Geant4  10.01.p03
DicomDetectorConstruction.cc
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26 // $Id: DicomDetectorConstruction.cc 84839 2014-10-21 13:44:55Z gcosmo $
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30 //
31 
32 #include "globals.hh"
33 
34 #include "G4Box.hh"
35 #include "G4LogicalVolume.hh"
36 #include "G4VPhysicalVolume.hh"
37 #include "G4PVPlacement.hh"
38 #include "G4Material.hh"
39 #include "G4Element.hh"
40 #include "G4UIcommand.hh"
41 #include "G4PhysicalConstants.hh"
42 #include "G4SystemOfUnits.hh"
43 
46 
47 #include "DicomRunAction.hh"
48 #include "DicomRun.hh"
49 
50 #include "G4VisAttributes.hh"
51 
52 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
55  fAir(0),
56 
57  fWorld_solid(0),
58  fWorld_logic(0),
59  fWorld_phys(0),
60 
61  fContainer_solid(0),
62  fContainer_logic(0),
63  fContainer_phys(0),
64 
65  fNoFiles(0),
66  fMateIDs(0),
67 
68  fZSliceHeaderMerged(0),
69 
70  fNVoxelX(0),
71  fNVoxelY(0),
72  fNVoxelZ(0),
73  fVoxelHalfDimX(0),
74  fVoxelHalfDimY(0),
75  fVoxelHalfDimZ(0),
76 
77  fConstructed(false)
78 {
79 
80 }
81 
82 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
84 {
85 }
86 
87 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
89 {
90  if(!fConstructed || fWorld_phys == 0) {
91  fConstructed = true;
93 
94  //----- Build world
95  G4double worldXDimension = 1.*m;
96  G4double worldYDimension = 1.*m;
97  G4double worldZDimension = 1.*m;
98 
99  fWorld_solid = new G4Box( "WorldSolid",
100  worldXDimension,
101  worldYDimension,
102  worldZDimension );
103 
105  fAir,
106  "WorldLogical",
107  0, 0, 0 );
108 
109  fWorld_phys = new G4PVPlacement( 0,
110  G4ThreeVector(0,0,0),
111  "World",
112  fWorld_logic,
113  0,
114  false,
115  0 );
116 
117  ReadPhantomData();
118 
121  }
122  return fWorld_phys;
123 }
124 
125 
126 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
128 {
129  // Creating elements :
130  G4double z, a, density;
132 
133  G4Element* elC = new G4Element( name = "Carbon",
134  symbol = "C",
135  z = 6.0, a = 12.011 * g/mole );
136  G4Element* elH = new G4Element( name = "Hydrogen",
137  symbol = "H",
138  z = 1.0, a = 1.008 * g/mole );
139  G4Element* elN = new G4Element( name = "Nitrogen",
140  symbol = "N",
141  z = 7.0, a = 14.007 * g/mole );
142  G4Element* elO = new G4Element( name = "Oxygen",
143  symbol = "O",
144  z = 8.0, a = 16.00 * g/mole );
145  G4Element* elNa = new G4Element( name = "Sodium",
146  symbol = "Na",
147  z= 11.0, a = 22.98977* g/mole );
148  G4Element* elS = new G4Element( name = "Sulfur",
149  symbol = "S",
150  z = 16.0,a = 32.065* g/mole );
151  G4Element* elCl = new G4Element( name = "Chlorine",
152  symbol = "P",
153  z = 17.0, a = 35.453* g/mole );
154  G4Element* elK = new G4Element( name = "Potassium",
155  symbol = "P",
156  z = 19.0, a = 30.0983* g/mole );
157  G4Element* elP = new G4Element( name = "Phosphorus",
158  symbol = "P",
159  z = 30.0, a = 30.973976* g/mole );
160  G4Element* elFe = new G4Element( name = "Iron",
161  symbol = "Fe",
162  z = 26, a = 56.845* g/mole );
163  G4Element* elMg = new G4Element( name = "Magnesium",
164  symbol = "Mg",
165  z = 12.0, a = 24.3050* g/mole );
166  G4Element* elCa = new G4Element( name="Calcium",
167  symbol = "Ca",
168  z = 20.0, a = 40.078* g/mole );
169 
170  // Creating Materials :
171  G4int numberofElements;
172 
173  // Air
174  fAir = new G4Material( "Air",
175  1.290*mg/cm3,
176  numberofElements = 2 );
177  fAir->AddElement(elN, 0.7);
178  fAir->AddElement(elO, 0.3);
179 
180  // Lung Inhale
181  G4Material* lunginhale = new G4Material( "LungInhale",
182  density = 0.217*g/cm3,
183  numberofElements = 9);
184  lunginhale->AddElement(elH,0.103);
185  lunginhale->AddElement(elC,0.105);
186  lunginhale->AddElement(elN,0.031);
187  lunginhale->AddElement(elO,0.749);
188  lunginhale->AddElement(elNa,0.002);
189  lunginhale->AddElement(elP,0.002);
190  lunginhale->AddElement(elS,0.003);
191  lunginhale->AddElement(elCl,0.002);
192  lunginhale->AddElement(elK,0.003);
193 
194  // Lung exhale
195  G4Material* lungexhale = new G4Material( "LungExhale",
196  density = 0.508*g/cm3,
197  numberofElements = 9 );
198  lungexhale->AddElement(elH,0.103);
199  lungexhale->AddElement(elC,0.105);
200  lungexhale->AddElement(elN,0.031);
201  lungexhale->AddElement(elO,0.749);
202  lungexhale->AddElement(elNa,0.002);
203  lungexhale->AddElement(elP,0.002);
204  lungexhale->AddElement(elS,0.003);
205  lungexhale->AddElement(elCl,0.002);
206  lungexhale->AddElement(elK,0.003);
207 
208  // Adipose tissue
209  G4Material* adiposeTissue = new G4Material( "AdiposeTissue",
210  density = 0.967*g/cm3,
211  numberofElements = 7);
212  adiposeTissue->AddElement(elH,0.114);
213  adiposeTissue->AddElement(elC,0.598);
214  adiposeTissue->AddElement(elN,0.007);
215  adiposeTissue->AddElement(elO,0.278);
216  adiposeTissue->AddElement(elNa,0.001);
217  adiposeTissue->AddElement(elS,0.001);
218  adiposeTissue->AddElement(elCl,0.001);
219 
220  // Breast
221  G4Material* breast = new G4Material( "Breast",
222  density = 0.990*g/cm3,
223  numberofElements = 8 );
224  breast->AddElement(elH,0.109);
225  breast->AddElement(elC,0.506);
226  breast->AddElement(elN,0.023);
227  breast->AddElement(elO,0.358);
228  breast->AddElement(elNa,0.001);
229  breast->AddElement(elP,0.001);
230  breast->AddElement(elS,0.001);
231  breast->AddElement(elCl,0.001);
232 
233  // Water
234  G4Material* water = new G4Material( "Water",
235  density = 1.0*g/cm3,
236  numberofElements = 2 );
237  water->AddElement(elH,0.112);
238  water->AddElement(elO,0.888);
239 
240  // Muscle
241  G4Material* muscle = new G4Material( "Muscle",
242  density = 1.061*g/cm3,
243  numberofElements = 9 );
244  muscle->AddElement(elH,0.102);
245  muscle->AddElement(elC,0.143);
246  muscle->AddElement(elN,0.034);
247  muscle->AddElement(elO,0.710);
248  muscle->AddElement(elNa,0.001);
249  muscle->AddElement(elP,0.002);
250  muscle->AddElement(elS,0.003);
251  muscle->AddElement(elCl,0.001);
252  muscle->AddElement(elK,0.004);
253 
254  // Liver
255  G4Material* liver = new G4Material( "Liver",
256  density = 1.071*g/cm3,
257  numberofElements = 9);
258  liver->AddElement(elH,0.102);
259  liver->AddElement(elC,0.139);
260  liver->AddElement(elN,0.030);
261  liver->AddElement(elO,0.716);
262  liver->AddElement(elNa,0.002);
263  liver->AddElement(elP,0.003);
264  liver->AddElement(elS,0.003);
265  liver->AddElement(elCl,0.002);
266  liver->AddElement(elK,0.003);
267 
268  // Trabecular Bone
269  G4Material* trabecularBone = new G4Material( "TrabecularBone",
270  density = 1.159*g/cm3,
271  numberofElements = 12 );
272  trabecularBone->AddElement(elH,0.085);
273  trabecularBone->AddElement(elC,0.404);
274  trabecularBone->AddElement(elN,0.058);
275  trabecularBone->AddElement(elO,0.367);
276  trabecularBone->AddElement(elNa,0.001);
277  trabecularBone->AddElement(elMg,0.001);
278  trabecularBone->AddElement(elP,0.034);
279  trabecularBone->AddElement(elS,0.002);
280  trabecularBone->AddElement(elCl,0.002);
281  trabecularBone->AddElement(elK,0.001);
282  trabecularBone->AddElement(elCa,0.044);
283  trabecularBone->AddElement(elFe,0.001);
284 
285  // Dense Bone
286  G4Material* denseBone = new G4Material( "DenseBone",
287  density = 1.575*g/cm3,
288  numberofElements = 11 );
289  denseBone->AddElement(elH,0.056);
290  denseBone->AddElement(elC,0.235);
291  denseBone->AddElement(elN,0.050);
292  denseBone->AddElement(elO,0.434);
293  denseBone->AddElement(elNa,0.001);
294  denseBone->AddElement(elMg,0.001);
295  denseBone->AddElement(elP,0.072);
296  denseBone->AddElement(elS,0.003);
297  denseBone->AddElement(elCl,0.001);
298  denseBone->AddElement(elK,0.001);
299  denseBone->AddElement(elCa,0.146);
300 
301  //----- Put the materials in a vector
302  fOriginalMaterials.push_back(fAir); // rho = 0.00129
303  fOriginalMaterials.push_back(lunginhale); // rho = 0.217
304  fOriginalMaterials.push_back(lungexhale); // rho = 0.508
305  fOriginalMaterials.push_back(adiposeTissue); // rho = 0.967
306  fOriginalMaterials.push_back(breast ); // rho = 0.990
307  fOriginalMaterials.push_back(water); // rho = 1.018
308  fOriginalMaterials.push_back(muscle); // rho = 1.061
309  fOriginalMaterials.push_back(liver); // rho = 1.071
310  fOriginalMaterials.push_back(trabecularBone); // rho = 1.159
311  fOriginalMaterials.push_back(denseBone); // rho = 1.575
312 
313 }
314 
315 
316 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
318 {
319 
320  G4String dataFile = "Data.dat";
321  std::ifstream finDF(dataFile.c_str());
322  G4String fname;
323  if(finDF.good() != 1 ) {
324  G4String descript = "Problem reading data file: "+dataFile;
325  G4Exception(" DicomDetectorConstruction::ReadPhantomData",
326  "",
328  descript);
329  }
330 
331  G4int compression;
332  finDF >> compression; // not used here
333 
334  finDF >> fNoFiles;
335  for(G4int i = 0; i < fNoFiles; i++ ) {
336  finDF >> fname;
337  //--- Read one data file
338  fname += ".g4dcm";
339  ReadPhantomDataFile(fname);
340  }
341 
342  //----- Merge data headers
344 
345  finDF.close();
346 
347 }
348 
349 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
351 {
352 #ifdef G4VERBOSE
353  G4cout << " DicomDetectorConstruction::ReadPhantomDataFile opening file "
354  << fname << G4endl;
355 #endif
356  std::ifstream fin(fname.c_str(), std::ios_base::in);
357  if( !fin.is_open() ) {
358  G4Exception("DicomDetectorConstruction::ReadPhantomDataFile",
359  "",
361  G4String("File not found " + fname ).c_str());
362  }
363  //----- Define density differences (maximum density difference to create
364  // a new material)
365  char* part = getenv( "DICOM_CHANGE_MATERIAL_DENSITY" );
366  G4double densityDiff = -1.;
367  if( part ) densityDiff = G4UIcommand::ConvertToDouble(part);
368  if( densityDiff != -1. ) {
369  for( unsigned int ii = 0; ii < fOriginalMaterials.size(); ii++ ){
370  fDensityDiffs[ii] = densityDiff; //currently all materials with
371  // same difference
372  }
373  }else {
374  if( fMaterials.size() == 0 ) { // do it only for first slice
375  for( unsigned int ii = 0; ii < fOriginalMaterials.size(); ii++ ){
376  fMaterials.push_back( fOriginalMaterials[ii] );
377  }
378  }
379  }
380 
381  //----- Read data header
382  DicomPhantomZSliceHeader* sliceHeader = new DicomPhantomZSliceHeader( fin );
383  fZSliceHeaders.push_back( sliceHeader );
384 
385  //----- Read material indices
386  G4int nVoxels = sliceHeader->GetNoVoxels();
387 
388  //--- If first slice, initiliaze fMateIDs
389  if( fZSliceHeaders.size() == 1 ) {
390  //fMateIDs = new unsigned int[fNoFiles*nVoxels];
391  fMateIDs = new size_t[fNoFiles*nVoxels];
392 
393  }
394 
395  unsigned int mateID;
396  // number of voxels from previously read slices
397  G4int voxelCopyNo = (fZSliceHeaders.size()-1)*nVoxels;
398  for( G4int ii = 0; ii < nVoxels; ii++, voxelCopyNo++ ){
399  fin >> mateID;
400  fMateIDs[voxelCopyNo] = mateID;
401  }
402 
403  //----- Read material densities and build new materials if two voxels have
404  // same material but its density is in a different density interval
405  // (size of density intervals defined by densityDiff)
407  // number of voxels from previously read slices
408  voxelCopyNo = (fZSliceHeaders.size()-1)*nVoxels;
409  for( G4int ii = 0; ii < nVoxels; ii++, voxelCopyNo++ ){
410  fin >> density;
411 
412  //-- Get material from list of original materials
413  mateID = fMateIDs[voxelCopyNo];
414  G4Material* mateOrig = fOriginalMaterials[mateID];
415 
416  //-- Get density bin: middle point of the bin in which the current
417  // density is included
418  G4String newMateName = mateOrig->GetName();
419  float densityBin = 0.;
420  if( densityDiff != -1.) {
421  densityBin = fDensityDiffs[mateID] *
422  (G4int(density/fDensityDiffs[mateID])+0.5);
423  //-- Build the new material name
424  newMateName += G4UIcommand::ConvertToString(densityBin);
425  }
426 
427  //-- Look if a material with this name is already created
428  // (because a previous voxel was already in this density bin)
429  unsigned int im;
430  for( im = 0; im < fMaterials.size(); im++ ){
431  if( fMaterials[im]->GetName() == newMateName ) {
432  break;
433  }
434  }
435  //-- If material is already created use index of this material
436  if( im != fMaterials.size() ) {
437  fMateIDs[voxelCopyNo] = im;
438  //-- else, create the material
439  } else {
440  if( densityDiff != -1.) {
441  fMaterials.push_back( BuildMaterialWithChangingDensity( mateOrig,
442  densityBin, newMateName ) );
443  fMateIDs[voxelCopyNo] = fMaterials.size()-1;
444  } else {
445  G4cerr << " im " << im << " < " << fMaterials.size() << " name "
446  << newMateName << G4endl;
447  G4Exception("DicomDetectorConstruction::ReadPhantomDataFile",
448  "",
450  "Wrong index in material"); //it should never reach here
451  }
452  }
453  }
454 
455 }
456 
457 
458 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
460 {
461  //----- Images must have the same dimension ...
463  for( unsigned int ii = 1; ii < fZSliceHeaders.size(); ii++ ) {
465  };
466 
467 }
468 
469 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
471  const G4Material* origMate, float density, G4String newMateName )
472 {
473  //----- Copy original material, but with new density
474  G4int nelem = origMate->GetNumberOfElements();
475  G4Material* mate = new G4Material( newMateName, density*g/cm3, nelem,
476  kStateUndefined, STP_Temperature );
477 
478  for( G4int ii = 0; ii < nelem; ii++ ){
479  G4double frac = origMate->GetFractionVector()[ii];
480  G4Element* elem = const_cast<G4Element*>(origMate->GetElement(ii));
481  mate->AddElement( elem, frac );
482  }
483 
484  return mate;
485 }
486 
487 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
489 {
490  //---- Extract number of voxels and voxel dimensions
494 
498 #ifdef G4VERBOSE
499  G4cout << " fNVoxelX " << fNVoxelX << " fVoxelHalfDimX " << fVoxelHalfDimX
500  <<G4endl;
501  G4cout << " fNVoxelY " << fNVoxelY << " fVoxelHalfDimY " << fVoxelHalfDimY
502  <<G4endl;
503  G4cout << " fNVoxelZ " << fNVoxelZ << " fVoxelHalfDimZ " << fVoxelHalfDimZ
504  <<G4endl;
505  G4cout << " totalPixels " << fNVoxelX*fNVoxelY*fNVoxelZ << G4endl;
506 #endif
507 
508  //----- Define the volume that contains all the voxels
509  fContainer_solid = new G4Box("phantomContainer",fNVoxelX*fVoxelHalfDimX,
514  //the material is not important, it will be fully filled by the voxels
515  fMaterials[0],
516  "phantomContainer",
517  0, 0, 0 );
518  //--- Place it on the world
519  G4double fOffsetX = (fZSliceHeaderMerged->GetMaxX() +
520  fZSliceHeaderMerged->GetMinX() ) /2.;
521  G4double fOffsetY = (fZSliceHeaderMerged->GetMaxY() +
522  fZSliceHeaderMerged->GetMinY() ) /2.;
523  G4double fOffsetZ = (fZSliceHeaderMerged->GetMaxZ() +
524  fZSliceHeaderMerged->GetMinZ() ) /2.;
525  G4ThreeVector posCentreVoxels(fOffsetX,fOffsetY,fOffsetZ);
526 #ifdef G4VERBOSE
527  G4cout << " placing voxel container volume at " << posCentreVoxels << G4endl;
528 #endif
530  new G4PVPlacement(0, // rotation
531  posCentreVoxels,
532  fContainer_logic, // The logic volume
533  "phantomContainer", // Name
534  fWorld_logic, // Mother
535  false, // No op. bool.
536  1); // Copy number
537 
538  //fContainer_logic->SetVisAttributes(new G4VisAttributes(G4Colour(1.,0.,0.)));
539 }
540 
541 
542 #include "G4SDManager.hh"
544 #include "G4PSDoseDeposit.hh"
545 #include "G4PSDoseDeposit3D.hh"
546 
547 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
549 {
550 
551  G4cout << "\n\n\n\n\t SET SCORER : " << voxel_logic->GetName()
552  << " \n\n\n" << G4endl;
553 
554  scorers.insert(voxel_logic);
555 
556 }
557 
558 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
559 
561 {
562 
563  G4cout << "\n\n\n\n\t CONSTRUCT SD AND FIELD \n\n\n" << G4endl;
564 
565  //G4SDManager* SDman = G4SDManager::GetSDMpointer();
566 
567  //SDman->SetVerboseLevel(1);
568 
569  //
570  // Sensitive Detector Name
571  G4String concreteSDname = "phantomSD";
572  std::vector<G4String> scorer_names;
573  scorer_names.push_back(concreteSDname);
574  //------------------------
575  // MultiFunctionalDetector
576  //------------------------
577  //
578  // Define MultiFunctionalDetector with name.
579  // declare MFDet as a MultiFunctionalDetector scorer
580  G4MultiFunctionalDetector* MFDet =
581  new G4MultiFunctionalDetector(concreteSDname);
582  //SDman->AddNewDetector( MFDet ); // Register SD to SDManager
583  //G4VPrimitiveScorer* dosedep = new G4PSDoseDeposit("DoseDeposit");
584  G4VPrimitiveScorer* dosedep =
585  new G4PSDoseDeposit3D("DoseDeposit", fNVoxelX, fNVoxelY, fNVoxelZ);
586  MFDet->RegisterPrimitive(dosedep);
587 
588  for(std::set<G4LogicalVolume*>::iterator ite = scorers.begin();
589  ite != scorers.end(); ++ite) {
590  SetSensitiveDetector(*ite, MFDet);
591  }
592 
593  /*if(DicomRunAction::Instance()->GetDicomRun()) {
594  DicomRunAction::Instance()->GetDicomRun()->ConstructMFD(scorer_names);
595  }*/
596 
597 
598 }
599 
600 
G4bool RegisterPrimitive(G4VPrimitiveScorer *)
void SetScorer(G4LogicalVolume *voxel_logic)
Definition of the DicomDetectorConstruction class.
G4String symbol
Definition: TRTMaterials.hh:40
G4String GetName() const
CLHEP::Hep3Vector G4ThreeVector
G4double z
Definition: TRTMaterials.hh:39
Definition: G4Box.hh:64
Definition of the DicomRunAction class.
G4String name
Definition: TRTMaterials.hh:40
const G4String & GetName() const
Definition: G4Material.hh:178
std::vector< DicomPhantomZSliceHeader * > fZSliceHeaders
std::set< G4LogicalVolume * > scorers
G4Element * elC
Definition: TRTMaterials.hh:48
static G4String ConvertToString(G4bool boolVal)
Definition: G4UIcommand.cc:371
virtual G4VPhysicalVolume * Construct()
G4double a
Definition: TRTMaterials.hh:39
static const double mg
Definition: G4SIunits.hh:163
const G4Element * GetElement(G4int iel) const
Definition: G4Material.hh:202
int G4int
Definition: G4Types.hh:78
Definition of the DicomRun class.
DicomPhantomZSliceHeader * fZSliceHeaderMerged
G4Element * elN
Definition: TRTMaterials.hh:44
G4Element * elH
Definition: TRTMaterials.hh:50
G4double density
Definition: TRTMaterials.hh:39
G4Material * BuildMaterialWithChangingDensity(const G4Material *origMate, float density, G4String newMateName)
G4GLOB_DLL std::ostream G4cout
G4Element * elO
Definition: TRTMaterials.hh:46
DicomPhantomZSliceHeader class.
static G4double ConvertToDouble(const char *st)
Definition: G4UIcommand.cc:443
static const double cm3
Definition: G4SIunits.hh:108
void SetSensitiveDetector(const G4String &logVolName, G4VSensitiveDetector *aSD, G4bool multi=false)
void G4Exception(const char *originOfException, const char *exceptionCode, G4ExceptionSeverity severity, const char *comments)
Definition: G4Exception.cc:41
static const double g
Definition: G4SIunits.hh:162
static const double mole
Definition: G4SIunits.hh:265
#define G4endl
Definition: G4ios.hh:61
static const double m
Definition: G4SIunits.hh:110
void AddElement(G4Element *element, G4int nAtoms)
Definition: G4Material.cc:364
size_t GetNumberOfElements() const
Definition: G4Material.hh:186
Definition of the DicomPhantomZSliceHeader class.
double G4double
Definition: G4Types.hh:76
std::vector< G4Material * > fMaterials
std::vector< G4Material * > fOriginalMaterials
void ReadPhantomDataFile(const G4String &fname)
const G4double * GetFractionVector() const
Definition: G4Material.hh:194
virtual void ConstructPhantom()=0
G4GLOB_DLL std::ostream G4cerr
std::map< G4int, G4double > fDensityDiffs