Changeset 1313 for trunk/examples/advanced/hadrontherapy/src/HadrontherapyMatrix.cc

Timestamp:

Jun 14, 2010, 3:54:58 PM (14 years ago)

Author:

garnier

Message:

geant4.9.4 beta rc0

File:

• trunk/examples/advanced/hadrontherapy/src/HadrontherapyMatrix.cc (modified) (1 diff)

trunk/examples/advanced/hadrontherapy/src/HadrontherapyMatrix.cc

@@ -1 @@
-//
-// ********************************************************************
-// * 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.          *
-// ********************************************************************
-//
-// $Id: HadrontherapyMatrix.cc;
-// See more at: http://g4advancedexamples.lngs.infn.it/Examples/hadrontherapy//
+        //
+        // ********************************************************************
+        // * 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.          *
+        // ********************************************************************
+        //
+        // $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"
-#include <fstream>
-
+
+// Units definition: CLHEP/Units/SystemOfUnits.h
+//
 HadrontherapyMatrix* HadrontherapyMatrix::instance = NULL;
-// Static method that only return a pointer to the matrix object
-HadrontherapyMatrix* HadrontherapyMatrix::getInstance() 
-{
-  return instance;
-}
-// This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it
-HadrontherapyMatrix* HadrontherapyMatrix::getInstance(G4int voxelX, G4int voxelY, G4int voxelZ)  
-{
-    if (instance) delete instance;
-    instance = new HadrontherapyMatrix(voxelX, voxelY, voxelZ);
-    instance -> Initialize();   
-    return instance;
-}
-
-HadrontherapyMatrix::HadrontherapyMatrix(G4int voxelX, G4int voxelY, G4int voxelZ):
-    matrix(0)
+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
-  numberVoxelX = voxelX;
-  numberVoxelY = voxelY;
-  numberVoxelZ = voxelZ; 
-  // Create the dose matrix
-  matrix = new G4double[numberVoxelX*numberVoxelY*numberVoxelZ];
-  if (matrix) G4cout << "Matrix: Memory space to store physical dose into " <<  
-                        numberVoxelX*numberVoxelY*numberVoxelZ <<
-                        " voxels has been allocated " << G4endl;
-  else G4Exception("Can't allocate memory to store physical dose!");
-}
-
+        // 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;
-}
-
-void HadrontherapyMatrix::flush()
-{
-        if(matrix)
-        for(int i=0; i<numberVoxelX*numberVoxelY*numberVoxelZ; i++)
-        {
-          matrix[i] = 0;
-        }
-}
+    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()
 { 
-// Initialise the elements of the matrix to zero
-  for(G4int i = 0; i < numberVoxelX; i++)
-    {
-      for(G4int j = 0; j < numberVoxelY; j++)
-           {
-              for(G4int k = 0; k < numberVoxelZ; k++)
-
-              matrix[Index(i,j,k)] = 0.;
-           } 
-    }
-}
+    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  i, j, k
-}
-
+    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
 
-  G4int k;
-  G4int j;
-  G4int i;
-  
-  if (matrix)
+#ifdef G4ANALYSIS_USE_ROOT
+    HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance();
+#endif
+    if (matrix)
     {  
-      std::ofstream ofs;        
-      ofs.open("DoseDistribution.out"); 
-      
-      for(G4int l = 0; l < numberVoxelZ; l++) 
-        {
-          k = l;
-          
-          for(G4int m = 0; m < numberVoxelY; m++) 
-            { 
-              j = m * numberVoxelZ + k; 
-                
-                for(G4int n = 0; n <  numberVoxelX; n++)
-                  {
-                    i =  n* numberVoxelZ * numberVoxelY + j;
-                    if(matrix[i] != 0)
-                      { 
-                        ofs << n << '\t' << m << '\t' <<
-                          k << '\t' << matrix[i] << G4endl;
-                        
-#ifdef ANALYSIS_USE
-                        HadrontherapyAnalysisManager* analysis = 
-                        HadrontherapyAnalysisManager::getInstance();
-                        analysis -> FillEnergyDeposit(n, m, k, matrix[i]);
-                        analysis -> BraggPeak(n, matrix[i]);
+        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
-                      }
-}       
-              }
-          }
-    }
-}
+                }
+    }
+}
+