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DicomFileMgr.cc
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26 #include "DicomFileMgr.hh"
27 
28 #include "DicomFileCT.hh"
29 #include "DicomFilePET.hh"
30 #include "DicomFileStructure.hh"
31 #include "DicomFilePlan.hh"
32 
33 #include "dcmtk/dcmdata/dcdeftag.h"
34 #include "G4tgrFileIn.hh"
35 #include "G4UIcommand.hh"
36 
37 DicomFileMgr* DicomFileMgr::theInstance = 0;
38 int DicomFileMgr::verbose = 1;
39 
40 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
41 DicomFileMgr* DicomFileMgr::GetInstance()
42 {
43  if( !theInstance ) {
44  theInstance = new DicomFileMgr;
45  }
46  return theInstance;
47 }
48 
49 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
50 DicomFileMgr::DicomFileMgr()
51 {
52  fCompression = 1.;
53  theCTFileAll = 0;
54  theStructureNCheck = 4;
55  theStructureNMaxROI = 100;
56 }
57 
58 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
59 void DicomFileMgr::Convert( G4String fileName )
60 {
61  G4tgrFileIn fin = G4tgrFileIn::GetInstance(fileName);
62  std::vector<G4String> wl;
63  // Read each file in file list
64  theFileOutName = "test.g4dcm";
65  int ii;
66  for( ii = 0;; ii++) {
67  if( ! fin.GetWordsInLine(wl) ) break;
68  if( wl[0] == ":COMPRESSION" ) {
69  CheckNColumns(wl,2);
70  SetCompression(wl[1]);
71  } else if( wl[0] == ":FILE" ) {
72  CheckNColumns(wl,2);
73  G4cout << "@@@@@@@ Reading FILE: " << wl[1] << G4endl;
74  AddFile(wl[1]);
75  } else if( wl[0] == ":FILE_OUT" ) {
76  CheckNColumns(wl,2);
77  theFileOutName = wl[1];
78  } else if( wl[0] == ":MATE_DENS" ) {
79  CheckNColumns(wl,3);
80  AddMaterialDensity(wl);
81  } else if( wl[0] == ":MATE" ) {
82  CheckNColumns(wl,3);
83  AddMaterial(wl);
84  } else if( wl[0] == ":CT2D" ) {
85  CheckNColumns(wl,3);
86  AddCT2Density(wl);
87  } else {
88  G4Exception("DICOM2G4",
89  "Wrong argument",
90  FatalErrorInArgument,
91  G4String("UNKNOWN TAG IN FILE "+wl[0]).c_str());
92  }
93 
94  }
95 
96 
97  //@@@@@@ Process files
98  ProcessFiles();
99 
100 }
101 
102 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
103 void DicomFileMgr::CheckNColumns(std::vector<G4String> wl, size_t vsizeTh )
104 {
105  if( wl.size() != vsizeTh ) {
106  G4cerr << " Reading line " << G4endl;
107  for( size_t ii = 0; ii < wl.size(); ii++){
108  G4cerr << wl[ii] << " ";
109  }
110  G4cerr << G4endl;
111  G4Exception("DICOM2G4",
112  "D2G0010",
113  FatalErrorInArgument,
114  ("Wrong number of columns in line " + std::to_string(wl.size()) + " <> "
115  + std::to_string(vsizeTh)).c_str());
116  }
117 
118 }
119 
120 
121 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
122 void DicomFileMgr::SetCompression( G4String fComp )
123 {
124  fCompression = G4UIcommand::ConvertToDouble(fComp);
125 }
126 
127 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
128 void DicomFileMgr::AddFile( G4String fileName )
129 {
130  DcmFileFormat dfile;
131  if( ! (dfile.loadFile(fileName.c_str())).good() ) {
132  G4Exception("DicomHandler::ReadFile",
133  "dfile.loadFile",
134  FatalErrorInArgument,
135  ("Error reading file " + fileName).c_str());
136  }
137  DcmDataset* dset = dfile.getDataset();
138 
139  OFString dModality;
140  if( !dset->findAndGetOFString(DCM_Modality,dModality).good() ) {
141  G4Exception("DicomHandler::ReadData ",
142  "",
143  FatalException,
144  " Have not read Modality");
145  }
146 
147  if( dModality == "CT" ) {
148  DicomFileCT* df = new DicomFileCT(dset);
149  df->ReadData();
150  df->SetFileName( fileName );
151  // reorder by location
152  theCTFiles[df->GetMaxZ()] = df;
153  } else if( dModality == "RTSTRUCT" ) {
154  DicomFileStructure* df = new DicomFileStructure(dset);
155  df->ReadData();
156  df->SetFileName( fileName );
157  // theFiles.insert(msd::value_type(dModality,df));
158  theStructFiles.push_back(df);
159  } else if( dModality == "RTPLAN" ) {
160  DicomFilePlan* df = new DicomFilePlan(dset);
161  df->ReadData();
162  df->SetFileName( fileName );
163  // theFiles.insert(msd::value_type(dModality,df));
164  thePlanFiles.push_back(df);
165  } else if( dModality == "PT" ) {
166  DicomFilePET* df = new DicomFilePET(dset);
167  df->ReadData();
168  df->SetFileName( fileName );
169  // theFiles.insert(msd::value_type(dModality,df));
170  thePETFiles[df->GetMaxZ()] = df;
171  // thePETFiles.push_back(df);
172  } else {
173  G4Exception("DicomFileMgr::AddFIle()",
174  "DFM001",
175  FatalErrorInArgument,
176  (G4String("File is not of type CT or RTSTRUCT or RTPLAN, but: ")
177  + dModality).c_str());
178  }
179 
180 }
181 
182 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
183 void DicomFileMgr::AddMaterial( std::vector<G4String> wl )
184 {
185  if( theMaterials.size() > 0 && bMaterialsDensity ) {
186  G4Exception("DicomFileMgr::AddMaterial",
187  "DFM005",
188  FatalException,
189  "Trying to add a Material with :MATE and another with :MATE_DENS, check your input file");
190  }
191  bMaterialsDensity = false;
192  theMaterials[G4UIcommand::ConvertToDouble(wl[2])] = wl[1];
193 }
194 
195 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
196 void DicomFileMgr::AddMaterialDensity( std::vector<G4String> wl )
197 {
198  if( theMaterialsDensity.size() > 0 && !bMaterialsDensity ) {
199  G4Exception("DicomFileMgr::AddMaterial",
200  "DFM005",
201  FatalException,
202  "Trying to add a Material with :MATE and another with :MATE_DENS, check your input file");
203  }
204  bMaterialsDensity = true;
205  theMaterialsDensity[G4UIcommand::ConvertToDouble(wl[2])] = wl[1];
206 }
207 
208 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
209 void DicomFileMgr::AddCT2Density( std::vector<G4String> wl)
210 {
211  theCT2Density[G4UIcommand::ConvertToInt(wl[1])] = G4UIcommand::ConvertToDouble(wl[2]);
212  G4cout << this << " AddCT2density " << theCT2Density.size() << G4endl;//GDEB
213 
214 }
215 
216 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
217 G4double DicomFileMgr::Hounsfield2density(Uint32 Hval)
218 {
219  if( theCT2Density.size() == 0 ) {
220  G4Exception("Hounsfield2density",
221  "DCM004",
222  FatalException,
223  "No :CT2D line in input file");
224  }
225  std::map<G4int,G4double>::const_iterator ite = theCT2Density.begin();
226  G4int minHval = (*ite).first;
227  if( G4int(Hval) < minHval ) {
228  G4Exception("DicomHandler::Hounsfield2density",
229  "",
230  FatalException,
231  ("Hval value too small, change input file "+std::to_string(Hval) + " < "
232  + std::to_string(minHval)).c_str());
233  }
234 
235  ite = theCT2Density.end(); ite--;
236  G4int maxHval = (*ite).first;
237  if( G4int(Hval) > maxHval ) {
238  G4Exception("DicomHandler::Hval2density",
239  "",
240  FatalException,
241  ("Hval value too big, change CT2Density.dat file "+std::to_string(Hval) + " > "
242  + std::to_string(maxHval)).c_str());
243  }
244 
245  G4float density = -1.;
246  G4double deltaCT = 0;
247  G4double deltaDensity = 0;
248 
249  ite = theCT2Density.upper_bound(Hval);
250  std::map<G4int,G4double>::const_iterator itePrev = ite; itePrev--;
251 
252  deltaCT = (*ite).first - (*itePrev).first;
253  deltaDensity = (*ite).second - (*itePrev).second;
254 
255  // interpolating linearly
256  density = (*ite).second - (((*ite).first-Hval)*deltaDensity/deltaCT );
257 
258  if(density < 0.) {
259  G4Exception("DicomFileMgr::Hounsfiled2Density",
260  "DFM002",
261  FatalException,
262  G4String("@@@ Error negative density = " + std::to_string(density) + " from HV = "
263  + std::to_string(Hval)).c_str());
264  }
265 
266  // G4cout << " Hval2density " << Hval << " -> " << density << G4endl;//GDEB
267  return density;
268 
269 }
270 
271 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
272 size_t DicomFileMgr::GetMaterialIndex( G4double Hval)
273 {
274  std::map<G4double,G4String>::iterator ite = theMaterials.upper_bound(Hval);
275  if( ite == theMaterials.end() ) {
276  ite--;
277  G4Exception("DicomFileMgr::GetMaterialIndex",
278  "DFM004",
279  FatalException,
280  ("Hounsfiled value too big, change input file "+std::to_string(Hval) + " > "
281  + std::to_string((*ite).first)).c_str());
282  }
283 
284  size_t dist = std::distance( theMaterials.begin(), ite );
285 
286  return dist;
287 
288 }
289 
290 
291 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
292 size_t DicomFileMgr::GetMaterialIndexByDensity( G4double density )
293 {
294  std::map<G4double,G4String>::iterator ite = theMaterialsDensity.upper_bound(density);
295  if( ite == theMaterialsDensity.end() ) {
296  ite--;
297  G4Exception("DicomFileMgr::GetMaterialIndexByDensity",
298  "DFM003",
299  FatalException,
300  ("Density too big, change input file "+std::to_string(density) + " > "
301  + std::to_string((*ite).first)).c_str());
302  }
303 
304  size_t dist = std::distance( theMaterialsDensity.begin(), ite );
305 
306  return dist;
307 
308 }
309 
310 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
311 void DicomFileMgr::ProcessFiles()
312 {
313  if( theCTFiles.size() == 0 ) {
314  G4Exception("CheckCTSlices",
315  "DCM004",
316  JustWarning,
317  "No :FILE of type CT in input file");
318  } else {
319 
320  CheckCTSlices();
321 
322  BuildCTMaterials();
323 
324  MergeCTFiles();
325 
326  }
327 
328  G4cout << " PROCESSING PET FILES " << thePETFiles.size() << G4endl; //GDEB
329  if( thePETFiles.size() != 0 ) {
330 
331  CheckPETSlices();
332 
333  BuildPETActivities();
334 
335  MergePETFiles();
336 
337  }
338 
339  DumpToTextFile();
340 
341 }
342 
343 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
344 void DicomFileMgr::CheckCTSlices()
345 {
346  size_t nSlices = theCTFiles.size();
347  G4cout << " DicomFileMgr::Checking CT slices: " << nSlices << G4endl;
348 
349  G4bool uniformSliceThickness = true;
350 
351  if(nSlices > 1) {
352  if(nSlices == 2) {
353  mdct::const_iterator ite = theCTFiles.begin();
354  DicomFileCT* one = (*ite).second;
355  ite++;
356  DicomFileCT* two = (*ite).second;
357 
358  G4double real_distance = (two->GetLocation()-one->GetLocation())/2.;
359 
360  if(one->GetMaxZ() != two->GetMinZ()) {
361  one->SetMaxZ(one->GetLocation()+real_distance);
362  two->SetMinZ(two->GetLocation()-real_distance);
363  //one->SetMinZ(one->GetLocation()-real_distance);
364  //two->SetMaxZ(two->GetLocation()+real_distance);
365  if(uniformSliceThickness) {
366  one->SetMinZ(one->GetLocation()-real_distance);
367  two->SetMaxZ(two->GetLocation()+real_distance);
368  }
369  }
370  } else {
371  mdct::iterator ite0 = theCTFiles.begin();
372  mdct::iterator ite1 = ite0; ite1++;
373  mdct::iterator ite2 = ite1; ite2++;
374  for(; ite2 != theCTFiles.end(); ++ite0, ++ite1, ++ite2) {
375  DicomFileCT* prev = (DicomFileCT*)((*ite0).second);
376  DicomFileCT* slice = (DicomFileCT*)((*ite1).second);
377  DicomFileCT* next = (DicomFileCT*)((*ite2).second);
378  G4double real_up_distance = (next->GetLocation() -
379  slice->GetLocation())/2.;
380  G4double real_down_distance = (slice->GetLocation() -
381  prev->GetLocation())/2.;
382  G4double real_distance = real_up_distance + real_down_distance;
383  G4double stated_distance = slice->GetMaxZ()-slice->GetMinZ();
384 
385  if(std::fabs(real_distance - stated_distance) > 1.E-9) {
386  unsigned int sliceNum = std::distance(theCTFiles.begin(),ite1);
387  G4cerr << "\tDicomFileMgr::CheckCTSlices - Slice Distance Error in slice [" << sliceNum
388  << "]: Distance between this slice and slices up and down = "
389  << real_distance
390  << " <> Slice width = " << stated_distance
391  << " Slice locations " <<prev->GetLocation() << " : " << slice->GetLocation()
392  << " : " << next->GetLocation()
393  << " DIFFERENCE= " << real_distance - stated_distance
394  << G4endl;
395  G4cerr << "!! WARNING: Geant4 will reset slice width so that it extends between "
396  << "lower and upper slice " << G4endl;
397 
398  slice->SetMinZ(slice->GetLocation()-real_down_distance);
399  slice->SetMaxZ(slice->GetLocation()+real_up_distance);
400 
401  if(ite0 == theCTFiles.begin()) {
402  prev->SetMaxZ(slice->GetMinZ());
403  // Using below would make all slice same thickness
404  //prev->SetMinZ(prev->GetLocation()-real_min_distance);
405  if(uniformSliceThickness) {
406  prev->SetMinZ(prev->GetLocation()-real_down_distance);
407  }
408  }
409  if(static_cast<unsigned int>(std::distance(theCTFiles.begin(),ite2)+1)==
410  nSlices) {
411  next->SetMinZ(slice->GetMaxZ());
412  // Using below would make all slice same thickness
413  //next->SetMaxZ(next->GetLocation()+real_max_distance);
414  if(uniformSliceThickness) {
415  next->SetMaxZ(next->GetLocation()+real_up_distance); }
416  }
417  }
418  }
419  }
420  }
421 
422 }
423 
424 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
425 void DicomFileMgr::CheckPETSlices()
426 {
427  size_t nSlices = thePETFiles.size();
428  G4cout << " DicomFileMgr::Checking PET slices: " << nSlices << G4endl;
429 
430  G4bool uniformSliceThickness = true;
431 
432  if(nSlices > 1) {
433  if(nSlices == 2) {
434  mdpet::const_iterator ite = thePETFiles.begin();
435  DicomFilePET* one = (*ite).second;
436  ite++;
437  DicomFilePET* two = (*ite).second;
438 
439  G4double real_distance = (two->GetLocation()-one->GetLocation())/2.;
440 
441  if(one->GetMaxZ() != two->GetMinZ()) {
442  one->SetMaxZ(one->GetLocation()+real_distance);
443  two->SetMinZ(two->GetLocation()-real_distance);
444  //one->SetMinZ(one->GetLocation()-real_distance);
445  //two->SetMaxZ(two->GetLocation()+real_distance);
446  if(uniformSliceThickness) {
447  one->SetMinZ(one->GetLocation()-real_distance);
448  two->SetMaxZ(two->GetLocation()+real_distance);
449  }
450  }
451  } else {
452  mdpet::iterator ite0 = thePETFiles.begin();
453  mdpet::iterator ite1 = ite0; ite1++;
454  mdpet::iterator ite2 = ite1; ite2++;
455  for(; ite2 != thePETFiles.end(); ++ite0, ++ite1, ++ite2) {
456  DicomFilePET* prev = (DicomFilePET*)((*ite0).second);
457  DicomFilePET* slice = (DicomFilePET*)((*ite1).second);
458  DicomFilePET* next = (DicomFilePET*)((*ite2).second);
459  G4double real_up_distance = (next->GetLocation() -
460  slice->GetLocation())/2.;
461  G4double real_down_distance = (slice->GetLocation() -
462  prev->GetLocation())/2.;
463  G4double real_distance = real_up_distance + real_down_distance;
464  G4double stated_distance = slice->GetMaxZ()-slice->GetMinZ();
465 
466  if(std::fabs(real_distance - stated_distance) > 1.E-9) {
467  unsigned int sliceNum = std::distance(thePETFiles.begin(),ite1);
468  G4cerr << "\tDicomFileMgr::CheckPETSlices - Slice Distance Error in slice [" << sliceNum
469  << "]: Distance between this slice and slices up and down = "
470  << real_distance
471  << " <> Slice width = " << stated_distance
472  << " Slice locations " <<prev->GetLocation() << " : " << slice->GetLocation()
473  << " : " << next->GetLocation()
474  << " DIFFERENCE= " << real_distance - stated_distance
475  << G4endl;
476  G4cerr << "!! WARNING: Geant4 will reset slice width so that it extends between "
477  << "lower and upper slice " << G4endl;
478 
479  slice->SetMinZ(slice->GetLocation()-real_down_distance);
480  slice->SetMaxZ(slice->GetLocation()+real_up_distance);
481 
482  if(ite0 == thePETFiles.begin()) {
483  prev->SetMaxZ(slice->GetMinZ());
484  // Using below would make all slice same thickness
485  //prev->SetMinZ(prev->GetLocation()-real_min_distance);
486  if(uniformSliceThickness) {
487  prev->SetMinZ(prev->GetLocation()-real_down_distance);
488  }
489  }
490  if(static_cast<unsigned int>(std::distance(thePETFiles.begin(),ite2)+1)==
491  nSlices) {
492  next->SetMinZ(slice->GetMaxZ());
493  // Using below would make all slice same thickness
494  //next->SetMaxZ(next->GetLocation()+real_max_distance);
495  if(uniformSliceThickness) {
496  next->SetMaxZ(next->GetLocation()+real_up_distance); }
497  }
498  }
499  }
500  }
501  }
502 
503 }
504 
505 
506 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
507 void DicomFileMgr::BuildCTMaterials()
508 {
509  G4cout << " DicomFileMgr::Building Materials " << theCTFiles.size() << G4endl;//GDEB
510  mdct::const_iterator ite = theCTFiles.begin();
511  for( ; ite != theCTFiles.end(); ite++ ) {
512  (*ite).second->BuildMaterials();
513  }
514 }
515 
516 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
517 void DicomFileMgr::BuildPETActivities()
518 {
519  G4cout << " DicomFileMgr::Building PETData " << thePETFiles.size() << G4endl;//GDEB
520  mdpet::const_iterator ite = thePETFiles.begin();
521  for( ; ite != thePETFiles.end(); ite++ ) {
522  (*ite).second->BuildActivities();
523  }
524 }
525 
526 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
527 void DicomFileMgr::MergeCTFiles()
528 {
529  G4cout << " DicomFileMgr::Merging CT Files " << theCTFiles.size() << G4endl;//GDEB
530  mdct::const_iterator ite = theCTFiles.begin();
531  theCTFileAll = new DicomFileCT( *((*ite).second) );
532  ite++;
533  for( ; ite != theCTFiles.end(); ite++ ) {
534  (*theCTFileAll) += *((*ite).second);
535  }
536 }
537 
538 
539 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
540 void DicomFileMgr::MergePETFiles()
541 {
542  G4cout << " DicomFileMgr::Merging PET Files " << thePETFiles.size() << G4endl;//GDEB
543  mdpet::const_iterator ite = thePETFiles.begin();
544  thePETFileAll = new DicomFilePET( *((*ite).second) );
545  ite++;
546  for( ; ite != thePETFiles.end(); ite++ ) {
547  (*thePETFileAll) += *((*ite).second);
548  }
549 }
550 
551 
552 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
553 void DicomFileMgr::DumpToTextFile()
554 {
555  G4cout << " DicomFileMgr::Dumping To Text File " << G4endl; //GDEB
556  if( theCTFiles.size() != 0 ) {
557  std::ofstream fout(theFileOutName);
558 
559  if( !bMaterialsDensity ) {
560  fout << theMaterials.size() << std::endl;
561  std::map<G4double,G4String>::const_iterator ite;
562  G4int ii = 0;
563  for(ite = theMaterials.begin(); ite != theMaterials.end(); ite++, ii++){
564  fout << ii << " \"" << (*ite).second << "\"" << std::endl;
565  }
566  } else {
567  fout << theMaterialsDensity.size() << std::endl;
568  std::map<G4double,G4String>::const_iterator ite;
569  G4int ii = 0;
570  for(ite = theMaterialsDensity.begin(); ite != theMaterialsDensity.end(); ite++, ii++){
571  fout << ii << " \"" << (*ite).second << "\"" << std::endl;
572  }
573  }
574 
575  theCTFileAll->DumpHeaderToTextFile(fout);
576  for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
577  (*itect).second->DumpMateIDsToTextFile(fout);
578  }
579  for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
580  (*itect).second->DumpDensitiesToTextFile(fout);
581  }
582  for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
583  (*itect).second->BuildStructureIDs();
584  (*itect).second->DumpStructureIDsToTextFile(fout);
585  }
586 
587  std::vector<DicomFileStructure*> dfs = GetStructFiles();
588  for( size_t i1 = 0; i1 < dfs.size(); i1++ ){
589  std::vector<DicomROI*> rois = dfs[i1]->GetROIs();
590  for( size_t i2 = 0; i2 < rois.size(); i2++ ){
591  fout << rois[i2]->GetNumber()+1 << " \"" << rois[i2]->GetName() << "\"" <<G4endl;
592  }
593  }
594  }
595 
596  if( thePETFiles.size() != 0 ) {
597  std::ofstream fout(theFileOutName);
598 
599  thePETFileAll->DumpHeaderToTextFile(fout);
600  for( mdpet::const_iterator itect = thePETFiles.begin(); itect != thePETFiles.end(); itect++ ) {
601  (*itect).second->DumpActivitiesToTextFile(fout);
602  }
603  }
604 
605  for( size_t i1 = 0; i1 < thePlanFiles.size(); i1++ ){
606  thePlanFiles[i1]->DumpToFile();
607  }
608 
609 }