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