add README.md, a little clean up

.vscode/c_cpp_properties.json

@@ -0,0 +1,17 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/opt/root/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++14",
+            "intelliSenseMode": "linux-gcc-x64"
+        }
+    ],
+    "version": 4
+}

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+  "files.associations": {
+    "DecayFinder.C": "cpp",
+    "script.C": "cpp",
+    "peachCake.C": "cpp",
+    "PIDCutCreator.C": "cpp",
+    "plotPID.C": "cpp",
+    "PIDCutChecker.C": "cpp"
+  }
+}

DecayFinder.C

@@ -41,7 +41,7 @@ int numCut = 0;
 
 int numMatch = 0;
 
-vector<vector<int>> isotopes = {
+std::vector<std::vector<int>> isotopes = {
                             {19,  7}, {20,  7}, {21,  7},
                             {22,  8}, {23,  8}, {24,  8},
                   {24,  9}, {25,  9}, {26,  9}, {27,  9},           {29,  9},
@@ -53,7 +53,7 @@ vector<vector<int>> isotopes = {
                             {43, 15}, {44, 15}
                           }; 
 
-string isoSym(int Z){
+std::string isoSym(int Z){
   switch (Z) {
     case  3 : return "Li"; break;
     case  4 : return "Be"; break;

README.md

@@ -0,0 +1,98 @@
+# Introduction
+
+This is analysis code package for FRIB iFDS (FRIB Decay Staion initiative) experiment e21061. 
+
+My personal analysis logbook can be found in [Here](https://fsu-my.sharepoint.com/:p:/g/personal/rtang_fsu_edu/EdnWBI0J1g9FovvbKVvvgHoBoHy1rokedIF7f-Sr9XA6aA). The experimental setup can also be found there. 
+
+The elog can be found in [Here](https://fsunuc.physics.fsu.edu/elog/2022_05_e21062_FRIB/)
+
+Other information of the experiment can be found [Here](https://fsunuc.physics.fsu.edu/wiki/index.php/FRIB_FDSi_e21062)
+
+# Programs
+
+### convertPixie.sh
+
+convert NSCL-evt (raw data) to pixie-evt, ripe off the NSCL header.
+
+### convertRoot.sh
+
+convert pixie-evt to root with event building and mapping.h applied.
+
+### mapping.h
+
+Thsi define the mapping
+
+### peachCake.C/h
+
+Analysis class from TSelector. It do the primary analysis and apply corrections. It has option to output a new root file (with prefix "zzz_") with tree branches:
+
+- eventID | eventID 
+- runID | runID
+- AoQ  | A/Q value of PID
+- Z    | Z value of PID
+- crossTime | cross scint. T2 analog time
+- crossEnergy | croos scint. T2 analog energy
+- flag | event identification flag, +1 = has Beta, +2 = has Ions, +4 = has Beam
+- vetoFlag | veto, +1 = has Front trigger, +2 = has Rear trigger, +4 = has cross scint T2/B2 
+- xIons | x-pos of Ions
+- yIons | y-pos of Ions
+- xBeta | x-pos of beta
+- yBeta | y-pos of beta
+- dyIonsTime | dinode Ions time 
+- dyBetaTime | dinode Beta time
+- veto_f  | front veto detector energy
+- veto_r  | rear veto detector energy
+
+### DecayFinder.C/h
+
+The DecayFinder.C/h analysis the zzz_XXX files to obtain the decay curve for various isotopes. 
+
+### PIDCutCreator.C and PIDCutChecker.C
+
+Create/Check the PID cut.
+
+### scipt.C
+
+root macro to run analysis flow at once.
+
+# Analysis Flow
+
+1. The NSCL-evt file to pixie-evt file (nscl2pixie)
+2. Use the EventBuilder to build event and apply the mapping.h
+3. Use peachCake.C/h to analysis and output a new root file. 
+4. Use DecayFinder.C/h to obtain the decay histogram. 
+
+
+# inside the Armory
+
+### DataBlock.h
+This defines a class **DataBlock** to store data from pixie digitizer
+
+### nsclEvtReader.h
+
+This defines a class **NSCLEvtReader** to read NSCL evt file.
+
+### nscl2pixie
+
+This is a program to convert NSCL-evt file to evt file. Basically ripe out all NSCL header.
+
+The bash script **converPixie.sh** use this program to batch convert NSCL-evt to evt file.
+
+### evtReader.h
+
+This defines a class **evtReader** to read pixie evt file.
+
+### EventBuilder
+
+This is a program to convert pixie-evt to root file with event building. This program will apply the mapping.h. The output tree has branches
+
+1. evtID | event ID, unsigned int
+2. multi | event multiplicity, int
+3. detID | detector ID defined in mapping.h, int 
+4. e     | energy, double
+5. e_t   | timestamp, ULong64_t
+6. cfd   | fine time from cfd, int
+7. qdc   | 8-section of intergrated trace, int[8]
+8. multiClover | multiplicity of Clover 
+9. multiBeam  | multiplicity of beam-line detector
+10. runID | runID, e.g. run-0330-17 = 330*100 + 17 = 33017

peachCake.C

@@ -52,7 +52,7 @@ TH1F * hvetoFlag;
 //TObjArray * cutList;
 //int numCut = 0;
 
-vector<vector<double>> eCorr;
+std::vector<std::vector<double>> eCorr;
 
 double TOFCorrection(double x){   
   ///========= for run 250

peachCake.h

@@ -83,7 +83,7 @@ public :
    ClassDef(peachCake,0);
    
    TString pidCorrFileName;
-   vector<vector<double>> pidCorr;
+   std::vector<std::vector<double>> pidCorr;
    
    //=========== varibales in new tree
    bool saveNewTree;

script.C

@@ -2,7 +2,9 @@
 
 ///evtReader * evt = new evtReader("run-0238-00.evt", true);
 
-#include "peachCake.C+"
+#inlcude "TString.h"
+
+#include "peachCake.C+" // the + sign is make sure the peachCake is compiled.
 
 void script() {
 
@@ -18,19 +20,19 @@ void script() {
   
   // new beam 
   chain->Add("root_data/run-024[6-8]*.root");
-  chain->Add("root_data/run-0250*.root");
+  // chain->Add("root_data/run-0250*.root");
-  chain->Add("root_data/run-025[1-4].root");
+  // chain->Add("root_data/run-025[1-4].root");
-  chain->Add("root_data/run-025[6-9].root");
+  // chain->Add("root_data/run-025[6-9].root");
-  chain->Add("root_data/run-026[1-4]*.root");
+  // chain->Add("root_data/run-026[1-4]*.root");
-  chain->Add("root_data/run-0269*.root");
+  // chain->Add("root_data/run-0269*.root");
-  chain->Add("root_data/run-027[0-1]*.root");
+  // chain->Add("root_data/run-027[0-1]*.root");
-  chain->Add("root_data/run-028[3-4]*.root");
+  // chain->Add("root_data/run-028[3-4]*.root");
-  chain->Add("root_data/run-028[6-8]*.root");
+  // chain->Add("root_data/run-028[6-8]*.root");
-  chain->Add("root_data/run-0292*.root");
+  // chain->Add("root_data/run-0292*.root");
-  chain->Add("root_data/run-029[4-6]*.root");
+  // chain->Add("root_data/run-029[4-6]*.root");
-  chain->Add("root_data/run-029[8-9]*.root");
+  // chain->Add("root_data/run-029[8-9]*.root");
-  chain->Add("root_data/run-031*.root");
+  // chain->Add("root_data/run-031*.root");
-  chain->Add("root_data/run-032*.root");
+  // chain->Add("root_data/run-032*.root");
 
   
   //chain->Add("root_data/run-0246-00.root");