castor-datafileConversionEx.cc

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#include "gVariables.hh"
#include "gOptions.hh"
#include "iDataFilePET.hh"
#include "sOutputManager.hh"
#include "sScannerManager.hh"
#include <iomanip> //std::setprecision

#ifdef CASTOR_ROOT
  #include "TROOT.h"
  #include "TApplication.h"
  #include "TGClient.h"
  #include "TCanvas.h"
  #include "TSystem.h"
  #include "TTree.h"
  #include "TBranch.h"
  #include "TFile.h"
#endif

void ShowHelp(int a_returnCode)
{
  cout << endl;
  cout << "NOTE : This program is an example code providing guidance regarding how to generate a PET CASToR datafile from any system datafile " << endl;
  cout << "       It does NOT perform any conversion by itself and must be adjusted to the conversion of any system dataset !" << endl;
  cout << endl;
  cout << endl;
  cout << "Usage:  castor-datafileConversionEx -ih input_datafile : (if datafile is histogram mode)" << endl;
  cout << "                                    -il input_datafile : (if datafile is list-mode)" << endl;
  cout << "                                    -o  output_datafile" << endl;
  cout << "                                    -s  scanner_alias "<< endl;
  cout << "                                   [-nc  norm_factors_file" << endl;
  cout << "                                   [-sc  scat_factors_file" << endl;
  cout << "                                   [-rc  rdm_factors_file" << endl;
  cout << "                                   [-ac  atn_factors_file" << endl;
  cout << "                                   [-cf  calibration factor" << endl;
  cout << "                                   [-ist isotope_alias" << endl;
  //cout << "                                [-poi  flag for POI]" << endl;
  //cout << "                                [-tof  flag for TOF]" << endl;
  cout << "                                   [-vb   verbosity]" << endl;
  cout << endl;
  cout << endl;
  cout << "[Main settings]:" << endl;
  cout << "  -ih path_to_histo_datafile   : provide an input histogram datafile to convert" << endl;
  cout << "  -il path_to_listm_datafile   : provide an input list-mode datafile to convert" << endl;
  cout << "  -o  path_to_cstr_file.cdh    : provide the path to the output file will be created inside this folder (no default)" << endl;
  cout << "  -s  scanner_alias            : provide the name of the scanner used for to acquire the original data" << endl;
  cout << "                               : Must correspond to a .geom or .hscan file in the config/scanner repository." << endl;
  cout << endl;
  cout << "[Optional settings]:" << endl;
  cout << "  -nc norm_factors_file        : provide a file containing normalization correction factors" << endl;
  cout << "  -sc scat_factors_file        : provide a file containing scatter correction factors" << endl;
  cout << "  -rc rdm_factors_file         : provide a file containing random correction factors" << endl;
  cout << "  -ac atn_factors_file         : provide a file containing attenuation correction factors" << endl;
  cout << "  -cf calibration factor       : provide a calibration factor" << endl;
  cout << "  -ist isotope_alias           : provide alias of the isotope used in the input datafile"<< endl;
  cout << "                                 Supported PET isotopes and their parameters are listed in config/misc/isotopes_pet"<< endl;
  cout << "                                 Other isotopes can be added in the same file"<< endl;
  cout << endl;
  cout << "[Miscellaneous settings]:" << endl;
  cout << "  -vb                          : give the verbosity level, from 0 (no verbose) to above 5 (at the event level) (default: 1)." << endl;
  cout << endl;
  #ifdef CASTOR_VERSION
  cout << "  This program is part of the CASToR release version " << CASTOR_VERSION << "." << endl;
  cout << endl;
  #endif
  Exit(a_returnCode);
}


/*
  Main program
*/
int main(int argc, char** argv)
{
  // No argument, then show help
  if (argc==1) ShowHelp(0);

  // ============================================================================================================
  // Parameterized variables with their default values
  // ============================================================================================================

  // String containing the path to the input data filename provided by the user
  string path_to_input_file = "";

  // Datafile mode (histogram or list (default)
  int data_mode = MODE_LIST;
  
  // Path to user provided data
  string path_to_out_file = "";
  string path_to_data_file = "";
  string path_to_header_file = "";
  string path_to_norm_file = "";
  string path_to_scat_file = "";
  string path_to_rdm_file = "";
  string path_to_acf_file = "";
  FLTNB calib_factor = 1.;

  string scanner_alias = "";
  string istp_alias = "";
  
  // Verbosity
  int vb = 1;
  
  // Input datafile is histogram
  bool is_histogram_flag = 0;


  // ============================================================================================================
  // Read command-line parameters
  // ============================================================================================================

  for (int i=1; i<argc; i++)
  {
    string option = (string)argv[i];
    
    // Provide an histogram datafile to convert
    if (option=="-ih")
    {
      if (!path_to_input_file.empty())
      {
        Cerr("***** castor-datafileConversionEx :: the following file names have already been provided (either -ih or -il option must be used): " << endl);    
        Cout(path_to_input_file << endl); 
        Exit(EXIT_FAILURE);
      }
      else
      {
        if (argv[i+1] == NULL)
        {
          Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
          Exit(EXIT_FAILURE);
        }
        else
          path_to_input_file = (string)argv[i+1];
        
        data_mode = MODE_HISTOGRAM;
        i++;
      }
    }

    // Provide a list-mode datafile to convert
    if (option=="-il")
    {
      if (!path_to_input_file.empty())
      {
        Cerr("***** castor-datafileConversionEx :: the following file names have already been provided (either -ih or -il option must be used): " << endl);    
        Cout(path_to_input_file << endl); 
        Exit(EXIT_FAILURE);
      }
      else
      {
        if (argv[i+1] == NULL)
        {
          Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
          Exit(EXIT_FAILURE);
        }
        else
          path_to_input_file = (string)argv[i+1];
        
        data_mode = MODE_LIST;
        i++;
      }
    }

    // Output CASToR datafile
    else if (option=="-o")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        path_to_out_file = (string)argv[i+1];
      i++;
    }

    // Scanner alias
    else if (option=="-s")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        scanner_alias = (string)argv[i+1];
      i++;
    }

    // Provide a norm correction file
    else if (option=="-nc")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        path_to_norm_file = (string)argv[i+1];
        
      i++;
    }

    // Provide a scatter correction file
    else if (option=="-sc")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        path_to_scat_file = (string)argv[i+1];
        
      i++;
    }
    
    // Provide a rdm correction file
    else if (option=="-rc")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        path_to_rdm_file = (string)argv[i+1];
        
      i++;
    }

    // Provide an acf correction file
    else if (option=="-ac")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        path_to_acf_file = (string)argv[i+1];
        
      i++;
    }

    // Provide a calibration factor
    else if (option=="-cf")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
      {
        string val_str = (string)argv[i+1];
        if(ConvertFromString(val_str, &calib_factor) )
        {
          Cerr("***** castor-datafileConversionEx :: Exception when trying to read'" << val_str << " for option: " << option << endl);
          Exit(EXIT_FAILURE);
        }
      }
      i++;
    }
    
    // Provide an isotope alias
    else if (option=="-ist")
    {
      if (argv[i+1] == NULL)
      {
        Cerr("***** castor-datafileConversionEx :: argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      else
        istp_alias = (string)argv[i+1];
        
      i++;
    }
    
    // Verbosity level
    else if (option=="-vb")
    {
      if (i>=argc-1)
      {
        Cerr("***** castor-datafileConversionEx :: Argument missing for option: " << option << endl);
        Exit(EXIT_FAILURE);
      }
      vb = atoi(argv[i+1]);
      i++;
    }

    else
    {
      Cerr("***** castor-datafileConversionEx :: Unknown option '" << option << "' !" << endl);
      Exit(EXIT_FAILURE);
    }
  }


  // ============================================================================================================
  // Basic initialization checks (minimal initializations mandatory for the next steps)
  // ============================================================================================================

  // data files
  if (path_to_input_file.empty() )
  {
    Cerr("***** castor-datafileConversionEx :: Please provide at least one data filename (-ih for histogram, -il for list-mode)" << endl);
    cout << "  -input filename   : give an input datafile (no default)." << endl;
    Exit(EXIT_FAILURE);
  }
  
  // output directory
  if (path_to_out_file.empty() )
  {
    Cerr("***** castor-datafileConversionEx :: Please provide the output file name (-o)" << endl);
    Exit(EXIT_FAILURE);
  }

  // scanner
  if (scanner_alias.empty())
  {
    Cerr("***** castor-datafileConversionEx :: Please provide a scanner alias (-s) :" << endl);
    Cout("                                     It must correspond to a .geom or .hscan (user-made LUT) file in the config/scanner directory." << endl);
    ShowHelp(0);
    Exit(EXIT_FAILURE);
  }
  
  // Throw error by default.
  // These two lines must be erased when implementing any datafile converter!
  //Cerr("castor-GATERootToCastor :: This script is only for demonstration purposes " << endl);
  //Exit(EXIT_FAILURE);


  // ============================================================================================================
  // SOutputManager object initialisation:
  // (Used for log file)
  // ============================================================================================================

  sOutputManager* p_outputManager = sOutputManager::GetInstance();  
  // Set verbose level
  p_outputManager->SetVerbose(vb);
  // Set MPI rank
  p_outputManager->SetMPIRank(0);

  // Set path to the config directory
  if (p_outputManager->CheckConfigDir(""))
  {
    Cerr("***** castor-datafileConversionEx :: A problem occured while checking for the config directory path !" << endl);
    Exit(EXIT_FAILURE);
  }
  // Initialize output directory and base name
  if (p_outputManager->InitOutputDirectory(path_to_out_file, ""))
  {
    Cerr("***** castor-datafileConversionEx :: A problem occured while initializing output directory !" << endl);

    Exit(EXIT_FAILURE);
  }
  // Log command line
  if (p_outputManager->LogCommandLine(argc,argv))
  {
    Cerr("***** castor-datafileConversionEx :: A problem occured while logging command line arguments !" << endl);
    Exit(EXIT_FAILURE);
  }

  // Output progression options
  cout << std::fixed;
  cout << std::setprecision(2);

  // ============================================================================================================
  // ScannerManager object initialization
  // (Basic initialization to locate scanner geometry files)
  // ============================================================================================================
  
  sScannerManager* p_scannermanager = sScannerManager::GetInstance();  
  p_scannermanager->SetVerbose(vb);
    
  // Check if the scanner exists and get the name from ScannerManager
  scanner_alias = (scanner_alias.find(OS_SEP)) ? 
                  scanner_alias.substr(scanner_alias.find_last_of(OS_SEP)+1) :
                  scanner_alias;

  if(p_scannermanager->FindScannerSystem(scanner_alias) )
  {
    Cerr("**** castor-datafileConversionEx :: A problem occurred while searching for scanner system !" << endl);
    Exit(EXIT_FAILURE);
  } 

  // Build output file names
  path_to_data_file = path_to_out_file + ".Cdf";
  path_to_header_file = path_to_out_file + ".Cdh";

  // ============================================================================================================
  // Instanciate/Initialize CASToR Datafile
  // (Enable/Disable optionnal field to be written)
  // ============================================================================================================
  
  // Instantiate & Initialize oImageDimensionsAndQuantification object, required for datafile generation (number of threads)
  oImageDimensionsAndQuantification* p_ID = new oImageDimensionsAndQuantification(); 
  
  // Instanciate & Initialize iDataFilePET and Event objects
  iDataFilePET* Out_data_file = NULL;
  vEvent* Event = NULL;

  // ===> This variable set the maximum number of LORs contained in one event
  // ===> in the whole dataset (for compression purposes)
  // ===> This depends on the dataset to convert
  uint16_t max_nb_lines_per_event = 1;

  // Create datafile and set variables
  Out_data_file = new iDataFilePET();
  
  // Set the image oImageDimensionsAndQuantification object (required for initialization)
  Out_data_file->SetImageDimensionsAndQuantification(p_ID);
  
  // Set path to header datafile
  Out_data_file->SetHeaderDataFileName(path_to_header_file);
  
  // Just required for initialization
  Out_data_file->SetPercentageLoad(0);

  // Set verbosity
  Out_data_file->SetVerbose(vb);

  // Set data mode (list/hitogram)
  Out_data_file->SetDataMode(data_mode);

  // Set modality
  Out_data_file->SetDataType(TYPE_PET);
  
  // Set maximum number of LORs contained in one event
  Out_data_file->SetMaxNumberOfLinesPerEvent(max_nb_lines_per_event);
  
  // Set calibration factor
  Out_data_file->SetCalibrationFactor(calib_factor);

  // Set isotope
  if(!istp_alias.empty())
  {
    if(p_ID->SetPETIsotope(0, istp_alias) )
    {
      Cerr("**** castor-datafileConversionEx :: A problem occurred while checking isotope name !" << endl);
      Exit(EXIT_FAILURE);  
    }
    Out_data_file->SetIsotope(istp_alias);
  }

  // Allocate the Event structure (containing all information for a listmode
  // or histogram event, depending on data mode)
  if(data_mode == MODE_HISTOGRAM)
  {
    // Instanciate list-mode Event 
    Event = new iEventHistoPET();
    Event->SetNbLines(max_nb_lines_per_event);
    Event->AllocateID();
  }
  else
  {
    // Instanciate histogram Event 
    Event = new iEventListPET();
    Event->SetNbLines(max_nb_lines_per_event);
    Event->AllocateID();
  }


  // ============================================================================================================
  // ===> Read sinogram correction file(s) (if any) and set datafile flag for each correction
  // ============================================================================================================
  
  // ===> Compute sinogram dimensions.
  // ===> Values must be adjusted to the dataset to convert.
  uint32_t nbins = 1;
  uint32_t nangles = 1;
  uint32_t nsinos = 1;
  uint32_t nb_cor_factors = nbins 
                          * nangles 
                          * nsinos;
  
  // --- Normalization correction factors ---
  
  // FLTNBDATA is either a float (default) or double type.
  // Defined in /management/gVariables.hh
  FLTNBDATA *p_norm = NULL;
  bool norm_flag = false; 
  
  if( !path_to_norm_file.empty() )
  {
    if(vb>=2) Cout("--> Reading the norm correction factors file = " << path_to_norm_file << "..." << endl);
    ifstream ifile(path_to_norm_file.c_str(), ios::binary | ios::in);
    
    if (!ifile)
    {
      Cerr("***** castor-datafileConversionEx ::  Error reading normalization factor file: "<< path_to_norm_file <<" !" << endl);
      Exit(EXIT_FAILURE);
    }
    else
    {
      // Allocate buffer storing the normalisation
      p_norm = new FLTNBDATA [nb_cor_factors * sizeof( FLTNBDATA )];
      ifile.read(reinterpret_cast < char* > (p_norm), nb_cor_factors * sizeof( FLTNBDATA));
      ifile.close();
    }
    
    // ===> Set normalization correction flag in datafile objet
    // ===> (required to indicate that normalization correction will be provided)
    Out_data_file->SetNormCorrectionFlagOn();
    norm_flag = true;
  }

  // --- Scatter correction factors file ---
  FLTNBDATA *p_scat = NULL;
  bool scat_flag = false; 
  
  if( !path_to_scat_file.empty() )
  {
    if(vb>=2) Cout("--> Reading the scatter correction factors file = " << path_to_scat_file << "..." << endl);
    ifstream ifile(path_to_scat_file.c_str(), ios::binary | ios::in);
    
    if (!ifile)
    {
      Cerr("***** castor-datafileConversionEx ::  Error reading scatter factor file: "<< path_to_scat_file <<" !" << endl);
      Exit(EXIT_FAILURE);
    }
    else
    {
      // Allocating buffer storing the scatter
      p_scat = new FLTNBDATA [nb_cor_factors * sizeof( FLTNBDATA )];
      ifile.read(reinterpret_cast < char* > (p_scat), nb_cor_factors * sizeof( FLTNBDATA));
      ifile.close();
    }

    // ===> Set scatter correction flag in datafile objet
    // ===> (required to indicate that scatter correction will be provided)
    Out_data_file->SetScatterCorrectionFlagOn();
    scat_flag = true;
  }

  // --- Random correction factors file ---
  FLTNBDATA *p_rdm = NULL;
  bool rdm_flag = false; 
  
  if( !path_to_rdm_file.empty() )
  {
    if(vb>=2) Cout("--> Reading the random correction factors file = " << path_to_rdm_file << "..." << endl);
    ifstream ifile(path_to_rdm_file.c_str(), ios::binary | ios::in);
    
    if (!ifile)
    {
      Cerr("***** castor-datafileConversionEx ::  Error reading random correction factor file: "<< path_to_rdm_file <<" !" << endl);
      Exit(EXIT_FAILURE);
    }
    else
    {
      // Allocating buffer storing the random
      p_rdm = new FLTNBDATA [nb_cor_factors * sizeof( FLTNBDATA )];
      ifile.read(reinterpret_cast < char* > (p_rdm), nb_cor_factors * sizeof( FLTNBDATA));
      ifile.close();
    }

    // ===> Set random correction flag in datafile objet
    // ===> (required to indicate that random correction will be provided)
    Out_data_file->SetRandomCorrectionFlagOn();
    rdm_flag = true;
  }

  // --- Attenuation correction factors file ---
  FLTNBDATA *p_acf = NULL;
  bool acf_flag = false; 
  
  if( !path_to_acf_file.empty() )
  {
    if(vb>=2) Cout("--> Reading the attenuation correction factors file = " << path_to_acf_file << "..." << endl);
    ifstream ifile(path_to_acf_file.c_str(), ios::binary | ios::in);
    
    if (!ifile)
    {
      Cerr("***** castor-datafileConversionEx ::  Error reading attenuation correction factor file: "<< path_to_acf_file <<" !" << endl);
      Exit(EXIT_FAILURE);
    }
    else
    {
      // Allocating buffer storing the acf
      p_acf = new FLTNBDATA [nb_cor_factors * sizeof( FLTNBDATA )];
      ifile.read(reinterpret_cast < char* > (p_acf), nb_cor_factors* sizeof( FLTNBDATA));
      ifile.close();
    }
    
    // ===> Set attenuation correction flag in datafile objet
    // ===> (required to indicate that attenuation correction will be provided)
    Out_data_file->SetAtnCorrectionFlagOn();
    acf_flag = true;
  }
  
  // Initialize datafile object
  Out_data_file->PROJ_InitFile();
  
  // Compute the event size relatively to the mandatory 
  // and optionnal (correction factors) elements
  Out_data_file->ComputeSizeEvent();
  
  // Init Datafile
  Out_data_file->PrepareDataFile();


  // ============================================================================================================
  // *********************************************** CONVERSION *************************************************
  // ============================================================================================================
  Cout(" --- Start conversion of datafile : " << path_to_input_file <<  endl
    << "     CASToR output header datafile: " << path_to_header_file << endl
    << "     CASToR output binary datafile: " << path_to_data_file << endl << endl);
  

  // ============================================================================================================
  // Init variables
  // ============================================================================================================
  
  // Index for progression printing
  uint32_t printing_index = 0;

  // ===> Recover the total number of events (number of coincidences or 
  // ===> histogram bins) from the dataset metadata
  uint32_t nEvents = 0;


  // ===> Acquisition duration and start time in seconds
  // ===> This should be recovered from the dataset metadata)
  FLTNB start_time_sec = 0.; 
  FLTNB stop_time_sec = 1.; 
  FLTNB duration_sec = stop_time_sec - start_time_sec; 
  
  // ===> Scanner variables (blocs, modules, submodules, crystals etc..)
  // ===> depending on the system.
  uint32_t nRsectorsPerRing = 70;
  uint32_t nb_crystals_trs = 9, 
           nb_crystals_axl = 6; 
  uint32_t nb_crystals_per_ring = nRsectorsPerRing
                                * nb_crystals_trs;
  
  // ===> Variables to recover indices of the two crystals for each potential
  // ===> LORs contributing to the event
  uint32_t *castor_id1 = new uint32_t[max_nb_lines_per_event]; 
  uint32_t *castor_id2 = new uint32_t[max_nb_lines_per_event];
  
  // --------------------------------
  // Initialization of root variables
  // The following lines are just required for the demonstration dataset used in this sample code,
  // Must be erased when adjusting this code to the conversion of any dataset
  
  // ROOT objects/variables
  int32_t rSectorID1, rSectorID2;
  int32_t moduleID1, moduleID2;
  int32_t crystalID1, crystalID2;
    
  #ifdef CASTOR_ROOT
    TApplication *Tapp = new TApplication("tapp",0,0);
    TTree* Coincidences = new TTree;
    TFile* Tfile_root = new TFile(path_to_input_file.c_str(),"READ","ROOT file with histograms");
    Coincidences = (TTree*)Tfile_root->Get("Coincidences");
    nEvents += Coincidences->GetEntries();

    //------------- ROOT branches
    double_t time1=0; 
    Coincidences->SetBranchAddress("time1",&time1);
    Coincidences->SetBranchAddress("rsectorID1",&rSectorID1);
    Coincidences->SetBranchAddress("moduleID1",&moduleID1);
    Coincidences->SetBranchAddress("crystalID1",&crystalID1);

    double_t time2=0;
    Coincidences->SetBranchAddress("time2",&time2);
    Coincidences->SetBranchAddress("rsectorID2",&rSectorID2);
    Coincidences->SetBranchAddress("moduleID2",&moduleID2);
    Coincidences->SetBranchAddress("crystalID2",&crystalID2); 

    // Recover acquisition start time from the first event
    Coincidences->GetEntry(0);
  #endif
  // --------------------------------

  // Just for progression output
  uint32_t printing_ratio = (nEvents>1000) ? 1000 : nEvents/10;
  
  // Loop on the data elements (histogram bins or LORs)
  for (uint32_t i=0; i<nEvents ; i++)
  {
    // ===> Recover event value (list-mode, or dynamic histogram dataset)
    uint32_t time_ms = 0;
    stop_time_sec = (FLTNB)time_ms/1000;
    
    // ===> Recover the number of lines in the event (if compression).
    int nb_lines_in_event = 1;

    // -----------------------------------------------------------------
    // The following lines are just required for the demonstration dataset used in this sample code.
    // Must be erased/adapted when adjusting this code to the conversion of any dataset
    #ifdef CASTOR_ROOT
    Coincidences->GetEntry(i);
    time_ms = time1;
    #endif

    // ===> Compute CASToR indexation depending on the system layout
    // ===> This directly depends on the type of scanner file used to
    // ===> described the system geometry.
    // ===> See documentation for more information
    uint32_t crystals_trs_id1 = (uint32_t)(crystalID1/nb_crystals_trs);
    
    uint32_t ringID1 = moduleID1*nb_crystals_axl 
                     + crystals_trs_id1;
                     
    uint32_t crystals_trs_id2 = (uint32_t)(crystalID2/nb_crystals_trs);
    
    uint32_t ringID2 = moduleID2*nb_crystals_axl 
                     + crystals_trs_id2;

    // Loop on the LORs contained in the event
    for(int l=0 ; l<nb_lines_in_event ; l++)
    {
      // Recover the CASToR ID position of the two crystals according to
      // the LUT corresponding to this scanner
      castor_id1[l] = ringID1*nb_crystals_per_ring 
                    + rSectorID1*nb_crystals_trs 
                    + crystalID1%nb_crystals_trs ;
                    
      castor_id2[l] = ringID2*nb_crystals_per_ring 
                    + rSectorID2*nb_crystals_trs
                    + crystalID2%nb_crystals_trs ;
    }
    // -----------------------------------------------------------------
    
    // --- Histo-mode event ---
    if(is_histogram_flag) // histogram mode event
    {
      // Set the number of lines in this event
      Event->SetNbLines(nb_lines_in_event);
  
      // Set CASToR IDs in the event structure for each contributing line
      for(int l=0 ; l<nb_lines_in_event ; l++)
      {
        Event->SetID1(l, castor_id1[l]);  // 1st argument : line, 2nd argument : index
        Event->SetID2(l, castor_id2[l]);  // 1st argument : line, 2nd argument : index
      }

      // Set information related to each TOF bin
      int nb_tof_bins = 1;
      for (int b=0; b<nb_tof_bins; b++)
      {
        // ===> Recover and set event value (histogram dataset)
        FLTNB event_value = 1.;
        Event->SetEventValue(b, event_value);  // 1st argument : TOF bin, 2nd argument : event value
      
        // ===> Set scatter correction factor (if any)
        // ===> Require computation of the scatter correction value for
        // ===> this LOR from the factors loaded in the "p_scat" buffer
        if(scat_flag)
        {
          FLTNB scat_correction_coeff = 0.; // computed from p_scat
          ((iEventHistoPET*)Event)->SetScatterRate(b, scat_correction_coeff);
        }
      }
      
      // ===> Set timestamp of the event in ms (global timestamp for histogram)
      // ===> i.e : 0, or timestamp of a dynamic frame
      Event->SetTimeInMs(time_ms); // uint32_t

      // ===> Set random correction factor (if any)
      // ===> Require computation of the random correction value for
      // ===> this LOR from the factors loaded in the "p_rdm" buffer
      if(rdm_flag)
      {
        FLTNB rdm_correction_coeff = 0.; // computed from p_rdm
        ((iEventPET*)Event)->SetRandomRate(rdm_correction_coeff);
      }
      
      // ===> Set normalization correction factor (if any)
      // ===> Require computation of the norm correction value for
      // ===> this LOR from the factors loaded in the "p_norm" buffer
      if(norm_flag)
      {
        FLTNB norm_correction_coeff = 0.; // computed from p_norm
       ((iEventPET*)Event)->SetNormalizationFactor(norm_correction_coeff);
      }

      // ===> Set attenuation correction factor (if any)
      // ===> Require computation of the atn correction value for
      // ===> this LOR from the factors loaded in the "p_acf" buffer
      if(acf_flag)
      {
        FLTNB atn_correction_coeff = 0.; // computed from p_acf
        ((iEventPET*)Event)->SetAttenuationCorrectionFactor(atn_correction_coeff);
      }

      // Write event in the datafile
      // ('0' argument is just thread-related. No change required)
      Out_data_file->PROJ_WriteEvent(Event, 0);
    }
    
    // --- List-mode event ---
    else 
    {
      // Set the number of lines in this event
      Event->SetNbLines(nb_lines_in_event);
      
      // Set CASToR ID in the event structure
      for(int l=0 ; l<nb_lines_in_event ; l++)
      {
        Event->SetID1(l, castor_id1[l]); // 1st argument : line, 2nd argument :index
        Event->SetID2(l, castor_id2[l]); // 1st argument : line, 2nd argument :index
      }

      // ===> Set scatter correction factor (if any)
      // ===> Require computation of the scatter correction value for
      // ===> this LOR from the factors loaded in the "p_scat" buffer
      if(scat_flag)
      {
        FLTNB scat_correction_coeff = 0.; // computed from p_scat
        // First argument '0' by default for list-mode (it is used for histograms with TOF bins).
        ((iEventListPET*)Event)->SetScatterRate(0, scat_correction_coeff); 
      }
        
      // ===> Set timestamp of the event in ms
      Event->SetTimeInMs(time_ms); // uint32_t
      
      // ===> Set random correction factor (if any)
      // ===> Require computation of the random correction value for
      // ===> this LOR from the factors loaded in the "p_rdm" buffer
      if(rdm_flag)
      {
        FLTNB rdm_correction_coeff = 0.; // computed from p_rdm
        ((iEventPET*)Event)->SetRandomRate(rdm_correction_coeff);
      }
      
      // ===> Set normalization correction factor (if any)
      // ===> Require computation of the norm correction value for
      // ===> this LOR from the factors loaded in the "p_norm" buffer
      if(norm_flag)
      {
        FLTNB norm_correction_coeff = 0.; // computed from p_norm
       ((iEventPET*)Event)->SetNormalizationFactor(norm_correction_coeff);
      }

      // ===> Set attenuation correction factor (if any)
      // ===> Require computation of the atn correction value for
      // ===> this LOR from the factors loaded in the "p_acf" buffer
      if(acf_flag)
      {
        FLTNB atn_correction_coeff = 0.; // computed from p_acf
        ((iEventPET*)Event)->SetAttenuationCorrectionFactor(atn_correction_coeff);
      }
      
      // Write event in the datafile
      // ('0' argument is just thread-related. No change required)
      Out_data_file->PROJ_WriteEvent(Event, 0);
    }
    
    // Progression output
    if (printing_index%printing_ratio==0)
    {
      FLTNB percent = ( ((FLTNB)(printing_index+1))/((FLTNB)nEvents) ) * ((FLTNB)100);
      cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b      "
           << percent << " \%                    ";
    }
    printing_index++;
  }
   
  Cout("The simulated dataset contained " << nEvents << " coincidences / bins" << endl);

  // Set duration and nb of events in datafile
  Out_data_file->SetStartTime(start_time_sec); 
  Out_data_file->SetDuration(duration_sec); 
  Out_data_file->SetNbEvents(nEvents);
  
  // Write datafile header
  Out_data_file->PROJ_WriteHeader(); 
  
  // Write raw datafile
  Out_data_file->PROJ_WriteData(); 

  // Delete tmp writing file (if any)
  Out_data_file->PROJ_DeleteTmpDatafile();

  cout << endl;
  
  // ============================================================================================================
  // End
  // ============================================================================================================

  // Free Root objects
  #ifdef CASTOR_ROOT
  delete Coincidences;
  delete Tfile_root;
  delete Tapp;
  #endif

  delete[] castor_id1;
  delete[] castor_id2;

  if(p_acf != NULL) delete[] p_acf;
  if(p_rdm != NULL) delete[] p_rdm;
  if(p_scat != NULL) delete[] p_scat;
  if(p_norm != NULL) delete[] p_norm;
  
  // Delete objects
  if (Event)
  {
    if (is_histogram_flag) 
      delete (iEventHistoPET*)Event; 
    else 
      delete (iEventListPET*)Event;
  }

  delete Out_data_file;
  delete p_ID;
  
  return 0;
}