modified: TrackRecon.C

modified:   anasen_fem/wires2d.sif
	modified:   run_tr.sh

.gitignore

@@ -1,12 +1,40 @@
-EventBuilder*
 *.d
 *.so
 *.pcm
 *.root
 *.exe
-
+*.txt
+*.err
+*.seq
+*.png
+*.gif
+*.msh
+*.vtk
 Mapper
 AnasenMS
 
 data/
 data_proton/
+Sudarshan/
+wires2d/
+myenv/
+Analyzer_C_ACLiC_dict0713aaa966_dictContent.h
+.gitignore
+Analyzer_C_ACLiC_dict5411fecd5c_dictUmbrella.h
+gainmatch.C
+gainmatch.h
+MakePlotsQQQ.C
+MakePlotsQQQ.h
+MakePlotsSX3.C
+MakePlotsSX3.h
+Armory/CorrelateQQQ.h
+QQQStage2.C
+anasen_fem/scalars.dat.names
+anasen_fem/He96_CO2_4_260Torr.gas
+anasen_fem/heavy_ion_track.csv
+Armory/EventBuilder
+EventBuilder
+anasen_fem/anode_to_cathode_1d_17.43.csv
+pc_calib_raw/
+AutoFit.C
+scratch/images/WedgeChVAnode.jpeg

.vscode/c_cpp_properties.json

@@ -1,23 +1,11 @@
 {
     "configurations": [
         {
-            "name": "splitpole",
+            "name": "Hades",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/home/splitpole/cern/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
-            ],
+                "/usr/local/cern/root_v6.26.06/include/**"
-            "defines": [],
-            "compilerPath": "/usr/bin/gcc",
-            "cStandard": "c17",
-            "cppStandard": "gnu++17",
-            "intelliSenseMode": "linux-gcc-x64"
-        },
-        {
-            "name": "Ryan",
-            "includePath": [
-                "${workspaceFolder}/**",
-                "/home/ryan/Downloads/root_build/**",
-                "/home/ryan/Downloads/root_build/include"
             ],
             "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 +40,39 @@
             "intelliSenseMode": "linux-gcc-x64"
         },
         {
-            "name": "Dirac",
+            "name": "Splitpole",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/usr/opt/root/**"
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/home/splitpole/cern/root/include/**",
+                "/usr/include/x86_64-linux-gnu/qt6/QtWidgets",
+                "/usr/include/x86_64-linux-gnu/qt6/QtCore"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "Penguin",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/usr/include/x86_64-linux-gnu/qt6/**",
+                "/usr/local/cern/root/include/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        },
+        {
+            "name": "VigneshROG",
+            "includePath": [
+                "/home/vsitaraman/**",
+                "${workspaceFolder}/**",
+                "/home/vsitaraman/root/include/**"
             ],
             "defines": [],
             "compilerPath": "/usr/bin/gcc",

.vscode/settings.json

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

Analysis.C

@@ -1,20 +0,0 @@
-#include "TChain.h"
-#include <iostream>
-
-
-
-void Analysis(int start, int end) {
-    // Create a TChain
-    TChain *chain = new TChain("tree");
-    for(int i = start; i < end+1; i++) {
-        chain->Add(Form("data/root_data/Run_%03d_mapped.root", i));
-    }
-
-    // Process the chain using Analyzer.C+
-    chain->Process("Analyzer.C+");
-}
-
-// Define a macro with the same name as the script
-void Analysis() {
-    Analysis(72, 194); // Adjust the range if needed
-}

Armory/ANASEN_model.C

@@ -42,7 +42,7 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
   //--- making ANASEN
   const int nWire = 24;
   const int wireShift = 3;
-  const int zLen = 300; //mm
+  const int zLen = 350; //mm
   const int radiusA = 38;
   const int radiusC = 43;
 
@@ -103,8 +103,8 @@ void ANASEN_model(int anodeID1 = -1, int anodeID2 = -1, int cathodeID1 = -1, int
                                                        new TGeoRotation("rot1", 360/nSX3 * (i + 0.5), 0., 0.)));
   }
 
-  const int qqqR1 = 10;
+  const int qqqR1 = 50;
-  const int qqqR2 = 50;
+  const int qqqR2 = 100;
   TGeoVolume *qqq = geom->MakeTubs("qqq", Al, qqqR1, qqqR2, 0.5, 5, 85);
   qqq->SetLineColor(7);
   for( int i = 0; i < 4; i++){

Armory/ClassDet.h

@@ -5,60 +5,67 @@
 
 #define MAXMULTI 1000
 
-class Det{
+class Det
+{
 public:
-  Det(): multi(0) {Clear(); }
+  Det() : multi(0) { Clear(); }
 
-  unsigned short       multi; // max 65535
+  unsigned short multi; // max 65535
-  unsigned short       id[MAXMULTI];
+  unsigned short id[MAXMULTI];
-  unsigned short       ch[MAXMULTI];
+  unsigned short ch[MAXMULTI];
-  unsigned short       e[MAXMULTI];
+  unsigned short e[MAXMULTI];
-  unsigned long long   t[MAXMULTI];
+  unsigned long long t[MAXMULTI];
+  unsigned long long tf[MAXMULTI];
 
-  unsigned short         sn[MAXMULTI];
+  unsigned short sn[MAXMULTI];
-  unsigned short     digiCh[MAXMULTI];
+  unsigned short digiCh[MAXMULTI];
 
-  unsigned short  index[MAXMULTI]; // id * nCh + ch;
+  unsigned short index[MAXMULTI]; // id * nCh + ch;
-  bool  used[MAXMULTI];
+  bool used[MAXMULTI];
 
-  void Clear(){
+  void Clear()
+  {
     multi = 0;
-    for( int i = 0; i < MAXMULTI; i++){
+    for (int i = 0; i < MAXMULTI; i++)
+    {
       id[i] = 0;
       ch[i] = 0;
-       e[i] = 0;
+      e[i] = 0;
-       t[i] = 0;
+      t[i] = 0;
-       index[i] = 0;
+      tf[i] = 0;
-       sn[i] = 0;
+      index[i] = 0;
-       digiCh[i] = 0;
+      sn[i] = 0;
-       used[i] = false;
+      digiCh[i] = 0;
+      used[i] = false;
     }
   }
 
-  void Print(){
+  void Print()
+  {
     printf("=============================== multi : %u\n", multi);
-    for( int i = 0; i < multi; i++) {
+    for (int i = 0; i < multi; i++)
-      printf(" %3d | %2d-%-2d(%5d) %5u %15llu \n", i, id[i], ch[i], index[i], e[i], t[i]);
+    {
+      printf(" %3d | %2d-%-2d(%5d) %5u %15llu %15llu \n", i, id[i], ch[i], index[i], e[i], t[i], tf[i]);
     }
   }
 
-  void SetDetDimension(unsigned short maxID, unsigned maxCh){
+  void SetDetDimension(unsigned short maxID, unsigned maxCh)
+  {
     nID = maxID;
     nCh = maxCh;
   }
 
-  void CalIndex(){
+  void CalIndex()
-    for( int i = 0; i < multi; i++){
+  {
-      index[i] = id[i] * nCh + ch[i] ;
+    for (int i = 0; i < multi; i++)
+    {
+      index[i] = id[i] * nCh + ch[i];
     }
   }
 
 private:
-
   unsigned short nID;
   unsigned short nCh;
-
 };
 
-
+#endif
-#endif 

Armory/ClassPC1An.h

@@ -1,246 +0,0 @@
-#ifndef ClassPC_h
-#define ClassPC_h
-
-#include <cstdio>
-#include <TMath.h>
-#include <TVector3.h>
-#include <TRandom.h>
-
-struct PCHit_1An{
-  std::pair<short, short>   nearestWire; // anode, cathode
-  std::pair<double, double> nearestDist; // anode, cathode
-
-  short   nextNearestWire; // cathode
-  double nextNearestDist; // cathode
-
-  void Clear(){
-    nearestWire.first = -1;
-    nearestWire.second = -1;
-    nearestDist.first = 999999999;
-    nearestDist.second = 999999999;
-    nextNearestWire= -1;
-    nextNearestDist = 999999999;
-  }
-};
-
-//!########################################################
-class PC{ // proportional wire
-public: 
-  PC(){ ClearHitInfo();};
-  ~PC(){};
-  
-  PCHit_1An GetHitInfo() const {return hitInfo;}
-  std::pair<short, short>   GetNearestID()          const {return hitInfo.nearestWire;}
-  std::pair<double, double> GetNearestDistance()    const {return hitInfo.nearestDist;}
-  short   Get2ndNearestID()       const {return hitInfo.nextNearestWire;}
-  double Get2ndNearestDistance() const {return hitInfo.nextNearestDist;}
-
-  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;}
-
-  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();}
-
-  void ClearHitInfo();
-  void ConstructGeo();
-  void FindWireID(TVector3 pos, TVector3 direction, bool verbose = false);
-  void CalTrack3(TVector3 sx3Pos, PCHit_1An hitInfo, double sigmaA = 0, double sigmaC = 0, bool verbose = false);
-
-  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 Cathode: %2d(%5.2f)\n", hitInfo.nextNearestWire, 
-                                                     hitInfo.nextNearestDist);
-  }
-
-private:
-
-  // PCHitInfo hitInfo;
-  PCHit_1An hitInfo;
-
-  TVector3 trackPos;
-  TVector3 trackVec;
-
-  const int nWire = 24;
-  const int wireShift = 3;
-  const float zLen = 380; //mm
-  const float radiusA = 37;
-  const float radiusC = 43;
-
-  double dAngle;
-  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 
-
-  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2){
-    TVector3 na = a1 - a2;
-    TVector3 nb = b1 - b2;
-    TVector3 nd = (na.Cross(nb)).Unit();
-    return TMath::Abs(nd.Dot(a1-b2));
-  } 
-
-};
-
-inline void PC::ClearHitInfo(){
-  hitInfo.Clear();
-}
-
-inline void PC::ConstructGeo(){
-
-  An.clear();
-  Ca.clear();
-
-  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.
-
-  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);
-    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);
-    Ca.push_back(q1);
-  }
-
-  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) );
-}
-
-inline void PC::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
-
-  hitInfo.Clear();
-  double phi = direction.Phi();
-
-  for( int i = 0; i < nWire; i++){
-
-    double disA = 99999999;
-    double phiS = An[i].first.Phi()  - TMath::PiOver4();
-    double phiL = An[i].second.Phi() + TMath::PiOver4();
-    // printf("A%2d: %f %f | %f\n", i, phiS * TMath::RadToDeg(), phiL * TMath::RadToDeg(), phi * TMath::RadToDeg());
-    if( phi > 0 && phiS > phiL )  phiL = phiL + TMath::TwoPi();
-    if( phi < 0 && phiS > phiL )  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 ){
-        hitInfo.nearestDist.first = disA;
-        hitInfo.nearestWire.first = i;
-      }
-    }
-
-    double disC = 99999999;
-    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(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);
-  }
-
-  short cathode1 = hitInfo.nearestWire.second;
-  short ccc1 = cathode1 - 1; if( ccc1 < 0 ) ccc1 += nWire;
-  short ccc2 = (cathode1 + 1) % nWire; 
-
-   double haha1 = Distance( pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
-   double haha2 = Distance( pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
-  if( haha1 < haha2){
-    hitInfo.nextNearestWire = ccc1;
-    hitInfo.nextNearestDist = haha1;
-  }else{
-    hitInfo.nextNearestWire = ccc2;
-    hitInfo.nextNearestDist= haha2;
-  }
-
-  if( verbose ) Print();
-}
-
-
-inline void PC::CalTrack3(TVector3 sx3Pos, PCHit_1An hitInfo, double sigmaA, double sigmaC, bool verbose){
-
-  trackPos = sx3Pos;
-
-  double p1 = TMath::Abs(hitInfo.nearestDist.first + gRandom->Gaus(0, sigmaA));
-  short anodeID1 = hitInfo.nearestWire.first;
-
-  double q1 = TMath::Abs(hitInfo.nearestDist.second + gRandom->Gaus(0, sigmaC));
-  double q2 = TMath::Abs(hitInfo.nextNearestDist+ gRandom->Gaus(0, sigmaC));
-  double fracC = q1 / (q1 + q2);
-  short cathodeID1 = hitInfo.nearestWire.second;
-  short cathodeID2 = hitInfo.nextNearestWire;
-  TVector3 shiftC1 = (Ca[cathodeID2].first - Ca[cathodeID1].first) * fracC;
-  TVector3 shiftC2 = (Ca[cathodeID2].second - Ca[cathodeID1].second) * fracC;
-
-  TVector3 a1 = An[anodeID1].first;
-
-  TVector3 c1 = Ca[cathodeID1].first + shiftC1;
-  TVector3 c2 = Ca[cathodeID1].second + shiftC2;
-
-  TVector3 n1 = (sx3Pos - a1).Unit();
-  TVector3 n2 = (c1 - c2).Cross((sx3Pos - c2)).Unit();
-
-  // 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()); 
-
-}
-
-inline double PC::GetZ0(){
-
-  double x = trackPos.X();
-  double y = trackPos.Y();
-  double rho = TMath::Sqrt(x*x + y*y);
-  double theta = trackVec.Theta();
-  
-  return trackPos.Z() - rho / TMath::Tan(theta);
-
-}
-
-#endif 

Armory/ClassPW.h

@@ -2,17 +2,21 @@
 #define ClassPW_h
 
 #include <cstdio>
+#include <iostream>
 #include <TMath.h>
 #include <TVector3.h>
+#include <TRandom.h>
 
-struct PWHitInfo{
+struct PWHitInfo
-  std::pair<short, short>   nearestWire; // anode, cathode
+{
+  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;
@@ -24,95 +28,125 @@ struct PWHitInfo{
   }
 };
 
-//!########################################################
+struct Coord
-class PW{ // proportional wire
+{
-public: 
+  float x, y, z;
-  PW(){ ClearHitInfo();};
+  Coord() : x(0), y(0), z(0) {}
-  ~PW(){};
+  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;}
+class PW
-  std::pair<double, double> GetNearestDistance()    const {return hitInfo.nearestDist;}
+{ // proportional wire
-  std::pair<short, short>   Get2ndNearestID()       const {return hitInfo.nextNearestWire;}
+public:
-  std::pair<double, double> Get2ndNearestDistance() const {return hitInfo.nextNearestDist;}
+  PW() { ClearHitInfo(); };
+  ~PW() {};
 
-  TVector3 GetTrackPos() const {return trackPos;}
+  PWHitInfo GetHitInfo() const { return hitInfo; }
-  TVector3 GetTrackVec() const {return trackVec;}
+  std::pair<short, short> GetNearestID() const { return hitInfo.nearestWire; }
-  double GetTrackTheta() const {return trackVec.Theta();}
+  std::pair<double, double> GetNearestDistance() const { return hitInfo.nearestDist; }
-  double GetTrackPhi()   const {return trackVec.Phi();}
+  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;}
+  Coord Crossover[24][24][2];
-  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; }
+  inline TVector3 getClosestWirePosAtWirePhi(std::pair<TVector3, TVector3>, double phi);
-  double   GetAnodeTheta(short id) const {return (An[id].first - An[id].second).Theta();}
+  inline TVector3 getClosestWirePosAtWirePhiOld(std::pair<TVector3, TVector3>, double phi);
-  double   GetAnodePhi(short id)   const {return (An[id].first - An[id].second).Phi();}
+  inline std::tuple<std::pair<TVector3, TVector3>, double, double, double> GetPseudoWire(const std::vector<std::tuple<int, double, double>> &cluster, std::string type);
 
-  TVector3 GetCathodneMid(short id)  const {return (Ca[id].first + Ca[id].second) * 0.5; }
+  inline std::tuple<TVector3, double, double, double, double, double, double, double>
-  double   GetCathodeTheta(short id) const {return (Ca[id].first - Ca[id].second).Theta();}
+  FindCrossoverProperties(const std::vector<std::tuple<int, double, double>> &a_cluster, const std::vector<std::tuple<int, double, double>> &c_cluster);
-  double   GetCathodePhi(short id)   const {return (Ca[id].first - Ca[id].second).Phi();}
+
+  inline std::vector<std::vector<std::tuple<int, double, double>>>
+  Make_Clusters(const std::unordered_map<int, std::tuple<int, double, double>> &wireEvents);
+
+  int GetNumWire() const { return nWire; }
+  double GetDeltaAngle() const { return dAngle; }
+  double GetAnodeLength() const { return anodeLength; }
+  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 GetCathodeMid(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();
   void FindWireID(TVector3 pos, TVector3 direction, bool verbose = false);
   void CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose = false);
-  void CalTrack2(TVector3 sx3Pos, PWHitInfo hitInfo, double sigmaA = 0, double sigmaC = 0, bool verbose = false);
+  void CalTrack2(TVector3 sx3Pos, TVector3 anodeInt, bool verbose = false);
 
-  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 2nd nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nextNearestWire.first,
-    printf("     The nearest | Anode: %2d(%5.2f) Cathode: %2d(%5.2f)\n", hitInfo.nearestWire.first, 
+           hitInfo.nextNearestDist.first,
-                                                                         hitInfo.nearestDist.first, 
+           hitInfo.nextNearestWire.second,
-                                                                         hitInfo.nearestWire.second, 
+           hitInfo.nextNearestDist.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);
   }
 
 private:
-
   PWHitInfo hitInfo;
 
   TVector3 trackPos;
   TVector3 trackVec;
 
   const int nWire = 24;
-  const int wireShift = 3;
+  const int wireShift = 4;
-  const float zLen = 380; //mm
+  // const float zLen = 380; // mm
+  //  const float zLen = 348.6; // mm
+  const float zLen = 174.3 * 2; // mm
   const float radiusA = 37;
-  const float radiusC = 43;
+  const float radiusC = 42;
 
   double dAngle;
   double anodeLength;
   double cathodeLength;
 
-  std::vector<std::pair<TVector3,TVector3>> An; // the anode wire position vector in space 
+  // std::vector<std::pair<TVector3, TVector3>> An; // the anode wire position vector in space
-  std::vector<std::pair<TVector3,TVector3>> Ca; // the cathode wire position vector in space 
+  // std::vector<std::pair<TVector3, TVector3>> Ca; // the cathode wire position vector in space
 
-  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2){
+  double Distance(TVector3 a1, TVector3 a2, TVector3 b1, TVector3 b2)
+  {
     TVector3 na = a1 - a2;
     TVector3 nb = b1 - b2;
     TVector3 nd = (na.Cross(nb)).Unit();
-    return TMath::Abs(nd.Dot(a1-b2));
+    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 +154,416 @@ 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
+  double k = TMath::TwoPi() / 24.;     // 48 solder thru holes, wires in every other one
-  //anode wire shift is right-hand.
+  double offset_a1 = -6 * k - 4 * k;   // -6 to go from 0,0 to 90degree up, and 4 for the wire offset //old version -5 * k - 5 * k;
-  //cathode wire shift is left-hand.
+  double offset_c1 = -6 * k + k / 2.0; // correct for a half-turn
+  // std::cerr << "Here!" << std::endl;
+  // #include "../scratch/testing.h"
+  double offset_a2 = offset_a1 + wireShift * k;
+  double offset_c2 = offset_c1 - wireShift * k;
 
-  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()),
+    // Anode rotate right-hand coming in towards +z riding with the beam. In this frame, +x is to the right, and +y down
-                    radiusA * TMath::Sin( TMath::TwoPi() / nWire * (i)  + TMath::PiOver2()),
+    // updated Feb 2026, Sudarsan B. Photographs indicate that anode wires twist right handed, as one moves from -z to +z with the convention above
-                    zLen/2);
+    // wire indices increase leftward as one moves to +z (hence -k factor), but wires themselves twist rightward - as indicated by offset_a2 being more +ve w.r.t offset_a1
-    p1.second.SetXYZ( radiusA * TMath::Cos( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+    //'First' is -z locus, 'second' is +z locus
-                      radiusA * TMath::Sin( TMath::TwoPi() / nWire * (i + wireShift) + TMath::PiOver2()),
+    p1.first.SetXYZ(radiusA * TMath::Cos(-k * i + offset_a1),
-                    -zLen/2);
+                    radiusA * TMath::Sin(-k * i + offset_a1),
+                    -zLen / 2);
+    p1.second.SetXYZ(radiusA * TMath::Cos(-k * i + offset_a2),
+                     radiusA * TMath::Sin(-k * i + offset_a2),
+                     +zLen / 2);
+
+    // Cathodes twist left-hand as indicated by offset_c2 being more negative than offset_c1, under the same system, while wires increase rightward (hence +k factor)
+    q1.first.SetXYZ(radiusC * TMath::Cos(k * i + offset_c1),
+                    radiusC * TMath::Sin(k * i + offset_c1),
+                    -zLen / 2);
+    q1.second.SetXYZ(radiusC * TMath::Cos(k * i + offset_c2),
+                     radiusC * TMath::Sin(k * i + offset_c2),
+                     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);
     Ca.push_back(q1);
   }
 
+  // Calculate Crossover Geometry ONCE
+  TVector3 a, c, diff;
+  double a2, ac, c2, adiff, cdiff, denom, alpha;
+
+  for (size_t i = 0; i < An.size(); i++)
+  {
+    // a = An[i].first - An[i].second;
+    a = An[i].second - An[i].first;
+    for (size_t j = 0; j < Ca.size(); j++)
+    {
+      c = Ca[j].second - Ca[j].first;
+      diff = An[i].second - Ca[j].second;
+      a2 = a.Dot(a);
+      c2 = c.Dot(c);
+      ac = a.Dot(c);
+      adiff = a.Dot(diff);
+      cdiff = c.Dot(diff);
+      denom = a2 * c2 - ac * ac;
+      alpha = (ac * cdiff - c2 * adiff) / denom;
+
+      Crossover[i][j][0].x = An[i].second.X() + alpha * a.X();
+      Crossover[i][j][0].y = An[i].second.Y() + alpha * a.Y();
+      Crossover[i][j][0].z = An[i].second.Z() + alpha * a.Z();
+
+      if (Crossover[i][j][0].z < -190 || Crossover[i][j][0].z > 190)
+      {
+        // std::cout << "Weird crossover but ok" << std::endl;
+      }
+      if ((i + j) % 24 == 12 || Crossover[i][j][0].z < -190 || Crossover[i][j][0].z > 190)
+      {
+        Crossover[i][j][0].z = 9999999;
+        // std::cout << "Weird crossover" << std::endl;
+      }
+
+      Crossover[i][j][1].x = alpha;
+      Crossover[i][j][1].y = 0;
+    }
+  }
+
   dAngle = wireShift * TMath::TwoPi() / nWire;
-  anodeLength = TMath::Sqrt( zLen*zLen + TMath::Power(2* radiusA * 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) );
+  cathodeLength = TMath::Sqrt(zLen * zLen + TMath::Power(2 * radiusC * TMath::Sin(dAngle / 2), 2)); // chord length subtending an angle alpha is 2rsin(alpha/2)
 }
 
-inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose ){
+inline TVector3 PW::getClosestWirePosAtWirePhiOld(std::pair<TVector3, TVector3> awire, double sx3phi_radian)
+{
+  // 1. Get wire geometry
+  TVector3 a1 = awire.first;  // Top of the wire
+  TVector3 a2 = awire.second; // Bottom of the wire
+  TVector3 wireVec = a2 - a1; // Vector pointing down the wire
+
+  // Variables to track our minimums during the scan
+  double min_delta_phi = 9999.0;
+  double best_t = -1.0;
+  TVector3 best_pcz_intersect;
+
+  // 2. THE SCAN: Walk down the wire in 1000 tiny steps
+  // (For a 380mm wire, this is checking every 0.38 mm)
+  int num_steps = 1000;
+  for (int i = 0; i <= num_steps; ++i)
+  {
+    double t_test = (double)i / num_steps;    // Ranges from 0.0 to 1.0
+    TVector3 test_pt = a1 + t_test * wireVec; // The 3D point at this step
+
+    // Calculate absolute Delta Phi between Si hit and this specific point on the wire
+    if (TMath::IsNaN(sx3phi_radian - test_pt.Phi()))
+      continue;
+    double dPhi = TMath::Abs(TVector2::Phi_mpi_pi(sx3phi_radian - test_pt.Phi())); // Phi_mpi_pi just puts the angle in the range -180 to 180
+
+    // If this is the smallest Delta Phi we've seen so far, save it!
+    if (dPhi < min_delta_phi)
+    {
+      min_delta_phi = dPhi;
+      best_t = t_test;
+      best_pcz_intersect = test_pt;
+    }
+  }
+  return best_pcz_intersect;
+}
+
+inline TVector3 PW::getClosestWirePosAtWirePhi(std::pair<TVector3, TVector3> awire, double phi)
+{
+  const TVector3 &a1 = awire.first;
+  const TVector3 &a2 = awire.second;
+  const double s = TMath::Sin(phi), c = TMath::Cos(phi);
+  const double dx = a2.X() - a1.X(), dy = a2.Y() - a1.Y();
+  const double t = (a1.Y() * c - a1.X() * s) / (dx * s - dy * c);
+
+  auto nearerEndpoint = [&]() -> TVector3
+  {
+    auto dphi = [&](const TVector3 &p)
+    {
+      return TMath::Abs(TVector2::Phi_mpi_pi(phi - p.Phi()));
+    };
+    return dphi(a1) <= dphi(a2) ? a1 : a2;
+  };
+
+  if (t < 0.0 || t > 1.0)
+    return nearerEndpoint();
+
+  const TVector3 hit = a1 + t * (a2 - a1);
+  if (hit.X() * c + hit.Y() * s <= 0.0) // wrong half-plane (anti-phi side)
+    return nearerEndpoint();
+
+  return hit;
+}
+
+inline std::vector<std::vector<std::tuple<int, double, double>>>
+
+PW::Make_Clusters(const std::unordered_map<int, std::tuple<int, double, double>> &wireEvents)
+{
+  std::vector<std::vector<std::tuple<int, double, double>>> wireClusters;
+  std::vector<std::tuple<int, double, double>> wireCluster;
+  // TODO: Write a macro once, call it twice
+  int wirecount = 0;
+  while (wirecount < 24)
+  {
+    if (wireEvents.find(wirecount) == wireEvents.end())
+    {
+      wirecount++;
+      continue;
+    }
+    wireCluster.clear();
+    int ctr2 = wirecount;
+    do
+    {
+      wireCluster.emplace_back(wireEvents.at(ctr2));
+      ctr2 += 1;
+      if (ctr2 == 24 || ctr2 - wirecount == 7)
+        break; // loose logic, needs to be looked at.
+    } while (wireEvents.find(ctr2) != wireEvents.end());
+    wireClusters.push_back(std::move(wireCluster));
+    wirecount = ctr2; // we already dealt with wires until the last value of ctr2
+  }
+
+  if (wireClusters.size() > 1)
+  {                                            // Deal with wraparound if required
+    auto first_cluster = wireClusters.front(); // front and back provide references to the elements themselves. less copy, can modify etc
+    auto last_cluster = wireClusters.back();
+    if (std::get<0>(last_cluster.back()) == 23 && std::get<0>(first_cluster.front()) == 0)
+    {
+      last_cluster.insert(last_cluster.end(), first_cluster.begin(), first_cluster.end());
+    }
+    wireClusters.erase(wireClusters.begin()); // canonically, erase() needs an iterator, hence begin() not front()
+    // TODO: Can also deal with 'gaps' of missing wires similarly. end of one segment and beginning of another segment will be separated by missing wire --> combine the two
+    // TODO: Also needs some development regarding the time-correlation. Don't put wires in the same cluster if they aren't time coincident
+  }
+  return wireClusters;
+
+  /*if(aClusters.size()>1 || cClusters.size() > 1) {
+    std::cout << " ============== " << std::endl;
+  }
+  if(aClusters.size()>1 && cClusters.size() >=1) {
+    std::cout << aClusters.size() << " new anode clusters ----> " << std::endl;
+    int cc=1;
+    for(auto ac : aClusters) {
+      std::cout << "  Cluster " << cc << std::endl;
+      double first_ts = std::get<2>(ac.at(0));
+      for(auto item : ac) {
+        std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+      }
+      std::cout << "  ------" << std::endl;
+      cc++;
+    }
+  }
+
+  if(cClusters.size()>=1 ) {
+    std::cout << cClusters.size() << " new cathode clusters ----> " << std::endl;
+    int cc=1;
+    for(auto ac : cClusters) {
+      std::cout << "  Cluster " << cc << std::endl;
+      double first_ts = std::get<2>(ac.at(0));
+      for(auto item : ac) {
+        std::cout << "  \t" << std::get<0>(item) << " " << std::get<1>(item) << " " << std::get<2>(item)-first_ts << std::endl;
+      }
+      std::cout << "  ------" << std::endl;
+      cc++;
+    }
+  } 	*/
+}
+
+inline std::tuple<std::pair<TVector3, TVector3>, double, double, double>
+PW::GetPseudoWire(const std::vector<std::tuple<int, double, double>> &cluster, std::string type)
+{
+  std::pair<TVector3, TVector3> avgvec = std::pair(TVector3(0, 0, 0), TVector3(0, 0, 0));
+  double sumEnergy = 0;
+  double maxEnergy = 0;
+  double tsMaxEnergy = 0;
+  if (type == "ANODE")
+  {
+    // if(cluster.size()>1) std::cout << " -------anodes" << std::endl;
+    for (auto wire : cluster)
+    {
+      avgvec.first += std::get<1>(wire) * TVector3(An.at(std::get<0>(wire)).first.X(), An.at(std::get<0>(wire)).first.Y(), 0);
+      avgvec.second += std::get<1>(wire) * TVector3(An.at(std::get<0>(wire)).second.X(), An.at(std::get<0>(wire)).second.Y(), 0);
+      sumEnergy += std::get<1>(wire);
+      if (std::get<1>(wire) > maxEnergy)
+      {
+        maxEnergy = std::get<1>(wire);
+        tsMaxEnergy = std::get<2>(wire);
+      }
+      /*if(cluster.size()>1) {
+        std::cout << "\t\t ch:" << std::get<0>(wire) << " " << std::get<1>(wire) << " " << std::get<2>(wire) << std::endl;
+        std::cout << "\t\t w1(r,phi,z):" << An.at(std::get<0>(wire)).first.Perp() << " " << An.at(std::get<0>(wire)).first.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).first.Z() << std::endl;
+        std::cout << "\t\t w2(r,phi,z):" << An.at(std::get<0>(wire)).second.Perp() << " " << An.at(std::get<0>(wire)).second.Phi()*180/M_PI << " " << An.at(std::get<0>(wire)).second.Z() << std::endl;
+      }*/
+    }
+    avgvec.first = avgvec.first * (1.0 / sumEnergy);
+    avgvec.second = avgvec.second * (1.0 / sumEnergy);
+    double phi1 = avgvec.first.Phi();
+    double phi2 = avgvec.second.Phi();
+    avgvec.first.SetXYZ(radiusA * TMath::Cos(phi1), radiusA * TMath::Sin(phi1), -zLen / 2);
+    avgvec.second.SetXYZ(radiusA * TMath::Cos(phi2), radiusA * TMath::Sin(phi2), zLen / 2);
+    /*if(cluster.size()>1) {
+      std::cout << "\t\t avg1(r,phi,z):" << avgvec.first.Perp() << " " << avgvec.first.Phi()*180/M_PI << " " << avgvec.first.Z() << std::endl;
+      std::cout << "\t\t avg2(r,phi,z):" << avgvec.second.Perp() << " " << avgvec.second.Phi()*180/M_PI << " " << avgvec.second.Z() << std::endl;
+    }*/
+  }
+  else if (type == "CATHODE")
+  {
+    for (auto wire : cluster)
+    {
+      avgvec.first += std::get<1>(wire) * TVector3(Ca.at(std::get<0>(wire)).first.X(), Ca.at(std::get<0>(wire)).first.Y(), 0);
+      avgvec.second += std::get<1>(wire) * TVector3(Ca.at(std::get<0>(wire)).second.X(), Ca.at(std::get<0>(wire)).second.Y(), 0);
+      sumEnergy += std::get<1>(wire);
+      if (std::get<1>(wire) > maxEnergy)
+      {
+        maxEnergy = std::get<1>(wire);
+        tsMaxEnergy = std::get<2>(wire);
+      }
+    }
+    avgvec.first = avgvec.first * (1.0 / sumEnergy);
+    avgvec.second = avgvec.second * (1.0 / sumEnergy);
+    double phi1 = avgvec.first.Phi();
+    double phi2 = avgvec.second.Phi();
+    avgvec.first.SetXYZ(radiusC * TMath::Cos(phi1), radiusC * TMath::Sin(phi1), -zLen / 2);
+    avgvec.second.SetXYZ(radiusC * TMath::Cos(phi2), radiusC * TMath::Sin(phi2), zLen / 2);
+  }
+  return std::tuple(avgvec, sumEnergy, maxEnergy, tsMaxEnergy);
+}
+
+inline std::tuple<TVector3, double, double, double, double, double, double, double> PW::FindCrossoverProperties(const std::vector<std::tuple<int, double, double>> &a_cluster,
+                                                                                                                const std::vector<std::tuple<int, double, double>> &c_cluster)
+{
+  // std::pair<TVector3, TVector3> apwire = GetPseudoWire(a_cluster,"ANODE",anodeSumE);
+  // std::pair<TVector3, TVector3> cpwire = GetPseudoWire(c_cluster,"CATHODE",cathodeSumE);
+  auto [apwire, apSumE, apMaxE, apTSMaxE] = GetPseudoWire(a_cluster, "ANODE");
+  auto [cpwire, cpSumE, cpMaxE, cpTSMaxE] = GetPseudoWire(c_cluster, "CATHODE");
+
+  TVector3 crossover;
+  crossover.Clear();
+  TVector3 a, c, diff;
+  double a2, ac, c2, adiff, cdiff, denom, alpha = 0;
+
+  if (apSumE && cpSumE)
+  {
+    a = apwire.first - apwire.second;
+    c = cpwire.first - cpwire.second;
+    diff = apwire.first - cpwire.first;
+    a2 = a.Dot(a);
+    c2 = c.Dot(c);
+    ac = a.Dot(c);
+    adiff = a.Dot(diff);
+    cdiff = c.Dot(diff);
+    denom = a2 * c2 - ac * ac;
+    alpha = (ac * cdiff - c2 * adiff) / denom;
+    crossover = apwire.first + alpha * a;
+    if (crossover.z() < -190 || crossover.Z() > 190)
+    {
+      alpha = 9999999;
+      apSumE = -1;
+      cpSumE = -1;
+      apMaxE = -1;
+      cpMaxE = -1;
+      apTSMaxE = -1;
+      cpTSMaxE = -1;
+    }
+  }
+  // std::cout << apSumE << " " << cpSumE << " " << " " <<  crossover.Perp() << std::endl;
+  return std::tuple(crossover, alpha, apSumE, cpSumE, apMaxE, cpMaxE, apTSMaxE, cpTSMaxE);
+}
+
+inline void PW::FindWireID(TVector3 pos, TVector3 direction, bool verbose)
+{
 
   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)
-    if( phi < 0 && phiS > phiL )  phiS = phiS - TMath::TwoPi();
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();
 
-    if( phiS < phi && phi < phiL) {
+    if (phiS < phi && phi < phiL)
-      disA = Distance( pos, pos + direction, An[i].first, An[i].second);
+    {
-      if( disA < hitInfo.nearestDist.first ){
+      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)
-    if( phi < 0 && phiS > phiL ) phiS = phiS - TMath::TwoPi();
+      phiL = phiL + TMath::TwoPi();
+    if (phi < 0 && phiS > phiL)
+      phiS = phiS - TMath::TwoPi();
 
-    if(phiS < phi && phi < phiL) {
+    if (phiS < phi && phi < phiL)
-      disC = Distance( pos, pos + direction, Ca[i].first, Ca[i].second);
+    {
-      if( disC < hitInfo.nearestDist.second ){
+      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 aaa1 = anode1 - 1;
-  short aaa2 = (anode1 + 1) % nWire; 
+  if (aaa1 < 0)
+    aaa1 += nWire;
+  short aaa2 = (anode1 + 1) % nWire;
 
-  double haha1 = Distance( pos, pos + direction, An[aaa1].first, An[aaa1].second);
+  double haha1 = Distance(pos, pos + direction, An[aaa1].first, An[aaa1].second);
-  double haha2 = Distance( pos, pos + direction, An[aaa2].first, An[aaa2].second);
+  double haha2 = Distance(pos, pos + direction, An[aaa2].first, An[aaa2].second);
-  if( haha1 < haha2){
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.first = aaa1;
     hitInfo.nextNearestDist.first = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.first = aaa2;
     hitInfo.nextNearestDist.first = haha2;
   }
 
   short cathode1 = hitInfo.nearestWire.second;
-  short ccc1 = cathode1 - 1; if( ccc1 < 0 ) ccc1 += nWire;
+  short ccc1 = cathode1 - 1;
-  short ccc2 = (cathode1 + 1) % nWire; 
+  if (ccc1 < 0)
+    ccc1 += nWire;
+  short ccc2 = (cathode1 + 1) % nWire;
 
-  haha1 = Distance( pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
+  haha1 = Distance(pos, pos + direction, Ca[ccc1].first, Ca[ccc1].second);
-  haha2 = Distance( pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
+  haha2 = Distance(pos, pos + direction, Ca[ccc2].first, Ca[ccc2].second);
-  if( haha1 < haha2){
+  if (haha1 < haha2)
+  {
     hitInfo.nextNearestWire.second = ccc1;
     hitInfo.nextNearestDist.second = haha1;
-  }else{
+  }
+  else
+  {
     hitInfo.nextNearestWire.second = ccc2;
     hitInfo.nextNearestDist.second = haha2;
   }
 
-  if( verbose ) Print();
+  if (verbose)
+    Print();
 }
 
-inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose){
+inline void PW::CalTrack(TVector3 sx3Pos, int anodeID, int cathodeID, bool verbose)
+{
 
   trackPos = sx3Pos;
 
@@ -231,72 +573,116 @@ 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 siPos, TVector3 anodeInt, bool verbose)
+{
 
-  trackPos = sx3Pos;
+  double mx, my;
-
+  double z;
-  double p1 = TMath::Abs(hitInfo.nearestDist.first + gRandom->Gaus(0, sigmaA));
+  mx = siPos.X() / (siPos.X() - anodeInt.X());
-  double p2 = TMath::Abs(hitInfo.nextNearestDist.first + gRandom->Gaus(0, sigmaA));
+  my = siPos.Y() / (siPos.Y() - anodeInt.Y());
-  double fracA = p1 / (p1 + p2);
+  z = siPos.Z() + mx * (anodeInt.Z() - siPos.Z());
-  short anodeID1 = hitInfo.nearestWire.first;
+  // if (mx == my)
-  short anodeID2 = hitInfo.nextNearestWire.first;
+  {
-  TVector3 shiftA1 = (An[anodeID2].first - An[anodeID1].first) * fracA;
+    trackVec = TVector3(0, 0, z);
-  TVector3 shiftA2 = (An[anodeID2].second - An[anodeID1].second) * fracA;
+  }
-
-  double q1 = TMath::Abs(hitInfo.nearestDist.second + gRandom->Gaus(0, sigmaC));
-  double q2 = TMath::Abs(hitInfo.nextNearestDist.second + gRandom->Gaus(0, sigmaC));
-  double fracC = q1 / (q1 + q2);
-  short cathodeID1 = hitInfo.nearestWire.second;
-  short cathodeID2 = hitInfo.nextNearestWire.second;
-  TVector3 shiftC1 = (Ca[cathodeID2].first - Ca[cathodeID1].first) * fracC;
-  TVector3 shiftC2 = (Ca[cathodeID2].second - Ca[cathodeID1].second) * fracC;
-
-  TVector3 a1 = An[anodeID1].first + shiftA1;
-  TVector3 a2 = An[anodeID1].second + shiftA2;
-
-  TVector3 c1 = Ca[cathodeID1].first + shiftC1;
-  TVector3 c2 = Ca[cathodeID1].second + shiftC2;
-
-  TVector3 n1 = (a1 - a2).Cross((sx3Pos - a2)).Unit();
-  TVector3 n2 = (c1 - c2).Cross((sx3Pos - c2)).Unit();
-
-  // 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("X slope = %f and Y slope = %f \n", mx, my);
 }
 
-inline double PW::GetZ0(){
+/*inline TVector3 PW::CalTrack3(TVector3 siPos, TVector3 anodeInt, bool verbose)
+{
+
+  TVector3 v = anodeInt-siPos;
+  double t_minimum = -1.0*(siPos.X()*v.X()+siPos.Y()*v.Y())/(v.X()*v.X()+v.Y()*v.Y());
+  TVector3 vector_closest_to_z = siPos + t_minimum*v;
+
+  return vector_closest_to_z;
+  if (verbose)
+    printf("X slope = %f and Y slope = %f \n", mx, my);
+}*/
+
+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);
 
+  return trackVec.Z();
+}
+// Each wire family is strung as straight skew chords between two rings, so it sweeps a
+// one-sheet hyperboloid (x*x+y*y)/(a*a) - (z*z)/(c*c) = 1 whose waist 'a' is smaller than
+// the ring radius. The anode waist was fit to the measured anode crossover points; the
+// other families share the flare 'c' and scale their waist with the ring radius.
+//
+// Radial ordering, inner to outer:  guard (ring 32) < anode (ring 37) < cathode (ring 43).
+// Charge collection spans guard -> cathode. The anodes in the middle are the readout, the
+// cathodes see the induced/mirror charge, and the guard wires are field-shaping, not read out.
+const double kPCHyperbC = 301.895;
+const double kPCAnodeWaist = 32.0429;                 // ring radius 37 mm -- readout
+const double kPCCathodeWaist = 32.0429 * 42.0 / 37.0; // ring radius 43 mm -- induced charge
+const double kPCGuardWaist = 32.0429 * 32.0 / 37.0;   // ring radius 32 mm -- not read out
+
+// Intersection of the segment x1 -> x1+dx with the one-sheet hyperboloid of waist a, flare c.
+// Returns TVector3(0, 0, 54321) when the segment does not cross the surface.
+inline TVector3 pc_hyperboloid_intersect(const TVector3 &x1, const TVector3 &dx, double a, double c)
+{
+  double t2 = 1.0; // value of 't' at the destination point, by definition t=(z(t)-z0)/dz
+  auto A = pow(dx.Perp(), 2) / (a * a) - pow(dx.Z(), 2) / (c * c);
+  auto B = 2 * (dx.X() * x1.X() + dx.Y() * x1.Y()) / (a * a) - 2 * (dx.Z() * x1.Z()) / (c * c);
+  auto C = pow(x1.Perp(), 2) / (a * a) - pow(x1.Z(), 2) / (c * c) - 1.0;
+  double disc = B * B - 4 * A * C;
+  if (disc < 0)
+    return TVector3(0, 0, 54321);
+  double tsol1 = (-B + TMath::Sqrt(disc)) / (2 * A);
+  double tsol2 = (-B - TMath::Sqrt(disc)) / (2 * A);
+  if (tsol1 >= 0 && tsol1 <= t2)
+    return x1 + tsol1 * dx;
+  else if (tsol2 >= 0 && tsol2 <= t2)
+    return x1 + tsol2 * dx;
+  else
+    return TVector3(0, 0, 54321);
 }
 
-inline double PW::CircularMean(std::vector<std::pair<int, double>> wireList){
+inline std::tuple<TVector3, TVector3, double> find_PC_PathLength(const TVector3 &x1, const TVector3 &x2)
-
+{
-  //use unit vector, wireID start from Zero
+  /*
-  double xCom = 0, yCom = 0;
+      Anode -> cathode segment for a particle moving from x1 to x2.
-  for( size_t i = 0; i < wireList.size() ; i++){
+      * Typical arguments here will be x1=r_rhoMin, x2=qqqevent.pos or sx3event.pos
-    xCom += TMath::Cos(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
+      * Returns {cathode_intersect, anode_intersect, gap_in_cm}; gap == 54321 sentinel on failure.
-    yCom += TMath::Sin(TMath::TwoPi() * wireList[i].first / nWire) * wireList[i].second;
+      * NOTE: this is the anode->cathode gap, NOT the full charge-collection region.
-  }
+        For the anode energy calibration use find_PC_CollectionPath() instead.
-
+  */
-  //calculate the angle of the summed unit vectors
+  TVector3 dx = x2 - x1; // direction vector
-  double angle = TMath::ATan2(yCom, xCom);
+  TVector3 anode_intersect = pc_hyperboloid_intersect(x1, dx, kPCAnodeWaist, kPCHyperbC);
-  if( angle < 0 ) angle += TMath::TwoPi(); // convert the angle from 0 to 2 pi
+  TVector3 cathode_intersect = pc_hyperboloid_intersect(x1, dx, kPCCathodeWaist, kPCHyperbC);
-
+  if (anode_intersect.Z() != 54321 && cathode_intersect.Z() != 54321)
-  return angle/ TMath::TwoPi() * nWire;
+    return std::tuple(cathode_intersect, anode_intersect, (cathode_intersect - anode_intersect).Mag() * 0.1);
-
+  else
+    return std::tuple(TVector3(0, 0, 0), TVector3(0, 0, 0), 54321);
 }
 
-#endif 
+inline std::tuple<TVector3, TVector3, double> find_PC_CollectionPath(const TVector3 &x1, const TVector3 &x2)
+{
+  /*
+      Charge-collection region for a particle moving from x1 to x2: it begins where the track
+      passes the guard wires and ends at the cathode. This is the segment whose energy deposit
+      the anodes actually collect, so it is the dE target for the anode energy calibration.
+      * Returns {guard_intersect, cathode_intersect, thickness_in_cm}; 54321 sentinel on failure.
+  */
+  TVector3 dx = x2 - x1;
+  TVector3 guard_intersect = pc_hyperboloid_intersect(x1, dx, kPCGuardWaist, kPCHyperbC);
+  TVector3 cathode_intersect = pc_hyperboloid_intersect(x1, dx, kPCCathodeWaist, kPCHyperbC);
+  if (guard_intersect.Z() != 54321 && cathode_intersect.Z() != 54321)
+    return std::tuple(guard_intersect, cathode_intersect, (cathode_intersect - guard_intersect).Mag() * 0.1);
+  else
+    return std::tuple(TVector3(0, 0, 0), TVector3(0, 0, 0), 54321);
+}
+
+#endif

Armory/EventBuilder.cpp

@@ -0,0 +1,355 @@
+#include "fsuReader.h"
+
+#include "TROOT.h"
+#include "TSystem.h"
+#include "TClonesArray.h"
+#include "TGraph.h"
+#include "TFile.h"
+#include "TTree.h"
+#include "TMacro.h"
+
+
+#define MAX_MULTI  2000
+
+struct FileInfo{
+
+  std::string fileName;
+  int fileID;
+  unsigned long hitCount;
+
+};
+
+//^#############################################################
+//^#############################################################
+int main(int argc, char **argv) {
+  
+  printf("=========================================\n");
+  printf("===      *.fsu Events Builder         ===\n");
+  printf("=========================================\n");  
+  if (argc < 6)    {
+    printf("Incorrect number of arguments:\n");
+    printf("%s [timeWindow] [withTrace] [verbose] [batchSize] [inFile1]  [inFile2] .... \n", argv[0]);
+    printf("    timeWindow : in ns, -1 = no event building \n");   
+    printf("     withTrace : 0 for no trace, 1 for trace \n");   
+    printf("       verbose : > 0 for debug  \n");   
+    printf("     batchSize : the size of hit in a batch \n");   
+    printf("    Output file name is contructed from inFile1 \n");   
+    printf("\n");
+    printf(" Example: %s 0 0 0 10000 '\\ls -1 *001*.fsu'\n", argv[0]);
+    printf("\n\n");
+
+    return 1;
+  }
+
+  uInt runStartTime = getTime_us();
+
+  ///============= read input
+  long timeWindow = atoi(argv[1]);
+  bool traceOn = atoi(argv[2]);
+  unsigned int debug = atoi(argv[3]);
+  unsigned int batchSize = atoi(argv[4]);
+  int nFile = argc - 5;
+  TString inFileName[nFile];
+  for( int i = 0 ; i < nFile ; i++){ inFileName[i] = argv[i+5];}
+  
+  /// Form outFileName;
+  TString outFileName = inFileName[0];
+  int pos = outFileName.Last('/');
+  pos = outFileName.Index("_", pos+1); // find next "_"
+  pos = outFileName.Index("_", pos+1); // find next "_"
+  if( nFile == 1 ) pos = outFileName.Index("_", pos+1); // find next "_", S/N
+  outFileName.Remove(pos); // remove the rest
+  outFileName += "_" + std::to_string(timeWindow);
+  outFileName += ".root";
+  printf("-------> Out file name : %s \n", outFileName.Data());
+  printf("========================================= Number of Files : %d \n", nFile);
+  for( int i = 0; i < nFile; i++) printf("%2d | %s \n", i, inFileName[i].Data());
+  printf("=========================================\n"); 
+  printf("    Time Window = %ld ns = %.1f us\n", timeWindow, timeWindow/1000.);
+  printf("  Include Trace = %s\n", traceOn ? "Yes" : "No");
+  printf("    Debug level = %d\n", debug);
+  printf("     Batch size = %d events/file\n", batchSize);
+  printf(" Max multiplity = %d hits/event (hard coded)\n", MAX_MULTI);
+  printf("========================================= Grouping files\n");  
+
+  std::vector<std::vector<FileInfo>> fileGroupList; // fileName and ID = SN * 1000 + index
+  std::vector<FileInfo> fileList;
+
+  unsigned long long int totalHitCount = 0;
+
+  FSUReader * readerA = new FSUReader(inFileName[0].Data(), 1, 1);
+  readerA->ScanNumBlock(0,0);
+  FileInfo fileInfo = {inFileName[0].Data(), readerA->GetSN() * 1000 +  readerA->GetFileOrder(), readerA->GetHitCount()};
+  fileList.push_back(fileInfo);
+  totalHitCount += readerA->GetHitCount();
+
+  for( int i = 1; i < nFile; i++){
+    FSUReader * readerB = new FSUReader(inFileName[i].Data(), 1, 0);
+    readerB->ScanNumBlock(0,0);
+    totalHitCount += readerB->GetHitCount();
+    fileInfo = {inFileName[i].Data(), readerB->GetSN() * 1000 +  readerB->GetFileOrder(), readerB->GetHitCount()};
+    
+    if( readerA->GetSN() == readerB->GetSN() ){
+      fileList.push_back(fileInfo);
+    }else{
+      fileGroupList.push_back(fileList);
+      fileList.clear();
+      fileList.push_back(fileInfo);
+    }
+  
+    delete readerA;
+    readerA = readerB;
+  }
+  fileGroupList.push_back(fileList);
+  delete readerA;
+
+  printf("======================= total Hit Count : %llu\n", totalHitCount);
+
+  for( size_t i = 0; i < fileGroupList.size(); i++){
+    printf("group ----- %ld \n", i);
+
+    //sort by ID
+    std::sort(fileGroupList[i].begin(), fileGroupList[i].end(), [](const FileInfo & a, const FileInfo & b) {
+      return a.fileID < b.fileID;
+    });
+
+    for( size_t j = 0; j < fileGroupList[i].size(); j++){
+      printf("%3ld | %8d | %9lu| %s \n", j, fileGroupList[i][j].fileID, fileGroupList[i][j].hitCount, fileGroupList[i][j].fileName.c_str() );
+    }
+
+  }
+
+  // //*====================================== create tree
+  TFile * outRootFile = new TFile(outFileName, "recreate");
+  TTree * tree = new TTree("tree", outFileName);
+
+  unsigned long long                evID = 0;
+  unsigned int                     multi = 0;
+  unsigned short           sn[MAX_MULTI] = {0}; /// board SN
+  unsigned short           ch[MAX_MULTI] = {0}; /// chID
+  unsigned short            e[MAX_MULTI] = {0}; /// 15 bit
+  unsigned short           e2[MAX_MULTI] = {0}; /// 15 bit
+  unsigned long long      e_t[MAX_MULTI] = {0}; /// timestamp 47 bit
+  unsigned short          e_f[MAX_MULTI] = {0}; /// fine time 10 bit 
+  unsigned short  traceLength[MAX_MULTI];
+
+  tree->Branch("evID",           &evID, "event_ID/l"); 
+  tree->Branch("multi",         &multi, "multi/i"); 
+  tree->Branch("sn",                sn, "sn[multi]/s");
+  tree->Branch("ch",                ch, "ch[multi]/s");
+  tree->Branch("e",                  e, "e[multi]/s");
+  tree->Branch("e2",                e2, "e2[multi]/s");
+  tree->Branch("e_t",              e_t, "e_timestamp[multi]/l");
+  tree->Branch("e_f",              e_f, "e_fineTime[multi]/s");
+  tree->Branch("traceLength", traceLength, "traceLength[multi]/s");
+  
+  TClonesArray * arrayTrace = nullptr;
+  TGraph * trace = nullptr;
+
+  if( traceOn ) {
+    arrayTrace = new TClonesArray("TGraph");
+    tree->Branch("trace",       arrayTrace, 2560000);
+    arrayTrace->BypassStreamer();
+  }
+
+  //*======================================= Open files
+  printf("========================================= Open files & Build Events.\n"); 
+
+  const short nGroup = fileGroupList.size();
+  std::vector<Hit> hitList[nGroup];
+  
+  FSUReader ** reader = new FSUReader * [nGroup];
+  ulong ID[nGroup];
+  for( short i = 0; i < nGroup; i++){
+    std::vector<std::string> fList;
+    for( size_t j = 0; j < fileGroupList[i].size(); j++){
+      fList.push_back( fileGroupList[i][j].fileName );
+    }
+    reader[i] = new FSUReader(fList, 600, debug);
+    hitList[i] = reader[i]->ReadBatch(batchSize, debug );
+    reader[i]->PrintHitListInfo(&hitList[i], "hitList-" + std::to_string(reader[i]->GetSN()));
+    ID[i] = 0;
+    if( debug ) {
+
+      for( size_t p = 0; p < 10; p ++ ){
+        if( hitList[i].size() <= p ) break;
+        hitList[i][p].Print();
+      }
+
+    }
+  }
+
+  unsigned long long tStart = 0;
+  unsigned long long tEnd = 0;
+
+  //find earliest time group;
+  unsigned long long t0 = -1;
+  short g0 = 0 ;
+  for( short i = 0; i < nGroup; i++){
+    if( hitList[i].size() == 0 ) continue;
+    if( hitList[i][0].timestamp < t0 ) {
+      t0 = hitList[i][0].timestamp;
+      g0 = i;
+    }
+  }
+  tStart = t0;
+  if( debug ) printf("First timestamp is %llu, group : %u\n", t0, g0);
+
+  int nFileFinished = 0;
+  multi = 0;
+  evID = 0;
+  std::vector<Hit> events;
+
+  unsigned long long hitProcessed = 0;
+
+  do{
+
+    //*============= Build events from hitList[i]
+    if( debug ) printf("################################ ev build %llu \n", evID);
+    events.clear();
+
+    for( short i = 0; i < nGroup; i++){
+      short ig = (i + g0 ) % nGroup;
+
+      if( hitList[ig].size() == 0 ) continue;
+
+      //chekc if reached the end of hitList
+      if( ID[ig] >= hitList[ig].size() ) {
+        hitList[ig] = reader[ig]->ReadBatch(batchSize, debug + 1);
+        if( debug ) reader[ig]->PrintHitListInfo( &hitList[ig], "hitList-" + std::to_string(ig));
+        ID[ig] = 0;
+        if( hitList[ig].size() == 0 ) continue;
+      }
+
+      if( timeWindow >= 0 ){
+      
+        do{
+
+          if( (long int)(hitList[ig].at(ID[ig]).timestamp  - t0) <= timeWindow ){
+            events.push_back(hitList[ig].at(ID[ig]));
+            ID[ig] ++;
+          }else{
+            break;
+          }
+
+          //check if reached the end of hitList
+          if( ID[ig] >= hitList[ig].size() ) {
+            hitList[ig] = reader[ig]->ReadBatch(batchSize, debug);
+            if( debug ) reader[ig]->PrintHitListInfo( &hitList[ig], "hitList-" + std::to_string(ig));
+            ID[ig] = 0;
+            if( hitList[ig].size() == 0 ) break;
+          }
+      
+        }while(ID[ig] < hitList[ig].size());
+
+      }else{
+        events.push_back(hitList[ig].at(ID[ig]));
+        ID[ig] ++;
+      }
+
+      if( timeWindow < 0) break;
+
+    }
+
+    if( events.size() > 1 ){
+      std::sort(events.begin(), events.end(), [](const Hit& a, const Hit& b) {
+        return a.timestamp < b.timestamp;
+      });
+    }
+    
+    tEnd = events.back().timestamp;
+
+    hitProcessed += events.size();    
+    if( hitProcessed % 10000 == 0 ) printf("hit Porcessed %llu/%llu hit....%.2f%%\n\033[A\r", hitProcessed, totalHitCount, hitProcessed*100./totalHitCount);
+    
+
+    multi = events.size() ;
+    if( events.size() >= MAX_MULTI ) {
+      printf("event %lld has size = %d > MAX_MULTI = %d\n", evID, multi, MAX_MULTI);
+      multi = MAX_MULTI;
+    }
+    if( debug ) printf("=================================== filling data | %u \n", multi);
+    for( size_t p = 0; p < multi ; p ++ ) {
+      if( debug ) {printf("%4zu | ", p); events[p].Print();}
+
+      sn[p] = events[p].sn;
+      ch[p] = events[p].ch;
+      e[p] = events[p].energy;
+      e2[p] = events[p].energy2;
+      e_t[p] = events[p].timestamp;
+      e_f[p] = events[p].fineTime;
+      
+      traceLength[p] = events[p].traceLength;
+      if( traceOn ){
+        trace = (TGraph *) arrayTrace->ConstructedAt(multi, "C");
+        trace->Clear();
+        for( int hh = 0; hh < traceLength[multi]; hh++){
+          trace->SetPoint(hh, hh, events[p].trace[hh]);
+        }
+      }
+    }
+
+    outRootFile->cd();
+    tree->Fill();
+    // tree->Write();
+    multi = 0;
+    evID ++;
+
+    ///===================== find the next first timestamp
+    t0 = -1;
+    g0 = -1;
+
+    for( int i = 0; i < nGroup; i++) {
+      if( hitList[i].size() == 0 ) continue;
+      if( hitList[i][ID[i]].timestamp < t0 ) {
+        t0 = hitList[i][ID[i]].timestamp;
+        g0 = i;
+      }
+    } 
+    if( debug ) printf("Next First timestamp is %llu, group : %u\n", t0, g0);
+
+    //*=============
+    nFileFinished = 0;
+    for( int i = 0 ; i < nGroup; i++) {
+      if( hitList[i].size() == 0 ) {
+        nFileFinished ++;
+        continue;
+      }else{
+        if( ID[i] >= hitList[i].size( )) {
+          hitList[i] = reader[i]->ReadBatch(batchSize, debug);
+          ID[i] = 0;
+          if( hitList[i].size() == 0 ) nFileFinished ++;
+        }
+      }
+    }
+    if( debug > 1 ) printf("========== nFileFinished : %d\n", nFileFinished);
+
+  }while( nFileFinished < nGroup);
+
+  tree->Write();
+
+  uInt runEndTime = getTime_us();
+  double runTime = (runEndTime - runStartTime) * 1e-6;
+  printf("========================================= finished.\n");
+  printf(" event building time = %.2f sec = %.2f min\n", runTime, runTime/60.);
+  printf("  total events built = %llu by event builder (%llu in tree)\n", evID, tree->GetEntriesFast());
+  double tDuration_sec = (tEnd - tStart) * 1e-9;
+  printf("     first timestamp = %20llu ns\n", tStart);
+  printf("      last timestamp = %20llu ns\n", tEnd);
+  printf(" total data duration = %.2f sec = %.2f min\n", tDuration_sec, tDuration_sec/60.);
+  printf("==============> saved to %s \n", outFileName.Data());
+
+  TMacro info;
+  info.AddLine(Form("tStart= %20llu ns",tStart));
+  info.AddLine(Form("  tEnd= %20llu ns",tEnd));
+  info.Write("info");
+
+  outRootFile->Close();
+  
+  for( int i = 0; i < nGroup; i++) delete reader[i];
+  delete [] reader;
+
+  return 0;
+
+}
+

Armory/HistPlotter.h

@@ -0,0 +1,491 @@
+#ifndef HISTPLOTTER_H
+#define HISTPLOTTER_H
+#include <TCanvas.h>
+#include <TROOT.h>
+#include <TSystem.h>
+#include <TStyle.h>
+#include <iostream>
+#include <TFile.h>
+#include <TMemFile.h>
+#include <TH1.h>
+#include <TH2.h>
+#include <TCutG.h>
+#include <signal.h>
+#include <cstdlib>
+#include <utility>
+#include <fstream>
+#include <sstream>
+#include <map>
+#include <unordered_map>
+#include <set>
+#include <TGraphErrors.h>
+
+class HistPlotter
+{
+private:
+    long long barrier_count, barrier_limit; // meant to keep track of how often to call FillN() on histograms
+    enum
+    {
+        TFILE,
+        TMEMFILE
+    } filetype;
+    std::map<std::string, TObject *> oMap;                        //!< Maps std::string to all TH1, TH2 objects in the class
+    std::unordered_map<std::string, TObject *> cutsMap;           //!< Maps std::string to TCutG objects held by the class
+    std::set<std::string> folderList;                             //!< List of all folder names used to nest objects
+    std::unordered_map<TObject *, std::string> foldersForObjects; //!< Map that returns the folder corresponding to the object whose pointer is specified
+    TFile *ofile = nullptr;                                       //!< TFile pointer for the output file
+    TMemFile *omfile = nullptr;                                   //!< TFile pointer for the output memfile
+
+    // Caches to permit FillN() calls
+    std::map<std::string, std::vector<double>> onedimcache;
+    std::map<std::string, std::pair<std::vector<double>, std::vector<double>>> twodimcache;
+    inline void FillN_All_Histograms();
+
+public:
+    HistPlotter(std::string outfile, std::string type);
+    inline void FlushToDisk(int integral); //!< Writes all objects to file before closing, nesting objects in folders as is found necessary
+    inline void PrintObjects();            //!< Dump objects to std::cout for inspection
+    inline void ReadCuts(std::string);
+    inline TCutG *FindCut(std::string cut)
+    {
+        return static_cast<TCutG *>(cutsMap.at(cut));
+    }
+    inline void set_barrier_limit(long long limit) { barrier_limit = limit; }
+    inline void barrier_increment()
+    {
+        barrier_count++;
+        if (barrier_count == barrier_limit)
+        {
+            FillN_All_Histograms();
+            barrier_count = 0;
+        }
+    }
+
+    inline void force_flush_caches()
+    {
+        FillN_All_Histograms();
+        barrier_count = 0;
+    }
+    /*! \fn void FindCut()
+        \brief
+            - Searches for a cut by name 'cut' in the internal list of cuts 'cutsMap'. Ugly fails (via unresolved at()) if such a cut isn't found.
+        \param filename - name of the plainxtext file containing the cut file locations and identifiers
+        \return Pointer to the TCutG object that matches the name. Very useful to use this as plotter.FindCut("protonbarrelpid")->IsInside(deltaE, E) for instance.
+    */
+
+    inline void SetNewTitle(std::string name, std::string title)
+    {
+        auto result = oMap.find(name); // result is an iterator
+        if (result == oMap.end())
+            return; // no warnings, could be changed in future
+        else
+            static_cast<TNamed *>(oMap.at(name))->SetTitle(title.c_str()); // set new title
+    }
+
+    // Smart functions that create a new histogram if it doesn't exist.
+    inline void FillGraph(const std::string &name, float valuex, float valuey, float errx = 0, float erry = 0);
+    inline void Fill1D(const std::string &name, int nbinsx, float xlow, float xhigh, float value);
+    inline void Fill2D(const std::string &name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey);
+    inline void Fill1D(const std::string &name, int nbinsx, float xlow, float xhigh, float value, const std::string &folder);
+    inline void Fill2D(const std::string &name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string &folder);
+    // TObject* findObject(std::string key);
+};
+
+HistPlotter::HistPlotter(std::string outfile, std::string type = "")
+{
+    /*!
+        \brief Constructor. Opens a TFile instance with the specified filename
+        \param outfile : std::string that holds the desired output ROOT filename
+        \return None
+    */
+    if (type == "" || type == "TFILE")
+    {
+        ofile = new TFile(outfile.c_str(), "recreate");
+        filetype = TFILE;
+    }
+    else if (type == "TMEMFILE")
+    {
+        omfile = new TMemFile(outfile.c_str(), "recreate");
+        filetype = TMEMFILE;
+    }
+    else
+    {
+        std::cout << "Unknown type " << type << " specified for HistPlotter (use \"TFILE\" or \"TMEMFILE\"), using default \"TFILE\"  " << std::endl;
+        ofile = new TFile(outfile.c_str(), "recreate");
+        filetype = TFILE;
+    }
+    barrier_count = 0;
+    barrier_limit = 1000;
+}
+
+void HistPlotter::FillN_All_Histograms()
+{
+    for (auto it = oMap.begin(); it != oMap.end(); it++)
+    {
+        // it->first is std::string 'name', it->second is the TObject
+        if (it->second->InheritsFrom("TH1F"))
+        {
+            // FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size)
+            static_cast<TH1F *>(it->second)->FillN(onedimcache[it->first].size(),                                   // size
+                                                   onedimcache[it->first].data(),                                   // array
+                                                   std::vector<double>(onedimcache[it->first].size(), 1.0).data()); // weight of ones
+            onedimcache[it->first].clear();
+        }
+        else if (it->second->InheritsFrom("TH2F"))
+        {
+            // FillN(size, array-of-doubles, array-of-weights); //we set array-of-weights to (1,1,1,.. (size))
+            static_cast<TH2F *>(it->second)->FillN(twodimcache[it->first].first.size(),                                   // size
+                                                   twodimcache[it->first].first.data(),                                   // x array
+                                                   twodimcache[it->first].second.data(),                                  // y array
+                                                   std::vector<double>(twodimcache[it->first].first.size(), 1.0).data()); // weight of ones
+            twodimcache[it->first].first.clear();
+            twodimcache[it->first].second.clear();
+        }
+    }
+    std::cout << "." << std::endl;
+}
+
+void HistPlotter::FlushToDisk(int min_integral = 0)
+{
+    /*! \fn void FlushToDisk()
+        \brief         Function that can be used at any point to exit smoothly by saving all ROOT objects in memory
+        to the output file before closing it. Obeys the binding of histograms to separate folders, if so specified.
+        \return No return -- void
+    */
+    if (filetype == TMEMFILE && omfile)
+    {
+        std::cout << "Not flushing a TMemfile .. exiting .." << std::endl;
+        delete omfile;
+        return;
+    }
+    if (ofile->IsZombie() || !ofile)
+    {
+        std::cerr << "Output file is zombie, finishing up without writing to disk!" << std::endl;
+        return;
+    }
+    FillN_All_Histograms();
+    for (auto it = oMap.begin(); it != oMap.end(); it++)
+    {
+        // omap maps: name(first) to object address(second).
+        //  foldersForObjects maps: object address(first) to foldername(second)
+        auto result = foldersForObjects.find(it->second); // returns <TObject* histogram,std::string foldername> pair if found
+        if (result != foldersForObjects.end())
+        {                                                    // we try to create folder if needed and cd to it
+            ofile->mkdir(result->second.c_str(), "", kTRUE); // args: name, title, returnExistingDirectory
+            ofile->cd(result->second.c_str());
+        }
+        else
+        {
+            ofile->cd(); // toplevel for all default histograms. Default setting
+        }
+        if (((TH1F *)it->second)->Integral() > min_integral)
+            it->second->Write();
+    }
+
+    // Create a directory for all cuts, and save all cuts in them
+    ofile->mkdir("gCUTS", "", kTRUE);
+    ofile->cd("gCUTS");
+    for (auto it = cutsMap.begin(); it != cutsMap.end(); it++)
+    {
+        (static_cast<TNamed *>(it->second))->SetName(it->first.c_str());
+        it->second->Write();
+    }
+    ofile->Close();
+    std::cout << "Wrote " << oMap.size() << " histograms to TFile " << std::string(ofile->GetName()) << std::endl;
+}
+
+void HistPlotter::FillGraph(const std::string &name, float valuex, float valuey, float errx, float erry)
+{
+    /*! \fn void FillGraph()
+        \brief
+        - Creates a TGraphError in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TGraph*
+
+        \param name name of the TGraph
+        \param valuex The xvalue
+        \param valuey The yvalue
+        \param errx The x error
+        \param erry The y error
+        \return No return void
+    */
+    auto result = oMap.find(name);
+    if (result == oMap.end())
+    {
+        TGraphErrors *tempG = new TGraphErrors();
+        tempG->SetName(name.c_str());
+        oMap.insert(std::make_pair(name, static_cast<TObject *>(tempG)));
+    }
+    if (!oMap.at(name)->InheritsFrom("TGraphErrors"))
+    {
+        std::cerr << "Object " << name << " refers to something other than a TGraph*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    // static_cast<TGraphErrors*>(oMap.at(name))->AddPointError(valuex,valuey,errx,erry);
+}
+
+void HistPlotter::Fill1D(const std::string &name, int nbinsx, float xlow, float xhigh, float value)
+{
+    /*! \fn void Fill1D()
+        \brief
+        - Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+        - Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \return No return void
+    */
+    auto result = oMap.find(name); // result is an iterator
+    if (result == oMap.end())
+    {
+        TH1F *temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name, static_cast<TObject *>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+    }
+    else if (foldersForObjects.find(oMap.at(name)) != foldersForObjects.end())
+    { // shouldn't have a folder associated with it
+        std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] << ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    // Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if (!oMap.at(name)->InheritsFrom("TH1F"))
+    {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    // static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill1D(const std::string &name, int nbinsx, float xlow, float xhigh, float value, const std::string &foldername)
+{
+    /*! \fn void Fill1D()
+        \brief
+      -  Creates a TH1F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH1*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not, defaults to toplevel.
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of bins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param value The bin corresponding to value in (nbinsx, xlow, xhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); // result is an iterator
+    if (result == oMap.end())
+    {
+        TH1F *temp1D = new TH1F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh);
+        oMap.insert(std::make_pair(name, static_cast<TObject *>(temp1D)));
+        onedimcache.insert(std::make_pair(name, std::vector<double>()));
+        onedimcache[name].reserve(16384);
+        if (foldername != "")
+        {
+            if (folderList.find(foldername) == folderList.end())
+            {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject *>(temp1D), foldername));
+        }
+    }
+    else
+    {
+        // object is present in map, but we enforce unique names
+        // it must already have a folder attached to it
+        if (foldersForObjects.find(oMap.at(name)) == foldersForObjects.end())
+        {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+        else if (foldersForObjects[oMap[name]] != foldername)
+        {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] << ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+    // Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if (!oMap.at(name)->InheritsFrom("TH1F"))
+    {
+        std::cerr << "Object " << name << " refers to something other than a TH1*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    onedimcache[name].emplace_back(value);
+    // static_cast<TH1F*>(oMap.at(name))->Fill(value);
+}
+
+void HistPlotter::Fill2D(const std::string &name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey)
+{
+    /*! \fn void Fill2D()
+        \brief
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); // result is an iterator
+    if (result == oMap.end())
+    {
+        TH2F *temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name, static_cast<TObject *>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(), std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+    }
+    else if (foldersForObjects.find(oMap.at(name)) != foldersForObjects.end())
+    { // shouldn't have a folder associated with it
+        std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] << ", choose a different name for the histogram to be stored in toplevel .." << std::endl;
+    }
+
+    // Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if (!oMap.at(name)->InheritsFrom("TH2F"))
+    {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    // static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::Fill2D(const std::string &name, int nbinsx, float xlow, float xhigh, int nbinsy, float ylow, float yhigh, float valuex, float valuey, const std::string &foldername)
+{
+    /*! \fn void Fill2D()
+        \brief
+      -  Creates a TH2F in memory with name 'name' if it doesn't exist, and fills it with valuex, valuey
+      -  Writes present state to disk and fails with return value -1 if the name clashes with another object that's not of type TH2*
+      -  Remembers the foldername this particular histogram maps to, if provided. If not defaults to toplevel
+
+        \param name name of the TH1F histogram
+        \param nbinsx Number of xbins in the histogram
+        \param xlow Lower limit on x-axis
+        \param xhigh Upper limit on x-axis
+        \param nbinsy Number of ybins in the histogram
+        \param ylow Lower limit on y-axis
+        \param yhigh Upper limit on y-axis
+        \param valuex
+        \param valuey The bin corresponding to (valuex, valuey) in (nbinsx, xlow, xhigh, ybinsx, ylow, yhigh) is incremented by 1
+        \param foldername Name of the folder to put this histogram into. Defaults to toplevel if left empty
+        \return No return -- void
+    */
+
+    auto result = oMap.find(name); // result is an iterator
+    if (result == oMap.end())
+    {
+        TH2F *temp2D = new TH2F(name.c_str(), name.c_str(), nbinsx, xlow, xhigh, nbinsy, ylow, yhigh);
+        oMap.insert(std::make_pair(name, static_cast<TObject *>(temp2D)));
+        twodimcache.insert(std::make_pair(name, std::make_pair(std::vector<double>(), std::vector<double>())));
+        twodimcache[name].first.reserve(16384);
+        twodimcache[name].second.reserve(16384);
+        if (foldername != "")
+        {
+            if (folderList.find(foldername) == folderList.end())
+            {
+                folderList.insert(foldername);
+            }
+            foldersForObjects.insert(std::make_pair(static_cast<TObject *>(temp2D), foldername));
+        }
+    }
+    else
+    {
+        // object is present in map, but we enforce unique names
+        // it must already have a folder attached to it
+        if (foldersForObjects.find(oMap.at(name)) == foldersForObjects.end())
+        {
+            std::cerr << "Object " << name << " already registered at toplevel, choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+        else if (foldersForObjects[oMap.at(name)] != foldername)
+        {
+            std::cerr << "Object " << name << " already registered at " << foldersForObjects[oMap[name]] << ", choose a different name for the histogram to be stored in " << foldername << " folder .." << std::endl;
+        }
+    }
+
+    // Check if the string 'name' maps to a 1D hist. If there's any other object by this name raise issue
+    if (!oMap.at(name)->InheritsFrom("TH2F"))
+    {
+        std::cerr << "Object " << name << " refers to something other than a TH2*, not filling it hence!" << std::endl;
+        std::cerr << "Abort.." << std::endl;
+        FlushToDisk();
+        exit(-1);
+    }
+    twodimcache[name].first.emplace_back(valuex);
+    twodimcache[name].second.emplace_back(valuey);
+    // static_cast<TH2F*>(oMap.at(name))->Fill(valuex,valuey);
+}
+
+void HistPlotter::ReadCuts(std::string filename)
+{
+    /*! \fn void ReadCuts()
+        \brief  Reads a list of cuts from a file. The file must have the format below, two columns
+                   - Column#1 - path to a file that contains a single TCutG object named "CUTG", the default name in ROOT.
+                   - Column#2 - The identifier name you plan to use in the code, like 'protonbarrelpid' or something, that will be searched by FindCut()
+        \param filename name of the plainxtext file containing the cut file locations and identifiers
+        \return No return -- void
+    */
+
+    std::ifstream infile;
+    infile.open(filename);
+    std::string cutfilename, cutname;
+    for (std::string line; std::getline(infile, line);)
+    {
+        if (line.size() != 0 && line[0] == '#')
+            ; // don't do anything with '#' lines
+        else
+        {
+            std::stringstream ss(line);
+            ss >> cutfilename >> cutname;
+
+            TFile f(cutfilename.c_str());
+            if (f.IsZombie())
+            {
+                std::cerr << "Cannot open cutfile " << cutfilename << " .. skipping.." << std::endl;
+                continue;
+            }
+            TCutG *cut = (TCutG *)(f.Get("CUTG"));
+            cutsMap.insert(std::make_pair(cutname, static_cast<TObject *>(cut)));
+            f.Close();
+        } // else
+    } // for loop
+    infile.close();
+}
+
+void HistPlotter::PrintObjects()
+{
+    /*
+        void PrintObjects()
+        Prints the contents of the unordered_maps oMap and cutsMap to facilitate debugging
+
+    */
+    std::cout << "Type | Name " << std::endl;
+    std::cout << "---- | --------------------- " << std::endl;
+    for (auto it = oMap.begin(); it != oMap.end(); it++)
+    {
+        std::cout << it->second->ClassName() << " | " << it->first << std::endl;
+    }
+    for (auto it = cutsMap.begin(); it != cutsMap.end(); it++)
+    {
+        std::cout << it->second->ClassName() << " | " << it->first << std::endl;
+    }
+    std::cout << "---- | --------------------- " << std::endl;
+}
+
+#endif

Armory/Hit.h

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

Armory/Kinematics.cpp

@@ -0,0 +1,111 @@
+#include "Kinematics.h"
+//#include "elastcaller.h"
+//double Kinematics::getQval(double m1, double m2, double m3, double t1, double t3, double angle3)
+double Kinematics::getExc(double t3, double angle3)
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \return Excitation energy of the heavy-recoil nucleus in MeV
+*/
+{
+    double m1 = m_A;
+    double m2 = m_d;
+    double m3 = m_p;
+    double m4 = m_B;
+    double t1 = E_beam;
+    //t1 = slowitdown("75Ga",t1,"1(12C)2(2H)",1.2);
+
+    m1 *= u_MeV;
+    m2 *= u_MeV;
+    m3 *= u_MeV;
+    m4 *= u_MeV;
+
+    double e1 = m1 + t1;
+    double e3 = m3 + t3;
+    ET = t1 + m1 + m2;
+    double p1 = TMath::Sqrt(t1*t1 + 2*m1*t1);
+    double p3 = TMath::Sqrt(t3*t3 + 2*m3*t3);
+    double cosTheta = TMath::Cos(angle3*TMath::Pi()/180.);
+//    return m1+m2-m3-TMath::Sqrt(m1*m1 + m2*m2 + m3*m3 + 2.*m2*e1 - 2.*e3*(e1+m2)+ 2.*p1*p3*cosTheta);
+    double Q =  m1+m2-m3-TMath::Sqrt(m1*m1 + m2*m2 + m3*m3 + 2.*m2*e1 - 2.*e3*(e1+m2)+ 2.*p1*p3*cosTheta);
+
+    Qx = Q;
+    T4 = ET - e3 - (m1+m2-m3-Q);
+    //T4 = slowitdown("75Ga",T4,"1(12C)2(2H)",1.2);
+    P4 = TMath::Sqrt(T4*T4 + 2*m4*T4);
+
+    //this angle will not be affected by eloss
+    theta4 = (180./M_PI)*TMath::ASin((p3/P4)*TMath::Sin(angle3*M_PI/180.));
+
+//    T4-=16.5; //eloss in about 1.4 mg CD2
+    T4-=15.5; //eloss in 1.35 mg CD2 //TODO: actually degrade recoil/ejectiles in target
+//    T4-=14.1; //eloss in about 1.2 mg CD2
+//    T4-=31.7; //eloss in 2.7 mg CD2
+
+    //recalculate everything other than angle with lowered Kinetic energy
+    P4 = TMath::Sqrt(T4*T4 + 2*m4*T4);
+    gamma4 = T4/m4+1.;
+    beta4 = TMath::Sqrt(1. - 1./(gamma4*gamma4));
+    //beta4 = TMath::Sqrt((P4*P4)/(P4*P4 + m4*m4));
+    theta4 = (180./M_PI)*TMath::ASin((p3/P4)*TMath::Sin(angle3*M_PI/180.));
+
+    return Q0 - Q;//Q0  = Q + Exc
+
+}
+
+double Kinematics::getBeta4(double t3, double angle3) 
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \return doppler-shift beta (=v/c) of the heavy-recoil nucleus, calls getExc() to fill the value
+*/
+{
+    getExc(t3, angle3);
+    return beta4;
+}
+
+double Kinematics::getBrho(double t3, double angle3, double charge_state) {
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \param charge_state charge state of the intended nucleus, in units of elementary charge (= +1 for H+, +2 for He2+ etc).
+  \return b-rho value, generated from P4*3.3359e-3/charge_state where P4 is 4momentum of heavy-recoil calculated from orruba kinematics
+*/
+	getExc(t3,angle3);
+	return P4*3.3359e-3/charge_state;
+}
+
+double Kinematics::getTheta4(double t3, double angle3) {
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \param charge_state charge state of the intended nucleus, in units of elementary charge (= +1 for H+, +2 for He2+ etc).
+  \return lab theta value of heavy recoil in degrees
+*/
+	getExc(t3,angle3);
+	return theta4;
+}

Armory/Kinematics.h

@@ -0,0 +1,207 @@
+#ifndef KINEMATICS_H
+#define KINEMATICS_H
+#include <TMath.h>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <TVector3.h>
+const double u_MeV = 931.49410372; //u in MeV
+
+class Kinematics {
+public:
+	/*
+		A(d,p)B is used as template, with A being beam, and p being ejectile.
+		Always, make m3 the thing you detect, and m1 the beam
+	*/
+    double m_A, m_d, m_p, m_B;
+    double E_beam;
+
+/**
+ * @{ \name List of funny impossible default values
+ */
+/**
+ * \brief Default values used for all the physics values
+ */
+    double Q0=-9999, Qx=-9999;
+    double P4=-9999, E4=-9999, T4=-9999; //heavy recoil momentum, totE, KE
+    double P3=-9999, E3=-9999, T3=-9999; //light recoil
+    double ET=-9999;
+    double gamma4=-9999, beta4=-9999, theta4=-9999; //theta=heavy-recoil lab angle
+    double brho=-9999;
+/**
+ * @}
+ */
+    Kinematics(double m1, double m2, double m3, double m4, double ebeam) {
+	/*
+		A(d,p)B is used as template, with A being beam, and p being ejectile.
+		Always, make m3 the thing you detect, m2 the target, and m1 the beam
+		
+		ebeam is in MeV/u, all others are in amu
+	*/
+        m_A = m1;
+        m_d = m2;
+        m_p = m3, m_B = m4, E_beam = ebeam*m_A;
+        Q0 = (- m_B - m_p + m_d + m_A)*u_MeV;
+    }
+    Kinematics() {}
+
+    void setValues(double m1, double m2, double m3, double m4, double ebeam) {
+	/*
+		Can be used to 'live update' say the beam energy in the case of active target detectors.
+	*/
+
+        m_A = m1;
+        m_d = m2;
+        m_p = m3, m_B = m4, E_beam = ebeam*m_A;
+        Q0 = (- m_B - m_p + m_d + m_A)*u_MeV;
+        //std::cout << "Q0 MeV: " << Q0 << std::endl;
+    }
+
+    void setEBeam(double Ebeam) {E_beam = Ebeam;}
+
+    double getBeta4(double t3, double angle3);
+    double getTheta4(double t3, double angle3);
+    double getBrho(double t3, double angle3, double charge_state);
+    double getExc(double t3, double angle3); //t3 is proton energy detected in ORRUBA, angle3 is proton angle in degrees
+
+    double getBeta4_fromvec(double t3, const TVector3 &pos, const TVector3 &origin) {
+        TVector3 local = pos - origin; //position w.r.t origin
+        float angle = local.Theta()*180./M_PI;
+        return getBeta4(t3, angle);
+    }
+
+    double getExc_fromvec(double t3, const TVector3 &pos, const TVector3 &origin) {
+        TVector3 local = pos - origin; //position w.r.t origin
+        float angle = local.Theta()*180./M_PI;
+        return getExc(t3, angle);
+    }
+
+    void setValuesFromFile(const std::string& filename) {
+    	(void) filename;
+        /*std::ifstream in;
+        in.open(filename);
+        if(!in) {
+            std::cerr<< "File not open at " << filename << std::endl;
+            return;
+        }
+        for(std::string line; std::getline(in, line); ) {
+            if(line.size()!=0 && line[0]=='#')
+                ; //don't do anything with '#' lines
+            else {
+                std::stringstream ss(line);
+                ss>>m_A>>m_d>>m_p>>m_B>>E_beam;
+            }
+        }
+        in.close();*/
+
+    }
+};
+
+//double Kinematics::getQval(double m1, double m2, double m3, double t1, double t3, double angle3)
+double Kinematics::getExc(double t3, double angle3)
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  
+  All calculations are done here, and other wrapper functions written make derived quantities from stuff calculated here.
+  
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \return Excitation energy of the heavy-recoil nucleus in MeV
+*/
+{
+    double m1 = m_A;
+    double m2 = m_d;
+    double m3 = m_p;
+    double m4 = m_B;
+    double t1 = E_beam; 
+
+    m1 *= u_MeV;
+    m2 *= u_MeV;
+    m3 *= u_MeV;
+    m4 *= u_MeV;
+
+    double e1 = m1 + t1;
+    double e3 = m3 + t3;
+    ET = t1 + m1 + m2;
+    double p1 = TMath::Sqrt(t1*t1 + 2*m1*t1);
+    double p3 = TMath::Sqrt(t3*t3 + 2*m3*t3);
+    double cosTheta = TMath::Cos(angle3*TMath::Pi()/180.);
+//    return m1+m2-m3-TMath::Sqrt(m1*m1 + m2*m2 + m3*m3 + 2.*m2*e1 - 2.*e3*(e1+m2)+ 2.*p1*p3*cosTheta);
+    double Q =  m1+m2-m3-TMath::Sqrt(m1*m1 + m2*m2 + m3*m3 + 2.*m2*e1 - 2.*e3*(e1+m2)+ 2.*p1*p3*cosTheta);
+
+    Qx = Q;
+    //Recoil properties just in case it's useful
+    T4 = ET - e3 - (m1+m2-m3-Q);
+    P4 = TMath::Sqrt(T4*T4 + 2*m4*T4);
+
+    //this angle will not be affected by eloss
+    theta4 = (180./M_PI)*TMath::ASin((p3/P4)*TMath::Sin(angle3*M_PI/180.));
+
+    //recalculate everything other than angle with lowered Kinetic energy
+    P4 = TMath::Sqrt(T4*T4 + 2*m4*T4);
+    gamma4 = T4/m4+1.;
+    beta4 = TMath::Sqrt(1. - 1./(gamma4*gamma4));
+    theta4 = (180./M_PI)*TMath::ASin((p3/P4)*TMath::Sin(angle3*M_PI/180.));
+
+    return Q0 - Q;//Q0  = Q + Exc
+
+}
+
+double Kinematics::getBeta4(double t3, double angle3) 
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \return doppler-shift beta (=v/c) of the heavy-recoil nucleus, calls getExc() to fill the value
+*/
+{
+    getExc(t3, angle3);
+    return beta4;
+}
+
+double Kinematics::getBrho(double t3, double angle3, double charge_state) {
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \param charge_state charge state of the intended nucleus, in units of elementary charge (= +1 for H+, +2 for He2+ etc).
+  \return b-rho value, generated from P4*3.3359e-3/charge_state where P4 is 4momentum of heavy-recoil calculated from orruba kinematics
+*/
+	getExc(t3,angle3);
+	return P4*3.3359e-3/charge_state;
+}
+
+double Kinematics::getTheta4(double t3, double angle3) {
+/*
+  \brief Follows convention in Marion, 2013: (1 - beam, 2- target, 3-ejectile, 4-recoil)
+
+  m1 is beam, (typically heavy nucleus)
+  m2 is 'd', (light target)
+  m3 is 'p', (light ejectile mass)
+  t1 is beam kinetic energy,
+  \param t3 lab-kinetic-energy in MeV
+  \param angle3 lab-angle in deg of detected proton (if d,p) or other charged particle
+  \param charge_state charge state of the intended nucleus, in units of elementary charge (= +1 for H+, +2 for He2+ etc).
+  \return lab theta value of heavy recoil in degrees
+*/
+	getExc(t3,angle3);
+	return theta4;
+}
+
+
+#endif

Armory/LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
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+have designed this version of the GPL to prohibit the practice for those
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+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
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Armory/Makefile

@@ -10,7 +10,7 @@ COPTS	=	-fPIC -DLINUX -g -O0 -Wall -std=c++17 -lpthread
 
 ROOTLIBS = `root-config --cflags --glibs`
 
-ALL = Mapper AnasenMS
+ALL = Mapper EventBuilder#AnasenMS
 
 #########################################################################
 
@@ -23,6 +23,10 @@ Mapper	:	Mapper.cpp  ../mapping.h ClassDet.h
 		@echo "--------- making Mapper"
 		$(CC) $(COPTS) -o Mapper Mapper.cpp $(ROOTLIBS)
 
-AnasenMS : constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h anasenMS.cpp 
+# AnasenMS : constant.h Isotope.h ClassTransfer.h ClassSX3.h ClassPW.h ClassAnasen.h anasenMS.cpp 
-		@echo "--------- making ANASEN Monte Carlo"
+# 		@echo "--------- making ANASEN Monte Carlo"
-		$(CC) $(COPTS) -o AnasenMS anasenMS.cpp $(ROOTLIBS)
+# 		$(CC) $(COPTS) -o AnasenMS anasenMS.cpp $(ROOTLIBS)
+
+EventBuilder : EventBuilder.cpp ClassData.h fsuReader.h Hit.h
+		@echo "--------- making EventBuilder"
+		$(CC) $(COPTS) -o EventBuilder EventBuilder.cpp $(ROOTLIBS) 

Armory/Mapper.cpp

@@ -11,12 +11,14 @@
 #include "ClassDet.h"
 
 //===============================
-int main(int argc, char **argv){
+int main(int argc, char **argv)
+{
 
   printf("=========================================\n");
   printf("===               Mapper              ===\n");
-  printf("=========================================\n");  
+  printf("=========================================\n");
-  if (argc != 2)    {
+  if (argc != 2)
+  {
     printf("Incorrect number of arguments:\n");
     printf("%s [inFile]\n", argv[0]);
     printf("\n\n");
@@ -28,155 +30,188 @@ int main(int argc, char **argv){
 
   PrintMapping();
 
-  TFile * inFile = new TFile(inFileName.c_str(), "READ");
+  TFile *inFile = new TFile(inFileName.c_str(), "READ");
-  TTree * tree = (TTree*) inFile->Get("tree");
+  TTree *tree = (TTree *)inFile->Get("tree");
   unsigned long long totnumEntry = tree->GetEntries();
 
-  ULong64_t       evID;
+  ULong64_t evID;
-  UInt_t          multi;
+  UInt_t multi;
-  UShort_t         sn[MAXMULTI];
+  UShort_t sn[MAXMULTI];
-  UShort_t         ch[MAXMULTI];
+  UShort_t ch[MAXMULTI];
-  UShort_t          e[MAXMULTI];
+  UShort_t e[MAXMULTI];
-  UShort_t         e2[MAXMULTI];
+  UShort_t e2[MAXMULTI];
-  ULong64_t       e_t[MAXMULTI];
+  ULong64_t e_t[MAXMULTI];
-  UShort_t        e_f[MAXMULTI];
+  UShort_t e_f[MAXMULTI];
 
-  tree->SetBranchAddress("evID",  &evID);
+  tree->SetBranchAddress("evID", &evID);
   tree->SetBranchAddress("multi", &multi);
-  tree->SetBranchAddress("sn",    sn);
+  tree->SetBranchAddress("sn", sn);
-  tree->SetBranchAddress("ch",    ch);
+  tree->SetBranchAddress("ch", ch);
-  tree->SetBranchAddress("e",     e);
+  tree->SetBranchAddress("e", e);
-  tree->SetBranchAddress("e2",    e2);
+  tree->SetBranchAddress("e2", e2);
-  tree->SetBranchAddress("e_t",   e_t);
+  tree->SetBranchAddress("e_t", e_t);
-  tree->SetBranchAddress("e_f",   e_f);
+  tree->SetBranchAddress("e_f", e_f);
 
   ///================== new tree
   TString outFileName = inFileName;
-  TString runStr = outFileName; 
+  TString runStr = outFileName;
   int pos = outFileName.Last('/');
-  pos = outFileName.Index("_", pos+1); // find next "_"
+  pos = outFileName.Index("_", pos + 1); // find next "_"
-  runStr.Remove(0, pos+1);
+  runStr.Remove(0, pos + 1);
   runStr.Remove(3);
-  pos = outFileName.Index("_", pos+1); // find next "_"
+  pos = outFileName.Index("_", pos + 1); // find next "_"
-  outFileName.Remove(pos); // remove the rest
+  outFileName.Remove(pos);               // remove the rest
   outFileName += "_mapped.root";
 
   ULong_t eventID;
   UInt_t run = runStr.Atoi();
-  
+
   Det sx3;
   Det qqq;
-  Det pc ;
+  Det pc;
+  Det misc;
 
   printf(" Raw root file : %s\n", inFileName.c_str());
   printf("           Run : %03d\n", run);
   printf("   total Entry : %lld \n", totnumEntry);
   printf(" Out file name : %s \n", outFileName.Data());
 
-  TFile * saveFile = new TFile( outFileName,"RECREATE");
+  TFile *saveFile = new TFile(outFileName, "RECREATE");
-  TTree * newTree =  new TTree("tree","tree");
+  TTree *newTree = new TTree("tree", "tree");
-  
 
-  newTree->Branch("evID",   &eventID,"eventID/l"); 
+  newTree->Branch("evID", &eventID, "eventID/l");
-  newTree->Branch("run",        &run,"run/i");  
+  newTree->Branch("run", &run, "run/i");
 
   newTree->Branch("sx3Multi", &sx3.multi, "sx3Multi/s");
-  newTree->Branch("sx3ID",    &sx3.id,    "sx3ID[sx3Multi]/s");
+  newTree->Branch("sx3ID", &sx3.id, "sx3ID[sx3Multi]/s");
-  newTree->Branch("sx3Ch",    &sx3.ch,    "sx3Ch[sx3Multi]/s");
+  newTree->Branch("sx3Ch", &sx3.ch, "sx3Ch[sx3Multi]/s");
-  newTree->Branch("sx3E",     &sx3.e,     "sx3Energy[sx3Multi]/s");
+  newTree->Branch("sx3E", &sx3.e, "sx3Energy[sx3Multi]/s");
-  newTree->Branch("sx3T",     &sx3.t,     "sx3Time[sx3Multi]/l");
+  newTree->Branch("sx3T", &sx3.t, "sx3Time[sx3Multi]/l");
 
   newTree->Branch("qqqMulti", &qqq.multi, "qqqMulti/s");
-  newTree->Branch("qqqID",    &qqq.id,    "qqqID[qqqMulti]/s");
+  newTree->Branch("qqqID", &qqq.id, "qqqID[qqqMulti]/s");
-  newTree->Branch("qqqCh",    &qqq.ch,    "qqqCh[qqqMulti]/s");
+  newTree->Branch("qqqCh", &qqq.ch, "qqqCh[qqqMulti]/s");
-  newTree->Branch("qqqE",     &qqq.e,     "qqqEnergy[qqqMulti]/s");
+  newTree->Branch("qqqE", &qqq.e, "qqqEnergy[qqqMulti]/s");
-  newTree->Branch("qqqT",     &qqq.t,     "qqqTime[qqqMulti]/l");
+  newTree->Branch("qqqT", &qqq.t, "qqqTime[qqqMulti]/l");
-  newTree->Branch("qqqSN",    &qqq.sn,     "qqqSN[qqqMulti]/s");
+  newTree->Branch("qqqSN", &qqq.sn, "qqqSN[qqqMulti]/s");
 
   newTree->Branch("pcMulti", &pc.multi, "pcMulti/s");
-  newTree->Branch("pcID",    &pc.id,    "pcID[pcMulti]/s");
+  newTree->Branch("pcID", &pc.id, "pcID[pcMulti]/s");
-  newTree->Branch("pcCh",    &pc.ch,    "pcCh[pcMulti]/s");
+  newTree->Branch("pcCh", &pc.ch, "pcCh[pcMulti]/s");
-  newTree->Branch("pcE",     &pc.e,     "pcEnergy[pcMulti]/s");
+  newTree->Branch("pcE", &pc.e, "pcEnergy[pcMulti]/s");
-  newTree->Branch("pcT",     &pc.t,     "pcTime[pcMulti]/l");
+  newTree->Branch("pcT", &pc.t, "pcTime[pcMulti]/l");
+
+  newTree->Branch("miscMulti", &misc.multi, "miscMulti/s");
+  newTree->Branch("miscID", &misc.id, "miscID[miscMulti]/s");
+  newTree->Branch("miscCh", &misc.ch, "miscCh[miscMulti]/s");
+  newTree->Branch("miscE", &misc.e, "miscEnergy[miscMulti]/s");
+  newTree->Branch("miscT", &misc.t, "miscTime[miscMulti]/l");
+  newTree->Branch("miscF", &misc.tf, "miscFineTime[miscMulti]/l");
 
   ///================== looping old tree and apply mapping
 
-  //clock   
+  // clock
-  // TBenchmark clock;
+  //  TBenchmark clock;
-  // Bool_t shown;
+  //  Bool_t shown;
 
-  for( unsigned long long ev = 0; ev < totnumEntry; ev++){
+  for (unsigned long long ev = 0; ev < totnumEntry; ev++)
+  {
     tree->GetEntry(ev);
 
     eventID = evID;
     sx3.multi = 0;
     qqq.multi = 0;
     pc.multi = 0;
+    misc.multi = 0;
 
+    sx3.Clear();
+    sx3.Clear();
     qqq.Clear();
+    pc.Clear();
+    misc.Clear();
+    pc.Clear();
+    misc.Clear();
 
-    for( unsigned int i = 0; i < multi; i++){
+    for (unsigned int i = 0; i < multi; i++)
+    {
 
       // printf("%10u/%10u| %5d, %2u, %6u, %14llu\n", i, multi, sn[i], ch[i], e[i], e_t[i] );
-      
+
-      //globalCh = digi-ID * nCh(digi-iD) + ch
+      // globalCh = digi-ID * nCh(digi-iD) + ch
       int globalCh = -1;
 
-      for( int j = 0; j < nBd; j++){
+      for (int j = 0; j < nBd; j++)
-        if( board.at(j) == sn[i]){
+      {
-          globalCh = (sn[i] > 1000 ? j * 64 :  7*64 + (j-7) * 16) + ch[i]; //& = number V1740
+        if (board.at(j) == sn[i])
+        {
+          globalCh = (sn[i] > 1000 ? j * 64 : 7 * 64 + (j - 7) * 16) + ch[i]; //& = number V1740
           break;
         }
       }
-      
+
-      if( globalCh == -1) printf("ev %llu\n", ev);
+      if (globalCh == -1)
+        printf("ev %llu\n", ev);
 
       unsigned short ID = mapping[globalCh];
 
       //=================================== sx3
-      if( ID < 10000 ) {
+      if (ID < 10000)
+      {
         sx3.id[sx3.multi] = ID / 100;
         sx3.ch[sx3.multi] = ID % 100;
         sx3.e[sx3.multi] = e[i];
         sx3.t[sx3.multi] = e_t[i];
-        sx3.multi ++;
+        sx3.multi++;
       }
 
       //=================================== qqq
-      if( 10000 <= ID && ID < 20000 ) {
+      if (10000 <= ID && ID < 20000)
+      {
         qqq.id[qqq.multi] = (ID - 10000) / 100;
         qqq.ch[qqq.multi] = (ID - 10000) % 100;
         qqq.e[qqq.multi] = e[i];
         qqq.t[qqq.multi] = e_t[i];
         qqq.sn[qqq.multi] = sn[i];
-        qqq.multi ++;
+        qqq.multi++;
       }
 
       //=================================== pc
-      if( 20000 <= ID && ID < 30000 ) {
+      if (20000 <= ID && ID < 30000)
+      {
         pc.id[pc.multi] = (ID - 20000) / 100;
         pc.ch[pc.multi] = (ID - 20000) % 100;
         pc.e[pc.multi] = e[i];
         pc.t[pc.multi] = e_t[i];
-        pc.multi ++;
+        pc.multi++;
+      }
+
+      //=================================== misc
+      if (30000 <= ID && ID < 40000)
+      {
+        misc.id[misc.multi] = (ID - 30000) / 100;
+        misc.ch[misc.multi] = (ID - 30000) % 100;
+        misc.e[misc.multi] = e[i];
+        misc.t[misc.multi] = e_t[i];
+        misc.tf[misc.multi] = e_f[i];
+        // if( ID == 30002 || ID == 30004 ) printf("sn : %d ch: %2d | gID %3d | ID %6d | e_f : %d\n", sn[i], ch[i], globalCh, ID, e_f[i]);
+        misc.multi++;
       }
     }
-    
-    saveFile->cd(); //set focus on this file
-    newTree->Fill();
-    
-    if( eventID % 100 == 0 ) printf("%6lu/%6llu [%2d%%]\n\033[A\r", eventID, totnumEntry, TMath::Nint((eventID+1)*100./totnumEntry));
 
+    saveFile->cd(); // set focus on this file
+    newTree->Fill();
+
+    if (eventID % 100 == 0)
+      printf("%6lu/%6llu [%2d%%]\n\033[A\r", eventID, totnumEntry, TMath::Nint((eventID + 1) * 100. / totnumEntry));
   }
 
   inFile->Close();
 
-  saveFile->cd(); //set focus on this file
+  saveFile->cd(); // set focus on this file
-  newTree->Write(); 
+  newTree->Write();
   UInt_t eventNumber = newTree->GetEntries();
   saveFile->Close();
   printf("-------------- done,  %u\n", eventNumber);
-  
-  return 0;
 
+  return 0;
 }

Armory/PCZRecon.h

@@ -0,0 +1,331 @@
+#ifndef PCZRecon_h
+#define PCZRecon_h
+
+// PC Z-position reconstruction, one section per anode/cathode topology:
+// A1C0 (single anode wire only), A2C0 (two-wire anode cluster, no cathode --
+// same math as A1C0, see that section), A1C1 (anode + single cathode, charge
+// division), A1C2 (anode + two cathodes, "step ladder" correction). Each topology gets one
+// well-defined entry point instead of the math being split across files by
+// historical accident (A1C0/A1C1 used to live in TrackRecon.C itself; A1C2's
+// underlying model lives in the separately-shared PC_StepLadder_Correction.h
+// -- see the A1C2 section below for why that one isn't just moved in).
+//
+// This header holds the reconstruction MATH only. The per-dataset tuning
+// constants it reads (cfrac fit parameters, dead-wire lists, Z calibration,
+// beam-axis origin) are still owned and set by TrackRecon.C's Begin() --
+// this header just declares them `extern` so the same single translation
+// unit (TrackRecon.C is compiled as one .C file via ACLiC) can see them.
+// Moving the constants themselves out is a separate, riskier change and is
+// deliberately NOT done here.
+//
+// Relocated verbatim from TrackRecon.C (no logic changes): A1C1CellSol,
+// A1C1Sol, solve_cell, a1c1_solve, SideChoice, a1c1_pick_side, a1c1_zcorr,
+// a1c0_hybrid_pcz (split into a1c0_wirePos + a1c0_hybrid_pcz).
+//
+// New in this header (see call-site migration notes where each is used):
+// a1c1_solve_pick, a1c1_cfrac_pcz, a1c2_zfix.
+
+#include <TVector3.h>
+#include <TRandom3.h>
+#include <TMath.h>
+#include "ClassPW.h"
+
+// --- Per-dataset tuning constants, defined and set in TrackRecon.C ---
+extern PW pwinstance;
+extern const double a1c1_zg[8];
+extern double a1c1_cfmin_cell[7];
+extern double a1c1_k_cell[7];
+extern double a1c1_cfmin2_cell[7];
+extern double a1c1_k2_cell[7];
+extern double a1c1_cfrac_split;
+extern double a1c1_lowband_rfactor;
+extern double a1c1_missing_fmax;
+extern double a1c1_z_scale_qqq;
+extern double a1c1_z_off_qqq;
+extern double a1c1_z_scale_sx3;
+extern double a1c1_z_off_sx3;
+bool a1c1_missing_neighbor(int awire, int cwire); // TrackRecon.C: dead-wire-adjacency check
+TVector3 beamVertex(const TVector3 &si, const TVector3 &dir);
+double beamPerp(const TVector3 &p);
+
+// ---------------------------------------------------------------------
+// A1C0: single-wire (anode only) position reconstruction
+// ---------------------------------------------------------------------
+
+// Anode-wire Z, corrected by the a1c1-derived scale+offset (a1c1_zcorr),
+// same reference frame the a1c1 solve below reports in.
+inline double a1c1_zcorr(double z_a1c0, bool isQQQ)
+{
+  double scale = isQQQ ? a1c1_z_scale_qqq : a1c1_z_scale_sx3;
+  double off = isQQQ ? a1c1_z_off_qqq : a1c1_z_off_sx3;
+  return z_a1c0 * (1.0 - scale) - off;
+}
+
+// The raw (undithered) A1C0 wire position: nearest-wire XY at the given
+// track phi, Z corrected into the same frame a1c1 uses. This is what
+// _rawZ_a1c0 / phi cuts / _dPhi_a1c0-style diagnostics should read --
+// anywhere you want the true discretized wire position, not a smoothed one.
+inline TVector3 a1c0_wirePos(const std::pair<TVector3, TVector3> &apwire, double phi, bool isQQQ)
+{
+  TVector3 pc = pwinstance.getClosestWirePosAtWirePhi(apwire, phi);
+  pc.SetZ(a1c1_zcorr(pc.Z(), isQQQ));
+  return pc;
+}
+
+// a1c0_wirePos, then Gaussian-dithered in Z to hide wire-pitch quantization.
+// sigma is the caller's choice (dither_sigma or dither_sigma_c0/2.0 etc in
+// TrackRecon.C) -- this function doesn't know which convention is "correct"
+// for a given call site, only how to apply whichever sigma it's given.
+inline TVector3 a1c0_hybrid_pcz(const std::pair<TVector3, TVector3> &apwire, double phi,
+                                bool isQQQ, double sigma, TRandom3 &rand)
+{
+  TVector3 pc = a1c0_wirePos(apwire, phi, isQQQ);
+  pc.SetZ(rand.Gaus(pc.Z(), sigma));
+  return pc;
+}
+
+// ---------------------------------------------------------------------
+// A2C0: two-wire anode-cluster (charge-shared), no-cathode position
+// reconstruction
+// ---------------------------------------------------------------------
+//
+// Same math as A1C0 above -- pseudowire + phi-minimization, no dither --
+// just handed a genuine 2-wire energy-weighted pseudowire (GetPseudoWire
+// over a 2-wire anode cluster) instead of a single real wire. a1c0_wirePos
+// already treats its `apwire` argument as an opaque pseudowire pair
+// regardless of how many physical wires went into it, so this is a
+// documented, named entry point rather than new math: call sites can say
+// what topology they mean instead of reusing a1c0_wirePos silently and
+// trusting a comment to explain why.
+//
+// Deliberately no dithered twin (no a2c0_hybrid_pcz): A2C0 is meant to feed
+// the reaction-analysis plots at its raw, undithered resolution, not stand
+// in for a1c0_hybrid_pcz's benchmark-truth-comparison role. If a "genuine
+// A2C0" BenchMark validation block is ever wanted (mirroring the existing
+// aClusters.size()==1 && cClusters.size()==0 A1C0 block in TrackRecon.C),
+// add one there rather than adding dithering here.
+inline TVector3 a2c0_wirePos(const std::pair<TVector3, TVector3> &apwire, double phi, bool isQQQ)
+{
+  return a1c0_wirePos(apwire, phi, isQQQ);
+}
+
+// ---------------------------------------------------------------------
+// A1C1: single-anode + single-cathode charge-division position reconstruction
+// ---------------------------------------------------------------------
+
+struct A1C1CellSol
+{
+  int cell = -1;
+  double pcz = -99999;
+  double f = 0.0;
+  double pitch = 0.0;
+  bool inband = false;
+  bool pitchok = false;
+};
+
+struct A1C1Sol
+{
+  int band;
+  double cfrac_used;
+  double pcz_lo;
+  double pcz_hi;
+  A1C1CellSol hi;
+  A1C1CellSol lo;
+};
+
+inline A1C1CellSol solve_cell(int cell, int wf, double zf, double cfrac,
+                              const double *cfmin, const double *kk, bool dead_neighbor)
+{
+  A1C1CellSol s;
+  s.cell = cell;
+  s.pcz = zf; // safe sentinel: fired-wire position so edge-wire defaults don't read as z=0
+
+  if (cell < 0 || cell > 6)
+    return s;
+
+  double zc = 0.5 * (a1c1_zg[cell] + a1c1_zg[cell + 1]);   // cell centre
+  double half = 0.5 * (a1c1_zg[cell] - a1c1_zg[cell + 1]); // half-cell width
+  double pitch = a1c1_zg[cell] - a1c1_zg[cell + 1];        // full wire spacing
+
+  if (half <= 0.0 || kk[cell] <= 0.0)
+    return s;
+
+  s.pitch = pitch;
+
+  // f = 0 -> cell centre, f = 1 -> fired wire. Outside [0,1] = outside the band.
+  s.f = (cfrac - cfmin[cell]) / kk[cell];
+
+  // sign maps increasing f toward the fired cathode wire.
+  double sgn = (a1c1_zg[wf] >= zc) ? +1.0 : -1.0;
+  s.pcz = zc + sgn * s.f * half;
+
+  double fmax = dead_neighbor ? a1c1_missing_fmax : 1.0;
+  s.inband = (s.f >= 0.0 && s.f <= fmax);
+
+  // Reconstructed position should remain within one cell pitch of the fired wire.
+  s.pitchok = (TMath::Abs(s.pcz - zf) <= pitch);
+
+  return s;
+}
+
+inline A1C1Sol a1c1_solve(double cfrac, double zf, int cwire = -1, double anodeE = -1, int awire = -1)
+{
+  A1C1Sol s{0, cfrac, zf, zf, {}, {}};
+  const double *cfmin = a1c1_cfmin_cell;
+  const double *kk = a1c1_k_cell;
+  if (a1c1_cfrac_split > 0.0 && cfrac >= 0.0 && cfrac < a1c1_cfrac_split)
+  {
+    s.band = 1;
+    if (a1c1_lowband_rfactor > 0.0 && cfrac > 0.0 && cfrac < 1.0)
+    {
+      double r = cfrac / (1.0 - cfrac);
+      r *= a1c1_lowband_rfactor;
+      cfrac = r / (1.0 + r);
+    }
+    else
+    {
+      cfmin = a1c1_cfmin2_cell;
+      kk = a1c1_k2_cell;
+    }
+  }
+  s.cfrac_used = cfrac;
+
+  int wf = 0;
+  for (int i = 1; i < 8; ++i)
+    if (TMath::Abs(a1c1_zg[i] - zf) < TMath::Abs(a1c1_zg[wf] - zf))
+      wf = i;
+
+  bool dead_neighbor = a1c1_missing_neighbor(awire, cwire);           // same for both cells; hoist to avoid double scan
+  s.hi = solve_cell(wf - 1, wf, zf, cfrac, cfmin, kk, dead_neighbor); // cell above (higher z)
+  s.lo = solve_cell(wf, wf, zf, cfrac, cfmin, kk, dead_neighbor);     // cell below (lower z)
+  s.pcz_hi = s.hi.pcz;
+  s.pcz_lo = s.lo.pcz;
+  return s;
+}
+
+// Which of the two candidate cells the beam-axis test selects.
+enum class SideChoice
+{
+  High, // the cell ABOVE the fired wire (pcz_hi)
+  Low   // the cell BELOW the fired wire (pcz_lo)
+};
+
+// Picks between the two candidate cells (lo/hi) a1c1_solve returns.
+//
+// This used to compare beamVertex(si, ...)'s beamPerp for each candidate, but
+// that check is a no-op: both candidates share the same (cx, cy), so
+// beamVertex's t-parameter -- computed purely from dir.X()/dir.Y() -- comes out
+// identical for both, and therefore so does the resulting vertex X/Y and
+// beamPerp. The two disambiguating branches below were consequently dead code;
+// the function always fell through to returning Low regardless of the actual
+// physics.
+//
+// inband/pitchok DO differ between the two cells (each depends on cfrac's
+// position within that cell's own band), so they're used here for status
+// instead. The final tie-break prefers whichever candidate sits closer to the
+// fired wire itself, rather than farther into the next cell over.
+inline SideChoice a1c1_pick_side(const A1C1CellSol &lo, const A1C1CellSol &hi, double zf, int &status)
+{
+  bool okl = lo.inband && lo.pitchok;
+  bool okh = hi.inband && hi.pitchok;
+  status = (okl || okh) ? ((okl && okh) ? 1 : 0) : 2;
+  if (okl && !okh)
+    return SideChoice::Low;
+  if (okh && !okl)
+    return SideChoice::High;
+  double dl = TMath::Abs(lo.pcz - zf);
+  double dh = TMath::Abs(hi.pcz - zf);
+  return (dl <= dh) ? SideChoice::Low : SideChoice::High;
+}
+
+// a1c1_solve() + a1c1_pick_side() together, with the picked cell already
+// resolved. Every call site that needs more than just the final pcz (side
+// status, cell index, f, inband, pitchok -- e.g. for benchmark/diagnostic
+// histograms) was previously re-deriving this same 4-line pattern by hand;
+// this is that pattern, named once.
+struct A1C1PickedSol
+{
+  A1C1Sol sol;
+  SideChoice side = SideChoice::Low;
+  int side_status = -1;
+
+  const A1C1CellSol &best() const { return (side == SideChoice::High) ? sol.hi : sol.lo; }
+};
+
+inline A1C1PickedSol a1c1_solve_pick(double cfrac, double zf, const TVector3 &si, double cx, double cy,
+                                     int cwire = -1, double anodeE = -1, int awire = -1)
+{
+  // si/cx/cy are no longer used by the pick itself (see a1c1_pick_side above)
+  // but are kept in the signature so the ~10 existing call sites throughout
+  // TrackRecon.C don't need to change.
+  A1C1PickedSol out;
+  out.sol = a1c1_solve(cfrac, zf, cwire, anodeE, awire);
+  out.side = a1c1_pick_side(out.sol.lo, out.sol.hi, zf, out.side_status);
+  return out;
+}
+
+// Full pipeline: raw anode/cathode energies -> cfrac -> solve -> pick side ->
+// picked Z, plus whether the pick landed in-band. This is what most call
+// sites actually want (they don't need the intermediate A1C1Sol/side_status
+// unless they're doing benchmark diagnostics -- for that, call
+// a1c1_solve_pick directly instead).
+//
+// Takes primitives rather than TrackRecon.C's `Event` type so this header
+// has no dependency on TrackRecon.C's class definitions; see the thin
+// `Event`-taking overload kept in TrackRecon.C next to the `Event` class
+// for the short call-site spelling existing code uses.
+inline double a1c1_cfrac_pcz(double pcz_raw, double energyAnode, double energyCathode,
+                             double cx, double cy, int cathodeCh, int anodeCh,
+                             const TVector3 &si, bool &inband)
+{
+  inband = false;
+  double ac = energyAnode + energyCathode;
+  double cfrac = (ac > 0.0) ? energyCathode / ac : -1.0;
+  if (cfrac < 0.0)
+    return pcz_raw;
+  A1C1PickedSol picked = a1c1_solve_pick(cfrac, pcz_raw, si, cx, cy, cathodeCh, energyAnode, anodeCh);
+  const A1C1CellSol &best = picked.best();
+  inband = (best.inband && picked.side_status != 2);
+  return best.pcz;
+}
+
+// ---------------------------------------------------------------------
+// A1C2: two-cathode "step ladder" Z reconstruction
+// ---------------------------------------------------------------------
+//
+// Same step-ladder, pivot-about-cell-midpoint model as Armory/
+// PC_StepLadder_Correction.h's model_invert. That file is shared with
+// MakeVertex.C (a separate, parallel branch of development, out of scope
+// here) and a few scratch macros, so rather than include it or edit it,
+// this is a standalone copy -- keeping every TrackRecon.C reconstruction
+// path (A1C0/A1C1/A1C2) self-contained in this one header rather than
+// reaching into a file with unrelated consumers. If the underlying model
+// ever changes, both copies need the same edit; there are exactly two.
+//
+// Rewritten as a plain scalar function rather than kept in model_invert's
+// original `double f(double *y, double *p)` shape -- that signature only
+// existed to match TF1's raw-function-pointer constructor. TrackRecon.C
+// used to go through a `TF1 pcfix_func` purely to get a callable out of it,
+// calling only pcfix_func.Eval(z) at every site (npar `p` was never used,
+// and nothing called .Draw()/.Integral()/anything else TF1-specific) --
+// so the TF1 wrapper bought nothing. a1c2_zfix has the same scalar
+// in/scalar out shape as a1c0_wirePos/a1c1_solve above instead.
+inline double a1c2_zfix(double z)
+{
+  double result = z;
+  double slope = 0.52;
+  double z_grid[8] = {148.2677, 102.1111, 59.8527, 19.7248, -19.7248, -59.8527, -102.1111, -148.2677};
+
+  for (int i = 0; i < 7; i++)
+  {
+    if (z <= z_grid[i] && z > z_grid[i + 1])
+    {
+      double zavg = (z_grid[i] + z_grid[i + 1]) * 0.5; // midpoint about which we pivot
+      result = (z - zavg) / slope + zavg;
+      break;
+    }
+  }
+  return result;
+}
+
+#endif

Armory/PC_StepLadder_Correction.h

@@ -0,0 +1,82 @@
+#include <TF1.h>
+
+double model_invert(double *y, double *p)
+{
+    double result = y[0];
+    double slope = 0.52;
+    double z_grid[8] = {147.998, 101.946, 59.7634, 19.6965, -19.6965, -59.7634, -101.946, -147.998};
+    for (int i = 0; i < 7; i++)
+    {
+        if (y[0] <= z_grid[i] && y[0] > z_grid[i + 1])
+        {
+            double zavg = (z_grid[i] + z_grid[i + 1]) * 0.5; // midpoint about which we pivot
+            result = (y[0] - zavg) / slope + zavg;
+            break;
+        }
+    }
+    return result;
+}
+// ---- Parabola variant (now takes optional slope; out-of-band -> Si, no clamp-snap) ----
+inline double model_invert_a1c1(double cfrac, double z_si, double z_pivot,
+                                double C, const double* c0_table, bool& ok,
+                                double slope = 1.0)
+{
+    ok = false;
+    static const double z_grid[8] =
+        {147.998, 101.946, 59.7634, 19.6965, -19.6965, -59.7634, -101.946, -147.998};
+    const double cfrac_hi = 0.90, cfrac_lo = 0.12;
+    if (cfrac > cfrac_hi || cfrac < cfrac_lo) return z_si;
+
+    const double sgn = (z_si >= z_pivot) ? +1.0 : -1.0;
+    int gnb = -1; double z_nb = (sgn > 0) ? +1.0e30 : -1.0e30;
+    for (int i = 0; i < 8; ++i) {
+        if (sgn > 0 && z_grid[i] > z_pivot + 1e-6 && z_grid[i] < z_nb) { z_nb = z_grid[i]; gnb = i; }
+        if (sgn < 0 && z_grid[i] < z_pivot - 1e-6 && z_grid[i] > z_nb) { z_nb = z_grid[i]; gnb = i; }
+    }
+    if (gnb < 0) return z_si;
+    const double W = TMath::Abs(z_nb - z_pivot);
+    if (W <= 0.0) return z_si;
+    int cell = (sgn > 0) ? gnb : gnb - 1;
+    if (cell < 0) cell = 0; if (cell > 6) cell = 6;
+
+    double s2 = (c0_table[cell] - cfrac) / C;
+    if (s2 < 0.0 || s2 > 1.0) return z_si;          // out-of-band -> Si (no boundary snap)
+    double s = TMath::Sqrt(s2);
+    double z_rec = z_pivot + sgn * s * W;
+    if (slope > 0.0 && slope != 1.0) {
+        const double zc = 0.5 * (z_grid[cell] + z_grid[cell + 1]);
+        z_rec = (z_rec - zc) / slope + zc;
+    }
+    if (TMath::Abs(z_rec - z_si) > W) return z_si;
+    ok = true;
+    return z_rec;
+}
+
+// ---- Linear centre-fold variant ----
+inline double model_invert_a1c1_linear(double cfrac, double z_si, double z_pivot,
+                                        double k, const double* cfmin_table, bool& ok)
+{
+    ok = false;
+    static const double z_grid[8] =
+        {147.998, 101.946, 59.7634, 19.6965, -19.6965, -59.7634, -101.946, -147.998};
+    const double cfrac_hi = 0.90, cfrac_lo = 0.12;
+    if (cfrac > cfrac_hi || cfrac < cfrac_lo) return z_si;
+
+    int cell = -1;
+    for (int i = 0; i < 7; ++i)
+        if (z_si <= z_grid[i] && z_si > z_grid[i + 1]) { cell = i; break; }
+    if (cell < 0) return z_si;
+    const double zc   = 0.5 * (z_grid[cell] + z_grid[cell + 1]);
+    const double half = 0.5 * (z_grid[cell] - z_grid[cell + 1]);
+    if (half <= 0.0 || k <= 0.0) return z_si;
+
+    double f = (cfrac - cfmin_table[cell]) / k;
+    if (f < 0.0) f = 0.0;
+    if (f > 1.0) return z_si;
+    const double d   = f * half;
+    const double sgn = (z_pivot >= zc) ? +1.0 : -1.0;
+    const double z_rec = zc + sgn * d;
+    if (TMath::Abs(z_rec - z_si) > half) return z_si;
+    ok = true;
+    return z_rec;
+}

Armory/SX3Geom.h

@@ -0,0 +1,190 @@
+#ifndef SX3Geom_h
+#define SX3Geom_h
+#include <vector>
+
+const double DEFAULT_NULL=-987654321.;
+
+class sx3_geometry_scalefactors {
+public:
+    //If sx3 has L, R being the left and right extremities, we choose add, stretch here such that
+    // x_mm = (x_raw+add)*stretch; so add=abs(L), stretch=75/(abs(L)+R)
+    float add[4];
+    float stretch[4];
+};
+
+class qqq5_finegains {
+public:
+    std::array<std::pair<float,float>,32> front;
+    //front.at(30).first = slope at clkpos 0, ring 30 for E front layer
+    //front.at(30).second = intercept for the same as above
+    std::array<std::pair<float,float>,4> back;
+};
+class sx3_fbgains {
+public:
+    //Order of indices is [pad][strip]
+    float padoffsets[4][4];
+    float padgains[4][4];
+
+    float stripLoffsets[4][4];
+    float stripLgains[4][4];
+
+    float stripRoffsets[4][4];
+    float stripRgains[4][4];
+};
+
+std::array<sx3_fbgains,24> sx3_xtalk_gains; //every sx3 needs to be gainmatched as a frontL-back, frontR-back pair (pad strip pair)
+std::array<sx3_geometry_scalefactors,24> sx3gs;
+
+class sx3 {
+public:
+    //TODO: Convert to std::array
+    //Holds all information in an event, including ped subtraction+scaling. back[2].at(0) will have the largest energy seen in ch2, if any
+    std::vector<float> back[4];
+    std::vector<float> frontL[4];
+    std::vector<float> frontR[4];
+
+    double ts = DEFAULT_NULL;
+    //Easy lookup of final calibrated event. Only filled for valid cases, assumed for now to be 1L, 1R, 1B
+    float frontX=DEFAULT_NULL;
+    float frontXmm=DEFAULT_NULL;
+    float frontE=DEFAULT_NULL;
+    float backE=DEFAULT_NULL;
+    int stripF=DEFAULT_NULL;
+    int stripB=DEFAULT_NULL;
+    float frontEL=DEFAULT_NULL;
+    float frontER=DEFAULT_NULL;
+
+    float phi=DEFAULT_NULL; //
+
+    std::set<int> valid_front_chans;
+    std::set<int> valid_back_chans;
+    std::set<int> unmatched_front_chans; //every front channel is unmatched and invalid at first. when it gets matched, it gets removed and sent to valid
+
+    bool foundevent=false;
+    bool valid=false;//valid will be set to false in all cases where we have ambiguity
+    int flags=-1;//flags settable to different types of values to indicate different invalid situations
+
+    void fillevent(const std::string& position, const int subchannel, const float value); //make 'const' what functions don't need to change, helps with performance
+    void validate(const sx3_fbgains&, const sx3_geometry_scalefactors&);
+    void validate();
+};
+
+
+void sx3::fillevent(const std::string& positionstring, const int subchannel, const float value) {
+    assert(subchannel>=0 && subchannel<4);
+    foundevent=1;
+    if(positionstring=="FRONT_L") {
+        frontL[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="FRONT_R") {
+        frontR[subchannel].push_back(value);
+        unmatched_front_chans.insert(subchannel);
+    } else if(positionstring=="BACK") {
+        back[subchannel].push_back(value);
+        valid_back_chans.insert(subchannel);
+    } else {
+        std::cout << "Unknown string "+positionstring+" encountered in sx3::fillevent \n" << std::endl;
+    }
+    if(frontL[subchannel].size()!=0 && frontR[subchannel].size()!=0 ) {
+        unmatched_front_chans.erase(subchannel);
+        valid_front_chans.insert(subchannel); //std::set, so no duplication will happen
+    }
+}
+
+
+//void sx3::validate(const sx3_fbgains& fbgains, const sx3_geometry_scalefactors& sx3gs) {
+void sx3::validate() {
+    if(valid_front_chans.size()!=0 && valid_back_chans.size()!=0) {
+        valid=true;
+        float maxFE=0;
+        float maxBE=0;
+        //float zpos=0;
+        int bchan=-1;
+        int fchan=-1;
+/*            	for(auto cc: valid_front_chans) {
+            		std::cout << "fc" << cc << std::endl;// " " << frontL[cc].at(0) << " " << frontR[cc].at(0) << std::endl;
+            	}
+            	for(auto cc: valid_back_chans) {
+            		std::cout << "bc" << cc << std::endl; //" " << back[cc].at(0) << std::endl;
+            	}
+*/
+        for(auto chan: valid_front_chans) {
+            if(frontL[chan].size()>1) {
+                printf("\nmultihit sx3 at Lsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontL[chan]) printf("e: %f\t",e);
+                std::sort(frontL[chan].begin(), frontL[chan].end(), std::greater<float>());
+                flags += (-1000);
+            }
+            if(frontR[chan].size()>1) {
+                printf("\nmultihit sx3 at Rsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: frontR[chan]) printf("e: %f\t",e);
+                std::sort(frontR[chan].begin(), frontR[chan].end(), std::greater<float>());
+                flags += (-2000);
+            }
+            //assign position using max L+R value
+            /*printf("chan:%d sizeL: %d sizeR: %d\n",chan, frontL[chan].size(), frontR[chan].size()); fflush(stdout);
+			printf("foo\n");
+			std::cout << "\nL:" << std::endl;
+			for(auto thing: frontL[chan]) std::cout << thing << " " << std::flush;
+			std::cout << "\nR:" << std::endl;
+			for(auto thing: frontR[chan]) std::cout << thing << " " << std::flush;*/
+            if(frontL[chan].at(0) + frontR[chan].at(0)>= maxFE) {
+                maxFE = frontL[chan].at(0) + frontR[chan].at(0);
+                //zpos = (frontL[chan].at(0)-frontR[chan].at(0))/maxFE;
+                fchan = chan;
+            }
+        }
+        for(auto chan: valid_back_chans) {
+            if(back[chan].size()>1) {
+                printf("\nmultihit sx3 at Bsubchan:%d, ts:%1.13g\n",chan,ts);
+                for(const auto& e: back[chan]) printf("e: %f\t",e);
+                std::sort(back[chan].begin(), back[chan].end(), std::greater<float>());
+                flags += (-3000);
+            }
+            if(back[chan].size() ==0 ) {
+            	printf("foo\n");
+            	//continue;
+            }
+            if(back[chan].at(0) >= maxBE) {
+                maxBE = back[chan].at(0);
+                bchan = chan;
+            }
+        }
+        /*
+        	Cross-talk corrections are important when evaluating 'energy' signals from strips/pads.
+        	They can cause unexpected behavior when used universally for all EL, ER cases, so we split scenarios in two.
+        		- Positions along each strip (frontX) *are not* corrected for crosstalk.
+        		- Total F and B energies (frontE, backE) *are*.
+        	Sudarsan B, 31 Oct 2024
+        */
+        
+        if(fchan==-1 || bchan==-1) {
+        	std::cout << "how" << std::endl;
+        	std::cout << "fc " << std::flush; for(auto fc : valid_front_chans) std::cout << fc << " (" << frontL[fc].at(0) << "," << frontR[fc].at(0)<< ") "; std::cout << std::endl;
+        	std::cout << "bc " << std::flush; for(auto bc : valid_back_chans) std::cout << bc << " " << back[bc].at(0) << std::flush; std::cout << std::endl;
+       	}
+        float Eleft = frontL[fchan].at(0);
+        float Eright = frontR[fchan].at(0);
+        frontEL = Eleft;
+        frontER = Eright;
+        frontX = (Eleft-Eright)/(Eleft+Eright);
+        //frontXmm = (frontX+sx3gs.add[fchan])*sx3gs.stretch[fchan]; //convert to mm
+
+        //frontE = Eleft*fbgains.stripLgains[bchan][fchan] + fbgains.stripLoffsets[bchan][fchan]
+         //        + Eright*fbgains.stripRgains[bchan][fchan]  + fbgains.stripRoffsets[bchan][fchan];
+        //backE = back[bchan].at(0)*fbgains.padgains[bchan][fchan]+fbgains.padoffsets[bchan][fchan];
+        frontE = Eleft+Eright;
+        backE = maxBE;
+        stripF=fchan;
+        stripB=bchan;
+
+        flags = 0;
+    } else if(valid_front_chans.size()!=0 && valid_back_chans.size()==0) {
+        flags = -10;
+    } else if(valid_front_chans.size()==0 && valid_back_chans.size()!=0) {
+        flags = -20;
+    }
+}
+
+typedef sx3 sx3det;
+#endif

Armory/fsuReader.h

@@ -0,0 +1,795 @@
+#include "ClassData.h"
+#include "Hit.h"
+#include <algorithm>
+#include <filesystem>
+
+// #include "AggSeparator.h"
+
+class FSUReader{
+
+  public:
+    FSUReader();
+    FSUReader(std::string fileName, uInt dataSize = 100, int verbose = 1);
+    FSUReader(std::vector<std::string> fileList, uInt dataSize = 100, int verbose = 1);
+    ~FSUReader();
+
+    void OpenFile(std::string fileName, uInt dataSize, int verbose = 1);
+    bool IsOpen() const{return inFile == nullptr ? false : true;}
+    bool IsEndOfFile() const { 
+      // printf("%s : %d | %ld |%ld\n", __func__, feof(inFile), ftell(inFile), inFileSize);
+      if(fileList.empty() ) {
+        if( (uLong )ftell(inFile) >= inFileSize){
+          return true;
+        }else{
+          return false;
+        }
+      }else{
+        if( fileID + 1 == (int) fileList.size() && ((uLong)ftell(inFile) >= inFileSize) ) {
+          return true;
+        }else{
+          return false;
+        }
+      }
+    }
+
+    void ScanNumBlock(int verbose = 1, uShort saveData = 0); // saveData = 0 (no save), 1 (no trace), 2 (with trace);
+    int  ReadNextBlock(bool traceON = false, int verbose = 0, uShort saveData = 0); // saveData = 0 (no save), 1 (no trace), 2 (with trace);
+    int  ReadBlock(unsigned int ID, int verbose = 0);
+
+    unsigned int GetFilePos() const {return filePos;}
+    unsigned long GetTotNumBlock() const{ return totNumBlock;}
+    std::vector<unsigned int> GetBlockTimestamp() const {return blockTimeStamp;}
+
+    Data * GetData() const{return data;}
+
+    std::string GetFileName() const{return fileName;}
+    int GetDPPType()   const{return DPPType;}
+    int GetSN()        const{return sn;}
+    int GetTick2ns()   const{return tick2ns;}
+    int GetNumCh()     const{return numCh;}
+    int GetFileOrder() const{return order;}  
+    int GetChMask()    const{return chMask;}
+    unsigned long GetFileByteSize() const {return inFileSize;}
+
+    void ClearHitList() { hit.clear();}
+    ulong GetHitListLength() const {return hit.size();}
+    std::vector<Hit> GetHitVector() const {return hit;}
+    void SortHit(int verbose = false);
+    Hit GetHit(int id) const {
+      if( id < 0 ) id = hit.size() + id;
+      return hit[id];
+    }
+
+    void ClearHitCount() {hitCount = 0;}
+    ulong GetHitCount() const{return hitCount;}
+
+    std::vector<Hit> ReadBatch(unsigned int batchSize = 1000000, bool verbose = false); // output the sorted Hit
+
+    // std::string SaveHit(std::vector<Hit> hitList, bool isAppend = false);
+    // std::string SaveHit2NewFile(std::string saveFolder = "./", std::string indexStr = "");
+    // void SortAndSaveTS(unsigned int batchSize = 1000000, bool verbose = false);
+    // off_t GetTSFileSize() const {return tsFileSize;}
+
+    //TODO 
+    //void SplitFile(unsigned long hitSizePreFile);
+
+    void PrintHit(ulong numHit = -1, ulong startIndex = 0) {
+      for( ulong i = startIndex; i < std::min(numHit, hitCount); i++){
+        printf("%10zu ", i); hit[i].Print();
+      }
+    }
+
+    static void PrintHitListInfo(std::vector<Hit> * hitList, std::string name){
+      size_t n = hitList->size();
+      size_t s = sizeof(Hit);
+      printf("============== %s, size : %zu | %.2f MByte\n", name.c_str(), n, n*s/1024./1024.);
+      if( n > 0 ){
+        printf("t0 : %15llu ns\n", hitList->front().timestamp);
+        printf("t1 : %15llu ns\n", hitList->back().timestamp);
+        printf("dt : %15.3f ms\n", (hitList->back().timestamp - hitList->front().timestamp)/1e6);
+      }
+    }
+
+    void PrintHitListInfo(){
+      size_t n = hit.size();
+      size_t s = sizeof(Hit);
+      printf("============== reader.hit, size : %zu | %.2f MByte\n", n, n*s/1024./1024.);
+      if( n > 0 ){
+        printf("t0 : %15llu ns\n", hit.at(0).timestamp);
+        printf("t1 : %15llu ns\n", hit.back().timestamp);
+        printf("dt : %15.3f ms\n", (hit.back().timestamp - hit.front().timestamp)/1e6);
+      }
+    }
+
+
+    //void SaveAsCAENCoMPASSFormat();
+
+  private:
+
+    FILE * inFile;
+    Data * data;
+
+    std::string fileName;
+    std::vector<std::string> fileList;
+    short fileID;
+    unsigned long inFileSize;
+    unsigned int  filePos;
+    unsigned long totNumBlock;
+    unsigned int  blockID;
+
+    bool isDualBlock;
+
+    uShort sn;
+    uShort DPPType;
+    uShort tick2ns;
+    uShort order;
+    uShort chMask;
+    uShort numCh;
+
+    std::vector<unsigned int> blockPos;
+    std::vector<unsigned int > blockTimeStamp;
+
+    unsigned long hitCount;
+
+    std::vector<Hit> hit;
+
+    unsigned int word[1]; /// 4 byte
+    size_t dummy;
+    char * buffer;
+
+    off_t  tsFileSize;
+
+};
+
+inline FSUReader::~FSUReader(){
+  delete data;
+
+  if( inFile  ) fclose(inFile);
+
+}
+
+inline FSUReader::FSUReader(){
+  inFile = nullptr;
+  data = nullptr;
+
+  blockPos.clear();
+  blockTimeStamp.clear();
+  hit.clear();
+
+  fileList.clear();
+  fileID = -1;
+
+}
+
+inline FSUReader::FSUReader(std::string fileName, uInt dataSize, int verbose){
+  inFile = nullptr;
+  data = nullptr;
+
+  blockPos.clear();
+  blockTimeStamp.clear();
+  hit.clear();
+
+  fileList.clear();
+  fileID = -1;
+  OpenFile(fileName, dataSize, verbose);
+}
+
+inline FSUReader::FSUReader(std::vector<std::string> fileList, uInt dataSize, int verbose){
+  inFile = nullptr;
+  data = nullptr;
+
+  blockPos.clear();
+  blockTimeStamp.clear();
+  hit.clear();
+  //The files are the same DPPType and sn
+  this->fileList = fileList;
+  fileID = 0;
+  OpenFile(fileList[fileID], dataSize, verbose);
+
+}
+
+inline void FSUReader::OpenFile(std::string fileName, uInt dataSize, int verbose){
+
+  /// File format must be YYY...Y_runXXX_AAA_BBB_TT_CCC.fsu
+  /// YYY...Y  = prefix
+  /// XXX = runID, 3 digits
+  /// AAA = board Serial Number, 3 digits
+  /// BBB = DPPtype, 3 digits
+  ///  TT = tick2ns, any digits
+  /// CCC = over size index, 3 digits
+
+  if( inFile != nullptr ) fclose(inFile);
+
+  inFile = fopen(fileName.c_str(), "r");
+
+  if( inFile == NULL ){
+    printf("FSUReader::Cannot open file : %s \n", fileName.c_str());
+    this->fileName = "";
+    return;
+  }
+
+  this->fileName = fileName;
+
+  fseek(inFile, 0L, SEEK_END);
+  inFileSize = ftell(inFile);
+  if(verbose) printf("%s | file size : %ld Byte = %.2f MB\n", fileName.c_str() , inFileSize, inFileSize/1024./1024.);
+  fseek(inFile, 0L, SEEK_SET);
+  filePos = 0;
+
+  if( fileID > 0 ) return;
+
+  totNumBlock = 0;
+  blockID = 0;
+  blockPos.clear();
+  blockTimeStamp.clear();
+
+  hitCount = 0;
+  hit.clear();
+
+  //check is the file is *.fsu or *.fsu.X
+  size_t found = fileName.find_last_of('.');
+  std::string ext = fileName.substr(found + 1);
+
+  if( ext.find("fsu") != std::string::npos ) {
+    if(verbose > 1) printf("It is an raw data *.fsu format\n");
+    isDualBlock = false;
+    chMask = -1;
+  }else{
+    chMask = atoi(ext.c_str());
+    isDualBlock = true;
+    if(verbose > 1) printf("It is a splitted dual block data *.fsu.X format, dual channel mask : %d \n", chMask);
+  }
+
+  std::string fileNameNoExt;
+  found = fileName.find_last_of(".fsu");
+  size_t found2 = fileName.find_last_of('/');
+  if( found2 == std::string::npos ){
+    fileNameNoExt = fileName.substr(0, found-4);
+  }else{
+    fileNameNoExt = fileName.substr(found2+1, found-4);
+  }
+
+  // Split the string by underscores
+  std::istringstream iss(fileNameNoExt);
+  std::vector<std::string> tokens;
+  std::string token;
+
+  while (std::getline(iss, token, '_')) { tokens.push_back(token); }
+  sn = atoi(tokens[2].c_str());
+  tick2ns = atoi(tokens[4].c_str());
+  order = atoi(tokens[5].c_str());
+
+  DPPType = 0;
+  if( fileName.find("PHA") != std::string::npos ) DPPType = DPPTypeCode::DPP_PHA_CODE;
+  if( fileName.find("PSD") != std::string::npos ) DPPType = DPPTypeCode::DPP_PSD_CODE;
+  if( fileName.find("QDC") != std::string::npos ) DPPType = DPPTypeCode::DPP_QDC_CODE;
+  if( DPPType == 0 ){
+    fclose(inFile);
+    inFile = nullptr;
+    printf("Cannot find DPPType in the filename. Abort.");
+    return ;
+  }
+
+  numCh = (DPPType == DPPTypeCode::DPP_QDC_CODE ? 64 : 16);
+
+  data = new Data(numCh, dataSize);
+  data->tick2ns = tick2ns;
+  data->boardSN = sn;
+  data->DPPType = DPPType;
+
+}
+
+inline int FSUReader::ReadNextBlock(bool traceON, int verbose, uShort saveData){
+  if( inFile == NULL ) return -1;
+  if( feof(inFile) || filePos >= inFileSize) {
+    if( fileID >= 0 && fileID + 1  < (short) fileList.size() ){
+      printf("-------------- next file\n");
+      fileID ++;
+      OpenFile(fileList[fileID], data->GetDataSize(), 1 );
+    }else{
+      return -1;
+    }
+  }
+  
+  dummy = fread(word, 4, 1, inFile);
+  fseek(inFile, -4, SEEK_CUR);
+
+  if( dummy != 1) {
+    printf("fread error, should read 4 bytes, but read %ld x 4 byte, file pos: %ld / %ld byte\n", 
+            dummy, ftell(inFile), inFileSize);
+    return -10;
+  }
+  short header = ((word[0] >> 28 ) & 0xF);
+
+  Hit temp;
+
+  if( header == 0xA ) { ///normal header
+ 
+    unsigned int aggSize = (word[0] & 0x0FFFFFFF) * 4; ///byte
+    if( aggSize > inFileSize - ftell(inFile)) aggSize = inFileSize - ftell(inFile);
+    buffer = new char[aggSize];
+    dummy = fread(buffer, aggSize, 1, inFile);
+    filePos = ftell(inFile);
+    if( dummy != 1) {
+      printf("fread error, should read %d bytes, but read %ld x %d byte, file pos: %ld / %ld byte \n", 
+             aggSize, dummy, aggSize, ftell(inFile), inFileSize);
+      return -30;
+    }
+
+    data->DecodeBuffer(buffer, aggSize, !traceON, verbose); // data will own the buffer
+    //printf(" word Index = %u | filePos : %u | ", data->GetWordIndex(), filePos);
+
+  }else if( (header & 0xF ) == 0x8 ) { /// dual channel header
+
+    unsigned int dualSize = (word[0] & 0x7FFFFFFF) * 4; ///byte    
+    buffer = new char[dualSize];
+    dummy = fread(buffer, dualSize, 1, inFile);
+    filePos = ftell(inFile);
+
+    data->buffer = buffer;
+    data->DecodeDualBlock(buffer, dualSize, DPPType, chMask, !traceON, verbose);
+
+  }else{
+    printf("incorrect header.\n trminate.");
+    return -20;
+  }
+
+  unsigned int eventCout  = 0;
+
+  for( int ch = 0; ch < data->GetNChannel(); ch++){
+    if( data->NumEventsDecoded[ch] == 0 ) continue;
+
+    hitCount += data->NumEventsDecoded[ch];
+    eventCout += data->NumEventsDecoded[ch];
+
+    if( saveData ){
+      int start = data->GetDataIndex(ch) - data->NumEventsDecoded[ch] + 1;
+      if( start < 0 ) start = start + data->GetDataSize();
+
+      for( int i = start; i < start + data->NumEventsDecoded[ch]; i++ ){
+        int k  = i % data->GetDataSize();
+        
+        temp.sn = sn;
+        temp.ch = ch;
+        temp.energy    = data->GetEnergy(ch, k);
+        temp.energy2   = data->GetEnergy2(ch, k);
+        temp.timestamp = data->GetTimestamp(ch, k);
+        temp.fineTime  = data->GetFineTime(ch, k);
+        temp.pileUp    = data->GetPileUp(ch, k);
+        if( saveData > 1 ) {
+          temp.traceLength = data->Waveform1[ch][k].size();
+          temp.trace = data->Waveform1[ch][k];
+        }else{
+          temp.traceLength = 0;
+          if( temp.trace.size() > 0 ) temp.trace.clear();
+        }
+
+        hit.push_back(temp);
+      }
+    }
+  }
+
+  data->ClearTriggerRate();
+  data->ClearNumEventsDecoded();
+  data->ClearBuffer(); // this will clear the buffer.
+  return 0;
+}
+
+inline int FSUReader::ReadBlock(unsigned int ID, int verbose){
+  if( totNumBlock == 0 )return -1;
+  if( ID >= totNumBlock )return -1;
+
+  data->ClearData();
+
+  fseek( inFile, 0L, SEEK_SET);
+
+  if( verbose ) printf("Block index: %u, File Pos: %u byte\n", ID, blockPos[ID]);
+
+  fseek(inFile, blockPos[ID], SEEK_CUR);
+  filePos = blockPos[ID];
+  blockID = ID;
+  return ReadNextBlock(false, verbose, false);
+
+}
+
+inline void FSUReader::SortHit(int verbose){
+  if( verbose) printf("\nQuick Sort hit array according to time...");
+  std::sort(hit.begin(), hit.end(), [](const Hit& a, const Hit& b) {
+    return a.timestamp < b.timestamp;
+  });
+  if( verbose) printf(".......done.\n");
+}
+
+inline void FSUReader::ScanNumBlock(int verbose, uShort saveData){
+  if( inFile == nullptr ) return;
+  if( feof(inFile) ) return;
+
+  blockID = 0;
+  blockPos.push_back(0);
+
+  data->ClearData();
+  rewind(inFile);
+  filePos = 0;
+
+  bool isTraceOn = saveData < 2 ? false : true;
+
+  while( ReadNextBlock(isTraceOn, verbose - 1, saveData) == 0 ){
+    blockPos.push_back(filePos);
+    blockTimeStamp.push_back(data->aggTime);
+    blockID ++;
+    if(verbose && blockID % 10000 == 0) printf("%u, %.2f%% %u/%lu\n\033[A\r", blockID, filePos*100./inFileSize, filePos, inFileSize);
+  }
+
+  totNumBlock = blockID;
+  if(verbose) {
+    printf("\nScan complete: number of data Block : %lu\n", totNumBlock);
+    printf(  "                      number of hit : %lu", hitCount);
+    if( hitCount > 1e6 ) printf(" = %.3f million", hitCount/1e6); 
+    printf("\n");
+    if( saveData )printf(  "              size of the hit array : %lu\n", hit.size());
+
+    if( saveData ){
+      size_t sizeT = sizeof(hit[0]) * hit.size();
+      printf("size of hit array : %lu byte = %.2f kByte, = %.2f MByte\n", sizeT, sizeT/1024., sizeT/1024./1024.);
+    }
+  } 
+
+  if( fileList.size() > 0  ){
+    fileID = 0;
+    OpenFile(fileList[fileID], data->GetDataSize(), 0);
+  }
+
+  rewind(inFile);
+  blockID = 0;  
+  filePos = 0;
+
+  //check is the hitCount == hit.size();
+  if( saveData ){
+    if( hitCount != hit.size()){
+      printf("!!!!!! the Data::dataSize is not big enough. !!!!!!!!!!!!!!!\n");
+    }else{
+      SortHit(verbose+1);
+    }
+  }
+}
+
+inline std::vector<Hit> FSUReader::ReadBatch(unsigned int batchSize, bool verbose){
+
+  // printf("%s sn:%d. filePos : %lu\n", __func__, sn, ftell(inFile));
+
+  std::vector<Hit> hitList_A;
+  if( IsEndOfFile() ) {
+    hitList_A = hit;
+    hit.clear();  
+    return hitList_A;
+  }
+
+  if( hit.size() == 0 ){
+    int res = 0;
+    do{
+      res = ReadNextBlock(true, 0, 3);
+    }while ( hit.size() < batchSize && res == 0);
+    SortHit();
+    uLong t0_B = hit.at(0).timestamp;
+    uLong t1_B = hit.back().timestamp;
+    if( verbose ) {
+      printf(" hit in memeory : %7zu | %u | %lu \n", hit.size(), filePos, inFileSize);
+      printf("t0 : %15lu ns\n", t0_B);
+      printf("t1 : %15lu ns\n", t1_B);
+      printf("dt : %15.3f ms\n", (t1_B - t0_B)/1e6);
+    }
+
+    hitList_A = hit;
+    hit.clear();
+
+  }else{
+
+    hitList_A = hit;
+    hit.clear();
+
+  }
+
+  if( IsEndOfFile() ) return hitList_A; // when file finished for 1st batch read
+
+  int res = 0;
+  do{
+    res = ReadNextBlock(true, 0, 3);
+  }while ( hit.size() < batchSize && res == 0);
+  SortHit();
+  uLong t0_B = hit.at(0).timestamp;
+  uLong t1_B = hit.back().timestamp;
+
+  if( verbose ) {
+    printf(" hit in memeory : %7zu | %u | %lu \n", hit.size(), filePos, inFileSize);
+    printf("t0 : %15lu\n", t0_B);
+    printf("t1 : %15lu\n", t1_B);
+    printf("dt : %15.3f ms\n", (t1_B - t0_B)/1e6);
+  }
+
+  uLong t0_A = hitList_A.at(0).timestamp;
+  uLong t1_A = hitList_A.back().timestamp;
+  ulong ID_A = 0;
+  ulong ID_B = 0;
+
+  if( t0_A >= t0_B) {
+    printf("\033[0;31m!!!!!!!!!!!!!!!!! %s | Need to increase the batch size. \033[0m\n", __func__);
+    return std::vector<Hit> ();
+  }
+
+  if( t1_A > t0_B) { // need to sort between two hitList
+
+    if( verbose ) {
+      printf("############# need to sort \n");
+      printf("=========== sume of A + B : %zu \n", hitList_A.size() + hit.size());
+    }
+
+    std::vector<Hit> hitTemp;
+
+    // find the hit that is >= t0_B, save them to hitTemp
+    for( size_t j = 0; j < hitList_A.size() ; j++){
+      if( hitList_A[j].timestamp < t0_B ) continue;;
+      if( ID_A == 0 ) ID_A = j;
+      hitTemp.push_back(hitList_A[j]);
+    }
+
+    // remove hitList_A element that is >= t0_B
+    hitList_A.erase(hitList_A.begin() + ID_A, hitList_A.end() );
+    
+    // find the hit that is <= t1_A, save them to hitTemp
+    for( size_t j = 0; j < hit.size(); j++){
+      if( hit[j].timestamp > t1_A ) {
+        break;
+      }
+      hitTemp.push_back(hit[j]);
+      ID_B = j + 1;
+    }
+
+    // remove hit elements that is <= t1_A
+    hit.erase(hit.begin(), hit.begin() + ID_B  );
+
+    // sort hitTemp
+    std::sort(hitTemp.begin(), hitTemp.end(), [](const Hit& a, const Hit& b) {
+      return a.timestamp < b.timestamp;
+    });
+
+
+    if( verbose ) {
+      printf("----------------- ID_A : %lu, Drop\n", ID_A);
+      printf("----------------- ID_B : %lu, Drop\n", ID_B);
+      PrintHitListInfo(&hitList_A, "hitList_A");
+      PrintHitListInfo(&hitTemp, "hitTemp");
+      PrintHitListInfo();
+      printf("=========== sume of A + B + Temp : %zu \n", hitList_A.size() + hit.size()  + hitTemp.size());
+      printf("----------------- refill hitList_A \n");
+    }
+
+    for( size_t j = 0; j < hitTemp.size(); j++){
+      hitList_A.push_back(hitTemp[j]);
+    }
+    hitTemp.clear();
+    
+    if( verbose ) {
+      PrintHitListInfo(&hitList_A, "hitList_A");
+      PrintHitListInfo();
+      printf("=========== sume of A + B : %zu \n", hitList_A.size() + hit.size());
+    }
+   
+  }
+
+  return hitList_A;
+
+}
+
+/*
+inline void FSUReader::SortAndSaveTS(unsigned int batchSize, bool verbose){
+
+  int count = 0;
+  std::vector<Hit> hitList_A ;
+
+  do{
+
+    if( verbose ) printf("***************************************************\n");
+
+    int res = 0;
+    do{
+      res = ReadNextBlock(true, 0, 3);
+    }while ( hit.size() < batchSize && res == 0);
+
+    SortHit();
+    uLong t0_B = hit.at(0).timestamp;
+    uLong t1_B = hit.back().timestamp;
+
+    if( verbose ) {
+      printf(" hit in memeory : %7zu | %u | %lu \n", hit.size(), filePos, inFileSize);
+      printf("t0 : %15lu\n", t0_B);
+      printf("t1 : %15lu\n", t1_B);
+    }
+
+    if( count == 0 ) {
+      hitList_A = hit; // copy hit
+    }else{
+
+      uLong t0_A = hitList_A.at(0).timestamp;
+      uLong t1_A = hitList_A.back().timestamp;
+      ulong ID_A = 0;
+      ulong ID_B = 0;
+
+      if( t0_A > t0_B) {
+        printf("Need to increase the batch size. \n");
+        return;
+      }
+
+      if( t1_A > t0_B) { // need to sort between two hitList
+
+        if( verbose ) {
+          printf("############# need to sort \n");
+          printf("=========== sume of A + B : %zu \n", hitList_A.size() + hit.size());
+        }
+
+        std::vector<Hit> hitTemp;
+
+        for( size_t j = 0; j < hitList_A.size() ; j++){
+          if( hitList_A[j].timestamp < t0_B ) continue;
+          if( ID_A == 0 ) ID_A = j;
+          hitTemp.push_back(hitList_A[j]);
+        }
+
+        hitList_A.erase(hitList_A.begin() + ID_A, hitList_A.end() );
+        if( verbose ) {
+          printf("----------------- ID_A : %lu, Drop\n", ID_A);
+          PrintHitListInfo(hitList_A, "hitList_A");
+        }
+  
+      
+        for( size_t j = 0; j < hit.size(); j++){
+          if( hit[j].timestamp > t1_A ) {
+            ID_B = j;
+            break;
+          }
+          hitTemp.push_back(hit[j]);
+        }
+
+        std::sort(hitTemp.begin(), hitTemp.end(), [](const Hit& a, const Hit& b) {
+          return a.timestamp < b.timestamp;
+        });
+
+        hit.erase(hit.begin(), hit.begin() + ID_B  );
+
+        if( verbose ) {
+          PrintHitListInfo(hitTemp, "hitTemp");
+          printf("----------------- ID_B : %lu, Drop\n", ID_B);
+          PrintHitListInfo(hit, "hit");
+          printf("=========== sume of A + B + Temp : %zu \n", hitList_A.size() + hit.size()  + hitTemp.size());
+          printf("----------------- refill hitList_A \n");
+        }
+        ulong ID_Temp = 0;
+        for( size_t j = 0; j < hitTemp.size(); j++){
+          hitList_A.push_back(hitTemp[j]);
+          if( hitList_A.size() >= batchSize ) {
+            ID_Temp = j+1;
+            break;
+          }
+        }
+
+        hitTemp.erase(hitTemp.begin(), hitTemp.begin() + ID_Temp );
+        for( size_t j = 0 ; j < hit.size(); j ++){
+          hitTemp.push_back(hit[j]);
+        }
+        SaveHit(hitList_A, count <= 1 ? false : true);
+
+        if( verbose ) {
+          PrintHitListInfo(hitList_A, "hitList_A");
+          PrintHitListInfo(hitTemp, "hitTemp");
+          printf("----------------- replace hitList_A by hitTemp \n");
+        }
+
+        hitList_A.clear();
+        hitList_A = hitTemp;
+        hit.clear();
+
+        if( verbose ) {
+          PrintHitListInfo(hitList_A, "hitList_A");
+          printf("===========================================\n");
+        }
+
+      }else{ // save hitList_A, replace hitList_A 
+        
+        SaveHit(hitList_A, count <= 1? false : true);
+        hitList_A.clear();
+        hitList_A = hit;
+        if( verbose ) PrintHitListInfo(hitList_A, "hitList_A");
+
+      }
+    }
+
+    ClearHitList();
+    count ++;
+  }while(filePos < inFileSize);  
+
+  SaveHit(hitList_A, count <= 1 ? false : true);
+
+  printf("================= finished.\n");
+}
+*/
+
+/*
+inline std::string FSUReader::SaveHit(std::vector<Hit> hitList, bool isAppend){
+
+  std::string outFileName;
+  if( fileList.empty() ) {
+    outFileName =  fileName + ".ts" ;
+  }else{
+    outFileName =  fileList[0] + ".ts" ;
+  }
+  uint64_t hitSize = hitList.size();
+
+  FILE * outFile ;
+  if( isAppend ) {
+    outFile = fopen(outFileName.c_str(), "rb+"); //read/write bineary
+
+    rewind(outFile);
+    fseek( outFile, 4, SEEK_CUR);
+    uint64_t org_hitSize;
+    fread(&org_hitSize, 8, 1, outFile);
+
+    rewind(outFile);
+    fseek( outFile, 4, SEEK_CUR);
+
+    org_hitSize += hitSize;
+
+    fwrite(&org_hitSize, 8, 1, outFile);
+    fseek(outFile, 0, SEEK_END);
+
+  }else{
+    outFile = fopen(outFileName.c_str(), "wb"); //overwrite binary
+    uint32_t header = 0xAA000000;
+    header += sn;
+    fwrite( &header, 4, 1, outFile );
+    fwrite( &hitSize, 8, 1, outFile);
+  }
+
+
+  for( ulong i = 0; i < hitSize; i++){
+
+    if( i% 10000 == 0 ) printf("Saving %lu/%lu Hit (%.2f%%)\n\033[A\r", i, hitSize, i*100./hitSize);
+
+    uint16_t flag = hitList[i].ch + (hitList[i].pileUp << 8) ;
+
+    if( DPPType == DPPTypeCode::DPP_PSD_CODE ) flag += ( 1 << 15);
+    if( hitList[i].traceLength > 0 ) flag += (1 << 14);
+
+    // fwrite( &(hit[i].ch), 1, 1, outFile);
+    fwrite( &flag, 2, 1, outFile);
+    fwrite( &(hitList[i].energy), 2, 1, outFile);
+    if( DPPType == DPPTypeCode::DPP_PSD_CODE ) fwrite( &(hitList[i].energy2), 2, 1, outFile);
+    fwrite( &(hitList[i].timestamp), 6, 1, outFile);
+    fwrite( &(hitList[i].fineTime), 2, 1, outFile);
+    if( hitList[i].traceLength > 0 ) fwrite( &(hitList[i].traceLength), 2, 1, outFile);
+    
+    for( uShort j = 0; j < hitList[i].traceLength; j++){
+      fwrite( &(hitList[i].trace[j]), 2, 1, outFile);
+    }
+    
+  }
+
+  off_t tsFileSize = ftello(outFile);  // unsigned int =  Max ~4GB
+  fclose(outFile);
+
+  printf("Saved to %s, size: ", outFileName.c_str());
+  if( tsFileSize < 1024 ) {
+    printf(" %ld Byte", tsFileSize);
+  }else if( tsFileSize < 1024*1024 ) {
+    printf(" %.2f kB", tsFileSize/1024.);
+  }else if( tsFileSize < 1024*1024*1024){
+    printf(" %.2f MB", tsFileSize/1024./1024.);
+  }else{
+    printf(" %.2f GB", tsFileSize/1024./1024./1024.);
+  }
+  printf("\n");
+
+  return outFileName;
+
+}
+*/
+
+

Armory/macro.h

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

BatchProcess.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+#parallel -j 6 echo ./ProcessRun.sh {1} 2000 0 ::: {020..400}
+
+parallel  --jobs 1 --results log/log_{}.txt --memfree 1G --ctag -j 1 ./ProcessRun.sh {1} 2000 0 ::: {109..400} # for 17F
+
+# parallel --results log/log_{}.txt --ctag -j 6 ./ProcessRun.sh {1} 4000 0 ::: {5..21}  

CLAUDE.md

@@ -0,0 +1,45 @@
+# ANASEN Analysis — working notes for Claude
+
+## Agent behavior
+- ALWAYS output a brief, step-by-step plan before modifying files or running commands.
+- Commit only when explicitly asked. Do not push to remote on your own initiative; pushing is allowed only when the session's instructions name a branch to push to (e.g. a `claude/*` working branch), and never to `devel_vignesh` or any other shared branch.
+- **Targeted edits only.** Never regenerate a whole file to make a local change.
+- **Never read `MakeVertex.C`** (4,003 lines, 240 KB). Same rule as `TrackRecon.C` below if you must touch it: grep, then Read with offset/limit.
+- **Never read `TrackRecon.C` end to end** (4,268 lines, 218 KB; ~60k tokens, and it stays in the prefix for the rest of the session). Grep for the symbol, then Read with offset/limit around the hit. If a question genuinely needs the whole file, say so first. Do not explore the codebase open-endedly.
+- **Do not spawn subagents** for work that can be done inline — each starts cold and re-derives context already loaded. Worth it only for wide parallel searches where the conclusion is all that's needed.
+- **You cannot verify your own work here.** No test suite, no CI, no data in the repo; validation is visual, via ROOT `TBrowser`, on a machine that has the data. Say explicitly when a change is unverified — never report a physics change as working because it compiled. The dangerous bugs are silent: a flipped sign in a kinematics term, an inverted spline direction, a wrong argument order, an off-by-one in a wire mask. None of them throw. The run completes, the plot renders, and the spectrum is wrong.
+- **Review once per coherent change, not per edit.** Scale depth to blast radius: scratch macros, shell, and docs are shallow; `TrackRecon.C`, `MakeVertex.C`, `Armory/`, or any calibration fit is deep and should tolerate uncertain findings — silent failure is what's being hunted. Run `/security-review` only for file I/O or shell interpolation in the `run_*.sh` drivers; it is not a physics tool.
+
+## Build & execution
+- ROOT macros (`.C`) compile via ACLiC inside ROOT. Do not link into binaries.
+- Standalone binaries (`EventBuilder`, `Mapper`): `cd Armory && make`
+- Pre-compile for parallel runs: `root -q -l -b -e '.L TrackRecon.C++O'`
+- Batch runs: `./run_17F.sh`, `./run_27Al.sh`, `./run_tr.sh`
+- `run_tr.sh` gates its stages with `if [[ 1 -eq 0 ]]` / `if [[ 1 -eq 1 ]]`. Flip the literal to enable a block.
+- Data is NOT in the repo. Mapped ROOT files live at `../ANASEN_analysis/data/${DATASET}_Data/${PREFIX}${run}_mapped.root`.
+
+## Runtime configuration
+All config is `getenv`-driven; the run scripts `export` it. Defaults are in `TrackRecon.C::Begin()`.
+
+Physics / results-affecting:
+`DATASET` `reactiondata` `CO2percent` `pressure_in_torr` `CATHODE_GAIN` `PC_ENERGY_CALIBRATION`
+`source_vertex` `CUTLIST` `DITHER_SIGMA` `RNG_SEED` `BEAM_AXIS_X` `BEAM_AXIS_Y`
+`timecut_low` `timecut_high` `DISABLE_BAD_ANODE_WIRES` `A1C1_LOWBAND_RFACTOR`
+`A1C1_Z_SCALE_QQQ` `A1C1_Z_SCALE_SX3` `A1C1_Z_OFF_QQQ` `A1C1_Z_OFF_SX3`
+
+Plumbing: `OUT_DIR` `RUN_NUMBER` `FLUSH_BARRIER` `MAX_RSS_MB` `MEMCHECK_STRIDE`
+
+**`DEDX_SCALE` is read by `eloss_calculations/Eloss.py`, NOT by `TrackRecon.C`.**
+It multiplies `catima.dedx` when the lookup tables are generated. Changing it invalidates every `.dat` table — re-run `Eloss.py` (the run scripts do this automatically before processing). Tables are keyed `eloss_calculations/<species>_lookup_<E>MeV_<P>torr_<CO2>pc.dat` (e.g. `alpha_lookup_50MeV_250torr_3pc.dat`).
+
+## Footguns
+- **`HistPlotter` keys `oMap` by histogram NAME only.** The folder argument does not namespace. Two `Fill` calls with the same name and the *same* folder merge silently — no warning, no error, wrong plot. A same-name/different-folder (or toplevel-vs-folder) clash does print to `stderr` and then merges anyway, but the run scripts send stdout+stderr to `/dev/null`, so in a batch run it is invisible either way. Always make names unique.
+- **Si–PC coincidence sits at negative dt.** The band is centred well below zero, not near it. The one gate of record is `siPcCoincident()` in `TrackRecon.C` (`kSiPcDtMin = -500`, `kSiPcDtMax = 150` ns); anything else is a plotting range, not a cut. Do not "correct" a timing gate toward zero.
+- **RNG**: in `TrackRecon.C`, one shared `anasenRandom` (`TRandom3`, seed 4357, `RNG_SEED` to override), aliased by reference wherever a local `rnd`/`rand` appears — do not introduce fresh `TRandom3(0)` instances; it breaks reproducibility. `MakeVertex.C` predates this and still has ~12 independent default-seeded `TRandom3` objects; do not assume its output is reproducible against `TrackRecon.C`.
+- **Pass By Reference in Event Loops:** Always iterate via `const auto&` over cluster/hit vectors to prevent expensive struct copies in multi-million event runs.
+
+## Invariants to check on any physics change
+Units (MeV vs keV, cm vs mm); sign conventions on `z` and beam direction; eloss spline domain and extrapolation; energy conservation in the kinematics; dead-wire / neighbour masking; RNG seeding. When reviewing, include the `.dat` and `run_*.sh` parameter deltas — the most consequential recent changes have been constants, not code.
+
+## Docs
+`README.md` has the pipeline documentation and full file references.

CalibrationQQQ.C

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

CalibrationQQQ.h

@@ -0,0 +1,114 @@
+#ifndef CalibrationQQQ_h
+#define CalibrationQQQ_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+
+#include "Armory/ClassDet.h"
+
+class CalibrationQQQ : 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;   //!
+
+   CalibrationQQQ(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~CalibrationQQQ() { }
+   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(CalibrationQQQ,0);
+};
+
+#endif
+
+#ifdef CalibrationQQQ_cxx
+void CalibrationQQQ::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 CalibrationQQQ::Notify(){
+
+   return kTRUE;
+}
+
+void CalibrationQQQ::SlaveBegin(TTree * /*tree*/){
+
+   TString option = GetOption();
+
+}
+
+void CalibrationQQQ::SlaveTerminate(){
+
+}
+
+
+#endif // #ifdef CalibrationQQQ_cxx

FitHistogramsWithTSpectrum_Sequential_Improved.C

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

GainMatchQQQ.C

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

GainMatchQQQ.h

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

MakeVertex.h

@@ -0,0 +1,133 @@
+#ifndef MakeVertex_h
+#define MakeVertex_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TApplication.h>
+#include <TFile.h>
+#include <TSelector.h>
+#include <iomanip>
+#include <vector>         // Required for vectors
+#include <utility>        // Required for std::pair
+
+#include "Armory/ClassDet.h"
+#include "Armory/ClassPW.h" // YOU ADDED THIS (Correct! Defines Coord)
+
+class MakeVertex : public TSelector {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc ;
+   Det misc;
+
+   ULong64_t       evID;
+   UInt_t          run;
+
+   // List of branches
+   TBranch        *b_eventID;   //!
+   TBranch        *b_run;   //!
+   TBranch        *b_sx3Multi;   //!
+   TBranch        *b_sx3ID;   //!
+   TBranch        *b_sx3Ch;   //!
+   TBranch        *b_sx3E;   //!
+   TBranch        *b_sx3T;   //!
+   TBranch        *b_qqqMulti;   //!
+   TBranch        *b_qqqID;   //!
+   TBranch        *b_qqqCh;   //!
+   TBranch        *b_qqqE;   //!
+   TBranch        *b_qqqT;   //!
+   TBranch        *b_pcMulti;   //!
+   TBranch        *b_pcID;   //!
+   TBranch        *b_pcCh;   //!
+   TBranch        *b_pcE;   //!
+   TBranch        *b_pcT;   //!
+   TBranch        *b_miscMulti;   //!
+   TBranch        *b_miscID;   //!
+   TBranch        *b_miscCh;   //!
+   TBranch        *b_miscE;   //!
+   TBranch        *b_miscT;   //!
+   TBranch        *b_miscTf;   //!
+
+   // 1. Geometry Cache
+   Coord Crossover[24][24][2];
+
+   // 2. Persistent Vectors (REQUIRED for the optimized .cxx to work)
+   std::vector<std::pair<int, double>> anodeHits;
+   std::vector<std::pair<int, double>> cathodeHits;
+   std::vector<std::pair<int, double>> corrcatMax;
+   std::vector<std::pair<int, double>> corranoMax;
+   std::vector<double> cathodeTimes;
+   std::vector<double> anodeTimes;
+   
+   MakeVertex(TTree * /*tree*/ =0) : fChain(0) { }
+   virtual ~MakeVertex() { }
+   virtual Int_t   Version() const { return 2; }
+   virtual void    Begin(TTree *tree);
+   virtual void    SlaveBegin(TTree *tree);
+   virtual void    Init(TTree *tree);
+   virtual Bool_t  Notify();
+   virtual Bool_t  Process(Long64_t entry);
+   virtual Int_t   GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void    SetOption(const char *option) { fOption = option; }
+   virtual void    SetObject(TObject *obj) { fObject = obj; }
+   virtual void    SetInputList(TList *input) { fInput = input; }
+   virtual TList  *GetOutputList() const { return fOutput; }
+   virtual void    SlaveTerminate();
+   virtual void    Terminate();
+
+   ClassDef(MakeVertex,0);
+};
+
+#endif
+
+#ifdef MakeVertex_cxx
+void MakeVertex::Init(TTree *tree){
+
+   if (!tree) return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24,12);
+   qqq.SetDetDimension(4,32);
+   pc.SetDetDimension(2,24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID",    &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch",    &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E",     &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T",     &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID",    &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh",    &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE",     &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT",     &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti",  &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID",     &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh",     &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE",      &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT",      &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID",    &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh",    &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE",     &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT",     &misc.t, &b_miscT);
+   fChain->SetBranchAddress("miscf",    &misc.tf, &b_miscTf);
+}
+
+Bool_t MakeVertex::Notify(){
+   return kTRUE;
+}
+
+void MakeVertex::SlaveBegin(TTree * /*tree*/){
+   // TString option = GetOption();
+}
+
+void MakeVertex::SlaveTerminate(){
+}
+#endif // #ifdef MakeVertex_cxx

MatchAndPlotCentroids.C

@@ -0,0 +1,139 @@
+#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_27Al.txt");
+    // std::ifstream inputFile("centroids_17F.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.dat");
+    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
+
+    // 1. Create a SINGLE canvas BEFORE the loop
+    TCanvas *c1 = new TCanvas("c1", "Centroid Fit Viewer", 800, 600);
+
+    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
+       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); 
+        graph->SetMarkerSize(1.0);
+        graph->SetMarkerColor(kBlue);
+        
+        graph->Draw("AP");
+        // 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;
+}

MiscEdE.C

@@ -0,0 +1,359 @@
+#include "TFile.h"
+#include "TTree.h"
+#include "TChain.h"
+#include "TH1D.h"
+#include "TH2D.h"
+#include "TCutG.h"
+#include "TKey.h"
+#include "TString.h"
+#include "TSystem.h"
+#include <map>
+#include <vector>
+#include <utility>
+#include <cstdlib>
+
+namespace
+{
+    constexpr double kAdcMax = 16384; // 14-bit-ish ADC range for axes
+
+    struct HitData
+    {
+        double e;
+        unsigned long long t;
+    };
+}
+
+void MiscEdE(const char *f0,
+             const char *f1 = "", const char *f2 = "", const char *f3 = "",
+             const char *f4 = "", const char *f5 = "", const char *f6 = "",
+             const char *f7 = "", const char *f8 = "", const char *f9 = "")
+{
+    std::vector<TString> inputs;
+    for (const char *f : {f0, f1, f2, f3, f4, f5, f6, f7, f8, f9})
+        if (f && f[0])
+            inputs.emplace_back(f);
+    if (inputs.empty())
+    {
+        printf("MiscEdE: no input files given.\n");
+        return;
+    }
+
+    TChain *tree = new TChain("tree");
+    for (auto &in : inputs)
+    {
+        if (gSystem->AccessPathName(in))
+        {
+            printf("MiscEdE: WARNING input not found, skipping: %s\n", in.Data());
+            continue;
+        }
+        tree->Add(in);
+    }
+    if (tree->GetNtrees() == 0)
+    {
+        printf("MiscEdE: no readable inputs.\n");
+        return;
+    }
+
+    // ---------------------------------------------------------
+    // Bash Environment Variable Extraction
+    // ---------------------------------------------------------
+    int runNumber = -1;
+    if (gSystem->Getenv("CURRENT_RUN")) {
+        runNumber = std::atoi(gSystem->Getenv("CURRENT_RUN"));
+    }
+    printf("MiscEdE: Run Number loaded from Bash: %d\n", runNumber);
+
+    TString cutDir = "~/ANASEN_analysis"; // Fallback if not run via bash
+    if (gSystem->Getenv("CUT_DIR")) {
+        cutDir = gSystem->Getenv("CUT_DIR");
+    }
+
+    // ---------------------------------------------------------
+    // Run-Dependent Channel Routing
+    // ---------------------------------------------------------
+    // Defaults (Run <= 180)
+    int snLolli = 405, chLolli = 9;
+    int snSi    = 405, chSi    = 11;
+    int snRF    = 405, chRF    = 15;
+    int snMCP   = 405, chMCP   = 14;
+
+    if (runNumber > 180 && runNumber <= 282) {
+        chRF = 10;
+    } 
+    else if (runNumber > 282 && runNumber <= 322) {
+        snRF = 89; chRF = 0;
+        snMCP = 89; chMCP = 1;
+    } 
+    else if (runNumber > 322) {
+        snRF = 89; chRF = 0;
+        snMCP = 89; chMCP = 2;
+    }
+
+    // Composite Unique IDs (UID = Board * 100 + Channel) to prevent collisions
+    int uidLollipop = snLolli * 100 + chLolli;
+    int uidSiMon    = snSi * 100 + chSi;
+    int uidRF       = snRF * 100 + chRF;
+    int uidMCP      = snMCP * 100 + chMCP;
+
+    printf("  -> Routed Lollipop : Board %d, Ch %d (UID: %d)\n", snLolli, chLolli, uidLollipop);
+    printf("  -> Routed Si Monitor: Board %d, Ch %d (UID: %d)\n", snSi, chSi, uidSiMon);
+    printf("  -> Routed RF       : Board %d, Ch %d (UID: %d)\n", snRF, chRF, uidRF);
+    printf("  -> Routed MCP      : Board %d, Ch %d (UID: %d)\n", snMCP, chMCP, uidMCP);
+
+    // ---------------------------------------------------------
+    // Exact schema matching EventBuilder.cpp
+    // ---------------------------------------------------------
+    const int MAX_MULTI = 2000;
+    unsigned int multi = 0;
+    unsigned short sn[MAX_MULTI];
+    unsigned short ch[MAX_MULTI];
+    unsigned short e[MAX_MULTI];
+    unsigned long long e_t[MAX_MULTI]; // Timestamp branch is "e_t"
+
+    tree->SetBranchAddress("multi", &multi);
+    tree->SetBranchAddress("sn", sn);
+    tree->SetBranchAddress("ch", ch);
+    tree->SetBranchAddress("e", e);
+    tree->SetBranchAddress("e_t", e_t);
+
+    TString stem = gSystem->BaseName(inputs[0].Data());
+    if (stem.EndsWith(".root"))
+        stem.Remove(stem.Length() - 5);
+    TString outName = "MiscEdE_" + stem + ".root";
+    TFile *out = new TFile(outName, "recreate");
+
+    // ---------------------------------------------------------
+    // Load the 17F and 16O TCutGs from file
+    // ---------------------------------------------------------
+    TCutG *cut17F = nullptr;
+    TString path17F = gSystem->ExpandPathName(Form("%s/17FCut.root", cutDir.Data()));
+    if (!gSystem->AccessPathName(path17F))
+    {
+        TFile *fCut = TFile::Open(path17F);
+        if (fCut && !fCut->IsZombie())
+        {
+            for (auto keyObj : *fCut->GetListOfKeys())
+            {
+                TKey *key = (TKey *)keyObj;
+                if (TString(key->GetClassName()) == "TCutG")
+                {
+                    cut17F = (TCutG *)key->ReadObj()->Clone("cut17F");
+                    break;
+                }
+            }
+            fCut->Close();
+        }
+    }
+
+    TCutG *cut16O = nullptr;
+    TString path16O = gSystem->ExpandPathName(Form("%s/16OCut.root", cutDir.Data()));
+    if (!gSystem->AccessPathName(path16O))
+    {
+        TFile *fCut = TFile::Open(path16O);
+        if (fCut && !fCut->IsZombie())
+        {
+            for (auto keyObj : *fCut->GetListOfKeys())
+            {
+                TKey *key = (TKey *)keyObj;
+                if (TString(key->GetClassName()) == "TCutG")
+                {
+                    cut16O = (TCutG *)key->ReadObj()->Clone("cut16O");
+                    break;
+                }
+            }
+            fCut->Close();
+        }
+    }
+
+    out->cd();
+
+    // ---------------------------------------------------------
+    // Prepare Histograms
+    // ---------------------------------------------------------
+    std::map<int, TH2D*> hEvsChMap;
+    auto getEvsCh = [&](int boardSN) -> TH2D* {
+        if (hEvsChMap.count(boardSN)) return hEvsChMap[boardSN];
+        TH2D *h = new TH2D(Form("h2_E_vs_ch_bd%d", boardSN), Form("Board %d: E vs channel;board channel;E [ADC]", boardSN), 16, -0.5, 15.5, 800, 0, kAdcMax);
+        hEvsChMap[boardSN] = h;
+        return h;
+    };
+
+    TH2D *h2_EvsdT_LolliSi = new TH2D("EvsdT_Lollipop_Si", "Energy Si vs dT (Lollipop - Si);dT [ticks];Si E [ADC]", 500, 0, 2000, 400, 0, kAdcMax);
+    TH2D *h2_TOF_SiRF = new TH2D("TOF_Si_RF", "Time of Flight: Energy Si vs (T_Si - T_RF);T_Si - T_RF [ticks];Si E [ADC]", 500, 0, 2000, 400, 0, kAdcMax);
+
+    // Dynamic Pairwise E-dE mapped by UID
+    std::map<std::pair<int, int>, TH2D *> hEdE;
+    auto getEdE = [&](int uidA, int uidB) -> TH2D * {
+        if (uidA > uidB) std::swap(uidA, uidB);
+        auto key = std::make_pair(uidA, uidB);
+        auto it = hEdE.find(key);
+        if (it != hEdE.end()) return it->second;
+        
+        TString name = Form("h2_ede_bd%d_ch%d_vs_bd%d_ch%d", uidA/100, uidA%100, uidB/100, uidB%100);
+        TString title = Form("E-dE: Bd %d Ch %d (x) vs Bd %d Ch %d (y);X E [ADC];Y E [ADC]", uidA/100, uidA%100, uidB/100, uidB%100);
+        
+        TH2D *h = new TH2D(name, title, 400, 0, kAdcMax, 400, 0, kAdcMax);
+        hEdE[key] = h;
+        return h;
+    };
+
+    // 17F Gated Plots
+    TH2D *hEdE_17F = nullptr;
+    TH2D *hEdE_inv = nullptr;
+    TH2D *h2_EvsdT_LolliSi_17F = nullptr;
+    TH2D *h2_TOF_SiRF_17F = nullptr;
+    TH1D *h1_dT_17F = nullptr;
+
+    if (cut17F)
+    {
+        hEdE_17F = new TH2D("EdE_lollipopIC_vs_SiMonitor_17FCut", "lollipop IC vs Si monitor (17F Gated);Si monitor E [ADC];lollipop IC E [ADC]", 400, 0, kAdcMax, 400, 0, kAdcMax);
+        hEdE_inv = new TH2D("EdE_lollipopIC_vs_SiMonitor_17FCut_Inverse", "lollipop IC vs Si monitor (Inverse 17F Gated);Si monitor E [ADC];lollipop IC E [ADC]", 400, 0, kAdcMax, 400, 0, kAdcMax);
+        h2_EvsdT_LolliSi_17F = new TH2D("EvsdT_Lollipop_Si_17FCut", "Energy Si vs dT (17F Gated);dT (Lollipop - Si) [ticks];Si E [ADC]", 500, 0, 2000, 400, 0, kAdcMax);
+        h2_TOF_SiRF_17F = new TH2D("TOF_Si_RF_17FCut", "Si TOF vs Energy (17F Gated);T_Si - T_RF [ticks];Si E [ADC]", 500, 0, 2000, 400, 0, kAdcMax);
+        h1_dT_17F = new TH1D("dT_Lollipop_Si_17FCut", "dT Lollipop-Si (17F Gated);T_Lollipop - T_Si [ticks]", 500, 0, 2000);
+    }
+
+    // 16O Gated Plots
+    TH2D *hEdE_16O = nullptr;
+    TH2D *h2_EvsdT_LolliSi_16O = nullptr;
+    TH2D *h2_TOF_SiRF_16O = nullptr;
+    TH1D *h1_dT_16O = nullptr;
+
+    if (cut16O)
+    {
+        hEdE_16O = new TH2D("EdE_lollipopIC_vs_SiMonitor_16OCut", "lollipop IC vs Si monitor (16O Gated);Si monitor E [ADC];lollipop IC E [ADC]", 400, 0, kAdcMax, 400, 0, kAdcMax);
+        h2_EvsdT_LolliSi_16O = new TH2D("EvsdT_Lollipop_Si_16OCut", "Energy Si vs dT (16O Gated);dT (Lollipop - Si) [ticks];Si E [ADC]", 500, 0, 2000, 400, 0, kAdcMax);
+        h2_TOF_SiRF_16O = new TH2D("TOF_Si_RF_16OCut", "Si TOF vs Energy (16O Gated);T_Si - T_RF [ticks];Si E [ADC]", 500, 0, 2000, 800, 0, kAdcMax);
+        h1_dT_16O = new TH1D("dT_Lollipop_Si_16OCut", "dT Lollipop-Si (16O Gated);T_Lollipop - T_Si [ticks]", 500, 0, 2000);
+    }
+
+    Long64_t nEnt = tree->GetEntries();
+    printf("MiscEdE: %lld entries across %d file(s) -> %s\n", nEnt, tree->GetNtrees(), outName.Data());
+
+    Long64_t used = 0;
+    for (Long64_t i = 0; i < nEnt; ++i)
+    {
+        tree->GetEntry(i);
+
+        // We map hits by UID instead of standard channel to prevent overlaps between Bd405 and Bd89
+        std::map<int, HitData> hit;
+        for (unsigned int j = 0; j < multi && j < (unsigned)MAX_MULTI; ++j)
+        {
+            // Only care about MISC boards 405 and 89
+            if (sn[j] != 405 && sn[j] != 89)
+                continue;
+
+            int c = ch[j];
+            int uid = (sn[j] * 100) + ch[j]; 
+            double en = e[j];
+            unsigned long long ts = e_t[j];
+
+            auto it = hit.find(uid);
+            if (it == hit.end() || en > it->second.e)
+                hit[uid] = {en, ts};
+                
+            getEvsCh(sn[j])->Fill(c, en);
+        }
+
+        if (hit.empty())
+            continue;
+        ++used;
+
+        // ---------------------------------------------------------
+        // Generic Dynamic Pairwise E-dE Logic across all UIDs
+        // ---------------------------------------------------------
+        for (auto a = hit.begin(); a != hit.end(); ++a)
+        {
+            for (auto b = std::next(a); b != hit.end(); ++b)
+            {
+                if (a->second.e > 500 && b->second.e > 500)
+                {
+                    getEdE(a->first, b->first)->Fill(a->second.e, b->second.e);
+                }
+            }
+        }
+
+        // ---------------------------------------------------------
+        // Core Timing and PID Gating Logic (Lollipop-Si specific)
+        // ---------------------------------------------------------
+        if (hit.count(uidLollipop) && hit.count(uidSiMon))
+        {
+            double e_lol = hit[uidLollipop].e;
+            double e_si = hit[uidSiMon].e;
+
+            // Calculate delta T safely across potential CAEN rollovers
+            double dt_lol_si = static_cast<double>(hit[uidLollipop].t) - static_cast<double>(hit[uidSiMon].t);
+
+            if (e_lol > 500 && e_si > 500)
+            {
+                h2_EvsdT_LolliSi->Fill(dt_lol_si, e_si);
+
+                bool is17F = cut17F && cut17F->IsInside(e_si, e_lol);
+                bool is16O = cut16O && cut16O->IsInside(e_si, e_lol);
+
+                if (is17F)
+                {
+                    hEdE_17F->Fill(e_si, e_lol);
+                    h2_EvsdT_LolliSi_17F->Fill(dt_lol_si, e_si);
+                    h1_dT_17F->Fill(dt_lol_si);
+                }
+                else if (cut17F)
+                {
+                    hEdE_inv->Fill(e_si, e_lol);
+                }
+
+                if (is16O)
+                {
+                    hEdE_16O->Fill(e_si, e_lol);
+                    h2_EvsdT_LolliSi_16O->Fill(dt_lol_si, e_si);
+                    h1_dT_16O->Fill(dt_lol_si);
+                }
+
+                // Generate absolute TOF if the RF channel fired
+                if (hit.count(uidRF))
+                {
+                    double tof = static_cast<double>(hit[uidSiMon].t) - static_cast<double>(hit[uidRF].t);
+                    h2_TOF_SiRF->Fill(tof, e_si);
+
+                    if (is17F)
+                        h2_TOF_SiRF_17F->Fill(tof, e_si);
+                    if (is16O)
+                        h2_TOF_SiRF_16O->Fill(tof, e_si);
+                }
+            }
+        }
+    }
+
+    // ---------------------------------------------------------
+    // Purge Sparse E-dE Histograms (< 500 counts)
+    // ---------------------------------------------------------
+    for (auto it = hEdE.begin(); it != hEdE.end();)
+    {
+        if (it->second->GetEntries() < 500)
+        {
+            delete it->second; // Free memory and remove from ROOT file
+            it = hEdE.erase(it);
+        }
+        else
+        {
+            ++it;
+        }
+    }
+
+    // Convenience alias: Transpose generic plot to correctly place stopping E on X
+    if (hEdE.count({uidLollipop, uidSiMon}))
+    {
+        TH2D *src = hEdE[{uidLollipop, uidSiMon}];
+        TH2D *alias = new TH2D("EdE_lollipopIC_vs_SiMonitor_Ungated",
+                               Form("lollipop IC vs Si monitor (Ungated);Bd %d Ch %d (Si) E [ADC];Bd %d Ch %d (Lolli) E [ADC]", snSi, chSi, snLolli, chLolli),
+                               src->GetNbinsY(), src->GetYaxis()->GetXmin(), src->GetYaxis()->GetXmax(),
+                               src->GetNbinsX(), src->GetXaxis()->GetXmin(), src->GetXaxis()->GetXmax());
+        for (int ix = 1; ix <= src->GetNbinsX(); ++ix)
+            for (int iy = 1; iy <= src->GetNbinsY(); ++iy)
+                alias->SetBinContent(iy, ix, src->GetBinContent(ix, iy)); // (x,y) -> (y,x)
+    }
+
+    out->Write();
+    out->Close();
+    printf("MiscEdE: Processed %lld valid MISC events. Wrote %s\n", used, outName.Data());
+}

PCGainMatch.C

@@ -1,14 +1,13 @@
-#define Analyzer_cxx
+#define PCGainMatch_cxx
 
-#include "Analyzer.h"
+#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"
 
@@ -28,6 +27,13 @@ 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;
@@ -36,13 +42,20 @@ 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 Analyzer::Begin(TTree * /*tree*/){
+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, 400, 0, 4000); hpcIndexVE->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);
@@ -66,20 +79,37 @@ void Analyzer::Begin(TTree * /*tree*/){
   hsx3VpcE->SetNdivisions( -612, "x");
   hsx3VpcE->SetNdivisions( -12, "y");
 
-  hZProj = new TH1F("hZProj", "Z Projection", 200, -600, 600);
+  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);
-  hanVScatsum = new TH2F("hanVScatsum", "Anode vs Cathode Sum; Anode E; Cathode E", 400,0 , 10000, 400, 0 , 16000);
+  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 Analyzer::Process(Long64_t entry){
+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();
@@ -111,24 +141,140 @@ Bool_t Analyzer::Process(Long64_t entry){
   // 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 ++){
-    ID.push_back(std::pair<int, int>(sx3.id[i], 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] );
 
-    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 = i+1; j < sx3.multi; j++){
+      for( int j = 0; j < pc.multi; j++){
-      hsx3Coin->Fill( sx3.index[i], sx3.index[j]);
+        hsx3VpcIndex->Fill( sx3.index[i], pc.index[j] );
-    }
+        //  if( sx3.ch[index] > 8 ){
-
+        //    hsx3VpcE->Fill( sx3.e[i], pc.e[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] );
-      //   }
-    }
   }
 
 
@@ -179,8 +325,9 @@ Bool_t Analyzer::Process(Long64_t entry){
           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 ){
+            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] );
             }
@@ -198,125 +345,30 @@ Bool_t Analyzer::Process(Long64_t entry){
 
   // //======================= QQQ
   for( int i = 0; i < qqq.multi; i ++){
-    // for( int j = 0; j < pc.multi; j++){
+
-        // if(pc.index[j]==4){
+      // 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;
-    for( int j = 0; j < qqq.multi; j++){
+            hqqqCoin->Fill( qqq.index[i], qqq.index[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 && E[l].first!=20 && E[l].first!=12){
-          if(!multi_an){
-            aE = E[l].second;
           }
-          multi_an=true;
+
-        }
+
-        else {
+          for( int j = i + 1; j < qqq.multi; j++){
-          cE = E[l].second + cE;
+            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( ID[0].first < 1 ) {
+        }  
-      aID = pc.ch[ID[0].second];
+      // }
-      cID = pc.ch[ID[1].second];
+  }
-    }else{
+
-      cID = pc.ch[ID[0].second];
+    // hanVScatsum->Fill(aE,cE);
-      aID = pc.ch[ID[1].second];
+    
-    }
 
     if( HitNonZero){
       pw_contr.CalTrack( hitPos, aID, cID);
@@ -324,7 +376,7 @@ Bool_t Analyzer::Process(Long64_t entry){
     }
 
   
-  }
+  
   
 
 
@@ -337,7 +389,7 @@ Bool_t Analyzer::Process(Long64_t entry){
   return kTRUE;
 }
 
-void Analyzer::Terminate(){
+void PCGainMatch::Terminate(){
 
   gStyle->SetOptStat("neiou");
   TCanvas * canvas = new TCanvas("cANASEN", "ANASEN", 2000, 2000); 
@@ -396,7 +448,7 @@ void Analyzer::Terminate(){
   // hqqqPolar->Draw("same colz pol");
 
  canvas->cd(padID); canvas->cd(padID)->SetGrid(1);
-//  hZProj->Draw();
   hanVScatsum->Draw("colz");
-
+  // hAnodeHits->Draw("colz");
+  // hAnodeMultiplicity->Draw();
 }

PCGainMatch.h

@@ -1,5 +1,5 @@
-#ifndef Analyzer_h
+#ifndef PCGainMatch_h
-#define Analyzer_h
+#define PCGainMatch_h
 
 #include <TROOT.h>
 #include <TChain.h>
@@ -8,7 +8,7 @@
 
 #include "Armory/ClassDet.h"
 
-class Analyzer : public TSelector {
+class PCGainMatch : public TSelector {
 public :
    TTree          *fChain;   //!pointer to the analyzed TTree or TChain
 
@@ -41,8 +41,8 @@ public :
    TBranch        *b_pcE;   //!
    TBranch        *b_pcT;   //!
 
-   Analyzer(TTree * /*tree*/ =0) : fChain(0) { }
+   PCGainMatch(TTree * /*tree*/ =0) : fChain(0) { }
-   virtual ~Analyzer() { }
+   virtual ~PCGainMatch() { }
    virtual Int_t   Version() const { return 2; }
    virtual void    Begin(TTree *tree);
    virtual void    SlaveBegin(TTree *tree);
@@ -57,13 +57,13 @@ public :
    virtual void    SlaveTerminate();
    virtual void    Terminate();
 
-   ClassDef(Analyzer,0);
+   ClassDef(PCGainMatch,0);
 };
 
 #endif
 
-#ifdef Analyzer_cxx
+#ifdef PCGainMatch_cxx
-void Analyzer::Init(TTree *tree){
+void PCGainMatch::Init(TTree *tree){
 
    // Set branch addresses and branch pointers
    if (!tree) return;
@@ -95,18 +95,18 @@ void Analyzer::Init(TTree *tree){
 
 }
 
-Bool_t Analyzer::Notify(){
+Bool_t PCGainMatch::Notify(){
 
    return kTRUE;
 }
 
-void Analyzer::SlaveBegin(TTree * /*tree*/){
+void PCGainMatch::SlaveBegin(TTree * /*tree*/){
 
    TString option = GetOption();
 
 }
 
-void Analyzer::SlaveTerminate(){
+void PCGainMatch::SlaveTerminate(){
 
 }
 

ProcessRun.sh

@@ -1,27 +1,38 @@
 #!/bin/bash
 
-if [ "$#" -ne 2 ]; then
+if [ "$#" -ne 3 ]; then
-    echo "Usage: $0 runID timeWindow_ns"
+    echo "Usage: $0 runID timeWindow_ns option"
+    echo "option: 0 - process raw data, 1 - process mapped data"
     echo "Exiting..."
     exit 1
 fi
 
-runID=$1
+runID=$(printf "%03d" $1)
 timeWindow=$2
 
-rawFolder=/home/tandem/Desktop/analysis/data
+option=$3
-rootFolder=/home/tandem/Desktop/analysis/data/root_data
 
-rsync -a splitpole@128.186.111.223:/media/nvmeData/ANASEN27Alap/*.fsu /home/tandem/Desktop/analysis/data
+# rawFolder=/home/tandem/data1/2024_09_17Fap/data
+# rawFolder=/mnt/d/17F
+# rootFolder=/mnt/d/Remapped_files/17F_data/root_data
+# rawFolder=/mnt/data1/vs19g/2024_06_27Al
+# rootFolder=/home/vs19g/Desktop/27Al_Data/root_data
+rawFolder=/mnt/data1/vs19g/2024_09_17Fap/data
+rootFolder=/home/vs19g/Desktop/17F_Data/root_data
 
-fileList=`\ls -1 ${rawFolder}/Run_${runID}_*.fsu`
+if [ $option -eq 0 ]; then
 
-./EventBuilder ${timeWindow} 0 0 10000000 ${fileList}
+    # rsync -auh --info=progress2 splitpole@128.186.111.223:/media/nvmeData/2024_09_17Fap/*.fsu /home/tandem/data1/2024_09_17Fap/data
 
-outFile=${rawFolder}/*${runID}*${timeWindow}.root
+    fileList=`\ls -1 ${rawFolder}/*Run*_${runID}_*.fsu`
 
-mv -vf ${outFile} ${rootFolder}/.
+    time ./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}/.
+
+    time ./Mapper ${rootFolder}/*${runID}*${timeWindow}.root
+fi
+
+# root "processRun.C(\"${rootFolder}/Run_${runID}_mapped.root\")"

QQQ_Calcheck.C

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

QQQ_Calcheck.h

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

README.md

@@ -0,0 +1,238 @@
+# ANASEN Analysis
+
+Analysis code for the **Array for Nuclear Astrophysics and Structure with Exotic Nuclei (ANASEN)** detector at FSU. Processes raw .fsu data through event building, channel mapping, calibration, and physics-level vertex reconstruction for transfer reaction experiments.
+
+---
+
+## Detector Overview
+
+| Detector | Type | Role |
+|----------|------|------|
+| **SX3** | Double-sided silicon strip (barrel, ~88 mm radius) | Energy and Z-position of recoils/ejectiles |
+| **QQQ** | Annular silicon (forward, z = 100 mm) | Energy and polar angle of forward-going particles |
+| **PC** | Helical proportional counter | dE and azimuthal/Z position via 24 anode + 24 cathode wires |
+
+The PC uses 24 twisted anode wires and 24 cathode wires. Wire geometry, crossover positions, pseudo-wire interpolation, and track-plane intersection are all handled by `Armory/ClassPW.h`.
+
+---
+
+## Full Analysis Chain
+
+```
+Raw .fsu files  (FSU digitizer output)
+      │
+      ▼
+┌─────────────────────────────────────────────────────────────────┐
+│  1. EVENT BUILDING                                              │
+│  Binary: EventBuilder  (Armory/EventBuilder.cpp)                │
+│  Script: buildEvents.sh  or  ProcessRun.sh <run> <tw> 0         │
+│  Input : *.fsu files                                            │
+│  Output: Run_NNN_<timeWindow>ns.root  (raw, unmapped TTree)     │
+│  Hits within a configurable time window are grouped as events.  │
+└─────────────────────────────────────────────────────────────────┘
+      │
+      ▼
+┌─────────────────────────────────────────────────────────────────┐
+│  3. PRE-ANALYSIS CHECKS  (optional)                             │
+│  Macro: PreAnalysis.C                                           │
+│  Plots raw rates and energy spectra per channel from unmapped   │
+│  data — useful for identifying dead/noisy channels before       │
+│  mapping.                                                       │
+└─────────────────────────────────────────────────────────────────┘
+      │
+      ▼
+┌─────────────────────────────────────────────────────────────────┐
+│  2. CHANNEL MAPPING                                             │
+│  Binary: Mapper  (Armory/Mapper.cpp)                            │
+│  Script: ProcessRun.sh <run> <tw> 0  (calls Mapper internally)  │
+│  Config: mapping.h                                              │
+│  Input : Eventbuilt ROOT tree                                   │
+│  Output: Run_NNN_mapped.root                                    │
+│  Translates hardware (digitizer SN, channel) to logical         │
+│  detector identity (SX3/QQQ/PC, strip/wire number).             │
+└─────────────────────────────────────────────────────────────────┘
+      │
+      ▼
+┌─────────────────────────────────────────────────────────────────┐
+│  4. CALIBRATION                                                 │
+│                                                                 │
+|  SX3 — two-pass procedure:                                      │
+│  Pass 1 — Left/Right matching  (sx3cal/LRFit.C)                 │
+│  │  Start with unity gains:                                     │
+│  │  LRFit.C fits the left/right charge ratio                    │
+│  │  Collate per-detector results into a single rightgains.dat   │
+|  │                                                              │
+│  Pass 2 — Back/Front gain matching  (sx3cal/EXFit.C)            │
+│  │  Run on data that is unity-gain sorted but L/R matched       │
+│  │  EXFit.C :                                                   │
+│  │    1) gain-matches the back strips (backgains.dat)           │
+│  │    2) corrects dynamic range non-linearity in the fronts     │
+│  │       (frontgains.dat)                                       │
+│  │  Run for every detector, collate into master backgains.dat   │
+│  │  and frontgains.dat.                                         │
+│  │                                                              |
+│  ├── GainMatchQQQ.C                                             │
+│  │       QQQ ring/wedge gain matching                           │
+│  │       Output: qqq_GainMatch.dat                              │
+│  ├── CalibrationQQQ.C                                           │
+│  │        Final absolute energy calibration for all detectors   │
+│  │        Output: qqq_Calib.dat                                 │
+│  ├── PCGainMatch.C                                              │
+│  │       PC anode and cathode gain matching                     │
+│  │       Output: slope_intercept_*.dat                          │
+│  ├── FitHistogramsWithTSpectrum_Sequential_Improved.C           │
+│  │       Automated peak finding on PC wire spectra              │
+│  │       done separately for anodes and cathodes then combined  │
+│  │       (TSpectrum-based; writes centroids for gain match)     │
+│  └──QQQ_Calcheck.C                                              │
+│      Verifies QQQ calibration against known sources             │
+└─────────────────────────────────────────────────────────────────┘
+      │
+      ▼
+┌─────────────────────────────────────────────────────────────────┐
+│  5.  VERTEX RECONSTRUCTION  (MakeVertex)                        │
+│  Macro : MakeVertex.C  (ROOT TSelector)                         │
+│  Batch : run_sx3.sh  (choose dataset, wireflip and offset)      │
+│  Input : Run_NNN_mapped.root                                    │
+│  Output: result_runNNN.root  (calibrated TTree                  │
+│          + diagnostic histograms)                               │
+│  Applies energy calibrations, reconstructs PC hit positions     │
+│  (anode energy + cathode charge division), clusters wires,      │
+│  and builds SX3/QQQ/PC event objects.                           │
+│  3D track-reconstruction diagnostics using                      │
+│  PC wire geometry and Si hit positions.                         │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Channel Mapping (`mapping.h` / `mapping_alpha.h`)
+
+The Mapper binary reads the raw TTree (digitizer serial number + channel) and rewrites it with logical detector labels. `mapping.h` is used for standard beam runs; `mapping_alpha.h` for source/alpha calibration runs where the electronics configuration differs. The active mapping is selected by editing the `#include` at the top of `Armory/Mapper.cpp` before building.
+
+`PrintMapping()` (defined in the mapping header) prints the full channel table at runtime for verification.
+
+---
+
+## MakeVertex — Vertex Reconstruction
+
+`MakeVertex.C` is a ROOT `TSelector` that loops over the analyzed event tree and fills diagnostic and physics histograms. It loads energy-loss lookup tables from `eloss_calculations/` and uses `Armory/Kinematics.h` for two-body reaction kinematics.
+
+### Diagnostic Section Toggles
+
+Comment out any `#define` at the top of `MakeVertex.C` to skip that block at compile time:
+
+```cpp
+#define DIAG_WIREMULT   // anode/cathode cluster multiplicity plots
+#define DIAG_1WIRE      // raw per-wire dE vs Si (no PC required)
+#define DIAG_PC_SX3     // PC-SX3 coincidence analysis
+#define DIAG_1A0C_SX3   // 1A0C single-wire vertex with SX3
+#define DIAG_1A0C_QQQ   // 1A0C single-wire vertex with QQQ
+#define DIAG_NA0C_SX3   // nA0C (n>=2) pseudo-wire vertex with SX3
+#define DIAG_NA0C_QQQ   // nA0C (n>=2) pseudo-wire vertex with QQQ
+#define DIAG_PC_QQQ     // PC-QQQ coincidence analysis
+```
+
+### Histogram Output Folders
+
+| ROOT Folder | Content |
+|-------------|---------|
+| `wiremult` | Anode/cathode cluster size and multiplicity matrices |
+| `1wire` | Raw single-wire dE vs SX3/QQQ energy and phi correlations |
+| `hTiming` | PC-Si timing spectra |
+| `hPCZSX3` | PC-Z reconstruction with SX3 coincidence |
+| `hPCzQQQ` | PC-Z projection with QQQ coincidence |
+| `1A0C`,`2A0C`, `3A0C`, … | n anodes (n≥1), 0 cathode: pseudo-wire vertex + excitation spectra |
+| `ainterp_noc` | Pseudo-wire interpolation diagnostics (no cathode gate) |
+| `phicut` | PC-QQQ with phi coincidence gate |
+
+### Vertex Reconstruction Methods
+
+**nA0C (n ≥ 1 anodes, `DIAG_NA0C_SX3/QQQ`):** All anode clusters are flattened and passed to `GetPseudoWire()` to produce an energy-weighted average wire. `getClosestWirePosAtWirePhi()` then finds the point on that pseudo-wire at the Si phi. Histograms land in a folder named `{n}A0C` (e.g. `2A0C`).
+
+---
+
+## Energy Loss (`eloss_calculations/`)
+
+Lookup tables pre-computed with [pycatima](https://github.com/hrosiak/pycatima) for the isobutane/helium fill gas at 250 Torr. Tables cover protons, alphas, aluminum beam, fluorine, and oxygen. `Eloss.py` regenerates the tables; `make_eloss_table.C` is a ROOT-based alternative generator.
+
+The `cm_to_MeV` / `MeV_to_cm` TGraph pairs loaded in `MakeVertex.C` provide fast range–energy conversion for correcting energy loss in the Si detectors.
+
+---
+
+## Geometry Utilities
+
+| File | Purpose |
+|------|---------|
+| `grid_generate.py` | Generates `detector_geometry.dat` — calculates SX3, QQQ, and PC wire azimuthal angles from first principles given detector radii and strip positions |
+| `shadowplay.py` | Exports ANASEN geometry (wires, SX3, QQQ) as a VTK file + `anasen_labels.csv` for visualisation in ParaView |
+| `detector_geometry.dat` | Pre-generated geometry reference (SX3 strip angles, wire positions) |
+| `anasen_labels.csv` | Label table for ParaView geometry display |
+
+---
+
+## FEM Simulations (`anasen_fem/`)
+
+Finite-element simulations of the PC electric field using gmsh (meshing), Elmer (FEM solver), and ParaView (visualisation). See `anasen_fem/README.md` for full setup and installation instructions.
+
+```bash
+cd anasen_fem
+python3 run.py    # mesh → FEM solve → field extraction → ParaView output
+```
+
+---
+
+## Batch Processing Scripts
+
+| Script | Purpose |
+|--------|---------|
+| `buildEvents.sh <run> <tw>` | Build events from raw .fsu for a single run |
+| `ProcessRun.sh <run> <tw> <opt>` | Full single-run pipeline: event build (opt=0) or analysis (opt=1) |
+| `BatchProcess.sh` | Parallel batch processing over a run range via GNU parallel |
+| `process_mapped_run.sh <start> <end>` | Run `TrackRecon.C` in parallel over a range of mapped files |
+| `run_sx3.sh/run_27Al.sh/run_17F.sh` | Run `VertexRecon.C` in parallel over a range of mapped files and hAdds them for analysis|
+
+---
+
+## Dependencies
+
+- [ROOT](https://root.cern) ≥ 6.x (TSelector, TChain, TVector3, TF1, TGraph, TSpectrum)
+- [GNU parallel](https://www.gnu.org/software/parallel/) — for batch scripts
+- [pycatima](https://github.com/hrosiak/pycatima) — for regenerating energy-loss tables
+- gmsh + Elmer + ParaView — for FEM simulations only
+
+---
+
+## Key Files Reference
+
+| File | Purpose |
+|------|---------|
+| `mapping.h` / `mapping_alpha.h` | Hardware→logical channel mapping (beam / alpha-source configs) |
+| `Armory/EventBuilder.cpp` | Time-window coincidence event builder (compiled binary) |
+| `Armory/Mapper.cpp` | Channel remapper: SN+ch → detector ID (compiled binary) |
+| `PreAnalysis.C / .h` | Raw rate and energy checks on mapped data |
+| `sx3cal/EXFit.C`, `EXFit2.C` | SX3 front/back gain coefficient extraction |
+| `sx3cal/LRFit.C` | SX3 left-right position calibration |
+| `sx3cal/{17F,27Al}/` | Per-experiment gain coefficient files (frontgains, backgains, rightgains) |
+| `GainMatchQQQ.C` | QQQ gain matching |
+| `Calibration.C / .h` | Absolute energy calibration |
+| `QQQ_Calcheck.C` | QQQ calibration verification |
+| `PCGainMatch.C` | PC anode/cathode gain matching |
+| `FitHistogramsWithTSpectrum_Sequential_Improved.C` | Automated PC anode peak fitting |
+| `Analyzer.C / .h` | Event-level clustering and PC hit reconstruction, (older in need of rehaul)|
+| `Analysis.C` | TChain wrapper to run Analyzer over a run range |
+| `processRun.C` | Single-file wrapper to run Analyzer on one ROOT file |
+| `MakeVertex.C / .h` | Vertex reconstruction and physics histogram production |
+| `TrackRecon.C / .h` | Alternate to VertexRecon, to track changes through code, eventaully plan to clean up one for actual data analysis |
+| `RunTimeSummary.C` | Run-by-run timing/rate summary across a run range |
+| `Armory/ClassPW.h` | PC wire geometry: crossovers, pseudo-wire, track-plane intersection |
+| `Armory/Kinematics.h/.cpp` | Two-body reaction kinematics (excitation energy, Q-value) |
+| `Armory/HistPlotter.h` | Histogram management with named ROOT folders |
+| `Armory/SX3Geom.h` | SX3 detector geometry |
+| `Armory/PC_StepLadder_Correction.h` | PC Z-position slope correction |
+| `eloss_calculations/Eloss.py` | Energy-loss table generator (pycatima) |
+| `grid_generate.py` | Generates `detector_geometry.dat` from first principles |
+| `shadowplay.py` | Exports ANASEN geometry to VTK + CSV for ParaView |
+| `detector_geometry.dat` | Pre-generated detector geometry reference |
+| `anasen_labels.csv` | Label table for ParaView geometry visualisation |
+| `anasen_fem/` | FEM electric field simulations for the PC |

RunTimeSummary.C

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

TrackRecon.h

@@ -0,0 +1,141 @@
+#ifndef TrackRecon_h
+#define TrackRecon_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <TSelector.h>
+#include <vector>
+#include <utility>
+#include <unordered_map>
+#include <tuple>
+
+#include "Armory/ClassDet.h"
+#include "Armory/ClassPW.h"
+
+class TrackRecon : public TSelector
+{
+public:
+   TTree *fChain; //! pointer to the analyzed TTree or TChain
+
+   // Declaration of leaf types
+   Det sx3;
+   Det qqq;
+   Det pc;
+   Det misc;
+
+   ULong64_t evID;
+   UInt_t run;
+
+   // List of branches
+   TBranch *b_eventID;   //!
+   TBranch *b_run;       //!
+   TBranch *b_sx3Multi;  //!
+   TBranch *b_sx3ID;     //!
+   TBranch *b_sx3Ch;     //!
+   TBranch *b_sx3E;      //!
+   TBranch *b_sx3T;      //!
+   TBranch *b_qqqMulti;  //!
+   TBranch *b_qqqID;     //!
+   TBranch *b_qqqCh;     //!
+   TBranch *b_qqqE;      //!
+   TBranch *b_qqqT;      //!
+   TBranch *b_pcMulti;   //!
+   TBranch *b_pcID;      //!
+   TBranch *b_pcCh;      //!
+   TBranch *b_pcE;       //!
+   TBranch *b_pcT;       //!
+   TBranch *b_miscMulti; //!
+   TBranch *b_miscID;    //!
+   TBranch *b_miscCh;    //!
+   TBranch *b_miscE;     //!
+   TBranch *b_miscT;     //!
+   TBranch *b_miscTf;    //!
+
+   // 1. Geometry Cache
+   Coord Crossover[24][24][2];
+
+   // 2. Persistent Vectors (REQUIRED for the optimized .cxx to work)
+   std::vector<std::pair<int, double>> anodeHits;
+   std::vector<std::pair<int, double>> cathodeHits;
+   std::vector<std::pair<int, double>> corrcatMax;
+   std::vector<std::pair<int, double>> corranoMax;
+   std::vector<double> cathodeTimes;
+   std::vector<double> anodeTimes;
+   std::unordered_map<int, std::tuple<int, double, double>> aWireEvents, cWireEvents;
+
+   TrackRecon(TTree * /*tree*/ = 0) : fChain(0) {}
+   virtual ~TrackRecon() {}
+   virtual Int_t Version() const { return 2; }
+   virtual void Begin(TTree *tree);
+   virtual void SlaveBegin(TTree *tree);
+   virtual void Init(TTree *tree);
+   virtual Bool_t Notify();
+   virtual Bool_t Process(Long64_t entry);
+   virtual Int_t GetEntry(Long64_t entry, Int_t getall = 0) { return fChain ? fChain->GetTree()->GetEntry(entry, getall) : 0; }
+   virtual void SetOption(const char *option) { fOption = option; }
+   virtual void SetObject(TObject *obj) { fObject = obj; }
+   virtual void SetInputList(TList *input) { fInput = input; }
+   virtual TList *GetOutputList() const { return fOutput; }
+   virtual void SlaveTerminate();
+   virtual void Terminate();
+   void OldAnalysis();
+
+   ClassDef(TrackRecon, 0);
+};
+
+#endif
+
+#ifdef TrackRecon_cxx
+void TrackRecon::Init(TTree *tree)
+{
+
+   if (!tree)
+      return;
+   fChain = tree;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("evID", &evID, &b_eventID);
+   fChain->SetBranchAddress("run", &run, &b_run);
+
+   sx3.SetDetDimension(24, 12);
+   qqq.SetDetDimension(4, 32);
+   pc.SetDetDimension(2, 24);
+
+   fChain->SetBranchAddress("sx3Multi", &sx3.multi, &b_sx3Multi);
+   fChain->SetBranchAddress("sx3ID", &sx3.id, &b_sx3ID);
+   fChain->SetBranchAddress("sx3Ch", &sx3.ch, &b_sx3Ch);
+   fChain->SetBranchAddress("sx3E", &sx3.e, &b_sx3E);
+   fChain->SetBranchAddress("sx3T", &sx3.t, &b_sx3T);
+   fChain->SetBranchAddress("qqqMulti", &qqq.multi, &b_qqqMulti);
+   fChain->SetBranchAddress("qqqID", &qqq.id, &b_qqqID);
+   fChain->SetBranchAddress("qqqCh", &qqq.ch, &b_qqqCh);
+   fChain->SetBranchAddress("qqqE", &qqq.e, &b_qqqE);
+   fChain->SetBranchAddress("qqqT", &qqq.t, &b_qqqT);
+   fChain->SetBranchAddress("pcMulti", &pc.multi, &b_pcMulti);
+   fChain->SetBranchAddress("pcID", &pc.id, &b_pcID);
+   fChain->SetBranchAddress("pcCh", &pc.ch, &b_pcCh);
+   fChain->SetBranchAddress("pcE", &pc.e, &b_pcE);
+   fChain->SetBranchAddress("pcT", &pc.t, &b_pcT);
+   fChain->SetBranchAddress("miscMulti", &misc.multi, &b_miscMulti);
+   fChain->SetBranchAddress("miscID", &misc.id, &b_miscID);
+   fChain->SetBranchAddress("miscCh", &misc.ch, &b_miscCh);
+   fChain->SetBranchAddress("miscE", &misc.e, &b_miscE);
+   fChain->SetBranchAddress("miscT", &misc.t, &b_miscT);
+   fChain->SetBranchAddress("miscF", &misc.tf, &b_miscTf);
+}
+
+Bool_t TrackRecon::Notify()
+{
+   return kTRUE;
+}
+
+void TrackRecon::SlaveBegin(TTree * /*tree*/)
+{
+   // TString option = GetOption();
+}
+
+void TrackRecon::SlaveTerminate()
+{
+}
+#endif // #ifdef TrackRecon_cxx

anasen_fem/1dpotplot.py

@@ -0,0 +1,187 @@
+#!/home/vsitaraman/ParaView-6.1.0-RC1-MPI-Linux-Python3.12-x86_64/bin/pvbatch
+
+import sys
+import numpy as np
+from paraview.simple import *
+import paraview.servermanager as sm
+from paraview.vtk.numpy_interface import dataset_adapter as dsa
+
+# ==========================================
+# COMMAND LINE ARGUMENTS
+# ==========================================
+if len(sys.argv) < 2:
+ print("Usage: pvbatch 1dpotplot.py <z_locus in mm>")
+ sys.exit(1)
+
+z_loc = float(sys.argv[1])
+
+INPUT_FILE = f"wires2d/elfield_anasen_t0001.vtu"
+OUTPUT_CSV = f"anode_to_cathode_1d_{z_loc}.csv"
+OUTPUT_IMAGE = f"1D_Variation_Plot_{z_loc}.png"
+
+print(f"--- Starting 1D Potential Extraction for Z = {z_loc} mm ---")
+
+# ==========================================
+# 1. EXACT GEOMETRIC CALCULATION
+# ==========================================
+print("Calculating theoretical wire coordinates...")
+
+wireShift = 4.0
+k = 2 * np.pi / 24.0
+
+offset_a1 = -10.0 * k
+offset_c1 = -5.5 * k
+offset_a2 = offset_a1 + (wireShift * k)
+offset_c2 = offset_c1 - (wireShift * k)
+
+t = (z_loc + 174.3) / (2 * 174.3)
+
+# Anode 0 theoretical position
+xa_loc = (37.0 * np.cos(offset_a1)) + t * (37.0 * np.cos(offset_a2) - 37.0 * np.cos(offset_a1))
+ya_loc = (37.0 * np.sin(offset_a1)) + t * (37.0 * np.sin(offset_a2) - 37.0 * np.sin(offset_a1))
+
+# All Cathodes theoretical positions
+xc1_all = np.array([42.0 * np.cos(k * i + offset_c1) for i in range(24)])
+yc1_all = np.array([42.0 * np.sin(k * i + offset_c1) for i in range(24)])
+xc2_all = np.array([42.0 * np.cos(k * i + offset_c2) for i in range(24)])
+yc2_all = np.array([42.0 * np.sin(k * i + offset_c2) for i in range(24)])
+
+xc_loc_all = xc1_all + t * (xc2_all - xc1_all)
+yc_loc_all = yc1_all + t * (yc2_all - yc1_all)
+
+# Nearest Cathode theoretical position
+distances = np.sqrt((xc_loc_all - xa_loc)**2 + (yc_loc_all - ya_loc)**2)
+nearest_c_idx = np.argmin(distances)
+xc_loc = xc_loc_all[nearest_c_idx]
+yc_loc = yc_loc_all[nearest_c_idx]
+
+# Theoretical targets in meters
+math_anode = np.array([xa_loc / 1000.0, ya_loc / 1000.0, 0.0])
+math_cathode = np.array([xc_loc / 1000.0, yc_loc / 1000.0, 0.0])
+# ==========================================
+# 2. MESH DATA SNAPPING (Electrode-Constrained)
+# ==========================================
+print(f"Loading VTU file: {INPUT_FILE} to snap to electrode nodes...")
+
+reader = XMLUnstructuredGridReader(FileName=[INPUT_FILE])
+UpdatePipeline()
+
+# Fetch data to Python
+raw_data = sm.Fetch(reader)
+wrapped_data = dsa.WrapDataObject(raw_data)
+
+pts = wrapped_data.Points
+pot = wrapped_data.PointData['potential']
+
+print("\nPotential range:")
+print(" min =", np.min(pot))
+print(" max =", np.max(pot))
+
+# -------------------------------------------------
+# Find actual electrode nodes
+# -------------------------------------------------
+
+anode_candidates = np.where(pot > 640.0)[0]
+
+if len(anode_candidates) == 0:
+ raise RuntimeError("No anode nodes found near 650 V")
+
+cathode_candidates = np.where(np.abs(pot) < 1.0)[0]
+
+if len(cathode_candidates) == 0:
+ raise RuntimeError("No cathode nodes found near 0 V")
+
+print(f"Found {len(anode_candidates)} anode nodes")
+print(f"Found {len(cathode_candidates)} cathode nodes")
+
+# -------------------------------------------------
+# Snap theoretical anode location to nearest
+# actual anode node
+# -------------------------------------------------
+
+anode_dist = np.linalg.norm(
+ pts[anode_candidates] - math_anode,
+ axis=1
+)
+
+anode_idx = anode_candidates[np.argmin(anode_dist)]
+
+true_anode_pos = pts[anode_idx]
+true_anode_pot = pot[anode_idx]
+
+# -------------------------------------------------
+# Snap theoretical cathode location to nearest
+# actual cathode node
+# -------------------------------------------------
+
+cathode_dist = np.linalg.norm(
+ pts[cathode_candidates] - math_cathode,
+ axis=1
+)
+
+cathode_idx = cathode_candidates[np.argmin(cathode_dist)]
+
+true_cathode_pos = pts[cathode_idx]
+true_cathode_pot = pot[cathode_idx]
+
+# -------------------------------------------------
+# Diagnostics
+# -------------------------------------------------
+
+anode_snap_error = np.linalg.norm(
+ true_anode_pos - math_anode
+)
+
+cathode_snap_error = np.linalg.norm(
+ true_cathode_pos - math_cathode
+)
+
+print("\nSelected electrode nodes:")
+print(f"Anode:")
+print(f" position = {true_anode_pos}")
+print(f" potential = {true_anode_pot:.3f} V")
+print(f" distance = {anode_snap_error*1e6:.1f} um")
+
+print(f"\nCathode:")
+print(f" position = {true_cathode_pos}")
+print(f" potential = {true_cathode_pot:.3f} V")
+print(f" distance = {cathode_snap_error*1e6:.1f} um")
+# ==========================================
+# 3. PARAVIEW EXTRACTION & PLOTTING
+# ==========================================
+print("Extracting data along the snapped line...")
+plot_over_line = PlotOverLine(Input=reader)
+
+# Apply the SNAPPED coordinates (converted to standard Python lists)
+plot_over_line.Point1 = true_anode_pos.tolist()
+plot_over_line.Point2 = true_cathode_pos.tolist()
+plot_over_line.Resolution = 1000 
+
+SaveData(OUTPUT_CSV, proxy=plot_over_line)
+
+print("Rendering plot...")
+line_chart_view = CreateView('XYChartView')
+line_chart_view.ViewSize = [1000, 600]
+line_chart_view.ChartTitle = f'Potential & E-Field: Anode to Cathode (Z = {z_loc} mm)'
+line_chart_view.LeftAxisTitle = 'Potential (V)'
+line_chart_view.BottomAxisTitle = 'Distance from Anode (m)'
+
+line_display = Show(plot_over_line, line_chart_view)
+
+# Tell ParaView to draw BOTH variables
+# line_display.SeriesVisibility = ['potential', 'electric field_Magnitude']
+line_display.SeriesVisibility = ['potential']
+
+# Style Potential (Red)
+line_display.SeriesColor = ['potential', '1.0', '0.0', '0.0'] 
+line_display.SeriesLineThickness = ['potential', '3']
+
+# # Style Electric Field (Blue, Right Axis)
+# line_display.SeriesColor = ['electric field_Magnitude', '0.0', '0.5', '1.0'] 
+# line_display.SeriesLineThickness = ['electric field_Magnitude', '3']
+# line_display.SeriesPlotCorner = ['electric field_Magnitude', '1']
+# line_chart_view.RightAxisTitle = 'Electric Field (V/m)'
+
+SaveScreenshot(OUTPUT_IMAGE, view=line_chart_view)
+print(f"Saved plot screenshot to: {OUTPUT_IMAGE}")
+print("--- Extraction Complete ---")

anasen_fem/README.md

@@ -0,0 +1,46 @@
+### README for ANASEN fem simulations:
+
+* There are a few iterations of these simulations that already exist. Be sure to also locate and refer to them if necessary.
+* Install gmsh and its python api by running (Ubuntu 22.04 LTS)
+
+```
+		sudo apt install gmsh python3-gmsh 
+```
+
+* Gmsh gives us the tools to create a meshgrid that samples the 2d space appropriately to plot the field/equipotential lines.
+* The output file typically has the .msh extension. This is read as input to Elmer, which is the FEM differential-equation solver.
+
+* Install Elmer via the following steps:
+
+```
+		sudo add-apt-repository ppa:elmer-csc-ubuntu/elmer-csc-ppa
+		sudo apt install elmerfem-csc-eg
+```
+
+* Install ParaView for visualizations by downloading from the Linux .tar.gz link at https://www.paraview.org/download/
+	- The current version is tested to work on Paraview 6.1.0. The default version in Ubuntu 22.04 repositories has some trouble with scripting
+* v0.0.1, March 10 2026
+	- 2d simulations of fields only. gmsh for meshing, elmer for fem, paraview to plot
+	- Before running, open `paraview_plotter.py` to make the bash shebang (#!) point to the location of `pvpython` or `pvbatch`
+	- `python3 run.py` should run everything in order, and is hopefully all the files are self-documenting
+* v0.0.2, September 2026
+	- Adds the Ramo weighting field and the `E . E_w` dot product for one cathode wire.
+	- `wires_gmsh2d_bc.py` now cuts the wires into the gas disk with `occ.fragment` instead of `mesh.embed`, so each wire boundary is a real edge of the domain. One cathode (optional 2nd argument, default 1) gets its own physical group, **tag 40**; the other 23 stay in tag 30.
+	- Two solves, same mesh, identical apart from the potentials:
+
+	| file | tag 40 | output |
+	|---|---|---|
+	| `wires2d.sif` | 0 V, like every other cathode | `wires2d/elfield_anasen_t0001.vtu` |
+	| `wires2d_weight.sif` | 1 V, all else 0 V | `wires2d/elfield_weight_t0001.vtu` |
+
+	- `dotproduct.py` reads both and writes `wires2d/dotproduct.vtu` with `DotProduct = E . E_w` (V/m^2). It aborts if the node sets differ or if either field is all zeros — both are silent failures otherwise.
+	- `paraview_dotproduct.py` renders it. `DOT_MIN`/`DOT_MAX` set the colour range and decide whether the picture shows anything.
+	- `paraview_plotter.py` gains two views: the equipotentials over one quadrant, and streamlines over the same quadrant. Streamlines are drift paths up to diffusion, so they show which wire collects charge from where; `SEED_POTENTIAL` and `SEED_STRIDE` control them.
+	- Six PNGs per z-locus, archived as before (`<Stem>_z_<count>_<z>[_quarter].png`). `Field_ouput` keeps its typo so the new files sort with the dozen already in `png/`.
+	- `STAGE` in `run.py`: `1` = mesh + physical solve, `2` = weighting solve + dot product reusing stage 1's mesh, `0` = both. Stage 2 never re-meshes, so it applies to whichever z stage 1 ran last.
+	- **Do not pass `-autoclean` to ElmerGrid.** It renumbers the physical groups (13/10/20/30/40 become 1/4/5/6/7), so every `Target Bodies`/`Target Boundaries` in the sifs matches nothing, Elmer solves nothing, and the potential comes out identically zero with no error.
+	- `mesh.recombine()` and `mesh.refine()` are both off: recombination ran over half an hour on the barrel surface without finishing, and refine took the mesh to ~16M nodes.
+	- Note on the solver stack: both sifs are the same file bar the potentials, so whatever `FluxSolver` does to `Electric Field` it does equally to both and the dot product stays consistent.
+* v0.0.3, planned TODO
+	- Garfield to take Elmer results and perform charge-transport
+	- Sweep the weighting solve over all 24 cathodes rather than one at a time

anasen_fem/clean.sh

@@ -0,0 +1,2 @@
+rm -f wires2d.msh
+rm -rf wires2d/*

anasen_fem/dielectrics.dat

@@ -0,0 +1,2 @@
+1
+13 1.0

anasen_fem/dotproduct.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+"""Node-by-node dot product of the physical field with a Ramo weighting field.
+
+Reads the two Elmer VTUs from wires2d.sif and wires2d_weight.sif and writes one
+carrying DotProduct = E . E_w. E is in V/m and E_w in 1/m (its electrode is
+driven to 1 V), so DotProduct is in V/m^2.
+
+By Shockley-Ramo a charge q drifting at v induces i = -q v . E_w, and for
+v = mu E that is -q mu (E . E_w). So this map is the induced-current density up
+to the constant -q*mu; --scale folds it in. The signs of q and mu differ
+between the electron and ion components, so they are left to the caller.
+
+    python3 dotproduct.py
+    python3 dotproduct.py --scale -1.0e-4
+"""
+
+import argparse
+import sys
+
+import numpy as np
+
+try:
+    import meshio
+except ImportError:
+    sys.exit("meshio is required: pip install meshio")
+
+
+def find_array(point_data, wanted, label):
+    """Look up a point-data array, ignoring case and spacing.
+
+    Elmer lowercases variable names into the VTU and the spelling has varied
+    between versions, so match loosely and list what is there on failure.
+    """
+    def norm(s):
+        return "".join(s.lower().split())
+
+    target = norm(wanted)
+    for key in point_data:
+        if norm(key) == target:
+            return point_data[key]
+    sys.exit(
+        "%s: no point-data array matching %r.\nAvailable arrays: %s"
+        % (label, wanted, sorted(point_data))
+    )
+
+
+def as_vectors(arr, label):
+    """Return an (N, ncomp) float array, tolerating flat or 2-component data."""
+    a = np.asarray(arr, dtype=float)
+    if a.ndim == 1:
+        sys.exit("%s: expected a vector field, got a scalar array" % label)
+    if a.ndim != 2:
+        sys.exit("%s: expected a 2D array, got shape %s" % (label, a.shape))
+    return a
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--phys", default="wires2d/elfield_anasen_t0001.vtu",
+                    help="VTU from the physical solve (wires2d.sif)")
+    ap.add_argument("--weight", default="wires2d/elfield_weight_t0001.vtu",
+                    help="VTU from the weighting solve (wires2d_weight.sif)")
+    ap.add_argument("--out", default="wires2d/dotproduct.vtu",
+                    help="output VTU")
+    ap.add_argument("--field", default="electric field",
+                    help="name of the electric-field array in both inputs")
+    ap.add_argument("--scale", type=float, default=None,
+                    help="constant (e.g. -q*mu) multiplying the dot product; "
+                         "writes an extra ScaledDotProduct array")
+    ap.add_argument("--rtol", type=float, default=0.0,
+                    help="relative tolerance for the node-position check")
+    ap.add_argument("--atol", type=float, default=1e-12,
+                    help="absolute tolerance (m) for the node-position check")
+    args = ap.parse_args()
+
+    phys = meshio.read(args.phys)
+    weight = meshio.read(args.weight)
+
+    # Taken node by node, so both solves must have produced the same node list.
+    # If they did not, every value below is meaningless and nothing else checks.
+    if phys.points.shape != weight.points.shape:
+        sys.exit(
+            "Node counts differ: %s has %d nodes, %s has %d. Both solves must "
+            "read the same mesh (same wires2d/ directory)."
+            % (args.phys, len(phys.points), args.weight, len(weight.points))
+        )
+    if not np.allclose(phys.points, weight.points, rtol=args.rtol, atol=args.atol):
+        worst = np.max(np.linalg.norm(phys.points - weight.points, axis=1))
+        sys.exit(
+            "Node positions do not match (largest discrepancy %.3e m). The two "
+            "solves were run on different meshes." % worst
+        )
+
+    E = as_vectors(find_array(phys.point_data, args.field, args.phys), args.phys)
+    Ew = as_vectors(find_array(weight.point_data, args.field, args.weight), args.weight)
+
+    # A zero field means the solve never ran: Laplace with no Dirichlet
+    # condition applied has the trivial solution and Elmer reports no error.
+    # Without this the chain completes and writes zeros, and the only symptom
+    # is a blank plot.
+    for label, arr, path in (
+        ("physical", E, args.phys),
+        ("weighting", Ew, args.weight),
+    ):
+        if not np.any(arr):
+            sys.exit(
+                "the %s field in %s is identically zero.\n"
+                "Elmer returned the trivial solution, which means no boundary "
+                "condition was applied. Compare the Target Bodies and Target "
+                "Boundaries numbers in the .sif against wires2d/mesh.names -- "
+                "ElmerGrid's -autoclean renumbers them." % (label, path)
+            )
+
+    # Elmer may pad 2D vectors to three components; compare only the
+    # components both arrays actually carry.
+    ncomp = min(E.shape[1], Ew.shape[1])
+    if E.shape[1] != Ew.shape[1]:
+        print("note: component counts differ (%d vs %d), using the first %d"
+              % (E.shape[1], Ew.shape[1], ncomp))
+    dot = np.einsum("ij,ij->i", E[:, :ncomp], Ew[:, :ncomp])
+
+    out = meshio.Mesh(
+        points=phys.points,
+        cells=phys.cells,
+        point_data=dict(phys.point_data),
+        cell_data=dict(phys.cell_data),
+    )
+    out.point_data["DotProduct"] = dot
+    out.point_data["WeightingField"] = Ew
+    if args.scale is not None:
+        out.point_data["ScaledDotProduct"] = args.scale * dot
+
+    meshio.write(args.out, out)
+
+    finite = dot[np.isfinite(dot)]
+    print("nodes            : %d" % len(dot))
+    print("components used  : %d" % ncomp)
+    print("DotProduct min   : %.6e V/m^2" % finite.min())
+    print("DotProduct max   : %.6e V/m^2" % finite.max())
+    print("DotProduct mean  : %.6e V/m^2" % finite.mean())
+    if len(finite) != len(dot):
+        print("WARNING: %d non-finite nodes" % (len(dot) - len(finite)))
+    print("wrote %s" % args.out)
+
+
+if __name__ == "__main__":
+    main()

anasen_fem/garfield_sim.py

@@ -0,0 +1,107 @@
+import ROOT
+import os
+import sys
+
+# 1. FIX: Manually load the Garfield library if it's not in the ROOT namespace
+# Update this path to your actual installation location
+garfield_lib_path = "/home/vs19g/garfieldpp/install/lib/libGarfield.so" #penguin path
+# garfield_lib_path = "/home/vsitaraman/garfieldpp/install/lib/libGarfield.so" #laptop path
+
+if os.path.exists(garfield_lib_path):
+    ROOT.gSystem.Load(garfield_lib_path)
+else:
+    print(f"CRITICAL ERROR: {garfield_lib_path} not found.")
+    sys.exit(1)
+
+# Verify access
+try:
+    test_gas = ROOT.Garfield.MediumMagboltz()
+except AttributeError:
+    print("ERROR: Garfield shared library loaded, but 'Garfield' namespace not found.")
+    sys.exit(1)
+
+# --- 2. GAS SETUP (96% He, 4% CO2) ---
+gas = ROOT.Garfield.MediumMagboltz()
+gas_file = "He96_CO2_4_260Torr.gas"
+
+if not os.path.exists(gas_file):
+    print("Generating new Magboltz gas table (260 Torr)...")
+    # --- Optimized Magboltz Settings ---
+    gas.SetComposition("he", 96.0, "co2", 4.0)
+    gas.SetTemperature(293.15)
+    gas.SetPressure(260.0)
+
+    # 1. Limit the Field Grid: 
+    gas.SetFieldGrid(10., 80000., 20, True) 
+
+    # 2. Reduce the precision slightly for the first run:
+    gas.GenerateGasTable(8) 
+    gas.WriteGasFile(gas_file)
+else:
+    print(f"Loading existing gas table: {gas_file}")
+    gas.LoadGasFile(gas_file)
+
+# --- 3. FIELD MAP SETUP ---
+fm = ROOT.Garfield.ComponentElmer2d()
+
+
+fm.Initialise("wires2d/mesh.header", 
+              "wires2d/mesh.elements", 
+              "wires2d/mesh.nodes", 
+              "dielectrics.dat", 
+              "wires2d/elstatics.result", 
+              "mm")
+
+# Set the medium (Body 13 from your Gmsh script)
+fm.SetMedium(0, gas)
+
+# --- 4. SENSOR AND DRIFT SETUP ---
+sensor = ROOT.Garfield.Sensor()
+sensor.AddComponent(fm)
+sensor.SetArea(-50.0, -50.0, -5.0, 50.0, 50.0, 5.0) #hardcoding the sesnsor area to define a psuedo 3d geometry
+
+# Heavy Ion Drift (RKF) - Best for the general track
+drift = ROOT.Garfield.DriftLineRKF()
+drift.SetSensor(sensor)
+
+# Electron Avalanche (Microscopic) - Best for high-field gain
+aval = ROOT.Garfield.AvalancheMicroscopic()
+aval.SetSensor(sensor)
+
+# --- 5. EXECUTION ---
+# Starting position (e.g., near the IC wires at r=23mm or closer to Anodes)
+x0, y0, z0, t0 = 3.50, 0.0, 0.0, 0.0
+
+print(f"Simulating heavy ion drift from r={x0}...")
+drift.DriftIon(x0, y0, z0, t0)
+
+# Create a file to store the heavy ion track
+with open("heavy_ion_track.csv", "w") as f:
+    f.write("x,y,z,t\n")
+    
+    # After running drift.DriftIon(x0, y0, z0, t0):
+    n_points = drift.GetNumberOfDriftLinePoints()
+    for i in range(n_points):
+        xi, yi, zi, ti = ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.double(0)
+        drift.GetDriftLinePoint(i, xi, yi, zi, ti)
+        f.write(f"{xi},{yi},{zi},{ti}\n")
+
+print(f"Simulating electron avalanche from r={x0}...")
+# AvalancheElectron(x, y, z, t, energy, dx, dy, dz)
+aval.AvalancheElectron(x0, y0, z0, t0, 0.1, 0.0, 0.0, 0.0)
+
+with open("avalanche_endpoints.csv", "w") as f:
+    f.write("x,y,z,t\n")
+    
+    # After aval.AvalancheElectron(...)
+    n_endpoints = aval.GetNumberOfEndpoints()
+    for i in range(n_endpoints):
+        # Get start and end points of each electron in the avalanche
+        x1, y1, z1, t1, e1 = ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.double(0)
+        x2, y2, z2, t2, e2, status = ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.double(0), ROOT.int(0)
+        
+        aval.GetEndpoint(i, x1, y1, z1, t1, e1, x2, y2, z2, t2, e2, status)
+        # We save the endpoint (x2, y2, z2) where the electron was collected or attached
+        f.write(f"{x2},{y2},{z2},{t2}\n")
+
+print("Simulation complete.")

anasen_fem/junk/wires.py

@@ -0,0 +1,114 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+
+acolors = plt.get_cmap('tab20',24)
+ccolors = plt.get_cmap('tab20',24)
+
+k=-2*np.pi/24.
+offset = 6*k + 3*k #-pi/2
+xarra_1 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_1 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+labelsa_1 = np.array([i for i in np.arange(0,24)])
+
+fig,ax = plt.subplots(figsize=(10,10))
+ax.invert_yaxis()
+ax.plot(xarra_1,yarra_1,"x",label="anode, z=-L/2")
+
+for x,y,label in zip(xarra_1,yarra_1,labelsa_1):
+    ax.text(x,y,label)
+
+kc=2*np.pi/24.
+offsetc = -4*kc + 2*kc -  np.pi/24 #-pi/4
+xarrc_1 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_1 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+labelsc_1 = np.array([i for i in np.arange(0,24)])
+
+ax.plot(xarrc_1,yarrc_1,"o",label="cathode, z=-L/2, where they are picked up")
+
+for x,y,label in zip(xarrc_1,yarrc_1,labelsc_1):
+    ax.text(x,y,label)
+plt.title("z=-L/2 plane, beam going into the plane along +z, (+x right, +y down)")
+plt.grid()
+plt.legend()
+plt.savefig("plane1.png")
+plt.show()
+
+fig,ax = plt.subplots(figsize=(10,10))
+ax.invert_yaxis()
+
+offset = offset-3*k
+xarra_2 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_2 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+labelsa_2 = np.array([i for i in np.arange(0,24)])
+
+ax.plot(xarra_2,yarra_2,"x",label="anode, z=+L/2, where they are picked up")
+
+for x,y,label in zip(xarra_2,yarra_2,labelsa_2):
+    ax.text(x,y,label)
+
+offsetc = offsetc-3*kc
+xarrc_2 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_2 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+labelsc_2 = np.array([i for i in np.arange(0,24)])
+
+ax.plot(xarrc_2,yarrc_2,"o",label="cathode, z=+L/2")
+
+for x,y,label in zip(xarrc_2,yarrc_2,labelsc_2):
+    ax.text(x,y,label)
+plt.title("z=+L/2 plane, beam going into the plane along +z, (+x right, +y down)")
+plt.grid()
+plt.legend()
+plt.savefig("plane2.png")
+plt.show()
+
+fig = plt.figure(figsize=(10,10))
+ax = fig.add_subplot(111,projection='3d')
+ax.set_xlabel("x")
+ax.set_ylabel("y")
+ax.set_zlabel("z")
+
+xx_a = np.array([[x1,x2] for x1,x2 in zip(xarra_1,xarra_2)])
+yy_a = np.array([[y1,y2] for y1,y2 in zip(yarra_1,yarra_2)])
+zz_a = np.array([[-173.5,173.5] for x1,x2 in zip(xarra_1,xarra_2)])
+for i,[xx,yy,zz] in enumerate(zip(xx_a,yy_a,zz_a)):
+    ax.plot(xx,yy,zz,'-',color=acolors(i/24))
+
+for i,[x,y,label] in enumerate(zip(xarra_1,yarra_1,labelsa_1)):
+    ax.text(x,y,-173,"a"+str(label),color=acolors(i/24))
+for i,[x,y,label] in enumerate(zip(xarra_2,yarra_2,labelsa_2)):
+    ax.text(x,y,+173,"a"+str(label),color=acolors(i/24))
+
+xx_c = np.array([[x1,x2] for x1,x2 in zip(xarrc_1,xarrc_2)])
+yy_c = np.array([[y1,y2] for y1,y2 in zip(yarrc_1,yarrc_2)])
+zz_c = np.array([[-173.5,173.5] for x1,x2 in zip(xarrc_1,xarrc_2)])
+for i,[xx,yy,zz] in enumerate(zip(xx_c,yy_c,zz_c)):
+    ax.plot(xx,yy,zz,'--',color=ccolors(((47-i)%24)/24))
+
+for i,[x,y,label] in enumerate(zip(xarrc_1,yarrc_1,labelsc_1)):
+    ax.text(x,y,-173,"c"+str(label),color=ccolors(((25-i)%24)/24))
+for i,[x,y,label] in enumerate(zip(xarrc_2,yarrc_2,labelsc_2)):
+    ax.text(x,y,+173,"c"+str(label),color=ccolors(((47-i)%24)/24))
+ax.view_init(elev=-53, azim=-106, roll=18)
+plt.tight_layout()
+plt.show()
+phi_qqq = np.array([[2*np.pi*(-i*16+j+0.5)/(16*4) for i in range(4)] for j in range(16)])
+print(phi_qqq)
+#'''
+for i,[phi1,phi2,phi3,phi4] in enumerate(phi_qqq):
+    ax.plot([50*np.cos(phi1),100*np.cos(phi1)],[50*np.sin(phi1),100*np.sin(phi1)],[100,100],'-',color='red')
+    ax.text(104*np.cos(phi1),104*np.sin(phi1),100,"0_%d"%(i),color="red")
+
+    ax.plot([50*np.cos(phi2),100*np.cos(phi2)],[50*np.sin(phi2),100*np.sin(phi2)],[100,100],'-',color='green')
+    ax.text(104*np.cos(phi2),104*np.sin(phi2),100,"1_%d"%(i),color="green")
+
+    ax.plot([50*np.cos(phi3),100*np.cos(phi3)],[50*np.sin(phi3),100*np.sin(phi3)],[100,100],'-',color='blue')
+    ax.text(104*np.cos(phi3),104*np.sin(phi3),100,"2_%d"%(i),color="blue")
+
+    ax.plot([50*np.cos(phi4),100*np.cos(phi4)],[50*np.sin(phi4),100*np.sin(phi4)],[100,100],'-',color='brown')
+    ax.text(104*np.cos(phi4),104*np.sin(phi4),100,"3_%d"%(i),color="brown")
+#'''
+#coords_qqq = np.array([[50*np.cos(phi),100*np.sin(phi),100] for phi in phi_qqq]).T
+plt.tight_layout()
+plt.show()
+

anasen_fem/junk/wires2d_test.sif

@@ -0,0 +1,71 @@
+Check Keywords Warn
+
+Header
+  Mesh DB "." "wires2d"
+End
+
+Simulation
+  Coordinate System = Cartesian 2D
+  Simulation Type = Steady State
+  Steady State Max Iterations = 1
+  Output File = "elstatics.result"
+  Post File = "elstatics.ep"
+End
+
+Constants
+  Permittivity Of Vacuum = 8.8542e-12
+End
+
+
+Body 1
+  Target Bodies(1) = 13
+  Equation = 1
+  Material = 1
+End
+
+
+Equation 1
+  Active Solvers(2) = 1 2
+End
+
+
+Material 1
+  Relative Permittivity = 1
+End
+
+
+Solver 1
+  Equation = Electrostatics
+  Procedure = "StatElecSolve" "StatElecSolver"
+
+  Variable = Potential
+  Variable DOFs = 1
+
+  Calculate Electric Field = True
+  Calculate Electric Flux = False
+
+  Linear System Solver = Iterative
+  Linear System Iterative Method = CG
+  Linear System Max Iterations = 500
+  Linear System Convergence Tolerance = 1.0e-8
+  Linear System Preconditioning = ILU1
+End
+
+
+Solver 2
+  Equation = Electric Force
+  Procedure = "ElectricForce" "StatElecForce"
+End
+
+
+Boundary Condition 1
+  Target Boundaries = 10
+  Potential = 650
+  Calculate Electric Force = True
+End
+
+
+Boundary Condition 2
+  Target Boundaries = 20
+  Potential = 0
+End

anasen_fem/junk/wires_gmsh.py

@@ -0,0 +1,91 @@
+import numpy as np
+import gmsh
+
+gmsh.initialize()
+gmsh.model.add("adaptive_mesh")
+gmsh.option.setNumber('General.NumThreads', 4)
+#gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfElements", 200000)
+#gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfNodes", 200000)
+#gmsh.option.setNumber("Mesh.Adapt.MaxIter",5)
+#gmsh.option.setNumber("Mesh.MeshSizeMin", 5e-3)
+#gmsh.option.setNumber("Mesh.MeshSizeMax", 10.0)
+#gmsh.option.setNumber("Mesh.CharacteristicLengthFromCurvature", 0)
+
+lc = 0.01
+
+#anodes, plane 1 at -zmax/2
+k=-2*np.pi/24.
+offset = 6*k + 3*k #-pi/2
+xarra_1 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_1 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+
+#cathodes, plane 1 at -zmax/2
+kc=2*np.pi/24.
+offsetc = -4*kc + 2*kc -  np.pi/24 #-pi/4
+xarrc_1 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_1 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+
+#anodes, plane 2 at +zmax/2
+offset = offset-3*k
+xarra_2 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_2 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+
+#cathodes, plane2 at +zmax/2
+offsetc = offsetc-3*kc
+xarrc_2 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_2 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+
+pa1 = []
+pa2 = []
+pc1 = []
+pc2 = []
+
+wire_radius = 0.254 #mm
+anode_wires = []
+cathode_wires = []
+aw_tags = [(3,i) for i in range(24)]
+cw_tags = [(3,i+24) for i in range(24)]
+
+for i,[xa,ya,xc,yc,xa2,ya2,xc2,yc2] in enumerate(zip(xarra_1,yarra_1,xarrc_1,yarrc_1,xarra_2,yarra_2,xarrc_2,yarrc_2)):
+    print(i,xa,ya,-178.3,xc,yc,-178.3,xa2,ya2,178.3,xc2,yc2,178.3)
+    anode_wires.append(gmsh.model.occ.addCylinder(xa,ya,-178.3,(xa2-xa),(ya2-ya),178.3*2,wire_radius,i)) #x,y,z of first face center, dx,dy,dz of the axis, then the wire radius
+    cathode_wires.append(gmsh.model.occ.addCylinder(xc,yc,-178.3,(xc2-xc),(yc2-yc),178.3*2,wire_radius,i+24)) #cathode tags 24-47, anode 0-23
+
+
+anasen_barrel = gmsh.model.occ.addCylinder(0,0,-500,0,0,500+605,300,1234) #tag 1234
+#anasen_barrel = gmsh.model.occ.addCylinder(0,0,-500,0,0,500+605,300,1234) #tag 1234
+
+gmsh.model.occ.synchronize()
+
+all_wires = aw_tags+cw_tags
+gmsh.model.occ.fragment([(3,1234)],all_wires)
+gmsh.model.occ.removeAllDuplicates()
+gmsh.model.occ.synchronize()
+gmsh.option.setNumber("Geometry.Tolerance", 1e-6)
+gmsh.option.setNumber("Geometry.OCCFixDegenerated", 1)
+gmsh.option.setNumber("Geometry.OCCFixSmallEdges", 1)
+gmsh.option.setNumber("Geometry.OCCFixSmallFaces", 1)
+
+wire_surfs = []
+for w in anode_wires + cathode_wires:
+    wire_surfs += [s[1] for s in gmsh.model.getBoundary([(3,w)], oriented=False) if s[0] == 2]
+#'''
+f1 = gmsh.model.mesh.field.add("Distance")
+gmsh.model.mesh.field.setNumbers(f1, "FacesList", wire_surfs) # Example curves
+f2 = gmsh.model.mesh.field.add("Threshold")
+gmsh.model.mesh.field.setNumber(f2, "InField", f1)
+gmsh.model.mesh.field.setNumber(f2, "SizeMin", 0.05)
+gmsh.model.mesh.field.setNumber(f2, "SizeMax", 5.)
+gmsh.model.mesh.field.setNumber(f2, "DistMin", 1.)
+gmsh.model.mesh.field.setNumber(f2, "DistMax", 20.)
+gmsh.model.mesh.field.setAsBackgroundMesh(f2)
+#'''
+gmsh.option.setNumber("Mesh.Algorithm", 2)
+gmsh.option.setNumber("Mesh.Algorithm3D", 1) # For 3D meshes
+
+gmsh.model.mesh.generate(dim=3)
+#gmsh.model.mesh.refine()
+#gmsh.model.mesh.refine()
+#gmsh.model.mesh.refine()
+gmsh.fltk.run()
+gmsh.finalize()

anasen_fem/junk/wires_gmsh_bc.py

@@ -0,0 +1,87 @@
+import numpy as np
+import gmsh
+
+gmsh.initialize()
+#gmsh.model.add("adaptive_mesh")
+gmsh.option.setNumber('General.NumThreads', 4)
+#gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfElements", 200000)
+#gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfNodes", 200000)
+#gmsh.option.setNumber("Mesh.Adapt.MaxIter",5)
+#gmsh.option.setNumber("Mesh.MeshSizeMin", 5e-3)
+#gmsh.option.setNumber("Mesh.MeshSizeMax", 10.0)
+gmsh.option.setNumber("Geometry.Tolerance", 1e-2)
+#gmsh.option.setNumber("Mesh.CharacteristicLengthFromCurvature", 0)
+
+lc = 0.04
+#anodes, plane 1 at -zmax/2
+k=-2*np.pi/24.
+offset = 6*k + 3*k #-pi/2
+xarra_1 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_1 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+
+#cathodes, plane 1 at -zmax/2
+kc=2*np.pi/24.
+offsetc = -4*kc + 2*kc -  np.pi/24 #-pi/4
+xarrc_1 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_1 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+
+#anodes, plane 2 at +zmax/2
+offset = offset-3*k
+xarra_2 = np.array([37*np.cos(k*i+offset) for i in np.arange(0,24)])
+yarra_2 = np.array([37*np.sin(k*i+offset) for i in np.arange(0,24)])
+
+#cathodes, plane2 at +zmax/2
+offsetc = offsetc-3*kc
+xarrc_2 = np.array([42*np.cos(kc*i+offsetc) for i in np.arange(0,24)])
+yarrc_2 = np.array([42*np.sin(kc*i+offsetc) for i in np.arange(0,24)])
+
+wire_radius = 0.254 #mm
+anode_wires = []
+cathode_wires = []
+aw_tags = [(3,i) for i in range(24)]
+cw_tags = [(3,i+24) for i in range(24)]
+
+for i,[xa,ya,xc,yc,xa2,ya2,xc2,yc2] in enumerate(zip(xarra_1,yarra_1,xarrc_1,yarrc_1,xarra_2,yarra_2,xarrc_2,yarrc_2)):
+    print(i,xa,ya,-178.3,xc,yc,-178.3,xa2,ya2,178.3,xc2,yc2,178.3)
+    pa1 = gmsh.model.occ.addPoint(xa,ya,-178.3,lc)
+    pa2 = gmsh.model.occ.addPoint(xa2,ya2,178.3,lc)
+    pc1 = gmsh.model.occ.addPoint(xc,yc,-178.3,lc)
+    pc2 = gmsh.model.occ.addPoint(xc2,yc2,178.3,lc)
+    linea = gmsh.model.occ.addLine(pa1,pa2)
+    linec = gmsh.model.occ.addLine(pc1,pc2)
+    anode_wires.append(linea)
+    cathode_wires.append(linec)
+
+#anasen_barrel = gmsh.model.occ.addCylinder(0,0,-500,0,0,500+605,300,1234) #tag 1234
+anasen_barrel = gmsh.model.occ.addCylinder(0,0,-200, 0,0,400, 300) #tag 1234
+
+gmsh.model.occ.synchronize()
+gmsh.model.mesh.embed(1,anode_wires+cathode_wires,3,anasen_barrel)
+
+f1 = gmsh.model.mesh.field.add("Distance")
+gmsh.model.mesh.field.setNumbers(f1,"CurvesList",anode_wires+cathode_wires)
+
+f2 = gmsh.model.mesh.field.add("Threshold")
+gmsh.model.mesh.field.setNumber(f2,"InField",f1)
+gmsh.model.mesh.field.setNumber(f2,"SizeMin",0.08)
+gmsh.model.mesh.field.setNumber(f2,"SizeMax",5)
+gmsh.model.mesh.field.setNumber(f2,"DistMin",1)
+gmsh.model.mesh.field.setNumber(f2,"DistMax",20)
+
+gmsh.model.mesh.field.setAsBackgroundMesh(f2)
+
+gmsh.model.addPhysicalGroup(1, anode_wires, tag=10)
+gmsh.model.setPhysicalName(1,10,"anode_wires")
+
+gmsh.model.addPhysicalGroup(1, cathode_wires, tag=20)
+gmsh.model.setPhysicalName(1,20,"cathode_wires")
+
+gmsh.option.setNumber("Mesh.Algorithm",6)
+gmsh.option.setNumber("Mesh.Algorithm3D", 10) # For 3D meshes
+
+gmsh.model.mesh.generate(dim=3)
+gmsh.model.mesh.refine()
+#gmsh.model.mesh.refine()
+#gmsh.model.mesh.refine()
+gmsh.fltk.run()
+gmsh.finalize()

anasen_fem/paraview_dotproduct.py

@@ -0,0 +1,279 @@
+#!/home/vsitaraman/ParaView-6.1.0-RC1-MPI-Linux-Python3.12-x86_64/bin/pvbatch
+# Point the shebang above at your own pvbatch/pvpython, as for paraview_plotter.py.
+#
+# Renders the E . E_w map written by dotproduct.py.
+#
+# By Shockley-Ramo the dot product describes the current induced on ONE
+# electrode: the cathode that wires2d_weight.sif held at 1 V. Everywhere else
+# the number is just the tail of that electrode's weighting field, so the view
+# is centred on that wire and nothing else. Its position is read out of the
+# weighting solve rather than recomputed from the geometry -- the driven
+# electrode is wherever the weighting potential reaches 1.
+#
+# Usage (from anasen_fem/):
+#   ./paraview_dotproduct.py [dotproduct.vtu] [output.png] [weight.vtu]
+#
+# Re-plotting an archived z needs its archived weighting solve as well, since
+# that is where the driven cathode's position is read from:
+#   ./paraview_dotproduct.py wires2d/vtu_files/dotproduct_10_0.0000.vtu \
+#       png/DotProduct_output_z_10_0.0000.png \
+#       wires2d/vtu_files/elfield_weight_10_0.0000.vtu
+
+import sys
+
+import numpy as np
+from paraview.simple import *
+
+INPUT_VTU = sys.argv[1] if len(sys.argv) > 1 else "wires2d/dotproduct.vtu"
+OUTPUT_IMAGE = sys.argv[2] if len(sys.argv) > 2 else "DotProduct_output.png"
+
+# Weighting solve, used only to locate the driven cathode. Must be the one that
+# belongs to this dot product -- the wire moves with z.
+WEIGHT_VTU = sys.argv[3] if len(sys.argv) > 3 else "wires2d/elfield_weight_t0001.vtu"
+
+# Half-height of the view in metres. Cathodes sit every 15 degrees at a radius
+# of about 36.4 mm, so the neighbours either side are 9.5 mm away; 14 mm takes
+# them both in with a margin.
+# Image size. The structure round the driven cathode is much wider than it is
+# tall, so a square frame spends most of its area on empty gas.
+VIEW_SIZE = [2000, 1200]
+
+# CameraParallelScale, which is the half-HEIGHT of the view in metres. The
+# width follows from the aspect: half-height * (VIEW_SIZE[0] / VIEW_SIZE[1]).
+# So widening the frame alone does not crop anything, it just shows more
+# sideways; the scale has to come down with it. 0.0084 at 2000x1200 keeps the
+# same 28 mm width as the old square 0.014 and trims the height to 16.8 mm.
+ZOOM_SCALE = 0.0084
+
+# The driven cathode swings round the axis as z changes, so with a fixed "up"
+# every z comes out rotated by a different amount and the shots cannot be laid
+# side by side. Aligning up with the outward radial direction through the
+# cathode puts the detector axis below and the barrel wall above in every
+# frame, whatever z. Set False for plain screen-aligned axes.
+ALIGN_RADIAL = True
+
+# Shift of the view centre along the outward radial, in metres. Up in the frame
+# is the outward radial, so a NEGATIVE value walks the camera in towards the
+# detector axis and the cathode rides higher in the picture. Positive drops it.
+# Purely framing; it does not move the wire.
+CENTER_SHIFT = -0.0036
+
+# Second, wider shot over the same quadrant paraview_plotter.py frames, so the
+# dot product can be laid beside the field and contour views of that z. Centre
+# is at x < 0, y > 0; negate the y for the lower-left quadrant instead.
+
+# Colour range for DotProduct. Both ends negative: E and E_w point in broadly
+# opposite senses over most of the drift volume.
+# Most of the painted patch lies between -2e7 and -2e6. Against a range
+# reaching -3.1e8 that is the top few percent of the scale, so it all came out
+# at the white end of Greens. Narrowing the range spreads those values over the
+# green; anything stronger simply clamps to the darkest end, which only affects
+# the last fraction of a millimetre at the wire surface.
+DOT_MIN, DOT_MAX = -8.0e7, -3.0e6
+
+# Opacity of the painted map. Anything at least as strong as OPAQUE_BELOW is
+# drawn solid; from there it ramps down to transparent at FADE_TO, so the grey
+# shows through with a soft round edge rather than the ragged one a hard cut
+# leaves.
+#
+# The plateau matters more than either endpoint. Ramping all the way from
+# DOT_MIN (-3.1e8) meant the opacity at -5e7 was only about 0.13, so the whole
+# patch read as washed out however the fade point was set.
+OPAQUE_BELOW = -2.0e7
+FADE_TO = -2.0e6
+
+# Coarse cut, only to keep the far field out of the render. Must be nearer zero
+# than FADE_TO so its hard edge lands where the surface is already fully
+# transparent and cannot be seen.
+PAINT_CUT = -5.0e5
+
+# "signed-log" maps sign and magnitude together through a signed logarithm and
+# a diverging colour map; "linear" is the earlier one-sided Greens scale, which
+# the constants above still drive.
+COLOR_MODE = "signed-log"
+# X0 sets where the mapping turns from linear to logarithmic, and so how much
+# of the weak far field survives at all: at 1e6 the data map to -2.51 .. 1.62,
+# against -3.51 .. 2.61 at 1e5. Raise it to paint less.
+SYMLOG_X0 = 1.0e6
+SYMLOG_LIMIT = 2.5       # symmetric colour limit; match it to the mapped range
+SYMLOG_OPAQUE = 0.6      # |value| at which the map is fully opaque
+SYMLOG_FADE = 0.3        # |value| below which it is transparent
+
+# Shape of the two opacity ramps, as opposed to where they sit.
+#
+# A piecewise function's midpoint describes the segment running RIGHTWARD from
+# each node, and the two ramps run in opposite senses -- falling on the
+# negative side, rising on the positive. So a single midpoint below 0.5 applied
+# to both makes the negative lobe fade out sooner while the positive lobe goes
+# opaque sooner, rendering the two polarities at different effective
+# thresholds. Mirroring it keeps them symmetric: below 0.5 both sides go opaque
+# sooner, so more is painted, equally on each.
+#
+# Sharpness is the independent dial for how abrupt the edge is: 0 smooth, 1 a
+# hard step. 0.5 is already close to a step.
+SYMLOG_MIDPOINT = 0.3
+SYMLOG_SHARPNESS = 0.0
+DIVERGING_PRESET = "PRGn"   # purple / white / green; zero sits at white
+
+BACKGROUND = [0.35, 0.34, 0.33]   # grey
+
+# Equipotential lines over the whole frame, painted gas or not. Off by default:
+# the map is the subject here, and the lines are already in the contour plots.
+SHOW_CONTOURS = False
+CONTOUR_BY = "potential"
+CONTOUR_LEVELS = list(np.arange(0, 660, 660 / 40.0))
+
+
+def threshold_between(source, array, low, high):
+    """Threshold filter, tolerating the pre-5.10 property names."""
+    t = Threshold(Input=source, Scalars=["POINTS", array])
+    try:
+        t.LowerThreshold = low
+        t.UpperThreshold = high
+        t.ThresholdMethod = "Between"
+    except Exception:
+        t.ThresholdRange = [low, high]
+    return t
+
+
+# --- locate the driven cathode: the weighting potential is 1 on it ---
+weight_reader = XMLUnstructuredGridReader(FileName=[WEIGHT_VTU])
+driven = threshold_between(weight_reader, "potential", 0.99, 1.01)
+driven.UpdatePipeline()
+
+info = driven.GetDataInformation()
+if info.GetNumberOfPoints() == 0:
+    sys.exit(
+        "no nodes with weighting potential ~1 in %s -- the weighting solve did\n"
+        "not drive any electrode, so there is nothing to centre on." % WEIGHT_VTU
+    )
+b = info.GetBounds()
+CATHODE = [0.5 * (b[0] + b[1]), 0.5 * (b[2] + b[3]), 0.0]
+print("driven cathode at x = %.5f m, y = %.5f m" % (CATHODE[0], CATHODE[1]))
+
+radius = (CATHODE[0] ** 2 + CATHODE[1] ** 2) ** 0.5
+outward = [CATHODE[0] / radius, CATHODE[1] / radius, 0.0] if radius > 0 else [0.0, 1.0, 0.0]
+
+# Frame centre, offset from the wire along that radial.
+CENTER = [
+    CATHODE[0] + CENTER_SHIFT * outward[0],
+    CATHODE[1] + CENTER_SHIFT * outward[1],
+    0.0,
+]
+
+Delete(driven)
+Delete(weight_reader)
+
+# --- the dot product map ---
+reader = XMLUnstructuredGridReader(FileName=[INPUT_VTU])
+
+renderView = GetActiveViewOrCreate("RenderView")
+renderView.ViewSize = VIEW_SIZE
+renderView.OrientationAxesVisibility = 1
+renderView.UseColorPaletteForBackground = 0
+renderView.Background = BACKGROUND
+renderView.MultiSamples = 8
+
+if COLOR_MODE == "signed-log":
+    # E . E_w spans about 3.5 decades negative and 2.6 positive, and 38% of the
+    # nodes are positive -- charge drifting there induces current of the
+    # opposite polarity on the cathode. A linear scale over one sign shows
+    # neither the decades nor the sign, so map through a signed log:
+    #
+    #     sign(d) * log10(1 + |d| / SYMLOG_X0)
+    #
+    # sign() is not in the calculator namespace, hence d/(|d|+1); the +1 is
+    # negligible beside the 1e5 scale and the expression tends to 0 anyway
+    # where d does.
+    calc = PythonCalculator(Input=reader)
+    calc.ArrayName = "SignedLogDot"
+    calc.ArrayAssociation = "Point Data"
+    calc.Expression = (
+        "(DotProduct/(abs(DotProduct)+1.0))*log10(1.0+abs(DotProduct)/%g)"
+        % SYMLOG_X0
+    )
+    painted = calc
+    array = "SignedLogDot"
+    colour_range = (-SYMLOG_LIMIT, SYMLOG_LIMIT)   # symmetric, so zero is neutral
+    preset = DIVERGING_PRESET
+    # Transparent either side of zero, opaque past SYMLOG_OPAQUE, both signs.
+    _m, _s = SYMLOG_MIDPOINT, SYMLOG_SHARPNESS
+    opacity_points = [
+        -SYMLOG_LIMIT, 1.0, 0.5, _s,
+        -SYMLOG_OPAQUE, 1.0, 1.0 - _m, _s,   # mirrored: this ramp falls
+        -SYMLOG_FADE, 0.0, 0.5, _s,
+        SYMLOG_FADE, 0.0, _m, _s,            # this one rises
+        SYMLOG_OPAQUE, 1.0, 0.5, _s,
+        SYMLOG_LIMIT, 1.0, 0.5, _s,
+    ]
+    bar_title = "sign(E.Ew) log10(1+|E.Ew|/%g)" % SYMLOG_X0
+else:
+    painted = threshold_between(reader, "DotProduct", -1.0e30, PAINT_CUT)
+    array = "DotProduct"
+    colour_range = (DOT_MIN, DOT_MAX)
+    preset = "Greens"
+    opacity_points = [
+        DOT_MIN, 1.0, 0.5, 0.0,
+        OPAQUE_BELOW, 1.0, 0.5, 0.0,
+        FADE_TO, 0.0, 0.5, 0.0,
+    ]
+    bar_title = "E . E_w  (V/m^2)"
+
+surface_display = Show(painted, renderView)
+surface_display.Representation = "Surface"
+ColorBy(surface_display, ("POINTS", array))
+
+dotLUT = GetColorTransferFunction(array)
+dotLUT.ApplyPreset(preset, True)
+dotLUT.RescaleTransferFunction(colour_range[0], colour_range[1])
+
+# Points go (value, opacity, midpoint, sharpness) in ascending value.
+dotPWF = GetOpacityTransferFunction(array)
+dotPWF.Points = opacity_points
+dotLUT.ScalarOpacityFunction = dotPWF
+dotLUT.EnableOpacityMapping = 1
+
+surface_display.SetScalarBarVisibility(renderView, True)
+try:
+    GetScalarBar(dotLUT, renderView).Title = bar_title
+except Exception as exc:
+    print("note: could not set the scalar bar title (%s)" % exc)
+
+# --- contour lines over the whole field, including the unpainted gas ---
+if SHOW_CONTOURS:
+    contour_filter = Contour(Input=reader, ContourBy=["POINTS", CONTOUR_BY])
+    contour_filter.Isosurfaces = CONTOUR_LEVELS
+
+    contour_display = Show(contour_filter, renderView)
+    contour_display.LineWidth = 1.0
+    contour_display.DiffuseColor = [1.0, 1.0, 1.0]
+    # ColorBy(rep, None) is rejected by ParaView 6.1 -- it forwards the
+    # association as the string 'NONE' and raises -- so set the property.
+    contour_display.ColorArrayName = [None, ""]
+    contour_display.SetScalarBarVisibility(renderView, False)
+
+# --- camera: parallel projection, centred on the driven cathode ---
+# ParaView resets the camera on a view's FIRST render, throwing away anything
+# set beforehand, so burn that render here and set the camera after it.
+# Measured: scale 0.008 set before the first Render comes back as 0.021; set
+# again afterwards it holds.
+Render()
+
+view = GetActiveView()
+view.CameraParallelScale = ZOOM_SCALE
+view.CenterOfRotation = CENTER
+view.CameraPosition = [CENTER[0], CENTER[1], 1.0]
+view.CameraFocalPoint = CENTER
+if ALIGN_RADIAL:
+    up = outward
+    print("view rotated %.1f deg so the outward radial is up"
+          % np.degrees(np.arctan2(up[0], up[1])))
+else:
+    up = [0.0, 1.0, 0.0]
+view.CameraViewUp = up
+view.CameraParallelProjection = 1
+
+Render()
+SaveScreenshot(OUTPUT_IMAGE)
+print("Saved %s" % OUTPUT_IMAGE)
+

anasen_fem/paraview_plotter.py

@@ -0,0 +1,268 @@
+#!/home/vsitaraman/ParaView-6.1.0-RC1-MPI-Linux-Python3.12-x86_64/bin/pvbatch
+# #######!/home/vsitaraman/ParaView-6.1.0-MPI-Linux-Python3.12-x86_64/bin/pvbatch
+import numpy as np
+import sys
+from paraview.simple import *
+
+# Optional argument so an archived VTU can be re-plotted without re-solving:
+#   ./paraview_plotter.py wires2d/vtu_files/elfield_anasen_10_0.0000.vtu
+INPUT_VTU = sys.argv[1] if len(sys.argv) > 1 else "wires2d/elfield_anasen_t0001.vtu"
+
+# --- contour settings ---
+# The whole-PC view keeps the original sparse, evenly spaced levels; at that
+# scale more lines just fill in solid. The quadrant gets the denser, biased
+# set, since that is where the structure between wires is actually readable.
+POT_MIN, POT_MAX = 0.0, 660.0
+N_CONTOURS_FULL, CONTOUR_BIAS_FULL = 40, 1.0
+N_CONTOURS_QUARTER, CONTOUR_BIAS_QUARTER = 80, 1.0
+
+# Line widths. Thin lines wash out their own colour, so the quadrant views draw
+# heavier than the full-PC one; tubes keep them smooth at 2000 px.
+LINE_WIDTH_FULL = 3.0
+LINE_WIDTH_QUARTER = 2.5
+STREAM_LINE_WIDTH = 2.5
+
+# Arrows are glyphed onto the contour points, so doubling the quadrant contour
+# density doubled the arrow count too. This offsets that.
+GLYPH_STRIDE = 96
+
+# --- quadrant view ---
+# Centre sits at radius 35.4 mm, near the outer edge of the wire band, which
+# pushes the wires to one side and leaves the far corner empty. Pulled in to
+# 31.8 mm so the band sits more centrally.
+ZOOM_CENTER = [-0.0225, 0.0225, 0.0]
+ZOOM_SCALE = 0.022   # half-height of the view in metres; larger = more in frame
+
+
+def contour_levels(n, bias):
+    """Isosurface values.
+
+    phi ~ ln(r) around a wire, so evenly spaced levels crowd onto the wire
+    surfaces and thin out in the gas. Raising a symmetric parameter to `bias`
+    pulls levels towards mid-range, where the saddles between wires are,
+    without adding more of them. 1.0 is plain linear spacing; much above 1.5
+    and the middle levels start landing on top of each other.
+    """
+    u = np.linspace(-1.0, 1.0, n)
+    u = np.sign(u) * np.abs(u) ** bias
+    mid = 0.5 * (POT_MIN + POT_MAX)
+    return list(mid + 0.5 * (POT_MAX - POT_MIN) * u)
+
+
+reader = XMLUnstructuredGridReader(FileName=[INPUT_VTU])
+
+contour_filter = Contour(Input=reader,ContourBy = 'potential')
+contour_filter.Isosurfaces = contour_levels(N_CONTOURS_FULL, CONTOUR_BIAS_FULL)
+
+renderView = GetActiveViewOrCreate('RenderView')
+renderView.ViewSize = [2000,2000]
+renderView.OrientationAxesVisibility = 0 # Hide axis
+renderView.UseColorPaletteForBackground=0
+renderView.Background = [0.1, 0.1, 0.1] # Set background to dark gray (RGB 0-1)
+
+renderView.MultiSamples = 8  # 0 disables it, 4-8 is usually sufficient
+
+ResetCamera()
+
+contour_display = Show(contour_filter, renderView)
+contour_display.LineWidth = LINE_WIDTH_FULL
+contour_display.RenderLinesAsTubes = 1    # Makes lines look smoother at high res
+#colorbar
+contour_display_potentialLUT = GetColorTransferFunction('potential', contour_display, separate=True)
+contour_display_potentialLUT.ApplyPreset('Cool to Warm', True)
+contour_display.SetScalarBarVisibility(renderView, True)
+
+#axesGrid = renderView.AxesGridrfcxgdtv
+#axesGrid.Visibility = 1
+#axesGrid.XTitle = "x (mm)"
+#axesGrid.YTitle = "y (mm)"
+
+# 1. Get the active view
+view = GetActiveView()
+
+# 2. Define your desired coordinate ranges (x_min, x_max, y_min, y_max, z_min, z_max)
+x_min, x_max = -0.05, 0.05
+y_min, y_max = -0.05, 0.05
+z_min, z_max = -0.05, 0.05
+
+# 3. Calculate Center, Position, and Parallel Scale
+center = [(x_min + x_max) / 2.0, (y_min + y_max) / 2.0, (z_min + z_max) / 2.0]
+# Position the camera far away along Z to look at the center
+position = [center[0], center[1], 1.0] 
+# Parallel scale defines how much of the scene is visible. 
+# It is usually half the height of the viewed area.
+view.CameraParallelScale = max((x_max - x_min), (y_max - y_min))/1.6
+
+# 4. Apply settings
+view.CenterOfRotation = center
+view.CameraPosition = position
+view.CameraFocalPoint = center
+view.CameraViewUp = [0.0, 1.0, 0.0] # Y-axis is up
+
+# 5. Enable Parallel Projection (optional, often better for exact mapping)
+view.CameraParallelProjection = 1
+
+#ResetCamera()
+Render()
+
+SaveScreenshot("contour_output.png")
+
+# Everything from here on is a quadrant view: denser levels, heavier lines.
+contour_filter.Isosurfaces = contour_levels(N_CONTOURS_QUARTER, CONTOUR_BIAS_QUARTER)
+contour_display.LineWidth = LINE_WIDTH_QUARTER
+contour_display.RenderLinesAsTubes = 1
+
+# 1. Get the active view
+view = GetActiveView()
+
+# 1. Set the Focal Point to the middle of the quadrant in metres
+zoom_center = ZOOM_CENTER
+
+# 2. Tighten the Parallel Scale 
+view.CameraParallelScale = ZOOM_SCALE
+
+# 3. Position the Camera (0.5m away is fine)
+view.CameraPosition = [zoom_center[0], zoom_center[1], 0.5]
+view.CameraFocalPoint = zoom_center
+view.CameraViewUp = [0.0, 1.0, 0.0]
+
+# Equipotentials over one quadrant, saved before the arrows go on so this and
+# Field_output.png below share a camera and overlay exactly.
+Render()
+SaveScreenshot("contour_quarter_output.png")
+
+# pot_threshold = Threshold(Input=reader)
+# pot_threshold.Scalars = ['POINTS', 'potential']
+# pot_threshold.ThresholdMethod = 'Above Upper Threshold'
+# pot_threshold.UpperThreshold = 100.0  
+
+# --- 2. Create the Glyph Filter (The Arrows) ---
+# IMPORTANT: Use 'pot_threshold' as the Input, not the 'reader'
+glyph = Glyph(Input=contour_filter, GlyphType='Arrow') #
+# glyph = Glyph(Input=reader, GlyphType='Arrow') #this uses all field line snot just the ones from the equipotential lines shown
+
+# Orientation Array: Use the 'electric field' vector from Elmer
+glyph.OrientationArray = ['POINTS', 'electric field']
+glyph.ScaleArray = ['POINTS', 'No scale array']
+glyph.ScaleFactor = 0.001  
+
+glyph.GlyphMode = 'Every Nth Point'
+glyph.Stride = GLYPH_STRIDE
+
+# --- 3. Display the Glyphs ---
+glyph_display = Show(glyph, renderView)
+
+# Set the representation to Surface so we see the full arrow colors
+glyph_display.Representation = 'Surface'
+
+
+# This is the critical line: Color the arrows by the 'potential' scalar
+ColorBy(glyph_display, ('POINTS', 'potential'))
+glyph_display.LookupTable = contour_display_potentialLUT
+contour_display_potentialLUT.RescaleTransferFunction(POT_MIN, POT_MAX)
+
+# Optional: Disable the scalar bar for the arrows to avoid cluttering 
+# the existing 'potential' scalar bar.
+glyph_display.SetScalarBarVisibility(renderView, False)
+
+# --- 4. Final Render ---
+Render()
+SaveScreenshot("Field_output.png")
+
+
+# --- Streamlines over the same quadrant ---
+# Field lines rather than arrows: with no B field the drift velocity is
+# parallel to E, so these are drift paths up to diffusion, i.e. a map of which
+# wire collects charge from where. The glyphs above are fixed length, so they
+# show direction only. Quadrant only; over the whole PC it is an unreadable mat.
+# Equipotentials the streamlines start from. One level near the anodes seeds
+# lines only in a ring around each anode, so with the lines truncated short the
+# rest of the frame comes out empty. Spanning the range instead puts seeds
+# right across the gas: every equipotential is a closed curve winding between
+# the wires, so together they cover the volume.
+SEED_POTENTIALS = [660.0, 600.0, 550.0, 500.0, 450.0, 400.0,350.0, 300.0,250.0, 250.0, 200.0, 150.0, 100.0, 50.0]
+
+# Keep 1 seed point in N along the seed contours. Measured point counts per
+# level, for working out the total:
+#
+#     600 V   4970      300 V  29971
+#     500 V   8861      200 V  51558
+#     400 V  16331      100 V  51645
+#                        50 V  27259
+#
+# 250 V and 150 V are not measured; from the trend they are of order 40000 and
+# 50000, putting the nine levels near 280000 points. Stride 3 is then ~94000
+# seeds, of which roughly an eighth land in the rendered quadrant. That is
+# three times the previous seed count, but each line is now 4 mm instead of
+# 20 mm, so the integration work is comparable.
+SEED_STRIDE = 3
+# Arc length each line is allowed to run, in metres. Field lines terminate on
+# electrodes, so any line long enough to reach one will converge with every
+# other line reaching the same wire -- that convergence is the field, not a
+# plotting artefact, and the only way to avoid drawing it is to stop the lines
+# short. The anode-cathode gap runs 4.3-6.2 mm depending on z, so 3 mm keeps
+# every line clear of the cathodes. Raise it towards 0.005 for longer lines,
+# and they will start meeting again at the wires.
+# Short lines, and the gaps between them closed by seeding more planes rather
+# than by making each line longer. 4 mm is just under the 4.3 mm closest
+# anode-cathode approach, so no line quite reaches a wire and they stay
+# separate instead of converging.
+STREAM_MAX_LENGTH = 0.0005
+
+# StreamTracer counts steps as well as length, and its step sizes are in
+# cell-length units rather than metres: 0.2 of a cell by default, and cells are
+# 0.05 mm at the wires. 2000 steps therefore buys about 20 mm at best and less
+# wherever the mesh is fine, so the default caps the lines before
+# STREAM_MAX_LENGTH ever does. Raise it well past what the length needs.
+MAX_STEPS = 20000
+STREAM_DIRECTION = 'BOTH'   # 'BOTH' also draws the half that runs into the anode
+STREAM_RANGE = [-200.0, 650.0]   # full electrode span, needle to anode
+
+# Clear the quadrant view of everything else so only the field lines show.
+Hide(glyph, renderView)
+Hide(contour_filter, renderView)
+
+seed_contour = Contour(Input=reader, ContourBy=['POINTS', 'potential'])
+seed_contour.Isosurfaces = SEED_POTENTIALS
+
+# StreamTracer's own Point Cloud and Line seeds are 3D and this mesh is a
+# single plane at z = 0, so they would mostly land outside it. Seeding from a
+# contour of the mesh keeps every seed in the plane by construction.
+seed_points = MaskPoints(Input=seed_contour)
+seed_points.OnRatio = SEED_STRIDE
+seed_points.RandomSampling = 0
+
+stream = StreamTracerWithCustomSource(Input=reader, SeedSource=seed_points)
+stream.Vectors = ['POINTS', 'electric field']
+# FORWARD follows E, which runs from the anode outwards, so each line leaves
+# its seed and heads for a cathode. With BOTH, the backward half of every line
+# also climbs to the anode the seed ring encircles, and all of them meet there
+# -- that is the joining. BOTH is still the honest full field line if you want
+# it; this only changes what gets drawn.
+stream.IntegrationDirection = STREAM_DIRECTION
+stream.MaximumStreamlineLength = STREAM_MAX_LENGTH
+stream.MaximumSteps = MAX_STEPS
+
+# Keep integration in the z = 0 plane. Newer ParaView only, so tolerate it
+# being absent.
+try:
+    stream.SurfaceStreamlines = 1
+except Exception as exc:
+    print("note: SurfaceStreamlines unavailable (%s)" % exc)
+
+stream_display = Show(stream, renderView)
+stream_display.Representation = 'Surface'
+stream_display.LineWidth = STREAM_LINE_WIDTH
+stream_display.RenderLinesAsTubes = 1
+
+ColorBy(stream_display, ('POINTS', 'potential'))
+streamLUT = GetColorTransferFunction('potential', stream_display, separate=True)
+streamLUT.ApplyPreset('Cool to Warm', True)
+streamLUT.RescaleTransferFunction(STREAM_RANGE[0], STREAM_RANGE[1])
+stream_display.LookupTable = streamLUT
+stream_display.SetScalarBarVisibility(renderView, True)
+
+renderView.Background = [0.0, 0.0, 0.0]
+
+Render()
+SaveScreenshot("Streamlines_quarter_output.png")

anasen_fem/run.py

@@ -0,0 +1,113 @@
+import os
+import sys
+
+# Cathode wire (0..23) that wires2d_weight.sif drives to 1 V. Passed to the
+# mesher, which puts that one wire in its own physical group, tag 40.
+SELECTED_CATHODE = 1
+
+# 0 = everything in one pass
+# 1 = mesh and the physical field only
+# 2 = weighting field and dot product only, reusing stage 1's mesh
+STAGE = 0
+
+# gmsh comes from apt and lives in the system python3; meshio is pip-installed
+# into the venv, which cannot see apt packages. Neither interpreter has both,
+# so name them explicitly rather than relying on whichever python3 is on PATH.
+MESH_PY = "/usr/bin/python3"
+DOT_PY = os.path.expanduser("~/myenv/bin/python3")
+
+
+def run(cmd):
+    """os.system that stops on failure.
+
+    Worth the four lines: a solve that quietly did nothing once produced a
+    field of zeros, and every later step ran happily on it.
+    """
+    print(cmd)
+    if os.system(cmd) != 0:
+        sys.exit("failed: " + cmd)
+
+
+# z-loci to run, in mm.
+#
+# The wires twist: over z = 0 -> 174.3 the anode lattice turns 60 deg against
+# the cathode lattice, which is exactly 4 cathode pitches of 15 deg. So the
+# field pattern goes through the same cycle four times across that range, while
+# the wire radii drift slowly and monotonically (anodes 32.0 -> 37.0 mm).
+#
+# A uniform 17.43 step samples the fast cycle 2.75 times per period, which
+# aliases it -- consecutive slices land at relative azimuths 7.5, 14.1, 5.7,
+# 12.2, 3.5 deg, jumping around rather than sweeping. Sample the two variations
+# separately instead:
+#   - 8 slices across one pitch, which walks the azimuth in even ~2 deg steps
+#     at essentially fixed radius
+#   - 5 slices one whole pitch apart, which holds the azimuth near-fixed and
+#     walks the radius over its full range
+# 12 z-loci in total, against 11 for the uniform sweep.
+PITCH_Z = 174.3 / 4.0
+
+Z_VALUES = sorted(set(
+    [round(i * PITCH_Z / 8.0, 4) for i in range(8)]
+    + [round(i * PITCH_Z, 4) for i in range(5)]
+))
+
+# Running only two loci for now; delete this line for the full sweep.
+# 19.794 is the crossover: the relative azimuth wraps through zero there, so an
+# anode sits directly radially outside a cathode, and the closest anode-cathode
+# approach over the whole range (4.339 mm) is at 19.707. It is deliberately off
+# the grid above, whose nearest point is 21.7875.
+# Z_VALUES = [19.690]
+
+# Stage 2 reuses whatever single mesh is sitting in wires2d/, so it cannot span
+# several z. Without this it would happily solve the weighting field on one z's
+# mesh and archive the result under another z's name -- and dotproduct.py could
+# not catch it, since the node sets would agree perfectly.
+if STAGE == 2 and len(Z_VALUES) > 1:
+    sys.exit(
+        "STAGE 2 applies to the one mesh in wires2d/, which is whichever z\n"
+        "stage 1 ran last. Set Z_VALUES to that single z."
+    )
+
+for count, val in enumerate(Z_VALUES, start=10):
+    print(val)
+    os.system("mkdir -p wires2d/mesh_files wires2d/sif_files wires2d/vtu_files png")
+
+    # Each stage archives its own output before the next one starts, so a
+    # failure in stage 2 does not throw away what stage 1 already produced.
+    if STAGE in (0, 1):
+        run("%s wires_gmsh2d_bc.py %s %d" % (MESH_PY, val, SELECTED_CATHODE))
+        run("ElmerGrid 14 2 wires2d.msh -2d")
+        run("ElmerSolver wires2d.sif")
+        run("./paraview_plotter.py")
+
+        os.system("cp wires2d.msh wires2d/mesh_files/wires2d%02d_%1.4f.msh"%(count,val))
+        os.system("cp wires2d.sif wires2d/sif_files/wires2d_%02d_%1.4f.sif"%(count,val))
+        os.system("cp wires2d/elfield_anasen_t0001.vtu wires2d/vtu_files/elfield_anasen_%02d_%1.4f.vtu"%(count,val))
+        os.system("cp contour_output.png png/Contour_output_z_%02d_%1.4f.png"%(count,val))
+        os.system("cp contour_quarter_output.png png/Contour_output_z_%02d_%1.4f_quarter.png"%(count,val))
+        os.system("cp Field_output.png png/Field_ouput_z_%02d_%1.4f.png"%(count,val))
+        os.system("cp Streamlines_quarter_output.png png/Streamlines_output_z_%02d_%1.4f_quarter.png"%(count,val))
+
+    # Stage 2 does not re-mesh: it reuses wires2d/ as stage 1 left it, which is
+    # what makes the node-by-node dot product valid.
+    if STAGE in (0, 2):
+        run("ElmerSolver wires2d_weight.sif")
+        run("%s dotproduct.py" % DOT_PY)
+        run("./paraview_dotproduct.py")
+
+        os.system("cp wires2d_weight.sif wires2d/sif_files/wires2d_weight_%02d_%1.4f.sif"%(count,val))
+        os.system("cp wires2d/elfield_weight_t0001.vtu wires2d/vtu_files/elfield_weight_%02d_%1.4f.vtu"%(count,val))
+        os.system("cp wires2d/dotproduct.vtu wires2d/vtu_files/dotproduct_%02d_%1.4f.vtu"%(count,val))
+        os.system("cp DotProduct_output.png png/DotProduct_output_z_%02d_%1.4f.png"%(count,val))
+        os.system("cp DotProduct_quarter_output.png png/DotProduct_output_z_%02d_%1.4f_quarter.png"%(count,val))
+
+    # os.system("python3 garfield_sim.py")
+
+    # (a bare "break" here runs only the first z, as the original did)
+
+# os.system("tar -cvzf wiress2d/mesh.tar.gz wires2d/mesh_files")
+# os.system("rm -rf wires2d/mesh_files/*")
+# os.system("tar -cvzf wires2d/sif.tar.gz wires2d/sif_files")
+# os.system("rm -rf wires2d/sif_files/*")
+# os.system("tar -cvzf wires2d/vtu.tar.gz wires2d/vtu_files")
+# os.system("rm -rf wires2d/vtu_files/*")

anasen_fem/scalars.dat

@@ -0,0 +1 @@
+   8.500000000000E+002

anasen_fem/scalars.dat.names

@@ -0,0 +1,8 @@
+Metadata for SaveScalars file: ./scalars.dat
+Elmer version: 26.2
+Elmer compilation date: 2026-06-10
+Solver input file: wires2d.sif
+File started at: 2026/09/23 14:27:47
+ 
+Variables in columns of matrix: 
+   1: res: potential difference

anasen_fem/scalars_weight.dat

@@ -0,0 +1 @@
+   1.000000000000E+000

anasen_fem/scalars_weight.dat.names

@@ -0,0 +1,8 @@
+Metadata for SaveScalars file: ./scalars_weight.dat
+Elmer version: 26.2
+Elmer compilation date: 2026-06-10
+Solver input file: wires2d_weight.sif
+File started at: 2026/09/23 14:50:46
+ 
+Variables in columns of matrix: 
+   1: res: potential difference

anasen_fem/wires2d.sif

@@ -0,0 +1,127 @@
+Check Keywords Warn
+
+Header
+  Mesh DB "." "wires2d"
+End
+
+Simulation
+  Coordinate System = Cartesian 2D
+  Simulation Type = Steady State
+  Steady State Max Iterations = 1
+  Output File = "elstatics.result"
+  Post File = "elstatics.ep"
+  Coordinate Scaling = 0.001  ! Converts mm from Gmsh to meters for Elmer
+End
+
+Constants
+  Permittivity Of Vacuum = 8.8542e-12
+End
+
+
+Body 1
+  Target Bodies(1) = 13
+  Equation = 1
+  Material = 1
+End
+
+
+Equation 1
+  Active Solvers(2) = 1 2
+End
+
+
+Material 1
+  Relative Permittivity = 1
+End
+
+
+Solver 1
+  Equation = Electrostatics
+  Procedure = "StatElecSolve" "StatElecSolver"
+
+  Variable = Potential
+  Variable DOFs = 1
+
+  Calculate Electric Field = True
+  Calculate Electric Flux = False
+
+  Linear System Solver = Iterative
+  Linear System Iterative Method = CG
+  Linear System Max Iterations = 5000
+  Linear System Convergence Tolerance = 1.0e-8
+  Linear System Preconditioning = ILU1
+  Calculate Vectors = Logical True
+End
+
+Solver 2
+  Equation = "Electric Field"
+  Procedure = "FluxSolver" "FluxSolver"
+  
+  ! Calculate from the potential
+  Target Variable = "Potential"
+  ! Name of the output vector field in VTU
+  Flux Variable = String "Electric Field"
+  
+  ! Use 2D components (x, y)
+  Flux Coefficient = String "Permittivity"
+  
+  Calculate Vectors = Logical True
+End
+
+Solver 3
+  Equation = Result Output
+  Procedure = "ResultOutputSolve" "ResultOutputSolver"
+  Output File Name = elfield_anasen  ! Sets prefix for output files
+  Output Format = Vtu
+  ! Optional: Select specific variables to save
+  Scalar Field 1 = Potential
+  Vector Field 1 = Electric Field
+End
+
+Solver 4
+ Exec Solver = After All
+ Equation = SaveScalars
+ Procedure = "SaveData" "SaveScalars"
+ Filename = "scalars.dat"
+End
+
+Boundary Condition 1
+  Target Boundaries = 1 
+  Potential = -200
+  Calculate Electric Force = True
+End
+
+Boundary Condition 2
+  Target Boundaries = 2
+  Potential = 150
+  Calculate Electric Force = True
+End
+
+Boundary Condition 3
+  Target Boundaries = 3
+  Potential = 250
+  Calculate Electric Force = True
+End
+
+Boundary Condition 4
+  Target Boundaries = 10
+  Potential = 0
+End
+
+Boundary Condition 5
+  Target Boundaries = 20
+  Potential = 660
+  Calculate Electric Force = True
+End
+
+Boundary Condition 6
+  Target Boundaries = 30
+  Potential = 0
+End
+
+! The one cathode singled out in wires_gmsh2d_bc.py. Grounded here, exactly
+! like the other 23; it is only separate so wires2d_weight.sif can drive it.
+Boundary Condition 7
+  Target Boundaries = 40
+  Potential = 0
+End

anasen_fem/wires2d_weight.sif

@@ -0,0 +1,132 @@
+Check Keywords Warn
+
+! Ramo weighting potential for the single cathode at tag 40: that electrode
+! sits at 1 V and every other one at 0 V. Identical to wires2d.sif apart from
+! the potentials and the output names, so both solves discretise the same way
+! and E . E_w is meaningful node by node.
+
+Header
+  Mesh DB "." "wires2d"
+End
+
+Simulation
+  Coordinate System = Cartesian 2D
+  Simulation Type = Steady State
+  Steady State Max Iterations = 1
+  Output File = "elstatics_weight.result"
+  Post File = "elstatics_weight.ep"
+  Coordinate Scaling = 0.001  ! Converts mm from Gmsh to meters for Elmer
+End
+
+Constants
+  Permittivity Of Vacuum = 8.8542e-12
+End
+
+
+Body 1
+  Target Bodies(1) = 13
+  Equation = 1
+  Material = 1
+End
+
+
+Equation 1
+  Active Solvers(2) = 1 2
+End
+
+
+Material 1
+  Relative Permittivity = 1
+End
+
+
+Solver 1
+  Equation = Electrostatics
+  Procedure = "StatElecSolve" "StatElecSolver"
+
+  Variable = Potential
+  Variable DOFs = 1
+
+  Calculate Electric Field = True
+  Calculate Electric Flux = False
+
+  Linear System Solver = Iterative
+  Linear System Iterative Method = CG
+  Linear System Max Iterations = 5000
+  Linear System Convergence Tolerance = 1.0e-8
+  Linear System Preconditioning = ILU1
+  Calculate Vectors = Logical True
+End
+
+Solver 2
+  Equation = "Electric Field"
+  Procedure = "FluxSolver" "FluxSolver"
+  
+  ! Calculate from the potential
+  Target Variable = "Potential"
+  ! Name of the output vector field in VTU
+  Flux Variable = String "Electric Field"
+  
+  ! Use 2D components (x, y)
+  Flux Coefficient = String "Permittivity"
+  
+  Calculate Vectors = Logical True
+End
+
+Solver 3
+  Equation = Result Output
+  Procedure = "ResultOutputSolve" "ResultOutputSolver"
+  Output File Name = elfield_weight  ! Sets prefix for output files
+  Output Format = Vtu
+  ! Optional: Select specific variables to save
+  Scalar Field 1 = Potential
+  Vector Field 1 = Electric Field
+End
+
+Solver 4
+ Exec Solver = After All
+ Equation = SaveScalars
+ Procedure = "SaveData" "SaveScalars"
+ Filename = "scalars_weight.dat"
+End
+
+Boundary Condition 1
+  Target Boundaries = 1 
+  Potential = 0
+  Calculate Electric Force = True
+End
+
+Boundary Condition 2
+  Target Boundaries = 2
+  Potential = 0
+  Calculate Electric Force = True
+End
+
+Boundary Condition 3
+  Target Boundaries = 3
+  Potential = 0
+  Calculate Electric Force = True
+End
+
+Boundary Condition 4
+  Target Boundaries = 10
+  Potential = 0
+End
+
+Boundary Condition 5
+  Target Boundaries = 20
+  Potential = 0
+  Calculate Electric Force = True
+End
+
+Boundary Condition 6
+  Target Boundaries = 30
+  Potential = 0
+End
+
+! The one cathode singled out in wires_gmsh2d_bc.py. Grounded here, exactly
+! like the other 23; it is only separate so wires2d_weight.sif can drive it.
+Boundary Condition 7
+  Target Boundaries = 40
+  Potential = 1
+End

anasen_fem/wires_gmsh2d_bc.py

@@ -0,0 +1,295 @@
+# This script generates a 2D Gmsh geometry for the ANASEN detector's wire planes, including an optional hot needle and IC wires. The geometry is designed for adaptive meshing, with finer mesh near the wires and coarser mesh in empty space. The script takes a z-locus as a command-line argument to determine the interpolation between the two wire planes.
+import numpy as np
+import gmsh, sys
+
+# --- Configuration Flags ---
+include_ic_wires = True
+include_needle = True
+
+gmsh.initialize()
+gmsh.model.add("adaptive_mesh")
+gmsh.option.setNumber("General.NumThreads", 10)
+# gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfElements", 200000)
+# gmsh.option.setNumber("Mesh.Adapt.MaxNumberOfNodes", 200000)
+# gmsh.option.setNumber("Mesh.Adapt.MaxIter",5)
+# gmsh.option.setNumber("Mesh.MeshSizeMin", 5e-3)
+# gmsh.option.setNumber("Mesh.MeshSizeMax", 10.0)
+gmsh.option.setNumber("Geometry.Tolerance", 4e-2)
+# gmsh.option.setNumber("Mesh.MeshSizeExtendFromBoundary", 0)
+# Only needed alongside mesh.recombine(), which is off. See the note there.
+# gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
+# gmsh.option.setNumber("Mesh.SubdivisionAlgorithm", 1)
+gmsh.option.setNumber("Mesh.SecondOrderIncomplete", 1)
+
+lc = 0.04
+# z_loc = -174.3
+
+if len(sys.argv) < 2:
+    print("Usage: python3 wires_gmsh2d_bc.py <z_locus in mm> [selected_cathode_index]")
+    quit()
+
+z_loc = float(sys.argv[1])
+
+# Cathode wire (0..23) given its own physical group, tag 40, so that
+# wires2d_weight.sif can hold it at 1 V while everything else stays grounded.
+selected_cathode = int(sys.argv[2]) if len(sys.argv) > 2 else 1
+
+wireShift = 4.0
+k = 2 * np.pi / 24.0
+kg = k/2.0
+
+# Plane 1 Offsets (-zmax/2)
+# Anodes: -6*k (base) - 4*k (correction) = -10*k
+offset_a1 = -6 * k - 4 * k
+# Cathodes: -6*k (base) + 0.5*k (half-placement)
+offset_c1 = -6 * k + (k / 2.0)
+# Guard wires: aligned with cathodes
+offset_g1 = offset_c1
+
+# Plane 2 Offsets (+zmax/2) with Twist
+offset_a2 = offset_a1 + (wireShift * k)
+offset_c2 = offset_c1 - (wireShift * k)
+offset_g2 = offset_c2
+
+# 1 needle, 24 ic1, 24 ic2, 48 guard wires, 24 anodes, 24 cathodes
+
+# needle at plane 1 at -zmax/2 no rotation
+xarr_needle = np.array([0])
+yarr_needle = np.array([0])
+
+# ic1 wires, plane 1 at -zmax/2 no rotation
+xarr_i11 = np.array([23 * np.cos(k * i) for i in range(24)])
+yarr_i11 = np.array([23 * np.sin(k * i) for i in range(24)])
+
+# ic1 wires, plane 1 at -zmax/2 no rotation
+xarr_i21 = np.array([23 * np.cos(k * i + k / 2.0) for i in range(24)])
+yarr_i21 = np.array([23 * np.sin(k * i + k / 2.0) for i in range(24)])
+
+# --- Coordinate Arrays (Plane 1) ---
+# Anodes: -k*i (Left-handed twist direction)
+xarra_1 = np.array([37 * np.cos(-k * i + offset_a1) for i in range(24)])
+yarra_1 = np.array([37 * np.sin(-k * i + offset_a1) for i in range(24)])
+
+# Cathodes: +k*i (Right-handed twist direction)
+xarrc_1 = np.array([42 * np.cos(k * i + offset_c1) for i in range(24)])
+yarrc_1 = np.array([42 * np.sin(k * i + offset_c1) for i in range(24)])
+
+# Guard Wires (48 wires, use kg spacing)
+xarrg_1 = np.array([32 * np.cos(kg * i + offset_g1) for i in range(48)])
+yarrg_1 = np.array([32 * np.sin(kg * i + offset_g1) for i in range(48)])
+
+# needle at plane 2 at zmax/2
+xarr_needle_2 = np.array([0])
+yarr_needle_2 = np.array([0])
+
+# #ic1 wires, plane 2 at zmax/2
+xarr_i12 = np.array([23 * np.cos(k * i) for i in range(24)])
+yarr_i12 = np.array([23 * np.sin(k * i) for i in range(24)])
+
+# #ic2 wires, plane 2 at zmax/2
+xarr_i22 = np.array([23 * np.cos(k * i + k / 2.0) for i in range(24)])
+yarr_i22 = np.array([23 * np.sin(k * i + k / 2.0) for i in range(24)])
+
+# --- Coordinate Arrays (Plane 2) ---
+xarra_2 = np.array([37 * np.cos(-k * i + offset_a2) for i in range(24)])
+yarra_2 = np.array([37 * np.sin(-k * i + offset_a2) for i in range(24)])
+
+xarrc_2 = np.array([42 * np.cos(k * i + offset_c2) for i in range(24)])
+yarrc_2 = np.array([42 * np.sin(k * i + offset_c2) for i in range(24)])
+
+xarrg_2 = np.array([32 * np.cos(kg * i + offset_g2) for i in range(48)])
+yarrg_2 = np.array([32 * np.sin(kg * i + offset_g2) for i in range(48)])
+
+direction_needle_x = xarr_needle_2 - xarr_needle
+direction_needle_y = yarr_needle_2 - yarr_needle
+
+direction_ic1_x = xarr_i12 - xarr_i11
+direction_ic1_y = yarr_i12 - yarr_i11
+
+direction_ic2_x = xarr_i22 - xarr_i21
+direction_ic2_y = yarr_i22 - yarr_i21
+
+direction_guard_x = xarrg_2 - xarrg_1
+direction_guard_y = yarrg_2 - yarrg_1
+
+direction_anodes_x = xarra_2 - xarra_1
+direction_anodes_y = yarra_2 - yarra_1
+
+direction_cathodes_x = xarrc_2 - xarrc_1
+direction_cathodes_y = yarrc_2 - yarrc_1
+
+t = (z_loc + 174.3) / (2 * 174.3)  # z=-174.3 is 0, z=+174.3 is 1
+
+xloc_needle = xarr_needle + t * direction_needle_x
+yloc_needle = yarr_needle + t * direction_needle_y
+xloc_i1 = xarr_i11 + t * direction_ic1_x
+yloc_i1 = yarr_i11 + t * direction_ic1_y
+xloc_i2 = xarr_i21 + t * direction_ic2_x
+yloc_i2 = yarr_i21 + t * direction_ic2_y
+xloc_g = xarrg_1 + t * direction_guard_x
+yloc_g = yarrg_1 + t * direction_guard_y
+xloc_a = xarra_1 + t * direction_anodes_x
+yloc_a = yarra_1 + t * direction_anodes_y
+xloc_c = xarrc_1 + t * direction_cathodes_x
+yloc_c = yarrc_1 + t * direction_cathodes_y
+
+# wire_radius_a = 0.018 #mm
+# wire_radius_c = 0.0762 #mm
+# wire_radius_g = 0.0762 #mm
+wire_radius = 0.254  # mm
+needle = []
+ic1_wires = []
+ic2_wires = []
+guard_wires = []
+anode_wires = []
+cathode_wires = []
+iw1_tags = [(3, i) for i in range(24)]
+iw2_tags = [(3, i + 24) for i in range(24)]
+gw_tags = [(3, i + 48) for i in range(48)]
+aw_tags = [(3, i) for i in range(24)]
+cw_tags = [(3, i + 24) for i in range(24)]
+
+# for i,[xa,ya,xc,yc] in enumerate(zip(xarra_1,yarra_1,xarrc_1,yarrc_1)):
+# create Hot Needle (1 total)
+for i, (xn, yn) in enumerate(zip(xloc_needle, yloc_needle)):
+    if include_needle:
+        ndisk = gmsh.model.occ.addDisk(xn, yn, 0, wire_radius, wire_radius)
+        needle.append(ndisk)
+
+# create Guard Wires (48 total)
+for xg, yg in zip(xloc_g, yloc_g):
+    gdisk = gmsh.model.occ.addDisk(xg, yg, 0, wire_radius, wire_radius)
+    guard_wires.append(gdisk)
+
+# create Cathode Wires (24 total)
+for xc, yc in zip(xloc_c, yloc_c):
+    cdisk = gmsh.model.occ.addDisk(xc, yc, 0, wire_radius, wire_radius)
+    cathode_wires.append(cdisk)
+
+# create IC Anode and Cathode Wires (24 total each)
+for i, (xa, ya) in enumerate(zip(xloc_a, yloc_a)):
+    adisk = gmsh.model.occ.addDisk(xa, ya, 0, wire_radius, wire_radius)
+    anode_wires.append(adisk)
+
+    # Place IC wires only if flag is True
+    if include_ic_wires:
+        i1disk = gmsh.model.occ.addDisk(
+            xloc_i1[i], yloc_i1[i], 0, wire_radius, wire_radius
+        )
+        i2disk = gmsh.model.occ.addDisk(
+            xloc_i2[i], yloc_i2[i], 0, wire_radius, wire_radius
+        )
+        ic1_wires.append(i1disk)
+        ic2_wires.append(i2disk)
+
+anasen_barrel = gmsh.model.occ.addDisk(0, 0, 0, 500, 500)
+# gmsh.model.occ.synchronize()
+# gmsh.model.mesh.embed(1,anode_wires+cathode_wires,2,anasen_barrel)
+
+gmsh.option.setNumber("Geometry.Tolerance", 1e-6)
+gmsh.option.setNumber("Geometry.OCCFixDegenerated", 1)
+gmsh.model.occ.synchronize()
+
+
+# --- Surface Extraction ---
+def get_surfs(disks):
+    surfs = []
+    for d in disks:
+        surfs += [
+            s[1] for s in gmsh.model.getBoundary([(2, d)], oriented=False) if s[0] == 1
+        ]
+    return surfs
+
+
+if not 0 <= selected_cathode < len(cathode_wires):
+    print("selected_cathode must be 0..%d" % (len(cathode_wires) - 1))
+    quit()
+
+cathode_wires_other = [
+    disk for i, disk in enumerate(cathode_wires) if i != selected_cathode
+]
+
+# Cut the wire disks into the gas disk, replacing the old mesh.embed() call.
+# embed only makes the mesher honour the curves; fragment splits the barrel
+# into conforming surfaces, which is what lets one wire carry its own BC.
+gmsh.model.occ.synchronize()
+
+all_wire_disks = needle + guard_wires + cathode_wires + anode_wires
+if include_ic_wires:
+    all_wire_disks += ic1_wires + ic2_wires
+
+gmsh.model.occ.fragment([(2, anasen_barrel)], [(2, d) for d in all_wire_disks])
+gmsh.model.occ.synchronize()
+
+# fragment re-derives the bounding curves, so re-extract them.
+needle_surfs = get_surfs(needle) if include_needle else []
+gwire_surfs = get_surfs(guard_wires)
+awire_surfs = get_surfs(anode_wires)
+cwire_surfs = get_surfs(cathode_wires_other)
+cwire_sel_surfs = get_surfs([cathode_wires[selected_cathode]])
+i1wire_surfs = get_surfs(ic1_wires) if include_ic_wires else []
+i2wire_surfs = get_surfs(ic2_wires) if include_ic_wires else []
+
+all_active_wire_surfs = (
+    needle_surfs
+    + gwire_surfs
+    + awire_surfs
+    + cwire_surfs
+    + cwire_sel_surfs
+    + i1wire_surfs
+    + i2wire_surfs
+)
+
+f1 = gmsh.model.mesh.field.add("Distance")
+gmsh.model.mesh.field.setNumbers(f1, "CurvesList", all_active_wire_surfs)
+
+f2 = gmsh.model.mesh.field.add("Threshold")
+gmsh.model.mesh.field.setNumber(f2, "InField", f1)
+gmsh.model.mesh.field.setNumber(f2, "SizeMin", 0.05)  # Fine mesh near wires
+gmsh.model.mesh.field.setNumber(f2, "SizeMax", 5.0)  # Large mesh in empty space
+gmsh.model.mesh.field.setNumber(f2, "DistMin", 0.5)  # Apply SizeMin within 1mm
+gmsh.model.mesh.field.setNumber(f2, "DistMax", 15.0)  # Transition to SizeMax by 20mm
+
+gmsh.model.mesh.field.setAsBackgroundMesh(f2)
+
+
+# --- Physical Groups ---
+# These tags are the Target Bodies / Target Boundaries numbers in the .sif
+# files. Do not renumber them without changing both sifs -- and note that
+# ElmerGrid's -autoclean renumbers them for you, which silently breaks every
+# boundary condition.
+# Needle
+if include_needle:
+    gmsh.model.addPhysicalGroup(1, needle_surfs, tag=1, name="hot_needle")
+
+# IC Wires
+if include_ic_wires:
+    gmsh.model.addPhysicalGroup(1, i1wire_surfs, tag=2, name="ic_wire_1")
+    gmsh.model.addPhysicalGroup(1, i2wire_surfs, tag=3, name="ic_wire_2")
+
+# Proportional Counter Wires
+gmsh.model.addPhysicalGroup(1, gwire_surfs, tag=10, name="guard_wires")
+gmsh.model.addPhysicalGroup(1, awire_surfs, tag=20, name="anode_wires")
+gmsh.model.addPhysicalGroup(1, cwire_surfs, tag=30, name="cathode_wires")
+
+# The one cathode the weighting potential is solved for, kept out of tag 30 so
+# wires2d_weight.sif can drive it independently.
+gmsh.model.addPhysicalGroup(1, cwire_sel_surfs, tag=40, name="cathode_wire_selected")
+
+# Gas Volume (2D). fragment split the barrel into many surfaces, so collect
+# them all; naming the original disk alone would solve one sliver of the domain.
+all_surfaces_2d = [s[1] for s in gmsh.model.getEntities(dim=2)]
+gmsh.model.addPhysicalGroup(2, all_surfaces_2d, tag=13, name="gas")
+
+gmsh.option.setNumber("Mesh.Algorithm", 5)
+
+gmsh.model.mesh.generate(2)
+gmsh.model.mesh.setOrder(2)
+# recombine() ran for over half an hour on the barrel surface without
+# finishing, and refine() took the mesh to ~16M nodes. Neither is needed: the
+# Threshold field above already gives 0.05 mm elements on 0.254 mm wires.
+# gmsh.model.mesh.recombine()
+# gmsh.model.mesh.refine()
+gmsh.write("wires2d.msh")
+# gmsh.fltk.run()
+gmsh.finalize()

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

detector_geometry.dat

@@ -0,0 +1,48 @@
+=========================================================
+          SX3 BARREL AZIMUTHAL ANGLES (Degrees)          
+=========================================================
+ Det ID | Strip 0 | Strip 1 | Strip 2 | Strip 3 | Det Center
+---------------------------------------------------------
+    0   |   85.08 |   78.39 |   71.61 |   64.92 |    75.00
+    1   |   55.08 |   48.39 |   41.61 |   34.92 |    45.00
+    2   |   25.08 |   18.39 |   11.61 |    4.92 |    15.00
+    3   |   -4.92 |  -11.61 |  -18.39 |  -25.08 |   -15.00
+    4   |  -34.92 |  -41.61 |  -48.39 |  -55.08 |   -45.00
+    5   |  -64.92 |  -71.61 |  -78.39 |  -85.08 |   -75.00
+    6   |  -94.92 |  -101.61 |  -108.39 |  -115.08 |   -105.00
+    7   |  -124.92 |  -131.61 |  -138.39 |  -145.08 |   -135.00
+    8   |  -154.92 |  -161.61 |  -168.39 |  -175.08 |   -165.00
+    9   |  175.08 |  168.39 |  161.61 |  154.92 |   165.00
+   10   |  145.08 |  138.39 |  131.61 |  124.92 |   135.00
+   11   |  115.08 |  108.39 |  101.61 |   94.92 |   105.00
+
+
+=========================================================
+     PROPORTIONAL COUNTER WIRE ANGLES (Degrees)          
+=========================================================
+ Wire ID | Anode (-z) | Anode (+z) | Cathode (-z) | Cathode (+z)
+----------------------------------------------------------------
+     0   |  -135.00   |   -90.00   |    -97.50    |   -142.50
+     1   |  -150.00   |  -105.00   |    -82.50    |   -127.50
+     2   |  -165.00   |  -120.00   |    -67.50    |   -112.50
+     3   |  -180.00   |  -135.00   |    -52.50    |    -97.50
+     4   |   165.00   |  -150.00   |    -37.50    |    -82.50
+     5   |   150.00   |  -165.00   |    -22.50    |    -67.50
+     6   |   135.00   |  -180.00   |     -7.50    |    -52.50
+     7   |   120.00   |   165.00   |      7.50    |    -37.50
+     8   |   105.00   |   150.00   |     22.50    |    -22.50
+     9   |    90.00   |   135.00   |     37.50    |     -7.50
+    10   |    75.00   |   120.00   |     52.50    |      7.50
+    11   |    60.00   |   105.00   |     67.50    |     22.50
+    12   |    45.00   |    90.00   |     82.50    |     37.50
+    13   |    30.00   |    75.00   |     97.50    |     52.50
+    14   |    15.00   |    60.00   |    112.50    |     67.50
+    15   |     0.00   |    45.00   |    127.50    |     82.50
+    16   |   -15.00   |    30.00   |    142.50    |     97.50
+    17   |   -30.00   |    15.00   |    157.50    |    112.50
+    18   |   -45.00   |     0.00   |    172.50    |    127.50
+    19   |   -60.00   |   -15.00   |   -172.50    |    142.50
+    20   |   -75.00   |   -30.00   |   -157.50    |    157.50
+    21   |   -90.00   |   -45.00   |   -142.50    |    172.50
+    22   |  -105.00   |   -60.00   |   -127.50    |   -172.50
+    23   |  -120.00   |   -75.00   |   -112.50    |   -157.50

eloss_calculations/Eloss.py

@@ -0,0 +1,104 @@
+import pycatima as catima
+import numpy as np
+import os
+
+DEDX_SCALE = float(os.environ.get("DEDX_SCALE", "0.89"))
+print(f"Using dEdX scale factor: {DEDX_SCALE}")
+
+# --- 1. Constants ---
+P_TORR = 250
+TEMP_K = 293.15 
+R = 8.3144
+MEV2U = 1.0 / 931.494
+P_CO2 = 3
+
+# Gas Density Calculations
+p_pa = P_TORR * 133.322
+molar_density = p_pa / (R * TEMP_K)
+m_he, m_c, m_o= 4.0026, 12.0000, 15.9949
+m_mix_avg = ((1 - P_CO2 / 100) * m_he) + (P_CO2 / 100 * (m_c + 2*m_o))
+rho_g_cm3 = (molar_density * m_mix_avg) / 1e6
+print(f"Gas density at {P_TORR} Torr: {rho_g_cm3:.6e} g/cm^3")
+
+# --- 2. Material & Step Setup ---
+material_def = [(m_he, 2, (1 - P_CO2 / 100)), (m_c, 6, P_CO2 / 100), (m_o, 8, 2*P_CO2 / 100)]
+gas_mix = catima.Material(material_def)
+gas_mix.density(rho_g_cm3)
+
+# Thickness step settings
+step_mg_cm2 = 0.001           # 1 ug/cm2 steps as per your example -- kept fine for
+                               # numerical accuracy of the dedx integration itself.
+step_g_cm2 = step_mg_cm2 / 1000.0
+max_steps = 1000000000             # Adjust based on how far you want to track
+
+coarse_step_cm = 0.2   # row spacing over most of the track
+fine_step_cm = 0.03     # row spacing near the Bragg peak
+fine_zone_frac = 0.085   # fraction of the *total* range treated as "near the peak"
+
+def generate_lookup(z, mass_u, e_start_mev, label):
+    filename = f"/home/vsitaraman/ANASEN_analysis/eloss_calculations/{label}_lookup_{e_start_mev}MeV_{P_TORR}torr_{P_CO2}pc.dat"
+    header = f"Energy(MeV) \tmg/cm2 \tcm\nStarting Energy: {e_start_mev} MeV"
+
+    # Pass 1: integrate at full precision just to find the total range (needed
+    # to know where the "last fine_zone_frac" of the track begins).
+    projectile = catima.Projectile(mass_u, z)
+    e_u = e_start_mev / mass_u
+    total_thickness_g_cm2 = 0.0
+    while e_u >= 0.0001:
+        projectile.T(e_u)
+        loss_mev = catima.dedx(projectile, gas_mix) * step_g_cm2
+        e_u = (e_u * mass_u - loss_mev) / mass_u
+        total_thickness_g_cm2 += step_g_cm2
+    total_range_cm = total_thickness_g_cm2 / rho_g_cm3
+    fine_zone_start_cm = total_range_cm * (1.0 - fine_zone_frac)
+
+    projectile = catima.Projectile(mass_u, z)
+    current_e_total = e_start_mev
+    current_thickness_g_cm2 = 0.0
+    next_checkpoint_cm = 0.0
+
+    output = []
+    last_dist_cm = None
+
+    def append_row(e_total, thickness_g_cm2, dist_cm):
+        if last_dist_cm is not None and dist_cm <= last_dist_cm:
+            return False
+        output.append([e_total, thickness_g_cm2 * 1000.0, dist_cm])
+        return True
+
+    for i in range(max_steps):
+        dist_cm = current_thickness_g_cm2 / rho_g_cm3
+        if dist_cm >= next_checkpoint_cm:
+            if append_row(current_e_total, current_thickness_g_cm2, dist_cm):
+                last_dist_cm = dist_cm
+            step_cm = fine_step_cm if dist_cm >= fine_zone_start_cm else coarse_step_cm
+            next_checkpoint_cm = dist_cm + step_cm
+
+        e_u = current_e_total / mass_u
+        if e_u < 0.0001:  # Stop at ATIMA limit
+            append_row(current_e_total, current_thickness_g_cm2, dist_cm)
+            break
+
+        projectile.T(e_u)
+        # dedx returns MeV / (g/cm2)
+        loss_mev = catima.dedx(projectile, gas_mix) * step_g_cm2 * DEDX_SCALE
+        # if(mass_u >=10.0):
+            # loss_mev = catima.dedx(projectile, gas_mix) * step_g_cm2 * DEDX_SCALE
+        # else:
+        #     loss_mev = catima.dedx(projectile, gas_mix) * step_g_cm2
+
+        current_e_total = max(0.0, current_e_total - loss_mev)
+        current_thickness_g_cm2 += step_g_cm2
+
+    np.savetxt(filename, output, fmt='%.6f', delimiter='\t', header=header)
+    print(f"Lookup table created: {filename} ({len(output)} rows, "
+          f"range {total_range_cm:.2f} cm, fine zone below {fine_zone_start_cm:.2f} cm)")
+
+# --- 3. Run ---
+# Format: generate_lookup(Z, mass_u, E_start_MeV, label)
+generate_lookup(1, 1.0078, 30, "proton")
+generate_lookup(1, 2.01355, 30, "deutron")
+generate_lookup(2, 4.0026, 50, "alpha")
+generate_lookup(13,26.9815, 80, "aluminum")
+generate_lookup(9,17.0021, 70, "fluorine")
+generate_lookup(8,15.9949, 70, "oxygen")

eloss_calculations/aluminum_lookup_80MeV_250torr_3pc.dat

@@ -0,0 +1,579 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 80 MeV
+80.000000	0.000000	0.000000
+79.792337	0.015000	0.210854
+79.584426	0.030000	0.421708
+79.376267	0.045000	0.632562
+79.167859	0.060000	0.843416
+78.959201	0.075000	1.054270
+78.750292	0.090000	1.265124
+78.541131	0.105000	1.475978
+78.331717	0.120000	1.686832
+78.122050	0.135000	1.897686
+77.912127	0.150000	2.108540
+77.701950	0.165000	2.319394
+77.491515	0.180000	2.530248
+77.280823	0.195000	2.741102
+77.069873	0.210000	2.951956
+76.858662	0.225000	3.162810
+76.647192	0.240000	3.373664
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eloss_calculations/aluminum_lookup_80MeV_250torr_4pc.dat

@@ -0,0 +1,554 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 80 MeV
+80.000000	0.000000	0.000000
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eloss_calculations/aluminum_lookup_80MeV_350torr_3pc.dat

@@ -0,0 +1,326 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 80 MeV
+80.000000	0.000000	0.000000
+79.688803	0.020000	0.200813
+79.377050	0.040000	0.401627
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+76.862636	0.200000	2.008133
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+75.910173	0.260000	2.610573
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+70.737624	0.580000	5.823587
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+67.420696	0.780000	7.831720
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+63.691353	1.000000	10.040667
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+56.313258	1.420000	14.257747
+55.952762	1.440000	14.458561
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+55.229117	1.480000	14.860187
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+54.136907	1.540000	15.462627
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+53.404187	1.580000	15.864254
+53.036430	1.600000	16.065067
+52.667731	1.620000	16.265881
+52.298082	1.640000	16.466694
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+51.183352	1.700000	17.069134
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+47.785067	1.880000	18.876454
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+47.018388	1.920000	19.278081
+46.633419	1.940000	19.478894
+46.247348	1.960000	19.679708
+45.860166	1.980000	19.880521
+45.471861	2.000000	20.081334
+45.082420	2.020000	20.282148
+44.691832	2.040000	20.482961
+44.300085	2.060000	20.683774
+43.907166	2.080000	20.884588
+43.513062	2.100000	21.085401
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+41.122807	2.220000	22.290281
+40.720025	2.240000	22.491094
+40.315943	2.260000	22.691908
+39.910545	2.280000	22.892721
+39.503814	2.300000	23.093534
+39.095734	2.320000	23.294348
+38.686285	2.340000	23.495161
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+37.863212	2.380000	23.896788
+37.449548	2.400000	24.097601
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+36.617866	2.440000	24.499228
+36.199805	2.460000	24.700041
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+35.359130	2.500000	25.101668
+34.936469	2.520000	25.302481
+34.512226	2.540000	25.503294
+34.086374	2.560000	25.704108
+33.658887	2.580000	25.904921
+33.229737	2.600000	26.105734
+32.798893	2.620000	26.306548
+32.366325	2.640000	26.507361
+31.932000	2.660000	26.708174
+31.495886	2.680000	26.908988
+31.058108	2.700000	27.109801
+30.618942	2.720000	27.310614
+30.178391	2.740000	27.511428
+29.736448	2.760000	27.712241
+29.293103	2.780000	27.913055
+28.848348	2.800000	28.113868
+28.402175	2.820000	28.314681
+27.954576	2.840000	28.515495
+27.505544	2.860000	28.716308
+27.055071	2.880000	28.917121
+26.603148	2.900000	29.117935
+26.149770	2.920000	29.318748
+25.694928	2.940000	29.519561
+25.238617	2.960000	29.720375
+24.780830	2.980000	29.921188
+24.321560	3.000000	30.122001
+23.860803	3.020000	30.322815
+23.398554	3.040000	30.523628
+22.934808	3.060000	30.724441
+22.469563	3.080000	30.925255
+22.002814	3.100000	31.126068
+21.534561	3.120000	31.326881
+21.064804	3.140000	31.527695
+20.593543	3.160000	31.728508
+20.120781	3.180000	31.929321
+19.646523	3.200000	32.130135
+19.170777	3.220000	32.330948
+18.693552	3.240000	32.531761
+18.215161	3.260000	32.732575
+17.736573	3.280000	32.933388
+17.257970	3.300000	33.134201
+16.779470	3.320000	33.335015
+16.301199	3.340000	33.535828
+15.823299	3.360000	33.736641
+15.345927	3.380000	33.937455
+14.869258	3.400000	34.138268
+14.393487	3.420000	34.339081
+13.918832	3.440000	34.539895
+13.445535	3.460000	34.740708
+12.973871	3.480000	34.941521
+12.504146	3.500000	35.142335
+12.036705	3.520000	35.343148
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+10.652203	3.580000	35.945588
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+9.749100	3.620000	36.347215
+9.305192	3.640000	36.548028
+8.864425	3.660000	36.748842
+8.426224	3.680000	36.949655
+7.991228	3.700000	37.150468
+7.560188	3.720000	37.351282
+7.133965	3.740000	37.552095
+6.713536	3.760000	37.752908
+6.299994	3.780000	37.953722
+5.894542	3.800000	38.154535
+5.498474	3.820000	38.355348
+5.113148	3.840000	38.556162
+4.739951	3.860000	38.756975
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+4.035323	3.900000	39.158602
+3.706328	3.920000	39.359415
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+3.099704	3.960000	39.761042
+2.823232	3.980000	39.961855
+2.564958	4.000000	40.162668
+2.324760	4.020000	40.363482
+2.102259	4.040000	40.564295
+1.896859	4.060000	40.765108
+1.867478	4.063000	40.795230
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+1.781512	4.072000	40.885596
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+1.671855	4.084000	41.006084
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+1.619097	4.090000	41.066328
+1.593224	4.093000	41.096450
+1.567684	4.096000	41.126572
+1.542474	4.099000	41.156694
+1.517589	4.102000	41.186816
+1.493028	4.105000	41.216938
+1.468785	4.108000	41.247060
+1.444859	4.111000	41.277182
+1.421244	4.114000	41.307304
+1.397939	4.117000	41.337426
+1.374939	4.120000	41.367548
+1.352240	4.123000	41.397670
+1.329840	4.126000	41.427792
+1.307734	4.129000	41.457914
+1.285919	4.132000	41.488036
+1.264393	4.135000	41.518158
+1.243150	4.138000	41.548280
+1.222187	4.141000	41.578402
+1.201502	4.144000	41.608524
+1.181090	4.147000	41.638646
+1.160949	4.150000	41.668768
+1.141073	4.153000	41.698890
+1.121461	4.156000	41.729012
+1.102109	4.159000	41.759134
+1.083012	4.162000	41.789256
+1.064168	4.165000	41.819378
+1.045574	4.168000	41.849500
+1.027225	4.171000	41.879622
+1.009119	4.174000	41.909744
+0.991252	4.177000	41.939866
+0.973621	4.180000	41.969988
+0.956222	4.183000	42.000110
+0.939052	4.186000	42.030232
+0.922108	4.189000	42.060354
+0.905387	4.192000	42.090476
+0.888885	4.195000	42.120598
+0.872600	4.198000	42.150720
+0.856527	4.201000	42.180842
+0.840663	4.204000	42.210964
+0.825007	4.207000	42.241086
+0.809554	4.210000	42.271208
+0.794301	4.213000	42.301330
+0.779247	4.216000	42.331452
+0.764386	4.219000	42.361574
+0.749717	4.222000	42.391696
+0.735236	4.225000	42.421818
+0.720941	4.228000	42.451940
+0.706828	4.231000	42.482062
+0.692895	4.234000	42.512184
+0.679139	4.237000	42.542306
+0.665555	4.240000	42.572428
+0.652102	4.243000	42.602550
+0.638755	4.246000	42.632672
+0.625511	4.249000	42.662794
+0.612371	4.252000	42.692916
+0.599334	4.255000	42.723038
+0.586400	4.258000	42.753160
+0.573569	4.261000	42.783282
+0.560839	4.264000	42.813404
+0.548205	4.267000	42.843526
+0.535662	4.270000	42.873648
+0.523219	4.273000	42.903770
+0.510875	4.276000	42.933892
+0.498630	4.279000	42.964014
+0.486484	4.282000	42.994136
+0.474435	4.285000	43.024258
+0.462483	4.288000	43.054381
+0.450627	4.291000	43.084503
+0.438867	4.294000	43.114625
+0.427202	4.297000	43.144747
+0.415631	4.300000	43.174869
+0.404153	4.303000	43.204991
+0.392767	4.306000	43.235113
+0.381471	4.309000	43.265235
+0.370262	4.312000	43.295357
+0.359141	4.315000	43.325479
+0.348106	4.318000	43.355601
+0.337155	4.321000	43.385723
+0.326286	4.324000	43.415845
+0.315500	4.327000	43.445967
+0.304795	4.330000	43.476089
+0.294169	4.333000	43.506211
+0.283622	4.336000	43.536333
+0.273151	4.339000	43.566455
+0.262756	4.342000	43.596577
+0.252434	4.345000	43.626699
+0.242183	4.348000	43.656821
+0.232002	4.351000	43.686943
+0.221888	4.354000	43.717065
+0.211839	4.357000	43.747187
+0.201851	4.360000	43.777309
+0.191922	4.363000	43.807431
+0.182047	4.366000	43.837553
+0.172222	4.369000	43.867675
+0.162443	4.372000	43.897797
+0.152704	4.375000	43.927919
+0.142999	4.378000	43.958041
+0.133320	4.381000	43.988163
+0.123659	4.384000	44.018285
+0.114004	4.387000	44.048407
+0.104345	4.390000	44.078529
+0.094664	4.393000	44.108651
+0.084944	4.396000	44.138773
+0.075160	4.399000	44.168895
+0.065281	4.402000	44.199017
+0.055267	4.405000	44.229139
+0.045062	4.408000	44.259261
+0.034588	4.411000	44.289383
+0.023738	4.414000	44.319505
+0.012376	4.417000	44.349627
+0.000722	4.420000	44.379749

eloss_calculations/aluminum_lookup_80MeV_350torr_4pc.dat

@@ -0,0 +1,275 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 80 MeV
+80.000000	0.000000	0.000000
+79.652863	0.022000	0.205127
+79.305036	0.044000	0.410255
+78.956514	0.066000	0.615382
+78.607294	0.088000	0.820510
+78.257370	0.110000	1.025637
+77.906739	0.132000	1.230764
+77.555397	0.154000	1.435892
+77.203338	0.176000	1.641019
+76.850558	0.198000	1.846147
+76.497053	0.220000	2.051274
+76.142818	0.242000	2.256402
+75.787848	0.264000	2.461529
+75.432139	0.286000	2.666656
+75.075687	0.308000	2.871784
+74.718485	0.330000	3.076911
+74.360529	0.352000	3.282039
+74.001815	0.374000	3.487166
+73.642337	0.396000	3.692293
+73.282091	0.418000	3.897421
+72.921071	0.440000	4.102548
+72.559271	0.462000	4.307676
+72.196688	0.484000	4.512803
+71.833315	0.506000	4.717930
+71.469148	0.528000	4.923058
+71.104181	0.550000	5.128185
+70.738407	0.572000	5.333313
+70.371823	0.594000	5.538440
+70.004422	0.616000	5.743568
+69.636199	0.638000	5.948695
+69.267147	0.660000	6.153822
+68.897262	0.682000	6.358950
+68.526536	0.704000	6.564077
+68.154965	0.726000	6.769205
+67.782542	0.748000	6.974332
+67.409261	0.770000	7.179459
+67.035116	0.792000	7.384587
+66.660101	0.814000	7.589714
+66.284209	0.836000	7.794842
+65.907434	0.858000	7.999969
+65.529769	0.880000	8.205097
+65.151207	0.902000	8.410224
+64.771743	0.924000	8.615351
+64.391369	0.946000	8.820479
+64.010078	0.968000	9.025606
+63.627864	0.990000	9.230734
+63.244719	1.012000	9.435861
+62.860636	1.034000	9.640988
+62.475608	1.056000	9.846116
+62.089627	1.078000	10.051243
+61.702686	1.100000	10.256371
+61.314778	1.122000	10.461498
+60.925894	1.144000	10.666625
+60.536028	1.166000	10.871753
+60.145170	1.188000	11.076880
+59.753313	1.210000	11.282008
+59.360448	1.232000	11.487135
+58.966568	1.254000	11.692263
+58.571664	1.276000	11.897390
+58.175727	1.298000	12.102517
+57.778749	1.320000	12.307645
+57.380720	1.342000	12.512772
+56.981633	1.364000	12.717900
+56.581477	1.386000	12.923027
+56.180243	1.408000	13.128154
+55.777922	1.430000	13.333282
+55.374504	1.452000	13.538409
+54.969980	1.474000	13.743537
+54.564339	1.496000	13.948664
+54.157572	1.518000	14.153791
+53.749667	1.540000	14.358919
+53.340616	1.562000	14.564046
+52.930406	1.584000	14.769174
+52.519026	1.606000	14.974301
+52.106467	1.628000	15.179429
+51.692716	1.650000	15.384556
+51.277762	1.672000	15.589683
+50.861594	1.694000	15.794811
+50.444198	1.716000	15.999938
+50.025563	1.738000	16.205066
+49.605677	1.760000	16.410193
+49.184526	1.782000	16.615320
+48.762097	1.804000	16.820448
+48.338378	1.826000	17.025575
+47.913354	1.848000	17.230703
+47.487012	1.870000	17.435830
+47.059337	1.892000	17.640958
+46.630315	1.914000	17.846085
+46.199931	1.936000	18.051212
+45.768168	1.958000	18.256340
+45.335013	1.980000	18.461467
+44.900448	2.002000	18.666595
+44.464457	2.024000	18.871722
+44.027023	2.046000	19.076849
+43.588129	2.068000	19.281977
+43.147757	2.090000	19.487104
+42.705888	2.112000	19.692232
+42.262504	2.134000	19.897359
+41.817584	2.156000	20.102486
+41.371110	2.178000	20.307614
+40.923060	2.200000	20.512741
+40.473413	2.222000	20.717869
+40.022147	2.244000	20.922996
+39.569239	2.266000	21.128124
+39.114666	2.288000	21.333251
+38.658404	2.310000	21.538378
+38.200427	2.332000	21.743506
+37.740710	2.354000	21.948633
+37.279224	2.376000	22.153761
+36.815944	2.398000	22.358888
+36.350838	2.420000	22.564015
+35.883878	2.442000	22.769143
+35.415030	2.464000	22.974270
+34.944264	2.486000	23.179398
+34.471544	2.508000	23.384525
+33.996834	2.530000	23.589652
+33.520097	2.552000	23.794780
+33.041294	2.574000	23.999907
+32.560384	2.596000	24.205035
+32.077324	2.618000	24.410162
+31.592067	2.640000	24.615290
+31.104689	2.662000	24.820417
+30.615570	2.684000	25.025544
+30.124743	2.706000	25.230672
+29.632198	2.728000	25.435799
+29.137922	2.750000	25.640927
+28.641906	2.772000	25.846054
+28.144138	2.794000	26.051181
+27.644608	2.816000	26.256309
+27.143305	2.838000	26.461436
+26.640219	2.860000	26.666564
+26.135342	2.882000	26.871691
+25.628663	2.904000	27.076819
+25.120174	2.926000	27.281946
+24.609866	2.948000	27.487073
+24.097733	2.970000	27.692201
+23.583768	2.992000	27.897328
+23.067964	3.014000	28.102456
+22.550318	3.036000	28.307583
+22.030825	3.058000	28.512710
+21.509485	3.080000	28.717838
+20.986298	3.102000	28.922965
+20.461265	3.124000	29.128093
+19.934392	3.146000	29.333220
+19.405688	3.168000	29.538347
+18.875166	3.190000	29.743475
+18.342952	3.212000	29.948602
+17.810238	3.234000	30.153730
+17.277504	3.256000	30.358857
+16.744907	3.278000	30.563985
+16.212626	3.300000	30.769112
+15.680858	3.322000	30.974239
+15.149825	3.344000	31.179367
+14.619780	3.366000	31.384494
+14.091004	3.388000	31.589622
+13.563818	3.410000	31.794749
+13.038586	3.432000	31.999876
+12.515722	3.454000	32.205004
+11.995696	3.476000	32.410131
+11.479043	3.498000	32.615259
+10.966373	3.520000	32.820386
+10.458376	3.542000	33.025513
+9.955836	3.564000	33.230641
+9.459634	3.586000	33.435768
+8.968587	3.608000	33.640896
+8.480624	3.630000	33.846023
+7.996543	3.652000	34.051151
+7.517365	3.674000	34.256278
+7.044277	3.696000	34.461405
+6.578645	3.718000	34.666533
+6.122008	3.740000	34.871660
+5.676063	3.762000	35.076788
+5.242633	3.784000	35.281915
+4.823608	3.806000	35.487042
+4.420872	3.828000	35.692170
+4.036211	3.850000	35.897297
+3.671213	3.872000	36.102425
+3.327175	3.894000	36.307552
+3.005018	3.916000	36.512679
+2.705246	3.938000	36.717807
+2.427930	3.960000	36.922934
+2.172726	3.982000	37.128062
+1.938931	4.004000	37.333189
+1.898649	4.008000	37.370485
+1.859036	4.012000	37.407781
+1.820084	4.016000	37.445077
+1.781787	4.020000	37.482373
+1.744136	4.024000	37.519669
+1.707124	4.028000	37.556965
+1.670744	4.032000	37.594260
+1.634987	4.036000	37.631556
+1.599846	4.040000	37.668852
+1.565312	4.044000	37.706148
+1.531376	4.048000	37.743444
+1.498031	4.052000	37.780740
+1.465269	4.056000	37.818036
+1.433080	4.060000	37.855332
+1.401456	4.064000	37.892628
+1.370389	4.068000	37.929923
+1.339869	4.072000	37.967219
+1.309889	4.076000	38.004515
+1.280440	4.080000	38.041811
+1.251512	4.084000	38.079107
+1.223098	4.088000	38.116403
+1.195189	4.092000	38.153699
+1.167776	4.096000	38.190995
+1.140850	4.100000	38.228291
+1.114403	4.104000	38.265586
+1.088427	4.108000	38.302882
+1.062913	4.112000	38.340178
+1.037853	4.116000	38.377474
+1.013238	4.120000	38.414770
+0.989061	4.124000	38.452066
+0.965312	4.128000	38.489362
+0.941984	4.132000	38.526658
+0.919069	4.136000	38.563954
+0.896559	4.140000	38.601250
+0.874445	4.144000	38.638545
+0.852720	4.148000	38.675841
+0.831375	4.152000	38.713137
+0.810405	4.156000	38.750433
+0.789800	4.160000	38.787729
+0.769555	4.164000	38.825025
+0.749659	4.168000	38.862321
+0.730108	4.172000	38.899617
+0.710893	4.176000	38.936913
+0.692007	4.180000	38.974208
+0.673444	4.184000	39.011504
+0.655169	4.188000	39.048800
+0.637097	4.192000	39.086096
+0.619219	4.196000	39.123392
+0.601533	4.200000	39.160688
+0.584039	4.204000	39.197984
+0.566734	4.208000	39.235280
+0.549617	4.212000	39.272576
+0.532668	4.216000	39.309871
+0.515903	4.220000	39.347167
+0.499322	4.224000	39.384463
+0.482922	4.228000	39.421759
+0.466703	4.232000	39.459055
+0.450662	4.236000	39.496351
+0.434797	4.240000	39.533647
+0.419107	4.244000	39.570943
+0.403589	4.248000	39.608239
+0.388240	4.252000	39.645535
+0.373053	4.256000	39.682830
+0.358025	4.260000	39.720126
+0.343153	4.264000	39.757422
+0.328433	4.268000	39.794718
+0.313862	4.272000	39.832014
+0.299437	4.276000	39.869310
+0.285156	4.280000	39.906606
+0.271013	4.284000	39.943902
+0.257007	4.288000	39.981198
+0.243132	4.292000	40.018493
+0.229383	4.296000	40.055789
+0.215754	4.300000	40.093085
+0.202240	4.304000	40.130381
+0.188830	4.308000	40.167677
+0.175518	4.312000	40.204973
+0.162291	4.316000	40.242269
+0.149136	4.320000	40.279565
+0.136037	4.324000	40.316861
+0.122975	4.328000	40.354156
+0.109923	4.332000	40.391452
+0.096850	4.336000	40.428748
+0.083713	4.340000	40.466044
+0.070453	4.344000	40.503340
+0.056987	4.348000	40.540636
+0.043192	4.352000	40.577932
+0.028879	4.356000	40.615228
+0.013760	4.360000	40.652524
+0.001928	4.363000	40.680496

eloss_calculations/fluorine_lookup_70MeV_250torr_3pc.dat

@@ -0,0 +1,920 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
+70.000000	0.000000	0.000000
+69.905134	0.015000	0.210854
+69.810187	0.030000	0.421708
+69.715160	0.045000	0.632562
+69.620053	0.060000	0.843416
+69.524866	0.075000	1.054270
+69.429597	0.090000	1.265124
+69.334248	0.105000	1.475978
+69.238817	0.120000	1.686832
+69.143304	0.135000	1.897686
+69.047710	0.150000	2.108540
+68.952034	0.165000	2.319394
+68.856277	0.180000	2.530248
+68.760436	0.195000	2.741102
+68.664513	0.210000	2.951956
+68.568508	0.225000	3.162810
+68.472419	0.240000	3.373664
+68.376248	0.255000	3.584518
+68.279993	0.270000	3.795372
+68.183654	0.285000	4.006226
+68.087231	0.300000	4.217080
+67.990725	0.315000	4.427934
+67.894134	0.330000	4.638788
+67.797459	0.345000	4.849642
+67.700699	0.360000	5.060496
+67.603854	0.375000	5.271350
+67.506924	0.390000	5.482204
+67.409908	0.405000	5.693058
+67.312807	0.420000	5.903912
+67.215620	0.435000	6.114766
+67.118347	0.450000	6.325620
+67.020988	0.465000	6.536474
+66.923542	0.480000	6.747328
+66.826009	0.495000	6.958182
+66.728389	0.510000	7.169036
+66.630682	0.525000	7.379890
+66.532888	0.540000	7.590744
+66.435006	0.555000	7.801598
+66.337036	0.570000	8.012452
+66.238977	0.585000	8.223306
+66.140831	0.600000	8.434160
+66.042595	0.615000	8.645014
+65.944271	0.630000	8.855868
+65.845858	0.645000	9.066722
+65.747355	0.660000	9.277576
+65.648762	0.675000	9.488430
+65.550080	0.690000	9.699284
+65.451307	0.705000	9.910138
+65.352444	0.720000	10.120992
+65.253491	0.735000	10.331846
+65.154446	0.750000	10.542700
+65.055311	0.765000	10.753554
+64.956084	0.780000	10.964408
+64.856765	0.795000	11.175262
+64.757355	0.810000	11.386116
+64.657852	0.825000	11.596970
+64.558257	0.840000	11.807825
+64.458569	0.855000	12.018679
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eloss_calculations/fluorine_lookup_70MeV_250torr_4pc.dat

@@ -0,0 +1,881 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
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eloss_calculations/fluorine_lookup_70MeV_350torr_3pc.dat

@@ -0,0 +1,522 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
+70.000000	0.000000	0.000000
+69.857849	0.020000	0.200813
+69.715518	0.040000	0.401627
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eloss_calculations/fluorine_lookup_70MeV_350torr_4pc.dat

@@ -0,0 +1,437 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
+70.000000	0.000000	0.000000
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eloss_calculations/oxygen_lookup_70MeV_350torr_3pc.dat

@@ -0,0 +1,641 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
+70.000000	0.000000	0.000000
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eloss_calculations/oxygen_lookup_70MeV_350torr_4pc.dat

@@ -0,0 +1,538 @@
+# Energy(MeV) 	mg/cm2 	cm
+# Starting Energy: 70 MeV
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fit_a1c1_cfrac.C

@@ -0,0 +1,296 @@
+// fit_a1c1_cfrac.C
+// =============================================================================
+// Offline per-cell "gain match" for the A1C1 linear centre-fold model.
+//
+// The raw cfrac = cpMax/(apSum+cpMax) pedestal floats with the arbitrary
+// anode/cathode gain, so the model cfrac = cfmin[cell] + k[cell]*fold has to be
+// re-fit per dataset. This macro does that fit OFFLINE from an already-processed
+// results file (no reprocessing of raw data), replacing the in-line autocal that
+// used to live in TrackRecon.C.
+//
+// It reads the reference histograms
+//     Benchmark_QQQ_A1C1_cfrac_vs_ref   (X = true z = pcz_ref, Y = cfrac)
+//     Benchmark_SX3_A1C1_cfrac_vs_ref
+// filled from A1C2 events (where the true z is known from the crossover), folds
+// each cell about its centre (fold = |z - z_centre| / halfcell, in [0,1]) and
+// does a weighted least-squares fit of cfrac vs fold per cathode cell. QQQ and
+// SX3 are combined (same proportional-counter cells).
+//
+// Output: a per-cell table, paste-ready C++ array literals for TrackRecon.C
+// (a1c1_cfmin_<DATASET>[7] / a1c1_k_<DATASET>[7]), and optionally a .dat file.
+//
+// Usage (compile once with + then call):
+//   root -l -b -q 'fit_a1c1_cfrac.C+("Output_17F/Output_17F.root")'   // build
+//   MAIN band:  fit_a1c1_cfrac("Output_17F/Output_17F.root","17F",0.25,1.05)
+//   LOW band:   fit_a1c1_cfrac("Output_17F/Output_17F.root","17F",0.00,0.25,50,false,"2")
+//   27Al:       fit_a1c1_cfrac("Output_27Al/output_27Al.root","27Al",0.10,1.05)
+// Args: cfrac_min, cfrac_max (band window), min_counts (per-cell fit threshold),
+//       write_dat (dump a1c1_cfrac_<DATASET>.dat), band ("" main, "2" low band ->
+//       prints a1c1_cfmin2_<DATASET>), all_cells (pool all 7 cells into one fit
+//       and broadcast -- robust when per-cell stats are thin / pedestals uniform).
+//   ALL-CELLS: fit_a1c1_cfrac("Output_cal/17F.root","17F",0.25,1.05,50,false,"",true)
+// =============================================================================
+
+#include <TFile.h>
+#include <TH1.h>
+#include <TH2.h>
+#include <TKey.h>
+#include <TDirectory.h>
+#include <TMath.h>
+#include <TString.h>
+#include <algorithm>
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <vector>
+
+namespace {
+// cathode wire grid; cell i spans zg[i] (high) .. zg[i+1] (low)
+const double zg[8] = {147.998, 101.946, 59.7634, 19.6965,
+                      -19.6965, -59.7634, -101.946, -147.998};
+
+int cellOf(double z) {
+  for (int i = 0; i < 7; ++i)
+    if (z <= zg[i] && z > zg[i + 1]) return i;
+  return -1;
+}
+
+// recursively search a directory tree for a TH2 by name (folders vary by group)
+TH2 *findTH2(TDirectory *dir, const std::string &name) {
+  if (TH2 *h = dynamic_cast<TH2 *>(dir->Get(name.c_str()))) return h;
+  TIter next(dir->GetListOfKeys());
+  TKey *key;
+  while ((key = (TKey *)next())) {
+    TObject *obj = key->ReadObj();
+    if (TDirectory *sub = dynamic_cast<TDirectory *>(obj)) {
+      if (TH2 *h = findTH2(sub, name)) return h;
+    }
+  }
+  return nullptr;
+}
+} // namespace
+
+// cfrac_min/cfrac_max bracket the band to fit: [0.25, 1.05] for the MAIN band,
+// [0.0, 0.25] for the 17F low (incomplete-integration) band. band="" prints the
+// a1c1_cfmin_<dataset> arrays; band="2" prints a1c1_cfmin2_<dataset> (the low band).
+void fit_a1c1_cfrac(const char *filename, const char *dataset = "DATA",
+                    double cfrac_min = 0.0, double cfrac_max = 1.05,
+                    long min_counts = 50, bool write_dat = false,
+                    const char *band = "", bool all_cells = false) {
+  TFile *f = TFile::Open(filename, "READ");
+  if (!f || f->IsZombie()) {
+    std::cerr << "fit_a1c1_cfrac: cannot open " << filename << std::endl;
+    return;
+  }
+
+  const char *names[2] = {"Benchmark_QQQ_A1C1_cfrac_vs_ref",
+                          "Benchmark_SX3_A1C1_cfrac_vs_ref"};
+
+  // weighted OLS accumulators per cell:  cfrac = cfmin + k*fold
+  double n[7] = {0}, sf[7] = {0}, sff[7] = {0}, sc[7] = {0}, sfc[7] = {0};
+
+  for (int s = 0; s < 2; ++s) {
+    TH2 *h = findTH2(f, names[s]);
+    if (!h) {
+      std::cout << "  (note: " << names[s] << " not found -- skipping)" << std::endl;
+      continue;
+    }
+    std::cout << "Using " << names[s] << "  (" << h->GetEntries() << " entries)" << std::endl;
+    const int nx = h->GetNbinsX(), ny = h->GetNbinsY();
+    for (int ix = 1; ix <= nx; ++ix) {
+      const double z = h->GetXaxis()->GetBinCenter(ix);
+      const int c = cellOf(z);
+      if (c < 0) continue;
+      const double zc = 0.5 * (zg[c] + zg[c + 1]);
+      const double half = 0.5 * (zg[c] - zg[c + 1]);
+      if (half <= 0.0) continue;
+      const double fold = TMath::Abs(z - zc) / half; // [0,1]
+      for (int iy = 1; iy <= ny; ++iy) {
+        const double w = h->GetBinContent(ix, iy);
+        if (w <= 0.0) continue;
+        const double cfrac = h->GetYaxis()->GetBinCenter(iy);
+        if (cfrac < cfrac_min || cfrac > cfrac_max) continue;
+        n[c] += w;
+        sf[c] += w * fold;
+        sff[c] += w * fold * fold;
+        sc[c] += w * cfrac;
+        sfc[c] += w * fold * cfrac;
+      }
+    }
+  }
+
+  // per-cell weighted least-squares; keep a fallback for starved cells
+  const double cfmin_fallback = 0.40, k_fallback = 0.075;
+  double cfmin[7], k[7];
+
+  if (all_cells) {
+    // pool every cell into one fit. fold is already cell-relative (|z-zc|/half),
+    // so pooling the (fold, cfrac) pairs is valid -- robust when per-cell stats
+    // are thin and the pedestals are ~uniform. Same value written to all 7 cells.
+    double N = 0, SF = 0, SFF = 0, SC = 0, SFC = 0;
+    for (int c = 0; c < 7; ++c) { N += n[c]; SF += sf[c]; SFF += sff[c]; SC += sc[c]; SFC += sfc[c]; }
+    double cf = cfmin_fallback, kk = k_fallback;
+    const char *status = "FALLBACK (starved)";
+    if (N > min_counts) {
+      const double denom = N * SFF - SF * SF;
+      if (TMath::Abs(denom) > 1e-9) {
+        const double kfit = (N * SFC - SF * SC) / denom;
+        const double cffit = (SC - kfit * SF) / N;
+        if (kfit > 0.01) { cf = cffit; kk = kfit; status = "fit"; }
+        else status = "FALLBACK (flat k)";
+      }
+    }
+    for (int c = 0; c < 7; ++c) { cfmin[c] = cf; k[c] = kk; }
+    printf("\n ALL-CELLS pooled fit: cfmin=%.6f  k=%.6f  n(eff)=%.0f   %s\n", cf, kk, N, status);
+  } else {
+    std::cout << "\n cell    cfmin         k         n(eff)   status" << std::endl;
+    std::cout << " ----  ---------   ---------   --------   ------" << std::endl;
+    for (int c = 0; c < 7; ++c) {
+      double cf = cfmin_fallback, kk = k_fallback;
+      const char *status = "FALLBACK (starved)";
+      if (n[c] > min_counts) {
+        const double denom = n[c] * sff[c] - sf[c] * sf[c];
+        if (TMath::Abs(denom) > 1e-9) {
+          const double kfit = (n[c] * sfc[c] - sf[c] * sc[c]) / denom;
+          const double cffit = (sc[c] - kfit * sf[c]) / n[c];
+          if (kfit > 0.01) { // reject degenerate/flat fit
+            cf = cffit;
+            kk = kfit;
+            status = "fit";
+          } else {
+            status = "FALLBACK (flat k)";
+          }
+        }
+      }
+      cfmin[c] = cf;
+      k[c] = kk;
+      printf("  %d    %9.6f   %9.6f   %8.0f   %s\n", c, cf, kk, n[c], status);
+    }
+  }
+
+  // paste-ready literals for TrackRecon.C (band="" -> main set, "2" -> low band)
+  printf("\n// ---- paste into TrackRecon.C (cfrac in [%.2f, %.2f]) ----\n", cfrac_min, cfrac_max);
+  printf("static const double a1c1_cfmin%s_%s[7] = {", band, dataset);
+  for (int c = 0; c < 7; ++c) printf("%.6f%s", cfmin[c], c < 6 ? ", " : "};\n");
+  printf("static const double a1c1_k%s_%s[7]     = {", band, dataset);
+  for (int c = 0; c < 7; ++c) printf("%.6f%s", k[c], c < 6 ? ", " : "};\n");
+
+  if (write_dat) {
+    const std::string fn = std::string("a1c1_cfrac_") + dataset + ".dat";
+    std::ofstream out(fn);
+    out << "# cell  cfmin  k    (offline fit cfrac = cfmin + k*fold; dataset=" << dataset << ")\n";
+    for (int c = 0; c < 7; ++c) out << c << "  " << cfmin[c] << "  " << k[c] << "\n";
+    out.close();
+    std::cout << "\nwrote " << fn << std::endl;
+  }
+
+  f->Close();
+}
+
+// =============================================================================
+// REFERENCE-FREE gain match.
+//
+// Does NOT use the A1C2 true-z reference. Reads the per-cell A1C1 cfrac
+// histogram Benchmark_{QQQ,SX3}_trueA1C1_cfrac_vs_cell (cell assignment is pure
+// geometry) and recovers the constants from the EDGES of each cell's cfrac
+// distribution: within a cell cfrac = cfmin + k*fold with fold in [0,1], so the
+// low percentile ~ cfmin (fold->0, cell centre) and the high percentile ~
+// cfmin+k (fold->1, at the wire). Robust percentiles (plo/phi) are used instead
+// of min/max.
+//
+// This aligns the per-cell pedestals (the actual gain match) WITHOUT a reference,
+// but it cannot fix the absolute z scale -- it assumes the linear model and that
+// each cell is illuminated across its length. If shared_k=true, a single
+// geometric k (median of the per-cell spans) is used for every cell and only the
+// per-cell cfmin pedestal is taken from the data -- the most robust mode.
+//
+// Usage:
+//   root -l -b -q 'fit_a1c1_cfrac.C+("Output_17F/Output_17F.root")'   // compile
+//   root -l -b -q 'fit_a1c1_cfrac_reffree("Output_17F/Output_17F.root","17F")'
+// =============================================================================
+void fit_a1c1_cfrac_reffree(const char *filename, const char *dataset = "DATA",
+                            double plo = 0.05, double phi = 0.95,
+                            bool shared_k = false, double min_counts = 50,
+                            bool write_dat = false) {
+  TFile *f = TFile::Open(filename, "READ");
+  if (!f || f->IsZombie()) {
+    std::cerr << "fit_a1c1_cfrac_reffree: cannot open " << filename << std::endl;
+    return;
+  }
+
+  const char *names[2] = {"Benchmark_QQQ_trueA1C1_cfrac_vs_cell",
+                          "Benchmark_SX3_trueA1C1_cfrac_vs_cell"};
+
+  // sum the QQQ + SX3 per-cell cfrac histograms into one (cell x cfrac)
+  TH2 *acc = nullptr;
+  for (int s = 0; s < 2; ++s) {
+    TH2 *h = findTH2(f, names[s]);
+    if (!h) {
+      std::cout << "  (note: " << names[s] << " not found -- skipping)" << std::endl;
+      continue;
+    }
+    std::cout << "Using " << names[s] << "  (" << h->GetEntries() << " entries)" << std::endl;
+    if (!acc) { acc = (TH2 *)h->Clone("acc_cfrac_vs_cell"); acc->SetDirectory(nullptr); }
+    else acc->Add(h);
+  }
+  if (!acc) { std::cerr << "no cfrac_vs_cell histograms found" << std::endl; f->Close(); return; }
+
+  const double cfmin_fallback = 0.40, k_fallback = 0.075;
+  double cfmin[7], k[7], span[7];
+  bool ok[7];
+
+  std::cout << "\n cell    cfmin       cfmin+k        k        n     status" << std::endl;
+  std::cout << " ----  ---------   ---------   ---------   ------   ------" << std::endl;
+  for (int c = 0; c < 7; ++c) {
+    TH1D *proj = acc->ProjectionY(Form("proj_c%d", c), c + 1, c + 1);
+    const double n = proj->Integral();
+    double lo = cfmin_fallback, hi = cfmin_fallback + k_fallback;
+    ok[c] = false;
+    if (n > min_counts) {
+      double q[2], p[2] = {plo, phi};
+      proj->GetQuantiles(2, q, p);
+      lo = q[0];
+      hi = q[1];
+      ok[c] = (hi - lo > 0.01);
+    }
+    cfmin[c] = ok[c] ? lo : cfmin_fallback;
+    span[c] = ok[c] ? (hi - lo) : k_fallback;
+    k[c] = span[c];
+    printf("  %d    %9.6f   %9.6f   %9.6f   %6.0f   %s\n", c, cfmin[c],
+           cfmin[c] + span[c], span[c], n, ok[c] ? "fit" : "FALLBACK");
+    delete proj;
+  }
+
+  if (shared_k) {
+    // median of the well-determined per-cell spans -> one geometric k for all cells
+    double v[7];
+    int m = 0;
+    for (int c = 0; c < 7; ++c) if (ok[c]) v[m++] = span[c];
+    double kg = k_fallback;
+    if (m > 0) {
+      std::sort(v, v + m);
+      kg = (m % 2) ? v[m / 2] : 0.5 * (v[m / 2 - 1] + v[m / 2]);
+    }
+    for (int c = 0; c < 7; ++c) k[c] = kg;
+    std::cout << "\nshared geometric k = " << kg << " (median of " << m << " fitted cells)" << std::endl;
+  }
+
+  printf("\n// ---- paste into TrackRecon.C (reference-free gain match) ----\n");
+  printf("static const double a1c1_cfmin_%s[7] = {", dataset);
+  for (int c = 0; c < 7; ++c) printf("%.6f%s", cfmin[c], c < 6 ? ", " : "};\n");
+  printf("static const double a1c1_k_%s[7]     = {", dataset);
+  for (int c = 0; c < 7; ++c) printf("%.6f%s", k[c], c < 6 ? ", " : "};\n");
+
+  if (write_dat) {
+    const std::string fn = std::string("a1c1_cfrac_") + dataset + ".dat";
+    std::ofstream out(fn);
+    out << "# cell  cfmin  k   (reference-free gain match, percentiles " << plo << "/" << phi
+        << "; dataset=" << dataset << ")\n";
+    for (int c = 0; c < 7; ++c) out << c << "  " << cfmin[c] << "  " << k[c] << "\n";
+    out.close();
+    std::cout << "\nwrote " << fn << std::endl;
+  }
+
+  delete acc;
+  f->Close();
+}

gmsx3/func1.h

@@ -0,0 +1,41 @@
+#include "TF1.h"
+
+double model2(double *x, double *par) {
+    /*  'Potential Well' of width 2a from from xx-a to xx+a
+        xx is coordinate about the point of origin, set at x=center
+        v0 is the y-offset of the potential
+        k is the 'steepness' of the potential
+
+        continuous across xx-a and xx+a, and differentiable
+    */
+
+    double center= par[3];
+    double xx = x[0]-center;
+    double a = TMath::Abs(par[0]);
+    double k = TMath::Abs(par[1]);
+    double v0 = par[2];
+
+    if(xx < -a)
+        return k*(xx+a)*(xx+a) + v0;
+    else if(xx > a)
+        return k*(xx-a)*(xx-a) + v0;
+    else
+        return v0;
+}
+
+void func1() {
+    //TF1 f1("bowl",model,-2.,2.,2);
+    TCanvas c("c1","c1",800,600);
+    TF1 f1("bowl",model2,-10.,10.,4);
+    f1.SetMaximum(10);
+
+    for(int i=-4; i<4; i++) {
+        f1.SetParameters(.4,100,2,i); //a, k, v0, center
+        f1.SetNpx(100000);
+        if(i==-4) f1.Draw("L");
+        f1.DrawCopy("L SAME");
+        c.Modified(); c.Update();
+        //c.SaveAs(Form("%d.png",out));
+        while(c.WaitPrimitive());
+   }
+}

gmsx3/intgm_sx3.h

@@ -0,0 +1,216 @@
+#include "../Armory/HistPlotter.h"
+#include <Minuit2/FCNBase.h>
+#include <Math/Minimizer.h>
+#include <Math/Factory.h>
+#include <Math/Functor.h>
+#include <TMath.h>
+#include <TPad.h>
+#include <cassert>
+#include <vector>
+#include <array>
+#include <iostream>
+#include <TF1.h>
+#include "func1.h"
+static long iters=0;
+
+//class intgm_sx3 : public ROOT::Minuit2::FCNBase {
+class intgm_sx3 {
+        int N;
+
+        //L.at(0).at(3).at(n) is front strip = 0, back pad = 3, nth datapoint
+        std::array<std::array<std::vector<double>,4>,4> L,R,B;
+        //std::array<std::array<double,5>,4> stripedge; //stripedge.at(i).at(j) is the jth edge of the ith strip. there are five edges for the four strips 'i'=0 to 3, (0,1) (1,2) (2,3) (3,4) for each
+        //the edges are at  -2a, -a, 0, a, 2a respectively so we enforce four ratios in the chi2 value - 'a' can be held constant, no need to fit it.
+
+        //assume z = M*(aL-bR)
+        //stripedge[i][1] = max(z) when pad==0 = min(z) when pad==1  this should be -1
+        //stripedge[i][2] = max(z) when pad==1 = min(z) when pad==2. this should be 0
+        //stripedge[i][3] = max(z) when pad==2 = min(z) when pad==3. this should be 1
+
+        //i.e. stripedge[i][j] = max(z) when pad == j-1, min(z) when pad==j, for i= 1,2,3
+
+        //ncounts.at(frontch).at(backch) is the number of (L,R,B) tuples we've filled (frontch,backch) coordinates in the detector
+        std::array<std::array<long,4>,4> ncounts;
+        TH1F *localhists[4][4]; //one histogram for each fc, bc combination
+        HistPlotter *plotter;
+        TF1 *pos_weight[4];
+        TF1 *energywell;
+    public:
+        intgm_sx3() {
+            for(int bc=0; bc<4; bc++) {
+                for(int fc=0; fc<4; fc++) {
+                    L[fc][bc].reserve(1000);
+                    R[fc][bc].reserve(1000);
+                    B[fc][bc].reserve(1000);
+                    //localhists[fc][bc] = new TH1F(Form("h_%d_%d",fc,bc),Form("h_%d_%d",fc,bc),1000,-4.,4.);
+                    ncounts[fc][bc] = 0;
+                }
+                pos_weight[bc] = new TF1(Form("b_strip%d",bc),model2,-10,10,4); //from -10, to 10, 4 parameters
+                pos_weight[bc]->SetParameters(1.0,10,1.,3-2*bc); //centers at 1, 3.,5,7 Width 2a with a=1.0
+                pos_weight[bc]->SetNpx(1'000'000);
+            }
+            energywell = new TF1("ewell",model2,0,2000,4); //0 to 2000 channels, 4 params
+            energywell->SetParameters(1000,20,1,1500); //center the back E values at 1500 +/- 500
+            energywell->SetNpx(1'000'000);
+            N=0;
+        }
+        void set_plotter(HistPlotter *p) {plotter=p;}
+        void set_iters(long i) { iters=i;}
+        intgm_sx3(HistPlotter *p) : plotter(p) {
+            for(int bc=0; bc<4; bc++) {
+                for(int fc=0; fc<4; fc++) {
+                    L[fc][bc].reserve(1000);
+                    R[fc][bc].reserve(1000);
+                    B[fc][bc].reserve(1000);
+                    //localhists[fc][bc] = new TH1F(Form("h_%d_%d",fc,bc),Form("h_%d_%d",fc,bc),1000,-4.,4.);
+                    ncounts[fc][bc] = 0;
+                }
+                pos_weight[bc] = new TF1(Form("b_strip%d",bc),model2,-10,10,4); //from -10, to 10, 4 parameters
+                                                //a/2, k, v0, center
+                pos_weight[bc]->SetParameters(0.92,10,1.,-1.*(3-2*bc)); //centers at 7, 5.,3,1 Width 2a with a=1.0
+                pos_weight[bc]->SetNpx(1'000'000);
+            }
+            energywell = new TF1("ewell",model2,0,8000,4); //0 to 2000 channels, 4 params
+//            energywell->SetParameters(60,10,0,1430); //center the back E values at 1430 +/- 60
+            energywell->SetParameters(400,10,0,5246); //center the back E values at 5486 +/- 600
+            energywell->SetNpx(1'000'000);
+            N=0;
+        }
+
+        inline void fill(int fc, int bc, double leftE, double rightE, double backE) {
+            /*
+             *
+             */
+            assert(fc>=0 && fc<=3 && "Front channels should fit the range 0 to 3 inclusive!");
+            assert(bc>=0 && bc<=3 && "Back channels should fit the range 0 to 3 inclusive!");
+            if(leftE>0 && rightE >0 && backE>0) {
+                L[fc][bc].emplace_back(leftE);
+                R[fc][bc].emplace_back(rightE);
+                B[fc][bc].emplace_back(backE);
+                ncounts[fc][bc]+=1;
+                N+=1;
+            }
+        }
+
+        inline void print() {
+            for(int i=0; i<16; i++) {
+                std::cout << ncounts[i%4][i/4] << std::endl;
+            }
+        }
+        inline void plot(std::string comment, const double* params) {
+            std::array<double,4> l,r,b,bo,ro,lo,offset,stretch; //aliases to help with book-keeping
+            std::array<std::array<double,4>,4> back_gains;// back_gains[fc][bc] are for fc,bc firing in combo
+            for(int ctr=0; ctr<4; ctr++) {
+                r[ctr] = params[ctr];
+            }
+            for(int ctr=4; ctr<20; ctr++) {
+                int bch = (ctr-4)%4;
+                int fch = (ctr-4)/4;
+                back_gains[bch][fch] = params[ctr];
+            }
+            for(int ctr=20; ctr<24; ctr++) {
+                stretch[ctr-20] = params[ctr];
+            }
+            for(int ctr=24; ctr<28; ctr++) {
+                l[ctr-24] = params[ctr];
+            }
+            for(int fc=0; fc<4; fc++) {
+                for(int bc=0; bc<4; bc++) {
+                    for(int n=0; n<ncounts[fc][bc]; n++) {
+                        if(plotter) {
+                            double left = l[fc]*L[fc][bc].at(n);
+                            double right = r[fc]*R[fc][bc].at(n);
+                            double back = back_gains[bc][fc]*B[fc][bc].at(n);
+                            //double zpos = (left - right)/(left+right);
+                            double zpos = stretch[fc]*(left - right)/(left+right);// + offset[fc]; //back;
+                            plotter->Fill2D(Form("normlf_fc%d_%d_%s",fc,bc,comment.c_str()),800,0,1.,800,0,1.,left/back, right/back,"l_vs_r");
+                            plotter->Fill2D(Form("normlf_all_%s",comment.c_str()),800, 0, 1., 800, 0, 1.,left/back, right/back);
+                            plotter->Fill2D(Form("case_f%d_b%d_%s",fc,bc,comment.c_str()),800,0,8192,800,0,8192,left+right,back,"l_vs_r");
+                            plotter->Fill2D(Form("case_all_%s",comment.c_str()),800,0,8192,800,0,8192,left+right,back);
+                            //plotter->Fill2D(Form("z_vs_backe_f%d_b%d_%s",fc,bc,comment.c_str()),800,-10,10,800,0,8192,zpos,back,"z_vs_be");
+                            plotter->Fill2D(Form("z_vs_backe_all_%s",comment.c_str()),800,-10,10,800,0,8192,zpos,back);
+                        } //end if plotter
+                    }// end for-n
+                }//end for-bc
+            }//end for-fc
+        }//end plot()
+
+    //    double operator()(const std::vector<double>& params) const override{
+        double eval(const double* params) const {
+            iters+=1;
+
+            std::array<double,4> l,r,b,bo,ro,lo, offset, stretch; //aliases to help with book-keeping
+            std::array<std::array<double,4>,4> back_gains;// back_gains[fc][bc] are for fc,bc firing in combo
+            for(int ctr=0; ctr<16; ctr++) {
+                int bch = (ctr)%4;
+                int fch = (ctr)/4;
+                back_gains[bch][fch] = params[ctr];
+            }
+            for(int ctr=16; ctr<20; ctr++) {
+                r[ctr-16] = params[ctr];
+                l[ctr-16] = 1.0;
+            }
+            for(int ctr=20; ctr<24; ctr++) {
+            	stretch[ctr-20] = params[ctr];
+            }
+            double result=0, sumcount=0;
+            for(int fc=0; fc<4; fc++) {
+                for(int bc=0; bc<4; bc++) {
+                    //if(bc >= 1 || fc >= 1 ) continue;
+                    if(ncounts[fc][bc] == 0 && iters ==0) {
+                        std::cout << "Missing any data in front:" << fc << " back:" << bc << " combination." << std::endl;
+                    }
+
+                    for(int n=0; n<ncounts[fc][bc] ; n++) {
+                        //double left = l[fc]*L[fc][bc].at(n) + lo[fc];
+                        //double right = r[fc]*R[fc][bc].at(n) + ro[fc];
+                        //double back = b[bc]*B[fc][bc].at(n) + bo[bc];
+                        //double add = TMath::Power(left + right - back,2);
+                        if(B[fc][bc].at(n)<100) continue;//ignore events too close to noise threshold
+
+                        double left = l[fc]*L[fc][bc].at(n);
+                        double right = r[fc]*R[fc][bc].at(n);
+                        double back = back_gains[bc][fc]*B[fc][bc].at(n);
+                        double lnorm = left/B[fc][bc].at(n);
+                        double rnorm = right/B[fc][bc].at(n);
+
+                        //double add = TMath::Power(left/back + right/back - 1.0,2);
+                        double add = TMath::Power(left + right - back,2);
+                        double zpos = stretch[fc]*(left - right)/(left+right); //back;
+                        std::cout << zpos << " " << pos_weight[bc]->Eval(zpos) << " " << bc << std::endl;
+                        double add_position = pos_weight[bc]->Eval(zpos);
+                        double eback_align_penalty = energywell->Eval(back);
+/*                      if(back>1000) zmid[fc][bc] += zpos;
+                        if(back>1000 && zpos < zmin[fc][bc]) zmin[fc][bc] = zpos;
+                        if(back> 1000 && zpos > zmax[fc][bc]) zmax[fc][bc] = zpos;
+
+                        if(back>1000) {
+                            localhists[fc][bc]->Fill(zpos);
+                        }*/
+
+                        result += add_position;
+                        //result += add;
+                        result += eback_align_penalty;
+                        sumcount+=1;
+                        //if(bc==0) std::cout << add << " " << add_position << " " <<  zpos << std::endl;
+                        //To avoid drift towards (0,0,0) trivial solution. This value ~1 close to (1,1,1)
+                        //result+=(1e-3/(TMath::Power(l[fc],2)+TMath::Power(r[fc],2)+TMath::Power(b[bc],2)+1e-9));
+						//result+=(1e-3/(TMath::Power(l[fc],2)+TMath::Power(r[fc],2)+TMath::Power(b[bc],2)+1e-9));
+                    } //end for-n
+                } //end for-bc
+            } //end for-fc
+            result/=sumcount; //normalize, so the value doesn't scream
+            if(iters%1'000==0) {
+                std::cout << "iters : " << iters << " params: " << std::endl ;
+                for(int i=0 ; i< 10; i++) std::cout << params[i] << " " << std::flush;
+                std::cout<< std::endl;
+                for(int i=10 ; i< 20; i++) std::cout << params[i] << " " << std::flush;
+                std::cout << std::endl <<  " result: " << result << std::endl;
+            } //end if
+            return result;
+        } //end eval()
+
+        //double Up() const override { return 1.0; } // Required by minuit2 FCBase
+
+};
+

gmsx3/utilities_orr.h

@@ -0,0 +1,338 @@
+#ifndef UTILS_ORR_H
+#define UTILS_ORR_H
+#include "datatypes.h"
+#include "HistPlotter.h"
+#include "Geometry_orr.h" //contains orruba geometry constants
+#include <cassert>
+#include <stdio.h>
+#include <cassert>
+#include <cstdint>
+#include <fcntl.h>
+#include <unistd.h>
+#include <vector>
+//#include <cstring>
+#include <string>
+#include <fstream>
+#include <sstream>
+#include <iostream>
+#include <cmath>
+#include <iomanip>
+#include <set>
+#include <sys/stat.h>
+#include "TMath.h"
+#include "counters.h"
+
+static named_counter oc("named orruba counters");
+
+inline float get_filesize(std::string filename) {
+    struct stat st;
+    stat(filename.c_str(), &st);
+    return st.st_size;
+}
+
+class orruba_params {
+    /*
+    *   
+    */
+public:
+    int chnum=DEFAULT_NULL; //!< global channel number
+    std::string type = "-";
+    int id=DEFAULT_NULL;
+    int layer=DEFAULT_NULL;
+    int frontback=DEFAULT_NULL;
+    int updown=DEFAULT_NULL;
+    int subid=DEFAULT_NULL;
+    int leftright=DEFAULT_NULL;
+
+    float ped=DEFAULT_NULL;
+    float offset=DEFAULT_NULL;
+    float gain=DEFAULT_NULL;
+    float gain2=DEFAULT_NULL; //for use with sx3's
+};
+
+class sx3_geometry_scalefactors {
+public:
+    //If sx3 has L, R being the left and right extremities, we choose add, stretch here such that
+    // x_mm = (x_raw+add)*stretch; so add=abs(L), stretch=75/(abs(L)+R)
+    float add[4];
+    float stretch[4];
+};
+
+class qqq5_finegains {
+public:
+    std::array<std::pair<float,float>,32> front;
+    //front.at(30).first = slope at clkpos 0, ring 30 for E front layer
+    //front.at(30).second = intercept for the same as above
+    std::array<std::pair<float,float>,4> back;
+};
+class sx3_fbgains {
+public:
+    //Order of indices is [pad][strip]
+    float padoffsets[4][4];
+    float padgains[4][4];
+
+    float stripLoffsets[4][4];
+    float stripLgains[4][4];
+
+    float stripRoffsets[4][4];
+    float stripRgains[4][4];
+};
+
+//Metadata ORRUBA needs to know about itself, to be configured at the start
+extern std::array<orruba_params,MAX_ORRUBA_CHANS> o_params;
+extern std::array<sx3_fbgains,24> sx3_xtalk_gains; //every sx3 needs to be gainmatched as a frontL-back, frontR-back pair (pad strip pair)
+extern std::array<sx3_geometry_scalefactors,24> sx3gs;
+extern std::array<qqq5_finegains,4> qqq5_fg_dE, qqq5_fg_E;
+
+class type19Raw {
+public:
+    long int timestamp;
+    std::vector<unsigned short> ch;
+    std::vector<unsigned short> val;
+
+    type19Raw() : timestamp(0), ch(50,0), val(50,0) {} //Reserve 50 for size of these vectors, initial value of zero
+    void print() const {
+        /*
+            print()
+            Prints type19Raw's contents to stdout for monitoring
+        */
+        std::cout << "------" << std::endl;
+        for(unsigned int ii=0; ii<ch.size(); ii++) {
+            std::cout << ch.at(ii) << " " << val.at(ii) << std::endl;
+        }
+    }
+};
+
+class sx3 {
+public:
+    //TODO: Convert to std::array
+    //Holds all information in an event, including ped subtraction+scaling. back[2].at(0) will have the largest energy seen in ch2, if any
+    std::vector<float> back[4];
+    std::vector<float> frontL[4];
+    std::vector<float> frontR[4];
+
+    double ts = DEFAULT_NULL;
+    //Easy lookup of final calibrated event. Only filled for valid cases, assumed for now to be 1L, 1R, 1B
+    float frontX=DEFAULT_NULL;
+    float frontXmm=DEFAULT_NULL;
+    float frontE=DEFAULT_NULL;
+    float backE=DEFAULT_NULL;
+    int stripF=DEFAULT_NULL;
+    int stripB=DEFAULT_NULL;
+    float frontEL=DEFAULT_NULL;
+    float frontER=DEFAULT_NULL;
+
+    float phi=DEFAULT_NULL; //
+
+    std::set<int> valid_front_chans;
+    std::set<int> valid_back_chans;
+    std::set<int> unmatched_front_chans; //every front channel is unmatched and invalid at first. when it gets matched, it gets removed and sent to valid
+
+    bool foundevent=false;
+    bool valid=false;//valid will be set to false in all cases where we have ambiguity
+    int flags=-1;//flags settable to different types of values to indicate different invalid situations
+
+    void fillevent(const std::string& position, const int subchannel, const float value); //make 'const' what functions don't need to change, helps with performance
+    void validate(const sx3_fbgains&, const sx3_geometry_scalefactors&);
+};
+
+class qqq5 {
+public:
+    //Holds all information in an event, including ped subtraction+scaling. front[2].at(0) will have the largest energy seen in ch2, if any
+    //TODO: Convert to std::array
+    std::vector<float> back[4];
+    std::vector<float> front[32];
+
+    double ts = DEFAULT_NULL;
+    float selftheta=DEFAULT_NULL,selfrho=DEFAULT_NULL;
+    //Easy lookup of the final calibrated event. Only filled for valid cases.
+    double frontE=DEFAULT_NULL;
+    double backE=DEFAULT_NULL;
+    int frontch;
+    int backch;
+
+    std::pair<int,int> adj_front_strips = {-1,-1};
+    std::pair<int,int> adj_back_strips = {-1,-1};
+    std::set<int> valid_front_chans; //list of channels that fire. can inspect size() of these to see if there are front/back events
+    std::set<int> valid_back_chans; // we use std::set since it makes for very readable code
+
+    bool foundevent=false;
+    bool valid=false; //valid will be set to false in all cases where we have ambiguity
+    int flags=-1; //flags settable to different types of values to indicate different invalid situations
+
+    void fillevent(const std::string& position, const int subchannel, const float value); //make 'const' what functions don't need to change, helps with performance
+    void validate();
+};
+
+struct orrubaevent {
+    //Every clean, valid charged-particle event will have these four parts
+    float dE=DEFAULT_NULL;  //!< true energy-loss in the dE layer. Found by gainmatching ADC readout to alpha data
+    float E=DEFAULT_NULL;   //!< energy deposited in the  E layer. When summed with dE, gives true energy in keV deposited by the particle in ORRUBA
+    float dE_PID = DEFAULT_NULL; //!< dE scaled for dE-layer's thickness, reducing the spread due to angular straggling by explicitly accounting for it. This will give a sharper pid plot that can be gated on better
+    float dE_linPID = DEFAULT_NULL; //!< dE_PID, but linearized using the prescription described in, say, PhysRevC.90.034601 (2014). dE_linPID = ((dE+E)^a-E^a)^(1/a) where a ~ 1.68 is chosen empirically
+    float Theta=DEFAULT_NULL; //!< Laboratory polar angle of event in radians, deprecated
+    float Phi=DEFAULT_NULL; //!< Lab azimuthal angle of event in radians, deprecated
+
+    //Helpful indices to make dE-E plots
+    std::string type; //!< "endcap" vs "barrel"
+    //!< Identify the position of the detector in the barrel, usually in accordance with the channel map: say we might learn detector is at "Quad 4" or "clk_pos 10", together with 'type'. Useful with HistPlotter class
+    int position=DEFAULT_NULL;
+	int subchdE_1=DEFAULT_NULL, subchdE_2=DEFAULT_NULL; //!< Identify the subchannels corresponding to the two sides of the dE detector. To avoid confusion, 1=strip(sx3), ring(qqq) and 2=pad(sx3), wedge(qqq)
+	int subchE_1=DEFAULT_NULL, subchE_2=DEFAULT_NULL; //!< Identify the subchannels corresponding to the two sides of the E detector. Same convention as above
+
+    float x=DEFAULT_NULL,y=DEFAULT_NULL,z=DEFAULT_NULL; //!< Laboratory x,y,z coordinates of the event from the E layer
+    float r0=DEFAULT_NULL,theta0=DEFAULT_NULL,phi0=DEFAULT_NULL; //!< vector elements from hit to origin for E layer
+    float r1=DEFAULT_NULL,theta1=DEFAULT_NULL,phi1=DEFAULT_NULL; //!< vector elements from hit to origin for dE layer
+};
+
+/*TODO:
+    * There will be some use for a class such that it stores 
+        PhysicsEvent = <Ex, Brho, THeta4, ...orrubaevent >
+    * Once the 'orrubaevent' structs are made, it should be callable. like 
+    std::vector<PhysicsEvent> getPhysicsFromVertices(Kinematics dpkin, std::vector<orrubaevent> orvec);?
+    * should the physics just go sit in orrubaevent? maybe orruba2024 class can have a kinematics object in it?
+*/
+
+class orruba2024 {
+private:
+//Class expected to be changed for each version of the analysis code
+public:
+    bool found_trk, found_trkpresc, found_tdcq, found_s800e1, found_s800trg,
+         found_rf, found_gt, found_si, found_siup;
+
+	bool found_de, found_e, found_qqq, found_sx3;//orruba
+    long long timestamp=DEFAULT_NULL;
+    std::vector<type19Raw> o_rawvec;
+
+    std::array<qqq5,4> uendcapE;
+    std::array<qqq5,4> uendcapdE;
+    std::array<sx3,12> ubarrelE;
+    std::array<sx3,12> ubarreldE;
+
+    std::array<sx3,2> dbarrelE;
+    //Results after post-processing, including possible multiplicities
+    std::vector<orrubaevent> events;
+
+    double target_z_offset;
+
+    //void initialize(const std::string & filename1, const std::string& filename2, const std::string& filename3);
+	float tdc_trk = DEFAULT_NULL;
+	float tdc_trksi = DEFAULT_NULL; //trackerpr+si stops are combined into one channel
+	float tdc_trkp = DEFAULT_NULL;
+	float tdc_q = DEFAULT_NULL;
+	float tdc_s800e1 = DEFAULT_NULL;
+	float tdc_s800trg = DEFAULT_NULL;
+	float tdc_rf = DEFAULT_NULL;
+	float tdc_rf_unwrap = DEFAULT_NULL;
+	float tdc_gt = DEFAULT_NULL;
+	float tdc_si = DEFAULT_NULL;
+	float tdc_siup = DEFAULT_NULL;
+    orruba2024(const std::vector<type19Raw>& orvec);
+    void postprocess(); //generates 'events', and performs validations on freshly entered data. performs fine gainmatching for front-back-pairs
+    void print() const {
+    	std::cout << Form("TDCs\n trk:%1.4f\ntrkp:%1.4f\nq:%1.4f\ns800e1:%1.4f\ns800trg:%1.4f\nrf:%1.4f\nrfuw:%1.4f\ngt:%1.4f\nsi:%1.4f\nsiup:%1.4f\n-----\nevents_size:%lu\ntimestamp:%lld\nfound_de:%d, found_e:%d\n-------\n-------\n",
+    	tdc_trk, tdc_trkp, tdc_q, tdc_s800e1, tdc_s800trg, tdc_rf, tdc_rf_unwrap, tdc_gt, tdc_si, tdc_siup, events.size(), timestamp, found_de, found_e) << std::endl;
+    }
+};
+
+class trackingdet {
+public:
+    double timestamp=DEFAULT_NULL;
+    //TODO: Convert all to std::array
+    std::vector<float> xwires[MAXNWIRES_TRACK];
+    std::vector<float> ywires[MAXNWIRES_TRACK];
+    std::vector<float> xwiresf[MAXNWIRES_TRACK];
+    std::vector<float> ywiresf[MAXNWIRES_TRACK];
+    std::vector<float> xwiresf_nn[MAXNWIRES_TRACK];
+    std::vector<float> ywiresf_nn[MAXNWIRES_TRACK];
+
+    std::vector<float> xtimes[MAXNWIRES_TRACK];
+    std::vector<float> ytimes[MAXNWIRES_TRACK];
+    std::vector<float> xtimesf[MAXNWIRES_TRACK];
+    std::vector<float> ytimesf[MAXNWIRES_TRACK];
+    std::vector<float> cathode;
+
+    int multx; //how many x-wires fired?
+    int multy; //how many y-wires fired?
+    int multxf; //how many filtered x-wires fired?
+    int multyf; //how many filtered y-wires fired?
+
+    int multxt; //how many x-tdcwires fired?
+    int multyt; //how many y-tdcwires fired?
+
+    int multxtf; //how many x-tdcwires fired in window?
+    int multytf; //how many y-tdcwires fired in window?
+
+    float tot_cathode=0;
+    float tot_x=0;
+    float tot_y=0;
+    float tot_anode=0;
+
+    //list of x and y wires fired above energy threshold, within timing gate window
+    std::set<int> list_ywires;
+    std::set<int> list_xwires;
+
+    std::set<int> list_ytwires;
+    std::set<int> list_xtwires;
+
+    //position of the vertex estimated by up to 2 neighbouring wires firing together within window  
+    double xpos=DEFAULT_NULL;
+    double ypos=DEFAULT_NULL;
+    bool clean_event = false;
+    int maxnx=-124, maxny=-124;
+    int nnx = 0; //nearest neighbour x wires set this to +/- 1 if present w.r.t. wire maxnx
+    int nny = 0; //nearest neighbour y wires set this to +/- 1 if present w.r.t  wire maxny
+    bool clean_event_no_timing = false;
+    bool clean_single_xy_event = false;
+    bool clean_single_xy_event_no_timing = false;
+    void Reset() {
+        /***
+        Resets all data members.
+        **/
+        cathode.clear();
+        for(int i=0; i<MAXNWIRES_TRACK; i++) {
+            xwires[i].clear();
+            ywires[i].clear();
+            xwiresf[i].clear();
+            ywiresf[i].clear();
+            xwiresf_nn[i].clear();
+            ywiresf_nn[i].clear();
+            xtimes[i].clear();
+            ytimes[i].clear();
+            xtimesf[i].clear();
+            ytimesf[i].clear();
+        }
+        list_xwires.clear();
+        list_ywires.clear();
+        list_xtwires.clear();
+        list_ytwires.clear();
+
+        nnx = 0;
+        nny = 0;
+        clean_event_no_timing = false;
+        clean_event = false; //x, y both fire above thresh, xt, yt present within broad coinc window
+        xpos=DEFAULT_NULL;
+        ypos=DEFAULT_NULL;
+        maxnx=-124;
+        maxny=-124;
+        multx=0; //how many x-wires fired?
+        multy=0; //how many y-wires fired?
+        multxf=0; //how many filt x-wires fired?
+        multyf=0; //how many filt y-wires fired?
+        multxt=0; //how many tdc x-wires fired?
+        multyt=0; //how many tdc y-wires fired?
+        multxtf=0; //how many tdc x-wires fired?
+        multytf=0; //how many tdc y-wires fired?
+    }
+
+    trackingdet() {
+        Reset();
+    };
+    trackingdet(const std::vector<type19Raw>& orvec);
+};
+
+const float alpha = 0.0;
+int matchchantype(unsigned short chan, const std::array<orruba_params,MAX_ORRUBA_CHANS>& index, const std::string& label);
+void initialize_orruba(const std::string & filename1, const std::string& filename2, const std::string& filename3, const std::string& filename4);//,
+int parse_orruba_data(const unsigned short* buffer, int32_t length, type19Raw& oraw_event);
+#endif

mapping.h

@@ -12,213 +12,261 @@
 #include <TMath.h>
 
 const std::map<int, unsigned short> board = {
-   {0, 17122},  // id, sn
+    {0, 17122}, // id, sn
-   {1, 17123},
+    {1, 17123},
-   {2, 22320},
+    {2, 22320},
-   {3, 22130},
+    {3, 22130},
-   {4, 22129},
+    {4, 22129},
-   {5, 15529},
+    {5, 15529},
-   {6, 15528},
+    {6, 15528},
-   {7,   334},
+    //  {7,89},
-   {8,   379},
+    {7, 334},
-   {9,   325},
+    {8, 379},
-   {10,  405}
+    {9, 325},
-};
+    {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
 
-
+// use the GenMapping() to get that
-// use the GenMapping() to get that 
 const std::vector<int> mapping = {
 
-  //================== 17122
+    //================== 17122
-   806,   807,   804,   805,   803,   802,   801,   800,  1006,  1007,  1004,  1005,  1003,  1002,  1001,  1000,
+    806, 807, 804, 805, 803, 802, 801, 800, 1006, 1007, 1004, 1005, 1003, 1002, 1001, 1000,
-   606,   607,   604,   605,   603,   602,   601,   600,  1106,  1107,  1104,  1105,  1103,  1102,  1101,  1100,
+    606, 607, 604, 605, 603, 602, 601, 600, 1106, 1107, 1104, 1105, 1103, 1102, 1101, 1100,
-   711,   710,   709,   708,   911,   910,   909,   908,  1011,  1010,  1009,  1008,   811,   810,   809,   808,
+    711, 710, 709, 708, 911, 910, 909, 908, 1011, 1010, 1009, 1008, 811, 810, 809, 808,
-   706,   707,   704,   705,   703,   702,   701,   700,   906,   907,   904,   905,   903,   902,   901,   900,
+    706, 707, 704, 705, 703, 702, 701, 700, 906, 907, 904, 905, 903, 902, 901, 900,
-  //================== 17123
+    //================== 17123
-  1406,  1407,  1404,  1405,  1403,  1402,  1401,  1400,  1606,  1607,  1604,  1605,  1603,  1602,  1601,  1600,
+    1406, 1407, 1404, 1405, 1403, 1402, 1401, 1400, 1606, 1607, 1604, 1605, 1603, 1602, 1601, 1600,
-  1306,  1307,  1304,  1305,  1303,  1302,  1301,  1300,  1506,  1507,  1504,  1505,  1503,  1502,  1501,  1500,
+    1306, 1307, 1304, 1305, 1303, 1302, 1301, 1300, 1506, 1507, 1504, 1505, 1503, 1502, 1501, 1500,
-  1311,  1310,  1309,  1308,  1711,  1710,  1709,  1708,  1611,  1610,  1609,  1608,  1411,  1410,  1409,  1408,
+    1311, 1310, 1309, 1308, 1711, 1710, 1709, 1708, 1611, 1610, 1609, 1608, 1411, 1410, 1409, 1408,
-  1206,  1207,  1204,  1205,  1203,  1202,  1201,  1200,  1706,  1707,  1704,  1705,  1703,  1702,  1701,  1700,
+    1206, 1207, 1204, 1205, 1203, 1202, 1201, 1200, 1706, 1707, 1704, 1705, 1703, 1702, 1701, 1700,
-  //================== 22320
+    //================== 22320
-     6,     7,     4,     5,     3,     2,     1,     0,   506,   507,   504,   505,   503,   502,   501,   500,
+    6, 7, 4, 5, 3, 2, 1, 0, 506, 507, 504, 505, 503, 502, 501, 500,
-   111,   110,   109,   108,   311,   310,   309,   308,   411,   410,   409,   408,   211,   210,   209,   208,
+    111, 110, 109, 108, 311, 310, 309, 308, 411, 410, 409, 408, 211, 210, 209, 208,
-   206,   207,   204,   205,   203,   202,   201,   200,   406,   407,   404,   405,   403,   402,   401,   400,
+    206, 207, 204, 205, 203, 202, 201, 200, 406, 407, 404, 405, 403, 402, 401, 400,
-   106,   107,   104,   105,   103,   102,   101,   100,   306,   307,   304,   305,   303,   302,   301,   300,
+    106, 107, 104, 105, 103, 102, 101, 100, 306, 307, 304, 305, 303, 302, 301, 300,
-  //================== 22130
+    //================== 22130
-  1911,  1910,  1909,  1908,  2111,  2110,  2109,  2108,  2211,  2210,  2209,  2208,  2011,  2010,  2009,  2008,
+    1911, 1910, 1909, 1908, 2111, 2110, 2109, 2108, 2211, 2210, 2209, 2208, 2011, 2010, 2009, 2008,
-    11,    10,     9,     8,   511,   510,   509,   508,   611,   610,   609,   608,  1111,  1110,  1109,  1108,
+    11, 10, 9, 8, 511, 510, 509, 508, 611, 610, 609, 608, 1111, 1110, 1109, 1108,
-  2006,  2007,  2004,  2005,  2003,  2002,  2001,  2000,  2206,  2207,  2204,  2205,  2203,  2202,  2201,  2200,
+    2006, 2007, 2004, 2005, 2003, 2002, 2001, 2000, 2206, 2207, 2204, 2205, 2203, 2202, 2201, 2200,
-  1906,  1907,  1904,  1905,  1903,  1902,  1901,  1900,  2106,  2107,  2104,  2105,  2103,  2102,  2101,  2100,
+    1906, 1907, 1904, 1905, 1903, 1902, 1901, 1900, 2106, 2107, 2104, 2105, 2103, 2102, 2101, 2100,
-  //================== 22129
+    //================== 22129
-  1806,  1807,  1804,  1805,  1803,  1802,  1801,  1800,  2306,  2307,  2304,  2305,  2303,  2302,  2301,  2300,
+    1806, 1807, 1804, 1805, 1803, 1802, 1801, 1800, 2306, 2307, 2304, 2305, 2303, 2302, 2301, 2300,
- 10016, 10017, 10018, 10019, 10020, 10021, 10022, 10023, 10024, 10025, 10026, 10027, 10028, 10029, 10030, 10031,
+    10031, 10030, 10029, 10028, 10027, 10026, 10025, 10024, 10023, 10022, 10021, 10020, 10019, 10018, 10017, 10016,
- 10116, 10117, 10118, 10119, 10120, 10121, 10122, 10123, 10124, 10125, 10126, 10127, 10128, 10129, 10130, 10131,
+    // 10016, 10017, 10018, 10019, 10020, 10021, 10022, 10023, 10024, 10025, 10026, 10027, 10028, 10029, 10030, 10031,
- 10015, 10014, 10013, 10012, 10011, 10010, 10009, 10008, 10007, 10006, 10005, 10004, 10003, 10002, 10001, 10000,
+    10116, 10117, 10118, 10119, 10120, 10121, 10122, 10123, 10124, 10125, 10126, 10127, 10128, 10129, 10130, 10131,
-  //================== 15529
+    10015, 10014, 10013, 10012, 10011, 10010, 10009, 10008, 10007, 10006, 10005, 10004, 10003, 10002, 10001, 10000,
- 10231, 10230, 10229, 10228, 10227, 10226, 10225, 10224, 10223, 10222, 10221, 10220, 10219, 10218, 10217, 10216,
+    //================== 15529
- 10115, 10114, 10113, 10112, 10111, 10110, 10109, 10108, 10107, 10106, 10105, 10104, 10103, 10102, 10101, 10100,
+    10231, 10230, 10229, 10228, 10227, 10226, 10225, 10224, 10223, 10222, 10221, 10220, 10219, 10218, 10217, 10216,
- 10315, 10314, 10313, 10312, 10311, 10310, 10309, 10308, 10307, 10306, 10305, 10304, 10303, 10302, 10301, 10300,
+    10100, 10101, 10102, 10103, 10104, 10105, 10106, 10107, 10108, 10109, 10110, 10111, 10112, 10113, 10114, 10115,
- 10215, 10214, 10213, 10212, 10211, 10210, 10209, 10208, 10207, 10206, 10205, 10204, 10203, 10202, 10201, 10200,
+    //  10115, 10114, 10113, 10112, 10111, 10110, 10109, 10108, 10107, 10106, 10105, 10104, 10103, 10102, 10101, 10100,
-  //================== 15528
+    10300, 10301, 10302, 10303, 10304, 10305, 10306, 10307, 10308, 10309, 10310, 10311, 10312, 10313, 10314, 10315,
- 10316, 10317, 10318, 10319, 10320, 10321, 10322, 10323, 10324, 10325, 10326, 10327, 10328, 10329, 10330, 10331,
+    //  10315, 10314, 10313, 10312, 10311, 10310, 10309, 10308, 10307, 10306, 10305, 10304, 10303, 10302, 10301, 10300,
-    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
+    10215, 10214, 10213, 10212, 10211, 10210, 10209, 10208, 10207, 10206, 10205, 10204, 10203, 10202, 10201, 10200,
-    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
+    //================== 15528
-    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,
+    10316, 10317, 10318, 10319, 10320, 10321, 10322, 10323, 10324, 10325, 10326, 10327, 10328, 10329, 10330, 10331,
-  //================== 334
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 20116, 20117, 20118, 20119, 20120, 20121, 20122, 20123, 20016, 20017, 20018, 20019, 20020, 20021, 20022, 20023,
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-  //================== 379
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 20000, 20001, 20002, 20003, 20004, 20005,    -1, 20007, 20008,    -1, 20010, 20011, 20012, 20013, 20014, 20015,
+    //================== 89
-  //================== 325
+    //  0     1      2      3      4      5      6      7      8      9     10     11     12     13     14     15
- 20100, 20101, 20102, 20103, 20104, 20105, 20106, 20107, 20108, 20109, 20110, 20111, 20112, 20113, 20114, 20115,
+    //  30004,    -1, 30003,    -1,    -1,    -1,    -1,    -1,     -1,   -1,    -1,    -1,    -1,    -1,    -1,    -1,
-  //================== 405
+    //================== 334
- 20006,    -1,    -1, 20009,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1,    -1
+    20116, 20117, 20118, 20119, -1, 20121, 20122, 20123, 20016, 20017, 20018, -1, 20020, 20021, 20022, 20023,
+    //================== 379
+    -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, -1, 20114, 20115,
+    //================== 405
+    //  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
-void PrintMapping(){
+// moved back to ch
+void PrintMapping()
+{
 
   int digiID = 0;
   int count = 0;
   printf("==================== ID-MAP: \n");
-  printf("%11s|", "");  for(int i = 0 ; i < 16; i++ ) printf("%7d|", i);
+  printf("%11s|", "");
+  for (int i = 0; i < 16; i++)
+    printf("%7d|", i);
   printf("\n");
-  for(int i = 0 ; i < 12 + 16*8; i++ ) printf("-");
+  for (int i = 0; i < 12 + 16 * 8; i++)
-  for(size_t i = 0 ; i < mapping.size(); i ++){
+    printf("-");
-    if( (i) % 16 == 0 ) {
+  for (size_t i = 0; i < mapping.size(); i++)
+  {
+    if ((i) % 16 == 0)
+    {
       printf("\n");
 
-      if( digiID < nBd ){
+      if (digiID < nBd)
-        if( board.at(digiID) > 1000 ) {
+      {
-          if( count == 3 ) digiID ++;
+        if (board.at(digiID) > 1000)
-          if( i % 64 == 0 ) {
+        {
+          if (count == 3)
+            digiID++;
+          if (i % 64 == 0)
+          {
             printf("%11d|", board.at(digiID));
             count = 0;
           }
-        }else{
+        }
-          if( count == 1 ) digiID ++;
+        else
-          if( i % 16 == 0 ) {
+        {
+          if (count == 1)
+            digiID++;
+          if (i % 16 == 0)
+          {
             printf("%11d|", board.at(digiID));
             count = 0;
           }
         }
       }
 
-      if( count != 0) printf("%11s|", "");
+      if (count != 0)
-      count ++;
+        printf("%11s|", "");
+      count++;
     }
 
     int typeID = mapping[i] / 10000;
-    int detID = (mapping[i] - typeID*10000 )/100;
+    int detID = (mapping[i] - typeID * 10000) / 100;
-    int ch = mapping[i] - typeID*10000 - detID * 100;
+    int ch = mapping[i] - typeID * 10000 - detID * 100;
 
-    if( mapping[i] == -1 ) {
+    if (mapping[i] == -1)
+    {
 
       printf("%7s|", "");
+    }
+    else
+    {
 
-    }else{
+      if (typeID == 0)
+      { // SX3
 
-      if( typeID == 0){ // SX3
+        printf("\033[36m%3d(%2d)\033[0m|", detID, ch);
-
+      }
-        printf("\033[36m%3d(%2d)\033[0m|", detID, ch); 
+      else if (typeID == 1)
-
+      { // QQQ
-      }else if( typeID == 1){ // QQQ
 
         printf("\033[91m%3d(%2d)\033[0m|", detID, ch);
-        
+      }
-      }else if( typeID == 2){ // PC
+      else if (typeID == 2)
+      { // PC
 
         printf("\033[35m%3d(%2d)\033[0m|", detID, ch);
-        
+      }
-      }else{
+      else if (typeID == 3)
-
+      { // MISC
 
+        printf("\033[33m%3d(%2d)\033[0m|", detID, ch);
       }
     }
   }
   printf("\n");
-  for(int i = 0 ; i < 12 + 16*8; i++ ) printf("-");
+  for (int i = 0; i < 12 + 16 * 8; i++)
+    printf("-");
   printf("\n");
-
 }
 
-
+void GenMapping(std::string mapFile)
-void GenMapping(std::string mapFile){
+{
-
 
   std::vector<int> map;
 
+  std::ifstream inputFile(mapFile); // Replace "your_file.txt" with the actual file path
 
-  std::ifstream inputFile(mapFile);  // Replace "your_file.txt" with the actual file path
+  if (!inputFile.is_open())
-
+  {
-  if (!inputFile.is_open()) {
     printf("Error: Could not open the file (%s).\n", mapFile.c_str());
-    return ;
+    return;
   }
 
   std::string line;
 
   // Read the file line by line
-  while (std::getline(inputFile, line)) {
+  while (std::getline(inputFile, line))
+  {
     std::vector<std::string> words;
     std::istringstream iss(line);
 
     // Extract words from the current line
-    while (true) {
+    while (true)
+    {
       std::string word;
-      if (!(iss >> word)) break;  // Break if there are no more words
+      if (!(iss >> word))
+        break; // Break if there are no more words
 
       word.erase(std::remove_if(word.begin(), word.end(), ::isspace), word.end());
       words.push_back(word);
-    
     }
 
-    if( atoi(words[0].c_str()) % 16 == 0 ) printf("=================\n");
+    if (atoi(words[0].c_str()) % 16 == 0)
+      printf("=================\n");
 
-
+    int detID = atoi(words[1].c_str()) * 100;
-    int detID = atoi(words[1].c_str())*100;
+    if (words.size() < 5)
-    if(words.size() < 5 ) printf(" hahhahha %s\n", line.c_str()); 
+      printf(" hahhahha %s\n", line.c_str());
-    if( words[2] == "BARREL" ) {
+    if (words[2] == "BARREL")
-      if( words[3] == "FRONTDOWN" ){
+    {
+      if (words[3] == "FRONTDOWN")
+      {
         int chID = atoi(words[4].c_str());
-        if( chID % 2 != 0 ) chID -= 1;
+        if (chID % 2 != 0)
+          chID -= 1;
         detID += chID;
       }
 
-      if( words[3] == "FRONTUP" ){
+      if (words[3] == "FRONTUP")
+      {
         int chID = atoi(words[4].c_str());
-        if( chID % 2 == 0 ) chID += 1;
+        if (chID % 2 == 0)
+          chID += 1;
         detID += chID;
       }
 
-      if( words[3] == "BACK") detID += atoi(words[4].c_str()) + 8;
+      if (words[3] == "BACK")
+        detID += atoi(words[4].c_str()) + 8;
     }
 
-    if( words[2] == "FQQQ" ) {
+    if (words[2] == "FQQQ")
+    {
       detID += 10000;
-      if( words[3] == "WEDGE") detID += atoi(words[4].c_str());
+      if (words[3] == "WEDGE")
-      if( words[3] == "RING") detID += atoi(words[4].c_str()) + 16;
+        detID += atoi(words[4].c_str());
+      if (words[3] == "RING")
+        detID += atoi(words[4].c_str()) + 16;
     }
 
-    if( words[2] == "PC" ) {
+    if (words[2] == "PC")
+    {
       detID += 20000;
-      if( words[3] == "ANODE") detID += atoi(words[4].c_str());
+      if (words[3] == "ANODE")
-      if( words[3] == "CATHODE") detID += 100 + atoi(words[4].c_str());
+        detID += atoi(words[4].c_str());
-
+      if (words[3] == "CATHODE")
+        detID += 100 + atoi(words[4].c_str());
     }
 
-    if( words[2] == "blank") {
+    if(words[2] == "MISC")
+    {
+      detID += 30000;
+    }
+
+    if (words[2] == "blank")
+    {
       detID = -1;
     }
 
@@ -234,29 +282,42 @@ void GenMapping(std::string mapFile){
   int digiID = 0;
   int count = 0;
   printf("===============================\n");
-  for( size_t i = 0; i < ((map.size() +15)/16) * 16; i++){
+  for (size_t i = 0; i < ((map.size() + 15) / 16) * 16; i++)
-    if( i % 16 == 0) {
+  {
+    if (i % 16 == 0)
+    {
       printf("\n");
-      if( digiID < nBd ){
+      if (digiID < nBd)
-        if( board.at(digiID) > 1000 ) {
+      {
-          if( count == 3 ) digiID ++;
+        if (board.at(digiID) > 1000)
-          if( i % 64 == 0 ) {
+        {
+          if (count == 3)
+            digiID++;
+          if (i % 64 == 0)
+          {
             printf("  //================== %d\n", board.at(digiID));
             count = 0;
           }
-        }else{
+        }
-          if( count == 1 ) digiID ++;
+        else
-          if( i % 16 == 0 ) {
+        {
+          if (count == 1)
+            digiID++;
+          if (i % 16 == 0)
+          {
             printf("  //================== %d\n", board.at(digiID));
             count = 0;
           }
         }
       }
-      count ++;
+      count++;
     }
-    if( i < map.size() ){
+    if (i < map.size())
+    {
       printf(" %5d,", map[i]);
-    }else{
+    }
+    else
+    {
       printf(" %5d,", -1);
     }
   }
@@ -265,13 +326,14 @@ void GenMapping(std::string mapFile){
   printf("sorting mapping and see if there any repeated\n");
   std::sort(map.begin(), map.end());
 
-  for( size_t i = 1; i < map.size(); i++){
+  for (size_t i = 1; i < map.size(); i++)
-    if( map[i] == -1 ) continue;
+  {
-    if( map[i] == map[i-1] ) printf("%5d \n", map[i]);
+    if (map[i] == -1)
+      continue;
+    if (map[i] == map[i - 1])
+      printf("%5d \n", map[i]);
   }
   printf("=========== Done. if nothing show, no repeat. \n");
-
-
 }
 
-#endif 
+#endif

mapping_old.txt

@@ -302,22 +302,22 @@
 301	1	FQQQ	RING	13
 302	1	FQQQ	RING	14
 303	1	FQQQ	RING	15
-304	1	FQQQ	WEDGE	15
+304	1	FQQQ	WEDGE	0
-305	1	FQQQ	WEDGE	14
+305	1	FQQQ	WEDGE	1
-306	1	FQQQ	WEDGE	13
+306	1	FQQQ	WEDGE	2
-307	1	FQQQ	WEDGE	12
+307	1	FQQQ	WEDGE	3
-308	1	FQQQ	WEDGE	11
+308	1	FQQQ	WEDGE	4
-309	1	FQQQ	WEDGE	10
+309	1	FQQQ	WEDGE	5
-310	1	FQQQ	WEDGE	9
+310	1	FQQQ	WEDGE   6
-311	1	FQQQ	WEDGE	8
+311	1	FQQQ	WEDGE   7
-312	1	FQQQ	WEDGE	7
+312	1	FQQQ	WEDGE   8
-313	1	FQQQ	WEDGE	6
+313	1	FQQQ	WEDGE   9
-314	1	FQQQ	WEDGE	5
+314	1	FQQQ	WEDGE   10
-315	1	FQQQ	WEDGE	4
+315	1	FQQQ	WEDGE   11
-316	1	FQQQ	WEDGE	3
+316	1	FQQQ	WEDGE   12
-317	1	FQQQ	WEDGE	2
+317	1	FQQQ	WEDGE   13
-318	1	FQQQ	WEDGE	1
+318	1	FQQQ	WEDGE   14
-319	1	FQQQ	WEDGE	0
+319	1	FQQQ	WEDGE   15
 320	2	FQQQ	RING	15
 321	2	FQQQ	RING	14
 322	2	FQQQ	RING	13
@@ -366,22 +366,22 @@
 365	2	FQQQ	WEDGE	2
 366	2	FQQQ	WEDGE	1
 367	2	FQQQ	WEDGE	0
-368	3	FQQQ	WEDGE	15
+368	3	FQQQ	WEDGE	0
-369	3	FQQQ	WEDGE	14
+369	3	FQQQ	WEDGE	1
-370	3	FQQQ	WEDGE	13
+370	3	FQQQ	WEDGE	2
-371	3	FQQQ	WEDGE	12
+371	3	FQQQ	WEDGE	3
-372	3	FQQQ	WEDGE	11
+372	3	FQQQ	WEDGE	4
-373	3	FQQQ	WEDGE	10
+373	3	FQQQ	WEDGE	5
-374	3	FQQQ	WEDGE	9
+374	3	FQQQ	WEDGE   6
-375	3	FQQQ	WEDGE	8
+375	3	FQQQ	WEDGE	7
-376	3	FQQQ	WEDGE	7
+376	3	FQQQ	WEDGE	8
-377	3	FQQQ	WEDGE	6
+377	3	FQQQ	WEDGE	9
-378	3	FQQQ	WEDGE	5
+378	3	FQQQ	WEDGE   10
-379	3	FQQQ	WEDGE	4
+379	3	FQQQ	WEDGE   11
-380	3	FQQQ	WEDGE	3
+380	3	FQQQ	WEDGE   12
-381	3	FQQQ	WEDGE	2
+381	3	FQQQ	WEDGE   13
-382	3	FQQQ	WEDGE	1
+382	3	FQQQ	WEDGE   14
-383	3	FQQQ	WEDGE	0
+383	3	FQQQ	WEDGE	15
 384	3	FQQQ	RING	0
 385	3	FQQQ	RING	1
 386	3	FQQQ	RING	2

pc_energy_calibration.dat

@@ -0,0 +1,48 @@
+0	7.569000E-06	0.000000E+00	1
+1	1.283082E-05	0.000000E+00	1
+2	1.283082E-05	0.000000E+00	1
+3	1.283082E-05	0.000000E+00	1
+4	1.283082E-05	0.000000E+00	1
+5	1.496409E-05	0.000000E+00	2
+6	2.036882E-05	0.000000E+00	1
+7	1.124799E-05	0.000000E+00	1
+8	1.123432E-05	0.000000E+00	1
+9	3.333333E-01	0.000000E+00	3
+10	1.292001E-05	0.000000E+00	1
+11	8.787520E-06	0.000000E+00	1
+12	3.333333E-01	0.000000E+00	3
+13	7.867300E-06	0.000000E+00	1
+14	6.707640E-06	0.000000E+00	1
+15	8.515706E-06	0.000000E+00	1
+16	1.041633E-05	0.000000E+00	1
+17	1.041633E-05	0.000000E+00	1
+18	1.283082E-05	0.000000E+00	1
+19	9.043133E-06	0.000000E+00	2
+20	1.046743E-05	0.000000E+00	1
+21	1.046743E-05	0.000000E+00	2
+22	1.047560E-05	0.000000E+00	2
+23	1.283082E-05	0.000000E+00	2
+24	1.008216E-05	0.000000E+00	1
+25	1.244045E-05	0.000000E+00	1
+26	1.162146E-05	0.000000E+00	1
+27	1.837130E-05	0.000000E+00	1
+28	1.490705E-05	0.000000E+00	1
+29	1.218593E-05	0.000000E+00	1
+30	1.193124E-05	0.000000E+00	1
+31	1.169320E-05	0.000000E+00	1
+32	1.204609E-05	0.000000E+00	1
+33	9.622476E-06	0.000000E+00	1
+34	1.010416E-05	0.000000E+00	1
+35	9.946100E-06	0.000000E+00	1
+36	1.245206E-05	0.000000E+00	1
+37	2.004189E-05	0.000000E+00	2
+38	1.101200E-05	0.000000E+00	1
+39	2.013155E-05	0.000000E+00	1
+40	1.503905E-05	0.000000E+00	1
+41	1.695527E-05	0.000000E+00	1
+42	1.255106E-05	0.000000E+00	1
+43	1.885628E-05	0.000000E+00	1
+44	3.987430E-05	0.000000E+00	2
+45	9.909176E-06	0.000000E+00	1
+46	9.432880E-06	0.000000E+00	1
+47	1.103287E-05	0.000000E+00	1

pccal/anode_gainmatch.C

@@ -0,0 +1,67 @@
+void anode_gainmatch(){
+    TFile *f = new TFile("../results_run16.root");
+
+    TH2F *pc_index_h2d = (TH2F*)(f->Get("hRawPC/PC_Index_Vs_Energy"));
+    std::cout << pc_index_h2d << std::endl;
+    TCanvas c("c1","c1",0,0,1600,800);
+    //TCanvas c_g("cg","cg",0,900,400,400);
+    c.Divide(2,1);
+    auto c1=c.cd(1);
+    pc_index_h2d->Draw("COLZ");
+    pc_index_h2d->GetYaxis()->SetRangeUser(240,5000);
+    auto c2=c.cd(2);
+    c2->SetLogy();
+    TH1F *h_1d=NULL;
+    int bin_index=1;
+    std::vector<std::vector<double>> all_peaks;
+    std::vector<int> found_wire_list;
+    while(bin_index<=24) {
+        h_1d=(TH1F*)(pc_index_h2d->ProjectionY("_py",bin_index,bin_index));
+        auto c1 = c.cd(1);
+        TBox box(pc_index_h2d->GetXaxis()->GetBinLowEdge(bin_index),0,pc_index_h2d->GetXaxis()->GetBinUpEdge(bin_index),pc_index_h2d->GetYaxis()->GetXmax());
+        box.SetFillColorAlpha(kYellow+3,0.3);
+        box.Draw("SAME");
+        c1->Modified(); c1->Update();
+        //while(c1->WaitPrimitive());
+
+        TSpectrum s;
+        auto c2 = c.cd(2);
+        h_1d->Draw();
+        c2->Modified(); c2->Update();
+        int npeaks = s.Search(h_1d,8,"",0.02); std::cout << npeaks << std::endl;
+        if(npeaks>=3) {
+            std::vector<double> xpeaks(s.GetPositionX(),s.GetPositionX()+npeaks);
+            std::sort(xpeaks.begin(),xpeaks.end(),std::greater());
+            found_wire_list.push_back((int)pc_index_h2d->GetXaxis()->GetBinCenter(bin_index));
+            all_peaks.push_back(xpeaks);
+        }
+        while(c2->WaitPrimitive());
+        bin_index++;
+    }
+    c.cd(2)->SetLogy(kFALSE);
+    gStyle->SetOptFit(1111);
+
+    std::ofstream outfile("anode_gm_coeffs.dat");
+    outfile <<  found_wire_list.at(0) << " "
+            << 1.0  << " "
+            << 0.0  << std::endl;
+
+    for(int i=0; i<all_peaks.size(); i++){
+        if(i==1) continue;
+        TGraph g(all_peaks.at(i).size(), all_peaks.at(i).data(), all_peaks.at(1).data());
+        auto c2 = c.cd(2);
+        g.SetMarkerStyle(20);
+        //g.Print();
+        g.Draw("AP");
+        g.Fit("pol1");
+        outfile <<  found_wire_list.at(i) << " "
+                << ((TF1*)g.FindObject("pol1"))->GetParameter(1) << " "
+                << ((TF1*)g.FindObject("pol1"))->GetParameter(0) << std::endl;
+        c2->Modified();
+        c2->Update();
+        while(c2->WaitPrimitive());
+    }
+    outfile.close();
+    f->Close();
+    return;
+}

pccal/anode_gm_coeffs.dat

@@ -0,0 +1,24 @@
+0 1 0
+0 0.937314 -16.871
+2 0.965461 -1.54376
+3 0.926501 -3.27662
+4 0.905634 2.54577
+5 0.905634 -11.0387
+6 0.853919 6.23079
+7 0.945588 -9.54044
+8 0.884454 -11.8262
+9 0.922501 -3.42538
+10 0.903053 9.28069
+11 0.914653 9.87642
+12 0.965332 13.2526
+13 0.923847 -3.41775
+14 0.93845 25.9901
+15 0.955424 12.324
+16 0.95116 4.99595
+17 0.910745 2.86648
+18 0.941376 4.57217
+19 0.871622 932.111
+20 1.00624 7.86358
+21 0.969834 -45.001
+22 0.89304 -31.5635
+23 0.933226 4.02193

pccal/cathode_gainmatch.C

@@ -0,0 +1,69 @@
+void cathode_gainmatch(){
+    TFile *f = new TFile("../results_run17.root");
+    TH2F *pc_index_h2d = (TH2F*)(f->Get("hRawPC/PC_Index_Vs_Energy"));
+    std::cout << pc_index_h2d << std::endl;
+    TCanvas c("c1","c1",0,0,1600,800);
+    //TCanvas c_g("cg","cg",0,900,400,400);
+    c.Divide(2,1);
+    auto c1=c.cd(1);
+    pc_index_h2d->Draw("COLZ");
+    pc_index_h2d->GetYaxis()->SetRangeUser(600,pc_index_h2d->GetYaxis()->GetXmax());
+    auto c2=c.cd(2);
+    c2->SetLogy();
+    TH1F *h_1d=NULL;
+    int bin_index=25;
+    std::vector<double> pulser_heights = {0.01,0.05,0.1,0.15,0.2,0.25,0.3,0.5};
+    std::vector<std::vector<double>> all_peaks;
+    std::vector<int> found_wire_list;
+    while(bin_index<=48) {
+        h_1d=(TH1F*)(pc_index_h2d->ProjectionY("_py",bin_index,bin_index));
+        auto c1 = c.cd(1);
+        TBox box(pc_index_h2d->GetXaxis()->GetBinLowEdge(bin_index),0,pc_index_h2d->GetXaxis()->GetBinUpEdge(bin_index),pc_index_h2d->GetYaxis()->GetXmax());
+        box.SetFillColorAlpha(kYellow+3,0.3);
+        box.Draw("SAME");
+        c1->Modified(); c1->Update();
+        //while(c1->WaitPrimitive());
+
+        TSpectrum s;
+        auto c2 = c.cd(2);
+        h_1d->Draw();
+        c2->Modified(); c2->Update();
+        int npeaks = s.Search(h_1d,20,"",0.1); std::cout << npeaks << std::endl;
+        if(npeaks==8) {
+            std::vector<double> xpeaks(s.GetPositionX(),s.GetPositionX()+npeaks);
+            for(int i=0; i<8; i++) {
+                std::cout << pc_index_h2d->GetXaxis()->GetBinCenter(bin_index) << " " << xpeaks.at(i) << " " << xpeaks.at(i)/pulser_heights.at(i) << std::endl;
+            }
+            std::sort(xpeaks.begin(),xpeaks.end(),std::greater());
+            found_wire_list.push_back((int)pc_index_h2d->GetXaxis()->GetBinCenter(bin_index));
+            all_peaks.push_back(xpeaks);
+        }
+        while(c2->WaitPrimitive());
+        bin_index++;
+    }
+    c.cd(2)->SetLogy(kFALSE);
+    gStyle->SetOptFit(1111);
+
+    std::ofstream outfile("cathode_gm_coeffs.dat");
+    outfile <<  found_wire_list.at(0) << " "
+            << 1.0  << " "
+            << 0.0  << std::endl;
+
+    for(int i=1; i<all_peaks.size(); i++){
+        TGraph g(all_peaks.at(i).size(), all_peaks.at(i).data(), all_peaks.at(0).data());
+        auto c2 = c.cd(2);
+        g.SetMarkerStyle(20);
+        //g.Print();
+        g.Draw("AP");
+        g.Fit("pol1");
+        outfile <<  found_wire_list.at(i) << " "
+                << ((TF1*)g.FindObject("pol1"))->GetParameter(1) << " "
+                << ((TF1*)g.FindObject("pol1"))->GetParameter(0) << std::endl;
+        c2->Modified();
+        c2->Update();
+        while(c2->WaitPrimitive());
+    }
+    outfile.close();
+    f->Close();
+    return;
+}