IORTMatrix.cc

이 파일의 문서화 페이지로 가기

//
// ********************************************************************
// * License and Disclaimer                                           *
// *                                                                  *
// * The  Geant4 software  is  copyright of the Copyright Holders  of *
// * the Geant4 Collaboration.  It is provided  under  the terms  and *
// * conditions of the Geant4 Software License,  included in the file *
// * LICENSE and available at  http://cern.ch/geant4/license .  These *
// * include a list of copyright holders.                             *
// *                                                                  *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work  make  any representation or  warranty, express or implied, *
// * regarding  this  software system or assume any liability for its *
// * use.  Please see the license in the file  LICENSE  and URL above *
// * for the full disclaimer and the limitation of liability.         *
// *                                                                  *
// * This  code  implementation is the result of  the  scientific and *
// * technical work of the GEANT4 collaboration.                      *
// * By using,  copying,  modifying or  distributing the software (or *
// * any work based  on the software)  you  agree  to acknowledge its *
// * use  in  resulting  scientific  publications,  and indicate your *
// * acceptance of all terms of the Geant4 Software license.          *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//    
//   (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
//   (b) IBFM-CNR , Segrate (Milano), Italy
//   (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
//   (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
//   (e) University of Wallongong, Australia
//
//   *Corresponding author, email to carlo.casarino@polooncologicocefalu.it

#include <fstream>
#include <iostream>
#include <sstream>
#include <iomanip>

#include "IORTMatrix.hh"
#include "IORTAnalysisManager.hh"
#include "IORTPrimaryGeneratorAction.hh"

#include "globals.hh"
#include "G4SystemOfUnits.hh"
#include "G4RunManager.hh"
#include "G4ParticleGun.hh"

// Units definition: CLHEP/Units/SystemOfUnits.h
//
IORTMatrix* IORTMatrix::instance = NULL;
G4bool IORTMatrix::secondary = false;

// Only return a pointer to matrix
IORTMatrix* IORTMatrix::GetInstance() 
{
  return instance;
}
  // This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it
  // TODO A check on the parameters is required!
IORTMatrix* IORTMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass)  
{
  if (instance) delete instance;
  instance = new IORTMatrix(voxelX, voxelY, voxelZ, mass);
  instance -> Initialize(); 
  return instance;
}
IORTMatrix::IORTMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass):
    stdFile("Dose.out"),
    doseUnit(MeV/g)
{  
  // Number of the voxels of the phantom
  // For Y = Z = 1 the phantom is divided in slices (and not in voxels)
  // orthogonal to the beam axis
  numberOfVoxelAlongX = voxelX;
  numberOfVoxelAlongY = voxelY;
  numberOfVoxelAlongZ = voxelZ; 
  massOfVoxel = mass;
  // Create the dose matrix
  matrix = new G4double[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
  if (matrix)
  {
    G4cout << "IORTMatrix: Memory space to store physical dose into " <<  
    numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
    " voxels has been allocated " << G4endl;
  }
  else G4Exception("IORTMatrix::IORTMatrix()", "IORT0005", FatalException, "Error: can't allocate memory to store physical dose!");
    // Hit voxel (TrackID) marker
    // This array mark the status of voxel, if a hit occur, with the trackID of the particle
    // Must be initialized
  hitTrack = new G4int[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
  ClearHitTrack();
}

IORTMatrix::~IORTMatrix()
{
    delete[] matrix;
    delete[] hitTrack;
    // free fluences/dose data memory
    Clear();
}

void IORTMatrix::Clear()
{
    for (size_t i=0; i<ionStore.size(); i++)
    {
  delete[] ionStore[i].dose; 
  delete[] ionStore[i].fluence; 
    }
    ionStore.clear();
}

// Initialise the elements of the matrix to zero
void IORTMatrix::Initialize()
{ 
    // Clear ions store
    Clear();
    // Clear dose
    for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
    {
    matrix[i] = 0;
    }
}
  // Print generated nuclides list
void IORTMatrix::PrintNuclides()
{
    for (size_t i=0; i<ionStore.size(); i++)
    {
    G4cout << ionStore[i].name << G4endl;
    }
}
  // Clear Hit voxel (TrackID) markers
void IORTMatrix::ClearHitTrack()
{
  for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
}
  // Return Hit status
G4int* IORTMatrix::GetHitTrack(G4int i, G4int j, G4int k)
{
  return &(hitTrack[Index(i,j,k)]);
}
// Dose methods...
// Fill DOSE/fluence matrix for secondary particles: 
// If fluence parameter is true (default value is FALSE) then fluence at voxel (i, j, k) is increased. 
// The energyDeposit parameter fill the dose matrix for voxel (i,j,k) 

G4bool IORTMatrix::Fill(G4int trackID,
         G4ParticleDefinition* particleDef,
         G4int i, G4int j, G4int k, 
         G4double energyDeposit,
         G4bool fluence) 
{
    if ( (energyDeposit <=0. && !fluence) || !secondary) return false;
    // Get Particle Data Group particle ID 
    G4int PDGencoding = particleDef -> GetPDGEncoding();
    PDGencoding -= PDGencoding%10;
  
    // Search for already allocated data...
    for (size_t l=0; l < ionStore.size(); l++)
    {
    if (ionStore[l].PDGencoding == PDGencoding ) 
    {   // Is it a primary or a secondary particle? 
      if ( ((trackID == 1) && (ionStore[l].isPrimary)) || ((trackID !=1) && (!ionStore[l].isPrimary)))
      {
        if (energyDeposit > 0.) ionStore[l].dose[Index(i, j, k)] += energyDeposit/massOfVoxel;
        
          // Fill a matrix per each ion with the fluence
        if (fluence) ionStore[l].fluence[Index(i, j, k)]++;
        return true;
      }
    }
    }
  
    G4int Z = particleDef-> GetAtomicNumber();
    G4int A = particleDef-> GetAtomicMass();

    G4String fullName = particleDef -> GetParticleName();
    G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy  
  // Let's put a new particle in our store...
    ion newIon = 
    {
    (trackID == 1) ? true:false,
    PDGencoding,
    name,
    name.length(), 
    Z, 
    A, 
    new G4double[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ],
    new unsigned int[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ]
    }; 
    // Initialize data
    if (newIon.dose && newIon.fluence)
    {
    for(G4int q=0; q<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; q++)
    {
      newIon.dose[q] = 0.;
      newIon.fluence[q] = 0;
    }
    if (energyDeposit > 0.) newIon.dose[Index(i, j, k)] += energyDeposit/massOfVoxel;
    if (fluence) newIon.fluence[Index(i, j, k)]++;
    
    ionStore.push_back(newIon);
    
    // TODO Put some verbosity check
    /*
     G4cout << "Memory space to store the DOSE/FLUENCE into " <<  
     numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ << 
     " voxels has been allocated for the nuclide " << newIon.name << 
     " (Z = " << Z << ", A = " << A << ")" << G4endl ;
     */
    return true;
    }
    else // XXX Out of memory! XXX
    {
    return false;
    }
  
}
  
  // Methods to store data to filenames...
  //
  // General method to store matrix data to filename
void IORTMatrix::StoreMatrix(G4String file, void* data, size_t psize)
{
    if (data)
    {
    ofs.open(file, std::ios::out);
    if (ofs.is_open())
    {
      for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
        for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
          for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
          {
            G4int n = Index(i, j, k);
              // Check for data type: u_int, G4double, XXX 
            if (psize == sizeof(unsigned int))
            {
              unsigned int* pdata = (unsigned int*)data;
              if (pdata[n]) ofs << i << '\t' << j << '\t' <<
                k << '\t' << pdata[n] << G4endl;
            }
            else if (psize == sizeof(G4double))
            {
              G4double* pdata = (G4double*)data;
              if (pdata[n]) ofs << i << '\t' << j << '\t' <<
                k << '\t' << pdata[n] << G4endl;
            }
          }
      ofs.close();
    }
    }
}

  // Store fluence per single ion in multiple files
void IORTMatrix::StoreFluenceData()
{
    for (size_t i=0; i < ionStore.size(); i++){
    StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int));
    }
}
  // Store dose per single ion in multiple files
void IORTMatrix::StoreDoseData()
{
  
    for (size_t i=0; i < ionStore.size(); i++){
    StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double));
    }
}
  // Store dose for all ions into a single file and into ntuples.
  // Please note that this function is called via messenger commands
  // defined in the IORTAnalysisFileMessenger.cc class file
void IORTMatrix::StoreDoseFluenceAscii(G4String file)
{
#define width 15L
    filename = (file=="") ? stdFile:file;
    // Sort like periodic table
    std::sort(ionStore.begin(), ionStore.end());
    G4cout << "Dose is being written to " << filename << G4endl;
    ofs.open(filename, std::ios::out);
    if (ofs.is_open())
    {
  // Write the voxels index and the list of particles/ions 
  ofs << std::setprecision(6) << std::left <<
      "i\tj\tk\t"; 
  // Total dose 
  ofs << std::setw(width) << "Dose(MeV/g)";
  if (secondary)
  {
      for (size_t l=0; l < ionStore.size(); l++)
      {
    G4String a = (ionStore[l].isPrimary) ? "_1":""; // is it a primary?
    ofs << std::setw(width) << ionStore[l].name + a <<
        std::setw(width) << ionStore[l].name  + a;
      }
      ofs << G4endl;

      /*
       * PDGencondig
       */
      /*
      ofs << std::setprecision(6) << std::left <<
      "0\t0\t0\t"; 

      // Total dose 
      ofs << std::setw(width) << '0';
      for (size_t l=0; l < ionStore.size(); l++)
      {
      ofs << std::setw(width) << ionStore[l].PDGencoding  <<
      std::setw(width) << ionStore[l].PDGencoding;
      }
      ofs << G4endl;
      */
  }
  // Write data
  for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
      for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
    for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
    {
        G4int n = Index(i, j, k);
        // Write only not identically null data lines
        if (matrix[n])
        {
      ofs << G4endl;
      ofs << i << '\t' << j << '\t' << k << '\t';
      // Total dose 
      ofs << std::setw(width) << matrix[n]/massOfVoxel/doseUnit; 
      if (secondary)
      {
          for (size_t l=0; l < ionStore.size(); l++)
          {
        // Fill ASCII file rows
        ofs << std::setw(width) << ionStore[l].dose[n]/massOfVoxel/doseUnit <<
            std::setw(width) << ionStore[l].fluence[n]; 
          }
      }
        }
    }
  ofs.close();
    }
}

void IORTMatrix::StoreDoseFluenceRoot()
{
    IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
    for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
      for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
  for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
    {
      G4int n = Index(i, j, k);
      for (size_t l=0; l < ionStore.size(); l++)
        
        {
    // Do the same work for .root file: fill dose/fluence ntuple  
    analysis -> FillVoxelFragmentTuple( i, j, k, 
                ionStore[l].A, 
                ionStore[l].Z, 
                ionStore[l].dose[n]/massOfVoxel/doseUnit, 
                ionStore[l].fluence[n] );
    
    
        }
      
    }
}

void IORTMatrix::Fill(G4int i, G4int j, G4int k, 
             G4double energyDeposit)
{
    if (matrix)
    matrix[Index(i,j,k)] += energyDeposit;
  
    // Store the energy deposit in the matrix element corresponding 
    // to the phantom voxel  
}
void IORTMatrix::TotalEnergyDeposit()
{
    // Store the information of the matrix in a ntuple and in 
    // a 1D Histogram
}