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// $Id: HadrontherapyMatrix.cc;
// See more at: http://g4advancedexamples.lngs.infn.it/Examples/hadrontherapy//

#include "HadrontherapyMatrix.hh"
#include "HadrontherapyAnalysisManager.hh"
#include "G4RunManager.hh"
#include "HadrontherapyPrimaryGeneratorAction.hh"
#include "G4ParticleGun.hh"

#include <fstream>
#include <unistd.h>
#include <iostream>
#include <sstream>
#include <iomanip>
#include "globals.hh"

// Units definition: CLHEP/Units/SystemOfUnits.h
//
HadrontherapyMatrix* HadrontherapyMatrix::instance = NULL;
G4bool HadrontherapyMatrix::secondaries = false;
	// Only return a pointer to matrix
HadrontherapyMatrix* HadrontherapyMatrix::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!
HadrontherapyMatrix* HadrontherapyMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass)  
{
	if (instance) delete instance;
	instance = new HadrontherapyMatrix(voxelX, voxelY, voxelZ, mass);
	instance -> Initialize();// XXX
	return instance;
}
HadrontherapyMatrix::HadrontherapyMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass):
    filename("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 << "HadrontherapyMatrix: Memory space to store physical dose into " <<  
		numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
		" voxels has been allocated " << G4endl;
	}
	else G4Exception(" HadrontherapyMatrix::HadrontherapyMatrix. 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();
}

/////////////////////////////////////////////////////////////////////////////
HadrontherapyMatrix::~HadrontherapyMatrix()
{
    delete[] matrix;
    delete[] hitTrack;
		// clear fluences/dose data
    Clear();
}

/////////////////////////////////////////////////////////////////////////////
void HadrontherapyMatrix::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 HadrontherapyMatrix::Initialize()
{ 
    Clear();
    for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
    {
		matrix[i] = 0;
    }
}
	/////////////////////////////////////////////////////////////////////////////
	/////////////////////////////////////////////////////////////////////////////
	// Print generated nuclides list
void HadrontherapyMatrix::PrintNuclides()
{
    for (size_t i=0; i<ionStore.size(); i++)
    {
		G4cout << ionStore[i].name << G4endl;
    }
}
	/////////////////////////////////////////////////////////////////////////////
	// Clear Hit voxel (TrackID) markers
void HadrontherapyMatrix::ClearHitTrack()
{
	for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
}
	// Return Hit status
G4int* HadrontherapyMatrix::GetHitTrack(G4int i, G4int j, G4int k)
{
	return &(hitTrack[Index(i,j,k)]);
}
/////////////////////////////////////////////////////////////////////////////
// Dose methods...
// Fill DOSE/fluence matrix for particle/ion: 
// 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 HadrontherapyMatrix::Fill(G4int trackID,
				 G4ParticleDefinition* particleDef,
				 G4int i, G4int j, G4int k, 
				 G4double energyDeposit,
				 G4bool fluence) 
{
    if (energyDeposit <=0. && !fluence || !secondaries) 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 m=0; m<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; m++)
		{
			newIon.dose[m] = 0.;
			newIon.fluence[m] = 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 HadrontherapyMatrix::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 HadrontherapyMatrix::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 HadrontherapyMatrix::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 HadrontherapyAnalysisFileMessenger.cc class file
void HadrontherapyMatrix::StoreDoseFluenceAscii()
{
    // Sort like periodic table
    std::sort(ionStore.begin(), ionStore.end());
#define width 15L
    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"; 
/*	    
	    G4RunManager *runManager = G4RunManager::GetRunManager();
	    HadrontherapyPrimaryGeneratorAction *pPGA = (HadrontherapyPrimaryGeneratorAction*)runManager -> GetUserPrimaryGeneratorAction();
	    G4String name = pPGA -> GetParticleGun() -> GetParticleDefinition() -> GetParticleName();
*/         
	// Total dose 
	ofs << std::setw(width) << "Dose";

	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;

/*
	// PDGencoding
	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]/(doseUnit); 
			{
			    for (size_t l=0; l < ionStore.size(); l++)
			    {
				// Fill ASCII file rows
				ofs << std::setw(width) << ionStore[l].dose[n]/(doseUnit) <<
				    std::setw(width) << ionStore[l].fluence[n]; 
			    }
			}
		    }
		}
	ofs.close();
    }
}
/////////////////////////////////////////////////////////////////////////////

#ifdef G4ANALYSIS_USE_ROOT
void HadrontherapyMatrix::StoreDoseFluenceRoot()
{
    HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::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]/(doseUnit), 
							ionStore[l].fluence[n] );


		}
	    }
}
#endif

void HadrontherapyMatrix::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 HadrontherapyMatrix::TotalEnergyDeposit()
{
  // Convert energy deposited to dose.
  // Store the information of the matrix in a ntuple and in 
  // a 1D Histogram

#ifdef G4ANALYSIS_USE_ROOT
    HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance();
#endif
    if (matrix)
    {  
	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);
	            matrix[n] = matrix[n] / massOfVoxel;
#ifdef G4ANALYSIS_USE_ROOT
		    analysis -> FillEnergyDeposit(i, j, k, matrix[n]/doseUnit);
		    analysis -> BraggPeak(i, matrix[n]/doseUnit);
#endif
		}
    }
}