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25 // 25 //
26 // 26 //
>> 27 // $Id: G4GMocrenIO.cc,v 1.4.2.1 2010/03/18 10:29:16 gcosmo Exp $
>> 28 // GEANT4 tag $Name: geant4-09-03-patch-02 $
27 // 29 //
28 // 30 //
29 // File I/O manager class for writing or readi 31 // File I/O manager class for writing or reading calcuated dose
30 // distribution and some event information 32 // distribution and some event information
31 // 33 //
32 // Created: Mar. 31, 2009 Akinori Kimura : r 34 // Created: Mar. 31, 2009 Akinori Kimura : release for the gMocrenFile driver
33 // 35 //
34 // Akinori Kimur 36 // Akinori Kimura
35 // gMocren home 37 // gMocren home page:
36 // http://geant4 38 // http://geant4.kek.jp/gMocren/
37 // 39 //
38 // 40 //
39 #include "G4GMocrenIO.hh" 41 #include "G4GMocrenIO.hh"
>> 42
40 #include <iostream> 43 #include <iostream>
41 #include <ctime> 44 #include <ctime>
42 #include <sstream> 45 #include <sstream>
43 #include <iomanip> 46 #include <iomanip>
44 #include <cstdlib> 47 #include <cstdlib>
45 #include <cstring> 48 #include <cstring>
46 <<
47 #include "globals.hh" <<
48 #include "G4VisManager.hh" <<
49 <<
50 #if defined(_WIN32) 49 #if defined(_WIN32)
51 #define LITTLE_ENDIAN 1234 50 #define LITTLE_ENDIAN 1234
52 #define BYTE_ORDER LITTLE_ENDIAN 51 #define BYTE_ORDER LITTLE_ENDIAN
53 #endif 52 #endif
54 53
55 const int DOSERANGE = 25000; 54 const int DOSERANGE = 25000;
56 55
57 //----- GMocrenDataPrimitive class in the GMoc 56 //----- GMocrenDataPrimitive class in the GMocrenDataIO class-----//
58 template <typename T> 57 template <typename T>
59 GMocrenDataPrimitive<T>::GMocrenDataPrimitive 58 GMocrenDataPrimitive<T>::GMocrenDataPrimitive () {
60 clear(); 59 clear();
61 } 60 }
62 template <typename T> 61 template <typename T>
63 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive 62 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive () {
64 /* 63 /*
65 std::vector<short *>::iterator itr = image 64 std::vector<short *>::iterator itr = image.begin();
66 for(; itr != image.end(); itr++) { 65 for(; itr != image.end(); itr++) {
67 delete [] *itr; 66 delete [] *itr;
68 } 67 }
69 */ 68 */
70 } 69 }
71 70
72 template <typename T> GMocrenDataPrimitive<T> 71 template <typename T> GMocrenDataPrimitive<T> &
73 GMocrenDataPrimitive<T>::operator = (const GMo 72 GMocrenDataPrimitive<T>::operator = (const GMocrenDataPrimitive<T> & _right) {
74 if (this == &_right) return *this; <<
75 for(int i = 0; i < 3; i++) { 73 for(int i = 0; i < 3; i++) {
76 kSize[i] = _right.kSize[i]; 74 kSize[i] = _right.kSize[i];
77 kCenter[i] = _right.kCenter[i]; 75 kCenter[i] = _right.kCenter[i];
78 } 76 }
79 kScale = _right.kScale; 77 kScale = _right.kScale;
80 for(int i = 0; i < 2; i++) kMinmax[i] = _rig 78 for(int i = 0; i < 2; i++) kMinmax[i] = _right.kMinmax[i];
81 int num = kSize[0]*kSize[1]; 79 int num = kSize[0]*kSize[1];
82 kImage.clear(); 80 kImage.clear();
83 for(int z = 0; z < kSize[2]; z++) { 81 for(int z = 0; z < kSize[2]; z++) {
84 T * img = new T[num]; 82 T * img = new T[num];
85 for(int i = 0; i < num; i++) img[i] =_righ 83 for(int i = 0; i < num; i++) img[i] =_right.kImage[z][i];
86 kImage.push_back(img); 84 kImage.push_back(img);
87 } 85 }
88 return *this; 86 return *this;
89 } 87 }
90 88
91 template <typename T> GMocrenDataPrimitive<T> 89 template <typename T> GMocrenDataPrimitive<T> &
92 GMocrenDataPrimitive<T>::operator + (const GMo 90 GMocrenDataPrimitive<T>::operator + (const GMocrenDataPrimitive<T> & _right) {
93 91
94 GMocrenDataPrimitive<T> rprim; 92 GMocrenDataPrimitive<T> rprim;
95 bool stat = true; 93 bool stat = true;
96 for(int i = 0; i < 3; i++) { 94 for(int i = 0; i < 3; i++) {
97 if(kSize[i] != _right.kSize[i]) stat = fal 95 if(kSize[i] != _right.kSize[i]) stat = false;
98 if(kCenter[i] != _right.kCenter[i]) stat = 96 if(kCenter[i] != _right.kCenter[i]) stat = false;
99 } 97 }
100 if(!stat) { 98 if(!stat) {
101 if (G4VisManager::GetVerbosity() >= G4VisM << 99 std::cerr << "Warning: operator + "
102 G4cout << "Warning: operator + " << 100 << " Cannot do the operator +"
103 << " Cannot do the operator +" << 101 << std::endl;
104 << G4endl; <<
105 return *this; 102 return *this;
106 } 103 }
107 104
108 rprim.setSize(kSize); 105 rprim.setSize(kSize);
109 rprim.setCenterPosition(kCenter); 106 rprim.setCenterPosition(kCenter);
110 107
111 T mms[2] = {9e100,-9e100}; << 108 T mm[2] = {9e100,-9e100};
112 //if(mms[0] > _right.minmax[0]) mms[0] = _ri << 109 //if(mm[0] > _right.minmax[0]) mm[0] = _right.minmax[0];
113 //if(mms[1] < _right.minmax[1]) mms[1] = _ri << 110 //if(mm[1] < _right.minmax[1]) mm[1] = _right.minmax[1];
114 111
115 int num = kSize[0]*kSize[1]; 112 int num = kSize[0]*kSize[1];
116 for(int z = 0; z < kSize[2]; z++) { 113 for(int z = 0; z < kSize[2]; z++) {
117 T * img = new T[num]; 114 T * img = new T[num];
118 for(int xy = 0; xy < num; xy++) { 115 for(int xy = 0; xy < num; xy++) {
119 img[xy] = kImage[z][xy] + _right.kImage[ 116 img[xy] = kImage[z][xy] + _right.kImage[z][xy];
120 if(mms[0] > img[xy]) mms[0] = img[xy]; << 117 if(mm[0] > img[xy]) mm[0] = img[xy];
121 if(mms[1] < img[xy]) mms[1] = img[xy]; << 118 if(mm[1] < img[xy]) mm[1] = img[xy];
122 } 119 }
123 rprim.addImage(img); 120 rprim.addImage(img);
124 } 121 }
125 rprim.setMinMax(mms); << 122 rprim.setMinMax(mm);
126 123
127 T scl = mms[1]/DOSERANGE; << 124 T scl = mm[1]/DOSERANGE;
128 rprim.setScale(scl); 125 rprim.setScale(scl);
129 126
130 return rprim; 127 return rprim;
131 } 128 }
132 129
133 template <typename T> GMocrenDataPrimitive<T> 130 template <typename T> GMocrenDataPrimitive<T> &
134 GMocrenDataPrimitive<T>::operator += (const GM 131 GMocrenDataPrimitive<T>::operator += (const GMocrenDataPrimitive<T> & _right) {
135 132
136 bool stat = true; 133 bool stat = true;
137 for(int i = 0; i < 3; i++) { 134 for(int i = 0; i < 3; i++) {
138 if(kSize[i] != _right.kSize[i]) stat = fal 135 if(kSize[i] != _right.kSize[i]) stat = false;
139 if(kCenter[i] != _right.kCenter[i]) stat = 136 if(kCenter[i] != _right.kCenter[i]) stat = false;
140 } 137 }
141 if(!stat) { 138 if(!stat) {
142 if (G4VisManager::GetVerbosity() >= G4VisM << 139 std::cerr << "Warning: operator += " << std::endl
143 G4cout << "Warning: operator += " << G4e << 140 << " Cannot do the operator +="
144 << " Cannot do the operator +=" << 141 << std::endl;
145 << G4endl; <<
146 return *this; 142 return *this;
147 } 143 }
148 144
149 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0 145 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0] = _right.kMinmax[0];
150 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1 146 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1] = _right.kMinmax[1];
151 147
152 int num = kSize[0]*kSize[1]; 148 int num = kSize[0]*kSize[1];
153 for(int z = 0; z < kSize[2]; z++) { 149 for(int z = 0; z < kSize[2]; z++) {
154 for(int xy = 0; xy < num; xy++) { 150 for(int xy = 0; xy < num; xy++) {
155 kImage[z][xy] += _right.kImage[z][xy]; 151 kImage[z][xy] += _right.kImage[z][xy];
156 if(kMinmax[0] > kImage[z][xy]) kMinmax[0 152 if(kMinmax[0] > kImage[z][xy]) kMinmax[0] = kImage[z][xy];
157 if(kMinmax[1] < kImage[z][xy]) kMinmax[1 153 if(kMinmax[1] < kImage[z][xy]) kMinmax[1] = kImage[z][xy];
158 } 154 }
159 } 155 }
160 156
161 kScale = kMinmax[1]/DOSERANGE; 157 kScale = kMinmax[1]/DOSERANGE;
162 158
163 return *this; 159 return *this;
164 } 160 }
165 161
166 template <typename T> 162 template <typename T>
167 void GMocrenDataPrimitive<T>::clear() { 163 void GMocrenDataPrimitive<T>::clear() {
168 for(int i = 0; i < 3; i++) { 164 for(int i = 0; i < 3; i++) {
169 kSize[i] = 0; 165 kSize[i] = 0;
170 kCenter[i] = 0.; 166 kCenter[i] = 0.;
171 } 167 }
172 kScale = 1.; 168 kScale = 1.;
173 kMinmax[0] = (T)32109; 169 kMinmax[0] = (T)32109;
174 kMinmax[1] = (T)-32109; 170 kMinmax[1] = (T)-32109;
175 171
176 clearImage(); 172 clearImage();
177 } 173 }
178 template <typename T> 174 template <typename T>
179 void GMocrenDataPrimitive<T>::clearImage() { 175 void GMocrenDataPrimitive<T>::clearImage() {
180 typename std::vector<T *>::iterator itr; 176 typename std::vector<T *>::iterator itr;
181 for(itr = kImage.begin(); itr != kImage.end( 177 for(itr = kImage.begin(); itr != kImage.end(); itr++) {
182 delete [] *itr; 178 delete [] *itr;
183 } 179 }
184 kImage.clear(); 180 kImage.clear();
185 } 181 }
186 template <typename T> 182 template <typename T>
187 void GMocrenDataPrimitive<T>::setSize(int _siz 183 void GMocrenDataPrimitive<T>::setSize(int _size[3]) {
188 for(int i = 0; i < 3; i++) kSize[i] = _size[ 184 for(int i = 0; i < 3; i++) kSize[i] = _size[i];
189 } 185 }
190 template <typename T> 186 template <typename T>
191 void GMocrenDataPrimitive<T>::getSize(int _siz 187 void GMocrenDataPrimitive<T>::getSize(int _size[3]) {
192 for(int i = 0; i < 3; i++) _size[i] = kSize[ 188 for(int i = 0; i < 3; i++) _size[i] = kSize[i];
193 } 189 }
194 template <typename T> 190 template <typename T>
195 void GMocrenDataPrimitive<T>::setScale(double 191 void GMocrenDataPrimitive<T>::setScale(double & _scale) {
196 kScale = _scale; 192 kScale = _scale;
197 } 193 }
198 template <typename T> 194 template <typename T>
199 double GMocrenDataPrimitive<T>::getScale() { 195 double GMocrenDataPrimitive<T>::getScale() {
200 return kScale; 196 return kScale;
201 } 197 }
202 template <typename T> 198 template <typename T>
203 void GMocrenDataPrimitive<T>::setMinMax(T _min 199 void GMocrenDataPrimitive<T>::setMinMax(T _minmax[2]) {
204 for(int i = 0; i < 2; i++) kMinmax[i] = _min 200 for(int i = 0; i < 2; i++) kMinmax[i] = _minmax[i];
205 } 201 }
206 template <typename T> 202 template <typename T>
207 void GMocrenDataPrimitive<T>::getMinMax(T _min 203 void GMocrenDataPrimitive<T>::getMinMax(T _minmax[2]) {
208 for(int i = 0; i < 2; i++) _minmax[i] = kMin 204 for(int i = 0; i < 2; i++) _minmax[i] = kMinmax[i];
209 205
210 } 206 }
211 template <typename T> 207 template <typename T>
212 void GMocrenDataPrimitive<T>::setImage(std::ve 208 void GMocrenDataPrimitive<T>::setImage(std::vector<T *> & _image) {
213 kImage = _image; 209 kImage = _image;
214 } 210 }
215 template <typename T> 211 template <typename T>
216 void GMocrenDataPrimitive<T>::addImage(T * _im 212 void GMocrenDataPrimitive<T>::addImage(T * _image) {
217 kImage.push_back(_image); 213 kImage.push_back(_image);
218 } 214 }
219 template <typename T> 215 template <typename T>
220 std::vector<T *> & GMocrenDataPrimitive<T>::ge 216 std::vector<T *> & GMocrenDataPrimitive<T>::getImage() {
221 return kImage; 217 return kImage;
222 } 218 }
223 template <typename T> 219 template <typename T>
224 T * GMocrenDataPrimitive<T>::getImage(int _z) 220 T * GMocrenDataPrimitive<T>::getImage(int _z) {
225 if(_z >= (int)kImage.size()) return 0; 221 if(_z >= (int)kImage.size()) return 0;
226 return kImage[_z]; 222 return kImage[_z];
227 } 223 }
228 template <typename T> 224 template <typename T>
229 void GMocrenDataPrimitive<T>::setCenterPositio 225 void GMocrenDataPrimitive<T>::setCenterPosition(float _center[3]) {
230 for(int i = 0; i < 3; i++) kCenter[i] = _cen 226 for(int i = 0; i < 3; i++) kCenter[i] = _center[i];
231 } 227 }
232 template <typename T> 228 template <typename T>
233 void GMocrenDataPrimitive<T>::getCenterPositio 229 void GMocrenDataPrimitive<T>::getCenterPosition(float _center[3]) {
234 for(int i = 0; i < 3; i++) _center[i] = kCen 230 for(int i = 0; i < 3; i++) _center[i] = kCenter[i];
235 } 231 }
236 template <typename T> 232 template <typename T>
237 void GMocrenDataPrimitive<T>::setName(std::str 233 void GMocrenDataPrimitive<T>::setName(std::string & _name) {
238 kDataName = _name; 234 kDataName = _name;
239 } 235 }
240 template <typename T> 236 template <typename T>
241 std::string GMocrenDataPrimitive<T>::getName() 237 std::string GMocrenDataPrimitive<T>::getName() {
242 return kDataName; 238 return kDataName;
243 } 239 }
244 240
245 241
246 242
247 243
248 244
249 GMocrenTrack::GMocrenTrack() { 245 GMocrenTrack::GMocrenTrack() {
250 kTrack.clear(); 246 kTrack.clear();
251 for(int i = 0; i < 3; i++) kColor[i] = 0; 247 for(int i = 0; i < 3; i++) kColor[i] = 0;
252 } 248 }
253 249
254 void GMocrenTrack::addStep(float _startx, floa 250 void GMocrenTrack::addStep(float _startx, float _starty, float _startz,
255 float _endx, float _endy, float _endz 251 float _endx, float _endy, float _endz) {
256 struct Step step; 252 struct Step step;
257 step.startPoint[0] = _startx; 253 step.startPoint[0] = _startx;
258 step.startPoint[1] = _starty; 254 step.startPoint[1] = _starty;
259 step.startPoint[2] = _startz; 255 step.startPoint[2] = _startz;
260 step.endPoint[0] = _endx; 256 step.endPoint[0] = _endx;
261 step.endPoint[1] = _endy; 257 step.endPoint[1] = _endy;
262 step.endPoint[2] = _endz; 258 step.endPoint[2] = _endz;
263 kTrack.push_back(step); 259 kTrack.push_back(step);
264 } 260 }
265 void GMocrenTrack::getStep(float & _startx, fl 261 void GMocrenTrack::getStep(float & _startx, float & _starty, float & _startz,
266 float & _endx, float & _endy, float & 262 float & _endx, float & _endy, float & _endz,
267 int _num) { 263 int _num) {
268 if(_num >= (int)kTrack.size()) { 264 if(_num >= (int)kTrack.size()) {
269 if (G4VisManager::GetVerbosity() >= G4VisM << 265 std::cerr << "GMocrenTrack::getStep(...) Error: "
270 G4cout << "GMocrenTrack::getStep(...) Er << 266 << "invalid step # : " << _num << std::endl;
271 << "invalid step # : " << _num << G4end <<
272 return; 267 return;
273 } 268 }
274 269
275 _startx = kTrack[_num].startPoint[0]; 270 _startx = kTrack[_num].startPoint[0];
276 _starty = kTrack[_num].startPoint[1]; 271 _starty = kTrack[_num].startPoint[1];
277 _startz = kTrack[_num].startPoint[2]; 272 _startz = kTrack[_num].startPoint[2];
278 _endx = kTrack[_num].endPoint[0]; 273 _endx = kTrack[_num].endPoint[0];
279 _endy = kTrack[_num].endPoint[1]; 274 _endy = kTrack[_num].endPoint[1];
280 _endz = kTrack[_num].endPoint[2]; 275 _endz = kTrack[_num].endPoint[2];
281 } 276 }
282 void GMocrenTrack::translate(std::vector<float 277 void GMocrenTrack::translate(std::vector<float> & _translate) {
283 std::vector<struct Step>::iterator itr = kTr 278 std::vector<struct Step>::iterator itr = kTrack.begin();
284 for(; itr != kTrack.end(); itr++) { 279 for(; itr != kTrack.end(); itr++) {
285 for(int i = 0; i < 3; i++ ) { 280 for(int i = 0; i < 3; i++ ) {
286 itr->startPoint[i] += _translate[i]; 281 itr->startPoint[i] += _translate[i];
287 itr->endPoint[i] += _translate[i]; 282 itr->endPoint[i] += _translate[i];
288 } 283 }
289 } 284 }
290 } 285 }
291 286
292 287
293 288
294 289
295 290
296 291
297 292
298 293
299 294
300 GMocrenDetector::GMocrenDetector() { 295 GMocrenDetector::GMocrenDetector() {
301 kDetector.clear(); 296 kDetector.clear();
302 for(int i = 0; i < 3; i++) kColor[i] = 0; 297 for(int i = 0; i < 3; i++) kColor[i] = 0;
303 } 298 }
304 299
305 void GMocrenDetector::addEdge(float _startx, f 300 void GMocrenDetector::addEdge(float _startx, float _starty, float _startz,
306 float _endx, float _endy, float _e 301 float _endx, float _endy, float _endz) {
307 struct Edge edge; 302 struct Edge edge;
308 edge.startPoint[0] = _startx; 303 edge.startPoint[0] = _startx;
309 edge.startPoint[1] = _starty; 304 edge.startPoint[1] = _starty;
310 edge.startPoint[2] = _startz; 305 edge.startPoint[2] = _startz;
311 edge.endPoint[0] = _endx; 306 edge.endPoint[0] = _endx;
312 edge.endPoint[1] = _endy; 307 edge.endPoint[1] = _endy;
313 edge.endPoint[2] = _endz; 308 edge.endPoint[2] = _endz;
314 kDetector.push_back(edge); 309 kDetector.push_back(edge);
315 } 310 }
316 void GMocrenDetector::getEdge(float & _startx, 311 void GMocrenDetector::getEdge(float & _startx, float & _starty, float & _startz,
317 float & _endx, float & _endy, float & 312 float & _endx, float & _endy, float & _endz,
318 int _num) { 313 int _num) {
319 if(_num >= (int)kDetector.size()) { 314 if(_num >= (int)kDetector.size()) {
320 if (G4VisManager::GetVerbosity() >= G4VisM << 315 std::cerr << "GMocrenDetector::getEdge(...) Error: "
321 G4cout << "GMocrenDetector::getEdge(...) << 316 << "invalid edge # : " << _num << std::endl;
322 << "invalid edge # : " << _num << G4end <<
323 return; 317 return;
324 } 318 }
325 319
326 _startx = kDetector[_num].startPoint[0]; 320 _startx = kDetector[_num].startPoint[0];
327 _starty = kDetector[_num].startPoint[1]; 321 _starty = kDetector[_num].startPoint[1];
328 _startz = kDetector[_num].startPoint[2]; 322 _startz = kDetector[_num].startPoint[2];
329 _endx = kDetector[_num].endPoint[0]; 323 _endx = kDetector[_num].endPoint[0];
330 _endy = kDetector[_num].endPoint[1]; 324 _endy = kDetector[_num].endPoint[1];
331 _endz = kDetector[_num].endPoint[2]; 325 _endz = kDetector[_num].endPoint[2];
332 } 326 }
333 void GMocrenDetector::translate(std::vector<fl 327 void GMocrenDetector::translate(std::vector<float> & _translate) {
334 std::vector<struct Edge>::iterator itr = kDe 328 std::vector<struct Edge>::iterator itr = kDetector.begin();
335 for(; itr != kDetector.end(); itr++) { 329 for(; itr != kDetector.end(); itr++) {
336 for(int i = 0; i < 3; i++) { 330 for(int i = 0; i < 3; i++) {
337 itr->startPoint[i] += _translate[i]; 331 itr->startPoint[i] += _translate[i];
338 itr->endPoint[i] += _translate[i]; 332 itr->endPoint[i] += _translate[i];
339 } 333 }
340 } 334 }
341 } 335 }
342 336
343 337
344 338
345 339
346 340
347 341
348 342
349 343
350 344
351 // file information 345 // file information
352 std::string G4GMocrenIO::kId; 346 std::string G4GMocrenIO::kId;
353 std::string G4GMocrenIO::kVersion = "2.0.0"; 347 std::string G4GMocrenIO::kVersion = "2.0.0";
354 int G4GMocrenIO::kNumberOfEvents = 0; 348 int G4GMocrenIO::kNumberOfEvents = 0;
355 char G4GMocrenIO::kLittleEndianInput = true; 349 char G4GMocrenIO::kLittleEndianInput = true;
356 350
357 #if BYTE_ORDER == LITTLE_ENDIAN 351 #if BYTE_ORDER == LITTLE_ENDIAN
358 char G4GMocrenIO::kLittleEndianOutput = true; 352 char G4GMocrenIO::kLittleEndianOutput = true;
359 #else 353 #else
360 char G4GMocrenIO::kLittleEndianOutput = false; 354 char G4GMocrenIO::kLittleEndianOutput = false; // Big endian
361 #endif 355 #endif
362 std::string G4GMocrenIO::kComment; 356 std::string G4GMocrenIO::kComment;
363 // 357 //
364 std::string G4GMocrenIO::kFileName = "dose.gdd 358 std::string G4GMocrenIO::kFileName = "dose.gdd";
365 359
366 // 360 //
367 unsigned int G4GMocrenIO::kPointerToModalityDa 361 unsigned int G4GMocrenIO::kPointerToModalityData = 0;
368 std::vector<unsigned int> G4GMocrenIO::kPointe 362 std::vector<unsigned int> G4GMocrenIO::kPointerToDoseDistData;
369 unsigned int G4GMocrenIO::kPointerToROIData = 363 unsigned int G4GMocrenIO::kPointerToROIData = 0;
370 unsigned int G4GMocrenIO::kPointerToTrackData 364 unsigned int G4GMocrenIO::kPointerToTrackData = 0;
371 unsigned int G4GMocrenIO::kPointerToDetectorDa 365 unsigned int G4GMocrenIO::kPointerToDetectorData = 0;
372 366
373 // modality 367 // modality
374 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 368 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 0.};
375 class GMocrenDataPrimitive<short> G4GMocrenIO 369 class GMocrenDataPrimitive<short> G4GMocrenIO::kModality;
376 std::vector<float> G4GMocrenIO::kModalityImage 370 std::vector<float> G4GMocrenIO::kModalityImageDensityMap;
377 std::string G4GMocrenIO::kModalityUnit = "g/cm 371 std::string G4GMocrenIO::kModalityUnit = "g/cm3 "; // 12 Bytes
378 372
379 // dose 373 // dose
380 std::vector<class GMocrenDataPrimitive<double> 374 std::vector<class GMocrenDataPrimitive<double> > G4GMocrenIO::kDose;
381 std::string G4GMocrenIO::kDoseUnit = "keV 375 std::string G4GMocrenIO::kDoseUnit = "keV "; // 12 Bytes
382 376
383 // ROI 377 // ROI
384 std::vector<class GMocrenDataPrimitive<short> 378 std::vector<class GMocrenDataPrimitive<short> > G4GMocrenIO::kRoi;
385 379
386 // track 380 // track
387 std::vector<float *> G4GMocrenIO::kSteps; 381 std::vector<float *> G4GMocrenIO::kSteps;
388 std::vector<unsigned char *> G4GMocrenIO::kSte 382 std::vector<unsigned char *> G4GMocrenIO::kStepColors;
389 std::vector<class GMocrenTrack> G4GMocrenIO::k 383 std::vector<class GMocrenTrack> G4GMocrenIO::kTracks;
390 384
391 // detector 385 // detector
392 std::vector<class GMocrenDetector> G4GMocrenIO 386 std::vector<class GMocrenDetector> G4GMocrenIO::kDetectors;
393 387
394 // verbose 388 // verbose
395 int G4GMocrenIO::kVerbose = 0; 389 int G4GMocrenIO::kVerbose = 0;
396 390
397 const int IDLENGTH = 21; 391 const int IDLENGTH = 21;
398 const int VERLENGTH = 6; 392 const int VERLENGTH = 6;
399 393
400 // constructor 394 // constructor
401 G4GMocrenIO::G4GMocrenIO() 395 G4GMocrenIO::G4GMocrenIO()
402 : kTracksWillBeStored(true) { 396 : kTracksWillBeStored(true) {
403 ; 397 ;
404 } 398 }
405 399
406 // destructor 400 // destructor
407 G4GMocrenIO::~G4GMocrenIO() { 401 G4GMocrenIO::~G4GMocrenIO() {
408 ; 402 ;
409 } 403 }
410 404
411 // initialize 405 // initialize
412 void G4GMocrenIO::initialize() { 406 void G4GMocrenIO::initialize() {
413 407
414 kId.clear(); 408 kId.clear();
415 kVersion = "2.0.0"; 409 kVersion = "2.0.0";
416 kNumberOfEvents = 0; 410 kNumberOfEvents = 0;
417 kLittleEndianInput = true; 411 kLittleEndianInput = true;
418 #if BYTE_ORDER == LITTLE_ENDIAN 412 #if BYTE_ORDER == LITTLE_ENDIAN
419 kLittleEndianOutput = true; 413 kLittleEndianOutput = true;
420 #else // Big endian 414 #else // Big endian
421 kLittleEndianOutput = false; 415 kLittleEndianOutput = false;
422 #endif 416 #endif
423 kComment.clear(); 417 kComment.clear();
424 kFileName = "dose.gdd"; 418 kFileName = "dose.gdd";
425 kPointerToModalityData = 0; 419 kPointerToModalityData = 0;
426 kPointerToDoseDistData.clear(); 420 kPointerToDoseDistData.clear();
427 kPointerToROIData = 0; 421 kPointerToROIData = 0;
428 kPointerToTrackData = 0; 422 kPointerToTrackData = 0;
429 // modality 423 // modality
430 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 424 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = 0.;
431 kModality.clear(); 425 kModality.clear();
432 kModalityImageDensityMap.clear(); 426 kModalityImageDensityMap.clear();
433 kModalityUnit = "g/cm3 "; // 12 Bytes 427 kModalityUnit = "g/cm3 "; // 12 Bytes
434 // dose 428 // dose
435 kDose.clear(); 429 kDose.clear();
436 kDoseUnit = "keV "; // 12 Bytes 430 kDoseUnit = "keV "; // 12 Bytes
437 // ROI 431 // ROI
438 kRoi.clear(); 432 kRoi.clear();
439 // track 433 // track
440 std::vector<float *>::iterator itr; 434 std::vector<float *>::iterator itr;
441 for(itr = kSteps.begin(); itr != kSteps.end( 435 for(itr = kSteps.begin(); itr != kSteps.end(); itr++) delete [] *itr;
442 kSteps.clear(); 436 kSteps.clear();
443 std::vector<unsigned char *>::iterator citr; 437 std::vector<unsigned char *>::iterator citr;
444 for(citr = kStepColors.begin(); citr != kSte 438 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++)
445 delete [] *citr; 439 delete [] *citr;
446 kStepColors.clear(); 440 kStepColors.clear();
447 kTracksWillBeStored = true; 441 kTracksWillBeStored = true;
448 442
449 // verbose 443 // verbose
450 kVerbose = 0; 444 kVerbose = 0;
451 } 445 }
452 446
453 bool G4GMocrenIO::storeData() { 447 bool G4GMocrenIO::storeData() {
454 return storeData4(); 448 return storeData4();
455 } 449 }
456 // 450 //
457 bool G4GMocrenIO::storeData(char * _filename) 451 bool G4GMocrenIO::storeData(char * _filename) {
458 return storeData4(_filename); 452 return storeData4(_filename);
459 } 453 }
460 454
461 bool G4GMocrenIO::storeData4() { 455 bool G4GMocrenIO::storeData4() {
462 456
463 bool DEBUG = false;// 457 bool DEBUG = false;//
464 458
465 if(DEBUG || kVerbose > 0) 459 if(DEBUG || kVerbose > 0)
466 G4cout << ">>>>>>> store data (ver.4) <<< << 460 std::cout << ">>>>>>> store data (ver.4) <<<<<<<" << std::endl;
467 if(DEBUG || kVerbose > 0) 461 if(DEBUG || kVerbose > 0)
468 G4cout << " " << kFileName << G4en << 462 std::cout << " " << kFileName << std::endl;
469 463
470 // output file open 464 // output file open
471 std::ofstream ofile(kFileName.c_str(), 465 std::ofstream ofile(kFileName.c_str(),
472 std::ios_base::out|std::ios_base::bi 466 std::ios_base::out|std::ios_base::binary);
473 if(DEBUG || kVerbose > 0) 467 if(DEBUG || kVerbose > 0)
474 G4cout << " file open status: " << << 468 std::cout << " file open status: " << ofile << std::endl;
475 469
476 // file identifier 470 // file identifier
477 ofile.write("gMocren ", 8); 471 ofile.write("gMocren ", 8);
478 472
479 // file version 473 // file version
480 unsigned char ver = 0x04; 474 unsigned char ver = 0x04;
481 ofile.write((char *)&ver, 1); 475 ofile.write((char *)&ver, 1);
482 476
483 // endian 477 // endian
484 //ofile.write((char *)&kLittleEndianOutput, 478 //ofile.write((char *)&kLittleEndianOutput, sizeof(char));
485 char littleEndian = 0x01; 479 char littleEndian = 0x01;
486 ofile.write((char *)&littleEndian, sizeof(ch 480 ofile.write((char *)&littleEndian, sizeof(char));
487 if(DEBUG || kVerbose > 0) { 481 if(DEBUG || kVerbose > 0) {
488 //G4cout << "Endian: " << (int)kLittleEndi << 482 //std::cout << "Endian: " << (int)kLittleEndianOutput << std::endl;
489 G4cout << "Endian: " << (int)littleEndian << 483 std::cout << "Endian: " << (int)littleEndian << std::endl;
490 } 484 }
491 485
492 // for inverting the byte order 486 // for inverting the byte order
493 float ftmp[6]; 487 float ftmp[6];
494 int itmp[6]; 488 int itmp[6];
495 short stmp[6]; 489 short stmp[6];
496 490
497 // comment length (fixed size) 491 // comment length (fixed size)
498 int commentLength = 1024; 492 int commentLength = 1024;
499 if(kLittleEndianOutput) { 493 if(kLittleEndianOutput) {
500 ofile.write((char *)&commentLength, 4); 494 ofile.write((char *)&commentLength, 4);
501 } else { 495 } else {
502 invertByteOrder((char *)&commentLength, it 496 invertByteOrder((char *)&commentLength, itmp[0]);
503 ofile.write((char *)itmp, 4); 497 ofile.write((char *)itmp, 4);
504 } 498 }
505 499
506 // comment 500 // comment
507 char cmt[1025]; 501 char cmt[1025];
508 std::strncpy(cmt, kComment.c_str(), 1024); << 502 for(int i = 0; i < 1025; i++) cmt[i] = '\0';
509 cmt[1024] = '\0'; << 503 //std::strncpy(cmt, kComment.c_str(), 1024);
510 ofile.write(cmt, 1024); << 504 std::strcpy(cmt, kComment.c_str());
>> 505 ofile.write((char *)cmt, 1024);
511 if(DEBUG || kVerbose > 0) { 506 if(DEBUG || kVerbose > 0) {
512 G4cout << "Data comment : " << 507 std::cout << "Data comment : "
513 << kComment << G4endl; << 508 << kComment << std::endl;
514 } 509 }
515 510
516 // voxel spacings for all images 511 // voxel spacings for all images
517 if(kLittleEndianOutput) { 512 if(kLittleEndianOutput) {
518 ofile.write((char *)kVoxelSpacing, 12); 513 ofile.write((char *)kVoxelSpacing, 12);
519 } else { 514 } else {
520 for(int j = 0; j < 3; j++) 515 for(int j = 0; j < 3; j++)
521 invertByteOrder((char *)&kVoxelSpacing[j 516 invertByteOrder((char *)&kVoxelSpacing[j], ftmp[j]);
522 ofile.write((char *)ftmp, 12); 517 ofile.write((char *)ftmp, 12);
523 } 518 }
524 if(DEBUG || kVerbose > 0) { 519 if(DEBUG || kVerbose > 0) {
525 G4cout << "Voxel spacing : (" << 520 std::cout << "Voxel spacing : ("
526 << kVoxelSpacing[0] << ", " 521 << kVoxelSpacing[0] << ", "
527 << kVoxelSpacing[1] << ", " 522 << kVoxelSpacing[1] << ", "
528 << kVoxelSpacing[2] 523 << kVoxelSpacing[2]
529 << ") mm " << G4endl; << 524 << ") mm " << std::endl;
530 } 525 }
531 526
532 calcPointers4(); 527 calcPointers4();
533 if(!kTracksWillBeStored) kPointerToTrackData 528 if(!kTracksWillBeStored) kPointerToTrackData = 0;
534 529
535 // offset from file starting point to the mo 530 // offset from file starting point to the modality image data
536 if(kLittleEndianOutput) { 531 if(kLittleEndianOutput) {
537 ofile.write((char *)&kPointerToModalityDat 532 ofile.write((char *)&kPointerToModalityData, 4);
538 } else { 533 } else {
539 invertByteOrder((char *)&kPointerToModalit 534 invertByteOrder((char *)&kPointerToModalityData, itmp[0]);
540 ofile.write((char *)itmp, 4); 535 ofile.write((char *)itmp, 4);
541 } 536 }
542 537
543 // # of dose distributions 538 // # of dose distributions
544 //int nDoseDist = (int)pointerToDoseDistData 539 //int nDoseDist = (int)pointerToDoseDistData.size();
545 int nDoseDist = getNumDoseDist(); 540 int nDoseDist = getNumDoseDist();
546 if(kLittleEndianOutput) { 541 if(kLittleEndianOutput) {
547 ofile.write((char *)&nDoseDist, 4); 542 ofile.write((char *)&nDoseDist, 4);
548 } else { 543 } else {
549 invertByteOrder((char *)&nDoseDist, itmp[0 544 invertByteOrder((char *)&nDoseDist, itmp[0]);
550 ofile.write((char *)itmp, 4); 545 ofile.write((char *)itmp, 4);
551 } 546 }
552 547
553 // offset from file starting point to the do 548 // offset from file starting point to the dose image data
554 if(kLittleEndianOutput) { 549 if(kLittleEndianOutput) {
555 for(int i = 0; i < nDoseDist; i++) { 550 for(int i = 0; i < nDoseDist; i++) {
556 ofile.write((char *)&kPointerToDoseDistD 551 ofile.write((char *)&kPointerToDoseDistData[i], 4);
557 } 552 }
558 } else { 553 } else {
559 for(int i = 0; i < nDoseDist; i++) { 554 for(int i = 0; i < nDoseDist; i++) {
560 invertByteOrder((char *)&kPointerToDoseD 555 invertByteOrder((char *)&kPointerToDoseDistData[i], itmp[0]);
561 ofile.write((char *)itmp, 4); 556 ofile.write((char *)itmp, 4);
562 } 557 }
563 } 558 }
564 559
565 // offset from file starting point to the RO 560 // offset from file starting point to the ROI image data
566 if(kLittleEndianOutput) { 561 if(kLittleEndianOutput) {
567 ofile.write((char *)&kPointerToROIData, 4) 562 ofile.write((char *)&kPointerToROIData, 4);
568 } else { 563 } else {
569 invertByteOrder((char *)&kPointerToROIData 564 invertByteOrder((char *)&kPointerToROIData, itmp[0]);
570 ofile.write((char *)itmp, 4); 565 ofile.write((char *)itmp, 4);
571 } 566 }
572 567
573 // offset from file starting point to the tr 568 // offset from file starting point to the track data
574 if(kLittleEndianOutput) { 569 if(kLittleEndianOutput) {
575 ofile.write((char *)&kPointerToTrackData, 570 ofile.write((char *)&kPointerToTrackData, 4);
576 } else { 571 } else {
577 invertByteOrder((char *)&kPointerToTrackDa 572 invertByteOrder((char *)&kPointerToTrackData, itmp[0]);
578 ofile.write((char *)itmp, 4); 573 ofile.write((char *)itmp, 4);
579 } 574 }
580 575
581 // offset from file starting point to the de 576 // offset from file starting point to the detector data
582 if(kLittleEndianOutput) { 577 if(kLittleEndianOutput) {
583 ofile.write((char *)&kPointerToDetectorDat 578 ofile.write((char *)&kPointerToDetectorData, 4);
584 } else { 579 } else {
585 invertByteOrder((char *)&kPointerToDetecto 580 invertByteOrder((char *)&kPointerToDetectorData, itmp[0]);
586 ofile.write((char *)itmp, 4); 581 ofile.write((char *)itmp, 4);
587 } 582 }
588 583
589 if(DEBUG || kVerbose > 0) { 584 if(DEBUG || kVerbose > 0) {
590 G4cout << "Each pointer to data : " << 585 std::cout << "Each pointer to data : "
591 << kPointerToModalityData << ", "; 586 << kPointerToModalityData << ", ";
592 for(int i = 0; i < nDoseDist; i++) { 587 for(int i = 0; i < nDoseDist; i++) {
593 G4cout << kPointerToDoseDistData[i] << " << 588 std::cout << kPointerToDoseDistData[i] << ", ";
594 } 589 }
595 G4cout << kPointerToROIData << ", " << 590 std::cout << kPointerToROIData << ", "
596 << kPointerToTrackData << ", " 591 << kPointerToTrackData << ", "
597 << kPointerToDetectorData 592 << kPointerToDetectorData
598 << G4endl; << 593 << std::endl;
599 } 594 }
600 595
601 //----- modality image -----// 596 //----- modality image -----//
602 597
603 int size[3]; 598 int size[3];
604 float scale; 599 float scale;
605 short minmax[2]; 600 short minmax[2];
606 float fCenter[3]; 601 float fCenter[3];
607 int iCenter[3]; 602 int iCenter[3];
608 // modality image size 603 // modality image size
609 kModality.getSize(size); 604 kModality.getSize(size);
610 605
611 if(kLittleEndianOutput) { 606 if(kLittleEndianOutput) {
612 ofile.write((char *)size, 3*sizeof(int)); 607 ofile.write((char *)size, 3*sizeof(int));
613 } else { 608 } else {
614 for(int j = 0; j < 3; j++) 609 for(int j = 0; j < 3; j++)
615 invertByteOrder((char *)&size[j], itmp[j 610 invertByteOrder((char *)&size[j], itmp[j]);
616 ofile.write((char *)itmp, 12); 611 ofile.write((char *)itmp, 12);
617 } 612 }
618 613
619 if(DEBUG || kVerbose > 0) { 614 if(DEBUG || kVerbose > 0) {
620 G4cout << "Modality image size : (" << 615 std::cout << "Modality image size : ("
621 << size[0] << ", " 616 << size[0] << ", "
622 << size[1] << ", " 617 << size[1] << ", "
623 << size[2] << ")" 618 << size[2] << ")"
624 << G4endl; << 619 << std::endl;
625 } 620 }
626 621
627 // modality image max. & min. 622 // modality image max. & min.
628 kModality.getMinMax(minmax); 623 kModality.getMinMax(minmax);
629 if(kLittleEndianOutput) { 624 if(kLittleEndianOutput) {
630 ofile.write((char *)minmax, 4); 625 ofile.write((char *)minmax, 4);
631 } else { 626 } else {
632 for(int j = 0; j < 2; j++) 627 for(int j = 0; j < 2; j++)
633 invertByteOrder((char *)&minmax[j], stmp 628 invertByteOrder((char *)&minmax[j], stmp[j]);
634 ofile.write((char *)stmp, 4); 629 ofile.write((char *)stmp, 4);
635 } 630 }
636 631
637 // modality image unit 632 // modality image unit
638 char munit[13] = "g/cm3\0"; 633 char munit[13] = "g/cm3\0";
639 ofile.write((char *)munit, 12); 634 ofile.write((char *)munit, 12);
640 635
641 // modality image scale 636 // modality image scale
642 scale = (float)kModality.getScale(); 637 scale = (float)kModality.getScale();
643 if(kLittleEndianOutput) { 638 if(kLittleEndianOutput) {
644 ofile.write((char *)&scale, 4); 639 ofile.write((char *)&scale, 4);
645 } else { 640 } else {
646 invertByteOrder((char *)&scale, ftmp[0]); 641 invertByteOrder((char *)&scale, ftmp[0]);
647 ofile.write((char *)ftmp, 4); 642 ofile.write((char *)ftmp, 4);
648 } 643 }
649 if(DEBUG || kVerbose > 0) { 644 if(DEBUG || kVerbose > 0) {
650 G4cout << "Modality image min., max., scal << 645 std::cout << "Modality image min., max., scale : "
651 << minmax[0] << ", " 646 << minmax[0] << ", "
652 << minmax[1] << ", " 647 << minmax[1] << ", "
653 << scale << G4endl; << 648 << scale << std::endl;
654 } 649 }
655 650
656 // modality image 651 // modality image
657 int psize = size[0]*size[1]; 652 int psize = size[0]*size[1];
658 if(DEBUG || kVerbose > 0) G4cout << "Modalit << 653 if(DEBUG || kVerbose > 0) std::cout << "Modality image : ";
659 for(int i = 0; i < size[2]; i++) { 654 for(int i = 0; i < size[2]; i++) {
660 short * image = kModality.getImage(i); 655 short * image = kModality.getImage(i);
661 if(kLittleEndianOutput) { 656 if(kLittleEndianOutput) {
662 ofile.write((char *)image, psize*sizeof( 657 ofile.write((char *)image, psize*sizeof(short));
663 } else { 658 } else {
664 for(int j = 0; j < psize; j++) { 659 for(int j = 0; j < psize; j++) {
665 invertByteOrder((char *)&image[j], stmp[0]); 660 invertByteOrder((char *)&image[j], stmp[0]);
666 ofile.write((char *)stmp, 2); 661 ofile.write((char *)stmp, 2);
667 } 662 }
668 } 663 }
669 664
670 if(DEBUG || kVerbose > 0) G4cout << "[" << << 665 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
671 } 666 }
672 if(DEBUG || kVerbose > 0) G4cout << G4endl; << 667 if(DEBUG || kVerbose > 0) std::cout << std::endl;
673 668
674 // modality desity map for CT value 669 // modality desity map for CT value
675 size_t msize = minmax[1] - minmax[0]+1; 670 size_t msize = minmax[1] - minmax[0]+1;
676 if(DEBUG || kVerbose > 0) 671 if(DEBUG || kVerbose > 0)
677 G4cout << "modality image : " << minmax[0] << 672 std::cout << "modality image : " << minmax[0] << ", " << minmax[1] << std::endl;
678 float * pdmap = new float[msize]; 673 float * pdmap = new float[msize];
679 for(int i = 0; i < (int)msize; i++) pdmap[i] 674 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
680 675
681 if(kLittleEndianOutput) { 676 if(kLittleEndianOutput) {
682 ofile.write((char *)pdmap, msize*sizeof(fl 677 ofile.write((char *)pdmap, msize*sizeof(float));
683 } else { 678 } else {
684 for(int j = 0; j < (int)msize; j++) { 679 for(int j = 0; j < (int)msize; j++) {
685 invertByteOrder((char *)&pdmap[j], ftmp[ 680 invertByteOrder((char *)&pdmap[j], ftmp[0]);
686 ofile.write((char *)ftmp, 4); 681 ofile.write((char *)ftmp, 4);
687 } 682 }
688 } 683 }
689 684
690 if(DEBUG || kVerbose > 0) { 685 if(DEBUG || kVerbose > 0) {
691 G4cout << "density map : " << std::ends; << 686 std::cout << "density map : " << std::ends;
692 for(int i = 0; i < (int)msize; i+=50) 687 for(int i = 0; i < (int)msize; i+=50)
693 G4cout <<kModalityImageDensityMap[i] << << 688 std::cout <<kModalityImageDensityMap[i] << ", ";
694 G4cout << G4endl; << 689 std::cout << std::endl;
695 } 690 }
696 delete [] pdmap; 691 delete [] pdmap;
697 692
698 693
699 //----- dose distribution image -----// 694 //----- dose distribution image -----//
700 695
701 if(!isDoseEmpty()) { 696 if(!isDoseEmpty()) {
702 697
703 calcDoseDistScale(); 698 calcDoseDistScale();
704 699
705 for(int ndose = 0; ndose < nDoseDist; ndos 700 for(int ndose = 0; ndose < nDoseDist; ndose++) {
706 // dose distrbution image size 701 // dose distrbution image size
707 kDose[ndose].getSize(size); 702 kDose[ndose].getSize(size);
708 if(kLittleEndianOutput) { 703 if(kLittleEndianOutput) {
709 ofile.write((char *)size, 3*sizeof(int)); 704 ofile.write((char *)size, 3*sizeof(int));
710 } else { 705 } else {
711 for(int j = 0; j < 3; j++) 706 for(int j = 0; j < 3; j++)
712 invertByteOrder((char *)&size[j], itmp[j]) 707 invertByteOrder((char *)&size[j], itmp[j]);
713 ofile.write((char *)itmp, 12); 708 ofile.write((char *)itmp, 12);
714 } 709 }
715 if(DEBUG || kVerbose > 0) { 710 if(DEBUG || kVerbose > 0) {
716 G4cout << "Dose dist. [" << ndose << "] imag << 711 std::cout << "Dose dist. [" << ndose << "] image size : ("
717 << size[0] << ", " 712 << size[0] << ", "
718 << size[1] << ", " 713 << size[1] << ", "
719 << size[2] << ")" 714 << size[2] << ")"
720 << G4endl; << 715 << std::endl;
721 } 716 }
722 717
723 // dose distribution max. & min. 718 // dose distribution max. & min.
724 getShortDoseDistMinMax(minmax, ndose); 719 getShortDoseDistMinMax(minmax, ndose);
725 if(kLittleEndianOutput) { 720 if(kLittleEndianOutput) {
726 ofile.write((char *)minmax, 2*2); // sizeof( 721 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
727 } else { 722 } else {
728 for(int j = 0; j < 2; j++) 723 for(int j = 0; j < 2; j++)
729 invertByteOrder((char *)&minmax[j], stmp[j 724 invertByteOrder((char *)&minmax[j], stmp[j]);
730 ofile.write((char *)stmp, 4); 725 ofile.write((char *)stmp, 4);
731 } 726 }
732 727
733 // dose distribution unit 728 // dose distribution unit
734 char cdunit[13]; 729 char cdunit[13];
735 std::strncpy(cdunit, kDoseUnit.c_str(), << 730 for(int i = 0; i < 13; i++) cdunit[i] = '\0';
736 cdunit[12] = '\0'; << 731 std::strcpy(cdunit, kDoseUnit.c_str());
737 ofile.write(cdunit, 12); << 732 ofile.write((char *)cdunit, 12);
738 if(DEBUG || kVerbose > 0) { 733 if(DEBUG || kVerbose > 0) {
739 G4cout << "Dose dist. unit : " << kDoseUnit << 734 std::cout << "Dose dist. unit : " << kDoseUnit << std::endl;
740 } 735 }
741 736
742 // dose distribution scaling 737 // dose distribution scaling
743 double dscale; 738 double dscale;
744 dscale = getDoseDistScale(ndose); 739 dscale = getDoseDistScale(ndose);
745 scale = float(dscale); 740 scale = float(dscale);
746 if(kLittleEndianOutput) { 741 if(kLittleEndianOutput) {
747 ofile.write((char *)&scale, 4); 742 ofile.write((char *)&scale, 4);
748 } else { 743 } else {
749 invertByteOrder((char *)&scale, ftmp[0]); 744 invertByteOrder((char *)&scale, ftmp[0]);
750 ofile.write((char *)ftmp, 4); 745 ofile.write((char *)ftmp, 4);
751 } 746 }
752 if(DEBUG || kVerbose > 0) { 747 if(DEBUG || kVerbose > 0) {
753 G4cout << "Dose dist. [" << ndose << 748 std::cout << "Dose dist. [" << ndose
754 << "] image min., max., scale : " 749 << "] image min., max., scale : "
755 << minmax[0] << ", " 750 << minmax[0] << ", "
756 << minmax[1] << ", " 751 << minmax[1] << ", "
757 << scale << G4endl; << 752 << scale << std::endl;
758 } 753 }
759 754
760 // dose distribution image 755 // dose distribution image
761 int dsize = size[0]*size[1]; 756 int dsize = size[0]*size[1];
762 short * dimage = new short[dsize]; 757 short * dimage = new short[dsize];
763 for(int z = 0; z < size[2]; z++) { 758 for(int z = 0; z < size[2]; z++) {
764 getShortDoseDist(dimage, z, ndose); 759 getShortDoseDist(dimage, z, ndose);
765 if(kLittleEndianOutput) { 760 if(kLittleEndianOutput) {
766 ofile.write((char *)dimage, dsize*2); //si 761 ofile.write((char *)dimage, dsize*2); //sizeof(short)
767 } else { 762 } else {
768 for(int j = 0; j < dsize; j++) { 763 for(int j = 0; j < dsize; j++) {
769 invertByteOrder((char *)&dimage[j], stmp 764 invertByteOrder((char *)&dimage[j], stmp[0]);
770 ofile.write((char *)stmp, 2); 765 ofile.write((char *)stmp, 2);
771 } 766 }
772 } 767 }
773 768
774 if(DEBUG || kVerbose > 0) { 769 if(DEBUG || kVerbose > 0) {
775 for(int j = 0; j < dsize; j++) { 770 for(int j = 0; j < dsize; j++) {
776 if(dimage[j] < 0) 771 if(dimage[j] < 0)
777 G4cout << "[" << j << "," << z << "]" << 772 std::cout << "[" << j << "," << z << "]"
778 << dimage[j] << ", "; 773 << dimage[j] << ", ";
779 } 774 }
780 } 775 }
781 } 776 }
782 if(DEBUG || kVerbose > 0) G4cout << G4en << 777 if(DEBUG || kVerbose > 0) std::cout << std::endl;
783 delete [] dimage; 778 delete [] dimage;
784 779
785 // relative location of the dose distrib 780 // relative location of the dose distribution image for
786 // the modality image 781 // the modality image
787 getDoseDistCenterPosition(fCenter, ndose 782 getDoseDistCenterPosition(fCenter, ndose);
788 for(int i = 0; i < 3; i++) iCenter[i] = 783 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
789 if(kLittleEndianOutput) { 784 if(kLittleEndianOutput) {
790 ofile.write((char *)iCenter, 3*4); // 3*size 785 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
791 } else { 786 } else {
792 for(int j = 0; j < 3; j++) 787 for(int j = 0; j < 3; j++)
793 invertByteOrder((char *)&iCenter[j], itmp[ 788 invertByteOrder((char *)&iCenter[j], itmp[j]);
794 ofile.write((char *)itmp, 12); 789 ofile.write((char *)itmp, 12);
795 } 790 }
796 if(DEBUG || kVerbose > 0) { 791 if(DEBUG || kVerbose > 0) {
797 G4cout << "Dose dist. [" << ndose << 792 std::cout << "Dose dist. [" << ndose
798 << "]image relative location : (" 793 << "]image relative location : ("
799 << iCenter[0] << ", " 794 << iCenter[0] << ", "
800 << iCenter[1] << ", " 795 << iCenter[1] << ", "
801 << iCenter[2] << ")" << G4endl; << 796 << iCenter[2] << ")" << std::endl;
802 } 797 }
803 798
804 // dose distribution name 799 // dose distribution name
805 std::string name = getDoseDistName(ndose 800 std::string name = getDoseDistName(ndose);
806 if(name.size() == 0) name = "dose"; 801 if(name.size() == 0) name = "dose";
807 name.resize(80); 802 name.resize(80);
808 ofile.write((char *)name.c_str(), 80); 803 ofile.write((char *)name.c_str(), 80);
809 if(DEBUG || kVerbose > 0) { 804 if(DEBUG || kVerbose > 0) {
810 G4cout << "Dose dist. name : " << name << G4 << 805 std::cout << "Dose dist. name : " << name << std::endl;
811 } 806 }
812 807
813 } 808 }
814 } 809 }
815 810
816 //----- ROI image -----// 811 //----- ROI image -----//
817 if(!isROIEmpty()) { 812 if(!isROIEmpty()) {
818 // ROI image size 813 // ROI image size
819 kRoi[0].getSize(size); 814 kRoi[0].getSize(size);
820 if(kLittleEndianOutput) { 815 if(kLittleEndianOutput) {
821 ofile.write((char *)size, 3*sizeof(int)) 816 ofile.write((char *)size, 3*sizeof(int));
822 } else { 817 } else {
823 for(int j = 0; j < 3; j++) 818 for(int j = 0; j < 3; j++)
824 invertByteOrder((char *)&size[j], itmp[j]); 819 invertByteOrder((char *)&size[j], itmp[j]);
825 ofile.write((char *)itmp, 12); 820 ofile.write((char *)itmp, 12);
826 } 821 }
827 if(DEBUG || kVerbose > 0) { 822 if(DEBUG || kVerbose > 0) {
828 G4cout << "ROI image size : (" << 823 std::cout << "ROI image size : ("
829 << size[0] << ", " 824 << size[0] << ", "
830 << size[1] << ", " 825 << size[1] << ", "
831 << size[2] << ")" 826 << size[2] << ")"
832 << G4endl; << 827 << std::endl;
833 } 828 }
834 829
835 // ROI max. & min. 830 // ROI max. & min.
836 kRoi[0].getMinMax(minmax); 831 kRoi[0].getMinMax(minmax);
837 if(kLittleEndianOutput) { 832 if(kLittleEndianOutput) {
838 ofile.write((char *)minmax, sizeof(short 833 ofile.write((char *)minmax, sizeof(short)*2);
839 } else { 834 } else {
840 for(int j = 0; j < 2; j++) 835 for(int j = 0; j < 2; j++)
841 invertByteOrder((char *)&minmax[j], stmp[j]) 836 invertByteOrder((char *)&minmax[j], stmp[j]);
842 ofile.write((char *)stmp, 4); 837 ofile.write((char *)stmp, 4);
843 } 838 }
844 839
845 // ROI distribution scaling 840 // ROI distribution scaling
846 scale = (float)kRoi[0].getScale(); 841 scale = (float)kRoi[0].getScale();
847 if(kLittleEndianOutput) { 842 if(kLittleEndianOutput) {
848 ofile.write((char *)&scale, sizeof(float 843 ofile.write((char *)&scale, sizeof(float));
849 } else { 844 } else {
850 invertByteOrder((char *)&scale, ftmp[0]) 845 invertByteOrder((char *)&scale, ftmp[0]);
851 ofile.write((char *)ftmp, 4); 846 ofile.write((char *)ftmp, 4);
852 } 847 }
853 if(DEBUG || kVerbose > 0) { 848 if(DEBUG || kVerbose > 0) {
854 G4cout << "ROI image min., max., scale : << 849 std::cout << "ROI image min., max., scale : "
855 << minmax[0] << ", " 850 << minmax[0] << ", "
856 << minmax[1] << ", " 851 << minmax[1] << ", "
857 << scale << G4endl; << 852 << scale << std::endl;
858 } 853 }
859 854
860 // ROI image 855 // ROI image
861 int rsize = size[0]*size[1]; 856 int rsize = size[0]*size[1];
862 for(int i = 0; i < size[2]; i++) { 857 for(int i = 0; i < size[2]; i++) {
863 short * rimage = kRoi[0].getImage(i); 858 short * rimage = kRoi[0].getImage(i);
864 if(kLittleEndianOutput) { 859 if(kLittleEndianOutput) {
865 ofile.write((char *)rimage, rsize*sizeof(sho 860 ofile.write((char *)rimage, rsize*sizeof(short));
866 } else { 861 } else {
867 for(int j = 0; j < rsize; j++) { 862 for(int j = 0; j < rsize; j++) {
868 invertByteOrder((char *)&rimage[j], stmp[0 863 invertByteOrder((char *)&rimage[j], stmp[0]);
869 ofile.write((char *)stmp, 2); 864 ofile.write((char *)stmp, 2);
870 } 865 }
871 } 866 }
872 867
873 } 868 }
874 869
875 // ROI relative location 870 // ROI relative location
876 kRoi[0].getCenterPosition(fCenter); 871 kRoi[0].getCenterPosition(fCenter);
877 for(int i = 0; i < 3; i++) iCenter[i] = (i 872 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
878 if(kLittleEndianOutput) { 873 if(kLittleEndianOutput) {
879 ofile.write((char *)iCenter, 3*sizeof(in 874 ofile.write((char *)iCenter, 3*sizeof(int));
880 } else { 875 } else {
881 for(int j = 0; j < 3; j++) 876 for(int j = 0; j < 3; j++)
882 invertByteOrder((char *)&iCenter[j], itmp[j] 877 invertByteOrder((char *)&iCenter[j], itmp[j]);
883 ofile.write((char *)itmp, 12); 878 ofile.write((char *)itmp, 12);
884 } 879 }
885 if(DEBUG || kVerbose > 0) { 880 if(DEBUG || kVerbose > 0) {
886 G4cout << "ROI image relative location : << 881 std::cout << "ROI image relative location : ("
887 << iCenter[0] << ", " 882 << iCenter[0] << ", "
888 << iCenter[1] << ", " 883 << iCenter[1] << ", "
889 << iCenter[2] << ")" << G4endl; << 884 << iCenter[2] << ")" << std::endl;
890 } 885 }
891 } 886 }
892 887
893 //----- track information -----// 888 //----- track information -----//
894 // number of track 889 // number of track
895 if(kPointerToTrackData > 0) { 890 if(kPointerToTrackData > 0) {
896 891
897 int ntrk = (int)kTracks.size(); << 892 int ntrk = kTracks.size();
898 if(kLittleEndianOutput) { 893 if(kLittleEndianOutput) {
899 ofile.write((char *)&ntrk, sizeof(int)); 894 ofile.write((char *)&ntrk, sizeof(int));
900 } else { 895 } else {
901 invertByteOrder((char *)&ntrk, itmp[0]); 896 invertByteOrder((char *)&ntrk, itmp[0]);
902 ofile.write((char *)itmp, 4); 897 ofile.write((char *)itmp, 4);
903 } 898 }
904 if(DEBUG || kVerbose > 0) { 899 if(DEBUG || kVerbose > 0) {
905 G4cout << "# of tracks : " << 900 std::cout << "# of tracks : "
906 << ntrk << G4endl; << 901 << ntrk << std::endl;
907 } 902 }
908 903
909 for(int nt = 0; nt < ntrk; nt++) { 904 for(int nt = 0; nt < ntrk; nt++) {
910 905
911 // # of steps in a track 906 // # of steps in a track
912 int nsteps = kTracks[nt].getNumberOfStep 907 int nsteps = kTracks[nt].getNumberOfSteps();
913 if(kLittleEndianOutput) { 908 if(kLittleEndianOutput) {
914 ofile.write((char *)&nsteps, sizeof(int)); 909 ofile.write((char *)&nsteps, sizeof(int));
915 } else { 910 } else {
916 invertByteOrder((char *)&nsteps, itmp[0]); 911 invertByteOrder((char *)&nsteps, itmp[0]);
917 ofile.write((char *)itmp, 4); 912 ofile.write((char *)itmp, 4);
918 } 913 }
919 if(DEBUG || kVerbose > 0) { 914 if(DEBUG || kVerbose > 0) {
920 G4cout << "# of steps : " << nsteps << G4end << 915 std::cout << "# of steps : " << nsteps << std::endl;
921 } 916 }
922 917
923 // track color 918 // track color
924 unsigned char tcolor[3]; 919 unsigned char tcolor[3];
925 kTracks[nt].getColor(tcolor); 920 kTracks[nt].getColor(tcolor);
926 ofile.write((char *)tcolor, 3); 921 ofile.write((char *)tcolor, 3);
927 922
928 // steps 923 // steps
929 float stepPoints[6]; 924 float stepPoints[6];
930 for(int isteps = 0; isteps < nsteps; ist << 925 for(int ns = 0; ns < nsteps; ns++) {
931 kTracks[nt].getStep(stepPoints[0], stepPoint 926 kTracks[nt].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
932 stepPoints[3], stepPoints[4], stepPo 927 stepPoints[3], stepPoints[4], stepPoints[5],
933 isteps); << 928 ns);
934 929
935 if(kLittleEndianOutput) { 930 if(kLittleEndianOutput) {
936 ofile.write((char *)stepPoints, sizeof(flo 931 ofile.write((char *)stepPoints, sizeof(float)*6);
937 } else { 932 } else {
938 for(int j = 0; j < 6; j++) 933 for(int j = 0; j < 6; j++)
939 invertByteOrder((char *)&stepPoints[j], 934 invertByteOrder((char *)&stepPoints[j], ftmp[j]);
940 ofile.write((char *)ftmp, 24); 935 ofile.write((char *)ftmp, 24);
941 } 936 }
942 } 937 }
943 } 938 }
944 } 939 }
945 940
946 //----- detector information -----// 941 //----- detector information -----//
947 // number of detectors 942 // number of detectors
948 if(kPointerToDetectorData > 0) { 943 if(kPointerToDetectorData > 0) {
949 int ndet = (int)kDetectors.size(); << 944 int ndet = kDetectors.size();
950 if(kLittleEndianOutput) { 945 if(kLittleEndianOutput) {
951 ofile.write((char *)&ndet, sizeof(int)); 946 ofile.write((char *)&ndet, sizeof(int));
952 } else { 947 } else {
953 invertByteOrder((char *)&ndet, itmp[0]); 948 invertByteOrder((char *)&ndet, itmp[0]);
954 ofile.write((char *)itmp, 4); 949 ofile.write((char *)itmp, 4);
955 } 950 }
956 if(DEBUG || kVerbose > 0) { 951 if(DEBUG || kVerbose > 0) {
957 G4cout << "# of detectors : " << 952 std::cout << "# of detectors : "
958 << ndet << G4endl; << 953 << ndet << std::endl;
959 } 954 }
960 955
961 for(int nd = 0; nd < ndet; nd++) { 956 for(int nd = 0; nd < ndet; nd++) {
962 957
963 // # of edges of a detector 958 // # of edges of a detector
964 int nedges = kDetectors[nd].getNumberOfE 959 int nedges = kDetectors[nd].getNumberOfEdges();
965 if(kLittleEndianOutput) { 960 if(kLittleEndianOutput) {
966 ofile.write((char *)&nedges, sizeof(int)); 961 ofile.write((char *)&nedges, sizeof(int));
967 } else { 962 } else {
968 invertByteOrder((char *)&nedges, itmp[0]); 963 invertByteOrder((char *)&nedges, itmp[0]);
969 ofile.write((char *)itmp, 4); 964 ofile.write((char *)itmp, 4);
970 } 965 }
971 if(DEBUG || kVerbose > 0) { 966 if(DEBUG || kVerbose > 0) {
972 G4cout << "# of edges in a detector : " << n << 967 std::cout << "# of edges in a detector : " << nedges << std::endl;
973 } 968 }
974 969
975 // edges 970 // edges
976 float edgePoints[6]; 971 float edgePoints[6];
977 for(int ne = 0; ne < nedges; ne++) { 972 for(int ne = 0; ne < nedges; ne++) {
978 kDetectors[nd].getEdge(edgePoints[0], edgePo 973 kDetectors[nd].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
979 edgePoints[3], edgePoints[4], edg 974 edgePoints[3], edgePoints[4], edgePoints[5],
980 ne); 975 ne);
981 976
982 if(kLittleEndianOutput) { 977 if(kLittleEndianOutput) {
983 ofile.write((char *)edgePoints, sizeof(flo 978 ofile.write((char *)edgePoints, sizeof(float)*6);
984 } else { 979 } else {
985 for(int j = 0; j < 6; j++) 980 for(int j = 0; j < 6; j++)
986 invertByteOrder((char *)&edgePoints[j], 981 invertByteOrder((char *)&edgePoints[j], ftmp[j]);
987 ofile.write((char *)ftmp, 24); 982 ofile.write((char *)ftmp, 24);
988 } 983 }
989 984
990 if(DEBUG || kVerbose > 0) { 985 if(DEBUG || kVerbose > 0) {
991 if(ne < 1) { 986 if(ne < 1) {
992 G4cout << " edge : (" << edgePoints[0] < << 987 std::cout << " edge : (" << edgePoints[0] << ", "
993 << edgePoints[1] << ", " 988 << edgePoints[1] << ", "
994 << edgePoints[2] << ") - (" 989 << edgePoints[2] << ") - ("
995 << edgePoints[3] << ", " 990 << edgePoints[3] << ", "
996 << edgePoints[4] << ", " 991 << edgePoints[4] << ", "
997 << edgePoints[5] << ")" << G4endl; << 992 << edgePoints[5] << ")" << std::endl;
998 } 993 }
999 } 994 }
1000 } 995 }
1001 996
1002 // detector color 997 // detector color
1003 unsigned char dcolor[3]; 998 unsigned char dcolor[3];
1004 kDetectors[nd].getColor(dcolor); 999 kDetectors[nd].getColor(dcolor);
1005 ofile.write((char *)dcolor, 3); 1000 ofile.write((char *)dcolor, 3);
1006 if(DEBUG || kVerbose > 0) { 1001 if(DEBUG || kVerbose > 0) {
1007 G4cout << " rgb : (" << (int)dcolor[0] << " << 1002 std::cout << " rgb : (" << (int)dcolor[0] << ", "
1008 << (int)dcolor[1] << ", " 1003 << (int)dcolor[1] << ", "
1009 << (int)dcolor[2] << ")" << G4endl; << 1004 << (int)dcolor[2] << ")" << std::endl;
1010 } 1005 }
1011 1006
1012 // detector name 1007 // detector name
1013 std::string dname = kDetectors[nd].getN 1008 std::string dname = kDetectors[nd].getName();
1014 dname.resize(80); 1009 dname.resize(80);
1015 ofile.write((char *)dname.c_str(), 80); 1010 ofile.write((char *)dname.c_str(), 80);
1016 if(DEBUG || kVerbose > 0) { 1011 if(DEBUG || kVerbose > 0) {
1017 G4cout << " detector name : " << dname << G << 1012 std::cout << " detector name : " << dname << std::endl;
1018 1013
1019 } 1014 }
1020 } 1015 }
1021 } 1016 }
1022 1017
1023 // file end mark 1018 // file end mark
1024 ofile.write("END", 3); 1019 ofile.write("END", 3);
1025 1020
1026 ofile.close(); 1021 ofile.close();
1027 if(DEBUG || kVerbose > 0) 1022 if(DEBUG || kVerbose > 0)
1028 G4cout << ">>>> closed gdd file: " << kFi << 1023 std::cout << ">>>> closed gdd file: " << kFileName << std::endl;
1029 1024
1030 return true; 1025 return true;
1031 } 1026 }
1032 bool G4GMocrenIO::storeData3() { 1027 bool G4GMocrenIO::storeData3() {
1033 1028
1034 if(kVerbose > 0) G4cout << ">>>>>>> store << 1029 if(kVerbose > 0) std::cout << ">>>>>>> store data (ver.3) <<<<<<<" << std::endl;
1035 if(kVerbose > 0) G4cout << " " << k << 1030 if(kVerbose > 0) std::cout << " " << kFileName << std::endl;
1036 1031
1037 bool DEBUG = false;// 1032 bool DEBUG = false;//
1038 1033
1039 // output file open 1034 // output file open
1040 std::ofstream ofile(kFileName.c_str(), 1035 std::ofstream ofile(kFileName.c_str(),
1041 std::ios_base::out|std::ios_base::b 1036 std::ios_base::out|std::ios_base::binary);
1042 1037
1043 // file identifier 1038 // file identifier
1044 ofile.write("gMocren ", 8); 1039 ofile.write("gMocren ", 8);
1045 1040
1046 // file version 1041 // file version
1047 unsigned char ver = 0x03; 1042 unsigned char ver = 0x03;
1048 ofile.write((char *)&ver, 1); 1043 ofile.write((char *)&ver, 1);
1049 1044
1050 // endian 1045 // endian
1051 ofile.write((char *)&kLittleEndianOutput, s 1046 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1052 1047
1053 // comment length (fixed size) 1048 // comment length (fixed size)
1054 int commentLength = 1024; 1049 int commentLength = 1024;
1055 ofile.write((char *)&commentLength, 4); 1050 ofile.write((char *)&commentLength, 4);
1056 1051
1057 // comment 1052 // comment
1058 char cmt[1025]; 1053 char cmt[1025];
1059 std::strncpy(cmt, kComment.c_str(), 1024); 1054 std::strncpy(cmt, kComment.c_str(), 1024);
1060 ofile.write((char *)cmt, 1024); 1055 ofile.write((char *)cmt, 1024);
1061 if(DEBUG || kVerbose > 0) { 1056 if(DEBUG || kVerbose > 0) {
1062 G4cout << "Data comment : " << 1057 std::cout << "Data comment : "
1063 << kComment << G4endl; << 1058 << kComment << std::endl;
1064 } 1059 }
1065 1060
1066 // voxel spacings for all images 1061 // voxel spacings for all images
1067 ofile.write((char *)kVoxelSpacing, 12); 1062 ofile.write((char *)kVoxelSpacing, 12);
1068 if(DEBUG || kVerbose > 0) { 1063 if(DEBUG || kVerbose > 0) {
1069 G4cout << "Voxel spacing : (" << 1064 std::cout << "Voxel spacing : ("
1070 << kVoxelSpacing[0] << ", " 1065 << kVoxelSpacing[0] << ", "
1071 << kVoxelSpacing[1] << ", " 1066 << kVoxelSpacing[1] << ", "
1072 << kVoxelSpacing[2] 1067 << kVoxelSpacing[2]
1073 << ") mm " << G4endl; << 1068 << ") mm " << std::endl;
1074 } 1069 }
1075 1070
1076 calcPointers3(); 1071 calcPointers3();
1077 1072
1078 // offset from file starting point to the m 1073 // offset from file starting point to the modality image data
1079 ofile.write((char *)&kPointerToModalityData 1074 ofile.write((char *)&kPointerToModalityData, 4);
1080 1075
1081 // # of dose distributions 1076 // # of dose distributions
1082 //int nDoseDist = (int)pointerToDoseDistDat 1077 //int nDoseDist = (int)pointerToDoseDistData.size();
1083 int nDoseDist = getNumDoseDist(); 1078 int nDoseDist = getNumDoseDist();
1084 ofile.write((char *)&nDoseDist, 4); 1079 ofile.write((char *)&nDoseDist, 4);
1085 1080
1086 // offset from file starting point to the d 1081 // offset from file starting point to the dose image data
1087 for(int i = 0; i < nDoseDist; i++) { 1082 for(int i = 0; i < nDoseDist; i++) {
1088 ofile.write((char *)&kPointerToDoseDistDa 1083 ofile.write((char *)&kPointerToDoseDistData[i], 4);
1089 } 1084 }
1090 1085
1091 // offset from file starting point to the R 1086 // offset from file starting point to the ROI image data
1092 ofile.write((char *)&kPointerToROIData, 4); 1087 ofile.write((char *)&kPointerToROIData, 4);
1093 1088
1094 // offset from file starting point to the t 1089 // offset from file starting point to the track data
1095 ofile.write((char *)&kPointerToTrackData, 4 1090 ofile.write((char *)&kPointerToTrackData, 4);
1096 if(DEBUG || kVerbose > 0) { 1091 if(DEBUG || kVerbose > 0) {
1097 G4cout << "Each pointer to data : " << 1092 std::cout << "Each pointer to data : "
1098 << kPointerToModalityData << ", "; 1093 << kPointerToModalityData << ", ";
1099 for(int i = 0; i < nDoseDist; i++) { 1094 for(int i = 0; i < nDoseDist; i++) {
1100 G4cout << kPointerToDoseDistData[i] << << 1095 std::cout << kPointerToDoseDistData[i] << ", ";
1101 } 1096 }
1102 G4cout << kPointerToROIData << ", " << 1097 std::cout << kPointerToROIData << ", "
1103 << kPointerToTrackData << G4endl; << 1098 << kPointerToTrackData << std::endl;
1104 } 1099 }
1105 1100
1106 //----- modality image -----// 1101 //----- modality image -----//
1107 1102
1108 int size[3]; 1103 int size[3];
1109 float scale; 1104 float scale;
1110 short minmax[2]; 1105 short minmax[2];
1111 float fCenter[3]; 1106 float fCenter[3];
1112 int iCenter[3]; 1107 int iCenter[3];
1113 // modality image size 1108 // modality image size
1114 kModality.getSize(size); 1109 kModality.getSize(size);
1115 ofile.write((char *)size, 3*sizeof(int)); 1110 ofile.write((char *)size, 3*sizeof(int));
1116 if(DEBUG || kVerbose > 0) { 1111 if(DEBUG || kVerbose > 0) {
1117 G4cout << "Modality image size : (" << 1112 std::cout << "Modality image size : ("
1118 << size[0] << ", " 1113 << size[0] << ", "
1119 << size[1] << ", " 1114 << size[1] << ", "
1120 << size[2] << ")" 1115 << size[2] << ")"
1121 << G4endl; << 1116 << std::endl;
1122 } 1117 }
1123 1118
1124 // modality image max. & min. 1119 // modality image max. & min.
1125 kModality.getMinMax(minmax); 1120 kModality.getMinMax(minmax);
1126 ofile.write((char *)minmax, 4); 1121 ofile.write((char *)minmax, 4);
1127 1122
1128 // modality image unit 1123 // modality image unit
1129 char munit[13] = "g/cm3 "; 1124 char munit[13] = "g/cm3 ";
1130 ofile.write((char *)munit, 12); 1125 ofile.write((char *)munit, 12);
1131 1126
1132 // modality image scale 1127 // modality image scale
1133 scale = (float)kModality.getScale(); 1128 scale = (float)kModality.getScale();
1134 ofile.write((char *)&scale, 4); 1129 ofile.write((char *)&scale, 4);
1135 if(DEBUG || kVerbose > 0) { 1130 if(DEBUG || kVerbose > 0) {
1136 G4cout << "Modality image min., max., sca << 1131 std::cout << "Modality image min., max., scale : "
1137 << minmax[0] << ", " 1132 << minmax[0] << ", "
1138 << minmax[1] << ", " 1133 << minmax[1] << ", "
1139 << scale << G4endl; << 1134 << scale << std::endl;
1140 } 1135 }
1141 1136
1142 // modality image 1137 // modality image
1143 int psize = size[0]*size[1]; 1138 int psize = size[0]*size[1];
1144 if(DEBUG || kVerbose > 0) G4cout << "Modali << 1139 if(DEBUG || kVerbose > 0) std::cout << "Modality image : ";
1145 for(int i = 0; i < size[2]; i++) { 1140 for(int i = 0; i < size[2]; i++) {
1146 short * image = kModality.getImage(i); 1141 short * image = kModality.getImage(i);
1147 ofile.write((char *)image, psize*sizeof(s 1142 ofile.write((char *)image, psize*sizeof(short));
1148 1143
1149 if(DEBUG || kVerbose > 0) G4cout << "[" < << 1144 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1150 } 1145 }
1151 if(DEBUG || kVerbose > 0) G4cout << G4endl; << 1146 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1152 1147
1153 // modality desity map for CT value 1148 // modality desity map for CT value
1154 size_t msize = minmax[1] - minmax[0]+1; 1149 size_t msize = minmax[1] - minmax[0]+1;
1155 float * pdmap = new float[msize]; 1150 float * pdmap = new float[msize];
1156 for(int i = 0; i < (int)msize; i++) pdmap[i 1151 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1157 ofile.write((char *)pdmap, msize*sizeof(flo 1152 ofile.write((char *)pdmap, msize*sizeof(float));
1158 if(DEBUG || kVerbose > 0) { 1153 if(DEBUG || kVerbose > 0) {
1159 G4cout << "density map : " << std::ends; << 1154 std::cout << "density map : " << std::ends;
1160 for(int i = 0; i < (int)msize; i+=50) 1155 for(int i = 0; i < (int)msize; i+=50)
1161 G4cout <<kModalityImageDensityMap[i] << << 1156 std::cout <<kModalityImageDensityMap[i] << ", ";
1162 G4cout << G4endl; << 1157 std::cout << std::endl;
1163 } 1158 }
1164 delete [] pdmap; 1159 delete [] pdmap;
1165 1160
1166 1161
1167 //----- dose distribution image -----// 1162 //----- dose distribution image -----//
1168 1163
1169 if(!isDoseEmpty()) { 1164 if(!isDoseEmpty()) {
1170 1165
1171 calcDoseDistScale(); 1166 calcDoseDistScale();
1172 1167
1173 for(int ndose = 0; ndose < nDoseDist; ndo 1168 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1174 // dose distrbution image size 1169 // dose distrbution image size
1175 kDose[ndose].getSize(size); 1170 kDose[ndose].getSize(size);
1176 ofile.write((char *)size, 3*sizeof(int) 1171 ofile.write((char *)size, 3*sizeof(int));
1177 if(DEBUG || kVerbose > 0) { 1172 if(DEBUG || kVerbose > 0) {
1178 G4cout << "Dose dist. [" << ndose << "] ima << 1173 std::cout << "Dose dist. [" << ndose << "] image size : ("
1179 << size[0] << ", " 1174 << size[0] << ", "
1180 << size[1] << ", " 1175 << size[1] << ", "
1181 << size[2] << ")" 1176 << size[2] << ")"
1182 << G4endl; << 1177 << std::endl;
1183 } 1178 }
1184 1179
1185 // dose distribution max. & min. 1180 // dose distribution max. & min.
1186 getShortDoseDistMinMax(minmax, ndose); 1181 getShortDoseDistMinMax(minmax, ndose);
1187 ofile.write((char *)minmax, 2*2); // si 1182 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
1188 1183
1189 // dose distribution unit 1184 // dose distribution unit
1190 ofile.write((char *)kDoseUnit.c_str(), 1185 ofile.write((char *)kDoseUnit.c_str(), 12);
1191 if(DEBUG || kVerbose > 0) { 1186 if(DEBUG || kVerbose > 0) {
1192 G4cout << "Dose dist. unit : " << kDoseUnit << 1187 std::cout << "Dose dist. unit : " << kDoseUnit << std::endl;
1193 } 1188 }
1194 1189
1195 // dose distribution scaling 1190 // dose distribution scaling
1196 double dscale; 1191 double dscale;
1197 dscale = getDoseDistScale(ndose); 1192 dscale = getDoseDistScale(ndose);
1198 scale = float(dscale); 1193 scale = float(dscale);
1199 ofile.write((char *)&scale, 4); 1194 ofile.write((char *)&scale, 4);
1200 if(DEBUG || kVerbose > 0) { 1195 if(DEBUG || kVerbose > 0) {
1201 G4cout << "Dose dist. [" << ndose << 1196 std::cout << "Dose dist. [" << ndose
1202 << "] image min., max., scale : " 1197 << "] image min., max., scale : "
1203 << minmax[0] << ", " 1198 << minmax[0] << ", "
1204 << minmax[1] << ", " 1199 << minmax[1] << ", "
1205 << scale << G4endl; << 1200 << scale << std::endl;
1206 } 1201 }
1207 1202
1208 // dose distribution image 1203 // dose distribution image
1209 int dsize = size[0]*size[1]; 1204 int dsize = size[0]*size[1];
1210 short * dimage = new short[dsize]; 1205 short * dimage = new short[dsize];
1211 for(int z = 0; z < size[2]; z++) { 1206 for(int z = 0; z < size[2]; z++) {
1212 getShortDoseDist(dimage, z, ndose); 1207 getShortDoseDist(dimage, z, ndose);
1213 ofile.write((char *)dimage, dsize*2); //siz 1208 ofile.write((char *)dimage, dsize*2); //sizeof(short)
1214 1209
1215 if(DEBUG || kVerbose > 0) { 1210 if(DEBUG || kVerbose > 0) {
1216 for(int j = 0; j < dsize; j++) { 1211 for(int j = 0; j < dsize; j++) {
1217 if(dimage[j] < 0) 1212 if(dimage[j] < 0)
1218 G4cout << "[" << j << "," << z << "]" << 1213 std::cout << "[" << j << "," << z << "]"
1219 << dimage[j] << ", "; 1214 << dimage[j] << ", ";
1220 } 1215 }
1221 } 1216 }
1222 } 1217 }
1223 if(DEBUG || kVerbose > 0) G4cout << G4e << 1218 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1224 delete [] dimage; 1219 delete [] dimage;
1225 1220
1226 // relative location of the dose distri 1221 // relative location of the dose distribution image for
1227 // the modality image 1222 // the modality image
1228 getDoseDistCenterPosition(fCenter, ndos 1223 getDoseDistCenterPosition(fCenter, ndose);
1229 for(int i = 0; i < 3; i++) iCenter[i] = 1224 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1230 ofile.write((char *)iCenter, 3*4); // 3 1225 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
1231 if(DEBUG || kVerbose > 0) { 1226 if(DEBUG || kVerbose > 0) {
1232 G4cout << "Dose dist. [" << ndose << 1227 std::cout << "Dose dist. [" << ndose
1233 << "]image relative location : (" 1228 << "]image relative location : ("
1234 << iCenter[0] << ", " 1229 << iCenter[0] << ", "
1235 << iCenter[1] << ", " 1230 << iCenter[1] << ", "
1236 << iCenter[2] << ")" << G4endl; << 1231 << iCenter[2] << ")" << std::endl;
1237 } 1232 }
1238 } 1233 }
1239 } 1234 }
1240 1235
1241 //----- ROI image -----// 1236 //----- ROI image -----//
1242 if(!isROIEmpty()) { 1237 if(!isROIEmpty()) {
1243 // ROI image size 1238 // ROI image size
1244 kRoi[0].getSize(size); 1239 kRoi[0].getSize(size);
1245 ofile.write((char *)size, 3*sizeof(int)); 1240 ofile.write((char *)size, 3*sizeof(int));
1246 if(DEBUG || kVerbose > 0) { 1241 if(DEBUG || kVerbose > 0) {
1247 G4cout << "ROI image size : (" << 1242 std::cout << "ROI image size : ("
1248 << size[0] << ", " 1243 << size[0] << ", "
1249 << size[1] << ", " 1244 << size[1] << ", "
1250 << size[2] << ")" 1245 << size[2] << ")"
1251 << G4endl; << 1246 << std::endl;
1252 } 1247 }
1253 1248
1254 // ROI max. & min. 1249 // ROI max. & min.
1255 kRoi[0].getMinMax(minmax); 1250 kRoi[0].getMinMax(minmax);
1256 ofile.write((char *)minmax, sizeof(short) 1251 ofile.write((char *)minmax, sizeof(short)*2);
1257 1252
1258 // ROI distribution scaling 1253 // ROI distribution scaling
1259 scale = (float)kRoi[0].getScale(); 1254 scale = (float)kRoi[0].getScale();
1260 ofile.write((char *)&scale, sizeof(float) 1255 ofile.write((char *)&scale, sizeof(float));
1261 if(DEBUG || kVerbose > 0) { 1256 if(DEBUG || kVerbose > 0) {
1262 G4cout << "ROI image min., max., scale << 1257 std::cout << "ROI image min., max., scale : "
1263 << minmax[0] << ", " 1258 << minmax[0] << ", "
1264 << minmax[1] << ", " 1259 << minmax[1] << ", "
1265 << scale << G4endl; << 1260 << scale << std::endl;
1266 } 1261 }
1267 1262
1268 // ROI image 1263 // ROI image
1269 int rsize = size[0]*size[1]; 1264 int rsize = size[0]*size[1];
1270 for(int i = 0; i < size[2]; i++) { 1265 for(int i = 0; i < size[2]; i++) {
1271 short * rimage = kRoi[0].getImage(i); 1266 short * rimage = kRoi[0].getImage(i);
1272 ofile.write((char *)rimage, rsize*sizeo 1267 ofile.write((char *)rimage, rsize*sizeof(short));
1273 1268
1274 } 1269 }
1275 1270
1276 // ROI relative location 1271 // ROI relative location
1277 kRoi[0].getCenterPosition(fCenter); 1272 kRoi[0].getCenterPosition(fCenter);
1278 for(int i = 0; i < 3; i++) iCenter[i] = ( 1273 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1279 ofile.write((char *)iCenter, 3*sizeof(int 1274 ofile.write((char *)iCenter, 3*sizeof(int));
1280 if(DEBUG || kVerbose > 0) { 1275 if(DEBUG || kVerbose > 0) {
1281 G4cout << "ROI image relative location << 1276 std::cout << "ROI image relative location : ("
1282 << iCenter[0] << ", " 1277 << iCenter[0] << ", "
1283 << iCenter[1] << ", " 1278 << iCenter[1] << ", "
1284 << iCenter[2] << ")" << G4endl; << 1279 << iCenter[2] << ")" << std::endl;
1285 } 1280 }
1286 } 1281 }
1287 1282
1288 //----- track information -----// 1283 //----- track information -----//
1289 // number of track 1284 // number of track
1290 int ntrk = (int)kSteps.size(); << 1285 int ntrk = kSteps.size();
1291 ofile.write((char *)&ntrk, sizeof(int)); 1286 ofile.write((char *)&ntrk, sizeof(int));
1292 if(DEBUG || kVerbose > 0) { 1287 if(DEBUG || kVerbose > 0) {
1293 G4cout << "# of tracks : " << 1288 std::cout << "# of tracks : "
1294 << ntrk << G4endl; << 1289 << ntrk << std::endl;
1295 } 1290 }
1296 // track position 1291 // track position
1297 for(int i = 0; i < ntrk; i++) { 1292 for(int i = 0; i < ntrk; i++) {
1298 float * tp = kSteps[i]; 1293 float * tp = kSteps[i];
1299 ofile.write((char *)tp, sizeof(float)*6); 1294 ofile.write((char *)tp, sizeof(float)*6);
1300 } 1295 }
1301 // track color 1296 // track color
1302 int ntcolor = int(kStepColors.size()); 1297 int ntcolor = int(kStepColors.size());
1303 if(ntrk != ntcolor) 1298 if(ntrk != ntcolor)
1304 if (G4VisManager::GetVerbosity() >= G4Vis << 1299 std::cerr << "# of track color information must be the same as # of tracks."
1305 G4cout << "# of track color information << 1300 << std::endl;
1306 << G4endl; <<
1307 unsigned char white[3] = {255,255,255}; // 1301 unsigned char white[3] = {255,255,255}; // default color
1308 for(int i = 0; i < ntrk; i++) { 1302 for(int i = 0; i < ntrk; i++) {
1309 if(i < ntcolor) { 1303 if(i < ntcolor) {
1310 unsigned char * tcolor = kStepColors[i] 1304 unsigned char * tcolor = kStepColors[i];
1311 ofile.write((char *)tcolor, 3); 1305 ofile.write((char *)tcolor, 3);
1312 } else { 1306 } else {
1313 ofile.write((char *)white, 3); 1307 ofile.write((char *)white, 3);
1314 } 1308 }
1315 } 1309 }
1316 1310
1317 // file end mark 1311 // file end mark
1318 ofile.write("END", 3); 1312 ofile.write("END", 3);
1319 1313
1320 ofile.close(); 1314 ofile.close();
1321 1315
1322 return true; 1316 return true;
1323 } 1317 }
1324 // 1318 //
1325 bool G4GMocrenIO::storeData4(char * _filename 1319 bool G4GMocrenIO::storeData4(char * _filename) {
1326 kFileName = _filename; 1320 kFileName = _filename;
1327 return storeData4(); 1321 return storeData4();
1328 } 1322 }
1329 1323
1330 // version 2 1324 // version 2
1331 bool G4GMocrenIO::storeData2() { 1325 bool G4GMocrenIO::storeData2() {
1332 1326
1333 if(kVerbose > 0) G4cout << ">>>>>>> store << 1327 if(kVerbose > 0) std::cout << ">>>>>>> store data (ver.2) <<<<<<<" << std::endl;
1334 if(kVerbose > 0) G4cout << " " << k << 1328 if(kVerbose > 0) std::cout << " " << kFileName << std::endl;
1335 1329
1336 bool DEBUG = false;// 1330 bool DEBUG = false;//
1337 1331
1338 // output file open 1332 // output file open
1339 std::ofstream ofile(kFileName.c_str(), 1333 std::ofstream ofile(kFileName.c_str(),
1340 std::ios_base::out|std::ios_base::b 1334 std::ios_base::out|std::ios_base::binary);
1341 1335
1342 // file identifier 1336 // file identifier
1343 ofile.write("GRAPE ", 8); 1337 ofile.write("GRAPE ", 8);
1344 1338
1345 // file version 1339 // file version
1346 unsigned char ver = 0x02; 1340 unsigned char ver = 0x02;
1347 ofile.write((char *)&ver, 1); 1341 ofile.write((char *)&ver, 1);
1348 // file id for old file format support 1342 // file id for old file format support
1349 ofile.write(kId.c_str(), IDLENGTH); 1343 ofile.write(kId.c_str(), IDLENGTH);
1350 // file version for old file format support 1344 // file version for old file format support
1351 ofile.write(kVersion.c_str(), VERLENGTH); 1345 ofile.write(kVersion.c_str(), VERLENGTH);
1352 // endian 1346 // endian
1353 ofile.write((char *)&kLittleEndianOutput, s 1347 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1354 1348
1355 /* 1349 /*
1356 // event number 1350 // event number
1357 ofile.write((char *)&numberOfEvents, sizeof 1351 ofile.write((char *)&numberOfEvents, sizeof(int));
1358 float imageSpacing[3]; 1352 float imageSpacing[3];
1359 imageSpacing[0] = modalityImageVoxelSpacing 1353 imageSpacing[0] = modalityImageVoxelSpacing[0];
1360 imageSpacing[1] = modalityImageVoxelSpacing 1354 imageSpacing[1] = modalityImageVoxelSpacing[1];
1361 imageSpacing[2] = modalityImageVoxelSpacing 1355 imageSpacing[2] = modalityImageVoxelSpacing[2];
1362 ofile.write((char *)imageSpacing, 12); 1356 ofile.write((char *)imageSpacing, 12);
1363 */ 1357 */
1364 1358
1365 1359
1366 // voxel spacings for all images 1360 // voxel spacings for all images
1367 ofile.write((char *)kVoxelSpacing, 12); 1361 ofile.write((char *)kVoxelSpacing, 12);
1368 if(DEBUG || kVerbose > 0) { 1362 if(DEBUG || kVerbose > 0) {
1369 G4cout << "Voxel spacing : (" << 1363 std::cout << "Voxel spacing : ("
1370 << kVoxelSpacing[0] << ", " 1364 << kVoxelSpacing[0] << ", "
1371 << kVoxelSpacing[1] << ", " 1365 << kVoxelSpacing[1] << ", "
1372 << kVoxelSpacing[2] 1366 << kVoxelSpacing[2]
1373 << ") mm " << G4endl; << 1367 << ") mm " << std::endl;
1374 } 1368 }
1375 1369
1376 calcPointers2(); 1370 calcPointers2();
1377 // offset from file starting point to the m 1371 // offset from file starting point to the modality image data
1378 ofile.write((char *)&kPointerToModalityData 1372 ofile.write((char *)&kPointerToModalityData, 4);
1379 1373
1380 // offset from file starting point to the d 1374 // offset from file starting point to the dose image data
1381 ofile.write((char *)&kPointerToDoseDistData 1375 ofile.write((char *)&kPointerToDoseDistData[0], 4);
1382 1376
1383 // offset from file starting point to the R 1377 // offset from file starting point to the ROI image data
1384 ofile.write((char *)&kPointerToROIData, 4); 1378 ofile.write((char *)&kPointerToROIData, 4);
1385 1379
1386 // offset from file starting point to the t 1380 // offset from file starting point to the track data
1387 ofile.write((char *)&kPointerToTrackData, 4 1381 ofile.write((char *)&kPointerToTrackData, 4);
1388 if(DEBUG || kVerbose > 0) { 1382 if(DEBUG || kVerbose > 0) {
1389 G4cout << "Each pointer to data : " << 1383 std::cout << "Each pointer to data : "
1390 << kPointerToModalityData << ", " 1384 << kPointerToModalityData << ", "
1391 << kPointerToDoseDistData[0] << ", " 1385 << kPointerToDoseDistData[0] << ", "
1392 << kPointerToROIData << ", " 1386 << kPointerToROIData << ", "
1393 << kPointerToTrackData << G4endl; << 1387 << kPointerToTrackData << std::endl;
1394 } 1388 }
1395 1389
1396 //----- modality image -----// 1390 //----- modality image -----//
1397 1391
1398 int size[3]; 1392 int size[3];
1399 float scale; 1393 float scale;
1400 short minmax[2]; 1394 short minmax[2];
1401 float fCenter[3]; 1395 float fCenter[3];
1402 int iCenter[3]; 1396 int iCenter[3];
1403 // modality image size 1397 // modality image size
1404 kModality.getSize(size); 1398 kModality.getSize(size);
1405 ofile.write((char *)size, 3*sizeof(int)); 1399 ofile.write((char *)size, 3*sizeof(int));
1406 if(DEBUG || kVerbose > 0) { 1400 if(DEBUG || kVerbose > 0) {
1407 G4cout << "Modality image size : (" << 1401 std::cout << "Modality image size : ("
1408 << size[0] << ", " 1402 << size[0] << ", "
1409 << size[1] << ", " 1403 << size[1] << ", "
1410 << size[2] << ")" 1404 << size[2] << ")"
1411 << G4endl; << 1405 << std::endl;
1412 } 1406 }
1413 1407
1414 // modality image max. & min. 1408 // modality image max. & min.
1415 kModality.getMinMax(minmax); 1409 kModality.getMinMax(minmax);
1416 ofile.write((char *)minmax, 4); 1410 ofile.write((char *)minmax, 4);
1417 1411
1418 // modality image unit 1412 // modality image unit
1419 //char munit[13] = "g/cm3 "; 1413 //char munit[13] = "g/cm3 ";
1420 //ofile.write((char *)&munit, 12); 1414 //ofile.write((char *)&munit, 12);
1421 1415
1422 // modality image scale 1416 // modality image scale
1423 scale = (float)kModality.getScale(); 1417 scale = (float)kModality.getScale();
1424 ofile.write((char *)&scale, 4); 1418 ofile.write((char *)&scale, 4);
1425 if(DEBUG || kVerbose > 0) { 1419 if(DEBUG || kVerbose > 0) {
1426 G4cout << "Modality image min., max., sca << 1420 std::cout << "Modality image min., max., scale : "
1427 << minmax[0] << ", " 1421 << minmax[0] << ", "
1428 << minmax[1] << ", " 1422 << minmax[1] << ", "
1429 << scale << G4endl; << 1423 << scale << std::endl;
1430 } 1424 }
1431 1425
1432 // modality image 1426 // modality image
1433 int psize = size[0]*size[1]; 1427 int psize = size[0]*size[1];
1434 if(DEBUG || kVerbose > 0) G4cout << "Modali << 1428 if(DEBUG || kVerbose > 0) std::cout << "Modality image : ";
1435 for(int i = 0; i < size[2]; i++) { 1429 for(int i = 0; i < size[2]; i++) {
1436 short * image =kModality.getImage(i); 1430 short * image =kModality.getImage(i);
1437 ofile.write((char *)image, psize*sizeof(s 1431 ofile.write((char *)image, psize*sizeof(short));
1438 1432
1439 if(DEBUG || kVerbose > 0) G4cout << "[" < << 1433 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1440 } 1434 }
1441 if(DEBUG || kVerbose > 0) G4cout << G4endl; << 1435 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1442 1436
1443 // modality desity map for CT value 1437 // modality desity map for CT value
1444 size_t msize = minmax[1] - minmax[0]+1; 1438 size_t msize = minmax[1] - minmax[0]+1;
1445 float * pdmap = new float[msize]; 1439 float * pdmap = new float[msize];
1446 for(int i = 0; i < (int)msize; i++) pdmap[i 1440 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1447 ofile.write((char *)pdmap, msize*sizeof(flo 1441 ofile.write((char *)pdmap, msize*sizeof(float));
1448 if(DEBUG || kVerbose > 0) { 1442 if(DEBUG || kVerbose > 0) {
1449 G4cout << "density map : " << std::ends; << 1443 std::cout << "density map : " << std::ends;
1450 for(int i = 0; i < (int)msize; i+=50) 1444 for(int i = 0; i < (int)msize; i+=50)
1451 G4cout <<kModalityImageDensityMap[i] << << 1445 std::cout <<kModalityImageDensityMap[i] << ", ";
1452 G4cout << G4endl; << 1446 std::cout << std::endl;
1453 } 1447 }
1454 delete [] pdmap; 1448 delete [] pdmap;
1455 1449
1456 1450
1457 //----- dose distribution image -----// 1451 //----- dose distribution image -----//
1458 1452
1459 if(!isDoseEmpty()) { 1453 if(!isDoseEmpty()) {
1460 calcDoseDistScale(); 1454 calcDoseDistScale();
1461 1455
1462 // dose distrbution image size 1456 // dose distrbution image size
1463 kDose[0].getSize(size); 1457 kDose[0].getSize(size);
1464 ofile.write((char *)size, 3*sizeof(int)); 1458 ofile.write((char *)size, 3*sizeof(int));
1465 if(DEBUG || kVerbose > 0) { 1459 if(DEBUG || kVerbose > 0) {
1466 G4cout << "Dose dist. image size : (" << 1460 std::cout << "Dose dist. image size : ("
1467 << size[0] << ", " 1461 << size[0] << ", "
1468 << size[1] << ", " 1462 << size[1] << ", "
1469 << size[2] << ")" 1463 << size[2] << ")"
1470 << G4endl; << 1464 << std::endl;
1471 } 1465 }
1472 1466
1473 // dose distribution max. & min. 1467 // dose distribution max. & min.
1474 getShortDoseDistMinMax(minmax); 1468 getShortDoseDistMinMax(minmax);
1475 ofile.write((char *)minmax, sizeof(short) 1469 ofile.write((char *)minmax, sizeof(short)*2);
1476 1470
1477 // dose distribution scaling 1471 // dose distribution scaling
1478 scale = (float)kDose[0].getScale(); 1472 scale = (float)kDose[0].getScale();
1479 ofile.write((char *)&scale, sizeof(float) 1473 ofile.write((char *)&scale, sizeof(float));
1480 if(DEBUG || kVerbose > 0) { 1474 if(DEBUG || kVerbose > 0) {
1481 G4cout << "Dose dist. image min., max., << 1475 std::cout << "Dose dist. image min., max., scale : "
1482 << minmax[0] << ", " 1476 << minmax[0] << ", "
1483 << minmax[1] << ", " 1477 << minmax[1] << ", "
1484 << scale << G4endl; << 1478 << scale << std::endl;
1485 } 1479 }
1486 1480
1487 // dose distribution image 1481 // dose distribution image
1488 int dsize = size[0]*size[1]; 1482 int dsize = size[0]*size[1];
1489 short * dimage = new short[dsize]; 1483 short * dimage = new short[dsize];
1490 for(int z = 0; z < size[2]; z++) { 1484 for(int z = 0; z < size[2]; z++) {
1491 getShortDoseDist(dimage, z); 1485 getShortDoseDist(dimage, z);
1492 ofile.write((char *)dimage, dsize*sizeo 1486 ofile.write((char *)dimage, dsize*sizeof(short));
1493 1487
1494 if(DEBUG || kVerbose > 0) { 1488 if(DEBUG || kVerbose > 0) {
1495 for(int j = 0; j < dsize; j++) { 1489 for(int j = 0; j < dsize; j++) {
1496 if(dimage[j] < 0) 1490 if(dimage[j] < 0)
1497 G4cout << "[" << j << "," << z << "]" << 1491 std::cout << "[" << j << "," << z << "]"
1498 << dimage[j] << ", "; 1492 << dimage[j] << ", ";
1499 } 1493 }
1500 } 1494 }
1501 } 1495 }
1502 if(DEBUG || kVerbose > 0) G4cout << G4end << 1496 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1503 delete [] dimage; 1497 delete [] dimage;
1504 1498
1505 // relative location of the dose distribu 1499 // relative location of the dose distribution image for
1506 // the modality image 1500 // the modality image
1507 kDose[0].getCenterPosition(fCenter); 1501 kDose[0].getCenterPosition(fCenter);
1508 for(int i = 0; i < 3; i++) iCenter[i] = ( 1502 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1509 ofile.write((char *)iCenter, 3*sizeof(int 1503 ofile.write((char *)iCenter, 3*sizeof(int));
1510 if(DEBUG || kVerbose > 0) { 1504 if(DEBUG || kVerbose > 0) {
1511 G4cout << "Dose dist. image relative lo << 1505 std::cout << "Dose dist. image relative location : ("
1512 << iCenter[0] << ", " 1506 << iCenter[0] << ", "
1513 << iCenter[1] << ", " 1507 << iCenter[1] << ", "
1514 << iCenter[2] << ")" << G4endl; << 1508 << iCenter[2] << ")" << std::endl;
1515 } 1509 }
1516 1510
1517 } 1511 }
1518 1512
1519 //----- ROI image -----// 1513 //----- ROI image -----//
1520 if(!isROIEmpty()) { 1514 if(!isROIEmpty()) {
1521 // ROI image size 1515 // ROI image size
1522 kRoi[0].getSize(size); 1516 kRoi[0].getSize(size);
1523 ofile.write((char *)size, 3*sizeof(int)); 1517 ofile.write((char *)size, 3*sizeof(int));
1524 if(DEBUG || kVerbose > 0) { 1518 if(DEBUG || kVerbose > 0) {
1525 G4cout << "ROI image size : (" << 1519 std::cout << "ROI image size : ("
1526 << size[0] << ", " 1520 << size[0] << ", "
1527 << size[1] << ", " 1521 << size[1] << ", "
1528 << size[2] << ")" 1522 << size[2] << ")"
1529 << G4endl; << 1523 << std::endl;
1530 } 1524 }
1531 1525
1532 // ROI max. & min. 1526 // ROI max. & min.
1533 kRoi[0].getMinMax(minmax); 1527 kRoi[0].getMinMax(minmax);
1534 ofile.write((char *)minmax, sizeof(short) 1528 ofile.write((char *)minmax, sizeof(short)*2);
1535 1529
1536 // ROI distribution scaling 1530 // ROI distribution scaling
1537 scale = (float)kRoi[0].getScale(); 1531 scale = (float)kRoi[0].getScale();
1538 ofile.write((char *)&scale, sizeof(float) 1532 ofile.write((char *)&scale, sizeof(float));
1539 if(DEBUG || kVerbose > 0) { 1533 if(DEBUG || kVerbose > 0) {
1540 G4cout << "ROI image min., max., scale << 1534 std::cout << "ROI image min., max., scale : "
1541 << minmax[0] << ", " 1535 << minmax[0] << ", "
1542 << minmax[1] << ", " 1536 << minmax[1] << ", "
1543 << scale << G4endl; << 1537 << scale << std::endl;
1544 } 1538 }
1545 1539
1546 // ROI image 1540 // ROI image
1547 int rsize = size[0]*size[1]; 1541 int rsize = size[0]*size[1];
1548 for(int i = 0; i < size[2]; i++) { 1542 for(int i = 0; i < size[2]; i++) {
1549 short * rimage = kRoi[0].getImage(i); 1543 short * rimage = kRoi[0].getImage(i);
1550 ofile.write((char *)rimage, rsize*sizeo 1544 ofile.write((char *)rimage, rsize*sizeof(short));
1551 1545
1552 } 1546 }
1553 1547
1554 // ROI relative location 1548 // ROI relative location
1555 kRoi[0].getCenterPosition(fCenter); 1549 kRoi[0].getCenterPosition(fCenter);
1556 for(int i = 0; i < 3; i++) iCenter[i] = ( 1550 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1557 ofile.write((char *)iCenter, 3*sizeof(int 1551 ofile.write((char *)iCenter, 3*sizeof(int));
1558 if(DEBUG || kVerbose > 0) { 1552 if(DEBUG || kVerbose > 0) {
1559 G4cout << "ROI image relative location << 1553 std::cout << "ROI image relative location : ("
1560 << iCenter[0] << ", " 1554 << iCenter[0] << ", "
1561 << iCenter[1] << ", " 1555 << iCenter[1] << ", "
1562 << iCenter[2] << ")" << G4endl; << 1556 << iCenter[2] << ")" << std::endl;
1563 } 1557 }
1564 } 1558 }
1565 1559
1566 1560
1567 //----- track information -----// 1561 //----- track information -----//
1568 // track 1562 // track
1569 int ntrk = (int)kSteps.size(); << 1563 int ntrk = kSteps.size();
1570 ofile.write((char *)&ntrk, sizeof(int)); 1564 ofile.write((char *)&ntrk, sizeof(int));
1571 if(DEBUG || kVerbose > 0) { 1565 if(DEBUG || kVerbose > 0) {
1572 G4cout << "# of tracks : " << 1566 std::cout << "# of tracks : "
1573 << ntrk << G4endl; << 1567 << ntrk << std::endl;
1574 } 1568 }
1575 for(int i = 0; i < ntrk; i++) { 1569 for(int i = 0; i < ntrk; i++) {
1576 float * tp = kSteps[i]; 1570 float * tp = kSteps[i];
1577 ofile.write((char *)tp, sizeof(float)*6); 1571 ofile.write((char *)tp, sizeof(float)*6);
1578 } 1572 }
1579 1573
1580 1574
1581 // file end mark 1575 // file end mark
1582 ofile.write("END", 3); 1576 ofile.write("END", 3);
1583 1577
1584 ofile.close(); 1578 ofile.close();
1585 1579
1586 return true; 1580 return true;
1587 } 1581 }
1588 // 1582 //
1589 bool G4GMocrenIO::storeData2(char * _filename 1583 bool G4GMocrenIO::storeData2(char * _filename) {
1590 kFileName = _filename; 1584 kFileName = _filename;
1591 return storeData(); 1585 return storeData();
1592 } 1586 }
1593 1587
1594 bool G4GMocrenIO::retrieveData() { 1588 bool G4GMocrenIO::retrieveData() {
1595 1589
1596 // input file open 1590 // input file open
1597 std::ifstream ifile(kFileName.c_str(), std: 1591 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1598 if(!ifile) { 1592 if(!ifile) {
1599 if (G4VisManager::GetVerbosity() >= G4Vis << 1593 std::cerr << "Cannot open file: " << kFileName
1600 G4cout << "Cannot open file: " << kFile << 1594 << " in G4GMocrenIO::retrieveData()." << std::endl;
1601 << " in G4GMocrenIO::retrieveData()." <<
1602 return false; 1595 return false;
1603 } 1596 }
1604 1597
1605 // file identifier 1598 // file identifier
1606 char verid[9]; 1599 char verid[9];
1607 ifile.read((char *)verid, 8); 1600 ifile.read((char *)verid, 8);
1608 // file version 1601 // file version
1609 unsigned char ver; 1602 unsigned char ver;
1610 ifile.read((char *)&ver, 1); 1603 ifile.read((char *)&ver, 1);
1611 ifile.close(); 1604 ifile.close();
1612 1605
1613 if(std::strncmp(verid, "gMocren", 7) == 0) 1606 if(std::strncmp(verid, "gMocren", 7) == 0) {
1614 if(ver == 0x03) { 1607 if(ver == 0x03) {
1615 G4cout << ">>>>>>> retrieve data (ver. << 1608 std::cout << ">>>>>>> retrieve data (ver.3) <<<<<<<" << std::endl;
1616 G4cout << " " << kFileName << G << 1609 std::cout << " " << kFileName << std::endl;
1617 retrieveData3(); 1610 retrieveData3();
1618 } else if (ver == 0x04) { 1611 } else if (ver == 0x04) {
1619 G4cout << ">>>>>>> retrieve data (ver. << 1612 std::cout << ">>>>>>> retrieve data (ver.4) <<<<<<<" << std::endl;
1620 G4cout << " " << kFileName << G << 1613 std::cout << " " << kFileName << std::endl;
1621 retrieveData4(); 1614 retrieveData4();
1622 } else { 1615 } else {
1623 if (G4VisManager::GetVerbosity() >= G4V << 1616 std::cerr << "Error -- invalid file version : " << (int)ver
1624 G4cout << "Error -- invalid file version : << 1617 << std::endl;
1625 << G4endl; << 1618 std::cerr << " " << kFileName << std::endl;
1626 G4cout << " " << kFileName << G4end << 1619 std::exit(-1);
1627 } <<
1628 G4Exception("G4GMocrenIO::retrieveDadta <<
1629 "gMocren2001", FatalExcepti <<
1630 "Error."); <<
1631 <<
1632 } 1620 }
1633 } else if(std::strncmp(verid, "GRAPE", 5) = 1621 } else if(std::strncmp(verid, "GRAPE", 5) == 0) {
1634 G4cout << ">>>>>>> retrieve data (ver.2) << 1622 std::cout << ">>>>>>> retrieve data (ver.2) <<<<<<<" << std::endl;
1635 G4cout << " " << kFileName << G4e << 1623 std::cout << " " << kFileName << std::endl;
1636 retrieveData2(); 1624 retrieveData2();
1637 } else { 1625 } else {
1638 if (G4VisManager::GetVerbosity() >= G4Vis << 1626 std::cerr << kFileName << " was not gdd file." << std::endl;
1639 G4cout << kFileName << " was not gdd fi <<
1640 return false; 1627 return false;
1641 } 1628 }
1642 1629
1643 return true; 1630 return true;
1644 } 1631 }
1645 1632
1646 bool G4GMocrenIO::retrieveData(char * _filena 1633 bool G4GMocrenIO::retrieveData(char * _filename) {
1647 kFileName = _filename; 1634 kFileName = _filename;
1648 return retrieveData(); 1635 return retrieveData();
1649 } 1636 }
1650 1637
1651 // 1638 //
1652 bool G4GMocrenIO::retrieveData4() { 1639 bool G4GMocrenIO::retrieveData4() {
1653 1640
1654 bool DEBUG = false;// 1641 bool DEBUG = false;//
1655 1642
1656 // input file open 1643 // input file open
1657 std::ifstream ifile(kFileName.c_str(), std: 1644 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1658 if(!ifile) { 1645 if(!ifile) {
1659 if (G4VisManager::GetVerbosity() >= G4Vis << 1646 std::cerr << "Cannot open file: " << kFileName
1660 G4cout << "Cannot open file: " << kFile << 1647 << " in G4GMocrenIO::retrieveData3()." << std::endl;
1661 << " in G4GMocrenIO::retrieveData3()." << <<
1662 return false; 1648 return false;
1663 } 1649 }
1664 1650
1665 // data buffer 1651 // data buffer
1666 char ctmp[24]; << 1652 char ctmp[12];
1667 1653
1668 // file identifier 1654 // file identifier
1669 char verid[9]; 1655 char verid[9];
1670 ifile.read((char *)verid, 8); 1656 ifile.read((char *)verid, 8);
1671 1657
1672 // file version 1658 // file version
1673 unsigned char ver; 1659 unsigned char ver;
1674 ifile.read((char *)&ver, 1); 1660 ifile.read((char *)&ver, 1);
1675 std::stringstream ss; 1661 std::stringstream ss;
1676 ss << (int)ver; 1662 ss << (int)ver;
1677 kVersion = ss.str(); 1663 kVersion = ss.str();
1678 if(DEBUG || kVerbose > 0) G4cout << "File v << 1664 if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl;
1679 1665
1680 // endian 1666 // endian
1681 ifile.read((char *)&kLittleEndianInput, siz 1667 ifile.read((char *)&kLittleEndianInput, sizeof(char));
1682 if(DEBUG || kVerbose > 0) { 1668 if(DEBUG || kVerbose > 0) {
1683 G4cout << "Endian : "; << 1669 std::cout << "Endian : ";
1684 if(kLittleEndianInput == 1) 1670 if(kLittleEndianInput == 1)
1685 G4cout << " little" << G4endl; << 1671 std::cout << " little" << std::endl;
1686 else { 1672 else {
1687 G4cout << " big" << G4endl; << 1673 std::cout << " big" << std::endl;
1688 } 1674 }
1689 } 1675 }
1690 1676
1691 // comment length (fixed size) 1677 // comment length (fixed size)
1692 int clength; 1678 int clength;
1693 ifile.read((char *)ctmp, 4); 1679 ifile.read((char *)ctmp, 4);
1694 convertEndian(ctmp, clength); 1680 convertEndian(ctmp, clength);
1695 // comment 1681 // comment
1696 char cmt[1025]; 1682 char cmt[1025];
1697 ifile.read((char *)cmt, clength); 1683 ifile.read((char *)cmt, clength);
1698 std::string scmt = cmt; 1684 std::string scmt = cmt;
1699 scmt += '\0'; 1685 scmt += '\0';
1700 setComment(scmt); 1686 setComment(scmt);
1701 if(DEBUG || kVerbose > 0) { 1687 if(DEBUG || kVerbose > 0) {
1702 G4cout << "Data comment : " << 1688 std::cout << "Data comment : "
1703 << kComment << G4endl; << 1689 << kComment << std::endl;
1704 } 1690 }
1705 1691
1706 // voxel spacings for all images 1692 // voxel spacings for all images
1707 ifile.read((char *)ctmp, 12); 1693 ifile.read((char *)ctmp, 12);
1708 convertEndian(ctmp, kVoxelSpacing[0]); 1694 convertEndian(ctmp, kVoxelSpacing[0]);
1709 convertEndian(ctmp+4, kVoxelSpacing[1]); 1695 convertEndian(ctmp+4, kVoxelSpacing[1]);
1710 convertEndian(ctmp+8, kVoxelSpacing[2]); 1696 convertEndian(ctmp+8, kVoxelSpacing[2]);
1711 if(DEBUG || kVerbose > 0) { 1697 if(DEBUG || kVerbose > 0) {
1712 G4cout << "Voxel spacing : (" << 1698 std::cout << "Voxel spacing : ("
1713 << kVoxelSpacing[0] << ", " 1699 << kVoxelSpacing[0] << ", "
1714 << kVoxelSpacing[1] << ", " 1700 << kVoxelSpacing[1] << ", "
1715 << kVoxelSpacing[2] 1701 << kVoxelSpacing[2]
1716 << ") mm " << G4endl; << 1702 << ") mm " << std::endl;
1717 } 1703 }
1718 1704
1719 1705
1720 // offset from file starting point to the m 1706 // offset from file starting point to the modality image data
1721 ifile.read((char *)ctmp, 4); 1707 ifile.read((char *)ctmp, 4);
1722 convertEndian(ctmp, kPointerToModalityData) 1708 convertEndian(ctmp, kPointerToModalityData);
1723 1709
1724 // # of dose distributions 1710 // # of dose distributions
1725 ifile.read((char *)ctmp, 4); 1711 ifile.read((char *)ctmp, 4);
1726 int nDoseDist; 1712 int nDoseDist;
1727 convertEndian(ctmp, nDoseDist); 1713 convertEndian(ctmp, nDoseDist);
1728 1714
1729 // offset from file starting point to the d 1715 // offset from file starting point to the dose image data
1730 for(int i = 0; i < nDoseDist; i++) { 1716 for(int i = 0; i < nDoseDist; i++) {
1731 ifile.read((char *)ctmp, 4); 1717 ifile.read((char *)ctmp, 4);
1732 unsigned int dptr; 1718 unsigned int dptr;
1733 convertEndian(ctmp, dptr); 1719 convertEndian(ctmp, dptr);
1734 addPointerToDoseDistData(dptr); 1720 addPointerToDoseDistData(dptr);
1735 } 1721 }
1736 1722
1737 // offset from file starting point to the R 1723 // offset from file starting point to the ROI image data
1738 ifile.read((char *)ctmp, 4); 1724 ifile.read((char *)ctmp, 4);
1739 convertEndian(ctmp, kPointerToROIData); 1725 convertEndian(ctmp, kPointerToROIData);
1740 1726
1741 // offset from file starting point to the t 1727 // offset from file starting point to the track data
1742 ifile.read((char *)ctmp, 4); 1728 ifile.read((char *)ctmp, 4);
1743 convertEndian(ctmp, kPointerToTrackData); 1729 convertEndian(ctmp, kPointerToTrackData);
1744 1730
1745 // offset from file starting point to the d 1731 // offset from file starting point to the detector data
1746 ifile.read((char *)ctmp, 4); 1732 ifile.read((char *)ctmp, 4);
1747 convertEndian(ctmp, kPointerToDetectorData) 1733 convertEndian(ctmp, kPointerToDetectorData);
1748 1734
1749 if(DEBUG || kVerbose > 0) { 1735 if(DEBUG || kVerbose > 0) {
1750 G4cout << "Each pointer to data : " << 1736 std::cout << "Each pointer to data : "
1751 << kPointerToModalityData << ", "; 1737 << kPointerToModalityData << ", ";
1752 for(int i = 0; i < nDoseDist; i++) 1738 for(int i = 0; i < nDoseDist; i++)
1753 G4cout << kPointerToDoseDistData[i] << << 1739 std::cout << kPointerToDoseDistData[i] << ", ";
1754 G4cout << kPointerToROIData << ", " << 1740 std::cout << kPointerToROIData << ", "
1755 << kPointerToTrackData << ", " 1741 << kPointerToTrackData << ", "
1756 << kPointerToDetectorData 1742 << kPointerToDetectorData
1757 << G4endl; << 1743 << std::endl;
1758 } 1744 }
1759 1745
1760 1746
1761 1747
1762 if(kPointerToModalityData == 0 && kPointerT 1748 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
1763 kPointerToROIData == 0 && kPointerToTrac 1749 kPointerToROIData == 0 && kPointerToTrackData == 0) {
1764 if(DEBUG || kVerbose > 0) { 1750 if(DEBUG || kVerbose > 0) {
1765 G4cout << "No data." << G4endl; << 1751 std::cout << "No data." << std::endl;
1766 } 1752 }
1767 return false; 1753 return false;
1768 } 1754 }
1769 1755
1770 // event number 1756 // event number
1771 /* ver 1 1757 /* ver 1
1772 ifile.read(ctmp, sizeof(int)); 1758 ifile.read(ctmp, sizeof(int));
1773 convertEndian(ctmp, numberOfEvents); 1759 convertEndian(ctmp, numberOfEvents);
1774 */ 1760 */
1775 1761
1776 int size[3]; 1762 int size[3];
1777 float scale; 1763 float scale;
1778 double dscale; 1764 double dscale;
1779 short minmax[2]; 1765 short minmax[2];
1780 float fCenter[3]; 1766 float fCenter[3];
1781 int iCenter[3]; 1767 int iCenter[3];
1782 1768
1783 //----- Modality image -----// 1769 //----- Modality image -----//
1784 // modality image size 1770 // modality image size
1785 ifile.read(ctmp, 3*sizeof(int)); 1771 ifile.read(ctmp, 3*sizeof(int));
1786 convertEndian(ctmp, size[0]); 1772 convertEndian(ctmp, size[0]);
1787 convertEndian(ctmp+sizeof(int), size[1]); 1773 convertEndian(ctmp+sizeof(int), size[1]);
1788 convertEndian(ctmp+2*sizeof(int), size[2]); 1774 convertEndian(ctmp+2*sizeof(int), size[2]);
1789 if(DEBUG || kVerbose > 0) { 1775 if(DEBUG || kVerbose > 0) {
1790 G4cout << "Modality image size : (" << 1776 std::cout << "Modality image size : ("
1791 << size[0] << ", " 1777 << size[0] << ", "
1792 << size[1] << ", " 1778 << size[1] << ", "
1793 << size[2] << ")" 1779 << size[2] << ")"
1794 << G4endl; << 1780 << std::endl;
1795 } 1781 }
1796 kModality.setSize(size); 1782 kModality.setSize(size);
1797 1783
1798 // modality image voxel spacing 1784 // modality image voxel spacing
1799 /* 1785 /*
1800 ifile.read(ctmp, 3*sizeof(float)); 1786 ifile.read(ctmp, 3*sizeof(float));
1801 convertEndian(ctmp, modalityImageVoxelSpa 1787 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
1802 convertEndian(ctmp+sizeof(float), modalit 1788 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
1803 convertEndian(ctmp+2*sizeof(float), modal 1789 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
1804 */ 1790 */
1805 1791
1806 if(kPointerToModalityData != 0) { 1792 if(kPointerToModalityData != 0) {
1807 1793
1808 // modality density max. & min. 1794 // modality density max. & min.
1809 ifile.read((char *)ctmp, 4); 1795 ifile.read((char *)ctmp, 4);
1810 convertEndian(ctmp, minmax[0]); 1796 convertEndian(ctmp, minmax[0]);
1811 convertEndian(ctmp+2, minmax[1]); 1797 convertEndian(ctmp+2, minmax[1]);
1812 kModality.setMinMax(minmax); 1798 kModality.setMinMax(minmax);
1813 1799
1814 // modality image unit 1800 // modality image unit
1815 char munit[13]; 1801 char munit[13];
1816 munit[12] = '\0'; 1802 munit[12] = '\0';
1817 ifile.read((char *)munit, 12); 1803 ifile.read((char *)munit, 12);
1818 std::string smunit = munit; 1804 std::string smunit = munit;
1819 setModalityImageUnit(smunit); 1805 setModalityImageUnit(smunit);
1820 1806
1821 // modality density scale 1807 // modality density scale
1822 ifile.read((char *)ctmp, 4); 1808 ifile.read((char *)ctmp, 4);
1823 convertEndian(ctmp, scale); 1809 convertEndian(ctmp, scale);
1824 kModality.setScale(dscale = scale); 1810 kModality.setScale(dscale = scale);
1825 if(DEBUG || kVerbose > 0) { 1811 if(DEBUG || kVerbose > 0) {
1826 G4cout << "Modality image min., max., s << 1812 std::cout << "Modality image min., max., scale : "
1827 << minmax[0] << ", " 1813 << minmax[0] << ", "
1828 << minmax[1] << ", " 1814 << minmax[1] << ", "
1829 << scale << G4endl; << 1815 << scale << std::endl;
1830 } 1816 }
1831 1817
1832 // modality density 1818 // modality density
1833 int psize = size[0]*size[1]; 1819 int psize = size[0]*size[1];
1834 if(DEBUG || kVerbose > 0) G4cout << "Moda << 1820 if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): ";
1835 char * cimage = new char[psize*sizeof(sho 1821 char * cimage = new char[psize*sizeof(short)];
1836 for(int i = 0; i < size[2]; i++) { 1822 for(int i = 0; i < size[2]; i++) {
1837 ifile.read((char *)cimage, psize*sizeof 1823 ifile.read((char *)cimage, psize*sizeof(short));
1838 short * mimage = new short[psize]; 1824 short * mimage = new short[psize];
1839 for(int j = 0; j < psize; j++) { 1825 for(int j = 0; j < psize; j++) {
1840 convertEndian(cimage+j*sizeof(short), mimag 1826 convertEndian(cimage+j*sizeof(short), mimage[j]);
1841 } 1827 }
1842 kModality.addImage(mimage); 1828 kModality.addImage(mimage);
1843 1829
1844 if(DEBUG || kVerbose > 0) G4cout << "[" << 1830 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
1845 } 1831 }
1846 if(DEBUG || kVerbose > 0) G4cout << G4end << 1832 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1847 delete [] cimage; 1833 delete [] cimage;
1848 1834
1849 // modality desity map for CT value 1835 // modality desity map for CT value
1850 size_t msize = minmax[1]-minmax[0]+1; 1836 size_t msize = minmax[1]-minmax[0]+1;
1851 if(DEBUG || kVerbose > 0) G4cout << "msiz << 1837 if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl;
1852 char * pdmap = new char[msize*sizeof(floa 1838 char * pdmap = new char[msize*sizeof(float)];
1853 ifile.read((char *)pdmap, msize*sizeof(fl 1839 ifile.read((char *)pdmap, msize*sizeof(float));
1854 float ftmp; 1840 float ftmp;
1855 for(int i = 0; i < (int)msize; i++) { 1841 for(int i = 0; i < (int)msize; i++) {
1856 convertEndian(pdmap+i*sizeof(float), ft 1842 convertEndian(pdmap+i*sizeof(float), ftmp);
1857 kModalityImageDensityMap.push_back(ftmp 1843 kModalityImageDensityMap.push_back(ftmp);
1858 } 1844 }
1859 delete [] pdmap; <<
1860 <<
1861 if(DEBUG || kVerbose > 0) { 1845 if(DEBUG || kVerbose > 0) {
1862 G4cout << "density map : " << std::ends << 1846 std::cout << "density map : " << std::ends;
1863 for(int i = 0; i < 10; i++) 1847 for(int i = 0; i < 10; i++)
1864 G4cout <<kModalityImageDensityMap[i] << ", << 1848 std::cout <<kModalityImageDensityMap[i] << ", ";
1865 G4cout << G4endl; << 1849 std::cout << std::endl;
1866 for(int i = 0; i < 10; i++) G4cout << " << 1850 for(int i = 0; i < 10; i++) std::cout << "..";
1867 G4cout << G4endl; << 1851 std::cout << std::endl;
1868 for(size_t i =kModalityImageDensityMap. 1852 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
1869 G4cout <<kModalityImageDensityMap[i] << ", << 1853 std::cout <<kModalityImageDensityMap[i] << ", ";
1870 G4cout << G4endl; << 1854 std::cout << std::endl;
1871 } 1855 }
1872 1856
1873 } 1857 }
1874 1858
1875 1859
1876 //----- dose distribution image -----// 1860 //----- dose distribution image -----//
1877 for(int ndose = 0; ndose < nDoseDist; ndose 1861 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1878 1862
1879 newDoseDist(); 1863 newDoseDist();
1880 1864
1881 // dose distrbution image size 1865 // dose distrbution image size
1882 ifile.read((char *)ctmp, 3*sizeof(int)); 1866 ifile.read((char *)ctmp, 3*sizeof(int));
1883 convertEndian(ctmp, size[0]); 1867 convertEndian(ctmp, size[0]);
1884 convertEndian(ctmp+sizeof(int), size[1]); 1868 convertEndian(ctmp+sizeof(int), size[1]);
1885 convertEndian(ctmp+2*sizeof(int), size[2] 1869 convertEndian(ctmp+2*sizeof(int), size[2]);
1886 if(DEBUG || kVerbose > 0) { 1870 if(DEBUG || kVerbose > 0) {
1887 G4cout << "Dose dist. image size : (" << 1871 std::cout << "Dose dist. image size : ("
1888 << size[0] << ", " 1872 << size[0] << ", "
1889 << size[1] << ", " 1873 << size[1] << ", "
1890 << size[2] << ")" 1874 << size[2] << ")"
1891 << G4endl; << 1875 << std::endl;
1892 } 1876 }
1893 kDose[ndose].setSize(size); 1877 kDose[ndose].setSize(size);
1894 1878
1895 // dose distribution max. & min. 1879 // dose distribution max. & min.
1896 ifile.read((char *)ctmp, sizeof(short)*2) 1880 ifile.read((char *)ctmp, sizeof(short)*2);
1897 convertEndian(ctmp, minmax[0]); 1881 convertEndian(ctmp, minmax[0]);
1898 convertEndian(ctmp+2, minmax[1]); 1882 convertEndian(ctmp+2, minmax[1]);
1899 1883
1900 // dose distribution unit 1884 // dose distribution unit
1901 char dunit[13]; 1885 char dunit[13];
1902 dunit[12] = '\0'; 1886 dunit[12] = '\0';
1903 ifile.read((char *)dunit, 12); 1887 ifile.read((char *)dunit, 12);
1904 std::string sdunit = dunit; 1888 std::string sdunit = dunit;
1905 setDoseDistUnit(sdunit, ndose); 1889 setDoseDistUnit(sdunit, ndose);
1906 if(DEBUG || kVerbose > 0) { 1890 if(DEBUG || kVerbose > 0) {
1907 G4cout << "Dose dist. unit : " << kDose << 1891 std::cout << "Dose dist. unit : " << kDoseUnit << std::endl;
1908 } 1892 }
1909 1893
1910 // dose distribution scaling 1894 // dose distribution scaling
1911 ifile.read((char *)ctmp, 4); // sizeof(fl 1895 ifile.read((char *)ctmp, 4); // sizeof(float)
1912 convertEndian(ctmp, scale); 1896 convertEndian(ctmp, scale);
1913 kDose[ndose].setScale(dscale = scale); 1897 kDose[ndose].setScale(dscale = scale);
1914 1898
1915 double dminmax[2]; 1899 double dminmax[2];
1916 for(int i = 0; i < 2; i++) dminmax[i] = m 1900 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
1917 kDose[ndose].setMinMax(dminmax); 1901 kDose[ndose].setMinMax(dminmax);
1918 1902
1919 if(DEBUG || kVerbose > 0) { 1903 if(DEBUG || kVerbose > 0) {
1920 G4cout << "Dose dist. image min., max., << 1904 std::cout << "Dose dist. image min., max., scale : "
1921 << dminmax[0] << ", " 1905 << dminmax[0] << ", "
1922 << dminmax[1] << ", " 1906 << dminmax[1] << ", "
1923 << scale << G4endl; << 1907 << scale << std::endl;
1924 } 1908 }
1925 1909
1926 // dose distribution image 1910 // dose distribution image
1927 int dsize = size[0]*size[1]; 1911 int dsize = size[0]*size[1];
1928 if(DEBUG || kVerbose > 0) G4cout << "Dose << 1912 if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): ";
1929 char * di = new char[dsize*sizeof(short)] 1913 char * di = new char[dsize*sizeof(short)];
1930 short * shimage = new short[dsize]; 1914 short * shimage = new short[dsize];
1931 for(int z = 0; z < size[2]; z++) { 1915 for(int z = 0; z < size[2]; z++) {
1932 ifile.read((char *)di, dsize*sizeof(sho 1916 ifile.read((char *)di, dsize*sizeof(short));
1933 double * dimage = new double[dsize]; 1917 double * dimage = new double[dsize];
1934 for(int xy = 0; xy < dsize; xy++) { 1918 for(int xy = 0; xy < dsize; xy++) {
1935 convertEndian(di+xy*sizeof(short), shimage[ 1919 convertEndian(di+xy*sizeof(short), shimage[xy]);
1936 dimage[xy] = shimage[xy]*dscale; 1920 dimage[xy] = shimage[xy]*dscale;
1937 } 1921 }
1938 kDose[ndose].addImage(dimage); 1922 kDose[ndose].addImage(dimage);
1939 1923
1940 if(DEBUG || kVerbose > 0) G4cout << "[" << 1924 if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
1941 1925
1942 if(DEBUG || kVerbose > 0) { 1926 if(DEBUG || kVerbose > 0) {
1943 for(int j = 0; j < dsize; j++) { 1927 for(int j = 0; j < dsize; j++) {
1944 if(dimage[j] < 0) 1928 if(dimage[j] < 0)
1945 G4cout << "[" << j << "," << z << "]" << 1929 std::cout << "[" << j << "," << z << "]"
1946 << dimage[j] << ", "; 1930 << dimage[j] << ", ";
1947 } 1931 }
1948 } 1932 }
1949 } 1933 }
1950 delete [] shimage; 1934 delete [] shimage;
1951 delete [] di; 1935 delete [] di;
1952 if(DEBUG || kVerbose > 0) G4cout << G4end << 1936 if(DEBUG || kVerbose > 0) std::cout << std::endl;
1953 1937
1954 ifile.read((char *)ctmp, 3*4); // 3*sizeo 1938 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
1955 convertEndian(ctmp, iCenter[0]); 1939 convertEndian(ctmp, iCenter[0]);
1956 convertEndian(ctmp+4, iCenter[1]); 1940 convertEndian(ctmp+4, iCenter[1]);
1957 convertEndian(ctmp+8, iCenter[2]); 1941 convertEndian(ctmp+8, iCenter[2]);
1958 for(int i = 0; i < 3; i++) fCenter[i] = ( 1942 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
1959 kDose[ndose].setCenterPosition(fCenter); 1943 kDose[ndose].setCenterPosition(fCenter);
1960 1944
1961 if(DEBUG || kVerbose > 0) { 1945 if(DEBUG || kVerbose > 0) {
1962 G4cout << "Dose dist. image relative lo << 1946 std::cout << "Dose dist. image relative location : ("
1963 << fCenter[0] << ", " 1947 << fCenter[0] << ", "
1964 << fCenter[1] << ", " 1948 << fCenter[1] << ", "
1965 << fCenter[2] << ")" << G4endl; << 1949 << fCenter[2] << ")" << std::endl;
1966 } 1950 }
1967 1951
1968 1952
1969 // dose distribution name 1953 // dose distribution name
1970 char cname[81]; 1954 char cname[81];
1971 ifile.read((char *)cname, 80); 1955 ifile.read((char *)cname, 80);
1972 std::string dosename = cname; 1956 std::string dosename = cname;
1973 setDoseDistName(dosename, ndose); 1957 setDoseDistName(dosename, ndose);
1974 if(DEBUG || kVerbose > 0) { 1958 if(DEBUG || kVerbose > 0) {
1975 G4cout << "Dose dist. name : " << dosen << 1959 std::cout << "Dose dist. name : " << dosename << std::endl;
1976 } 1960 }
1977 1961
1978 } 1962 }
1979 1963
1980 //----- ROI image -----// 1964 //----- ROI image -----//
1981 if(kPointerToROIData != 0) { 1965 if(kPointerToROIData != 0) {
1982 1966
1983 newROI(); 1967 newROI();
1984 1968
1985 // ROI image size 1969 // ROI image size
1986 ifile.read((char *)ctmp, 3*sizeof(int)); 1970 ifile.read((char *)ctmp, 3*sizeof(int));
1987 convertEndian(ctmp, size[0]); 1971 convertEndian(ctmp, size[0]);
1988 convertEndian(ctmp+sizeof(int), size[1]); 1972 convertEndian(ctmp+sizeof(int), size[1]);
1989 convertEndian(ctmp+2*sizeof(int), size[2] 1973 convertEndian(ctmp+2*sizeof(int), size[2]);
1990 kRoi[0].setSize(size); 1974 kRoi[0].setSize(size);
1991 if(DEBUG || kVerbose > 0) { 1975 if(DEBUG || kVerbose > 0) {
1992 G4cout << "ROI image size : (" << 1976 std::cout << "ROI image size : ("
1993 << size[0] << ", " 1977 << size[0] << ", "
1994 << size[1] << ", " 1978 << size[1] << ", "
1995 << size[2] << ")" 1979 << size[2] << ")"
1996 << G4endl; << 1980 << std::endl;
1997 } 1981 }
1998 1982
1999 // ROI max. & min. 1983 // ROI max. & min.
2000 ifile.read((char *)ctmp, sizeof(short)*2) 1984 ifile.read((char *)ctmp, sizeof(short)*2);
2001 convertEndian(ctmp, minmax[0]); 1985 convertEndian(ctmp, minmax[0]);
2002 convertEndian(ctmp+sizeof(short), minmax[ 1986 convertEndian(ctmp+sizeof(short), minmax[1]);
2003 kRoi[0].setMinMax(minmax); 1987 kRoi[0].setMinMax(minmax);
2004 1988
2005 // ROI distribution scaling 1989 // ROI distribution scaling
2006 ifile.read((char *)ctmp, sizeof(float)); 1990 ifile.read((char *)ctmp, sizeof(float));
2007 convertEndian(ctmp, scale); 1991 convertEndian(ctmp, scale);
2008 kRoi[0].setScale(dscale = scale); 1992 kRoi[0].setScale(dscale = scale);
2009 if(DEBUG || kVerbose > 0) { 1993 if(DEBUG || kVerbose > 0) {
2010 G4cout << "ROI image min., max., scale << 1994 std::cout << "ROI image min., max., scale : "
2011 << minmax[0] << ", " 1995 << minmax[0] << ", "
2012 << minmax[1] << ", " 1996 << minmax[1] << ", "
2013 << scale << G4endl; << 1997 << scale << std::endl;
2014 } 1998 }
2015 1999
2016 // ROI image 2000 // ROI image
2017 int rsize = size[0]*size[1]; 2001 int rsize = size[0]*size[1];
2018 char * ri = new char[rsize*sizeof(short)] 2002 char * ri = new char[rsize*sizeof(short)];
2019 for(int i = 0; i < size[2]; i++) { 2003 for(int i = 0; i < size[2]; i++) {
2020 ifile.read((char *)ri, rsize*sizeof(sho 2004 ifile.read((char *)ri, rsize*sizeof(short));
2021 short * rimage = new short[rsize]; 2005 short * rimage = new short[rsize];
2022 for(int j = 0; j < rsize; j++) { 2006 for(int j = 0; j < rsize; j++) {
2023 convertEndian(ri+j*sizeof(short), rimage[j] 2007 convertEndian(ri+j*sizeof(short), rimage[j]);
2024 } 2008 }
2025 kRoi[0].addImage(rimage); 2009 kRoi[0].addImage(rimage);
2026 2010
2027 } 2011 }
2028 delete [] ri; 2012 delete [] ri;
2029 2013
2030 // ROI relative location 2014 // ROI relative location
2031 ifile.read((char *)ctmp, 3*sizeof(int)); 2015 ifile.read((char *)ctmp, 3*sizeof(int));
2032 convertEndian(ctmp, iCenter[0]); 2016 convertEndian(ctmp, iCenter[0]);
2033 convertEndian(ctmp+sizeof(int), iCenter[1 2017 convertEndian(ctmp+sizeof(int), iCenter[1]);
2034 convertEndian(ctmp+2*sizeof(int), iCenter 2018 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2035 for(int i = 0; i < 3; i++) fCenter[i] = i 2019 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2036 kRoi[0].setCenterPosition(fCenter); 2020 kRoi[0].setCenterPosition(fCenter);
2037 if(DEBUG || kVerbose > 0) { 2021 if(DEBUG || kVerbose > 0) {
2038 G4cout << "ROI image relative location << 2022 std::cout << "ROI image relative location : ("
2039 << fCenter[0] << ", " 2023 << fCenter[0] << ", "
2040 << fCenter[1] << ", " 2024 << fCenter[1] << ", "
2041 << fCenter[2] << ")" << G4endl; << 2025 << fCenter[2] << ")" << std::endl;
2042 } 2026 }
2043 2027
2044 } 2028 }
2045 2029
2046 //----- track information -----// 2030 //----- track information -----//
2047 if(kPointerToTrackData != 0) { 2031 if(kPointerToTrackData != 0) {
2048 2032
2049 // track 2033 // track
2050 ifile.read((char *)ctmp, sizeof(int)); 2034 ifile.read((char *)ctmp, sizeof(int));
2051 int ntrk; 2035 int ntrk;
2052 convertEndian(ctmp, ntrk); 2036 convertEndian(ctmp, ntrk);
2053 if(DEBUG || kVerbose > 0) { 2037 if(DEBUG || kVerbose > 0) {
2054 G4cout << "# of tracks: " << ntrk << G4 << 2038 std::cout << "# of tracks: " << ntrk << std::endl;
2055 } 2039 }
2056 2040
2057 // track position 2041 // track position
2058 unsigned char rgb[3]; 2042 unsigned char rgb[3];
2059 for(int i = 0; i < ntrk; i++) { 2043 for(int i = 0; i < ntrk; i++) {
2060 2044
2061 2045
2062 // # of steps in a track 2046 // # of steps in a track
2063 ifile.read((char *)ctmp, sizeof(int)); 2047 ifile.read((char *)ctmp, sizeof(int));
2064 int nsteps; 2048 int nsteps;
2065 convertEndian(ctmp, nsteps); 2049 convertEndian(ctmp, nsteps);
2066 2050
2067 // track color 2051 // track color
2068 ifile.read((char *)rgb, 3); 2052 ifile.read((char *)rgb, 3);
2069 2053
2070 std::vector<float *> steps; 2054 std::vector<float *> steps;
2071 // steps 2055 // steps
2072 for(int j = 0; j < nsteps; j++) { 2056 for(int j = 0; j < nsteps; j++) {
2073 2057
2074 float * steppoint = new float[6]; 2058 float * steppoint = new float[6];
2075 ifile.read((char *)ctmp, sizeof(float)*6); 2059 ifile.read((char *)ctmp, sizeof(float)*6);
2076 2060
2077 for(int k = 0; k < 6; k++) { 2061 for(int k = 0; k < 6; k++) {
2078 convertEndian(ctmp+k*sizeof(float), stepp 2062 convertEndian(ctmp+k*sizeof(float), steppoint[k]);
2079 } 2063 }
2080 2064
2081 steps.push_back(steppoint); 2065 steps.push_back(steppoint);
2082 } 2066 }
2083 2067
2084 // add a track to the track container 2068 // add a track to the track container
2085 addTrack(steps, rgb); 2069 addTrack(steps, rgb);
2086 2070
2087 if(DEBUG || kVerbose > 0) { 2071 if(DEBUG || kVerbose > 0) {
2088 if(i < 5) { 2072 if(i < 5) {
2089 G4cout << i << ": " ; << 2073 std::cout << i << ": " ;
2090 for(int j = 0; j < 3; j++) G4cout << step << 2074 for(int j = 0; j < 3; j++) std::cout << steps[0][j] << " ";
2091 int nstp = (int)steps.size(); << 2075 int nstp = steps.size();
2092 G4cout << "<-> "; << 2076 std::cout << "<-> ";
2093 for(int j = 3; j < 6; j++) G4cout << step << 2077 for(int j = 3; j < 6; j++) std::cout << steps[nstp-1][j] << " ";
2094 G4cout << " rgb( "; << 2078 std::cout << " rgb( ";
2095 for(int j = 0; j < 3; j++) G4cout << (int << 2079 for(int j = 0; j < 3; j++) std::cout << (int)rgb[j] << " ";
2096 G4cout << ")" << G4endl; << 2080 std::cout << ")" << std::endl;
2097 } 2081 }
2098 } 2082 }
2099 } 2083 }
2100 2084
2101 2085
2102 } 2086 }
2103 2087
2104 2088
2105 //----- detector information -----// 2089 //----- detector information -----//
2106 if(kPointerToDetectorData != 0) { 2090 if(kPointerToDetectorData != 0) {
2107 2091
2108 // number of detectors 2092 // number of detectors
2109 ifile.read((char *)ctmp, sizeof(int)); 2093 ifile.read((char *)ctmp, sizeof(int));
2110 int ndet; 2094 int ndet;
2111 convertEndian(ctmp, ndet); 2095 convertEndian(ctmp, ndet);
2112 2096
2113 if(DEBUG || kVerbose > 0) { 2097 if(DEBUG || kVerbose > 0) {
2114 G4cout << "# of detectors : " << 2098 std::cout << "# of detectors : "
2115 << ndet << G4endl; << 2099 << ndet << std::endl;
2116 } 2100 }
2117 2101
2118 for(int nd = 0; nd < ndet; nd++) { 2102 for(int nd = 0; nd < ndet; nd++) {
2119 2103
2120 // # of edges of a detector 2104 // # of edges of a detector
2121 ifile.read((char *)ctmp, sizeof(int)); 2105 ifile.read((char *)ctmp, sizeof(int));
2122 int nedges; 2106 int nedges;
2123 convertEndian(ctmp, nedges); 2107 convertEndian(ctmp, nedges);
2124 if(DEBUG || kVerbose > 0) { 2108 if(DEBUG || kVerbose > 0) {
2125 G4cout << "# of edges in a detector : " << << 2109 std::cout << "# of edges in a detector : " << nedges << std::endl;
2126 } 2110 }
2127 2111
2128 // edges 2112 // edges
2129 std::vector<float *> detector; 2113 std::vector<float *> detector;
2130 char cftmp[24]; 2114 char cftmp[24];
2131 for(int ne = 0; ne < nedges; ne++) { 2115 for(int ne = 0; ne < nedges; ne++) {
2132 2116
2133 ifile.read((char *)cftmp, sizeof(float)*6); 2117 ifile.read((char *)cftmp, sizeof(float)*6);
2134 float * edgePoints = new float[6]; 2118 float * edgePoints = new float[6];
2135 for(int j = 0; j < 6; j++) convertEndian(&c 2119 for(int j = 0; j < 6; j++) convertEndian(&cftmp[sizeof(float)*j], edgePoints[j]);
2136 detector.push_back(edgePoints); 2120 detector.push_back(edgePoints);
2137 2121
2138 } 2122 }
2139 2123
2140 if(DEBUG || kVerbose > 0) { 2124 if(DEBUG || kVerbose > 0) {
2141 G4cout << " first edge : (" << detector[0][ << 2125 std::cout << " first edge : (" << detector[0][0] << ", "
2142 << detector[0][1] << ", " 2126 << detector[0][1] << ", "
2143 << detector[0][2] << ") - (" 2127 << detector[0][2] << ") - ("
2144 << detector[0][3] << ", " 2128 << detector[0][3] << ", "
2145 << detector[0][4] << ", " 2129 << detector[0][4] << ", "
2146 << detector[0][5] << ")" << G4endl; << 2130 << detector[0][5] << ")" << std::endl;
2147 } 2131 }
2148 2132
2149 // detector color 2133 // detector color
2150 unsigned char dcolor[3]; 2134 unsigned char dcolor[3];
2151 ifile.read((char *)dcolor, 3); 2135 ifile.read((char *)dcolor, 3);
2152 if(DEBUG || kVerbose > 0) { 2136 if(DEBUG || kVerbose > 0) {
2153 G4cout << " detector color : rgb(" << 2137 std::cout << " detector color : rgb("
2154 << (int)dcolor[0] << ", " 2138 << (int)dcolor[0] << ", "
2155 << (int)dcolor[1] << ", " 2139 << (int)dcolor[1] << ", "
2156 << (int)dcolor[2] << G4endl; << 2140 << (int)dcolor[2] << std::endl;
2157 } 2141 }
2158 2142
2159 2143
2160 // detector name 2144 // detector name
2161 char cname[80]; 2145 char cname[80];
2162 ifile.read((char *)cname, 80); 2146 ifile.read((char *)cname, 80);
2163 std::string dname = cname; 2147 std::string dname = cname;
2164 if(DEBUG || kVerbose > 0) { 2148 if(DEBUG || kVerbose > 0) {
2165 G4cout << " detector name : " << dname << G << 2149 std::cout << " detector name : " << dname << std::endl;
2166 } 2150 }
2167 2151
2168 2152
2169 addDetector(dname, detector, dcolor); 2153 addDetector(dname, detector, dcolor);
2170 2154
2171 } 2155 }
2172 } 2156 }
2173 2157
2174 2158
2175 ifile.close(); 2159 ifile.close();
2176 2160
2177 return true; 2161 return true;
2178 } 2162 }
2179 bool G4GMocrenIO::retrieveData4(char * _filen 2163 bool G4GMocrenIO::retrieveData4(char * _filename) {
2180 kFileName = _filename; 2164 kFileName = _filename;
2181 return retrieveData(); 2165 return retrieveData();
2182 } 2166 }
2183 2167
2184 // 2168 //
2185 bool G4GMocrenIO::retrieveData3() { 2169 bool G4GMocrenIO::retrieveData3() {
2186 2170
2187 bool DEBUG = false;// 2171 bool DEBUG = false;//
2188 2172
2189 // input file open 2173 // input file open
2190 std::ifstream ifile(kFileName.c_str(), std: 2174 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2191 if(!ifile) { 2175 if(!ifile) {
2192 if (G4VisManager::GetVerbosity() >= G4Vis << 2176 std::cerr << "Cannot open file: " << kFileName
2193 G4cout << "Cannot open file: " << kFile << 2177 << " in G4GMocrenIO::retrieveData3()." << std::endl;
2194 << " in G4GMocrenIO::retrieveData3()." << <<
2195 return false; 2178 return false;
2196 } 2179 }
2197 2180
2198 // data buffer 2181 // data buffer
2199 char ctmp[12]; 2182 char ctmp[12];
2200 2183
2201 // file identifier 2184 // file identifier
2202 char verid[9]; 2185 char verid[9];
2203 ifile.read((char *)verid, 8); 2186 ifile.read((char *)verid, 8);
2204 2187
2205 // file version 2188 // file version
2206 unsigned char ver; 2189 unsigned char ver;
2207 ifile.read((char *)&ver, 1); 2190 ifile.read((char *)&ver, 1);
2208 std::stringstream ss; 2191 std::stringstream ss;
2209 ss << (int)ver; 2192 ss << (int)ver;
2210 kVersion = ss.str(); 2193 kVersion = ss.str();
2211 if(DEBUG || kVerbose > 0) G4cout << "File v << 2194 if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl;
2212 2195
2213 // endian 2196 // endian
2214 ifile.read((char *)&kLittleEndianInput, siz 2197 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2215 if(DEBUG || kVerbose > 0) { 2198 if(DEBUG || kVerbose > 0) {
2216 G4cout << "Endian : "; << 2199 std::cout << "Endian : ";
2217 if(kLittleEndianInput == 1) 2200 if(kLittleEndianInput == 1)
2218 G4cout << " little" << G4endl; << 2201 std::cout << " little" << std::endl;
2219 else { 2202 else {
2220 G4cout << " big" << G4endl; << 2203 std::cout << " big" << std::endl;
2221 } 2204 }
2222 } 2205 }
2223 2206
2224 // comment length (fixed size) 2207 // comment length (fixed size)
2225 int clength; 2208 int clength;
2226 ifile.read((char *)ctmp, 4); 2209 ifile.read((char *)ctmp, 4);
2227 convertEndian(ctmp, clength); 2210 convertEndian(ctmp, clength);
2228 // comment 2211 // comment
2229 char cmt[1025]; 2212 char cmt[1025];
2230 ifile.read((char *)cmt, clength); 2213 ifile.read((char *)cmt, clength);
2231 std::string scmt = cmt; 2214 std::string scmt = cmt;
2232 setComment(scmt); 2215 setComment(scmt);
2233 if(DEBUG || kVerbose > 0) { 2216 if(DEBUG || kVerbose > 0) {
2234 G4cout << "Data comment : " << 2217 std::cout << "Data comment : "
2235 << kComment << G4endl; << 2218 << kComment << std::endl;
2236 } 2219 }
2237 2220
2238 // voxel spacings for all images 2221 // voxel spacings for all images
2239 ifile.read((char *)ctmp, 12); 2222 ifile.read((char *)ctmp, 12);
2240 convertEndian(ctmp, kVoxelSpacing[0]); 2223 convertEndian(ctmp, kVoxelSpacing[0]);
2241 convertEndian(ctmp+4, kVoxelSpacing[1]); 2224 convertEndian(ctmp+4, kVoxelSpacing[1]);
2242 convertEndian(ctmp+8, kVoxelSpacing[2]); 2225 convertEndian(ctmp+8, kVoxelSpacing[2]);
2243 if(DEBUG || kVerbose > 0) { 2226 if(DEBUG || kVerbose > 0) {
2244 G4cout << "Voxel spacing : (" << 2227 std::cout << "Voxel spacing : ("
2245 << kVoxelSpacing[0] << ", " 2228 << kVoxelSpacing[0] << ", "
2246 << kVoxelSpacing[1] << ", " 2229 << kVoxelSpacing[1] << ", "
2247 << kVoxelSpacing[2] 2230 << kVoxelSpacing[2]
2248 << ") mm " << G4endl; << 2231 << ") mm " << std::endl;
2249 } 2232 }
2250 2233
2251 2234
2252 // offset from file starting point to the m 2235 // offset from file starting point to the modality image data
2253 ifile.read((char *)ctmp, 4); 2236 ifile.read((char *)ctmp, 4);
2254 convertEndian(ctmp, kPointerToModalityData) 2237 convertEndian(ctmp, kPointerToModalityData);
2255 2238
2256 // # of dose distributions 2239 // # of dose distributions
2257 ifile.read((char *)ctmp, 4); 2240 ifile.read((char *)ctmp, 4);
2258 int nDoseDist; 2241 int nDoseDist;
2259 convertEndian(ctmp, nDoseDist); 2242 convertEndian(ctmp, nDoseDist);
2260 2243
2261 // offset from file starting point to the d 2244 // offset from file starting point to the dose image data
2262 for(int i = 0; i < nDoseDist; i++) { 2245 for(int i = 0; i < nDoseDist; i++) {
2263 ifile.read((char *)ctmp, 4); 2246 ifile.read((char *)ctmp, 4);
2264 unsigned int dptr; 2247 unsigned int dptr;
2265 convertEndian(ctmp, dptr); 2248 convertEndian(ctmp, dptr);
2266 addPointerToDoseDistData(dptr); 2249 addPointerToDoseDistData(dptr);
2267 } 2250 }
2268 2251
2269 // offset from file starting point to the R 2252 // offset from file starting point to the ROI image data
2270 ifile.read((char *)ctmp, 4); 2253 ifile.read((char *)ctmp, 4);
2271 convertEndian(ctmp, kPointerToROIData); 2254 convertEndian(ctmp, kPointerToROIData);
2272 2255
2273 // offset from file starting point to the t 2256 // offset from file starting point to the track data
2274 ifile.read((char *)ctmp, 4); 2257 ifile.read((char *)ctmp, 4);
2275 convertEndian(ctmp, kPointerToTrackData); 2258 convertEndian(ctmp, kPointerToTrackData);
2276 if(DEBUG || kVerbose > 0) { 2259 if(DEBUG || kVerbose > 0) {
2277 G4cout << "Each pointer to data : " << 2260 std::cout << "Each pointer to data : "
2278 << kPointerToModalityData << ", "; 2261 << kPointerToModalityData << ", ";
2279 for(int i = 0; i < nDoseDist; i++) 2262 for(int i = 0; i < nDoseDist; i++)
2280 G4cout << kPointerToDoseDistData[0] << << 2263 std::cout << kPointerToDoseDistData[0] << ", ";
2281 G4cout << kPointerToROIData << ", " << 2264 std::cout << kPointerToROIData << ", "
2282 << kPointerToTrackData << G4endl; << 2265 << kPointerToTrackData << std::endl;
2283 } 2266 }
2284 2267
2285 if(kPointerToModalityData == 0 && kPointerT 2268 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2286 kPointerToROIData == 0 && kPointerToTrac 2269 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2287 if(DEBUG || kVerbose > 0) { 2270 if(DEBUG || kVerbose > 0) {
2288 G4cout << "No data." << G4endl; << 2271 std::cout << "No data." << std::endl;
2289 } 2272 }
2290 return false; 2273 return false;
2291 } 2274 }
2292 2275
2293 // event number 2276 // event number
2294 /* ver 1 2277 /* ver 1
2295 ifile.read(ctmp, sizeof(int)); 2278 ifile.read(ctmp, sizeof(int));
2296 convertEndian(ctmp, numberOfEvents); 2279 convertEndian(ctmp, numberOfEvents);
2297 */ 2280 */
2298 2281
2299 int size[3]; 2282 int size[3];
2300 float scale; 2283 float scale;
2301 double dscale; 2284 double dscale;
2302 short minmax[2]; 2285 short minmax[2];
2303 float fCenter[3]; 2286 float fCenter[3];
2304 int iCenter[3]; 2287 int iCenter[3];
2305 2288
2306 //----- Modality image -----// 2289 //----- Modality image -----//
2307 // modality image size 2290 // modality image size
2308 ifile.read(ctmp, 3*sizeof(int)); 2291 ifile.read(ctmp, 3*sizeof(int));
2309 convertEndian(ctmp, size[0]); 2292 convertEndian(ctmp, size[0]);
2310 convertEndian(ctmp+sizeof(int), size[1]); 2293 convertEndian(ctmp+sizeof(int), size[1]);
2311 convertEndian(ctmp+2*sizeof(int), size[2]); 2294 convertEndian(ctmp+2*sizeof(int), size[2]);
2312 if(DEBUG || kVerbose > 0) { 2295 if(DEBUG || kVerbose > 0) {
2313 G4cout << "Modality image size : (" << 2296 std::cout << "Modality image size : ("
2314 << size[0] << ", " 2297 << size[0] << ", "
2315 << size[1] << ", " 2298 << size[1] << ", "
2316 << size[2] << ")" 2299 << size[2] << ")"
2317 << G4endl; << 2300 << std::endl;
2318 } 2301 }
2319 kModality.setSize(size); 2302 kModality.setSize(size);
2320 2303
2321 // modality image voxel spacing 2304 // modality image voxel spacing
2322 /* 2305 /*
2323 ifile.read(ctmp, 3*sizeof(float)); 2306 ifile.read(ctmp, 3*sizeof(float));
2324 convertEndian(ctmp, modalityImageVoxelSpa 2307 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2325 convertEndian(ctmp+sizeof(float), modalit 2308 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2326 convertEndian(ctmp+2*sizeof(float), modal 2309 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2327 */ 2310 */
2328 2311
2329 if(kPointerToModalityData != 0) { 2312 if(kPointerToModalityData != 0) {
2330 2313
2331 // modality density max. & min. 2314 // modality density max. & min.
2332 ifile.read((char *)ctmp, 4); 2315 ifile.read((char *)ctmp, 4);
2333 convertEndian(ctmp, minmax[0]); 2316 convertEndian(ctmp, minmax[0]);
2334 convertEndian(ctmp+2, minmax[1]); 2317 convertEndian(ctmp+2, minmax[1]);
2335 kModality.setMinMax(minmax); 2318 kModality.setMinMax(minmax);
2336 2319
2337 // modality image unit 2320 // modality image unit
2338 char munit[13]; 2321 char munit[13];
2339 ifile.read((char *)munit, 12); 2322 ifile.read((char *)munit, 12);
2340 std::string smunit = munit; 2323 std::string smunit = munit;
2341 setModalityImageUnit(smunit); 2324 setModalityImageUnit(smunit);
2342 2325
2343 // modality density scale 2326 // modality density scale
2344 ifile.read((char *)ctmp, 4); 2327 ifile.read((char *)ctmp, 4);
2345 convertEndian(ctmp, scale); 2328 convertEndian(ctmp, scale);
2346 kModality.setScale(dscale = scale); 2329 kModality.setScale(dscale = scale);
2347 if(DEBUG || kVerbose > 0) { 2330 if(DEBUG || kVerbose > 0) {
2348 G4cout << "Modality image min., max., s << 2331 std::cout << "Modality image min., max., scale : "
2349 << minmax[0] << ", " 2332 << minmax[0] << ", "
2350 << minmax[1] << ", " 2333 << minmax[1] << ", "
2351 << scale << G4endl; << 2334 << scale << std::endl;
2352 } 2335 }
2353 2336
2354 // modality density 2337 // modality density
2355 int psize = size[0]*size[1]; 2338 int psize = size[0]*size[1];
2356 if(DEBUG || kVerbose > 0) G4cout << "Moda << 2339 if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): ";
2357 char * cimage = new char[psize*sizeof(sho 2340 char * cimage = new char[psize*sizeof(short)];
2358 for(int i = 0; i < size[2]; i++) { 2341 for(int i = 0; i < size[2]; i++) {
2359 ifile.read((char *)cimage, psize*sizeof 2342 ifile.read((char *)cimage, psize*sizeof(short));
2360 short * mimage = new short[psize]; 2343 short * mimage = new short[psize];
2361 for(int j = 0; j < psize; j++) { 2344 for(int j = 0; j < psize; j++) {
2362 convertEndian(cimage+j*sizeof(short), mimag 2345 convertEndian(cimage+j*sizeof(short), mimage[j]);
2363 } 2346 }
2364 kModality.addImage(mimage); 2347 kModality.addImage(mimage);
2365 2348
2366 if(DEBUG || kVerbose > 0) G4cout << "[" << 2349 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2367 } 2350 }
2368 if(DEBUG || kVerbose > 0) G4cout << G4end << 2351 if(DEBUG || kVerbose > 0) std::cout << std::endl;
2369 delete [] cimage; 2352 delete [] cimage;
2370 2353
2371 // modality desity map for CT value 2354 // modality desity map for CT value
2372 size_t msize = minmax[1]-minmax[0]+1; 2355 size_t msize = minmax[1]-minmax[0]+1;
2373 if(DEBUG || kVerbose > 0) G4cout << "msiz << 2356 if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl;
2374 char * pdmap = new char[msize*sizeof(floa 2357 char * pdmap = new char[msize*sizeof(float)];
2375 ifile.read((char *)pdmap, msize*sizeof(fl 2358 ifile.read((char *)pdmap, msize*sizeof(float));
2376 float ftmp; 2359 float ftmp;
2377 for(int i = 0; i < (int)msize; i++) { 2360 for(int i = 0; i < (int)msize; i++) {
2378 convertEndian(pdmap+i*sizeof(float), ft 2361 convertEndian(pdmap+i*sizeof(float), ftmp);
2379 kModalityImageDensityMap.push_back(ftmp 2362 kModalityImageDensityMap.push_back(ftmp);
2380 } 2363 }
2381 delete [] pdmap; <<
2382 if(DEBUG || kVerbose > 0) { 2364 if(DEBUG || kVerbose > 0) {
2383 G4cout << "density map : " << std::ends << 2365 std::cout << "density map : " << std::ends;
2384 for(int i = 0; i < 10; i++) 2366 for(int i = 0; i < 10; i++)
2385 G4cout <<kModalityImageDensityMap[i] << ", << 2367 std::cout <<kModalityImageDensityMap[i] << ", ";
2386 G4cout << G4endl; << 2368 std::cout << std::endl;
2387 for(int i = 0; i < 10; i++) G4cout << " << 2369 for(int i = 0; i < 10; i++) std::cout << "..";
2388 G4cout << G4endl; << 2370 std::cout << std::endl;
2389 for(size_t i =kModalityImageDensityMap. 2371 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2390 G4cout <<kModalityImageDensityMap[i] << ", << 2372 std::cout <<kModalityImageDensityMap[i] << ", ";
2391 G4cout << G4endl; << 2373 std::cout << std::endl;
2392 } 2374 }
2393 2375
2394 } 2376 }
2395 2377
2396 2378
2397 //----- dose distribution image -----// 2379 //----- dose distribution image -----//
2398 for(int ndose = 0; ndose < nDoseDist; ndose 2380 for(int ndose = 0; ndose < nDoseDist; ndose++) {
2399 2381
2400 newDoseDist(); 2382 newDoseDist();
2401 2383
2402 // dose distrbution image size 2384 // dose distrbution image size
2403 ifile.read((char *)ctmp, 3*sizeof(int)); 2385 ifile.read((char *)ctmp, 3*sizeof(int));
2404 convertEndian(ctmp, size[0]); 2386 convertEndian(ctmp, size[0]);
2405 convertEndian(ctmp+sizeof(int), size[1]); 2387 convertEndian(ctmp+sizeof(int), size[1]);
2406 convertEndian(ctmp+2*sizeof(int), size[2] 2388 convertEndian(ctmp+2*sizeof(int), size[2]);
2407 if(DEBUG || kVerbose > 0) { 2389 if(DEBUG || kVerbose > 0) {
2408 G4cout << "Dose dist. image size : (" << 2390 std::cout << "Dose dist. image size : ("
2409 << size[0] << ", " 2391 << size[0] << ", "
2410 << size[1] << ", " 2392 << size[1] << ", "
2411 << size[2] << ")" 2393 << size[2] << ")"
2412 << G4endl; << 2394 << std::endl;
2413 } 2395 }
2414 kDose[ndose].setSize(size); 2396 kDose[ndose].setSize(size);
2415 2397
2416 // dose distribution max. & min. 2398 // dose distribution max. & min.
2417 ifile.read((char *)ctmp, sizeof(short)*2) 2399 ifile.read((char *)ctmp, sizeof(short)*2);
2418 convertEndian(ctmp, minmax[0]); 2400 convertEndian(ctmp, minmax[0]);
2419 convertEndian(ctmp+2, minmax[1]); 2401 convertEndian(ctmp+2, minmax[1]);
2420 2402
2421 // dose distribution unit 2403 // dose distribution unit
2422 char dunit[13]; 2404 char dunit[13];
2423 ifile.read((char *)dunit, 12); 2405 ifile.read((char *)dunit, 12);
2424 std::string sdunit = dunit; 2406 std::string sdunit = dunit;
2425 setDoseDistUnit(sdunit, ndose); 2407 setDoseDistUnit(sdunit, ndose);
2426 if(DEBUG || kVerbose > 0) { 2408 if(DEBUG || kVerbose > 0) {
2427 G4cout << "Dose dist. unit : " << kDose << 2409 std::cout << "Dose dist. unit : " << kDoseUnit << std::endl;
2428 } 2410 }
2429 2411
2430 // dose distribution scaling 2412 // dose distribution scaling
2431 ifile.read((char *)ctmp, 4); // sizeof(fl 2413 ifile.read((char *)ctmp, 4); // sizeof(float)
2432 convertEndian(ctmp, scale); 2414 convertEndian(ctmp, scale);
2433 kDose[ndose].setScale(dscale = scale); 2415 kDose[ndose].setScale(dscale = scale);
2434 2416
2435 double dminmax[2]; 2417 double dminmax[2];
2436 for(int i = 0; i < 2; i++) dminmax[i] = m 2418 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2437 kDose[ndose].setMinMax(dminmax); 2419 kDose[ndose].setMinMax(dminmax);
2438 2420
2439 if(DEBUG || kVerbose > 0) { 2421 if(DEBUG || kVerbose > 0) {
2440 G4cout << "Dose dist. image min., max., << 2422 std::cout << "Dose dist. image min., max., scale : "
2441 << dminmax[0] << ", " 2423 << dminmax[0] << ", "
2442 << dminmax[1] << ", " 2424 << dminmax[1] << ", "
2443 << scale << G4endl; << 2425 << scale << std::endl;
2444 } 2426 }
2445 2427
2446 // dose distribution image 2428 // dose distribution image
2447 int dsize = size[0]*size[1]; 2429 int dsize = size[0]*size[1];
2448 if(DEBUG || kVerbose > 0) G4cout << "Dose << 2430 if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): ";
2449 char * di = new char[dsize*sizeof(short)] 2431 char * di = new char[dsize*sizeof(short)];
2450 short * shimage = new short[dsize]; 2432 short * shimage = new short[dsize];
2451 for(int z = 0; z < size[2]; z++) { 2433 for(int z = 0; z < size[2]; z++) {
2452 ifile.read((char *)di, dsize*sizeof(sho 2434 ifile.read((char *)di, dsize*sizeof(short));
2453 double * dimage = new double[dsize]; 2435 double * dimage = new double[dsize];
2454 for(int xy = 0; xy < dsize; xy++) { 2436 for(int xy = 0; xy < dsize; xy++) {
2455 convertEndian(di+xy*sizeof(short), shimage[ 2437 convertEndian(di+xy*sizeof(short), shimage[xy]);
2456 dimage[xy] = shimage[xy]*dscale; 2438 dimage[xy] = shimage[xy]*dscale;
2457 } 2439 }
2458 kDose[ndose].addImage(dimage); 2440 kDose[ndose].addImage(dimage);
2459 2441
2460 if(DEBUG || kVerbose > 0) G4cout << "[" << 2442 if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2461 2443
2462 if(DEBUG || kVerbose > 0) { 2444 if(DEBUG || kVerbose > 0) {
2463 for(int j = 0; j < dsize; j++) { 2445 for(int j = 0; j < dsize; j++) {
2464 if(dimage[j] < 0) 2446 if(dimage[j] < 0)
2465 G4cout << "[" << j << "," << z << "]" << 2447 std::cout << "[" << j << "," << z << "]"
2466 << dimage[j] << ", "; 2448 << dimage[j] << ", ";
2467 } 2449 }
2468 } 2450 }
2469 } 2451 }
2470 delete [] shimage; 2452 delete [] shimage;
2471 delete [] di; 2453 delete [] di;
2472 if(DEBUG || kVerbose > 0) G4cout << G4end << 2454 if(DEBUG || kVerbose > 0) std::cout << std::endl;
2473 2455
2474 ifile.read((char *)ctmp, 3*4); // 3*sizeo 2456 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
2475 convertEndian(ctmp, iCenter[0]); 2457 convertEndian(ctmp, iCenter[0]);
2476 convertEndian(ctmp+4, iCenter[1]); 2458 convertEndian(ctmp+4, iCenter[1]);
2477 convertEndian(ctmp+8, iCenter[2]); 2459 convertEndian(ctmp+8, iCenter[2]);
2478 for(int i = 0; i < 3; i++) fCenter[i] = ( 2460 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2479 kDose[ndose].setCenterPosition(fCenter); 2461 kDose[ndose].setCenterPosition(fCenter);
2480 2462
2481 if(DEBUG || kVerbose > 0) { 2463 if(DEBUG || kVerbose > 0) {
2482 G4cout << "Dose dist. image relative lo << 2464 std::cout << "Dose dist. image relative location : ("
2483 << fCenter[0] << ", " 2465 << fCenter[0] << ", "
2484 << fCenter[1] << ", " 2466 << fCenter[1] << ", "
2485 << fCenter[2] << ")" << G4endl; << 2467 << fCenter[2] << ")" << std::endl;
2486 } 2468 }
2487 2469
2488 2470
2489 } 2471 }
2490 2472
2491 //----- ROI image -----// 2473 //----- ROI image -----//
2492 if(kPointerToROIData != 0) { 2474 if(kPointerToROIData != 0) {
2493 2475
2494 newROI(); 2476 newROI();
2495 2477
2496 // ROI image size 2478 // ROI image size
2497 ifile.read((char *)ctmp, 3*sizeof(int)); 2479 ifile.read((char *)ctmp, 3*sizeof(int));
2498 convertEndian(ctmp, size[0]); 2480 convertEndian(ctmp, size[0]);
2499 convertEndian(ctmp+sizeof(int), size[1]); 2481 convertEndian(ctmp+sizeof(int), size[1]);
2500 convertEndian(ctmp+2*sizeof(int), size[2] 2482 convertEndian(ctmp+2*sizeof(int), size[2]);
2501 kRoi[0].setSize(size); 2483 kRoi[0].setSize(size);
2502 if(DEBUG || kVerbose > 0) { 2484 if(DEBUG || kVerbose > 0) {
2503 G4cout << "ROI image size : (" << 2485 std::cout << "ROI image size : ("
2504 << size[0] << ", " 2486 << size[0] << ", "
2505 << size[1] << ", " 2487 << size[1] << ", "
2506 << size[2] << ")" 2488 << size[2] << ")"
2507 << G4endl; << 2489 << std::endl;
2508 } 2490 }
2509 2491
2510 // ROI max. & min. 2492 // ROI max. & min.
2511 ifile.read((char *)ctmp, sizeof(short)*2) 2493 ifile.read((char *)ctmp, sizeof(short)*2);
2512 convertEndian(ctmp, minmax[0]); 2494 convertEndian(ctmp, minmax[0]);
2513 convertEndian(ctmp+sizeof(short), minmax[ 2495 convertEndian(ctmp+sizeof(short), minmax[1]);
2514 kRoi[0].setMinMax(minmax); 2496 kRoi[0].setMinMax(minmax);
2515 2497
2516 // ROI distribution scaling 2498 // ROI distribution scaling
2517 ifile.read((char *)ctmp, sizeof(float)); 2499 ifile.read((char *)ctmp, sizeof(float));
2518 convertEndian(ctmp, scale); 2500 convertEndian(ctmp, scale);
2519 kRoi[0].setScale(dscale = scale); 2501 kRoi[0].setScale(dscale = scale);
2520 if(DEBUG || kVerbose > 0) { 2502 if(DEBUG || kVerbose > 0) {
2521 G4cout << "ROI image min., max., scale << 2503 std::cout << "ROI image min., max., scale : "
2522 << minmax[0] << ", " 2504 << minmax[0] << ", "
2523 << minmax[1] << ", " 2505 << minmax[1] << ", "
2524 << scale << G4endl; << 2506 << scale << std::endl;
2525 } 2507 }
2526 2508
2527 // ROI image 2509 // ROI image
2528 int rsize = size[0]*size[1]; 2510 int rsize = size[0]*size[1];
2529 char * ri = new char[rsize*sizeof(short)] 2511 char * ri = new char[rsize*sizeof(short)];
2530 for(int i = 0; i < size[2]; i++) { 2512 for(int i = 0; i < size[2]; i++) {
2531 ifile.read((char *)ri, rsize*sizeof(sho 2513 ifile.read((char *)ri, rsize*sizeof(short));
2532 short * rimage = new short[rsize]; 2514 short * rimage = new short[rsize];
2533 for(int j = 0; j < rsize; j++) { 2515 for(int j = 0; j < rsize; j++) {
2534 convertEndian(ri+j*sizeof(short), rimage[j] 2516 convertEndian(ri+j*sizeof(short), rimage[j]);
2535 } 2517 }
2536 kRoi[0].addImage(rimage); 2518 kRoi[0].addImage(rimage);
2537 2519
2538 } 2520 }
2539 delete [] ri; 2521 delete [] ri;
2540 2522
2541 // ROI relative location 2523 // ROI relative location
2542 ifile.read((char *)ctmp, 3*sizeof(int)); 2524 ifile.read((char *)ctmp, 3*sizeof(int));
2543 convertEndian(ctmp, iCenter[0]); 2525 convertEndian(ctmp, iCenter[0]);
2544 convertEndian(ctmp+sizeof(int), iCenter[1 2526 convertEndian(ctmp+sizeof(int), iCenter[1]);
2545 convertEndian(ctmp+2*sizeof(int), iCenter 2527 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2546 for(int i = 0; i < 3; i++) fCenter[i] = i 2528 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2547 kRoi[0].setCenterPosition(fCenter); 2529 kRoi[0].setCenterPosition(fCenter);
2548 if(DEBUG || kVerbose > 0) { 2530 if(DEBUG || kVerbose > 0) {
2549 G4cout << "ROI image relative location << 2531 std::cout << "ROI image relative location : ("
2550 << fCenter[0] << ", " 2532 << fCenter[0] << ", "
2551 << fCenter[1] << ", " 2533 << fCenter[1] << ", "
2552 << fCenter[2] << ")" << G4endl; << 2534 << fCenter[2] << ")" << std::endl;
2553 } 2535 }
2554 2536
2555 } 2537 }
2556 2538
2557 //----- track information -----// 2539 //----- track information -----//
2558 if(kPointerToTrackData != 0) { 2540 if(kPointerToTrackData != 0) {
2559 2541
2560 // track 2542 // track
2561 ifile.read((char *)ctmp, sizeof(int)); 2543 ifile.read((char *)ctmp, sizeof(int));
2562 int ntrk; 2544 int ntrk;
2563 convertEndian(ctmp, ntrk); 2545 convertEndian(ctmp, ntrk);
2564 if(DEBUG || kVerbose > 0) { 2546 if(DEBUG || kVerbose > 0) {
2565 G4cout << "# of tracks: " << ntrk << G4 << 2547 std::cout << "# of tracks: " << ntrk << std::endl;
2566 } 2548 }
2567 2549
2568 // v4 2550 // v4
2569 std::vector<float *> trkv4; 2551 std::vector<float *> trkv4;
2570 2552
2571 // track position 2553 // track position
2572 for(int i = 0; i < ntrk; i++) { 2554 for(int i = 0; i < ntrk; i++) {
2573 float * tp = new float[6]; 2555 float * tp = new float[6];
2574 2556
2575 ifile.read((char *)ctmp, sizeof(float)* 2557 ifile.read((char *)ctmp, sizeof(float)*3);
2576 if(DEBUG || kVerbose > 0) if(i < 10) G4 << 2558 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << i << ": " ;
2577 for(int j = 0; j < 3; j++) { 2559 for(int j = 0; j < 3; j++) {
2578 convertEndian(ctmp+j*sizeof(float), tp[j]); 2560 convertEndian(ctmp+j*sizeof(float), tp[j]);
2579 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << 2561 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j] << ", ";
2580 } 2562 }
2581 2563
2582 ifile.read((char *)ctmp, sizeof(float)* 2564 ifile.read((char *)ctmp, sizeof(float)*3);
2583 for(int j = 0; j < 3; j++) { 2565 for(int j = 0; j < 3; j++) {
2584 convertEndian(ctmp+j*sizeof(float), tp[j+3] 2566 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
2585 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << 2567 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j+3] << ", ";
2586 } 2568 }
2587 addTrack(tp); 2569 addTrack(tp);
2588 if(DEBUG || kVerbose > 0) if(i < 10) G4 << 2570 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << std::endl;
2589 2571
2590 // v4 2572 // v4
2591 trkv4.push_back(tp); 2573 trkv4.push_back(tp);
2592 } 2574 }
2593 2575
2594 //v4 2576 //v4
2595 unsigned char trkcolorv4[3]; 2577 unsigned char trkcolorv4[3];
2596 2578
2597 // track color 2579 // track color
2598 for(int i = 0; i < ntrk; i++) { 2580 for(int i = 0; i < ntrk; i++) {
2599 unsigned char * rgb = new unsigned char 2581 unsigned char * rgb = new unsigned char[3];
2600 ifile.read((char *)rgb, 3); 2582 ifile.read((char *)rgb, 3);
2601 addTrackColor(rgb); 2583 addTrackColor(rgb);
2602 2584
2603 // v4 2585 // v4
2604 for(int j = 0; j < 3; j++) trkcolorv4[j 2586 for(int j = 0; j < 3; j++) trkcolorv4[j] = rgb[j];
2605 std::vector<float *> trk; 2587 std::vector<float *> trk;
2606 trk.push_back(trkv4[i]); 2588 trk.push_back(trkv4[i]);
2607 addTrack(trk, trkcolorv4); 2589 addTrack(trk, trkcolorv4);
2608 2590
2609 } 2591 }
2610 2592
2611 } 2593 }
2612 2594
2613 ifile.close(); 2595 ifile.close();
2614 2596
2615 return true; 2597 return true;
2616 } 2598 }
2617 bool G4GMocrenIO::retrieveData3(char * _filen 2599 bool G4GMocrenIO::retrieveData3(char * _filename) {
2618 kFileName = _filename; 2600 kFileName = _filename;
2619 return retrieveData(); 2601 return retrieveData();
2620 } 2602 }
2621 2603
2622 // 2604 //
2623 bool G4GMocrenIO::retrieveData2() { 2605 bool G4GMocrenIO::retrieveData2() {
2624 2606
2625 bool DEBUG = false;// 2607 bool DEBUG = false;//
2626 2608
2627 // input file open 2609 // input file open
2628 std::ifstream ifile(kFileName.c_str(), std: 2610 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2629 if(!ifile) { 2611 if(!ifile) {
2630 if (G4VisManager::GetVerbosity() >= G4Vis << 2612 std::cerr << "Cannot open file: " << kFileName
2631 G4cout << "Cannot open file: " << kFile << 2613 << " in G4GMocrenIO::retrieveData2()." << std::endl;
2632 << " in G4GMocrenIO::retrieveData2()." << <<
2633 return false; 2614 return false;
2634 } 2615 }
2635 2616
2636 // data buffer 2617 // data buffer
2637 char ctmp[12]; 2618 char ctmp[12];
2638 2619
2639 // file identifier 2620 // file identifier
2640 char verid[9]; 2621 char verid[9];
2641 ifile.read((char *)verid, 8); 2622 ifile.read((char *)verid, 8);
2642 2623
2643 // file version 2624 // file version
2644 unsigned char ver; 2625 unsigned char ver;
2645 ifile.read((char *)&ver, 1); 2626 ifile.read((char *)&ver, 1);
2646 std::stringstream ss; 2627 std::stringstream ss;
2647 ss << (int)ver; 2628 ss << (int)ver;
2648 kVersion = ss.str(); 2629 kVersion = ss.str();
2649 if(DEBUG || kVerbose > 0) G4cout << "File v << 2630 if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl;
2650 2631
2651 // id of version 1 2632 // id of version 1
2652 char idtmp[IDLENGTH]; 2633 char idtmp[IDLENGTH];
2653 ifile.read((char *)idtmp, IDLENGTH); 2634 ifile.read((char *)idtmp, IDLENGTH);
2654 kId = idtmp; 2635 kId = idtmp;
2655 // version of version 1 2636 // version of version 1
2656 char vertmp[VERLENGTH]; 2637 char vertmp[VERLENGTH];
2657 ifile.read((char *)vertmp, VERLENGTH); 2638 ifile.read((char *)vertmp, VERLENGTH);
2658 2639
2659 // endian 2640 // endian
2660 ifile.read((char *)&kLittleEndianInput, siz 2641 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2661 if(DEBUG || kVerbose > 0) { 2642 if(DEBUG || kVerbose > 0) {
2662 G4cout << "Endian : "; << 2643 std::cout << "Endian : ";
2663 if(kLittleEndianInput == 1) 2644 if(kLittleEndianInput == 1)
2664 G4cout << " little" << G4endl; << 2645 std::cout << " little" << std::endl;
2665 else { 2646 else {
2666 G4cout << " big" << G4endl; << 2647 std::cout << " big" << std::endl;
2667 } 2648 }
2668 } 2649 }
2669 2650
2670 // voxel spacings for all images 2651 // voxel spacings for all images
2671 ifile.read((char *)ctmp, 12); 2652 ifile.read((char *)ctmp, 12);
2672 convertEndian(ctmp, kVoxelSpacing[0]); 2653 convertEndian(ctmp, kVoxelSpacing[0]);
2673 convertEndian(ctmp+4, kVoxelSpacing[1]); 2654 convertEndian(ctmp+4, kVoxelSpacing[1]);
2674 convertEndian(ctmp+8, kVoxelSpacing[2]); 2655 convertEndian(ctmp+8, kVoxelSpacing[2]);
2675 if(DEBUG || kVerbose > 0) { 2656 if(DEBUG || kVerbose > 0) {
2676 G4cout << "Voxel spacing : (" << 2657 std::cout << "Voxel spacing : ("
2677 << kVoxelSpacing[0] << ", " 2658 << kVoxelSpacing[0] << ", "
2678 << kVoxelSpacing[1] << ", " 2659 << kVoxelSpacing[1] << ", "
2679 << kVoxelSpacing[2] 2660 << kVoxelSpacing[2]
2680 << ") mm " << G4endl; << 2661 << ") mm " << std::endl;
2681 } 2662 }
2682 2663
2683 2664
2684 // offset from file starting point to the m 2665 // offset from file starting point to the modality image data
2685 ifile.read((char *)ctmp, 4); 2666 ifile.read((char *)ctmp, 4);
2686 convertEndian(ctmp, kPointerToModalityData) 2667 convertEndian(ctmp, kPointerToModalityData);
2687 2668
2688 // offset from file starting point to the d 2669 // offset from file starting point to the dose image data
2689 unsigned int ptddd; 2670 unsigned int ptddd;
2690 ifile.read((char *)ctmp, 4); 2671 ifile.read((char *)ctmp, 4);
2691 convertEndian(ctmp, ptddd); 2672 convertEndian(ctmp, ptddd);
2692 kPointerToDoseDistData.push_back(ptddd); 2673 kPointerToDoseDistData.push_back(ptddd);
2693 2674
2694 // offset from file starting point to the R 2675 // offset from file starting point to the ROI image data
2695 ifile.read((char *)ctmp, 4); 2676 ifile.read((char *)ctmp, 4);
2696 convertEndian(ctmp, kPointerToROIData); 2677 convertEndian(ctmp, kPointerToROIData);
2697 2678
2698 // offset from file starting point to the t 2679 // offset from file starting point to the track data
2699 ifile.read((char *)ctmp, 4); 2680 ifile.read((char *)ctmp, 4);
2700 convertEndian(ctmp, kPointerToTrackData); 2681 convertEndian(ctmp, kPointerToTrackData);
2701 if(DEBUG || kVerbose > 0) { 2682 if(DEBUG || kVerbose > 0) {
2702 G4cout << "Each pointer to data : " << 2683 std::cout << "Each pointer to data : "
2703 << kPointerToModalityData << ", " 2684 << kPointerToModalityData << ", "
2704 << kPointerToDoseDistData[0] << ", " 2685 << kPointerToDoseDistData[0] << ", "
2705 << kPointerToROIData << ", " 2686 << kPointerToROIData << ", "
2706 << kPointerToTrackData << G4endl; << 2687 << kPointerToTrackData << std::endl;
2707 } 2688 }
2708 2689
2709 if(kPointerToModalityData == 0 && kPointerT 2690 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2710 kPointerToROIData == 0 && kPointerToTrac 2691 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2711 if(DEBUG || kVerbose > 0) { 2692 if(DEBUG || kVerbose > 0) {
2712 G4cout << "No data." << G4endl; << 2693 std::cout << "No data." << std::endl;
2713 } 2694 }
2714 return false; 2695 return false;
2715 } 2696 }
2716 2697
2717 // event number 2698 // event number
2718 /* ver 1 2699 /* ver 1
2719 ifile.read(ctmp, sizeof(int)); 2700 ifile.read(ctmp, sizeof(int));
2720 convertEndian(ctmp, numberOfEvents); 2701 convertEndian(ctmp, numberOfEvents);
2721 */ 2702 */
2722 2703
2723 int size[3]; 2704 int size[3];
2724 float scale; 2705 float scale;
2725 double dscale; 2706 double dscale;
2726 short minmax[2]; 2707 short minmax[2];
2727 float fCenter[3]; 2708 float fCenter[3];
2728 int iCenter[3]; 2709 int iCenter[3];
2729 2710
2730 //----- Modality image -----// 2711 //----- Modality image -----//
2731 // modality image size 2712 // modality image size
2732 ifile.read(ctmp, 3*sizeof(int)); 2713 ifile.read(ctmp, 3*sizeof(int));
2733 convertEndian(ctmp, size[0]); 2714 convertEndian(ctmp, size[0]);
2734 convertEndian(ctmp+sizeof(int), size[1]); 2715 convertEndian(ctmp+sizeof(int), size[1]);
2735 convertEndian(ctmp+2*sizeof(int), size[2]); 2716 convertEndian(ctmp+2*sizeof(int), size[2]);
2736 if(DEBUG || kVerbose > 0) { 2717 if(DEBUG || kVerbose > 0) {
2737 G4cout << "Modality image size : (" << 2718 std::cout << "Modality image size : ("
2738 << size[0] << ", " 2719 << size[0] << ", "
2739 << size[1] << ", " 2720 << size[1] << ", "
2740 << size[2] << ")" 2721 << size[2] << ")"
2741 << G4endl; << 2722 << std::endl;
2742 } 2723 }
2743 kModality.setSize(size); 2724 kModality.setSize(size);
2744 2725
2745 // modality image voxel spacing 2726 // modality image voxel spacing
2746 /* 2727 /*
2747 ifile.read(ctmp, 3*sizeof(float)); 2728 ifile.read(ctmp, 3*sizeof(float));
2748 convertEndian(ctmp, modalityImageVoxelSpa 2729 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2749 convertEndian(ctmp+sizeof(float), modalit 2730 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2750 convertEndian(ctmp+2*sizeof(float), modal 2731 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2751 */ 2732 */
2752 2733
2753 if(kPointerToModalityData != 0) { 2734 if(kPointerToModalityData != 0) {
2754 2735
2755 // modality density max. & min. 2736 // modality density max. & min.
2756 ifile.read((char *)ctmp, 4); 2737 ifile.read((char *)ctmp, 4);
2757 convertEndian(ctmp, minmax[0]); 2738 convertEndian(ctmp, minmax[0]);
2758 convertEndian(ctmp+2, minmax[1]); 2739 convertEndian(ctmp+2, minmax[1]);
2759 kModality.setMinMax(minmax); 2740 kModality.setMinMax(minmax);
2760 2741
2761 // modality density scale 2742 // modality density scale
2762 ifile.read((char *)ctmp, 4); 2743 ifile.read((char *)ctmp, 4);
2763 convertEndian(ctmp, scale); 2744 convertEndian(ctmp, scale);
2764 kModality.setScale(dscale = scale); 2745 kModality.setScale(dscale = scale);
2765 if(DEBUG || kVerbose > 0) { 2746 if(DEBUG || kVerbose > 0) {
2766 G4cout << "Modality image min., max., s << 2747 std::cout << "Modality image min., max., scale : "
2767 << minmax[0] << ", " 2748 << minmax[0] << ", "
2768 << minmax[1] << ", " 2749 << minmax[1] << ", "
2769 << scale << G4endl; << 2750 << scale << std::endl;
2770 } 2751 }
2771 2752
2772 // modality density 2753 // modality density
2773 int psize = size[0]*size[1]; 2754 int psize = size[0]*size[1];
2774 if(DEBUG || kVerbose > 0) G4cout << "Moda << 2755 if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): ";
2775 char * cimage = new char[psize*sizeof(sho 2756 char * cimage = new char[psize*sizeof(short)];
2776 for(int i = 0; i < size[2]; i++) { 2757 for(int i = 0; i < size[2]; i++) {
2777 ifile.read((char *)cimage, psize*sizeof 2758 ifile.read((char *)cimage, psize*sizeof(short));
2778 short * mimage = new short[psize]; 2759 short * mimage = new short[psize];
2779 for(int j = 0; j < psize; j++) { 2760 for(int j = 0; j < psize; j++) {
2780 convertEndian(cimage+j*sizeof(short), mimag 2761 convertEndian(cimage+j*sizeof(short), mimage[j]);
2781 } 2762 }
2782 kModality.addImage(mimage); 2763 kModality.addImage(mimage);
2783 2764
2784 if(DEBUG || kVerbose > 0) G4cout << "[" << 2765 if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2785 } 2766 }
2786 if(DEBUG || kVerbose > 0) G4cout << G4end << 2767 if(DEBUG || kVerbose > 0) std::cout << std::endl;
2787 delete [] cimage; 2768 delete [] cimage;
2788 2769
2789 // modality desity map for CT value 2770 // modality desity map for CT value
2790 size_t msize = minmax[1]-minmax[0]+1; 2771 size_t msize = minmax[1]-minmax[0]+1;
2791 if(DEBUG || kVerbose > 0) G4cout << "msiz << 2772 if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl;
2792 char * pdmap = new char[msize*sizeof(floa 2773 char * pdmap = new char[msize*sizeof(float)];
2793 ifile.read((char *)pdmap, msize*sizeof(fl 2774 ifile.read((char *)pdmap, msize*sizeof(float));
2794 float ftmp; 2775 float ftmp;
2795 for(int i = 0; i < (int)msize; i++) { 2776 for(int i = 0; i < (int)msize; i++) {
2796 convertEndian(pdmap+i*sizeof(float), ft 2777 convertEndian(pdmap+i*sizeof(float), ftmp);
2797 kModalityImageDensityMap.push_back(ftmp 2778 kModalityImageDensityMap.push_back(ftmp);
2798 } 2779 }
2799 delete [] pdmap; <<
2800 if(DEBUG || kVerbose > 0) { 2780 if(DEBUG || kVerbose > 0) {
2801 G4cout << "density map : " << std::ends << 2781 std::cout << "density map : " << std::ends;
2802 for(int i = 0; i < 10; i++) 2782 for(int i = 0; i < 10; i++)
2803 G4cout <<kModalityImageDensityMap[i] << ", << 2783 std::cout <<kModalityImageDensityMap[i] << ", ";
2804 G4cout << G4endl; << 2784 std::cout << std::endl;
2805 for(int i = 0; i < 10; i++) G4cout << " << 2785 for(int i = 0; i < 10; i++) std::cout << "..";
2806 G4cout << G4endl; << 2786 std::cout << std::endl;
2807 for(size_t i =kModalityImageDensityMap. 2787 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2808 G4cout <<kModalityImageDensityMap[i] << ", << 2788 std::cout <<kModalityImageDensityMap[i] << ", ";
2809 G4cout << G4endl; << 2789 std::cout << std::endl;
2810 } 2790 }
2811 2791
2812 } 2792 }
2813 2793
2814 2794
2815 //----- dose distribution image -----// 2795 //----- dose distribution image -----//
2816 if(kPointerToDoseDistData[0] != 0) { 2796 if(kPointerToDoseDistData[0] != 0) {
2817 2797
2818 newDoseDist(); 2798 newDoseDist();
2819 2799
2820 // dose distrbution image size 2800 // dose distrbution image size
2821 ifile.read((char *)ctmp, 3*sizeof(int)); 2801 ifile.read((char *)ctmp, 3*sizeof(int));
2822 convertEndian(ctmp, size[0]); 2802 convertEndian(ctmp, size[0]);
2823 convertEndian(ctmp+sizeof(int), size[1]); 2803 convertEndian(ctmp+sizeof(int), size[1]);
2824 convertEndian(ctmp+2*sizeof(int), size[2] 2804 convertEndian(ctmp+2*sizeof(int), size[2]);
2825 if(DEBUG || kVerbose > 0) { 2805 if(DEBUG || kVerbose > 0) {
2826 G4cout << "Dose dist. image size : (" << 2806 std::cout << "Dose dist. image size : ("
2827 << size[0] << ", " 2807 << size[0] << ", "
2828 << size[1] << ", " 2808 << size[1] << ", "
2829 << size[2] << ")" 2809 << size[2] << ")"
2830 << G4endl; << 2810 << std::endl;
2831 } 2811 }
2832 kDose[0].setSize(size); 2812 kDose[0].setSize(size);
2833 2813
2834 // dose distribution max. & min. 2814 // dose distribution max. & min.
2835 ifile.read((char *)ctmp, sizeof(short)*2) 2815 ifile.read((char *)ctmp, sizeof(short)*2);
2836 convertEndian(ctmp, minmax[0]); 2816 convertEndian(ctmp, minmax[0]);
2837 convertEndian(ctmp+2, minmax[1]); 2817 convertEndian(ctmp+2, minmax[1]);
2838 // dose distribution scaling 2818 // dose distribution scaling
2839 ifile.read((char *)ctmp, sizeof(float)); 2819 ifile.read((char *)ctmp, sizeof(float));
2840 convertEndian(ctmp, scale); 2820 convertEndian(ctmp, scale);
2841 kDose[0].setScale(dscale = scale); 2821 kDose[0].setScale(dscale = scale);
2842 2822
2843 double dminmax[2]; 2823 double dminmax[2];
2844 for(int i = 0; i < 2; i++) dminmax[i] = m 2824 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2845 kDose[0].setMinMax(dminmax); 2825 kDose[0].setMinMax(dminmax);
2846 2826
2847 if(DEBUG || kVerbose > 0) { 2827 if(DEBUG || kVerbose > 0) {
2848 G4cout << "Dose dist. image min., max., << 2828 std::cout << "Dose dist. image min., max., scale : "
2849 << dminmax[0] << ", " 2829 << dminmax[0] << ", "
2850 << dminmax[1] << ", " 2830 << dminmax[1] << ", "
2851 << scale << G4endl; << 2831 << scale << std::endl;
2852 } 2832 }
2853 2833
2854 // dose distribution image 2834 // dose distribution image
2855 int dsize = size[0]*size[1]; 2835 int dsize = size[0]*size[1];
2856 if(DEBUG || kVerbose > 0) G4cout << "Dose << 2836 if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): ";
2857 char * di = new char[dsize*sizeof(short)] 2837 char * di = new char[dsize*sizeof(short)];
2858 short * shimage = new short[dsize]; 2838 short * shimage = new short[dsize];
2859 for(int z = 0; z < size[2]; z++) { 2839 for(int z = 0; z < size[2]; z++) {
2860 ifile.read((char *)di, dsize*sizeof(sho 2840 ifile.read((char *)di, dsize*sizeof(short));
2861 double * dimage = new double[dsize]; 2841 double * dimage = new double[dsize];
2862 for(int xy = 0; xy < dsize; xy++) { 2842 for(int xy = 0; xy < dsize; xy++) {
2863 convertEndian(di+xy*sizeof(short), shimage[ 2843 convertEndian(di+xy*sizeof(short), shimage[xy]);
2864 dimage[xy] = shimage[xy]*dscale; 2844 dimage[xy] = shimage[xy]*dscale;
2865 } 2845 }
2866 kDose[0].addImage(dimage); 2846 kDose[0].addImage(dimage);
2867 2847
2868 if(DEBUG || kVerbose > 0) G4cout << "[" << 2848 if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2869 2849
2870 if(DEBUG || kVerbose > 0) { 2850 if(DEBUG || kVerbose > 0) {
2871 for(int j = 0; j < dsize; j++) { 2851 for(int j = 0; j < dsize; j++) {
2872 if(dimage[j] < 0) 2852 if(dimage[j] < 0)
2873 G4cout << "[" << j << "," << z << "]" << 2853 std::cout << "[" << j << "," << z << "]"
2874 << dimage[j] << ", "; 2854 << dimage[j] << ", ";
2875 } 2855 }
2876 } 2856 }
2877 } 2857 }
2878 delete [] shimage; 2858 delete [] shimage;
2879 delete [] di; 2859 delete [] di;
2880 if(DEBUG || kVerbose > 0) G4cout << G4end << 2860 if(DEBUG || kVerbose > 0) std::cout << std::endl;
2881 2861
2882 /* ver 1 2862 /* ver 1
2883 float doseDist; 2863 float doseDist;
2884 int dosePid; 2864 int dosePid;
2885 double * doseData = new double[numDose 2865 double * doseData = new double[numDoseImageVoxels];
2886 for(int i = 0; i < numDose; i++) { 2866 for(int i = 0; i < numDose; i++) {
2887 ifile.read(ctmp, sizeof(int)); 2867 ifile.read(ctmp, sizeof(int));
2888 convertEndian(ctmp, dosePid); 2868 convertEndian(ctmp, dosePid);
2889 for(int j = 0; j < numDoseImageVoxels; 2869 for(int j = 0; j < numDoseImageVoxels; j++) {
2890 ifile.read(ctmp, sizeof(float)); 2870 ifile.read(ctmp, sizeof(float));
2891 convertEndian(ctmp, doseDist); 2871 convertEndian(ctmp, doseDist);
2892 doseData[j] = doseDist; 2872 doseData[j] = doseDist;
2893 } 2873 }
2894 setDose(dosePid, doseData); 2874 setDose(dosePid, doseData);
2895 } 2875 }
2896 delete [] doseData; 2876 delete [] doseData;
2897 if(totalDose == NULL) totalDose = new 2877 if(totalDose == NULL) totalDose = new double[numDoseImageVoxels];
2898 for(int i = 0; i < numDoseImageVoxels; 2878 for(int i = 0; i < numDoseImageVoxels; i++) {
2899 ifile.read(ctmp, sizeof(float)); 2879 ifile.read(ctmp, sizeof(float));
2900 convertEndian(ctmp, doseDist); 2880 convertEndian(ctmp, doseDist);
2901 totalDose[i] = doseDist; 2881 totalDose[i] = doseDist;
2902 } 2882 }
2903 */ 2883 */
2904 2884
2905 /* ver 1 2885 /* ver 1
2906 // relative location between the two imag 2886 // relative location between the two images
2907 ifile.read(ctmp, 3*sizeof(float)); 2887 ifile.read(ctmp, 3*sizeof(float));
2908 convertEndian(ctmp, relativeLocation[0]); 2888 convertEndian(ctmp, relativeLocation[0]);
2909 convertEndian(ctmp+sizeof(float), relativ 2889 convertEndian(ctmp+sizeof(float), relativeLocation[1]);
2910 convertEndian(ctmp+2*sizeof(float), relat 2890 convertEndian(ctmp+2*sizeof(float), relativeLocation[2]);
2911 */ 2891 */
2912 2892
2913 // relative location of the dose distribu 2893 // relative location of the dose distribution image for
2914 // the modality image 2894 // the modality image
2915 //ofile.write((char *)relativeLocation, 3 2895 //ofile.write((char *)relativeLocation, 3*sizeof(float));
2916 ifile.read((char *)ctmp, 3*sizeof(int)); 2896 ifile.read((char *)ctmp, 3*sizeof(int));
2917 convertEndian(ctmp, iCenter[0]); 2897 convertEndian(ctmp, iCenter[0]);
2918 convertEndian(ctmp+sizeof(int), iCenter[1 2898 convertEndian(ctmp+sizeof(int), iCenter[1]);
2919 convertEndian(ctmp+2*sizeof(int), iCenter 2899 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2920 for(int i = 0; i < 3; i++) fCenter[i] = ( 2900 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2921 kDose[0].setCenterPosition(fCenter); 2901 kDose[0].setCenterPosition(fCenter);
2922 2902
2923 if(DEBUG || kVerbose > 0) { 2903 if(DEBUG || kVerbose > 0) {
2924 G4cout << "Dose dist. image relative lo << 2904 std::cout << "Dose dist. image relative location : ("
2925 << fCenter[0] << ", " 2905 << fCenter[0] << ", "
2926 << fCenter[1] << ", " 2906 << fCenter[1] << ", "
2927 << fCenter[2] << ")" << G4endl; << 2907 << fCenter[2] << ")" << std::endl;
2928 } 2908 }
2929 2909
2930 2910
2931 } 2911 }
2932 2912
2933 //----- ROI image -----// 2913 //----- ROI image -----//
2934 if(kPointerToROIData != 0) { 2914 if(kPointerToROIData != 0) {
2935 2915
2936 newROI(); 2916 newROI();
2937 2917
2938 // ROI image size 2918 // ROI image size
2939 ifile.read((char *)ctmp, 3*sizeof(int)); 2919 ifile.read((char *)ctmp, 3*sizeof(int));
2940 convertEndian(ctmp, size[0]); 2920 convertEndian(ctmp, size[0]);
2941 convertEndian(ctmp+sizeof(int), size[1]); 2921 convertEndian(ctmp+sizeof(int), size[1]);
2942 convertEndian(ctmp+2*sizeof(int), size[2] 2922 convertEndian(ctmp+2*sizeof(int), size[2]);
2943 kRoi[0].setSize(size); 2923 kRoi[0].setSize(size);
2944 if(DEBUG || kVerbose > 0) { 2924 if(DEBUG || kVerbose > 0) {
2945 G4cout << "ROI image size : (" << 2925 std::cout << "ROI image size : ("
2946 << size[0] << ", " 2926 << size[0] << ", "
2947 << size[1] << ", " 2927 << size[1] << ", "
2948 << size[2] << ")" 2928 << size[2] << ")"
2949 << G4endl; << 2929 << std::endl;
2950 } 2930 }
2951 2931
2952 // ROI max. & min. 2932 // ROI max. & min.
2953 ifile.read((char *)ctmp, sizeof(short)*2) 2933 ifile.read((char *)ctmp, sizeof(short)*2);
2954 convertEndian(ctmp, minmax[0]); 2934 convertEndian(ctmp, minmax[0]);
2955 convertEndian(ctmp+sizeof(short), minmax[ 2935 convertEndian(ctmp+sizeof(short), minmax[1]);
2956 kRoi[0].setMinMax(minmax); 2936 kRoi[0].setMinMax(minmax);
2957 2937
2958 // ROI distribution scaling 2938 // ROI distribution scaling
2959 ifile.read((char *)ctmp, sizeof(float)); 2939 ifile.read((char *)ctmp, sizeof(float));
2960 convertEndian(ctmp, scale); 2940 convertEndian(ctmp, scale);
2961 kRoi[0].setScale(dscale = scale); 2941 kRoi[0].setScale(dscale = scale);
2962 if(DEBUG || kVerbose > 0) { 2942 if(DEBUG || kVerbose > 0) {
2963 G4cout << "ROI image min., max., scale << 2943 std::cout << "ROI image min., max., scale : "
2964 << minmax[0] << ", " 2944 << minmax[0] << ", "
2965 << minmax[1] << ", " 2945 << minmax[1] << ", "
2966 << scale << G4endl; << 2946 << scale << std::endl;
2967 } 2947 }
2968 2948
2969 // ROI image 2949 // ROI image
2970 int rsize = size[0]*size[1]; 2950 int rsize = size[0]*size[1];
2971 char * ri = new char[rsize*sizeof(short)] 2951 char * ri = new char[rsize*sizeof(short)];
2972 for(int i = 0; i < size[2]; i++) { 2952 for(int i = 0; i < size[2]; i++) {
2973 ifile.read((char *)ri, rsize*sizeof(sho 2953 ifile.read((char *)ri, rsize*sizeof(short));
2974 short * rimage = new short[rsize]; 2954 short * rimage = new short[rsize];
2975 for(int j = 0; j < rsize; j++) { 2955 for(int j = 0; j < rsize; j++) {
2976 convertEndian(ri+j*sizeof(short), rimage[j] 2956 convertEndian(ri+j*sizeof(short), rimage[j]);
2977 } 2957 }
2978 kRoi[0].addImage(rimage); 2958 kRoi[0].addImage(rimage);
2979 2959
2980 } 2960 }
2981 delete [] ri; 2961 delete [] ri;
2982 2962
2983 // ROI relative location 2963 // ROI relative location
2984 ifile.read((char *)ctmp, 3*sizeof(int)); 2964 ifile.read((char *)ctmp, 3*sizeof(int));
2985 convertEndian(ctmp, iCenter[0]); 2965 convertEndian(ctmp, iCenter[0]);
2986 convertEndian(ctmp+sizeof(int), iCenter[1 2966 convertEndian(ctmp+sizeof(int), iCenter[1]);
2987 convertEndian(ctmp+2*sizeof(int), iCenter 2967 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2988 for(int i = 0; i < 3; i++) fCenter[i] = i 2968 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2989 kRoi[0].setCenterPosition(fCenter); 2969 kRoi[0].setCenterPosition(fCenter);
2990 if(DEBUG || kVerbose > 0) { 2970 if(DEBUG || kVerbose > 0) {
2991 G4cout << "ROI image relative location << 2971 std::cout << "ROI image relative location : ("
2992 << fCenter[0] << ", " 2972 << fCenter[0] << ", "
2993 << fCenter[1] << ", " 2973 << fCenter[1] << ", "
2994 << fCenter[2] << ")" << G4endl; << 2974 << fCenter[2] << ")" << std::endl;
2995 } 2975 }
2996 2976
2997 } 2977 }
2998 2978
2999 //----- track information -----// 2979 //----- track information -----//
3000 if(kPointerToTrackData != 0) { 2980 if(kPointerToTrackData != 0) {
3001 2981
3002 // track 2982 // track
3003 ifile.read((char *)ctmp, sizeof(int)); 2983 ifile.read((char *)ctmp, sizeof(int));
3004 int ntrk; 2984 int ntrk;
3005 convertEndian(ctmp, ntrk); 2985 convertEndian(ctmp, ntrk);
3006 if(DEBUG || kVerbose > 0) { 2986 if(DEBUG || kVerbose > 0) {
3007 G4cout << "# of tracks: " << ntrk << G4 << 2987 std::cout << "# of tracks: " << ntrk << std::endl;
3008 } 2988 }
3009 2989
3010 //v4 2990 //v4
3011 unsigned char trkcolorv4[3] = {255, 0, 0} 2991 unsigned char trkcolorv4[3] = {255, 0, 0};
3012 2992
3013 for(int i = 0; i < ntrk; i++) { 2993 for(int i = 0; i < ntrk; i++) {
3014 float * tp = new float[6]; 2994 float * tp = new float[6];
3015 // v4 2995 // v4
3016 std::vector<float *> trkv4; 2996 std::vector<float *> trkv4;
3017 2997
3018 ifile.read((char *)ctmp, sizeof(float)* 2998 ifile.read((char *)ctmp, sizeof(float)*3);
3019 if(DEBUG || kVerbose > 0) if(i < 10) G4 << 2999 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << i << ": " ;
3020 for(int j = 0; j < 3; j++) { 3000 for(int j = 0; j < 3; j++) {
3021 convertEndian(ctmp+j*sizeof(float), tp[j]); 3001 convertEndian(ctmp+j*sizeof(float), tp[j]);
3022 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << 3002 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j] << ", ";
3023 } 3003 }
3024 3004
3025 ifile.read((char *)ctmp, sizeof(float)* 3005 ifile.read((char *)ctmp, sizeof(float)*3);
3026 for(int j = 0; j < 3; j++) { 3006 for(int j = 0; j < 3; j++) {
3027 convertEndian(ctmp+j*sizeof(float), tp[j+3] 3007 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
3028 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << 3008 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j+3] << ", ";
3029 } 3009 }
3030 3010
3031 kSteps.push_back(tp); 3011 kSteps.push_back(tp);
3032 // v4 3012 // v4
3033 trkv4.push_back(tp); 3013 trkv4.push_back(tp);
3034 addTrack(trkv4, trkcolorv4); 3014 addTrack(trkv4, trkcolorv4);
3035 3015
3036 if(DEBUG || kVerbose > 0) if(i < 10) G4 << 3016 if(DEBUG || kVerbose > 0) if(i < 10) std::cout << std::endl;
3037 } 3017 }
3038 3018
3039 } 3019 }
3040 3020
3041 /* ver 1 3021 /* ver 1
3042 // track 3022 // track
3043 int ntracks; 3023 int ntracks;
3044 ifile.read(ctmp, sizeof(int)); 3024 ifile.read(ctmp, sizeof(int));
3045 convertEndian(ctmp, ntracks); 3025 convertEndian(ctmp, ntracks);
3046 // track displacement 3026 // track displacement
3047 ifile.read(ctmp, 3*sizeof(float)); 3027 ifile.read(ctmp, 3*sizeof(float));
3048 convertEndian(ctmp, trackDisplacement[0]); 3028 convertEndian(ctmp, trackDisplacement[0]);
3049 convertEndian(ctmp+sizeof(float), trackDisp 3029 convertEndian(ctmp+sizeof(float), trackDisplacement[2]); // exchanged with [1]
3050 convertEndian(ctmp+2*sizeof(float), trackDi 3030 convertEndian(ctmp+2*sizeof(float), trackDisplacement[1]);
3051 // 3031 //
3052 //for(int i = 0; i < ntracks && i < 100; i+ 3032 //for(int i = 0; i < ntracks && i < 100; i++) {
3053 for(int i = 0; i < ntracks; i++) { 3033 for(int i = 0; i < ntracks; i++) {
3054 DicomDoseTrack trk; 3034 DicomDoseTrack trk;
3055 short trackid, parentid, pid; 3035 short trackid, parentid, pid;
3056 int npoints; 3036 int npoints;
3057 ifile.read(ctmp, sizeof(short)); 3037 ifile.read(ctmp, sizeof(short));
3058 convertEndian(ctmp, trackid); 3038 convertEndian(ctmp, trackid);
3059 trk.setID(trackid); 3039 trk.setID(trackid);
3060 ifile.read(ctmp, sizeof(short)); 3040 ifile.read(ctmp, sizeof(short));
3061 convertEndian(ctmp, parentid); 3041 convertEndian(ctmp, parentid);
3062 trk.setParentID(parentid); 3042 trk.setParentID(parentid);
3063 ifile.read(ctmp, sizeof(short)); 3043 ifile.read(ctmp, sizeof(short));
3064 convertEndian(ctmp, pid); 3044 convertEndian(ctmp, pid);
3065 trk.setPID(pid); 3045 trk.setPID(pid);
3066 ifile.read(ctmp, sizeof(int)); 3046 ifile.read(ctmp, sizeof(int));
3067 convertEndian(ctmp, npoints); 3047 convertEndian(ctmp, npoints);
3068 for(int i = 0; i < npoints; i++) { 3048 for(int i = 0; i < npoints; i++) {
3069 ifile.read(ctmp, 3*sizeof(float)); 3049 ifile.read(ctmp, 3*sizeof(float));
3070 // storing only start and end points 3050 // storing only start and end points
3071 //if(i == 0 || i == npoints - 1) { 3051 //if(i == 0 || i == npoints - 1) {
3072 float * point = new float[3]; 3052 float * point = new float[3];
3073 convertEndian(ctmp, point[0]); 3053 convertEndian(ctmp, point[0]);
3074 convertEndian(ctmp+sizeof(float), point[1]) 3054 convertEndian(ctmp+sizeof(float), point[1]);
3075 convertEndian(ctmp+2*sizeof(float), point[2 3055 convertEndian(ctmp+2*sizeof(float), point[2]);
3076 trk.addPoint(point); 3056 trk.addPoint(point);
3077 //} 3057 //}
3078 } 3058 }
3079 track.push_back(trk); 3059 track.push_back(trk);
3080 } 3060 }
3081 */ 3061 */
3082 3062
3083 ifile.close(); 3063 ifile.close();
3084 3064
3085 return true; 3065 return true;
3086 } 3066 }
3087 3067
3088 bool G4GMocrenIO::retrieveData2(char * _filen 3068 bool G4GMocrenIO::retrieveData2(char * _filename) {
3089 kFileName = _filename; 3069 kFileName = _filename;
3090 return retrieveData(); 3070 return retrieveData();
3091 } 3071 }
3092 3072
3093 void G4GMocrenIO::setID() { 3073 void G4GMocrenIO::setID() {
3094 time_t t; 3074 time_t t;
3095 time(&t); 3075 time(&t);
3096 3076
3097 tm * ti; 3077 tm * ti;
3098 ti = localtime(&t); 3078 ti = localtime(&t);
3099 3079
3100 char cmonth[12][4] = {"Jan", "Feb", "Mar", 3080 char cmonth[12][4] = {"Jan", "Feb", "Mar", "Apr",
3101 "May", "Jun", "Jul", "Aug", 3081 "May", "Jun", "Jul", "Aug",
3102 "Sep", "Oct", "Nov", "Dec"}; 3082 "Sep", "Oct", "Nov", "Dec"};
3103 std::stringstream ss; 3083 std::stringstream ss;
3104 ss << std::setfill('0') 3084 ss << std::setfill('0')
3105 << std::setw(2) 3085 << std::setw(2)
3106 << ti->tm_hour << ":" 3086 << ti->tm_hour << ":"
3107 << std::setw(2) 3087 << std::setw(2)
3108 << ti->tm_min << ":" 3088 << ti->tm_min << ":"
3109 << std::setw(2) 3089 << std::setw(2)
3110 << ti->tm_sec << "," 3090 << ti->tm_sec << ","
3111 << cmonth[ti->tm_mon] << "." 3091 << cmonth[ti->tm_mon] << "."
3112 << std::setw(2) 3092 << std::setw(2)
3113 << ti->tm_mday << "," 3093 << ti->tm_mday << ","
3114 << ti->tm_year+1900; 3094 << ti->tm_year+1900;
3115 3095
3116 kId = ss.str(); 3096 kId = ss.str();
3117 } 3097 }
3118 3098
3119 // get & set the file version 3099 // get & set the file version
3120 std::string & G4GMocrenIO::getVersion() {retu 3100 std::string & G4GMocrenIO::getVersion() {return kVersion;}
3121 void G4GMocrenIO::setVersion(std::string & _v 3101 void G4GMocrenIO::setVersion(std::string & _version) {kVersion = _version;}
3122 3102
3123 // set endians of input/output data 3103 // set endians of input/output data
3124 void G4GMocrenIO::setLittleEndianInput(bool _ 3104 void G4GMocrenIO::setLittleEndianInput(bool _little) {kLittleEndianInput = _little;}
3125 void G4GMocrenIO::setLittleEndianOutput(bool 3105 void G4GMocrenIO::setLittleEndianOutput(bool _little) {kLittleEndianOutput = _little;}
3126 3106
3127 // voxel spacing 3107 // voxel spacing
3128 void G4GMocrenIO::setVoxelSpacing(float _spac 3108 void G4GMocrenIO::setVoxelSpacing(float _spacing[3]) {
3129 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 3109 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = _spacing[i];
3130 } 3110 }
3131 void G4GMocrenIO::getVoxelSpacing(float _spac 3111 void G4GMocrenIO::getVoxelSpacing(float _spacing[3]) {
3132 for(int i = 0; i < 3; i++) _spacing[i] = kV 3112 for(int i = 0; i < 3; i++) _spacing[i] = kVoxelSpacing[i];
3133 } 3113 }
3134 3114
3135 // get & set number of events 3115 // get & set number of events
3136 int & G4GMocrenIO::getNumberOfEvents() { 3116 int & G4GMocrenIO::getNumberOfEvents() {
3137 return kNumberOfEvents; 3117 return kNumberOfEvents;
3138 } 3118 }
3139 void G4GMocrenIO::setNumberOfEvents(int & _nu 3119 void G4GMocrenIO::setNumberOfEvents(int & _numberOfEvents) {
3140 kNumberOfEvents = _numberOfEvents; 3120 kNumberOfEvents = _numberOfEvents;
3141 } 3121 }
3142 void G4GMocrenIO::addOneEvent() { 3122 void G4GMocrenIO::addOneEvent() {
3143 kNumberOfEvents++; 3123 kNumberOfEvents++;
3144 } 3124 }
3145 3125
3146 // set/get pointer the modality image data 3126 // set/get pointer the modality image data
3147 void G4GMocrenIO::setPointerToModalityData(un 3127 void G4GMocrenIO::setPointerToModalityData(unsigned int & _pointer) {
3148 kPointerToModalityData = _pointer; 3128 kPointerToModalityData = _pointer;
3149 } 3129 }
3150 unsigned int G4GMocrenIO::getPointerToModalit 3130 unsigned int G4GMocrenIO::getPointerToModalityData() {
3151 return kPointerToModalityData; 3131 return kPointerToModalityData;
3152 } 3132 }
3153 // set/get pointer the dose distribution imag 3133 // set/get pointer the dose distribution image data
3154 void G4GMocrenIO::addPointerToDoseDistData(un 3134 void G4GMocrenIO::addPointerToDoseDistData(unsigned int & _pointer) {
3155 kPointerToDoseDistData.push_back(_pointer); 3135 kPointerToDoseDistData.push_back(_pointer);
3156 } 3136 }
3157 unsigned int G4GMocrenIO::getPointerToDoseDis 3137 unsigned int G4GMocrenIO::getPointerToDoseDistData(int _elem) {
3158 if(kPointerToDoseDistData.size() == 0 || 3138 if(kPointerToDoseDistData.size() == 0 ||
3159 kPointerToDoseDistData.size() < (size_t) 3139 kPointerToDoseDistData.size() < (size_t)_elem)
3160 return 0; 3140 return 0;
3161 else 3141 else
3162 return kPointerToDoseDistData[_elem]; 3142 return kPointerToDoseDistData[_elem];
3163 } 3143 }
3164 3144
3165 // set/get pointer the ROI image data 3145 // set/get pointer the ROI image data
3166 void G4GMocrenIO::setPointerToROIData(unsigne 3146 void G4GMocrenIO::setPointerToROIData(unsigned int & _pointer) {
3167 kPointerToROIData = _pointer; 3147 kPointerToROIData = _pointer;
3168 } 3148 }
3169 unsigned int G4GMocrenIO::getPointerToROIData 3149 unsigned int G4GMocrenIO::getPointerToROIData() {
3170 return kPointerToROIData; 3150 return kPointerToROIData;
3171 } 3151 }
3172 // set/get pointer the track data 3152 // set/get pointer the track data
3173 void G4GMocrenIO::setPointerToTrackData(unsig 3153 void G4GMocrenIO::setPointerToTrackData(unsigned int & _pointer) {
3174 kPointerToTrackData = _pointer; 3154 kPointerToTrackData = _pointer;
3175 } 3155 }
3176 unsigned int G4GMocrenIO::getPointerToTrackDa 3156 unsigned int G4GMocrenIO::getPointerToTrackData() {
3177 return kPointerToTrackData; 3157 return kPointerToTrackData;
3178 } 3158 }
3179 3159
3180 // calculate pointers for version 4 3160 // calculate pointers for version 4
3181 void G4GMocrenIO::calcPointers4() { 3161 void G4GMocrenIO::calcPointers4() {
3182 3162
3183 // pointer to modality data 3163 // pointer to modality data
3184 unsigned int pointer = 1070; // up to "poin 3164 unsigned int pointer = 1070; // up to "pointer to the detector data" except for "pointer to the dose dist data"
3185 int nDoseDist = getNumDoseDist(); 3165 int nDoseDist = getNumDoseDist();
3186 pointer += nDoseDist*4; 3166 pointer += nDoseDist*4;
3187 3167
3188 setPointerToModalityData(pointer); 3168 setPointerToModalityData(pointer);
3189 3169
3190 // pointer to dose data 3170 // pointer to dose data
3191 // ct-density map for modality data 3171 // ct-density map for modality data
3192 int msize[3]; 3172 int msize[3];
3193 getModalityImageSize(msize); 3173 getModalityImageSize(msize);
3194 short mminmax[2]; 3174 short mminmax[2];
3195 getModalityImageMinMax(mminmax); 3175 getModalityImageMinMax(mminmax);
3196 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3176 int pmsize = 2*msize[0]*msize[1]*msize[2];
3197 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3177 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3198 pointer += 32 + pmsize + pmmap; 3178 pointer += 32 + pmsize + pmmap;
3199 // 3179 //
3200 kPointerToDoseDistData.clear(); 3180 kPointerToDoseDistData.clear();
3201 if(nDoseDist == 0) { 3181 if(nDoseDist == 0) {
3202 unsigned int pointer0 = 0; 3182 unsigned int pointer0 = 0;
3203 addPointerToDoseDistData(pointer0); 3183 addPointerToDoseDistData(pointer0);
3204 } 3184 }
3205 for(int ndose = 0; ndose < nDoseDist; ndose 3185 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3206 addPointerToDoseDistData(pointer); 3186 addPointerToDoseDistData(pointer);
3207 int dsize[3]; 3187 int dsize[3];
3208 getDoseDistSize(dsize); 3188 getDoseDistSize(dsize);
3209 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3189 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2 + 80;
3210 } 3190 }
3211 3191
3212 // pointer to roi data 3192 // pointer to roi data
3213 if(!isROIEmpty()) { 3193 if(!isROIEmpty()) {
3214 setPointerToROIData(pointer); 3194 setPointerToROIData(pointer);
3215 3195
3216 int rsize[3]; 3196 int rsize[3];
3217 getROISize(rsize); 3197 getROISize(rsize);
3218 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3198 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3219 pointer += 20 + prsize + 12; 3199 pointer += 20 + prsize + 12;
3220 } else { 3200 } else {
3221 unsigned int pointer0 = 0; 3201 unsigned int pointer0 = 0;
3222 setPointerToROIData(pointer0); 3202 setPointerToROIData(pointer0);
3223 } 3203 }
3224 3204
3225 // pointer to track data 3205 // pointer to track data
3226 int ntrk = (int)kTracks.size(); << 3206 int ntrk = kTracks.size();
3227 if(ntrk != 0) { 3207 if(ntrk != 0) {
3228 setPointerToTrackData(pointer); 3208 setPointerToTrackData(pointer);
3229 3209
3230 pointer += 4; // # of tracks 3210 pointer += 4; // # of tracks
3231 for(int nt = 0; nt < ntrk; nt++) { 3211 for(int nt = 0; nt < ntrk; nt++) {
3232 int nsteps = kTracks[nt].getNumberOfSte 3212 int nsteps = kTracks[nt].getNumberOfSteps();
3233 pointer += 4 + 3 + nsteps*(4*6); // # o 3213 pointer += 4 + 3 + nsteps*(4*6); // # of steps + color + steps(float*6)
3234 } 3214 }
3235 } else { 3215 } else {
3236 unsigned int pointer0 = 0; 3216 unsigned int pointer0 = 0;
3237 setPointerToTrackData(pointer0); 3217 setPointerToTrackData(pointer0);
3238 } 3218 }
3239 if(kVerbose > 0) G4cout << " pointer to the << 3219 if(kVerbose > 0) std::cout << " pointer to the track data :"
3240 << kPointerToTrackData << G4endl; << 3220 << kPointerToTrackData << std::endl;
3241 3221
3242 // pointer to detector data 3222 // pointer to detector data
3243 int ndet = (int)kDetectors.size(); << 3223 int ndet = kDetectors.size();
3244 if(ndet != 0) { 3224 if(ndet != 0) {
3245 kPointerToDetectorData = pointer; 3225 kPointerToDetectorData = pointer;
3246 } else { 3226 } else {
3247 kPointerToDetectorData = 0; 3227 kPointerToDetectorData = 0;
3248 } 3228 }
3249 if(kVerbose > 0) G4cout << " pointer to the << 3229 if(kVerbose > 0) std::cout << " pointer to the detector data :"
3250 << kPointerToDetectorData << G4end << 3230 << kPointerToDetectorData << std::endl;
3251 3231
3252 } 3232 }
3253 3233
3254 // calculate pointers for ver.3 3234 // calculate pointers for ver.3
3255 void G4GMocrenIO::calcPointers3() { 3235 void G4GMocrenIO::calcPointers3() {
3256 3236
3257 // pointer to modality data 3237 // pointer to modality data
3258 unsigned int pointer = 1066; // up to "poin 3238 unsigned int pointer = 1066; // up to "pointer to the track data" except for "pointer to the dose dist data"
3259 int nDoseDist = getNumDoseDist(); 3239 int nDoseDist = getNumDoseDist();
3260 pointer += nDoseDist*4; 3240 pointer += nDoseDist*4;
3261 3241
3262 setPointerToModalityData(pointer); 3242 setPointerToModalityData(pointer);
3263 3243
3264 // pointer to dose data 3244 // pointer to dose data
3265 // ct-density map for modality data 3245 // ct-density map for modality data
3266 int msize[3]; 3246 int msize[3];
3267 getModalityImageSize(msize); 3247 getModalityImageSize(msize);
3268 short mminmax[2]; 3248 short mminmax[2];
3269 getModalityImageMinMax(mminmax); 3249 getModalityImageMinMax(mminmax);
3270 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3250 int pmsize = 2*msize[0]*msize[1]*msize[2];
3271 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3251 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3272 pointer += 32 + pmsize + pmmap; 3252 pointer += 32 + pmsize + pmmap;
3273 // 3253 //
3274 kPointerToDoseDistData.clear(); 3254 kPointerToDoseDistData.clear();
3275 if(nDoseDist == 0) { 3255 if(nDoseDist == 0) {
3276 unsigned int pointer0 = 0; 3256 unsigned int pointer0 = 0;
3277 addPointerToDoseDistData(pointer0); 3257 addPointerToDoseDistData(pointer0);
3278 } 3258 }
3279 for(int ndose = 0; ndose < nDoseDist; ndose 3259 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3280 addPointerToDoseDistData(pointer); 3260 addPointerToDoseDistData(pointer);
3281 int dsize[3]; 3261 int dsize[3];
3282 getDoseDistSize(dsize); 3262 getDoseDistSize(dsize);
3283 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3263 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2;
3284 } 3264 }
3285 3265
3286 // pointer to roi data 3266 // pointer to roi data
3287 if(!isROIEmpty()) { 3267 if(!isROIEmpty()) {
3288 setPointerToROIData(pointer); 3268 setPointerToROIData(pointer);
3289 3269
3290 int rsize[3]; 3270 int rsize[3];
3291 getROISize(rsize); 3271 getROISize(rsize);
3292 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3272 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3293 pointer += 20 + prsize + 12; 3273 pointer += 20 + prsize + 12;
3294 } else { 3274 } else {
3295 unsigned int pointer0 = 0; 3275 unsigned int pointer0 = 0;
3296 setPointerToROIData(pointer0); 3276 setPointerToROIData(pointer0);
3297 } 3277 }
3298 3278
3299 // 3279 //
3300 if(getNumTracks() != 0) 3280 if(getNumTracks() != 0)
3301 setPointerToTrackData(pointer); 3281 setPointerToTrackData(pointer);
3302 else { 3282 else {
3303 unsigned int pointer0 = 0; 3283 unsigned int pointer0 = 0;
3304 setPointerToTrackData(pointer0); 3284 setPointerToTrackData(pointer0);
3305 } 3285 }
3306 3286
3307 } 3287 }
3308 3288
3309 // calculate pointers for ver.2 3289 // calculate pointers for ver.2
3310 void G4GMocrenIO::calcPointers2() { 3290 void G4GMocrenIO::calcPointers2() {
3311 3291
3312 // pointer to modality data 3292 // pointer to modality data
3313 unsigned int pointer = 65; 3293 unsigned int pointer = 65;
3314 setPointerToModalityData(pointer); 3294 setPointerToModalityData(pointer);
3315 3295
3316 // pointer to dose data 3296 // pointer to dose data
3317 int msize[3]; 3297 int msize[3];
3318 getModalityImageSize(msize); 3298 getModalityImageSize(msize);
3319 short mminmax[2]; 3299 short mminmax[2];
3320 getModalityImageMinMax(mminmax); 3300 getModalityImageMinMax(mminmax);
3321 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3301 int pmsize = 2*msize[0]*msize[1]*msize[2];
3322 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3302 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3323 pointer += 20 + pmsize + pmmap; 3303 pointer += 20 + pmsize + pmmap;
3324 int dsize[3]; 3304 int dsize[3];
3325 getDoseDistSize(dsize); 3305 getDoseDistSize(dsize);
3326 kPointerToDoseDistData.clear(); 3306 kPointerToDoseDistData.clear();
3327 if(dsize[0] != 0) { 3307 if(dsize[0] != 0) {
3328 kPointerToDoseDistData.push_back(pointer) 3308 kPointerToDoseDistData.push_back(pointer);
3329 3309
3330 int pdsize = 2*dsize[0]*dsize[1]*dsize[2] 3310 int pdsize = 2*dsize[0]*dsize[1]*dsize[2];
3331 pointer += 20 + pdsize + 12; 3311 pointer += 20 + pdsize + 12;
3332 } else { 3312 } else {
3333 unsigned int pointer0 = 0; 3313 unsigned int pointer0 = 0;
3334 kPointerToDoseDistData.push_back(pointer0 3314 kPointerToDoseDistData.push_back(pointer0);
3335 } 3315 }
3336 3316
3337 // pointer to roi data 3317 // pointer to roi data
3338 if(!isROIEmpty()) { 3318 if(!isROIEmpty()) {
3339 int rsize[3]; 3319 int rsize[3];
3340 getROISize(rsize); 3320 getROISize(rsize);
3341 setPointerToROIData(pointer); 3321 setPointerToROIData(pointer);
3342 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3322 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3343 pointer += 20 + prsize + 12; 3323 pointer += 20 + prsize + 12;
3344 3324
3345 } else { 3325 } else {
3346 unsigned int pointer0 = 0; 3326 unsigned int pointer0 = 0;
3347 setPointerToROIData(pointer0); 3327 setPointerToROIData(pointer0);
3348 } 3328 }
3349 3329
3350 // 3330 //
3351 if(getNumTracks() != 0) 3331 if(getNumTracks() != 0)
3352 setPointerToTrackData(pointer); 3332 setPointerToTrackData(pointer);
3353 else { 3333 else {
3354 unsigned int pointer0 = 0; 3334 unsigned int pointer0 = 0;
3355 setPointerToTrackData(pointer0); 3335 setPointerToTrackData(pointer0);
3356 } 3336 }
3357 3337
3358 } 3338 }
3359 3339
3360 3340
3361 //----- Modality image -----// 3341 //----- Modality image -----//
3362 void G4GMocrenIO::getModalityImageSize(int _s 3342 void G4GMocrenIO::getModalityImageSize(int _size[3]) {
3363 3343
3364 kModality.getSize(_size); 3344 kModality.getSize(_size);
3365 } 3345 }
3366 void G4GMocrenIO::setModalityImageSize(int _s 3346 void G4GMocrenIO::setModalityImageSize(int _size[3]) {
3367 3347
3368 kModality.setSize(_size); 3348 kModality.setSize(_size);
3369 } 3349 }
3370 3350
3371 // get & set the modality image size 3351 // get & set the modality image size
3372 void G4GMocrenIO::setModalityImageScale(doubl 3352 void G4GMocrenIO::setModalityImageScale(double & _scale) {
3373 3353
3374 kModality.setScale(_scale); 3354 kModality.setScale(_scale);
3375 } 3355 }
3376 double G4GMocrenIO::getModalityImageScale() { 3356 double G4GMocrenIO::getModalityImageScale() {
3377 3357
3378 return kModality.getScale(); 3358 return kModality.getScale();
3379 } 3359 }
3380 3360
3381 // set the modality image in CT 3361 // set the modality image in CT
3382 void G4GMocrenIO::setModalityImage(short * _i 3362 void G4GMocrenIO::setModalityImage(short * _image) {
3383 3363
3384 kModality.addImage(_image); 3364 kModality.addImage(_image);
3385 } 3365 }
3386 short * G4GMocrenIO::getModalityImage(int _z) 3366 short * G4GMocrenIO::getModalityImage(int _z) {
3387 3367
3388 return kModality.getImage(_z); 3368 return kModality.getImage(_z);
3389 } 3369 }
3390 void G4GMocrenIO::clearModalityImage() { 3370 void G4GMocrenIO::clearModalityImage() {
3391 3371
3392 kModality.clearImage(); 3372 kModality.clearImage();
3393 } 3373 }
3394 // set/get the modality image density map 3374 // set/get the modality image density map
3395 void G4GMocrenIO::setModalityImageDensityMap( 3375 void G4GMocrenIO::setModalityImageDensityMap(std::vector<float> & _map) {
3396 kModalityImageDensityMap = _map; 3376 kModalityImageDensityMap = _map;
3397 } 3377 }
3398 std::vector<float> & G4GMocrenIO::getModality 3378 std::vector<float> & G4GMocrenIO::getModalityImageDensityMap() {
3399 return kModalityImageDensityMap; 3379 return kModalityImageDensityMap;
3400 } 3380 }
3401 // set the modality image min./max. 3381 // set the modality image min./max.
3402 void G4GMocrenIO::setModalityImageMinMax(shor 3382 void G4GMocrenIO::setModalityImageMinMax(short _minmax[2]) {
3403 3383
3404 kModality.setMinMax(_minmax); 3384 kModality.setMinMax(_minmax);
3405 } 3385 }
3406 // get the modality image min./max. 3386 // get the modality image min./max.
3407 void G4GMocrenIO::getModalityImageMinMax(shor 3387 void G4GMocrenIO::getModalityImageMinMax(short _minmax[2]) {
3408 3388
3409 short minmax[2]; 3389 short minmax[2];
3410 kModality.getMinMax(minmax); 3390 kModality.getMinMax(minmax);
3411 for(int i = 0; i < 2; i++) _minmax[i] = min 3391 for(int i = 0; i < 2; i++) _minmax[i] = minmax[i];
3412 } 3392 }
3413 short G4GMocrenIO::getModalityImageMax() { 3393 short G4GMocrenIO::getModalityImageMax() {
3414 3394
3415 short minmax[2]; 3395 short minmax[2];
3416 kModality.getMinMax(minmax); 3396 kModality.getMinMax(minmax);
3417 return minmax[1]; 3397 return minmax[1];
3418 } 3398 }
3419 short G4GMocrenIO::getModalityImageMin() { 3399 short G4GMocrenIO::getModalityImageMin() {
3420 3400
3421 short minmax[2]; 3401 short minmax[2];
3422 kModality.getMinMax(minmax); 3402 kModality.getMinMax(minmax);
3423 return minmax[0]; 3403 return minmax[0];
3424 } 3404 }
3425 // set/get position of the modality image cen 3405 // set/get position of the modality image center
3426 void G4GMocrenIO::setModalityCenterPosition(f 3406 void G4GMocrenIO::setModalityCenterPosition(float _center[3]) {
3427 3407
3428 kModality.setCenterPosition(_center); 3408 kModality.setCenterPosition(_center);
3429 } 3409 }
3430 void G4GMocrenIO::getModalityCenterPosition(f 3410 void G4GMocrenIO::getModalityCenterPosition(float _center[3]) {
3431 3411
3432 if(isROIEmpty()) 3412 if(isROIEmpty())
3433 for(int i = 0; i < 3; i++) _center[i] = 0 3413 for(int i = 0; i < 3; i++) _center[i] = 0;
3434 else 3414 else
3435 kModality.getCenterPosition(_center); 3415 kModality.getCenterPosition(_center);
3436 } 3416 }
3437 // get & set the modality image unit 3417 // get & set the modality image unit
3438 std::string G4GMocrenIO::getModalityImageUnit 3418 std::string G4GMocrenIO::getModalityImageUnit() {
3439 return kModalityUnit; 3419 return kModalityUnit;
3440 } 3420 }
3441 void G4GMocrenIO::setModalityImageUnit(std::s 3421 void G4GMocrenIO::setModalityImageUnit(std::string & _unit) {
3442 kModalityUnit = _unit; 3422 kModalityUnit = _unit;
3443 } 3423 }
3444 // 3424 //
3445 short G4GMocrenIO::convertDensityToHU(float & 3425 short G4GMocrenIO::convertDensityToHU(float & _dens) {
3446 short rval = -1024; // default: air 3426 short rval = -1024; // default: air
3447 int nmap = (int)kModalityImageDensityMap.si 3427 int nmap = (int)kModalityImageDensityMap.size();
3448 if(nmap != 0) { 3428 if(nmap != 0) {
3449 short minmax[2]; 3429 short minmax[2];
3450 kModality.getMinMax(minmax); 3430 kModality.getMinMax(minmax);
3451 rval = minmax[1]; 3431 rval = minmax[1];
3452 for(int i = 0; i < nmap; i++) { 3432 for(int i = 0; i < nmap; i++) {
3453 //G4cout << kModalityImageDensityMap[i] << 3433 //std::cout << kModalityImageDensityMap[i] << std::endl;
3454 if(_dens <= kModalityImageDensityMap[i] 3434 if(_dens <= kModalityImageDensityMap[i]) {
3455 rval = i + minmax[0]; 3435 rval = i + minmax[0];
3456 break; 3436 break;
3457 } 3437 }
3458 } 3438 }
3459 } 3439 }
3460 return rval; 3440 return rval;
3461 } 3441 }
3462 3442
3463 3443
3464 //----- Dose distribution -----// 3444 //----- Dose distribution -----//
3465 // 3445 //
3466 void G4GMocrenIO::newDoseDist() { 3446 void G4GMocrenIO::newDoseDist() {
3467 GMocrenDataPrimitive<double> doseData; 3447 GMocrenDataPrimitive<double> doseData;
3468 kDose.push_back(doseData); 3448 kDose.push_back(doseData);
3469 } 3449 }
3470 int G4GMocrenIO::getNumDoseDist() { 3450 int G4GMocrenIO::getNumDoseDist() {
3471 return (int)kDose.size(); 3451 return (int)kDose.size();
3472 } 3452 }
3473 3453
3474 // get & set the dose distribution unit 3454 // get & set the dose distribution unit
3475 std::string G4GMocrenIO::getDoseDistUnit(int 3455 std::string G4GMocrenIO::getDoseDistUnit(int _num) {
3476 // to avoid a warning in the compile proces 3456 // to avoid a warning in the compile process
3477 if(kDoseUnit.size() > static_cast<size_t>(_ << 3457 int dummynum;
>> 3458 dummynum = _num;
3478 3459
3479 return kDoseUnit; 3460 return kDoseUnit;
3480 } 3461 }
3481 void G4GMocrenIO::setDoseDistUnit(std::string 3462 void G4GMocrenIO::setDoseDistUnit(std::string & _unit, int _num) {
3482 // to avoid a warning in the compile proces 3463 // to avoid a warning in the compile process
3483 if(_unit.size() > static_cast<size_t>(_num) << 3464 int dummynum;
>> 3465 dummynum = _num;
3484 3466
3485 //char unit[13]; 3467 //char unit[13];
3486 //std::strncpy(unit, _unit.c_str(), 12); 3468 //std::strncpy(unit, _unit.c_str(), 12);
3487 //doseUnit = unit; 3469 //doseUnit = unit;
3488 kDoseUnit = _unit; 3470 kDoseUnit = _unit;
3489 } 3471 }
3490 // 3472 //
3491 void G4GMocrenIO::getDoseDistSize(int _size[3 3473 void G4GMocrenIO::getDoseDistSize(int _size[3], int _num) {
3492 if(isDoseEmpty()) 3474 if(isDoseEmpty())
3493 for(int i = 0; i < 3; i++) _size[i] = 0; 3475 for(int i = 0; i < 3; i++) _size[i] = 0;
3494 else 3476 else
3495 kDose[_num].getSize(_size); 3477 kDose[_num].getSize(_size);
3496 } 3478 }
3497 void G4GMocrenIO::setDoseDistSize(int _size[3 3479 void G4GMocrenIO::setDoseDistSize(int _size[3], int _num) {
3498 3480
3499 kDose[_num].setSize(_size); 3481 kDose[_num].setSize(_size);
3500 3482
3501 //resetDose(); 3483 //resetDose();
3502 } 3484 }
3503 3485
3504 void G4GMocrenIO::setDoseDistMinMax(short _mi 3486 void G4GMocrenIO::setDoseDistMinMax(short _minmax[2], int _num) {
3505 3487
3506 double minmax[2]; 3488 double minmax[2];
3507 double scale = kDose[_num].getScale(); 3489 double scale = kDose[_num].getScale();
3508 for(int i = 0; i < 2; i++) minmax[i] = (dou 3490 for(int i = 0; i < 2; i++) minmax[i] = (double)_minmax[i]*scale;
3509 kDose[_num].setMinMax(minmax); 3491 kDose[_num].setMinMax(minmax);
3510 } 3492 }
3511 void G4GMocrenIO::getDoseDistMinMax(short _mi 3493 void G4GMocrenIO::getDoseDistMinMax(short _minmax[2], int _num) {
3512 3494
3513 if(isDoseEmpty()) 3495 if(isDoseEmpty())
3514 for(int i = 0; i < 2; i++) _minmax[i] = 0 3496 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3515 else { 3497 else {
3516 double minmax[2]; 3498 double minmax[2];
3517 kDose[_num].getMinMax(minmax); 3499 kDose[_num].getMinMax(minmax);
3518 double scale = kDose[_num].getScale(); 3500 double scale = kDose[_num].getScale();
3519 for(int i = 0; i < 2; i++) _minmax[i] = ( 3501 for(int i = 0; i < 2; i++) _minmax[i] = (short)(minmax[i]/scale+0.5);
3520 } 3502 }
3521 } 3503 }
3522 void G4GMocrenIO::setDoseDistMinMax(double _m 3504 void G4GMocrenIO::setDoseDistMinMax(double _minmax[2], int _num) {
3523 3505
3524 kDose[_num].setMinMax(_minmax); 3506 kDose[_num].setMinMax(_minmax);
3525 } 3507 }
3526 void G4GMocrenIO::getDoseDistMinMax(double _m 3508 void G4GMocrenIO::getDoseDistMinMax(double _minmax[2], int _num) {
3527 3509
3528 if(isDoseEmpty()) 3510 if(isDoseEmpty())
3529 for(int i = 0; i < 2; i++) _minmax[i] = 0 3511 for(int i = 0; i < 2; i++) _minmax[i] = 0.;
3530 else 3512 else
3531 kDose[_num].getMinMax(_minmax); 3513 kDose[_num].getMinMax(_minmax);
3532 } 3514 }
3533 3515
3534 // get & set the dose distribution image scal 3516 // get & set the dose distribution image scale
3535 void G4GMocrenIO::setDoseDistScale(double & _ 3517 void G4GMocrenIO::setDoseDistScale(double & _scale, int _num) {
3536 3518
3537 kDose[_num].setScale(_scale); 3519 kDose[_num].setScale(_scale);
3538 } 3520 }
3539 double G4GMocrenIO::getDoseDistScale(int _num 3521 double G4GMocrenIO::getDoseDistScale(int _num) {
3540 3522
3541 if(isDoseEmpty()) 3523 if(isDoseEmpty())
3542 return 0.; 3524 return 0.;
3543 else 3525 else
3544 return kDose[_num].getScale(); 3526 return kDose[_num].getScale();
3545 } 3527 }
3546 3528
3547 /* 3529 /*
3548 void G4GMocrenIO::initializeShortDoseDist() 3530 void G4GMocrenIO::initializeShortDoseDist() {
3549 ; 3531 ;
3550 } 3532 }
3551 void G4GMocrenIO::finalizeShortDoseDist() { 3533 void G4GMocrenIO::finalizeShortDoseDist() {
3552 ; 3534 ;
3553 } 3535 }
3554 */ 3536 */
3555 // set the dose distribution image 3537 // set the dose distribution image
3556 void G4GMocrenIO::setShortDoseDist(short * _i 3538 void G4GMocrenIO::setShortDoseDist(short * _image, int _num) {
3557 3539
3558 int size[3]; 3540 int size[3];
3559 kDose[_num].getSize(size); 3541 kDose[_num].getSize(size);
3560 int dsize = size[0]*size[1]; 3542 int dsize = size[0]*size[1];
3561 double * ddata = new double[dsize]; 3543 double * ddata = new double[dsize];
3562 double scale = kDose[_num].getScale(); 3544 double scale = kDose[_num].getScale();
3563 double minmax[2]; 3545 double minmax[2];
3564 kDose[_num].getMinMax(minmax); 3546 kDose[_num].getMinMax(minmax);
3565 for(int xy = 0; xy < dsize; xy++) { 3547 for(int xy = 0; xy < dsize; xy++) {
3566 ddata[xy] = _image[xy]*scale; 3548 ddata[xy] = _image[xy]*scale;
3567 if(ddata[xy] < minmax[0]) minmax[0] = dda 3549 if(ddata[xy] < minmax[0]) minmax[0] = ddata[xy];
3568 if(ddata[xy] > minmax[1]) minmax[1] = dda 3550 if(ddata[xy] > minmax[1]) minmax[1] = ddata[xy];
3569 } 3551 }
3570 kDose[_num].addImage(ddata); 3552 kDose[_num].addImage(ddata);
3571 3553
3572 // set min./max. 3554 // set min./max.
3573 kDose[_num].setMinMax(minmax); 3555 kDose[_num].setMinMax(minmax);
3574 } 3556 }
3575 void G4GMocrenIO::getShortDoseDist(short * _d 3557 void G4GMocrenIO::getShortDoseDist(short * _data, int _z, int _num) {
3576 3558
3577 if(_data == NULL) { 3559 if(_data == NULL) {
3578 if (G4VisManager::GetVerbosity() >= G4Vis << 3560 std::cerr << "In G4GMocrenIO::getShortDoseDist(), "
3579 G4cout << "In G4GMocrenIO::getShortDose << 3561 << "first argument is NULL pointer. "
3580 << "first argument is NULL pointer. " << 3562 << "The argument must be allocated array."
3581 << "The argument must be allocated array. << 3563 << std::endl;
3582 << G4endl; << 3564 std::exit(-1);
3583 G4Exception("G4GMocrenIO::getShortDoseDis <<
3584 "gMocren2002", FatalException <<
3585 "Error."); <<
3586 return; <<
3587 } 3565 }
3588 3566
3589 int size[3]; 3567 int size[3];
3590 kDose[_num].getSize(size); 3568 kDose[_num].getSize(size);
3591 //short * shdata = new short[size[0]*size[1 3569 //short * shdata = new short[size[0]*size[1]];
3592 double * ddata = kDose[_num].getImage(_z); 3570 double * ddata = kDose[_num].getImage(_z);
3593 double scale = kDose[_num].getScale(); 3571 double scale = kDose[_num].getScale();
3594 for(int xy = 0; xy < size[0]*size[1]; xy++) 3572 for(int xy = 0; xy < size[0]*size[1]; xy++) {
3595 _data[xy] = (short)(ddata[xy]/scale+0.5); 3573 _data[xy] = (short)(ddata[xy]/scale+0.5); //there is never negative value
3596 } 3574 }
3597 } 3575 }
3598 void G4GMocrenIO::getShortDoseDistMinMax(shor 3576 void G4GMocrenIO::getShortDoseDistMinMax(short _minmax[2], int _num) {
3599 double scale = kDose[_num].getScale(); 3577 double scale = kDose[_num].getScale();
3600 double minmax[2]; 3578 double minmax[2];
3601 kDose[_num].getMinMax(minmax); 3579 kDose[_num].getMinMax(minmax);
3602 for(int i = 0; i < 2; i++) 3580 for(int i = 0; i < 2; i++)
3603 _minmax[i] = (short)(minmax[i]/scale+0.5) 3581 _minmax[i] = (short)(minmax[i]/scale+0.5);
3604 } 3582 }
3605 // 3583 //
3606 void G4GMocrenIO::setDoseDist(double * _image 3584 void G4GMocrenIO::setDoseDist(double * _image, int _num) {
3607 3585
3608 kDose[_num].addImage(_image); 3586 kDose[_num].addImage(_image);
3609 } 3587 }
3610 double * G4GMocrenIO::getDoseDist(int _z, int 3588 double * G4GMocrenIO::getDoseDist(int _z, int _num) {
3611 3589
3612 double * image; 3590 double * image;
3613 if(isDoseEmpty()) { 3591 if(isDoseEmpty()) {
3614 image = 0; 3592 image = 0;
3615 } else { 3593 } else {
3616 image = kDose[_num].getImage(_z); 3594 image = kDose[_num].getImage(_z);
3617 } 3595 }
3618 return image; 3596 return image;
3619 } 3597 }
3620 /* 3598 /*
3621 void G4GMocrenIO::getDoseDist(double * & _i 3599 void G4GMocrenIO::getDoseDist(double * & _image, int _z, int _num) {
3622 3600
3623 G4cout << " <" << (void*)_image << "> "; << 3601 std::cout << " <" << (void*)_image << "> ";
3624 if(isDoseEmpty()) { 3602 if(isDoseEmpty()) {
3625 _image = 0; 3603 _image = 0;
3626 } else { 3604 } else {
3627 _image = kDose[_num].getImage(_z); 3605 _image = kDose[_num].getImage(_z);
3628 G4cout << " <" << (void*)_image << "> "; << 3606 std::cout << " <" << (void*)_image << "> ";
3629 G4cout << _image[100] << " "; << 3607 std::cout << _image[100] << " ";
3630 } 3608 }
3631 } 3609 }
3632 */ 3610 */
3633 bool G4GMocrenIO::addDoseDist(std::vector<dou 3611 bool G4GMocrenIO::addDoseDist(std::vector<double *> & _image, int _num) {
3634 3612
3635 int size[3]; 3613 int size[3];
3636 getDoseDistSize(size, _num); 3614 getDoseDistSize(size, _num);
3637 std::vector<double *> dosedist = kDose[_num 3615 std::vector<double *> dosedist = kDose[_num].getImage();
3638 3616
3639 int nimg = size[0]*size[1]; 3617 int nimg = size[0]*size[1];
3640 for(int z = 0; z < size[2]; z++) { 3618 for(int z = 0; z < size[2]; z++) {
3641 for(int xy = 0; xy < nimg; xy++) { 3619 for(int xy = 0; xy < nimg; xy++) {
3642 dosedist[z][xy] += _image[z][xy]; 3620 dosedist[z][xy] += _image[z][xy];
3643 } 3621 }
3644 } 3622 }
3645 3623
3646 return true; 3624 return true;
3647 } 3625 }
3648 //void setDoseDistDensityMap(float * _map) {d 3626 //void setDoseDistDensityMap(float * _map) {doseImageDensityMap = _map;};
3649 // set the dose distribution image displaceme 3627 // set the dose distribution image displacement
3650 void G4GMocrenIO::setDoseDistCenterPosition(f 3628 void G4GMocrenIO::setDoseDistCenterPosition(float _center[3], int _num) {
3651 3629
3652 kDose[_num].setCenterPosition(_center); 3630 kDose[_num].setCenterPosition(_center);
3653 } 3631 }
3654 void G4GMocrenIO::getDoseDistCenterPosition(f 3632 void G4GMocrenIO::getDoseDistCenterPosition(float _center[3], int _num) {
3655 3633
3656 if(isDoseEmpty()) 3634 if(isDoseEmpty())
3657 for(int i = 0; i < 3; i++) _center[i] = 0 3635 for(int i = 0; i < 3; i++) _center[i] = 0;
3658 else 3636 else
3659 kDose[_num].getCenterPosition(_center); 3637 kDose[_num].getCenterPosition(_center);
3660 } 3638 }
3661 // set & get name of dose distribution 3639 // set & get name of dose distribution
3662 void G4GMocrenIO::setDoseDistName(std::string 3640 void G4GMocrenIO::setDoseDistName(std::string _name, int _num) {
3663 3641
3664 kDose[_num].setName(_name); 3642 kDose[_num].setName(_name);
3665 } 3643 }
3666 std::string G4GMocrenIO::getDoseDistName(int 3644 std::string G4GMocrenIO::getDoseDistName(int _num) {
3667 3645
3668 std::string name; 3646 std::string name;
3669 if(isDoseEmpty()) 3647 if(isDoseEmpty())
3670 return name; 3648 return name;
3671 else 3649 else
3672 return kDose[_num].getName(); 3650 return kDose[_num].getName();
3673 } 3651 }
3674 // copy dose distributions 3652 // copy dose distributions
3675 void G4GMocrenIO::copyDoseDist(std::vector<cl 3653 void G4GMocrenIO::copyDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3676 std::vector<class GMocrenDataPrimitive<doub 3654 std::vector<class GMocrenDataPrimitive<double> >::iterator itr;
3677 for(itr = kDose.begin(); itr != kDose.end() 3655 for(itr = kDose.begin(); itr != kDose.end(); itr++) {
3678 _dose.push_back(*itr); 3656 _dose.push_back(*itr);
3679 } 3657 }
3680 } 3658 }
3681 // merge two dose distributions 3659 // merge two dose distributions
3682 bool G4GMocrenIO::mergeDoseDist(std::vector<c 3660 bool G4GMocrenIO::mergeDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3683 if(kDose.size() != _dose.size()) { 3661 if(kDose.size() != _dose.size()) {
3684 if (G4VisManager::GetVerbosity() >= G4Vis << 3662 std::cerr << "G4GMocrenIO::mergeDoseDist() : Error" << std::endl;
3685 G4cout << "G4GMocrenIO::mergeDoseDist() << 3663 std::cerr << " Unable to merge the dose distributions,"<< std::endl;
3686 G4cout << " Unable to merge the dose << 3664 std::cerr << " because of different size of dose maps."<< std::endl;
3687 G4cout << " because of different size <<
3688 } <<
3689 return false; 3665 return false;
3690 } 3666 }
3691 3667
3692 int num = (int)kDose.size(); << 3668 int num = kDose.size();
3693 std::vector<class GMocrenDataPrimitive<doub 3669 std::vector<class GMocrenDataPrimitive<double> >::iterator itr1 = kDose.begin();
3694 std::vector<class GMocrenDataPrimitive<doub 3670 std::vector<class GMocrenDataPrimitive<double> >::iterator itr2 = _dose.begin();
3695 for(int i = 0; i < num; i++, itr1++, itr2++ 3671 for(int i = 0; i < num; i++, itr1++, itr2++) {
3696 if (G4VisManager::GetVerbosity() >= G4Vis << 3672 if(kVerbose > 0) std::cerr << "merged dose distribution [" << i << "]" << std::endl;
3697 if(kVerbose > 0) <<
3698 G4cout << "merged dose distribution [" << i <<
3699 *itr1 += *itr2; 3673 *itr1 += *itr2;
3700 } 3674 }
3701 3675
3702 return true; 3676 return true;
3703 } 3677 }
3704 // 3678 //
3705 void G4GMocrenIO::clearDoseDistAll() { 3679 void G4GMocrenIO::clearDoseDistAll() {
3706 3680
3707 if(!isDoseEmpty()) { 3681 if(!isDoseEmpty()) {
3708 for(int i = 0; i < getNumDoseDist(); i++) 3682 for(int i = 0; i < getNumDoseDist(); i++) {
3709 kDose[i].clear(); 3683 kDose[i].clear();
3710 } 3684 }
3711 kDose.clear(); 3685 kDose.clear();
3712 } 3686 }
3713 } 3687 }
3714 // 3688 //
3715 bool G4GMocrenIO::isDoseEmpty() { 3689 bool G4GMocrenIO::isDoseEmpty() {
3716 if(kDose.empty()) { 3690 if(kDose.empty()) {
3717 //if (G4VisManager::GetVerbosity() >= G4V << 3691 //std::cerr << "!!! dose distribution data is empty." << std::endl;
3718 // G4cout << "!!! dose distribution data <<
3719 return true; 3692 return true;
3720 } else { 3693 } else {
3721 return false; 3694 return false;
3722 } 3695 }
3723 } 3696 }
3724 3697
3725 // 3698 //
3726 void G4GMocrenIO::calcDoseDistScale() { 3699 void G4GMocrenIO::calcDoseDistScale() {
3727 3700
3728 double scale; 3701 double scale;
3729 double minmax[2]; 3702 double minmax[2];
3730 3703
3731 for(int i = 0; i < (int)kDose.size(); i++) 3704 for(int i = 0; i < (int)kDose.size(); i++) {
3732 kDose[i].getMinMax(minmax); 3705 kDose[i].getMinMax(minmax);
3733 scale = minmax[1]/DOSERANGE; 3706 scale = minmax[1]/DOSERANGE;
3734 kDose[i].setScale(scale); 3707 kDose[i].setScale(scale);
3735 } 3708 }
3736 } 3709 }
3737 3710
3738 3711
3739 //----- RoI -----// 3712 //----- RoI -----//
3740 3713
3741 // add one RoI data 3714 // add one RoI data
3742 void G4GMocrenIO::newROI() { 3715 void G4GMocrenIO::newROI() {
3743 GMocrenDataPrimitive<short> roiData; 3716 GMocrenDataPrimitive<short> roiData;
3744 kRoi.push_back(roiData); 3717 kRoi.push_back(roiData);
3745 } 3718 }
3746 int G4GMocrenIO::getNumROI() { 3719 int G4GMocrenIO::getNumROI() {
3747 return (int)kRoi.size(); 3720 return (int)kRoi.size();
3748 } 3721 }
3749 3722
3750 // set/get the ROI image scale 3723 // set/get the ROI image scale
3751 void G4GMocrenIO::setROIScale(double & _scale 3724 void G4GMocrenIO::setROIScale(double & _scale, int _num) {
3752 3725
3753 kRoi[_num].setScale(_scale); 3726 kRoi[_num].setScale(_scale);
3754 } 3727 }
3755 double G4GMocrenIO::getROIScale(int _num) { 3728 double G4GMocrenIO::getROIScale(int _num) {
3756 3729
3757 if(isROIEmpty()) 3730 if(isROIEmpty())
3758 return 0.; 3731 return 0.;
3759 else 3732 else
3760 return kRoi[_num].getScale(); 3733 return kRoi[_num].getScale();
3761 } 3734 }
3762 // set the ROI image 3735 // set the ROI image
3763 void G4GMocrenIO::setROI(short * _image, int 3736 void G4GMocrenIO::setROI(short * _image, int _num) {
3764 3737
3765 kRoi[_num].addImage(_image); 3738 kRoi[_num].addImage(_image);
3766 } 3739 }
3767 short * G4GMocrenIO::getROI(int _z, int _num) 3740 short * G4GMocrenIO::getROI(int _z, int _num) {
3768 3741
3769 if(isROIEmpty()) 3742 if(isROIEmpty())
3770 return 0; 3743 return 0;
3771 else 3744 else
3772 return kRoi[_num].getImage(_z); 3745 return kRoi[_num].getImage(_z);
3773 } 3746 }
3774 // set/get the ROI image size 3747 // set/get the ROI image size
3775 void G4GMocrenIO::setROISize(int _size[3], in 3748 void G4GMocrenIO::setROISize(int _size[3], int _num) {
3776 3749
3777 return kRoi[_num].setSize(_size); 3750 return kRoi[_num].setSize(_size);
3778 } 3751 }
3779 void G4GMocrenIO::getROISize(int _size[3], in 3752 void G4GMocrenIO::getROISize(int _size[3], int _num) {
3780 3753
3781 if(isROIEmpty()) 3754 if(isROIEmpty())
3782 for(int i = 0; i < 3; i++) _size[i] = 0; 3755 for(int i = 0; i < 3; i++) _size[i] = 0;
3783 else 3756 else
3784 return kRoi[_num].getSize(_size); 3757 return kRoi[_num].getSize(_size);
3785 } 3758 }
3786 // set/get the ROI image min. and max. 3759 // set/get the ROI image min. and max.
3787 void G4GMocrenIO::setROIMinMax(short _minmax[ 3760 void G4GMocrenIO::setROIMinMax(short _minmax[2], int _num) {
3788 3761
3789 kRoi[_num].setMinMax(_minmax); 3762 kRoi[_num].setMinMax(_minmax);
3790 } 3763 }
3791 void G4GMocrenIO::getROIMinMax(short _minmax[ 3764 void G4GMocrenIO::getROIMinMax(short _minmax[2], int _num) {
3792 3765
3793 if(isROIEmpty()) 3766 if(isROIEmpty())
3794 for(int i = 0; i < 2; i++) _minmax[i] = 0 3767 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3795 else 3768 else
3796 kRoi[_num].getMinMax(_minmax); 3769 kRoi[_num].getMinMax(_minmax);
3797 } 3770 }
3798 // set/get the ROI image displacement 3771 // set/get the ROI image displacement
3799 void G4GMocrenIO::setROICenterPosition(float 3772 void G4GMocrenIO::setROICenterPosition(float _center[3], int _num) {
3800 3773
3801 kRoi[_num].setCenterPosition(_center); 3774 kRoi[_num].setCenterPosition(_center);
3802 } 3775 }
3803 void G4GMocrenIO::getROICenterPosition(float 3776 void G4GMocrenIO::getROICenterPosition(float _center[3], int _num) {
3804 3777
3805 if(isROIEmpty()) 3778 if(isROIEmpty())
3806 for(int i = 0; i < 3; i++) _center[i] = 0 3779 for(int i = 0; i < 3; i++) _center[i] = 0;
3807 else 3780 else
3808 kRoi[_num].getCenterPosition(_center); 3781 kRoi[_num].getCenterPosition(_center);
3809 } 3782 }
3810 // 3783 //
3811 void G4GMocrenIO::clearROIAll() { 3784 void G4GMocrenIO::clearROIAll() {
3812 3785
3813 if(!isROIEmpty()) { 3786 if(!isROIEmpty()) {
3814 for(int i = 0; i < getNumROI(); i++) { 3787 for(int i = 0; i < getNumROI(); i++) {
3815 kRoi[i].clear(); 3788 kRoi[i].clear();
3816 } 3789 }
3817 kRoi.clear(); 3790 kRoi.clear();
3818 } 3791 }
3819 } 3792 }
3820 // 3793 //
3821 bool G4GMocrenIO::isROIEmpty() { 3794 bool G4GMocrenIO::isROIEmpty() {
3822 if(kRoi.empty()) { 3795 if(kRoi.empty()) {
3823 //if (G4VisManager::GetVerbosity() >= G4V << 3796 //std::cerr << "!!! ROI data is empty." << std::endl;
3824 // G4cout << "!!! ROI data is empty." << <<
3825 return true; 3797 return true;
3826 } else { 3798 } else {
3827 return false; 3799 return false;
3828 } 3800 }
3829 } 3801 }
3830 3802
3831 3803
3832 3804
3833 //----- Track information -----// 3805 //----- Track information -----//
3834 3806
3835 int G4GMocrenIO::getNumTracks() { 3807 int G4GMocrenIO::getNumTracks() {
3836 return (int)kSteps.size(); 3808 return (int)kSteps.size();
3837 } 3809 }
3838 int G4GMocrenIO::getNumTracks4() { 3810 int G4GMocrenIO::getNumTracks4() {
3839 return (int)kTracks.size(); 3811 return (int)kTracks.size();
3840 } 3812 }
3841 void G4GMocrenIO::addTrack(float * _tracks) { 3813 void G4GMocrenIO::addTrack(float * _tracks) {
3842 kSteps.push_back(_tracks); 3814 kSteps.push_back(_tracks);
3843 } 3815 }
3844 void G4GMocrenIO::setTracks(std::vector<float 3816 void G4GMocrenIO::setTracks(std::vector<float *> & _tracks) {
3845 kSteps = _tracks; 3817 kSteps = _tracks;
3846 } 3818 }
3847 std::vector<float *> & G4GMocrenIO::getTracks 3819 std::vector<float *> & G4GMocrenIO::getTracks() {
3848 return kSteps; 3820 return kSteps;
3849 } 3821 }
3850 void G4GMocrenIO::addTrackColor(unsigned char 3822 void G4GMocrenIO::addTrackColor(unsigned char * _colors) {
3851 kStepColors.push_back(_colors); 3823 kStepColors.push_back(_colors);
3852 } 3824 }
3853 void G4GMocrenIO::setTrackColors(std::vector< 3825 void G4GMocrenIO::setTrackColors(std::vector<unsigned char *> & _trackColors) {
3854 kStepColors = _trackColors; 3826 kStepColors = _trackColors;
3855 } 3827 }
3856 std::vector<unsigned char *> & G4GMocrenIO::g 3828 std::vector<unsigned char *> & G4GMocrenIO::getTrackColors() {
3857 return kStepColors; 3829 return kStepColors;
3858 } 3830 }
3859 void G4GMocrenIO::copyTracks(std::vector<floa 3831 void G4GMocrenIO::copyTracks(std::vector<float *> & _tracks,
3860 std::vector<unsigned char *> & _ 3832 std::vector<unsigned char *> & _colors) {
3861 std::vector<float *>::iterator titr; 3833 std::vector<float *>::iterator titr;
3862 for(titr = kSteps.begin(); titr != kSteps.e 3834 for(titr = kSteps.begin(); titr != kSteps.end(); titr++) {
3863 float * pts = new float[6]; 3835 float * pts = new float[6];
3864 for(int i = 0; i < 6; i++) { 3836 for(int i = 0; i < 6; i++) {
3865 pts[i] = (*titr)[i]; 3837 pts[i] = (*titr)[i];
3866 } 3838 }
3867 _tracks.push_back(pts); 3839 _tracks.push_back(pts);
3868 } 3840 }
3869 3841
3870 std::vector<unsigned char *>::iterator citr 3842 std::vector<unsigned char *>::iterator citr;
3871 for(citr = kStepColors.begin(); citr != kSt 3843 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++) {
3872 unsigned char * pts = new unsigned char[3 3844 unsigned char * pts = new unsigned char[3];
3873 for(int i = 0; i < 3; i++) { 3845 for(int i = 0; i < 3; i++) {
3874 pts[i] = (*citr)[i]; 3846 pts[i] = (*citr)[i];
3875 } 3847 }
3876 _colors.push_back(pts); 3848 _colors.push_back(pts);
3877 } 3849 }
3878 } 3850 }
3879 void G4GMocrenIO::mergeTracks(std::vector<flo 3851 void G4GMocrenIO::mergeTracks(std::vector<float *> & _tracks,
3880 std::vector<unsigned char *> & _color 3852 std::vector<unsigned char *> & _colors) {
3881 std::vector<float *>::iterator titr; 3853 std::vector<float *>::iterator titr;
3882 for(titr = _tracks.begin(); titr != _tracks 3854 for(titr = _tracks.begin(); titr != _tracks.end(); titr++) {
3883 addTrack(*titr); 3855 addTrack(*titr);
3884 } 3856 }
3885 3857
3886 std::vector<unsigned char *>::iterator citr 3858 std::vector<unsigned char *>::iterator citr;
3887 for(citr = _colors.begin(); citr != _colors 3859 for(citr = _colors.begin(); citr != _colors.end(); citr++) {
3888 addTrackColor(*citr); 3860 addTrackColor(*citr);
3889 } 3861 }
3890 } 3862 }
3891 void G4GMocrenIO::addTrack(std::vector<float 3863 void G4GMocrenIO::addTrack(std::vector<float *> & _steps, unsigned char _color[3]) {
3892 3864
3893 std::vector<float *>::iterator itr = _steps 3865 std::vector<float *>::iterator itr = _steps.begin();
3894 std::vector<struct GMocrenTrack::Step> st 3866 std::vector<struct GMocrenTrack::Step> steps;
3895 for(; itr != _steps.end(); itr++) { 3867 for(; itr != _steps.end(); itr++) {
3896 struct GMocrenTrack::Step step; 3868 struct GMocrenTrack::Step step;
3897 for(int i = 0; i < 3; i++) { 3869 for(int i = 0; i < 3; i++) {
3898 step.startPoint[i] = (*itr)[i]; 3870 step.startPoint[i] = (*itr)[i];
3899 step.endPoint[i] = (*itr)[i+3]; 3871 step.endPoint[i] = (*itr)[i+3];
3900 } 3872 }
3901 steps.push_back(step); 3873 steps.push_back(step);
3902 } 3874 }
3903 GMocrenTrack track; 3875 GMocrenTrack track;
3904 track.setTrack(steps); 3876 track.setTrack(steps);
3905 track.setColor(_color); 3877 track.setColor(_color);
3906 kTracks.push_back(track); 3878 kTracks.push_back(track);
3907 3879
3908 } 3880 }
3909 void G4GMocrenIO::getTrack(int _num, std::vec 3881 void G4GMocrenIO::getTrack(int _num, std::vector<float *> & _steps,
3910 std::vector<unsigned char *> & _co 3882 std::vector<unsigned char *> & _color) {
3911 3883
3912 if(_num > (int)kTracks.size()) { 3884 if(_num > (int)kTracks.size()) {
3913 if (G4VisManager::GetVerbosity() >= G4Vis << 3885 std::cerr << "ERROR in getTrack() : " << std::endl;
3914 G4cout << "ERROR in getTrack() : " << G << 3886 std::exit(-1);
3915 G4Exception("G4GMocrenIO::getTrack()", <<
3916 "gMocren2003", FatalException <<
3917 "Error."); <<
3918 } 3887 }
3919 unsigned char * color = new unsigned char[3 3888 unsigned char * color = new unsigned char[3];
3920 kTracks[_num].getColor(color); 3889 kTracks[_num].getColor(color);
3921 _color.push_back(color); 3890 _color.push_back(color);
3922 3891
3923 // steps 3892 // steps
3924 int nsteps = kTracks[_num].getNumberOfSteps 3893 int nsteps = kTracks[_num].getNumberOfSteps();
3925 for(int isteps = 0; isteps < nsteps; isteps << 3894 for(int ns = 0; ns < nsteps; ns++) {
3926 float * stepPoints = new float[6]; 3895 float * stepPoints = new float[6];
3927 kTracks[_num].getStep(stepPoints[0], step 3896 kTracks[_num].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
3928 stepPoints[3], stepPoints[4], stepPoi 3897 stepPoints[3], stepPoints[4], stepPoints[5],
3929 isteps); << 3898 ns);
3930 _steps.push_back(stepPoints); 3899 _steps.push_back(stepPoints);
3931 } 3900 }
3932 } 3901 }
3933 3902
3934 void G4GMocrenIO::translateTracks(std::vector 3903 void G4GMocrenIO::translateTracks(std::vector<float> & _translate) {
3935 std::vector<class GMocrenTrack>::iterator i 3904 std::vector<class GMocrenTrack>::iterator itr = kTracks.begin();
3936 for(; itr != kTracks.end(); itr++) { 3905 for(; itr != kTracks.end(); itr++) {
3937 itr->translate(_translate); 3906 itr->translate(_translate);
3938 } 3907 }
3939 } 3908 }
3940 3909
3941 3910
3942 3911
3943 3912
3944 //----- Detector information -----// 3913 //----- Detector information -----//
3945 int G4GMocrenIO::getNumberOfDetectors() { 3914 int G4GMocrenIO::getNumberOfDetectors() {
3946 return (int)kDetectors.size(); 3915 return (int)kDetectors.size();
3947 } 3916 }
3948 void G4GMocrenIO::addDetector(std::string & _ 3917 void G4GMocrenIO::addDetector(std::string & _name,
3949 std::vector<float *> & _det, 3918 std::vector<float *> & _det,
3950 unsigned char _color[3]) { 3919 unsigned char _color[3]) {
3951 3920
3952 std::vector<float *>::iterator itr = _det 3921 std::vector<float *>::iterator itr = _det.begin();
3953 std::vector<struct GMocrenDetector::Edge> 3922 std::vector<struct GMocrenDetector::Edge> edges;
3954 for(; itr != _det.end(); itr++) { 3923 for(; itr != _det.end(); itr++) {
3955 struct GMocrenDetector::Edge edge; 3924 struct GMocrenDetector::Edge edge;
3956 for(int i = 0; i < 3; i++) { 3925 for(int i = 0; i < 3; i++) {
3957 edge.startPoint[i] = (*itr)[i]; 3926 edge.startPoint[i] = (*itr)[i];
3958 edge.endPoint[i] = (*itr)[i+3]; 3927 edge.endPoint[i] = (*itr)[i+3];
3959 } 3928 }
3960 edges.push_back(edge); 3929 edges.push_back(edge);
3961 } 3930 }
3962 GMocrenDetector detector; 3931 GMocrenDetector detector;
3963 detector.setDetector(edges); 3932 detector.setDetector(edges);
3964 detector.setColor(_color); 3933 detector.setColor(_color);
3965 detector.setName(_name); 3934 detector.setName(_name);
3966 kDetectors.push_back(detector); 3935 kDetectors.push_back(detector);
3967 3936
3968 } 3937 }
3969 3938
3970 void G4GMocrenIO::getDetector(int _num, std:: 3939 void G4GMocrenIO::getDetector(int _num, std::vector<float *> & _edges,
3971 std::vector<unsigned char *> & _color 3940 std::vector<unsigned char *> & _color,
3972 std::string & _detName) { 3941 std::string & _detName) {
3973 3942
3974 if(_num > (int)kDetectors.size()) { 3943 if(_num > (int)kDetectors.size()) {
3975 if (G4VisManager::GetVerbosity() >= G4Vis << 3944 std::cerr << "ERROR in getDetector() : " << std::endl;
3976 G4cout << "ERROR in getDetector() : " < << 3945 std::exit(-1);
3977 <<
3978 G4Exception("G4GMocrenIO::getDetector()", <<
3979 "gMocren2004", FatalException <<
3980 "Error."); <<
3981 } 3946 }
3982 3947
3983 _detName = kDetectors[_num].getName(); 3948 _detName = kDetectors[_num].getName();
3984 3949
3985 unsigned char * color = new unsigned char[3 3950 unsigned char * color = new unsigned char[3];
3986 kDetectors[_num].getColor(color); 3951 kDetectors[_num].getColor(color);
3987 _color.push_back(color); 3952 _color.push_back(color);
3988 3953
3989 // edges 3954 // edges
3990 int nedges = kDetectors[_num].getNumberOfEd 3955 int nedges = kDetectors[_num].getNumberOfEdges();
3991 for(int ne = 0; ne < nedges; ne++) { 3956 for(int ne = 0; ne < nedges; ne++) {
3992 float * edgePoints = new float[6]; 3957 float * edgePoints = new float[6];
3993 kDetectors[_num].getEdge(edgePoints[0], e 3958 kDetectors[_num].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
3994 edgePoints[3], edgePoints[4], edge 3959 edgePoints[3], edgePoints[4], edgePoints[5],
3995 ne); 3960 ne);
3996 _edges.push_back(edgePoints); 3961 _edges.push_back(edgePoints);
3997 } 3962 }
3998 } 3963 }
3999 3964
4000 void G4GMocrenIO::translateDetector(std::vect 3965 void G4GMocrenIO::translateDetector(std::vector<float> & _translate) {
4001 std::vector<class GMocrenDetector>::iterato 3966 std::vector<class GMocrenDetector>::iterator itr = kDetectors.begin();
4002 for(; itr != kDetectors.end(); itr++) { 3967 for(; itr != kDetectors.end(); itr++) {
4003 itr->translate(_translate); 3968 itr->translate(_translate);
4004 } 3969 }
4005 } 3970 }
4006 3971
4007 // endian conversion 3972 // endian conversion
4008 template <typename T> 3973 template <typename T>
4009 void G4GMocrenIO::convertEndian(char * _val, 3974 void G4GMocrenIO::convertEndian(char * _val, T & _rval) {
4010 3975
4011 if((kLittleEndianOutput && !kLittleEndianIn 3976 if((kLittleEndianOutput && !kLittleEndianInput) || // big endian
4012 (!kLittleEndianOutput && kLittleEndianIn 3977 (!kLittleEndianOutput && kLittleEndianInput)) { // little endian
4013 3978
4014 const int SIZE = sizeof(_rval); 3979 const int SIZE = sizeof(_rval);
4015 char ctemp; 3980 char ctemp;
4016 for(int i = 0; i < SIZE/2; i++) { 3981 for(int i = 0; i < SIZE/2; i++) {
4017 ctemp = _val[i]; 3982 ctemp = _val[i];
4018 _val[i] = _val[SIZE - 1 - i]; 3983 _val[i] = _val[SIZE - 1 - i];
4019 _val[SIZE - 1 - i] = ctemp; 3984 _val[SIZE - 1 - i] = ctemp;
4020 } 3985 }
4021 } 3986 }
4022 _rval = *(T *)_val; 3987 _rval = *(T *)_val;
4023 } 3988 }
4024 3989
4025 // inversion of byte order 3990 // inversion of byte order
4026 template <typename T> 3991 template <typename T>
4027 void G4GMocrenIO::invertByteOrder(char * _val 3992 void G4GMocrenIO::invertByteOrder(char * _val, T & _rval) {
4028 3993
4029 const int SIZE = sizeof(_rval); 3994 const int SIZE = sizeof(_rval);
4030 //char * cval = new char[SIZE]; 3995 //char * cval = new char[SIZE];
4031 union { 3996 union {
4032 char cu[16]; 3997 char cu[16];
4033 T tu; 3998 T tu;
4034 } uni; 3999 } uni;
4035 for(int i = 0; i < SIZE; i++) { 4000 for(int i = 0; i < SIZE; i++) {
4036 uni.cu[i] = _val[SIZE-1-i]; 4001 uni.cu[i] = _val[SIZE-1-i];
4037 //cval[i] = _val[SIZE-i-1]; 4002 //cval[i] = _val[SIZE-i-1];
4038 } 4003 }
4039 //_rval = *(T *)cval; 4004 //_rval = *(T *)cval;
4040 _rval = uni.tu; 4005 _rval = uni.tu;
4041 //delete [] cval; 4006 //delete [] cval;
4042 } 4007 }
4043 4008
4044 //----- kVerbose information -----// 4009 //----- kVerbose information -----//
4045 void G4GMocrenIO::setVerboseLevel(int _level) 4010 void G4GMocrenIO::setVerboseLevel(int _level) {
4046 kVerbose = _level; 4011 kVerbose = _level;
4047 } 4012 }
4048 4013
4049 4014