 20109, 20110, 20111, 20112,    -1, 20114, 20115,
  //================== 405
- 20006,    -1,    -1, 20009,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1
-
+  //  0     1      2      3      4      5      6      7      8      9     10     11     12     13     14     15
+ 20006,    -1, 30005, 20009,    -1, 20120, 20000, 20019, 20113, 30000, 30004, 30001, 30002,    -1, 30003,   -1
 };

+//MCP moved from channel 1 to 2 after Run number 322
+//MCP and Rf moved to ch 0 and 1 after Run number after Run282
+//moved back to ch 
 void PrintMapping(){

  int digiID = 0;
@ -141,8 +149,9 @@ void PrintMapping(){

        printf("\033[35m%3d(%2d)\033[0m|", detID, ch);
        
-      }else{
+      }else if( typeID == 3){ // MISC

+        printf("\033[33m%3d(%2d)\033[0m|", detID, ch);

      }
    }
@ -215,7 +224,6 @@ void GenMapping(std::string mapFile){
      detID += 20000;
      if( words[3] == "ANODE") detID += atoi(words[4].c_str());
      if( words[3] == "CATHODE") detID += 100 + atoi(words[4].c_str());
-
    }

    if( words[2] == "blank") {
--- a/slope_intercept_cathode.txt
+++ b/slope_intercept_cathode.txt
@ -0,0 +1,23 @@
+Histogram Number	Slope	Intercept
+24	1	-2.89219e-10
+25	0.942098	-0.105169
+26	0.980862	-0.732032
+27	0.982975	-2.22704
+28	0.978815	-1.51477
+29	0.965245	-2.19515
+30	0.945384	-0.892599
+31	0.977408	-0.908592
+32	0.919546	3.25464
+33	0.972194	2.44956
+34	0.92852	5.44745
+35	0.947098	1.40531
+36	0.875491	-1.13145
+37	1.95496	-1735.58
+38	0.970862	2.86019
+40	0.91793	-3.80615
+41	0.913897	-2.12964
+42	0.954014	-0.760604
+43	0.993616	-1.40278
+45	0.926169	-21.2016
+46	1.00577	-2.14281
+47	0.943312	-1.26464
--- a/slope_intercept_results.txt
+++ b/slope_intercept_results.txt
@ -0,0 +1,49 @@
+Histogram Number	Slope	Intercept
+0	0.931015	-1.35431
+1	1	-1.87356e-10
+2	0.964185	1.49989
+3	0.92638	-1.30621
+4	0.905569	1.00834
+5	0.901182	0.470903
+6	0.853932	3.32687
+7	0.942785	1.08887
+8	0.878904	-0.0107433
+9	0.922662	-2.32259
+10	0.903343	8.38332
+11	0.914227	6.56108
+12	0.961008	23.0982
+13	0.920976	5.22104
+14	0.936584	31.5073
+15	0.959044	5.43267
+16	0.95263	-0.404053
+17	0.90953	4.82833
+18	0.940277	10.3629
+19	0.86746	-17.8678
+20	1.00683	4.76371
+21	0.968342	-43.9496
+22	0.892882	-32.0742
+23	0.933615	1.10704
+24	1	-2.89219e-10
+25	0.942098	-0.105169
+26	0.980862	-0.732032
+27	0.982975	-2.22704
+28	0.978815	-1.51477
+29	0.965245	-2.19515
+30	0.945384	-0.892599
+31	0.977408	-0.908592
+32	0.919546	3.25464
+33	0.972194	2.44956
+34	0.92852	5.44745
+35	0.947098	1.40531
+36	0.875491	-1.13145
+37	1	0
+38	0.970862	2.86019
+39	1	0
+40	0.91793	-3.80615
+41	0.913897	-2.12964
+42	0.954014	-0.760604
+43	0.993616	-1.40278
+44	1	0
+45	0.926169	-21.2016
+46	1.00577	-2.14281
+47	0.943312	-1.26464
--- a/slope_intercept_results_anode.txt
+++ b/slope_intercept_results_anode.txt
@ -0,0 +1,21 @@
+Histogram Number	Slope	Intercept
+1	1	-1.87356e-10
+2	0.964185	1.49989
+3	0.92638	-1.30621
+4	0.905569	1.00834
+5	0.901182	0.470903
+7	0.942785	1.08887
+8	0.878904	-0.0107433
+10	0.903343	8.38332
+11	0.914227	6.56108
+12	0.961008	23.0982
+13	0.920976	5.22104
+14	0.936584	31.5073
+15	0.959044	5.43267
+16	0.95263	-0.404053
+17	0.90953	4.82833
+18	0.940277	10.3629
+20	1.00683	4.76371
+21	0.968342	-43.9496
+22	0.892882	-32.0742
+23	0.933615	1.10704
Author	SHA1	Message	Date
Vignesh Sitaraman	2225b3a942	modified: .gitignore	2025-02-17 17:06:33 -05:00
Vignesh Sitaraman	6cfb38b564	modified: Analyzer.C	2025-02-17 17:03:58 -05:00
Vignesh Sitaraman	cb72c14ca4	modified: Analyzer.C modfied the algorithm for selection of valid cathodes, the section is now based on geometry modified: Armory/ClassPW.h the rotation of the cathodes was reversed	2025-02-17 16:59:08 -05:00
Vignesh Sitaraman	5995081396	modified: Analyzer.C modified: Armory/ClassPW.h adjusted the Cathode geometry to incorporate the offsett of 3 wires	2025-02-05 14:59:02 -05:00
Vignesh Sitaraman	d623e0cd17	modified: Analyzer.C made changes to correct for geomtry and eliminating redundant variables to a make the code more readable modified: Armory/ClassPW.h made changes to correct for the fact that the physical geometry of the detector is not the same as the geometry in the simulation, it is reversed and has an offset of 3	2025-02-05 08:23:23 -05:00
Vignesh Sitaraman	8d7322cf5a	modified: Analyzer.C	2025-02-03 10:32:07 -05:00
Vignesh Sitaraman	699b0f8701	modified: Analyzer.C HPZProjection implemented, testing seems to result in a plot with 0s. Need to debug	2025-01-31 09:25:37 -05:00
Vignesh Sitaraman	02213caaee	modified: Analyzer.C implementation of function to fgiure out the cqreelated cathodes in events	2025-01-28 10:19:14 -05:00
Vignesh Sitaraman	56a6389b4f	modified: Analyzer.C modified the analyser to include gain matching for the anodes and the cathodes modified: FitHistogramsWithTSpectrum_Sequential_Improved.C modified: MatchAndPlotCentroids.C modified: centroids.txt modified: slope_intercept_results.txt	2025-01-27 16:34:39 -05:00
Vignesh Sitaraman	b99ad4e4d7	new file: FitHistogramsWithTSpectrum_Sequential_Improved.C new file: MatchAndPlotCentroids.C new file: centroids.txt new file: centroids_edited.txt new file: slope_intercept_cathode.txt new file: slope_intercept_results.txt new file: slope_intercept_results_anode.txt	2025-01-27 15:11:27 -05:00
Vignesh Sitaraman	a5dfa2ecd3	modified: .vscode/settings.json modified: Analyzer.C modified: Analyzer.h modified: ProcessRun.sh	2025-01-27 10:55:22 -05:00
Vignesh Sitaraman	26e943adc8	modified: .vscode/settings.json modified: Analyzer.C	2025-01-27 09:51:25 -05:00
vs19g	42e093b104	modified: .vscode/c_cpp_properties.json modified: .vscode/settings.json modified: Analyzer.C new file: Armory/#ClassPW.h# modified: Armory/ClassDet.h modified: Armory/ClassPW.h modified: Armory/Mapper.cpp	2025-01-17 11:18:07 -05:00
dirac	3129339647	modified: Analyzer.C modified: ProcessRun.sh modified: mapping.h	2024-11-05 08:48:21 -05:00
dirac	7a70340b18	modified: Analyzer.C modified: mapping.h	2024-10-30 09:28:01 -04:00
dirac	a10081ea81	modified: .vscode/settings.json modified: Analyzer.C modified: Analyzer.h modified: Armory/ClassDet.h modified: Armory/ClassPW.h modified: Armory/Mapper.cpp modified: PCGainMatch.C modified: ProcessRun.sh modified: mapping.h	2024-10-25 15:02:59 -04:00
vs19g	4cb8a2c48c	new file: Analyzer1.C new file: Analyzer1.h	2024-10-04 12:43:24 -04:00
vs19g	fe6dbee171	Refactor PCGainMatch.C and Analyzer.C for improved efficiency and readability	2024-10-01 14:13:53 -04:00
vs19g	7805481ead	Refactor PCGainMatch.C and Analyzer.C for improved efficiency and readability	2024-09-16 10:25:13 -04:00
vs19g	511b4aa808	modified: PCGainMatch.C	2024-09-06 15:06:32 -04:00
vs19g	43233ceb02	modified: PCGainMatch.C	2024-09-06 14:32:22 -04:00
vs19g	68fc36a8f6	modified: PCGainMatch.C	2024-09-03 16:41:17 -04:00
vs19g	a6e754b958	modified: Analyzer.C new file: PCGainMatch.C new file: PCGainMatch.h	2024-08-28 10:49:36 -04:00
vs19g	48ede97992	modified: Analyzer.C implemented cuts and histograms for the 2D histograms	2024-08-26 11:41:06 -04:00
vs19g	f0a393abe2	modified: Analyzer.C	2024-08-26 10:34:13 -04:00
vs19g	4ba9c73b98	modified: Analyzer.C	2024-08-26 10:33:29 -04:00
vs19g	238ec8961e	modified: Analyzer.C	2024-08-26 10:33:29 -04:00