//************************************************
// Author: Federica Lionetto
// Created on: 24/02/2015
//************************************************

/*
CCE reads all the ROOT files of a given CCE data taking and calculates the CCE.

The CCE data taking is identified by the following information:
- <sensor>, that is, the type of sensor (Hans410, ...);
- <filename>, that is, the filename excluding the position value and the run type.
- <z>, that is, the position along z;
- <firstx>, that is, the first position along x;
- <lastx>, that is, the last position along x;
- <stepx>, that is, the step between two subsequent data acquisitions in x (1 step = 5 microns).

Compile with:

make

Run with:

./CCE [sensor] [filename] [z] [firstx] [lastx] [stepx] [additional folder]

For example:

./CCE Hans410 ProcessRawData-20141121 0 0 75 3

A folder named AnalysisResults will be created in a fixed location and a ROOT file will be saved in there. A folder named Figures will be created inside the folder named AnalysisResults, with some monitoring plots.

If needed, an additional folder can be specified, that will be created inside the folder named AnalysisResults.
*/

#include "../Tools/Lib.C"
#include "../Tools/lhcbStyle.C"
#include "../Tools/Style.C"

#include "../Tools/FindStrip.C"
#include "../Tools/SCurve.C"
#include "../Tools/Par.C"

void CCE(char *sensor, char *filename, const Float_t z, const Float_t firstx, const Float_t lastx, const Float_t stepx, char *externalPath=0);

int main(int argc, char *argv[])
{
  getLHCbStyle();
  PersonalStyle();

  if ((argc == 2) && (string(argv[1]) == "--info"))
  {
    cout << "**************************************************" << endl;

    cout << "Some comments." << endl;
    
    cout << "**************************************************" << endl;

    return 0;
  }
  else if (argc < 7)
  {
    cout << "**************************************************" << endl;

    cout << "Error! Arguments missing..." << endl;
    cout << "Please use the following format:" << endl;
    cout << "./CCE [1] [2] [3] [4] [5] [6] [7]" << endl;
    cout << "with:" << endl;
    cout << "[1] = Type of sensor (Hans410, ...);" << endl;
    cout << "[2] = Filename, excluding the position value and the run type;" << endl;
    cout << "[3] = Position along z;" << endl;
    cout << "[4] = First position along x;" << endl;
    cout << "[5] = Last position along x" << endl;
    cout << "[6] = Step between two subsequent data acquisitions (1 step = 5 microns);" << endl;
    cout << "[7] = Additional folder, optional." << endl;
    cout << "Type ./CCE --info for more information." << endl;
    
    cout << "**************************************************" << endl;

    return 0;
  }
  else
  {
    cout << "Type of sensor: " << argv[1] << endl;
    cout << "Filename: " << argv[2] << endl;
    cout << "Position along z: " << argv[3] << endl;
    cout << "First position along x: " << argv[4] << endl;
    cout << "Last position along x: " << argv[5] << endl;
    cout << "Step between two subsequent data acquisitions: " << argv[6] << endl;
    if (argc == 7)
      CCE(argv[1],argv[2],atoi(argv[3]),atoi(argv[4]),atoi(argv[5]),atoi(argv[6]));
    else if (argc == 8)
      CCE(argv[1],argv[2],atoi(argv[3]),atoi(argv[4]),atoi(argv[5]),atoi(argv[6]),argv[7]);
    else
    {
      cout << "Error! Too many arguments given..." << endl;
      
      return 0;
    }
    
    return 0;  
  }
}

void CCE(char *sensor, char *filename, const Float_t z, const Float_t firstx, const Float_t lastx, const Float_t stepx, char *externalPath)
{
  cout << "**************************************************" << endl;
  cout << "Measuring CCE..." << endl;
  cout << "**************************************************" << endl;

  // Do not comment this line.
  gROOT->ProcessLine("#include <vector>");

  // Do some fanciness to get the directory right.
  // string inputDirectory = "/disk/groups/hep/flionett/TestStand/AnalysisResults/"+string(sensor)+"/CCE";
  // CHANGE inputDirectory!!!
  string inputDirectory = "/disk/groups/hep/flionett/TestStand/AnalysisResults/"+string(sensor)+"/Alignment";  
  string outputDirectory = "/disk/groups/hep/flionett/TestStand/AnalysisResults/"+string(sensor)+"/CCE";
  if (externalPath!=0)
    outputDirectory = string(outputDirectory+"/"+externalPath);
  cout << "The input directory is: " << inputDirectory << endl;
  cout << "The output directory is: " << outputDirectory << endl;

  // Create the outputDirectory directory if it does not exist.
  string path_to_make = "mkdir -p "+outputDirectory;
  system(path_to_make.c_str());

  ostringstream convertx;
  ostringstream convertz;
  string tempx;
  string tempz;

  convertz.str("");
  convertz << z;
  tempz = convertz.str();  

  cout << "Figures stored in: " << outputDirectory+"/Figures/"+filename+"-"+tempz+"z" << endl;

  // Create a directory named Figures inside the directory named outputDirectory if it does not exist.
  string path_to_make_figures = "mkdir -p "+outputDirectory+"/Figures/"+filename+"-"+tempz+"z";
  system(path_to_make_figures.c_str());

  TString path_to_figures = (string(path_to_make_figures)).substr((string(path_to_make_figures)).find_last_of(' ')+1);

  int strip;
  string direction;

  char char_input_ROOT[200];
  string input_ROOT;
  string output_ROOT;

  string inputFindStrip;
  string outputFindStrip;

  Float_t noise[N];

  const Int_t steps = (Int_t)((lastx-firstx)/stepx+1);
  Float_t x[steps];
  Float_t signalOverNoise1Left[steps];
  Float_t signalOverNoise1Right[steps];
  Float_t signalOverNoise2[steps];
  Float_t signalOverNoise4[steps];

  // Parameters of the fitting functions.
  Float_t aLeft;
  Float_t bLeft;
  Float_t muLeft;
  Float_t sigmaLeft;

  Float_t aRight;
  Float_t bRight;
  Float_t muRight;
  Float_t sigmaRight;

  // Uncertainties on the parameters of the fitting functions.
  // u = uncertainty.
  Float_t uaLeft;
  Float_t ubLeft;
  Float_t umuLeft;
  Float_t usigmaLeft;

  Float_t uaRight;
  Float_t ubRight;
  Float_t umuRight;
  Float_t usigmaRight;

  // Open output ROOT file.
  output_ROOT = outputDirectory+"/CCE-"+filename+"-"+tempz+"z.root";
  TFile *output = TFile::Open(TString(output_ROOT),"RECREATE");

  for (Int_t step=0;step<steps;step++) {
    x[step] = firstx+step*stepx;

    // Open input data ROOT files.
    // I did not find a better way to create a string containing the bias voltage.
    sprintf(char_input_ROOT,"%s/%s-%dx-%dz-las.root",inputDirectory.c_str(),filename,(int)x[step],(int)z);
    input_ROOT = string(char_input_ROOT);
    // Check that the filename provided corresponds to a ROOT file.
    int found = input_ROOT.find(".root");
    if (found==string::npos)  {
      cout << "Error! The filename provided is not associated to a ROOT file." << endl;
      return;
    }

    cout << "Open ROOT file #" << step+1 << ": " << input_ROOT << endl;
    TFile *input = TFile::Open(TString(input_ROOT));

    inputFindStrip = input_ROOT;
    convertx.str("");
    convertx << x[step];
    tempx = convertx.str();
    outputFindStrip = outputDirectory+"/FindStrip-"+filename+"-"+tempx+"x-"+tempz+"z-las.root";
    FindStrip(inputFindStrip,outputFindStrip,path_to_figures,&strip,&direction);
  
    cout << "Histograms: " << endl;
    cout << Form("hADCPedSub%d",strip) << endl;
    cout << Form("hADCPedSub%d",strip+NSkip) << endl;
    cout << Form("hADCPedSub%d",strip-NSkip) << endl;
    cout << Form("hADCPedSub%d",strip-2*NSkip) << endl;
    cout << Form("hADCPedSub%d",strip+2*NSkip) << endl;

    // Find the pedestal run from which pedestals have been calculated and get the noise of each Beetle channel.
    string *PedFilename = new string();
    TBranch *b_PedFilename = 0;

    TTree *Header = (TTree *)input->Get("Header");
    int EventsHeader = Header->GetEntries();
    if (EventsHeader != 1)
    {
      cout << "Error! The ROOT file has been corrupted..." << endl;
      
      return ;
    }
    else 
    {
      Header->SetBranchAddress("PedFilename",&PedFilename,&b_PedFilename);
      
      Header->GetEntry();

      cout << "Pedestals calculated from: " << *PedFilename << endl; 

      // Get the noise of each Beetle channel.
      // Open input pedestal&noise text file.
      FILE *inputText = fopen(PedFilename->c_str(),"r");
      
      // Read noise.  
      for (int iChannel=0; iChannel<N; ++iChannel) {
	fscanf(inputText,"%*d%*c%*f%*c%f%*c",&(noise[iChannel]));
	// cout << iChannel << ", " << noise[iChannel] << endl;
      }
  
      // Close input pedestal&noise text file.
      fclose(inputText);
    }

    // Beetle channels where to look for signal.
    int ch1 = strip;
    int ch2 = strip+NSkip;
    int ch3 = strip-NSkip;
    int ch4;   
    if (direction == "left")
      ch4 = strip-2*NSkip;
    else if (direction == "right")
      ch4 = strip+2*NSkip;
    
    // Four adjacent strips.
    TH1D *hist1 = (TH1D *)input->Get(Form("hADCPedSub%d",ch1));
    TH1D *hist2 = (TH1D *)input->Get(Form("hADCPedSub%d",ch2));
    TH1D *hist3 = (TH1D *)input->Get(Form("hADCPedSub%d",ch3));
    TH1D *hist4 = (TH1D *)input->Get(Form("hADCPedSub%d",ch4));

    if (direction == "left") {
      signalOverNoise1Left[step] = (hist3->GetMean())/noise[ch3];
      signalOverNoise1Right[step] = (hist1->GetMean())/noise[ch1];
      signalOverNoise2[step] = (hist1->GetMean())/noise[ch1]+(hist3->GetMean())/noise[ch3];
    }
    else if (direction == "right") {
      signalOverNoise1Left[step] = (hist1->GetMean())/noise[ch1];
      signalOverNoise1Right[step] = (hist2->GetMean())/noise[ch2];
      signalOverNoise2[step] = (hist1->GetMean())/noise[ch1]+(hist2->GetMean())/noise[ch2];
    }
    signalOverNoise4[step] = (hist1->GetMean())/noise[ch1]+(hist2->GetMean())/noise[ch2]+(hist3->GetMean())/noise[ch3]+(hist4->GetMean())/noise[ch4];

    // Close input data ROOT files.
    input->Close();
  }

  output->cd();

  for (Int_t step=0;step<steps;step++)
    x[step] = x[step]*5.; // One step corresponds to 5 microns.

  // Four adjacent strips.
  TGraph *gcheckAlignmentSignalOverNoise4 = new TGraph(steps,x,signalOverNoise4);
  InitGraph(gcheckAlignmentSignalOverNoise4,"Check alignment - 4 adjacent strips","x (#mum)","S/N");

  // Fit the two s-curves and set the range for the CCE measurement.
  // The range for the CCE measurement is defined as [muRight+(muLeft-muRight)*0.05,muLeft-(muLeft-muRight)*0.05].
  // This is not used at the moment!!!

  // Right side (increasing y).
  Float_t minRight;
  Float_t maxRight;
  
  // Left side (decreasing y).
  Float_t minLeft;
  Float_t maxLeft;
  
  // Array of the parameters necessary for fitting with fitRight and fitLeft.
  // The array contains par0, par1, par2, par3, par0low, par0high, par1low, par1high, par2low, par2high, par3low, par3high for fitRight and the same for fitLeft.
  const Int_t lengthParSCurves = 24;
  Float_t parSCurves[lengthParSCurves];
  
  assignParInfoSCurves(string(filename),z,&minRight,&maxRight,&minLeft,&maxLeft,parSCurves,lengthParSCurves);

  // Right side (increasing y).
  TF1 *fitSCurveRight = new TF1("fitSCurveRight",fRight,minRight,maxRight,4);
  fitSCurve(r,gcheckAlignmentSignalOverNoise4,fitSCurveRight,parSCurves,lengthParSCurves,&aRight,&muRight,&sigmaRight,&bRight,&uaRight,&umuRight,&usigmaRight,&ubRight);

  // Left side (decreasing y).
  TF1 *fitSCurveLeft = new TF1("fitSCurveLeft",fLeft,minLeft,maxLeft,4);
  fitSCurve(l,gcheckAlignmentSignalOverNoise4,fitSCurveLeft,parSCurves,lengthParSCurves,&aLeft,&muLeft,&sigmaLeft,&bLeft,&uaLeft,&umuLeft,&usigmaLeft,&ubLeft);

  TCanvas *ccheckAlignmentSignalOverNoise4 = new TCanvas(Form("ccheckAlignmentSignalOverNoise4-%s",filename),"",400,300);
  DrawGraphFunc2(ccheckAlignmentSignalOverNoise4,gcheckAlignmentSignalOverNoise4,fitSCurveRight,fitSCurveLeft,"AP",path_to_figures);

  Float_t zMicrons = z*5.; // One step corresponds to 5 microns.

  cout << "Right side, z = " << zMicrons << ", a = " << aRight << ", mu = " << muRight << ", sigma = " << sigmaRight << ", b = " << bRight << endl;
  
  cout << "Left side, z = " << zMicrons << ", a = " << aLeft << ", mu = " << muLeft << ", sigma = " << sigmaLeft << ", b = " << bLeft << endl;
  
  Float_t minPosCCE = muRight+(muLeft-muRight)*0.05;
  Float_t maxPosCCE = muLeft-(muLeft-muRight)*0.05; 

  // Set the four Beetle channels that will form the cluster where to look for collected charge.
  // These are ch1, ch2, ch3, and ch4.

  // CCE.
  // Charge collected by the different strips.
  TCanvas *cCCESignalOverNoise = new TCanvas(Form("cCCESignalOverNoise-%s",filename),"",550,300);

  TMultiGraph *mgCCESignalOverNoise = new TMultiGraph();

  TGraph *gCCESignalOverNoise1Left = new TGraph(steps,x,signalOverNoise1Left);
  TGraph *gCCESignalOverNoise1Right = new TGraph(steps,x,signalOverNoise1Right);
  TGraph *gCCESignalOverNoise2 = new TGraph(steps,x,signalOverNoise2);
  TGraph *gCCESignalOverNoise4 = new TGraph(steps,x,signalOverNoise4);

  InitGraph(gCCESignalOverNoise1Left,"CCE","x (#mum)","S/N");
  InitGraph(gCCESignalOverNoise1Right,"CCE","x (#mum)","S/N");
  InitGraph(gCCESignalOverNoise2,"CCE","x (#mum)","S/N");
  InitGraph(gCCESignalOverNoise4,"CCE","x (#mum)","S/N");

  gCCESignalOverNoise1Left->SetMarkerColor(kMagenta);
  gCCESignalOverNoise1Right->SetMarkerColor(kOrange);
  gCCESignalOverNoise2->SetMarkerColor(kRed);
  gCCESignalOverNoise4->SetMarkerColor(kRed+2);

  gCCESignalOverNoise1Left->SetLineColor(kMagenta);
  gCCESignalOverNoise1Right->SetLineColor(kOrange);
  gCCESignalOverNoise2->SetLineColor(kRed);
  gCCESignalOverNoise4->SetLineColor(kRed+2);

  gCCESignalOverNoise1Left->SetLineWidth(2);
  gCCESignalOverNoise1Right->SetLineWidth(2);
  gCCESignalOverNoise2->SetLineWidth(2);
  gCCESignalOverNoise4->SetLineWidth(2);

  TLegend *legCCESignalOverNoise = CreateLegend4(gCCESignalOverNoise1Left,"left strip",gCCESignalOverNoise1Right,"right strip",gCCESignalOverNoise2,"2 strips",gCCESignalOverNoise4,"4 strips","lpw",0.72,0.62,0.92,0.92);

  mgCCESignalOverNoise->Add(gCCESignalOverNoise1Left);
  mgCCESignalOverNoise->Add(gCCESignalOverNoise1Right);
  mgCCESignalOverNoise->Add(gCCESignalOverNoise2);
  mgCCESignalOverNoise->Add(gCCESignalOverNoise4);

  DrawGraphCompare(cCCESignalOverNoise,mgCCESignalOverNoise,legCCESignalOverNoise,"CCE","x (#mum)","S/N","APCE",path_to_figures);

  // Write output ROOT file.
  output->Write();

  // Close output ROOT file.
  output->Close();

  return;
}