deleted: Armory/mass20.txt

modified:   TrackRecon.C paap gating
	modified:   run_17F.sh
	modified:   run_27Al.sh
	modified:   run_tr.sh
	modified:   scratch/overlay_2d.C

TrackRecon.C

@@ -45,7 +45,7 @@ bool process_alpha_proton_scattering = false,
      doPCSX3ClusterAnalysis = true,
      doPCQQQClusterAnalysis = true,
      doOldAnalysis = false,
-     BenchMark = false,
+     BenchMark = true,
      onewire_analysis = true,
      diagnostic_eplots = false,
      diagnostic_tplots = true,
@@ -3605,7 +3605,15 @@ void protonAlphaElastic_core(HistPlotter *plotter, const std::vector<Event> &Si_
 
       auto fillHypothesis = [&](bool alphaHyp)
       {
-        const std::string ejtag = (alphaHyp && sievent.Energy1 < 5) ? "_a" : "_p";
+        // const std::string ejtag = (alphaHyp && sievent.Energy1 < 5) ? "_a" : "_p";
+        std::string ejtag;
+        if (alphaHyp && sievent.Energy1 < 5)
+          ejtag = "_a";
+        else if (sievent.Energy1 >= 6.4 && sievent.Energy1 < 7.0)
+          ejtag = "_p";
+        else
+          ejtag = "_maybep";
+
         std::string pmlabel = misclabel + ejtag;
         TSpline3 *ej_fwd = alphaHyp ? MeV_to_cm_spl : MeV_to_cm_p_spl;
         TSpline3 *ej_inv = alphaHyp ? cm_to_MeV_spl : cm_to_MeVp_spl;
@@ -3684,9 +3692,9 @@ void protonAlphaElastic_core(HistPlotter *plotter, const std::vector<Event> &Si_
         }
       };
 
-      if (pid != SiPcPid::kAlpha)
+      if (pid != SiPcPid::kAlpha && sievent.Energy1 >= 6.4 && sievent.Energy1 < 7.0)
         fillHypothesis(false); // proton, or PID unavailable (legacy default)
-      if (pid == SiPcPid::kAlpha)
+      if (pid == SiPcPid::kAlpha && sievent.Energy1 < 6.2)
         fillHypothesis(true);
     };
 
@@ -3964,8 +3972,6 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
 
       plotter->Fill2D(rx + "_BeamEnergy_vs_VertexZ" + sfx, 800, -400, 400, 400, 0, beamE0, vertex_z, beam_energy_at_vertex, folderPrefix + globaltag + "_" + rx + "+misc_" + det);
 
-      bool trueProton = (beam_energy_at_vertex < 10.0);
-
       double ex_as_proton = 0.0, ex_as_alpha = 0.0;
       auto fillHypothesis = [&](double m3, double m4, TSpline3 *ej_fwd, TSpline3 *ej_inv, const std::string &ejtag)
       {
@@ -4016,28 +4022,25 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
           if (ebeam_kin_MeV > 0.0)
             plotter->Fill2D(rx + "_BeamEnergy_ETrack_vs_EKin" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_MeV, pmlabel);
-          if (ejtag == "_p")
+
+          if (beam_energy_at_vertex > 4.0 && beam_energy_at_vertex <= 12.0)
+          {
+            plotter->Fill2D(rx + "_EKin-ETrack2235keV_vs_phi" + ejtag + t + sfx, 45, -180, 180, 600, -20, 40, phi * 180 / M_PI, ebeam_kin_2235keV - beam_energy_at_vertex, pmlabel);
+          }
+          if (ejtag == "_p" && rx == "m27Alax")
           {
-            // if (beam_energy_at_vertex < 4.0 && beam_energy_at_vertex > 0.1)
             plotter->Fill2D(rx + "_ETrack_vs_EKinGS" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_GS, folderPrefix + "ETrackvsKin_assumed");
-            // else if (beam_energy_at_vertex <= 12.0)
             plotter->Fill2D(rx + "_ETrack_vs_EKin2235keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_2235keV, folderPrefix + "ETrackvsKin_assumed");
-            // else if (beam_energy_at_vertex < 24.0)
-            {
             plotter->Fill2D(rx + "_ETrack_vs_EKin3498keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_3498keV, folderPrefix + "ETrackvsKin_assumed");
             plotter->Fill2D(rx + "_ETrack_vs_EKin3774keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_3774keV, folderPrefix + "ETrackvsKin_assumed");
-            }
-            // else if (beam_energy_at_vertex <= 36.00)
             plotter->Fill2D(rx + "_ETrack_vs_EKin4809keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_4809keV, folderPrefix + "ETrackvsKin_assumed");
-            // else if (beam_energy_at_vertex < 42.0)
             plotter->Fill2D(rx + "_ETrack_vs_EKin5614keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_5614keV, folderPrefix + "ETrackvsKin_assumed");
-            // else
             plotter->Fill2D(rx + "_ETrack_vs_EKin6550keV" + ejtag + t + sfx, 400, 0, beamE0 * 1.5, 400, 0, beamE0 * 1.5,
                             beam_energy_at_vertex, ebeam_kin_6550keV, folderPrefix + "ETrackvsKin_assumed");
           }
@@ -4045,7 +4048,6 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
 
         plotter->Fill2D(rx + "_dE_E_Anode" + sfx, 400, 0, dEa_max, 800, 0, 40000, sievent.Energy1, anodeE, pmlabel);
 
-        plotter->Fill2D(rx + "_dE_E_Anode" + sfx + "_E<10MeV" + std::to_string(beam_energy_at_vertex < 10), 400, 0, dEa_max, 800, 0, 40000, sievent.Energy1, anodeE, pmlabel);
         if (cathodeE >= 0.0)
         {
           plotter->Fill2D(rx + "_dE_E_Cathode" + sfx, 400, 0, dEa_max, 800, 0, dEc_max, sievent.Energy1, cathodeE, pmlabel);
@@ -4055,7 +4057,7 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
         }
         plotter->Fill1D(rx + "_pczfix" + sfx, 600, -300, 300, pcz_fix, pmlabel);
         plotter->Fill2D(rx + "_Ef_vs_theta" + ejtag + sfx, 100, 0, 180, 800, 0, ef_max, theta * 180 / M_PI, Efix, pmlabel);
-        plotter->Fill2D(rx + "_Ex_vs_phi" + ejtag + sfx, 180, -180, 180, 600, -10, 20, phi * 180 / M_PI, Ex, pmlabel);
+        plotter->Fill2D(rx + "_Ex_vs_phi" + ejtag + sfx, 45, -180, 180, 600, -10, 20, phi * 180 / M_PI, Ex, pmlabel);
 
         for (const auto &pcevent : PC_Events)
         {
@@ -4065,6 +4067,7 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
             continue;
           plotter->Fill2D(rx + "_Ex_vs_dT" + ejtag + sfx, 500, -2000, 2000, 600, -10, 20, (sievent.Time1 - pcevent.Time1), Ex, pmlabel);
           plotter->Fill2D(rx + "_dEgasCalib_vs_dT" + ejtag + sfx, 500, -2000, 2000, 800, 0, 0.6, (sievent.Time1 - pcevent.Time1), anodeE_MeV, pmlabel);
+          plotter->Fill2D(rx + "_dEgasCalibCathode_vs_dT" + ejtag + sfx, 500, -2000, 2000, 800, 0, 0.6, (sievent.Time1 - pcevent.Time1), cathodeE_MeV, pmlabel);
         }
 
         if (dt_rf_mcp > -900000000)
@@ -4072,8 +4075,6 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
         plotter->Fill1D(rx + "_VertexReconZ" + sfx, 800, -400, 400, vertex_z, pmlabel);
 
         forEachTier(topo1, topo2, methodGroup, plot_with_tag);
-        if (trueProton)
-          plot_with_tag("trueProton"); // clean, alpha-free proton sub-sample
 
         // Gas segmentation validation
         PCCollect pcc = pcCollectionPath(r_rhoMin_fix, sievent.pos);
@@ -4095,7 +4096,7 @@ static void reaction_ax_core(HistPlotter *plotter, const std::vector<Event> &Si_
             plotter->Fill2D(rx + "_dEgasRaw_vs_VertexZ" + ejtag + sfx, 800, -400, 400, 800, 0, 20000, vertex_z, anodeE, pmlabel);
             plotter->Fill2D(rx + "_dEgasRaw_vs_theta" + ejtag + sfx, 180, 0, 180, 800, 0, 20000, theta * 180 / M_PI, anodeE, pmlabel);
             plotter->Fill2D(rx + "_dEgasCalib_vs_theta" + ejtag + sfx, 360, 0, 180, 800, 0, 0.6, theta * 180 / M_PI, anodeE_MeV, pmlabel);
-            plotter->Fill2D(rx + "_dEgasCalib_vs_phi" + ejtag + sfx, 90, -200, 200, 800, 0, 0.6, phi * 180 / M_PI, anodeE_MeV, pmlabel);
+            plotter->Fill2D(rx + "_dEgasCalib_vs_phi" + ejtag + sfx, 90, -180, 180, 800, 0, 0.6, phi * 180 / M_PI, anodeE_MeV, pmlabel);
             // if (anodeCh >= 0)
             //   plotter->Fill2D(rx + "_dEgasCalib_vs_E" + ejtag + sfx + "_anode" + pad2(anodeCh), 400, 0, ef_max, 800, 0, 0.6, sievent.Energy1, anodeE_MeV, pmlabel);
             plotter->Fill2D(rx + "_dEgasCalib_vs_Ex" + ejtag + sfx, 600, -10, 20, 800, 0, 0.6, Ex, anodeE_MeV, pmlabel);

run_17F.sh

@@ -35,7 +35,7 @@ export -f run_once
 export DATASET="17F"
 export PREFIX="Run_"
 export OUT_DIR="Output_17F"
-export source_vertex=-57.28
+export source_vertex=-200.0
 export CATHODE_GAIN=1
 # A1C1 cfrac low-band fold + z autocal (see TrackRecon.C Begin()). Defaults are the
 # 17F values; override here to re-tune without recompiling.

run_27Al.sh

@@ -23,8 +23,8 @@ process_run() {
     local infile="../ANASEN_analysis/data/${DATASET}_Data/${prefix}${wrun}_mapped.root"
     
     # Dynamically point to the correct output directory for this X/Y iteration
-    # local current_out_dir="Output_27Al_X${BEAM_AXIS_X}_Y${BEAM_AXIS_Y}"
     local current_out_dir="Output_27Al"
+    # local current_out_dir="Output_27Al_X${BEAM_AXIS_X}_Y${BEAM_AXIS_Y}"
     local out="${current_out_dir}/results_run${wrun}.root"
 
     root -q -l -b -x "$infile" \
@@ -47,9 +47,9 @@ export -f process_run
 #         BEAM_AXIS_Y=$y  
 
         # Define and create a clean directory name BEFORE running parallel tasks
-        # CURRENT_OUT_DIR="Output_27Al_X${BEAM_AXIS_X}_Y${BEAM_AXIS_Y}"
         CURRENT_OUT_DIR="Output_27Al"
-        # CURRENT_OUT_DIR="Output_27Al_run_48"
+        # CURRENT_OUT_DIR="Output_27Al_X${BEAM_AXIS_X}_Y${BEAM_AXIS_Y}"
+        rm -f ${OUT_DIR}/*.root
         mkdir -p "$CURRENT_OUT_DIR"
 
         echo "Running Eloss.py with a scaling parameter of $DEDX_SCALE"
@@ -57,9 +57,11 @@ export -f process_run
         python3 eloss_calculations/Eloss.py
         
         echo "Starting parallel processing..."
-        time parallel --bar -j 10 process_run ::: {24..41} 
+        time parallel --bar -j 12 process_run ::: {24..41} 44 45 46 {50..59}
-        time parallel --bar -j 10 process_run ::: 44 45 46 {50..59}
+        # time parallel --bar -j 10 process_run ::: {24..41} 
-        # time parallel --bar -j 10 process_run ::: 48 # pc without coincidence
+        # time parallel --bar -j 10 process_run ::: 44 45 46 {50..59}
+        time parallel --bar -j 1 process_run ::: 48 # pc without coincidence
+        mv "${CURRENT_OUT_DIR}/results_run048.root" "Output_27Al_run48/."
         # time parallel --bar -j 4 process_run ::: 62 63 66 67 68
         # time parallel --bar -j 1 process_run ::: 73
         # time parallel --bar -j 1 process_run ::: 74
@@ -67,7 +69,7 @@ export -f process_run
 
         echo "Merging files..."
         # Fixed: Safely merge using the clean directory variable (added -f to overwrite if re-running)
-        hadd -k -f -j 4 "${CURRENT_OUT_DIR}/output_27Al.root" "${CURRENT_OUT_DIR}/results_run"*.root
+        hadd -k -f -j 4 "${CURRENT_OUT_DIR}/Output_27Al.root" "${CURRENT_OUT_DIR}/results_run"*.root
 #     done
 # done
 

run_tr.sh

@@ -70,7 +70,7 @@ if [[ 1 -eq 1 ]]; then
     unset CATHODE_GAIN
     unset timecut_low
     unset pressure_in_torr
-    exit
+    # exit
 fi
 
 # --- Block 4: 17F Alpha+Gas Runs (18-21) ---
@@ -102,8 +102,8 @@ if [[ 1 -eq 1 ]]; then
     echo "Starting parallel processing for 27Al proton runs..."
 
     # process_run 18
-    parallel --bar -j 8 process_run ::: 15 {17..22}
+    # parallel --bar -j 8 process_run ::: 15 {17..22}
-    # parallel --bar -j 8 process_run :::  {17..22}
+    parallel --bar -j 8 process_run :::  {17..22}
     hadd -j 4 -k ${OUT_DIR}/Al_protons.root ${OUT_DIR}/results_run0{15..22}.root
     unset CATHODE_GAIN
     # exit

scratch/overlay_2d.C

@@ -48,6 +48,7 @@
 // Call, now just: rootFile, axis labels, and the drawing knobs --
 //
 //   root -l -b -q 'scratch/overlay_2d.C("Output_27Al/output_27Al.root", "Tracked Beam Energy (MeV)", "Kinematic Energy (MeV)", 2, 2, 2.0)'
+//   root -l -b -q 'scratch/overlay_2d.C("Output_27Al/output_27Al.root", "Tracked Beam Energy (MeV)", "Kinematic Energy (MeV)")'
 
 #include "TFile.h"
 #include "TH2.h"
@@ -59,7 +60,7 @@
 #include <vector>
 
 void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
-                int rebinX = 8, int rebinY = 8, double minz = 5.0)
+                int rebinX = 4, int rebinY = 4, double minz = 8.0)
 {
     gROOT->SetStyle("Plain");
     gStyle->SetOptStat(0);
@@ -67,7 +68,7 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
     // ---- Hardcoded selection: edit these to choose what to plot ----
     TString reaction = "m27Alax"; // reaction tag, e.g. "m27Alax", "m17Fax"
     TString ejtag = "p";          // ejectile: "p" (proton) or "a" (alpha)
-    TString topology = "a2c0";    // e.g. "a1c0", "a1c1", "a1c2fix", "a2c0", "a1c1c2"
+    TString topology = "a1c1_inband";    // e.g. "a1c0", "a1c1", "a1c2fix", "a2c0", "a1c1c2"
     TString detector = "sx3";     // "sx3" or "qqq"
 
     // Excited states to overlay, in the same order as labels[]/xlo[]/xhi[]
@@ -75,14 +76,16 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
     // note 3498's tag is lowercase "kev" (TrackRecon.C:4028), unlike every
     // other state's "keV". 3774 keV is deliberately left out (too close
     // to 3498, spin-parity predicts it's weaker anyway).
-    TString states[] = {"GS", "2235keV", "3498kev", "4809keV", "5614keV", "6550keV"};
+    TString states[] = {"GS", "2235keV", "3498keV", "4810keV", "6550keV"};
     TString labels[] = {"Ground State", "2.235 MeV", "3.498 MeV",
-                        "4.809 MeV", "5.614 MeV", "6.550 MeV"};
+                        "4.810 MeV", "6.550 MeV"};
 
     // Per-state display window (MeV), same order as states[] above.
     // See the header comment for why these are currently a no-op.
-    double xlo[] = {0, 4, 12, 24, 36, 42};
+    // double xlo[] = {0, 4, 12, 24, 36};
-    double xhi[] = {4, 12, 24, 36, 42, 90};
+    // double xhi[] = {4, 12, 24, 36, 90};
+    double xlo[] = {0, 4, 16, 28, 36};
+    double xhi[] = {4, 16, 28, 36, 90};
 
     const size_t nStates = sizeof(states) / sizeof(states[0]);
     if (sizeof(labels) / sizeof(labels[0]) != nStates ||
@@ -94,8 +97,18 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
         return;
     }
 
-    // Standard ANASEN color sequence
+    // Custom 12-color set (named ROOT colors + hex via TColor::GetColor), not the
-    int colors[] = {kBlack, kRed + 1, kAzure + 2, kGreen + 2, kMagenta + 1};
+    // ANASEN colors[40] sequence in TrackRecon.C -- 12 distinct colors is plenty of
+    // headroom for however many states get overlaid here without collisions.
+    int colors[] = {kBlack, kRed + 1, kAzure + 2, kGreen + 2, kMagenta + 1,
+                    TColor::GetColor("#3f90da"),
+                    TColor::GetColor("#bc1e00"),
+                    kGreen + 2,
+                    TColor::GetColor("#832db5"),
+                    kPink - 7,
+                    TColor::GetColor("#e76300"),
+                    TColor::GetColor("#b8ab6f")};
+    const int nColors = sizeof(colors) / sizeof(colors[0]);
     std::vector<TH2 *> hists;
     std::vector<TString> usedLabels;
 
@@ -144,6 +157,12 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
         hists[i]->SetMinimum(minz);
     }
 
+    double globalMax = 0;
+    for (size_t i = 0; i < hists.size(); i++)
+        globalMax = std::max(globalMax, hists[i]->GetMaximum());
+    for (size_t i = 0; i < hists.size(); i++)
+        hists[i]->SetMaximum(globalMax);
+
     TCanvas *c = new TCanvas("c", "", 1800, 1800);
     c->SetLeftMargin(0.15);
     c->SetBottomMargin(0.15);
@@ -152,7 +171,15 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
     c->SetGridx(1);
     c->SetGridy(1);
 
-    TLegend *leg = new TLegend(0.65, 0.75, 0.9, 0.9);
+    // Box height scales with the number of series instead of a fixed constant --
+    // at SetTextSize(0.03) a fixed 0.15 NDC-tall box only gives each of 6 rows
+    // 0.025 NDC, less than the text height itself, which is what made the legend
+    // look crowded. 0.045 NDC/row leaves real padding and stays correctly sized
+    // for however many states are overlaid.
+    const double legEntryHeight = 0.045;
+    const double legY2 = 0.9;
+    double legY1 = legY2 - legEntryHeight * hists.size();
+    TLegend *leg = new TLegend(0.65, legY1, 0.9, legY2);
     leg->SetBorderSize(1);
     leg->SetFillStyle(1001); // Solid background so grid doesn't bleed through
     leg->SetFillColor(kWhite);
@@ -160,7 +187,12 @@ void overlay_2d(TString rootFile, TString xAxisLabel, TString yAxisLabel,
 
     for (size_t i = 0; i < hists.size(); i++)
     {
-        hists[i]->SetFillColor(colors[i % 5]);
+        int color = colors[i % nColors];
+        hists[i]->SetMarkerColor(color);
+        hists[i]->SetLineColor(color);
+        hists[i]->SetFillColor(color);
+        hists[i]->SetFillStyle(1001); // solid fill for the "box" boxes below --
+                                      // "Plain" style's default fill is hollow
         if (i == 0)
         {
             hists[i]->SetTitle("");