| Geant4 Cross Reference |
1 //
2 // ********************************************************************
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4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
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15 // * use. Please see the license in the file LICENSE and URL above *
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17 // * *
18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboration. *
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21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publications, and indicate your *
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24 // ********************************************************************
25 //
26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708
30 // J. Comput. Phys. 274 (2014) 841-882
31 // The Geant4-DNA web site is available at http://geant4-dna.org
32 //
33 // Authors: J. Naoki D. Kondo (UCSF, US)
34 // J. Ramos-Mendez and B. Faddegon (UCSF, US)
35 //
36 /// \file ScoreStrandBreaks.cc
37 /// \brief Implementation of the ScoreStrandBreaks class
38
39 #include "ScoreStrandBreaks.hh"
40
41 #include "G4AnalysisManager.hh"
42 #include "G4DNAChemistryManager.hh"
43 #include "G4Event.hh"
44 #include "G4EventManager.hh"
45 #include "G4Scheduler.hh"
46 #include "G4UImessenger.hh"
47 #include "G4UnitsTable.hh"
48
49 #include <G4EventManager.hh>
50 #include <G4SystemOfUnits.hh>
51 #include <globals.hh>
52
53 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
54
55 ScoreStrandBreaks::ScoreStrandBreaks(G4String name, DetectorConstruction* detect, G4double* radius)
56 : G4VPrimitiveScorer(name), G4UImessenger(), fpDetector(detect)
57 {
58 fpOutputFileUI = new G4UIcmdWithAString("/scorer/StrandBreak/OutputFile", this);
59 fpOutputFileUI->SetGuidance("Set output file name");
60
61 fpOutputTypeUI = new G4UIcmdWithAString("/scorer/StrandBreak/OutputFormat", this);
62 fpOutputTypeUI->SetGuidance("Set output file format: ASCII by default");
63
64 fpBreakEnergyUI = new G4UIcmdWithADoubleAndUnit("/scorer/StrandBreak/BreakEnergy", this);
65 fpBreakEnergyUI->SetDefaultUnit("eV");
66 fpBreakEnergyUI->SetGuidance("Direct SSB energy treshold");
67
68 fRadius = radius;
69 fpGun = new MoleculeInserter(true);
70 // G4DNAChemistryManager::Instance()->SetGun(fpGun);
71 }
72
73 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
74
75 ScoreStrandBreaks::~ScoreStrandBreaks()
76 {
77 delete fpOutputFileUI;
78 delete fpBreakEnergyUI;
79 delete fpOutputTypeUI;
80 delete fpGun;
81 }
82
83 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
84
85 void ScoreStrandBreaks::SetNewValue(G4UIcommand* command, G4String newValue)
86 {
87 if (command == fpOutputFileUI) {
88 fOutputName = newValue;
89 }
90
91 if (command == fpBreakEnergyUI) {
92 fBreakEnergy = fpBreakEnergyUI->GetNewDoubleValue(newValue);
93 }
94
95 if (command == fpOutputTypeUI) {
96 fOutputType = newValue;
97 G4StrUtil::to_lower(fOutputType);
98 }
99 }
100
101 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
102
103 G4bool ScoreStrandBreaks::ProcessHits(G4Step* aStep, G4TouchableHistory*)
104 {
105 G4double edep = aStep->GetTotalEnergyDeposit();
106 if (edep <= 0) {
107 return FALSE;
108 }
109 fEnergyDeposit += edep;
110
111 G4StepPoint* aStepPoint = aStep->GetTrack()->GetStep()->GetPreStepPoint();
112 G4TouchableHandle aTouchable = aStepPoint->GetTouchableHandle();
113 G4String volumeName = aTouchable->GetVolume()->GetName();
114 G4StrUtil::to_lower(volumeName);
115 G4int strand = 0;
116
117 if (G4StrUtil::contains(volumeName, "deoxyribose")
118 || G4StrUtil::contains(volumeName, "phosphate"))
119 {
120 if (G4StrUtil::contains(volumeName, "1"))
121 strand = 1;
122 else if (G4StrUtil::contains(volumeName, "2"))
123 strand = 2;
124
125 G4int StrandID = strand;
126 G4int BaseID = aTouchable->GetReplicaNumber(0);
127 G4int PlasmidID = aTouchable->GetReplicaNumber(1);
128 G4int EventID = G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
129
130 fEnergyDepositMap[EventID][PlasmidID][BaseID][StrandID] += edep;
131 return TRUE;
132 }
133
134 if (!fDNAInserted) {
135 // Insert DNA molecules
136 std::vector<std::vector<G4int>> DNADetails = fpDetector->GetDNADetails();
137 std::vector<G4ThreeVector> DNAPositions = fpDetector->GetDNAPositions();
138 std::vector<G4String> DNAMolecules = fpDetector->GetDNANames();
139
140 fpGun->Clean();
141 for (size_t i = 0; i < DNAPositions.size(); i++) {
142 fpGun->AddMolecule(DNAMolecules[i], DNAPositions[i], 1.0 * ps);
143 }
144 fpGun->DefineTracks();
145
146 fDNAInserted = true;
147 }
148 return FALSE;
149 }
150
151 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
152
153 void ScoreStrandBreaks::Initialize(G4HCofThisEvent*) {}
154
155 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
156
157 void ScoreStrandBreaks::EndOfEvent(G4HCofThisEvent*)
158 {
159 // Get EventID
160 G4int EventID = G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
161
162 // Absorbed Dose
163 G4double volume = 4.0 / 3 * 3.14159 * (*fRadius) * (*fRadius) * (*fRadius) / 8;
164 G4double density = 1.0 * g / cm3;
165 G4double mass = density * volume;
166 G4double Dose = fEnergyDeposit / mass;
167 fDoseArray[EventID] = Dose / gray;
168
169 // Direct Strand Breaks
170 for (auto EventAndElse : fEnergyDepositMap) {
171 G4int event = EventAndElse.first;
172 for (auto PlasmidAndElse : EventAndElse.second) {
173 G4int plasmid = PlasmidAndElse.first;
174 for (auto BaseAndElse : PlasmidAndElse.second) {
175 G4int base = BaseAndElse.first;
176 for (auto StrandAndEdep : BaseAndElse.second) {
177 G4int strand = StrandAndEdep.first;
178 G4double edep = StrandAndEdep.second;
179 if (edep > fBreakEnergy) fDirectDamageMap[event].push_back({plasmid, base, strand});
180 }
181 }
182 }
183 }
184 fEnergyDepositMap.clear();
185
186 // Indirect Strand Breaks
187 std::vector<std::vector<G4int>> DNADetails = fpDetector->GetDNADetails();
188 std::vector<G4Track*> InsertedTracks = fpGun->GetInsertedTracks();
189 std::vector<std::vector<G4int>> IndirectBreaks;
190
191 for (size_t i = 0; i < InsertedTracks.size(); i++) {
192 if (InsertedTracks[i]->GetTrackStatus() == fStopAndKill)
193 IndirectBreaks.push_back(DNADetails[i]);
194 }
195
196 for (size_t i = 0; i < IndirectBreaks.size(); i++) {
197 fIndirectDamageMap[EventID].push_back(IndirectBreaks[i]);
198 }
199
200 fEnergyDeposit = 0;
201 fDNAInserted = false;
202 fnbOfEvents++;
203 }
204
205 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
206
207 void ScoreStrandBreaks::AbsorbResultsFromWorkerScorer(G4VPrimitiveScorer* workerScorer)
208 {
209 ScoreStrandBreaks* right =
210 dynamic_cast<ScoreStrandBreaks*>(dynamic_cast<G4VPrimitiveScorer*>(workerScorer));
211
212 if (right == 0) return;
213 if (right == this) return;
214
215 DamageMap WorkerDirectDamageMap = right->fDirectDamageMap;
216 DamageMap WorkerIndirectDamageMap = right->fIndirectDamageMap;
217 std::map<G4int, G4double> WorkerDose = right->fDoseArray;
218
219 for (auto EventAndBreaks : WorkerDirectDamageMap) {
220 G4int EventID = EventAndBreaks.first;
221 std::vector<std::vector<G4int>> Breaks = EventAndBreaks.second;
222 for (size_t i = 0; i < Breaks.size(); i++) {
223 fDirectDamageMap[EventID].push_back(Breaks[i]);
224 }
225 }
226
227 for (auto EventAndBreaks : WorkerIndirectDamageMap) {
228 G4int EventID = EventAndBreaks.first;
229 std::vector<std::vector<G4int>> Breaks = EventAndBreaks.second;
230 for (size_t i = 0; i < Breaks.size(); i++) {
231 fIndirectDamageMap[EventID].push_back(Breaks[i]);
232 }
233 }
234
235 for (auto EventAndDose : WorkerDose) {
236 G4int EventID = EventAndDose.first;
237 G4double dose = EventAndDose.second;
238 fDoseArray[EventID] = dose;
239 }
240
241 fnbOfEvents += right->fnbOfEvents;
242 right->Clear();
243 }
244
245 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
246
247 void ScoreStrandBreaks::Clear()
248 {
249 if (fDirectDamageMap.size() != 0) fDirectDamageMap.clear();
250
251 if (fIndirectDamageMap.size() != 0) fIndirectDamageMap.clear();
252
253 if (fEnergyDepositMap.size() != 0) fEnergyDepositMap.clear();
254
255 if (fDoseArray.size() != 0) fDoseArray.clear();
256 }
257
258 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
259
260 void ScoreStrandBreaks::DrawAll() {}
261
262 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
263
264 void ScoreStrandBreaks::PrintAll() {}
265
266 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
267
268 void ScoreStrandBreaks::OutputAndClear(G4double LET, G4double LET_STD)
269 {
270 if (G4Threading::IsWorkerThread()) return;
271
272 if (fOutputType != "ascii") {
273 G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
274
275 if (fOutputType == "csv")
276 analysisManager->SetDefaultFileType("csv");
277
278 else if (fOutputType == "root")
279 analysisManager->SetDefaultFileType("root");
280
281 else if (fOutputType == "xml")
282 analysisManager->SetDefaultFileType("xml");
283
284 WriteWithAnalysisManager(analysisManager);
285 }
286
287 else
288 ASCII(LET, LET_STD);
289
290 Clear();
291 }
292
293 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
294
295 void ScoreStrandBreaks::WriteWithAnalysisManager(G4VAnalysisManager* analysisManager)
296 {
297 analysisManager->OpenFile(fOutputName);
298 int fNtupleID = analysisManager->CreateNtuple("SB", "Direct And Indirect SBs");
299 analysisManager->CreateNtupleIColumn(fNtupleID, "EventID");
300 analysisManager->CreateNtupleIColumn(fNtupleID, "PlasmidID");
301 analysisManager->CreateNtupleIColumn(fNtupleID, "StrandID");
302 analysisManager->CreateNtupleIColumn(fNtupleID, "BaseID");
303 analysisManager->CreateNtupleIColumn(fNtupleID, "DamageID");
304 analysisManager->CreateNtupleIColumn(fNtupleID, "BreakID");
305 analysisManager->FinishNtuple(fNtupleID);
306
307 for (G4int i = 0; i < fnbOfEvents; i++) {
308 if (fDirectDamageMap.find(i) != fDirectDamageMap.end()) {
309 for (size_t j = 0; j < fDirectDamageMap[i].size(); j++) {
310 std::vector<G4int> Break = fDirectDamageMap[i][j];
311 analysisManager->FillNtupleIColumn(fNtupleID, 0, i);
312 analysisManager->FillNtupleIColumn(fNtupleID, 1, Break[0]);
313 analysisManager->FillNtupleIColumn(fNtupleID, 2, Break[1]);
314 analysisManager->FillNtupleIColumn(fNtupleID, 3, Break[2]);
315 analysisManager->FillNtupleIColumn(fNtupleID, 4, 1);
316 analysisManager->AddNtupleRow(fNtupleID);
317 }
318 }
319
320 if (fIndirectDamageMap.find(i) != fIndirectDamageMap.end()) {
321 for (size_t j = 0; j < fIndirectDamageMap[i].size(); j++) {
322 std::vector<G4int> Break = fIndirectDamageMap[i][j];
323 analysisManager->FillNtupleIColumn(fNtupleID, 0, i);
324 analysisManager->FillNtupleIColumn(fNtupleID, 1, Break[0]);
325 analysisManager->FillNtupleIColumn(fNtupleID, 2, Break[1]);
326 analysisManager->FillNtupleIColumn(fNtupleID, 3, Break[2]);
327 analysisManager->FillNtupleIColumn(fNtupleID, 4, 2);
328 analysisManager->AddNtupleRow(fNtupleID);
329 }
330 }
331 }
332
333 analysisManager->Write();
334 analysisManager->CloseFile();
335 }
336
337 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
338
339 void ScoreStrandBreaks::ASCII(G4double LET, G4double LET_STD)
340 {
341 std::ofstream dna(fOutputName + ".txt");
342
343 dna << "# DNA SB Map File" << G4endl;
344 dna << "# LET = " << LET / (keV / um) << " +- " << LET_STD / (keV / um) << " keV / um" << G4endl;
345 dna << "#" << std::setw(11) << "Event-ID" << std::setw(12) << "Plasmid-ID" << std::setw(12)
346 << "BP-ID" << std::setw(12) << "Strand-ID" << std::setw(10) << "Break-ID" << std::setw(12)
347 << "Dose (Gy) " << G4endl;
348
349 for (G4int i = 0; i < fnbOfEvents; i++) {
350 if (fDirectDamageMap.find(i) != fDirectDamageMap.end()) {
351 for (size_t j = 0; j < fDirectDamageMap[i].size(); j++) {
352 std::vector<G4int> Break = fDirectDamageMap[i][j];
353 dna << std::setw(12) << i << std::setw(12) << Break[0] << std::setw(12) << Break[1]
354 << std::setw(12) << Break[2] << std::setw(10) << 1 << std::setw(12) << fDoseArray[i]
355 << G4endl;
356 }
357 }
358
359 if (fIndirectDamageMap.find(i) != fIndirectDamageMap.end()) {
360 for (size_t j = 0; j < fIndirectDamageMap[i].size(); j++) {
361 std::vector<G4int> Break = fIndirectDamageMap[i][j];
362 dna << std::setw(12) << i << std::setw(12) << Break[0] << std::setw(12) << Break[1]
363 << std::setw(12) << Break[2] << std::setw(10) << 2 << std::setw(12) << fDoseArray[i]
364 << G4endl;
365 }
366 }
367 }
368
369 dna.close();
370 }
371
372 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......