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1 // 1 //
2 // ******************************************* 2 // ********************************************************************
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4 // * 4 // * *
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24 // ******************************************* 24 // ********************************************************************
25 // 25 //
>> 26 // $Id: DicomHandler.cc 92820 2015-09-17 15:22:14Z 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::fInstance = 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 fInstance;
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), fNbrequali(0),
>> 88 fValueDensity(NULL),fValueCT(NULL),fReadCalibration(false),
>> 89 fMergedSlices(NULL),fDriverFile("Data.dat"),fCt2DensityFile("CT2Density.dat")
84 { 90 {
85 // default is current directory << 91 fMergedSlices = 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 94 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
114 95
115 G4String DicomHandler::GetDicomDataFile() << 96 DicomHandler::~DicomHandler()
116 { 97 {
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 <<
124 //....oooOO0OOooo........oooOO0OOooo........oo <<
125 98
126 #ifdef DICOM_USE_HEAD <<
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 { <<
154 fMergedSlices = new DicomPhantomZSliceMerged <<
155 fDriverFile = GetDicomDataFile(); <<
156 G4cout << "Reading the DICOM_HEAD project " <<
157 } 99 }
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 <<
192 DicomHandler::~DicomHandler() {} <<
193 100
194 //....oooOO0OOooo........oooOO0OOooo........oo 101 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
195 102
196 G4int DicomHandler::ReadFile(FILE* dicom, char 103 G4int DicomHandler::ReadFile(FILE* dicom, char* filename2)
197 { 104 {
198 G4cout << " ReadFile " << filename2 << G4end << 105 G4cout << " ReadFile " << filename2 << G4endl;
199 << 106 G4int returnvalue = 0; size_t rflag = 0;
200 G4int returnvalue = 0; << 107 char * buffer = new char[LINEBUFFSIZE];
201 size_t rflag = 0; << 108
202 char* buffer = new char[LINEBUFFSIZE]; << 109 fImplicitEndian = false;
203 << 110 fLittleEndian = true;
204 fImplicitEndian = false; << 111
205 fLittleEndian = true; << 112 rflag = std::fread( buffer, 1, 128, dicom ); // The first 128 bytes
206 << 113 //are not important
207 rflag = std::fread(buffer, 1, 128, dicom); << 114 // Reads the "DICOM" letters
208 << 115 rflag = std::fread( buffer, 1, 4, dicom );
209 << 116 // if there is no preamble, the FILE pointer is rewinded.
210 rflag = std::fread(buffer, 1, 4, dicom); << 117 if(std::strncmp("DICM", buffer, 4) != 0) {
211 // if there is no preamble, the FILE pointer << 118 std::fseek(dicom, 0, SEEK_SET);
212 if (std::strncmp("DICM", buffer, 4) != 0) { << 119 fImplicitEndian = true;
213 std::fseek(dicom, 0, SEEK_SET); << 120 }
214 fImplicitEndian = true; << 121
215 } << 122 short readGroupId; // identify the kind of input data
216 << 123 short readElementId; // identify a particular type information
217 short readGroupId; // identify the kind of << 124 short elementLength2; // deal with element length in 2 bytes
218 short readElementId; // identify a particul << 125 //unsigned int elementLength4;
219 short elementLength2; // deal with element << 126 // deal with element length in 4 bytes
220 // unsigned int eleme << 127 unsigned long elementLength4; // deal with element length in 4 bytes
221 // deal with element length in 4 bytes << 128
222 unsigned long elementLength4; // deal with << 129 char * data = new char[DATABUFFSIZE];
223 << 130
224 char* data = new char[DATABUFFSIZE]; << 131 // Read information up to the pixel data
225 << 132 while(true) {
226 // Read information up to the pixel data << 133
227 while (true) { << 134 //Reading groups and elements :
228 // Reading groups and elements : << 135 readGroupId = 0;
229 readGroupId = 0; << 136 readElementId = 0;
230 readElementId = 0; << 137 // group ID
231 // group ID << 138 rflag = std::fread(buffer, 2, 1, dicom);
232 rflag = std::fread(buffer, 2, 1, dicom); << 139 GetValue(buffer, readGroupId);
233 GetValue(buffer, readGroupId); << 140 // element ID
234 // element ID << 141 rflag = std::fread(buffer, 2, 1, dicom);
235 rflag = std::fread(buffer, 2, 1, dicom); << 142 GetValue(buffer, readElementId);
236 GetValue(buffer, readElementId); << 143
237 << 144 // Creating a tag to be identified afterward
238 // Creating a tag to be identified afterwa << 145 G4int tagDictionary = readGroupId*0x10000 + readElementId;
239 G4int tagDictionary = readGroupId * 0x1000 << 146
240 << 147 // beginning of the pixels
241 // beginning of the pixels << 148 if(tagDictionary == 0x7FE00010) {
242 if (tagDictionary == 0x7FE00010) { << 149 // Folling 2 fread's are modifications to original DICOM example
243 // Following 2 fread's are modifications << 150 //(Jonathan Madsen)
244 // (Jonathan Madsen) << 151 rflag = std::fread(buffer,2,1,dicom); // Reserved 2 bytes
245 if (!fImplicitEndian) rflag = std::fread << 152 // (not used for pixels)
246 // (not used for pixels) << 153 rflag = std::fread(buffer,4,1,dicom); // Element Length
247 rflag = std::fread(buffer, 4, 1, dicom); << 154 // (not used for pixels)
248 // (not used for pixels) << 155 break; // Exit to ReadImageData()
249 break; // Exit to ReadImageData() << 156 }
250 } << 157
251 << 158 // VR or element length
252 // VR or element length << 159 rflag = std::fread(buffer,2,1,dicom);
253 rflag = std::fread(buffer, 2, 1, dicom); << 160 GetValue(buffer, elementLength2);
254 GetValue(buffer, elementLength2); << 161
255 << 162 // If value representation (VR) is OB, OW, SQ, UN, added OF and UT
256 // If value representation (VR) is OB, OW, << 163 //the next length is 32 bits
257 // the next length is 32 bits << 164 if((elementLength2 == 0x424f || // "OB"
258 if ((elementLength2 == 0x424f || // "OB" << 165 elementLength2 == 0x574f || // "OW"
259 elementLength2 == 0x574f || // "OW" << 166 elementLength2 == 0x464f || // "OF"
260 elementLength2 == 0x464f || // "OF" << 167 elementLength2 == 0x5455 || // "UT"
261 elementLength2 == 0x5455 || // "UT" << 168 elementLength2 == 0x5153 || // "SQ"
262 elementLength2 == 0x5153 || // "SQ" << 169 elementLength2 == 0x4e55) && // "UN"
263 elementLength2 == 0x4e55) << 170 !fImplicitEndian ) { // explicit VR
264 && // "UN" << 171
265 !fImplicitEndian) << 172 rflag = std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes
266 { // explicit VR << 173
267 <<
268 rflag = std::fread(buffer, 2, 1, dicom); <<
269 <<
270 // element length 174 // element length
271 rflag = std::fread(buffer, 4, 1, dicom); 175 rflag = std::fread(buffer, 4, 1, dicom);
272 GetValue(buffer, elementLength4); 176 GetValue(buffer, elementLength4);
273 << 177
274 if (elementLength2 == 0x5153) { << 178 if(elementLength2 == 0x5153)
275 if (elementLength4 == 0xFFFFFFFF) { << 179 {
276 read_undefined_nested(dicom); << 180 if(elementLength4 == 0xFFFFFFFF)
277 elementLength4 = 0; << 181 {
278 } << 182 read_undefined_nested( dicom );
279 else { << 183 elementLength4=0;
280 if (read_defined_nested(dicom, eleme << 184 } else{
281 G4Exception("DicomHandler::ReadFil << 185 if(read_defined_nested( dicom, elementLength4 )==0){
282 "Function read_defined << 186 G4Exception("DicomHandler::ReadFile",
>> 187 "DICOM001",
>> 188 FatalException,
>> 189 "Function read_defined_nested() failed!");
>> 190 }
283 } 191 }
284 } << 192 } else {
285 } <<
286 else { <<
287 // Reading the information with data 193 // Reading the information with data
288 rflag = std::fread(data, elementLength << 194 rflag = std::fread(data, elementLength4,1,dicom);
289 } 195 }
290 } << 196
291 else { << 197 } else {
>> 198
292 // explicit with VR different than prev 199 // explicit with VR different than previous ones
293 if (!fImplicitEndian || readGroupId == 2 << 200 if(!fImplicitEndian || readGroupId == 2) {
294 // G4cout << "Reading DICOM files wit << 201
295 // element length (2 bytes) << 202 //G4cout << "Reading DICOM files with Explicit VR"<< G4endl;
>> 203 // element length (2 bytes)
296 rflag = std::fread(buffer, 2, 1, dicom 204 rflag = std::fread(buffer, 2, 1, dicom);
297 GetValue(buffer, elementLength2); 205 GetValue(buffer, elementLength2);
298 elementLength4 = elementLength2; 206 elementLength4 = elementLength2;
299 << 207
300 rflag = std::fread(data, elementLength 208 rflag = std::fread(data, elementLength4, 1, dicom);
301 } << 209
302 else { // Implicit VR << 210 } else { // Implicit VR
303 << 211
304 // G4cout << "Reading DICOM files wit << 212 //G4cout << "Reading DICOM files with Implicit VR"<< G4endl;
305 << 213
306 // element length (4 bytes) 214 // element length (4 bytes)
307 if (std::fseek(dicom, -2, SEEK_CUR) != << 215 if(std::fseek(dicom, -2, SEEK_CUR) != 0) {
308 G4Exception("DicomHandler::ReadFile" << 216 G4Exception("DicomHandler::ReadFile",
>> 217 "DICOM001",
>> 218 FatalException,
>> 219 "fseek failed");
309 } 220 }
310 << 221
311 rflag = std::fread(buffer, 4, 1, dicom 222 rflag = std::fread(buffer, 4, 1, dicom);
312 GetValue(buffer, elementLength4); 223 GetValue(buffer, elementLength4);
313 << 224
314 // G4cout << std::hex<< elementLength << 225 //G4cout << std::hex<< elementLength4 << G4endl;
315 << 226
316 if (elementLength4 == 0xFFFFFFFF) { << 227 if(elementLength4 == 0xFFFFFFFF)
317 read_undefined_nested(dicom); << 228 {
318 elementLength4 = 0; << 229 read_undefined_nested(dicom);
319 } << 230 elementLength4=0;
320 else { << 231 } else{
321 rflag = std::fread(data, elementLeng 232 rflag = std::fread(data, elementLength4, 1, dicom);
322 } 233 }
>> 234
>> 235 }
323 } 236 }
>> 237
>> 238 // NULL termination
>> 239 data[elementLength4] = '\0';
>> 240
>> 241 // analyzing information
>> 242 GetInformation(tagDictionary, data);
324 } 243 }
>> 244
>> 245 G4String fnameG4DCM = G4String(filename2) + ".g4dcm";
325 246
326 // NULL termination << 247 // Perform functions originally written straight to file
327 data[elementLength4] = '\0'; << 248 DicomPhantomZSliceHeader* zslice = new DicomPhantomZSliceHeader(fnameG4DCM);
328 <<
329 // analyzing information <<
330 GetInformation(tagDictionary, data); <<
331 } <<
332 <<
333 G4String fnameG4DCM = G4String(filename2) + <<
334 249
335 // Perform functions originally written stra << 250 std::map<G4float,G4String>::const_iterator ite;
336 DicomPhantomZSliceHeader* zslice = new Dicom << 251 for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ++ite){
337 for (auto ite = fMaterialIndices.cbegin(); i << 252 zslice->AddMaterial(ite->second);
338 zslice->AddMaterial(ite->second); << 253 }
339 } << 254
340 << 255 zslice->SetNoVoxelX(fColumns/fCompression);
341 zslice->SetNoVoxelsX(fColumns / fCompression << 256 zslice->SetNoVoxelY(fRows/fCompression);
342 zslice->SetNoVoxelsY(fRows / fCompression); << 257 zslice->SetNoVoxelZ(1);
343 zslice->SetNoVoxelsZ(1); <<
344 258
345 zslice->SetMinX(-fPixelSpacingX * fColumns / << 259 zslice->SetMinX(-fPixelSpacingX*fColumns/2.);
346 zslice->SetMaxX(fPixelSpacingX * fColumns / << 260 zslice->SetMaxX(fPixelSpacingX*fColumns/2.);
347 261
348 zslice->SetMinY(-fPixelSpacingY * fRows / 2. << 262 zslice->SetMinY(-fPixelSpacingY*fRows/2.);
349 zslice->SetMaxY(fPixelSpacingY * fRows / 2.) << 263 zslice->SetMaxY(fPixelSpacingY*fRows/2.);
350 264
351 zslice->SetMinZ(fSliceLocation - fSliceThick << 265 zslice->SetMinZ(fSliceLocation-fSliceThickness/2.);
352 zslice->SetMaxZ(fSliceLocation + fSliceThick << 266 zslice->SetMaxZ(fSliceLocation+fSliceThickness/2.);
353 267
354 //=== << 268 //===
355 269
356 ReadData(dicom, filename2); << 270 ReadData( dicom, filename2 );
357 271
358 // DEPRECIATED << 272 // DEPRECIATED
359 // StoreData( foutG4DCM ); << 273 //StoreData( foutG4DCM );
360 // foutG4DCM.close(); << 274 //foutG4DCM.close();
361 275
362 StoreData(zslice); << 276 StoreData( zslice );
363 277
364 // Dumped 2 file after DicomPhantomZSliceMer << 278 // Dumped 2 file after DicomPhantomZSliceMerged has checked for consistency
365 // zslice->DumpToFile(); << 279 //zslice->DumpToFile();
366 280
367 fMergedSlices->AddZSlice(zslice); << 281 fMergedSlices->AddZSlice(zslice);
368 282
369 // << 283 //
370 delete[] buffer; << 284 delete [] buffer;
371 delete[] data; << 285 delete [] data;
372 286
373 if (rflag) return returnvalue; << 287 if (rflag) return returnvalue;
374 return returnvalue; << 288 return returnvalue;
375 } 289 }
376 290
377 //....oooOO0OOooo........oooOO0OOooo........oo 291 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
378 292
379 void DicomHandler::GetInformation(G4int& tagDi << 293 void DicomHandler::GetInformation(G4int & tagDictionary, char * data)
380 { 294 {
381 if (tagDictionary == 0x00280010) { // Numbe << 295 if(tagDictionary == 0x00280010 ) { // Number of Rows
382 GetValue(data, fRows); << 296 GetValue(data, fRows);
383 std::printf("[0x00280010] Rows -> %i\n", f << 297 std::printf("[0x00280010] Rows -> %i\n",fRows);
384 } << 298
385 else if (tagDictionary == 0x00280011) { // << 299 } else if(tagDictionary == 0x00280011 ) { // Number of fColumns
386 GetValue(data, fColumns); << 300 GetValue(data, fColumns);
387 std::printf("[0x00280011] Columns -> %i\n" << 301 std::printf("[0x00280011] Columns -> %i\n",fColumns);
388 } << 302
389 else if (tagDictionary == 0x00280102) { // << 303 } else if(tagDictionary == 0x00280102 ) { // High bits ( not used )
390 short highBits; << 304 short highBits;
391 GetValue(data, highBits); << 305 GetValue(data, highBits);
392 std::printf("[0x00280102] High bits -> %i\ << 306 std::printf("[0x00280102] High bits -> %i\n",highBits);
393 } << 307
394 else if (tagDictionary == 0x00280100) { // << 308 } else if(tagDictionary == 0x00280100 ) { // Bits allocated
395 GetValue(data, fBitAllocated); << 309 GetValue(data, fBitAllocated);
396 std::printf("[0x00280100] Bits allocated - << 310 std::printf("[0x00280100] Bits allocated -> %i\n", fBitAllocated);
397 } << 311
398 else if (tagDictionary == 0x00280101) { // << 312 } else if(tagDictionary == 0x00280101 ) { // Bits stored ( not used )
399 short bitStored; << 313 short bitStored;
400 GetValue(data, bitStored); << 314 GetValue(data, bitStored);
401 std::printf("[0x00280101] Bits stored -> % << 315 std::printf("[0x00280101] Bits stored -> %i\n",bitStored);
402 } << 316
403 else if (tagDictionary == 0x00280106) { // << 317 } else if(tagDictionary == 0x00280106 ) { // Min. pixel value
404 GetValue(data, fMinPixelValue); << 318 GetValue(data, fMinPixelValue);
405 std::printf("[0x00280106] Min. pixel value << 319 std::printf("[0x00280106] Min. pixel value -> %i\n", fMinPixelValue);
406 } << 320
407 else if (tagDictionary == 0x00280107) { // << 321 } else if(tagDictionary == 0x00280107 ) { // Max. pixel value
408 GetValue(data, fMaxPixelValue); << 322 GetValue(data, fMaxPixelValue);
409 std::printf("[0x00280107] Max. pixel value << 323 std::printf("[0x00280107] Max. pixel value -> %i\n", fMaxPixelValue);
410 } << 324
411 else if (tagDictionary == 0x00281053) { // << 325 } else if(tagDictionary == 0x00281053) { // Rescale slope
412 fRescaleSlope = atoi(data); << 326 fRescaleSlope = atoi(data);
413 std::printf("[0x00281053] Rescale Slope -> << 327 std::printf("[0x00281053] Rescale Slope -> %d\n", fRescaleSlope);
414 } << 328
415 else if (tagDictionary == 0x00281052) { // << 329 } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept
416 fRescaleIntercept = atoi(data); << 330 fRescaleIntercept = atoi(data);
417 std::printf("[0x00281052] Rescale Intercep << 331 std::printf("[0x00281052] Rescale Intercept -> %d\n",
418 } << 332 fRescaleIntercept );
419 else if (tagDictionary == 0x00280103) { << 333
420 // Pixel representation ( functions not d << 334 } else if(tagDictionary == 0x00280103 ) {
421 fPixelRepresentation = atoi(data); // 0: << 335 // Pixel representation ( functions not design to read signed bits )
422 std::printf("[0x00280103] Pixel Representa << 336 fPixelRepresentation = atoi(data); // 0: unsigned 1: signed
423 if (fPixelRepresentation == 1) { << 337 std::printf("[0x00280103] Pixel Representation -> %i\n",
424 std::printf("### PIXEL REPRESENTATION = << 338 fPixelRepresentation);
425 std::printf("DICOM READING SCAN FOR UNSI << 339 if(fPixelRepresentation == 1 ) {
426 std::printf("ERROR !!!!!! -> \n"); << 340 std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, ");
>> 341 std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE ");
>> 342 std::printf("ERROR !!!!!! -> \n");
>> 343 }
>> 344
>> 345 } else if(tagDictionary == 0x00080006 ) { // Modality
>> 346 std::printf("[0x00080006] Modality -> %s\n", data);
>> 347
>> 348 } else if(tagDictionary == 0x00080070 ) { // Manufacturer
>> 349 std::printf("[0x00080070] Manufacturer -> %s\n", data);
>> 350
>> 351 } else if(tagDictionary == 0x00080080 ) { // Institution Name
>> 352 std::printf("[0x00080080] Institution Name -> %s\n", data);
>> 353
>> 354 } else if(tagDictionary == 0x00080081 ) { // Institution Address
>> 355 std::printf("[0x00080081] Institution Address -> %s\n", data);
>> 356
>> 357 } else if(tagDictionary == 0x00081040 ) { // Institution Department Name
>> 358 std::printf("[0x00081040] Institution Department Name -> %s\n", data);
>> 359
>> 360 } else if(tagDictionary == 0x00081090 ) { // Manufacturer's Model Name
>> 361 std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data);
>> 362
>> 363 } else if(tagDictionary == 0x00181000 ) { // Device Serial Number
>> 364 std::printf("[0x00181000] Device Serial Number -> %s\n", data);
>> 365
>> 366 } else if(tagDictionary == 0x00080008 ) { // Image type ( not used )
>> 367 std::printf("[0x00080008] Image Types -> %s\n", data);
>> 368
>> 369 } else if(tagDictionary == 0x00283000 ) { //Modality LUT Sequence(not used)
>> 370 std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data);
>> 371
>> 372 } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used )
>> 373 std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data);
>> 374
>> 375 } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used )
>> 376 std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data);
>> 377
>> 378 } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used )
>> 379 std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data);
>> 380
>> 381 } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used )
>> 382 std::printf("[0x00283006] LUT Data US or SS -> %s\n", data);
>> 383
>> 384 } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used )
>> 385 std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data);
>> 386
>> 387 } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value (not used)
>> 388 std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data);
>> 389
>> 390 } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing
>> 391 G4String datas(data);
>> 392 int iss = datas.find('\\');
>> 393 fPixelSpacingX = atof( datas.substr(0,iss).c_str() );
>> 394 fPixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() );
>> 395
>> 396 } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used )
>> 397 std::printf("[0x00200037] Image Orientation (Phantom) -> %s\n", data);
>> 398
>> 399 } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used )
>> 400 std::printf("[0x00200032] Image Position (Phantom,mm) -> %s\n", data);
>> 401
>> 402 } else if(tagDictionary == 0x00180050 ) { // Slice Thickness
>> 403 fSliceThickness = atof(data);
>> 404 std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", fSliceThickness);
>> 405
>> 406 } else if(tagDictionary == 0x00201041 ) { // Slice Location
>> 407 fSliceLocation = atof(data);
>> 408 std::printf("[0x00201041] Slice Location -> %f\n", fSliceLocation);
>> 409
>> 410 } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation
>> 411 // ( not used )
>> 412 std::printf("[0x00280004] Photometric Interpretation -> %s\n", data);
>> 413
>> 414 } else if(tagDictionary == 0x00020010) { // Endian
>> 415 if(strcmp(data, "1.2.840.10008.1.2") == 0)
>> 416 fImplicitEndian = true;
>> 417 else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0)
>> 418 fLittleEndian = false;
>> 419 //else 1.2.840..10008.1.2.1 (explicit little endian)
>> 420
>> 421 std::printf("[0x00020010] Endian -> %s\n", data);
427 } 422 }
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 <<
504 423
505 std::printf("[0x00020010] Endian -> %s\n", << 424 // others
506 } << 425 else {
>> 426 //std::printf("[0x%x] -> %s\n", tagDictionary, data);
>> 427 ;
>> 428 }
507 429
508 // others <<
509 else { <<
510 // std::printf("[0x%x] -> %s\n", tagDictio <<
511 ; <<
512 } <<
513 } 430 }
514 431
515 //....oooOO0OOooo........oooOO0OOooo........oo 432 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
516 433
517 void DicomHandler::StoreData(DicomPhantomZSlic 434 void DicomHandler::StoreData(DicomPhantomZSliceHeader* dcmPZSH)
518 { 435 {
519 G4int mean; << 436 G4int mean;
520 G4double density; << 437 G4double density;
521 G4bool overflow = false; << 438 G4bool overflow = false;
522 << 439
523 if (!dcmPZSH) { << 440 if(!dcmPZSH) { return; }
524 return; << 441
525 } << 442 dcmPZSH->SetSliceLocation(fSliceLocation);
526 << 443
527 dcmPZSH->SetSliceLocation(fSliceLocation); << 444 //----- Print indices of material
528 << 445 if(fCompression == 1) { // no fCompression: each pixel has a density value)
529 //----- Print indices of material << 446 for( G4int ww = 0; ww < fRows; ww++) {
530 if (fCompression == 1) { // no fCompression << 447 dcmPZSH->AddRow();
531 for (G4int ww = 0; ww < fRows; ++ww) { << 448 for( G4int xx = 0; xx < fColumns; xx++) {
532 dcmPZSH->AddRow(); << 449 mean = fTab[ww][xx];
533 for (G4int xx = 0; xx < fColumns; ++xx) << 450 density = Pixel2density(mean);
534 mean = fTab[ww][xx]; << 451 dcmPZSH->AddValue(density);
535 density = Pixel2density(mean); << 452 dcmPZSH->AddMateID(GetMaterialIndex(density));
536 dcmPZSH->AddValue(density); << 453 }
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 } 454 }
556 mean /= fCompression * fCompression; <<
557 455
558 if (!overflow) { << 456 } else {
559 density = Pixel2density(mean); << 457 // density value is the average of a square region of
560 dcmPZSH->AddValue(density); << 458 // fCompression*fCompression pixels
561 dcmPZSH->AddMateID(GetMaterialIndex( << 459 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
>> 460 dcmPZSH->AddRow();
>> 461 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
>> 462 overflow = false;
>> 463 mean = 0;
>> 464 for(int sumx = 0; sumx < fCompression; sumx++) {
>> 465 for(int sumy = 0; sumy < fCompression; sumy++) {
>> 466 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
>> 467 mean += fTab[ww+sumy][xx+sumx];
>> 468 }
>> 469 if(overflow) break;
>> 470 }
>> 471 mean /= fCompression*fCompression;
>> 472
>> 473 if(!overflow) {
>> 474 density = Pixel2density(mean);
>> 475 dcmPZSH->AddValue(density);
>> 476 dcmPZSH->AddMateID(GetMaterialIndex(density));
>> 477 }
562 } 478 }
563 } 479 }
564 } 480 }
565 } << 481
566 << 482 dcmPZSH->FlipData();
567 dcmPZSH->FlipData(); <<
568 } 483 }
569 484
570 //....oooOO0OOooo........oooOO0OOooo........oo 485 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
571 // This function is depreciated as it is handl << 486 // This function is depreciated as it is handled by
572 // DicomPhantomZSliceHeader::DumpToFile 487 // DicomPhantomZSliceHeader::DumpToFile
573 void DicomHandler::StoreData(std::ofstream& fo 488 void DicomHandler::StoreData(std::ofstream& foutG4DCM)
574 { 489 {
575 G4int mean; 490 G4int mean;
576 G4double density; 491 G4double density;
577 G4bool overflow = false; 492 G4bool overflow = false;
578 << 493
579 //----- Print indices of material 494 //----- Print indices of material
580 if (fCompression == 1) { // no fCompression << 495 if(fCompression == 1) { // no fCompression: each pixel has a density value)
581 for (G4int ww = 0; ww < fRows; ++ww) { << 496 for( G4int ww = 0; ww < fRows; ww++) {
582 for (G4int xx = 0; xx < fColumns; ++xx) << 497 for( G4int xx = 0; xx < fColumns; xx++) {
583 mean = fTab[ww][xx]; 498 mean = fTab[ww][xx];
584 density = Pixel2density(mean); 499 density = Pixel2density(mean);
585 foutG4DCM << GetMaterialIndex(G4float( << 500 foutG4DCM << GetMaterialIndex( density ) << " ";
586 } 501 }
587 foutG4DCM << G4endl; 502 foutG4DCM << G4endl;
588 } 503 }
589 } << 504
590 else { << 505 } else {
591 // density value is the average of a squar 506 // density value is the average of a square region of
592 // fCompression*fCompression pixels 507 // fCompression*fCompression pixels
593 for (G4int ww = 0; ww < fRows; ww += fComp << 508 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
594 for (G4int xx = 0; xx < fColumns; xx += << 509 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
595 overflow = false; 510 overflow = false;
596 mean = 0; 511 mean = 0;
597 for (G4int sumx = 0; sumx < fCompressi << 512 for(int sumx = 0; sumx < fCompression; sumx++) {
598 for (G4int sumy = 0; sumy < fCompres << 513 for(int sumy = 0; sumy < fCompression; sumy++) {
599 if (ww + sumy >= fRows || xx + sum << 514 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
600 mean += fTab[ww + sumy][xx + sumx] << 515 mean += fTab[ww+sumy][xx+sumx];
601 } 516 }
602 if (overflow) break; << 517 if(overflow) break;
603 } 518 }
604 mean /= fCompression * fCompression; << 519 mean /= fCompression*fCompression;
605 << 520
606 if (!overflow) { << 521 if(!overflow) {
607 density = Pixel2density(mean); 522 density = Pixel2density(mean);
608 foutG4DCM << GetMaterialIndex(G4floa << 523 foutG4DCM << GetMaterialIndex( density ) << " ";
609 } 524 }
610 } 525 }
611 foutG4DCM << G4endl; 526 foutG4DCM << G4endl;
612 } 527 }
>> 528
613 } 529 }
614 << 530
615 //----- Print densities 531 //----- Print densities
616 if (fCompression == 1) { // no fCompression << 532 if(fCompression == 1) { // no fCompression: each pixel has a density value)
617 for (G4int ww = 0; ww < fRows; ww++) { << 533 for( G4int ww = 0; ww < fRows; ww++) {
618 for (G4int xx = 0; xx < fColumns; xx++) << 534 for( G4int xx = 0; xx < fColumns; xx++) {
619 mean = fTab[ww][xx]; 535 mean = fTab[ww][xx];
620 density = Pixel2density(mean); 536 density = Pixel2density(mean);
621 foutG4DCM << density << " "; 537 foutG4DCM << density << " ";
622 if (xx % 8 == 3) foutG4DCM << G4endl; << 538 if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading
623 } 539 }
624 } 540 }
625 } << 541
626 else { << 542 } else {
627 // density value is the average of a squar 543 // density value is the average of a square region of
628 // fCompression*fCompression pixels 544 // fCompression*fCompression pixels
629 for (G4int ww = 0; ww < fRows; ww += fComp << 545 for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
630 for (G4int xx = 0; xx < fColumns; xx += << 546 for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
631 overflow = false; 547 overflow = false;
632 mean = 0; 548 mean = 0;
633 for (G4int sumx = 0; sumx < fCompressi << 549 for(int sumx = 0; sumx < fCompression; sumx++) {
634 for (G4int sumy = 0; sumy < fCompres << 550 for(int sumy = 0; sumy < fCompression; sumy++) {
635 if (ww + sumy >= fRows || xx + sum << 551 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
636 mean += fTab[ww + sumy][xx + sumx] << 552 mean += fTab[ww+sumy][xx+sumx];
637 } 553 }
638 if (overflow) break; << 554 if(overflow) break;
639 } 555 }
640 mean /= fCompression * fCompression; << 556 mean /= fCompression*fCompression;
641 << 557
642 if (!overflow) { << 558 if(!overflow) {
643 density = Pixel2density(mean); 559 density = Pixel2density(mean);
644 foutG4DCM << density << " "; << 560 foutG4DCM << density << " ";
645 if (xx / fCompression % 8 == 3) fout << 561 if( xx/fCompression%8 == 3 ) foutG4DCM << G4endl; // just for nicer
646 // reading 562 // reading
647 } 563 }
648 } 564 }
649 } 565 }
>> 566
650 } 567 }
>> 568
651 } 569 }
652 570
653 //....oooOO0OOooo........oooOO0OOooo........oo << 571 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
654 void DicomHandler::ReadMaterialIndices(std::if << 572 void DicomHandler::ReadMaterialIndices( std::ifstream& finData)
655 { 573 {
656 unsigned int nMate; 574 unsigned int nMate;
657 G4String mateName; 575 G4String mateName;
658 G4float densityMax; 576 G4float densityMax;
659 finData >> nMate; 577 finData >> nMate;
660 if (finData.eof()) return; << 578 if( finData.eof() ) return;
661 << 579
662 G4cout << " ReadMaterialIndices " << nMate < 580 G4cout << " ReadMaterialIndices " << nMate << G4endl;
663 for (unsigned int ii = 0; ii < nMate; ++ii) << 581 for( unsigned int ii = 0; ii < nMate; ii++ ){
664 finData >> mateName >> densityMax; 582 finData >> mateName >> densityMax;
665 fMaterialIndices[densityMax] = mateName; 583 fMaterialIndices[densityMax] = mateName;
666 // G4cout << ii << " ReadMaterialIndice << 584 G4cout << ii << " ReadMaterialIndices " << mateName << " "
667 // << densityMax << G4endl; << 585 << densityMax << G4endl;
668 } 586 }
>> 587
669 } 588 }
670 589
671 //....oooOO0OOooo........oooOO0OOooo........oo 590 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
672 591
673 unsigned int DicomHandler::GetMaterialIndex(G4 << 592 unsigned int DicomHandler::GetMaterialIndex( G4float density )
674 { 593 {
675 std::map<G4float, G4String>::const_reverse_i << 594 std::map<G4float,G4String>::reverse_iterator ite;
676 std::size_t ii = fMaterialIndices.size(); << 595 G4int ii = fMaterialIndices.size();
677 << 596 for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend();
678 for (ite = fMaterialIndices.crbegin(); ite ! << 597 ite++, ii-- ) {
679 if (density >= (*ite).first) { << 598 if( density >= (*ite).first ) {
680 break; 599 break;
681 } 600 }
682 } 601 }
683 << 602 //- G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl;
684 if (ii == fMaterialIndices.size()) { << 603
685 ii = fMaterialIndices.size() - 1; << 604 if(static_cast<unsigned int>(ii) == fMaterialIndices.size())
686 } << 605 { ii = fMaterialIndices.size()-1; }
687 << 606
688 return unsigned(ii); << 607 return ii;
>> 608
689 } 609 }
690 610
691 //....oooOO0OOooo........oooOO0OOooo........oo 611 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
692 612
693 G4int DicomHandler::ReadData(FILE* dicom, char << 613 G4int DicomHandler::ReadData(FILE *dicom,char * filename2)
694 { 614 {
695 G4int returnvalue = 0; << 615 G4int returnvalue = 0; size_t rflag = 0;
696 size_t rflag = 0; << 616
697 << 617 // READING THE PIXELS :
698 // READING THE PIXELS << 618 G4int w = 0;
699 << 619
700 fTab = new G4int*[fRows]; 620 fTab = new G4int*[fRows];
701 for (G4int i = 0; i < fRows; ++i) { << 621 for ( G4int i = 0; i < fRows; i ++ ) {
702 fTab[i] = new G4int[fColumns]; << 622 fTab[i] = new G4int[fColumns];
703 } << 623 }
704 << 624
705 if (fBitAllocated == 8) { // Case 8 bits : << 625 if(fBitAllocated == 8) { // Case 8 bits :
706 << 626
707 std::printf("@@@ Error! Picture != 16 bits 627 std::printf("@@@ Error! Picture != 16 bits...\n");
708 std::printf("@@@ Error! Picture != 16 bits 628 std::printf("@@@ Error! Picture != 16 bits...\n");
709 std::printf("@@@ Error! Picture != 16 bits 629 std::printf("@@@ Error! Picture != 16 bits...\n");
710 << 630
711 unsigned char ch = 0; 631 unsigned char ch = 0;
712 << 632
713 for (G4int j = 0; j < fRows; ++j) { << 633 for(G4int j = 0; j < fRows; j++) {
714 for (G4int i = 0; i < fColumns; ++i) { << 634 for(G4int i = 0; i < fColumns; i++) {
715 rflag = std::fread(&ch, 1, 1, dicom); << 635 w++;
716 fTab[j][i] = ch * fRescaleSlope + fRes << 636 rflag = std::fread( &ch, 1, 1, dicom);
>> 637 fTab[j][i] = ch*fRescaleSlope + fRescaleIntercept;
717 } 638 }
718 } 639 }
719 returnvalue = 1; 640 returnvalue = 1;
720 } << 641
721 else { // from 12 to 16 bits : << 642 } else { // from 12 to 16 bits :
722 char sbuff[2]; 643 char sbuff[2];
723 short pixel; 644 short pixel;
724 for (G4int j = 0; j < fRows; ++j) { << 645 for( G4int j = 0; j < fRows; j++) {
725 for (G4int i = 0; i < fColumns; ++i) { << 646 for( G4int i = 0; i < fColumns; i++) {
>> 647 w++;
726 rflag = std::fread(sbuff, 2, 1, dicom) 648 rflag = std::fread(sbuff, 2, 1, dicom);
727 GetValue(sbuff, pixel); 649 GetValue(sbuff, pixel);
728 fTab[j][i] = pixel * fRescaleSlope + f << 650 fTab[j][i] = pixel*fRescaleSlope + fRescaleIntercept;
729 } 651 }
730 } 652 }
731 } 653 }
732 << 654
733 // Creation of .g4 files wich contains avera 655 // Creation of .g4 files wich contains averaged density data
734 G4String nameProcessed = filename2 + G4Strin << 656 char * nameProcessed = new char[FILENAMESIZE];
735 FILE* fileOut = std::fopen(nameProcessed.c_s << 657 FILE* fileOut;
736 << 658
737 G4cout << "### Writing of " << nameProcessed << 659 std::sprintf(nameProcessed,"%s.g4dcmb",filename2);
738 << 660 fileOut = std::fopen(nameProcessed,"w+b");
>> 661 std::printf("### Writing of %s ###\n",nameProcessed);
>> 662
739 unsigned int nMate = fMaterialIndices.size() 663 unsigned int nMate = fMaterialIndices.size();
740 rflag = std::fwrite(&nMate, sizeof(unsigned 664 rflag = std::fwrite(&nMate, sizeof(unsigned int), 1, fileOut);
741 //--- Write materials 665 //--- Write materials
742 for (auto ite = fMaterialIndices.cbegin(); i << 666 std::map<G4float,G4String>::const_iterator ite;
>> 667 for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++ ){
743 G4String mateName = (*ite).second; 668 G4String mateName = (*ite).second;
744 for (std::size_t ii = (*ite).second.length << 669 for( G4int ii = (*ite).second.length(); ii < 40; ii++ ) {
745 mateName += " "; 670 mateName += " ";
746 } // mateName = const_cast<char*>(((*ite) << 671 } //mateName = const_cast<char*>(((*ite).second).c_str());
747 << 672
748 const char* mateNameC = mateName.c_str(); 673 const char* mateNameC = mateName.c_str();
749 rflag = std::fwrite(mateNameC, sizeof(char << 674 rflag = std::fwrite(mateNameC, sizeof(char),40, fileOut);
750 } 675 }
751 << 676
752 unsigned int fRowsC = fRows / fCompression; << 677 unsigned int fRowsC = fRows/fCompression;
753 unsigned int fColumnsC = fColumns / fCompres << 678 unsigned int fColumnsC = fColumns/fCompression;
754 unsigned int planesC = 1; 679 unsigned int planesC = 1;
755 G4float pixelLocationXM = -G4float(fPixelSpa << 680 G4float pixelLocationXM = -fPixelSpacingX*fColumns/2.;
756 G4float pixelLocationXP = G4float(fPixelSpac << 681 G4float pixelLocationXP = fPixelSpacingX*fColumns/2.;
757 G4float pixelLocationYM = -G4float(fPixelSpa << 682 G4float pixelLocationYM = -fPixelSpacingY*fRows/2.;
758 G4float pixelLocationYP = G4float(fPixelSpac << 683 G4float pixelLocationYP = fPixelSpacingY*fRows/2.;
759 G4float fSliceLocationZM = G4float(fSliceLoc << 684 G4float fSliceLocationZM = fSliceLocation-fSliceThickness/2.;
760 G4float fSliceLocationZP = G4float(fSliceLoc << 685 G4float fSliceLocationZP = fSliceLocation+fSliceThickness/2.;
761 //--- Write number of voxels (assume only on 686 //--- Write number of voxels (assume only one voxel in Z)
762 rflag = std::fwrite(&fRowsC, sizeof(unsigned 687 rflag = std::fwrite(&fRowsC, sizeof(unsigned int), 1, fileOut);
763 rflag = std::fwrite(&fColumnsC, sizeof(unsig 688 rflag = std::fwrite(&fColumnsC, sizeof(unsigned int), 1, fileOut);
764 rflag = std::fwrite(&planesC, sizeof(unsigne 689 rflag = std::fwrite(&planesC, sizeof(unsigned int), 1, fileOut);
765 //--- Write minimum and maximum extensions 690 //--- Write minimum and maximum extensions
766 rflag = std::fwrite(&pixelLocationXM, sizeof 691 rflag = std::fwrite(&pixelLocationXM, sizeof(G4float), 1, fileOut);
767 rflag = std::fwrite(&pixelLocationXP, sizeof 692 rflag = std::fwrite(&pixelLocationXP, sizeof(G4float), 1, fileOut);
768 rflag = std::fwrite(&pixelLocationYM, sizeof 693 rflag = std::fwrite(&pixelLocationYM, sizeof(G4float), 1, fileOut);
769 rflag = std::fwrite(&pixelLocationYP, sizeof 694 rflag = std::fwrite(&pixelLocationYP, sizeof(G4float), 1, fileOut);
770 rflag = std::fwrite(&fSliceLocationZM, sizeo 695 rflag = std::fwrite(&fSliceLocationZM, sizeof(G4float), 1, fileOut);
771 rflag = std::fwrite(&fSliceLocationZP, sizeo 696 rflag = std::fwrite(&fSliceLocationZP, sizeof(G4float), 1, fileOut);
772 // rflag = std::fwrite(&fCompression, sizeof 697 // rflag = std::fwrite(&fCompression, sizeof(unsigned int), 1, fileOut);
773 << 698
774 std::printf("%8i %8i\n", fRows, fColumns); << 699 std::printf("%8i %8i\n",fRows,fColumns);
775 std::printf("%8f %8f\n", fPixelSpacingX, f << 700 std::printf("%8f %8f\n",fPixelSpacingX,fPixelSpacingY);
776 std::printf("%8f\n", fSliceThickness); 701 std::printf("%8f\n", fSliceThickness);
777 std::printf("%8f\n", fSliceLocation); 702 std::printf("%8f\n", fSliceLocation);
778 std::printf("%8i\n", fCompression); 703 std::printf("%8i\n", fCompression);
779 << 704
780 G4int compSize = fCompression; 705 G4int compSize = fCompression;
781 G4int mean; 706 G4int mean;
782 G4float density; 707 G4float density;
783 G4bool overflow = false; 708 G4bool overflow = false;
784 << 709
785 //----- Write index of material for each pix 710 //----- Write index of material for each pixel
786 if (compSize == 1) { // no fCompression: ea << 711 if(compSize == 1) { // no fCompression: each pixel has a density value)
787 for (G4int ww = 0; ww < fRows; ++ww) { << 712 for( G4int ww = 0; ww < fRows; ww++) {
788 for (G4int xx = 0; xx < fColumns; ++xx) << 713 for( G4int xx = 0; xx < fColumns; xx++) {
789 mean = fTab[ww][xx]; 714 mean = fTab[ww][xx];
790 density = Pixel2density(mean); 715 density = Pixel2density(mean);
791 unsigned int mateID = GetMaterialIndex << 716 unsigned int mateID = GetMaterialIndex( density );
792 rflag = std::fwrite(&mateID, sizeof(un 717 rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
793 } 718 }
794 } 719 }
795 } << 720
796 else { << 721 } else {
797 // density value is the average of a squar 722 // density value is the average of a square region of
798 // fCompression*fCompression pixels 723 // fCompression*fCompression pixels
799 for (G4int ww = 0; ww < fRows; ww += compS << 724 for(G4int ww = 0; ww < fRows ;ww += compSize ) {
800 for (G4int xx = 0; xx < fColumns; xx += << 725 for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
801 overflow = false; 726 overflow = false;
802 mean = 0; 727 mean = 0;
803 for (G4int sumx = 0; sumx < compSize; << 728 for(int sumx = 0; sumx < compSize; sumx++) {
804 for (G4int sumy = 0; sumy < compSize << 729 for(int sumy = 0; sumy < compSize; sumy++) {
805 if (ww + sumy >= fRows || xx + sum << 730 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
806 mean += fTab[ww + sumy][xx + sumx] << 731 mean += fTab[ww+sumy][xx+sumx];
807 } 732 }
808 if (overflow) break; << 733 if(overflow) break;
809 } 734 }
810 mean /= compSize * compSize; << 735 mean /= compSize*compSize;
811 << 736
812 if (!overflow) { << 737 if(!overflow) {
813 density = Pixel2density(mean); 738 density = Pixel2density(mean);
814 unsigned int mateID = GetMaterialInd << 739 unsigned int mateID = GetMaterialIndex( density );
815 rflag = std::fwrite(&mateID, sizeof( 740 rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
816 } 741 }
817 } 742 }
>> 743
818 } 744 }
819 } 745 }
820 << 746
821 //----- Write density for each pixel 747 //----- Write density for each pixel
822 if (compSize == 1) { // no fCompression: ea << 748 if(compSize == 1) { // no fCompression: each pixel has a density value)
823 for (G4int ww = 0; ww < fRows; ++ww) { << 749 for( G4int ww = 0; ww < fRows; ww++) {
824 for (G4int xx = 0; xx < fColumns; ++xx) << 750 for( G4int xx = 0; xx < fColumns; xx++) {
825 mean = fTab[ww][xx]; 751 mean = fTab[ww][xx];
826 density = Pixel2density(mean); 752 density = Pixel2density(mean);
827 rflag = std::fwrite(&density, sizeof(G 753 rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
828 } 754 }
829 } 755 }
830 } << 756
831 else { << 757 } else {
832 // density value is the average of a squar 758 // density value is the average of a square region of
833 // fCompression*fCompression pixels 759 // fCompression*fCompression pixels
834 for (G4int ww = 0; ww < fRows; ww += compS << 760 for(G4int ww = 0; ww < fRows ;ww += compSize ) {
835 for (G4int xx = 0; xx < fColumns; xx += << 761 for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
836 overflow = false; 762 overflow = false;
837 mean = 0; 763 mean = 0;
838 for (G4int sumx = 0; sumx < compSize; << 764 for(int sumx = 0; sumx < compSize; sumx++) {
839 for (G4int sumy = 0; sumy < compSize << 765 for(int sumy = 0; sumy < compSize; sumy++) {
840 if (ww + sumy >= fRows || xx + sum << 766 if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
841 mean += fTab[ww + sumy][xx + sumx] << 767 mean += fTab[ww+sumy][xx+sumx];
842 } 768 }
843 if (overflow) break; << 769 if(overflow) break;
844 } 770 }
845 mean /= compSize * compSize; << 771 mean /= compSize*compSize;
846 << 772
847 if (!overflow) { << 773 if(!overflow) {
848 density = Pixel2density(mean); 774 density = Pixel2density(mean);
849 rflag = std::fwrite(&density, sizeof 775 rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
850 } 776 }
851 } 777 }
>> 778
852 } 779 }
853 } 780 }
854 << 781
855 rflag = std::fclose(fileOut); 782 rflag = std::fclose(fileOut);
856 << 783
857 delete[] nameProcessed; << 784 delete [] nameProcessed;
858 << 785
859 /* for ( G4int i = 0; i < fRows; i ++ ) { 786 /* for ( G4int i = 0; i < fRows; i ++ ) {
860 delete [] fTab[i]; 787 delete [] fTab[i];
861 } 788 }
862 delete [] fTab; 789 delete [] fTab;
863 */ 790 */
864 << 791
865 if (rflag) return returnvalue; 792 if (rflag) return returnvalue;
866 return returnvalue; 793 return returnvalue;
867 } 794 }
868 795
869 //....oooOO0OOooo........oooOO0OOooo........oo << 796 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
870 <<
871 // DICOM HEAD does not use the calibration cur <<
872 <<
873 #ifdef DICOM_USE_HEAD <<
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 797 // Separated out of Pixel2density
882 // No need to read in same calibration EVERY t 798 // No need to read in same calibration EVERY time
883 // Increases the speed of reading file by seve 799 // Increases the speed of reading file by several orders of magnitude
884 <<
885 void DicomHandler::ReadCalibration() 800 void DicomHandler::ReadCalibration()
886 { 801 {
887 fNbrequali = 0; 802 fNbrequali = 0;
>> 803
888 // CT2Density.dat contains the calibration c 804 // CT2Density.dat contains the calibration curve to convert CT (Hounsfield)
889 // number to physical density 805 // number to physical density
890 std::ifstream calibration(fCt2DensityFile.c_ 806 std::ifstream calibration(fCt2DensityFile.c_str());
891 calibration >> fNbrequali; 807 calibration >> fNbrequali;
>> 808
892 fValueDensity = new G4double[fNbrequali]; 809 fValueDensity = new G4double[fNbrequali];
893 fValueCT = new G4double[fNbrequali]; 810 fValueCT = new G4double[fNbrequali];
894 << 811
895 if (!calibration) { << 812 if(!calibration) {
896 G4Exception("DicomHandler::ReadFile", "DIC << 813 G4Exception("DicomHandler::ReadFile",
>> 814 "DICOM001",
>> 815 FatalException,
897 "@@@ No value to transform pix 816 "@@@ No value to transform pixels in density!");
898 } << 817
899 else { // calibration was successfully open << 818 } else { // calibration was successfully opened
900 for (G4int i = 0; i < fNbrequali; ++i) { << 819 for(G4int i = 0; i < fNbrequali; i++) { // Loop to store all the
>> 820 //pts in CT2Density.dat
901 calibration >> fValueCT[i] >> fValueDens 821 calibration >> fValueCT[i] >> fValueDensity[i];
902 } 822 }
903 } 823 }
904 calibration.close(); 824 calibration.close();
>> 825
905 fReadCalibration = true; 826 fReadCalibration = true;
906 } 827 }
907 #endif <<
908 828
909 #ifdef DICOM_USE_HEAD << 829 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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 } <<
940 <<
941 #else <<
942 //....oooOO0OOooo........oooOO0OOooo........oo <<
943 830
944 G4float DicomHandler::Pixel2density(G4int pixe 831 G4float DicomHandler::Pixel2density(G4int pixel)
945 { 832 {
946 if (!fReadCalibration) { << 833 if(!fReadCalibration) { ReadCalibration(); }
947 ReadCalibration(); << 834
948 } <<
949 <<
950 G4float density = -1.; 835 G4float density = -1.;
951 G4double deltaCT = 0; 836 G4double deltaCT = 0;
952 G4double deltaDensity = 0; 837 G4double deltaDensity = 0;
953 << 838
954 for (G4int j = 1; j < fNbrequali; ++j) { << 839
955 if (pixel >= fValueCT[j - 1] && pixel < fV << 840 for(G4int j = 1; j < fNbrequali; j++) {
956 deltaCT = fValueCT[j] - fValueCT[j - 1]; << 841 if( pixel >= fValueCT[j-1] && pixel < fValueCT[j]) {
957 deltaDensity = fValueDensity[j] - fValue << 842
958 << 843 deltaCT = fValueCT[j] - fValueCT[j-1];
>> 844 deltaDensity = fValueDensity[j] - fValueDensity[j-1];
>> 845
959 // interpolating linearly 846 // interpolating linearly
960 density = G4float(fValueDensity[j] - ((f << 847 density = fValueDensity[j] - ((fValueCT[j] - pixel)*deltaDensity/deltaCT );
961 break; 848 break;
962 } 849 }
963 } 850 }
964 << 851
965 if (density < 0.) { << 852 if(density < 0.) {
966 std::printf( << 853 std::printf("@@@ Error density = %f && Pixel = %i \
967 "@@@ Error density = %f && Pixel = %i \ << 854 (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel,
968 (0x%x) && deltaDensity/deltaCT = %f\n", << 855 deltaDensity/deltaCT);
969 density, pixel, pixel, deltaDensity / de <<
970 } 856 }
971 << 857
972 return density; 858 return density;
973 } 859 }
974 #endif << 860
975 //....oooOO0OOooo........oooOO0OOooo........oo 861 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
976 862
977 void DicomHandler::CheckFileFormat() 863 void DicomHandler::CheckFileFormat()
978 { 864 {
979 std::ifstream checkData(fDriverFile.c_str()) 865 std::ifstream checkData(fDriverFile.c_str());
980 char* oneLine = new char[128]; << 866 char * oneLine = new char[128];
981 << 867
982 if (!(checkData.is_open())) { // Check exis << 868 if(!(checkData.is_open())) { //Check existance of Data.dat
983 << 869
984 G4String message = "\nDicomG4 needs Data.d << 870 G4String message =
>> 871 "\nDicomG4 needs Data.dat (or another driver file specified";
985 message += " in command line):\n"; 872 message += " in command line):\n";
986 message += "\tFirst line: number of image 873 message += "\tFirst line: number of image pixel for a voxel (G4Box)\n";
987 message += "\tSecond line: number of image 874 message += "\tSecond line: number of images (CT slices) to read\n";
988 message += "\tEach following line contains 875 message += "\tEach following line contains the name of a Dicom image";
989 message += " except for the .dcm extension 876 message += " except for the .dcm extension";
990 G4Exception("DicomHandler::ReadFile", "DIC << 877 G4Exception("DicomHandler::ReadFile",
>> 878 "DICOM001",
>> 879 FatalException,
>> 880 message.c_str());
991 } 881 }
992 << 882
993 checkData >> fCompression; 883 checkData >> fCompression;
994 checkData >> fNFiles; 884 checkData >> fNFiles;
995 G4String oneName; 885 G4String oneName;
996 checkData.getline(oneLine, 100); << 886 checkData.getline(oneLine,100);
997 std::ifstream testExistence; 887 std::ifstream testExistence;
998 G4bool existAlready = true; 888 G4bool existAlready = true;
999 for (G4int rep = 0; rep < fNFiles; ++rep) { << 889 for(G4int rep = 0; rep < fNFiles; rep++) {
1000 checkData.getline(oneLine, 100); << 890 checkData.getline(oneLine,100);
1001 oneName = oneLine; 891 oneName = oneLine;
1002 oneName += ".g4dcm"; // create dicomFile << 892 oneName += ".g4dcm"; // create dicomFile.g4dcm
1003 G4cout << fNFiles << " test file " << one 893 G4cout << fNFiles << " test file " << oneName << G4endl;
1004 testExistence.open(oneName.data()); 894 testExistence.open(oneName.data());
1005 if (!(testExistence.is_open())) { << 895 if(!(testExistence.is_open())) {
1006 existAlready = false; 896 existAlready = false;
1007 testExistence.clear(); 897 testExistence.clear();
1008 testExistence.close(); 898 testExistence.close();
1009 } 899 }
1010 testExistence.clear(); 900 testExistence.clear();
1011 testExistence.close(); 901 testExistence.close();
1012 } 902 }
1013 << 903
1014 ReadMaterialIndices(checkData); << 904 ReadMaterialIndices( checkData );
1015 << 905
1016 checkData.close(); 906 checkData.close();
1017 delete[] oneLine; << 907 delete [] oneLine;
1018 << 908
1019 if (existAlready == false) { // The files << 909 if( existAlready == false ) { // The files *.g4dcm have to be created
1020 << 910
1021 G4cout << "\nAll the necessary images wer 911 G4cout << "\nAll the necessary images were not found in processed form "
1022 << ", starting with .dcm images\n" 912 << ", starting with .dcm images\n";
1023 << 913
1024 FILE* dicom; << 914 FILE * dicom;
1025 FILE* lecturePref; << 915 FILE * lecturePref;
1026 char* fCompressionc = new char[LINEBUFFSI << 916 char * fCompressionc = new char[LINEBUFFSIZE];
1027 char* maxc = new char[LINEBUFFSIZE]; << 917 char * maxc = new char[LINEBUFFSIZE];
1028 // char name[300], inputFile[300]; << 918 //char name[300], inputFile[300];
1029 char* inputFile = new char[FILENAMESIZE]; << 919 char * name = new char[FILENAMESIZE];
>> 920 char * inputFile = new char[FILENAMESIZE];
1030 G4int rflag; 921 G4int rflag;
1031 lecturePref = std::fopen(fDriverFile.c_st << 922
1032 << 923 lecturePref = std::fopen(fDriverFile.c_str(),"r");
1033 rflag = std::fscanf(lecturePref, "%s", fC << 924 rflag = std::fscanf(lecturePref,"%s",fCompressionc);
1034 fCompression = atoi(fCompressionc); 925 fCompression = atoi(fCompressionc);
1035 rflag = std::fscanf(lecturePref, "%s", ma << 926 rflag = std::fscanf(lecturePref,"%s",maxc);
1036 fNFiles = atoi(maxc); 927 fNFiles = atoi(maxc);
1037 G4cout << " fNFiles " << fNFiles << G4end 928 G4cout << " fNFiles " << fNFiles << G4endl;
1038 << 929
1039 ///////////////////// << 930 for( G4int i = 1; i <= fNFiles; i++ ) { // Begin loop on filenames
1040 << 931
1041 #ifdef DICOM_USE_HEAD << 932 rflag = std::fscanf(lecturePref,"%s",inputFile);
1042 for (G4int i = 1; i <= fNFiles; ++i) { / << 933 std::sprintf(name,"%s.dcm",inputFile);
1043 rflag = std::fscanf(lecturePref, "%s", << 934 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 935 // Open input file and give it to gestion_dicom :
1051 G4cout << "### Opening " << name2 << " << 936 std::printf("### Opening %s and reading :\n",name);
1052 dicom = std::fopen(name2.c_str(), "rb") << 937 dicom = std::fopen(name,"rb");
1053 // Reading the .dcm in two steps: 938 // Reading the .dcm in two steps:
1054 // 1. reading the header 939 // 1. reading the header
1055 // 2. reading the pixel data and s 940 // 2. reading the pixel data and store the density in Moyenne.dat
1056 if (dicom != 0) { << 941 if( dicom != 0 ) {
1057 ReadFile(dicom, inputFile); << 942 ReadFile(dicom,inputFile);
1058 } << 943 } 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 : " < 944 G4cout << "\nError opening file : " << name << G4endl;
1084 } 945 }
1085 rflag = std::fclose(dicom); 946 rflag = std::fclose(dicom);
1086 } 947 }
1087 #endif <<
1088 <<
1089 rflag = std::fclose(lecturePref); 948 rflag = std::fclose(lecturePref);
1090 << 949
1091 // Checks the spacing is correct. Dumps t 950 // Checks the spacing is correct. Dumps to files
1092 fMergedSlices->CheckSlices(); 951 fMergedSlices->CheckSlices();
1093 << 952
1094 delete[] fCompressionc; << 953 delete [] fCompressionc;
1095 delete[] maxc; << 954 delete [] maxc;
1096 delete[] inputFile; << 955 delete [] name;
>> 956 delete [] inputFile;
1097 if (rflag) return; 957 if (rflag) return;
>> 958
1098 } 959 }
1099 << 960
1100 if (fValueDensity) { << 961 if(fValueDensity) { delete [] fValueDensity; }
1101 delete[] fValueDensity; << 962 if(fValueCT) { delete [] fValueCT; }
1102 } << 963 if(fMergedSlices) { delete fMergedSlices; }
1103 if (fValueCT) { << 964
1104 delete[] fValueCT; <<
1105 } <<
1106 if (fMergedSlices) { <<
1107 delete fMergedSlices; <<
1108 } <<
1109 } 965 }
1110 966
1111 //....oooOO0OOooo........oooOO0OOooo........o << 967 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1112 968
1113 G4int DicomHandler::read_defined_nested(FILE* << 969 G4int DicomHandler::read_defined_nested(FILE * nested,G4int SQ_Length)
1114 { 970 {
1115 // VARIABLES 971 // VARIABLES
1116 unsigned short item_GroupNumber; 972 unsigned short item_GroupNumber;
1117 unsigned short item_ElementNumber; 973 unsigned short item_ElementNumber;
1118 G4int item_Length; 974 G4int item_Length;
1119 G4int items_array_length = 0; << 975 G4int items_array_length=0;
1120 char* buffer = new char[LINEBUFFSIZE]; << 976 char * buffer= new char[LINEBUFFSIZE];
1121 size_t rflag = 0; 977 size_t rflag = 0;
1122 << 978
1123 while (items_array_length < SQ_Length) { << 979 while(items_array_length < SQ_Length)
1124 rflag = std::fread(buffer, 2, 1, nested); << 980 {
1125 GetValue(buffer, item_GroupNumber); << 981 rflag = std::fread(buffer, 2, 1, nested);
1126 << 982 GetValue(buffer, item_GroupNumber);
1127 rflag = std::fread(buffer, 2, 1, nested); << 983
1128 GetValue(buffer, item_ElementNumber); << 984 rflag = std::fread(buffer, 2, 1, nested);
1129 << 985 GetValue(buffer, item_ElementNumber);
1130 rflag = std::fread(buffer, 4, 1, nested); << 986
1131 GetValue(buffer, item_Length); << 987 rflag = std::fread(buffer, 4, 1, nested);
1132 << 988 GetValue(buffer, item_Length);
1133 rflag = std::fread(buffer, item_Length, 1 << 989
1134 << 990 rflag = std::fread(buffer, item_Length, 1, nested);
1135 items_array_length = items_array_length + << 991
1136 } << 992 items_array_length= items_array_length+8+item_Length;
1137 << 993 }
1138 delete[] buffer; << 994
1139 << 995 delete [] buffer;
1140 if (SQ_Length > items_array_length) << 996
>> 997 if( SQ_Length>items_array_length )
1141 return 0; 998 return 0;
1142 else 999 else
1143 return 1; 1000 return 1;
1144 if (rflag) return 1; 1001 if (rflag) return 1;
1145 } 1002 }
1146 1003
1147 //....oooOO0OOooo........oooOO0OOooo........o << 1004 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1148 1005
1149 void DicomHandler::read_undefined_nested(FILE << 1006 void DicomHandler::read_undefined_nested(FILE * nested)
1150 { 1007 {
1151 // VARIABLES 1008 // VARIABLES
1152 unsigned short item_GroupNumber; 1009 unsigned short item_GroupNumber;
1153 unsigned short item_ElementNumber; 1010 unsigned short item_ElementNumber;
1154 unsigned int item_Length; 1011 unsigned int item_Length;
1155 char* buffer = new char[LINEBUFFSIZE]; << 1012 char * buffer= new char[LINEBUFFSIZE];
1156 size_t rflag = 0; 1013 size_t rflag = 0;
1157 << 1014
1158 do { << 1015 do
1159 rflag = std::fread(buffer, 2, 1, nested); << 1016 {
1160 GetValue(buffer, item_GroupNumber); << 1017 rflag = std::fread(buffer, 2, 1, nested);
1161 << 1018 GetValue(buffer, item_GroupNumber);
1162 rflag = std::fread(buffer, 2, 1, nested); << 1019
1163 GetValue(buffer, item_ElementNumber); << 1020 rflag = std::fread(buffer, 2, 1, nested);
1164 << 1021 GetValue(buffer, item_ElementNumber);
1165 rflag = std::fread(buffer, 4, 1, nested); << 1022
1166 GetValue(buffer, item_Length); << 1023 rflag = std::fread(buffer, 4, 1, nested);
1167 << 1024 GetValue(buffer, item_Length);
1168 if (item_Length != 0xffffffff) << 1025
1169 rflag = std::fread(buffer, item_Length, << 1026 if(item_Length!=0xffffffff)
1170 else << 1027 rflag = std::fread(buffer, item_Length, 1, nested);
1171 read_undefined_item(nested); << 1028 else
1172 << 1029 read_undefined_item(nested);
1173 } while (item_GroupNumber != 0xFFFE || item << 1030
1174 << 1031
1175 delete[] buffer; << 1032 } while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE0DD
1176 if (rflag) return; << 1033 || item_Length!=0);
>> 1034
>> 1035 delete [] buffer;
>> 1036 if (rflag) return;
1177 } 1037 }
1178 1038
1179 //....oooOO0OOooo........oooOO0OOooo........o << 1039 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1180 1040
1181 void DicomHandler::read_undefined_item(FILE* << 1041 void DicomHandler::read_undefined_item(FILE * nested)
1182 { 1042 {
1183 // VARIABLES 1043 // VARIABLES
1184 unsigned short item_GroupNumber; 1044 unsigned short item_GroupNumber;
1185 unsigned short item_ElementNumber; 1045 unsigned short item_ElementNumber;
1186 G4int item_Length; << 1046 G4int item_Length; size_t rflag = 0;
1187 size_t rflag = 0; << 1047 char *buffer= new char[LINEBUFFSIZE];
1188 char* buffer = new char[LINEBUFFSIZE]; << 1048
1189 << 1049 do
1190 do { << 1050 {
1191 rflag = std::fread(buffer, 2, 1, nested); << 1051 rflag = std::fread(buffer, 2, 1, nested);
1192 GetValue(buffer, item_GroupNumber); << 1052 GetValue(buffer, item_GroupNumber);
1193 << 1053
1194 rflag = std::fread(buffer, 2, 1, nested); << 1054 rflag = std::fread(buffer, 2, 1, nested);
1195 GetValue(buffer, item_ElementNumber); << 1055 GetValue(buffer, item_ElementNumber);
1196 << 1056
1197 rflag = std::fread(buffer, 4, 1, nested); << 1057 rflag = std::fread(buffer, 4, 1, nested);
1198 GetValue(buffer, item_Length); << 1058 GetValue(buffer, item_Length);
1199 << 1059
1200 if (item_Length != 0) rflag = std::fread( << 1060
1201 << 1061 if(item_Length!=0)
1202 } while (item_GroupNumber != 0xFFFE || item << 1062 rflag = std::fread(buffer,item_Length,1,nested);
1203 << 1063
1204 delete[] buffer; << 1064 }
>> 1065 while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE00D
>> 1066 || item_Length!=0);
>> 1067
>> 1068 delete [] buffer;
1205 if (rflag) return; 1069 if (rflag) return;
1206 } 1070 }
1207 1071
1208 //....oooOO0OOooo........oooOO0OOooo........o << 1072 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1209 1073
1210 template<class Type> << 1074 template <class Type>
1211 void DicomHandler::GetValue(char* _val, Type& << 1075 void DicomHandler::GetValue(char * _val, Type & _rval) {
1212 { << 1076
1213 #if BYTE_ORDER == BIG_ENDIAN 1077 #if BYTE_ORDER == BIG_ENDIAN
1214 if (fLittleEndian) { // little endian << 1078 if(fLittleEndian) { // little endian
1215 #else // BYTE_ORDER == LITTLE_ENDIAN << 1079 #else // BYTE_ORDER == LITTLE_ENDIAN
1216 if (!fLittleEndian) { // big endian << 1080 if(!fLittleEndian) { // big endian
1217 #endif 1081 #endif
1218 const G4int SIZE = sizeof(_rval); << 1082 const int SIZE = sizeof(_rval);
1219 char ctemp; << 1083 char ctemp;
1220 for (G4int i = 0; i < SIZE / 2; ++i) { << 1084 for(int i = 0; i < SIZE/2; i++) {
1221 ctemp = _val[i]; << 1085 ctemp = _val[i];
1222 _val[i] = _val[SIZE - 1 - i]; << 1086 _val[i] = _val[SIZE - 1 - i];
1223 _val[SIZE - 1 - i] = ctemp; << 1087 _val[SIZE - 1 - i] = ctemp;
>> 1088 }
1224 } 1089 }
>> 1090 _rval = *(Type *)_val;
1225 } 1091 }
1226 _rval = *(Type*)_val; << 1092
1227 } << 1093 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
1228 1094
1229 //....oooOO0OOooo........oooOO0OOooo........o <<
1230 1095