void runAngleOpt() {

  gSystem->AddIncludePath("-I${ANITA_UTIL_INSTALL_DIR}/include");

  double startVal=0;               
  double stepSize=0.1;       
  double minVal=-2;           
  double maxVal=2;            
  Double_t p0 = 0;

  //Load libraries. Need to have ANITA_UTIL_INSTALL_DIR/lib and ROOTSYS/lib in the LD_LIBRARY_PATH               
  gSystem->Load("libfftw3.so");
  gSystem->Load("libMathMore.so");
  gSystem->Load("libPhysics.so");  
  gSystem->Load("libGeom.so");  
  gSystem->Load("libMinuit.so");  
  gSystem->Load("libRootFftwWrapper.so");         
  gSystem->Load("libAnitaEvent.so");      
  gSystem->Load("libAnitaCorrelator.so");

  AnitaGeomTool *fGeomTool = AnitaGeomTool::Instance();
  gSystem->CompileMacro("anglePlotterOpt.C","k");
  
  Double_t relDeltaOut=0;

  TMinuit *myMin = new TMinuit(1);
  myMin->SetObjectFit(anglePlotterOpt);
  myMin->SetFCN(iHateRoot);
  //setArray();

  for(int u = 0; u < 1; u++){

    int middle = 16;

      for(int y = 16; y <32; y++){

	int leftOpt, rightOpt;
	fGeomTool->getThetaPartners(middle,leftOpt,rightOpt); 


	myMin->DefineParameter(0, "antNum", middle, stepSize, minVal, maxVal);
	myMin->FixParameter(0);  
    
	myMin->DefineParameter(1, "deltaT", startVal, stepSize, minVal, maxVal);

  
	Double_t deltaT,deltaTErr;
  
	//*********MINUIT METHOD*******************
	myMin->SetPrintLevel(-1);
	myMin->Migrad();   
	myMin->GetParameter(1,deltaT,deltaTErr);

  

	setValue(rightOpt,deltaT);

	//	printArray();

	//	cout << middle << "  " << rightOpt << "  " << deltaT << endl;
  
	cout << "deltaTArrayMod[" << rightOpt << "] = " << deltaT << ";" << endl;

	middle = rightOpt;

      }

  }

  
  //   myMin->DeleteArrays();

  //   myMin->DeleteArrays();

  
}
void runQuickOptAllAntFixedZ() {
  
  gSystem->AddIncludePath("-I${ANITA_UTIL_INSTALL_DIR}/include");
  
  double startVal=0;               
  double stepSize=0.05;       
  double minVal=-0.5;           
  double maxVal=0.5;            
  Double_t p0 = 0;

  //Load libraries. Need to have ANITA_UTIL_INSTALL_DIR/lib and ROOTSYS/lib in the LD_LIBRARY_PATH               
  gSystem->Load("libfftw3.so");
  gSystem->Load("libMathMore.so");
  gSystem->Load("libPhysics.so");  
  gSystem->Load("libGeom.so");  
  gSystem->Load("libMinuit.so");  
  gSystem->Load("libRootFftwWrapper.so");         
  gSystem->Load("libAnitaEvent.so");      
  gSystem->Load("libAnitaCorrelator.so");

  AnitaGeomTool *fGeomTool = AnitaGeomTool::Instance();
  gSystem->CompileMacro("quickOptAllAntFixedZ.C","k");

  fillArrays(eventNumberIndex, thetaWaveIndex, phiWaveIndex, antIndex1, antIndex2, maxCorrTimeIndex, adjacent);
  
  Double_t relDeltaOut=0;

  TMinuit *myMin = new TMinuit(192);
  myMin->SetObjectFit(quickOptAllAntFixedZ);
  myMin->SetFCN(iHateRoot);
//   myMin->SetMaxIterations(2);
  //myMin->SetErrorDef(1000);

//   int ierflg;
//   double eps[1] = {2.};
//   myMin->mnexcm("SET EPS", eps, 1, ierflg);
  //setArray();

  double startValR[MAX_ANTENNAS] ={0};
  double startValZ[MAX_ANTENNAS] ={0};
  double startValPhi[MAX_ANTENNAS] ={0};
  double startValCableDelays[MAX_ANTENNAS] ={0};
  
  
  for(int y = 0; y <MAX_ANTENNAS; y++){
    
    char name[30];
    sprintf(name,"r%d",y);
    myMin->DefineParameter(y, name, startValR[y], stepSize, -0.1, 0.1);
    sprintf(name,"z%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS, name, startValZ[y], stepSize, -0.1, 0.1);
    myMin->FixParameter(y+MAX_ANTENNAS);
    sprintf(name,"phi%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS*2, name, startValPhi[y], stepSize, -0.1, 0.1);
    sprintf(name,"cable%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS*3, name, startValCableDelays[y], stepSize, -0.5, 0.5);
  }
  
  
  
  Double_t deltaR[MAX_ANTENNAS],deltaRErr[MAX_ANTENNAS];
  Double_t deltaZ[MAX_ANTENNAS],deltaZErr[MAX_ANTENNAS];
  Double_t deltaPhi[MAX_ANTENNAS],deltaPhiErr[MAX_ANTENNAS];
  Double_t deltaCableDelays[MAX_ANTENNAS],deltaCableDelaysErr[MAX_ANTENNAS];
  
  //*********MINUIT METHOD*******************
//   myMin->SetPrintLevel(-1);
  myMin->Migrad();
  //  int error_flag;
  //  myMin->mnexcm("MINOS",0,0,error_flag);  

  ofstream newfile("newLindaNumbersCableDelays_ALLANTENNAS_RMS_GRAD_FixedZ.txt");
  for(int u = 0; u <MAX_ANTENNAS; u++){
    myMin->GetParameter(u,deltaR[u],deltaRErr[u]);
    cout << "deltaR[" << u << "] = " << deltaR[u] << " +/- " << deltaRErr[u] << endl;
	
    
    myMin->GetParameter(u+MAX_ANTENNAS,deltaZ[u],deltaZErr[u]);
    cout << " deltaZ[" << u << "] = " << deltaZ[u] << " +/- " << deltaZErr[u] << endl;
    
    myMin->GetParameter(u+MAX_ANTENNAS*2,deltaPhi[u],deltaPhiErr[u]);
    cout << " deltaPhi[" << u << "] = " << deltaPhi[u] << " +/- " << deltaPhiErr[u] << endl;

    myMin->GetParameter(u+MAX_ANTENNAS*3,deltaCableDelays[u],deltaCableDelaysErr[u]);
    cout << " deltaCableDelays[" << u << "] = " << deltaCableDelays[u]  << " +/- " << deltaCableDelaysErr[u] << endl;
    
    newfile << u << "  " << deltaR[u]<< "  " << deltaZ[u]<< "  " << deltaPhi[u]<< "  " << deltaCableDelays[u] << endl;


  }
  
  
  cout << "Easy table" << endl;
  for(int u = 0; u <MAX_ANTENNAS; u++)  cout << u << " & " << deltaR[u]<< " & " << deltaZ[u]<< " & " << deltaPhi[u]<< " & " << deltaCableDelays[u] << endl;

  
}
void runTopRingOpt() {

  gSystem->AddIncludePath("-I${ANITA_UTIL_INSTALL_DIR}/include");

  double startVal=0;               
  double stepSize=0.1;       
  double minVal=-0.5;           
  double maxVal=0.5;            
  Double_t p0 = 0;

  //Load libraries. Need to have ANITA_UTIL_INSTALL_DIR/lib and ROOTSYS/lib in the LD_LIBRARY_PATH               
  gSystem->Load("libfftw3.so");
  gSystem->Load("libMathMore.so");
  gSystem->Load("libPhysics.so");  
  gSystem->Load("libGeom.so");  
  gSystem->Load("libMinuit.so");  
  gSystem->Load("libRootFftwWrapper.so");         
  gSystem->Load("libAnitaEvent.so");      
  gSystem->Load("libAnitaCorrelator.so");

  AnitaGeomTool *fGeomTool = AnitaGeomTool::Instance();
  gSystem->CompileMacro("topRingOpt.C","k");
  
  Double_t relDeltaOut=0;

  TMinuit *myMin = new TMinuit(150);
  myMin->SetObjectFit(topRingOpt);
  myMin->SetFCN(iHateRoot);
  //setArray();

  double startValDeltaT[16] ={0};
  double startValR[16] ={0};
  double startValPhi[16] ={0};

 //    startValDeltaT[0] =  -0.0519515;     startValR[0] =   -0.0101463;         startValPhi[0] =      -0.00473836 ;   
//     startValDeltaT[1] =     -0.0597062;   startValR[1] =      -0.02577;       startValPhi[1] =   0.00864501 ; 
//     startValDeltaT[2] =     -0.081435;     startValR[2] =     -0.000224044;    startValPhi[2] =   -0.000630649;
//     startValDeltaT[3] =     0.0118873;     startValR[3] =      0.019945;       startValPhi[3] =    0.014016;   
//     startValDeltaT[4] =      0.017917;      startValR[4] =     -0.00297559;    startValPhi[4] =    0.0224936 ;
//     startValDeltaT[5] =      0.0377119;     startValR[5] =     -0.014872;       startValPhi[5] =   0.0163349; 
//     startValDeltaT[6] =     -0.0426158;     startValR[6] =    -0.0562555;      startValPhi[6] =    0.0220065 ; 
//     startValDeltaT[7] =     -0.0221673;     startValR[7] =    -0.034104 ;      startValPhi[7] =    0.0158545 ; 
//     startValDeltaT[8] =      0.0263739;     startValR[8] =     0.00248804;      startValPhi[8] =    0.013246 ; 
//     startValDeltaT[9] =      -0.0938419;    startValR[9] =     -0.00344703;     startValPhi[9] =    -0.00718616; 
//     startValDeltaT[10] =      0.145264;      startValR[10] =     -0.0121874 ;     startValPhi[10] =     0.0156988 ;  
//     startValDeltaT[11] =      0.118105;      startValR[11] =     -0.0337033 ;      startValPhi[11] =   -0.00324182 ;
//     startValDeltaT[12] =      0.321805;      startValR[12] =     0.0134362  ;      startValPhi[12] =   -0.00190277 ;
//     startValDeltaT[13] =      0.0197693;     startValR[13] =     -0.000656063;      startValPhi[13] =   -0.0162318  ;
//     startValDeltaT[14] =      -0.115263;     startValR[14] =     0.0495637   ;      startValPhi[14] =   -0.0198119 ; 
//     startValDeltaT[15] =      -0.255707;   startValR[15] =     0.00189892  ;     startValPhi[15] =     0.0383932  ;
    


 for(int y = 0; y <16; y++){

   ofstream newfile("newSimonNumbers.txt");

   char name[30];
   sprintf(name,"r%d",y);
	myMin->DefineParameter(y, name, startValR[y], stepSize, minVal, maxVal);
   sprintf(name,"z%d",y);
	myMin->DefineParameter(y+16, name, startValDeltaT[y], stepSize, minVal, maxVal);
	   sprintf(name,"phi%d",y);
	myMin->DefineParameter(y+32, name, startValPhi[y], stepSize, minVal, maxVal);
 }


  
	Double_t deltaR[32],deltaRErr[32];
	Double_t deltaZ[32],deltaZErr[32];
	Double_t deltaPhi[32],deltaPhiErr[32];
  
	//*********MINUIT METHOD*******************
	myMin->SetPrintLevel(-1);
	myMin->Migrad();   

	for(int u = 0; u <16; u++){
	  myMin->GetParameter(u,deltaR[u],deltaRErr[u]);
	  //cout << "deltaR[" << u << "] = " << deltaR[u] ;
	
	
	  myMin->GetParameter(u+16,deltaZ[u],deltaZErr[u]);
	  //cout << " deltaZ[" << u << "] = " << deltaZ[u] ;
	
	  myMin->GetParameter(u+32,deltaPhi[u],deltaPhiErr[u]);
	  //cout << " deltaPhi[" << u << "] = " << deltaPhi[u] << ";" << endl;

	  newfile << u << "  " << deltaZ[u]<< "  " << deltaR[u]<< "  " << deltaPhi[u]<< "  " << 0 << endl;


	}


  
}
void runQuickOptAllAntStepsLDBHPOL() {
  
  gSystem->AddIncludePath("-I${ANITA_UTIL_INSTALL_DIR}/include");
  
  double startVal=0;               
  double stepSize=0.01;       
  double minVal=-0.5;           
  double maxVal=0.5;            
  Double_t p0 = 0;

  //Load libraries. Need to have ANITA_UTIL_INSTALL_DIR/lib and ROOTSYS/lib in the LD_LIBRARY_PATH               
  gSystem->Load("libfftw3.so");
  gSystem->Load("libMathMore.so");
  gSystem->Load("libPhysics.so");  
  gSystem->Load("libGeom.so");  
  gSystem->Load("libMinuit.so");  
  gSystem->Load("libRootFftwWrapper.so");         
  gSystem->Load("libAnitaEvent.so");      
  gSystem->Load("libAnitaCorrelator.so");

  AnitaGeomTool *fGeomTool = AnitaGeomTool::Instance();
  fGeomTool->useKurtAnita3Numbers(1);
  gSystem->CompileMacro("quickOptAllAntStepsLDBHPOL.C","k");

  fillArrays(eventNumberIndex, thetaWaveIndex, phiWaveIndex, antIndex1, antIndex2, maxCorrTimeIndex, adjacent);
  
  Double_t relDeltaOut=0;

  TMinuit *myMin = new TMinuit(192);
  myMin->SetObjectFit(quickOptAllAntStepsLDBHPOL);
  myMin->SetFCN(iHateRoot);
 //   myMin->SetMaxIterations(2);
  //myMin->SetErrorDef(1000);

//   int ierflg;
//   double eps[1] = {2.};
//   myMin->mnexcm("SET EPS", eps, 1, ierflg);
  //setArray();

  double minValCableDelays[MAX_ANTENNAS] ={0};
  double maxValCableDelays[MAX_ANTENNAS] ={0};

  Double_t deltaR[MAX_ANTENNAS] = {0};
  Double_t deltaRErr[MAX_ANTENNAS] = {0};
  Double_t deltaZ[MAX_ANTENNAS] = {0};
  Double_t deltaZErr[MAX_ANTENNAS] = {0};
  Double_t deltaPhi[MAX_ANTENNAS] = {0};
  Double_t deltaPhiErr[MAX_ANTENNAS] = {0};
  Double_t deltaCableDelays[MAX_ANTENNAS] = {0};
  Double_t deltaCableDelaysErr[MAX_ANTENNAS] = {0};

  //  Double_t globalDeltaz = 0.242575;
  Double_t globalDeltaz = 0.03;
  
  //Min global   deltaZ[] = -0.242575 +/- 0.00198264

  for(int y = 0; y <MAX_ANTENNAS; y++){
 
    deltaR[y] = 0;//-0.05;
    deltaCableDelays[y] = 0. - (y==47)*0.35;
    minValCableDelays[y] = deltaCableDelays[y] - 0.15;
    maxValCableDelays[y] = deltaCableDelays[y] + 0.15;
    deltaZ[y] = 0;//(y<16)*(-globalDeltaz) + (y>15)*globalDeltaz;

    char name[30];
    sprintf(name,"r%d",y);
    myMin->DefineParameter(y, name, deltaR[y], stepSize, -0.3, 0.3);
    sprintf(name,"z%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS, name, deltaZ[y], stepSize, -0.3, 0.3);
    sprintf(name,"phi%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS*2, name, deltaPhi[y], stepSize, -0.3, 0.3);
    sprintf(name,"cable%d",y);
    myMin->DefineParameter(y+MAX_ANTENNAS*3, name, deltaCableDelays[y], stepSize, minValCableDelays[y], maxValCableDelays[y]);
  }



  for(int y = 0; y <MAX_ANTENNAS; y++){
    myMin->FixParameter(y); // fixed R 
    myMin->FixParameter(y+MAX_ANTENNAS); // fixed Z
    myMin->FixParameter(y+MAX_ANTENNAS*2); // fixed phi
    //    myMin->FixParameter(y+MAX_ANTENNAS*3); // fixed t

  }

  myMin->FixParameter(MAX_ANTENNAS*3); // fixed t0

  //*********MINUIT METHOD*******************
//   myMin->SetPrintLevel(-1);
  myMin->Migrad();
  //  int error_flag;
  //  myMin->mnexcm("MINOS",0,0,error_flag);  



  for(int u = 0; u <MAX_ANTENNAS; u++){
    myMin->GetParameter(u+MAX_ANTENNAS*3,deltaCableDelays[u],deltaCableDelaysErr[u]);
    cout << " deltaCableDelays[" << u << "] = " << deltaCableDelays[u]  << " +/- " << deltaCableDelaysErr[u] << endl;

    //    myMin->GetParameter(u+MAX_ANTENNAS,deltaZ[u],deltaZErr[u]);
    //    cout << " deltaZ[" << u << "] = " << deltaZ[u] << " +/- " << deltaZErr[u] << endl;

  }

  cout << " ################## first step done ##############" << endl;

  TMinuit *myMin2 = new TMinuit(192);
  myMin2->SetObjectFit(quickOptAllAntStepsLDBHPOL);
  myMin2->SetFCN(iHateRoot);

  for(int y = 0; y <MAX_ANTENNAS; y++){    
    char name[30];
    sprintf(name,"r%d",y);
    myMin2->DefineParameter(y, name, deltaR[y], stepSize, -0.15, 0.15);
    sprintf(name,"z%d",y);
    myMin2->DefineParameter(y+MAX_ANTENNAS, name, deltaZ[y], stepSize, -0.3, 0.3);
    sprintf(name,"phi%d",y);
    myMin2->DefineParameter(y+MAX_ANTENNAS*2, name, deltaPhi[y], stepSize, -0.15, 0.15);
    sprintf(name,"cable%d",y);
    myMin2->DefineParameter(y+MAX_ANTENNAS*3, name, deltaCableDelays[y], stepSize, minValCableDelays[y], maxValCableDelays[y]);
  }


  for(int y = 0; y <MAX_ANTENNAS; y++){
    myMin2->FixParameter(y); // fixed R 
    myMin2->FixParameter(y+MAX_ANTENNAS); // fixed Z
    // myMin2->FixParameter(y+MAX_ANTENNAS*2); // fixed phi
    myMin2->FixParameter(y+MAX_ANTENNAS*3); // fixed t

  }

  myMin2->Migrad();


  for(int u = 0; u <MAX_ANTENNAS; u++){
    // myMin2->GetParameter(u,deltaR[u],deltaRErr[u]);
    // cout << "deltaR[" << u << "] = " << deltaR[u] << " +/- " << deltaRErr[u] << endl;
    myMin2->GetParameter(u+MAX_ANTENNAS*2,deltaPhi[u],deltaPhiErr[u]);
    cout << " deltaPhi[" << u << "] = " << deltaPhi[u] << " +/- " << deltaPhiErr[u] << endl;
  }


  cout << " ################## second step done ##############" << endl;

  TMinuit *myMin3 = new TMinuit(192);
  myMin3->SetObjectFit(quickOptAllAntStepsLDBHPOL);
  myMin3->SetFCN(iHateRoot);

  for(int y = 0; y <MAX_ANTENNAS; y++){    
    char name[30];
    sprintf(name,"r%d",y);
    myMin3->DefineParameter(y, name, deltaR[y], stepSize, -0.15,0.15);
    sprintf(name,"z%d",y);
    myMin3->DefineParameter(y+MAX_ANTENNAS, name, deltaZ[y], stepSize, -0.3, 0.3);
    sprintf(name,"phi%d",y);
    myMin3->DefineParameter(y+MAX_ANTENNAS*2, name, deltaPhi[y], stepSize, -0.3, 0.3);
    sprintf(name,"cable%d",y);
    myMin3->DefineParameter(y+MAX_ANTENNAS*3, name, deltaCableDelays[y], stepSize, minValCableDelays[y], maxValCableDelays[y]);
  }



  for(int y = 0; y <MAX_ANTENNAS; y++){
    // myMin3->FixParameter(y); // fixed R 
    myMin3->FixParameter(y+MAX_ANTENNAS); // fixed Z
    myMin3->FixParameter(y+MAX_ANTENNAS*2); // fixed phi
    myMin3->FixParameter(y+MAX_ANTENNAS*3); // fixed t

  }

  myMin3->Migrad();


  for(int u = 0; u <MAX_ANTENNAS; u++){
    // myMin3->GetParameter(u+MAX_ANTENNAS*2,deltaPhi[u],deltaPhiErr[u]);
    // cout << " deltaPhi[" << u << "] = " << deltaPhi[u] << " +/- " << deltaPhiErr[u] << endl;
    myMin3->GetParameter(u,deltaR[u],deltaRErr[u]);
    cout << "deltaR[" << u << "] = " << deltaR[u] << " +/- " << deltaRErr[u] << endl;

  }

  cout << " ################## third step done ##############" << endl;

  TMinuit *myMin4 = new TMinuit(192);
  myMin4->SetObjectFit(quickOptAllAntStepsLDBHPOL);
  myMin4->SetFCN(iHateRoot);

  for(int y = 0; y <MAX_ANTENNAS; y++){    

    sprintf(name,"r%d",y);
    myMin4->DefineParameter(y, name, deltaR[y],stepSize, -0.3, 0.3);
    sprintf(name,"z%d",y);
    myMin4->DefineParameter(y+MAX_ANTENNAS, name, deltaZ[y], stepSize, -0.15, 0.15);
    sprintf(name,"phi%d",y);
    myMin4->DefineParameter(y+MAX_ANTENNAS*2, name, deltaPhi[y], stepSize, -0.3, 0.3);
    sprintf(name,"cable%d",y);
    myMin4->DefineParameter(y+MAX_ANTENNAS*3, name, deltaCableDelays[y], stepSize, minValCableDelays[y], maxValCableDelays[y]);
  }


  for(int y = 0; y <MAX_ANTENNAS; y++){
     myMin4->FixParameter(y); // fixed R 
     //myMin4->FixParameter(y+MAX_ANTENNAS); // fixed Z
     myMin4->FixParameter(y+MAX_ANTENNAS*2); // fixed phi
     myMin4->FixParameter(y+MAX_ANTENNAS*3); // fixed t

  }

  //*********MINUIT METHOD*******************
//   myMin->SetPrintLevel(-1);
  myMin4->Migrad();
  //  int error_flag;
  //  myMin->mnexcm("MINOS",0,0,error_flag);  

  std::time_t now = std::time(NULL);
  std::tm * ptm = std::localtime(&now);
  char buffer[32];
  std::strftime(buffer, 32, "%Y_%m_%d_time_%H_%M_%S", ptm); 


  ofstream newfile(Form("RETEST/newLindaNumbers_LDBHPOL_NEW12_fixedBug_%s.txt", buffer));
  for(int u = 0; u <MAX_ANTENNAS; u++){
    myMin4->GetParameter(u,deltaR[u],deltaRErr[u]);
    cout << "deltaR[" << u << "] = " << deltaR[u] << " +/- " << deltaRErr[u] << endl;
	
    
    myMin4->GetParameter(u+MAX_ANTENNAS,deltaZ[u],deltaZErr[u]);
    cout << " deltaZ[" << u << "] = " << deltaZ[u] << " +/- " << deltaZErr[u] << endl;
    
    myMin4->GetParameter(u+MAX_ANTENNAS*2,deltaPhi[u],deltaPhiErr[u]);
    cout << " deltaPhi[" << u << "] = " << deltaPhi[u] << " +/- " << deltaPhiErr[u] << endl;

    myMin4->GetParameter(u+MAX_ANTENNAS*3,deltaCableDelays[u],deltaCableDelaysErr[u]);
    cout << " deltaCableDelays[" << u << "] = " << deltaCableDelays[u]  << " +/- " << deltaCableDelaysErr[u] << endl;
    
    newfile << u << "  " << deltaR[u]<< "  " << deltaZ[u]<< "  " << deltaPhi[u]<< "  " << deltaCableDelays[u] << endl;


  }
  
  
  cout << "Easy table" << endl;
  for(int u = 0; u <MAX_ANTENNAS; u++)  cout << u << " & " << deltaR[u]<< " & " << deltaZ[u]<< " & " << deltaPhi[u]<< " & " << deltaCableDelays[u] << endl;

  
}