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1 // 1 //
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24 // ******************************************* 24 // ********************************************************************
25 // 25 //
>> 26 // $Id: DicomHandler.cc 84839 2014-10-21 13:44:55Z gcosmo $
26 // 27 //
27 /// \file medical/DICOM/src/DicomHandler.cc 28 /// \file medical/DICOM/src/DicomHandler.cc
28 /// \brief Implementation of the DicomHandler 29 /// \brief Implementation of the DicomHandler class
29 // 30 //
30 // The code was written by : 31 // The code was written by :
31 // *Louis Archambault louis.archambault@p 32 // *Louis Archambault louis.archambault@phy.ulaval.ca,
32 // *Luc Beaulieu beaulieu@phy.ulaval.ca 33 // *Luc Beaulieu beaulieu@phy.ulaval.ca
33 // +Vincent Hubert-Tremblay at tigre.2@sy 34 // +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
34 // 35 //
35 // 36 //
36 // *Centre Hospitalier Universitaire de Quebec 37 // *Centre Hospitalier Universitaire de Quebec (CHUQ),
37 // Hotel-Dieu de Quebec, departement de Radio- 38 // Hotel-Dieu de Quebec, departement de Radio-oncologie
38 // 11 cote du palais. Quebec, QC, Canada, G1R 39 // 11 cote du palais. Quebec, QC, Canada, G1R 2J6
39 // tel (418) 525-4444 #6720 40 // tel (418) 525-4444 #6720
40 // fax (418) 691 5268 41 // fax (418) 691 5268
41 // 42 //
42 // + University Laval, Quebec (QC) Canada 43 // + University Laval, Quebec (QC) Canada
43 //******************************************** 44 //*******************************************************
44 // 45 //
45 //******************************************** 46 //*******************************************************
46 // 47 //
47 /// DicomHandler.cc : 48 /// DicomHandler.cc :
48 /// - Handling of DICM images 49 /// - Handling of DICM images
49 /// - Reading headers and pixels 50 /// - Reading headers and pixels
50 /// - Transforming pixel to density and 51 /// - Transforming pixel to density and creating *.g4dcm
51 /// files 52 /// files
52 //******************************************** 53 //*******************************************************
53 54
54 #include "DicomHandler.hh" 55 #include "DicomHandler.hh"
55 <<
56 #include "DicomPhantomZSliceHeader.hh" <<
57 #include "DicomPhantomZSliceMerged.hh" <<
58 <<
59 #include "G4ios.hh" <<
60 #include "globals.hh" 56 #include "globals.hh"
>> 57 #include "G4ios.hh"
>> 58 #include <fstream>
61 59
62 #include <cctype> 60 #include <cctype>
63 #include <cstring> 61 #include <cstring>
64 #include <fstream> << 62
>> 63 #include "DicomPhantomZSliceHeader.hh"
>> 64 #include "DicomPhantomZSliceMerged.hh"
65 65
66 //....oooOO0OOooo........oooOO0OOooo........oo 66 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
67 67
68 DicomHandler* DicomHandler::fInstance = 0; << 68 DicomHandler* DicomHandler::fgInstance = 0;
69 69
70 //....oooOO0OOooo........oooOO0OOooo........oo 70 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
71 71
72 DicomHandler* DicomHandler::Instance() 72 DicomHandler* DicomHandler::Instance()
73 { 73 {
74 if (fInstance == 0) { << 74 return fgInstance;
75 static DicomHandler dicomhandler; <<
76 fInstance = &dicomhandler; <<
77 } <<
78 return fInstance; <<
79 } 75 }
80 76
81 //....oooOO0OOooo........oooOO0OOooo........oo 77 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
82 78
83 G4String DicomHandler::GetDicomDataPath() << 79 DicomHandler::DicomHandler()
>> 80 : DATABUFFSIZE(8192), LINEBUFFSIZE(5020), FILENAMESIZE(512),
>> 81 fCompression(0), fNFiles(0), fRows(0), fColumns(0),
>> 82 fBitAllocated(0), fMaxPixelValue(0), fMinPixelValue(0),
>> 83 fPixelSpacingX(0.), fPixelSpacingY(0.),
>> 84 fSliceThickness(0.), fSliceLocation(0.),
>> 85 fRescaleIntercept(0), fRescaleSlope(0),
>> 86 fLittleEndian(true), fImplicitEndian(false),
>> 87 fPixelRepresentation(0), nbrequali(0),
>> 88 valuedensity(NULL),valueCT(NULL),readCalibration(false),
>> 89 mergedSlices(NULL),driverFile("Data.dat"),ct2densityFile("CT2Density.dat")
84 { 90 {
85 // default is current directory << 91 mergedSlices = new DicomPhantomZSliceMerged;
86 G4String driverPath = "."; <<
87 // check environment <<
88 const char* path = std::getenv("DICOM_PATH") <<
89 <<
90 if (path) { <<
91 // if is set in environment <<
92 return G4String(path); <<
93 } <<
94 else { <<
95 // if DICOM_USE_HEAD, look for data instal <<
96 #ifdef DICOM_USE_HEAD <<
97 G4cerr << "Warning! DICOM was compiled wit <<
98 << "the DICOM_PATH was not set!" << <<
99 G4String datadir = G4GetEnv<G4String>("G4E <<
100 if (datadir.length() > 0) { <<
101 auto _last = datadir.rfind("/"); <<
102 if (_last != std::string::npos) datadir. <<
103 driverPath = datadir + "/DICOM1.1/DICOM_ <<
104 G4int rc = setenv("DICOM_PATH", driverPa <<
105 G4cerr << "\t --> Using '" << driverPath <<
106 G4ConsumeParameters(rc); <<
107 } <<
108 #endif <<
109 } <<
110 return driverPath; <<
111 } 92 }
112 93
113 //....oooOO0OOooo........oooOO0OOooo........oo <<
114 <<
115 G4String DicomHandler::GetDicomDataFile() <<
116 { <<
117 #if defined(DICOM_USE_HEAD) && defined(G4_DCMT <<
118 return GetDicomDataPath() + "/Data.dat.new"; <<
119 #else <<
120 return GetDicomDataPath() + "/Data.dat"; <<
121 #endif <<
122 } <<
123 94
124 //....oooOO0OOooo........oooOO0OOooo........oo 95 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
125 96
126 #ifdef DICOM_USE_HEAD << 97 DicomHandler::~DicomHandler()
127 DicomHandler::DicomHandler() <<
128 : DATABUFFSIZE(8192), <<
129 LINEBUFFSIZE(5020), <<
130 FILENAMESIZE(512), <<
131 fCompression(0), <<
132 fNFiles(0), <<
133 fRows(0), <<
134 fColumns(0), <<
135 fBitAllocated(0), <<
136 fMaxPixelValue(0), <<
137 fMinPixelValue(0), <<
138 fPixelSpacingX(0.), <<
139 fPixelSpacingY(0.), <<
140 fSliceThickness(0.), <<
141 fSliceLocation(0.), <<
142 fRescaleIntercept(0), <<
143 fRescaleSlope(0), <<
144 fLittleEndian(true), <<
145 fImplicitEndian(false), <<
146 fPixelRepresentation(0), <<
147 fNbrequali(0), <<
148 fValueDensity(NULL), <<
149 fValueCT(NULL), <<
150 fReadCalibration(false), <<
151 fMergedSlices(NULL), <<
152 fCt2DensityFile("null.dat") <<
153 { 98 {
154 fMergedSlices = new DicomPhantomZSliceMerged <<
155 fDriverFile = GetDicomDataFile(); <<
156 G4cout << "Reading the DICOM_HEAD project " <<
157 } <<
158 #else <<
159 DicomHandler::DicomHandler() <<
160 : DATABUFFSIZE(8192), <<
161 LINEBUFFSIZE(5020), <<
162 FILENAMESIZE(512), <<
163 fCompression(0), <<
164 fNFiles(0), <<
165 fRows(0), <<
166 fColumns(0), <<
167 fBitAllocated(0), <<
168 fMaxPixelValue(0), <<
169 fMinPixelValue(0), <<
170 fPixelSpacingX(0.), <<
171 fPixelSpacingY(0.), <<
172 fSliceThickness(0.), <<
173 fSliceLocation(0.), <<
174 fRescaleIntercept(0), <<
175 fRescaleSlope(0), <<
176 fLittleEndian(true), <<
177 fImplicitEndian(false), <<
178 fPixelRepresentation(0), <<
179 fNbrequali(0), <<
180 fValueDensity(NULL), <<
181 fValueCT(NULL), <<
182 fReadCalibration(false), <<
183 fMergedSlices(NULL), <<
184 fDriverFile("Data.dat"), <<
185 fCt2DensityFile("CT2Density.dat") <<
186 { <<
187 fMergedSlices = new DicomPhantomZSliceMerged <<
188 } <<
189 #endif <<
190 //....oooOO0OOooo........oooOO0OOooo........oo <<
191 99
192 DicomHandler::~DicomHandler() {} << 100 }
193 101
194 //....oooOO0OOooo........oooOO0OOooo........oo 102 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
195 103
196 G4int DicomHandler::ReadFile(FILE* dicom, char 104 G4int DicomHandler::ReadFile(FILE* dicom, char* filename2)
197 { 105 {
198 G4cout << " ReadFile " << filename2 << G4end << 106 G4cout << " ReadFile " << filename2 << G4endl;
199 << 107 G4int returnvalue = 0; size_t rflag = 0;
200 G4int returnvalue = 0; << 108 char * buffer = new char[LINEBUFFSIZE];
201 size_t rflag = 0; << 109
202 char* buffer = new char[LINEBUFFSIZE]; << 110 fImplicitEndian = false;
203 << 111 fLittleEndian = true;
204 fImplicitEndian = false; << 112
205 fLittleEndian = true; << 113 rflag = std::fread( buffer, 1, 128, dicom ); // The first 128 bytes
206 << 114 //are not important
207 rflag = std::fread(buffer, 1, 128, dicom); << 115 // Reads the "DICOM" letters
208 << 116 rflag = std::fread( buffer, 1, 4, dicom );
209 << 117 // if there is no preamble, the FILE pointer is rewinded.
210 rflag = std::fread(buffer, 1, 4, dicom); << 118 if(std::strncmp("DICM", buffer, 4) != 0) {
211 // if there is no preamble, the FILE pointer << 119 std::fseek(dicom, 0, SEEK_SET);
212 if (std::strncmp("DICM", buffer, 4) != 0) { << 120 fImplicitEndian = true;
213 std::fseek(dicom, 0, SEEK_SET); << 121 }
214 fImplicitEndian = true; << 122
215 } << 123 short readGroupId; // identify the kind of input data
216 << 124 short readElementId; // identify a particular type information
217 short readGroupId; // identify the kind of << 125 short elementLength2; // deal with element length in 2 bytes
218 short readElementId; // identify a particul << 126 //unsigned int elementLength4;
219 short elementLength2; // deal with element << 127 // deal with element length in 4 bytes
220 // unsigned int eleme << 128 unsigned long elementLength4; // deal with element length in 4 bytes
221 // deal with element length in 4 bytes << 129
222 unsigned long elementLength4; // deal with << 130 char * data = new char[DATABUFFSIZE];
223 << 131
224 char* data = new char[DATABUFFSIZE]; << 132
225 << 133 // Read information up to the pixel data
226 // Read information up to the pixel data << 134 while(true) {
227 while (true) { << 135
228 // Reading groups and elements : << 136 //Reading groups and elements :
229 readGroupId = 0; << 137 readGroupId = 0;
230 readElementId = 0; << 138 readElementId = 0;
231 // group ID << 139 // group ID
232 rflag = std::fread(buffer, 2, 1, dicom); << 140 rflag = std::fread(buffer, 2, 1, dicom);
233 GetValue(buffer, readGroupId); << 141 GetValue(buffer, readGroupId);
234 // element ID << 142 // element ID
235 rflag = std::fread(buffer, 2, 1, dicom); << 143 rflag = std::fread(buffer, 2, 1, dicom);
236 GetValue(buffer, readElementId); << 144 GetValue(buffer, readElementId);
237 << 145
238 // Creating a tag to be identified afterwa << 146 // Creating a tag to be identified afterward
239 G4int tagDictionary = readGroupId * 0x1000 << 147 G4int tagDictionary = readGroupId*0x10000 + readElementId;
240 << 148
241 // beginning of the pixels << 149 // beginning of the pixels
242 if (tagDictionary == 0x7FE00010) { << 150 if(tagDictionary == 0x7FE00010) {
243 // Following 2 fread's are modifications << 151 // Folling 2 fread's are modifications to original DICOM example
244 // (Jonathan Madsen) << 152 //(Jonathan Madsen)
245 if (!fImplicitEndian) rflag = std::fread << 153 rflag = std::fread(buffer,2,1,dicom); // Reserved 2 bytes
246 // (not used for pixels) << 154 // (not used for pixels)
247 rflag = std::fread(buffer, 4, 1, dicom); << 155 rflag = std::fread(buffer,4,1,dicom); // Element Length
248 // (not used for pixels) << 156 // (not used for pixels)
249 break; // Exit to ReadImageData() << 157 break; // Exit to ReadImageData()
250 } << 158 }
251 << 159
252 // VR or element length << 160 // VR or element length
253 rflag = std::fread(buffer, 2, 1, dicom); << 161 rflag = std::fread(buffer,2,1,dicom);
254 GetValue(buffer, elementLength2); << 162 GetValue(buffer, elementLength2);
255 << 163
256 // If value representation (VR) is OB, OW, << 164 // If value representation (VR) is OB, OW, SQ, UN, added OF and UT
257 // the next length is 32 bits << 165 //the next length is 32 bits
258 if ((elementLength2 == 0x424f || // "OB" << 166 if((elementLength2 == 0x424f || // "OB"
259 elementLength2 == 0x574f || // "OW" << 167 elementLength2 == 0x574f || // "OW"
260 elementLength2 == 0x464f || // "OF" << 168 elementLength2 == 0x464f || // "OF"
261 elementLength2 == 0x5455 || // "UT" << 169 elementLength2 == 0x5455 || // "UT"
262 elementLength2 == 0x5153 || // "SQ" << 170 elementLength2 == 0x5153 || // "SQ"
263 elementLength2 == 0x4e55) << 171 elementLength2 == 0x4e55) && // "UN"
264 && // "UN" << 172 !fImplicitEndian ) { // explicit VR
265 !fImplicitEndian) << 173
266 { // explicit VR << 174 rflag = std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes
267 << 175
268 rflag = std::fread(buffer, 2, 1, dicom); <<
269 <<
270 // element length 176 // element length
271 rflag = std::fread(buffer, 4, 1, dicom); 177 rflag = std::fread(buffer, 4, 1, dicom);
272 GetValue(buffer, elementLength4); 178 GetValue(buffer, elementLength4);
273 << 179
274 if (elementLength2 == 0x5153) { << 180 if(elementLength2 == 0x5153)
275 if (elementLength4 == 0xFFFFFFFF) { << 181 {
276 read_undefined_nested(dicom); << 182 if(elementLength4 == 0xFFFFFFFF)
277 elementLength4 = 0; << 183 {
278 } << 184 read_undefined_nested( dicom );
279 else { << 185 elementLength4=0;
280 if (read_defined_nested(dicom, eleme << 186 } else{
281 G4Exception("DicomHandler::ReadFil << 187 if(read_defined_nested( dicom, elementLength4 )==0){
282 "Function read_defined << 188 G4Exception("DicomHandler::ReadFile",
>> 189 "DICOM001",
>> 190 FatalException,
>> 191 "Function read_defined_nested() failed!");
>> 192 }
283 } 193 }
284 } << 194 } else {
285 } <<
286 else { <<
287 // Reading the information with data 195 // Reading the information with data
288 rflag = std::fread(data, elementLength << 196 rflag = std::fread(data, elementLength4,1,dicom);
289 } 197 }
290 } << 198
291 else { << 199
>> 200 } else {
>> 201
292 // explicit with VR different than prev 202 // explicit with VR different than previous ones
293 if (!fImplicitEndian || readGroupId == 2 << 203 if(!fImplicitEndian || readGroupId == 2) {
294 // G4cout << "Reading DICOM files wit << 204
295 // element length (2 bytes) << 205 //G4cout << "Reading DICOM files with Explicit VR"<< G4endl;
>> 206 // element length (2 bytes)
296 rflag = std::fread(buffer, 2, 1, dicom 207 rflag = std::fread(buffer, 2, 1, dicom);
297 GetValue(buffer, elementLength2); 208 GetValue(buffer, elementLength2);
298 elementLength4 = elementLength2; 209 elementLength4 = elementLength2;
299 << 210
300 rflag = std::fread(data, elementLength 211 rflag = std::fread(data, elementLength4, 1, dicom);
301 } << 212
302 else { // Implicit VR << 213 } else { // Implicit VR
303 << 214
304 // G4cout << "Reading DICOM files wit << 215 //G4cout << "Reading DICOM files with Implicit VR"<< G4endl;
305 << 216
306 // element length (4 bytes) 217 // element length (4 bytes)
307 if (std::fseek(dicom, -2, SEEK_CUR) != << 218 if(std::fseek(dicom, -2, SEEK_CUR) != 0) {
308 G4Exception("DicomHandler::ReadFile" << 219 G4Exception("DicomHandler::ReadFile",
>> 220 "DICOM001",
>> 221 FatalException,
>> 222 "fseek failed");
309 } 223 }
310 << 224
311 rflag = std::fread(buffer, 4, 1, dicom 225 rflag = std::fread(buffer, 4, 1, dicom);
312 GetValue(buffer, elementLength4); 226 GetValue(buffer, elementLength4);
313 << 227
314 // G4cout << std::hex<< elementLength << 228 //G4cout << std::hex<< elementLength4 << G4endl;
315 << 229
316 if (elementLength4 == 0xFFFFFFFF) { << 230 if(elementLength4 == 0xFFFFFFFF)
317 read_undefined_nested(dicom); << 231 {
318 elementLength4 = 0; << 232 read_undefined_nested(dicom);
319 } << 233 elementLength4=0;
320 else { << 234 } else{
321 rflag = std::fread(data, elementLeng 235 rflag = std::fread(data, elementLength4, 1, dicom);
322 } 236 }
>> 237
>> 238 }
323 } 239 }
>> 240
>> 241 // NULL termination
>> 242 data[elementLength4] = '\0';
>> 243
>> 244 // analyzing information
>> 245 GetInformation(tagDictionary, data);
324 } 246 }
>> 247
>> 248 G4String fnameG4DCM = G4String(filename2) + ".g4dcm";
325 249
326 // NULL termination << 250 // Perform functions originally written straight to file
327 data[elementLength4] = '\0'; << 251 DicomPhantomZSliceHeader* zslice = new DicomPhantomZSliceHeader(fnameG4DCM);
328 <<
329 // analyzing information <<
330 GetInformation(tagDictionary, data); <<
331 } <<
332 252
333 G4String fnameG4DCM = G4String(filename2) + << 253 std::map<G4float,G4String>::const_iterator ite;
334 << 254 for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ++ite){
335 // Perform functions originally written stra << 255 zslice->AddMaterial(ite->second);
336 DicomPhantomZSliceHeader* zslice = new Dicom << 256 }
337 for (auto ite = fMaterialIndices.cbegin(); i << 257
338 zslice->AddMaterial(ite->second); << 258 zslice->SetNoVoxelX(fColumns/fCompression);
339 } << 259 zslice->SetNoVoxelY(fRows/fCompression);
340 << 260 zslice->SetNoVoxelZ(1);
341 zslice->SetNoVoxelsX(fColumns / fCompression <<
342 zslice->SetNoVoxelsY(fRows / fCompression); <<
343 zslice->SetNoVoxelsZ(1); <<
344 261
345 zslice->SetMinX(-fPixelSpacingX * fColumns / << 262 zslice->SetMinX(-fPixelSpacingX*fColumns/2.);
346 zslice->SetMaxX(fPixelSpacingX * fColumns / << 263 zslice->SetMaxX(fPixelSpacingX*fColumns/2.);
347 264
348 zslice->SetMinY(-fPixelSpacingY * fRows / 2. << 265 zslice->SetMinY(-fPixelSpacingY*fRows/2.);
349 zslice->SetMaxY(fPixelSpacingY * fRows / 2.) << 266 zslice->SetMaxY(fPixelSpacingY*fRows/2.);
350 267
351 zslice->SetMinZ(fSliceLocation - fSliceThick << 268 zslice->SetMinZ(fSliceLocation-fSliceThickness/2.);
352 zslice->SetMaxZ(fSliceLocation + fSliceThick << 269 zslice->SetMaxZ(fSliceLocation+fSliceThickness/2.);
353 270
354 //=== << 271 //===
355 272
356 ReadData(dicom, filename2); << 273 ReadData( dicom, filename2 );
357 274
358 // DEPRECIATED << 275 // DEPRECIATED
359 // StoreData( foutG4DCM ); << 276 //StoreData( foutG4DCM );
360 // foutG4DCM.close(); << 277 //foutG4DCM.close();
361 278
362 StoreData(zslice); << 279 StoreData( zslice );
363 280
364 // Dumped 2 file after DicomPhantomZSliceMer << 281 // Dumped 2 file after DicomPhantomZSliceMerged has checked for consistency
365 // zslice->DumpToFile(); << 282 //zslice->DumpToFile();
366 283
367 fMergedSlices->AddZSlice(zslice); << 284 mergedSlices->AddZSlice(zslice);
368 285
369 // << 286 //
370 delete[] buffer; << 287 delete [] buffer;
371 delete[] data; << 288 delete [] data;
372 289
373 if (rflag) return returnvalue; << 290 if (rflag) return returnvalue;
374 return returnvalue; << 291 return returnvalue;
375 } 292 }
376 293
377 //....oooOO0OOooo........oooOO0OOooo........oo 294 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
378 295
379 void DicomHandler::GetInformation(G4int& tagDi << 296 void DicomHandler::GetInformation(G4int & tagDictionary, char * data)
380 { 297 {
381 if (tagDictionary == 0x00280010) { // Numbe << 298 if(tagDictionary == 0x00280010 ) { // Number of Rows
382 GetValue(data, fRows); << 299 GetValue(data, fRows);
383 std::printf("[0x00280010] Rows -> %i\n", f << 300 std::printf("[0x00280010] Rows -> %i\n",fRows);
384 } << 301
385 else if (tagDictionary == 0x00280011) { // << 302 } else if(tagDictionary == 0x00280011 ) { // Number of fColumns
386 GetValue(data, fColumns); << 303 GetValue(data, fColumns);
387 std::printf("[0x00280011] Columns -> %i\n" << 304 std::printf("[0x00280011] Columns -> %i\n",fColumns);
388 } << 305
389 else if (tagDictionary == 0x00280102) { // << 306 } else if(tagDictionary == 0x00280102 ) { // High bits ( not used )
390 short highBits; << 307 short highBits;
391 GetValue(data, highBits); << 308 GetValue(data, highBits);
392 std::printf("[0x00280102] High bits -> %i\ << 309 std::printf("[0x00280102] High bits -> %i\n",highBits);
393 } << 310
394 else if (tagDictionary == 0x00280100) { // << 311 } else if(tagDictionary == 0x00280100 ) { // Bits allocated
395 GetValue(data, fBitAllocated); << 312 GetValue(data, fBitAllocated);
396 std::printf("[0x00280100] Bits allocated - << 313 std::printf("[0x00280100] Bits allocated -> %i\n", fBitAllocated);
397 } << 314
398 else if (tagDictionary == 0x00280101) { // << 315 } else if(tagDictionary == 0x00280101 ) { // Bits stored ( not used )
399 short bitStored; << 316 short bitStored;
400 GetValue(data, bitStored); << 317 GetValue(data, bitStored);
401 std::printf("[0x00280101] Bits stored -> % << 318 std::printf("[0x00280101] Bits stored -> %i\n",bitStored);
402 } << 319
403 else if (tagDictionary == 0x00280106) { // << 320 } else if(tagDictionary == 0x00280106 ) { // Min. pixel value
404 GetValue(data, fMinPixelValue); << 321 GetValue(data, fMinPixelValue);
405 std::printf("[0x00280106] Min. pixel value << 322 std::printf("[0x00280106] Min. pixel value -> %i\n", fMinPixelValue);
406 } << 323
407 else if (tagDictionary == 0x00280107) { // << 324 } else if(tagDictionary == 0x00280107 ) { // Max. pixel value
408 GetValue(data, fMaxPixelValue); << 325 GetValue(data, fMaxPixelValue);
409 std::printf("[0x00280107] Max. pixel value << 326 std::printf("[0x00280107] Max. pixel value -> %i\n", fMaxPixelValue);
410 } << 327
411 else if (tagDictionary == 0x00281053) { // << 328 } else if(tagDictionary == 0x00281053) { // Rescale slope
412 fRescaleSlope = atoi(data); << 329 fRescaleSlope = atoi(data);
413 std::printf("[0x00281053] Rescale Slope -> << 330 std::printf("[0x00281053] Rescale Slope -> %d\n", fRescaleSlope);
414 } << 331
415 else if (tagDictionary == 0x00281052) { // << 332 } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept
416 fRescaleIntercept = atoi(data); << 333 fRescaleIntercept = atoi(data);
417 std::printf("[0x00281052] Rescale Intercep << 334 std::printf("[0x00281052] Rescale Intercept -> %d\n",
418 } << 335 fRescaleIntercept );
419 else if (tagDictionary == 0x00280103) { << 336
420 // Pixel representation ( functions not d << 337 } else if(tagDictionary == 0x00280103 ) {
421 fPixelRepresentation = atoi(data); // 0: << 338 // Pixel representation ( functions not design to read signed bits )
422 std::printf("[0x00280103] Pixel Representa << 339 fPixelRepresentation = atoi(data); // 0: unsigned 1: signed
423 if (fPixelRepresentation == 1) { << 340 std::printf("[0x00280103] Pixel Representation -> %i\n",
424 std::printf("### PIXEL REPRESENTATION = << 341 fPixelRepresentation);
425 std::printf("DICOM READING SCAN FOR UNSI << 342 if(fPixelRepresentation == 1 ) {
426 std::printf("ERROR !!!!!! -> \n"); << 343 std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, ");
>> 344 std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE ");
>> 345 std::printf("ERROR !!!!!! -> \n");
>> 346 }
>> 347
>> 348 } else if(tagDictionary == 0x00080006 ) { // Modality
>> 349 std::printf("[0x00080006] Modality -> %s\n", data);
>> 350
>> 351 } else if(tagDictionary == 0x00080070 ) { // Manufacturer
>> 352 std::printf("[0x00080070] Manufacturer -> %s\n", data);
>> 353
>> 354 } else if(tagDictionary == 0x00080080 ) { // Institution Name
>> 355 std::printf("[0x00080080] Institution Name -> %s\n", data);
>> 356
>> 357 } else if(tagDictionary == 0x00080081 ) { // Institution Address
>> 358 std::printf("[0x00080081] Institution Address -> %s\n", data);
>> 359
>> 360 } else if(tagDictionary == 0x00081040 ) { // Institution Department Name
>> 361 std::printf("[0x00081040] Institution Department Name -> %s\n", data);
>> 362
>> 363 } else if(tagDictionary == 0x00081090 ) { // Manufacturer's Model Name
>> 364 std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data);
>> 365
>> 366 } else if(tagDictionary == 0x00181000 ) { // Device Serial Number
>> 367 std::printf("[0x00181000] Device Serial Number -> %s\n", data);
>> 368
>> 369 } else if(tagDictionary == 0x00080008 ) { // Image type ( not used )
>> 370 std::printf("[0x00080008] Image Types -> %s\n", data);
>> 371
>> 372 } else if(tagDictionary == 0x00283000 ) { //Modality LUT Sequence(not used)
>> 373 std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data);
>> 374
>> 375 } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used )
>> 376 std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data);
>> 377
>> 378 } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used )
>> 379 std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data);
>> 380
>> 381 } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used )
>> 382 std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data);
>> 383
>> 384 } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used )
>> 385 std::printf("[0x00283006] LUT Data US or SS -> %s\n", data);
>> 386
>> 387 } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used )
>> 388 std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data);
>> 389
>> 390 } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value (not used)
>> 391 std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data);
>> 392
>> 393 } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing
>> 394 G4String datas(data);
>> 395 int iss = datas.find('\\');
>> 396 fPixelSpacingX = atof( datas.substr(0,iss).c_str() );
>> 397 fPixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() );
>> 398
>> 399 } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used )
>> 400 std::printf("[0x00200037] Image Orientation (Phantom) -> %s\n", data);
>> 401
>> 402 } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used )
>> 403 std::printf("[0x00200032] Image Position (Phantom,mm) -> %s\n", data);
>> 404
>> 405 } else if(tagDictionary == 0x00180050 ) { // Slice Thickness
>> 406 fSliceThickness = atof(data);
>> 407 std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", fSliceThickness);
>> 408
>> 409 } else if(tagDictionary == 0x00201041 ) { // Slice Location
>> 410 fSliceLocation = atof(data);
>> 411 std::printf("[0x00201041] Slice Location -> %f\n", fSliceLocation);
>> 412
>> 413 } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation
>> 414 // ( not used )
>> 415 std::printf("[0x00280004] Photometric Interpretation -> %s\n", data);
>> 416
>> 417 } else if(tagDictionary == 0x00020010) { // Endian
>> 418 if(strcmp(data, "1.2.840.10008.1.2") == 0)
>> 419 fImplicitEndian = true;
>> 420 else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0)
>> 421 fLittleEndian = false;
>> 422 //else 1.2.840..10008.1.2.1 (explicit little endian)
>> 423
>> 424 std::printf("[0x00020010] Endian -> %s\n", data);
427 } 425 }
428 } <<
429 else if (tagDictionary == 0x00080006) { // <<
430 std::printf("[0x00080006] Modality -> %s\n <<
431 } <<
432 else if (tagDictionary == 0x00080070) { // <<
433 std::printf("[0x00080070] Manufacturer -> <<
434 } <<
435 else if (tagDictionary == 0x00080080) { // <<
436 std::printf("[0x00080080] Institution Name <<
437 } <<
438 else if (tagDictionary == 0x00080081) { // <<
439 std::printf("[0x00080081] Institution Addr <<
440 } <<
441 else if (tagDictionary == 0x00081040) { // <<
442 std::printf("[0x00081040] Institution Depa <<
443 } <<
444 else if (tagDictionary == 0x00081090) { // <<
445 std::printf("[0x00081090] Manufacturer's M <<
446 } <<
447 else if (tagDictionary == 0x00181000) { // <<
448 std::printf("[0x00181000] Device Serial Nu <<
449 } <<
450 else if (tagDictionary == 0x00080008) { // <<
451 std::printf("[0x00080008] Image Types -> % <<
452 } <<
453 else if (tagDictionary == 0x00283000) { // <<
454 std::printf("[0x00283000] Modality LUT Seq <<
455 } <<
456 else if (tagDictionary == 0x00283002) { // <<
457 std::printf("[0x00283002] LUT Descriptor U <<
458 } <<
459 else if (tagDictionary == 0x00283003) { // <<
460 std::printf("[0x00283003] LUT Explanation <<
461 } <<
462 else if (tagDictionary == 0x00283004) { // <<
463 std::printf("[0x00283004] Modality LUT Typ <<
464 } <<
465 else if (tagDictionary == 0x00283006) { // <<
466 std::printf("[0x00283006] LUT Data US or S <<
467 } <<
468 else if (tagDictionary == 0x00283010) { // <<
469 std::printf("[0x00283010] VOI LUT Sequence <<
470 } <<
471 else if (tagDictionary == 0x00280120) { // <<
472 std::printf("[0x00280120] Pixel Padding Va <<
473 } <<
474 else if (tagDictionary == 0x00280030) { // <<
475 G4String datas(data); <<
476 G4int iss = G4int(datas.find('\\')); <<
477 fPixelSpacingX = atof(datas.substr(0, iss) <<
478 fPixelSpacingY = atof(datas.substr(iss + 1 <<
479 } <<
480 else if (tagDictionary == 0x00200037) { // <<
481 std::printf("[0x00200037] Image Orientatio <<
482 } <<
483 else if (tagDictionary == 0x00200032) { // <<
484 std::printf("[0x00200032] Image Position ( <<
485 } <<
486 else if (tagDictionary == 0x00180050) { // <<
487 fSliceThickness = atof(data); <<
488 std::printf("[0x00180050] Slice Thickness <<
489 } <<
490 else if (tagDictionary == 0x00201041) { // <<
491 fSliceLocation = atof(data); <<
492 std::printf("[0x00201041] Slice Location - <<
493 } <<
494 else if (tagDictionary == 0x00280004) { // <<
495 // ( not used ) <<
496 std::printf("[0x00280004] Photometric Inte <<
497 } <<
498 else if (tagDictionary == 0x00020010) { // <<
499 if (strcmp(data, "1.2.840.10008.1.2") == 0 <<
500 fImplicitEndian = true; <<
501 else if (strncmp(data, "1.2.840.10008.1.2. <<
502 fLittleEndian = false; <<
503 // else 1.2.840..10008.1.2.1 (explicit lit <<
504 426
505 std::printf("[0x00020010] Endian -> %s\n", << 427 // others
506 } << 428 else {
>> 429 //std::printf("[0x%x] -> %s\n", tagDictionary, data);
>> 430 ;
>> 431 }
507 432
508 // others <<
509 else { <<
510 // std::printf("[0x%x] -> %s\n", tagDictio <<
511 ; <<
512 } <<
513 } 433 }
514 434
515 //....oooOO0OOooo........oooOO0OOooo........oo 435 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
516 436
517 void DicomHandler::StoreData(DicomPhantomZSlic 437 void DicomHandler::StoreData(DicomPhantomZSliceHeader* dcmPZSH)
518 { 438 {
519 G4int mean; << 439 G4int mean;
520 G4double density; << 440 G4double density;
521 G4bool overflow = false; << 441 G4bool overflow = false;
522 << 442
523 if (!dcmPZSH) { << 443 if(!dcmPZSH) { return; }
524 return; << 444
525 } << 445 dcmPZSH->SetSliceLocation(fSliceLocation);
526 << 446
527 dcmPZSH->SetSliceLocation(fSliceLocation); << 447 //----- Print indices of material
528 << 448 if(fCompression == 1) { // no fCompression: each pixel has a density value)
529 //----- Print indices of material << 449 for( G4int ww = 0; ww < fRows; ww++) {
530 if (fCompression == 1) { // no fCompression << 450 dcmPZSH->AddRow();
531 for (G4int ww = 0; ww < fRows; ++ww) { << 451 for( G4int xx = 0; xx < fColumns; xx++) {
532 dcmPZSH->AddRow(); << 452 mean = fTab[ww][xx];
533 for (G4int xx = 0; xx < fColumns; ++xx) << 453 density = Pixel2density(mean);
534 mean = fTab[ww][xx]; << 454 dcmPZSH->AddValue(density);
535 density = Pixel2density(mean); << 455 dcmPZSH->AddMateID(GetMaterialIndex(density));
536 dcmPZSH->AddValue(density); << 456 }
537 dcmPZSH->AddMateID(GetMaterialIndex(G4 <<
538 } <<
539 } <<
540 } <<
541 else { <<
542 // density value is the average of a squar <<
543 // fCompression*fCompression pixels <<
544 for (G4int ww = 0; ww < fRows; ww += fComp <<
545 dcmPZSH->AddRow(); <<
546 for (G4int xx = 0; xx < fColumns; xx += <<
547 overflow = false; <<
548 mean = 0; <<
549 for (G4int sumx = 0; sumx < fCompressi <<
550 for (G4int sumy = 0; sumy < fCompres <<
551 if (ww + sumy >= fRows || xx + sum <<
552 mean += fTab[ww + sumy][xx + sumx] <<
553 } <<
554 if (overflow) break; <<
555 } 457 }
556 mean /= fCompression * fCompression; <<
557 458
558 if (!overflow) { << 459 } else {
559 density = Pixel2density(mean); << 460 // density value is the average of a square region of
560 dcmPZSH->AddValue(density); << 461 // fCompression*fCompression pixels
561 dcmPZSH->AddMateID(GetMaterialIndex( << 462 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
>> 463 dcmPZSH->AddRow();
>> 464 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
>> 465 overflow = false;
>> 466 mean = 0;
>> 467 for(int sumx = 0; sumx < fCompression; sumx++) {
>> 468 for(int sumy = 0; sumy < fCompression; sumy++) {
>> 469 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
>> 470 mean += fTab[ww+sumy][xx+sumx];
>> 471 }
>> 472 if(overflow) break;
>> 473 }
>> 474 mean /= fCompression*fCompression;
>> 475
>> 476 if(!overflow) {
>> 477 density = Pixel2density(mean);
>> 478 dcmPZSH->AddValue(density);
>> 479 dcmPZSH->AddMateID(GetMaterialIndex(density));
>> 480 }
562 } 481 }
563 } 482 }
564 } 483 }
565 } << 484
566 << 485 dcmPZSH->FlipData();
567 dcmPZSH->FlipData(); <<
568 } 486 }
569 487
570 //....oooOO0OOooo........oooOO0OOooo........oo 488 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
571 // This function is depreciated as it is handl << 489 // This function is depreciated as it is handled by
572 // DicomPhantomZSliceHeader::DumpToFile 490 // DicomPhantomZSliceHeader::DumpToFile
573 void DicomHandler::StoreData(std::ofstream& fo 491 void DicomHandler::StoreData(std::ofstream& foutG4DCM)
574 { 492 {
575 G4int mean; 493 G4int mean;
576 G4double density; 494 G4double density;
577 G4bool overflow = false; 495 G4bool overflow = false;
578 << 496
579 //----- Print indices of material 497 //----- Print indices of material
580 if (fCompression == 1) { // no fCompression << 498 if(fCompression == 1) { // no fCompression: each pixel has a density value)
581 for (G4int ww = 0; ww < fRows; ++ww) { << 499 for( G4int ww = 0; ww < fRows; ww++) {
582 for (G4int xx = 0; xx < fColumns; ++xx) << 500 for( G4int xx = 0; xx < fColumns; xx++) {
583 mean = fTab[ww][xx]; 501 mean = fTab[ww][xx];
584 density = Pixel2density(mean); 502 density = Pixel2density(mean);
585 foutG4DCM << GetMaterialIndex(G4float( << 503 foutG4DCM << GetMaterialIndex( density ) << " ";
586 } 504 }
587 foutG4DCM << G4endl; 505 foutG4DCM << G4endl;
588 } 506 }
589 } << 507
590 else { << 508 } else {
591 // density value is the average of a squar 509 // density value is the average of a square region of
592 // fCompression*fCompression pixels 510 // fCompression*fCompression pixels
593 for (G4int ww = 0; ww < fRows; ww += fComp << 511 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
594 for (G4int xx = 0; xx < fColumns; xx += << 512 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
595 overflow = false; 513 overflow = false;
596 mean = 0; 514 mean = 0;
597 for (G4int sumx = 0; sumx < fCompressi << 515 for(int sumx = 0; sumx < fCompression; sumx++) {
598 for (G4int sumy = 0; sumy < fCompres << 516 for(int sumy = 0; sumy < fCompression; sumy++) {
599 if (ww + sumy >= fRows || xx + sum << 517 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
600 mean += fTab[ww + sumy][xx + sumx] << 518 mean += fTab[ww+sumy][xx+sumx];
601 } 519 }
602 if (overflow) break; << 520 if(overflow) break;
603 } 521 }
604 mean /= fCompression * fCompression; << 522 mean /= fCompression*fCompression;
605 << 523
606 if (!overflow) { << 524 if(!overflow) {
607 density = Pixel2density(mean); 525 density = Pixel2density(mean);
608 foutG4DCM << GetMaterialIndex(G4floa << 526 foutG4DCM << GetMaterialIndex( density ) << " ";
609 } 527 }
610 } 528 }
611 foutG4DCM << G4endl; 529 foutG4DCM << G4endl;
612 } 530 }
>> 531
613 } 532 }
614 << 533
615 //----- Print densities 534 //----- Print densities
616 if (fCompression == 1) { // no fCompression << 535 if(fCompression == 1) { // no fCompression: each pixel has a density value)
617 for (G4int ww = 0; ww < fRows; ww++) { << 536 for( G4int ww = 0; ww < fRows; ww++) {
618 for (G4int xx = 0; xx < fColumns; xx++) << 537 for( G4int xx = 0; xx < fColumns; xx++) {
619 mean = fTab[ww][xx]; 538 mean = fTab[ww][xx];
620 density = Pixel2density(mean); 539 density = Pixel2density(mean);
621 foutG4DCM << density << " "; 540 foutG4DCM << density << " ";
622 if (xx % 8 == 3) foutG4DCM << G4endl; << 541 if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading
623 } 542 }
624 } 543 }
625 } << 544
626 else { << 545 } else {
627 // density value is the average of a squar 546 // density value is the average of a square region of
628 // fCompression*fCompression pixels 547 // fCompression*fCompression pixels
629 for (G4int ww = 0; ww < fRows; ww += fComp << 548 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
630 for (G4int xx = 0; xx < fColumns; xx += << 549 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
631 overflow = false; 550 overflow = false;
632 mean = 0; 551 mean = 0;
633 for (G4int sumx = 0; sumx < fCompressi << 552 for(int sumx = 0; sumx < fCompression; sumx++) {
634 for (G4int sumy = 0; sumy < fCompres << 553 for(int sumy = 0; sumy < fCompression; sumy++) {
635 if (ww + sumy >= fRows || xx + sum << 554 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
636 mean += fTab[ww + sumy][xx + sumx] << 555 mean += fTab[ww+sumy][xx+sumx];
637 } 556 }
638 if (overflow) break; << 557 if(overflow) break;
639 } 558 }
640 mean /= fCompression * fCompression; << 559 mean /= fCompression*fCompression;
641 << 560
642 if (!overflow) { << 561 if(!overflow) {
643 density = Pixel2density(mean); 562 density = Pixel2density(mean);
644 foutG4DCM << density << " "; << 563 foutG4DCM << density << " ";
645 if (xx / fCompression % 8 == 3) fout << 564 if( xx/fCompression%8 == 3 ) foutG4DCM << G4endl; // just for nicer
646 // reading 565 // reading
647 } 566 }
648 } 567 }
649 } 568 }
>> 569
650 } 570 }
>> 571
651 } 572 }
652 573
653 //....oooOO0OOooo........oooOO0OOooo........oo << 574 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
654 void DicomHandler::ReadMaterialIndices(std::if << 575 void DicomHandler::ReadMaterialIndices( std::ifstream& finData)
655 { 576 {
656 unsigned int nMate; 577 unsigned int nMate;
657 G4String mateName; 578 G4String mateName;
658 G4float densityMax; 579 G4float densityMax;
659 finData >> nMate; 580 finData >> nMate;
660 if (finData.eof()) return; << 581 if( finData.eof() ) return;
661 << 582
662 G4cout << " ReadMaterialIndices " << nMate < 583 G4cout << " ReadMaterialIndices " << nMate << G4endl;
663 for (unsigned int ii = 0; ii < nMate; ++ii) << 584 for( unsigned int ii = 0; ii < nMate; ii++ ){
664 finData >> mateName >> densityMax; 585 finData >> mateName >> densityMax;
665 fMaterialIndices[densityMax] = mateName; 586 fMaterialIndices[densityMax] = mateName;
666 // G4cout << ii << " ReadMaterialIndice << 587 G4cout << ii << " ReadMaterialIndices " << mateName << " "
667 // << densityMax << G4endl; << 588 << densityMax << G4endl;
668 } 589 }
>> 590
669 } 591 }
670 592
671 //....oooOO0OOooo........oooOO0OOooo........oo 593 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
672 594
673 unsigned int DicomHandler::GetMaterialIndex(G4 << 595 unsigned int DicomHandler::GetMaterialIndex( G4float density )
674 { 596 {
675 std::map<G4float, G4String>::const_reverse_i << 597 std::map<G4float,G4String>::reverse_iterator ite;
676 std::size_t ii = fMaterialIndices.size(); << 598 G4int ii = fMaterialIndices.size();
677 << 599 for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend();
678 for (ite = fMaterialIndices.crbegin(); ite ! << 600 ite++, ii-- ) {
679 if (density >= (*ite).first) { << 601 if( density >= (*ite).first ) {
680 break; 602 break;
681 } 603 }
682 } 604 }
683 << 605 //- G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl;
684 if (ii == fMaterialIndices.size()) { << 606
685 ii = fMaterialIndices.size() - 1; << 607 if(static_cast<unsigned int>(ii) == fMaterialIndices.size())
686 } << 608 { ii = fMaterialIndices.size()-1; }
687 << 609
688 return unsigned(ii); << 610 return ii;
>> 611
689 } 612 }
690 613
691 //....oooOO0OOooo........oooOO0OOooo........oo 614 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
692 615
693 G4int DicomHandler::ReadData(FILE* dicom, char << 616 G4int DicomHandler::ReadData(FILE *dicom,char * filename2)
694 { 617 {
695 G4int returnvalue = 0; << 618 G4int returnvalue = 0; size_t rflag = 0;
696 size_t rflag = 0; << 619
697 << 620 // READING THE PIXELS :
698 // READING THE PIXELS << 621 G4int w = 0;
699 << 622
700 fTab = new G4int*[fRows]; 623 fTab = new G4int*[fRows];
701 for (G4int i = 0; i < fRows; ++i) { << 624 for ( G4int i = 0; i < fRows; i ++ ) {
702 fTab[i] = new G4int[fColumns]; << 625 fTab[i] = new G4int[fColumns];
703 } << 626 }
704 << 627
705 if (fBitAllocated == 8) { // Case 8 bits : << 628 if(fBitAllocated == 8) { // Case 8 bits :
706 << 629
707 std::printf("@@@ Error! Picture != 16 bits 630 std::printf("@@@ Error! Picture != 16 bits...\n");
708 std::printf("@@@ Error! Picture != 16 bits 631 std::printf("@@@ Error! Picture != 16 bits...\n");
709 std::printf("@@@ Error! Picture != 16 bits 632 std::printf("@@@ Error! Picture != 16 bits...\n");
710 << 633
711 unsigned char ch = 0; 634 unsigned char ch = 0;
712 << 635
713 for (G4int j = 0; j < fRows; ++j) { << 636 for(G4int j = 0; j < fRows; j++) {
714 for (G4int i = 0; i < fColumns; ++i) { << 637 for(G4int i = 0; i < fColumns; i++) {
715 rflag = std::fread(&ch, 1, 1, dicom); << 638 w++;
716 fTab[j][i] = ch * fRescaleSlope + fRes << 639 rflag = std::fread( &ch, 1, 1, dicom);
>> 640 fTab[j][i] = ch*fRescaleSlope + fRescaleIntercept;
717 } 641 }
718 } 642 }
719 returnvalue = 1; 643 returnvalue = 1;
720 } << 644
721 else { // from 12 to 16 bits : << 645 } else { // from 12 to 16 bits :
722 char sbuff[2]; 646 char sbuff[2];
723 short pixel; 647 short pixel;
724 for (G4int j = 0; j < fRows; ++j) { << 648 for( G4int j = 0; j < fRows; j++) {
725 for (G4int i = 0; i < fColumns; ++i) { << 649 for( G4int i = 0; i < fColumns; i++) {
>> 650 w++;
726 rflag = std::fread(sbuff, 2, 1, dicom) 651 rflag = std::fread(sbuff, 2, 1, dicom);
727 GetValue(sbuff, pixel); 652 GetValue(sbuff, pixel);
728 fTab[j][i] = pixel * fRescaleSlope + f << 653 fTab[j][i] = pixel*fRescaleSlope + fRescaleIntercept;
729 } 654 }
730 } 655 }
731 } 656 }
732 << 657
733 // Creation of .g4 files wich contains avera 658 // Creation of .g4 files wich contains averaged density data
734 G4String nameProcessed = filename2 + G4Strin << 659 char * nameProcessed = new char[FILENAMESIZE];
735 FILE* fileOut = std::fopen(nameProcessed.c_s << 660 FILE* fileOut;
736 << 661
737 G4cout << "### Writing of " << nameProcessed << 662 std::sprintf(nameProcessed,"%s.g4dcmb",filename2);
738 << 663 fileOut = std::fopen(nameProcessed,"w+b");
>> 664 std::printf("### Writing of %s ###\n",nameProcessed);
>> 665
739 unsigned int nMate = fMaterialIndices.size() 666 unsigned int nMate = fMaterialIndices.size();
740 rflag = std::fwrite(&nMate, sizeof(unsigned 667 rflag = std::fwrite(&nMate, sizeof(unsigned int), 1, fileOut);
741 //--- Write materials 668 //--- Write materials
742 for (auto ite = fMaterialIndices.cbegin(); i << 669 std::map<G4float,G4String>::const_iterator ite;
>> 670 for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++ ){
743 G4String mateName = (*ite).second; 671 G4String mateName = (*ite).second;
744 for (std::size_t ii = (*ite).second.length << 672 for( G4int ii = (*ite).second.length(); ii < 40; ii++ ) {
745 mateName += " "; 673 mateName += " ";
746 } // mateName = const_cast<char*>(((*ite) << 674 } //mateName = const_cast<char*>(((*ite).second).c_str());
747 << 675
748 const char* mateNameC = mateName.c_str(); 676 const char* mateNameC = mateName.c_str();
749 rflag = std::fwrite(mateNameC, sizeof(char << 677 rflag = std::fwrite(mateNameC, sizeof(char),40, fileOut);
750 } 678 }
751 << 679
752 unsigned int fRowsC = fRows / fCompression; << 680 unsigned int fRowsC = fRows/fCompression;
753 unsigned int fColumnsC = fColumns / fCompres << 681 unsigned int fColumnsC = fColumns/fCompression;
754 unsigned int planesC = 1; 682 unsigned int planesC = 1;
755 G4float pixelLocationXM = -G4float(fPixelSpa << 683 G4float pixelLocationXM = -fPixelSpacingX*fColumns/2.;
756 G4float pixelLocationXP = G4float(fPixelSpac << 684 G4float pixelLocationXP = fPixelSpacingX*fColumns/2.;
757 G4float pixelLocationYM = -G4float(fPixelSpa << 685 G4float pixelLocationYM = -fPixelSpacingY*fRows/2.;
758 G4float pixelLocationYP = G4float(fPixelSpac << 686 G4float pixelLocationYP = fPixelSpacingY*fRows/2.;
759 G4float fSliceLocationZM = G4float(fSliceLoc << 687 G4float fSliceLocationZM = fSliceLocation-fSliceThickness/2.;
760 G4float fSliceLocationZP = G4float(fSliceLoc << 688 G4float fSliceLocationZP = fSliceLocation+fSliceThickness/2.;
761 //--- Write number of voxels (assume only on 689 //--- Write number of voxels (assume only one voxel in Z)
762 rflag = std::fwrite(&fRowsC, sizeof(unsigned 690 rflag = std::fwrite(&fRowsC, sizeof(unsigned int), 1, fileOut);
763 rflag = std::fwrite(&fColumnsC, sizeof(unsig 691 rflag = std::fwrite(&fColumnsC, sizeof(unsigned int), 1, fileOut);
764 rflag = std::fwrite(&planesC, sizeof(unsigne 692 rflag = std::fwrite(&planesC, sizeof(unsigned int), 1, fileOut);
765 //--- Write minimum and maximum extensions 693 //--- Write minimum and maximum extensions
766 rflag = std::fwrite(&pixelLocationXM, sizeof 694 rflag = std::fwrite(&pixelLocationXM, sizeof(G4float), 1, fileOut);
767 rflag = std::fwrite(&pixelLocationXP, sizeof 695 rflag = std::fwrite(&pixelLocationXP, sizeof(G4float), 1, fileOut);
768 rflag = std::fwrite(&pixelLocationYM, sizeof 696 rflag = std::fwrite(&pixelLocationYM, sizeof(G4float), 1, fileOut);
769 rflag = std::fwrite(&pixelLocationYP, sizeof 697 rflag = std::fwrite(&pixelLocationYP, sizeof(G4float), 1, fileOut);
770 rflag = std::fwrite(&fSliceLocationZM, sizeo 698 rflag = std::fwrite(&fSliceLocationZM, sizeof(G4float), 1, fileOut);
771 rflag = std::fwrite(&fSliceLocationZP, sizeo 699 rflag = std::fwrite(&fSliceLocationZP, sizeof(G4float), 1, fileOut);
772 // rflag = std::fwrite(&fCompression, sizeof 700 // rflag = std::fwrite(&fCompression, sizeof(unsigned int), 1, fileOut);
773 << 701
774 std::printf("%8i %8i\n", fRows, fColumns); << 702 std::printf("%8i %8i\n",fRows,fColumns);
775 std::printf("%8f %8f\n", fPixelSpacingX, f << 703 std::printf("%8f %8f\n",fPixelSpacingX,fPixelSpacingY);
776 std::printf("%8f\n", fSliceThickness); 704 std::printf("%8f\n", fSliceThickness);
777 std::printf("%8f\n", fSliceLocation); 705 std::printf("%8f\n", fSliceLocation);
778 std::printf("%8i\n", fCompression); 706 std::printf("%8i\n", fCompression);
779 << 707
780 G4int compSize = fCompression; 708 G4int compSize = fCompression;
781 G4int mean; 709 G4int mean;
782 G4float density; 710 G4float density;
783 G4bool overflow = false; 711 G4bool overflow = false;
784 << 712
785 //----- Write index of material for each pix 713 //----- Write index of material for each pixel
786 if (compSize == 1) { // no fCompression: ea << 714 if(compSize == 1) { // no fCompression: each pixel has a density value)
787 for (G4int ww = 0; ww < fRows; ++ww) { << 715 for( G4int ww = 0; ww < fRows; ww++) {
788 for (G4int xx = 0; xx < fColumns; ++xx) << 716 for( G4int xx = 0; xx < fColumns; xx++) {
789 mean = fTab[ww][xx]; 717 mean = fTab[ww][xx];
790 density = Pixel2density(mean); 718 density = Pixel2density(mean);
791 unsigned int mateID = GetMaterialIndex << 719 unsigned int mateID = GetMaterialIndex( density );
792 rflag = std::fwrite(&mateID, sizeof(un 720 rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
793 } 721 }
794 } 722 }
795 } << 723
796 else { << 724 } else {
797 // density value is the average of a squar 725 // density value is the average of a square region of
798 // fCompression*fCompression pixels 726 // fCompression*fCompression pixels
799 for (G4int ww = 0; ww < fRows; ww += compS << 727 for(G4int ww = 0; ww < fRows ;ww += compSize ) {
800 for (G4int xx = 0; xx < fColumns; xx += << 728 for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
801 overflow = false; 729 overflow = false;
802 mean = 0; 730 mean = 0;
803 for (G4int sumx = 0; sumx < compSize; << 731 for(int sumx = 0; sumx < compSize; sumx++) {
804 for (G4int sumy = 0; sumy < compSize << 732 for(int sumy = 0; sumy < compSize; sumy++) {
805 if (ww + sumy >= fRows || xx + sum << 733 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
806 mean += fTab[ww + sumy][xx + sumx] << 734 mean += fTab[ww+sumy][xx+sumx];
807 } 735 }
808 if (overflow) break; << 736 if(overflow) break;
809 } 737 }
810 mean /= compSize * compSize; << 738 mean /= compSize*compSize;
811 << 739
812 if (!overflow) { << 740 if(!overflow) {
813 density = Pixel2density(mean); 741 density = Pixel2density(mean);
814 unsigned int mateID = GetMaterialInd << 742 unsigned int mateID = GetMaterialIndex( density );
815 rflag = std::fwrite(&mateID, sizeof( 743 rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
816 } 744 }
817 } 745 }
>> 746
818 } 747 }
819 } 748 }
820 << 749
821 //----- Write density for each pixel 750 //----- Write density for each pixel
822 if (compSize == 1) { // no fCompression: ea << 751 if(compSize == 1) { // no fCompression: each pixel has a density value)
823 for (G4int ww = 0; ww < fRows; ++ww) { << 752 for( G4int ww = 0; ww < fRows; ww++) {
824 for (G4int xx = 0; xx < fColumns; ++xx) << 753 for( G4int xx = 0; xx < fColumns; xx++) {
825 mean = fTab[ww][xx]; 754 mean = fTab[ww][xx];
826 density = Pixel2density(mean); 755 density = Pixel2density(mean);
827 rflag = std::fwrite(&density, sizeof(G 756 rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
828 } 757 }
829 } 758 }
830 } << 759
831 else { << 760 } else {
832 // density value is the average of a squar 761 // density value is the average of a square region of
833 // fCompression*fCompression pixels 762 // fCompression*fCompression pixels
834 for (G4int ww = 0; ww < fRows; ww += compS << 763 for(G4int ww = 0; ww < fRows ;ww += compSize ) {
835 for (G4int xx = 0; xx < fColumns; xx += << 764 for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
836 overflow = false; 765 overflow = false;
837 mean = 0; 766 mean = 0;
838 for (G4int sumx = 0; sumx < compSize; << 767 for(int sumx = 0; sumx < compSize; sumx++) {
839 for (G4int sumy = 0; sumy < compSize << 768 for(int sumy = 0; sumy < compSize; sumy++) {
840 if (ww + sumy >= fRows || xx + sum << 769 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
841 mean += fTab[ww + sumy][xx + sumx] << 770 mean += fTab[ww+sumy][xx+sumx];
842 } 771 }
843 if (overflow) break; << 772 if(overflow) break;
844 } 773 }
845 mean /= compSize * compSize; << 774 mean /= compSize*compSize;
846 << 775
847 if (!overflow) { << 776 if(!overflow) {
848 density = Pixel2density(mean); 777 density = Pixel2density(mean);
849 rflag = std::fwrite(&density, sizeof 778 rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
850 } 779 }
851 } 780 }
>> 781
852 } 782 }
853 } 783 }
854 << 784
855 rflag = std::fclose(fileOut); 785 rflag = std::fclose(fileOut);
856 << 786
857 delete[] nameProcessed; << 787 delete [] nameProcessed;
858 << 788
859 /* for ( G4int i = 0; i < fRows; i ++ ) { 789 /* for ( G4int i = 0; i < fRows; i ++ ) {
860 delete [] fTab[i]; 790 delete [] fTab[i];
861 } 791 }
862 delete [] fTab; 792 delete [] fTab;
863 */ 793 */
864 << 794
865 if (rflag) return returnvalue; 795 if (rflag) return returnvalue;
866 return returnvalue; 796 return returnvalue;
867 } 797 }
868 798
869 //....oooOO0OOooo........oooOO0OOooo........oo <<
870 <<
871 // DICOM HEAD does not use the calibration cur <<
872 799
873 #ifdef DICOM_USE_HEAD << 800 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
874 void DicomHandler::ReadCalibration() <<
875 { <<
876 fNbrequali = 0; <<
877 fReadCalibration = false; <<
878 G4cout << "No calibration curve for the DICO <<
879 } <<
880 #else <<
881 // Separated out of Pixel2density 801 // Separated out of Pixel2density
882 // No need to read in same calibration EVERY t 802 // No need to read in same calibration EVERY time
883 // Increases the speed of reading file by seve 803 // Increases the speed of reading file by several orders of magnitude
884 <<
885 void DicomHandler::ReadCalibration() 804 void DicomHandler::ReadCalibration()
886 { 805 {
887 fNbrequali = 0; << 806 nbrequali = 0;
>> 807
888 // CT2Density.dat contains the calibration c 808 // CT2Density.dat contains the calibration curve to convert CT (Hounsfield)
889 // number to physical density 809 // number to physical density
890 std::ifstream calibration(fCt2DensityFile.c_ << 810 std::ifstream calibration(ct2densityFile.c_str());
891 calibration >> fNbrequali; << 811 calibration >> nbrequali;
892 fValueDensity = new G4double[fNbrequali]; << 812
893 fValueCT = new G4double[fNbrequali]; << 813 valuedensity = new G4double[nbrequali];
894 << 814 valueCT = new G4double[nbrequali];
895 if (!calibration) { << 815
896 G4Exception("DicomHandler::ReadFile", "DIC << 816 if(!calibration) {
>> 817 G4Exception("DicomHandler::ReadFile",
>> 818 "DICOM001",
>> 819 FatalException,
897 "@@@ No value to transform pix 820 "@@@ No value to transform pixels in density!");
898 } << 821
899 else { // calibration was successfully open << 822 } else { // calibration was successfully opened
900 for (G4int i = 0; i < fNbrequali; ++i) { << 823 for(G4int i = 0; i < nbrequali; i++) { // Loop to store all the
901 calibration >> fValueCT[i] >> fValueDens << 824 //pts in CT2Density.dat
>> 825 calibration >> valueCT[i] >> valuedensity[i];
902 } 826 }
903 } 827 }
904 calibration.close(); 828 calibration.close();
905 fReadCalibration = true; << 829
906 } << 830 readCalibration = true;
907 #endif <<
908 <<
909 #ifdef DICOM_USE_HEAD <<
910 G4float DicomHandler::Pixel2density(G4int pixe <<
911 { <<
912 G4float density = -1; <<
913 <<
914 // Air <<
915 if (pixel == -998.) density = 0.001290; <<
916 // Soft Tissue <<
917 else if (pixel == 24.) <<
918 density = 1.00; <<
919 // Brain <<
920 else if (pixel == 52.) <<
921 density = 1.03; <<
922 // Spinal disc <<
923 else if (pixel == 92.) <<
924 density = 1.10; <<
925 // Trabecular bone <<
926 else if (pixel == 197.) <<
927 density = 1.18; <<
928 // Cortical Bone <<
929 else if (pixel == 923.) <<
930 density = 1.85; <<
931 // Tooth dentine <<
932 else if (pixel == 1280.) <<
933 density = 2.14; <<
934 // Tooth enamel <<
935 else if (pixel == 2310.) <<
936 density = 2.89; <<
937 <<
938 return density; <<
939 } 831 }
940 832
941 #else << 833 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
942 //....oooOO0OOooo........oooOO0OOooo........oo <<
943 834
944 G4float DicomHandler::Pixel2density(G4int pixe 835 G4float DicomHandler::Pixel2density(G4int pixel)
945 { 836 {
946 if (!fReadCalibration) { << 837 if(!readCalibration) { ReadCalibration(); }
947 ReadCalibration(); << 838
948 } <<
949 <<
950 G4float density = -1.; 839 G4float density = -1.;
951 G4double deltaCT = 0; 840 G4double deltaCT = 0;
952 G4double deltaDensity = 0; 841 G4double deltaDensity = 0;
953 << 842
954 for (G4int j = 1; j < fNbrequali; ++j) { << 843
955 if (pixel >= fValueCT[j - 1] && pixel < fV << 844 for(G4int j = 1; j < nbrequali; j++) {
956 deltaCT = fValueCT[j] - fValueCT[j - 1]; << 845 if( pixel >= valueCT[j-1] && pixel < valueCT[j]) {
957 deltaDensity = fValueDensity[j] - fValue << 846
958 << 847 deltaCT = valueCT[j] - valueCT[j-1];
>> 848 deltaDensity = valuedensity[j] - valuedensity[j-1];
>> 849
959 // interpolating linearly 850 // interpolating linearly
960 density = G4float(fValueDensity[j] - ((f << 851 density = valuedensity[j] - ((valueCT[j] - pixel)*deltaDensity/deltaCT );
961 break; 852 break;
962 } 853 }
963 } 854 }
964 << 855
965 if (density < 0.) { << 856 if(density < 0.) {
966 std::printf( << 857 std::printf("@@@ Error density = %f && Pixel = %i \
967 "@@@ Error density = %f && Pixel = %i \ << 858 (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel,
968 (0x%x) && deltaDensity/deltaCT = %f\n", << 859 deltaDensity/deltaCT);
969 density, pixel, pixel, deltaDensity / de <<
970 } 860 }
971 << 861
972 return density; 862 return density;
973 } 863 }
974 #endif << 864
975 //....oooOO0OOooo........oooOO0OOooo........oo 865 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
976 866
977 void DicomHandler::CheckFileFormat() 867 void DicomHandler::CheckFileFormat()
978 { 868 {
979 std::ifstream checkData(fDriverFile.c_str()) << 869 std::ifstream checkData(driverFile.c_str());
980 char* oneLine = new char[128]; << 870 char * oneLine = new char[128];
981 << 871
982 if (!(checkData.is_open())) { // Check exis << 872 if(!(checkData.is_open())) { //Check existance of Data.dat
983 << 873
984 G4String message = "\nDicomG4 needs Data.d << 874 G4String message =
>> 875 "\nDicomG4 needs Data.dat (or another driver file specified";
985 message += " in command line):\n"; 876 message += " in command line):\n";
986 message += "\tFirst line: number of image 877 message += "\tFirst line: number of image pixel for a voxel (G4Box)\n";
987 message += "\tSecond line: number of image 878 message += "\tSecond line: number of images (CT slices) to read\n";
988 message += "\tEach following line contains 879 message += "\tEach following line contains the name of a Dicom image";
989 message += " except for the .dcm extension 880 message += " except for the .dcm extension";
990 G4Exception("DicomHandler::ReadFile", "DIC << 881 G4Exception("DicomHandler::ReadFile",
>> 882 "DICOM001",
>> 883 FatalException,
>> 884 message.c_str());
991 } 885 }
992 << 886
993 checkData >> fCompression; 887 checkData >> fCompression;
994 checkData >> fNFiles; 888 checkData >> fNFiles;
995 G4String oneName; 889 G4String oneName;
996 checkData.getline(oneLine, 100); << 890 checkData.getline(oneLine,100);
997 std::ifstream testExistence; 891 std::ifstream testExistence;
998 G4bool existAlready = true; 892 G4bool existAlready = true;
999 for (G4int rep = 0; rep < fNFiles; ++rep) { << 893 for(G4int rep = 0; rep < fNFiles; rep++) {
1000 checkData.getline(oneLine, 100); << 894 checkData.getline(oneLine,100);
1001 oneName = oneLine; 895 oneName = oneLine;
1002 oneName += ".g4dcm"; // create dicomFile << 896 oneName += ".g4dcm"; // create dicomFile.g4dcm
1003 G4cout << fNFiles << " test file " << one 897 G4cout << fNFiles << " test file " << oneName << G4endl;
1004 testExistence.open(oneName.data()); 898 testExistence.open(oneName.data());
1005 if (!(testExistence.is_open())) { << 899 if(!(testExistence.is_open())) {
1006 existAlready = false; 900 existAlready = false;
1007 testExistence.clear(); 901 testExistence.clear();
1008 testExistence.close(); 902 testExistence.close();
1009 } 903 }
1010 testExistence.clear(); 904 testExistence.clear();
1011 testExistence.close(); 905 testExistence.close();
1012 } 906 }
1013 << 907
1014 ReadMaterialIndices(checkData); << 908 ReadMaterialIndices( checkData );
1015 << 909
1016 checkData.close(); 910 checkData.close();
1017 delete[] oneLine; << 911 delete [] oneLine;
1018 << 912
1019 if (existAlready == false) { // The files << 913 if( existAlready == false ) { // The files *.g4dcm have to be created
1020 << 914
1021 G4cout << "\nAll the necessary images wer 915 G4cout << "\nAll the necessary images were not found in processed form "
1022 << ", starting with .dcm images\n" 916 << ", starting with .dcm images\n";
1023 << 917
1024 FILE* dicom; << 918 FILE * dicom;
1025 FILE* lecturePref; << 919 FILE * lecturePref;
1026 char* fCompressionc = new char[LINEBUFFSI << 920 char * fCompressionc = new char[LINEBUFFSIZE];
1027 char* maxc = new char[LINEBUFFSIZE]; << 921 char * maxc = new char[LINEBUFFSIZE];
1028 // char name[300], inputFile[300]; << 922 //char name[300], inputFile[300];
1029 char* inputFile = new char[FILENAMESIZE]; << 923 char * name = new char[FILENAMESIZE];
>> 924 char * inputFile = new char[FILENAMESIZE];
1030 G4int rflag; 925 G4int rflag;
1031 lecturePref = std::fopen(fDriverFile.c_st << 926
1032 << 927 lecturePref = std::fopen(driverFile.c_str(),"r");
1033 rflag = std::fscanf(lecturePref, "%s", fC << 928 rflag = std::fscanf(lecturePref,"%s",fCompressionc);
1034 fCompression = atoi(fCompressionc); 929 fCompression = atoi(fCompressionc);
1035 rflag = std::fscanf(lecturePref, "%s", ma << 930 rflag = std::fscanf(lecturePref,"%s",maxc);
1036 fNFiles = atoi(maxc); 931 fNFiles = atoi(maxc);
1037 G4cout << " fNFiles " << fNFiles << G4end 932 G4cout << " fNFiles " << fNFiles << G4endl;
1038 << 933
1039 ///////////////////// << 934 for( G4int i = 1; i <= fNFiles; i++ ) { // Begin loop on filenames
1040 << 935
1041 #ifdef DICOM_USE_HEAD << 936 rflag = std::fscanf(lecturePref,"%s",inputFile);
1042 for (G4int i = 1; i <= fNFiles; ++i) { / << 937 std::sprintf(name,"%s.dcm",inputFile);
1043 rflag = std::fscanf(lecturePref, "%s", << 938 G4cout << "check 1: " << name << G4endl;
1044 G4String path = GetDicomDataPath() + "/ <<
1045 <<
1046 G4String name = inputFile + G4String(". <<
1047 // Writes the results to a character st <<
1048 <<
1049 G4String name2 = path + name; <<
1050 // Open input file and give it to gest 939 // Open input file and give it to gestion_dicom :
1051 G4cout << "### Opening " << name2 << " << 940 std::printf("### Opening %s and reading :\n",name);
1052 dicom = std::fopen(name2.c_str(), "rb") << 941 dicom = std::fopen(name,"rb");
1053 // Reading the .dcm in two steps: 942 // Reading the .dcm in two steps:
1054 // 1. reading the header 943 // 1. reading the header
1055 // 2. reading the pixel data and s 944 // 2. reading the pixel data and store the density in Moyenne.dat
1056 if (dicom != 0) { << 945 if( dicom != 0 ) {
1057 ReadFile(dicom, inputFile); << 946 ReadFile(dicom,inputFile);
1058 } << 947 } else {
1059 else { <<
1060 G4cout << "\nError opening file : " < <<
1061 } <<
1062 rflag = std::fclose(dicom); <<
1063 } <<
1064 #else <<
1065 <<
1066 for (G4int i = 1; i <= fNFiles; ++i) { / <<
1067 rflag = std::fscanf(lecturePref, "%s", <<
1068 <<
1069 G4String name = inputFile + G4String(". <<
1070 // Writes the results to a character st <<
1071 <<
1072 // G4cout << "check: " << name << G4end <<
1073 // Open input file and give it to gest <<
1074 G4cout << "### Opening " << name << " a <<
1075 dicom = std::fopen(name.c_str(), "rb"); <<
1076 // Reading the .dcm in two steps: <<
1077 // 1. reading the header <<
1078 // 2. reading the pixel data and s <<
1079 if (dicom != 0) { <<
1080 ReadFile(dicom, inputFile); <<
1081 } <<
1082 else { <<
1083 G4cout << "\nError opening file : " < 948 G4cout << "\nError opening file : " << name << G4endl;
1084 } 949 }
1085 rflag = std::fclose(dicom); 950 rflag = std::fclose(dicom);
1086 } 951 }
1087 #endif <<
1088 <<
1089 rflag = std::fclose(lecturePref); 952 rflag = std::fclose(lecturePref);
1090 << 953
1091 // Checks the spacing is correct. Dumps t 954 // Checks the spacing is correct. Dumps to files
1092 fMergedSlices->CheckSlices(); << 955 mergedSlices->CheckSlices();
1093 << 956
1094 delete[] fCompressionc; << 957 delete [] fCompressionc;
1095 delete[] maxc; << 958 delete [] maxc;
1096 delete[] inputFile; << 959 delete [] name;
>> 960 delete [] inputFile;
1097 if (rflag) return; 961 if (rflag) return;
>> 962
1098 } 963 }
1099 << 964
1100 if (fValueDensity) { << 965 if(valuedensity) { delete [] valuedensity; }
1101 delete[] fValueDensity; << 966 if(valueCT) { delete [] valueCT; }
1102 } << 967 if(mergedSlices) { delete mergedSlices; }
1103 if (fValueCT) { << 968
1104 delete[] fValueCT; <<
1105 } <<
1106 if (fMergedSlices) { <<
1107 delete fMergedSlices; <<
1108 } <<
1109 } 969 }
1110 970
1111 //....oooOO0OOooo........oooOO0OOooo........o << 971 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1112 972
1113 G4int DicomHandler::read_defined_nested(FILE* << 973 G4int DicomHandler::read_defined_nested(FILE * nested,G4int SQ_Length)
1114 { 974 {
1115 // VARIABLES 975 // VARIABLES
1116 unsigned short item_GroupNumber; 976 unsigned short item_GroupNumber;
1117 unsigned short item_ElementNumber; 977 unsigned short item_ElementNumber;
1118 G4int item_Length; 978 G4int item_Length;
1119 G4int items_array_length = 0; << 979 G4int items_array_length=0;
1120 char* buffer = new char[LINEBUFFSIZE]; << 980 char * buffer= new char[LINEBUFFSIZE];
1121 size_t rflag = 0; 981 size_t rflag = 0;
1122 << 982
1123 while (items_array_length < SQ_Length) { << 983 while(items_array_length < SQ_Length)
1124 rflag = std::fread(buffer, 2, 1, nested); << 984 {
1125 GetValue(buffer, item_GroupNumber); << 985 rflag = std::fread(buffer, 2, 1, nested);
1126 << 986 GetValue(buffer, item_GroupNumber);
1127 rflag = std::fread(buffer, 2, 1, nested); << 987
1128 GetValue(buffer, item_ElementNumber); << 988 rflag = std::fread(buffer, 2, 1, nested);
1129 << 989 GetValue(buffer, item_ElementNumber);
1130 rflag = std::fread(buffer, 4, 1, nested); << 990
1131 GetValue(buffer, item_Length); << 991 rflag = std::fread(buffer, 4, 1, nested);
1132 << 992 GetValue(buffer, item_Length);
1133 rflag = std::fread(buffer, item_Length, 1 << 993
1134 << 994 rflag = std::fread(buffer, item_Length, 1, nested);
1135 items_array_length = items_array_length + << 995
1136 } << 996 items_array_length= items_array_length+8+item_Length;
1137 << 997 }
1138 delete[] buffer; << 998
1139 << 999 delete [] buffer;
1140 if (SQ_Length > items_array_length) << 1000
>> 1001 if( SQ_Length>items_array_length )
1141 return 0; 1002 return 0;
1142 else 1003 else
1143 return 1; 1004 return 1;
1144 if (rflag) return 1; 1005 if (rflag) return 1;
1145 } 1006 }
1146 1007
1147 //....oooOO0OOooo........oooOO0OOooo........o << 1008 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1148 1009
1149 void DicomHandler::read_undefined_nested(FILE << 1010 void DicomHandler::read_undefined_nested(FILE * nested)
1150 { 1011 {
1151 // VARIABLES 1012 // VARIABLES
1152 unsigned short item_GroupNumber; 1013 unsigned short item_GroupNumber;
1153 unsigned short item_ElementNumber; 1014 unsigned short item_ElementNumber;
1154 unsigned int item_Length; 1015 unsigned int item_Length;
1155 char* buffer = new char[LINEBUFFSIZE]; << 1016 char * buffer= new char[LINEBUFFSIZE];
1156 size_t rflag = 0; 1017 size_t rflag = 0;
1157 << 1018
1158 do { << 1019 do
1159 rflag = std::fread(buffer, 2, 1, nested); << 1020 {
1160 GetValue(buffer, item_GroupNumber); << 1021 rflag = std::fread(buffer, 2, 1, nested);
1161 << 1022 GetValue(buffer, item_GroupNumber);
1162 rflag = std::fread(buffer, 2, 1, nested); << 1023
1163 GetValue(buffer, item_ElementNumber); << 1024 rflag = std::fread(buffer, 2, 1, nested);
1164 << 1025 GetValue(buffer, item_ElementNumber);
1165 rflag = std::fread(buffer, 4, 1, nested); << 1026
1166 GetValue(buffer, item_Length); << 1027 rflag = std::fread(buffer, 4, 1, nested);
1167 << 1028 GetValue(buffer, item_Length);
1168 if (item_Length != 0xffffffff) << 1029
1169 rflag = std::fread(buffer, item_Length, << 1030 if(item_Length!=0xffffffff)
1170 else << 1031 rflag = std::fread(buffer, item_Length, 1, nested);
1171 read_undefined_item(nested); << 1032 else
1172 << 1033 read_undefined_item(nested);
1173 } while (item_GroupNumber != 0xFFFE || item << 1034
1174 << 1035
1175 delete[] buffer; << 1036 } while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE0DD
1176 if (rflag) return; << 1037 || item_Length!=0);
>> 1038
>> 1039 delete [] buffer;
>> 1040 if (rflag) return;
1177 } 1041 }
1178 1042
1179 //....oooOO0OOooo........oooOO0OOooo........o << 1043 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1180 1044
1181 void DicomHandler::read_undefined_item(FILE* << 1045 void DicomHandler::read_undefined_item(FILE * nested)
1182 { 1046 {
1183 // VARIABLES 1047 // VARIABLES
1184 unsigned short item_GroupNumber; 1048 unsigned short item_GroupNumber;
1185 unsigned short item_ElementNumber; 1049 unsigned short item_ElementNumber;
1186 G4int item_Length; << 1050 G4int item_Length; size_t rflag = 0;
1187 size_t rflag = 0; << 1051 char *buffer= new char[LINEBUFFSIZE];
1188 char* buffer = new char[LINEBUFFSIZE]; << 1052
1189 << 1053 do
1190 do { << 1054 {
1191 rflag = std::fread(buffer, 2, 1, nested); << 1055 rflag = std::fread(buffer, 2, 1, nested);
1192 GetValue(buffer, item_GroupNumber); << 1056 GetValue(buffer, item_GroupNumber);
1193 << 1057
1194 rflag = std::fread(buffer, 2, 1, nested); << 1058 rflag = std::fread(buffer, 2, 1, nested);
1195 GetValue(buffer, item_ElementNumber); << 1059 GetValue(buffer, item_ElementNumber);
1196 << 1060
1197 rflag = std::fread(buffer, 4, 1, nested); << 1061 rflag = std::fread(buffer, 4, 1, nested);
1198 GetValue(buffer, item_Length); << 1062 GetValue(buffer, item_Length);
1199 << 1063
1200 if (item_Length != 0) rflag = std::fread( << 1064
1201 << 1065 if(item_Length!=0)
1202 } while (item_GroupNumber != 0xFFFE || item << 1066 rflag = std::fread(buffer,item_Length,1,nested);
1203 << 1067
1204 delete[] buffer; << 1068 }
>> 1069 while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE00D
>> 1070 || item_Length!=0);
>> 1071
>> 1072 delete [] buffer;
1205 if (rflag) return; 1073 if (rflag) return;
1206 } 1074 }
1207 1075
1208 //....oooOO0OOooo........oooOO0OOooo........o << 1076 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1209 1077
1210 template<class Type> << 1078 template <class Type>
1211 void DicomHandler::GetValue(char* _val, Type& << 1079 void DicomHandler::GetValue(char * _val, Type & _rval) {
1212 { << 1080
1213 #if BYTE_ORDER == BIG_ENDIAN 1081 #if BYTE_ORDER == BIG_ENDIAN
1214 if (fLittleEndian) { // little endian << 1082 if(fLittleEndian) { // little endian
1215 #else // BYTE_ORDER == LITTLE_ENDIAN << 1083 #else // BYTE_ORDER == LITTLE_ENDIAN
1216 if (!fLittleEndian) { // big endian << 1084 if(!fLittleEndian) { // big endian
1217 #endif 1085 #endif
1218 const G4int SIZE = sizeof(_rval); << 1086 const int SIZE = sizeof(_rval);
1219 char ctemp; << 1087 char ctemp;
1220 for (G4int i = 0; i < SIZE / 2; ++i) { << 1088 for(int i = 0; i < SIZE/2; i++) {
1221 ctemp = _val[i]; << 1089 ctemp = _val[i];
1222 _val[i] = _val[SIZE - 1 - i]; << 1090 _val[i] = _val[SIZE - 1 - i];
1223 _val[SIZE - 1 - i] = ctemp; << 1091 _val[SIZE - 1 - i] = ctemp;
>> 1092 }
1224 } 1093 }
>> 1094 _rval = *(Type *)_val;
1225 } 1095 }
1226 _rval = *(Type*)_val; << 1096
1227 } << 1097 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1228 << 1098
1229 //....oooOO0OOooo........oooOO0OOooo........o <<
1230 1099