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25 //
26 // Hadrontherapy advanced example for Geant4
27 // See more at: https://twiki.cern.ch/twiki/bin/view/Geant4/AdvancedExamplesHadrontherapy
28
29 #include <fstream>
30 #include <iostream>
31 #include <sstream>
32 #include <iomanip>
33
34 #include "HadrontherapyMatrix.hh"
35 #include "HadrontherapyPrimaryGeneratorAction.hh"
36 #include "globals.hh"
37 #include "G4SystemOfUnits.hh"
38 #include "G4RunManager.hh"
39 #include "G4ParticleGun.hh"
40 #include "HadrontherapySteppingAction.hh"
41 #include "HadrontherapyAnalysisFileMessenger.hh"
42 #include "G4SystemOfUnits.hh"
43 #include <time.h>
44
45 HadrontherapyAnalysis* HadrontherapyAnalysis::instance = 0;
46 /////////////////////////////////////////////////////////////////////////////
47
48 HadrontherapyAnalysis::HadrontherapyAnalysis()
49 {
50 fMess = new HadrontherapyAnalysisFileMessenger(this);
51 }
52
53 /////////////////////////////////////////////////////////////////////////////
54 HadrontherapyAnalysis::~HadrontherapyAnalysis()
55 {
56 delete fMess;
57 }
58
59 /////////////////////////////////////////////////////////////////////////////
60 HadrontherapyAnalysis* HadrontherapyAnalysis::GetInstance(){
61
62 if (instance == 0) instance = new HadrontherapyAnalysis;
63 return instance;
64 }
65
66 HadrontherapyMatrix* HadrontherapyMatrix::instance = NULL;
67 G4bool HadrontherapyMatrix::secondary = false;
68
69
70 // Only return a pointer to matrix
71 HadrontherapyMatrix* HadrontherapyMatrix::GetInstance()
72 {
73 return instance;
74 }
75
76 /////////////////////////////////////////////////////////////////////////////
77 // This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it
78 // TODO A check on the parameters is required!
79 HadrontherapyMatrix* HadrontherapyMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass)
80 {
81 if (instance) delete instance;
82 instance = new HadrontherapyMatrix(voxelX, voxelY, voxelZ, mass);
83 instance -> Initialize();
84 return instance;
85 }
86
87 /////////////////////////////////////////////////////////////////////////////
88 HadrontherapyMatrix::HadrontherapyMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass):
89 stdFile("Dose.out"),
90 doseUnit(gray)
91 {
92 // Number of the voxels of the phantom
93 // For Y = Z = 1 the phantom is divided in slices (and not in voxels)
94 // orthogonal to the beam axis
95 numberOfVoxelAlongX = voxelX;
96 numberOfVoxelAlongY = voxelY;
97 numberOfVoxelAlongZ = voxelZ;
98 massOfVoxel = mass;
99
100
101 // Create the dose matrix
102 matrix = new G4double[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
103 if (matrix)
104 {
105 G4cout << "HadrontherapyMatrix: Memory space to store physical dose into " <<
106 numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
107 " voxels has been allocated " << G4endl;
108 }
109
110 else G4Exception("HadrontherapyMatrix::HadrontherapyMatrix()", "Hadrontherapy0005", FatalException, "Can't allocate memory to store physical dose!");
111
112
113 // Hit voxel (TrackID) marker
114 // This array mark the status of voxel, if a hit occur, with the trackID of the particle
115 // Must be initialized
116
117 hitTrack = new G4int[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
118 ClearHitTrack();
119 }
120
121 /////////////////////////////////////////////////////////////////////////////
122 HadrontherapyMatrix::~HadrontherapyMatrix()
123 {
124 delete[] matrix;
125 delete[] hitTrack;
126 Clear();
127 }
128
129 /////////////////////////////////////////////////////////////////////////////
130 void HadrontherapyMatrix::Clear()
131 {
132 for (size_t i=0; i<ionStore.size(); i++)
133 {
134 delete[] ionStore[i].dose;
135 delete[] ionStore[i].fluence;
136 }
137 ionStore.clear();
138 }
139
140 /////////////////////////////////////////////////////////////////////////////
141 // Initialise the elements of the matrix to zero
142
143 void HadrontherapyMatrix::Initialize()
144 {
145 // Clear ions store
146 Clear();
147 // Clear dose
148 for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
149 {
150 matrix[i] = 0;
151 }
152 }
153
154 /////////////////////////////////////////////////////////////////////////////
155 // Print generated nuclides list
156
157 /////////////////////////////////////////////////////////////////////////////
158 void HadrontherapyMatrix::PrintNuclides()
159 {
160 for (size_t i=0; i<ionStore.size(); i++)
161 {
162 G4cout << ionStore[i].name << G4endl;
163 }
164 }
165
166 /////////////////////////////////////////////////////////////////////////////
167 // Clear Hit voxel (TrackID) markers
168
169 void HadrontherapyMatrix::ClearHitTrack()
170 {
171 for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
172 }
173
174 // Return Hit status
175 G4int* HadrontherapyMatrix::GetHitTrack(G4int i, G4int j, G4int k)
176 {
177 return &(hitTrack[Index(i,j,k)]);
178 }
179
180 /////////////////////////////////////////////////////////////////////////////
181 // Dose methods...
182 // Fill DOSE/fluence matrix for secondary particles:
183 // If fluence parameter is true (default value is FALSE) then fluence at voxel (i, j, k) is increased.
184 // The energyDeposit parameter fill the dose matrix for voxel (i,j,k)
185 /////////////////////////////////////////////////////////////////////////////
186 G4bool HadrontherapyMatrix::Fill(G4int trackID,
187 G4ParticleDefinition* particleDef,
188 G4int i, G4int j, G4int k,
189 G4double energyDeposit,
190 G4bool fluence)
191 {
192
193 if ( (energyDeposit <=0. && !fluence) || !secondary) return false;
194
195 // Get Particle Data Group particle ID
196 G4int PDGencoding = particleDef -> GetPDGEncoding();
197 PDGencoding -= PDGencoding%10;
198
199 // Search for already allocated data...
200 for (size_t l=0; l < ionStore.size(); l++)
201 {
202 if (ionStore[l].PDGencoding == PDGencoding )
203 { // Is it a primary or a secondary particle?
204
205 if ( (trackID ==1 && ionStore[l].isPrimary) || (trackID !=1 && !ionStore[l].isPrimary))
206 {
207 if (energyDeposit > 0.)
208
209 ionStore[l].dose[Index(i, j, k)] += energyDeposit;
210
211 // Fill a matrix per each ion with the fluence
212
213 if (fluence) ionStore[l].fluence[Index(i, j, k)]++;
214 return true;
215 }
216 }
217 }
218 G4int Z = particleDef-> GetAtomicNumber();
219 G4int A = particleDef-> GetAtomicMass();
220 G4String fullName = particleDef -> GetParticleName();
221 G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy
222
223 // Let's put a new particle in our store...
224 ion newIon =
225 {
226 (trackID == 1) ? true:false,
227 PDGencoding,
228 name,
229 name.length(),
230 Z,
231 A,
232 new G4double[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ],
233 new unsigned int[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ]
234 };
235
236
237 // Initialize data
238 if (newIon.dose && newIon.fluence)
239 {
240 for(G4int q=0; q<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; q++)
241 {
242 newIon.dose[q] = 0.;
243 newIon.fluence[q] = 0;
244 }
245
246 if (energyDeposit > 0.) newIon.dose[Index(i, j, k)] += energyDeposit;
247 if (fluence) newIon.fluence[Index(i, j, k)]++;
248
249 ionStore.push_back(newIon);
250 return true;
251 }
252
253 else // XXX Out of memory! XXX
254
255 {
256 return false;
257 }
258 }
259
260 /////////////////////////////////////////////////////////////////////////////
261 /////////////////////////////////////////////////////////////////////////////
262 // Methods to store data to filenames...
263 ////////////////////////////////////////////////////////////////////////////
264 ////////////////////////////////////////////////////////////////////////////
265 //
266 // General method to store matrix data to filename
267 void HadrontherapyMatrix::StoreMatrix(G4String file, void* data, size_t psize)
268 {
269 if (data)
270 {
271 ofs.open(file, std::ios::out);
272 if (ofs.is_open())
273 {
274 for(G4int i = 0; i < numberOfVoxelAlongX; i++)
275 for(G4int j = 0; j < numberOfVoxelAlongY; j++)
276 for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
277 {
278 G4int n = Index(i, j, k);
279
280 if (psize == sizeof(unsigned int))
281 {
282 unsigned int* pdata = (unsigned int*)data;
283
284 if (pdata[n])
285
286 ofs << i << '\t' << j << '\t' << k << '\t' << pdata[n] << G4endl;
287 }
288
289 else if (psize == sizeof(G4double))
290
291 {
292 G4double* pdata = (G4double*)data;
293 if (pdata[n]) ofs << i << '\t' << j << '\t' << k << '\t' << pdata[n] << G4endl;
294 }
295 }
296 ofs.close();
297 }
298 }
299 }
300
301 /////////////////////////////////////////////////////////////////////////////
302 // Store fluence per single ion in multiple files
303 void HadrontherapyMatrix::StoreFluenceData()
304 {
305 for (size_t i=0; i < ionStore.size(); i++){
306 StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int));
307 }
308 }
309
310 /////////////////////////////////////////////////////////////////////////////
311 // Store dose per single ion in multiple files
312 void HadrontherapyMatrix::StoreDoseData()
313 {
314
315 for (size_t i=0; i < ionStore.size(); i++){
316 StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double));
317 }
318 }
319
320 ////////////////////////////////////////////////////////////////////////
321 // Store dose into a single file
322 // or in histograms. Please, note that this function is called via
323 // messenger commands
324 // defined in the HadrontherapyAnalysisFileMessenger.cc class file
325 void HadrontherapyMatrix::StoreDoseFluenceAscii(G4String file)
326 {
327 #define width 15L
328 filename = (file=="") ? stdFile:file;
329
330 // Sort like periodic table
331
332 std::sort(ionStore.begin(), ionStore.end());
333 G4cout << "Dose is being written to " << filename << G4endl;
334 ofs.open(filename, std::ios::out);
335
336 if (ofs.is_open())
337 {
338 // Write the voxels index and the list of particles/ions
339 //ofs << std::setprecision(6) << std::left << "i\tj\tk\t";
340 ofs << "i" << '\t' << "j" << '\t' << "k";
341 G4cout << "i" << '\t' << "j" << '\t' << "k";
342
343 // Total dose
344 ofs <<'\t' <<"Dose(Gy)";
345 //ofs << std::setw(width) << "Dose(Gy)";
346 G4cout << '\t' << "Dose(Gy)";
347
348 G4String fluence = "_f";
349 if (secondary)
350 {
351 for (size_t l=0; l < ionStore.size(); l++)
352 {
353 G4String a = (ionStore[l].isPrimary) ? "_1":""; // is it a primary?
354
355 // ofs << std::setw(width) << ionStore[l].name + a <<
356 // std::setw(width) << ionStore[l].name + a + fluence;
357
358 ofs << '\t' << ionStore[l].name + a <<
359 '\t' << ionStore[l].name + a + fluence;
360
361 G4cout << '\t' << ionStore[l].name + a <<
362 '\t' << ionStore[l].name + a + fluence;
363
364 }
365 //ofs << G4endl;
366 }
367
368 // Write data
369 for(G4int i = 0; i < numberOfVoxelAlongX; i++)
370 for(G4int j = 0; j < numberOfVoxelAlongY; j++)
371 for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
372 {
373 G4int n = Index(i, j, k);
374
375 if (matrix[n])
376 {
377 ofs << G4endl;
378 ofs << i << '\t' << j << '\t' << k << '\t';
379
380 // Total dose
381 //ofs << std::setw(width) << (matrix[n]/massOfVoxel)/doseUnit;
382 ofs << (matrix[n]/massOfVoxel)/doseUnit;
383
384 if (secondary)
385 {
386 for (size_t l=0; l < ionStore.size(); l++)
387 {
388 // Fill ASCII file rows
389 //ofs << std::setw(width) << ionStore[l].dose[n]/massOfVoxel/doseUnit <<
390 // std::setw(width) << ionStore[l].fluence[n];
391
392 ofs << '\t' << ionStore[l].dose[n]/massOfVoxel/doseUnit <<
393 '\t' << ionStore[l].fluence[n];
394 }
395 }
396 }
397 }
398 ofs.close();
399 }
400 }
401 //////////////////////////////////////////////////////////////////////////////
402 void HadrontherapyMatrix::Fill(G4int i, G4int j, G4int k,
403 G4double energyDeposit)
404 {
405 if (matrix)
406 matrix[Index(i,j,k)] += energyDeposit;
407
408 // Store the energy deposit in the matrix element corresponding
409 // to the phantom voxel
410 }
411
412
413
414
415