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25 // 25 //
26 // 26 //
>> 27 // $Id: G4GMocrenIO.cc,v 1.6 2010-11-10 23:53:23 akimura Exp $
>> 28 // GEANT4 tag $Name: not supported by cvs2svn $
27 // 29 //
28 // 30 //
29 // File I/O manager class for writing or readi 31 // File I/O manager class for writing or reading calcuated dose
30 // distribution and some event information 32 // distribution and some event information
31 // 33 //
32 // Created: Mar. 31, 2009 Akinori Kimura : r 34 // Created: Mar. 31, 2009 Akinori Kimura : release for the gMocrenFile driver
33 // 35 //
34 // Akinori Kimur 36 // Akinori Kimura
35 // gMocren home 37 // gMocren home page:
36 // http://geant4 38 // http://geant4.kek.jp/gMocren/
37 // 39 //
38 // 40 //
39 #include "G4GMocrenIO.hh" 41 #include "G4GMocrenIO.hh"
40 #include <iostream> 42 #include <iostream>
41 #include <ctime> 43 #include <ctime>
42 #include <sstream> 44 #include <sstream>
43 #include <iomanip> 45 #include <iomanip>
44 #include <cstdlib> 46 #include <cstdlib>
45 #include <cstring> 47 #include <cstring>
46 48
47 #include "globals.hh" 49 #include "globals.hh"
48 #include "G4VisManager.hh" 50 #include "G4VisManager.hh"
49 51
50 #if defined(_WIN32) 52 #if defined(_WIN32)
51 #define LITTLE_ENDIAN 1234 53 #define LITTLE_ENDIAN 1234
52 #define BYTE_ORDER LITTLE_ENDIAN 54 #define BYTE_ORDER LITTLE_ENDIAN
53 #endif 55 #endif
54 56
55 const int DOSERANGE = 25000; 57 const int DOSERANGE = 25000;
56 58
57 //----- GMocrenDataPrimitive class in the GMoc 59 //----- GMocrenDataPrimitive class in the GMocrenDataIO class-----//
58 template <typename T> 60 template <typename T>
59 GMocrenDataPrimitive<T>::GMocrenDataPrimitive 61 GMocrenDataPrimitive<T>::GMocrenDataPrimitive () {
60 clear(); 62 clear();
61 } 63 }
62 template <typename T> 64 template <typename T>
63 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive 65 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive () {
64 /* 66 /*
65 std::vector<short *>::iterator itr = image 67 std::vector<short *>::iterator itr = image.begin();
66 for(; itr != image.end(); itr++) { 68 for(; itr != image.end(); itr++) {
67 delete [] *itr; 69 delete [] *itr;
68 } 70 }
69 */ 71 */
70 } 72 }
71 73
72 template <typename T> GMocrenDataPrimitive<T> 74 template <typename T> GMocrenDataPrimitive<T> &
73 GMocrenDataPrimitive<T>::operator = (const GMo 75 GMocrenDataPrimitive<T>::operator = (const GMocrenDataPrimitive<T> & _right) {
74 if (this == &_right) return *this; <<
75 for(int i = 0; i < 3; i++) { 76 for(int i = 0; i < 3; i++) {
76 kSize[i] = _right.kSize[i]; 77 kSize[i] = _right.kSize[i];
77 kCenter[i] = _right.kCenter[i]; 78 kCenter[i] = _right.kCenter[i];
78 } 79 }
79 kScale = _right.kScale; 80 kScale = _right.kScale;
80 for(int i = 0; i < 2; i++) kMinmax[i] = _rig 81 for(int i = 0; i < 2; i++) kMinmax[i] = _right.kMinmax[i];
81 int num = kSize[0]*kSize[1]; 82 int num = kSize[0]*kSize[1];
82 kImage.clear(); 83 kImage.clear();
83 for(int z = 0; z < kSize[2]; z++) { 84 for(int z = 0; z < kSize[2]; z++) {
84 T * img = new T[num]; 85 T * img = new T[num];
85 for(int i = 0; i < num; i++) img[i] =_righ 86 for(int i = 0; i < num; i++) img[i] =_right.kImage[z][i];
86 kImage.push_back(img); 87 kImage.push_back(img);
87 } 88 }
88 return *this; 89 return *this;
89 } 90 }
90 91
91 template <typename T> GMocrenDataPrimitive<T> 92 template <typename T> GMocrenDataPrimitive<T> &
92 GMocrenDataPrimitive<T>::operator + (const GMo 93 GMocrenDataPrimitive<T>::operator + (const GMocrenDataPrimitive<T> & _right) {
93 94
94 GMocrenDataPrimitive<T> rprim; 95 GMocrenDataPrimitive<T> rprim;
95 bool stat = true; 96 bool stat = true;
96 for(int i = 0; i < 3; i++) { 97 for(int i = 0; i < 3; i++) {
97 if(kSize[i] != _right.kSize[i]) stat = fal 98 if(kSize[i] != _right.kSize[i]) stat = false;
98 if(kCenter[i] != _right.kCenter[i]) stat = 99 if(kCenter[i] != _right.kCenter[i]) stat = false;
99 } 100 }
100 if(!stat) { 101 if(!stat) {
101 if (G4VisManager::GetVerbosity() >= G4VisM 102 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
102 G4cout << "Warning: operator + " 103 G4cout << "Warning: operator + "
103 << " Cannot do the operator +" 104 << " Cannot do the operator +"
104 << G4endl; 105 << G4endl;
105 return *this; 106 return *this;
106 } 107 }
107 108
108 rprim.setSize(kSize); 109 rprim.setSize(kSize);
109 rprim.setCenterPosition(kCenter); 110 rprim.setCenterPosition(kCenter);
110 111
111 T mms[2] = {9e100,-9e100}; << 112 T mm[2] = {9e100,-9e100};
112 //if(mms[0] > _right.minmax[0]) mms[0] = _ri << 113 //if(mm[0] > _right.minmax[0]) mm[0] = _right.minmax[0];
113 //if(mms[1] < _right.minmax[1]) mms[1] = _ri << 114 //if(mm[1] < _right.minmax[1]) mm[1] = _right.minmax[1];
114 115
115 int num = kSize[0]*kSize[1]; 116 int num = kSize[0]*kSize[1];
116 for(int z = 0; z < kSize[2]; z++) { 117 for(int z = 0; z < kSize[2]; z++) {
117 T * img = new T[num]; 118 T * img = new T[num];
118 for(int xy = 0; xy < num; xy++) { 119 for(int xy = 0; xy < num; xy++) {
119 img[xy] = kImage[z][xy] + _right.kImage[ 120 img[xy] = kImage[z][xy] + _right.kImage[z][xy];
120 if(mms[0] > img[xy]) mms[0] = img[xy]; << 121 if(mm[0] > img[xy]) mm[0] = img[xy];
121 if(mms[1] < img[xy]) mms[1] = img[xy]; << 122 if(mm[1] < img[xy]) mm[1] = img[xy];
122 } 123 }
123 rprim.addImage(img); 124 rprim.addImage(img);
124 } 125 }
125 rprim.setMinMax(mms); << 126 rprim.setMinMax(mm);
126 127
127 T scl = mms[1]/DOSERANGE; << 128 T scl = mm[1]/DOSERANGE;
128 rprim.setScale(scl); 129 rprim.setScale(scl);
129 130
130 return rprim; 131 return rprim;
131 } 132 }
132 133
133 template <typename T> GMocrenDataPrimitive<T> 134 template <typename T> GMocrenDataPrimitive<T> &
134 GMocrenDataPrimitive<T>::operator += (const GM 135 GMocrenDataPrimitive<T>::operator += (const GMocrenDataPrimitive<T> & _right) {
135 136
136 bool stat = true; 137 bool stat = true;
137 for(int i = 0; i < 3; i++) { 138 for(int i = 0; i < 3; i++) {
138 if(kSize[i] != _right.kSize[i]) stat = fal 139 if(kSize[i] != _right.kSize[i]) stat = false;
139 if(kCenter[i] != _right.kCenter[i]) stat = 140 if(kCenter[i] != _right.kCenter[i]) stat = false;
140 } 141 }
141 if(!stat) { 142 if(!stat) {
142 if (G4VisManager::GetVerbosity() >= G4VisM 143 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
143 G4cout << "Warning: operator += " << G4e 144 G4cout << "Warning: operator += " << G4endl
144 << " Cannot do the operator +=" 145 << " Cannot do the operator +="
145 << G4endl; 146 << G4endl;
146 return *this; 147 return *this;
147 } 148 }
148 149
149 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0 150 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0] = _right.kMinmax[0];
150 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1 151 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1] = _right.kMinmax[1];
151 152
152 int num = kSize[0]*kSize[1]; 153 int num = kSize[0]*kSize[1];
153 for(int z = 0; z < kSize[2]; z++) { 154 for(int z = 0; z < kSize[2]; z++) {
154 for(int xy = 0; xy < num; xy++) { 155 for(int xy = 0; xy < num; xy++) {
155 kImage[z][xy] += _right.kImage[z][xy]; 156 kImage[z][xy] += _right.kImage[z][xy];
156 if(kMinmax[0] > kImage[z][xy]) kMinmax[0 157 if(kMinmax[0] > kImage[z][xy]) kMinmax[0] = kImage[z][xy];
157 if(kMinmax[1] < kImage[z][xy]) kMinmax[1 158 if(kMinmax[1] < kImage[z][xy]) kMinmax[1] = kImage[z][xy];
158 } 159 }
159 } 160 }
160 161
161 kScale = kMinmax[1]/DOSERANGE; 162 kScale = kMinmax[1]/DOSERANGE;
162 163
163 return *this; 164 return *this;
164 } 165 }
165 166
166 template <typename T> 167 template <typename T>
167 void GMocrenDataPrimitive<T>::clear() { 168 void GMocrenDataPrimitive<T>::clear() {
168 for(int i = 0; i < 3; i++) { 169 for(int i = 0; i < 3; i++) {
169 kSize[i] = 0; 170 kSize[i] = 0;
170 kCenter[i] = 0.; 171 kCenter[i] = 0.;
171 } 172 }
172 kScale = 1.; 173 kScale = 1.;
173 kMinmax[0] = (T)32109; 174 kMinmax[0] = (T)32109;
174 kMinmax[1] = (T)-32109; 175 kMinmax[1] = (T)-32109;
175 176
176 clearImage(); 177 clearImage();
177 } 178 }
178 template <typename T> 179 template <typename T>
179 void GMocrenDataPrimitive<T>::clearImage() { 180 void GMocrenDataPrimitive<T>::clearImage() {
180 typename std::vector<T *>::iterator itr; 181 typename std::vector<T *>::iterator itr;
181 for(itr = kImage.begin(); itr != kImage.end( 182 for(itr = kImage.begin(); itr != kImage.end(); itr++) {
182 delete [] *itr; 183 delete [] *itr;
183 } 184 }
184 kImage.clear(); 185 kImage.clear();
185 } 186 }
186 template <typename T> 187 template <typename T>
187 void GMocrenDataPrimitive<T>::setSize(int _siz 188 void GMocrenDataPrimitive<T>::setSize(int _size[3]) {
188 for(int i = 0; i < 3; i++) kSize[i] = _size[ 189 for(int i = 0; i < 3; i++) kSize[i] = _size[i];
189 } 190 }
190 template <typename T> 191 template <typename T>
191 void GMocrenDataPrimitive<T>::getSize(int _siz 192 void GMocrenDataPrimitive<T>::getSize(int _size[3]) {
192 for(int i = 0; i < 3; i++) _size[i] = kSize[ 193 for(int i = 0; i < 3; i++) _size[i] = kSize[i];
193 } 194 }
194 template <typename T> 195 template <typename T>
195 void GMocrenDataPrimitive<T>::setScale(double 196 void GMocrenDataPrimitive<T>::setScale(double & _scale) {
196 kScale = _scale; 197 kScale = _scale;
197 } 198 }
198 template <typename T> 199 template <typename T>
199 double GMocrenDataPrimitive<T>::getScale() { 200 double GMocrenDataPrimitive<T>::getScale() {
200 return kScale; 201 return kScale;
201 } 202 }
202 template <typename T> 203 template <typename T>
203 void GMocrenDataPrimitive<T>::setMinMax(T _min 204 void GMocrenDataPrimitive<T>::setMinMax(T _minmax[2]) {
204 for(int i = 0; i < 2; i++) kMinmax[i] = _min 205 for(int i = 0; i < 2; i++) kMinmax[i] = _minmax[i];
205 } 206 }
206 template <typename T> 207 template <typename T>
207 void GMocrenDataPrimitive<T>::getMinMax(T _min 208 void GMocrenDataPrimitive<T>::getMinMax(T _minmax[2]) {
208 for(int i = 0; i < 2; i++) _minmax[i] = kMin 209 for(int i = 0; i < 2; i++) _minmax[i] = kMinmax[i];
209 210
210 } 211 }
211 template <typename T> 212 template <typename T>
212 void GMocrenDataPrimitive<T>::setImage(std::ve 213 void GMocrenDataPrimitive<T>::setImage(std::vector<T *> & _image) {
213 kImage = _image; 214 kImage = _image;
214 } 215 }
215 template <typename T> 216 template <typename T>
216 void GMocrenDataPrimitive<T>::addImage(T * _im 217 void GMocrenDataPrimitive<T>::addImage(T * _image) {
217 kImage.push_back(_image); 218 kImage.push_back(_image);
218 } 219 }
219 template <typename T> 220 template <typename T>
220 std::vector<T *> & GMocrenDataPrimitive<T>::ge 221 std::vector<T *> & GMocrenDataPrimitive<T>::getImage() {
221 return kImage; 222 return kImage;
222 } 223 }
223 template <typename T> 224 template <typename T>
224 T * GMocrenDataPrimitive<T>::getImage(int _z) 225 T * GMocrenDataPrimitive<T>::getImage(int _z) {
225 if(_z >= (int)kImage.size()) return 0; 226 if(_z >= (int)kImage.size()) return 0;
226 return kImage[_z]; 227 return kImage[_z];
227 } 228 }
228 template <typename T> 229 template <typename T>
229 void GMocrenDataPrimitive<T>::setCenterPositio 230 void GMocrenDataPrimitive<T>::setCenterPosition(float _center[3]) {
230 for(int i = 0; i < 3; i++) kCenter[i] = _cen 231 for(int i = 0; i < 3; i++) kCenter[i] = _center[i];
231 } 232 }
232 template <typename T> 233 template <typename T>
233 void GMocrenDataPrimitive<T>::getCenterPositio 234 void GMocrenDataPrimitive<T>::getCenterPosition(float _center[3]) {
234 for(int i = 0; i < 3; i++) _center[i] = kCen 235 for(int i = 0; i < 3; i++) _center[i] = kCenter[i];
235 } 236 }
236 template <typename T> 237 template <typename T>
237 void GMocrenDataPrimitive<T>::setName(std::str 238 void GMocrenDataPrimitive<T>::setName(std::string & _name) {
238 kDataName = _name; 239 kDataName = _name;
239 } 240 }
240 template <typename T> 241 template <typename T>
241 std::string GMocrenDataPrimitive<T>::getName() 242 std::string GMocrenDataPrimitive<T>::getName() {
242 return kDataName; 243 return kDataName;
243 } 244 }
244 245
245 246
246 247
247 248
248 249
249 GMocrenTrack::GMocrenTrack() { 250 GMocrenTrack::GMocrenTrack() {
250 kTrack.clear(); 251 kTrack.clear();
251 for(int i = 0; i < 3; i++) kColor[i] = 0; 252 for(int i = 0; i < 3; i++) kColor[i] = 0;
252 } 253 }
253 254
254 void GMocrenTrack::addStep(float _startx, floa 255 void GMocrenTrack::addStep(float _startx, float _starty, float _startz,
255 float _endx, float _endy, float _endz 256 float _endx, float _endy, float _endz) {
256 struct Step step; 257 struct Step step;
257 step.startPoint[0] = _startx; 258 step.startPoint[0] = _startx;
258 step.startPoint[1] = _starty; 259 step.startPoint[1] = _starty;
259 step.startPoint[2] = _startz; 260 step.startPoint[2] = _startz;
260 step.endPoint[0] = _endx; 261 step.endPoint[0] = _endx;
261 step.endPoint[1] = _endy; 262 step.endPoint[1] = _endy;
262 step.endPoint[2] = _endz; 263 step.endPoint[2] = _endz;
263 kTrack.push_back(step); 264 kTrack.push_back(step);
264 } 265 }
265 void GMocrenTrack::getStep(float & _startx, fl 266 void GMocrenTrack::getStep(float & _startx, float & _starty, float & _startz,
266 float & _endx, float & _endy, float & 267 float & _endx, float & _endy, float & _endz,
267 int _num) { 268 int _num) {
268 if(_num >= (int)kTrack.size()) { 269 if(_num >= (int)kTrack.size()) {
269 if (G4VisManager::GetVerbosity() >= G4VisM 270 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
270 G4cout << "GMocrenTrack::getStep(...) Er 271 G4cout << "GMocrenTrack::getStep(...) Error: "
271 << "invalid step # : " << _num << G4end 272 << "invalid step # : " << _num << G4endl;
272 return; 273 return;
273 } 274 }
274 275
275 _startx = kTrack[_num].startPoint[0]; 276 _startx = kTrack[_num].startPoint[0];
276 _starty = kTrack[_num].startPoint[1]; 277 _starty = kTrack[_num].startPoint[1];
277 _startz = kTrack[_num].startPoint[2]; 278 _startz = kTrack[_num].startPoint[2];
278 _endx = kTrack[_num].endPoint[0]; 279 _endx = kTrack[_num].endPoint[0];
279 _endy = kTrack[_num].endPoint[1]; 280 _endy = kTrack[_num].endPoint[1];
280 _endz = kTrack[_num].endPoint[2]; 281 _endz = kTrack[_num].endPoint[2];
281 } 282 }
282 void GMocrenTrack::translate(std::vector<float 283 void GMocrenTrack::translate(std::vector<float> & _translate) {
283 std::vector<struct Step>::iterator itr = kTr 284 std::vector<struct Step>::iterator itr = kTrack.begin();
284 for(; itr != kTrack.end(); itr++) { 285 for(; itr != kTrack.end(); itr++) {
285 for(int i = 0; i < 3; i++ ) { 286 for(int i = 0; i < 3; i++ ) {
286 itr->startPoint[i] += _translate[i]; 287 itr->startPoint[i] += _translate[i];
287 itr->endPoint[i] += _translate[i]; 288 itr->endPoint[i] += _translate[i];
288 } 289 }
289 } 290 }
290 } 291 }
291 292
292 293
293 294
294 295
295 296
296 297
297 298
298 299
299 300
300 GMocrenDetector::GMocrenDetector() { 301 GMocrenDetector::GMocrenDetector() {
301 kDetector.clear(); 302 kDetector.clear();
302 for(int i = 0; i < 3; i++) kColor[i] = 0; 303 for(int i = 0; i < 3; i++) kColor[i] = 0;
303 } 304 }
304 305
305 void GMocrenDetector::addEdge(float _startx, f 306 void GMocrenDetector::addEdge(float _startx, float _starty, float _startz,
306 float _endx, float _endy, float _e 307 float _endx, float _endy, float _endz) {
307 struct Edge edge; 308 struct Edge edge;
308 edge.startPoint[0] = _startx; 309 edge.startPoint[0] = _startx;
309 edge.startPoint[1] = _starty; 310 edge.startPoint[1] = _starty;
310 edge.startPoint[2] = _startz; 311 edge.startPoint[2] = _startz;
311 edge.endPoint[0] = _endx; 312 edge.endPoint[0] = _endx;
312 edge.endPoint[1] = _endy; 313 edge.endPoint[1] = _endy;
313 edge.endPoint[2] = _endz; 314 edge.endPoint[2] = _endz;
314 kDetector.push_back(edge); 315 kDetector.push_back(edge);
315 } 316 }
316 void GMocrenDetector::getEdge(float & _startx, 317 void GMocrenDetector::getEdge(float & _startx, float & _starty, float & _startz,
317 float & _endx, float & _endy, float & 318 float & _endx, float & _endy, float & _endz,
318 int _num) { 319 int _num) {
319 if(_num >= (int)kDetector.size()) { 320 if(_num >= (int)kDetector.size()) {
320 if (G4VisManager::GetVerbosity() >= G4VisM 321 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
321 G4cout << "GMocrenDetector::getEdge(...) 322 G4cout << "GMocrenDetector::getEdge(...) Error: "
322 << "invalid edge # : " << _num << G4end 323 << "invalid edge # : " << _num << G4endl;
323 return; 324 return;
324 } 325 }
325 326
326 _startx = kDetector[_num].startPoint[0]; 327 _startx = kDetector[_num].startPoint[0];
327 _starty = kDetector[_num].startPoint[1]; 328 _starty = kDetector[_num].startPoint[1];
328 _startz = kDetector[_num].startPoint[2]; 329 _startz = kDetector[_num].startPoint[2];
329 _endx = kDetector[_num].endPoint[0]; 330 _endx = kDetector[_num].endPoint[0];
330 _endy = kDetector[_num].endPoint[1]; 331 _endy = kDetector[_num].endPoint[1];
331 _endz = kDetector[_num].endPoint[2]; 332 _endz = kDetector[_num].endPoint[2];
332 } 333 }
333 void GMocrenDetector::translate(std::vector<fl 334 void GMocrenDetector::translate(std::vector<float> & _translate) {
334 std::vector<struct Edge>::iterator itr = kDe 335 std::vector<struct Edge>::iterator itr = kDetector.begin();
335 for(; itr != kDetector.end(); itr++) { 336 for(; itr != kDetector.end(); itr++) {
336 for(int i = 0; i < 3; i++) { 337 for(int i = 0; i < 3; i++) {
337 itr->startPoint[i] += _translate[i]; 338 itr->startPoint[i] += _translate[i];
338 itr->endPoint[i] += _translate[i]; 339 itr->endPoint[i] += _translate[i];
339 } 340 }
340 } 341 }
341 } 342 }
342 343
343 344
344 345
345 346
346 347
347 348
348 349
349 350
350 351
351 // file information 352 // file information
352 std::string G4GMocrenIO::kId; 353 std::string G4GMocrenIO::kId;
353 std::string G4GMocrenIO::kVersion = "2.0.0"; 354 std::string G4GMocrenIO::kVersion = "2.0.0";
354 int G4GMocrenIO::kNumberOfEvents = 0; 355 int G4GMocrenIO::kNumberOfEvents = 0;
355 char G4GMocrenIO::kLittleEndianInput = true; 356 char G4GMocrenIO::kLittleEndianInput = true;
356 357
357 #if BYTE_ORDER == LITTLE_ENDIAN 358 #if BYTE_ORDER == LITTLE_ENDIAN
358 char G4GMocrenIO::kLittleEndianOutput = true; 359 char G4GMocrenIO::kLittleEndianOutput = true;
359 #else 360 #else
360 char G4GMocrenIO::kLittleEndianOutput = false; 361 char G4GMocrenIO::kLittleEndianOutput = false; // Big endian
361 #endif 362 #endif
362 std::string G4GMocrenIO::kComment; 363 std::string G4GMocrenIO::kComment;
363 // 364 //
364 std::string G4GMocrenIO::kFileName = "dose.gdd 365 std::string G4GMocrenIO::kFileName = "dose.gdd";
365 366
366 // 367 //
367 unsigned int G4GMocrenIO::kPointerToModalityDa 368 unsigned int G4GMocrenIO::kPointerToModalityData = 0;
368 std::vector<unsigned int> G4GMocrenIO::kPointe 369 std::vector<unsigned int> G4GMocrenIO::kPointerToDoseDistData;
369 unsigned int G4GMocrenIO::kPointerToROIData = 370 unsigned int G4GMocrenIO::kPointerToROIData = 0;
370 unsigned int G4GMocrenIO::kPointerToTrackData 371 unsigned int G4GMocrenIO::kPointerToTrackData = 0;
371 unsigned int G4GMocrenIO::kPointerToDetectorDa 372 unsigned int G4GMocrenIO::kPointerToDetectorData = 0;
372 373
373 // modality 374 // modality
374 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 375 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 0.};
375 class GMocrenDataPrimitive<short> G4GMocrenIO 376 class GMocrenDataPrimitive<short> G4GMocrenIO::kModality;
376 std::vector<float> G4GMocrenIO::kModalityImage 377 std::vector<float> G4GMocrenIO::kModalityImageDensityMap;
377 std::string G4GMocrenIO::kModalityUnit = "g/cm 378 std::string G4GMocrenIO::kModalityUnit = "g/cm3 "; // 12 Bytes
378 379
379 // dose 380 // dose
380 std::vector<class GMocrenDataPrimitive<double> 381 std::vector<class GMocrenDataPrimitive<double> > G4GMocrenIO::kDose;
381 std::string G4GMocrenIO::kDoseUnit = "keV 382 std::string G4GMocrenIO::kDoseUnit = "keV "; // 12 Bytes
382 383
383 // ROI 384 // ROI
384 std::vector<class GMocrenDataPrimitive<short> 385 std::vector<class GMocrenDataPrimitive<short> > G4GMocrenIO::kRoi;
385 386
386 // track 387 // track
387 std::vector<float *> G4GMocrenIO::kSteps; 388 std::vector<float *> G4GMocrenIO::kSteps;
388 std::vector<unsigned char *> G4GMocrenIO::kSte 389 std::vector<unsigned char *> G4GMocrenIO::kStepColors;
389 std::vector<class GMocrenTrack> G4GMocrenIO::k 390 std::vector<class GMocrenTrack> G4GMocrenIO::kTracks;
390 391
391 // detector 392 // detector
392 std::vector<class GMocrenDetector> G4GMocrenIO 393 std::vector<class GMocrenDetector> G4GMocrenIO::kDetectors;
393 394
394 // verbose 395 // verbose
395 int G4GMocrenIO::kVerbose = 0; 396 int G4GMocrenIO::kVerbose = 0;
396 397
397 const int IDLENGTH = 21; 398 const int IDLENGTH = 21;
398 const int VERLENGTH = 6; 399 const int VERLENGTH = 6;
399 400
400 // constructor 401 // constructor
401 G4GMocrenIO::G4GMocrenIO() 402 G4GMocrenIO::G4GMocrenIO()
402 : kTracksWillBeStored(true) { 403 : kTracksWillBeStored(true) {
403 ; 404 ;
404 } 405 }
405 406
406 // destructor 407 // destructor
407 G4GMocrenIO::~G4GMocrenIO() { 408 G4GMocrenIO::~G4GMocrenIO() {
408 ; 409 ;
409 } 410 }
410 411
411 // initialize 412 // initialize
412 void G4GMocrenIO::initialize() { 413 void G4GMocrenIO::initialize() {
413 414
414 kId.clear(); 415 kId.clear();
415 kVersion = "2.0.0"; 416 kVersion = "2.0.0";
416 kNumberOfEvents = 0; 417 kNumberOfEvents = 0;
417 kLittleEndianInput = true; 418 kLittleEndianInput = true;
418 #if BYTE_ORDER == LITTLE_ENDIAN 419 #if BYTE_ORDER == LITTLE_ENDIAN
419 kLittleEndianOutput = true; 420 kLittleEndianOutput = true;
420 #else // Big endian 421 #else // Big endian
421 kLittleEndianOutput = false; 422 kLittleEndianOutput = false;
422 #endif 423 #endif
423 kComment.clear(); 424 kComment.clear();
424 kFileName = "dose.gdd"; 425 kFileName = "dose.gdd";
425 kPointerToModalityData = 0; 426 kPointerToModalityData = 0;
426 kPointerToDoseDistData.clear(); 427 kPointerToDoseDistData.clear();
427 kPointerToROIData = 0; 428 kPointerToROIData = 0;
428 kPointerToTrackData = 0; 429 kPointerToTrackData = 0;
429 // modality 430 // modality
430 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 431 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = 0.;
431 kModality.clear(); 432 kModality.clear();
432 kModalityImageDensityMap.clear(); 433 kModalityImageDensityMap.clear();
433 kModalityUnit = "g/cm3 "; // 12 Bytes 434 kModalityUnit = "g/cm3 "; // 12 Bytes
434 // dose 435 // dose
435 kDose.clear(); 436 kDose.clear();
436 kDoseUnit = "keV "; // 12 Bytes 437 kDoseUnit = "keV "; // 12 Bytes
437 // ROI 438 // ROI
438 kRoi.clear(); 439 kRoi.clear();
439 // track 440 // track
440 std::vector<float *>::iterator itr; 441 std::vector<float *>::iterator itr;
441 for(itr = kSteps.begin(); itr != kSteps.end( 442 for(itr = kSteps.begin(); itr != kSteps.end(); itr++) delete [] *itr;
442 kSteps.clear(); 443 kSteps.clear();
443 std::vector<unsigned char *>::iterator citr; 444 std::vector<unsigned char *>::iterator citr;
444 for(citr = kStepColors.begin(); citr != kSte 445 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++)
445 delete [] *citr; 446 delete [] *citr;
446 kStepColors.clear(); 447 kStepColors.clear();
447 kTracksWillBeStored = true; 448 kTracksWillBeStored = true;
448 449
449 // verbose 450 // verbose
450 kVerbose = 0; 451 kVerbose = 0;
451 } 452 }
452 453
453 bool G4GMocrenIO::storeData() { 454 bool G4GMocrenIO::storeData() {
454 return storeData4(); 455 return storeData4();
455 } 456 }
456 // 457 //
457 bool G4GMocrenIO::storeData(char * _filename) 458 bool G4GMocrenIO::storeData(char * _filename) {
458 return storeData4(_filename); 459 return storeData4(_filename);
459 } 460 }
460 461
461 bool G4GMocrenIO::storeData4() { 462 bool G4GMocrenIO::storeData4() {
462 463
463 bool DEBUG = false;// 464 bool DEBUG = false;//
464 465
465 if(DEBUG || kVerbose > 0) 466 if(DEBUG || kVerbose > 0)
466 G4cout << ">>>>>>> store data (ver.4) <<< 467 G4cout << ">>>>>>> store data (ver.4) <<<<<<<" << G4endl;
467 if(DEBUG || kVerbose > 0) 468 if(DEBUG || kVerbose > 0)
468 G4cout << " " << kFileName << G4en 469 G4cout << " " << kFileName << G4endl;
469 470
470 // output file open 471 // output file open
471 std::ofstream ofile(kFileName.c_str(), 472 std::ofstream ofile(kFileName.c_str(),
472 std::ios_base::out|std::ios_base::bi 473 std::ios_base::out|std::ios_base::binary);
473 if(DEBUG || kVerbose > 0) 474 if(DEBUG || kVerbose > 0)
474 G4cout << " file open status: " << << 475 G4cout << " file open status: " << ofile << G4endl;
475 476
476 // file identifier 477 // file identifier
477 ofile.write("gMocren ", 8); 478 ofile.write("gMocren ", 8);
478 479
479 // file version 480 // file version
480 unsigned char ver = 0x04; 481 unsigned char ver = 0x04;
481 ofile.write((char *)&ver, 1); 482 ofile.write((char *)&ver, 1);
482 483
483 // endian 484 // endian
484 //ofile.write((char *)&kLittleEndianOutput, 485 //ofile.write((char *)&kLittleEndianOutput, sizeof(char));
485 char littleEndian = 0x01; 486 char littleEndian = 0x01;
486 ofile.write((char *)&littleEndian, sizeof(ch 487 ofile.write((char *)&littleEndian, sizeof(char));
487 if(DEBUG || kVerbose > 0) { 488 if(DEBUG || kVerbose > 0) {
488 //G4cout << "Endian: " << (int)kLittleEndi 489 //G4cout << "Endian: " << (int)kLittleEndianOutput << G4endl;
489 G4cout << "Endian: " << (int)littleEndian 490 G4cout << "Endian: " << (int)littleEndian << G4endl;
490 } 491 }
491 492
492 // for inverting the byte order 493 // for inverting the byte order
493 float ftmp[6]; 494 float ftmp[6];
494 int itmp[6]; 495 int itmp[6];
495 short stmp[6]; 496 short stmp[6];
496 497
497 // comment length (fixed size) 498 // comment length (fixed size)
498 int commentLength = 1024; 499 int commentLength = 1024;
499 if(kLittleEndianOutput) { 500 if(kLittleEndianOutput) {
500 ofile.write((char *)&commentLength, 4); 501 ofile.write((char *)&commentLength, 4);
501 } else { 502 } else {
502 invertByteOrder((char *)&commentLength, it 503 invertByteOrder((char *)&commentLength, itmp[0]);
503 ofile.write((char *)itmp, 4); 504 ofile.write((char *)itmp, 4);
504 } 505 }
505 506
506 // comment 507 // comment
507 char cmt[1025]; 508 char cmt[1025];
508 std::strncpy(cmt, kComment.c_str(), 1024); << 509 for(int i = 0; i < 1025; i++) cmt[i] = '\0';
509 cmt[1024] = '\0'; << 510 //std::strncpy(cmt, kComment.c_str(), 1024);
510 ofile.write(cmt, 1024); << 511 std::strcpy(cmt, kComment.c_str());
>> 512 ofile.write((char *)cmt, 1024);
511 if(DEBUG || kVerbose > 0) { 513 if(DEBUG || kVerbose > 0) {
512 G4cout << "Data comment : " 514 G4cout << "Data comment : "
513 << kComment << G4endl; 515 << kComment << G4endl;
514 } 516 }
515 517
516 // voxel spacings for all images 518 // voxel spacings for all images
517 if(kLittleEndianOutput) { 519 if(kLittleEndianOutput) {
518 ofile.write((char *)kVoxelSpacing, 12); 520 ofile.write((char *)kVoxelSpacing, 12);
519 } else { 521 } else {
520 for(int j = 0; j < 3; j++) 522 for(int j = 0; j < 3; j++)
521 invertByteOrder((char *)&kVoxelSpacing[j 523 invertByteOrder((char *)&kVoxelSpacing[j], ftmp[j]);
522 ofile.write((char *)ftmp, 12); 524 ofile.write((char *)ftmp, 12);
523 } 525 }
524 if(DEBUG || kVerbose > 0) { 526 if(DEBUG || kVerbose > 0) {
525 G4cout << "Voxel spacing : (" 527 G4cout << "Voxel spacing : ("
526 << kVoxelSpacing[0] << ", " 528 << kVoxelSpacing[0] << ", "
527 << kVoxelSpacing[1] << ", " 529 << kVoxelSpacing[1] << ", "
528 << kVoxelSpacing[2] 530 << kVoxelSpacing[2]
529 << ") mm " << G4endl; 531 << ") mm " << G4endl;
530 } 532 }
531 533
532 calcPointers4(); 534 calcPointers4();
533 if(!kTracksWillBeStored) kPointerToTrackData 535 if(!kTracksWillBeStored) kPointerToTrackData = 0;
534 536
535 // offset from file starting point to the mo 537 // offset from file starting point to the modality image data
536 if(kLittleEndianOutput) { 538 if(kLittleEndianOutput) {
537 ofile.write((char *)&kPointerToModalityDat 539 ofile.write((char *)&kPointerToModalityData, 4);
538 } else { 540 } else {
539 invertByteOrder((char *)&kPointerToModalit 541 invertByteOrder((char *)&kPointerToModalityData, itmp[0]);
540 ofile.write((char *)itmp, 4); 542 ofile.write((char *)itmp, 4);
541 } 543 }
542 544
543 // # of dose distributions 545 // # of dose distributions
544 //int nDoseDist = (int)pointerToDoseDistData 546 //int nDoseDist = (int)pointerToDoseDistData.size();
545 int nDoseDist = getNumDoseDist(); 547 int nDoseDist = getNumDoseDist();
546 if(kLittleEndianOutput) { 548 if(kLittleEndianOutput) {
547 ofile.write((char *)&nDoseDist, 4); 549 ofile.write((char *)&nDoseDist, 4);
548 } else { 550 } else {
549 invertByteOrder((char *)&nDoseDist, itmp[0 551 invertByteOrder((char *)&nDoseDist, itmp[0]);
550 ofile.write((char *)itmp, 4); 552 ofile.write((char *)itmp, 4);
551 } 553 }
552 554
553 // offset from file starting point to the do 555 // offset from file starting point to the dose image data
554 if(kLittleEndianOutput) { 556 if(kLittleEndianOutput) {
555 for(int i = 0; i < nDoseDist; i++) { 557 for(int i = 0; i < nDoseDist; i++) {
556 ofile.write((char *)&kPointerToDoseDistD 558 ofile.write((char *)&kPointerToDoseDistData[i], 4);
557 } 559 }
558 } else { 560 } else {
559 for(int i = 0; i < nDoseDist; i++) { 561 for(int i = 0; i < nDoseDist; i++) {
560 invertByteOrder((char *)&kPointerToDoseD 562 invertByteOrder((char *)&kPointerToDoseDistData[i], itmp[0]);
561 ofile.write((char *)itmp, 4); 563 ofile.write((char *)itmp, 4);
562 } 564 }
563 } 565 }
564 566
565 // offset from file starting point to the RO 567 // offset from file starting point to the ROI image data
566 if(kLittleEndianOutput) { 568 if(kLittleEndianOutput) {
567 ofile.write((char *)&kPointerToROIData, 4) 569 ofile.write((char *)&kPointerToROIData, 4);
568 } else { 570 } else {
569 invertByteOrder((char *)&kPointerToROIData 571 invertByteOrder((char *)&kPointerToROIData, itmp[0]);
570 ofile.write((char *)itmp, 4); 572 ofile.write((char *)itmp, 4);
571 } 573 }
572 574
573 // offset from file starting point to the tr 575 // offset from file starting point to the track data
574 if(kLittleEndianOutput) { 576 if(kLittleEndianOutput) {
575 ofile.write((char *)&kPointerToTrackData, 577 ofile.write((char *)&kPointerToTrackData, 4);
576 } else { 578 } else {
577 invertByteOrder((char *)&kPointerToTrackDa 579 invertByteOrder((char *)&kPointerToTrackData, itmp[0]);
578 ofile.write((char *)itmp, 4); 580 ofile.write((char *)itmp, 4);
579 } 581 }
580 582
581 // offset from file starting point to the de 583 // offset from file starting point to the detector data
582 if(kLittleEndianOutput) { 584 if(kLittleEndianOutput) {
583 ofile.write((char *)&kPointerToDetectorDat 585 ofile.write((char *)&kPointerToDetectorData, 4);
584 } else { 586 } else {
585 invertByteOrder((char *)&kPointerToDetecto 587 invertByteOrder((char *)&kPointerToDetectorData, itmp[0]);
586 ofile.write((char *)itmp, 4); 588 ofile.write((char *)itmp, 4);
587 } 589 }
588 590
589 if(DEBUG || kVerbose > 0) { 591 if(DEBUG || kVerbose > 0) {
590 G4cout << "Each pointer to data : " 592 G4cout << "Each pointer to data : "
591 << kPointerToModalityData << ", "; 593 << kPointerToModalityData << ", ";
592 for(int i = 0; i < nDoseDist; i++) { 594 for(int i = 0; i < nDoseDist; i++) {
593 G4cout << kPointerToDoseDistData[i] << " 595 G4cout << kPointerToDoseDistData[i] << ", ";
594 } 596 }
595 G4cout << kPointerToROIData << ", " 597 G4cout << kPointerToROIData << ", "
596 << kPointerToTrackData << ", " 598 << kPointerToTrackData << ", "
597 << kPointerToDetectorData 599 << kPointerToDetectorData
598 << G4endl; 600 << G4endl;
599 } 601 }
600 602
601 //----- modality image -----// 603 //----- modality image -----//
602 604
603 int size[3]; 605 int size[3];
604 float scale; 606 float scale;
605 short minmax[2]; 607 short minmax[2];
606 float fCenter[3]; 608 float fCenter[3];
607 int iCenter[3]; 609 int iCenter[3];
608 // modality image size 610 // modality image size
609 kModality.getSize(size); 611 kModality.getSize(size);
610 612
611 if(kLittleEndianOutput) { 613 if(kLittleEndianOutput) {
612 ofile.write((char *)size, 3*sizeof(int)); 614 ofile.write((char *)size, 3*sizeof(int));
613 } else { 615 } else {
614 for(int j = 0; j < 3; j++) 616 for(int j = 0; j < 3; j++)
615 invertByteOrder((char *)&size[j], itmp[j 617 invertByteOrder((char *)&size[j], itmp[j]);
616 ofile.write((char *)itmp, 12); 618 ofile.write((char *)itmp, 12);
617 } 619 }
618 620
619 if(DEBUG || kVerbose > 0) { 621 if(DEBUG || kVerbose > 0) {
620 G4cout << "Modality image size : (" 622 G4cout << "Modality image size : ("
621 << size[0] << ", " 623 << size[0] << ", "
622 << size[1] << ", " 624 << size[1] << ", "
623 << size[2] << ")" 625 << size[2] << ")"
624 << G4endl; 626 << G4endl;
625 } 627 }
626 628
627 // modality image max. & min. 629 // modality image max. & min.
628 kModality.getMinMax(minmax); 630 kModality.getMinMax(minmax);
629 if(kLittleEndianOutput) { 631 if(kLittleEndianOutput) {
630 ofile.write((char *)minmax, 4); 632 ofile.write((char *)minmax, 4);
631 } else { 633 } else {
632 for(int j = 0; j < 2; j++) 634 for(int j = 0; j < 2; j++)
633 invertByteOrder((char *)&minmax[j], stmp 635 invertByteOrder((char *)&minmax[j], stmp[j]);
634 ofile.write((char *)stmp, 4); 636 ofile.write((char *)stmp, 4);
635 } 637 }
636 638
637 // modality image unit 639 // modality image unit
638 char munit[13] = "g/cm3\0"; 640 char munit[13] = "g/cm3\0";
639 ofile.write((char *)munit, 12); 641 ofile.write((char *)munit, 12);
640 642
641 // modality image scale 643 // modality image scale
642 scale = (float)kModality.getScale(); 644 scale = (float)kModality.getScale();
643 if(kLittleEndianOutput) { 645 if(kLittleEndianOutput) {
644 ofile.write((char *)&scale, 4); 646 ofile.write((char *)&scale, 4);
645 } else { 647 } else {
646 invertByteOrder((char *)&scale, ftmp[0]); 648 invertByteOrder((char *)&scale, ftmp[0]);
647 ofile.write((char *)ftmp, 4); 649 ofile.write((char *)ftmp, 4);
648 } 650 }
649 if(DEBUG || kVerbose > 0) { 651 if(DEBUG || kVerbose > 0) {
650 G4cout << "Modality image min., max., scal 652 G4cout << "Modality image min., max., scale : "
651 << minmax[0] << ", " 653 << minmax[0] << ", "
652 << minmax[1] << ", " 654 << minmax[1] << ", "
653 << scale << G4endl; 655 << scale << G4endl;
654 } 656 }
655 657
656 // modality image 658 // modality image
657 int psize = size[0]*size[1]; 659 int psize = size[0]*size[1];
658 if(DEBUG || kVerbose > 0) G4cout << "Modalit 660 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
659 for(int i = 0; i < size[2]; i++) { 661 for(int i = 0; i < size[2]; i++) {
660 short * image = kModality.getImage(i); 662 short * image = kModality.getImage(i);
661 if(kLittleEndianOutput) { 663 if(kLittleEndianOutput) {
662 ofile.write((char *)image, psize*sizeof( 664 ofile.write((char *)image, psize*sizeof(short));
663 } else { 665 } else {
664 for(int j = 0; j < psize; j++) { 666 for(int j = 0; j < psize; j++) {
665 invertByteOrder((char *)&image[j], stmp[0]); 667 invertByteOrder((char *)&image[j], stmp[0]);
666 ofile.write((char *)stmp, 2); 668 ofile.write((char *)stmp, 2);
667 } 669 }
668 } 670 }
669 671
670 if(DEBUG || kVerbose > 0) G4cout << "[" << 672 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
671 } 673 }
672 if(DEBUG || kVerbose > 0) G4cout << G4endl; 674 if(DEBUG || kVerbose > 0) G4cout << G4endl;
673 675
674 // modality desity map for CT value 676 // modality desity map for CT value
675 size_t msize = minmax[1] - minmax[0]+1; 677 size_t msize = minmax[1] - minmax[0]+1;
676 if(DEBUG || kVerbose > 0) 678 if(DEBUG || kVerbose > 0)
677 G4cout << "modality image : " << minmax[0] 679 G4cout << "modality image : " << minmax[0] << ", " << minmax[1] << G4endl;
678 float * pdmap = new float[msize]; 680 float * pdmap = new float[msize];
679 for(int i = 0; i < (int)msize; i++) pdmap[i] 681 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
680 682
681 if(kLittleEndianOutput) { 683 if(kLittleEndianOutput) {
682 ofile.write((char *)pdmap, msize*sizeof(fl 684 ofile.write((char *)pdmap, msize*sizeof(float));
683 } else { 685 } else {
684 for(int j = 0; j < (int)msize; j++) { 686 for(int j = 0; j < (int)msize; j++) {
685 invertByteOrder((char *)&pdmap[j], ftmp[ 687 invertByteOrder((char *)&pdmap[j], ftmp[0]);
686 ofile.write((char *)ftmp, 4); 688 ofile.write((char *)ftmp, 4);
687 } 689 }
688 } 690 }
689 691
690 if(DEBUG || kVerbose > 0) { 692 if(DEBUG || kVerbose > 0) {
691 G4cout << "density map : " << std::ends; 693 G4cout << "density map : " << std::ends;
692 for(int i = 0; i < (int)msize; i+=50) 694 for(int i = 0; i < (int)msize; i+=50)
693 G4cout <<kModalityImageDensityMap[i] << 695 G4cout <<kModalityImageDensityMap[i] << ", ";
694 G4cout << G4endl; 696 G4cout << G4endl;
695 } 697 }
696 delete [] pdmap; 698 delete [] pdmap;
697 699
698 700
699 //----- dose distribution image -----// 701 //----- dose distribution image -----//
700 702
701 if(!isDoseEmpty()) { 703 if(!isDoseEmpty()) {
702 704
703 calcDoseDistScale(); 705 calcDoseDistScale();
704 706
705 for(int ndose = 0; ndose < nDoseDist; ndos 707 for(int ndose = 0; ndose < nDoseDist; ndose++) {
706 // dose distrbution image size 708 // dose distrbution image size
707 kDose[ndose].getSize(size); 709 kDose[ndose].getSize(size);
708 if(kLittleEndianOutput) { 710 if(kLittleEndianOutput) {
709 ofile.write((char *)size, 3*sizeof(int)); 711 ofile.write((char *)size, 3*sizeof(int));
710 } else { 712 } else {
711 for(int j = 0; j < 3; j++) 713 for(int j = 0; j < 3; j++)
712 invertByteOrder((char *)&size[j], itmp[j]) 714 invertByteOrder((char *)&size[j], itmp[j]);
713 ofile.write((char *)itmp, 12); 715 ofile.write((char *)itmp, 12);
714 } 716 }
715 if(DEBUG || kVerbose > 0) { 717 if(DEBUG || kVerbose > 0) {
716 G4cout << "Dose dist. [" << ndose << "] imag 718 G4cout << "Dose dist. [" << ndose << "] image size : ("
717 << size[0] << ", " 719 << size[0] << ", "
718 << size[1] << ", " 720 << size[1] << ", "
719 << size[2] << ")" 721 << size[2] << ")"
720 << G4endl; 722 << G4endl;
721 } 723 }
722 724
723 // dose distribution max. & min. 725 // dose distribution max. & min.
724 getShortDoseDistMinMax(minmax, ndose); 726 getShortDoseDistMinMax(minmax, ndose);
725 if(kLittleEndianOutput) { 727 if(kLittleEndianOutput) {
726 ofile.write((char *)minmax, 2*2); // sizeof( 728 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
727 } else { 729 } else {
728 for(int j = 0; j < 2; j++) 730 for(int j = 0; j < 2; j++)
729 invertByteOrder((char *)&minmax[j], stmp[j 731 invertByteOrder((char *)&minmax[j], stmp[j]);
730 ofile.write((char *)stmp, 4); 732 ofile.write((char *)stmp, 4);
731 } 733 }
732 734
733 // dose distribution unit 735 // dose distribution unit
734 char cdunit[13]; 736 char cdunit[13];
735 std::strncpy(cdunit, kDoseUnit.c_str(), << 737 for(int i = 0; i < 13; i++) cdunit[i] = '\0';
736 cdunit[12] = '\0'; << 738 std::strcpy(cdunit, kDoseUnit.c_str());
737 ofile.write(cdunit, 12); << 739 ofile.write((char *)cdunit, 12);
738 if(DEBUG || kVerbose > 0) { 740 if(DEBUG || kVerbose > 0) {
739 G4cout << "Dose dist. unit : " << kDoseUnit 741 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
740 } 742 }
741 743
742 // dose distribution scaling 744 // dose distribution scaling
743 double dscale; 745 double dscale;
744 dscale = getDoseDistScale(ndose); 746 dscale = getDoseDistScale(ndose);
745 scale = float(dscale); 747 scale = float(dscale);
746 if(kLittleEndianOutput) { 748 if(kLittleEndianOutput) {
747 ofile.write((char *)&scale, 4); 749 ofile.write((char *)&scale, 4);
748 } else { 750 } else {
749 invertByteOrder((char *)&scale, ftmp[0]); 751 invertByteOrder((char *)&scale, ftmp[0]);
750 ofile.write((char *)ftmp, 4); 752 ofile.write((char *)ftmp, 4);
751 } 753 }
752 if(DEBUG || kVerbose > 0) { 754 if(DEBUG || kVerbose > 0) {
753 G4cout << "Dose dist. [" << ndose 755 G4cout << "Dose dist. [" << ndose
754 << "] image min., max., scale : " 756 << "] image min., max., scale : "
755 << minmax[0] << ", " 757 << minmax[0] << ", "
756 << minmax[1] << ", " 758 << minmax[1] << ", "
757 << scale << G4endl; 759 << scale << G4endl;
758 } 760 }
759 761
760 // dose distribution image 762 // dose distribution image
761 int dsize = size[0]*size[1]; 763 int dsize = size[0]*size[1];
762 short * dimage = new short[dsize]; 764 short * dimage = new short[dsize];
763 for(int z = 0; z < size[2]; z++) { 765 for(int z = 0; z < size[2]; z++) {
764 getShortDoseDist(dimage, z, ndose); 766 getShortDoseDist(dimage, z, ndose);
765 if(kLittleEndianOutput) { 767 if(kLittleEndianOutput) {
766 ofile.write((char *)dimage, dsize*2); //si 768 ofile.write((char *)dimage, dsize*2); //sizeof(short)
767 } else { 769 } else {
768 for(int j = 0; j < dsize; j++) { 770 for(int j = 0; j < dsize; j++) {
769 invertByteOrder((char *)&dimage[j], stmp 771 invertByteOrder((char *)&dimage[j], stmp[0]);
770 ofile.write((char *)stmp, 2); 772 ofile.write((char *)stmp, 2);
771 } 773 }
772 } 774 }
773 775
774 if(DEBUG || kVerbose > 0) { 776 if(DEBUG || kVerbose > 0) {
775 for(int j = 0; j < dsize; j++) { 777 for(int j = 0; j < dsize; j++) {
776 if(dimage[j] < 0) 778 if(dimage[j] < 0)
777 G4cout << "[" << j << "," << z << "]" 779 G4cout << "[" << j << "," << z << "]"
778 << dimage[j] << ", "; 780 << dimage[j] << ", ";
779 } 781 }
780 } 782 }
781 } 783 }
782 if(DEBUG || kVerbose > 0) G4cout << G4en 784 if(DEBUG || kVerbose > 0) G4cout << G4endl;
783 delete [] dimage; 785 delete [] dimage;
784 786
785 // relative location of the dose distrib 787 // relative location of the dose distribution image for
786 // the modality image 788 // the modality image
787 getDoseDistCenterPosition(fCenter, ndose 789 getDoseDistCenterPosition(fCenter, ndose);
788 for(int i = 0; i < 3; i++) iCenter[i] = 790 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
789 if(kLittleEndianOutput) { 791 if(kLittleEndianOutput) {
790 ofile.write((char *)iCenter, 3*4); // 3*size 792 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
791 } else { 793 } else {
792 for(int j = 0; j < 3; j++) 794 for(int j = 0; j < 3; j++)
793 invertByteOrder((char *)&iCenter[j], itmp[ 795 invertByteOrder((char *)&iCenter[j], itmp[j]);
794 ofile.write((char *)itmp, 12); 796 ofile.write((char *)itmp, 12);
795 } 797 }
796 if(DEBUG || kVerbose > 0) { 798 if(DEBUG || kVerbose > 0) {
797 G4cout << "Dose dist. [" << ndose 799 G4cout << "Dose dist. [" << ndose
798 << "]image relative location : (" 800 << "]image relative location : ("
799 << iCenter[0] << ", " 801 << iCenter[0] << ", "
800 << iCenter[1] << ", " 802 << iCenter[1] << ", "
801 << iCenter[2] << ")" << G4endl; 803 << iCenter[2] << ")" << G4endl;
802 } 804 }
803 805
804 // dose distribution name 806 // dose distribution name
805 std::string name = getDoseDistName(ndose 807 std::string name = getDoseDistName(ndose);
806 if(name.size() == 0) name = "dose"; 808 if(name.size() == 0) name = "dose";
807 name.resize(80); 809 name.resize(80);
808 ofile.write((char *)name.c_str(), 80); 810 ofile.write((char *)name.c_str(), 80);
809 if(DEBUG || kVerbose > 0) { 811 if(DEBUG || kVerbose > 0) {
810 G4cout << "Dose dist. name : " << name << G4 812 G4cout << "Dose dist. name : " << name << G4endl;
811 } 813 }
812 814
813 } 815 }
814 } 816 }
815 817
816 //----- ROI image -----// 818 //----- ROI image -----//
817 if(!isROIEmpty()) { 819 if(!isROIEmpty()) {
818 // ROI image size 820 // ROI image size
819 kRoi[0].getSize(size); 821 kRoi[0].getSize(size);
820 if(kLittleEndianOutput) { 822 if(kLittleEndianOutput) {
821 ofile.write((char *)size, 3*sizeof(int)) 823 ofile.write((char *)size, 3*sizeof(int));
822 } else { 824 } else {
823 for(int j = 0; j < 3; j++) 825 for(int j = 0; j < 3; j++)
824 invertByteOrder((char *)&size[j], itmp[j]); 826 invertByteOrder((char *)&size[j], itmp[j]);
825 ofile.write((char *)itmp, 12); 827 ofile.write((char *)itmp, 12);
826 } 828 }
827 if(DEBUG || kVerbose > 0) { 829 if(DEBUG || kVerbose > 0) {
828 G4cout << "ROI image size : (" 830 G4cout << "ROI image size : ("
829 << size[0] << ", " 831 << size[0] << ", "
830 << size[1] << ", " 832 << size[1] << ", "
831 << size[2] << ")" 833 << size[2] << ")"
832 << G4endl; 834 << G4endl;
833 } 835 }
834 836
835 // ROI max. & min. 837 // ROI max. & min.
836 kRoi[0].getMinMax(minmax); 838 kRoi[0].getMinMax(minmax);
837 if(kLittleEndianOutput) { 839 if(kLittleEndianOutput) {
838 ofile.write((char *)minmax, sizeof(short 840 ofile.write((char *)minmax, sizeof(short)*2);
839 } else { 841 } else {
840 for(int j = 0; j < 2; j++) 842 for(int j = 0; j < 2; j++)
841 invertByteOrder((char *)&minmax[j], stmp[j]) 843 invertByteOrder((char *)&minmax[j], stmp[j]);
842 ofile.write((char *)stmp, 4); 844 ofile.write((char *)stmp, 4);
843 } 845 }
844 846
845 // ROI distribution scaling 847 // ROI distribution scaling
846 scale = (float)kRoi[0].getScale(); 848 scale = (float)kRoi[0].getScale();
847 if(kLittleEndianOutput) { 849 if(kLittleEndianOutput) {
848 ofile.write((char *)&scale, sizeof(float 850 ofile.write((char *)&scale, sizeof(float));
849 } else { 851 } else {
850 invertByteOrder((char *)&scale, ftmp[0]) 852 invertByteOrder((char *)&scale, ftmp[0]);
851 ofile.write((char *)ftmp, 4); 853 ofile.write((char *)ftmp, 4);
852 } 854 }
853 if(DEBUG || kVerbose > 0) { 855 if(DEBUG || kVerbose > 0) {
854 G4cout << "ROI image min., max., scale : 856 G4cout << "ROI image min., max., scale : "
855 << minmax[0] << ", " 857 << minmax[0] << ", "
856 << minmax[1] << ", " 858 << minmax[1] << ", "
857 << scale << G4endl; 859 << scale << G4endl;
858 } 860 }
859 861
860 // ROI image 862 // ROI image
861 int rsize = size[0]*size[1]; 863 int rsize = size[0]*size[1];
862 for(int i = 0; i < size[2]; i++) { 864 for(int i = 0; i < size[2]; i++) {
863 short * rimage = kRoi[0].getImage(i); 865 short * rimage = kRoi[0].getImage(i);
864 if(kLittleEndianOutput) { 866 if(kLittleEndianOutput) {
865 ofile.write((char *)rimage, rsize*sizeof(sho 867 ofile.write((char *)rimage, rsize*sizeof(short));
866 } else { 868 } else {
867 for(int j = 0; j < rsize; j++) { 869 for(int j = 0; j < rsize; j++) {
868 invertByteOrder((char *)&rimage[j], stmp[0 870 invertByteOrder((char *)&rimage[j], stmp[0]);
869 ofile.write((char *)stmp, 2); 871 ofile.write((char *)stmp, 2);
870 } 872 }
871 } 873 }
872 874
873 } 875 }
874 876
875 // ROI relative location 877 // ROI relative location
876 kRoi[0].getCenterPosition(fCenter); 878 kRoi[0].getCenterPosition(fCenter);
877 for(int i = 0; i < 3; i++) iCenter[i] = (i 879 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
878 if(kLittleEndianOutput) { 880 if(kLittleEndianOutput) {
879 ofile.write((char *)iCenter, 3*sizeof(in 881 ofile.write((char *)iCenter, 3*sizeof(int));
880 } else { 882 } else {
881 for(int j = 0; j < 3; j++) 883 for(int j = 0; j < 3; j++)
882 invertByteOrder((char *)&iCenter[j], itmp[j] 884 invertByteOrder((char *)&iCenter[j], itmp[j]);
883 ofile.write((char *)itmp, 12); 885 ofile.write((char *)itmp, 12);
884 } 886 }
885 if(DEBUG || kVerbose > 0) { 887 if(DEBUG || kVerbose > 0) {
886 G4cout << "ROI image relative location : 888 G4cout << "ROI image relative location : ("
887 << iCenter[0] << ", " 889 << iCenter[0] << ", "
888 << iCenter[1] << ", " 890 << iCenter[1] << ", "
889 << iCenter[2] << ")" << G4endl; 891 << iCenter[2] << ")" << G4endl;
890 } 892 }
891 } 893 }
892 894
893 //----- track information -----// 895 //----- track information -----//
894 // number of track 896 // number of track
895 if(kPointerToTrackData > 0) { 897 if(kPointerToTrackData > 0) {
896 898
897 int ntrk = (int)kTracks.size(); << 899 int ntrk = kTracks.size();
898 if(kLittleEndianOutput) { 900 if(kLittleEndianOutput) {
899 ofile.write((char *)&ntrk, sizeof(int)); 901 ofile.write((char *)&ntrk, sizeof(int));
900 } else { 902 } else {
901 invertByteOrder((char *)&ntrk, itmp[0]); 903 invertByteOrder((char *)&ntrk, itmp[0]);
902 ofile.write((char *)itmp, 4); 904 ofile.write((char *)itmp, 4);
903 } 905 }
904 if(DEBUG || kVerbose > 0) { 906 if(DEBUG || kVerbose > 0) {
905 G4cout << "# of tracks : " 907 G4cout << "# of tracks : "
906 << ntrk << G4endl; 908 << ntrk << G4endl;
907 } 909 }
908 910
909 for(int nt = 0; nt < ntrk; nt++) { 911 for(int nt = 0; nt < ntrk; nt++) {
910 912
911 // # of steps in a track 913 // # of steps in a track
912 int nsteps = kTracks[nt].getNumberOfStep 914 int nsteps = kTracks[nt].getNumberOfSteps();
913 if(kLittleEndianOutput) { 915 if(kLittleEndianOutput) {
914 ofile.write((char *)&nsteps, sizeof(int)); 916 ofile.write((char *)&nsteps, sizeof(int));
915 } else { 917 } else {
916 invertByteOrder((char *)&nsteps, itmp[0]); 918 invertByteOrder((char *)&nsteps, itmp[0]);
917 ofile.write((char *)itmp, 4); 919 ofile.write((char *)itmp, 4);
918 } 920 }
919 if(DEBUG || kVerbose > 0) { 921 if(DEBUG || kVerbose > 0) {
920 G4cout << "# of steps : " << nsteps << G4end 922 G4cout << "# of steps : " << nsteps << G4endl;
921 } 923 }
922 924
923 // track color 925 // track color
924 unsigned char tcolor[3]; 926 unsigned char tcolor[3];
925 kTracks[nt].getColor(tcolor); 927 kTracks[nt].getColor(tcolor);
926 ofile.write((char *)tcolor, 3); 928 ofile.write((char *)tcolor, 3);
927 929
928 // steps 930 // steps
929 float stepPoints[6]; 931 float stepPoints[6];
930 for(int isteps = 0; isteps < nsteps; ist << 932 for(int ns = 0; ns < nsteps; ns++) {
931 kTracks[nt].getStep(stepPoints[0], stepPoint 933 kTracks[nt].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
932 stepPoints[3], stepPoints[4], stepPo 934 stepPoints[3], stepPoints[4], stepPoints[5],
933 isteps); << 935 ns);
934 936
935 if(kLittleEndianOutput) { 937 if(kLittleEndianOutput) {
936 ofile.write((char *)stepPoints, sizeof(flo 938 ofile.write((char *)stepPoints, sizeof(float)*6);
937 } else { 939 } else {
938 for(int j = 0; j < 6; j++) 940 for(int j = 0; j < 6; j++)
939 invertByteOrder((char *)&stepPoints[j], 941 invertByteOrder((char *)&stepPoints[j], ftmp[j]);
940 ofile.write((char *)ftmp, 24); 942 ofile.write((char *)ftmp, 24);
941 } 943 }
942 } 944 }
943 } 945 }
944 } 946 }
945 947
946 //----- detector information -----// 948 //----- detector information -----//
947 // number of detectors 949 // number of detectors
948 if(kPointerToDetectorData > 0) { 950 if(kPointerToDetectorData > 0) {
949 int ndet = (int)kDetectors.size(); << 951 int ndet = kDetectors.size();
950 if(kLittleEndianOutput) { 952 if(kLittleEndianOutput) {
951 ofile.write((char *)&ndet, sizeof(int)); 953 ofile.write((char *)&ndet, sizeof(int));
952 } else { 954 } else {
953 invertByteOrder((char *)&ndet, itmp[0]); 955 invertByteOrder((char *)&ndet, itmp[0]);
954 ofile.write((char *)itmp, 4); 956 ofile.write((char *)itmp, 4);
955 } 957 }
956 if(DEBUG || kVerbose > 0) { 958 if(DEBUG || kVerbose > 0) {
957 G4cout << "# of detectors : " 959 G4cout << "# of detectors : "
958 << ndet << G4endl; 960 << ndet << G4endl;
959 } 961 }
960 962
961 for(int nd = 0; nd < ndet; nd++) { 963 for(int nd = 0; nd < ndet; nd++) {
962 964
963 // # of edges of a detector 965 // # of edges of a detector
964 int nedges = kDetectors[nd].getNumberOfE 966 int nedges = kDetectors[nd].getNumberOfEdges();
965 if(kLittleEndianOutput) { 967 if(kLittleEndianOutput) {
966 ofile.write((char *)&nedges, sizeof(int)); 968 ofile.write((char *)&nedges, sizeof(int));
967 } else { 969 } else {
968 invertByteOrder((char *)&nedges, itmp[0]); 970 invertByteOrder((char *)&nedges, itmp[0]);
969 ofile.write((char *)itmp, 4); 971 ofile.write((char *)itmp, 4);
970 } 972 }
971 if(DEBUG || kVerbose > 0) { 973 if(DEBUG || kVerbose > 0) {
972 G4cout << "# of edges in a detector : " << n 974 G4cout << "# of edges in a detector : " << nedges << G4endl;
973 } 975 }
974 976
975 // edges 977 // edges
976 float edgePoints[6]; 978 float edgePoints[6];
977 for(int ne = 0; ne < nedges; ne++) { 979 for(int ne = 0; ne < nedges; ne++) {
978 kDetectors[nd].getEdge(edgePoints[0], edgePo 980 kDetectors[nd].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
979 edgePoints[3], edgePoints[4], edg 981 edgePoints[3], edgePoints[4], edgePoints[5],
980 ne); 982 ne);
981 983
982 if(kLittleEndianOutput) { 984 if(kLittleEndianOutput) {
983 ofile.write((char *)edgePoints, sizeof(flo 985 ofile.write((char *)edgePoints, sizeof(float)*6);
984 } else { 986 } else {
985 for(int j = 0; j < 6; j++) 987 for(int j = 0; j < 6; j++)
986 invertByteOrder((char *)&edgePoints[j], 988 invertByteOrder((char *)&edgePoints[j], ftmp[j]);
987 ofile.write((char *)ftmp, 24); 989 ofile.write((char *)ftmp, 24);
988 } 990 }
989 991
990 if(DEBUG || kVerbose > 0) { 992 if(DEBUG || kVerbose > 0) {
991 if(ne < 1) { 993 if(ne < 1) {
992 G4cout << " edge : (" << edgePoints[0] < 994 G4cout << " edge : (" << edgePoints[0] << ", "
993 << edgePoints[1] << ", " 995 << edgePoints[1] << ", "
994 << edgePoints[2] << ") - (" 996 << edgePoints[2] << ") - ("
995 << edgePoints[3] << ", " 997 << edgePoints[3] << ", "
996 << edgePoints[4] << ", " 998 << edgePoints[4] << ", "
997 << edgePoints[5] << ")" << G4endl; 999 << edgePoints[5] << ")" << G4endl;
998 } 1000 }
999 } 1001 }
1000 } 1002 }
1001 1003
1002 // detector color 1004 // detector color
1003 unsigned char dcolor[3]; 1005 unsigned char dcolor[3];
1004 kDetectors[nd].getColor(dcolor); 1006 kDetectors[nd].getColor(dcolor);
1005 ofile.write((char *)dcolor, 3); 1007 ofile.write((char *)dcolor, 3);
1006 if(DEBUG || kVerbose > 0) { 1008 if(DEBUG || kVerbose > 0) {
1007 G4cout << " rgb : (" << (int)dcolor[0] << " 1009 G4cout << " rgb : (" << (int)dcolor[0] << ", "
1008 << (int)dcolor[1] << ", " 1010 << (int)dcolor[1] << ", "
1009 << (int)dcolor[2] << ")" << G4endl; 1011 << (int)dcolor[2] << ")" << G4endl;
1010 } 1012 }
1011 1013
1012 // detector name 1014 // detector name
1013 std::string dname = kDetectors[nd].getN 1015 std::string dname = kDetectors[nd].getName();
1014 dname.resize(80); 1016 dname.resize(80);
1015 ofile.write((char *)dname.c_str(), 80); 1017 ofile.write((char *)dname.c_str(), 80);
1016 if(DEBUG || kVerbose > 0) { 1018 if(DEBUG || kVerbose > 0) {
1017 G4cout << " detector name : " << dname << G 1019 G4cout << " detector name : " << dname << G4endl;
1018 1020
1019 } 1021 }
1020 } 1022 }
1021 } 1023 }
1022 1024
1023 // file end mark 1025 // file end mark
1024 ofile.write("END", 3); 1026 ofile.write("END", 3);
1025 1027
1026 ofile.close(); 1028 ofile.close();
1027 if(DEBUG || kVerbose > 0) 1029 if(DEBUG || kVerbose > 0)
1028 G4cout << ">>>> closed gdd file: " << kFi 1030 G4cout << ">>>> closed gdd file: " << kFileName << G4endl;
1029 1031
1030 return true; 1032 return true;
1031 } 1033 }
1032 bool G4GMocrenIO::storeData3() { 1034 bool G4GMocrenIO::storeData3() {
1033 1035
1034 if(kVerbose > 0) G4cout << ">>>>>>> store 1036 if(kVerbose > 0) G4cout << ">>>>>>> store data (ver.3) <<<<<<<" << G4endl;
1035 if(kVerbose > 0) G4cout << " " << k 1037 if(kVerbose > 0) G4cout << " " << kFileName << G4endl;
1036 1038
1037 bool DEBUG = false;// 1039 bool DEBUG = false;//
1038 1040
1039 // output file open 1041 // output file open
1040 std::ofstream ofile(kFileName.c_str(), 1042 std::ofstream ofile(kFileName.c_str(),
1041 std::ios_base::out|std::ios_base::b 1043 std::ios_base::out|std::ios_base::binary);
1042 1044
1043 // file identifier 1045 // file identifier
1044 ofile.write("gMocren ", 8); 1046 ofile.write("gMocren ", 8);
1045 1047
1046 // file version 1048 // file version
1047 unsigned char ver = 0x03; 1049 unsigned char ver = 0x03;
1048 ofile.write((char *)&ver, 1); 1050 ofile.write((char *)&ver, 1);
1049 1051
1050 // endian 1052 // endian
1051 ofile.write((char *)&kLittleEndianOutput, s 1053 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1052 1054
1053 // comment length (fixed size) 1055 // comment length (fixed size)
1054 int commentLength = 1024; 1056 int commentLength = 1024;
1055 ofile.write((char *)&commentLength, 4); 1057 ofile.write((char *)&commentLength, 4);
1056 1058
1057 // comment 1059 // comment
1058 char cmt[1025]; 1060 char cmt[1025];
1059 std::strncpy(cmt, kComment.c_str(), 1024); 1061 std::strncpy(cmt, kComment.c_str(), 1024);
1060 ofile.write((char *)cmt, 1024); 1062 ofile.write((char *)cmt, 1024);
1061 if(DEBUG || kVerbose > 0) { 1063 if(DEBUG || kVerbose > 0) {
1062 G4cout << "Data comment : " 1064 G4cout << "Data comment : "
1063 << kComment << G4endl; 1065 << kComment << G4endl;
1064 } 1066 }
1065 1067
1066 // voxel spacings for all images 1068 // voxel spacings for all images
1067 ofile.write((char *)kVoxelSpacing, 12); 1069 ofile.write((char *)kVoxelSpacing, 12);
1068 if(DEBUG || kVerbose > 0) { 1070 if(DEBUG || kVerbose > 0) {
1069 G4cout << "Voxel spacing : (" 1071 G4cout << "Voxel spacing : ("
1070 << kVoxelSpacing[0] << ", " 1072 << kVoxelSpacing[0] << ", "
1071 << kVoxelSpacing[1] << ", " 1073 << kVoxelSpacing[1] << ", "
1072 << kVoxelSpacing[2] 1074 << kVoxelSpacing[2]
1073 << ") mm " << G4endl; 1075 << ") mm " << G4endl;
1074 } 1076 }
1075 1077
1076 calcPointers3(); 1078 calcPointers3();
1077 1079
1078 // offset from file starting point to the m 1080 // offset from file starting point to the modality image data
1079 ofile.write((char *)&kPointerToModalityData 1081 ofile.write((char *)&kPointerToModalityData, 4);
1080 1082
1081 // # of dose distributions 1083 // # of dose distributions
1082 //int nDoseDist = (int)pointerToDoseDistDat 1084 //int nDoseDist = (int)pointerToDoseDistData.size();
1083 int nDoseDist = getNumDoseDist(); 1085 int nDoseDist = getNumDoseDist();
1084 ofile.write((char *)&nDoseDist, 4); 1086 ofile.write((char *)&nDoseDist, 4);
1085 1087
1086 // offset from file starting point to the d 1088 // offset from file starting point to the dose image data
1087 for(int i = 0; i < nDoseDist; i++) { 1089 for(int i = 0; i < nDoseDist; i++) {
1088 ofile.write((char *)&kPointerToDoseDistDa 1090 ofile.write((char *)&kPointerToDoseDistData[i], 4);
1089 } 1091 }
1090 1092
1091 // offset from file starting point to the R 1093 // offset from file starting point to the ROI image data
1092 ofile.write((char *)&kPointerToROIData, 4); 1094 ofile.write((char *)&kPointerToROIData, 4);
1093 1095
1094 // offset from file starting point to the t 1096 // offset from file starting point to the track data
1095 ofile.write((char *)&kPointerToTrackData, 4 1097 ofile.write((char *)&kPointerToTrackData, 4);
1096 if(DEBUG || kVerbose > 0) { 1098 if(DEBUG || kVerbose > 0) {
1097 G4cout << "Each pointer to data : " 1099 G4cout << "Each pointer to data : "
1098 << kPointerToModalityData << ", "; 1100 << kPointerToModalityData << ", ";
1099 for(int i = 0; i < nDoseDist; i++) { 1101 for(int i = 0; i < nDoseDist; i++) {
1100 G4cout << kPointerToDoseDistData[i] << 1102 G4cout << kPointerToDoseDistData[i] << ", ";
1101 } 1103 }
1102 G4cout << kPointerToROIData << ", " 1104 G4cout << kPointerToROIData << ", "
1103 << kPointerToTrackData << G4endl; 1105 << kPointerToTrackData << G4endl;
1104 } 1106 }
1105 1107
1106 //----- modality image -----// 1108 //----- modality image -----//
1107 1109
1108 int size[3]; 1110 int size[3];
1109 float scale; 1111 float scale;
1110 short minmax[2]; 1112 short minmax[2];
1111 float fCenter[3]; 1113 float fCenter[3];
1112 int iCenter[3]; 1114 int iCenter[3];
1113 // modality image size 1115 // modality image size
1114 kModality.getSize(size); 1116 kModality.getSize(size);
1115 ofile.write((char *)size, 3*sizeof(int)); 1117 ofile.write((char *)size, 3*sizeof(int));
1116 if(DEBUG || kVerbose > 0) { 1118 if(DEBUG || kVerbose > 0) {
1117 G4cout << "Modality image size : (" 1119 G4cout << "Modality image size : ("
1118 << size[0] << ", " 1120 << size[0] << ", "
1119 << size[1] << ", " 1121 << size[1] << ", "
1120 << size[2] << ")" 1122 << size[2] << ")"
1121 << G4endl; 1123 << G4endl;
1122 } 1124 }
1123 1125
1124 // modality image max. & min. 1126 // modality image max. & min.
1125 kModality.getMinMax(minmax); 1127 kModality.getMinMax(minmax);
1126 ofile.write((char *)minmax, 4); 1128 ofile.write((char *)minmax, 4);
1127 1129
1128 // modality image unit 1130 // modality image unit
1129 char munit[13] = "g/cm3 "; 1131 char munit[13] = "g/cm3 ";
1130 ofile.write((char *)munit, 12); 1132 ofile.write((char *)munit, 12);
1131 1133
1132 // modality image scale 1134 // modality image scale
1133 scale = (float)kModality.getScale(); 1135 scale = (float)kModality.getScale();
1134 ofile.write((char *)&scale, 4); 1136 ofile.write((char *)&scale, 4);
1135 if(DEBUG || kVerbose > 0) { 1137 if(DEBUG || kVerbose > 0) {
1136 G4cout << "Modality image min., max., sca 1138 G4cout << "Modality image min., max., scale : "
1137 << minmax[0] << ", " 1139 << minmax[0] << ", "
1138 << minmax[1] << ", " 1140 << minmax[1] << ", "
1139 << scale << G4endl; 1141 << scale << G4endl;
1140 } 1142 }
1141 1143
1142 // modality image 1144 // modality image
1143 int psize = size[0]*size[1]; 1145 int psize = size[0]*size[1];
1144 if(DEBUG || kVerbose > 0) G4cout << "Modali 1146 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
1145 for(int i = 0; i < size[2]; i++) { 1147 for(int i = 0; i < size[2]; i++) {
1146 short * image = kModality.getImage(i); 1148 short * image = kModality.getImage(i);
1147 ofile.write((char *)image, psize*sizeof(s 1149 ofile.write((char *)image, psize*sizeof(short));
1148 1150
1149 if(DEBUG || kVerbose > 0) G4cout << "[" < 1151 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1150 } 1152 }
1151 if(DEBUG || kVerbose > 0) G4cout << G4endl; 1153 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1152 1154
1153 // modality desity map for CT value 1155 // modality desity map for CT value
1154 size_t msize = minmax[1] - minmax[0]+1; 1156 size_t msize = minmax[1] - minmax[0]+1;
1155 float * pdmap = new float[msize]; 1157 float * pdmap = new float[msize];
1156 for(int i = 0; i < (int)msize; i++) pdmap[i 1158 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1157 ofile.write((char *)pdmap, msize*sizeof(flo 1159 ofile.write((char *)pdmap, msize*sizeof(float));
1158 if(DEBUG || kVerbose > 0) { 1160 if(DEBUG || kVerbose > 0) {
1159 G4cout << "density map : " << std::ends; 1161 G4cout << "density map : " << std::ends;
1160 for(int i = 0; i < (int)msize; i+=50) 1162 for(int i = 0; i < (int)msize; i+=50)
1161 G4cout <<kModalityImageDensityMap[i] << 1163 G4cout <<kModalityImageDensityMap[i] << ", ";
1162 G4cout << G4endl; 1164 G4cout << G4endl;
1163 } 1165 }
1164 delete [] pdmap; 1166 delete [] pdmap;
1165 1167
1166 1168
1167 //----- dose distribution image -----// 1169 //----- dose distribution image -----//
1168 1170
1169 if(!isDoseEmpty()) { 1171 if(!isDoseEmpty()) {
1170 1172
1171 calcDoseDistScale(); 1173 calcDoseDistScale();
1172 1174
1173 for(int ndose = 0; ndose < nDoseDist; ndo 1175 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1174 // dose distrbution image size 1176 // dose distrbution image size
1175 kDose[ndose].getSize(size); 1177 kDose[ndose].getSize(size);
1176 ofile.write((char *)size, 3*sizeof(int) 1178 ofile.write((char *)size, 3*sizeof(int));
1177 if(DEBUG || kVerbose > 0) { 1179 if(DEBUG || kVerbose > 0) {
1178 G4cout << "Dose dist. [" << ndose << "] ima 1180 G4cout << "Dose dist. [" << ndose << "] image size : ("
1179 << size[0] << ", " 1181 << size[0] << ", "
1180 << size[1] << ", " 1182 << size[1] << ", "
1181 << size[2] << ")" 1183 << size[2] << ")"
1182 << G4endl; 1184 << G4endl;
1183 } 1185 }
1184 1186
1185 // dose distribution max. & min. 1187 // dose distribution max. & min.
1186 getShortDoseDistMinMax(minmax, ndose); 1188 getShortDoseDistMinMax(minmax, ndose);
1187 ofile.write((char *)minmax, 2*2); // si 1189 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
1188 1190
1189 // dose distribution unit 1191 // dose distribution unit
1190 ofile.write((char *)kDoseUnit.c_str(), 1192 ofile.write((char *)kDoseUnit.c_str(), 12);
1191 if(DEBUG || kVerbose > 0) { 1193 if(DEBUG || kVerbose > 0) {
1192 G4cout << "Dose dist. unit : " << kDoseUnit 1194 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
1193 } 1195 }
1194 1196
1195 // dose distribution scaling 1197 // dose distribution scaling
1196 double dscale; 1198 double dscale;
1197 dscale = getDoseDistScale(ndose); 1199 dscale = getDoseDistScale(ndose);
1198 scale = float(dscale); 1200 scale = float(dscale);
1199 ofile.write((char *)&scale, 4); 1201 ofile.write((char *)&scale, 4);
1200 if(DEBUG || kVerbose > 0) { 1202 if(DEBUG || kVerbose > 0) {
1201 G4cout << "Dose dist. [" << ndose 1203 G4cout << "Dose dist. [" << ndose
1202 << "] image min., max., scale : " 1204 << "] image min., max., scale : "
1203 << minmax[0] << ", " 1205 << minmax[0] << ", "
1204 << minmax[1] << ", " 1206 << minmax[1] << ", "
1205 << scale << G4endl; 1207 << scale << G4endl;
1206 } 1208 }
1207 1209
1208 // dose distribution image 1210 // dose distribution image
1209 int dsize = size[0]*size[1]; 1211 int dsize = size[0]*size[1];
1210 short * dimage = new short[dsize]; 1212 short * dimage = new short[dsize];
1211 for(int z = 0; z < size[2]; z++) { 1213 for(int z = 0; z < size[2]; z++) {
1212 getShortDoseDist(dimage, z, ndose); 1214 getShortDoseDist(dimage, z, ndose);
1213 ofile.write((char *)dimage, dsize*2); //siz 1215 ofile.write((char *)dimage, dsize*2); //sizeof(short)
1214 1216
1215 if(DEBUG || kVerbose > 0) { 1217 if(DEBUG || kVerbose > 0) {
1216 for(int j = 0; j < dsize; j++) { 1218 for(int j = 0; j < dsize; j++) {
1217 if(dimage[j] < 0) 1219 if(dimage[j] < 0)
1218 G4cout << "[" << j << "," << z << "]" 1220 G4cout << "[" << j << "," << z << "]"
1219 << dimage[j] << ", "; 1221 << dimage[j] << ", ";
1220 } 1222 }
1221 } 1223 }
1222 } 1224 }
1223 if(DEBUG || kVerbose > 0) G4cout << G4e 1225 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1224 delete [] dimage; 1226 delete [] dimage;
1225 1227
1226 // relative location of the dose distri 1228 // relative location of the dose distribution image for
1227 // the modality image 1229 // the modality image
1228 getDoseDistCenterPosition(fCenter, ndos 1230 getDoseDistCenterPosition(fCenter, ndose);
1229 for(int i = 0; i < 3; i++) iCenter[i] = 1231 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1230 ofile.write((char *)iCenter, 3*4); // 3 1232 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
1231 if(DEBUG || kVerbose > 0) { 1233 if(DEBUG || kVerbose > 0) {
1232 G4cout << "Dose dist. [" << ndose 1234 G4cout << "Dose dist. [" << ndose
1233 << "]image relative location : (" 1235 << "]image relative location : ("
1234 << iCenter[0] << ", " 1236 << iCenter[0] << ", "
1235 << iCenter[1] << ", " 1237 << iCenter[1] << ", "
1236 << iCenter[2] << ")" << G4endl; 1238 << iCenter[2] << ")" << G4endl;
1237 } 1239 }
1238 } 1240 }
1239 } 1241 }
1240 1242
1241 //----- ROI image -----// 1243 //----- ROI image -----//
1242 if(!isROIEmpty()) { 1244 if(!isROIEmpty()) {
1243 // ROI image size 1245 // ROI image size
1244 kRoi[0].getSize(size); 1246 kRoi[0].getSize(size);
1245 ofile.write((char *)size, 3*sizeof(int)); 1247 ofile.write((char *)size, 3*sizeof(int));
1246 if(DEBUG || kVerbose > 0) { 1248 if(DEBUG || kVerbose > 0) {
1247 G4cout << "ROI image size : (" 1249 G4cout << "ROI image size : ("
1248 << size[0] << ", " 1250 << size[0] << ", "
1249 << size[1] << ", " 1251 << size[1] << ", "
1250 << size[2] << ")" 1252 << size[2] << ")"
1251 << G4endl; 1253 << G4endl;
1252 } 1254 }
1253 1255
1254 // ROI max. & min. 1256 // ROI max. & min.
1255 kRoi[0].getMinMax(minmax); 1257 kRoi[0].getMinMax(minmax);
1256 ofile.write((char *)minmax, sizeof(short) 1258 ofile.write((char *)minmax, sizeof(short)*2);
1257 1259
1258 // ROI distribution scaling 1260 // ROI distribution scaling
1259 scale = (float)kRoi[0].getScale(); 1261 scale = (float)kRoi[0].getScale();
1260 ofile.write((char *)&scale, sizeof(float) 1262 ofile.write((char *)&scale, sizeof(float));
1261 if(DEBUG || kVerbose > 0) { 1263 if(DEBUG || kVerbose > 0) {
1262 G4cout << "ROI image min., max., scale 1264 G4cout << "ROI image min., max., scale : "
1263 << minmax[0] << ", " 1265 << minmax[0] << ", "
1264 << minmax[1] << ", " 1266 << minmax[1] << ", "
1265 << scale << G4endl; 1267 << scale << G4endl;
1266 } 1268 }
1267 1269
1268 // ROI image 1270 // ROI image
1269 int rsize = size[0]*size[1]; 1271 int rsize = size[0]*size[1];
1270 for(int i = 0; i < size[2]; i++) { 1272 for(int i = 0; i < size[2]; i++) {
1271 short * rimage = kRoi[0].getImage(i); 1273 short * rimage = kRoi[0].getImage(i);
1272 ofile.write((char *)rimage, rsize*sizeo 1274 ofile.write((char *)rimage, rsize*sizeof(short));
1273 1275
1274 } 1276 }
1275 1277
1276 // ROI relative location 1278 // ROI relative location
1277 kRoi[0].getCenterPosition(fCenter); 1279 kRoi[0].getCenterPosition(fCenter);
1278 for(int i = 0; i < 3; i++) iCenter[i] = ( 1280 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1279 ofile.write((char *)iCenter, 3*sizeof(int 1281 ofile.write((char *)iCenter, 3*sizeof(int));
1280 if(DEBUG || kVerbose > 0) { 1282 if(DEBUG || kVerbose > 0) {
1281 G4cout << "ROI image relative location 1283 G4cout << "ROI image relative location : ("
1282 << iCenter[0] << ", " 1284 << iCenter[0] << ", "
1283 << iCenter[1] << ", " 1285 << iCenter[1] << ", "
1284 << iCenter[2] << ")" << G4endl; 1286 << iCenter[2] << ")" << G4endl;
1285 } 1287 }
1286 } 1288 }
1287 1289
1288 //----- track information -----// 1290 //----- track information -----//
1289 // number of track 1291 // number of track
1290 int ntrk = (int)kSteps.size(); << 1292 int ntrk = kSteps.size();
1291 ofile.write((char *)&ntrk, sizeof(int)); 1293 ofile.write((char *)&ntrk, sizeof(int));
1292 if(DEBUG || kVerbose > 0) { 1294 if(DEBUG || kVerbose > 0) {
1293 G4cout << "# of tracks : " 1295 G4cout << "# of tracks : "
1294 << ntrk << G4endl; 1296 << ntrk << G4endl;
1295 } 1297 }
1296 // track position 1298 // track position
1297 for(int i = 0; i < ntrk; i++) { 1299 for(int i = 0; i < ntrk; i++) {
1298 float * tp = kSteps[i]; 1300 float * tp = kSteps[i];
1299 ofile.write((char *)tp, sizeof(float)*6); 1301 ofile.write((char *)tp, sizeof(float)*6);
1300 } 1302 }
1301 // track color 1303 // track color
1302 int ntcolor = int(kStepColors.size()); 1304 int ntcolor = int(kStepColors.size());
1303 if(ntrk != ntcolor) 1305 if(ntrk != ntcolor)
1304 if (G4VisManager::GetVerbosity() >= G4Vis 1306 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1305 G4cout << "# of track color information 1307 G4cout << "# of track color information must be the same as # of tracks."
1306 << G4endl; 1308 << G4endl;
1307 unsigned char white[3] = {255,255,255}; // 1309 unsigned char white[3] = {255,255,255}; // default color
1308 for(int i = 0; i < ntrk; i++) { 1310 for(int i = 0; i < ntrk; i++) {
1309 if(i < ntcolor) { 1311 if(i < ntcolor) {
1310 unsigned char * tcolor = kStepColors[i] 1312 unsigned char * tcolor = kStepColors[i];
1311 ofile.write((char *)tcolor, 3); 1313 ofile.write((char *)tcolor, 3);
1312 } else { 1314 } else {
1313 ofile.write((char *)white, 3); 1315 ofile.write((char *)white, 3);
1314 } 1316 }
1315 } 1317 }
1316 1318
1317 // file end mark 1319 // file end mark
1318 ofile.write("END", 3); 1320 ofile.write("END", 3);
1319 1321
1320 ofile.close(); 1322 ofile.close();
1321 1323
1322 return true; 1324 return true;
1323 } 1325 }
1324 // 1326 //
1325 bool G4GMocrenIO::storeData4(char * _filename 1327 bool G4GMocrenIO::storeData4(char * _filename) {
1326 kFileName = _filename; 1328 kFileName = _filename;
1327 return storeData4(); 1329 return storeData4();
1328 } 1330 }
1329 1331
1330 // version 2 1332 // version 2
1331 bool G4GMocrenIO::storeData2() { 1333 bool G4GMocrenIO::storeData2() {
1332 1334
1333 if(kVerbose > 0) G4cout << ">>>>>>> store 1335 if(kVerbose > 0) G4cout << ">>>>>>> store data (ver.2) <<<<<<<" << G4endl;
1334 if(kVerbose > 0) G4cout << " " << k 1336 if(kVerbose > 0) G4cout << " " << kFileName << G4endl;
1335 1337
1336 bool DEBUG = false;// 1338 bool DEBUG = false;//
1337 1339
1338 // output file open 1340 // output file open
1339 std::ofstream ofile(kFileName.c_str(), 1341 std::ofstream ofile(kFileName.c_str(),
1340 std::ios_base::out|std::ios_base::b 1342 std::ios_base::out|std::ios_base::binary);
1341 1343
1342 // file identifier 1344 // file identifier
1343 ofile.write("GRAPE ", 8); 1345 ofile.write("GRAPE ", 8);
1344 1346
1345 // file version 1347 // file version
1346 unsigned char ver = 0x02; 1348 unsigned char ver = 0x02;
1347 ofile.write((char *)&ver, 1); 1349 ofile.write((char *)&ver, 1);
1348 // file id for old file format support 1350 // file id for old file format support
1349 ofile.write(kId.c_str(), IDLENGTH); 1351 ofile.write(kId.c_str(), IDLENGTH);
1350 // file version for old file format support 1352 // file version for old file format support
1351 ofile.write(kVersion.c_str(), VERLENGTH); 1353 ofile.write(kVersion.c_str(), VERLENGTH);
1352 // endian 1354 // endian
1353 ofile.write((char *)&kLittleEndianOutput, s 1355 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1354 1356
1355 /* 1357 /*
1356 // event number 1358 // event number
1357 ofile.write((char *)&numberOfEvents, sizeof 1359 ofile.write((char *)&numberOfEvents, sizeof(int));
1358 float imageSpacing[3]; 1360 float imageSpacing[3];
1359 imageSpacing[0] = modalityImageVoxelSpacing 1361 imageSpacing[0] = modalityImageVoxelSpacing[0];
1360 imageSpacing[1] = modalityImageVoxelSpacing 1362 imageSpacing[1] = modalityImageVoxelSpacing[1];
1361 imageSpacing[2] = modalityImageVoxelSpacing 1363 imageSpacing[2] = modalityImageVoxelSpacing[2];
1362 ofile.write((char *)imageSpacing, 12); 1364 ofile.write((char *)imageSpacing, 12);
1363 */ 1365 */
1364 1366
1365 1367
1366 // voxel spacings for all images 1368 // voxel spacings for all images
1367 ofile.write((char *)kVoxelSpacing, 12); 1369 ofile.write((char *)kVoxelSpacing, 12);
1368 if(DEBUG || kVerbose > 0) { 1370 if(DEBUG || kVerbose > 0) {
1369 G4cout << "Voxel spacing : (" 1371 G4cout << "Voxel spacing : ("
1370 << kVoxelSpacing[0] << ", " 1372 << kVoxelSpacing[0] << ", "
1371 << kVoxelSpacing[1] << ", " 1373 << kVoxelSpacing[1] << ", "
1372 << kVoxelSpacing[2] 1374 << kVoxelSpacing[2]
1373 << ") mm " << G4endl; 1375 << ") mm " << G4endl;
1374 } 1376 }
1375 1377
1376 calcPointers2(); 1378 calcPointers2();
1377 // offset from file starting point to the m 1379 // offset from file starting point to the modality image data
1378 ofile.write((char *)&kPointerToModalityData 1380 ofile.write((char *)&kPointerToModalityData, 4);
1379 1381
1380 // offset from file starting point to the d 1382 // offset from file starting point to the dose image data
1381 ofile.write((char *)&kPointerToDoseDistData 1383 ofile.write((char *)&kPointerToDoseDistData[0], 4);
1382 1384
1383 // offset from file starting point to the R 1385 // offset from file starting point to the ROI image data
1384 ofile.write((char *)&kPointerToROIData, 4); 1386 ofile.write((char *)&kPointerToROIData, 4);
1385 1387
1386 // offset from file starting point to the t 1388 // offset from file starting point to the track data
1387 ofile.write((char *)&kPointerToTrackData, 4 1389 ofile.write((char *)&kPointerToTrackData, 4);
1388 if(DEBUG || kVerbose > 0) { 1390 if(DEBUG || kVerbose > 0) {
1389 G4cout << "Each pointer to data : " 1391 G4cout << "Each pointer to data : "
1390 << kPointerToModalityData << ", " 1392 << kPointerToModalityData << ", "
1391 << kPointerToDoseDistData[0] << ", " 1393 << kPointerToDoseDistData[0] << ", "
1392 << kPointerToROIData << ", " 1394 << kPointerToROIData << ", "
1393 << kPointerToTrackData << G4endl; 1395 << kPointerToTrackData << G4endl;
1394 } 1396 }
1395 1397
1396 //----- modality image -----// 1398 //----- modality image -----//
1397 1399
1398 int size[3]; 1400 int size[3];
1399 float scale; 1401 float scale;
1400 short minmax[2]; 1402 short minmax[2];
1401 float fCenter[3]; 1403 float fCenter[3];
1402 int iCenter[3]; 1404 int iCenter[3];
1403 // modality image size 1405 // modality image size
1404 kModality.getSize(size); 1406 kModality.getSize(size);
1405 ofile.write((char *)size, 3*sizeof(int)); 1407 ofile.write((char *)size, 3*sizeof(int));
1406 if(DEBUG || kVerbose > 0) { 1408 if(DEBUG || kVerbose > 0) {
1407 G4cout << "Modality image size : (" 1409 G4cout << "Modality image size : ("
1408 << size[0] << ", " 1410 << size[0] << ", "
1409 << size[1] << ", " 1411 << size[1] << ", "
1410 << size[2] << ")" 1412 << size[2] << ")"
1411 << G4endl; 1413 << G4endl;
1412 } 1414 }
1413 1415
1414 // modality image max. & min. 1416 // modality image max. & min.
1415 kModality.getMinMax(minmax); 1417 kModality.getMinMax(minmax);
1416 ofile.write((char *)minmax, 4); 1418 ofile.write((char *)minmax, 4);
1417 1419
1418 // modality image unit 1420 // modality image unit
1419 //char munit[13] = "g/cm3 "; 1421 //char munit[13] = "g/cm3 ";
1420 //ofile.write((char *)&munit, 12); 1422 //ofile.write((char *)&munit, 12);
1421 1423
1422 // modality image scale 1424 // modality image scale
1423 scale = (float)kModality.getScale(); 1425 scale = (float)kModality.getScale();
1424 ofile.write((char *)&scale, 4); 1426 ofile.write((char *)&scale, 4);
1425 if(DEBUG || kVerbose > 0) { 1427 if(DEBUG || kVerbose > 0) {
1426 G4cout << "Modality image min., max., sca 1428 G4cout << "Modality image min., max., scale : "
1427 << minmax[0] << ", " 1429 << minmax[0] << ", "
1428 << minmax[1] << ", " 1430 << minmax[1] << ", "
1429 << scale << G4endl; 1431 << scale << G4endl;
1430 } 1432 }
1431 1433
1432 // modality image 1434 // modality image
1433 int psize = size[0]*size[1]; 1435 int psize = size[0]*size[1];
1434 if(DEBUG || kVerbose > 0) G4cout << "Modali 1436 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
1435 for(int i = 0; i < size[2]; i++) { 1437 for(int i = 0; i < size[2]; i++) {
1436 short * image =kModality.getImage(i); 1438 short * image =kModality.getImage(i);
1437 ofile.write((char *)image, psize*sizeof(s 1439 ofile.write((char *)image, psize*sizeof(short));
1438 1440
1439 if(DEBUG || kVerbose > 0) G4cout << "[" < 1441 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1440 } 1442 }
1441 if(DEBUG || kVerbose > 0) G4cout << G4endl; 1443 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1442 1444
1443 // modality desity map for CT value 1445 // modality desity map for CT value
1444 size_t msize = minmax[1] - minmax[0]+1; 1446 size_t msize = minmax[1] - minmax[0]+1;
1445 float * pdmap = new float[msize]; 1447 float * pdmap = new float[msize];
1446 for(int i = 0; i < (int)msize; i++) pdmap[i 1448 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1447 ofile.write((char *)pdmap, msize*sizeof(flo 1449 ofile.write((char *)pdmap, msize*sizeof(float));
1448 if(DEBUG || kVerbose > 0) { 1450 if(DEBUG || kVerbose > 0) {
1449 G4cout << "density map : " << std::ends; 1451 G4cout << "density map : " << std::ends;
1450 for(int i = 0; i < (int)msize; i+=50) 1452 for(int i = 0; i < (int)msize; i+=50)
1451 G4cout <<kModalityImageDensityMap[i] << 1453 G4cout <<kModalityImageDensityMap[i] << ", ";
1452 G4cout << G4endl; 1454 G4cout << G4endl;
1453 } 1455 }
1454 delete [] pdmap; 1456 delete [] pdmap;
1455 1457
1456 1458
1457 //----- dose distribution image -----// 1459 //----- dose distribution image -----//
1458 1460
1459 if(!isDoseEmpty()) { 1461 if(!isDoseEmpty()) {
1460 calcDoseDistScale(); 1462 calcDoseDistScale();
1461 1463
1462 // dose distrbution image size 1464 // dose distrbution image size
1463 kDose[0].getSize(size); 1465 kDose[0].getSize(size);
1464 ofile.write((char *)size, 3*sizeof(int)); 1466 ofile.write((char *)size, 3*sizeof(int));
1465 if(DEBUG || kVerbose > 0) { 1467 if(DEBUG || kVerbose > 0) {
1466 G4cout << "Dose dist. image size : (" 1468 G4cout << "Dose dist. image size : ("
1467 << size[0] << ", " 1469 << size[0] << ", "
1468 << size[1] << ", " 1470 << size[1] << ", "
1469 << size[2] << ")" 1471 << size[2] << ")"
1470 << G4endl; 1472 << G4endl;
1471 } 1473 }
1472 1474
1473 // dose distribution max. & min. 1475 // dose distribution max. & min.
1474 getShortDoseDistMinMax(minmax); 1476 getShortDoseDistMinMax(minmax);
1475 ofile.write((char *)minmax, sizeof(short) 1477 ofile.write((char *)minmax, sizeof(short)*2);
1476 1478
1477 // dose distribution scaling 1479 // dose distribution scaling
1478 scale = (float)kDose[0].getScale(); 1480 scale = (float)kDose[0].getScale();
1479 ofile.write((char *)&scale, sizeof(float) 1481 ofile.write((char *)&scale, sizeof(float));
1480 if(DEBUG || kVerbose > 0) { 1482 if(DEBUG || kVerbose > 0) {
1481 G4cout << "Dose dist. image min., max., 1483 G4cout << "Dose dist. image min., max., scale : "
1482 << minmax[0] << ", " 1484 << minmax[0] << ", "
1483 << minmax[1] << ", " 1485 << minmax[1] << ", "
1484 << scale << G4endl; 1486 << scale << G4endl;
1485 } 1487 }
1486 1488
1487 // dose distribution image 1489 // dose distribution image
1488 int dsize = size[0]*size[1]; 1490 int dsize = size[0]*size[1];
1489 short * dimage = new short[dsize]; 1491 short * dimage = new short[dsize];
1490 for(int z = 0; z < size[2]; z++) { 1492 for(int z = 0; z < size[2]; z++) {
1491 getShortDoseDist(dimage, z); 1493 getShortDoseDist(dimage, z);
1492 ofile.write((char *)dimage, dsize*sizeo 1494 ofile.write((char *)dimage, dsize*sizeof(short));
1493 1495
1494 if(DEBUG || kVerbose > 0) { 1496 if(DEBUG || kVerbose > 0) {
1495 for(int j = 0; j < dsize; j++) { 1497 for(int j = 0; j < dsize; j++) {
1496 if(dimage[j] < 0) 1498 if(dimage[j] < 0)
1497 G4cout << "[" << j << "," << z << "]" 1499 G4cout << "[" << j << "," << z << "]"
1498 << dimage[j] << ", "; 1500 << dimage[j] << ", ";
1499 } 1501 }
1500 } 1502 }
1501 } 1503 }
1502 if(DEBUG || kVerbose > 0) G4cout << G4end 1504 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1503 delete [] dimage; 1505 delete [] dimage;
1504 1506
1505 // relative location of the dose distribu 1507 // relative location of the dose distribution image for
1506 // the modality image 1508 // the modality image
1507 kDose[0].getCenterPosition(fCenter); 1509 kDose[0].getCenterPosition(fCenter);
1508 for(int i = 0; i < 3; i++) iCenter[i] = ( 1510 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1509 ofile.write((char *)iCenter, 3*sizeof(int 1511 ofile.write((char *)iCenter, 3*sizeof(int));
1510 if(DEBUG || kVerbose > 0) { 1512 if(DEBUG || kVerbose > 0) {
1511 G4cout << "Dose dist. image relative lo 1513 G4cout << "Dose dist. image relative location : ("
1512 << iCenter[0] << ", " 1514 << iCenter[0] << ", "
1513 << iCenter[1] << ", " 1515 << iCenter[1] << ", "
1514 << iCenter[2] << ")" << G4endl; 1516 << iCenter[2] << ")" << G4endl;
1515 } 1517 }
1516 1518
1517 } 1519 }
1518 1520
1519 //----- ROI image -----// 1521 //----- ROI image -----//
1520 if(!isROIEmpty()) { 1522 if(!isROIEmpty()) {
1521 // ROI image size 1523 // ROI image size
1522 kRoi[0].getSize(size); 1524 kRoi[0].getSize(size);
1523 ofile.write((char *)size, 3*sizeof(int)); 1525 ofile.write((char *)size, 3*sizeof(int));
1524 if(DEBUG || kVerbose > 0) { 1526 if(DEBUG || kVerbose > 0) {
1525 G4cout << "ROI image size : (" 1527 G4cout << "ROI image size : ("
1526 << size[0] << ", " 1528 << size[0] << ", "
1527 << size[1] << ", " 1529 << size[1] << ", "
1528 << size[2] << ")" 1530 << size[2] << ")"
1529 << G4endl; 1531 << G4endl;
1530 } 1532 }
1531 1533
1532 // ROI max. & min. 1534 // ROI max. & min.
1533 kRoi[0].getMinMax(minmax); 1535 kRoi[0].getMinMax(minmax);
1534 ofile.write((char *)minmax, sizeof(short) 1536 ofile.write((char *)minmax, sizeof(short)*2);
1535 1537
1536 // ROI distribution scaling 1538 // ROI distribution scaling
1537 scale = (float)kRoi[0].getScale(); 1539 scale = (float)kRoi[0].getScale();
1538 ofile.write((char *)&scale, sizeof(float) 1540 ofile.write((char *)&scale, sizeof(float));
1539 if(DEBUG || kVerbose > 0) { 1541 if(DEBUG || kVerbose > 0) {
1540 G4cout << "ROI image min., max., scale 1542 G4cout << "ROI image min., max., scale : "
1541 << minmax[0] << ", " 1543 << minmax[0] << ", "
1542 << minmax[1] << ", " 1544 << minmax[1] << ", "
1543 << scale << G4endl; 1545 << scale << G4endl;
1544 } 1546 }
1545 1547
1546 // ROI image 1548 // ROI image
1547 int rsize = size[0]*size[1]; 1549 int rsize = size[0]*size[1];
1548 for(int i = 0; i < size[2]; i++) { 1550 for(int i = 0; i < size[2]; i++) {
1549 short * rimage = kRoi[0].getImage(i); 1551 short * rimage = kRoi[0].getImage(i);
1550 ofile.write((char *)rimage, rsize*sizeo 1552 ofile.write((char *)rimage, rsize*sizeof(short));
1551 1553
1552 } 1554 }
1553 1555
1554 // ROI relative location 1556 // ROI relative location
1555 kRoi[0].getCenterPosition(fCenter); 1557 kRoi[0].getCenterPosition(fCenter);
1556 for(int i = 0; i < 3; i++) iCenter[i] = ( 1558 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1557 ofile.write((char *)iCenter, 3*sizeof(int 1559 ofile.write((char *)iCenter, 3*sizeof(int));
1558 if(DEBUG || kVerbose > 0) { 1560 if(DEBUG || kVerbose > 0) {
1559 G4cout << "ROI image relative location 1561 G4cout << "ROI image relative location : ("
1560 << iCenter[0] << ", " 1562 << iCenter[0] << ", "
1561 << iCenter[1] << ", " 1563 << iCenter[1] << ", "
1562 << iCenter[2] << ")" << G4endl; 1564 << iCenter[2] << ")" << G4endl;
1563 } 1565 }
1564 } 1566 }
1565 1567
1566 1568
1567 //----- track information -----// 1569 //----- track information -----//
1568 // track 1570 // track
1569 int ntrk = (int)kSteps.size(); << 1571 int ntrk = kSteps.size();
1570 ofile.write((char *)&ntrk, sizeof(int)); 1572 ofile.write((char *)&ntrk, sizeof(int));
1571 if(DEBUG || kVerbose > 0) { 1573 if(DEBUG || kVerbose > 0) {
1572 G4cout << "# of tracks : " 1574 G4cout << "# of tracks : "
1573 << ntrk << G4endl; 1575 << ntrk << G4endl;
1574 } 1576 }
1575 for(int i = 0; i < ntrk; i++) { 1577 for(int i = 0; i < ntrk; i++) {
1576 float * tp = kSteps[i]; 1578 float * tp = kSteps[i];
1577 ofile.write((char *)tp, sizeof(float)*6); 1579 ofile.write((char *)tp, sizeof(float)*6);
1578 } 1580 }
1579 1581
1580 1582
1581 // file end mark 1583 // file end mark
1582 ofile.write("END", 3); 1584 ofile.write("END", 3);
1583 1585
1584 ofile.close(); 1586 ofile.close();
1585 1587
1586 return true; 1588 return true;
1587 } 1589 }
1588 // 1590 //
1589 bool G4GMocrenIO::storeData2(char * _filename 1591 bool G4GMocrenIO::storeData2(char * _filename) {
1590 kFileName = _filename; 1592 kFileName = _filename;
1591 return storeData(); 1593 return storeData();
1592 } 1594 }
1593 1595
1594 bool G4GMocrenIO::retrieveData() { 1596 bool G4GMocrenIO::retrieveData() {
1595 1597
1596 // input file open 1598 // input file open
1597 std::ifstream ifile(kFileName.c_str(), std: 1599 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1598 if(!ifile) { 1600 if(!ifile) {
1599 if (G4VisManager::GetVerbosity() >= G4Vis 1601 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1600 G4cout << "Cannot open file: " << kFile 1602 G4cout << "Cannot open file: " << kFileName
1601 << " in G4GMocrenIO::retrieveData()." 1603 << " in G4GMocrenIO::retrieveData()." << G4endl;
1602 return false; 1604 return false;
1603 } 1605 }
1604 1606
1605 // file identifier 1607 // file identifier
1606 char verid[9]; 1608 char verid[9];
1607 ifile.read((char *)verid, 8); 1609 ifile.read((char *)verid, 8);
1608 // file version 1610 // file version
1609 unsigned char ver; 1611 unsigned char ver;
1610 ifile.read((char *)&ver, 1); 1612 ifile.read((char *)&ver, 1);
1611 ifile.close(); 1613 ifile.close();
1612 1614
1613 if(std::strncmp(verid, "gMocren", 7) == 0) 1615 if(std::strncmp(verid, "gMocren", 7) == 0) {
1614 if(ver == 0x03) { 1616 if(ver == 0x03) {
1615 G4cout << ">>>>>>> retrieve data (ver. 1617 G4cout << ">>>>>>> retrieve data (ver.3) <<<<<<<" << G4endl;
1616 G4cout << " " << kFileName << G 1618 G4cout << " " << kFileName << G4endl;
1617 retrieveData3(); 1619 retrieveData3();
1618 } else if (ver == 0x04) { 1620 } else if (ver == 0x04) {
1619 G4cout << ">>>>>>> retrieve data (ver. 1621 G4cout << ">>>>>>> retrieve data (ver.4) <<<<<<<" << G4endl;
1620 G4cout << " " << kFileName << G 1622 G4cout << " " << kFileName << G4endl;
1621 retrieveData4(); 1623 retrieveData4();
1622 } else { 1624 } else {
1623 if (G4VisManager::GetVerbosity() >= G4V 1625 if (G4VisManager::GetVerbosity() >= G4VisManager::errors) {
1624 G4cout << "Error -- invalid file version : 1626 G4cout << "Error -- invalid file version : " << (int)ver
1625 << G4endl; 1627 << G4endl;
1626 G4cout << " " << kFileName << G4end 1628 G4cout << " " << kFileName << G4endl;
1627 } 1629 }
1628 G4Exception("G4GMocrenIO::retrieveDadta << 1630 std::exit(-1);
1629 "gMocren2001", FatalExcepti <<
1630 "Error."); <<
1631 <<
1632 } 1631 }
1633 } else if(std::strncmp(verid, "GRAPE", 5) = 1632 } else if(std::strncmp(verid, "GRAPE", 5) == 0) {
1634 G4cout << ">>>>>>> retrieve data (ver.2) 1633 G4cout << ">>>>>>> retrieve data (ver.2) <<<<<<<" << G4endl;
1635 G4cout << " " << kFileName << G4e 1634 G4cout << " " << kFileName << G4endl;
1636 retrieveData2(); 1635 retrieveData2();
1637 } else { 1636 } else {
1638 if (G4VisManager::GetVerbosity() >= G4Vis 1637 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1639 G4cout << kFileName << " was not gdd fi 1638 G4cout << kFileName << " was not gdd file." << G4endl;
1640 return false; 1639 return false;
1641 } 1640 }
1642 1641
1643 return true; 1642 return true;
1644 } 1643 }
1645 1644
1646 bool G4GMocrenIO::retrieveData(char * _filena 1645 bool G4GMocrenIO::retrieveData(char * _filename) {
1647 kFileName = _filename; 1646 kFileName = _filename;
1648 return retrieveData(); 1647 return retrieveData();
1649 } 1648 }
1650 1649
1651 // 1650 //
1652 bool G4GMocrenIO::retrieveData4() { 1651 bool G4GMocrenIO::retrieveData4() {
1653 1652
1654 bool DEBUG = false;// 1653 bool DEBUG = false;//
1655 1654
1656 // input file open 1655 // input file open
1657 std::ifstream ifile(kFileName.c_str(), std: 1656 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1658 if(!ifile) { 1657 if(!ifile) {
1659 if (G4VisManager::GetVerbosity() >= G4Vis 1658 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1660 G4cout << "Cannot open file: " << kFile 1659 G4cout << "Cannot open file: " << kFileName
1661 << " in G4GMocrenIO::retrieveData3()." << 1660 << " in G4GMocrenIO::retrieveData3()." << G4endl;
1662 return false; 1661 return false;
1663 } 1662 }
1664 1663
1665 // data buffer 1664 // data buffer
1666 char ctmp[24]; << 1665 char ctmp[12];
1667 1666
1668 // file identifier 1667 // file identifier
1669 char verid[9]; 1668 char verid[9];
1670 ifile.read((char *)verid, 8); 1669 ifile.read((char *)verid, 8);
1671 1670
1672 // file version 1671 // file version
1673 unsigned char ver; 1672 unsigned char ver;
1674 ifile.read((char *)&ver, 1); 1673 ifile.read((char *)&ver, 1);
1675 std::stringstream ss; 1674 std::stringstream ss;
1676 ss << (int)ver; 1675 ss << (int)ver;
1677 kVersion = ss.str(); 1676 kVersion = ss.str();
1678 if(DEBUG || kVerbose > 0) G4cout << "File v 1677 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
1679 1678
1680 // endian 1679 // endian
1681 ifile.read((char *)&kLittleEndianInput, siz 1680 ifile.read((char *)&kLittleEndianInput, sizeof(char));
1682 if(DEBUG || kVerbose > 0) { 1681 if(DEBUG || kVerbose > 0) {
1683 G4cout << "Endian : "; 1682 G4cout << "Endian : ";
1684 if(kLittleEndianInput == 1) 1683 if(kLittleEndianInput == 1)
1685 G4cout << " little" << G4endl; 1684 G4cout << " little" << G4endl;
1686 else { 1685 else {
1687 G4cout << " big" << G4endl; 1686 G4cout << " big" << G4endl;
1688 } 1687 }
1689 } 1688 }
1690 1689
1691 // comment length (fixed size) 1690 // comment length (fixed size)
1692 int clength; 1691 int clength;
1693 ifile.read((char *)ctmp, 4); 1692 ifile.read((char *)ctmp, 4);
1694 convertEndian(ctmp, clength); 1693 convertEndian(ctmp, clength);
1695 // comment 1694 // comment
1696 char cmt[1025]; 1695 char cmt[1025];
1697 ifile.read((char *)cmt, clength); 1696 ifile.read((char *)cmt, clength);
1698 std::string scmt = cmt; 1697 std::string scmt = cmt;
1699 scmt += '\0'; 1698 scmt += '\0';
1700 setComment(scmt); 1699 setComment(scmt);
1701 if(DEBUG || kVerbose > 0) { 1700 if(DEBUG || kVerbose > 0) {
1702 G4cout << "Data comment : " 1701 G4cout << "Data comment : "
1703 << kComment << G4endl; 1702 << kComment << G4endl;
1704 } 1703 }
1705 1704
1706 // voxel spacings for all images 1705 // voxel spacings for all images
1707 ifile.read((char *)ctmp, 12); 1706 ifile.read((char *)ctmp, 12);
1708 convertEndian(ctmp, kVoxelSpacing[0]); 1707 convertEndian(ctmp, kVoxelSpacing[0]);
1709 convertEndian(ctmp+4, kVoxelSpacing[1]); 1708 convertEndian(ctmp+4, kVoxelSpacing[1]);
1710 convertEndian(ctmp+8, kVoxelSpacing[2]); 1709 convertEndian(ctmp+8, kVoxelSpacing[2]);
1711 if(DEBUG || kVerbose > 0) { 1710 if(DEBUG || kVerbose > 0) {
1712 G4cout << "Voxel spacing : (" 1711 G4cout << "Voxel spacing : ("
1713 << kVoxelSpacing[0] << ", " 1712 << kVoxelSpacing[0] << ", "
1714 << kVoxelSpacing[1] << ", " 1713 << kVoxelSpacing[1] << ", "
1715 << kVoxelSpacing[2] 1714 << kVoxelSpacing[2]
1716 << ") mm " << G4endl; 1715 << ") mm " << G4endl;
1717 } 1716 }
1718 1717
1719 1718
1720 // offset from file starting point to the m 1719 // offset from file starting point to the modality image data
1721 ifile.read((char *)ctmp, 4); 1720 ifile.read((char *)ctmp, 4);
1722 convertEndian(ctmp, kPointerToModalityData) 1721 convertEndian(ctmp, kPointerToModalityData);
1723 1722
1724 // # of dose distributions 1723 // # of dose distributions
1725 ifile.read((char *)ctmp, 4); 1724 ifile.read((char *)ctmp, 4);
1726 int nDoseDist; 1725 int nDoseDist;
1727 convertEndian(ctmp, nDoseDist); 1726 convertEndian(ctmp, nDoseDist);
1728 1727
1729 // offset from file starting point to the d 1728 // offset from file starting point to the dose image data
1730 for(int i = 0; i < nDoseDist; i++) { 1729 for(int i = 0; i < nDoseDist; i++) {
1731 ifile.read((char *)ctmp, 4); 1730 ifile.read((char *)ctmp, 4);
1732 unsigned int dptr; 1731 unsigned int dptr;
1733 convertEndian(ctmp, dptr); 1732 convertEndian(ctmp, dptr);
1734 addPointerToDoseDistData(dptr); 1733 addPointerToDoseDistData(dptr);
1735 } 1734 }
1736 1735
1737 // offset from file starting point to the R 1736 // offset from file starting point to the ROI image data
1738 ifile.read((char *)ctmp, 4); 1737 ifile.read((char *)ctmp, 4);
1739 convertEndian(ctmp, kPointerToROIData); 1738 convertEndian(ctmp, kPointerToROIData);
1740 1739
1741 // offset from file starting point to the t 1740 // offset from file starting point to the track data
1742 ifile.read((char *)ctmp, 4); 1741 ifile.read((char *)ctmp, 4);
1743 convertEndian(ctmp, kPointerToTrackData); 1742 convertEndian(ctmp, kPointerToTrackData);
1744 1743
1745 // offset from file starting point to the d 1744 // offset from file starting point to the detector data
1746 ifile.read((char *)ctmp, 4); 1745 ifile.read((char *)ctmp, 4);
1747 convertEndian(ctmp, kPointerToDetectorData) 1746 convertEndian(ctmp, kPointerToDetectorData);
1748 1747
1749 if(DEBUG || kVerbose > 0) { 1748 if(DEBUG || kVerbose > 0) {
1750 G4cout << "Each pointer to data : " 1749 G4cout << "Each pointer to data : "
1751 << kPointerToModalityData << ", "; 1750 << kPointerToModalityData << ", ";
1752 for(int i = 0; i < nDoseDist; i++) 1751 for(int i = 0; i < nDoseDist; i++)
1753 G4cout << kPointerToDoseDistData[i] << 1752 G4cout << kPointerToDoseDistData[i] << ", ";
1754 G4cout << kPointerToROIData << ", " 1753 G4cout << kPointerToROIData << ", "
1755 << kPointerToTrackData << ", " 1754 << kPointerToTrackData << ", "
1756 << kPointerToDetectorData 1755 << kPointerToDetectorData
1757 << G4endl; 1756 << G4endl;
1758 } 1757 }
1759 1758
1760 1759
1761 1760
1762 if(kPointerToModalityData == 0 && kPointerT 1761 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
1763 kPointerToROIData == 0 && kPointerToTrac 1762 kPointerToROIData == 0 && kPointerToTrackData == 0) {
1764 if(DEBUG || kVerbose > 0) { 1763 if(DEBUG || kVerbose > 0) {
1765 G4cout << "No data." << G4endl; 1764 G4cout << "No data." << G4endl;
1766 } 1765 }
1767 return false; 1766 return false;
1768 } 1767 }
1769 1768
1770 // event number 1769 // event number
1771 /* ver 1 1770 /* ver 1
1772 ifile.read(ctmp, sizeof(int)); 1771 ifile.read(ctmp, sizeof(int));
1773 convertEndian(ctmp, numberOfEvents); 1772 convertEndian(ctmp, numberOfEvents);
1774 */ 1773 */
1775 1774
1776 int size[3]; 1775 int size[3];
1777 float scale; 1776 float scale;
1778 double dscale; 1777 double dscale;
1779 short minmax[2]; 1778 short minmax[2];
1780 float fCenter[3]; 1779 float fCenter[3];
1781 int iCenter[3]; 1780 int iCenter[3];
1782 1781
1783 //----- Modality image -----// 1782 //----- Modality image -----//
1784 // modality image size 1783 // modality image size
1785 ifile.read(ctmp, 3*sizeof(int)); 1784 ifile.read(ctmp, 3*sizeof(int));
1786 convertEndian(ctmp, size[0]); 1785 convertEndian(ctmp, size[0]);
1787 convertEndian(ctmp+sizeof(int), size[1]); 1786 convertEndian(ctmp+sizeof(int), size[1]);
1788 convertEndian(ctmp+2*sizeof(int), size[2]); 1787 convertEndian(ctmp+2*sizeof(int), size[2]);
1789 if(DEBUG || kVerbose > 0) { 1788 if(DEBUG || kVerbose > 0) {
1790 G4cout << "Modality image size : (" 1789 G4cout << "Modality image size : ("
1791 << size[0] << ", " 1790 << size[0] << ", "
1792 << size[1] << ", " 1791 << size[1] << ", "
1793 << size[2] << ")" 1792 << size[2] << ")"
1794 << G4endl; 1793 << G4endl;
1795 } 1794 }
1796 kModality.setSize(size); 1795 kModality.setSize(size);
1797 1796
1798 // modality image voxel spacing 1797 // modality image voxel spacing
1799 /* 1798 /*
1800 ifile.read(ctmp, 3*sizeof(float)); 1799 ifile.read(ctmp, 3*sizeof(float));
1801 convertEndian(ctmp, modalityImageVoxelSpa 1800 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
1802 convertEndian(ctmp+sizeof(float), modalit 1801 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
1803 convertEndian(ctmp+2*sizeof(float), modal 1802 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
1804 */ 1803 */
1805 1804
1806 if(kPointerToModalityData != 0) { 1805 if(kPointerToModalityData != 0) {
1807 1806
1808 // modality density max. & min. 1807 // modality density max. & min.
1809 ifile.read((char *)ctmp, 4); 1808 ifile.read((char *)ctmp, 4);
1810 convertEndian(ctmp, minmax[0]); 1809 convertEndian(ctmp, minmax[0]);
1811 convertEndian(ctmp+2, minmax[1]); 1810 convertEndian(ctmp+2, minmax[1]);
1812 kModality.setMinMax(minmax); 1811 kModality.setMinMax(minmax);
1813 1812
1814 // modality image unit 1813 // modality image unit
1815 char munit[13]; 1814 char munit[13];
1816 munit[12] = '\0'; 1815 munit[12] = '\0';
1817 ifile.read((char *)munit, 12); 1816 ifile.read((char *)munit, 12);
1818 std::string smunit = munit; 1817 std::string smunit = munit;
1819 setModalityImageUnit(smunit); 1818 setModalityImageUnit(smunit);
1820 1819
1821 // modality density scale 1820 // modality density scale
1822 ifile.read((char *)ctmp, 4); 1821 ifile.read((char *)ctmp, 4);
1823 convertEndian(ctmp, scale); 1822 convertEndian(ctmp, scale);
1824 kModality.setScale(dscale = scale); 1823 kModality.setScale(dscale = scale);
1825 if(DEBUG || kVerbose > 0) { 1824 if(DEBUG || kVerbose > 0) {
1826 G4cout << "Modality image min., max., s 1825 G4cout << "Modality image min., max., scale : "
1827 << minmax[0] << ", " 1826 << minmax[0] << ", "
1828 << minmax[1] << ", " 1827 << minmax[1] << ", "
1829 << scale << G4endl; 1828 << scale << G4endl;
1830 } 1829 }
1831 1830
1832 // modality density 1831 // modality density
1833 int psize = size[0]*size[1]; 1832 int psize = size[0]*size[1];
1834 if(DEBUG || kVerbose > 0) G4cout << "Moda 1833 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
1835 char * cimage = new char[psize*sizeof(sho 1834 char * cimage = new char[psize*sizeof(short)];
1836 for(int i = 0; i < size[2]; i++) { 1835 for(int i = 0; i < size[2]; i++) {
1837 ifile.read((char *)cimage, psize*sizeof 1836 ifile.read((char *)cimage, psize*sizeof(short));
1838 short * mimage = new short[psize]; 1837 short * mimage = new short[psize];
1839 for(int j = 0; j < psize; j++) { 1838 for(int j = 0; j < psize; j++) {
1840 convertEndian(cimage+j*sizeof(short), mimag 1839 convertEndian(cimage+j*sizeof(short), mimage[j]);
1841 } 1840 }
1842 kModality.addImage(mimage); 1841 kModality.addImage(mimage);
1843 1842
1844 if(DEBUG || kVerbose > 0) G4cout << "[" 1843 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
1845 } 1844 }
1846 if(DEBUG || kVerbose > 0) G4cout << G4end 1845 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1847 delete [] cimage; 1846 delete [] cimage;
1848 1847
1849 // modality desity map for CT value 1848 // modality desity map for CT value
1850 size_t msize = minmax[1]-minmax[0]+1; 1849 size_t msize = minmax[1]-minmax[0]+1;
1851 if(DEBUG || kVerbose > 0) G4cout << "msiz 1850 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
1852 char * pdmap = new char[msize*sizeof(floa 1851 char * pdmap = new char[msize*sizeof(float)];
1853 ifile.read((char *)pdmap, msize*sizeof(fl 1852 ifile.read((char *)pdmap, msize*sizeof(float));
1854 float ftmp; 1853 float ftmp;
1855 for(int i = 0; i < (int)msize; i++) { 1854 for(int i = 0; i < (int)msize; i++) {
1856 convertEndian(pdmap+i*sizeof(float), ft 1855 convertEndian(pdmap+i*sizeof(float), ftmp);
1857 kModalityImageDensityMap.push_back(ftmp 1856 kModalityImageDensityMap.push_back(ftmp);
1858 } 1857 }
1859 delete [] pdmap; <<
1860 <<
1861 if(DEBUG || kVerbose > 0) { 1858 if(DEBUG || kVerbose > 0) {
1862 G4cout << "density map : " << std::ends 1859 G4cout << "density map : " << std::ends;
1863 for(int i = 0; i < 10; i++) 1860 for(int i = 0; i < 10; i++)
1864 G4cout <<kModalityImageDensityMap[i] << ", 1861 G4cout <<kModalityImageDensityMap[i] << ", ";
1865 G4cout << G4endl; 1862 G4cout << G4endl;
1866 for(int i = 0; i < 10; i++) G4cout << " 1863 for(int i = 0; i < 10; i++) G4cout << "..";
1867 G4cout << G4endl; 1864 G4cout << G4endl;
1868 for(size_t i =kModalityImageDensityMap. 1865 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
1869 G4cout <<kModalityImageDensityMap[i] << ", 1866 G4cout <<kModalityImageDensityMap[i] << ", ";
1870 G4cout << G4endl; 1867 G4cout << G4endl;
1871 } 1868 }
1872 1869
1873 } 1870 }
1874 1871
1875 1872
1876 //----- dose distribution image -----// 1873 //----- dose distribution image -----//
1877 for(int ndose = 0; ndose < nDoseDist; ndose 1874 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1878 1875
1879 newDoseDist(); 1876 newDoseDist();
1880 1877
1881 // dose distrbution image size 1878 // dose distrbution image size
1882 ifile.read((char *)ctmp, 3*sizeof(int)); 1879 ifile.read((char *)ctmp, 3*sizeof(int));
1883 convertEndian(ctmp, size[0]); 1880 convertEndian(ctmp, size[0]);
1884 convertEndian(ctmp+sizeof(int), size[1]); 1881 convertEndian(ctmp+sizeof(int), size[1]);
1885 convertEndian(ctmp+2*sizeof(int), size[2] 1882 convertEndian(ctmp+2*sizeof(int), size[2]);
1886 if(DEBUG || kVerbose > 0) { 1883 if(DEBUG || kVerbose > 0) {
1887 G4cout << "Dose dist. image size : (" 1884 G4cout << "Dose dist. image size : ("
1888 << size[0] << ", " 1885 << size[0] << ", "
1889 << size[1] << ", " 1886 << size[1] << ", "
1890 << size[2] << ")" 1887 << size[2] << ")"
1891 << G4endl; 1888 << G4endl;
1892 } 1889 }
1893 kDose[ndose].setSize(size); 1890 kDose[ndose].setSize(size);
1894 1891
1895 // dose distribution max. & min. 1892 // dose distribution max. & min.
1896 ifile.read((char *)ctmp, sizeof(short)*2) 1893 ifile.read((char *)ctmp, sizeof(short)*2);
1897 convertEndian(ctmp, minmax[0]); 1894 convertEndian(ctmp, minmax[0]);
1898 convertEndian(ctmp+2, minmax[1]); 1895 convertEndian(ctmp+2, minmax[1]);
1899 1896
1900 // dose distribution unit 1897 // dose distribution unit
1901 char dunit[13]; 1898 char dunit[13];
1902 dunit[12] = '\0'; 1899 dunit[12] = '\0';
1903 ifile.read((char *)dunit, 12); 1900 ifile.read((char *)dunit, 12);
1904 std::string sdunit = dunit; 1901 std::string sdunit = dunit;
1905 setDoseDistUnit(sdunit, ndose); 1902 setDoseDistUnit(sdunit, ndose);
1906 if(DEBUG || kVerbose > 0) { 1903 if(DEBUG || kVerbose > 0) {
1907 G4cout << "Dose dist. unit : " << kDose 1904 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
1908 } 1905 }
1909 1906
1910 // dose distribution scaling 1907 // dose distribution scaling
1911 ifile.read((char *)ctmp, 4); // sizeof(fl 1908 ifile.read((char *)ctmp, 4); // sizeof(float)
1912 convertEndian(ctmp, scale); 1909 convertEndian(ctmp, scale);
1913 kDose[ndose].setScale(dscale = scale); 1910 kDose[ndose].setScale(dscale = scale);
1914 1911
1915 double dminmax[2]; 1912 double dminmax[2];
1916 for(int i = 0; i < 2; i++) dminmax[i] = m 1913 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
1917 kDose[ndose].setMinMax(dminmax); 1914 kDose[ndose].setMinMax(dminmax);
1918 1915
1919 if(DEBUG || kVerbose > 0) { 1916 if(DEBUG || kVerbose > 0) {
1920 G4cout << "Dose dist. image min., max., 1917 G4cout << "Dose dist. image min., max., scale : "
1921 << dminmax[0] << ", " 1918 << dminmax[0] << ", "
1922 << dminmax[1] << ", " 1919 << dminmax[1] << ", "
1923 << scale << G4endl; 1920 << scale << G4endl;
1924 } 1921 }
1925 1922
1926 // dose distribution image 1923 // dose distribution image
1927 int dsize = size[0]*size[1]; 1924 int dsize = size[0]*size[1];
1928 if(DEBUG || kVerbose > 0) G4cout << "Dose 1925 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
1929 char * di = new char[dsize*sizeof(short)] 1926 char * di = new char[dsize*sizeof(short)];
1930 short * shimage = new short[dsize]; 1927 short * shimage = new short[dsize];
1931 for(int z = 0; z < size[2]; z++) { 1928 for(int z = 0; z < size[2]; z++) {
1932 ifile.read((char *)di, dsize*sizeof(sho 1929 ifile.read((char *)di, dsize*sizeof(short));
1933 double * dimage = new double[dsize]; 1930 double * dimage = new double[dsize];
1934 for(int xy = 0; xy < dsize; xy++) { 1931 for(int xy = 0; xy < dsize; xy++) {
1935 convertEndian(di+xy*sizeof(short), shimage[ 1932 convertEndian(di+xy*sizeof(short), shimage[xy]);
1936 dimage[xy] = shimage[xy]*dscale; 1933 dimage[xy] = shimage[xy]*dscale;
1937 } 1934 }
1938 kDose[ndose].addImage(dimage); 1935 kDose[ndose].addImage(dimage);
1939 1936
1940 if(DEBUG || kVerbose > 0) G4cout << "[" 1937 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
1941 1938
1942 if(DEBUG || kVerbose > 0) { 1939 if(DEBUG || kVerbose > 0) {
1943 for(int j = 0; j < dsize; j++) { 1940 for(int j = 0; j < dsize; j++) {
1944 if(dimage[j] < 0) 1941 if(dimage[j] < 0)
1945 G4cout << "[" << j << "," << z << "]" 1942 G4cout << "[" << j << "," << z << "]"
1946 << dimage[j] << ", "; 1943 << dimage[j] << ", ";
1947 } 1944 }
1948 } 1945 }
1949 } 1946 }
1950 delete [] shimage; 1947 delete [] shimage;
1951 delete [] di; 1948 delete [] di;
1952 if(DEBUG || kVerbose > 0) G4cout << G4end 1949 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1953 1950
1954 ifile.read((char *)ctmp, 3*4); // 3*sizeo 1951 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
1955 convertEndian(ctmp, iCenter[0]); 1952 convertEndian(ctmp, iCenter[0]);
1956 convertEndian(ctmp+4, iCenter[1]); 1953 convertEndian(ctmp+4, iCenter[1]);
1957 convertEndian(ctmp+8, iCenter[2]); 1954 convertEndian(ctmp+8, iCenter[2]);
1958 for(int i = 0; i < 3; i++) fCenter[i] = ( 1955 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
1959 kDose[ndose].setCenterPosition(fCenter); 1956 kDose[ndose].setCenterPosition(fCenter);
1960 1957
1961 if(DEBUG || kVerbose > 0) { 1958 if(DEBUG || kVerbose > 0) {
1962 G4cout << "Dose dist. image relative lo 1959 G4cout << "Dose dist. image relative location : ("
1963 << fCenter[0] << ", " 1960 << fCenter[0] << ", "
1964 << fCenter[1] << ", " 1961 << fCenter[1] << ", "
1965 << fCenter[2] << ")" << G4endl; 1962 << fCenter[2] << ")" << G4endl;
1966 } 1963 }
1967 1964
1968 1965
1969 // dose distribution name 1966 // dose distribution name
1970 char cname[81]; 1967 char cname[81];
1971 ifile.read((char *)cname, 80); 1968 ifile.read((char *)cname, 80);
1972 std::string dosename = cname; 1969 std::string dosename = cname;
1973 setDoseDistName(dosename, ndose); 1970 setDoseDistName(dosename, ndose);
1974 if(DEBUG || kVerbose > 0) { 1971 if(DEBUG || kVerbose > 0) {
1975 G4cout << "Dose dist. name : " << dosen 1972 G4cout << "Dose dist. name : " << dosename << G4endl;
1976 } 1973 }
1977 1974
1978 } 1975 }
1979 1976
1980 //----- ROI image -----// 1977 //----- ROI image -----//
1981 if(kPointerToROIData != 0) { 1978 if(kPointerToROIData != 0) {
1982 1979
1983 newROI(); 1980 newROI();
1984 1981
1985 // ROI image size 1982 // ROI image size
1986 ifile.read((char *)ctmp, 3*sizeof(int)); 1983 ifile.read((char *)ctmp, 3*sizeof(int));
1987 convertEndian(ctmp, size[0]); 1984 convertEndian(ctmp, size[0]);
1988 convertEndian(ctmp+sizeof(int), size[1]); 1985 convertEndian(ctmp+sizeof(int), size[1]);
1989 convertEndian(ctmp+2*sizeof(int), size[2] 1986 convertEndian(ctmp+2*sizeof(int), size[2]);
1990 kRoi[0].setSize(size); 1987 kRoi[0].setSize(size);
1991 if(DEBUG || kVerbose > 0) { 1988 if(DEBUG || kVerbose > 0) {
1992 G4cout << "ROI image size : (" 1989 G4cout << "ROI image size : ("
1993 << size[0] << ", " 1990 << size[0] << ", "
1994 << size[1] << ", " 1991 << size[1] << ", "
1995 << size[2] << ")" 1992 << size[2] << ")"
1996 << G4endl; 1993 << G4endl;
1997 } 1994 }
1998 1995
1999 // ROI max. & min. 1996 // ROI max. & min.
2000 ifile.read((char *)ctmp, sizeof(short)*2) 1997 ifile.read((char *)ctmp, sizeof(short)*2);
2001 convertEndian(ctmp, minmax[0]); 1998 convertEndian(ctmp, minmax[0]);
2002 convertEndian(ctmp+sizeof(short), minmax[ 1999 convertEndian(ctmp+sizeof(short), minmax[1]);
2003 kRoi[0].setMinMax(minmax); 2000 kRoi[0].setMinMax(minmax);
2004 2001
2005 // ROI distribution scaling 2002 // ROI distribution scaling
2006 ifile.read((char *)ctmp, sizeof(float)); 2003 ifile.read((char *)ctmp, sizeof(float));
2007 convertEndian(ctmp, scale); 2004 convertEndian(ctmp, scale);
2008 kRoi[0].setScale(dscale = scale); 2005 kRoi[0].setScale(dscale = scale);
2009 if(DEBUG || kVerbose > 0) { 2006 if(DEBUG || kVerbose > 0) {
2010 G4cout << "ROI image min., max., scale 2007 G4cout << "ROI image min., max., scale : "
2011 << minmax[0] << ", " 2008 << minmax[0] << ", "
2012 << minmax[1] << ", " 2009 << minmax[1] << ", "
2013 << scale << G4endl; 2010 << scale << G4endl;
2014 } 2011 }
2015 2012
2016 // ROI image 2013 // ROI image
2017 int rsize = size[0]*size[1]; 2014 int rsize = size[0]*size[1];
2018 char * ri = new char[rsize*sizeof(short)] 2015 char * ri = new char[rsize*sizeof(short)];
2019 for(int i = 0; i < size[2]; i++) { 2016 for(int i = 0; i < size[2]; i++) {
2020 ifile.read((char *)ri, rsize*sizeof(sho 2017 ifile.read((char *)ri, rsize*sizeof(short));
2021 short * rimage = new short[rsize]; 2018 short * rimage = new short[rsize];
2022 for(int j = 0; j < rsize; j++) { 2019 for(int j = 0; j < rsize; j++) {
2023 convertEndian(ri+j*sizeof(short), rimage[j] 2020 convertEndian(ri+j*sizeof(short), rimage[j]);
2024 } 2021 }
2025 kRoi[0].addImage(rimage); 2022 kRoi[0].addImage(rimage);
2026 2023
2027 } 2024 }
2028 delete [] ri; 2025 delete [] ri;
2029 2026
2030 // ROI relative location 2027 // ROI relative location
2031 ifile.read((char *)ctmp, 3*sizeof(int)); 2028 ifile.read((char *)ctmp, 3*sizeof(int));
2032 convertEndian(ctmp, iCenter[0]); 2029 convertEndian(ctmp, iCenter[0]);
2033 convertEndian(ctmp+sizeof(int), iCenter[1 2030 convertEndian(ctmp+sizeof(int), iCenter[1]);
2034 convertEndian(ctmp+2*sizeof(int), iCenter 2031 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2035 for(int i = 0; i < 3; i++) fCenter[i] = i 2032 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2036 kRoi[0].setCenterPosition(fCenter); 2033 kRoi[0].setCenterPosition(fCenter);
2037 if(DEBUG || kVerbose > 0) { 2034 if(DEBUG || kVerbose > 0) {
2038 G4cout << "ROI image relative location 2035 G4cout << "ROI image relative location : ("
2039 << fCenter[0] << ", " 2036 << fCenter[0] << ", "
2040 << fCenter[1] << ", " 2037 << fCenter[1] << ", "
2041 << fCenter[2] << ")" << G4endl; 2038 << fCenter[2] << ")" << G4endl;
2042 } 2039 }
2043 2040
2044 } 2041 }
2045 2042
2046 //----- track information -----// 2043 //----- track information -----//
2047 if(kPointerToTrackData != 0) { 2044 if(kPointerToTrackData != 0) {
2048 2045
2049 // track 2046 // track
2050 ifile.read((char *)ctmp, sizeof(int)); 2047 ifile.read((char *)ctmp, sizeof(int));
2051 int ntrk; 2048 int ntrk;
2052 convertEndian(ctmp, ntrk); 2049 convertEndian(ctmp, ntrk);
2053 if(DEBUG || kVerbose > 0) { 2050 if(DEBUG || kVerbose > 0) {
2054 G4cout << "# of tracks: " << ntrk << G4 2051 G4cout << "# of tracks: " << ntrk << G4endl;
2055 } 2052 }
2056 2053
2057 // track position 2054 // track position
2058 unsigned char rgb[3]; 2055 unsigned char rgb[3];
2059 for(int i = 0; i < ntrk; i++) { 2056 for(int i = 0; i < ntrk; i++) {
2060 2057
2061 2058
2062 // # of steps in a track 2059 // # of steps in a track
2063 ifile.read((char *)ctmp, sizeof(int)); 2060 ifile.read((char *)ctmp, sizeof(int));
2064 int nsteps; 2061 int nsteps;
2065 convertEndian(ctmp, nsteps); 2062 convertEndian(ctmp, nsteps);
2066 2063
2067 // track color 2064 // track color
2068 ifile.read((char *)rgb, 3); 2065 ifile.read((char *)rgb, 3);
2069 2066
2070 std::vector<float *> steps; 2067 std::vector<float *> steps;
2071 // steps 2068 // steps
2072 for(int j = 0; j < nsteps; j++) { 2069 for(int j = 0; j < nsteps; j++) {
2073 2070
2074 float * steppoint = new float[6]; 2071 float * steppoint = new float[6];
2075 ifile.read((char *)ctmp, sizeof(float)*6); 2072 ifile.read((char *)ctmp, sizeof(float)*6);
2076 2073
2077 for(int k = 0; k < 6; k++) { 2074 for(int k = 0; k < 6; k++) {
2078 convertEndian(ctmp+k*sizeof(float), stepp 2075 convertEndian(ctmp+k*sizeof(float), steppoint[k]);
2079 } 2076 }
2080 2077
2081 steps.push_back(steppoint); 2078 steps.push_back(steppoint);
2082 } 2079 }
2083 2080
2084 // add a track to the track container 2081 // add a track to the track container
2085 addTrack(steps, rgb); 2082 addTrack(steps, rgb);
2086 2083
2087 if(DEBUG || kVerbose > 0) { 2084 if(DEBUG || kVerbose > 0) {
2088 if(i < 5) { 2085 if(i < 5) {
2089 G4cout << i << ": " ; 2086 G4cout << i << ": " ;
2090 for(int j = 0; j < 3; j++) G4cout << step 2087 for(int j = 0; j < 3; j++) G4cout << steps[0][j] << " ";
2091 int nstp = (int)steps.size(); << 2088 int nstp = steps.size();
2092 G4cout << "<-> "; 2089 G4cout << "<-> ";
2093 for(int j = 3; j < 6; j++) G4cout << step 2090 for(int j = 3; j < 6; j++) G4cout << steps[nstp-1][j] << " ";
2094 G4cout << " rgb( "; 2091 G4cout << " rgb( ";
2095 for(int j = 0; j < 3; j++) G4cout << (int 2092 for(int j = 0; j < 3; j++) G4cout << (int)rgb[j] << " ";
2096 G4cout << ")" << G4endl; 2093 G4cout << ")" << G4endl;
2097 } 2094 }
2098 } 2095 }
2099 } 2096 }
2100 2097
2101 2098
2102 } 2099 }
2103 2100
2104 2101
2105 //----- detector information -----// 2102 //----- detector information -----//
2106 if(kPointerToDetectorData != 0) { 2103 if(kPointerToDetectorData != 0) {
2107 2104
2108 // number of detectors 2105 // number of detectors
2109 ifile.read((char *)ctmp, sizeof(int)); 2106 ifile.read((char *)ctmp, sizeof(int));
2110 int ndet; 2107 int ndet;
2111 convertEndian(ctmp, ndet); 2108 convertEndian(ctmp, ndet);
2112 2109
2113 if(DEBUG || kVerbose > 0) { 2110 if(DEBUG || kVerbose > 0) {
2114 G4cout << "# of detectors : " 2111 G4cout << "# of detectors : "
2115 << ndet << G4endl; 2112 << ndet << G4endl;
2116 } 2113 }
2117 2114
2118 for(int nd = 0; nd < ndet; nd++) { 2115 for(int nd = 0; nd < ndet; nd++) {
2119 2116
2120 // # of edges of a detector 2117 // # of edges of a detector
2121 ifile.read((char *)ctmp, sizeof(int)); 2118 ifile.read((char *)ctmp, sizeof(int));
2122 int nedges; 2119 int nedges;
2123 convertEndian(ctmp, nedges); 2120 convertEndian(ctmp, nedges);
2124 if(DEBUG || kVerbose > 0) { 2121 if(DEBUG || kVerbose > 0) {
2125 G4cout << "# of edges in a detector : " << 2122 G4cout << "# of edges in a detector : " << nedges << G4endl;
2126 } 2123 }
2127 2124
2128 // edges 2125 // edges
2129 std::vector<float *> detector; 2126 std::vector<float *> detector;
2130 char cftmp[24]; 2127 char cftmp[24];
2131 for(int ne = 0; ne < nedges; ne++) { 2128 for(int ne = 0; ne < nedges; ne++) {
2132 2129
2133 ifile.read((char *)cftmp, sizeof(float)*6); 2130 ifile.read((char *)cftmp, sizeof(float)*6);
2134 float * edgePoints = new float[6]; 2131 float * edgePoints = new float[6];
2135 for(int j = 0; j < 6; j++) convertEndian(&c 2132 for(int j = 0; j < 6; j++) convertEndian(&cftmp[sizeof(float)*j], edgePoints[j]);
2136 detector.push_back(edgePoints); 2133 detector.push_back(edgePoints);
2137 2134
2138 } 2135 }
2139 2136
2140 if(DEBUG || kVerbose > 0) { 2137 if(DEBUG || kVerbose > 0) {
2141 G4cout << " first edge : (" << detector[0][ 2138 G4cout << " first edge : (" << detector[0][0] << ", "
2142 << detector[0][1] << ", " 2139 << detector[0][1] << ", "
2143 << detector[0][2] << ") - (" 2140 << detector[0][2] << ") - ("
2144 << detector[0][3] << ", " 2141 << detector[0][3] << ", "
2145 << detector[0][4] << ", " 2142 << detector[0][4] << ", "
2146 << detector[0][5] << ")" << G4endl; 2143 << detector[0][5] << ")" << G4endl;
2147 } 2144 }
2148 2145
2149 // detector color 2146 // detector color
2150 unsigned char dcolor[3]; 2147 unsigned char dcolor[3];
2151 ifile.read((char *)dcolor, 3); 2148 ifile.read((char *)dcolor, 3);
2152 if(DEBUG || kVerbose > 0) { 2149 if(DEBUG || kVerbose > 0) {
2153 G4cout << " detector color : rgb(" 2150 G4cout << " detector color : rgb("
2154 << (int)dcolor[0] << ", " 2151 << (int)dcolor[0] << ", "
2155 << (int)dcolor[1] << ", " 2152 << (int)dcolor[1] << ", "
2156 << (int)dcolor[2] << G4endl; 2153 << (int)dcolor[2] << G4endl;
2157 } 2154 }
2158 2155
2159 2156
2160 // detector name 2157 // detector name
2161 char cname[80]; 2158 char cname[80];
2162 ifile.read((char *)cname, 80); 2159 ifile.read((char *)cname, 80);
2163 std::string dname = cname; 2160 std::string dname = cname;
2164 if(DEBUG || kVerbose > 0) { 2161 if(DEBUG || kVerbose > 0) {
2165 G4cout << " detector name : " << dname << G 2162 G4cout << " detector name : " << dname << G4endl;
2166 } 2163 }
2167 2164
2168 2165
2169 addDetector(dname, detector, dcolor); 2166 addDetector(dname, detector, dcolor);
2170 2167
2171 } 2168 }
2172 } 2169 }
2173 2170
2174 2171
2175 ifile.close(); 2172 ifile.close();
2176 2173
2177 return true; 2174 return true;
2178 } 2175 }
2179 bool G4GMocrenIO::retrieveData4(char * _filen 2176 bool G4GMocrenIO::retrieveData4(char * _filename) {
2180 kFileName = _filename; 2177 kFileName = _filename;
2181 return retrieveData(); 2178 return retrieveData();
2182 } 2179 }
2183 2180
2184 // 2181 //
2185 bool G4GMocrenIO::retrieveData3() { 2182 bool G4GMocrenIO::retrieveData3() {
2186 2183
2187 bool DEBUG = false;// 2184 bool DEBUG = false;//
2188 2185
2189 // input file open 2186 // input file open
2190 std::ifstream ifile(kFileName.c_str(), std: 2187 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2191 if(!ifile) { 2188 if(!ifile) {
2192 if (G4VisManager::GetVerbosity() >= G4Vis 2189 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
2193 G4cout << "Cannot open file: " << kFile 2190 G4cout << "Cannot open file: " << kFileName
2194 << " in G4GMocrenIO::retrieveData3()." << 2191 << " in G4GMocrenIO::retrieveData3()." << G4endl;
2195 return false; 2192 return false;
2196 } 2193 }
2197 2194
2198 // data buffer 2195 // data buffer
2199 char ctmp[12]; 2196 char ctmp[12];
2200 2197
2201 // file identifier 2198 // file identifier
2202 char verid[9]; 2199 char verid[9];
2203 ifile.read((char *)verid, 8); 2200 ifile.read((char *)verid, 8);
2204 2201
2205 // file version 2202 // file version
2206 unsigned char ver; 2203 unsigned char ver;
2207 ifile.read((char *)&ver, 1); 2204 ifile.read((char *)&ver, 1);
2208 std::stringstream ss; 2205 std::stringstream ss;
2209 ss << (int)ver; 2206 ss << (int)ver;
2210 kVersion = ss.str(); 2207 kVersion = ss.str();
2211 if(DEBUG || kVerbose > 0) G4cout << "File v 2208 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
2212 2209
2213 // endian 2210 // endian
2214 ifile.read((char *)&kLittleEndianInput, siz 2211 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2215 if(DEBUG || kVerbose > 0) { 2212 if(DEBUG || kVerbose > 0) {
2216 G4cout << "Endian : "; 2213 G4cout << "Endian : ";
2217 if(kLittleEndianInput == 1) 2214 if(kLittleEndianInput == 1)
2218 G4cout << " little" << G4endl; 2215 G4cout << " little" << G4endl;
2219 else { 2216 else {
2220 G4cout << " big" << G4endl; 2217 G4cout << " big" << G4endl;
2221 } 2218 }
2222 } 2219 }
2223 2220
2224 // comment length (fixed size) 2221 // comment length (fixed size)
2225 int clength; 2222 int clength;
2226 ifile.read((char *)ctmp, 4); 2223 ifile.read((char *)ctmp, 4);
2227 convertEndian(ctmp, clength); 2224 convertEndian(ctmp, clength);
2228 // comment 2225 // comment
2229 char cmt[1025]; 2226 char cmt[1025];
2230 ifile.read((char *)cmt, clength); 2227 ifile.read((char *)cmt, clength);
2231 std::string scmt = cmt; 2228 std::string scmt = cmt;
2232 setComment(scmt); 2229 setComment(scmt);
2233 if(DEBUG || kVerbose > 0) { 2230 if(DEBUG || kVerbose > 0) {
2234 G4cout << "Data comment : " 2231 G4cout << "Data comment : "
2235 << kComment << G4endl; 2232 << kComment << G4endl;
2236 } 2233 }
2237 2234
2238 // voxel spacings for all images 2235 // voxel spacings for all images
2239 ifile.read((char *)ctmp, 12); 2236 ifile.read((char *)ctmp, 12);
2240 convertEndian(ctmp, kVoxelSpacing[0]); 2237 convertEndian(ctmp, kVoxelSpacing[0]);
2241 convertEndian(ctmp+4, kVoxelSpacing[1]); 2238 convertEndian(ctmp+4, kVoxelSpacing[1]);
2242 convertEndian(ctmp+8, kVoxelSpacing[2]); 2239 convertEndian(ctmp+8, kVoxelSpacing[2]);
2243 if(DEBUG || kVerbose > 0) { 2240 if(DEBUG || kVerbose > 0) {
2244 G4cout << "Voxel spacing : (" 2241 G4cout << "Voxel spacing : ("
2245 << kVoxelSpacing[0] << ", " 2242 << kVoxelSpacing[0] << ", "
2246 << kVoxelSpacing[1] << ", " 2243 << kVoxelSpacing[1] << ", "
2247 << kVoxelSpacing[2] 2244 << kVoxelSpacing[2]
2248 << ") mm " << G4endl; 2245 << ") mm " << G4endl;
2249 } 2246 }
2250 2247
2251 2248
2252 // offset from file starting point to the m 2249 // offset from file starting point to the modality image data
2253 ifile.read((char *)ctmp, 4); 2250 ifile.read((char *)ctmp, 4);
2254 convertEndian(ctmp, kPointerToModalityData) 2251 convertEndian(ctmp, kPointerToModalityData);
2255 2252
2256 // # of dose distributions 2253 // # of dose distributions
2257 ifile.read((char *)ctmp, 4); 2254 ifile.read((char *)ctmp, 4);
2258 int nDoseDist; 2255 int nDoseDist;
2259 convertEndian(ctmp, nDoseDist); 2256 convertEndian(ctmp, nDoseDist);
2260 2257
2261 // offset from file starting point to the d 2258 // offset from file starting point to the dose image data
2262 for(int i = 0; i < nDoseDist; i++) { 2259 for(int i = 0; i < nDoseDist; i++) {
2263 ifile.read((char *)ctmp, 4); 2260 ifile.read((char *)ctmp, 4);
2264 unsigned int dptr; 2261 unsigned int dptr;
2265 convertEndian(ctmp, dptr); 2262 convertEndian(ctmp, dptr);
2266 addPointerToDoseDistData(dptr); 2263 addPointerToDoseDistData(dptr);
2267 } 2264 }
2268 2265
2269 // offset from file starting point to the R 2266 // offset from file starting point to the ROI image data
2270 ifile.read((char *)ctmp, 4); 2267 ifile.read((char *)ctmp, 4);
2271 convertEndian(ctmp, kPointerToROIData); 2268 convertEndian(ctmp, kPointerToROIData);
2272 2269
2273 // offset from file starting point to the t 2270 // offset from file starting point to the track data
2274 ifile.read((char *)ctmp, 4); 2271 ifile.read((char *)ctmp, 4);
2275 convertEndian(ctmp, kPointerToTrackData); 2272 convertEndian(ctmp, kPointerToTrackData);
2276 if(DEBUG || kVerbose > 0) { 2273 if(DEBUG || kVerbose > 0) {
2277 G4cout << "Each pointer to data : " 2274 G4cout << "Each pointer to data : "
2278 << kPointerToModalityData << ", "; 2275 << kPointerToModalityData << ", ";
2279 for(int i = 0; i < nDoseDist; i++) 2276 for(int i = 0; i < nDoseDist; i++)
2280 G4cout << kPointerToDoseDistData[0] << 2277 G4cout << kPointerToDoseDistData[0] << ", ";
2281 G4cout << kPointerToROIData << ", " 2278 G4cout << kPointerToROIData << ", "
2282 << kPointerToTrackData << G4endl; 2279 << kPointerToTrackData << G4endl;
2283 } 2280 }
2284 2281
2285 if(kPointerToModalityData == 0 && kPointerT 2282 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2286 kPointerToROIData == 0 && kPointerToTrac 2283 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2287 if(DEBUG || kVerbose > 0) { 2284 if(DEBUG || kVerbose > 0) {
2288 G4cout << "No data." << G4endl; 2285 G4cout << "No data." << G4endl;
2289 } 2286 }
2290 return false; 2287 return false;
2291 } 2288 }
2292 2289
2293 // event number 2290 // event number
2294 /* ver 1 2291 /* ver 1
2295 ifile.read(ctmp, sizeof(int)); 2292 ifile.read(ctmp, sizeof(int));
2296 convertEndian(ctmp, numberOfEvents); 2293 convertEndian(ctmp, numberOfEvents);
2297 */ 2294 */
2298 2295
2299 int size[3]; 2296 int size[3];
2300 float scale; 2297 float scale;
2301 double dscale; 2298 double dscale;
2302 short minmax[2]; 2299 short minmax[2];
2303 float fCenter[3]; 2300 float fCenter[3];
2304 int iCenter[3]; 2301 int iCenter[3];
2305 2302
2306 //----- Modality image -----// 2303 //----- Modality image -----//
2307 // modality image size 2304 // modality image size
2308 ifile.read(ctmp, 3*sizeof(int)); 2305 ifile.read(ctmp, 3*sizeof(int));
2309 convertEndian(ctmp, size[0]); 2306 convertEndian(ctmp, size[0]);
2310 convertEndian(ctmp+sizeof(int), size[1]); 2307 convertEndian(ctmp+sizeof(int), size[1]);
2311 convertEndian(ctmp+2*sizeof(int), size[2]); 2308 convertEndian(ctmp+2*sizeof(int), size[2]);
2312 if(DEBUG || kVerbose > 0) { 2309 if(DEBUG || kVerbose > 0) {
2313 G4cout << "Modality image size : (" 2310 G4cout << "Modality image size : ("
2314 << size[0] << ", " 2311 << size[0] << ", "
2315 << size[1] << ", " 2312 << size[1] << ", "
2316 << size[2] << ")" 2313 << size[2] << ")"
2317 << G4endl; 2314 << G4endl;
2318 } 2315 }
2319 kModality.setSize(size); 2316 kModality.setSize(size);
2320 2317
2321 // modality image voxel spacing 2318 // modality image voxel spacing
2322 /* 2319 /*
2323 ifile.read(ctmp, 3*sizeof(float)); 2320 ifile.read(ctmp, 3*sizeof(float));
2324 convertEndian(ctmp, modalityImageVoxelSpa 2321 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2325 convertEndian(ctmp+sizeof(float), modalit 2322 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2326 convertEndian(ctmp+2*sizeof(float), modal 2323 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2327 */ 2324 */
2328 2325
2329 if(kPointerToModalityData != 0) { 2326 if(kPointerToModalityData != 0) {
2330 2327
2331 // modality density max. & min. 2328 // modality density max. & min.
2332 ifile.read((char *)ctmp, 4); 2329 ifile.read((char *)ctmp, 4);
2333 convertEndian(ctmp, minmax[0]); 2330 convertEndian(ctmp, minmax[0]);
2334 convertEndian(ctmp+2, minmax[1]); 2331 convertEndian(ctmp+2, minmax[1]);
2335 kModality.setMinMax(minmax); 2332 kModality.setMinMax(minmax);
2336 2333
2337 // modality image unit 2334 // modality image unit
2338 char munit[13]; 2335 char munit[13];
2339 ifile.read((char *)munit, 12); 2336 ifile.read((char *)munit, 12);
2340 std::string smunit = munit; 2337 std::string smunit = munit;
2341 setModalityImageUnit(smunit); 2338 setModalityImageUnit(smunit);
2342 2339
2343 // modality density scale 2340 // modality density scale
2344 ifile.read((char *)ctmp, 4); 2341 ifile.read((char *)ctmp, 4);
2345 convertEndian(ctmp, scale); 2342 convertEndian(ctmp, scale);
2346 kModality.setScale(dscale = scale); 2343 kModality.setScale(dscale = scale);
2347 if(DEBUG || kVerbose > 0) { 2344 if(DEBUG || kVerbose > 0) {
2348 G4cout << "Modality image min., max., s 2345 G4cout << "Modality image min., max., scale : "
2349 << minmax[0] << ", " 2346 << minmax[0] << ", "
2350 << minmax[1] << ", " 2347 << minmax[1] << ", "
2351 << scale << G4endl; 2348 << scale << G4endl;
2352 } 2349 }
2353 2350
2354 // modality density 2351 // modality density
2355 int psize = size[0]*size[1]; 2352 int psize = size[0]*size[1];
2356 if(DEBUG || kVerbose > 0) G4cout << "Moda 2353 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
2357 char * cimage = new char[psize*sizeof(sho 2354 char * cimage = new char[psize*sizeof(short)];
2358 for(int i = 0; i < size[2]; i++) { 2355 for(int i = 0; i < size[2]; i++) {
2359 ifile.read((char *)cimage, psize*sizeof 2356 ifile.read((char *)cimage, psize*sizeof(short));
2360 short * mimage = new short[psize]; 2357 short * mimage = new short[psize];
2361 for(int j = 0; j < psize; j++) { 2358 for(int j = 0; j < psize; j++) {
2362 convertEndian(cimage+j*sizeof(short), mimag 2359 convertEndian(cimage+j*sizeof(short), mimage[j]);
2363 } 2360 }
2364 kModality.addImage(mimage); 2361 kModality.addImage(mimage);
2365 2362
2366 if(DEBUG || kVerbose > 0) G4cout << "[" 2363 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2367 } 2364 }
2368 if(DEBUG || kVerbose > 0) G4cout << G4end 2365 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2369 delete [] cimage; 2366 delete [] cimage;
2370 2367
2371 // modality desity map for CT value 2368 // modality desity map for CT value
2372 size_t msize = minmax[1]-minmax[0]+1; 2369 size_t msize = minmax[1]-minmax[0]+1;
2373 if(DEBUG || kVerbose > 0) G4cout << "msiz 2370 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
2374 char * pdmap = new char[msize*sizeof(floa 2371 char * pdmap = new char[msize*sizeof(float)];
2375 ifile.read((char *)pdmap, msize*sizeof(fl 2372 ifile.read((char *)pdmap, msize*sizeof(float));
2376 float ftmp; 2373 float ftmp;
2377 for(int i = 0; i < (int)msize; i++) { 2374 for(int i = 0; i < (int)msize; i++) {
2378 convertEndian(pdmap+i*sizeof(float), ft 2375 convertEndian(pdmap+i*sizeof(float), ftmp);
2379 kModalityImageDensityMap.push_back(ftmp 2376 kModalityImageDensityMap.push_back(ftmp);
2380 } 2377 }
2381 delete [] pdmap; <<
2382 if(DEBUG || kVerbose > 0) { 2378 if(DEBUG || kVerbose > 0) {
2383 G4cout << "density map : " << std::ends 2379 G4cout << "density map : " << std::ends;
2384 for(int i = 0; i < 10; i++) 2380 for(int i = 0; i < 10; i++)
2385 G4cout <<kModalityImageDensityMap[i] << ", 2381 G4cout <<kModalityImageDensityMap[i] << ", ";
2386 G4cout << G4endl; 2382 G4cout << G4endl;
2387 for(int i = 0; i < 10; i++) G4cout << " 2383 for(int i = 0; i < 10; i++) G4cout << "..";
2388 G4cout << G4endl; 2384 G4cout << G4endl;
2389 for(size_t i =kModalityImageDensityMap. 2385 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2390 G4cout <<kModalityImageDensityMap[i] << ", 2386 G4cout <<kModalityImageDensityMap[i] << ", ";
2391 G4cout << G4endl; 2387 G4cout << G4endl;
2392 } 2388 }
2393 2389
2394 } 2390 }
2395 2391
2396 2392
2397 //----- dose distribution image -----// 2393 //----- dose distribution image -----//
2398 for(int ndose = 0; ndose < nDoseDist; ndose 2394 for(int ndose = 0; ndose < nDoseDist; ndose++) {
2399 2395
2400 newDoseDist(); 2396 newDoseDist();
2401 2397
2402 // dose distrbution image size 2398 // dose distrbution image size
2403 ifile.read((char *)ctmp, 3*sizeof(int)); 2399 ifile.read((char *)ctmp, 3*sizeof(int));
2404 convertEndian(ctmp, size[0]); 2400 convertEndian(ctmp, size[0]);
2405 convertEndian(ctmp+sizeof(int), size[1]); 2401 convertEndian(ctmp+sizeof(int), size[1]);
2406 convertEndian(ctmp+2*sizeof(int), size[2] 2402 convertEndian(ctmp+2*sizeof(int), size[2]);
2407 if(DEBUG || kVerbose > 0) { 2403 if(DEBUG || kVerbose > 0) {
2408 G4cout << "Dose dist. image size : (" 2404 G4cout << "Dose dist. image size : ("
2409 << size[0] << ", " 2405 << size[0] << ", "
2410 << size[1] << ", " 2406 << size[1] << ", "
2411 << size[2] << ")" 2407 << size[2] << ")"
2412 << G4endl; 2408 << G4endl;
2413 } 2409 }
2414 kDose[ndose].setSize(size); 2410 kDose[ndose].setSize(size);
2415 2411
2416 // dose distribution max. & min. 2412 // dose distribution max. & min.
2417 ifile.read((char *)ctmp, sizeof(short)*2) 2413 ifile.read((char *)ctmp, sizeof(short)*2);
2418 convertEndian(ctmp, minmax[0]); 2414 convertEndian(ctmp, minmax[0]);
2419 convertEndian(ctmp+2, minmax[1]); 2415 convertEndian(ctmp+2, minmax[1]);
2420 2416
2421 // dose distribution unit 2417 // dose distribution unit
2422 char dunit[13]; 2418 char dunit[13];
2423 ifile.read((char *)dunit, 12); 2419 ifile.read((char *)dunit, 12);
2424 std::string sdunit = dunit; 2420 std::string sdunit = dunit;
2425 setDoseDistUnit(sdunit, ndose); 2421 setDoseDistUnit(sdunit, ndose);
2426 if(DEBUG || kVerbose > 0) { 2422 if(DEBUG || kVerbose > 0) {
2427 G4cout << "Dose dist. unit : " << kDose 2423 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
2428 } 2424 }
2429 2425
2430 // dose distribution scaling 2426 // dose distribution scaling
2431 ifile.read((char *)ctmp, 4); // sizeof(fl 2427 ifile.read((char *)ctmp, 4); // sizeof(float)
2432 convertEndian(ctmp, scale); 2428 convertEndian(ctmp, scale);
2433 kDose[ndose].setScale(dscale = scale); 2429 kDose[ndose].setScale(dscale = scale);
2434 2430
2435 double dminmax[2]; 2431 double dminmax[2];
2436 for(int i = 0; i < 2; i++) dminmax[i] = m 2432 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2437 kDose[ndose].setMinMax(dminmax); 2433 kDose[ndose].setMinMax(dminmax);
2438 2434
2439 if(DEBUG || kVerbose > 0) { 2435 if(DEBUG || kVerbose > 0) {
2440 G4cout << "Dose dist. image min., max., 2436 G4cout << "Dose dist. image min., max., scale : "
2441 << dminmax[0] << ", " 2437 << dminmax[0] << ", "
2442 << dminmax[1] << ", " 2438 << dminmax[1] << ", "
2443 << scale << G4endl; 2439 << scale << G4endl;
2444 } 2440 }
2445 2441
2446 // dose distribution image 2442 // dose distribution image
2447 int dsize = size[0]*size[1]; 2443 int dsize = size[0]*size[1];
2448 if(DEBUG || kVerbose > 0) G4cout << "Dose 2444 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
2449 char * di = new char[dsize*sizeof(short)] 2445 char * di = new char[dsize*sizeof(short)];
2450 short * shimage = new short[dsize]; 2446 short * shimage = new short[dsize];
2451 for(int z = 0; z < size[2]; z++) { 2447 for(int z = 0; z < size[2]; z++) {
2452 ifile.read((char *)di, dsize*sizeof(sho 2448 ifile.read((char *)di, dsize*sizeof(short));
2453 double * dimage = new double[dsize]; 2449 double * dimage = new double[dsize];
2454 for(int xy = 0; xy < dsize; xy++) { 2450 for(int xy = 0; xy < dsize; xy++) {
2455 convertEndian(di+xy*sizeof(short), shimage[ 2451 convertEndian(di+xy*sizeof(short), shimage[xy]);
2456 dimage[xy] = shimage[xy]*dscale; 2452 dimage[xy] = shimage[xy]*dscale;
2457 } 2453 }
2458 kDose[ndose].addImage(dimage); 2454 kDose[ndose].addImage(dimage);
2459 2455
2460 if(DEBUG || kVerbose > 0) G4cout << "[" 2456 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2461 2457
2462 if(DEBUG || kVerbose > 0) { 2458 if(DEBUG || kVerbose > 0) {
2463 for(int j = 0; j < dsize; j++) { 2459 for(int j = 0; j < dsize; j++) {
2464 if(dimage[j] < 0) 2460 if(dimage[j] < 0)
2465 G4cout << "[" << j << "," << z << "]" 2461 G4cout << "[" << j << "," << z << "]"
2466 << dimage[j] << ", "; 2462 << dimage[j] << ", ";
2467 } 2463 }
2468 } 2464 }
2469 } 2465 }
2470 delete [] shimage; 2466 delete [] shimage;
2471 delete [] di; 2467 delete [] di;
2472 if(DEBUG || kVerbose > 0) G4cout << G4end 2468 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2473 2469
2474 ifile.read((char *)ctmp, 3*4); // 3*sizeo 2470 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
2475 convertEndian(ctmp, iCenter[0]); 2471 convertEndian(ctmp, iCenter[0]);
2476 convertEndian(ctmp+4, iCenter[1]); 2472 convertEndian(ctmp+4, iCenter[1]);
2477 convertEndian(ctmp+8, iCenter[2]); 2473 convertEndian(ctmp+8, iCenter[2]);
2478 for(int i = 0; i < 3; i++) fCenter[i] = ( 2474 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2479 kDose[ndose].setCenterPosition(fCenter); 2475 kDose[ndose].setCenterPosition(fCenter);
2480 2476
2481 if(DEBUG || kVerbose > 0) { 2477 if(DEBUG || kVerbose > 0) {
2482 G4cout << "Dose dist. image relative lo 2478 G4cout << "Dose dist. image relative location : ("
2483 << fCenter[0] << ", " 2479 << fCenter[0] << ", "
2484 << fCenter[1] << ", " 2480 << fCenter[1] << ", "
2485 << fCenter[2] << ")" << G4endl; 2481 << fCenter[2] << ")" << G4endl;
2486 } 2482 }
2487 2483
2488 2484
2489 } 2485 }
2490 2486
2491 //----- ROI image -----// 2487 //----- ROI image -----//
2492 if(kPointerToROIData != 0) { 2488 if(kPointerToROIData != 0) {
2493 2489
2494 newROI(); 2490 newROI();
2495 2491
2496 // ROI image size 2492 // ROI image size
2497 ifile.read((char *)ctmp, 3*sizeof(int)); 2493 ifile.read((char *)ctmp, 3*sizeof(int));
2498 convertEndian(ctmp, size[0]); 2494 convertEndian(ctmp, size[0]);
2499 convertEndian(ctmp+sizeof(int), size[1]); 2495 convertEndian(ctmp+sizeof(int), size[1]);
2500 convertEndian(ctmp+2*sizeof(int), size[2] 2496 convertEndian(ctmp+2*sizeof(int), size[2]);
2501 kRoi[0].setSize(size); 2497 kRoi[0].setSize(size);
2502 if(DEBUG || kVerbose > 0) { 2498 if(DEBUG || kVerbose > 0) {
2503 G4cout << "ROI image size : (" 2499 G4cout << "ROI image size : ("
2504 << size[0] << ", " 2500 << size[0] << ", "
2505 << size[1] << ", " 2501 << size[1] << ", "
2506 << size[2] << ")" 2502 << size[2] << ")"
2507 << G4endl; 2503 << G4endl;
2508 } 2504 }
2509 2505
2510 // ROI max. & min. 2506 // ROI max. & min.
2511 ifile.read((char *)ctmp, sizeof(short)*2) 2507 ifile.read((char *)ctmp, sizeof(short)*2);
2512 convertEndian(ctmp, minmax[0]); 2508 convertEndian(ctmp, minmax[0]);
2513 convertEndian(ctmp+sizeof(short), minmax[ 2509 convertEndian(ctmp+sizeof(short), minmax[1]);
2514 kRoi[0].setMinMax(minmax); 2510 kRoi[0].setMinMax(minmax);
2515 2511
2516 // ROI distribution scaling 2512 // ROI distribution scaling
2517 ifile.read((char *)ctmp, sizeof(float)); 2513 ifile.read((char *)ctmp, sizeof(float));
2518 convertEndian(ctmp, scale); 2514 convertEndian(ctmp, scale);
2519 kRoi[0].setScale(dscale = scale); 2515 kRoi[0].setScale(dscale = scale);
2520 if(DEBUG || kVerbose > 0) { 2516 if(DEBUG || kVerbose > 0) {
2521 G4cout << "ROI image min., max., scale 2517 G4cout << "ROI image min., max., scale : "
2522 << minmax[0] << ", " 2518 << minmax[0] << ", "
2523 << minmax[1] << ", " 2519 << minmax[1] << ", "
2524 << scale << G4endl; 2520 << scale << G4endl;
2525 } 2521 }
2526 2522
2527 // ROI image 2523 // ROI image
2528 int rsize = size[0]*size[1]; 2524 int rsize = size[0]*size[1];
2529 char * ri = new char[rsize*sizeof(short)] 2525 char * ri = new char[rsize*sizeof(short)];
2530 for(int i = 0; i < size[2]; i++) { 2526 for(int i = 0; i < size[2]; i++) {
2531 ifile.read((char *)ri, rsize*sizeof(sho 2527 ifile.read((char *)ri, rsize*sizeof(short));
2532 short * rimage = new short[rsize]; 2528 short * rimage = new short[rsize];
2533 for(int j = 0; j < rsize; j++) { 2529 for(int j = 0; j < rsize; j++) {
2534 convertEndian(ri+j*sizeof(short), rimage[j] 2530 convertEndian(ri+j*sizeof(short), rimage[j]);
2535 } 2531 }
2536 kRoi[0].addImage(rimage); 2532 kRoi[0].addImage(rimage);
2537 2533
2538 } 2534 }
2539 delete [] ri; 2535 delete [] ri;
2540 2536
2541 // ROI relative location 2537 // ROI relative location
2542 ifile.read((char *)ctmp, 3*sizeof(int)); 2538 ifile.read((char *)ctmp, 3*sizeof(int));
2543 convertEndian(ctmp, iCenter[0]); 2539 convertEndian(ctmp, iCenter[0]);
2544 convertEndian(ctmp+sizeof(int), iCenter[1 2540 convertEndian(ctmp+sizeof(int), iCenter[1]);
2545 convertEndian(ctmp+2*sizeof(int), iCenter 2541 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2546 for(int i = 0; i < 3; i++) fCenter[i] = i 2542 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2547 kRoi[0].setCenterPosition(fCenter); 2543 kRoi[0].setCenterPosition(fCenter);
2548 if(DEBUG || kVerbose > 0) { 2544 if(DEBUG || kVerbose > 0) {
2549 G4cout << "ROI image relative location 2545 G4cout << "ROI image relative location : ("
2550 << fCenter[0] << ", " 2546 << fCenter[0] << ", "
2551 << fCenter[1] << ", " 2547 << fCenter[1] << ", "
2552 << fCenter[2] << ")" << G4endl; 2548 << fCenter[2] << ")" << G4endl;
2553 } 2549 }
2554 2550
2555 } 2551 }
2556 2552
2557 //----- track information -----// 2553 //----- track information -----//
2558 if(kPointerToTrackData != 0) { 2554 if(kPointerToTrackData != 0) {
2559 2555
2560 // track 2556 // track
2561 ifile.read((char *)ctmp, sizeof(int)); 2557 ifile.read((char *)ctmp, sizeof(int));
2562 int ntrk; 2558 int ntrk;
2563 convertEndian(ctmp, ntrk); 2559 convertEndian(ctmp, ntrk);
2564 if(DEBUG || kVerbose > 0) { 2560 if(DEBUG || kVerbose > 0) {
2565 G4cout << "# of tracks: " << ntrk << G4 2561 G4cout << "# of tracks: " << ntrk << G4endl;
2566 } 2562 }
2567 2563
2568 // v4 2564 // v4
2569 std::vector<float *> trkv4; 2565 std::vector<float *> trkv4;
2570 2566
2571 // track position 2567 // track position
2572 for(int i = 0; i < ntrk; i++) { 2568 for(int i = 0; i < ntrk; i++) {
2573 float * tp = new float[6]; 2569 float * tp = new float[6];
2574 2570
2575 ifile.read((char *)ctmp, sizeof(float)* 2571 ifile.read((char *)ctmp, sizeof(float)*3);
2576 if(DEBUG || kVerbose > 0) if(i < 10) G4 2572 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << i << ": " ;
2577 for(int j = 0; j < 3; j++) { 2573 for(int j = 0; j < 3; j++) {
2578 convertEndian(ctmp+j*sizeof(float), tp[j]); 2574 convertEndian(ctmp+j*sizeof(float), tp[j]);
2579 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 2575 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j] << ", ";
2580 } 2576 }
2581 2577
2582 ifile.read((char *)ctmp, sizeof(float)* 2578 ifile.read((char *)ctmp, sizeof(float)*3);
2583 for(int j = 0; j < 3; j++) { 2579 for(int j = 0; j < 3; j++) {
2584 convertEndian(ctmp+j*sizeof(float), tp[j+3] 2580 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
2585 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 2581 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j+3] << ", ";
2586 } 2582 }
2587 addTrack(tp); 2583 addTrack(tp);
2588 if(DEBUG || kVerbose > 0) if(i < 10) G4 2584 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << G4endl;
2589 2585
2590 // v4 2586 // v4
2591 trkv4.push_back(tp); 2587 trkv4.push_back(tp);
2592 } 2588 }
2593 2589
2594 //v4 2590 //v4
2595 unsigned char trkcolorv4[3]; 2591 unsigned char trkcolorv4[3];
2596 2592
2597 // track color 2593 // track color
2598 for(int i = 0; i < ntrk; i++) { 2594 for(int i = 0; i < ntrk; i++) {
2599 unsigned char * rgb = new unsigned char 2595 unsigned char * rgb = new unsigned char[3];
2600 ifile.read((char *)rgb, 3); 2596 ifile.read((char *)rgb, 3);
2601 addTrackColor(rgb); 2597 addTrackColor(rgb);
2602 2598
2603 // v4 2599 // v4
2604 for(int j = 0; j < 3; j++) trkcolorv4[j 2600 for(int j = 0; j < 3; j++) trkcolorv4[j] = rgb[j];
2605 std::vector<float *> trk; 2601 std::vector<float *> trk;
2606 trk.push_back(trkv4[i]); 2602 trk.push_back(trkv4[i]);
2607 addTrack(trk, trkcolorv4); 2603 addTrack(trk, trkcolorv4);
2608 2604
2609 } 2605 }
2610 2606
2611 } 2607 }
2612 2608
2613 ifile.close(); 2609 ifile.close();
2614 2610
2615 return true; 2611 return true;
2616 } 2612 }
2617 bool G4GMocrenIO::retrieveData3(char * _filen 2613 bool G4GMocrenIO::retrieveData3(char * _filename) {
2618 kFileName = _filename; 2614 kFileName = _filename;
2619 return retrieveData(); 2615 return retrieveData();
2620 } 2616 }
2621 2617
2622 // 2618 //
2623 bool G4GMocrenIO::retrieveData2() { 2619 bool G4GMocrenIO::retrieveData2() {
2624 2620
2625 bool DEBUG = false;// 2621 bool DEBUG = false;//
2626 2622
2627 // input file open 2623 // input file open
2628 std::ifstream ifile(kFileName.c_str(), std: 2624 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2629 if(!ifile) { 2625 if(!ifile) {
2630 if (G4VisManager::GetVerbosity() >= G4Vis 2626 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
2631 G4cout << "Cannot open file: " << kFile 2627 G4cout << "Cannot open file: " << kFileName
2632 << " in G4GMocrenIO::retrieveData2()." << 2628 << " in G4GMocrenIO::retrieveData2()." << G4endl;
2633 return false; 2629 return false;
2634 } 2630 }
2635 2631
2636 // data buffer 2632 // data buffer
2637 char ctmp[12]; 2633 char ctmp[12];
2638 2634
2639 // file identifier 2635 // file identifier
2640 char verid[9]; 2636 char verid[9];
2641 ifile.read((char *)verid, 8); 2637 ifile.read((char *)verid, 8);
2642 2638
2643 // file version 2639 // file version
2644 unsigned char ver; 2640 unsigned char ver;
2645 ifile.read((char *)&ver, 1); 2641 ifile.read((char *)&ver, 1);
2646 std::stringstream ss; 2642 std::stringstream ss;
2647 ss << (int)ver; 2643 ss << (int)ver;
2648 kVersion = ss.str(); 2644 kVersion = ss.str();
2649 if(DEBUG || kVerbose > 0) G4cout << "File v 2645 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
2650 2646
2651 // id of version 1 2647 // id of version 1
2652 char idtmp[IDLENGTH]; 2648 char idtmp[IDLENGTH];
2653 ifile.read((char *)idtmp, IDLENGTH); 2649 ifile.read((char *)idtmp, IDLENGTH);
2654 kId = idtmp; 2650 kId = idtmp;
2655 // version of version 1 2651 // version of version 1
2656 char vertmp[VERLENGTH]; 2652 char vertmp[VERLENGTH];
2657 ifile.read((char *)vertmp, VERLENGTH); 2653 ifile.read((char *)vertmp, VERLENGTH);
2658 2654
2659 // endian 2655 // endian
2660 ifile.read((char *)&kLittleEndianInput, siz 2656 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2661 if(DEBUG || kVerbose > 0) { 2657 if(DEBUG || kVerbose > 0) {
2662 G4cout << "Endian : "; 2658 G4cout << "Endian : ";
2663 if(kLittleEndianInput == 1) 2659 if(kLittleEndianInput == 1)
2664 G4cout << " little" << G4endl; 2660 G4cout << " little" << G4endl;
2665 else { 2661 else {
2666 G4cout << " big" << G4endl; 2662 G4cout << " big" << G4endl;
2667 } 2663 }
2668 } 2664 }
2669 2665
2670 // voxel spacings for all images 2666 // voxel spacings for all images
2671 ifile.read((char *)ctmp, 12); 2667 ifile.read((char *)ctmp, 12);
2672 convertEndian(ctmp, kVoxelSpacing[0]); 2668 convertEndian(ctmp, kVoxelSpacing[0]);
2673 convertEndian(ctmp+4, kVoxelSpacing[1]); 2669 convertEndian(ctmp+4, kVoxelSpacing[1]);
2674 convertEndian(ctmp+8, kVoxelSpacing[2]); 2670 convertEndian(ctmp+8, kVoxelSpacing[2]);
2675 if(DEBUG || kVerbose > 0) { 2671 if(DEBUG || kVerbose > 0) {
2676 G4cout << "Voxel spacing : (" 2672 G4cout << "Voxel spacing : ("
2677 << kVoxelSpacing[0] << ", " 2673 << kVoxelSpacing[0] << ", "
2678 << kVoxelSpacing[1] << ", " 2674 << kVoxelSpacing[1] << ", "
2679 << kVoxelSpacing[2] 2675 << kVoxelSpacing[2]
2680 << ") mm " << G4endl; 2676 << ") mm " << G4endl;
2681 } 2677 }
2682 2678
2683 2679
2684 // offset from file starting point to the m 2680 // offset from file starting point to the modality image data
2685 ifile.read((char *)ctmp, 4); 2681 ifile.read((char *)ctmp, 4);
2686 convertEndian(ctmp, kPointerToModalityData) 2682 convertEndian(ctmp, kPointerToModalityData);
2687 2683
2688 // offset from file starting point to the d 2684 // offset from file starting point to the dose image data
2689 unsigned int ptddd; 2685 unsigned int ptddd;
2690 ifile.read((char *)ctmp, 4); 2686 ifile.read((char *)ctmp, 4);
2691 convertEndian(ctmp, ptddd); 2687 convertEndian(ctmp, ptddd);
2692 kPointerToDoseDistData.push_back(ptddd); 2688 kPointerToDoseDistData.push_back(ptddd);
2693 2689
2694 // offset from file starting point to the R 2690 // offset from file starting point to the ROI image data
2695 ifile.read((char *)ctmp, 4); 2691 ifile.read((char *)ctmp, 4);
2696 convertEndian(ctmp, kPointerToROIData); 2692 convertEndian(ctmp, kPointerToROIData);
2697 2693
2698 // offset from file starting point to the t 2694 // offset from file starting point to the track data
2699 ifile.read((char *)ctmp, 4); 2695 ifile.read((char *)ctmp, 4);
2700 convertEndian(ctmp, kPointerToTrackData); 2696 convertEndian(ctmp, kPointerToTrackData);
2701 if(DEBUG || kVerbose > 0) { 2697 if(DEBUG || kVerbose > 0) {
2702 G4cout << "Each pointer to data : " 2698 G4cout << "Each pointer to data : "
2703 << kPointerToModalityData << ", " 2699 << kPointerToModalityData << ", "
2704 << kPointerToDoseDistData[0] << ", " 2700 << kPointerToDoseDistData[0] << ", "
2705 << kPointerToROIData << ", " 2701 << kPointerToROIData << ", "
2706 << kPointerToTrackData << G4endl; 2702 << kPointerToTrackData << G4endl;
2707 } 2703 }
2708 2704
2709 if(kPointerToModalityData == 0 && kPointerT 2705 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2710 kPointerToROIData == 0 && kPointerToTrac 2706 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2711 if(DEBUG || kVerbose > 0) { 2707 if(DEBUG || kVerbose > 0) {
2712 G4cout << "No data." << G4endl; 2708 G4cout << "No data." << G4endl;
2713 } 2709 }
2714 return false; 2710 return false;
2715 } 2711 }
2716 2712
2717 // event number 2713 // event number
2718 /* ver 1 2714 /* ver 1
2719 ifile.read(ctmp, sizeof(int)); 2715 ifile.read(ctmp, sizeof(int));
2720 convertEndian(ctmp, numberOfEvents); 2716 convertEndian(ctmp, numberOfEvents);
2721 */ 2717 */
2722 2718
2723 int size[3]; 2719 int size[3];
2724 float scale; 2720 float scale;
2725 double dscale; 2721 double dscale;
2726 short minmax[2]; 2722 short minmax[2];
2727 float fCenter[3]; 2723 float fCenter[3];
2728 int iCenter[3]; 2724 int iCenter[3];
2729 2725
2730 //----- Modality image -----// 2726 //----- Modality image -----//
2731 // modality image size 2727 // modality image size
2732 ifile.read(ctmp, 3*sizeof(int)); 2728 ifile.read(ctmp, 3*sizeof(int));
2733 convertEndian(ctmp, size[0]); 2729 convertEndian(ctmp, size[0]);
2734 convertEndian(ctmp+sizeof(int), size[1]); 2730 convertEndian(ctmp+sizeof(int), size[1]);
2735 convertEndian(ctmp+2*sizeof(int), size[2]); 2731 convertEndian(ctmp+2*sizeof(int), size[2]);
2736 if(DEBUG || kVerbose > 0) { 2732 if(DEBUG || kVerbose > 0) {
2737 G4cout << "Modality image size : (" 2733 G4cout << "Modality image size : ("
2738 << size[0] << ", " 2734 << size[0] << ", "
2739 << size[1] << ", " 2735 << size[1] << ", "
2740 << size[2] << ")" 2736 << size[2] << ")"
2741 << G4endl; 2737 << G4endl;
2742 } 2738 }
2743 kModality.setSize(size); 2739 kModality.setSize(size);
2744 2740
2745 // modality image voxel spacing 2741 // modality image voxel spacing
2746 /* 2742 /*
2747 ifile.read(ctmp, 3*sizeof(float)); 2743 ifile.read(ctmp, 3*sizeof(float));
2748 convertEndian(ctmp, modalityImageVoxelSpa 2744 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2749 convertEndian(ctmp+sizeof(float), modalit 2745 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2750 convertEndian(ctmp+2*sizeof(float), modal 2746 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2751 */ 2747 */
2752 2748
2753 if(kPointerToModalityData != 0) { 2749 if(kPointerToModalityData != 0) {
2754 2750
2755 // modality density max. & min. 2751 // modality density max. & min.
2756 ifile.read((char *)ctmp, 4); 2752 ifile.read((char *)ctmp, 4);
2757 convertEndian(ctmp, minmax[0]); 2753 convertEndian(ctmp, minmax[0]);
2758 convertEndian(ctmp+2, minmax[1]); 2754 convertEndian(ctmp+2, minmax[1]);
2759 kModality.setMinMax(minmax); 2755 kModality.setMinMax(minmax);
2760 2756
2761 // modality density scale 2757 // modality density scale
2762 ifile.read((char *)ctmp, 4); 2758 ifile.read((char *)ctmp, 4);
2763 convertEndian(ctmp, scale); 2759 convertEndian(ctmp, scale);
2764 kModality.setScale(dscale = scale); 2760 kModality.setScale(dscale = scale);
2765 if(DEBUG || kVerbose > 0) { 2761 if(DEBUG || kVerbose > 0) {
2766 G4cout << "Modality image min., max., s 2762 G4cout << "Modality image min., max., scale : "
2767 << minmax[0] << ", " 2763 << minmax[0] << ", "
2768 << minmax[1] << ", " 2764 << minmax[1] << ", "
2769 << scale << G4endl; 2765 << scale << G4endl;
2770 } 2766 }
2771 2767
2772 // modality density 2768 // modality density
2773 int psize = size[0]*size[1]; 2769 int psize = size[0]*size[1];
2774 if(DEBUG || kVerbose > 0) G4cout << "Moda 2770 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
2775 char * cimage = new char[psize*sizeof(sho 2771 char * cimage = new char[psize*sizeof(short)];
2776 for(int i = 0; i < size[2]; i++) { 2772 for(int i = 0; i < size[2]; i++) {
2777 ifile.read((char *)cimage, psize*sizeof 2773 ifile.read((char *)cimage, psize*sizeof(short));
2778 short * mimage = new short[psize]; 2774 short * mimage = new short[psize];
2779 for(int j = 0; j < psize; j++) { 2775 for(int j = 0; j < psize; j++) {
2780 convertEndian(cimage+j*sizeof(short), mimag 2776 convertEndian(cimage+j*sizeof(short), mimage[j]);
2781 } 2777 }
2782 kModality.addImage(mimage); 2778 kModality.addImage(mimage);
2783 2779
2784 if(DEBUG || kVerbose > 0) G4cout << "[" 2780 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2785 } 2781 }
2786 if(DEBUG || kVerbose > 0) G4cout << G4end 2782 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2787 delete [] cimage; 2783 delete [] cimage;
2788 2784
2789 // modality desity map for CT value 2785 // modality desity map for CT value
2790 size_t msize = minmax[1]-minmax[0]+1; 2786 size_t msize = minmax[1]-minmax[0]+1;
2791 if(DEBUG || kVerbose > 0) G4cout << "msiz 2787 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
2792 char * pdmap = new char[msize*sizeof(floa 2788 char * pdmap = new char[msize*sizeof(float)];
2793 ifile.read((char *)pdmap, msize*sizeof(fl 2789 ifile.read((char *)pdmap, msize*sizeof(float));
2794 float ftmp; 2790 float ftmp;
2795 for(int i = 0; i < (int)msize; i++) { 2791 for(int i = 0; i < (int)msize; i++) {
2796 convertEndian(pdmap+i*sizeof(float), ft 2792 convertEndian(pdmap+i*sizeof(float), ftmp);
2797 kModalityImageDensityMap.push_back(ftmp 2793 kModalityImageDensityMap.push_back(ftmp);
2798 } 2794 }
2799 delete [] pdmap; <<
2800 if(DEBUG || kVerbose > 0) { 2795 if(DEBUG || kVerbose > 0) {
2801 G4cout << "density map : " << std::ends 2796 G4cout << "density map : " << std::ends;
2802 for(int i = 0; i < 10; i++) 2797 for(int i = 0; i < 10; i++)
2803 G4cout <<kModalityImageDensityMap[i] << ", 2798 G4cout <<kModalityImageDensityMap[i] << ", ";
2804 G4cout << G4endl; 2799 G4cout << G4endl;
2805 for(int i = 0; i < 10; i++) G4cout << " 2800 for(int i = 0; i < 10; i++) G4cout << "..";
2806 G4cout << G4endl; 2801 G4cout << G4endl;
2807 for(size_t i =kModalityImageDensityMap. 2802 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2808 G4cout <<kModalityImageDensityMap[i] << ", 2803 G4cout <<kModalityImageDensityMap[i] << ", ";
2809 G4cout << G4endl; 2804 G4cout << G4endl;
2810 } 2805 }
2811 2806
2812 } 2807 }
2813 2808
2814 2809
2815 //----- dose distribution image -----// 2810 //----- dose distribution image -----//
2816 if(kPointerToDoseDistData[0] != 0) { 2811 if(kPointerToDoseDistData[0] != 0) {
2817 2812
2818 newDoseDist(); 2813 newDoseDist();
2819 2814
2820 // dose distrbution image size 2815 // dose distrbution image size
2821 ifile.read((char *)ctmp, 3*sizeof(int)); 2816 ifile.read((char *)ctmp, 3*sizeof(int));
2822 convertEndian(ctmp, size[0]); 2817 convertEndian(ctmp, size[0]);
2823 convertEndian(ctmp+sizeof(int), size[1]); 2818 convertEndian(ctmp+sizeof(int), size[1]);
2824 convertEndian(ctmp+2*sizeof(int), size[2] 2819 convertEndian(ctmp+2*sizeof(int), size[2]);
2825 if(DEBUG || kVerbose > 0) { 2820 if(DEBUG || kVerbose > 0) {
2826 G4cout << "Dose dist. image size : (" 2821 G4cout << "Dose dist. image size : ("
2827 << size[0] << ", " 2822 << size[0] << ", "
2828 << size[1] << ", " 2823 << size[1] << ", "
2829 << size[2] << ")" 2824 << size[2] << ")"
2830 << G4endl; 2825 << G4endl;
2831 } 2826 }
2832 kDose[0].setSize(size); 2827 kDose[0].setSize(size);
2833 2828
2834 // dose distribution max. & min. 2829 // dose distribution max. & min.
2835 ifile.read((char *)ctmp, sizeof(short)*2) 2830 ifile.read((char *)ctmp, sizeof(short)*2);
2836 convertEndian(ctmp, minmax[0]); 2831 convertEndian(ctmp, minmax[0]);
2837 convertEndian(ctmp+2, minmax[1]); 2832 convertEndian(ctmp+2, minmax[1]);
2838 // dose distribution scaling 2833 // dose distribution scaling
2839 ifile.read((char *)ctmp, sizeof(float)); 2834 ifile.read((char *)ctmp, sizeof(float));
2840 convertEndian(ctmp, scale); 2835 convertEndian(ctmp, scale);
2841 kDose[0].setScale(dscale = scale); 2836 kDose[0].setScale(dscale = scale);
2842 2837
2843 double dminmax[2]; 2838 double dminmax[2];
2844 for(int i = 0; i < 2; i++) dminmax[i] = m 2839 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2845 kDose[0].setMinMax(dminmax); 2840 kDose[0].setMinMax(dminmax);
2846 2841
2847 if(DEBUG || kVerbose > 0) { 2842 if(DEBUG || kVerbose > 0) {
2848 G4cout << "Dose dist. image min., max., 2843 G4cout << "Dose dist. image min., max., scale : "
2849 << dminmax[0] << ", " 2844 << dminmax[0] << ", "
2850 << dminmax[1] << ", " 2845 << dminmax[1] << ", "
2851 << scale << G4endl; 2846 << scale << G4endl;
2852 } 2847 }
2853 2848
2854 // dose distribution image 2849 // dose distribution image
2855 int dsize = size[0]*size[1]; 2850 int dsize = size[0]*size[1];
2856 if(DEBUG || kVerbose > 0) G4cout << "Dose 2851 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
2857 char * di = new char[dsize*sizeof(short)] 2852 char * di = new char[dsize*sizeof(short)];
2858 short * shimage = new short[dsize]; 2853 short * shimage = new short[dsize];
2859 for(int z = 0; z < size[2]; z++) { 2854 for(int z = 0; z < size[2]; z++) {
2860 ifile.read((char *)di, dsize*sizeof(sho 2855 ifile.read((char *)di, dsize*sizeof(short));
2861 double * dimage = new double[dsize]; 2856 double * dimage = new double[dsize];
2862 for(int xy = 0; xy < dsize; xy++) { 2857 for(int xy = 0; xy < dsize; xy++) {
2863 convertEndian(di+xy*sizeof(short), shimage[ 2858 convertEndian(di+xy*sizeof(short), shimage[xy]);
2864 dimage[xy] = shimage[xy]*dscale; 2859 dimage[xy] = shimage[xy]*dscale;
2865 } 2860 }
2866 kDose[0].addImage(dimage); 2861 kDose[0].addImage(dimage);
2867 2862
2868 if(DEBUG || kVerbose > 0) G4cout << "[" 2863 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2869 2864
2870 if(DEBUG || kVerbose > 0) { 2865 if(DEBUG || kVerbose > 0) {
2871 for(int j = 0; j < dsize; j++) { 2866 for(int j = 0; j < dsize; j++) {
2872 if(dimage[j] < 0) 2867 if(dimage[j] < 0)
2873 G4cout << "[" << j << "," << z << "]" 2868 G4cout << "[" << j << "," << z << "]"
2874 << dimage[j] << ", "; 2869 << dimage[j] << ", ";
2875 } 2870 }
2876 } 2871 }
2877 } 2872 }
2878 delete [] shimage; 2873 delete [] shimage;
2879 delete [] di; 2874 delete [] di;
2880 if(DEBUG || kVerbose > 0) G4cout << G4end 2875 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2881 2876
2882 /* ver 1 2877 /* ver 1
2883 float doseDist; 2878 float doseDist;
2884 int dosePid; 2879 int dosePid;
2885 double * doseData = new double[numDose 2880 double * doseData = new double[numDoseImageVoxels];
2886 for(int i = 0; i < numDose; i++) { 2881 for(int i = 0; i < numDose; i++) {
2887 ifile.read(ctmp, sizeof(int)); 2882 ifile.read(ctmp, sizeof(int));
2888 convertEndian(ctmp, dosePid); 2883 convertEndian(ctmp, dosePid);
2889 for(int j = 0; j < numDoseImageVoxels; 2884 for(int j = 0; j < numDoseImageVoxels; j++) {
2890 ifile.read(ctmp, sizeof(float)); 2885 ifile.read(ctmp, sizeof(float));
2891 convertEndian(ctmp, doseDist); 2886 convertEndian(ctmp, doseDist);
2892 doseData[j] = doseDist; 2887 doseData[j] = doseDist;
2893 } 2888 }
2894 setDose(dosePid, doseData); 2889 setDose(dosePid, doseData);
2895 } 2890 }
2896 delete [] doseData; 2891 delete [] doseData;
2897 if(totalDose == NULL) totalDose = new 2892 if(totalDose == NULL) totalDose = new double[numDoseImageVoxels];
2898 for(int i = 0; i < numDoseImageVoxels; 2893 for(int i = 0; i < numDoseImageVoxels; i++) {
2899 ifile.read(ctmp, sizeof(float)); 2894 ifile.read(ctmp, sizeof(float));
2900 convertEndian(ctmp, doseDist); 2895 convertEndian(ctmp, doseDist);
2901 totalDose[i] = doseDist; 2896 totalDose[i] = doseDist;
2902 } 2897 }
2903 */ 2898 */
2904 2899
2905 /* ver 1 2900 /* ver 1
2906 // relative location between the two imag 2901 // relative location between the two images
2907 ifile.read(ctmp, 3*sizeof(float)); 2902 ifile.read(ctmp, 3*sizeof(float));
2908 convertEndian(ctmp, relativeLocation[0]); 2903 convertEndian(ctmp, relativeLocation[0]);
2909 convertEndian(ctmp+sizeof(float), relativ 2904 convertEndian(ctmp+sizeof(float), relativeLocation[1]);
2910 convertEndian(ctmp+2*sizeof(float), relat 2905 convertEndian(ctmp+2*sizeof(float), relativeLocation[2]);
2911 */ 2906 */
2912 2907
2913 // relative location of the dose distribu 2908 // relative location of the dose distribution image for
2914 // the modality image 2909 // the modality image
2915 //ofile.write((char *)relativeLocation, 3 2910 //ofile.write((char *)relativeLocation, 3*sizeof(float));
2916 ifile.read((char *)ctmp, 3*sizeof(int)); 2911 ifile.read((char *)ctmp, 3*sizeof(int));
2917 convertEndian(ctmp, iCenter[0]); 2912 convertEndian(ctmp, iCenter[0]);
2918 convertEndian(ctmp+sizeof(int), iCenter[1 2913 convertEndian(ctmp+sizeof(int), iCenter[1]);
2919 convertEndian(ctmp+2*sizeof(int), iCenter 2914 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2920 for(int i = 0; i < 3; i++) fCenter[i] = ( 2915 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2921 kDose[0].setCenterPosition(fCenter); 2916 kDose[0].setCenterPosition(fCenter);
2922 2917
2923 if(DEBUG || kVerbose > 0) { 2918 if(DEBUG || kVerbose > 0) {
2924 G4cout << "Dose dist. image relative lo 2919 G4cout << "Dose dist. image relative location : ("
2925 << fCenter[0] << ", " 2920 << fCenter[0] << ", "
2926 << fCenter[1] << ", " 2921 << fCenter[1] << ", "
2927 << fCenter[2] << ")" << G4endl; 2922 << fCenter[2] << ")" << G4endl;
2928 } 2923 }
2929 2924
2930 2925
2931 } 2926 }
2932 2927
2933 //----- ROI image -----// 2928 //----- ROI image -----//
2934 if(kPointerToROIData != 0) { 2929 if(kPointerToROIData != 0) {
2935 2930
2936 newROI(); 2931 newROI();
2937 2932
2938 // ROI image size 2933 // ROI image size
2939 ifile.read((char *)ctmp, 3*sizeof(int)); 2934 ifile.read((char *)ctmp, 3*sizeof(int));
2940 convertEndian(ctmp, size[0]); 2935 convertEndian(ctmp, size[0]);
2941 convertEndian(ctmp+sizeof(int), size[1]); 2936 convertEndian(ctmp+sizeof(int), size[1]);
2942 convertEndian(ctmp+2*sizeof(int), size[2] 2937 convertEndian(ctmp+2*sizeof(int), size[2]);
2943 kRoi[0].setSize(size); 2938 kRoi[0].setSize(size);
2944 if(DEBUG || kVerbose > 0) { 2939 if(DEBUG || kVerbose > 0) {
2945 G4cout << "ROI image size : (" 2940 G4cout << "ROI image size : ("
2946 << size[0] << ", " 2941 << size[0] << ", "
2947 << size[1] << ", " 2942 << size[1] << ", "
2948 << size[2] << ")" 2943 << size[2] << ")"
2949 << G4endl; 2944 << G4endl;
2950 } 2945 }
2951 2946
2952 // ROI max. & min. 2947 // ROI max. & min.
2953 ifile.read((char *)ctmp, sizeof(short)*2) 2948 ifile.read((char *)ctmp, sizeof(short)*2);
2954 convertEndian(ctmp, minmax[0]); 2949 convertEndian(ctmp, minmax[0]);
2955 convertEndian(ctmp+sizeof(short), minmax[ 2950 convertEndian(ctmp+sizeof(short), minmax[1]);
2956 kRoi[0].setMinMax(minmax); 2951 kRoi[0].setMinMax(minmax);
2957 2952
2958 // ROI distribution scaling 2953 // ROI distribution scaling
2959 ifile.read((char *)ctmp, sizeof(float)); 2954 ifile.read((char *)ctmp, sizeof(float));
2960 convertEndian(ctmp, scale); 2955 convertEndian(ctmp, scale);
2961 kRoi[0].setScale(dscale = scale); 2956 kRoi[0].setScale(dscale = scale);
2962 if(DEBUG || kVerbose > 0) { 2957 if(DEBUG || kVerbose > 0) {
2963 G4cout << "ROI image min., max., scale 2958 G4cout << "ROI image min., max., scale : "
2964 << minmax[0] << ", " 2959 << minmax[0] << ", "
2965 << minmax[1] << ", " 2960 << minmax[1] << ", "
2966 << scale << G4endl; 2961 << scale << G4endl;
2967 } 2962 }
2968 2963
2969 // ROI image 2964 // ROI image
2970 int rsize = size[0]*size[1]; 2965 int rsize = size[0]*size[1];
2971 char * ri = new char[rsize*sizeof(short)] 2966 char * ri = new char[rsize*sizeof(short)];
2972 for(int i = 0; i < size[2]; i++) { 2967 for(int i = 0; i < size[2]; i++) {
2973 ifile.read((char *)ri, rsize*sizeof(sho 2968 ifile.read((char *)ri, rsize*sizeof(short));
2974 short * rimage = new short[rsize]; 2969 short * rimage = new short[rsize];
2975 for(int j = 0; j < rsize; j++) { 2970 for(int j = 0; j < rsize; j++) {
2976 convertEndian(ri+j*sizeof(short), rimage[j] 2971 convertEndian(ri+j*sizeof(short), rimage[j]);
2977 } 2972 }
2978 kRoi[0].addImage(rimage); 2973 kRoi[0].addImage(rimage);
2979 2974
2980 } 2975 }
2981 delete [] ri; 2976 delete [] ri;
2982 2977
2983 // ROI relative location 2978 // ROI relative location
2984 ifile.read((char *)ctmp, 3*sizeof(int)); 2979 ifile.read((char *)ctmp, 3*sizeof(int));
2985 convertEndian(ctmp, iCenter[0]); 2980 convertEndian(ctmp, iCenter[0]);
2986 convertEndian(ctmp+sizeof(int), iCenter[1 2981 convertEndian(ctmp+sizeof(int), iCenter[1]);
2987 convertEndian(ctmp+2*sizeof(int), iCenter 2982 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2988 for(int i = 0; i < 3; i++) fCenter[i] = i 2983 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2989 kRoi[0].setCenterPosition(fCenter); 2984 kRoi[0].setCenterPosition(fCenter);
2990 if(DEBUG || kVerbose > 0) { 2985 if(DEBUG || kVerbose > 0) {
2991 G4cout << "ROI image relative location 2986 G4cout << "ROI image relative location : ("
2992 << fCenter[0] << ", " 2987 << fCenter[0] << ", "
2993 << fCenter[1] << ", " 2988 << fCenter[1] << ", "
2994 << fCenter[2] << ")" << G4endl; 2989 << fCenter[2] << ")" << G4endl;
2995 } 2990 }
2996 2991
2997 } 2992 }
2998 2993
2999 //----- track information -----// 2994 //----- track information -----//
3000 if(kPointerToTrackData != 0) { 2995 if(kPointerToTrackData != 0) {
3001 2996
3002 // track 2997 // track
3003 ifile.read((char *)ctmp, sizeof(int)); 2998 ifile.read((char *)ctmp, sizeof(int));
3004 int ntrk; 2999 int ntrk;
3005 convertEndian(ctmp, ntrk); 3000 convertEndian(ctmp, ntrk);
3006 if(DEBUG || kVerbose > 0) { 3001 if(DEBUG || kVerbose > 0) {
3007 G4cout << "# of tracks: " << ntrk << G4 3002 G4cout << "# of tracks: " << ntrk << G4endl;
3008 } 3003 }
3009 3004
3010 //v4 3005 //v4
3011 unsigned char trkcolorv4[3] = {255, 0, 0} 3006 unsigned char trkcolorv4[3] = {255, 0, 0};
3012 3007
3013 for(int i = 0; i < ntrk; i++) { 3008 for(int i = 0; i < ntrk; i++) {
3014 float * tp = new float[6]; 3009 float * tp = new float[6];
3015 // v4 3010 // v4
3016 std::vector<float *> trkv4; 3011 std::vector<float *> trkv4;
3017 3012
3018 ifile.read((char *)ctmp, sizeof(float)* 3013 ifile.read((char *)ctmp, sizeof(float)*3);
3019 if(DEBUG || kVerbose > 0) if(i < 10) G4 3014 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << i << ": " ;
3020 for(int j = 0; j < 3; j++) { 3015 for(int j = 0; j < 3; j++) {
3021 convertEndian(ctmp+j*sizeof(float), tp[j]); 3016 convertEndian(ctmp+j*sizeof(float), tp[j]);
3022 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 3017 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j] << ", ";
3023 } 3018 }
3024 3019
3025 ifile.read((char *)ctmp, sizeof(float)* 3020 ifile.read((char *)ctmp, sizeof(float)*3);
3026 for(int j = 0; j < 3; j++) { 3021 for(int j = 0; j < 3; j++) {
3027 convertEndian(ctmp+j*sizeof(float), tp[j+3] 3022 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
3028 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 3023 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j+3] << ", ";
3029 } 3024 }
3030 3025
3031 kSteps.push_back(tp); 3026 kSteps.push_back(tp);
3032 // v4 3027 // v4
3033 trkv4.push_back(tp); 3028 trkv4.push_back(tp);
3034 addTrack(trkv4, trkcolorv4); 3029 addTrack(trkv4, trkcolorv4);
3035 3030
3036 if(DEBUG || kVerbose > 0) if(i < 10) G4 3031 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << G4endl;
3037 } 3032 }
3038 3033
3039 } 3034 }
3040 3035
3041 /* ver 1 3036 /* ver 1
3042 // track 3037 // track
3043 int ntracks; 3038 int ntracks;
3044 ifile.read(ctmp, sizeof(int)); 3039 ifile.read(ctmp, sizeof(int));
3045 convertEndian(ctmp, ntracks); 3040 convertEndian(ctmp, ntracks);
3046 // track displacement 3041 // track displacement
3047 ifile.read(ctmp, 3*sizeof(float)); 3042 ifile.read(ctmp, 3*sizeof(float));
3048 convertEndian(ctmp, trackDisplacement[0]); 3043 convertEndian(ctmp, trackDisplacement[0]);
3049 convertEndian(ctmp+sizeof(float), trackDisp 3044 convertEndian(ctmp+sizeof(float), trackDisplacement[2]); // exchanged with [1]
3050 convertEndian(ctmp+2*sizeof(float), trackDi 3045 convertEndian(ctmp+2*sizeof(float), trackDisplacement[1]);
3051 // 3046 //
3052 //for(int i = 0; i < ntracks && i < 100; i+ 3047 //for(int i = 0; i < ntracks && i < 100; i++) {
3053 for(int i = 0; i < ntracks; i++) { 3048 for(int i = 0; i < ntracks; i++) {
3054 DicomDoseTrack trk; 3049 DicomDoseTrack trk;
3055 short trackid, parentid, pid; 3050 short trackid, parentid, pid;
3056 int npoints; 3051 int npoints;
3057 ifile.read(ctmp, sizeof(short)); 3052 ifile.read(ctmp, sizeof(short));
3058 convertEndian(ctmp, trackid); 3053 convertEndian(ctmp, trackid);
3059 trk.setID(trackid); 3054 trk.setID(trackid);
3060 ifile.read(ctmp, sizeof(short)); 3055 ifile.read(ctmp, sizeof(short));
3061 convertEndian(ctmp, parentid); 3056 convertEndian(ctmp, parentid);
3062 trk.setParentID(parentid); 3057 trk.setParentID(parentid);
3063 ifile.read(ctmp, sizeof(short)); 3058 ifile.read(ctmp, sizeof(short));
3064 convertEndian(ctmp, pid); 3059 convertEndian(ctmp, pid);
3065 trk.setPID(pid); 3060 trk.setPID(pid);
3066 ifile.read(ctmp, sizeof(int)); 3061 ifile.read(ctmp, sizeof(int));
3067 convertEndian(ctmp, npoints); 3062 convertEndian(ctmp, npoints);
3068 for(int i = 0; i < npoints; i++) { 3063 for(int i = 0; i < npoints; i++) {
3069 ifile.read(ctmp, 3*sizeof(float)); 3064 ifile.read(ctmp, 3*sizeof(float));
3070 // storing only start and end points 3065 // storing only start and end points
3071 //if(i == 0 || i == npoints - 1) { 3066 //if(i == 0 || i == npoints - 1) {
3072 float * point = new float[3]; 3067 float * point = new float[3];
3073 convertEndian(ctmp, point[0]); 3068 convertEndian(ctmp, point[0]);
3074 convertEndian(ctmp+sizeof(float), point[1]) 3069 convertEndian(ctmp+sizeof(float), point[1]);
3075 convertEndian(ctmp+2*sizeof(float), point[2 3070 convertEndian(ctmp+2*sizeof(float), point[2]);
3076 trk.addPoint(point); 3071 trk.addPoint(point);
3077 //} 3072 //}
3078 } 3073 }
3079 track.push_back(trk); 3074 track.push_back(trk);
3080 } 3075 }
3081 */ 3076 */
3082 3077
3083 ifile.close(); 3078 ifile.close();
3084 3079
3085 return true; 3080 return true;
3086 } 3081 }
3087 3082
3088 bool G4GMocrenIO::retrieveData2(char * _filen 3083 bool G4GMocrenIO::retrieveData2(char * _filename) {
3089 kFileName = _filename; 3084 kFileName = _filename;
3090 return retrieveData(); 3085 return retrieveData();
3091 } 3086 }
3092 3087
3093 void G4GMocrenIO::setID() { 3088 void G4GMocrenIO::setID() {
3094 time_t t; 3089 time_t t;
3095 time(&t); 3090 time(&t);
3096 3091
3097 tm * ti; 3092 tm * ti;
3098 ti = localtime(&t); 3093 ti = localtime(&t);
3099 3094
3100 char cmonth[12][4] = {"Jan", "Feb", "Mar", 3095 char cmonth[12][4] = {"Jan", "Feb", "Mar", "Apr",
3101 "May", "Jun", "Jul", "Aug", 3096 "May", "Jun", "Jul", "Aug",
3102 "Sep", "Oct", "Nov", "Dec"}; 3097 "Sep", "Oct", "Nov", "Dec"};
3103 std::stringstream ss; 3098 std::stringstream ss;
3104 ss << std::setfill('0') 3099 ss << std::setfill('0')
3105 << std::setw(2) 3100 << std::setw(2)
3106 << ti->tm_hour << ":" 3101 << ti->tm_hour << ":"
3107 << std::setw(2) 3102 << std::setw(2)
3108 << ti->tm_min << ":" 3103 << ti->tm_min << ":"
3109 << std::setw(2) 3104 << std::setw(2)
3110 << ti->tm_sec << "," 3105 << ti->tm_sec << ","
3111 << cmonth[ti->tm_mon] << "." 3106 << cmonth[ti->tm_mon] << "."
3112 << std::setw(2) 3107 << std::setw(2)
3113 << ti->tm_mday << "," 3108 << ti->tm_mday << ","
3114 << ti->tm_year+1900; 3109 << ti->tm_year+1900;
3115 3110
3116 kId = ss.str(); 3111 kId = ss.str();
3117 } 3112 }
3118 3113
3119 // get & set the file version 3114 // get & set the file version
3120 std::string & G4GMocrenIO::getVersion() {retu 3115 std::string & G4GMocrenIO::getVersion() {return kVersion;}
3121 void G4GMocrenIO::setVersion(std::string & _v 3116 void G4GMocrenIO::setVersion(std::string & _version) {kVersion = _version;}
3122 3117
3123 // set endians of input/output data 3118 // set endians of input/output data
3124 void G4GMocrenIO::setLittleEndianInput(bool _ 3119 void G4GMocrenIO::setLittleEndianInput(bool _little) {kLittleEndianInput = _little;}
3125 void G4GMocrenIO::setLittleEndianOutput(bool 3120 void G4GMocrenIO::setLittleEndianOutput(bool _little) {kLittleEndianOutput = _little;}
3126 3121
3127 // voxel spacing 3122 // voxel spacing
3128 void G4GMocrenIO::setVoxelSpacing(float _spac 3123 void G4GMocrenIO::setVoxelSpacing(float _spacing[3]) {
3129 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 3124 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = _spacing[i];
3130 } 3125 }
3131 void G4GMocrenIO::getVoxelSpacing(float _spac 3126 void G4GMocrenIO::getVoxelSpacing(float _spacing[3]) {
3132 for(int i = 0; i < 3; i++) _spacing[i] = kV 3127 for(int i = 0; i < 3; i++) _spacing[i] = kVoxelSpacing[i];
3133 } 3128 }
3134 3129
3135 // get & set number of events 3130 // get & set number of events
3136 int & G4GMocrenIO::getNumberOfEvents() { 3131 int & G4GMocrenIO::getNumberOfEvents() {
3137 return kNumberOfEvents; 3132 return kNumberOfEvents;
3138 } 3133 }
3139 void G4GMocrenIO::setNumberOfEvents(int & _nu 3134 void G4GMocrenIO::setNumberOfEvents(int & _numberOfEvents) {
3140 kNumberOfEvents = _numberOfEvents; 3135 kNumberOfEvents = _numberOfEvents;
3141 } 3136 }
3142 void G4GMocrenIO::addOneEvent() { 3137 void G4GMocrenIO::addOneEvent() {
3143 kNumberOfEvents++; 3138 kNumberOfEvents++;
3144 } 3139 }
3145 3140
3146 // set/get pointer the modality image data 3141 // set/get pointer the modality image data
3147 void G4GMocrenIO::setPointerToModalityData(un 3142 void G4GMocrenIO::setPointerToModalityData(unsigned int & _pointer) {
3148 kPointerToModalityData = _pointer; 3143 kPointerToModalityData = _pointer;
3149 } 3144 }
3150 unsigned int G4GMocrenIO::getPointerToModalit 3145 unsigned int G4GMocrenIO::getPointerToModalityData() {
3151 return kPointerToModalityData; 3146 return kPointerToModalityData;
3152 } 3147 }
3153 // set/get pointer the dose distribution imag 3148 // set/get pointer the dose distribution image data
3154 void G4GMocrenIO::addPointerToDoseDistData(un 3149 void G4GMocrenIO::addPointerToDoseDistData(unsigned int & _pointer) {
3155 kPointerToDoseDistData.push_back(_pointer); 3150 kPointerToDoseDistData.push_back(_pointer);
3156 } 3151 }
3157 unsigned int G4GMocrenIO::getPointerToDoseDis 3152 unsigned int G4GMocrenIO::getPointerToDoseDistData(int _elem) {
3158 if(kPointerToDoseDistData.size() == 0 || 3153 if(kPointerToDoseDistData.size() == 0 ||
3159 kPointerToDoseDistData.size() < (size_t) 3154 kPointerToDoseDistData.size() < (size_t)_elem)
3160 return 0; 3155 return 0;
3161 else 3156 else
3162 return kPointerToDoseDistData[_elem]; 3157 return kPointerToDoseDistData[_elem];
3163 } 3158 }
3164 3159
3165 // set/get pointer the ROI image data 3160 // set/get pointer the ROI image data
3166 void G4GMocrenIO::setPointerToROIData(unsigne 3161 void G4GMocrenIO::setPointerToROIData(unsigned int & _pointer) {
3167 kPointerToROIData = _pointer; 3162 kPointerToROIData = _pointer;
3168 } 3163 }
3169 unsigned int G4GMocrenIO::getPointerToROIData 3164 unsigned int G4GMocrenIO::getPointerToROIData() {
3170 return kPointerToROIData; 3165 return kPointerToROIData;
3171 } 3166 }
3172 // set/get pointer the track data 3167 // set/get pointer the track data
3173 void G4GMocrenIO::setPointerToTrackData(unsig 3168 void G4GMocrenIO::setPointerToTrackData(unsigned int & _pointer) {
3174 kPointerToTrackData = _pointer; 3169 kPointerToTrackData = _pointer;
3175 } 3170 }
3176 unsigned int G4GMocrenIO::getPointerToTrackDa 3171 unsigned int G4GMocrenIO::getPointerToTrackData() {
3177 return kPointerToTrackData; 3172 return kPointerToTrackData;
3178 } 3173 }
3179 3174
3180 // calculate pointers for version 4 3175 // calculate pointers for version 4
3181 void G4GMocrenIO::calcPointers4() { 3176 void G4GMocrenIO::calcPointers4() {
3182 3177
3183 // pointer to modality data 3178 // pointer to modality data
3184 unsigned int pointer = 1070; // up to "poin 3179 unsigned int pointer = 1070; // up to "pointer to the detector data" except for "pointer to the dose dist data"
3185 int nDoseDist = getNumDoseDist(); 3180 int nDoseDist = getNumDoseDist();
3186 pointer += nDoseDist*4; 3181 pointer += nDoseDist*4;
3187 3182
3188 setPointerToModalityData(pointer); 3183 setPointerToModalityData(pointer);
3189 3184
3190 // pointer to dose data 3185 // pointer to dose data
3191 // ct-density map for modality data 3186 // ct-density map for modality data
3192 int msize[3]; 3187 int msize[3];
3193 getModalityImageSize(msize); 3188 getModalityImageSize(msize);
3194 short mminmax[2]; 3189 short mminmax[2];
3195 getModalityImageMinMax(mminmax); 3190 getModalityImageMinMax(mminmax);
3196 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3191 int pmsize = 2*msize[0]*msize[1]*msize[2];
3197 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3192 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3198 pointer += 32 + pmsize + pmmap; 3193 pointer += 32 + pmsize + pmmap;
3199 // 3194 //
3200 kPointerToDoseDistData.clear(); 3195 kPointerToDoseDistData.clear();
3201 if(nDoseDist == 0) { 3196 if(nDoseDist == 0) {
3202 unsigned int pointer0 = 0; 3197 unsigned int pointer0 = 0;
3203 addPointerToDoseDistData(pointer0); 3198 addPointerToDoseDistData(pointer0);
3204 } 3199 }
3205 for(int ndose = 0; ndose < nDoseDist; ndose 3200 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3206 addPointerToDoseDistData(pointer); 3201 addPointerToDoseDistData(pointer);
3207 int dsize[3]; 3202 int dsize[3];
3208 getDoseDistSize(dsize); 3203 getDoseDistSize(dsize);
3209 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3204 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2 + 80;
3210 } 3205 }
3211 3206
3212 // pointer to roi data 3207 // pointer to roi data
3213 if(!isROIEmpty()) { 3208 if(!isROIEmpty()) {
3214 setPointerToROIData(pointer); 3209 setPointerToROIData(pointer);
3215 3210
3216 int rsize[3]; 3211 int rsize[3];
3217 getROISize(rsize); 3212 getROISize(rsize);
3218 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3213 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3219 pointer += 20 + prsize + 12; 3214 pointer += 20 + prsize + 12;
3220 } else { 3215 } else {
3221 unsigned int pointer0 = 0; 3216 unsigned int pointer0 = 0;
3222 setPointerToROIData(pointer0); 3217 setPointerToROIData(pointer0);
3223 } 3218 }
3224 3219
3225 // pointer to track data 3220 // pointer to track data
3226 int ntrk = (int)kTracks.size(); << 3221 int ntrk = kTracks.size();
3227 if(ntrk != 0) { 3222 if(ntrk != 0) {
3228 setPointerToTrackData(pointer); 3223 setPointerToTrackData(pointer);
3229 3224
3230 pointer += 4; // # of tracks 3225 pointer += 4; // # of tracks
3231 for(int nt = 0; nt < ntrk; nt++) { 3226 for(int nt = 0; nt < ntrk; nt++) {
3232 int nsteps = kTracks[nt].getNumberOfSte 3227 int nsteps = kTracks[nt].getNumberOfSteps();
3233 pointer += 4 + 3 + nsteps*(4*6); // # o 3228 pointer += 4 + 3 + nsteps*(4*6); // # of steps + color + steps(float*6)
3234 } 3229 }
3235 } else { 3230 } else {
3236 unsigned int pointer0 = 0; 3231 unsigned int pointer0 = 0;
3237 setPointerToTrackData(pointer0); 3232 setPointerToTrackData(pointer0);
3238 } 3233 }
3239 if(kVerbose > 0) G4cout << " pointer to the 3234 if(kVerbose > 0) G4cout << " pointer to the track data :"
3240 << kPointerToTrackData << G4endl; 3235 << kPointerToTrackData << G4endl;
3241 3236
3242 // pointer to detector data 3237 // pointer to detector data
3243 int ndet = (int)kDetectors.size(); << 3238 int ndet = kDetectors.size();
3244 if(ndet != 0) { 3239 if(ndet != 0) {
3245 kPointerToDetectorData = pointer; 3240 kPointerToDetectorData = pointer;
3246 } else { 3241 } else {
3247 kPointerToDetectorData = 0; 3242 kPointerToDetectorData = 0;
3248 } 3243 }
3249 if(kVerbose > 0) G4cout << " pointer to the 3244 if(kVerbose > 0) G4cout << " pointer to the detector data :"
3250 << kPointerToDetectorData << G4end 3245 << kPointerToDetectorData << G4endl;
3251 3246
3252 } 3247 }
3253 3248
3254 // calculate pointers for ver.3 3249 // calculate pointers for ver.3
3255 void G4GMocrenIO::calcPointers3() { 3250 void G4GMocrenIO::calcPointers3() {
3256 3251
3257 // pointer to modality data 3252 // pointer to modality data
3258 unsigned int pointer = 1066; // up to "poin 3253 unsigned int pointer = 1066; // up to "pointer to the track data" except for "pointer to the dose dist data"
3259 int nDoseDist = getNumDoseDist(); 3254 int nDoseDist = getNumDoseDist();
3260 pointer += nDoseDist*4; 3255 pointer += nDoseDist*4;
3261 3256
3262 setPointerToModalityData(pointer); 3257 setPointerToModalityData(pointer);
3263 3258
3264 // pointer to dose data 3259 // pointer to dose data
3265 // ct-density map for modality data 3260 // ct-density map for modality data
3266 int msize[3]; 3261 int msize[3];
3267 getModalityImageSize(msize); 3262 getModalityImageSize(msize);
3268 short mminmax[2]; 3263 short mminmax[2];
3269 getModalityImageMinMax(mminmax); 3264 getModalityImageMinMax(mminmax);
3270 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3265 int pmsize = 2*msize[0]*msize[1]*msize[2];
3271 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3266 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3272 pointer += 32 + pmsize + pmmap; 3267 pointer += 32 + pmsize + pmmap;
3273 // 3268 //
3274 kPointerToDoseDistData.clear(); 3269 kPointerToDoseDistData.clear();
3275 if(nDoseDist == 0) { 3270 if(nDoseDist == 0) {
3276 unsigned int pointer0 = 0; 3271 unsigned int pointer0 = 0;
3277 addPointerToDoseDistData(pointer0); 3272 addPointerToDoseDistData(pointer0);
3278 } 3273 }
3279 for(int ndose = 0; ndose < nDoseDist; ndose 3274 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3280 addPointerToDoseDistData(pointer); 3275 addPointerToDoseDistData(pointer);
3281 int dsize[3]; 3276 int dsize[3];
3282 getDoseDistSize(dsize); 3277 getDoseDistSize(dsize);
3283 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3278 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2;
3284 } 3279 }
3285 3280
3286 // pointer to roi data 3281 // pointer to roi data
3287 if(!isROIEmpty()) { 3282 if(!isROIEmpty()) {
3288 setPointerToROIData(pointer); 3283 setPointerToROIData(pointer);
3289 3284
3290 int rsize[3]; 3285 int rsize[3];
3291 getROISize(rsize); 3286 getROISize(rsize);
3292 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3287 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3293 pointer += 20 + prsize + 12; 3288 pointer += 20 + prsize + 12;
3294 } else { 3289 } else {
3295 unsigned int pointer0 = 0; 3290 unsigned int pointer0 = 0;
3296 setPointerToROIData(pointer0); 3291 setPointerToROIData(pointer0);
3297 } 3292 }
3298 3293
3299 // 3294 //
3300 if(getNumTracks() != 0) 3295 if(getNumTracks() != 0)
3301 setPointerToTrackData(pointer); 3296 setPointerToTrackData(pointer);
3302 else { 3297 else {
3303 unsigned int pointer0 = 0; 3298 unsigned int pointer0 = 0;
3304 setPointerToTrackData(pointer0); 3299 setPointerToTrackData(pointer0);
3305 } 3300 }
3306 3301
3307 } 3302 }
3308 3303
3309 // calculate pointers for ver.2 3304 // calculate pointers for ver.2
3310 void G4GMocrenIO::calcPointers2() { 3305 void G4GMocrenIO::calcPointers2() {
3311 3306
3312 // pointer to modality data 3307 // pointer to modality data
3313 unsigned int pointer = 65; 3308 unsigned int pointer = 65;
3314 setPointerToModalityData(pointer); 3309 setPointerToModalityData(pointer);
3315 3310
3316 // pointer to dose data 3311 // pointer to dose data
3317 int msize[3]; 3312 int msize[3];
3318 getModalityImageSize(msize); 3313 getModalityImageSize(msize);
3319 short mminmax[2]; 3314 short mminmax[2];
3320 getModalityImageMinMax(mminmax); 3315 getModalityImageMinMax(mminmax);
3321 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3316 int pmsize = 2*msize[0]*msize[1]*msize[2];
3322 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3317 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3323 pointer += 20 + pmsize + pmmap; 3318 pointer += 20 + pmsize + pmmap;
3324 int dsize[3]; 3319 int dsize[3];
3325 getDoseDistSize(dsize); 3320 getDoseDistSize(dsize);
3326 kPointerToDoseDistData.clear(); 3321 kPointerToDoseDistData.clear();
3327 if(dsize[0] != 0) { 3322 if(dsize[0] != 0) {
3328 kPointerToDoseDistData.push_back(pointer) 3323 kPointerToDoseDistData.push_back(pointer);
3329 3324
3330 int pdsize = 2*dsize[0]*dsize[1]*dsize[2] 3325 int pdsize = 2*dsize[0]*dsize[1]*dsize[2];
3331 pointer += 20 + pdsize + 12; 3326 pointer += 20 + pdsize + 12;
3332 } else { 3327 } else {
3333 unsigned int pointer0 = 0; 3328 unsigned int pointer0 = 0;
3334 kPointerToDoseDistData.push_back(pointer0 3329 kPointerToDoseDistData.push_back(pointer0);
3335 } 3330 }
3336 3331
3337 // pointer to roi data 3332 // pointer to roi data
3338 if(!isROIEmpty()) { 3333 if(!isROIEmpty()) {
3339 int rsize[3]; 3334 int rsize[3];
3340 getROISize(rsize); 3335 getROISize(rsize);
3341 setPointerToROIData(pointer); 3336 setPointerToROIData(pointer);
3342 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3337 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3343 pointer += 20 + prsize + 12; 3338 pointer += 20 + prsize + 12;
3344 3339
3345 } else { 3340 } else {
3346 unsigned int pointer0 = 0; 3341 unsigned int pointer0 = 0;
3347 setPointerToROIData(pointer0); 3342 setPointerToROIData(pointer0);
3348 } 3343 }
3349 3344
3350 // 3345 //
3351 if(getNumTracks() != 0) 3346 if(getNumTracks() != 0)
3352 setPointerToTrackData(pointer); 3347 setPointerToTrackData(pointer);
3353 else { 3348 else {
3354 unsigned int pointer0 = 0; 3349 unsigned int pointer0 = 0;
3355 setPointerToTrackData(pointer0); 3350 setPointerToTrackData(pointer0);
3356 } 3351 }
3357 3352
3358 } 3353 }
3359 3354
3360 3355
3361 //----- Modality image -----// 3356 //----- Modality image -----//
3362 void G4GMocrenIO::getModalityImageSize(int _s 3357 void G4GMocrenIO::getModalityImageSize(int _size[3]) {
3363 3358
3364 kModality.getSize(_size); 3359 kModality.getSize(_size);
3365 } 3360 }
3366 void G4GMocrenIO::setModalityImageSize(int _s 3361 void G4GMocrenIO::setModalityImageSize(int _size[3]) {
3367 3362
3368 kModality.setSize(_size); 3363 kModality.setSize(_size);
3369 } 3364 }
3370 3365
3371 // get & set the modality image size 3366 // get & set the modality image size
3372 void G4GMocrenIO::setModalityImageScale(doubl 3367 void G4GMocrenIO::setModalityImageScale(double & _scale) {
3373 3368
3374 kModality.setScale(_scale); 3369 kModality.setScale(_scale);
3375 } 3370 }
3376 double G4GMocrenIO::getModalityImageScale() { 3371 double G4GMocrenIO::getModalityImageScale() {
3377 3372
3378 return kModality.getScale(); 3373 return kModality.getScale();
3379 } 3374 }
3380 3375
3381 // set the modality image in CT 3376 // set the modality image in CT
3382 void G4GMocrenIO::setModalityImage(short * _i 3377 void G4GMocrenIO::setModalityImage(short * _image) {
3383 3378
3384 kModality.addImage(_image); 3379 kModality.addImage(_image);
3385 } 3380 }
3386 short * G4GMocrenIO::getModalityImage(int _z) 3381 short * G4GMocrenIO::getModalityImage(int _z) {
3387 3382
3388 return kModality.getImage(_z); 3383 return kModality.getImage(_z);
3389 } 3384 }
3390 void G4GMocrenIO::clearModalityImage() { 3385 void G4GMocrenIO::clearModalityImage() {
3391 3386
3392 kModality.clearImage(); 3387 kModality.clearImage();
3393 } 3388 }
3394 // set/get the modality image density map 3389 // set/get the modality image density map
3395 void G4GMocrenIO::setModalityImageDensityMap( 3390 void G4GMocrenIO::setModalityImageDensityMap(std::vector<float> & _map) {
3396 kModalityImageDensityMap = _map; 3391 kModalityImageDensityMap = _map;
3397 } 3392 }
3398 std::vector<float> & G4GMocrenIO::getModality 3393 std::vector<float> & G4GMocrenIO::getModalityImageDensityMap() {
3399 return kModalityImageDensityMap; 3394 return kModalityImageDensityMap;
3400 } 3395 }
3401 // set the modality image min./max. 3396 // set the modality image min./max.
3402 void G4GMocrenIO::setModalityImageMinMax(shor 3397 void G4GMocrenIO::setModalityImageMinMax(short _minmax[2]) {
3403 3398
3404 kModality.setMinMax(_minmax); 3399 kModality.setMinMax(_minmax);
3405 } 3400 }
3406 // get the modality image min./max. 3401 // get the modality image min./max.
3407 void G4GMocrenIO::getModalityImageMinMax(shor 3402 void G4GMocrenIO::getModalityImageMinMax(short _minmax[2]) {
3408 3403
3409 short minmax[2]; 3404 short minmax[2];
3410 kModality.getMinMax(minmax); 3405 kModality.getMinMax(minmax);
3411 for(int i = 0; i < 2; i++) _minmax[i] = min 3406 for(int i = 0; i < 2; i++) _minmax[i] = minmax[i];
3412 } 3407 }
3413 short G4GMocrenIO::getModalityImageMax() { 3408 short G4GMocrenIO::getModalityImageMax() {
3414 3409
3415 short minmax[2]; 3410 short minmax[2];
3416 kModality.getMinMax(minmax); 3411 kModality.getMinMax(minmax);
3417 return minmax[1]; 3412 return minmax[1];
3418 } 3413 }
3419 short G4GMocrenIO::getModalityImageMin() { 3414 short G4GMocrenIO::getModalityImageMin() {
3420 3415
3421 short minmax[2]; 3416 short minmax[2];
3422 kModality.getMinMax(minmax); 3417 kModality.getMinMax(minmax);
3423 return minmax[0]; 3418 return minmax[0];
3424 } 3419 }
3425 // set/get position of the modality image cen 3420 // set/get position of the modality image center
3426 void G4GMocrenIO::setModalityCenterPosition(f 3421 void G4GMocrenIO::setModalityCenterPosition(float _center[3]) {
3427 3422
3428 kModality.setCenterPosition(_center); 3423 kModality.setCenterPosition(_center);
3429 } 3424 }
3430 void G4GMocrenIO::getModalityCenterPosition(f 3425 void G4GMocrenIO::getModalityCenterPosition(float _center[3]) {
3431 3426
3432 if(isROIEmpty()) 3427 if(isROIEmpty())
3433 for(int i = 0; i < 3; i++) _center[i] = 0 3428 for(int i = 0; i < 3; i++) _center[i] = 0;
3434 else 3429 else
3435 kModality.getCenterPosition(_center); 3430 kModality.getCenterPosition(_center);
3436 } 3431 }
3437 // get & set the modality image unit 3432 // get & set the modality image unit
3438 std::string G4GMocrenIO::getModalityImageUnit 3433 std::string G4GMocrenIO::getModalityImageUnit() {
3439 return kModalityUnit; 3434 return kModalityUnit;
3440 } 3435 }
3441 void G4GMocrenIO::setModalityImageUnit(std::s 3436 void G4GMocrenIO::setModalityImageUnit(std::string & _unit) {
3442 kModalityUnit = _unit; 3437 kModalityUnit = _unit;
3443 } 3438 }
3444 // 3439 //
3445 short G4GMocrenIO::convertDensityToHU(float & 3440 short G4GMocrenIO::convertDensityToHU(float & _dens) {
3446 short rval = -1024; // default: air 3441 short rval = -1024; // default: air
3447 int nmap = (int)kModalityImageDensityMap.si 3442 int nmap = (int)kModalityImageDensityMap.size();
3448 if(nmap != 0) { 3443 if(nmap != 0) {
3449 short minmax[2]; 3444 short minmax[2];
3450 kModality.getMinMax(minmax); 3445 kModality.getMinMax(minmax);
3451 rval = minmax[1]; 3446 rval = minmax[1];
3452 for(int i = 0; i < nmap; i++) { 3447 for(int i = 0; i < nmap; i++) {
3453 //G4cout << kModalityImageDensityMap[i] 3448 //G4cout << kModalityImageDensityMap[i] << G4endl;
3454 if(_dens <= kModalityImageDensityMap[i] 3449 if(_dens <= kModalityImageDensityMap[i]) {
3455 rval = i + minmax[0]; 3450 rval = i + minmax[0];
3456 break; 3451 break;
3457 } 3452 }
3458 } 3453 }
3459 } 3454 }
3460 return rval; 3455 return rval;
3461 } 3456 }
3462 3457
3463 3458
3464 //----- Dose distribution -----// 3459 //----- Dose distribution -----//
3465 // 3460 //
3466 void G4GMocrenIO::newDoseDist() { 3461 void G4GMocrenIO::newDoseDist() {
3467 GMocrenDataPrimitive<double> doseData; 3462 GMocrenDataPrimitive<double> doseData;
3468 kDose.push_back(doseData); 3463 kDose.push_back(doseData);
3469 } 3464 }
3470 int G4GMocrenIO::getNumDoseDist() { 3465 int G4GMocrenIO::getNumDoseDist() {
3471 return (int)kDose.size(); 3466 return (int)kDose.size();
3472 } 3467 }
3473 3468
3474 // get & set the dose distribution unit 3469 // get & set the dose distribution unit
3475 std::string G4GMocrenIO::getDoseDistUnit(int 3470 std::string G4GMocrenIO::getDoseDistUnit(int _num) {
3476 // to avoid a warning in the compile proces 3471 // to avoid a warning in the compile process
3477 if(kDoseUnit.size() > static_cast<size_t>(_ << 3472 int dummynum;
>> 3473 dummynum = _num;
3478 3474
3479 return kDoseUnit; 3475 return kDoseUnit;
3480 } 3476 }
3481 void G4GMocrenIO::setDoseDistUnit(std::string 3477 void G4GMocrenIO::setDoseDistUnit(std::string & _unit, int _num) {
3482 // to avoid a warning in the compile proces 3478 // to avoid a warning in the compile process
3483 if(_unit.size() > static_cast<size_t>(_num) << 3479 int dummynum;
>> 3480 dummynum = _num;
3484 3481
3485 //char unit[13]; 3482 //char unit[13];
3486 //std::strncpy(unit, _unit.c_str(), 12); 3483 //std::strncpy(unit, _unit.c_str(), 12);
3487 //doseUnit = unit; 3484 //doseUnit = unit;
3488 kDoseUnit = _unit; 3485 kDoseUnit = _unit;
3489 } 3486 }
3490 // 3487 //
3491 void G4GMocrenIO::getDoseDistSize(int _size[3 3488 void G4GMocrenIO::getDoseDistSize(int _size[3], int _num) {
3492 if(isDoseEmpty()) 3489 if(isDoseEmpty())
3493 for(int i = 0; i < 3; i++) _size[i] = 0; 3490 for(int i = 0; i < 3; i++) _size[i] = 0;
3494 else 3491 else
3495 kDose[_num].getSize(_size); 3492 kDose[_num].getSize(_size);
3496 } 3493 }
3497 void G4GMocrenIO::setDoseDistSize(int _size[3 3494 void G4GMocrenIO::setDoseDistSize(int _size[3], int _num) {
3498 3495
3499 kDose[_num].setSize(_size); 3496 kDose[_num].setSize(_size);
3500 3497
3501 //resetDose(); 3498 //resetDose();
3502 } 3499 }
3503 3500
3504 void G4GMocrenIO::setDoseDistMinMax(short _mi 3501 void G4GMocrenIO::setDoseDistMinMax(short _minmax[2], int _num) {
3505 3502
3506 double minmax[2]; 3503 double minmax[2];
3507 double scale = kDose[_num].getScale(); 3504 double scale = kDose[_num].getScale();
3508 for(int i = 0; i < 2; i++) minmax[i] = (dou 3505 for(int i = 0; i < 2; i++) minmax[i] = (double)_minmax[i]*scale;
3509 kDose[_num].setMinMax(minmax); 3506 kDose[_num].setMinMax(minmax);
3510 } 3507 }
3511 void G4GMocrenIO::getDoseDistMinMax(short _mi 3508 void G4GMocrenIO::getDoseDistMinMax(short _minmax[2], int _num) {
3512 3509
3513 if(isDoseEmpty()) 3510 if(isDoseEmpty())
3514 for(int i = 0; i < 2; i++) _minmax[i] = 0 3511 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3515 else { 3512 else {
3516 double minmax[2]; 3513 double minmax[2];
3517 kDose[_num].getMinMax(minmax); 3514 kDose[_num].getMinMax(minmax);
3518 double scale = kDose[_num].getScale(); 3515 double scale = kDose[_num].getScale();
3519 for(int i = 0; i < 2; i++) _minmax[i] = ( 3516 for(int i = 0; i < 2; i++) _minmax[i] = (short)(minmax[i]/scale+0.5);
3520 } 3517 }
3521 } 3518 }
3522 void G4GMocrenIO::setDoseDistMinMax(double _m 3519 void G4GMocrenIO::setDoseDistMinMax(double _minmax[2], int _num) {
3523 3520
3524 kDose[_num].setMinMax(_minmax); 3521 kDose[_num].setMinMax(_minmax);
3525 } 3522 }
3526 void G4GMocrenIO::getDoseDistMinMax(double _m 3523 void G4GMocrenIO::getDoseDistMinMax(double _minmax[2], int _num) {
3527 3524
3528 if(isDoseEmpty()) 3525 if(isDoseEmpty())
3529 for(int i = 0; i < 2; i++) _minmax[i] = 0 3526 for(int i = 0; i < 2; i++) _minmax[i] = 0.;
3530 else 3527 else
3531 kDose[_num].getMinMax(_minmax); 3528 kDose[_num].getMinMax(_minmax);
3532 } 3529 }
3533 3530
3534 // get & set the dose distribution image scal 3531 // get & set the dose distribution image scale
3535 void G4GMocrenIO::setDoseDistScale(double & _ 3532 void G4GMocrenIO::setDoseDistScale(double & _scale, int _num) {
3536 3533
3537 kDose[_num].setScale(_scale); 3534 kDose[_num].setScale(_scale);
3538 } 3535 }
3539 double G4GMocrenIO::getDoseDistScale(int _num 3536 double G4GMocrenIO::getDoseDistScale(int _num) {
3540 3537
3541 if(isDoseEmpty()) 3538 if(isDoseEmpty())
3542 return 0.; 3539 return 0.;
3543 else 3540 else
3544 return kDose[_num].getScale(); 3541 return kDose[_num].getScale();
3545 } 3542 }
3546 3543
3547 /* 3544 /*
3548 void G4GMocrenIO::initializeShortDoseDist() 3545 void G4GMocrenIO::initializeShortDoseDist() {
3549 ; 3546 ;
3550 } 3547 }
3551 void G4GMocrenIO::finalizeShortDoseDist() { 3548 void G4GMocrenIO::finalizeShortDoseDist() {
3552 ; 3549 ;
3553 } 3550 }
3554 */ 3551 */
3555 // set the dose distribution image 3552 // set the dose distribution image
3556 void G4GMocrenIO::setShortDoseDist(short * _i 3553 void G4GMocrenIO::setShortDoseDist(short * _image, int _num) {
3557 3554
3558 int size[3]; 3555 int size[3];
3559 kDose[_num].getSize(size); 3556 kDose[_num].getSize(size);
3560 int dsize = size[0]*size[1]; 3557 int dsize = size[0]*size[1];
3561 double * ddata = new double[dsize]; 3558 double * ddata = new double[dsize];
3562 double scale = kDose[_num].getScale(); 3559 double scale = kDose[_num].getScale();
3563 double minmax[2]; 3560 double minmax[2];
3564 kDose[_num].getMinMax(minmax); 3561 kDose[_num].getMinMax(minmax);
3565 for(int xy = 0; xy < dsize; xy++) { 3562 for(int xy = 0; xy < dsize; xy++) {
3566 ddata[xy] = _image[xy]*scale; 3563 ddata[xy] = _image[xy]*scale;
3567 if(ddata[xy] < minmax[0]) minmax[0] = dda 3564 if(ddata[xy] < minmax[0]) minmax[0] = ddata[xy];
3568 if(ddata[xy] > minmax[1]) minmax[1] = dda 3565 if(ddata[xy] > minmax[1]) minmax[1] = ddata[xy];
3569 } 3566 }
3570 kDose[_num].addImage(ddata); 3567 kDose[_num].addImage(ddata);
3571 3568
3572 // set min./max. 3569 // set min./max.
3573 kDose[_num].setMinMax(minmax); 3570 kDose[_num].setMinMax(minmax);
3574 } 3571 }
3575 void G4GMocrenIO::getShortDoseDist(short * _d 3572 void G4GMocrenIO::getShortDoseDist(short * _data, int _z, int _num) {
3576 3573
3577 if(_data == NULL) { 3574 if(_data == NULL) {
3578 if (G4VisManager::GetVerbosity() >= G4Vis 3575 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3579 G4cout << "In G4GMocrenIO::getShortDose 3576 G4cout << "In G4GMocrenIO::getShortDoseDist(), "
3580 << "first argument is NULL pointer. " 3577 << "first argument is NULL pointer. "
3581 << "The argument must be allocated array. 3578 << "The argument must be allocated array."
3582 << G4endl; 3579 << G4endl;
3583 G4Exception("G4GMocrenIO::getShortDoseDis << 3580 std::exit(-1);
3584 "gMocren2002", FatalException <<
3585 "Error."); <<
3586 return; <<
3587 } 3581 }
3588 3582
3589 int size[3]; 3583 int size[3];
3590 kDose[_num].getSize(size); 3584 kDose[_num].getSize(size);
3591 //short * shdata = new short[size[0]*size[1 3585 //short * shdata = new short[size[0]*size[1]];
3592 double * ddata = kDose[_num].getImage(_z); 3586 double * ddata = kDose[_num].getImage(_z);
3593 double scale = kDose[_num].getScale(); 3587 double scale = kDose[_num].getScale();
3594 for(int xy = 0; xy < size[0]*size[1]; xy++) 3588 for(int xy = 0; xy < size[0]*size[1]; xy++) {
3595 _data[xy] = (short)(ddata[xy]/scale+0.5); 3589 _data[xy] = (short)(ddata[xy]/scale+0.5); //there is never negative value
3596 } 3590 }
3597 } 3591 }
3598 void G4GMocrenIO::getShortDoseDistMinMax(shor 3592 void G4GMocrenIO::getShortDoseDistMinMax(short _minmax[2], int _num) {
3599 double scale = kDose[_num].getScale(); 3593 double scale = kDose[_num].getScale();
3600 double minmax[2]; 3594 double minmax[2];
3601 kDose[_num].getMinMax(minmax); 3595 kDose[_num].getMinMax(minmax);
3602 for(int i = 0; i < 2; i++) 3596 for(int i = 0; i < 2; i++)
3603 _minmax[i] = (short)(minmax[i]/scale+0.5) 3597 _minmax[i] = (short)(minmax[i]/scale+0.5);
3604 } 3598 }
3605 // 3599 //
3606 void G4GMocrenIO::setDoseDist(double * _image 3600 void G4GMocrenIO::setDoseDist(double * _image, int _num) {
3607 3601
3608 kDose[_num].addImage(_image); 3602 kDose[_num].addImage(_image);
3609 } 3603 }
3610 double * G4GMocrenIO::getDoseDist(int _z, int 3604 double * G4GMocrenIO::getDoseDist(int _z, int _num) {
3611 3605
3612 double * image; 3606 double * image;
3613 if(isDoseEmpty()) { 3607 if(isDoseEmpty()) {
3614 image = 0; 3608 image = 0;
3615 } else { 3609 } else {
3616 image = kDose[_num].getImage(_z); 3610 image = kDose[_num].getImage(_z);
3617 } 3611 }
3618 return image; 3612 return image;
3619 } 3613 }
3620 /* 3614 /*
3621 void G4GMocrenIO::getDoseDist(double * & _i 3615 void G4GMocrenIO::getDoseDist(double * & _image, int _z, int _num) {
3622 3616
3623 G4cout << " <" << (void*)_image << "> "; 3617 G4cout << " <" << (void*)_image << "> ";
3624 if(isDoseEmpty()) { 3618 if(isDoseEmpty()) {
3625 _image = 0; 3619 _image = 0;
3626 } else { 3620 } else {
3627 _image = kDose[_num].getImage(_z); 3621 _image = kDose[_num].getImage(_z);
3628 G4cout << " <" << (void*)_image << "> "; 3622 G4cout << " <" << (void*)_image << "> ";
3629 G4cout << _image[100] << " "; 3623 G4cout << _image[100] << " ";
3630 } 3624 }
3631 } 3625 }
3632 */ 3626 */
3633 bool G4GMocrenIO::addDoseDist(std::vector<dou 3627 bool G4GMocrenIO::addDoseDist(std::vector<double *> & _image, int _num) {
3634 3628
3635 int size[3]; 3629 int size[3];
3636 getDoseDistSize(size, _num); 3630 getDoseDistSize(size, _num);
3637 std::vector<double *> dosedist = kDose[_num 3631 std::vector<double *> dosedist = kDose[_num].getImage();
3638 3632
3639 int nimg = size[0]*size[1]; 3633 int nimg = size[0]*size[1];
3640 for(int z = 0; z < size[2]; z++) { 3634 for(int z = 0; z < size[2]; z++) {
3641 for(int xy = 0; xy < nimg; xy++) { 3635 for(int xy = 0; xy < nimg; xy++) {
3642 dosedist[z][xy] += _image[z][xy]; 3636 dosedist[z][xy] += _image[z][xy];
3643 } 3637 }
3644 } 3638 }
3645 3639
3646 return true; 3640 return true;
3647 } 3641 }
3648 //void setDoseDistDensityMap(float * _map) {d 3642 //void setDoseDistDensityMap(float * _map) {doseImageDensityMap = _map;};
3649 // set the dose distribution image displaceme 3643 // set the dose distribution image displacement
3650 void G4GMocrenIO::setDoseDistCenterPosition(f 3644 void G4GMocrenIO::setDoseDistCenterPosition(float _center[3], int _num) {
3651 3645
3652 kDose[_num].setCenterPosition(_center); 3646 kDose[_num].setCenterPosition(_center);
3653 } 3647 }
3654 void G4GMocrenIO::getDoseDistCenterPosition(f 3648 void G4GMocrenIO::getDoseDistCenterPosition(float _center[3], int _num) {
3655 3649
3656 if(isDoseEmpty()) 3650 if(isDoseEmpty())
3657 for(int i = 0; i < 3; i++) _center[i] = 0 3651 for(int i = 0; i < 3; i++) _center[i] = 0;
3658 else 3652 else
3659 kDose[_num].getCenterPosition(_center); 3653 kDose[_num].getCenterPosition(_center);
3660 } 3654 }
3661 // set & get name of dose distribution 3655 // set & get name of dose distribution
3662 void G4GMocrenIO::setDoseDistName(std::string 3656 void G4GMocrenIO::setDoseDistName(std::string _name, int _num) {
3663 3657
3664 kDose[_num].setName(_name); 3658 kDose[_num].setName(_name);
3665 } 3659 }
3666 std::string G4GMocrenIO::getDoseDistName(int 3660 std::string G4GMocrenIO::getDoseDistName(int _num) {
3667 3661
3668 std::string name; 3662 std::string name;
3669 if(isDoseEmpty()) 3663 if(isDoseEmpty())
3670 return name; 3664 return name;
3671 else 3665 else
3672 return kDose[_num].getName(); 3666 return kDose[_num].getName();
3673 } 3667 }
3674 // copy dose distributions 3668 // copy dose distributions
3675 void G4GMocrenIO::copyDoseDist(std::vector<cl 3669 void G4GMocrenIO::copyDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3676 std::vector<class GMocrenDataPrimitive<doub 3670 std::vector<class GMocrenDataPrimitive<double> >::iterator itr;
3677 for(itr = kDose.begin(); itr != kDose.end() 3671 for(itr = kDose.begin(); itr != kDose.end(); itr++) {
3678 _dose.push_back(*itr); 3672 _dose.push_back(*itr);
3679 } 3673 }
3680 } 3674 }
3681 // merge two dose distributions 3675 // merge two dose distributions
3682 bool G4GMocrenIO::mergeDoseDist(std::vector<c 3676 bool G4GMocrenIO::mergeDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3683 if(kDose.size() != _dose.size()) { 3677 if(kDose.size() != _dose.size()) {
3684 if (G4VisManager::GetVerbosity() >= G4Vis 3678 if (G4VisManager::GetVerbosity() >= G4VisManager::errors) {
3685 G4cout << "G4GMocrenIO::mergeDoseDist() 3679 G4cout << "G4GMocrenIO::mergeDoseDist() : Error" << G4endl;
3686 G4cout << " Unable to merge the dose 3680 G4cout << " Unable to merge the dose distributions,"<< G4endl;
3687 G4cout << " because of different size 3681 G4cout << " because of different size of dose maps."<< G4endl;
3688 } 3682 }
3689 return false; 3683 return false;
3690 } 3684 }
3691 3685
3692 int num = (int)kDose.size(); << 3686 int num = kDose.size();
3693 std::vector<class GMocrenDataPrimitive<doub 3687 std::vector<class GMocrenDataPrimitive<double> >::iterator itr1 = kDose.begin();
3694 std::vector<class GMocrenDataPrimitive<doub 3688 std::vector<class GMocrenDataPrimitive<double> >::iterator itr2 = _dose.begin();
3695 for(int i = 0; i < num; i++, itr1++, itr2++ 3689 for(int i = 0; i < num; i++, itr1++, itr2++) {
3696 if (G4VisManager::GetVerbosity() >= G4Vis 3690 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3697 if(kVerbose > 0) 3691 if(kVerbose > 0)
3698 G4cout << "merged dose distribution [" << i 3692 G4cout << "merged dose distribution [" << i << "]" << G4endl;
3699 *itr1 += *itr2; 3693 *itr1 += *itr2;
3700 } 3694 }
3701 3695
3702 return true; 3696 return true;
3703 } 3697 }
3704 // 3698 //
3705 void G4GMocrenIO::clearDoseDistAll() { 3699 void G4GMocrenIO::clearDoseDistAll() {
3706 3700
3707 if(!isDoseEmpty()) { 3701 if(!isDoseEmpty()) {
3708 for(int i = 0; i < getNumDoseDist(); i++) 3702 for(int i = 0; i < getNumDoseDist(); i++) {
3709 kDose[i].clear(); 3703 kDose[i].clear();
3710 } 3704 }
3711 kDose.clear(); 3705 kDose.clear();
3712 } 3706 }
3713 } 3707 }
3714 // 3708 //
3715 bool G4GMocrenIO::isDoseEmpty() { 3709 bool G4GMocrenIO::isDoseEmpty() {
3716 if(kDose.empty()) { 3710 if(kDose.empty()) {
3717 //if (G4VisManager::GetVerbosity() >= G4V 3711 //if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3718 // G4cout << "!!! dose distribution data 3712 // G4cout << "!!! dose distribution data is empty." << G4endl;
3719 return true; 3713 return true;
3720 } else { 3714 } else {
3721 return false; 3715 return false;
3722 } 3716 }
3723 } 3717 }
3724 3718
3725 // 3719 //
3726 void G4GMocrenIO::calcDoseDistScale() { 3720 void G4GMocrenIO::calcDoseDistScale() {
3727 3721
3728 double scale; 3722 double scale;
3729 double minmax[2]; 3723 double minmax[2];
3730 3724
3731 for(int i = 0; i < (int)kDose.size(); i++) 3725 for(int i = 0; i < (int)kDose.size(); i++) {
3732 kDose[i].getMinMax(minmax); 3726 kDose[i].getMinMax(minmax);
3733 scale = minmax[1]/DOSERANGE; 3727 scale = minmax[1]/DOSERANGE;
3734 kDose[i].setScale(scale); 3728 kDose[i].setScale(scale);
3735 } 3729 }
3736 } 3730 }
3737 3731
3738 3732
3739 //----- RoI -----// 3733 //----- RoI -----//
3740 3734
3741 // add one RoI data 3735 // add one RoI data
3742 void G4GMocrenIO::newROI() { 3736 void G4GMocrenIO::newROI() {
3743 GMocrenDataPrimitive<short> roiData; 3737 GMocrenDataPrimitive<short> roiData;
3744 kRoi.push_back(roiData); 3738 kRoi.push_back(roiData);
3745 } 3739 }
3746 int G4GMocrenIO::getNumROI() { 3740 int G4GMocrenIO::getNumROI() {
3747 return (int)kRoi.size(); 3741 return (int)kRoi.size();
3748 } 3742 }
3749 3743
3750 // set/get the ROI image scale 3744 // set/get the ROI image scale
3751 void G4GMocrenIO::setROIScale(double & _scale 3745 void G4GMocrenIO::setROIScale(double & _scale, int _num) {
3752 3746
3753 kRoi[_num].setScale(_scale); 3747 kRoi[_num].setScale(_scale);
3754 } 3748 }
3755 double G4GMocrenIO::getROIScale(int _num) { 3749 double G4GMocrenIO::getROIScale(int _num) {
3756 3750
3757 if(isROIEmpty()) 3751 if(isROIEmpty())
3758 return 0.; 3752 return 0.;
3759 else 3753 else
3760 return kRoi[_num].getScale(); 3754 return kRoi[_num].getScale();
3761 } 3755 }
3762 // set the ROI image 3756 // set the ROI image
3763 void G4GMocrenIO::setROI(short * _image, int 3757 void G4GMocrenIO::setROI(short * _image, int _num) {
3764 3758
3765 kRoi[_num].addImage(_image); 3759 kRoi[_num].addImage(_image);
3766 } 3760 }
3767 short * G4GMocrenIO::getROI(int _z, int _num) 3761 short * G4GMocrenIO::getROI(int _z, int _num) {
3768 3762
3769 if(isROIEmpty()) 3763 if(isROIEmpty())
3770 return 0; 3764 return 0;
3771 else 3765 else
3772 return kRoi[_num].getImage(_z); 3766 return kRoi[_num].getImage(_z);
3773 } 3767 }
3774 // set/get the ROI image size 3768 // set/get the ROI image size
3775 void G4GMocrenIO::setROISize(int _size[3], in 3769 void G4GMocrenIO::setROISize(int _size[3], int _num) {
3776 3770
3777 return kRoi[_num].setSize(_size); 3771 return kRoi[_num].setSize(_size);
3778 } 3772 }
3779 void G4GMocrenIO::getROISize(int _size[3], in 3773 void G4GMocrenIO::getROISize(int _size[3], int _num) {
3780 3774
3781 if(isROIEmpty()) 3775 if(isROIEmpty())
3782 for(int i = 0; i < 3; i++) _size[i] = 0; 3776 for(int i = 0; i < 3; i++) _size[i] = 0;
3783 else 3777 else
3784 return kRoi[_num].getSize(_size); 3778 return kRoi[_num].getSize(_size);
3785 } 3779 }
3786 // set/get the ROI image min. and max. 3780 // set/get the ROI image min. and max.
3787 void G4GMocrenIO::setROIMinMax(short _minmax[ 3781 void G4GMocrenIO::setROIMinMax(short _minmax[2], int _num) {
3788 3782
3789 kRoi[_num].setMinMax(_minmax); 3783 kRoi[_num].setMinMax(_minmax);
3790 } 3784 }
3791 void G4GMocrenIO::getROIMinMax(short _minmax[ 3785 void G4GMocrenIO::getROIMinMax(short _minmax[2], int _num) {
3792 3786
3793 if(isROIEmpty()) 3787 if(isROIEmpty())
3794 for(int i = 0; i < 2; i++) _minmax[i] = 0 3788 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3795 else 3789 else
3796 kRoi[_num].getMinMax(_minmax); 3790 kRoi[_num].getMinMax(_minmax);
3797 } 3791 }
3798 // set/get the ROI image displacement 3792 // set/get the ROI image displacement
3799 void G4GMocrenIO::setROICenterPosition(float 3793 void G4GMocrenIO::setROICenterPosition(float _center[3], int _num) {
3800 3794
3801 kRoi[_num].setCenterPosition(_center); 3795 kRoi[_num].setCenterPosition(_center);
3802 } 3796 }
3803 void G4GMocrenIO::getROICenterPosition(float 3797 void G4GMocrenIO::getROICenterPosition(float _center[3], int _num) {
3804 3798
3805 if(isROIEmpty()) 3799 if(isROIEmpty())
3806 for(int i = 0; i < 3; i++) _center[i] = 0 3800 for(int i = 0; i < 3; i++) _center[i] = 0;
3807 else 3801 else
3808 kRoi[_num].getCenterPosition(_center); 3802 kRoi[_num].getCenterPosition(_center);
3809 } 3803 }
3810 // 3804 //
3811 void G4GMocrenIO::clearROIAll() { 3805 void G4GMocrenIO::clearROIAll() {
3812 3806
3813 if(!isROIEmpty()) { 3807 if(!isROIEmpty()) {
3814 for(int i = 0; i < getNumROI(); i++) { 3808 for(int i = 0; i < getNumROI(); i++) {
3815 kRoi[i].clear(); 3809 kRoi[i].clear();
3816 } 3810 }
3817 kRoi.clear(); 3811 kRoi.clear();
3818 } 3812 }
3819 } 3813 }
3820 // 3814 //
3821 bool G4GMocrenIO::isROIEmpty() { 3815 bool G4GMocrenIO::isROIEmpty() {
3822 if(kRoi.empty()) { 3816 if(kRoi.empty()) {
3823 //if (G4VisManager::GetVerbosity() >= G4V 3817 //if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3824 // G4cout << "!!! ROI data is empty." << 3818 // G4cout << "!!! ROI data is empty." << G4endl;
3825 return true; 3819 return true;
3826 } else { 3820 } else {
3827 return false; 3821 return false;
3828 } 3822 }
3829 } 3823 }
3830 3824
3831 3825
3832 3826
3833 //----- Track information -----// 3827 //----- Track information -----//
3834 3828
3835 int G4GMocrenIO::getNumTracks() { 3829 int G4GMocrenIO::getNumTracks() {
3836 return (int)kSteps.size(); 3830 return (int)kSteps.size();
3837 } 3831 }
3838 int G4GMocrenIO::getNumTracks4() { 3832 int G4GMocrenIO::getNumTracks4() {
3839 return (int)kTracks.size(); 3833 return (int)kTracks.size();
3840 } 3834 }
3841 void G4GMocrenIO::addTrack(float * _tracks) { 3835 void G4GMocrenIO::addTrack(float * _tracks) {
3842 kSteps.push_back(_tracks); 3836 kSteps.push_back(_tracks);
3843 } 3837 }
3844 void G4GMocrenIO::setTracks(std::vector<float 3838 void G4GMocrenIO::setTracks(std::vector<float *> & _tracks) {
3845 kSteps = _tracks; 3839 kSteps = _tracks;
3846 } 3840 }
3847 std::vector<float *> & G4GMocrenIO::getTracks 3841 std::vector<float *> & G4GMocrenIO::getTracks() {
3848 return kSteps; 3842 return kSteps;
3849 } 3843 }
3850 void G4GMocrenIO::addTrackColor(unsigned char 3844 void G4GMocrenIO::addTrackColor(unsigned char * _colors) {
3851 kStepColors.push_back(_colors); 3845 kStepColors.push_back(_colors);
3852 } 3846 }
3853 void G4GMocrenIO::setTrackColors(std::vector< 3847 void G4GMocrenIO::setTrackColors(std::vector<unsigned char *> & _trackColors) {
3854 kStepColors = _trackColors; 3848 kStepColors = _trackColors;
3855 } 3849 }
3856 std::vector<unsigned char *> & G4GMocrenIO::g 3850 std::vector<unsigned char *> & G4GMocrenIO::getTrackColors() {
3857 return kStepColors; 3851 return kStepColors;
3858 } 3852 }
3859 void G4GMocrenIO::copyTracks(std::vector<floa 3853 void G4GMocrenIO::copyTracks(std::vector<float *> & _tracks,
3860 std::vector<unsigned char *> & _ 3854 std::vector<unsigned char *> & _colors) {
3861 std::vector<float *>::iterator titr; 3855 std::vector<float *>::iterator titr;
3862 for(titr = kSteps.begin(); titr != kSteps.e 3856 for(titr = kSteps.begin(); titr != kSteps.end(); titr++) {
3863 float * pts = new float[6]; 3857 float * pts = new float[6];
3864 for(int i = 0; i < 6; i++) { 3858 for(int i = 0; i < 6; i++) {
3865 pts[i] = (*titr)[i]; 3859 pts[i] = (*titr)[i];
3866 } 3860 }
3867 _tracks.push_back(pts); 3861 _tracks.push_back(pts);
3868 } 3862 }
3869 3863
3870 std::vector<unsigned char *>::iterator citr 3864 std::vector<unsigned char *>::iterator citr;
3871 for(citr = kStepColors.begin(); citr != kSt 3865 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++) {
3872 unsigned char * pts = new unsigned char[3 3866 unsigned char * pts = new unsigned char[3];
3873 for(int i = 0; i < 3; i++) { 3867 for(int i = 0; i < 3; i++) {
3874 pts[i] = (*citr)[i]; 3868 pts[i] = (*citr)[i];
3875 } 3869 }
3876 _colors.push_back(pts); 3870 _colors.push_back(pts);
3877 } 3871 }
3878 } 3872 }
3879 void G4GMocrenIO::mergeTracks(std::vector<flo 3873 void G4GMocrenIO::mergeTracks(std::vector<float *> & _tracks,
3880 std::vector<unsigned char *> & _color 3874 std::vector<unsigned char *> & _colors) {
3881 std::vector<float *>::iterator titr; 3875 std::vector<float *>::iterator titr;
3882 for(titr = _tracks.begin(); titr != _tracks 3876 for(titr = _tracks.begin(); titr != _tracks.end(); titr++) {
3883 addTrack(*titr); 3877 addTrack(*titr);
3884 } 3878 }
3885 3879
3886 std::vector<unsigned char *>::iterator citr 3880 std::vector<unsigned char *>::iterator citr;
3887 for(citr = _colors.begin(); citr != _colors 3881 for(citr = _colors.begin(); citr != _colors.end(); citr++) {
3888 addTrackColor(*citr); 3882 addTrackColor(*citr);
3889 } 3883 }
3890 } 3884 }
3891 void G4GMocrenIO::addTrack(std::vector<float 3885 void G4GMocrenIO::addTrack(std::vector<float *> & _steps, unsigned char _color[3]) {
3892 3886
3893 std::vector<float *>::iterator itr = _steps 3887 std::vector<float *>::iterator itr = _steps.begin();
3894 std::vector<struct GMocrenTrack::Step> st 3888 std::vector<struct GMocrenTrack::Step> steps;
3895 for(; itr != _steps.end(); itr++) { 3889 for(; itr != _steps.end(); itr++) {
3896 struct GMocrenTrack::Step step; 3890 struct GMocrenTrack::Step step;
3897 for(int i = 0; i < 3; i++) { 3891 for(int i = 0; i < 3; i++) {
3898 step.startPoint[i] = (*itr)[i]; 3892 step.startPoint[i] = (*itr)[i];
3899 step.endPoint[i] = (*itr)[i+3]; 3893 step.endPoint[i] = (*itr)[i+3];
3900 } 3894 }
3901 steps.push_back(step); 3895 steps.push_back(step);
3902 } 3896 }
3903 GMocrenTrack track; 3897 GMocrenTrack track;
3904 track.setTrack(steps); 3898 track.setTrack(steps);
3905 track.setColor(_color); 3899 track.setColor(_color);
3906 kTracks.push_back(track); 3900 kTracks.push_back(track);
3907 3901
3908 } 3902 }
3909 void G4GMocrenIO::getTrack(int _num, std::vec 3903 void G4GMocrenIO::getTrack(int _num, std::vector<float *> & _steps,
3910 std::vector<unsigned char *> & _co 3904 std::vector<unsigned char *> & _color) {
3911 3905
3912 if(_num > (int)kTracks.size()) { 3906 if(_num > (int)kTracks.size()) {
3913 if (G4VisManager::GetVerbosity() >= G4Vis 3907 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3914 G4cout << "ERROR in getTrack() : " << G 3908 G4cout << "ERROR in getTrack() : " << G4endl;
3915 G4Exception("G4GMocrenIO::getTrack()", << 3909 std::exit(-1);
3916 "gMocren2003", FatalException <<
3917 "Error."); <<
3918 } 3910 }
3919 unsigned char * color = new unsigned char[3 3911 unsigned char * color = new unsigned char[3];
3920 kTracks[_num].getColor(color); 3912 kTracks[_num].getColor(color);
3921 _color.push_back(color); 3913 _color.push_back(color);
3922 3914
3923 // steps 3915 // steps
3924 int nsteps = kTracks[_num].getNumberOfSteps 3916 int nsteps = kTracks[_num].getNumberOfSteps();
3925 for(int isteps = 0; isteps < nsteps; isteps << 3917 for(int ns = 0; ns < nsteps; ns++) {
3926 float * stepPoints = new float[6]; 3918 float * stepPoints = new float[6];
3927 kTracks[_num].getStep(stepPoints[0], step 3919 kTracks[_num].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
3928 stepPoints[3], stepPoints[4], stepPoi 3920 stepPoints[3], stepPoints[4], stepPoints[5],
3929 isteps); << 3921 ns);
3930 _steps.push_back(stepPoints); 3922 _steps.push_back(stepPoints);
3931 } 3923 }
3932 } 3924 }
3933 3925
3934 void G4GMocrenIO::translateTracks(std::vector 3926 void G4GMocrenIO::translateTracks(std::vector<float> & _translate) {
3935 std::vector<class GMocrenTrack>::iterator i 3927 std::vector<class GMocrenTrack>::iterator itr = kTracks.begin();
3936 for(; itr != kTracks.end(); itr++) { 3928 for(; itr != kTracks.end(); itr++) {
3937 itr->translate(_translate); 3929 itr->translate(_translate);
3938 } 3930 }
3939 } 3931 }
3940 3932
3941 3933
3942 3934
3943 3935
3944 //----- Detector information -----// 3936 //----- Detector information -----//
3945 int G4GMocrenIO::getNumberOfDetectors() { 3937 int G4GMocrenIO::getNumberOfDetectors() {
3946 return (int)kDetectors.size(); 3938 return (int)kDetectors.size();
3947 } 3939 }
3948 void G4GMocrenIO::addDetector(std::string & _ 3940 void G4GMocrenIO::addDetector(std::string & _name,
3949 std::vector<float *> & _det, 3941 std::vector<float *> & _det,
3950 unsigned char _color[3]) { 3942 unsigned char _color[3]) {
3951 3943
3952 std::vector<float *>::iterator itr = _det 3944 std::vector<float *>::iterator itr = _det.begin();
3953 std::vector<struct GMocrenDetector::Edge> 3945 std::vector<struct GMocrenDetector::Edge> edges;
3954 for(; itr != _det.end(); itr++) { 3946 for(; itr != _det.end(); itr++) {
3955 struct GMocrenDetector::Edge edge; 3947 struct GMocrenDetector::Edge edge;
3956 for(int i = 0; i < 3; i++) { 3948 for(int i = 0; i < 3; i++) {
3957 edge.startPoint[i] = (*itr)[i]; 3949 edge.startPoint[i] = (*itr)[i];
3958 edge.endPoint[i] = (*itr)[i+3]; 3950 edge.endPoint[i] = (*itr)[i+3];
3959 } 3951 }
3960 edges.push_back(edge); 3952 edges.push_back(edge);
3961 } 3953 }
3962 GMocrenDetector detector; 3954 GMocrenDetector detector;
3963 detector.setDetector(edges); 3955 detector.setDetector(edges);
3964 detector.setColor(_color); 3956 detector.setColor(_color);
3965 detector.setName(_name); 3957 detector.setName(_name);
3966 kDetectors.push_back(detector); 3958 kDetectors.push_back(detector);
3967 3959
3968 } 3960 }
3969 3961
3970 void G4GMocrenIO::getDetector(int _num, std:: 3962 void G4GMocrenIO::getDetector(int _num, std::vector<float *> & _edges,
3971 std::vector<unsigned char *> & _color 3963 std::vector<unsigned char *> & _color,
3972 std::string & _detName) { 3964 std::string & _detName) {
3973 3965
3974 if(_num > (int)kDetectors.size()) { 3966 if(_num > (int)kDetectors.size()) {
3975 if (G4VisManager::GetVerbosity() >= G4Vis 3967 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3976 G4cout << "ERROR in getDetector() : " < 3968 G4cout << "ERROR in getDetector() : " << G4endl;
3977 << 3969 std::exit(-1);
3978 G4Exception("G4GMocrenIO::getDetector()", <<
3979 "gMocren2004", FatalException <<
3980 "Error."); <<
3981 } 3970 }
3982 3971
3983 _detName = kDetectors[_num].getName(); 3972 _detName = kDetectors[_num].getName();
3984 3973
3985 unsigned char * color = new unsigned char[3 3974 unsigned char * color = new unsigned char[3];
3986 kDetectors[_num].getColor(color); 3975 kDetectors[_num].getColor(color);
3987 _color.push_back(color); 3976 _color.push_back(color);
3988 3977
3989 // edges 3978 // edges
3990 int nedges = kDetectors[_num].getNumberOfEd 3979 int nedges = kDetectors[_num].getNumberOfEdges();
3991 for(int ne = 0; ne < nedges; ne++) { 3980 for(int ne = 0; ne < nedges; ne++) {
3992 float * edgePoints = new float[6]; 3981 float * edgePoints = new float[6];
3993 kDetectors[_num].getEdge(edgePoints[0], e 3982 kDetectors[_num].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
3994 edgePoints[3], edgePoints[4], edge 3983 edgePoints[3], edgePoints[4], edgePoints[5],
3995 ne); 3984 ne);
3996 _edges.push_back(edgePoints); 3985 _edges.push_back(edgePoints);
3997 } 3986 }
3998 } 3987 }
3999 3988
4000 void G4GMocrenIO::translateDetector(std::vect 3989 void G4GMocrenIO::translateDetector(std::vector<float> & _translate) {
4001 std::vector<class GMocrenDetector>::iterato 3990 std::vector<class GMocrenDetector>::iterator itr = kDetectors.begin();
4002 for(; itr != kDetectors.end(); itr++) { 3991 for(; itr != kDetectors.end(); itr++) {
4003 itr->translate(_translate); 3992 itr->translate(_translate);
4004 } 3993 }
4005 } 3994 }
4006 3995
4007 // endian conversion 3996 // endian conversion
4008 template <typename T> 3997 template <typename T>
4009 void G4GMocrenIO::convertEndian(char * _val, 3998 void G4GMocrenIO::convertEndian(char * _val, T & _rval) {
4010 3999
4011 if((kLittleEndianOutput && !kLittleEndianIn 4000 if((kLittleEndianOutput && !kLittleEndianInput) || // big endian
4012 (!kLittleEndianOutput && kLittleEndianIn 4001 (!kLittleEndianOutput && kLittleEndianInput)) { // little endian
4013 4002
4014 const int SIZE = sizeof(_rval); 4003 const int SIZE = sizeof(_rval);
4015 char ctemp; 4004 char ctemp;
4016 for(int i = 0; i < SIZE/2; i++) { 4005 for(int i = 0; i < SIZE/2; i++) {
4017 ctemp = _val[i]; 4006 ctemp = _val[i];
4018 _val[i] = _val[SIZE - 1 - i]; 4007 _val[i] = _val[SIZE - 1 - i];
4019 _val[SIZE - 1 - i] = ctemp; 4008 _val[SIZE - 1 - i] = ctemp;
4020 } 4009 }
4021 } 4010 }
4022 _rval = *(T *)_val; 4011 _rval = *(T *)_val;
4023 } 4012 }
4024 4013
4025 // inversion of byte order 4014 // inversion of byte order
4026 template <typename T> 4015 template <typename T>
4027 void G4GMocrenIO::invertByteOrder(char * _val 4016 void G4GMocrenIO::invertByteOrder(char * _val, T & _rval) {
4028 4017
4029 const int SIZE = sizeof(_rval); 4018 const int SIZE = sizeof(_rval);
4030 //char * cval = new char[SIZE]; 4019 //char * cval = new char[SIZE];
4031 union { 4020 union {
4032 char cu[16]; 4021 char cu[16];
4033 T tu; 4022 T tu;
4034 } uni; 4023 } uni;
4035 for(int i = 0; i < SIZE; i++) { 4024 for(int i = 0; i < SIZE; i++) {
4036 uni.cu[i] = _val[SIZE-1-i]; 4025 uni.cu[i] = _val[SIZE-1-i];
4037 //cval[i] = _val[SIZE-i-1]; 4026 //cval[i] = _val[SIZE-i-1];
4038 } 4027 }
4039 //_rval = *(T *)cval; 4028 //_rval = *(T *)cval;
4040 _rval = uni.tu; 4029 _rval = uni.tu;
4041 //delete [] cval; 4030 //delete [] cval;
4042 } 4031 }
4043 4032
4044 //----- kVerbose information -----// 4033 //----- kVerbose information -----//
4045 void G4GMocrenIO::setVerboseLevel(int _level) 4034 void G4GMocrenIO::setVerboseLevel(int _level) {
4046 kVerbose = _level; 4035 kVerbose = _level;
4047 } 4036 }
4048 4037
4049 4038