| Geant4 Cross Reference |
1 // 1 //
2 // ******************************************* 2 // ********************************************************************
3 // * License and Disclaimer 3 // * License and Disclaimer *
4 // * 4 // * *
5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided 6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License 7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/ 8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. 9 // * include a list of copyright holders. *
10 // * 10 // * *
11 // * Neither the authors of this software syst 11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing fin 12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warran 13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assum 14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file 15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. *
17 // * 17 // * *
18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publicati 22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. *
24 // ******************************************* 24 // ********************************************************************
25 // 25 //
26 // 26 //
27 // 27 //
28 // 28 //
29 // File I/O manager class for writing or readi 29 // File I/O manager class for writing or reading calcuated dose
30 // distribution and some event information 30 // distribution and some event information
31 // 31 //
32 // Created: Mar. 31, 2009 Akinori Kimura : r 32 // Created: Mar. 31, 2009 Akinori Kimura : release for the gMocrenFile driver
33 // 33 //
34 // Akinori Kimur 34 // Akinori Kimura
35 // gMocren home 35 // gMocren home page:
36 // http://geant4 36 // http://geant4.kek.jp/gMocren/
37 // 37 //
38 // 38 //
39 #include "G4GMocrenIO.hh" 39 #include "G4GMocrenIO.hh"
40 #include <iostream> 40 #include <iostream>
41 #include <ctime> 41 #include <ctime>
42 #include <sstream> 42 #include <sstream>
43 #include <iomanip> 43 #include <iomanip>
44 #include <cstdlib> 44 #include <cstdlib>
45 #include <cstring> 45 #include <cstring>
46 46
47 #include "globals.hh" 47 #include "globals.hh"
48 #include "G4VisManager.hh" 48 #include "G4VisManager.hh"
49 49
50 #if defined(_WIN32) 50 #if defined(_WIN32)
51 #define LITTLE_ENDIAN 1234 51 #define LITTLE_ENDIAN 1234
52 #define BYTE_ORDER LITTLE_ENDIAN 52 #define BYTE_ORDER LITTLE_ENDIAN
53 #endif 53 #endif
54 54
55 const int DOSERANGE = 25000; 55 const int DOSERANGE = 25000;
56 56
57 //----- GMocrenDataPrimitive class in the GMoc 57 //----- GMocrenDataPrimitive class in the GMocrenDataIO class-----//
58 template <typename T> 58 template <typename T>
59 GMocrenDataPrimitive<T>::GMocrenDataPrimitive 59 GMocrenDataPrimitive<T>::GMocrenDataPrimitive () {
60 clear(); 60 clear();
61 } 61 }
62 template <typename T> 62 template <typename T>
63 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive 63 GMocrenDataPrimitive<T>::~GMocrenDataPrimitive () {
64 /* 64 /*
65 std::vector<short *>::iterator itr = image 65 std::vector<short *>::iterator itr = image.begin();
66 for(; itr != image.end(); itr++) { 66 for(; itr != image.end(); itr++) {
67 delete [] *itr; 67 delete [] *itr;
68 } 68 }
69 */ 69 */
70 } 70 }
71 71
72 template <typename T> GMocrenDataPrimitive<T> 72 template <typename T> GMocrenDataPrimitive<T> &
73 GMocrenDataPrimitive<T>::operator = (const GMo 73 GMocrenDataPrimitive<T>::operator = (const GMocrenDataPrimitive<T> & _right) {
74 if (this == &_right) return *this; 74 if (this == &_right) return *this;
75 for(int i = 0; i < 3; i++) { 75 for(int i = 0; i < 3; i++) {
76 kSize[i] = _right.kSize[i]; 76 kSize[i] = _right.kSize[i];
77 kCenter[i] = _right.kCenter[i]; 77 kCenter[i] = _right.kCenter[i];
78 } 78 }
79 kScale = _right.kScale; 79 kScale = _right.kScale;
80 for(int i = 0; i < 2; i++) kMinmax[i] = _rig 80 for(int i = 0; i < 2; i++) kMinmax[i] = _right.kMinmax[i];
81 int num = kSize[0]*kSize[1]; 81 int num = kSize[0]*kSize[1];
82 kImage.clear(); 82 kImage.clear();
83 for(int z = 0; z < kSize[2]; z++) { 83 for(int z = 0; z < kSize[2]; z++) {
84 T * img = new T[num]; 84 T * img = new T[num];
85 for(int i = 0; i < num; i++) img[i] =_righ 85 for(int i = 0; i < num; i++) img[i] =_right.kImage[z][i];
86 kImage.push_back(img); 86 kImage.push_back(img);
87 } 87 }
88 return *this; 88 return *this;
89 } 89 }
90 90
91 template <typename T> GMocrenDataPrimitive<T> 91 template <typename T> GMocrenDataPrimitive<T> &
92 GMocrenDataPrimitive<T>::operator + (const GMo 92 GMocrenDataPrimitive<T>::operator + (const GMocrenDataPrimitive<T> & _right) {
93 93
94 GMocrenDataPrimitive<T> rprim; 94 GMocrenDataPrimitive<T> rprim;
95 bool stat = true; 95 bool stat = true;
96 for(int i = 0; i < 3; i++) { 96 for(int i = 0; i < 3; i++) {
97 if(kSize[i] != _right.kSize[i]) stat = fal 97 if(kSize[i] != _right.kSize[i]) stat = false;
98 if(kCenter[i] != _right.kCenter[i]) stat = 98 if(kCenter[i] != _right.kCenter[i]) stat = false;
99 } 99 }
100 if(!stat) { 100 if(!stat) {
101 if (G4VisManager::GetVerbosity() >= G4VisM 101 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
102 G4cout << "Warning: operator + " 102 G4cout << "Warning: operator + "
103 << " Cannot do the operator +" 103 << " Cannot do the operator +"
104 << G4endl; 104 << G4endl;
105 return *this; 105 return *this;
106 } 106 }
107 107
108 rprim.setSize(kSize); 108 rprim.setSize(kSize);
109 rprim.setCenterPosition(kCenter); 109 rprim.setCenterPosition(kCenter);
110 110
111 T mms[2] = {9e100,-9e100}; 111 T mms[2] = {9e100,-9e100};
112 //if(mms[0] > _right.minmax[0]) mms[0] = _ri 112 //if(mms[0] > _right.minmax[0]) mms[0] = _right.minmax[0];
113 //if(mms[1] < _right.minmax[1]) mms[1] = _ri 113 //if(mms[1] < _right.minmax[1]) mms[1] = _right.minmax[1];
114 114
115 int num = kSize[0]*kSize[1]; 115 int num = kSize[0]*kSize[1];
116 for(int z = 0; z < kSize[2]; z++) { 116 for(int z = 0; z < kSize[2]; z++) {
117 T * img = new T[num]; 117 T * img = new T[num];
118 for(int xy = 0; xy < num; xy++) { 118 for(int xy = 0; xy < num; xy++) {
119 img[xy] = kImage[z][xy] + _right.kImage[ 119 img[xy] = kImage[z][xy] + _right.kImage[z][xy];
120 if(mms[0] > img[xy]) mms[0] = img[xy]; 120 if(mms[0] > img[xy]) mms[0] = img[xy];
121 if(mms[1] < img[xy]) mms[1] = img[xy]; 121 if(mms[1] < img[xy]) mms[1] = img[xy];
122 } 122 }
123 rprim.addImage(img); 123 rprim.addImage(img);
124 } 124 }
125 rprim.setMinMax(mms); 125 rprim.setMinMax(mms);
126 126
127 T scl = mms[1]/DOSERANGE; 127 T scl = mms[1]/DOSERANGE;
128 rprim.setScale(scl); 128 rprim.setScale(scl);
129 129
130 return rprim; 130 return rprim;
131 } 131 }
132 132
133 template <typename T> GMocrenDataPrimitive<T> 133 template <typename T> GMocrenDataPrimitive<T> &
134 GMocrenDataPrimitive<T>::operator += (const GM 134 GMocrenDataPrimitive<T>::operator += (const GMocrenDataPrimitive<T> & _right) {
135 135
136 bool stat = true; 136 bool stat = true;
137 for(int i = 0; i < 3; i++) { 137 for(int i = 0; i < 3; i++) {
138 if(kSize[i] != _right.kSize[i]) stat = fal 138 if(kSize[i] != _right.kSize[i]) stat = false;
139 if(kCenter[i] != _right.kCenter[i]) stat = 139 if(kCenter[i] != _right.kCenter[i]) stat = false;
140 } 140 }
141 if(!stat) { 141 if(!stat) {
142 if (G4VisManager::GetVerbosity() >= G4VisM 142 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
143 G4cout << "Warning: operator += " << G4e 143 G4cout << "Warning: operator += " << G4endl
144 << " Cannot do the operator +=" 144 << " Cannot do the operator +="
145 << G4endl; 145 << G4endl;
146 return *this; 146 return *this;
147 } 147 }
148 148
149 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0 149 if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0] = _right.kMinmax[0];
150 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1 150 if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1] = _right.kMinmax[1];
151 151
152 int num = kSize[0]*kSize[1]; 152 int num = kSize[0]*kSize[1];
153 for(int z = 0; z < kSize[2]; z++) { 153 for(int z = 0; z < kSize[2]; z++) {
154 for(int xy = 0; xy < num; xy++) { 154 for(int xy = 0; xy < num; xy++) {
155 kImage[z][xy] += _right.kImage[z][xy]; 155 kImage[z][xy] += _right.kImage[z][xy];
156 if(kMinmax[0] > kImage[z][xy]) kMinmax[0 156 if(kMinmax[0] > kImage[z][xy]) kMinmax[0] = kImage[z][xy];
157 if(kMinmax[1] < kImage[z][xy]) kMinmax[1 157 if(kMinmax[1] < kImage[z][xy]) kMinmax[1] = kImage[z][xy];
158 } 158 }
159 } 159 }
160 160
161 kScale = kMinmax[1]/DOSERANGE; 161 kScale = kMinmax[1]/DOSERANGE;
162 162
163 return *this; 163 return *this;
164 } 164 }
165 165
166 template <typename T> 166 template <typename T>
167 void GMocrenDataPrimitive<T>::clear() { 167 void GMocrenDataPrimitive<T>::clear() {
168 for(int i = 0; i < 3; i++) { 168 for(int i = 0; i < 3; i++) {
169 kSize[i] = 0; 169 kSize[i] = 0;
170 kCenter[i] = 0.; 170 kCenter[i] = 0.;
171 } 171 }
172 kScale = 1.; 172 kScale = 1.;
173 kMinmax[0] = (T)32109; 173 kMinmax[0] = (T)32109;
174 kMinmax[1] = (T)-32109; 174 kMinmax[1] = (T)-32109;
175 175
176 clearImage(); 176 clearImage();
177 } 177 }
178 template <typename T> 178 template <typename T>
179 void GMocrenDataPrimitive<T>::clearImage() { 179 void GMocrenDataPrimitive<T>::clearImage() {
180 typename std::vector<T *>::iterator itr; 180 typename std::vector<T *>::iterator itr;
181 for(itr = kImage.begin(); itr != kImage.end( 181 for(itr = kImage.begin(); itr != kImage.end(); itr++) {
182 delete [] *itr; 182 delete [] *itr;
183 } 183 }
184 kImage.clear(); 184 kImage.clear();
185 } 185 }
186 template <typename T> 186 template <typename T>
187 void GMocrenDataPrimitive<T>::setSize(int _siz 187 void GMocrenDataPrimitive<T>::setSize(int _size[3]) {
188 for(int i = 0; i < 3; i++) kSize[i] = _size[ 188 for(int i = 0; i < 3; i++) kSize[i] = _size[i];
189 } 189 }
190 template <typename T> 190 template <typename T>
191 void GMocrenDataPrimitive<T>::getSize(int _siz 191 void GMocrenDataPrimitive<T>::getSize(int _size[3]) {
192 for(int i = 0; i < 3; i++) _size[i] = kSize[ 192 for(int i = 0; i < 3; i++) _size[i] = kSize[i];
193 } 193 }
194 template <typename T> 194 template <typename T>
195 void GMocrenDataPrimitive<T>::setScale(double 195 void GMocrenDataPrimitive<T>::setScale(double & _scale) {
196 kScale = _scale; 196 kScale = _scale;
197 } 197 }
198 template <typename T> 198 template <typename T>
199 double GMocrenDataPrimitive<T>::getScale() { 199 double GMocrenDataPrimitive<T>::getScale() {
200 return kScale; 200 return kScale;
201 } 201 }
202 template <typename T> 202 template <typename T>
203 void GMocrenDataPrimitive<T>::setMinMax(T _min 203 void GMocrenDataPrimitive<T>::setMinMax(T _minmax[2]) {
204 for(int i = 0; i < 2; i++) kMinmax[i] = _min 204 for(int i = 0; i < 2; i++) kMinmax[i] = _minmax[i];
205 } 205 }
206 template <typename T> 206 template <typename T>
207 void GMocrenDataPrimitive<T>::getMinMax(T _min 207 void GMocrenDataPrimitive<T>::getMinMax(T _minmax[2]) {
208 for(int i = 0; i < 2; i++) _minmax[i] = kMin 208 for(int i = 0; i < 2; i++) _minmax[i] = kMinmax[i];
209 209
210 } 210 }
211 template <typename T> 211 template <typename T>
212 void GMocrenDataPrimitive<T>::setImage(std::ve 212 void GMocrenDataPrimitive<T>::setImage(std::vector<T *> & _image) {
213 kImage = _image; 213 kImage = _image;
214 } 214 }
215 template <typename T> 215 template <typename T>
216 void GMocrenDataPrimitive<T>::addImage(T * _im 216 void GMocrenDataPrimitive<T>::addImage(T * _image) {
217 kImage.push_back(_image); 217 kImage.push_back(_image);
218 } 218 }
219 template <typename T> 219 template <typename T>
220 std::vector<T *> & GMocrenDataPrimitive<T>::ge 220 std::vector<T *> & GMocrenDataPrimitive<T>::getImage() {
221 return kImage; 221 return kImage;
222 } 222 }
223 template <typename T> 223 template <typename T>
224 T * GMocrenDataPrimitive<T>::getImage(int _z) 224 T * GMocrenDataPrimitive<T>::getImage(int _z) {
225 if(_z >= (int)kImage.size()) return 0; 225 if(_z >= (int)kImage.size()) return 0;
226 return kImage[_z]; 226 return kImage[_z];
227 } 227 }
228 template <typename T> 228 template <typename T>
229 void GMocrenDataPrimitive<T>::setCenterPositio 229 void GMocrenDataPrimitive<T>::setCenterPosition(float _center[3]) {
230 for(int i = 0; i < 3; i++) kCenter[i] = _cen 230 for(int i = 0; i < 3; i++) kCenter[i] = _center[i];
231 } 231 }
232 template <typename T> 232 template <typename T>
233 void GMocrenDataPrimitive<T>::getCenterPositio 233 void GMocrenDataPrimitive<T>::getCenterPosition(float _center[3]) {
234 for(int i = 0; i < 3; i++) _center[i] = kCen 234 for(int i = 0; i < 3; i++) _center[i] = kCenter[i];
235 } 235 }
236 template <typename T> 236 template <typename T>
237 void GMocrenDataPrimitive<T>::setName(std::str 237 void GMocrenDataPrimitive<T>::setName(std::string & _name) {
238 kDataName = _name; 238 kDataName = _name;
239 } 239 }
240 template <typename T> 240 template <typename T>
241 std::string GMocrenDataPrimitive<T>::getName() 241 std::string GMocrenDataPrimitive<T>::getName() {
242 return kDataName; 242 return kDataName;
243 } 243 }
244 244
245 245
246 246
247 247
248 248
249 GMocrenTrack::GMocrenTrack() { 249 GMocrenTrack::GMocrenTrack() {
250 kTrack.clear(); 250 kTrack.clear();
251 for(int i = 0; i < 3; i++) kColor[i] = 0; 251 for(int i = 0; i < 3; i++) kColor[i] = 0;
252 } 252 }
253 253
254 void GMocrenTrack::addStep(float _startx, floa 254 void GMocrenTrack::addStep(float _startx, float _starty, float _startz,
255 float _endx, float _endy, float _endz 255 float _endx, float _endy, float _endz) {
256 struct Step step; 256 struct Step step;
257 step.startPoint[0] = _startx; 257 step.startPoint[0] = _startx;
258 step.startPoint[1] = _starty; 258 step.startPoint[1] = _starty;
259 step.startPoint[2] = _startz; 259 step.startPoint[2] = _startz;
260 step.endPoint[0] = _endx; 260 step.endPoint[0] = _endx;
261 step.endPoint[1] = _endy; 261 step.endPoint[1] = _endy;
262 step.endPoint[2] = _endz; 262 step.endPoint[2] = _endz;
263 kTrack.push_back(step); 263 kTrack.push_back(step);
264 } 264 }
265 void GMocrenTrack::getStep(float & _startx, fl 265 void GMocrenTrack::getStep(float & _startx, float & _starty, float & _startz,
266 float & _endx, float & _endy, float & 266 float & _endx, float & _endy, float & _endz,
267 int _num) { 267 int _num) {
268 if(_num >= (int)kTrack.size()) { 268 if(_num >= (int)kTrack.size()) {
269 if (G4VisManager::GetVerbosity() >= G4VisM 269 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
270 G4cout << "GMocrenTrack::getStep(...) Er 270 G4cout << "GMocrenTrack::getStep(...) Error: "
271 << "invalid step # : " << _num << G4end 271 << "invalid step # : " << _num << G4endl;
272 return; 272 return;
273 } 273 }
274 274
275 _startx = kTrack[_num].startPoint[0]; 275 _startx = kTrack[_num].startPoint[0];
276 _starty = kTrack[_num].startPoint[1]; 276 _starty = kTrack[_num].startPoint[1];
277 _startz = kTrack[_num].startPoint[2]; 277 _startz = kTrack[_num].startPoint[2];
278 _endx = kTrack[_num].endPoint[0]; 278 _endx = kTrack[_num].endPoint[0];
279 _endy = kTrack[_num].endPoint[1]; 279 _endy = kTrack[_num].endPoint[1];
280 _endz = kTrack[_num].endPoint[2]; 280 _endz = kTrack[_num].endPoint[2];
281 } 281 }
282 void GMocrenTrack::translate(std::vector<float 282 void GMocrenTrack::translate(std::vector<float> & _translate) {
283 std::vector<struct Step>::iterator itr = kTr 283 std::vector<struct Step>::iterator itr = kTrack.begin();
284 for(; itr != kTrack.end(); itr++) { 284 for(; itr != kTrack.end(); itr++) {
285 for(int i = 0; i < 3; i++ ) { 285 for(int i = 0; i < 3; i++ ) {
286 itr->startPoint[i] += _translate[i]; 286 itr->startPoint[i] += _translate[i];
287 itr->endPoint[i] += _translate[i]; 287 itr->endPoint[i] += _translate[i];
288 } 288 }
289 } 289 }
290 } 290 }
291 291
292 292
293 293
294 294
295 295
296 296
297 297
298 298
299 299
300 GMocrenDetector::GMocrenDetector() { 300 GMocrenDetector::GMocrenDetector() {
301 kDetector.clear(); 301 kDetector.clear();
302 for(int i = 0; i < 3; i++) kColor[i] = 0; 302 for(int i = 0; i < 3; i++) kColor[i] = 0;
303 } 303 }
304 304
305 void GMocrenDetector::addEdge(float _startx, f 305 void GMocrenDetector::addEdge(float _startx, float _starty, float _startz,
306 float _endx, float _endy, float _e 306 float _endx, float _endy, float _endz) {
307 struct Edge edge; 307 struct Edge edge;
308 edge.startPoint[0] = _startx; 308 edge.startPoint[0] = _startx;
309 edge.startPoint[1] = _starty; 309 edge.startPoint[1] = _starty;
310 edge.startPoint[2] = _startz; 310 edge.startPoint[2] = _startz;
311 edge.endPoint[0] = _endx; 311 edge.endPoint[0] = _endx;
312 edge.endPoint[1] = _endy; 312 edge.endPoint[1] = _endy;
313 edge.endPoint[2] = _endz; 313 edge.endPoint[2] = _endz;
314 kDetector.push_back(edge); 314 kDetector.push_back(edge);
315 } 315 }
316 void GMocrenDetector::getEdge(float & _startx, 316 void GMocrenDetector::getEdge(float & _startx, float & _starty, float & _startz,
317 float & _endx, float & _endy, float & 317 float & _endx, float & _endy, float & _endz,
318 int _num) { 318 int _num) {
319 if(_num >= (int)kDetector.size()) { 319 if(_num >= (int)kDetector.size()) {
320 if (G4VisManager::GetVerbosity() >= G4VisM 320 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
321 G4cout << "GMocrenDetector::getEdge(...) 321 G4cout << "GMocrenDetector::getEdge(...) Error: "
322 << "invalid edge # : " << _num << G4end 322 << "invalid edge # : " << _num << G4endl;
323 return; 323 return;
324 } 324 }
325 325
326 _startx = kDetector[_num].startPoint[0]; 326 _startx = kDetector[_num].startPoint[0];
327 _starty = kDetector[_num].startPoint[1]; 327 _starty = kDetector[_num].startPoint[1];
328 _startz = kDetector[_num].startPoint[2]; 328 _startz = kDetector[_num].startPoint[2];
329 _endx = kDetector[_num].endPoint[0]; 329 _endx = kDetector[_num].endPoint[0];
330 _endy = kDetector[_num].endPoint[1]; 330 _endy = kDetector[_num].endPoint[1];
331 _endz = kDetector[_num].endPoint[2]; 331 _endz = kDetector[_num].endPoint[2];
332 } 332 }
333 void GMocrenDetector::translate(std::vector<fl 333 void GMocrenDetector::translate(std::vector<float> & _translate) {
334 std::vector<struct Edge>::iterator itr = kDe 334 std::vector<struct Edge>::iterator itr = kDetector.begin();
335 for(; itr != kDetector.end(); itr++) { 335 for(; itr != kDetector.end(); itr++) {
336 for(int i = 0; i < 3; i++) { 336 for(int i = 0; i < 3; i++) {
337 itr->startPoint[i] += _translate[i]; 337 itr->startPoint[i] += _translate[i];
338 itr->endPoint[i] += _translate[i]; 338 itr->endPoint[i] += _translate[i];
339 } 339 }
340 } 340 }
341 } 341 }
342 342
343 343
344 344
345 345
346 346
347 347
348 348
349 349
350 350
351 // file information 351 // file information
352 std::string G4GMocrenIO::kId; 352 std::string G4GMocrenIO::kId;
353 std::string G4GMocrenIO::kVersion = "2.0.0"; 353 std::string G4GMocrenIO::kVersion = "2.0.0";
354 int G4GMocrenIO::kNumberOfEvents = 0; 354 int G4GMocrenIO::kNumberOfEvents = 0;
355 char G4GMocrenIO::kLittleEndianInput = true; 355 char G4GMocrenIO::kLittleEndianInput = true;
356 356
357 #if BYTE_ORDER == LITTLE_ENDIAN 357 #if BYTE_ORDER == LITTLE_ENDIAN
358 char G4GMocrenIO::kLittleEndianOutput = true; 358 char G4GMocrenIO::kLittleEndianOutput = true;
359 #else 359 #else
360 char G4GMocrenIO::kLittleEndianOutput = false; 360 char G4GMocrenIO::kLittleEndianOutput = false; // Big endian
361 #endif 361 #endif
362 std::string G4GMocrenIO::kComment; 362 std::string G4GMocrenIO::kComment;
363 // 363 //
364 std::string G4GMocrenIO::kFileName = "dose.gdd 364 std::string G4GMocrenIO::kFileName = "dose.gdd";
365 365
366 // 366 //
367 unsigned int G4GMocrenIO::kPointerToModalityDa 367 unsigned int G4GMocrenIO::kPointerToModalityData = 0;
368 std::vector<unsigned int> G4GMocrenIO::kPointe 368 std::vector<unsigned int> G4GMocrenIO::kPointerToDoseDistData;
369 unsigned int G4GMocrenIO::kPointerToROIData = 369 unsigned int G4GMocrenIO::kPointerToROIData = 0;
370 unsigned int G4GMocrenIO::kPointerToTrackData 370 unsigned int G4GMocrenIO::kPointerToTrackData = 0;
371 unsigned int G4GMocrenIO::kPointerToDetectorDa 371 unsigned int G4GMocrenIO::kPointerToDetectorData = 0;
372 372
373 // modality 373 // modality
374 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 374 float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 0.};
375 class GMocrenDataPrimitive<short> G4GMocrenIO 375 class GMocrenDataPrimitive<short> G4GMocrenIO::kModality;
376 std::vector<float> G4GMocrenIO::kModalityImage 376 std::vector<float> G4GMocrenIO::kModalityImageDensityMap;
377 std::string G4GMocrenIO::kModalityUnit = "g/cm 377 std::string G4GMocrenIO::kModalityUnit = "g/cm3 "; // 12 Bytes
378 378
379 // dose 379 // dose
380 std::vector<class GMocrenDataPrimitive<double> 380 std::vector<class GMocrenDataPrimitive<double> > G4GMocrenIO::kDose;
381 std::string G4GMocrenIO::kDoseUnit = "keV 381 std::string G4GMocrenIO::kDoseUnit = "keV "; // 12 Bytes
382 382
383 // ROI 383 // ROI
384 std::vector<class GMocrenDataPrimitive<short> 384 std::vector<class GMocrenDataPrimitive<short> > G4GMocrenIO::kRoi;
385 385
386 // track 386 // track
387 std::vector<float *> G4GMocrenIO::kSteps; 387 std::vector<float *> G4GMocrenIO::kSteps;
388 std::vector<unsigned char *> G4GMocrenIO::kSte 388 std::vector<unsigned char *> G4GMocrenIO::kStepColors;
389 std::vector<class GMocrenTrack> G4GMocrenIO::k 389 std::vector<class GMocrenTrack> G4GMocrenIO::kTracks;
390 390
391 // detector 391 // detector
392 std::vector<class GMocrenDetector> G4GMocrenIO 392 std::vector<class GMocrenDetector> G4GMocrenIO::kDetectors;
393 393
394 // verbose 394 // verbose
395 int G4GMocrenIO::kVerbose = 0; 395 int G4GMocrenIO::kVerbose = 0;
396 396
397 const int IDLENGTH = 21; 397 const int IDLENGTH = 21;
398 const int VERLENGTH = 6; 398 const int VERLENGTH = 6;
399 399
400 // constructor 400 // constructor
401 G4GMocrenIO::G4GMocrenIO() 401 G4GMocrenIO::G4GMocrenIO()
402 : kTracksWillBeStored(true) { 402 : kTracksWillBeStored(true) {
403 ; 403 ;
404 } 404 }
405 405
406 // destructor 406 // destructor
407 G4GMocrenIO::~G4GMocrenIO() { 407 G4GMocrenIO::~G4GMocrenIO() {
408 ; 408 ;
409 } 409 }
410 410
411 // initialize 411 // initialize
412 void G4GMocrenIO::initialize() { 412 void G4GMocrenIO::initialize() {
413 413
414 kId.clear(); 414 kId.clear();
415 kVersion = "2.0.0"; 415 kVersion = "2.0.0";
416 kNumberOfEvents = 0; 416 kNumberOfEvents = 0;
417 kLittleEndianInput = true; 417 kLittleEndianInput = true;
418 #if BYTE_ORDER == LITTLE_ENDIAN 418 #if BYTE_ORDER == LITTLE_ENDIAN
419 kLittleEndianOutput = true; 419 kLittleEndianOutput = true;
420 #else // Big endian 420 #else // Big endian
421 kLittleEndianOutput = false; 421 kLittleEndianOutput = false;
422 #endif 422 #endif
423 kComment.clear(); 423 kComment.clear();
424 kFileName = "dose.gdd"; 424 kFileName = "dose.gdd";
425 kPointerToModalityData = 0; 425 kPointerToModalityData = 0;
426 kPointerToDoseDistData.clear(); 426 kPointerToDoseDistData.clear();
427 kPointerToROIData = 0; 427 kPointerToROIData = 0;
428 kPointerToTrackData = 0; 428 kPointerToTrackData = 0;
429 // modality 429 // modality
430 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 430 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = 0.;
431 kModality.clear(); 431 kModality.clear();
432 kModalityImageDensityMap.clear(); 432 kModalityImageDensityMap.clear();
433 kModalityUnit = "g/cm3 "; // 12 Bytes 433 kModalityUnit = "g/cm3 "; // 12 Bytes
434 // dose 434 // dose
435 kDose.clear(); 435 kDose.clear();
436 kDoseUnit = "keV "; // 12 Bytes 436 kDoseUnit = "keV "; // 12 Bytes
437 // ROI 437 // ROI
438 kRoi.clear(); 438 kRoi.clear();
439 // track 439 // track
440 std::vector<float *>::iterator itr; 440 std::vector<float *>::iterator itr;
441 for(itr = kSteps.begin(); itr != kSteps.end( 441 for(itr = kSteps.begin(); itr != kSteps.end(); itr++) delete [] *itr;
442 kSteps.clear(); 442 kSteps.clear();
443 std::vector<unsigned char *>::iterator citr; 443 std::vector<unsigned char *>::iterator citr;
444 for(citr = kStepColors.begin(); citr != kSte 444 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++)
445 delete [] *citr; 445 delete [] *citr;
446 kStepColors.clear(); 446 kStepColors.clear();
447 kTracksWillBeStored = true; 447 kTracksWillBeStored = true;
448 448
449 // verbose 449 // verbose
450 kVerbose = 0; 450 kVerbose = 0;
451 } 451 }
452 452
453 bool G4GMocrenIO::storeData() { 453 bool G4GMocrenIO::storeData() {
454 return storeData4(); 454 return storeData4();
455 } 455 }
456 // 456 //
457 bool G4GMocrenIO::storeData(char * _filename) 457 bool G4GMocrenIO::storeData(char * _filename) {
458 return storeData4(_filename); 458 return storeData4(_filename);
459 } 459 }
460 460
461 bool G4GMocrenIO::storeData4() { 461 bool G4GMocrenIO::storeData4() {
462 462
463 bool DEBUG = false;// 463 bool DEBUG = false;//
464 464
465 if(DEBUG || kVerbose > 0) 465 if(DEBUG || kVerbose > 0)
466 G4cout << ">>>>>>> store data (ver.4) <<< 466 G4cout << ">>>>>>> store data (ver.4) <<<<<<<" << G4endl;
467 if(DEBUG || kVerbose > 0) 467 if(DEBUG || kVerbose > 0)
468 G4cout << " " << kFileName << G4en 468 G4cout << " " << kFileName << G4endl;
469 469
470 // output file open 470 // output file open
471 std::ofstream ofile(kFileName.c_str(), 471 std::ofstream ofile(kFileName.c_str(),
472 std::ios_base::out|std::ios_base::bi 472 std::ios_base::out|std::ios_base::binary);
473 if(DEBUG || kVerbose > 0) 473 if(DEBUG || kVerbose > 0)
474 G4cout << " file open status: " << 474 G4cout << " file open status: " << ofile.rdbuf() << G4endl;
475 475
476 // file identifier 476 // file identifier
477 ofile.write("gMocren ", 8); 477 ofile.write("gMocren ", 8);
478 478
479 // file version 479 // file version
480 unsigned char ver = 0x04; 480 unsigned char ver = 0x04;
481 ofile.write((char *)&ver, 1); 481 ofile.write((char *)&ver, 1);
482 482
483 // endian 483 // endian
484 //ofile.write((char *)&kLittleEndianOutput, 484 //ofile.write((char *)&kLittleEndianOutput, sizeof(char));
485 char littleEndian = 0x01; 485 char littleEndian = 0x01;
486 ofile.write((char *)&littleEndian, sizeof(ch 486 ofile.write((char *)&littleEndian, sizeof(char));
487 if(DEBUG || kVerbose > 0) { 487 if(DEBUG || kVerbose > 0) {
488 //G4cout << "Endian: " << (int)kLittleEndi 488 //G4cout << "Endian: " << (int)kLittleEndianOutput << G4endl;
489 G4cout << "Endian: " << (int)littleEndian 489 G4cout << "Endian: " << (int)littleEndian << G4endl;
490 } 490 }
491 491
492 // for inverting the byte order 492 // for inverting the byte order
493 float ftmp[6]; 493 float ftmp[6];
494 int itmp[6]; 494 int itmp[6];
495 short stmp[6]; 495 short stmp[6];
496 496
497 // comment length (fixed size) 497 // comment length (fixed size)
498 int commentLength = 1024; 498 int commentLength = 1024;
499 if(kLittleEndianOutput) { 499 if(kLittleEndianOutput) {
500 ofile.write((char *)&commentLength, 4); 500 ofile.write((char *)&commentLength, 4);
501 } else { 501 } else {
502 invertByteOrder((char *)&commentLength, it 502 invertByteOrder((char *)&commentLength, itmp[0]);
503 ofile.write((char *)itmp, 4); 503 ofile.write((char *)itmp, 4);
504 } 504 }
505 505
506 // comment 506 // comment
507 char cmt[1025]; 507 char cmt[1025];
508 std::strncpy(cmt, kComment.c_str(), 1024); 508 std::strncpy(cmt, kComment.c_str(), 1024);
509 cmt[1024] = '\0'; 509 cmt[1024] = '\0';
510 ofile.write(cmt, 1024); 510 ofile.write(cmt, 1024);
511 if(DEBUG || kVerbose > 0) { 511 if(DEBUG || kVerbose > 0) {
512 G4cout << "Data comment : " 512 G4cout << "Data comment : "
513 << kComment << G4endl; 513 << kComment << G4endl;
514 } 514 }
515 515
516 // voxel spacings for all images 516 // voxel spacings for all images
517 if(kLittleEndianOutput) { 517 if(kLittleEndianOutput) {
518 ofile.write((char *)kVoxelSpacing, 12); 518 ofile.write((char *)kVoxelSpacing, 12);
519 } else { 519 } else {
520 for(int j = 0; j < 3; j++) 520 for(int j = 0; j < 3; j++)
521 invertByteOrder((char *)&kVoxelSpacing[j 521 invertByteOrder((char *)&kVoxelSpacing[j], ftmp[j]);
522 ofile.write((char *)ftmp, 12); 522 ofile.write((char *)ftmp, 12);
523 } 523 }
524 if(DEBUG || kVerbose > 0) { 524 if(DEBUG || kVerbose > 0) {
525 G4cout << "Voxel spacing : (" 525 G4cout << "Voxel spacing : ("
526 << kVoxelSpacing[0] << ", " 526 << kVoxelSpacing[0] << ", "
527 << kVoxelSpacing[1] << ", " 527 << kVoxelSpacing[1] << ", "
528 << kVoxelSpacing[2] 528 << kVoxelSpacing[2]
529 << ") mm " << G4endl; 529 << ") mm " << G4endl;
530 } 530 }
531 531
532 calcPointers4(); 532 calcPointers4();
533 if(!kTracksWillBeStored) kPointerToTrackData 533 if(!kTracksWillBeStored) kPointerToTrackData = 0;
534 534
535 // offset from file starting point to the mo 535 // offset from file starting point to the modality image data
536 if(kLittleEndianOutput) { 536 if(kLittleEndianOutput) {
537 ofile.write((char *)&kPointerToModalityDat 537 ofile.write((char *)&kPointerToModalityData, 4);
538 } else { 538 } else {
539 invertByteOrder((char *)&kPointerToModalit 539 invertByteOrder((char *)&kPointerToModalityData, itmp[0]);
540 ofile.write((char *)itmp, 4); 540 ofile.write((char *)itmp, 4);
541 } 541 }
542 542
543 // # of dose distributions 543 // # of dose distributions
544 //int nDoseDist = (int)pointerToDoseDistData 544 //int nDoseDist = (int)pointerToDoseDistData.size();
545 int nDoseDist = getNumDoseDist(); 545 int nDoseDist = getNumDoseDist();
546 if(kLittleEndianOutput) { 546 if(kLittleEndianOutput) {
547 ofile.write((char *)&nDoseDist, 4); 547 ofile.write((char *)&nDoseDist, 4);
548 } else { 548 } else {
549 invertByteOrder((char *)&nDoseDist, itmp[0 549 invertByteOrder((char *)&nDoseDist, itmp[0]);
550 ofile.write((char *)itmp, 4); 550 ofile.write((char *)itmp, 4);
551 } 551 }
552 552
553 // offset from file starting point to the do 553 // offset from file starting point to the dose image data
554 if(kLittleEndianOutput) { 554 if(kLittleEndianOutput) {
555 for(int i = 0; i < nDoseDist; i++) { 555 for(int i = 0; i < nDoseDist; i++) {
556 ofile.write((char *)&kPointerToDoseDistD 556 ofile.write((char *)&kPointerToDoseDistData[i], 4);
557 } 557 }
558 } else { 558 } else {
559 for(int i = 0; i < nDoseDist; i++) { 559 for(int i = 0; i < nDoseDist; i++) {
560 invertByteOrder((char *)&kPointerToDoseD 560 invertByteOrder((char *)&kPointerToDoseDistData[i], itmp[0]);
561 ofile.write((char *)itmp, 4); 561 ofile.write((char *)itmp, 4);
562 } 562 }
563 } 563 }
564 564
565 // offset from file starting point to the RO 565 // offset from file starting point to the ROI image data
566 if(kLittleEndianOutput) { 566 if(kLittleEndianOutput) {
567 ofile.write((char *)&kPointerToROIData, 4) 567 ofile.write((char *)&kPointerToROIData, 4);
568 } else { 568 } else {
569 invertByteOrder((char *)&kPointerToROIData 569 invertByteOrder((char *)&kPointerToROIData, itmp[0]);
570 ofile.write((char *)itmp, 4); 570 ofile.write((char *)itmp, 4);
571 } 571 }
572 572
573 // offset from file starting point to the tr 573 // offset from file starting point to the track data
574 if(kLittleEndianOutput) { 574 if(kLittleEndianOutput) {
575 ofile.write((char *)&kPointerToTrackData, 575 ofile.write((char *)&kPointerToTrackData, 4);
576 } else { 576 } else {
577 invertByteOrder((char *)&kPointerToTrackDa 577 invertByteOrder((char *)&kPointerToTrackData, itmp[0]);
578 ofile.write((char *)itmp, 4); 578 ofile.write((char *)itmp, 4);
579 } 579 }
580 580
581 // offset from file starting point to the de 581 // offset from file starting point to the detector data
582 if(kLittleEndianOutput) { 582 if(kLittleEndianOutput) {
583 ofile.write((char *)&kPointerToDetectorDat 583 ofile.write((char *)&kPointerToDetectorData, 4);
584 } else { 584 } else {
585 invertByteOrder((char *)&kPointerToDetecto 585 invertByteOrder((char *)&kPointerToDetectorData, itmp[0]);
586 ofile.write((char *)itmp, 4); 586 ofile.write((char *)itmp, 4);
587 } 587 }
588 588
589 if(DEBUG || kVerbose > 0) { 589 if(DEBUG || kVerbose > 0) {
590 G4cout << "Each pointer to data : " 590 G4cout << "Each pointer to data : "
591 << kPointerToModalityData << ", "; 591 << kPointerToModalityData << ", ";
592 for(int i = 0; i < nDoseDist; i++) { 592 for(int i = 0; i < nDoseDist; i++) {
593 G4cout << kPointerToDoseDistData[i] << " 593 G4cout << kPointerToDoseDistData[i] << ", ";
594 } 594 }
595 G4cout << kPointerToROIData << ", " 595 G4cout << kPointerToROIData << ", "
596 << kPointerToTrackData << ", " 596 << kPointerToTrackData << ", "
597 << kPointerToDetectorData 597 << kPointerToDetectorData
598 << G4endl; 598 << G4endl;
599 } 599 }
600 600
601 //----- modality image -----// 601 //----- modality image -----//
602 602
603 int size[3]; 603 int size[3];
604 float scale; 604 float scale;
605 short minmax[2]; 605 short minmax[2];
606 float fCenter[3]; 606 float fCenter[3];
607 int iCenter[3]; 607 int iCenter[3];
608 // modality image size 608 // modality image size
609 kModality.getSize(size); 609 kModality.getSize(size);
610 610
611 if(kLittleEndianOutput) { 611 if(kLittleEndianOutput) {
612 ofile.write((char *)size, 3*sizeof(int)); 612 ofile.write((char *)size, 3*sizeof(int));
613 } else { 613 } else {
614 for(int j = 0; j < 3; j++) 614 for(int j = 0; j < 3; j++)
615 invertByteOrder((char *)&size[j], itmp[j 615 invertByteOrder((char *)&size[j], itmp[j]);
616 ofile.write((char *)itmp, 12); 616 ofile.write((char *)itmp, 12);
617 } 617 }
618 618
619 if(DEBUG || kVerbose > 0) { 619 if(DEBUG || kVerbose > 0) {
620 G4cout << "Modality image size : (" 620 G4cout << "Modality image size : ("
621 << size[0] << ", " 621 << size[0] << ", "
622 << size[1] << ", " 622 << size[1] << ", "
623 << size[2] << ")" 623 << size[2] << ")"
624 << G4endl; 624 << G4endl;
625 } 625 }
626 626
627 // modality image max. & min. 627 // modality image max. & min.
628 kModality.getMinMax(minmax); 628 kModality.getMinMax(minmax);
629 if(kLittleEndianOutput) { 629 if(kLittleEndianOutput) {
630 ofile.write((char *)minmax, 4); 630 ofile.write((char *)minmax, 4);
631 } else { 631 } else {
632 for(int j = 0; j < 2; j++) 632 for(int j = 0; j < 2; j++)
633 invertByteOrder((char *)&minmax[j], stmp 633 invertByteOrder((char *)&minmax[j], stmp[j]);
634 ofile.write((char *)stmp, 4); 634 ofile.write((char *)stmp, 4);
635 } 635 }
636 636
637 // modality image unit 637 // modality image unit
638 char munit[13] = "g/cm3\0"; 638 char munit[13] = "g/cm3\0";
639 ofile.write((char *)munit, 12); 639 ofile.write((char *)munit, 12);
640 640
641 // modality image scale 641 // modality image scale
642 scale = (float)kModality.getScale(); 642 scale = (float)kModality.getScale();
643 if(kLittleEndianOutput) { 643 if(kLittleEndianOutput) {
644 ofile.write((char *)&scale, 4); 644 ofile.write((char *)&scale, 4);
645 } else { 645 } else {
646 invertByteOrder((char *)&scale, ftmp[0]); 646 invertByteOrder((char *)&scale, ftmp[0]);
647 ofile.write((char *)ftmp, 4); 647 ofile.write((char *)ftmp, 4);
648 } 648 }
649 if(DEBUG || kVerbose > 0) { 649 if(DEBUG || kVerbose > 0) {
650 G4cout << "Modality image min., max., scal 650 G4cout << "Modality image min., max., scale : "
651 << minmax[0] << ", " 651 << minmax[0] << ", "
652 << minmax[1] << ", " 652 << minmax[1] << ", "
653 << scale << G4endl; 653 << scale << G4endl;
654 } 654 }
655 655
656 // modality image 656 // modality image
657 int psize = size[0]*size[1]; 657 int psize = size[0]*size[1];
658 if(DEBUG || kVerbose > 0) G4cout << "Modalit 658 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
659 for(int i = 0; i < size[2]; i++) { 659 for(int i = 0; i < size[2]; i++) {
660 short * image = kModality.getImage(i); 660 short * image = kModality.getImage(i);
661 if(kLittleEndianOutput) { 661 if(kLittleEndianOutput) {
662 ofile.write((char *)image, psize*sizeof( 662 ofile.write((char *)image, psize*sizeof(short));
663 } else { 663 } else {
664 for(int j = 0; j < psize; j++) { 664 for(int j = 0; j < psize; j++) {
665 invertByteOrder((char *)&image[j], stmp[0]); 665 invertByteOrder((char *)&image[j], stmp[0]);
666 ofile.write((char *)stmp, 2); 666 ofile.write((char *)stmp, 2);
667 } 667 }
668 } 668 }
669 669
670 if(DEBUG || kVerbose > 0) G4cout << "[" << 670 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
671 } 671 }
672 if(DEBUG || kVerbose > 0) G4cout << G4endl; 672 if(DEBUG || kVerbose > 0) G4cout << G4endl;
673 673
674 // modality desity map for CT value 674 // modality desity map for CT value
675 size_t msize = minmax[1] - minmax[0]+1; 675 size_t msize = minmax[1] - minmax[0]+1;
676 if(DEBUG || kVerbose > 0) 676 if(DEBUG || kVerbose > 0)
677 G4cout << "modality image : " << minmax[0] 677 G4cout << "modality image : " << minmax[0] << ", " << minmax[1] << G4endl;
678 float * pdmap = new float[msize]; 678 float * pdmap = new float[msize];
679 for(int i = 0; i < (int)msize; i++) pdmap[i] 679 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
680 680
681 if(kLittleEndianOutput) { 681 if(kLittleEndianOutput) {
682 ofile.write((char *)pdmap, msize*sizeof(fl 682 ofile.write((char *)pdmap, msize*sizeof(float));
683 } else { 683 } else {
684 for(int j = 0; j < (int)msize; j++) { 684 for(int j = 0; j < (int)msize; j++) {
685 invertByteOrder((char *)&pdmap[j], ftmp[ 685 invertByteOrder((char *)&pdmap[j], ftmp[0]);
686 ofile.write((char *)ftmp, 4); 686 ofile.write((char *)ftmp, 4);
687 } 687 }
688 } 688 }
689 689
690 if(DEBUG || kVerbose > 0) { 690 if(DEBUG || kVerbose > 0) {
691 G4cout << "density map : " << std::ends; 691 G4cout << "density map : " << std::ends;
692 for(int i = 0; i < (int)msize; i+=50) 692 for(int i = 0; i < (int)msize; i+=50)
693 G4cout <<kModalityImageDensityMap[i] << 693 G4cout <<kModalityImageDensityMap[i] << ", ";
694 G4cout << G4endl; 694 G4cout << G4endl;
695 } 695 }
696 delete [] pdmap; 696 delete [] pdmap;
697 697
698 698
699 //----- dose distribution image -----// 699 //----- dose distribution image -----//
700 700
701 if(!isDoseEmpty()) { 701 if(!isDoseEmpty()) {
702 702
703 calcDoseDistScale(); 703 calcDoseDistScale();
704 704
705 for(int ndose = 0; ndose < nDoseDist; ndos 705 for(int ndose = 0; ndose < nDoseDist; ndose++) {
706 // dose distrbution image size 706 // dose distrbution image size
707 kDose[ndose].getSize(size); 707 kDose[ndose].getSize(size);
708 if(kLittleEndianOutput) { 708 if(kLittleEndianOutput) {
709 ofile.write((char *)size, 3*sizeof(int)); 709 ofile.write((char *)size, 3*sizeof(int));
710 } else { 710 } else {
711 for(int j = 0; j < 3; j++) 711 for(int j = 0; j < 3; j++)
712 invertByteOrder((char *)&size[j], itmp[j]) 712 invertByteOrder((char *)&size[j], itmp[j]);
713 ofile.write((char *)itmp, 12); 713 ofile.write((char *)itmp, 12);
714 } 714 }
715 if(DEBUG || kVerbose > 0) { 715 if(DEBUG || kVerbose > 0) {
716 G4cout << "Dose dist. [" << ndose << "] imag 716 G4cout << "Dose dist. [" << ndose << "] image size : ("
717 << size[0] << ", " 717 << size[0] << ", "
718 << size[1] << ", " 718 << size[1] << ", "
719 << size[2] << ")" 719 << size[2] << ")"
720 << G4endl; 720 << G4endl;
721 } 721 }
722 722
723 // dose distribution max. & min. 723 // dose distribution max. & min.
724 getShortDoseDistMinMax(minmax, ndose); 724 getShortDoseDistMinMax(minmax, ndose);
725 if(kLittleEndianOutput) { 725 if(kLittleEndianOutput) {
726 ofile.write((char *)minmax, 2*2); // sizeof( 726 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
727 } else { 727 } else {
728 for(int j = 0; j < 2; j++) 728 for(int j = 0; j < 2; j++)
729 invertByteOrder((char *)&minmax[j], stmp[j 729 invertByteOrder((char *)&minmax[j], stmp[j]);
730 ofile.write((char *)stmp, 4); 730 ofile.write((char *)stmp, 4);
731 } 731 }
732 732
733 // dose distribution unit 733 // dose distribution unit
734 char cdunit[13]; 734 char cdunit[13];
735 std::strncpy(cdunit, kDoseUnit.c_str(), 735 std::strncpy(cdunit, kDoseUnit.c_str(), 12);
736 cdunit[12] = '\0'; 736 cdunit[12] = '\0';
737 ofile.write(cdunit, 12); 737 ofile.write(cdunit, 12);
738 if(DEBUG || kVerbose > 0) { 738 if(DEBUG || kVerbose > 0) {
739 G4cout << "Dose dist. unit : " << kDoseUnit 739 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
740 } 740 }
741 741
742 // dose distribution scaling 742 // dose distribution scaling
743 double dscale; 743 double dscale;
744 dscale = getDoseDistScale(ndose); 744 dscale = getDoseDistScale(ndose);
745 scale = float(dscale); 745 scale = float(dscale);
746 if(kLittleEndianOutput) { 746 if(kLittleEndianOutput) {
747 ofile.write((char *)&scale, 4); 747 ofile.write((char *)&scale, 4);
748 } else { 748 } else {
749 invertByteOrder((char *)&scale, ftmp[0]); 749 invertByteOrder((char *)&scale, ftmp[0]);
750 ofile.write((char *)ftmp, 4); 750 ofile.write((char *)ftmp, 4);
751 } 751 }
752 if(DEBUG || kVerbose > 0) { 752 if(DEBUG || kVerbose > 0) {
753 G4cout << "Dose dist. [" << ndose 753 G4cout << "Dose dist. [" << ndose
754 << "] image min., max., scale : " 754 << "] image min., max., scale : "
755 << minmax[0] << ", " 755 << minmax[0] << ", "
756 << minmax[1] << ", " 756 << minmax[1] << ", "
757 << scale << G4endl; 757 << scale << G4endl;
758 } 758 }
759 759
760 // dose distribution image 760 // dose distribution image
761 int dsize = size[0]*size[1]; 761 int dsize = size[0]*size[1];
762 short * dimage = new short[dsize]; 762 short * dimage = new short[dsize];
763 for(int z = 0; z < size[2]; z++) { 763 for(int z = 0; z < size[2]; z++) {
764 getShortDoseDist(dimage, z, ndose); 764 getShortDoseDist(dimage, z, ndose);
765 if(kLittleEndianOutput) { 765 if(kLittleEndianOutput) {
766 ofile.write((char *)dimage, dsize*2); //si 766 ofile.write((char *)dimage, dsize*2); //sizeof(short)
767 } else { 767 } else {
768 for(int j = 0; j < dsize; j++) { 768 for(int j = 0; j < dsize; j++) {
769 invertByteOrder((char *)&dimage[j], stmp 769 invertByteOrder((char *)&dimage[j], stmp[0]);
770 ofile.write((char *)stmp, 2); 770 ofile.write((char *)stmp, 2);
771 } 771 }
772 } 772 }
773 773
774 if(DEBUG || kVerbose > 0) { 774 if(DEBUG || kVerbose > 0) {
775 for(int j = 0; j < dsize; j++) { 775 for(int j = 0; j < dsize; j++) {
776 if(dimage[j] < 0) 776 if(dimage[j] < 0)
777 G4cout << "[" << j << "," << z << "]" 777 G4cout << "[" << j << "," << z << "]"
778 << dimage[j] << ", "; 778 << dimage[j] << ", ";
779 } 779 }
780 } 780 }
781 } 781 }
782 if(DEBUG || kVerbose > 0) G4cout << G4en 782 if(DEBUG || kVerbose > 0) G4cout << G4endl;
783 delete [] dimage; 783 delete [] dimage;
784 784
785 // relative location of the dose distrib 785 // relative location of the dose distribution image for
786 // the modality image 786 // the modality image
787 getDoseDistCenterPosition(fCenter, ndose 787 getDoseDistCenterPosition(fCenter, ndose);
788 for(int i = 0; i < 3; i++) iCenter[i] = 788 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
789 if(kLittleEndianOutput) { 789 if(kLittleEndianOutput) {
790 ofile.write((char *)iCenter, 3*4); // 3*size 790 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
791 } else { 791 } else {
792 for(int j = 0; j < 3; j++) 792 for(int j = 0; j < 3; j++)
793 invertByteOrder((char *)&iCenter[j], itmp[ 793 invertByteOrder((char *)&iCenter[j], itmp[j]);
794 ofile.write((char *)itmp, 12); 794 ofile.write((char *)itmp, 12);
795 } 795 }
796 if(DEBUG || kVerbose > 0) { 796 if(DEBUG || kVerbose > 0) {
797 G4cout << "Dose dist. [" << ndose 797 G4cout << "Dose dist. [" << ndose
798 << "]image relative location : (" 798 << "]image relative location : ("
799 << iCenter[0] << ", " 799 << iCenter[0] << ", "
800 << iCenter[1] << ", " 800 << iCenter[1] << ", "
801 << iCenter[2] << ")" << G4endl; 801 << iCenter[2] << ")" << G4endl;
802 } 802 }
803 803
804 // dose distribution name 804 // dose distribution name
805 std::string name = getDoseDistName(ndose 805 std::string name = getDoseDistName(ndose);
806 if(name.size() == 0) name = "dose"; 806 if(name.size() == 0) name = "dose";
807 name.resize(80); 807 name.resize(80);
808 ofile.write((char *)name.c_str(), 80); 808 ofile.write((char *)name.c_str(), 80);
809 if(DEBUG || kVerbose > 0) { 809 if(DEBUG || kVerbose > 0) {
810 G4cout << "Dose dist. name : " << name << G4 810 G4cout << "Dose dist. name : " << name << G4endl;
811 } 811 }
812 812
813 } 813 }
814 } 814 }
815 815
816 //----- ROI image -----// 816 //----- ROI image -----//
817 if(!isROIEmpty()) { 817 if(!isROIEmpty()) {
818 // ROI image size 818 // ROI image size
819 kRoi[0].getSize(size); 819 kRoi[0].getSize(size);
820 if(kLittleEndianOutput) { 820 if(kLittleEndianOutput) {
821 ofile.write((char *)size, 3*sizeof(int)) 821 ofile.write((char *)size, 3*sizeof(int));
822 } else { 822 } else {
823 for(int j = 0; j < 3; j++) 823 for(int j = 0; j < 3; j++)
824 invertByteOrder((char *)&size[j], itmp[j]); 824 invertByteOrder((char *)&size[j], itmp[j]);
825 ofile.write((char *)itmp, 12); 825 ofile.write((char *)itmp, 12);
826 } 826 }
827 if(DEBUG || kVerbose > 0) { 827 if(DEBUG || kVerbose > 0) {
828 G4cout << "ROI image size : (" 828 G4cout << "ROI image size : ("
829 << size[0] << ", " 829 << size[0] << ", "
830 << size[1] << ", " 830 << size[1] << ", "
831 << size[2] << ")" 831 << size[2] << ")"
832 << G4endl; 832 << G4endl;
833 } 833 }
834 834
835 // ROI max. & min. 835 // ROI max. & min.
836 kRoi[0].getMinMax(minmax); 836 kRoi[0].getMinMax(minmax);
837 if(kLittleEndianOutput) { 837 if(kLittleEndianOutput) {
838 ofile.write((char *)minmax, sizeof(short 838 ofile.write((char *)minmax, sizeof(short)*2);
839 } else { 839 } else {
840 for(int j = 0; j < 2; j++) 840 for(int j = 0; j < 2; j++)
841 invertByteOrder((char *)&minmax[j], stmp[j]) 841 invertByteOrder((char *)&minmax[j], stmp[j]);
842 ofile.write((char *)stmp, 4); 842 ofile.write((char *)stmp, 4);
843 } 843 }
844 844
845 // ROI distribution scaling 845 // ROI distribution scaling
846 scale = (float)kRoi[0].getScale(); 846 scale = (float)kRoi[0].getScale();
847 if(kLittleEndianOutput) { 847 if(kLittleEndianOutput) {
848 ofile.write((char *)&scale, sizeof(float 848 ofile.write((char *)&scale, sizeof(float));
849 } else { 849 } else {
850 invertByteOrder((char *)&scale, ftmp[0]) 850 invertByteOrder((char *)&scale, ftmp[0]);
851 ofile.write((char *)ftmp, 4); 851 ofile.write((char *)ftmp, 4);
852 } 852 }
853 if(DEBUG || kVerbose > 0) { 853 if(DEBUG || kVerbose > 0) {
854 G4cout << "ROI image min., max., scale : 854 G4cout << "ROI image min., max., scale : "
855 << minmax[0] << ", " 855 << minmax[0] << ", "
856 << minmax[1] << ", " 856 << minmax[1] << ", "
857 << scale << G4endl; 857 << scale << G4endl;
858 } 858 }
859 859
860 // ROI image 860 // ROI image
861 int rsize = size[0]*size[1]; 861 int rsize = size[0]*size[1];
862 for(int i = 0; i < size[2]; i++) { 862 for(int i = 0; i < size[2]; i++) {
863 short * rimage = kRoi[0].getImage(i); 863 short * rimage = kRoi[0].getImage(i);
864 if(kLittleEndianOutput) { 864 if(kLittleEndianOutput) {
865 ofile.write((char *)rimage, rsize*sizeof(sho 865 ofile.write((char *)rimage, rsize*sizeof(short));
866 } else { 866 } else {
867 for(int j = 0; j < rsize; j++) { 867 for(int j = 0; j < rsize; j++) {
868 invertByteOrder((char *)&rimage[j], stmp[0 868 invertByteOrder((char *)&rimage[j], stmp[0]);
869 ofile.write((char *)stmp, 2); 869 ofile.write((char *)stmp, 2);
870 } 870 }
871 } 871 }
872 872
873 } 873 }
874 874
875 // ROI relative location 875 // ROI relative location
876 kRoi[0].getCenterPosition(fCenter); 876 kRoi[0].getCenterPosition(fCenter);
877 for(int i = 0; i < 3; i++) iCenter[i] = (i 877 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
878 if(kLittleEndianOutput) { 878 if(kLittleEndianOutput) {
879 ofile.write((char *)iCenter, 3*sizeof(in 879 ofile.write((char *)iCenter, 3*sizeof(int));
880 } else { 880 } else {
881 for(int j = 0; j < 3; j++) 881 for(int j = 0; j < 3; j++)
882 invertByteOrder((char *)&iCenter[j], itmp[j] 882 invertByteOrder((char *)&iCenter[j], itmp[j]);
883 ofile.write((char *)itmp, 12); 883 ofile.write((char *)itmp, 12);
884 } 884 }
885 if(DEBUG || kVerbose > 0) { 885 if(DEBUG || kVerbose > 0) {
886 G4cout << "ROI image relative location : 886 G4cout << "ROI image relative location : ("
887 << iCenter[0] << ", " 887 << iCenter[0] << ", "
888 << iCenter[1] << ", " 888 << iCenter[1] << ", "
889 << iCenter[2] << ")" << G4endl; 889 << iCenter[2] << ")" << G4endl;
890 } 890 }
891 } 891 }
892 892
893 //----- track information -----// 893 //----- track information -----//
894 // number of track 894 // number of track
895 if(kPointerToTrackData > 0) { 895 if(kPointerToTrackData > 0) {
896 896
897 int ntrk = (int)kTracks.size(); << 897 int ntrk = kTracks.size();
898 if(kLittleEndianOutput) { 898 if(kLittleEndianOutput) {
899 ofile.write((char *)&ntrk, sizeof(int)); 899 ofile.write((char *)&ntrk, sizeof(int));
900 } else { 900 } else {
901 invertByteOrder((char *)&ntrk, itmp[0]); 901 invertByteOrder((char *)&ntrk, itmp[0]);
902 ofile.write((char *)itmp, 4); 902 ofile.write((char *)itmp, 4);
903 } 903 }
904 if(DEBUG || kVerbose > 0) { 904 if(DEBUG || kVerbose > 0) {
905 G4cout << "# of tracks : " 905 G4cout << "# of tracks : "
906 << ntrk << G4endl; 906 << ntrk << G4endl;
907 } 907 }
908 908
909 for(int nt = 0; nt < ntrk; nt++) { 909 for(int nt = 0; nt < ntrk; nt++) {
910 910
911 // # of steps in a track 911 // # of steps in a track
912 int nsteps = kTracks[nt].getNumberOfStep 912 int nsteps = kTracks[nt].getNumberOfSteps();
913 if(kLittleEndianOutput) { 913 if(kLittleEndianOutput) {
914 ofile.write((char *)&nsteps, sizeof(int)); 914 ofile.write((char *)&nsteps, sizeof(int));
915 } else { 915 } else {
916 invertByteOrder((char *)&nsteps, itmp[0]); 916 invertByteOrder((char *)&nsteps, itmp[0]);
917 ofile.write((char *)itmp, 4); 917 ofile.write((char *)itmp, 4);
918 } 918 }
919 if(DEBUG || kVerbose > 0) { 919 if(DEBUG || kVerbose > 0) {
920 G4cout << "# of steps : " << nsteps << G4end 920 G4cout << "# of steps : " << nsteps << G4endl;
921 } 921 }
922 922
923 // track color 923 // track color
924 unsigned char tcolor[3]; 924 unsigned char tcolor[3];
925 kTracks[nt].getColor(tcolor); 925 kTracks[nt].getColor(tcolor);
926 ofile.write((char *)tcolor, 3); 926 ofile.write((char *)tcolor, 3);
927 927
928 // steps 928 // steps
929 float stepPoints[6]; 929 float stepPoints[6];
930 for(int isteps = 0; isteps < nsteps; ist 930 for(int isteps = 0; isteps < nsteps; isteps++) {
931 kTracks[nt].getStep(stepPoints[0], stepPoint 931 kTracks[nt].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
932 stepPoints[3], stepPoints[4], stepPo 932 stepPoints[3], stepPoints[4], stepPoints[5],
933 isteps); 933 isteps);
934 934
935 if(kLittleEndianOutput) { 935 if(kLittleEndianOutput) {
936 ofile.write((char *)stepPoints, sizeof(flo 936 ofile.write((char *)stepPoints, sizeof(float)*6);
937 } else { 937 } else {
938 for(int j = 0; j < 6; j++) 938 for(int j = 0; j < 6; j++)
939 invertByteOrder((char *)&stepPoints[j], 939 invertByteOrder((char *)&stepPoints[j], ftmp[j]);
940 ofile.write((char *)ftmp, 24); 940 ofile.write((char *)ftmp, 24);
941 } 941 }
942 } 942 }
943 } 943 }
944 } 944 }
945 945
946 //----- detector information -----// 946 //----- detector information -----//
947 // number of detectors 947 // number of detectors
948 if(kPointerToDetectorData > 0) { 948 if(kPointerToDetectorData > 0) {
949 int ndet = (int)kDetectors.size(); << 949 int ndet = kDetectors.size();
950 if(kLittleEndianOutput) { 950 if(kLittleEndianOutput) {
951 ofile.write((char *)&ndet, sizeof(int)); 951 ofile.write((char *)&ndet, sizeof(int));
952 } else { 952 } else {
953 invertByteOrder((char *)&ndet, itmp[0]); 953 invertByteOrder((char *)&ndet, itmp[0]);
954 ofile.write((char *)itmp, 4); 954 ofile.write((char *)itmp, 4);
955 } 955 }
956 if(DEBUG || kVerbose > 0) { 956 if(DEBUG || kVerbose > 0) {
957 G4cout << "# of detectors : " 957 G4cout << "# of detectors : "
958 << ndet << G4endl; 958 << ndet << G4endl;
959 } 959 }
960 960
961 for(int nd = 0; nd < ndet; nd++) { 961 for(int nd = 0; nd < ndet; nd++) {
962 962
963 // # of edges of a detector 963 // # of edges of a detector
964 int nedges = kDetectors[nd].getNumberOfE 964 int nedges = kDetectors[nd].getNumberOfEdges();
965 if(kLittleEndianOutput) { 965 if(kLittleEndianOutput) {
966 ofile.write((char *)&nedges, sizeof(int)); 966 ofile.write((char *)&nedges, sizeof(int));
967 } else { 967 } else {
968 invertByteOrder((char *)&nedges, itmp[0]); 968 invertByteOrder((char *)&nedges, itmp[0]);
969 ofile.write((char *)itmp, 4); 969 ofile.write((char *)itmp, 4);
970 } 970 }
971 if(DEBUG || kVerbose > 0) { 971 if(DEBUG || kVerbose > 0) {
972 G4cout << "# of edges in a detector : " << n 972 G4cout << "# of edges in a detector : " << nedges << G4endl;
973 } 973 }
974 974
975 // edges 975 // edges
976 float edgePoints[6]; 976 float edgePoints[6];
977 for(int ne = 0; ne < nedges; ne++) { 977 for(int ne = 0; ne < nedges; ne++) {
978 kDetectors[nd].getEdge(edgePoints[0], edgePo 978 kDetectors[nd].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
979 edgePoints[3], edgePoints[4], edg 979 edgePoints[3], edgePoints[4], edgePoints[5],
980 ne); 980 ne);
981 981
982 if(kLittleEndianOutput) { 982 if(kLittleEndianOutput) {
983 ofile.write((char *)edgePoints, sizeof(flo 983 ofile.write((char *)edgePoints, sizeof(float)*6);
984 } else { 984 } else {
985 for(int j = 0; j < 6; j++) 985 for(int j = 0; j < 6; j++)
986 invertByteOrder((char *)&edgePoints[j], 986 invertByteOrder((char *)&edgePoints[j], ftmp[j]);
987 ofile.write((char *)ftmp, 24); 987 ofile.write((char *)ftmp, 24);
988 } 988 }
989 989
990 if(DEBUG || kVerbose > 0) { 990 if(DEBUG || kVerbose > 0) {
991 if(ne < 1) { 991 if(ne < 1) {
992 G4cout << " edge : (" << edgePoints[0] < 992 G4cout << " edge : (" << edgePoints[0] << ", "
993 << edgePoints[1] << ", " 993 << edgePoints[1] << ", "
994 << edgePoints[2] << ") - (" 994 << edgePoints[2] << ") - ("
995 << edgePoints[3] << ", " 995 << edgePoints[3] << ", "
996 << edgePoints[4] << ", " 996 << edgePoints[4] << ", "
997 << edgePoints[5] << ")" << G4endl; 997 << edgePoints[5] << ")" << G4endl;
998 } 998 }
999 } 999 }
1000 } 1000 }
1001 1001
1002 // detector color 1002 // detector color
1003 unsigned char dcolor[3]; 1003 unsigned char dcolor[3];
1004 kDetectors[nd].getColor(dcolor); 1004 kDetectors[nd].getColor(dcolor);
1005 ofile.write((char *)dcolor, 3); 1005 ofile.write((char *)dcolor, 3);
1006 if(DEBUG || kVerbose > 0) { 1006 if(DEBUG || kVerbose > 0) {
1007 G4cout << " rgb : (" << (int)dcolor[0] << " 1007 G4cout << " rgb : (" << (int)dcolor[0] << ", "
1008 << (int)dcolor[1] << ", " 1008 << (int)dcolor[1] << ", "
1009 << (int)dcolor[2] << ")" << G4endl; 1009 << (int)dcolor[2] << ")" << G4endl;
1010 } 1010 }
1011 1011
1012 // detector name 1012 // detector name
1013 std::string dname = kDetectors[nd].getN 1013 std::string dname = kDetectors[nd].getName();
1014 dname.resize(80); 1014 dname.resize(80);
1015 ofile.write((char *)dname.c_str(), 80); 1015 ofile.write((char *)dname.c_str(), 80);
1016 if(DEBUG || kVerbose > 0) { 1016 if(DEBUG || kVerbose > 0) {
1017 G4cout << " detector name : " << dname << G 1017 G4cout << " detector name : " << dname << G4endl;
1018 1018
1019 } 1019 }
1020 } 1020 }
1021 } 1021 }
1022 1022
1023 // file end mark 1023 // file end mark
1024 ofile.write("END", 3); 1024 ofile.write("END", 3);
1025 1025
1026 ofile.close(); 1026 ofile.close();
1027 if(DEBUG || kVerbose > 0) 1027 if(DEBUG || kVerbose > 0)
1028 G4cout << ">>>> closed gdd file: " << kFi 1028 G4cout << ">>>> closed gdd file: " << kFileName << G4endl;
1029 1029
1030 return true; 1030 return true;
1031 } 1031 }
1032 bool G4GMocrenIO::storeData3() { 1032 bool G4GMocrenIO::storeData3() {
1033 1033
1034 if(kVerbose > 0) G4cout << ">>>>>>> store 1034 if(kVerbose > 0) G4cout << ">>>>>>> store data (ver.3) <<<<<<<" << G4endl;
1035 if(kVerbose > 0) G4cout << " " << k 1035 if(kVerbose > 0) G4cout << " " << kFileName << G4endl;
1036 1036
1037 bool DEBUG = false;// 1037 bool DEBUG = false;//
1038 1038
1039 // output file open 1039 // output file open
1040 std::ofstream ofile(kFileName.c_str(), 1040 std::ofstream ofile(kFileName.c_str(),
1041 std::ios_base::out|std::ios_base::b 1041 std::ios_base::out|std::ios_base::binary);
1042 1042
1043 // file identifier 1043 // file identifier
1044 ofile.write("gMocren ", 8); 1044 ofile.write("gMocren ", 8);
1045 1045
1046 // file version 1046 // file version
1047 unsigned char ver = 0x03; 1047 unsigned char ver = 0x03;
1048 ofile.write((char *)&ver, 1); 1048 ofile.write((char *)&ver, 1);
1049 1049
1050 // endian 1050 // endian
1051 ofile.write((char *)&kLittleEndianOutput, s 1051 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1052 1052
1053 // comment length (fixed size) 1053 // comment length (fixed size)
1054 int commentLength = 1024; 1054 int commentLength = 1024;
1055 ofile.write((char *)&commentLength, 4); 1055 ofile.write((char *)&commentLength, 4);
1056 1056
1057 // comment 1057 // comment
1058 char cmt[1025]; 1058 char cmt[1025];
1059 std::strncpy(cmt, kComment.c_str(), 1024); 1059 std::strncpy(cmt, kComment.c_str(), 1024);
1060 ofile.write((char *)cmt, 1024); 1060 ofile.write((char *)cmt, 1024);
1061 if(DEBUG || kVerbose > 0) { 1061 if(DEBUG || kVerbose > 0) {
1062 G4cout << "Data comment : " 1062 G4cout << "Data comment : "
1063 << kComment << G4endl; 1063 << kComment << G4endl;
1064 } 1064 }
1065 1065
1066 // voxel spacings for all images 1066 // voxel spacings for all images
1067 ofile.write((char *)kVoxelSpacing, 12); 1067 ofile.write((char *)kVoxelSpacing, 12);
1068 if(DEBUG || kVerbose > 0) { 1068 if(DEBUG || kVerbose > 0) {
1069 G4cout << "Voxel spacing : (" 1069 G4cout << "Voxel spacing : ("
1070 << kVoxelSpacing[0] << ", " 1070 << kVoxelSpacing[0] << ", "
1071 << kVoxelSpacing[1] << ", " 1071 << kVoxelSpacing[1] << ", "
1072 << kVoxelSpacing[2] 1072 << kVoxelSpacing[2]
1073 << ") mm " << G4endl; 1073 << ") mm " << G4endl;
1074 } 1074 }
1075 1075
1076 calcPointers3(); 1076 calcPointers3();
1077 1077
1078 // offset from file starting point to the m 1078 // offset from file starting point to the modality image data
1079 ofile.write((char *)&kPointerToModalityData 1079 ofile.write((char *)&kPointerToModalityData, 4);
1080 1080
1081 // # of dose distributions 1081 // # of dose distributions
1082 //int nDoseDist = (int)pointerToDoseDistDat 1082 //int nDoseDist = (int)pointerToDoseDistData.size();
1083 int nDoseDist = getNumDoseDist(); 1083 int nDoseDist = getNumDoseDist();
1084 ofile.write((char *)&nDoseDist, 4); 1084 ofile.write((char *)&nDoseDist, 4);
1085 1085
1086 // offset from file starting point to the d 1086 // offset from file starting point to the dose image data
1087 for(int i = 0; i < nDoseDist; i++) { 1087 for(int i = 0; i < nDoseDist; i++) {
1088 ofile.write((char *)&kPointerToDoseDistDa 1088 ofile.write((char *)&kPointerToDoseDistData[i], 4);
1089 } 1089 }
1090 1090
1091 // offset from file starting point to the R 1091 // offset from file starting point to the ROI image data
1092 ofile.write((char *)&kPointerToROIData, 4); 1092 ofile.write((char *)&kPointerToROIData, 4);
1093 1093
1094 // offset from file starting point to the t 1094 // offset from file starting point to the track data
1095 ofile.write((char *)&kPointerToTrackData, 4 1095 ofile.write((char *)&kPointerToTrackData, 4);
1096 if(DEBUG || kVerbose > 0) { 1096 if(DEBUG || kVerbose > 0) {
1097 G4cout << "Each pointer to data : " 1097 G4cout << "Each pointer to data : "
1098 << kPointerToModalityData << ", "; 1098 << kPointerToModalityData << ", ";
1099 for(int i = 0; i < nDoseDist; i++) { 1099 for(int i = 0; i < nDoseDist; i++) {
1100 G4cout << kPointerToDoseDistData[i] << 1100 G4cout << kPointerToDoseDistData[i] << ", ";
1101 } 1101 }
1102 G4cout << kPointerToROIData << ", " 1102 G4cout << kPointerToROIData << ", "
1103 << kPointerToTrackData << G4endl; 1103 << kPointerToTrackData << G4endl;
1104 } 1104 }
1105 1105
1106 //----- modality image -----// 1106 //----- modality image -----//
1107 1107
1108 int size[3]; 1108 int size[3];
1109 float scale; 1109 float scale;
1110 short minmax[2]; 1110 short minmax[2];
1111 float fCenter[3]; 1111 float fCenter[3];
1112 int iCenter[3]; 1112 int iCenter[3];
1113 // modality image size 1113 // modality image size
1114 kModality.getSize(size); 1114 kModality.getSize(size);
1115 ofile.write((char *)size, 3*sizeof(int)); 1115 ofile.write((char *)size, 3*sizeof(int));
1116 if(DEBUG || kVerbose > 0) { 1116 if(DEBUG || kVerbose > 0) {
1117 G4cout << "Modality image size : (" 1117 G4cout << "Modality image size : ("
1118 << size[0] << ", " 1118 << size[0] << ", "
1119 << size[1] << ", " 1119 << size[1] << ", "
1120 << size[2] << ")" 1120 << size[2] << ")"
1121 << G4endl; 1121 << G4endl;
1122 } 1122 }
1123 1123
1124 // modality image max. & min. 1124 // modality image max. & min.
1125 kModality.getMinMax(minmax); 1125 kModality.getMinMax(minmax);
1126 ofile.write((char *)minmax, 4); 1126 ofile.write((char *)minmax, 4);
1127 1127
1128 // modality image unit 1128 // modality image unit
1129 char munit[13] = "g/cm3 "; 1129 char munit[13] = "g/cm3 ";
1130 ofile.write((char *)munit, 12); 1130 ofile.write((char *)munit, 12);
1131 1131
1132 // modality image scale 1132 // modality image scale
1133 scale = (float)kModality.getScale(); 1133 scale = (float)kModality.getScale();
1134 ofile.write((char *)&scale, 4); 1134 ofile.write((char *)&scale, 4);
1135 if(DEBUG || kVerbose > 0) { 1135 if(DEBUG || kVerbose > 0) {
1136 G4cout << "Modality image min., max., sca 1136 G4cout << "Modality image min., max., scale : "
1137 << minmax[0] << ", " 1137 << minmax[0] << ", "
1138 << minmax[1] << ", " 1138 << minmax[1] << ", "
1139 << scale << G4endl; 1139 << scale << G4endl;
1140 } 1140 }
1141 1141
1142 // modality image 1142 // modality image
1143 int psize = size[0]*size[1]; 1143 int psize = size[0]*size[1];
1144 if(DEBUG || kVerbose > 0) G4cout << "Modali 1144 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
1145 for(int i = 0; i < size[2]; i++) { 1145 for(int i = 0; i < size[2]; i++) {
1146 short * image = kModality.getImage(i); 1146 short * image = kModality.getImage(i);
1147 ofile.write((char *)image, psize*sizeof(s 1147 ofile.write((char *)image, psize*sizeof(short));
1148 1148
1149 if(DEBUG || kVerbose > 0) G4cout << "[" < 1149 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1150 } 1150 }
1151 if(DEBUG || kVerbose > 0) G4cout << G4endl; 1151 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1152 1152
1153 // modality desity map for CT value 1153 // modality desity map for CT value
1154 size_t msize = minmax[1] - minmax[0]+1; 1154 size_t msize = minmax[1] - minmax[0]+1;
1155 float * pdmap = new float[msize]; 1155 float * pdmap = new float[msize];
1156 for(int i = 0; i < (int)msize; i++) pdmap[i 1156 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1157 ofile.write((char *)pdmap, msize*sizeof(flo 1157 ofile.write((char *)pdmap, msize*sizeof(float));
1158 if(DEBUG || kVerbose > 0) { 1158 if(DEBUG || kVerbose > 0) {
1159 G4cout << "density map : " << std::ends; 1159 G4cout << "density map : " << std::ends;
1160 for(int i = 0; i < (int)msize; i+=50) 1160 for(int i = 0; i < (int)msize; i+=50)
1161 G4cout <<kModalityImageDensityMap[i] << 1161 G4cout <<kModalityImageDensityMap[i] << ", ";
1162 G4cout << G4endl; 1162 G4cout << G4endl;
1163 } 1163 }
1164 delete [] pdmap; 1164 delete [] pdmap;
1165 1165
1166 1166
1167 //----- dose distribution image -----// 1167 //----- dose distribution image -----//
1168 1168
1169 if(!isDoseEmpty()) { 1169 if(!isDoseEmpty()) {
1170 1170
1171 calcDoseDistScale(); 1171 calcDoseDistScale();
1172 1172
1173 for(int ndose = 0; ndose < nDoseDist; ndo 1173 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1174 // dose distrbution image size 1174 // dose distrbution image size
1175 kDose[ndose].getSize(size); 1175 kDose[ndose].getSize(size);
1176 ofile.write((char *)size, 3*sizeof(int) 1176 ofile.write((char *)size, 3*sizeof(int));
1177 if(DEBUG || kVerbose > 0) { 1177 if(DEBUG || kVerbose > 0) {
1178 G4cout << "Dose dist. [" << ndose << "] ima 1178 G4cout << "Dose dist. [" << ndose << "] image size : ("
1179 << size[0] << ", " 1179 << size[0] << ", "
1180 << size[1] << ", " 1180 << size[1] << ", "
1181 << size[2] << ")" 1181 << size[2] << ")"
1182 << G4endl; 1182 << G4endl;
1183 } 1183 }
1184 1184
1185 // dose distribution max. & min. 1185 // dose distribution max. & min.
1186 getShortDoseDistMinMax(minmax, ndose); 1186 getShortDoseDistMinMax(minmax, ndose);
1187 ofile.write((char *)minmax, 2*2); // si 1187 ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2
1188 1188
1189 // dose distribution unit 1189 // dose distribution unit
1190 ofile.write((char *)kDoseUnit.c_str(), 1190 ofile.write((char *)kDoseUnit.c_str(), 12);
1191 if(DEBUG || kVerbose > 0) { 1191 if(DEBUG || kVerbose > 0) {
1192 G4cout << "Dose dist. unit : " << kDoseUnit 1192 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
1193 } 1193 }
1194 1194
1195 // dose distribution scaling 1195 // dose distribution scaling
1196 double dscale; 1196 double dscale;
1197 dscale = getDoseDistScale(ndose); 1197 dscale = getDoseDistScale(ndose);
1198 scale = float(dscale); 1198 scale = float(dscale);
1199 ofile.write((char *)&scale, 4); 1199 ofile.write((char *)&scale, 4);
1200 if(DEBUG || kVerbose > 0) { 1200 if(DEBUG || kVerbose > 0) {
1201 G4cout << "Dose dist. [" << ndose 1201 G4cout << "Dose dist. [" << ndose
1202 << "] image min., max., scale : " 1202 << "] image min., max., scale : "
1203 << minmax[0] << ", " 1203 << minmax[0] << ", "
1204 << minmax[1] << ", " 1204 << minmax[1] << ", "
1205 << scale << G4endl; 1205 << scale << G4endl;
1206 } 1206 }
1207 1207
1208 // dose distribution image 1208 // dose distribution image
1209 int dsize = size[0]*size[1]; 1209 int dsize = size[0]*size[1];
1210 short * dimage = new short[dsize]; 1210 short * dimage = new short[dsize];
1211 for(int z = 0; z < size[2]; z++) { 1211 for(int z = 0; z < size[2]; z++) {
1212 getShortDoseDist(dimage, z, ndose); 1212 getShortDoseDist(dimage, z, ndose);
1213 ofile.write((char *)dimage, dsize*2); //siz 1213 ofile.write((char *)dimage, dsize*2); //sizeof(short)
1214 1214
1215 if(DEBUG || kVerbose > 0) { 1215 if(DEBUG || kVerbose > 0) {
1216 for(int j = 0; j < dsize; j++) { 1216 for(int j = 0; j < dsize; j++) {
1217 if(dimage[j] < 0) 1217 if(dimage[j] < 0)
1218 G4cout << "[" << j << "," << z << "]" 1218 G4cout << "[" << j << "," << z << "]"
1219 << dimage[j] << ", "; 1219 << dimage[j] << ", ";
1220 } 1220 }
1221 } 1221 }
1222 } 1222 }
1223 if(DEBUG || kVerbose > 0) G4cout << G4e 1223 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1224 delete [] dimage; 1224 delete [] dimage;
1225 1225
1226 // relative location of the dose distri 1226 // relative location of the dose distribution image for
1227 // the modality image 1227 // the modality image
1228 getDoseDistCenterPosition(fCenter, ndos 1228 getDoseDistCenterPosition(fCenter, ndose);
1229 for(int i = 0; i < 3; i++) iCenter[i] = 1229 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1230 ofile.write((char *)iCenter, 3*4); // 3 1230 ofile.write((char *)iCenter, 3*4); // 3*sizeof(int)
1231 if(DEBUG || kVerbose > 0) { 1231 if(DEBUG || kVerbose > 0) {
1232 G4cout << "Dose dist. [" << ndose 1232 G4cout << "Dose dist. [" << ndose
1233 << "]image relative location : (" 1233 << "]image relative location : ("
1234 << iCenter[0] << ", " 1234 << iCenter[0] << ", "
1235 << iCenter[1] << ", " 1235 << iCenter[1] << ", "
1236 << iCenter[2] << ")" << G4endl; 1236 << iCenter[2] << ")" << G4endl;
1237 } 1237 }
1238 } 1238 }
1239 } 1239 }
1240 1240
1241 //----- ROI image -----// 1241 //----- ROI image -----//
1242 if(!isROIEmpty()) { 1242 if(!isROIEmpty()) {
1243 // ROI image size 1243 // ROI image size
1244 kRoi[0].getSize(size); 1244 kRoi[0].getSize(size);
1245 ofile.write((char *)size, 3*sizeof(int)); 1245 ofile.write((char *)size, 3*sizeof(int));
1246 if(DEBUG || kVerbose > 0) { 1246 if(DEBUG || kVerbose > 0) {
1247 G4cout << "ROI image size : (" 1247 G4cout << "ROI image size : ("
1248 << size[0] << ", " 1248 << size[0] << ", "
1249 << size[1] << ", " 1249 << size[1] << ", "
1250 << size[2] << ")" 1250 << size[2] << ")"
1251 << G4endl; 1251 << G4endl;
1252 } 1252 }
1253 1253
1254 // ROI max. & min. 1254 // ROI max. & min.
1255 kRoi[0].getMinMax(minmax); 1255 kRoi[0].getMinMax(minmax);
1256 ofile.write((char *)minmax, sizeof(short) 1256 ofile.write((char *)minmax, sizeof(short)*2);
1257 1257
1258 // ROI distribution scaling 1258 // ROI distribution scaling
1259 scale = (float)kRoi[0].getScale(); 1259 scale = (float)kRoi[0].getScale();
1260 ofile.write((char *)&scale, sizeof(float) 1260 ofile.write((char *)&scale, sizeof(float));
1261 if(DEBUG || kVerbose > 0) { 1261 if(DEBUG || kVerbose > 0) {
1262 G4cout << "ROI image min., max., scale 1262 G4cout << "ROI image min., max., scale : "
1263 << minmax[0] << ", " 1263 << minmax[0] << ", "
1264 << minmax[1] << ", " 1264 << minmax[1] << ", "
1265 << scale << G4endl; 1265 << scale << G4endl;
1266 } 1266 }
1267 1267
1268 // ROI image 1268 // ROI image
1269 int rsize = size[0]*size[1]; 1269 int rsize = size[0]*size[1];
1270 for(int i = 0; i < size[2]; i++) { 1270 for(int i = 0; i < size[2]; i++) {
1271 short * rimage = kRoi[0].getImage(i); 1271 short * rimage = kRoi[0].getImage(i);
1272 ofile.write((char *)rimage, rsize*sizeo 1272 ofile.write((char *)rimage, rsize*sizeof(short));
1273 1273
1274 } 1274 }
1275 1275
1276 // ROI relative location 1276 // ROI relative location
1277 kRoi[0].getCenterPosition(fCenter); 1277 kRoi[0].getCenterPosition(fCenter);
1278 for(int i = 0; i < 3; i++) iCenter[i] = ( 1278 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1279 ofile.write((char *)iCenter, 3*sizeof(int 1279 ofile.write((char *)iCenter, 3*sizeof(int));
1280 if(DEBUG || kVerbose > 0) { 1280 if(DEBUG || kVerbose > 0) {
1281 G4cout << "ROI image relative location 1281 G4cout << "ROI image relative location : ("
1282 << iCenter[0] << ", " 1282 << iCenter[0] << ", "
1283 << iCenter[1] << ", " 1283 << iCenter[1] << ", "
1284 << iCenter[2] << ")" << G4endl; 1284 << iCenter[2] << ")" << G4endl;
1285 } 1285 }
1286 } 1286 }
1287 1287
1288 //----- track information -----// 1288 //----- track information -----//
1289 // number of track 1289 // number of track
1290 int ntrk = (int)kSteps.size(); << 1290 int ntrk = kSteps.size();
1291 ofile.write((char *)&ntrk, sizeof(int)); 1291 ofile.write((char *)&ntrk, sizeof(int));
1292 if(DEBUG || kVerbose > 0) { 1292 if(DEBUG || kVerbose > 0) {
1293 G4cout << "# of tracks : " 1293 G4cout << "# of tracks : "
1294 << ntrk << G4endl; 1294 << ntrk << G4endl;
1295 } 1295 }
1296 // track position 1296 // track position
1297 for(int i = 0; i < ntrk; i++) { 1297 for(int i = 0; i < ntrk; i++) {
1298 float * tp = kSteps[i]; 1298 float * tp = kSteps[i];
1299 ofile.write((char *)tp, sizeof(float)*6); 1299 ofile.write((char *)tp, sizeof(float)*6);
1300 } 1300 }
1301 // track color 1301 // track color
1302 int ntcolor = int(kStepColors.size()); 1302 int ntcolor = int(kStepColors.size());
1303 if(ntrk != ntcolor) 1303 if(ntrk != ntcolor)
1304 if (G4VisManager::GetVerbosity() >= G4Vis 1304 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1305 G4cout << "# of track color information 1305 G4cout << "# of track color information must be the same as # of tracks."
1306 << G4endl; 1306 << G4endl;
1307 unsigned char white[3] = {255,255,255}; // 1307 unsigned char white[3] = {255,255,255}; // default color
1308 for(int i = 0; i < ntrk; i++) { 1308 for(int i = 0; i < ntrk; i++) {
1309 if(i < ntcolor) { 1309 if(i < ntcolor) {
1310 unsigned char * tcolor = kStepColors[i] 1310 unsigned char * tcolor = kStepColors[i];
1311 ofile.write((char *)tcolor, 3); 1311 ofile.write((char *)tcolor, 3);
1312 } else { 1312 } else {
1313 ofile.write((char *)white, 3); 1313 ofile.write((char *)white, 3);
1314 } 1314 }
1315 } 1315 }
1316 1316
1317 // file end mark 1317 // file end mark
1318 ofile.write("END", 3); 1318 ofile.write("END", 3);
1319 1319
1320 ofile.close(); 1320 ofile.close();
1321 1321
1322 return true; 1322 return true;
1323 } 1323 }
1324 // 1324 //
1325 bool G4GMocrenIO::storeData4(char * _filename 1325 bool G4GMocrenIO::storeData4(char * _filename) {
1326 kFileName = _filename; 1326 kFileName = _filename;
1327 return storeData4(); 1327 return storeData4();
1328 } 1328 }
1329 1329
1330 // version 2 1330 // version 2
1331 bool G4GMocrenIO::storeData2() { 1331 bool G4GMocrenIO::storeData2() {
1332 1332
1333 if(kVerbose > 0) G4cout << ">>>>>>> store 1333 if(kVerbose > 0) G4cout << ">>>>>>> store data (ver.2) <<<<<<<" << G4endl;
1334 if(kVerbose > 0) G4cout << " " << k 1334 if(kVerbose > 0) G4cout << " " << kFileName << G4endl;
1335 1335
1336 bool DEBUG = false;// 1336 bool DEBUG = false;//
1337 1337
1338 // output file open 1338 // output file open
1339 std::ofstream ofile(kFileName.c_str(), 1339 std::ofstream ofile(kFileName.c_str(),
1340 std::ios_base::out|std::ios_base::b 1340 std::ios_base::out|std::ios_base::binary);
1341 1341
1342 // file identifier 1342 // file identifier
1343 ofile.write("GRAPE ", 8); 1343 ofile.write("GRAPE ", 8);
1344 1344
1345 // file version 1345 // file version
1346 unsigned char ver = 0x02; 1346 unsigned char ver = 0x02;
1347 ofile.write((char *)&ver, 1); 1347 ofile.write((char *)&ver, 1);
1348 // file id for old file format support 1348 // file id for old file format support
1349 ofile.write(kId.c_str(), IDLENGTH); 1349 ofile.write(kId.c_str(), IDLENGTH);
1350 // file version for old file format support 1350 // file version for old file format support
1351 ofile.write(kVersion.c_str(), VERLENGTH); 1351 ofile.write(kVersion.c_str(), VERLENGTH);
1352 // endian 1352 // endian
1353 ofile.write((char *)&kLittleEndianOutput, s 1353 ofile.write((char *)&kLittleEndianOutput, sizeof(char));
1354 1354
1355 /* 1355 /*
1356 // event number 1356 // event number
1357 ofile.write((char *)&numberOfEvents, sizeof 1357 ofile.write((char *)&numberOfEvents, sizeof(int));
1358 float imageSpacing[3]; 1358 float imageSpacing[3];
1359 imageSpacing[0] = modalityImageVoxelSpacing 1359 imageSpacing[0] = modalityImageVoxelSpacing[0];
1360 imageSpacing[1] = modalityImageVoxelSpacing 1360 imageSpacing[1] = modalityImageVoxelSpacing[1];
1361 imageSpacing[2] = modalityImageVoxelSpacing 1361 imageSpacing[2] = modalityImageVoxelSpacing[2];
1362 ofile.write((char *)imageSpacing, 12); 1362 ofile.write((char *)imageSpacing, 12);
1363 */ 1363 */
1364 1364
1365 1365
1366 // voxel spacings for all images 1366 // voxel spacings for all images
1367 ofile.write((char *)kVoxelSpacing, 12); 1367 ofile.write((char *)kVoxelSpacing, 12);
1368 if(DEBUG || kVerbose > 0) { 1368 if(DEBUG || kVerbose > 0) {
1369 G4cout << "Voxel spacing : (" 1369 G4cout << "Voxel spacing : ("
1370 << kVoxelSpacing[0] << ", " 1370 << kVoxelSpacing[0] << ", "
1371 << kVoxelSpacing[1] << ", " 1371 << kVoxelSpacing[1] << ", "
1372 << kVoxelSpacing[2] 1372 << kVoxelSpacing[2]
1373 << ") mm " << G4endl; 1373 << ") mm " << G4endl;
1374 } 1374 }
1375 1375
1376 calcPointers2(); 1376 calcPointers2();
1377 // offset from file starting point to the m 1377 // offset from file starting point to the modality image data
1378 ofile.write((char *)&kPointerToModalityData 1378 ofile.write((char *)&kPointerToModalityData, 4);
1379 1379
1380 // offset from file starting point to the d 1380 // offset from file starting point to the dose image data
1381 ofile.write((char *)&kPointerToDoseDistData 1381 ofile.write((char *)&kPointerToDoseDistData[0], 4);
1382 1382
1383 // offset from file starting point to the R 1383 // offset from file starting point to the ROI image data
1384 ofile.write((char *)&kPointerToROIData, 4); 1384 ofile.write((char *)&kPointerToROIData, 4);
1385 1385
1386 // offset from file starting point to the t 1386 // offset from file starting point to the track data
1387 ofile.write((char *)&kPointerToTrackData, 4 1387 ofile.write((char *)&kPointerToTrackData, 4);
1388 if(DEBUG || kVerbose > 0) { 1388 if(DEBUG || kVerbose > 0) {
1389 G4cout << "Each pointer to data : " 1389 G4cout << "Each pointer to data : "
1390 << kPointerToModalityData << ", " 1390 << kPointerToModalityData << ", "
1391 << kPointerToDoseDistData[0] << ", " 1391 << kPointerToDoseDistData[0] << ", "
1392 << kPointerToROIData << ", " 1392 << kPointerToROIData << ", "
1393 << kPointerToTrackData << G4endl; 1393 << kPointerToTrackData << G4endl;
1394 } 1394 }
1395 1395
1396 //----- modality image -----// 1396 //----- modality image -----//
1397 1397
1398 int size[3]; 1398 int size[3];
1399 float scale; 1399 float scale;
1400 short minmax[2]; 1400 short minmax[2];
1401 float fCenter[3]; 1401 float fCenter[3];
1402 int iCenter[3]; 1402 int iCenter[3];
1403 // modality image size 1403 // modality image size
1404 kModality.getSize(size); 1404 kModality.getSize(size);
1405 ofile.write((char *)size, 3*sizeof(int)); 1405 ofile.write((char *)size, 3*sizeof(int));
1406 if(DEBUG || kVerbose > 0) { 1406 if(DEBUG || kVerbose > 0) {
1407 G4cout << "Modality image size : (" 1407 G4cout << "Modality image size : ("
1408 << size[0] << ", " 1408 << size[0] << ", "
1409 << size[1] << ", " 1409 << size[1] << ", "
1410 << size[2] << ")" 1410 << size[2] << ")"
1411 << G4endl; 1411 << G4endl;
1412 } 1412 }
1413 1413
1414 // modality image max. & min. 1414 // modality image max. & min.
1415 kModality.getMinMax(minmax); 1415 kModality.getMinMax(minmax);
1416 ofile.write((char *)minmax, 4); 1416 ofile.write((char *)minmax, 4);
1417 1417
1418 // modality image unit 1418 // modality image unit
1419 //char munit[13] = "g/cm3 "; 1419 //char munit[13] = "g/cm3 ";
1420 //ofile.write((char *)&munit, 12); 1420 //ofile.write((char *)&munit, 12);
1421 1421
1422 // modality image scale 1422 // modality image scale
1423 scale = (float)kModality.getScale(); 1423 scale = (float)kModality.getScale();
1424 ofile.write((char *)&scale, 4); 1424 ofile.write((char *)&scale, 4);
1425 if(DEBUG || kVerbose > 0) { 1425 if(DEBUG || kVerbose > 0) {
1426 G4cout << "Modality image min., max., sca 1426 G4cout << "Modality image min., max., scale : "
1427 << minmax[0] << ", " 1427 << minmax[0] << ", "
1428 << minmax[1] << ", " 1428 << minmax[1] << ", "
1429 << scale << G4endl; 1429 << scale << G4endl;
1430 } 1430 }
1431 1431
1432 // modality image 1432 // modality image
1433 int psize = size[0]*size[1]; 1433 int psize = size[0]*size[1];
1434 if(DEBUG || kVerbose > 0) G4cout << "Modali 1434 if(DEBUG || kVerbose > 0) G4cout << "Modality image : ";
1435 for(int i = 0; i < size[2]; i++) { 1435 for(int i = 0; i < size[2]; i++) {
1436 short * image =kModality.getImage(i); 1436 short * image =kModality.getImage(i);
1437 ofile.write((char *)image, psize*sizeof(s 1437 ofile.write((char *)image, psize*sizeof(short));
1438 1438
1439 if(DEBUG || kVerbose > 0) G4cout << "[" < 1439 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", ";
1440 } 1440 }
1441 if(DEBUG || kVerbose > 0) G4cout << G4endl; 1441 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1442 1442
1443 // modality desity map for CT value 1443 // modality desity map for CT value
1444 size_t msize = minmax[1] - minmax[0]+1; 1444 size_t msize = minmax[1] - minmax[0]+1;
1445 float * pdmap = new float[msize]; 1445 float * pdmap = new float[msize];
1446 for(int i = 0; i < (int)msize; i++) pdmap[i 1446 for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i];
1447 ofile.write((char *)pdmap, msize*sizeof(flo 1447 ofile.write((char *)pdmap, msize*sizeof(float));
1448 if(DEBUG || kVerbose > 0) { 1448 if(DEBUG || kVerbose > 0) {
1449 G4cout << "density map : " << std::ends; 1449 G4cout << "density map : " << std::ends;
1450 for(int i = 0; i < (int)msize; i+=50) 1450 for(int i = 0; i < (int)msize; i+=50)
1451 G4cout <<kModalityImageDensityMap[i] << 1451 G4cout <<kModalityImageDensityMap[i] << ", ";
1452 G4cout << G4endl; 1452 G4cout << G4endl;
1453 } 1453 }
1454 delete [] pdmap; 1454 delete [] pdmap;
1455 1455
1456 1456
1457 //----- dose distribution image -----// 1457 //----- dose distribution image -----//
1458 1458
1459 if(!isDoseEmpty()) { 1459 if(!isDoseEmpty()) {
1460 calcDoseDistScale(); 1460 calcDoseDistScale();
1461 1461
1462 // dose distrbution image size 1462 // dose distrbution image size
1463 kDose[0].getSize(size); 1463 kDose[0].getSize(size);
1464 ofile.write((char *)size, 3*sizeof(int)); 1464 ofile.write((char *)size, 3*sizeof(int));
1465 if(DEBUG || kVerbose > 0) { 1465 if(DEBUG || kVerbose > 0) {
1466 G4cout << "Dose dist. image size : (" 1466 G4cout << "Dose dist. image size : ("
1467 << size[0] << ", " 1467 << size[0] << ", "
1468 << size[1] << ", " 1468 << size[1] << ", "
1469 << size[2] << ")" 1469 << size[2] << ")"
1470 << G4endl; 1470 << G4endl;
1471 } 1471 }
1472 1472
1473 // dose distribution max. & min. 1473 // dose distribution max. & min.
1474 getShortDoseDistMinMax(minmax); 1474 getShortDoseDistMinMax(minmax);
1475 ofile.write((char *)minmax, sizeof(short) 1475 ofile.write((char *)minmax, sizeof(short)*2);
1476 1476
1477 // dose distribution scaling 1477 // dose distribution scaling
1478 scale = (float)kDose[0].getScale(); 1478 scale = (float)kDose[0].getScale();
1479 ofile.write((char *)&scale, sizeof(float) 1479 ofile.write((char *)&scale, sizeof(float));
1480 if(DEBUG || kVerbose > 0) { 1480 if(DEBUG || kVerbose > 0) {
1481 G4cout << "Dose dist. image min., max., 1481 G4cout << "Dose dist. image min., max., scale : "
1482 << minmax[0] << ", " 1482 << minmax[0] << ", "
1483 << minmax[1] << ", " 1483 << minmax[1] << ", "
1484 << scale << G4endl; 1484 << scale << G4endl;
1485 } 1485 }
1486 1486
1487 // dose distribution image 1487 // dose distribution image
1488 int dsize = size[0]*size[1]; 1488 int dsize = size[0]*size[1];
1489 short * dimage = new short[dsize]; 1489 short * dimage = new short[dsize];
1490 for(int z = 0; z < size[2]; z++) { 1490 for(int z = 0; z < size[2]; z++) {
1491 getShortDoseDist(dimage, z); 1491 getShortDoseDist(dimage, z);
1492 ofile.write((char *)dimage, dsize*sizeo 1492 ofile.write((char *)dimage, dsize*sizeof(short));
1493 1493
1494 if(DEBUG || kVerbose > 0) { 1494 if(DEBUG || kVerbose > 0) {
1495 for(int j = 0; j < dsize; j++) { 1495 for(int j = 0; j < dsize; j++) {
1496 if(dimage[j] < 0) 1496 if(dimage[j] < 0)
1497 G4cout << "[" << j << "," << z << "]" 1497 G4cout << "[" << j << "," << z << "]"
1498 << dimage[j] << ", "; 1498 << dimage[j] << ", ";
1499 } 1499 }
1500 } 1500 }
1501 } 1501 }
1502 if(DEBUG || kVerbose > 0) G4cout << G4end 1502 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1503 delete [] dimage; 1503 delete [] dimage;
1504 1504
1505 // relative location of the dose distribu 1505 // relative location of the dose distribution image for
1506 // the modality image 1506 // the modality image
1507 kDose[0].getCenterPosition(fCenter); 1507 kDose[0].getCenterPosition(fCenter);
1508 for(int i = 0; i < 3; i++) iCenter[i] = ( 1508 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1509 ofile.write((char *)iCenter, 3*sizeof(int 1509 ofile.write((char *)iCenter, 3*sizeof(int));
1510 if(DEBUG || kVerbose > 0) { 1510 if(DEBUG || kVerbose > 0) {
1511 G4cout << "Dose dist. image relative lo 1511 G4cout << "Dose dist. image relative location : ("
1512 << iCenter[0] << ", " 1512 << iCenter[0] << ", "
1513 << iCenter[1] << ", " 1513 << iCenter[1] << ", "
1514 << iCenter[2] << ")" << G4endl; 1514 << iCenter[2] << ")" << G4endl;
1515 } 1515 }
1516 1516
1517 } 1517 }
1518 1518
1519 //----- ROI image -----// 1519 //----- ROI image -----//
1520 if(!isROIEmpty()) { 1520 if(!isROIEmpty()) {
1521 // ROI image size 1521 // ROI image size
1522 kRoi[0].getSize(size); 1522 kRoi[0].getSize(size);
1523 ofile.write((char *)size, 3*sizeof(int)); 1523 ofile.write((char *)size, 3*sizeof(int));
1524 if(DEBUG || kVerbose > 0) { 1524 if(DEBUG || kVerbose > 0) {
1525 G4cout << "ROI image size : (" 1525 G4cout << "ROI image size : ("
1526 << size[0] << ", " 1526 << size[0] << ", "
1527 << size[1] << ", " 1527 << size[1] << ", "
1528 << size[2] << ")" 1528 << size[2] << ")"
1529 << G4endl; 1529 << G4endl;
1530 } 1530 }
1531 1531
1532 // ROI max. & min. 1532 // ROI max. & min.
1533 kRoi[0].getMinMax(minmax); 1533 kRoi[0].getMinMax(minmax);
1534 ofile.write((char *)minmax, sizeof(short) 1534 ofile.write((char *)minmax, sizeof(short)*2);
1535 1535
1536 // ROI distribution scaling 1536 // ROI distribution scaling
1537 scale = (float)kRoi[0].getScale(); 1537 scale = (float)kRoi[0].getScale();
1538 ofile.write((char *)&scale, sizeof(float) 1538 ofile.write((char *)&scale, sizeof(float));
1539 if(DEBUG || kVerbose > 0) { 1539 if(DEBUG || kVerbose > 0) {
1540 G4cout << "ROI image min., max., scale 1540 G4cout << "ROI image min., max., scale : "
1541 << minmax[0] << ", " 1541 << minmax[0] << ", "
1542 << minmax[1] << ", " 1542 << minmax[1] << ", "
1543 << scale << G4endl; 1543 << scale << G4endl;
1544 } 1544 }
1545 1545
1546 // ROI image 1546 // ROI image
1547 int rsize = size[0]*size[1]; 1547 int rsize = size[0]*size[1];
1548 for(int i = 0; i < size[2]; i++) { 1548 for(int i = 0; i < size[2]; i++) {
1549 short * rimage = kRoi[0].getImage(i); 1549 short * rimage = kRoi[0].getImage(i);
1550 ofile.write((char *)rimage, rsize*sizeo 1550 ofile.write((char *)rimage, rsize*sizeof(short));
1551 1551
1552 } 1552 }
1553 1553
1554 // ROI relative location 1554 // ROI relative location
1555 kRoi[0].getCenterPosition(fCenter); 1555 kRoi[0].getCenterPosition(fCenter);
1556 for(int i = 0; i < 3; i++) iCenter[i] = ( 1556 for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i];
1557 ofile.write((char *)iCenter, 3*sizeof(int 1557 ofile.write((char *)iCenter, 3*sizeof(int));
1558 if(DEBUG || kVerbose > 0) { 1558 if(DEBUG || kVerbose > 0) {
1559 G4cout << "ROI image relative location 1559 G4cout << "ROI image relative location : ("
1560 << iCenter[0] << ", " 1560 << iCenter[0] << ", "
1561 << iCenter[1] << ", " 1561 << iCenter[1] << ", "
1562 << iCenter[2] << ")" << G4endl; 1562 << iCenter[2] << ")" << G4endl;
1563 } 1563 }
1564 } 1564 }
1565 1565
1566 1566
1567 //----- track information -----// 1567 //----- track information -----//
1568 // track 1568 // track
1569 int ntrk = (int)kSteps.size(); << 1569 int ntrk = kSteps.size();
1570 ofile.write((char *)&ntrk, sizeof(int)); 1570 ofile.write((char *)&ntrk, sizeof(int));
1571 if(DEBUG || kVerbose > 0) { 1571 if(DEBUG || kVerbose > 0) {
1572 G4cout << "# of tracks : " 1572 G4cout << "# of tracks : "
1573 << ntrk << G4endl; 1573 << ntrk << G4endl;
1574 } 1574 }
1575 for(int i = 0; i < ntrk; i++) { 1575 for(int i = 0; i < ntrk; i++) {
1576 float * tp = kSteps[i]; 1576 float * tp = kSteps[i];
1577 ofile.write((char *)tp, sizeof(float)*6); 1577 ofile.write((char *)tp, sizeof(float)*6);
1578 } 1578 }
1579 1579
1580 1580
1581 // file end mark 1581 // file end mark
1582 ofile.write("END", 3); 1582 ofile.write("END", 3);
1583 1583
1584 ofile.close(); 1584 ofile.close();
1585 1585
1586 return true; 1586 return true;
1587 } 1587 }
1588 // 1588 //
1589 bool G4GMocrenIO::storeData2(char * _filename 1589 bool G4GMocrenIO::storeData2(char * _filename) {
1590 kFileName = _filename; 1590 kFileName = _filename;
1591 return storeData(); 1591 return storeData();
1592 } 1592 }
1593 1593
1594 bool G4GMocrenIO::retrieveData() { 1594 bool G4GMocrenIO::retrieveData() {
1595 1595
1596 // input file open 1596 // input file open
1597 std::ifstream ifile(kFileName.c_str(), std: 1597 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1598 if(!ifile) { 1598 if(!ifile) {
1599 if (G4VisManager::GetVerbosity() >= G4Vis 1599 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1600 G4cout << "Cannot open file: " << kFile 1600 G4cout << "Cannot open file: " << kFileName
1601 << " in G4GMocrenIO::retrieveData()." 1601 << " in G4GMocrenIO::retrieveData()." << G4endl;
1602 return false; 1602 return false;
1603 } 1603 }
1604 1604
1605 // file identifier 1605 // file identifier
1606 char verid[9]; 1606 char verid[9];
1607 ifile.read((char *)verid, 8); 1607 ifile.read((char *)verid, 8);
1608 // file version 1608 // file version
1609 unsigned char ver; 1609 unsigned char ver;
1610 ifile.read((char *)&ver, 1); 1610 ifile.read((char *)&ver, 1);
1611 ifile.close(); 1611 ifile.close();
1612 1612
1613 if(std::strncmp(verid, "gMocren", 7) == 0) 1613 if(std::strncmp(verid, "gMocren", 7) == 0) {
1614 if(ver == 0x03) { 1614 if(ver == 0x03) {
1615 G4cout << ">>>>>>> retrieve data (ver. 1615 G4cout << ">>>>>>> retrieve data (ver.3) <<<<<<<" << G4endl;
1616 G4cout << " " << kFileName << G 1616 G4cout << " " << kFileName << G4endl;
1617 retrieveData3(); 1617 retrieveData3();
1618 } else if (ver == 0x04) { 1618 } else if (ver == 0x04) {
1619 G4cout << ">>>>>>> retrieve data (ver. 1619 G4cout << ">>>>>>> retrieve data (ver.4) <<<<<<<" << G4endl;
1620 G4cout << " " << kFileName << G 1620 G4cout << " " << kFileName << G4endl;
1621 retrieveData4(); 1621 retrieveData4();
1622 } else { 1622 } else {
1623 if (G4VisManager::GetVerbosity() >= G4V 1623 if (G4VisManager::GetVerbosity() >= G4VisManager::errors) {
1624 G4cout << "Error -- invalid file version : 1624 G4cout << "Error -- invalid file version : " << (int)ver
1625 << G4endl; 1625 << G4endl;
1626 G4cout << " " << kFileName << G4end 1626 G4cout << " " << kFileName << G4endl;
1627 } 1627 }
1628 G4Exception("G4GMocrenIO::retrieveDadta 1628 G4Exception("G4GMocrenIO::retrieveDadta()",
1629 "gMocren2001", FatalExcepti 1629 "gMocren2001", FatalException,
1630 "Error."); 1630 "Error.");
1631 1631
1632 } 1632 }
1633 } else if(std::strncmp(verid, "GRAPE", 5) = 1633 } else if(std::strncmp(verid, "GRAPE", 5) == 0) {
1634 G4cout << ">>>>>>> retrieve data (ver.2) 1634 G4cout << ">>>>>>> retrieve data (ver.2) <<<<<<<" << G4endl;
1635 G4cout << " " << kFileName << G4e 1635 G4cout << " " << kFileName << G4endl;
1636 retrieveData2(); 1636 retrieveData2();
1637 } else { 1637 } else {
1638 if (G4VisManager::GetVerbosity() >= G4Vis 1638 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1639 G4cout << kFileName << " was not gdd fi 1639 G4cout << kFileName << " was not gdd file." << G4endl;
1640 return false; 1640 return false;
1641 } 1641 }
1642 1642
1643 return true; 1643 return true;
1644 } 1644 }
1645 1645
1646 bool G4GMocrenIO::retrieveData(char * _filena 1646 bool G4GMocrenIO::retrieveData(char * _filename) {
1647 kFileName = _filename; 1647 kFileName = _filename;
1648 return retrieveData(); 1648 return retrieveData();
1649 } 1649 }
1650 1650
1651 // 1651 //
1652 bool G4GMocrenIO::retrieveData4() { 1652 bool G4GMocrenIO::retrieveData4() {
1653 1653
1654 bool DEBUG = false;// 1654 bool DEBUG = false;//
1655 1655
1656 // input file open 1656 // input file open
1657 std::ifstream ifile(kFileName.c_str(), std: 1657 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
1658 if(!ifile) { 1658 if(!ifile) {
1659 if (G4VisManager::GetVerbosity() >= G4Vis 1659 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
1660 G4cout << "Cannot open file: " << kFile 1660 G4cout << "Cannot open file: " << kFileName
1661 << " in G4GMocrenIO::retrieveData3()." << 1661 << " in G4GMocrenIO::retrieveData3()." << G4endl;
1662 return false; 1662 return false;
1663 } 1663 }
1664 1664
1665 // data buffer 1665 // data buffer
1666 char ctmp[24]; 1666 char ctmp[24];
1667 1667
1668 // file identifier 1668 // file identifier
1669 char verid[9]; 1669 char verid[9];
1670 ifile.read((char *)verid, 8); 1670 ifile.read((char *)verid, 8);
1671 1671
1672 // file version 1672 // file version
1673 unsigned char ver; 1673 unsigned char ver;
1674 ifile.read((char *)&ver, 1); 1674 ifile.read((char *)&ver, 1);
1675 std::stringstream ss; 1675 std::stringstream ss;
1676 ss << (int)ver; 1676 ss << (int)ver;
1677 kVersion = ss.str(); 1677 kVersion = ss.str();
1678 if(DEBUG || kVerbose > 0) G4cout << "File v 1678 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
1679 1679
1680 // endian 1680 // endian
1681 ifile.read((char *)&kLittleEndianInput, siz 1681 ifile.read((char *)&kLittleEndianInput, sizeof(char));
1682 if(DEBUG || kVerbose > 0) { 1682 if(DEBUG || kVerbose > 0) {
1683 G4cout << "Endian : "; 1683 G4cout << "Endian : ";
1684 if(kLittleEndianInput == 1) 1684 if(kLittleEndianInput == 1)
1685 G4cout << " little" << G4endl; 1685 G4cout << " little" << G4endl;
1686 else { 1686 else {
1687 G4cout << " big" << G4endl; 1687 G4cout << " big" << G4endl;
1688 } 1688 }
1689 } 1689 }
1690 1690
1691 // comment length (fixed size) 1691 // comment length (fixed size)
1692 int clength; 1692 int clength;
1693 ifile.read((char *)ctmp, 4); 1693 ifile.read((char *)ctmp, 4);
1694 convertEndian(ctmp, clength); 1694 convertEndian(ctmp, clength);
1695 // comment 1695 // comment
1696 char cmt[1025]; 1696 char cmt[1025];
1697 ifile.read((char *)cmt, clength); 1697 ifile.read((char *)cmt, clength);
1698 std::string scmt = cmt; 1698 std::string scmt = cmt;
1699 scmt += '\0'; 1699 scmt += '\0';
1700 setComment(scmt); 1700 setComment(scmt);
1701 if(DEBUG || kVerbose > 0) { 1701 if(DEBUG || kVerbose > 0) {
1702 G4cout << "Data comment : " 1702 G4cout << "Data comment : "
1703 << kComment << G4endl; 1703 << kComment << G4endl;
1704 } 1704 }
1705 1705
1706 // voxel spacings for all images 1706 // voxel spacings for all images
1707 ifile.read((char *)ctmp, 12); 1707 ifile.read((char *)ctmp, 12);
1708 convertEndian(ctmp, kVoxelSpacing[0]); 1708 convertEndian(ctmp, kVoxelSpacing[0]);
1709 convertEndian(ctmp+4, kVoxelSpacing[1]); 1709 convertEndian(ctmp+4, kVoxelSpacing[1]);
1710 convertEndian(ctmp+8, kVoxelSpacing[2]); 1710 convertEndian(ctmp+8, kVoxelSpacing[2]);
1711 if(DEBUG || kVerbose > 0) { 1711 if(DEBUG || kVerbose > 0) {
1712 G4cout << "Voxel spacing : (" 1712 G4cout << "Voxel spacing : ("
1713 << kVoxelSpacing[0] << ", " 1713 << kVoxelSpacing[0] << ", "
1714 << kVoxelSpacing[1] << ", " 1714 << kVoxelSpacing[1] << ", "
1715 << kVoxelSpacing[2] 1715 << kVoxelSpacing[2]
1716 << ") mm " << G4endl; 1716 << ") mm " << G4endl;
1717 } 1717 }
1718 1718
1719 1719
1720 // offset from file starting point to the m 1720 // offset from file starting point to the modality image data
1721 ifile.read((char *)ctmp, 4); 1721 ifile.read((char *)ctmp, 4);
1722 convertEndian(ctmp, kPointerToModalityData) 1722 convertEndian(ctmp, kPointerToModalityData);
1723 1723
1724 // # of dose distributions 1724 // # of dose distributions
1725 ifile.read((char *)ctmp, 4); 1725 ifile.read((char *)ctmp, 4);
1726 int nDoseDist; 1726 int nDoseDist;
1727 convertEndian(ctmp, nDoseDist); 1727 convertEndian(ctmp, nDoseDist);
1728 1728
1729 // offset from file starting point to the d 1729 // offset from file starting point to the dose image data
1730 for(int i = 0; i < nDoseDist; i++) { 1730 for(int i = 0; i < nDoseDist; i++) {
1731 ifile.read((char *)ctmp, 4); 1731 ifile.read((char *)ctmp, 4);
1732 unsigned int dptr; 1732 unsigned int dptr;
1733 convertEndian(ctmp, dptr); 1733 convertEndian(ctmp, dptr);
1734 addPointerToDoseDistData(dptr); 1734 addPointerToDoseDistData(dptr);
1735 } 1735 }
1736 1736
1737 // offset from file starting point to the R 1737 // offset from file starting point to the ROI image data
1738 ifile.read((char *)ctmp, 4); 1738 ifile.read((char *)ctmp, 4);
1739 convertEndian(ctmp, kPointerToROIData); 1739 convertEndian(ctmp, kPointerToROIData);
1740 1740
1741 // offset from file starting point to the t 1741 // offset from file starting point to the track data
1742 ifile.read((char *)ctmp, 4); 1742 ifile.read((char *)ctmp, 4);
1743 convertEndian(ctmp, kPointerToTrackData); 1743 convertEndian(ctmp, kPointerToTrackData);
1744 1744
1745 // offset from file starting point to the d 1745 // offset from file starting point to the detector data
1746 ifile.read((char *)ctmp, 4); 1746 ifile.read((char *)ctmp, 4);
1747 convertEndian(ctmp, kPointerToDetectorData) 1747 convertEndian(ctmp, kPointerToDetectorData);
1748 1748
1749 if(DEBUG || kVerbose > 0) { 1749 if(DEBUG || kVerbose > 0) {
1750 G4cout << "Each pointer to data : " 1750 G4cout << "Each pointer to data : "
1751 << kPointerToModalityData << ", "; 1751 << kPointerToModalityData << ", ";
1752 for(int i = 0; i < nDoseDist; i++) 1752 for(int i = 0; i < nDoseDist; i++)
1753 G4cout << kPointerToDoseDistData[i] << 1753 G4cout << kPointerToDoseDistData[i] << ", ";
1754 G4cout << kPointerToROIData << ", " 1754 G4cout << kPointerToROIData << ", "
1755 << kPointerToTrackData << ", " 1755 << kPointerToTrackData << ", "
1756 << kPointerToDetectorData 1756 << kPointerToDetectorData
1757 << G4endl; 1757 << G4endl;
1758 } 1758 }
1759 1759
1760 1760
1761 1761
1762 if(kPointerToModalityData == 0 && kPointerT 1762 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
1763 kPointerToROIData == 0 && kPointerToTrac 1763 kPointerToROIData == 0 && kPointerToTrackData == 0) {
1764 if(DEBUG || kVerbose > 0) { 1764 if(DEBUG || kVerbose > 0) {
1765 G4cout << "No data." << G4endl; 1765 G4cout << "No data." << G4endl;
1766 } 1766 }
1767 return false; 1767 return false;
1768 } 1768 }
1769 1769
1770 // event number 1770 // event number
1771 /* ver 1 1771 /* ver 1
1772 ifile.read(ctmp, sizeof(int)); 1772 ifile.read(ctmp, sizeof(int));
1773 convertEndian(ctmp, numberOfEvents); 1773 convertEndian(ctmp, numberOfEvents);
1774 */ 1774 */
1775 1775
1776 int size[3]; 1776 int size[3];
1777 float scale; 1777 float scale;
1778 double dscale; 1778 double dscale;
1779 short minmax[2]; 1779 short minmax[2];
1780 float fCenter[3]; 1780 float fCenter[3];
1781 int iCenter[3]; 1781 int iCenter[3];
1782 1782
1783 //----- Modality image -----// 1783 //----- Modality image -----//
1784 // modality image size 1784 // modality image size
1785 ifile.read(ctmp, 3*sizeof(int)); 1785 ifile.read(ctmp, 3*sizeof(int));
1786 convertEndian(ctmp, size[0]); 1786 convertEndian(ctmp, size[0]);
1787 convertEndian(ctmp+sizeof(int), size[1]); 1787 convertEndian(ctmp+sizeof(int), size[1]);
1788 convertEndian(ctmp+2*sizeof(int), size[2]); 1788 convertEndian(ctmp+2*sizeof(int), size[2]);
1789 if(DEBUG || kVerbose > 0) { 1789 if(DEBUG || kVerbose > 0) {
1790 G4cout << "Modality image size : (" 1790 G4cout << "Modality image size : ("
1791 << size[0] << ", " 1791 << size[0] << ", "
1792 << size[1] << ", " 1792 << size[1] << ", "
1793 << size[2] << ")" 1793 << size[2] << ")"
1794 << G4endl; 1794 << G4endl;
1795 } 1795 }
1796 kModality.setSize(size); 1796 kModality.setSize(size);
1797 1797
1798 // modality image voxel spacing 1798 // modality image voxel spacing
1799 /* 1799 /*
1800 ifile.read(ctmp, 3*sizeof(float)); 1800 ifile.read(ctmp, 3*sizeof(float));
1801 convertEndian(ctmp, modalityImageVoxelSpa 1801 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
1802 convertEndian(ctmp+sizeof(float), modalit 1802 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
1803 convertEndian(ctmp+2*sizeof(float), modal 1803 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
1804 */ 1804 */
1805 1805
1806 if(kPointerToModalityData != 0) { 1806 if(kPointerToModalityData != 0) {
1807 1807
1808 // modality density max. & min. 1808 // modality density max. & min.
1809 ifile.read((char *)ctmp, 4); 1809 ifile.read((char *)ctmp, 4);
1810 convertEndian(ctmp, minmax[0]); 1810 convertEndian(ctmp, minmax[0]);
1811 convertEndian(ctmp+2, minmax[1]); 1811 convertEndian(ctmp+2, minmax[1]);
1812 kModality.setMinMax(minmax); 1812 kModality.setMinMax(minmax);
1813 1813
1814 // modality image unit 1814 // modality image unit
1815 char munit[13]; 1815 char munit[13];
1816 munit[12] = '\0'; 1816 munit[12] = '\0';
1817 ifile.read((char *)munit, 12); 1817 ifile.read((char *)munit, 12);
1818 std::string smunit = munit; 1818 std::string smunit = munit;
1819 setModalityImageUnit(smunit); 1819 setModalityImageUnit(smunit);
1820 1820
1821 // modality density scale 1821 // modality density scale
1822 ifile.read((char *)ctmp, 4); 1822 ifile.read((char *)ctmp, 4);
1823 convertEndian(ctmp, scale); 1823 convertEndian(ctmp, scale);
1824 kModality.setScale(dscale = scale); 1824 kModality.setScale(dscale = scale);
1825 if(DEBUG || kVerbose > 0) { 1825 if(DEBUG || kVerbose > 0) {
1826 G4cout << "Modality image min., max., s 1826 G4cout << "Modality image min., max., scale : "
1827 << minmax[0] << ", " 1827 << minmax[0] << ", "
1828 << minmax[1] << ", " 1828 << minmax[1] << ", "
1829 << scale << G4endl; 1829 << scale << G4endl;
1830 } 1830 }
1831 1831
1832 // modality density 1832 // modality density
1833 int psize = size[0]*size[1]; 1833 int psize = size[0]*size[1];
1834 if(DEBUG || kVerbose > 0) G4cout << "Moda 1834 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
1835 char * cimage = new char[psize*sizeof(sho 1835 char * cimage = new char[psize*sizeof(short)];
1836 for(int i = 0; i < size[2]; i++) { 1836 for(int i = 0; i < size[2]; i++) {
1837 ifile.read((char *)cimage, psize*sizeof 1837 ifile.read((char *)cimage, psize*sizeof(short));
1838 short * mimage = new short[psize]; 1838 short * mimage = new short[psize];
1839 for(int j = 0; j < psize; j++) { 1839 for(int j = 0; j < psize; j++) {
1840 convertEndian(cimage+j*sizeof(short), mimag 1840 convertEndian(cimage+j*sizeof(short), mimage[j]);
1841 } 1841 }
1842 kModality.addImage(mimage); 1842 kModality.addImage(mimage);
1843 1843
1844 if(DEBUG || kVerbose > 0) G4cout << "[" 1844 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
1845 } 1845 }
1846 if(DEBUG || kVerbose > 0) G4cout << G4end 1846 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1847 delete [] cimage; 1847 delete [] cimage;
1848 1848
1849 // modality desity map for CT value 1849 // modality desity map for CT value
1850 size_t msize = minmax[1]-minmax[0]+1; 1850 size_t msize = minmax[1]-minmax[0]+1;
1851 if(DEBUG || kVerbose > 0) G4cout << "msiz 1851 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
1852 char * pdmap = new char[msize*sizeof(floa 1852 char * pdmap = new char[msize*sizeof(float)];
1853 ifile.read((char *)pdmap, msize*sizeof(fl 1853 ifile.read((char *)pdmap, msize*sizeof(float));
1854 float ftmp; 1854 float ftmp;
1855 for(int i = 0; i < (int)msize; i++) { 1855 for(int i = 0; i < (int)msize; i++) {
1856 convertEndian(pdmap+i*sizeof(float), ft 1856 convertEndian(pdmap+i*sizeof(float), ftmp);
1857 kModalityImageDensityMap.push_back(ftmp 1857 kModalityImageDensityMap.push_back(ftmp);
1858 } 1858 }
1859 delete [] pdmap; 1859 delete [] pdmap;
1860 1860
1861 if(DEBUG || kVerbose > 0) { 1861 if(DEBUG || kVerbose > 0) {
1862 G4cout << "density map : " << std::ends 1862 G4cout << "density map : " << std::ends;
1863 for(int i = 0; i < 10; i++) 1863 for(int i = 0; i < 10; i++)
1864 G4cout <<kModalityImageDensityMap[i] << ", 1864 G4cout <<kModalityImageDensityMap[i] << ", ";
1865 G4cout << G4endl; 1865 G4cout << G4endl;
1866 for(int i = 0; i < 10; i++) G4cout << " 1866 for(int i = 0; i < 10; i++) G4cout << "..";
1867 G4cout << G4endl; 1867 G4cout << G4endl;
1868 for(size_t i =kModalityImageDensityMap. 1868 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
1869 G4cout <<kModalityImageDensityMap[i] << ", 1869 G4cout <<kModalityImageDensityMap[i] << ", ";
1870 G4cout << G4endl; 1870 G4cout << G4endl;
1871 } 1871 }
1872 1872
1873 } 1873 }
1874 1874
1875 1875
1876 //----- dose distribution image -----// 1876 //----- dose distribution image -----//
1877 for(int ndose = 0; ndose < nDoseDist; ndose 1877 for(int ndose = 0; ndose < nDoseDist; ndose++) {
1878 1878
1879 newDoseDist(); 1879 newDoseDist();
1880 1880
1881 // dose distrbution image size 1881 // dose distrbution image size
1882 ifile.read((char *)ctmp, 3*sizeof(int)); 1882 ifile.read((char *)ctmp, 3*sizeof(int));
1883 convertEndian(ctmp, size[0]); 1883 convertEndian(ctmp, size[0]);
1884 convertEndian(ctmp+sizeof(int), size[1]); 1884 convertEndian(ctmp+sizeof(int), size[1]);
1885 convertEndian(ctmp+2*sizeof(int), size[2] 1885 convertEndian(ctmp+2*sizeof(int), size[2]);
1886 if(DEBUG || kVerbose > 0) { 1886 if(DEBUG || kVerbose > 0) {
1887 G4cout << "Dose dist. image size : (" 1887 G4cout << "Dose dist. image size : ("
1888 << size[0] << ", " 1888 << size[0] << ", "
1889 << size[1] << ", " 1889 << size[1] << ", "
1890 << size[2] << ")" 1890 << size[2] << ")"
1891 << G4endl; 1891 << G4endl;
1892 } 1892 }
1893 kDose[ndose].setSize(size); 1893 kDose[ndose].setSize(size);
1894 1894
1895 // dose distribution max. & min. 1895 // dose distribution max. & min.
1896 ifile.read((char *)ctmp, sizeof(short)*2) 1896 ifile.read((char *)ctmp, sizeof(short)*2);
1897 convertEndian(ctmp, minmax[0]); 1897 convertEndian(ctmp, minmax[0]);
1898 convertEndian(ctmp+2, minmax[1]); 1898 convertEndian(ctmp+2, minmax[1]);
1899 1899
1900 // dose distribution unit 1900 // dose distribution unit
1901 char dunit[13]; 1901 char dunit[13];
1902 dunit[12] = '\0'; 1902 dunit[12] = '\0';
1903 ifile.read((char *)dunit, 12); 1903 ifile.read((char *)dunit, 12);
1904 std::string sdunit = dunit; 1904 std::string sdunit = dunit;
1905 setDoseDistUnit(sdunit, ndose); 1905 setDoseDistUnit(sdunit, ndose);
1906 if(DEBUG || kVerbose > 0) { 1906 if(DEBUG || kVerbose > 0) {
1907 G4cout << "Dose dist. unit : " << kDose 1907 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
1908 } 1908 }
1909 1909
1910 // dose distribution scaling 1910 // dose distribution scaling
1911 ifile.read((char *)ctmp, 4); // sizeof(fl 1911 ifile.read((char *)ctmp, 4); // sizeof(float)
1912 convertEndian(ctmp, scale); 1912 convertEndian(ctmp, scale);
1913 kDose[ndose].setScale(dscale = scale); 1913 kDose[ndose].setScale(dscale = scale);
1914 1914
1915 double dminmax[2]; 1915 double dminmax[2];
1916 for(int i = 0; i < 2; i++) dminmax[i] = m 1916 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
1917 kDose[ndose].setMinMax(dminmax); 1917 kDose[ndose].setMinMax(dminmax);
1918 1918
1919 if(DEBUG || kVerbose > 0) { 1919 if(DEBUG || kVerbose > 0) {
1920 G4cout << "Dose dist. image min., max., 1920 G4cout << "Dose dist. image min., max., scale : "
1921 << dminmax[0] << ", " 1921 << dminmax[0] << ", "
1922 << dminmax[1] << ", " 1922 << dminmax[1] << ", "
1923 << scale << G4endl; 1923 << scale << G4endl;
1924 } 1924 }
1925 1925
1926 // dose distribution image 1926 // dose distribution image
1927 int dsize = size[0]*size[1]; 1927 int dsize = size[0]*size[1];
1928 if(DEBUG || kVerbose > 0) G4cout << "Dose 1928 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
1929 char * di = new char[dsize*sizeof(short)] 1929 char * di = new char[dsize*sizeof(short)];
1930 short * shimage = new short[dsize]; 1930 short * shimage = new short[dsize];
1931 for(int z = 0; z < size[2]; z++) { 1931 for(int z = 0; z < size[2]; z++) {
1932 ifile.read((char *)di, dsize*sizeof(sho 1932 ifile.read((char *)di, dsize*sizeof(short));
1933 double * dimage = new double[dsize]; 1933 double * dimage = new double[dsize];
1934 for(int xy = 0; xy < dsize; xy++) { 1934 for(int xy = 0; xy < dsize; xy++) {
1935 convertEndian(di+xy*sizeof(short), shimage[ 1935 convertEndian(di+xy*sizeof(short), shimage[xy]);
1936 dimage[xy] = shimage[xy]*dscale; 1936 dimage[xy] = shimage[xy]*dscale;
1937 } 1937 }
1938 kDose[ndose].addImage(dimage); 1938 kDose[ndose].addImage(dimage);
1939 1939
1940 if(DEBUG || kVerbose > 0) G4cout << "[" 1940 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
1941 1941
1942 if(DEBUG || kVerbose > 0) { 1942 if(DEBUG || kVerbose > 0) {
1943 for(int j = 0; j < dsize; j++) { 1943 for(int j = 0; j < dsize; j++) {
1944 if(dimage[j] < 0) 1944 if(dimage[j] < 0)
1945 G4cout << "[" << j << "," << z << "]" 1945 G4cout << "[" << j << "," << z << "]"
1946 << dimage[j] << ", "; 1946 << dimage[j] << ", ";
1947 } 1947 }
1948 } 1948 }
1949 } 1949 }
1950 delete [] shimage; 1950 delete [] shimage;
1951 delete [] di; 1951 delete [] di;
1952 if(DEBUG || kVerbose > 0) G4cout << G4end 1952 if(DEBUG || kVerbose > 0) G4cout << G4endl;
1953 1953
1954 ifile.read((char *)ctmp, 3*4); // 3*sizeo 1954 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
1955 convertEndian(ctmp, iCenter[0]); 1955 convertEndian(ctmp, iCenter[0]);
1956 convertEndian(ctmp+4, iCenter[1]); 1956 convertEndian(ctmp+4, iCenter[1]);
1957 convertEndian(ctmp+8, iCenter[2]); 1957 convertEndian(ctmp+8, iCenter[2]);
1958 for(int i = 0; i < 3; i++) fCenter[i] = ( 1958 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
1959 kDose[ndose].setCenterPosition(fCenter); 1959 kDose[ndose].setCenterPosition(fCenter);
1960 1960
1961 if(DEBUG || kVerbose > 0) { 1961 if(DEBUG || kVerbose > 0) {
1962 G4cout << "Dose dist. image relative lo 1962 G4cout << "Dose dist. image relative location : ("
1963 << fCenter[0] << ", " 1963 << fCenter[0] << ", "
1964 << fCenter[1] << ", " 1964 << fCenter[1] << ", "
1965 << fCenter[2] << ")" << G4endl; 1965 << fCenter[2] << ")" << G4endl;
1966 } 1966 }
1967 1967
1968 1968
1969 // dose distribution name 1969 // dose distribution name
1970 char cname[81]; 1970 char cname[81];
1971 ifile.read((char *)cname, 80); 1971 ifile.read((char *)cname, 80);
1972 std::string dosename = cname; 1972 std::string dosename = cname;
1973 setDoseDistName(dosename, ndose); 1973 setDoseDistName(dosename, ndose);
1974 if(DEBUG || kVerbose > 0) { 1974 if(DEBUG || kVerbose > 0) {
1975 G4cout << "Dose dist. name : " << dosen 1975 G4cout << "Dose dist. name : " << dosename << G4endl;
1976 } 1976 }
1977 1977
1978 } 1978 }
1979 1979
1980 //----- ROI image -----// 1980 //----- ROI image -----//
1981 if(kPointerToROIData != 0) { 1981 if(kPointerToROIData != 0) {
1982 1982
1983 newROI(); 1983 newROI();
1984 1984
1985 // ROI image size 1985 // ROI image size
1986 ifile.read((char *)ctmp, 3*sizeof(int)); 1986 ifile.read((char *)ctmp, 3*sizeof(int));
1987 convertEndian(ctmp, size[0]); 1987 convertEndian(ctmp, size[0]);
1988 convertEndian(ctmp+sizeof(int), size[1]); 1988 convertEndian(ctmp+sizeof(int), size[1]);
1989 convertEndian(ctmp+2*sizeof(int), size[2] 1989 convertEndian(ctmp+2*sizeof(int), size[2]);
1990 kRoi[0].setSize(size); 1990 kRoi[0].setSize(size);
1991 if(DEBUG || kVerbose > 0) { 1991 if(DEBUG || kVerbose > 0) {
1992 G4cout << "ROI image size : (" 1992 G4cout << "ROI image size : ("
1993 << size[0] << ", " 1993 << size[0] << ", "
1994 << size[1] << ", " 1994 << size[1] << ", "
1995 << size[2] << ")" 1995 << size[2] << ")"
1996 << G4endl; 1996 << G4endl;
1997 } 1997 }
1998 1998
1999 // ROI max. & min. 1999 // ROI max. & min.
2000 ifile.read((char *)ctmp, sizeof(short)*2) 2000 ifile.read((char *)ctmp, sizeof(short)*2);
2001 convertEndian(ctmp, minmax[0]); 2001 convertEndian(ctmp, minmax[0]);
2002 convertEndian(ctmp+sizeof(short), minmax[ 2002 convertEndian(ctmp+sizeof(short), minmax[1]);
2003 kRoi[0].setMinMax(minmax); 2003 kRoi[0].setMinMax(minmax);
2004 2004
2005 // ROI distribution scaling 2005 // ROI distribution scaling
2006 ifile.read((char *)ctmp, sizeof(float)); 2006 ifile.read((char *)ctmp, sizeof(float));
2007 convertEndian(ctmp, scale); 2007 convertEndian(ctmp, scale);
2008 kRoi[0].setScale(dscale = scale); 2008 kRoi[0].setScale(dscale = scale);
2009 if(DEBUG || kVerbose > 0) { 2009 if(DEBUG || kVerbose > 0) {
2010 G4cout << "ROI image min., max., scale 2010 G4cout << "ROI image min., max., scale : "
2011 << minmax[0] << ", " 2011 << minmax[0] << ", "
2012 << minmax[1] << ", " 2012 << minmax[1] << ", "
2013 << scale << G4endl; 2013 << scale << G4endl;
2014 } 2014 }
2015 2015
2016 // ROI image 2016 // ROI image
2017 int rsize = size[0]*size[1]; 2017 int rsize = size[0]*size[1];
2018 char * ri = new char[rsize*sizeof(short)] 2018 char * ri = new char[rsize*sizeof(short)];
2019 for(int i = 0; i < size[2]; i++) { 2019 for(int i = 0; i < size[2]; i++) {
2020 ifile.read((char *)ri, rsize*sizeof(sho 2020 ifile.read((char *)ri, rsize*sizeof(short));
2021 short * rimage = new short[rsize]; 2021 short * rimage = new short[rsize];
2022 for(int j = 0; j < rsize; j++) { 2022 for(int j = 0; j < rsize; j++) {
2023 convertEndian(ri+j*sizeof(short), rimage[j] 2023 convertEndian(ri+j*sizeof(short), rimage[j]);
2024 } 2024 }
2025 kRoi[0].addImage(rimage); 2025 kRoi[0].addImage(rimage);
2026 2026
2027 } 2027 }
2028 delete [] ri; 2028 delete [] ri;
2029 2029
2030 // ROI relative location 2030 // ROI relative location
2031 ifile.read((char *)ctmp, 3*sizeof(int)); 2031 ifile.read((char *)ctmp, 3*sizeof(int));
2032 convertEndian(ctmp, iCenter[0]); 2032 convertEndian(ctmp, iCenter[0]);
2033 convertEndian(ctmp+sizeof(int), iCenter[1 2033 convertEndian(ctmp+sizeof(int), iCenter[1]);
2034 convertEndian(ctmp+2*sizeof(int), iCenter 2034 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2035 for(int i = 0; i < 3; i++) fCenter[i] = i 2035 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2036 kRoi[0].setCenterPosition(fCenter); 2036 kRoi[0].setCenterPosition(fCenter);
2037 if(DEBUG || kVerbose > 0) { 2037 if(DEBUG || kVerbose > 0) {
2038 G4cout << "ROI image relative location 2038 G4cout << "ROI image relative location : ("
2039 << fCenter[0] << ", " 2039 << fCenter[0] << ", "
2040 << fCenter[1] << ", " 2040 << fCenter[1] << ", "
2041 << fCenter[2] << ")" << G4endl; 2041 << fCenter[2] << ")" << G4endl;
2042 } 2042 }
2043 2043
2044 } 2044 }
2045 2045
2046 //----- track information -----// 2046 //----- track information -----//
2047 if(kPointerToTrackData != 0) { 2047 if(kPointerToTrackData != 0) {
2048 2048
2049 // track 2049 // track
2050 ifile.read((char *)ctmp, sizeof(int)); 2050 ifile.read((char *)ctmp, sizeof(int));
2051 int ntrk; 2051 int ntrk;
2052 convertEndian(ctmp, ntrk); 2052 convertEndian(ctmp, ntrk);
2053 if(DEBUG || kVerbose > 0) { 2053 if(DEBUG || kVerbose > 0) {
2054 G4cout << "# of tracks: " << ntrk << G4 2054 G4cout << "# of tracks: " << ntrk << G4endl;
2055 } 2055 }
2056 2056
2057 // track position 2057 // track position
2058 unsigned char rgb[3]; 2058 unsigned char rgb[3];
2059 for(int i = 0; i < ntrk; i++) { 2059 for(int i = 0; i < ntrk; i++) {
2060 2060
2061 2061
2062 // # of steps in a track 2062 // # of steps in a track
2063 ifile.read((char *)ctmp, sizeof(int)); 2063 ifile.read((char *)ctmp, sizeof(int));
2064 int nsteps; 2064 int nsteps;
2065 convertEndian(ctmp, nsteps); 2065 convertEndian(ctmp, nsteps);
2066 2066
2067 // track color 2067 // track color
2068 ifile.read((char *)rgb, 3); 2068 ifile.read((char *)rgb, 3);
2069 2069
2070 std::vector<float *> steps; 2070 std::vector<float *> steps;
2071 // steps 2071 // steps
2072 for(int j = 0; j < nsteps; j++) { 2072 for(int j = 0; j < nsteps; j++) {
2073 2073
2074 float * steppoint = new float[6]; 2074 float * steppoint = new float[6];
2075 ifile.read((char *)ctmp, sizeof(float)*6); 2075 ifile.read((char *)ctmp, sizeof(float)*6);
2076 2076
2077 for(int k = 0; k < 6; k++) { 2077 for(int k = 0; k < 6; k++) {
2078 convertEndian(ctmp+k*sizeof(float), stepp 2078 convertEndian(ctmp+k*sizeof(float), steppoint[k]);
2079 } 2079 }
2080 2080
2081 steps.push_back(steppoint); 2081 steps.push_back(steppoint);
2082 } 2082 }
2083 2083
2084 // add a track to the track container 2084 // add a track to the track container
2085 addTrack(steps, rgb); 2085 addTrack(steps, rgb);
2086 2086
2087 if(DEBUG || kVerbose > 0) { 2087 if(DEBUG || kVerbose > 0) {
2088 if(i < 5) { 2088 if(i < 5) {
2089 G4cout << i << ": " ; 2089 G4cout << i << ": " ;
2090 for(int j = 0; j < 3; j++) G4cout << step 2090 for(int j = 0; j < 3; j++) G4cout << steps[0][j] << " ";
2091 int nstp = (int)steps.size(); << 2091 int nstp = steps.size();
2092 G4cout << "<-> "; 2092 G4cout << "<-> ";
2093 for(int j = 3; j < 6; j++) G4cout << step 2093 for(int j = 3; j < 6; j++) G4cout << steps[nstp-1][j] << " ";
2094 G4cout << " rgb( "; 2094 G4cout << " rgb( ";
2095 for(int j = 0; j < 3; j++) G4cout << (int 2095 for(int j = 0; j < 3; j++) G4cout << (int)rgb[j] << " ";
2096 G4cout << ")" << G4endl; 2096 G4cout << ")" << G4endl;
2097 } 2097 }
2098 } 2098 }
2099 } 2099 }
2100 2100
2101 2101
2102 } 2102 }
2103 2103
2104 2104
2105 //----- detector information -----// 2105 //----- detector information -----//
2106 if(kPointerToDetectorData != 0) { 2106 if(kPointerToDetectorData != 0) {
2107 2107
2108 // number of detectors 2108 // number of detectors
2109 ifile.read((char *)ctmp, sizeof(int)); 2109 ifile.read((char *)ctmp, sizeof(int));
2110 int ndet; 2110 int ndet;
2111 convertEndian(ctmp, ndet); 2111 convertEndian(ctmp, ndet);
2112 2112
2113 if(DEBUG || kVerbose > 0) { 2113 if(DEBUG || kVerbose > 0) {
2114 G4cout << "# of detectors : " 2114 G4cout << "# of detectors : "
2115 << ndet << G4endl; 2115 << ndet << G4endl;
2116 } 2116 }
2117 2117
2118 for(int nd = 0; nd < ndet; nd++) { 2118 for(int nd = 0; nd < ndet; nd++) {
2119 2119
2120 // # of edges of a detector 2120 // # of edges of a detector
2121 ifile.read((char *)ctmp, sizeof(int)); 2121 ifile.read((char *)ctmp, sizeof(int));
2122 int nedges; 2122 int nedges;
2123 convertEndian(ctmp, nedges); 2123 convertEndian(ctmp, nedges);
2124 if(DEBUG || kVerbose > 0) { 2124 if(DEBUG || kVerbose > 0) {
2125 G4cout << "# of edges in a detector : " << 2125 G4cout << "# of edges in a detector : " << nedges << G4endl;
2126 } 2126 }
2127 2127
2128 // edges 2128 // edges
2129 std::vector<float *> detector; 2129 std::vector<float *> detector;
2130 char cftmp[24]; 2130 char cftmp[24];
2131 for(int ne = 0; ne < nedges; ne++) { 2131 for(int ne = 0; ne < nedges; ne++) {
2132 2132
2133 ifile.read((char *)cftmp, sizeof(float)*6); 2133 ifile.read((char *)cftmp, sizeof(float)*6);
2134 float * edgePoints = new float[6]; 2134 float * edgePoints = new float[6];
2135 for(int j = 0; j < 6; j++) convertEndian(&c 2135 for(int j = 0; j < 6; j++) convertEndian(&cftmp[sizeof(float)*j], edgePoints[j]);
2136 detector.push_back(edgePoints); 2136 detector.push_back(edgePoints);
2137 2137
2138 } 2138 }
2139 2139
2140 if(DEBUG || kVerbose > 0) { 2140 if(DEBUG || kVerbose > 0) {
2141 G4cout << " first edge : (" << detector[0][ 2141 G4cout << " first edge : (" << detector[0][0] << ", "
2142 << detector[0][1] << ", " 2142 << detector[0][1] << ", "
2143 << detector[0][2] << ") - (" 2143 << detector[0][2] << ") - ("
2144 << detector[0][3] << ", " 2144 << detector[0][3] << ", "
2145 << detector[0][4] << ", " 2145 << detector[0][4] << ", "
2146 << detector[0][5] << ")" << G4endl; 2146 << detector[0][5] << ")" << G4endl;
2147 } 2147 }
2148 2148
2149 // detector color 2149 // detector color
2150 unsigned char dcolor[3]; 2150 unsigned char dcolor[3];
2151 ifile.read((char *)dcolor, 3); 2151 ifile.read((char *)dcolor, 3);
2152 if(DEBUG || kVerbose > 0) { 2152 if(DEBUG || kVerbose > 0) {
2153 G4cout << " detector color : rgb(" 2153 G4cout << " detector color : rgb("
2154 << (int)dcolor[0] << ", " 2154 << (int)dcolor[0] << ", "
2155 << (int)dcolor[1] << ", " 2155 << (int)dcolor[1] << ", "
2156 << (int)dcolor[2] << G4endl; 2156 << (int)dcolor[2] << G4endl;
2157 } 2157 }
2158 2158
2159 2159
2160 // detector name 2160 // detector name
2161 char cname[80]; 2161 char cname[80];
2162 ifile.read((char *)cname, 80); 2162 ifile.read((char *)cname, 80);
2163 std::string dname = cname; 2163 std::string dname = cname;
2164 if(DEBUG || kVerbose > 0) { 2164 if(DEBUG || kVerbose > 0) {
2165 G4cout << " detector name : " << dname << G 2165 G4cout << " detector name : " << dname << G4endl;
2166 } 2166 }
2167 2167
2168 2168
2169 addDetector(dname, detector, dcolor); 2169 addDetector(dname, detector, dcolor);
2170 2170
2171 } 2171 }
2172 } 2172 }
2173 2173
2174 2174
2175 ifile.close(); 2175 ifile.close();
2176 2176
2177 return true; 2177 return true;
2178 } 2178 }
2179 bool G4GMocrenIO::retrieveData4(char * _filen 2179 bool G4GMocrenIO::retrieveData4(char * _filename) {
2180 kFileName = _filename; 2180 kFileName = _filename;
2181 return retrieveData(); 2181 return retrieveData();
2182 } 2182 }
2183 2183
2184 // 2184 //
2185 bool G4GMocrenIO::retrieveData3() { 2185 bool G4GMocrenIO::retrieveData3() {
2186 2186
2187 bool DEBUG = false;// 2187 bool DEBUG = false;//
2188 2188
2189 // input file open 2189 // input file open
2190 std::ifstream ifile(kFileName.c_str(), std: 2190 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2191 if(!ifile) { 2191 if(!ifile) {
2192 if (G4VisManager::GetVerbosity() >= G4Vis 2192 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
2193 G4cout << "Cannot open file: " << kFile 2193 G4cout << "Cannot open file: " << kFileName
2194 << " in G4GMocrenIO::retrieveData3()." << 2194 << " in G4GMocrenIO::retrieveData3()." << G4endl;
2195 return false; 2195 return false;
2196 } 2196 }
2197 2197
2198 // data buffer 2198 // data buffer
2199 char ctmp[12]; 2199 char ctmp[12];
2200 2200
2201 // file identifier 2201 // file identifier
2202 char verid[9]; 2202 char verid[9];
2203 ifile.read((char *)verid, 8); 2203 ifile.read((char *)verid, 8);
2204 2204
2205 // file version 2205 // file version
2206 unsigned char ver; 2206 unsigned char ver;
2207 ifile.read((char *)&ver, 1); 2207 ifile.read((char *)&ver, 1);
2208 std::stringstream ss; 2208 std::stringstream ss;
2209 ss << (int)ver; 2209 ss << (int)ver;
2210 kVersion = ss.str(); 2210 kVersion = ss.str();
2211 if(DEBUG || kVerbose > 0) G4cout << "File v 2211 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
2212 2212
2213 // endian 2213 // endian
2214 ifile.read((char *)&kLittleEndianInput, siz 2214 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2215 if(DEBUG || kVerbose > 0) { 2215 if(DEBUG || kVerbose > 0) {
2216 G4cout << "Endian : "; 2216 G4cout << "Endian : ";
2217 if(kLittleEndianInput == 1) 2217 if(kLittleEndianInput == 1)
2218 G4cout << " little" << G4endl; 2218 G4cout << " little" << G4endl;
2219 else { 2219 else {
2220 G4cout << " big" << G4endl; 2220 G4cout << " big" << G4endl;
2221 } 2221 }
2222 } 2222 }
2223 2223
2224 // comment length (fixed size) 2224 // comment length (fixed size)
2225 int clength; 2225 int clength;
2226 ifile.read((char *)ctmp, 4); 2226 ifile.read((char *)ctmp, 4);
2227 convertEndian(ctmp, clength); 2227 convertEndian(ctmp, clength);
2228 // comment 2228 // comment
2229 char cmt[1025]; 2229 char cmt[1025];
2230 ifile.read((char *)cmt, clength); 2230 ifile.read((char *)cmt, clength);
2231 std::string scmt = cmt; 2231 std::string scmt = cmt;
2232 setComment(scmt); 2232 setComment(scmt);
2233 if(DEBUG || kVerbose > 0) { 2233 if(DEBUG || kVerbose > 0) {
2234 G4cout << "Data comment : " 2234 G4cout << "Data comment : "
2235 << kComment << G4endl; 2235 << kComment << G4endl;
2236 } 2236 }
2237 2237
2238 // voxel spacings for all images 2238 // voxel spacings for all images
2239 ifile.read((char *)ctmp, 12); 2239 ifile.read((char *)ctmp, 12);
2240 convertEndian(ctmp, kVoxelSpacing[0]); 2240 convertEndian(ctmp, kVoxelSpacing[0]);
2241 convertEndian(ctmp+4, kVoxelSpacing[1]); 2241 convertEndian(ctmp+4, kVoxelSpacing[1]);
2242 convertEndian(ctmp+8, kVoxelSpacing[2]); 2242 convertEndian(ctmp+8, kVoxelSpacing[2]);
2243 if(DEBUG || kVerbose > 0) { 2243 if(DEBUG || kVerbose > 0) {
2244 G4cout << "Voxel spacing : (" 2244 G4cout << "Voxel spacing : ("
2245 << kVoxelSpacing[0] << ", " 2245 << kVoxelSpacing[0] << ", "
2246 << kVoxelSpacing[1] << ", " 2246 << kVoxelSpacing[1] << ", "
2247 << kVoxelSpacing[2] 2247 << kVoxelSpacing[2]
2248 << ") mm " << G4endl; 2248 << ") mm " << G4endl;
2249 } 2249 }
2250 2250
2251 2251
2252 // offset from file starting point to the m 2252 // offset from file starting point to the modality image data
2253 ifile.read((char *)ctmp, 4); 2253 ifile.read((char *)ctmp, 4);
2254 convertEndian(ctmp, kPointerToModalityData) 2254 convertEndian(ctmp, kPointerToModalityData);
2255 2255
2256 // # of dose distributions 2256 // # of dose distributions
2257 ifile.read((char *)ctmp, 4); 2257 ifile.read((char *)ctmp, 4);
2258 int nDoseDist; 2258 int nDoseDist;
2259 convertEndian(ctmp, nDoseDist); 2259 convertEndian(ctmp, nDoseDist);
2260 2260
2261 // offset from file starting point to the d 2261 // offset from file starting point to the dose image data
2262 for(int i = 0; i < nDoseDist; i++) { 2262 for(int i = 0; i < nDoseDist; i++) {
2263 ifile.read((char *)ctmp, 4); 2263 ifile.read((char *)ctmp, 4);
2264 unsigned int dptr; 2264 unsigned int dptr;
2265 convertEndian(ctmp, dptr); 2265 convertEndian(ctmp, dptr);
2266 addPointerToDoseDistData(dptr); 2266 addPointerToDoseDistData(dptr);
2267 } 2267 }
2268 2268
2269 // offset from file starting point to the R 2269 // offset from file starting point to the ROI image data
2270 ifile.read((char *)ctmp, 4); 2270 ifile.read((char *)ctmp, 4);
2271 convertEndian(ctmp, kPointerToROIData); 2271 convertEndian(ctmp, kPointerToROIData);
2272 2272
2273 // offset from file starting point to the t 2273 // offset from file starting point to the track data
2274 ifile.read((char *)ctmp, 4); 2274 ifile.read((char *)ctmp, 4);
2275 convertEndian(ctmp, kPointerToTrackData); 2275 convertEndian(ctmp, kPointerToTrackData);
2276 if(DEBUG || kVerbose > 0) { 2276 if(DEBUG || kVerbose > 0) {
2277 G4cout << "Each pointer to data : " 2277 G4cout << "Each pointer to data : "
2278 << kPointerToModalityData << ", "; 2278 << kPointerToModalityData << ", ";
2279 for(int i = 0; i < nDoseDist; i++) 2279 for(int i = 0; i < nDoseDist; i++)
2280 G4cout << kPointerToDoseDistData[0] << 2280 G4cout << kPointerToDoseDistData[0] << ", ";
2281 G4cout << kPointerToROIData << ", " 2281 G4cout << kPointerToROIData << ", "
2282 << kPointerToTrackData << G4endl; 2282 << kPointerToTrackData << G4endl;
2283 } 2283 }
2284 2284
2285 if(kPointerToModalityData == 0 && kPointerT 2285 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2286 kPointerToROIData == 0 && kPointerToTrac 2286 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2287 if(DEBUG || kVerbose > 0) { 2287 if(DEBUG || kVerbose > 0) {
2288 G4cout << "No data." << G4endl; 2288 G4cout << "No data." << G4endl;
2289 } 2289 }
2290 return false; 2290 return false;
2291 } 2291 }
2292 2292
2293 // event number 2293 // event number
2294 /* ver 1 2294 /* ver 1
2295 ifile.read(ctmp, sizeof(int)); 2295 ifile.read(ctmp, sizeof(int));
2296 convertEndian(ctmp, numberOfEvents); 2296 convertEndian(ctmp, numberOfEvents);
2297 */ 2297 */
2298 2298
2299 int size[3]; 2299 int size[3];
2300 float scale; 2300 float scale;
2301 double dscale; 2301 double dscale;
2302 short minmax[2]; 2302 short minmax[2];
2303 float fCenter[3]; 2303 float fCenter[3];
2304 int iCenter[3]; 2304 int iCenter[3];
2305 2305
2306 //----- Modality image -----// 2306 //----- Modality image -----//
2307 // modality image size 2307 // modality image size
2308 ifile.read(ctmp, 3*sizeof(int)); 2308 ifile.read(ctmp, 3*sizeof(int));
2309 convertEndian(ctmp, size[0]); 2309 convertEndian(ctmp, size[0]);
2310 convertEndian(ctmp+sizeof(int), size[1]); 2310 convertEndian(ctmp+sizeof(int), size[1]);
2311 convertEndian(ctmp+2*sizeof(int), size[2]); 2311 convertEndian(ctmp+2*sizeof(int), size[2]);
2312 if(DEBUG || kVerbose > 0) { 2312 if(DEBUG || kVerbose > 0) {
2313 G4cout << "Modality image size : (" 2313 G4cout << "Modality image size : ("
2314 << size[0] << ", " 2314 << size[0] << ", "
2315 << size[1] << ", " 2315 << size[1] << ", "
2316 << size[2] << ")" 2316 << size[2] << ")"
2317 << G4endl; 2317 << G4endl;
2318 } 2318 }
2319 kModality.setSize(size); 2319 kModality.setSize(size);
2320 2320
2321 // modality image voxel spacing 2321 // modality image voxel spacing
2322 /* 2322 /*
2323 ifile.read(ctmp, 3*sizeof(float)); 2323 ifile.read(ctmp, 3*sizeof(float));
2324 convertEndian(ctmp, modalityImageVoxelSpa 2324 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2325 convertEndian(ctmp+sizeof(float), modalit 2325 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2326 convertEndian(ctmp+2*sizeof(float), modal 2326 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2327 */ 2327 */
2328 2328
2329 if(kPointerToModalityData != 0) { 2329 if(kPointerToModalityData != 0) {
2330 2330
2331 // modality density max. & min. 2331 // modality density max. & min.
2332 ifile.read((char *)ctmp, 4); 2332 ifile.read((char *)ctmp, 4);
2333 convertEndian(ctmp, minmax[0]); 2333 convertEndian(ctmp, minmax[0]);
2334 convertEndian(ctmp+2, minmax[1]); 2334 convertEndian(ctmp+2, minmax[1]);
2335 kModality.setMinMax(minmax); 2335 kModality.setMinMax(minmax);
2336 2336
2337 // modality image unit 2337 // modality image unit
2338 char munit[13]; 2338 char munit[13];
2339 ifile.read((char *)munit, 12); 2339 ifile.read((char *)munit, 12);
2340 std::string smunit = munit; 2340 std::string smunit = munit;
2341 setModalityImageUnit(smunit); 2341 setModalityImageUnit(smunit);
2342 2342
2343 // modality density scale 2343 // modality density scale
2344 ifile.read((char *)ctmp, 4); 2344 ifile.read((char *)ctmp, 4);
2345 convertEndian(ctmp, scale); 2345 convertEndian(ctmp, scale);
2346 kModality.setScale(dscale = scale); 2346 kModality.setScale(dscale = scale);
2347 if(DEBUG || kVerbose > 0) { 2347 if(DEBUG || kVerbose > 0) {
2348 G4cout << "Modality image min., max., s 2348 G4cout << "Modality image min., max., scale : "
2349 << minmax[0] << ", " 2349 << minmax[0] << ", "
2350 << minmax[1] << ", " 2350 << minmax[1] << ", "
2351 << scale << G4endl; 2351 << scale << G4endl;
2352 } 2352 }
2353 2353
2354 // modality density 2354 // modality density
2355 int psize = size[0]*size[1]; 2355 int psize = size[0]*size[1];
2356 if(DEBUG || kVerbose > 0) G4cout << "Moda 2356 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
2357 char * cimage = new char[psize*sizeof(sho 2357 char * cimage = new char[psize*sizeof(short)];
2358 for(int i = 0; i < size[2]; i++) { 2358 for(int i = 0; i < size[2]; i++) {
2359 ifile.read((char *)cimage, psize*sizeof 2359 ifile.read((char *)cimage, psize*sizeof(short));
2360 short * mimage = new short[psize]; 2360 short * mimage = new short[psize];
2361 for(int j = 0; j < psize; j++) { 2361 for(int j = 0; j < psize; j++) {
2362 convertEndian(cimage+j*sizeof(short), mimag 2362 convertEndian(cimage+j*sizeof(short), mimage[j]);
2363 } 2363 }
2364 kModality.addImage(mimage); 2364 kModality.addImage(mimage);
2365 2365
2366 if(DEBUG || kVerbose > 0) G4cout << "[" 2366 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2367 } 2367 }
2368 if(DEBUG || kVerbose > 0) G4cout << G4end 2368 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2369 delete [] cimage; 2369 delete [] cimage;
2370 2370
2371 // modality desity map for CT value 2371 // modality desity map for CT value
2372 size_t msize = minmax[1]-minmax[0]+1; 2372 size_t msize = minmax[1]-minmax[0]+1;
2373 if(DEBUG || kVerbose > 0) G4cout << "msiz 2373 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
2374 char * pdmap = new char[msize*sizeof(floa 2374 char * pdmap = new char[msize*sizeof(float)];
2375 ifile.read((char *)pdmap, msize*sizeof(fl 2375 ifile.read((char *)pdmap, msize*sizeof(float));
2376 float ftmp; 2376 float ftmp;
2377 for(int i = 0; i < (int)msize; i++) { 2377 for(int i = 0; i < (int)msize; i++) {
2378 convertEndian(pdmap+i*sizeof(float), ft 2378 convertEndian(pdmap+i*sizeof(float), ftmp);
2379 kModalityImageDensityMap.push_back(ftmp 2379 kModalityImageDensityMap.push_back(ftmp);
2380 } 2380 }
2381 delete [] pdmap; 2381 delete [] pdmap;
2382 if(DEBUG || kVerbose > 0) { 2382 if(DEBUG || kVerbose > 0) {
2383 G4cout << "density map : " << std::ends 2383 G4cout << "density map : " << std::ends;
2384 for(int i = 0; i < 10; i++) 2384 for(int i = 0; i < 10; i++)
2385 G4cout <<kModalityImageDensityMap[i] << ", 2385 G4cout <<kModalityImageDensityMap[i] << ", ";
2386 G4cout << G4endl; 2386 G4cout << G4endl;
2387 for(int i = 0; i < 10; i++) G4cout << " 2387 for(int i = 0; i < 10; i++) G4cout << "..";
2388 G4cout << G4endl; 2388 G4cout << G4endl;
2389 for(size_t i =kModalityImageDensityMap. 2389 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2390 G4cout <<kModalityImageDensityMap[i] << ", 2390 G4cout <<kModalityImageDensityMap[i] << ", ";
2391 G4cout << G4endl; 2391 G4cout << G4endl;
2392 } 2392 }
2393 2393
2394 } 2394 }
2395 2395
2396 2396
2397 //----- dose distribution image -----// 2397 //----- dose distribution image -----//
2398 for(int ndose = 0; ndose < nDoseDist; ndose 2398 for(int ndose = 0; ndose < nDoseDist; ndose++) {
2399 2399
2400 newDoseDist(); 2400 newDoseDist();
2401 2401
2402 // dose distrbution image size 2402 // dose distrbution image size
2403 ifile.read((char *)ctmp, 3*sizeof(int)); 2403 ifile.read((char *)ctmp, 3*sizeof(int));
2404 convertEndian(ctmp, size[0]); 2404 convertEndian(ctmp, size[0]);
2405 convertEndian(ctmp+sizeof(int), size[1]); 2405 convertEndian(ctmp+sizeof(int), size[1]);
2406 convertEndian(ctmp+2*sizeof(int), size[2] 2406 convertEndian(ctmp+2*sizeof(int), size[2]);
2407 if(DEBUG || kVerbose > 0) { 2407 if(DEBUG || kVerbose > 0) {
2408 G4cout << "Dose dist. image size : (" 2408 G4cout << "Dose dist. image size : ("
2409 << size[0] << ", " 2409 << size[0] << ", "
2410 << size[1] << ", " 2410 << size[1] << ", "
2411 << size[2] << ")" 2411 << size[2] << ")"
2412 << G4endl; 2412 << G4endl;
2413 } 2413 }
2414 kDose[ndose].setSize(size); 2414 kDose[ndose].setSize(size);
2415 2415
2416 // dose distribution max. & min. 2416 // dose distribution max. & min.
2417 ifile.read((char *)ctmp, sizeof(short)*2) 2417 ifile.read((char *)ctmp, sizeof(short)*2);
2418 convertEndian(ctmp, minmax[0]); 2418 convertEndian(ctmp, minmax[0]);
2419 convertEndian(ctmp+2, minmax[1]); 2419 convertEndian(ctmp+2, minmax[1]);
2420 2420
2421 // dose distribution unit 2421 // dose distribution unit
2422 char dunit[13]; 2422 char dunit[13];
2423 ifile.read((char *)dunit, 12); 2423 ifile.read((char *)dunit, 12);
2424 std::string sdunit = dunit; 2424 std::string sdunit = dunit;
2425 setDoseDistUnit(sdunit, ndose); 2425 setDoseDistUnit(sdunit, ndose);
2426 if(DEBUG || kVerbose > 0) { 2426 if(DEBUG || kVerbose > 0) {
2427 G4cout << "Dose dist. unit : " << kDose 2427 G4cout << "Dose dist. unit : " << kDoseUnit << G4endl;
2428 } 2428 }
2429 2429
2430 // dose distribution scaling 2430 // dose distribution scaling
2431 ifile.read((char *)ctmp, 4); // sizeof(fl 2431 ifile.read((char *)ctmp, 4); // sizeof(float)
2432 convertEndian(ctmp, scale); 2432 convertEndian(ctmp, scale);
2433 kDose[ndose].setScale(dscale = scale); 2433 kDose[ndose].setScale(dscale = scale);
2434 2434
2435 double dminmax[2]; 2435 double dminmax[2];
2436 for(int i = 0; i < 2; i++) dminmax[i] = m 2436 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2437 kDose[ndose].setMinMax(dminmax); 2437 kDose[ndose].setMinMax(dminmax);
2438 2438
2439 if(DEBUG || kVerbose > 0) { 2439 if(DEBUG || kVerbose > 0) {
2440 G4cout << "Dose dist. image min., max., 2440 G4cout << "Dose dist. image min., max., scale : "
2441 << dminmax[0] << ", " 2441 << dminmax[0] << ", "
2442 << dminmax[1] << ", " 2442 << dminmax[1] << ", "
2443 << scale << G4endl; 2443 << scale << G4endl;
2444 } 2444 }
2445 2445
2446 // dose distribution image 2446 // dose distribution image
2447 int dsize = size[0]*size[1]; 2447 int dsize = size[0]*size[1];
2448 if(DEBUG || kVerbose > 0) G4cout << "Dose 2448 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
2449 char * di = new char[dsize*sizeof(short)] 2449 char * di = new char[dsize*sizeof(short)];
2450 short * shimage = new short[dsize]; 2450 short * shimage = new short[dsize];
2451 for(int z = 0; z < size[2]; z++) { 2451 for(int z = 0; z < size[2]; z++) {
2452 ifile.read((char *)di, dsize*sizeof(sho 2452 ifile.read((char *)di, dsize*sizeof(short));
2453 double * dimage = new double[dsize]; 2453 double * dimage = new double[dsize];
2454 for(int xy = 0; xy < dsize; xy++) { 2454 for(int xy = 0; xy < dsize; xy++) {
2455 convertEndian(di+xy*sizeof(short), shimage[ 2455 convertEndian(di+xy*sizeof(short), shimage[xy]);
2456 dimage[xy] = shimage[xy]*dscale; 2456 dimage[xy] = shimage[xy]*dscale;
2457 } 2457 }
2458 kDose[ndose].addImage(dimage); 2458 kDose[ndose].addImage(dimage);
2459 2459
2460 if(DEBUG || kVerbose > 0) G4cout << "[" 2460 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2461 2461
2462 if(DEBUG || kVerbose > 0) { 2462 if(DEBUG || kVerbose > 0) {
2463 for(int j = 0; j < dsize; j++) { 2463 for(int j = 0; j < dsize; j++) {
2464 if(dimage[j] < 0) 2464 if(dimage[j] < 0)
2465 G4cout << "[" << j << "," << z << "]" 2465 G4cout << "[" << j << "," << z << "]"
2466 << dimage[j] << ", "; 2466 << dimage[j] << ", ";
2467 } 2467 }
2468 } 2468 }
2469 } 2469 }
2470 delete [] shimage; 2470 delete [] shimage;
2471 delete [] di; 2471 delete [] di;
2472 if(DEBUG || kVerbose > 0) G4cout << G4end 2472 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2473 2473
2474 ifile.read((char *)ctmp, 3*4); // 3*sizeo 2474 ifile.read((char *)ctmp, 3*4); // 3*sizeof(int)
2475 convertEndian(ctmp, iCenter[0]); 2475 convertEndian(ctmp, iCenter[0]);
2476 convertEndian(ctmp+4, iCenter[1]); 2476 convertEndian(ctmp+4, iCenter[1]);
2477 convertEndian(ctmp+8, iCenter[2]); 2477 convertEndian(ctmp+8, iCenter[2]);
2478 for(int i = 0; i < 3; i++) fCenter[i] = ( 2478 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2479 kDose[ndose].setCenterPosition(fCenter); 2479 kDose[ndose].setCenterPosition(fCenter);
2480 2480
2481 if(DEBUG || kVerbose > 0) { 2481 if(DEBUG || kVerbose > 0) {
2482 G4cout << "Dose dist. image relative lo 2482 G4cout << "Dose dist. image relative location : ("
2483 << fCenter[0] << ", " 2483 << fCenter[0] << ", "
2484 << fCenter[1] << ", " 2484 << fCenter[1] << ", "
2485 << fCenter[2] << ")" << G4endl; 2485 << fCenter[2] << ")" << G4endl;
2486 } 2486 }
2487 2487
2488 2488
2489 } 2489 }
2490 2490
2491 //----- ROI image -----// 2491 //----- ROI image -----//
2492 if(kPointerToROIData != 0) { 2492 if(kPointerToROIData != 0) {
2493 2493
2494 newROI(); 2494 newROI();
2495 2495
2496 // ROI image size 2496 // ROI image size
2497 ifile.read((char *)ctmp, 3*sizeof(int)); 2497 ifile.read((char *)ctmp, 3*sizeof(int));
2498 convertEndian(ctmp, size[0]); 2498 convertEndian(ctmp, size[0]);
2499 convertEndian(ctmp+sizeof(int), size[1]); 2499 convertEndian(ctmp+sizeof(int), size[1]);
2500 convertEndian(ctmp+2*sizeof(int), size[2] 2500 convertEndian(ctmp+2*sizeof(int), size[2]);
2501 kRoi[0].setSize(size); 2501 kRoi[0].setSize(size);
2502 if(DEBUG || kVerbose > 0) { 2502 if(DEBUG || kVerbose > 0) {
2503 G4cout << "ROI image size : (" 2503 G4cout << "ROI image size : ("
2504 << size[0] << ", " 2504 << size[0] << ", "
2505 << size[1] << ", " 2505 << size[1] << ", "
2506 << size[2] << ")" 2506 << size[2] << ")"
2507 << G4endl; 2507 << G4endl;
2508 } 2508 }
2509 2509
2510 // ROI max. & min. 2510 // ROI max. & min.
2511 ifile.read((char *)ctmp, sizeof(short)*2) 2511 ifile.read((char *)ctmp, sizeof(short)*2);
2512 convertEndian(ctmp, minmax[0]); 2512 convertEndian(ctmp, minmax[0]);
2513 convertEndian(ctmp+sizeof(short), minmax[ 2513 convertEndian(ctmp+sizeof(short), minmax[1]);
2514 kRoi[0].setMinMax(minmax); 2514 kRoi[0].setMinMax(minmax);
2515 2515
2516 // ROI distribution scaling 2516 // ROI distribution scaling
2517 ifile.read((char *)ctmp, sizeof(float)); 2517 ifile.read((char *)ctmp, sizeof(float));
2518 convertEndian(ctmp, scale); 2518 convertEndian(ctmp, scale);
2519 kRoi[0].setScale(dscale = scale); 2519 kRoi[0].setScale(dscale = scale);
2520 if(DEBUG || kVerbose > 0) { 2520 if(DEBUG || kVerbose > 0) {
2521 G4cout << "ROI image min., max., scale 2521 G4cout << "ROI image min., max., scale : "
2522 << minmax[0] << ", " 2522 << minmax[0] << ", "
2523 << minmax[1] << ", " 2523 << minmax[1] << ", "
2524 << scale << G4endl; 2524 << scale << G4endl;
2525 } 2525 }
2526 2526
2527 // ROI image 2527 // ROI image
2528 int rsize = size[0]*size[1]; 2528 int rsize = size[0]*size[1];
2529 char * ri = new char[rsize*sizeof(short)] 2529 char * ri = new char[rsize*sizeof(short)];
2530 for(int i = 0; i < size[2]; i++) { 2530 for(int i = 0; i < size[2]; i++) {
2531 ifile.read((char *)ri, rsize*sizeof(sho 2531 ifile.read((char *)ri, rsize*sizeof(short));
2532 short * rimage = new short[rsize]; 2532 short * rimage = new short[rsize];
2533 for(int j = 0; j < rsize; j++) { 2533 for(int j = 0; j < rsize; j++) {
2534 convertEndian(ri+j*sizeof(short), rimage[j] 2534 convertEndian(ri+j*sizeof(short), rimage[j]);
2535 } 2535 }
2536 kRoi[0].addImage(rimage); 2536 kRoi[0].addImage(rimage);
2537 2537
2538 } 2538 }
2539 delete [] ri; 2539 delete [] ri;
2540 2540
2541 // ROI relative location 2541 // ROI relative location
2542 ifile.read((char *)ctmp, 3*sizeof(int)); 2542 ifile.read((char *)ctmp, 3*sizeof(int));
2543 convertEndian(ctmp, iCenter[0]); 2543 convertEndian(ctmp, iCenter[0]);
2544 convertEndian(ctmp+sizeof(int), iCenter[1 2544 convertEndian(ctmp+sizeof(int), iCenter[1]);
2545 convertEndian(ctmp+2*sizeof(int), iCenter 2545 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2546 for(int i = 0; i < 3; i++) fCenter[i] = i 2546 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2547 kRoi[0].setCenterPosition(fCenter); 2547 kRoi[0].setCenterPosition(fCenter);
2548 if(DEBUG || kVerbose > 0) { 2548 if(DEBUG || kVerbose > 0) {
2549 G4cout << "ROI image relative location 2549 G4cout << "ROI image relative location : ("
2550 << fCenter[0] << ", " 2550 << fCenter[0] << ", "
2551 << fCenter[1] << ", " 2551 << fCenter[1] << ", "
2552 << fCenter[2] << ")" << G4endl; 2552 << fCenter[2] << ")" << G4endl;
2553 } 2553 }
2554 2554
2555 } 2555 }
2556 2556
2557 //----- track information -----// 2557 //----- track information -----//
2558 if(kPointerToTrackData != 0) { 2558 if(kPointerToTrackData != 0) {
2559 2559
2560 // track 2560 // track
2561 ifile.read((char *)ctmp, sizeof(int)); 2561 ifile.read((char *)ctmp, sizeof(int));
2562 int ntrk; 2562 int ntrk;
2563 convertEndian(ctmp, ntrk); 2563 convertEndian(ctmp, ntrk);
2564 if(DEBUG || kVerbose > 0) { 2564 if(DEBUG || kVerbose > 0) {
2565 G4cout << "# of tracks: " << ntrk << G4 2565 G4cout << "# of tracks: " << ntrk << G4endl;
2566 } 2566 }
2567 2567
2568 // v4 2568 // v4
2569 std::vector<float *> trkv4; 2569 std::vector<float *> trkv4;
2570 2570
2571 // track position 2571 // track position
2572 for(int i = 0; i < ntrk; i++) { 2572 for(int i = 0; i < ntrk; i++) {
2573 float * tp = new float[6]; 2573 float * tp = new float[6];
2574 2574
2575 ifile.read((char *)ctmp, sizeof(float)* 2575 ifile.read((char *)ctmp, sizeof(float)*3);
2576 if(DEBUG || kVerbose > 0) if(i < 10) G4 2576 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << i << ": " ;
2577 for(int j = 0; j < 3; j++) { 2577 for(int j = 0; j < 3; j++) {
2578 convertEndian(ctmp+j*sizeof(float), tp[j]); 2578 convertEndian(ctmp+j*sizeof(float), tp[j]);
2579 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 2579 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j] << ", ";
2580 } 2580 }
2581 2581
2582 ifile.read((char *)ctmp, sizeof(float)* 2582 ifile.read((char *)ctmp, sizeof(float)*3);
2583 for(int j = 0; j < 3; j++) { 2583 for(int j = 0; j < 3; j++) {
2584 convertEndian(ctmp+j*sizeof(float), tp[j+3] 2584 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
2585 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 2585 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j+3] << ", ";
2586 } 2586 }
2587 addTrack(tp); 2587 addTrack(tp);
2588 if(DEBUG || kVerbose > 0) if(i < 10) G4 2588 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << G4endl;
2589 2589
2590 // v4 2590 // v4
2591 trkv4.push_back(tp); 2591 trkv4.push_back(tp);
2592 } 2592 }
2593 2593
2594 //v4 2594 //v4
2595 unsigned char trkcolorv4[3]; 2595 unsigned char trkcolorv4[3];
2596 2596
2597 // track color 2597 // track color
2598 for(int i = 0; i < ntrk; i++) { 2598 for(int i = 0; i < ntrk; i++) {
2599 unsigned char * rgb = new unsigned char 2599 unsigned char * rgb = new unsigned char[3];
2600 ifile.read((char *)rgb, 3); 2600 ifile.read((char *)rgb, 3);
2601 addTrackColor(rgb); 2601 addTrackColor(rgb);
2602 2602
2603 // v4 2603 // v4
2604 for(int j = 0; j < 3; j++) trkcolorv4[j 2604 for(int j = 0; j < 3; j++) trkcolorv4[j] = rgb[j];
2605 std::vector<float *> trk; 2605 std::vector<float *> trk;
2606 trk.push_back(trkv4[i]); 2606 trk.push_back(trkv4[i]);
2607 addTrack(trk, trkcolorv4); 2607 addTrack(trk, trkcolorv4);
2608 2608
2609 } 2609 }
2610 2610
2611 } 2611 }
2612 2612
2613 ifile.close(); 2613 ifile.close();
2614 2614
2615 return true; 2615 return true;
2616 } 2616 }
2617 bool G4GMocrenIO::retrieveData3(char * _filen 2617 bool G4GMocrenIO::retrieveData3(char * _filename) {
2618 kFileName = _filename; 2618 kFileName = _filename;
2619 return retrieveData(); 2619 return retrieveData();
2620 } 2620 }
2621 2621
2622 // 2622 //
2623 bool G4GMocrenIO::retrieveData2() { 2623 bool G4GMocrenIO::retrieveData2() {
2624 2624
2625 bool DEBUG = false;// 2625 bool DEBUG = false;//
2626 2626
2627 // input file open 2627 // input file open
2628 std::ifstream ifile(kFileName.c_str(), std: 2628 std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary);
2629 if(!ifile) { 2629 if(!ifile) {
2630 if (G4VisManager::GetVerbosity() >= G4Vis 2630 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
2631 G4cout << "Cannot open file: " << kFile 2631 G4cout << "Cannot open file: " << kFileName
2632 << " in G4GMocrenIO::retrieveData2()." << 2632 << " in G4GMocrenIO::retrieveData2()." << G4endl;
2633 return false; 2633 return false;
2634 } 2634 }
2635 2635
2636 // data buffer 2636 // data buffer
2637 char ctmp[12]; 2637 char ctmp[12];
2638 2638
2639 // file identifier 2639 // file identifier
2640 char verid[9]; 2640 char verid[9];
2641 ifile.read((char *)verid, 8); 2641 ifile.read((char *)verid, 8);
2642 2642
2643 // file version 2643 // file version
2644 unsigned char ver; 2644 unsigned char ver;
2645 ifile.read((char *)&ver, 1); 2645 ifile.read((char *)&ver, 1);
2646 std::stringstream ss; 2646 std::stringstream ss;
2647 ss << (int)ver; 2647 ss << (int)ver;
2648 kVersion = ss.str(); 2648 kVersion = ss.str();
2649 if(DEBUG || kVerbose > 0) G4cout << "File v 2649 if(DEBUG || kVerbose > 0) G4cout << "File version : " << kVersion << G4endl;
2650 2650
2651 // id of version 1 2651 // id of version 1
2652 char idtmp[IDLENGTH]; 2652 char idtmp[IDLENGTH];
2653 ifile.read((char *)idtmp, IDLENGTH); 2653 ifile.read((char *)idtmp, IDLENGTH);
2654 kId = idtmp; 2654 kId = idtmp;
2655 // version of version 1 2655 // version of version 1
2656 char vertmp[VERLENGTH]; 2656 char vertmp[VERLENGTH];
2657 ifile.read((char *)vertmp, VERLENGTH); 2657 ifile.read((char *)vertmp, VERLENGTH);
2658 2658
2659 // endian 2659 // endian
2660 ifile.read((char *)&kLittleEndianInput, siz 2660 ifile.read((char *)&kLittleEndianInput, sizeof(char));
2661 if(DEBUG || kVerbose > 0) { 2661 if(DEBUG || kVerbose > 0) {
2662 G4cout << "Endian : "; 2662 G4cout << "Endian : ";
2663 if(kLittleEndianInput == 1) 2663 if(kLittleEndianInput == 1)
2664 G4cout << " little" << G4endl; 2664 G4cout << " little" << G4endl;
2665 else { 2665 else {
2666 G4cout << " big" << G4endl; 2666 G4cout << " big" << G4endl;
2667 } 2667 }
2668 } 2668 }
2669 2669
2670 // voxel spacings for all images 2670 // voxel spacings for all images
2671 ifile.read((char *)ctmp, 12); 2671 ifile.read((char *)ctmp, 12);
2672 convertEndian(ctmp, kVoxelSpacing[0]); 2672 convertEndian(ctmp, kVoxelSpacing[0]);
2673 convertEndian(ctmp+4, kVoxelSpacing[1]); 2673 convertEndian(ctmp+4, kVoxelSpacing[1]);
2674 convertEndian(ctmp+8, kVoxelSpacing[2]); 2674 convertEndian(ctmp+8, kVoxelSpacing[2]);
2675 if(DEBUG || kVerbose > 0) { 2675 if(DEBUG || kVerbose > 0) {
2676 G4cout << "Voxel spacing : (" 2676 G4cout << "Voxel spacing : ("
2677 << kVoxelSpacing[0] << ", " 2677 << kVoxelSpacing[0] << ", "
2678 << kVoxelSpacing[1] << ", " 2678 << kVoxelSpacing[1] << ", "
2679 << kVoxelSpacing[2] 2679 << kVoxelSpacing[2]
2680 << ") mm " << G4endl; 2680 << ") mm " << G4endl;
2681 } 2681 }
2682 2682
2683 2683
2684 // offset from file starting point to the m 2684 // offset from file starting point to the modality image data
2685 ifile.read((char *)ctmp, 4); 2685 ifile.read((char *)ctmp, 4);
2686 convertEndian(ctmp, kPointerToModalityData) 2686 convertEndian(ctmp, kPointerToModalityData);
2687 2687
2688 // offset from file starting point to the d 2688 // offset from file starting point to the dose image data
2689 unsigned int ptddd; 2689 unsigned int ptddd;
2690 ifile.read((char *)ctmp, 4); 2690 ifile.read((char *)ctmp, 4);
2691 convertEndian(ctmp, ptddd); 2691 convertEndian(ctmp, ptddd);
2692 kPointerToDoseDistData.push_back(ptddd); 2692 kPointerToDoseDistData.push_back(ptddd);
2693 2693
2694 // offset from file starting point to the R 2694 // offset from file starting point to the ROI image data
2695 ifile.read((char *)ctmp, 4); 2695 ifile.read((char *)ctmp, 4);
2696 convertEndian(ctmp, kPointerToROIData); 2696 convertEndian(ctmp, kPointerToROIData);
2697 2697
2698 // offset from file starting point to the t 2698 // offset from file starting point to the track data
2699 ifile.read((char *)ctmp, 4); 2699 ifile.read((char *)ctmp, 4);
2700 convertEndian(ctmp, kPointerToTrackData); 2700 convertEndian(ctmp, kPointerToTrackData);
2701 if(DEBUG || kVerbose > 0) { 2701 if(DEBUG || kVerbose > 0) {
2702 G4cout << "Each pointer to data : " 2702 G4cout << "Each pointer to data : "
2703 << kPointerToModalityData << ", " 2703 << kPointerToModalityData << ", "
2704 << kPointerToDoseDistData[0] << ", " 2704 << kPointerToDoseDistData[0] << ", "
2705 << kPointerToROIData << ", " 2705 << kPointerToROIData << ", "
2706 << kPointerToTrackData << G4endl; 2706 << kPointerToTrackData << G4endl;
2707 } 2707 }
2708 2708
2709 if(kPointerToModalityData == 0 && kPointerT 2709 if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 &&
2710 kPointerToROIData == 0 && kPointerToTrac 2710 kPointerToROIData == 0 && kPointerToTrackData == 0) {
2711 if(DEBUG || kVerbose > 0) { 2711 if(DEBUG || kVerbose > 0) {
2712 G4cout << "No data." << G4endl; 2712 G4cout << "No data." << G4endl;
2713 } 2713 }
2714 return false; 2714 return false;
2715 } 2715 }
2716 2716
2717 // event number 2717 // event number
2718 /* ver 1 2718 /* ver 1
2719 ifile.read(ctmp, sizeof(int)); 2719 ifile.read(ctmp, sizeof(int));
2720 convertEndian(ctmp, numberOfEvents); 2720 convertEndian(ctmp, numberOfEvents);
2721 */ 2721 */
2722 2722
2723 int size[3]; 2723 int size[3];
2724 float scale; 2724 float scale;
2725 double dscale; 2725 double dscale;
2726 short minmax[2]; 2726 short minmax[2];
2727 float fCenter[3]; 2727 float fCenter[3];
2728 int iCenter[3]; 2728 int iCenter[3];
2729 2729
2730 //----- Modality image -----// 2730 //----- Modality image -----//
2731 // modality image size 2731 // modality image size
2732 ifile.read(ctmp, 3*sizeof(int)); 2732 ifile.read(ctmp, 3*sizeof(int));
2733 convertEndian(ctmp, size[0]); 2733 convertEndian(ctmp, size[0]);
2734 convertEndian(ctmp+sizeof(int), size[1]); 2734 convertEndian(ctmp+sizeof(int), size[1]);
2735 convertEndian(ctmp+2*sizeof(int), size[2]); 2735 convertEndian(ctmp+2*sizeof(int), size[2]);
2736 if(DEBUG || kVerbose > 0) { 2736 if(DEBUG || kVerbose > 0) {
2737 G4cout << "Modality image size : (" 2737 G4cout << "Modality image size : ("
2738 << size[0] << ", " 2738 << size[0] << ", "
2739 << size[1] << ", " 2739 << size[1] << ", "
2740 << size[2] << ")" 2740 << size[2] << ")"
2741 << G4endl; 2741 << G4endl;
2742 } 2742 }
2743 kModality.setSize(size); 2743 kModality.setSize(size);
2744 2744
2745 // modality image voxel spacing 2745 // modality image voxel spacing
2746 /* 2746 /*
2747 ifile.read(ctmp, 3*sizeof(float)); 2747 ifile.read(ctmp, 3*sizeof(float));
2748 convertEndian(ctmp, modalityImageVoxelSpa 2748 convertEndian(ctmp, modalityImageVoxelSpacing[0]);
2749 convertEndian(ctmp+sizeof(float), modalit 2749 convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]);
2750 convertEndian(ctmp+2*sizeof(float), modal 2750 convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]);
2751 */ 2751 */
2752 2752
2753 if(kPointerToModalityData != 0) { 2753 if(kPointerToModalityData != 0) {
2754 2754
2755 // modality density max. & min. 2755 // modality density max. & min.
2756 ifile.read((char *)ctmp, 4); 2756 ifile.read((char *)ctmp, 4);
2757 convertEndian(ctmp, minmax[0]); 2757 convertEndian(ctmp, minmax[0]);
2758 convertEndian(ctmp+2, minmax[1]); 2758 convertEndian(ctmp+2, minmax[1]);
2759 kModality.setMinMax(minmax); 2759 kModality.setMinMax(minmax);
2760 2760
2761 // modality density scale 2761 // modality density scale
2762 ifile.read((char *)ctmp, 4); 2762 ifile.read((char *)ctmp, 4);
2763 convertEndian(ctmp, scale); 2763 convertEndian(ctmp, scale);
2764 kModality.setScale(dscale = scale); 2764 kModality.setScale(dscale = scale);
2765 if(DEBUG || kVerbose > 0) { 2765 if(DEBUG || kVerbose > 0) {
2766 G4cout << "Modality image min., max., s 2766 G4cout << "Modality image min., max., scale : "
2767 << minmax[0] << ", " 2767 << minmax[0] << ", "
2768 << minmax[1] << ", " 2768 << minmax[1] << ", "
2769 << scale << G4endl; 2769 << scale << G4endl;
2770 } 2770 }
2771 2771
2772 // modality density 2772 // modality density
2773 int psize = size[0]*size[1]; 2773 int psize = size[0]*size[1];
2774 if(DEBUG || kVerbose > 0) G4cout << "Moda 2774 if(DEBUG || kVerbose > 0) G4cout << "Modality image (" << psize << "): ";
2775 char * cimage = new char[psize*sizeof(sho 2775 char * cimage = new char[psize*sizeof(short)];
2776 for(int i = 0; i < size[2]; i++) { 2776 for(int i = 0; i < size[2]; i++) {
2777 ifile.read((char *)cimage, psize*sizeof 2777 ifile.read((char *)cimage, psize*sizeof(short));
2778 short * mimage = new short[psize]; 2778 short * mimage = new short[psize];
2779 for(int j = 0; j < psize; j++) { 2779 for(int j = 0; j < psize; j++) {
2780 convertEndian(cimage+j*sizeof(short), mimag 2780 convertEndian(cimage+j*sizeof(short), mimage[j]);
2781 } 2781 }
2782 kModality.addImage(mimage); 2782 kModality.addImage(mimage);
2783 2783
2784 if(DEBUG || kVerbose > 0) G4cout << "[" 2784 if(DEBUG || kVerbose > 0) G4cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", ";
2785 } 2785 }
2786 if(DEBUG || kVerbose > 0) G4cout << G4end 2786 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2787 delete [] cimage; 2787 delete [] cimage;
2788 2788
2789 // modality desity map for CT value 2789 // modality desity map for CT value
2790 size_t msize = minmax[1]-minmax[0]+1; 2790 size_t msize = minmax[1]-minmax[0]+1;
2791 if(DEBUG || kVerbose > 0) G4cout << "msiz 2791 if(DEBUG || kVerbose > 0) G4cout << "msize: " << msize << G4endl;
2792 char * pdmap = new char[msize*sizeof(floa 2792 char * pdmap = new char[msize*sizeof(float)];
2793 ifile.read((char *)pdmap, msize*sizeof(fl 2793 ifile.read((char *)pdmap, msize*sizeof(float));
2794 float ftmp; 2794 float ftmp;
2795 for(int i = 0; i < (int)msize; i++) { 2795 for(int i = 0; i < (int)msize; i++) {
2796 convertEndian(pdmap+i*sizeof(float), ft 2796 convertEndian(pdmap+i*sizeof(float), ftmp);
2797 kModalityImageDensityMap.push_back(ftmp 2797 kModalityImageDensityMap.push_back(ftmp);
2798 } 2798 }
2799 delete [] pdmap; 2799 delete [] pdmap;
2800 if(DEBUG || kVerbose > 0) { 2800 if(DEBUG || kVerbose > 0) {
2801 G4cout << "density map : " << std::ends 2801 G4cout << "density map : " << std::ends;
2802 for(int i = 0; i < 10; i++) 2802 for(int i = 0; i < 10; i++)
2803 G4cout <<kModalityImageDensityMap[i] << ", 2803 G4cout <<kModalityImageDensityMap[i] << ", ";
2804 G4cout << G4endl; 2804 G4cout << G4endl;
2805 for(int i = 0; i < 10; i++) G4cout << " 2805 for(int i = 0; i < 10; i++) G4cout << "..";
2806 G4cout << G4endl; 2806 G4cout << G4endl;
2807 for(size_t i =kModalityImageDensityMap. 2807 for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++)
2808 G4cout <<kModalityImageDensityMap[i] << ", 2808 G4cout <<kModalityImageDensityMap[i] << ", ";
2809 G4cout << G4endl; 2809 G4cout << G4endl;
2810 } 2810 }
2811 2811
2812 } 2812 }
2813 2813
2814 2814
2815 //----- dose distribution image -----// 2815 //----- dose distribution image -----//
2816 if(kPointerToDoseDistData[0] != 0) { 2816 if(kPointerToDoseDistData[0] != 0) {
2817 2817
2818 newDoseDist(); 2818 newDoseDist();
2819 2819
2820 // dose distrbution image size 2820 // dose distrbution image size
2821 ifile.read((char *)ctmp, 3*sizeof(int)); 2821 ifile.read((char *)ctmp, 3*sizeof(int));
2822 convertEndian(ctmp, size[0]); 2822 convertEndian(ctmp, size[0]);
2823 convertEndian(ctmp+sizeof(int), size[1]); 2823 convertEndian(ctmp+sizeof(int), size[1]);
2824 convertEndian(ctmp+2*sizeof(int), size[2] 2824 convertEndian(ctmp+2*sizeof(int), size[2]);
2825 if(DEBUG || kVerbose > 0) { 2825 if(DEBUG || kVerbose > 0) {
2826 G4cout << "Dose dist. image size : (" 2826 G4cout << "Dose dist. image size : ("
2827 << size[0] << ", " 2827 << size[0] << ", "
2828 << size[1] << ", " 2828 << size[1] << ", "
2829 << size[2] << ")" 2829 << size[2] << ")"
2830 << G4endl; 2830 << G4endl;
2831 } 2831 }
2832 kDose[0].setSize(size); 2832 kDose[0].setSize(size);
2833 2833
2834 // dose distribution max. & min. 2834 // dose distribution max. & min.
2835 ifile.read((char *)ctmp, sizeof(short)*2) 2835 ifile.read((char *)ctmp, sizeof(short)*2);
2836 convertEndian(ctmp, minmax[0]); 2836 convertEndian(ctmp, minmax[0]);
2837 convertEndian(ctmp+2, minmax[1]); 2837 convertEndian(ctmp+2, minmax[1]);
2838 // dose distribution scaling 2838 // dose distribution scaling
2839 ifile.read((char *)ctmp, sizeof(float)); 2839 ifile.read((char *)ctmp, sizeof(float));
2840 convertEndian(ctmp, scale); 2840 convertEndian(ctmp, scale);
2841 kDose[0].setScale(dscale = scale); 2841 kDose[0].setScale(dscale = scale);
2842 2842
2843 double dminmax[2]; 2843 double dminmax[2];
2844 for(int i = 0; i < 2; i++) dminmax[i] = m 2844 for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale;
2845 kDose[0].setMinMax(dminmax); 2845 kDose[0].setMinMax(dminmax);
2846 2846
2847 if(DEBUG || kVerbose > 0) { 2847 if(DEBUG || kVerbose > 0) {
2848 G4cout << "Dose dist. image min., max., 2848 G4cout << "Dose dist. image min., max., scale : "
2849 << dminmax[0] << ", " 2849 << dminmax[0] << ", "
2850 << dminmax[1] << ", " 2850 << dminmax[1] << ", "
2851 << scale << G4endl; 2851 << scale << G4endl;
2852 } 2852 }
2853 2853
2854 // dose distribution image 2854 // dose distribution image
2855 int dsize = size[0]*size[1]; 2855 int dsize = size[0]*size[1];
2856 if(DEBUG || kVerbose > 0) G4cout << "Dose 2856 if(DEBUG || kVerbose > 0) G4cout << "Dose dist. (" << dsize << "): ";
2857 char * di = new char[dsize*sizeof(short)] 2857 char * di = new char[dsize*sizeof(short)];
2858 short * shimage = new short[dsize]; 2858 short * shimage = new short[dsize];
2859 for(int z = 0; z < size[2]; z++) { 2859 for(int z = 0; z < size[2]; z++) {
2860 ifile.read((char *)di, dsize*sizeof(sho 2860 ifile.read((char *)di, dsize*sizeof(short));
2861 double * dimage = new double[dsize]; 2861 double * dimage = new double[dsize];
2862 for(int xy = 0; xy < dsize; xy++) { 2862 for(int xy = 0; xy < dsize; xy++) {
2863 convertEndian(di+xy*sizeof(short), shimage[ 2863 convertEndian(di+xy*sizeof(short), shimage[xy]);
2864 dimage[xy] = shimage[xy]*dscale; 2864 dimage[xy] = shimage[xy]*dscale;
2865 } 2865 }
2866 kDose[0].addImage(dimage); 2866 kDose[0].addImage(dimage);
2867 2867
2868 if(DEBUG || kVerbose > 0) G4cout << "[" 2868 if(DEBUG || kVerbose > 0) G4cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", ";
2869 2869
2870 if(DEBUG || kVerbose > 0) { 2870 if(DEBUG || kVerbose > 0) {
2871 for(int j = 0; j < dsize; j++) { 2871 for(int j = 0; j < dsize; j++) {
2872 if(dimage[j] < 0) 2872 if(dimage[j] < 0)
2873 G4cout << "[" << j << "," << z << "]" 2873 G4cout << "[" << j << "," << z << "]"
2874 << dimage[j] << ", "; 2874 << dimage[j] << ", ";
2875 } 2875 }
2876 } 2876 }
2877 } 2877 }
2878 delete [] shimage; 2878 delete [] shimage;
2879 delete [] di; 2879 delete [] di;
2880 if(DEBUG || kVerbose > 0) G4cout << G4end 2880 if(DEBUG || kVerbose > 0) G4cout << G4endl;
2881 2881
2882 /* ver 1 2882 /* ver 1
2883 float doseDist; 2883 float doseDist;
2884 int dosePid; 2884 int dosePid;
2885 double * doseData = new double[numDose 2885 double * doseData = new double[numDoseImageVoxels];
2886 for(int i = 0; i < numDose; i++) { 2886 for(int i = 0; i < numDose; i++) {
2887 ifile.read(ctmp, sizeof(int)); 2887 ifile.read(ctmp, sizeof(int));
2888 convertEndian(ctmp, dosePid); 2888 convertEndian(ctmp, dosePid);
2889 for(int j = 0; j < numDoseImageVoxels; 2889 for(int j = 0; j < numDoseImageVoxels; j++) {
2890 ifile.read(ctmp, sizeof(float)); 2890 ifile.read(ctmp, sizeof(float));
2891 convertEndian(ctmp, doseDist); 2891 convertEndian(ctmp, doseDist);
2892 doseData[j] = doseDist; 2892 doseData[j] = doseDist;
2893 } 2893 }
2894 setDose(dosePid, doseData); 2894 setDose(dosePid, doseData);
2895 } 2895 }
2896 delete [] doseData; 2896 delete [] doseData;
2897 if(totalDose == NULL) totalDose = new 2897 if(totalDose == NULL) totalDose = new double[numDoseImageVoxels];
2898 for(int i = 0; i < numDoseImageVoxels; 2898 for(int i = 0; i < numDoseImageVoxels; i++) {
2899 ifile.read(ctmp, sizeof(float)); 2899 ifile.read(ctmp, sizeof(float));
2900 convertEndian(ctmp, doseDist); 2900 convertEndian(ctmp, doseDist);
2901 totalDose[i] = doseDist; 2901 totalDose[i] = doseDist;
2902 } 2902 }
2903 */ 2903 */
2904 2904
2905 /* ver 1 2905 /* ver 1
2906 // relative location between the two imag 2906 // relative location between the two images
2907 ifile.read(ctmp, 3*sizeof(float)); 2907 ifile.read(ctmp, 3*sizeof(float));
2908 convertEndian(ctmp, relativeLocation[0]); 2908 convertEndian(ctmp, relativeLocation[0]);
2909 convertEndian(ctmp+sizeof(float), relativ 2909 convertEndian(ctmp+sizeof(float), relativeLocation[1]);
2910 convertEndian(ctmp+2*sizeof(float), relat 2910 convertEndian(ctmp+2*sizeof(float), relativeLocation[2]);
2911 */ 2911 */
2912 2912
2913 // relative location of the dose distribu 2913 // relative location of the dose distribution image for
2914 // the modality image 2914 // the modality image
2915 //ofile.write((char *)relativeLocation, 3 2915 //ofile.write((char *)relativeLocation, 3*sizeof(float));
2916 ifile.read((char *)ctmp, 3*sizeof(int)); 2916 ifile.read((char *)ctmp, 3*sizeof(int));
2917 convertEndian(ctmp, iCenter[0]); 2917 convertEndian(ctmp, iCenter[0]);
2918 convertEndian(ctmp+sizeof(int), iCenter[1 2918 convertEndian(ctmp+sizeof(int), iCenter[1]);
2919 convertEndian(ctmp+2*sizeof(int), iCenter 2919 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2920 for(int i = 0; i < 3; i++) fCenter[i] = ( 2920 for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i];
2921 kDose[0].setCenterPosition(fCenter); 2921 kDose[0].setCenterPosition(fCenter);
2922 2922
2923 if(DEBUG || kVerbose > 0) { 2923 if(DEBUG || kVerbose > 0) {
2924 G4cout << "Dose dist. image relative lo 2924 G4cout << "Dose dist. image relative location : ("
2925 << fCenter[0] << ", " 2925 << fCenter[0] << ", "
2926 << fCenter[1] << ", " 2926 << fCenter[1] << ", "
2927 << fCenter[2] << ")" << G4endl; 2927 << fCenter[2] << ")" << G4endl;
2928 } 2928 }
2929 2929
2930 2930
2931 } 2931 }
2932 2932
2933 //----- ROI image -----// 2933 //----- ROI image -----//
2934 if(kPointerToROIData != 0) { 2934 if(kPointerToROIData != 0) {
2935 2935
2936 newROI(); 2936 newROI();
2937 2937
2938 // ROI image size 2938 // ROI image size
2939 ifile.read((char *)ctmp, 3*sizeof(int)); 2939 ifile.read((char *)ctmp, 3*sizeof(int));
2940 convertEndian(ctmp, size[0]); 2940 convertEndian(ctmp, size[0]);
2941 convertEndian(ctmp+sizeof(int), size[1]); 2941 convertEndian(ctmp+sizeof(int), size[1]);
2942 convertEndian(ctmp+2*sizeof(int), size[2] 2942 convertEndian(ctmp+2*sizeof(int), size[2]);
2943 kRoi[0].setSize(size); 2943 kRoi[0].setSize(size);
2944 if(DEBUG || kVerbose > 0) { 2944 if(DEBUG || kVerbose > 0) {
2945 G4cout << "ROI image size : (" 2945 G4cout << "ROI image size : ("
2946 << size[0] << ", " 2946 << size[0] << ", "
2947 << size[1] << ", " 2947 << size[1] << ", "
2948 << size[2] << ")" 2948 << size[2] << ")"
2949 << G4endl; 2949 << G4endl;
2950 } 2950 }
2951 2951
2952 // ROI max. & min. 2952 // ROI max. & min.
2953 ifile.read((char *)ctmp, sizeof(short)*2) 2953 ifile.read((char *)ctmp, sizeof(short)*2);
2954 convertEndian(ctmp, minmax[0]); 2954 convertEndian(ctmp, minmax[0]);
2955 convertEndian(ctmp+sizeof(short), minmax[ 2955 convertEndian(ctmp+sizeof(short), minmax[1]);
2956 kRoi[0].setMinMax(minmax); 2956 kRoi[0].setMinMax(minmax);
2957 2957
2958 // ROI distribution scaling 2958 // ROI distribution scaling
2959 ifile.read((char *)ctmp, sizeof(float)); 2959 ifile.read((char *)ctmp, sizeof(float));
2960 convertEndian(ctmp, scale); 2960 convertEndian(ctmp, scale);
2961 kRoi[0].setScale(dscale = scale); 2961 kRoi[0].setScale(dscale = scale);
2962 if(DEBUG || kVerbose > 0) { 2962 if(DEBUG || kVerbose > 0) {
2963 G4cout << "ROI image min., max., scale 2963 G4cout << "ROI image min., max., scale : "
2964 << minmax[0] << ", " 2964 << minmax[0] << ", "
2965 << minmax[1] << ", " 2965 << minmax[1] << ", "
2966 << scale << G4endl; 2966 << scale << G4endl;
2967 } 2967 }
2968 2968
2969 // ROI image 2969 // ROI image
2970 int rsize = size[0]*size[1]; 2970 int rsize = size[0]*size[1];
2971 char * ri = new char[rsize*sizeof(short)] 2971 char * ri = new char[rsize*sizeof(short)];
2972 for(int i = 0; i < size[2]; i++) { 2972 for(int i = 0; i < size[2]; i++) {
2973 ifile.read((char *)ri, rsize*sizeof(sho 2973 ifile.read((char *)ri, rsize*sizeof(short));
2974 short * rimage = new short[rsize]; 2974 short * rimage = new short[rsize];
2975 for(int j = 0; j < rsize; j++) { 2975 for(int j = 0; j < rsize; j++) {
2976 convertEndian(ri+j*sizeof(short), rimage[j] 2976 convertEndian(ri+j*sizeof(short), rimage[j]);
2977 } 2977 }
2978 kRoi[0].addImage(rimage); 2978 kRoi[0].addImage(rimage);
2979 2979
2980 } 2980 }
2981 delete [] ri; 2981 delete [] ri;
2982 2982
2983 // ROI relative location 2983 // ROI relative location
2984 ifile.read((char *)ctmp, 3*sizeof(int)); 2984 ifile.read((char *)ctmp, 3*sizeof(int));
2985 convertEndian(ctmp, iCenter[0]); 2985 convertEndian(ctmp, iCenter[0]);
2986 convertEndian(ctmp+sizeof(int), iCenter[1 2986 convertEndian(ctmp+sizeof(int), iCenter[1]);
2987 convertEndian(ctmp+2*sizeof(int), iCenter 2987 convertEndian(ctmp+2*sizeof(int), iCenter[2]);
2988 for(int i = 0; i < 3; i++) fCenter[i] = i 2988 for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i];
2989 kRoi[0].setCenterPosition(fCenter); 2989 kRoi[0].setCenterPosition(fCenter);
2990 if(DEBUG || kVerbose > 0) { 2990 if(DEBUG || kVerbose > 0) {
2991 G4cout << "ROI image relative location 2991 G4cout << "ROI image relative location : ("
2992 << fCenter[0] << ", " 2992 << fCenter[0] << ", "
2993 << fCenter[1] << ", " 2993 << fCenter[1] << ", "
2994 << fCenter[2] << ")" << G4endl; 2994 << fCenter[2] << ")" << G4endl;
2995 } 2995 }
2996 2996
2997 } 2997 }
2998 2998
2999 //----- track information -----// 2999 //----- track information -----//
3000 if(kPointerToTrackData != 0) { 3000 if(kPointerToTrackData != 0) {
3001 3001
3002 // track 3002 // track
3003 ifile.read((char *)ctmp, sizeof(int)); 3003 ifile.read((char *)ctmp, sizeof(int));
3004 int ntrk; 3004 int ntrk;
3005 convertEndian(ctmp, ntrk); 3005 convertEndian(ctmp, ntrk);
3006 if(DEBUG || kVerbose > 0) { 3006 if(DEBUG || kVerbose > 0) {
3007 G4cout << "# of tracks: " << ntrk << G4 3007 G4cout << "# of tracks: " << ntrk << G4endl;
3008 } 3008 }
3009 3009
3010 //v4 3010 //v4
3011 unsigned char trkcolorv4[3] = {255, 0, 0} 3011 unsigned char trkcolorv4[3] = {255, 0, 0};
3012 3012
3013 for(int i = 0; i < ntrk; i++) { 3013 for(int i = 0; i < ntrk; i++) {
3014 float * tp = new float[6]; 3014 float * tp = new float[6];
3015 // v4 3015 // v4
3016 std::vector<float *> trkv4; 3016 std::vector<float *> trkv4;
3017 3017
3018 ifile.read((char *)ctmp, sizeof(float)* 3018 ifile.read((char *)ctmp, sizeof(float)*3);
3019 if(DEBUG || kVerbose > 0) if(i < 10) G4 3019 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << i << ": " ;
3020 for(int j = 0; j < 3; j++) { 3020 for(int j = 0; j < 3; j++) {
3021 convertEndian(ctmp+j*sizeof(float), tp[j]); 3021 convertEndian(ctmp+j*sizeof(float), tp[j]);
3022 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 3022 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j] << ", ";
3023 } 3023 }
3024 3024
3025 ifile.read((char *)ctmp, sizeof(float)* 3025 ifile.read((char *)ctmp, sizeof(float)*3);
3026 for(int j = 0; j < 3; j++) { 3026 for(int j = 0; j < 3; j++) {
3027 convertEndian(ctmp+j*sizeof(float), tp[j+3] 3027 convertEndian(ctmp+j*sizeof(float), tp[j+3]);
3028 if(DEBUG || kVerbose > 0) if(i < 10) G4cout 3028 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << tp[j+3] << ", ";
3029 } 3029 }
3030 3030
3031 kSteps.push_back(tp); 3031 kSteps.push_back(tp);
3032 // v4 3032 // v4
3033 trkv4.push_back(tp); 3033 trkv4.push_back(tp);
3034 addTrack(trkv4, trkcolorv4); 3034 addTrack(trkv4, trkcolorv4);
3035 3035
3036 if(DEBUG || kVerbose > 0) if(i < 10) G4 3036 if(DEBUG || kVerbose > 0) if(i < 10) G4cout << G4endl;
3037 } 3037 }
3038 3038
3039 } 3039 }
3040 3040
3041 /* ver 1 3041 /* ver 1
3042 // track 3042 // track
3043 int ntracks; 3043 int ntracks;
3044 ifile.read(ctmp, sizeof(int)); 3044 ifile.read(ctmp, sizeof(int));
3045 convertEndian(ctmp, ntracks); 3045 convertEndian(ctmp, ntracks);
3046 // track displacement 3046 // track displacement
3047 ifile.read(ctmp, 3*sizeof(float)); 3047 ifile.read(ctmp, 3*sizeof(float));
3048 convertEndian(ctmp, trackDisplacement[0]); 3048 convertEndian(ctmp, trackDisplacement[0]);
3049 convertEndian(ctmp+sizeof(float), trackDisp 3049 convertEndian(ctmp+sizeof(float), trackDisplacement[2]); // exchanged with [1]
3050 convertEndian(ctmp+2*sizeof(float), trackDi 3050 convertEndian(ctmp+2*sizeof(float), trackDisplacement[1]);
3051 // 3051 //
3052 //for(int i = 0; i < ntracks && i < 100; i+ 3052 //for(int i = 0; i < ntracks && i < 100; i++) {
3053 for(int i = 0; i < ntracks; i++) { 3053 for(int i = 0; i < ntracks; i++) {
3054 DicomDoseTrack trk; 3054 DicomDoseTrack trk;
3055 short trackid, parentid, pid; 3055 short trackid, parentid, pid;
3056 int npoints; 3056 int npoints;
3057 ifile.read(ctmp, sizeof(short)); 3057 ifile.read(ctmp, sizeof(short));
3058 convertEndian(ctmp, trackid); 3058 convertEndian(ctmp, trackid);
3059 trk.setID(trackid); 3059 trk.setID(trackid);
3060 ifile.read(ctmp, sizeof(short)); 3060 ifile.read(ctmp, sizeof(short));
3061 convertEndian(ctmp, parentid); 3061 convertEndian(ctmp, parentid);
3062 trk.setParentID(parentid); 3062 trk.setParentID(parentid);
3063 ifile.read(ctmp, sizeof(short)); 3063 ifile.read(ctmp, sizeof(short));
3064 convertEndian(ctmp, pid); 3064 convertEndian(ctmp, pid);
3065 trk.setPID(pid); 3065 trk.setPID(pid);
3066 ifile.read(ctmp, sizeof(int)); 3066 ifile.read(ctmp, sizeof(int));
3067 convertEndian(ctmp, npoints); 3067 convertEndian(ctmp, npoints);
3068 for(int i = 0; i < npoints; i++) { 3068 for(int i = 0; i < npoints; i++) {
3069 ifile.read(ctmp, 3*sizeof(float)); 3069 ifile.read(ctmp, 3*sizeof(float));
3070 // storing only start and end points 3070 // storing only start and end points
3071 //if(i == 0 || i == npoints - 1) { 3071 //if(i == 0 || i == npoints - 1) {
3072 float * point = new float[3]; 3072 float * point = new float[3];
3073 convertEndian(ctmp, point[0]); 3073 convertEndian(ctmp, point[0]);
3074 convertEndian(ctmp+sizeof(float), point[1]) 3074 convertEndian(ctmp+sizeof(float), point[1]);
3075 convertEndian(ctmp+2*sizeof(float), point[2 3075 convertEndian(ctmp+2*sizeof(float), point[2]);
3076 trk.addPoint(point); 3076 trk.addPoint(point);
3077 //} 3077 //}
3078 } 3078 }
3079 track.push_back(trk); 3079 track.push_back(trk);
3080 } 3080 }
3081 */ 3081 */
3082 3082
3083 ifile.close(); 3083 ifile.close();
3084 3084
3085 return true; 3085 return true;
3086 } 3086 }
3087 3087
3088 bool G4GMocrenIO::retrieveData2(char * _filen 3088 bool G4GMocrenIO::retrieveData2(char * _filename) {
3089 kFileName = _filename; 3089 kFileName = _filename;
3090 return retrieveData(); 3090 return retrieveData();
3091 } 3091 }
3092 3092
3093 void G4GMocrenIO::setID() { 3093 void G4GMocrenIO::setID() {
3094 time_t t; 3094 time_t t;
3095 time(&t); 3095 time(&t);
3096 3096
3097 tm * ti; 3097 tm * ti;
3098 ti = localtime(&t); 3098 ti = localtime(&t);
3099 3099
3100 char cmonth[12][4] = {"Jan", "Feb", "Mar", 3100 char cmonth[12][4] = {"Jan", "Feb", "Mar", "Apr",
3101 "May", "Jun", "Jul", "Aug", 3101 "May", "Jun", "Jul", "Aug",
3102 "Sep", "Oct", "Nov", "Dec"}; 3102 "Sep", "Oct", "Nov", "Dec"};
3103 std::stringstream ss; 3103 std::stringstream ss;
3104 ss << std::setfill('0') 3104 ss << std::setfill('0')
3105 << std::setw(2) 3105 << std::setw(2)
3106 << ti->tm_hour << ":" 3106 << ti->tm_hour << ":"
3107 << std::setw(2) 3107 << std::setw(2)
3108 << ti->tm_min << ":" 3108 << ti->tm_min << ":"
3109 << std::setw(2) 3109 << std::setw(2)
3110 << ti->tm_sec << "," 3110 << ti->tm_sec << ","
3111 << cmonth[ti->tm_mon] << "." 3111 << cmonth[ti->tm_mon] << "."
3112 << std::setw(2) 3112 << std::setw(2)
3113 << ti->tm_mday << "," 3113 << ti->tm_mday << ","
3114 << ti->tm_year+1900; 3114 << ti->tm_year+1900;
3115 3115
3116 kId = ss.str(); 3116 kId = ss.str();
3117 } 3117 }
3118 3118
3119 // get & set the file version 3119 // get & set the file version
3120 std::string & G4GMocrenIO::getVersion() {retu 3120 std::string & G4GMocrenIO::getVersion() {return kVersion;}
3121 void G4GMocrenIO::setVersion(std::string & _v 3121 void G4GMocrenIO::setVersion(std::string & _version) {kVersion = _version;}
3122 3122
3123 // set endians of input/output data 3123 // set endians of input/output data
3124 void G4GMocrenIO::setLittleEndianInput(bool _ 3124 void G4GMocrenIO::setLittleEndianInput(bool _little) {kLittleEndianInput = _little;}
3125 void G4GMocrenIO::setLittleEndianOutput(bool 3125 void G4GMocrenIO::setLittleEndianOutput(bool _little) {kLittleEndianOutput = _little;}
3126 3126
3127 // voxel spacing 3127 // voxel spacing
3128 void G4GMocrenIO::setVoxelSpacing(float _spac 3128 void G4GMocrenIO::setVoxelSpacing(float _spacing[3]) {
3129 for(int i = 0; i < 3; i++) kVoxelSpacing[i] 3129 for(int i = 0; i < 3; i++) kVoxelSpacing[i] = _spacing[i];
3130 } 3130 }
3131 void G4GMocrenIO::getVoxelSpacing(float _spac 3131 void G4GMocrenIO::getVoxelSpacing(float _spacing[3]) {
3132 for(int i = 0; i < 3; i++) _spacing[i] = kV 3132 for(int i = 0; i < 3; i++) _spacing[i] = kVoxelSpacing[i];
3133 } 3133 }
3134 3134
3135 // get & set number of events 3135 // get & set number of events
3136 int & G4GMocrenIO::getNumberOfEvents() { 3136 int & G4GMocrenIO::getNumberOfEvents() {
3137 return kNumberOfEvents; 3137 return kNumberOfEvents;
3138 } 3138 }
3139 void G4GMocrenIO::setNumberOfEvents(int & _nu 3139 void G4GMocrenIO::setNumberOfEvents(int & _numberOfEvents) {
3140 kNumberOfEvents = _numberOfEvents; 3140 kNumberOfEvents = _numberOfEvents;
3141 } 3141 }
3142 void G4GMocrenIO::addOneEvent() { 3142 void G4GMocrenIO::addOneEvent() {
3143 kNumberOfEvents++; 3143 kNumberOfEvents++;
3144 } 3144 }
3145 3145
3146 // set/get pointer the modality image data 3146 // set/get pointer the modality image data
3147 void G4GMocrenIO::setPointerToModalityData(un 3147 void G4GMocrenIO::setPointerToModalityData(unsigned int & _pointer) {
3148 kPointerToModalityData = _pointer; 3148 kPointerToModalityData = _pointer;
3149 } 3149 }
3150 unsigned int G4GMocrenIO::getPointerToModalit 3150 unsigned int G4GMocrenIO::getPointerToModalityData() {
3151 return kPointerToModalityData; 3151 return kPointerToModalityData;
3152 } 3152 }
3153 // set/get pointer the dose distribution imag 3153 // set/get pointer the dose distribution image data
3154 void G4GMocrenIO::addPointerToDoseDistData(un 3154 void G4GMocrenIO::addPointerToDoseDistData(unsigned int & _pointer) {
3155 kPointerToDoseDistData.push_back(_pointer); 3155 kPointerToDoseDistData.push_back(_pointer);
3156 } 3156 }
3157 unsigned int G4GMocrenIO::getPointerToDoseDis 3157 unsigned int G4GMocrenIO::getPointerToDoseDistData(int _elem) {
3158 if(kPointerToDoseDistData.size() == 0 || 3158 if(kPointerToDoseDistData.size() == 0 ||
3159 kPointerToDoseDistData.size() < (size_t) 3159 kPointerToDoseDistData.size() < (size_t)_elem)
3160 return 0; 3160 return 0;
3161 else 3161 else
3162 return kPointerToDoseDistData[_elem]; 3162 return kPointerToDoseDistData[_elem];
3163 } 3163 }
3164 3164
3165 // set/get pointer the ROI image data 3165 // set/get pointer the ROI image data
3166 void G4GMocrenIO::setPointerToROIData(unsigne 3166 void G4GMocrenIO::setPointerToROIData(unsigned int & _pointer) {
3167 kPointerToROIData = _pointer; 3167 kPointerToROIData = _pointer;
3168 } 3168 }
3169 unsigned int G4GMocrenIO::getPointerToROIData 3169 unsigned int G4GMocrenIO::getPointerToROIData() {
3170 return kPointerToROIData; 3170 return kPointerToROIData;
3171 } 3171 }
3172 // set/get pointer the track data 3172 // set/get pointer the track data
3173 void G4GMocrenIO::setPointerToTrackData(unsig 3173 void G4GMocrenIO::setPointerToTrackData(unsigned int & _pointer) {
3174 kPointerToTrackData = _pointer; 3174 kPointerToTrackData = _pointer;
3175 } 3175 }
3176 unsigned int G4GMocrenIO::getPointerToTrackDa 3176 unsigned int G4GMocrenIO::getPointerToTrackData() {
3177 return kPointerToTrackData; 3177 return kPointerToTrackData;
3178 } 3178 }
3179 3179
3180 // calculate pointers for version 4 3180 // calculate pointers for version 4
3181 void G4GMocrenIO::calcPointers4() { 3181 void G4GMocrenIO::calcPointers4() {
3182 3182
3183 // pointer to modality data 3183 // pointer to modality data
3184 unsigned int pointer = 1070; // up to "poin 3184 unsigned int pointer = 1070; // up to "pointer to the detector data" except for "pointer to the dose dist data"
3185 int nDoseDist = getNumDoseDist(); 3185 int nDoseDist = getNumDoseDist();
3186 pointer += nDoseDist*4; 3186 pointer += nDoseDist*4;
3187 3187
3188 setPointerToModalityData(pointer); 3188 setPointerToModalityData(pointer);
3189 3189
3190 // pointer to dose data 3190 // pointer to dose data
3191 // ct-density map for modality data 3191 // ct-density map for modality data
3192 int msize[3]; 3192 int msize[3];
3193 getModalityImageSize(msize); 3193 getModalityImageSize(msize);
3194 short mminmax[2]; 3194 short mminmax[2];
3195 getModalityImageMinMax(mminmax); 3195 getModalityImageMinMax(mminmax);
3196 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3196 int pmsize = 2*msize[0]*msize[1]*msize[2];
3197 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3197 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3198 pointer += 32 + pmsize + pmmap; 3198 pointer += 32 + pmsize + pmmap;
3199 // 3199 //
3200 kPointerToDoseDistData.clear(); 3200 kPointerToDoseDistData.clear();
3201 if(nDoseDist == 0) { 3201 if(nDoseDist == 0) {
3202 unsigned int pointer0 = 0; 3202 unsigned int pointer0 = 0;
3203 addPointerToDoseDistData(pointer0); 3203 addPointerToDoseDistData(pointer0);
3204 } 3204 }
3205 for(int ndose = 0; ndose < nDoseDist; ndose 3205 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3206 addPointerToDoseDistData(pointer); 3206 addPointerToDoseDistData(pointer);
3207 int dsize[3]; 3207 int dsize[3];
3208 getDoseDistSize(dsize); 3208 getDoseDistSize(dsize);
3209 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3209 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2 + 80;
3210 } 3210 }
3211 3211
3212 // pointer to roi data 3212 // pointer to roi data
3213 if(!isROIEmpty()) { 3213 if(!isROIEmpty()) {
3214 setPointerToROIData(pointer); 3214 setPointerToROIData(pointer);
3215 3215
3216 int rsize[3]; 3216 int rsize[3];
3217 getROISize(rsize); 3217 getROISize(rsize);
3218 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3218 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3219 pointer += 20 + prsize + 12; 3219 pointer += 20 + prsize + 12;
3220 } else { 3220 } else {
3221 unsigned int pointer0 = 0; 3221 unsigned int pointer0 = 0;
3222 setPointerToROIData(pointer0); 3222 setPointerToROIData(pointer0);
3223 } 3223 }
3224 3224
3225 // pointer to track data 3225 // pointer to track data
3226 int ntrk = (int)kTracks.size(); << 3226 int ntrk = kTracks.size();
3227 if(ntrk != 0) { 3227 if(ntrk != 0) {
3228 setPointerToTrackData(pointer); 3228 setPointerToTrackData(pointer);
3229 3229
3230 pointer += 4; // # of tracks 3230 pointer += 4; // # of tracks
3231 for(int nt = 0; nt < ntrk; nt++) { 3231 for(int nt = 0; nt < ntrk; nt++) {
3232 int nsteps = kTracks[nt].getNumberOfSte 3232 int nsteps = kTracks[nt].getNumberOfSteps();
3233 pointer += 4 + 3 + nsteps*(4*6); // # o 3233 pointer += 4 + 3 + nsteps*(4*6); // # of steps + color + steps(float*6)
3234 } 3234 }
3235 } else { 3235 } else {
3236 unsigned int pointer0 = 0; 3236 unsigned int pointer0 = 0;
3237 setPointerToTrackData(pointer0); 3237 setPointerToTrackData(pointer0);
3238 } 3238 }
3239 if(kVerbose > 0) G4cout << " pointer to the 3239 if(kVerbose > 0) G4cout << " pointer to the track data :"
3240 << kPointerToTrackData << G4endl; 3240 << kPointerToTrackData << G4endl;
3241 3241
3242 // pointer to detector data 3242 // pointer to detector data
3243 int ndet = (int)kDetectors.size(); << 3243 int ndet = kDetectors.size();
3244 if(ndet != 0) { 3244 if(ndet != 0) {
3245 kPointerToDetectorData = pointer; 3245 kPointerToDetectorData = pointer;
3246 } else { 3246 } else {
3247 kPointerToDetectorData = 0; 3247 kPointerToDetectorData = 0;
3248 } 3248 }
3249 if(kVerbose > 0) G4cout << " pointer to the 3249 if(kVerbose > 0) G4cout << " pointer to the detector data :"
3250 << kPointerToDetectorData << G4end 3250 << kPointerToDetectorData << G4endl;
3251 3251
3252 } 3252 }
3253 3253
3254 // calculate pointers for ver.3 3254 // calculate pointers for ver.3
3255 void G4GMocrenIO::calcPointers3() { 3255 void G4GMocrenIO::calcPointers3() {
3256 3256
3257 // pointer to modality data 3257 // pointer to modality data
3258 unsigned int pointer = 1066; // up to "poin 3258 unsigned int pointer = 1066; // up to "pointer to the track data" except for "pointer to the dose dist data"
3259 int nDoseDist = getNumDoseDist(); 3259 int nDoseDist = getNumDoseDist();
3260 pointer += nDoseDist*4; 3260 pointer += nDoseDist*4;
3261 3261
3262 setPointerToModalityData(pointer); 3262 setPointerToModalityData(pointer);
3263 3263
3264 // pointer to dose data 3264 // pointer to dose data
3265 // ct-density map for modality data 3265 // ct-density map for modality data
3266 int msize[3]; 3266 int msize[3];
3267 getModalityImageSize(msize); 3267 getModalityImageSize(msize);
3268 short mminmax[2]; 3268 short mminmax[2];
3269 getModalityImageMinMax(mminmax); 3269 getModalityImageMinMax(mminmax);
3270 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3270 int pmsize = 2*msize[0]*msize[1]*msize[2];
3271 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3271 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3272 pointer += 32 + pmsize + pmmap; 3272 pointer += 32 + pmsize + pmmap;
3273 // 3273 //
3274 kPointerToDoseDistData.clear(); 3274 kPointerToDoseDistData.clear();
3275 if(nDoseDist == 0) { 3275 if(nDoseDist == 0) {
3276 unsigned int pointer0 = 0; 3276 unsigned int pointer0 = 0;
3277 addPointerToDoseDistData(pointer0); 3277 addPointerToDoseDistData(pointer0);
3278 } 3278 }
3279 for(int ndose = 0; ndose < nDoseDist; ndose 3279 for(int ndose = 0; ndose < nDoseDist; ndose++) {
3280 addPointerToDoseDistData(pointer); 3280 addPointerToDoseDistData(pointer);
3281 int dsize[3]; 3281 int dsize[3];
3282 getDoseDistSize(dsize); 3282 getDoseDistSize(dsize);
3283 pointer += 44 + dsize[0]*dsize[1]*dsize[2 3283 pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2;
3284 } 3284 }
3285 3285
3286 // pointer to roi data 3286 // pointer to roi data
3287 if(!isROIEmpty()) { 3287 if(!isROIEmpty()) {
3288 setPointerToROIData(pointer); 3288 setPointerToROIData(pointer);
3289 3289
3290 int rsize[3]; 3290 int rsize[3];
3291 getROISize(rsize); 3291 getROISize(rsize);
3292 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3292 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3293 pointer += 20 + prsize + 12; 3293 pointer += 20 + prsize + 12;
3294 } else { 3294 } else {
3295 unsigned int pointer0 = 0; 3295 unsigned int pointer0 = 0;
3296 setPointerToROIData(pointer0); 3296 setPointerToROIData(pointer0);
3297 } 3297 }
3298 3298
3299 // 3299 //
3300 if(getNumTracks() != 0) 3300 if(getNumTracks() != 0)
3301 setPointerToTrackData(pointer); 3301 setPointerToTrackData(pointer);
3302 else { 3302 else {
3303 unsigned int pointer0 = 0; 3303 unsigned int pointer0 = 0;
3304 setPointerToTrackData(pointer0); 3304 setPointerToTrackData(pointer0);
3305 } 3305 }
3306 3306
3307 } 3307 }
3308 3308
3309 // calculate pointers for ver.2 3309 // calculate pointers for ver.2
3310 void G4GMocrenIO::calcPointers2() { 3310 void G4GMocrenIO::calcPointers2() {
3311 3311
3312 // pointer to modality data 3312 // pointer to modality data
3313 unsigned int pointer = 65; 3313 unsigned int pointer = 65;
3314 setPointerToModalityData(pointer); 3314 setPointerToModalityData(pointer);
3315 3315
3316 // pointer to dose data 3316 // pointer to dose data
3317 int msize[3]; 3317 int msize[3];
3318 getModalityImageSize(msize); 3318 getModalityImageSize(msize);
3319 short mminmax[2]; 3319 short mminmax[2];
3320 getModalityImageMinMax(mminmax); 3320 getModalityImageMinMax(mminmax);
3321 int pmsize = 2*msize[0]*msize[1]*msize[2]; 3321 int pmsize = 2*msize[0]*msize[1]*msize[2];
3322 int pmmap = 4*(mminmax[1] - mminmax[0] + 1) 3322 int pmmap = 4*(mminmax[1] - mminmax[0] + 1);
3323 pointer += 20 + pmsize + pmmap; 3323 pointer += 20 + pmsize + pmmap;
3324 int dsize[3]; 3324 int dsize[3];
3325 getDoseDistSize(dsize); 3325 getDoseDistSize(dsize);
3326 kPointerToDoseDistData.clear(); 3326 kPointerToDoseDistData.clear();
3327 if(dsize[0] != 0) { 3327 if(dsize[0] != 0) {
3328 kPointerToDoseDistData.push_back(pointer) 3328 kPointerToDoseDistData.push_back(pointer);
3329 3329
3330 int pdsize = 2*dsize[0]*dsize[1]*dsize[2] 3330 int pdsize = 2*dsize[0]*dsize[1]*dsize[2];
3331 pointer += 20 + pdsize + 12; 3331 pointer += 20 + pdsize + 12;
3332 } else { 3332 } else {
3333 unsigned int pointer0 = 0; 3333 unsigned int pointer0 = 0;
3334 kPointerToDoseDistData.push_back(pointer0 3334 kPointerToDoseDistData.push_back(pointer0);
3335 } 3335 }
3336 3336
3337 // pointer to roi data 3337 // pointer to roi data
3338 if(!isROIEmpty()) { 3338 if(!isROIEmpty()) {
3339 int rsize[3]; 3339 int rsize[3];
3340 getROISize(rsize); 3340 getROISize(rsize);
3341 setPointerToROIData(pointer); 3341 setPointerToROIData(pointer);
3342 int prsize = 2*rsize[0]*rsize[1]*rsize[2] 3342 int prsize = 2*rsize[0]*rsize[1]*rsize[2];
3343 pointer += 20 + prsize + 12; 3343 pointer += 20 + prsize + 12;
3344 3344
3345 } else { 3345 } else {
3346 unsigned int pointer0 = 0; 3346 unsigned int pointer0 = 0;
3347 setPointerToROIData(pointer0); 3347 setPointerToROIData(pointer0);
3348 } 3348 }
3349 3349
3350 // 3350 //
3351 if(getNumTracks() != 0) 3351 if(getNumTracks() != 0)
3352 setPointerToTrackData(pointer); 3352 setPointerToTrackData(pointer);
3353 else { 3353 else {
3354 unsigned int pointer0 = 0; 3354 unsigned int pointer0 = 0;
3355 setPointerToTrackData(pointer0); 3355 setPointerToTrackData(pointer0);
3356 } 3356 }
3357 3357
3358 } 3358 }
3359 3359
3360 3360
3361 //----- Modality image -----// 3361 //----- Modality image -----//
3362 void G4GMocrenIO::getModalityImageSize(int _s 3362 void G4GMocrenIO::getModalityImageSize(int _size[3]) {
3363 3363
3364 kModality.getSize(_size); 3364 kModality.getSize(_size);
3365 } 3365 }
3366 void G4GMocrenIO::setModalityImageSize(int _s 3366 void G4GMocrenIO::setModalityImageSize(int _size[3]) {
3367 3367
3368 kModality.setSize(_size); 3368 kModality.setSize(_size);
3369 } 3369 }
3370 3370
3371 // get & set the modality image size 3371 // get & set the modality image size
3372 void G4GMocrenIO::setModalityImageScale(doubl 3372 void G4GMocrenIO::setModalityImageScale(double & _scale) {
3373 3373
3374 kModality.setScale(_scale); 3374 kModality.setScale(_scale);
3375 } 3375 }
3376 double G4GMocrenIO::getModalityImageScale() { 3376 double G4GMocrenIO::getModalityImageScale() {
3377 3377
3378 return kModality.getScale(); 3378 return kModality.getScale();
3379 } 3379 }
3380 3380
3381 // set the modality image in CT 3381 // set the modality image in CT
3382 void G4GMocrenIO::setModalityImage(short * _i 3382 void G4GMocrenIO::setModalityImage(short * _image) {
3383 3383
3384 kModality.addImage(_image); 3384 kModality.addImage(_image);
3385 } 3385 }
3386 short * G4GMocrenIO::getModalityImage(int _z) 3386 short * G4GMocrenIO::getModalityImage(int _z) {
3387 3387
3388 return kModality.getImage(_z); 3388 return kModality.getImage(_z);
3389 } 3389 }
3390 void G4GMocrenIO::clearModalityImage() { 3390 void G4GMocrenIO::clearModalityImage() {
3391 3391
3392 kModality.clearImage(); 3392 kModality.clearImage();
3393 } 3393 }
3394 // set/get the modality image density map 3394 // set/get the modality image density map
3395 void G4GMocrenIO::setModalityImageDensityMap( 3395 void G4GMocrenIO::setModalityImageDensityMap(std::vector<float> & _map) {
3396 kModalityImageDensityMap = _map; 3396 kModalityImageDensityMap = _map;
3397 } 3397 }
3398 std::vector<float> & G4GMocrenIO::getModality 3398 std::vector<float> & G4GMocrenIO::getModalityImageDensityMap() {
3399 return kModalityImageDensityMap; 3399 return kModalityImageDensityMap;
3400 } 3400 }
3401 // set the modality image min./max. 3401 // set the modality image min./max.
3402 void G4GMocrenIO::setModalityImageMinMax(shor 3402 void G4GMocrenIO::setModalityImageMinMax(short _minmax[2]) {
3403 3403
3404 kModality.setMinMax(_minmax); 3404 kModality.setMinMax(_minmax);
3405 } 3405 }
3406 // get the modality image min./max. 3406 // get the modality image min./max.
3407 void G4GMocrenIO::getModalityImageMinMax(shor 3407 void G4GMocrenIO::getModalityImageMinMax(short _minmax[2]) {
3408 3408
3409 short minmax[2]; 3409 short minmax[2];
3410 kModality.getMinMax(minmax); 3410 kModality.getMinMax(minmax);
3411 for(int i = 0; i < 2; i++) _minmax[i] = min 3411 for(int i = 0; i < 2; i++) _minmax[i] = minmax[i];
3412 } 3412 }
3413 short G4GMocrenIO::getModalityImageMax() { 3413 short G4GMocrenIO::getModalityImageMax() {
3414 3414
3415 short minmax[2]; 3415 short minmax[2];
3416 kModality.getMinMax(minmax); 3416 kModality.getMinMax(minmax);
3417 return minmax[1]; 3417 return minmax[1];
3418 } 3418 }
3419 short G4GMocrenIO::getModalityImageMin() { 3419 short G4GMocrenIO::getModalityImageMin() {
3420 3420
3421 short minmax[2]; 3421 short minmax[2];
3422 kModality.getMinMax(minmax); 3422 kModality.getMinMax(minmax);
3423 return minmax[0]; 3423 return minmax[0];
3424 } 3424 }
3425 // set/get position of the modality image cen 3425 // set/get position of the modality image center
3426 void G4GMocrenIO::setModalityCenterPosition(f 3426 void G4GMocrenIO::setModalityCenterPosition(float _center[3]) {
3427 3427
3428 kModality.setCenterPosition(_center); 3428 kModality.setCenterPosition(_center);
3429 } 3429 }
3430 void G4GMocrenIO::getModalityCenterPosition(f 3430 void G4GMocrenIO::getModalityCenterPosition(float _center[3]) {
3431 3431
3432 if(isROIEmpty()) 3432 if(isROIEmpty())
3433 for(int i = 0; i < 3; i++) _center[i] = 0 3433 for(int i = 0; i < 3; i++) _center[i] = 0;
3434 else 3434 else
3435 kModality.getCenterPosition(_center); 3435 kModality.getCenterPosition(_center);
3436 } 3436 }
3437 // get & set the modality image unit 3437 // get & set the modality image unit
3438 std::string G4GMocrenIO::getModalityImageUnit 3438 std::string G4GMocrenIO::getModalityImageUnit() {
3439 return kModalityUnit; 3439 return kModalityUnit;
3440 } 3440 }
3441 void G4GMocrenIO::setModalityImageUnit(std::s 3441 void G4GMocrenIO::setModalityImageUnit(std::string & _unit) {
3442 kModalityUnit = _unit; 3442 kModalityUnit = _unit;
3443 } 3443 }
3444 // 3444 //
3445 short G4GMocrenIO::convertDensityToHU(float & 3445 short G4GMocrenIO::convertDensityToHU(float & _dens) {
3446 short rval = -1024; // default: air 3446 short rval = -1024; // default: air
3447 int nmap = (int)kModalityImageDensityMap.si 3447 int nmap = (int)kModalityImageDensityMap.size();
3448 if(nmap != 0) { 3448 if(nmap != 0) {
3449 short minmax[2]; 3449 short minmax[2];
3450 kModality.getMinMax(minmax); 3450 kModality.getMinMax(minmax);
3451 rval = minmax[1]; 3451 rval = minmax[1];
3452 for(int i = 0; i < nmap; i++) { 3452 for(int i = 0; i < nmap; i++) {
3453 //G4cout << kModalityImageDensityMap[i] 3453 //G4cout << kModalityImageDensityMap[i] << G4endl;
3454 if(_dens <= kModalityImageDensityMap[i] 3454 if(_dens <= kModalityImageDensityMap[i]) {
3455 rval = i + minmax[0]; 3455 rval = i + minmax[0];
3456 break; 3456 break;
3457 } 3457 }
3458 } 3458 }
3459 } 3459 }
3460 return rval; 3460 return rval;
3461 } 3461 }
3462 3462
3463 3463
3464 //----- Dose distribution -----// 3464 //----- Dose distribution -----//
3465 // 3465 //
3466 void G4GMocrenIO::newDoseDist() { 3466 void G4GMocrenIO::newDoseDist() {
3467 GMocrenDataPrimitive<double> doseData; 3467 GMocrenDataPrimitive<double> doseData;
3468 kDose.push_back(doseData); 3468 kDose.push_back(doseData);
3469 } 3469 }
3470 int G4GMocrenIO::getNumDoseDist() { 3470 int G4GMocrenIO::getNumDoseDist() {
3471 return (int)kDose.size(); 3471 return (int)kDose.size();
3472 } 3472 }
3473 3473
3474 // get & set the dose distribution unit 3474 // get & set the dose distribution unit
3475 std::string G4GMocrenIO::getDoseDistUnit(int 3475 std::string G4GMocrenIO::getDoseDistUnit(int _num) {
3476 // to avoid a warning in the compile proces 3476 // to avoid a warning in the compile process
3477 if(kDoseUnit.size() > static_cast<size_t>(_ 3477 if(kDoseUnit.size() > static_cast<size_t>(_num)) return kDoseUnit;
3478 3478
3479 return kDoseUnit; 3479 return kDoseUnit;
3480 } 3480 }
3481 void G4GMocrenIO::setDoseDistUnit(std::string 3481 void G4GMocrenIO::setDoseDistUnit(std::string & _unit, int _num) {
3482 // to avoid a warning in the compile proces 3482 // to avoid a warning in the compile process
3483 if(_unit.size() > static_cast<size_t>(_num) 3483 if(_unit.size() > static_cast<size_t>(_num)) kDoseUnit = _unit;
3484 3484
3485 //char unit[13]; 3485 //char unit[13];
3486 //std::strncpy(unit, _unit.c_str(), 12); 3486 //std::strncpy(unit, _unit.c_str(), 12);
3487 //doseUnit = unit; 3487 //doseUnit = unit;
3488 kDoseUnit = _unit; 3488 kDoseUnit = _unit;
3489 } 3489 }
3490 // 3490 //
3491 void G4GMocrenIO::getDoseDistSize(int _size[3 3491 void G4GMocrenIO::getDoseDistSize(int _size[3], int _num) {
3492 if(isDoseEmpty()) 3492 if(isDoseEmpty())
3493 for(int i = 0; i < 3; i++) _size[i] = 0; 3493 for(int i = 0; i < 3; i++) _size[i] = 0;
3494 else 3494 else
3495 kDose[_num].getSize(_size); 3495 kDose[_num].getSize(_size);
3496 } 3496 }
3497 void G4GMocrenIO::setDoseDistSize(int _size[3 3497 void G4GMocrenIO::setDoseDistSize(int _size[3], int _num) {
3498 3498
3499 kDose[_num].setSize(_size); 3499 kDose[_num].setSize(_size);
3500 3500
3501 //resetDose(); 3501 //resetDose();
3502 } 3502 }
3503 3503
3504 void G4GMocrenIO::setDoseDistMinMax(short _mi 3504 void G4GMocrenIO::setDoseDistMinMax(short _minmax[2], int _num) {
3505 3505
3506 double minmax[2]; 3506 double minmax[2];
3507 double scale = kDose[_num].getScale(); 3507 double scale = kDose[_num].getScale();
3508 for(int i = 0; i < 2; i++) minmax[i] = (dou 3508 for(int i = 0; i < 2; i++) minmax[i] = (double)_minmax[i]*scale;
3509 kDose[_num].setMinMax(minmax); 3509 kDose[_num].setMinMax(minmax);
3510 } 3510 }
3511 void G4GMocrenIO::getDoseDistMinMax(short _mi 3511 void G4GMocrenIO::getDoseDistMinMax(short _minmax[2], int _num) {
3512 3512
3513 if(isDoseEmpty()) 3513 if(isDoseEmpty())
3514 for(int i = 0; i < 2; i++) _minmax[i] = 0 3514 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3515 else { 3515 else {
3516 double minmax[2]; 3516 double minmax[2];
3517 kDose[_num].getMinMax(minmax); 3517 kDose[_num].getMinMax(minmax);
3518 double scale = kDose[_num].getScale(); 3518 double scale = kDose[_num].getScale();
3519 for(int i = 0; i < 2; i++) _minmax[i] = ( 3519 for(int i = 0; i < 2; i++) _minmax[i] = (short)(minmax[i]/scale+0.5);
3520 } 3520 }
3521 } 3521 }
3522 void G4GMocrenIO::setDoseDistMinMax(double _m 3522 void G4GMocrenIO::setDoseDistMinMax(double _minmax[2], int _num) {
3523 3523
3524 kDose[_num].setMinMax(_minmax); 3524 kDose[_num].setMinMax(_minmax);
3525 } 3525 }
3526 void G4GMocrenIO::getDoseDistMinMax(double _m 3526 void G4GMocrenIO::getDoseDistMinMax(double _minmax[2], int _num) {
3527 3527
3528 if(isDoseEmpty()) 3528 if(isDoseEmpty())
3529 for(int i = 0; i < 2; i++) _minmax[i] = 0 3529 for(int i = 0; i < 2; i++) _minmax[i] = 0.;
3530 else 3530 else
3531 kDose[_num].getMinMax(_minmax); 3531 kDose[_num].getMinMax(_minmax);
3532 } 3532 }
3533 3533
3534 // get & set the dose distribution image scal 3534 // get & set the dose distribution image scale
3535 void G4GMocrenIO::setDoseDistScale(double & _ 3535 void G4GMocrenIO::setDoseDistScale(double & _scale, int _num) {
3536 3536
3537 kDose[_num].setScale(_scale); 3537 kDose[_num].setScale(_scale);
3538 } 3538 }
3539 double G4GMocrenIO::getDoseDistScale(int _num 3539 double G4GMocrenIO::getDoseDistScale(int _num) {
3540 3540
3541 if(isDoseEmpty()) 3541 if(isDoseEmpty())
3542 return 0.; 3542 return 0.;
3543 else 3543 else
3544 return kDose[_num].getScale(); 3544 return kDose[_num].getScale();
3545 } 3545 }
3546 3546
3547 /* 3547 /*
3548 void G4GMocrenIO::initializeShortDoseDist() 3548 void G4GMocrenIO::initializeShortDoseDist() {
3549 ; 3549 ;
3550 } 3550 }
3551 void G4GMocrenIO::finalizeShortDoseDist() { 3551 void G4GMocrenIO::finalizeShortDoseDist() {
3552 ; 3552 ;
3553 } 3553 }
3554 */ 3554 */
3555 // set the dose distribution image 3555 // set the dose distribution image
3556 void G4GMocrenIO::setShortDoseDist(short * _i 3556 void G4GMocrenIO::setShortDoseDist(short * _image, int _num) {
3557 3557
3558 int size[3]; 3558 int size[3];
3559 kDose[_num].getSize(size); 3559 kDose[_num].getSize(size);
3560 int dsize = size[0]*size[1]; 3560 int dsize = size[0]*size[1];
3561 double * ddata = new double[dsize]; 3561 double * ddata = new double[dsize];
3562 double scale = kDose[_num].getScale(); 3562 double scale = kDose[_num].getScale();
3563 double minmax[2]; 3563 double minmax[2];
3564 kDose[_num].getMinMax(minmax); 3564 kDose[_num].getMinMax(minmax);
3565 for(int xy = 0; xy < dsize; xy++) { 3565 for(int xy = 0; xy < dsize; xy++) {
3566 ddata[xy] = _image[xy]*scale; 3566 ddata[xy] = _image[xy]*scale;
3567 if(ddata[xy] < minmax[0]) minmax[0] = dda 3567 if(ddata[xy] < minmax[0]) minmax[0] = ddata[xy];
3568 if(ddata[xy] > minmax[1]) minmax[1] = dda 3568 if(ddata[xy] > minmax[1]) minmax[1] = ddata[xy];
3569 } 3569 }
3570 kDose[_num].addImage(ddata); 3570 kDose[_num].addImage(ddata);
3571 3571
3572 // set min./max. 3572 // set min./max.
3573 kDose[_num].setMinMax(minmax); 3573 kDose[_num].setMinMax(minmax);
3574 } 3574 }
3575 void G4GMocrenIO::getShortDoseDist(short * _d 3575 void G4GMocrenIO::getShortDoseDist(short * _data, int _z, int _num) {
3576 3576
3577 if(_data == NULL) { 3577 if(_data == NULL) {
3578 if (G4VisManager::GetVerbosity() >= G4Vis 3578 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3579 G4cout << "In G4GMocrenIO::getShortDose 3579 G4cout << "In G4GMocrenIO::getShortDoseDist(), "
3580 << "first argument is NULL pointer. " 3580 << "first argument is NULL pointer. "
3581 << "The argument must be allocated array. 3581 << "The argument must be allocated array."
3582 << G4endl; 3582 << G4endl;
3583 G4Exception("G4GMocrenIO::getShortDoseDis 3583 G4Exception("G4GMocrenIO::getShortDoseDist()",
3584 "gMocren2002", FatalException 3584 "gMocren2002", FatalException,
3585 "Error."); 3585 "Error.");
3586 return; 3586 return;
3587 } 3587 }
3588 3588
3589 int size[3]; 3589 int size[3];
3590 kDose[_num].getSize(size); 3590 kDose[_num].getSize(size);
3591 //short * shdata = new short[size[0]*size[1 3591 //short * shdata = new short[size[0]*size[1]];
3592 double * ddata = kDose[_num].getImage(_z); 3592 double * ddata = kDose[_num].getImage(_z);
3593 double scale = kDose[_num].getScale(); 3593 double scale = kDose[_num].getScale();
3594 for(int xy = 0; xy < size[0]*size[1]; xy++) 3594 for(int xy = 0; xy < size[0]*size[1]; xy++) {
3595 _data[xy] = (short)(ddata[xy]/scale+0.5); 3595 _data[xy] = (short)(ddata[xy]/scale+0.5); //there is never negative value
3596 } 3596 }
3597 } 3597 }
3598 void G4GMocrenIO::getShortDoseDistMinMax(shor 3598 void G4GMocrenIO::getShortDoseDistMinMax(short _minmax[2], int _num) {
3599 double scale = kDose[_num].getScale(); 3599 double scale = kDose[_num].getScale();
3600 double minmax[2]; 3600 double minmax[2];
3601 kDose[_num].getMinMax(minmax); 3601 kDose[_num].getMinMax(minmax);
3602 for(int i = 0; i < 2; i++) 3602 for(int i = 0; i < 2; i++)
3603 _minmax[i] = (short)(minmax[i]/scale+0.5) 3603 _minmax[i] = (short)(minmax[i]/scale+0.5);
3604 } 3604 }
3605 // 3605 //
3606 void G4GMocrenIO::setDoseDist(double * _image 3606 void G4GMocrenIO::setDoseDist(double * _image, int _num) {
3607 3607
3608 kDose[_num].addImage(_image); 3608 kDose[_num].addImage(_image);
3609 } 3609 }
3610 double * G4GMocrenIO::getDoseDist(int _z, int 3610 double * G4GMocrenIO::getDoseDist(int _z, int _num) {
3611 3611
3612 double * image; 3612 double * image;
3613 if(isDoseEmpty()) { 3613 if(isDoseEmpty()) {
3614 image = 0; 3614 image = 0;
3615 } else { 3615 } else {
3616 image = kDose[_num].getImage(_z); 3616 image = kDose[_num].getImage(_z);
3617 } 3617 }
3618 return image; 3618 return image;
3619 } 3619 }
3620 /* 3620 /*
3621 void G4GMocrenIO::getDoseDist(double * & _i 3621 void G4GMocrenIO::getDoseDist(double * & _image, int _z, int _num) {
3622 3622
3623 G4cout << " <" << (void*)_image << "> "; 3623 G4cout << " <" << (void*)_image << "> ";
3624 if(isDoseEmpty()) { 3624 if(isDoseEmpty()) {
3625 _image = 0; 3625 _image = 0;
3626 } else { 3626 } else {
3627 _image = kDose[_num].getImage(_z); 3627 _image = kDose[_num].getImage(_z);
3628 G4cout << " <" << (void*)_image << "> "; 3628 G4cout << " <" << (void*)_image << "> ";
3629 G4cout << _image[100] << " "; 3629 G4cout << _image[100] << " ";
3630 } 3630 }
3631 } 3631 }
3632 */ 3632 */
3633 bool G4GMocrenIO::addDoseDist(std::vector<dou 3633 bool G4GMocrenIO::addDoseDist(std::vector<double *> & _image, int _num) {
3634 3634
3635 int size[3]; 3635 int size[3];
3636 getDoseDistSize(size, _num); 3636 getDoseDistSize(size, _num);
3637 std::vector<double *> dosedist = kDose[_num 3637 std::vector<double *> dosedist = kDose[_num].getImage();
3638 3638
3639 int nimg = size[0]*size[1]; 3639 int nimg = size[0]*size[1];
3640 for(int z = 0; z < size[2]; z++) { 3640 for(int z = 0; z < size[2]; z++) {
3641 for(int xy = 0; xy < nimg; xy++) { 3641 for(int xy = 0; xy < nimg; xy++) {
3642 dosedist[z][xy] += _image[z][xy]; 3642 dosedist[z][xy] += _image[z][xy];
3643 } 3643 }
3644 } 3644 }
3645 3645
3646 return true; 3646 return true;
3647 } 3647 }
3648 //void setDoseDistDensityMap(float * _map) {d 3648 //void setDoseDistDensityMap(float * _map) {doseImageDensityMap = _map;};
3649 // set the dose distribution image displaceme 3649 // set the dose distribution image displacement
3650 void G4GMocrenIO::setDoseDistCenterPosition(f 3650 void G4GMocrenIO::setDoseDistCenterPosition(float _center[3], int _num) {
3651 3651
3652 kDose[_num].setCenterPosition(_center); 3652 kDose[_num].setCenterPosition(_center);
3653 } 3653 }
3654 void G4GMocrenIO::getDoseDistCenterPosition(f 3654 void G4GMocrenIO::getDoseDistCenterPosition(float _center[3], int _num) {
3655 3655
3656 if(isDoseEmpty()) 3656 if(isDoseEmpty())
3657 for(int i = 0; i < 3; i++) _center[i] = 0 3657 for(int i = 0; i < 3; i++) _center[i] = 0;
3658 else 3658 else
3659 kDose[_num].getCenterPosition(_center); 3659 kDose[_num].getCenterPosition(_center);
3660 } 3660 }
3661 // set & get name of dose distribution 3661 // set & get name of dose distribution
3662 void G4GMocrenIO::setDoseDistName(std::string 3662 void G4GMocrenIO::setDoseDistName(std::string _name, int _num) {
3663 3663
3664 kDose[_num].setName(_name); 3664 kDose[_num].setName(_name);
3665 } 3665 }
3666 std::string G4GMocrenIO::getDoseDistName(int 3666 std::string G4GMocrenIO::getDoseDistName(int _num) {
3667 3667
3668 std::string name; 3668 std::string name;
3669 if(isDoseEmpty()) 3669 if(isDoseEmpty())
3670 return name; 3670 return name;
3671 else 3671 else
3672 return kDose[_num].getName(); 3672 return kDose[_num].getName();
3673 } 3673 }
3674 // copy dose distributions 3674 // copy dose distributions
3675 void G4GMocrenIO::copyDoseDist(std::vector<cl 3675 void G4GMocrenIO::copyDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3676 std::vector<class GMocrenDataPrimitive<doub 3676 std::vector<class GMocrenDataPrimitive<double> >::iterator itr;
3677 for(itr = kDose.begin(); itr != kDose.end() 3677 for(itr = kDose.begin(); itr != kDose.end(); itr++) {
3678 _dose.push_back(*itr); 3678 _dose.push_back(*itr);
3679 } 3679 }
3680 } 3680 }
3681 // merge two dose distributions 3681 // merge two dose distributions
3682 bool G4GMocrenIO::mergeDoseDist(std::vector<c 3682 bool G4GMocrenIO::mergeDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) {
3683 if(kDose.size() != _dose.size()) { 3683 if(kDose.size() != _dose.size()) {
3684 if (G4VisManager::GetVerbosity() >= G4Vis 3684 if (G4VisManager::GetVerbosity() >= G4VisManager::errors) {
3685 G4cout << "G4GMocrenIO::mergeDoseDist() 3685 G4cout << "G4GMocrenIO::mergeDoseDist() : Error" << G4endl;
3686 G4cout << " Unable to merge the dose 3686 G4cout << " Unable to merge the dose distributions,"<< G4endl;
3687 G4cout << " because of different size 3687 G4cout << " because of different size of dose maps."<< G4endl;
3688 } 3688 }
3689 return false; 3689 return false;
3690 } 3690 }
3691 3691
3692 int num = (int)kDose.size(); << 3692 int num = kDose.size();
3693 std::vector<class GMocrenDataPrimitive<doub 3693 std::vector<class GMocrenDataPrimitive<double> >::iterator itr1 = kDose.begin();
3694 std::vector<class GMocrenDataPrimitive<doub 3694 std::vector<class GMocrenDataPrimitive<double> >::iterator itr2 = _dose.begin();
3695 for(int i = 0; i < num; i++, itr1++, itr2++ 3695 for(int i = 0; i < num; i++, itr1++, itr2++) {
3696 if (G4VisManager::GetVerbosity() >= G4Vis 3696 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3697 if(kVerbose > 0) 3697 if(kVerbose > 0)
3698 G4cout << "merged dose distribution [" << i 3698 G4cout << "merged dose distribution [" << i << "]" << G4endl;
3699 *itr1 += *itr2; 3699 *itr1 += *itr2;
3700 } 3700 }
3701 3701
3702 return true; 3702 return true;
3703 } 3703 }
3704 // 3704 //
3705 void G4GMocrenIO::clearDoseDistAll() { 3705 void G4GMocrenIO::clearDoseDistAll() {
3706 3706
3707 if(!isDoseEmpty()) { 3707 if(!isDoseEmpty()) {
3708 for(int i = 0; i < getNumDoseDist(); i++) 3708 for(int i = 0; i < getNumDoseDist(); i++) {
3709 kDose[i].clear(); 3709 kDose[i].clear();
3710 } 3710 }
3711 kDose.clear(); 3711 kDose.clear();
3712 } 3712 }
3713 } 3713 }
3714 // 3714 //
3715 bool G4GMocrenIO::isDoseEmpty() { 3715 bool G4GMocrenIO::isDoseEmpty() {
3716 if(kDose.empty()) { 3716 if(kDose.empty()) {
3717 //if (G4VisManager::GetVerbosity() >= G4V 3717 //if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3718 // G4cout << "!!! dose distribution data 3718 // G4cout << "!!! dose distribution data is empty." << G4endl;
3719 return true; 3719 return true;
3720 } else { 3720 } else {
3721 return false; 3721 return false;
3722 } 3722 }
3723 } 3723 }
3724 3724
3725 // 3725 //
3726 void G4GMocrenIO::calcDoseDistScale() { 3726 void G4GMocrenIO::calcDoseDistScale() {
3727 3727
3728 double scale; 3728 double scale;
3729 double minmax[2]; 3729 double minmax[2];
3730 3730
3731 for(int i = 0; i < (int)kDose.size(); i++) 3731 for(int i = 0; i < (int)kDose.size(); i++) {
3732 kDose[i].getMinMax(minmax); 3732 kDose[i].getMinMax(minmax);
3733 scale = minmax[1]/DOSERANGE; 3733 scale = minmax[1]/DOSERANGE;
3734 kDose[i].setScale(scale); 3734 kDose[i].setScale(scale);
3735 } 3735 }
3736 } 3736 }
3737 3737
3738 3738
3739 //----- RoI -----// 3739 //----- RoI -----//
3740 3740
3741 // add one RoI data 3741 // add one RoI data
3742 void G4GMocrenIO::newROI() { 3742 void G4GMocrenIO::newROI() {
3743 GMocrenDataPrimitive<short> roiData; 3743 GMocrenDataPrimitive<short> roiData;
3744 kRoi.push_back(roiData); 3744 kRoi.push_back(roiData);
3745 } 3745 }
3746 int G4GMocrenIO::getNumROI() { 3746 int G4GMocrenIO::getNumROI() {
3747 return (int)kRoi.size(); 3747 return (int)kRoi.size();
3748 } 3748 }
3749 3749
3750 // set/get the ROI image scale 3750 // set/get the ROI image scale
3751 void G4GMocrenIO::setROIScale(double & _scale 3751 void G4GMocrenIO::setROIScale(double & _scale, int _num) {
3752 3752
3753 kRoi[_num].setScale(_scale); 3753 kRoi[_num].setScale(_scale);
3754 } 3754 }
3755 double G4GMocrenIO::getROIScale(int _num) { 3755 double G4GMocrenIO::getROIScale(int _num) {
3756 3756
3757 if(isROIEmpty()) 3757 if(isROIEmpty())
3758 return 0.; 3758 return 0.;
3759 else 3759 else
3760 return kRoi[_num].getScale(); 3760 return kRoi[_num].getScale();
3761 } 3761 }
3762 // set the ROI image 3762 // set the ROI image
3763 void G4GMocrenIO::setROI(short * _image, int 3763 void G4GMocrenIO::setROI(short * _image, int _num) {
3764 3764
3765 kRoi[_num].addImage(_image); 3765 kRoi[_num].addImage(_image);
3766 } 3766 }
3767 short * G4GMocrenIO::getROI(int _z, int _num) 3767 short * G4GMocrenIO::getROI(int _z, int _num) {
3768 3768
3769 if(isROIEmpty()) 3769 if(isROIEmpty())
3770 return 0; 3770 return 0;
3771 else 3771 else
3772 return kRoi[_num].getImage(_z); 3772 return kRoi[_num].getImage(_z);
3773 } 3773 }
3774 // set/get the ROI image size 3774 // set/get the ROI image size
3775 void G4GMocrenIO::setROISize(int _size[3], in 3775 void G4GMocrenIO::setROISize(int _size[3], int _num) {
3776 3776
3777 return kRoi[_num].setSize(_size); 3777 return kRoi[_num].setSize(_size);
3778 } 3778 }
3779 void G4GMocrenIO::getROISize(int _size[3], in 3779 void G4GMocrenIO::getROISize(int _size[3], int _num) {
3780 3780
3781 if(isROIEmpty()) 3781 if(isROIEmpty())
3782 for(int i = 0; i < 3; i++) _size[i] = 0; 3782 for(int i = 0; i < 3; i++) _size[i] = 0;
3783 else 3783 else
3784 return kRoi[_num].getSize(_size); 3784 return kRoi[_num].getSize(_size);
3785 } 3785 }
3786 // set/get the ROI image min. and max. 3786 // set/get the ROI image min. and max.
3787 void G4GMocrenIO::setROIMinMax(short _minmax[ 3787 void G4GMocrenIO::setROIMinMax(short _minmax[2], int _num) {
3788 3788
3789 kRoi[_num].setMinMax(_minmax); 3789 kRoi[_num].setMinMax(_minmax);
3790 } 3790 }
3791 void G4GMocrenIO::getROIMinMax(short _minmax[ 3791 void G4GMocrenIO::getROIMinMax(short _minmax[2], int _num) {
3792 3792
3793 if(isROIEmpty()) 3793 if(isROIEmpty())
3794 for(int i = 0; i < 2; i++) _minmax[i] = 0 3794 for(int i = 0; i < 2; i++) _minmax[i] = 0;
3795 else 3795 else
3796 kRoi[_num].getMinMax(_minmax); 3796 kRoi[_num].getMinMax(_minmax);
3797 } 3797 }
3798 // set/get the ROI image displacement 3798 // set/get the ROI image displacement
3799 void G4GMocrenIO::setROICenterPosition(float 3799 void G4GMocrenIO::setROICenterPosition(float _center[3], int _num) {
3800 3800
3801 kRoi[_num].setCenterPosition(_center); 3801 kRoi[_num].setCenterPosition(_center);
3802 } 3802 }
3803 void G4GMocrenIO::getROICenterPosition(float 3803 void G4GMocrenIO::getROICenterPosition(float _center[3], int _num) {
3804 3804
3805 if(isROIEmpty()) 3805 if(isROIEmpty())
3806 for(int i = 0; i < 3; i++) _center[i] = 0 3806 for(int i = 0; i < 3; i++) _center[i] = 0;
3807 else 3807 else
3808 kRoi[_num].getCenterPosition(_center); 3808 kRoi[_num].getCenterPosition(_center);
3809 } 3809 }
3810 // 3810 //
3811 void G4GMocrenIO::clearROIAll() { 3811 void G4GMocrenIO::clearROIAll() {
3812 3812
3813 if(!isROIEmpty()) { 3813 if(!isROIEmpty()) {
3814 for(int i = 0; i < getNumROI(); i++) { 3814 for(int i = 0; i < getNumROI(); i++) {
3815 kRoi[i].clear(); 3815 kRoi[i].clear();
3816 } 3816 }
3817 kRoi.clear(); 3817 kRoi.clear();
3818 } 3818 }
3819 } 3819 }
3820 // 3820 //
3821 bool G4GMocrenIO::isROIEmpty() { 3821 bool G4GMocrenIO::isROIEmpty() {
3822 if(kRoi.empty()) { 3822 if(kRoi.empty()) {
3823 //if (G4VisManager::GetVerbosity() >= G4V 3823 //if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3824 // G4cout << "!!! ROI data is empty." << 3824 // G4cout << "!!! ROI data is empty." << G4endl;
3825 return true; 3825 return true;
3826 } else { 3826 } else {
3827 return false; 3827 return false;
3828 } 3828 }
3829 } 3829 }
3830 3830
3831 3831
3832 3832
3833 //----- Track information -----// 3833 //----- Track information -----//
3834 3834
3835 int G4GMocrenIO::getNumTracks() { 3835 int G4GMocrenIO::getNumTracks() {
3836 return (int)kSteps.size(); 3836 return (int)kSteps.size();
3837 } 3837 }
3838 int G4GMocrenIO::getNumTracks4() { 3838 int G4GMocrenIO::getNumTracks4() {
3839 return (int)kTracks.size(); 3839 return (int)kTracks.size();
3840 } 3840 }
3841 void G4GMocrenIO::addTrack(float * _tracks) { 3841 void G4GMocrenIO::addTrack(float * _tracks) {
3842 kSteps.push_back(_tracks); 3842 kSteps.push_back(_tracks);
3843 } 3843 }
3844 void G4GMocrenIO::setTracks(std::vector<float 3844 void G4GMocrenIO::setTracks(std::vector<float *> & _tracks) {
3845 kSteps = _tracks; 3845 kSteps = _tracks;
3846 } 3846 }
3847 std::vector<float *> & G4GMocrenIO::getTracks 3847 std::vector<float *> & G4GMocrenIO::getTracks() {
3848 return kSteps; 3848 return kSteps;
3849 } 3849 }
3850 void G4GMocrenIO::addTrackColor(unsigned char 3850 void G4GMocrenIO::addTrackColor(unsigned char * _colors) {
3851 kStepColors.push_back(_colors); 3851 kStepColors.push_back(_colors);
3852 } 3852 }
3853 void G4GMocrenIO::setTrackColors(std::vector< 3853 void G4GMocrenIO::setTrackColors(std::vector<unsigned char *> & _trackColors) {
3854 kStepColors = _trackColors; 3854 kStepColors = _trackColors;
3855 } 3855 }
3856 std::vector<unsigned char *> & G4GMocrenIO::g 3856 std::vector<unsigned char *> & G4GMocrenIO::getTrackColors() {
3857 return kStepColors; 3857 return kStepColors;
3858 } 3858 }
3859 void G4GMocrenIO::copyTracks(std::vector<floa 3859 void G4GMocrenIO::copyTracks(std::vector<float *> & _tracks,
3860 std::vector<unsigned char *> & _ 3860 std::vector<unsigned char *> & _colors) {
3861 std::vector<float *>::iterator titr; 3861 std::vector<float *>::iterator titr;
3862 for(titr = kSteps.begin(); titr != kSteps.e 3862 for(titr = kSteps.begin(); titr != kSteps.end(); titr++) {
3863 float * pts = new float[6]; 3863 float * pts = new float[6];
3864 for(int i = 0; i < 6; i++) { 3864 for(int i = 0; i < 6; i++) {
3865 pts[i] = (*titr)[i]; 3865 pts[i] = (*titr)[i];
3866 } 3866 }
3867 _tracks.push_back(pts); 3867 _tracks.push_back(pts);
3868 } 3868 }
3869 3869
3870 std::vector<unsigned char *>::iterator citr 3870 std::vector<unsigned char *>::iterator citr;
3871 for(citr = kStepColors.begin(); citr != kSt 3871 for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++) {
3872 unsigned char * pts = new unsigned char[3 3872 unsigned char * pts = new unsigned char[3];
3873 for(int i = 0; i < 3; i++) { 3873 for(int i = 0; i < 3; i++) {
3874 pts[i] = (*citr)[i]; 3874 pts[i] = (*citr)[i];
3875 } 3875 }
3876 _colors.push_back(pts); 3876 _colors.push_back(pts);
3877 } 3877 }
3878 } 3878 }
3879 void G4GMocrenIO::mergeTracks(std::vector<flo 3879 void G4GMocrenIO::mergeTracks(std::vector<float *> & _tracks,
3880 std::vector<unsigned char *> & _color 3880 std::vector<unsigned char *> & _colors) {
3881 std::vector<float *>::iterator titr; 3881 std::vector<float *>::iterator titr;
3882 for(titr = _tracks.begin(); titr != _tracks 3882 for(titr = _tracks.begin(); titr != _tracks.end(); titr++) {
3883 addTrack(*titr); 3883 addTrack(*titr);
3884 } 3884 }
3885 3885
3886 std::vector<unsigned char *>::iterator citr 3886 std::vector<unsigned char *>::iterator citr;
3887 for(citr = _colors.begin(); citr != _colors 3887 for(citr = _colors.begin(); citr != _colors.end(); citr++) {
3888 addTrackColor(*citr); 3888 addTrackColor(*citr);
3889 } 3889 }
3890 } 3890 }
3891 void G4GMocrenIO::addTrack(std::vector<float 3891 void G4GMocrenIO::addTrack(std::vector<float *> & _steps, unsigned char _color[3]) {
3892 3892
3893 std::vector<float *>::iterator itr = _steps 3893 std::vector<float *>::iterator itr = _steps.begin();
3894 std::vector<struct GMocrenTrack::Step> st 3894 std::vector<struct GMocrenTrack::Step> steps;
3895 for(; itr != _steps.end(); itr++) { 3895 for(; itr != _steps.end(); itr++) {
3896 struct GMocrenTrack::Step step; 3896 struct GMocrenTrack::Step step;
3897 for(int i = 0; i < 3; i++) { 3897 for(int i = 0; i < 3; i++) {
3898 step.startPoint[i] = (*itr)[i]; 3898 step.startPoint[i] = (*itr)[i];
3899 step.endPoint[i] = (*itr)[i+3]; 3899 step.endPoint[i] = (*itr)[i+3];
3900 } 3900 }
3901 steps.push_back(step); 3901 steps.push_back(step);
3902 } 3902 }
3903 GMocrenTrack track; 3903 GMocrenTrack track;
3904 track.setTrack(steps); 3904 track.setTrack(steps);
3905 track.setColor(_color); 3905 track.setColor(_color);
3906 kTracks.push_back(track); 3906 kTracks.push_back(track);
3907 3907
3908 } 3908 }
3909 void G4GMocrenIO::getTrack(int _num, std::vec 3909 void G4GMocrenIO::getTrack(int _num, std::vector<float *> & _steps,
3910 std::vector<unsigned char *> & _co 3910 std::vector<unsigned char *> & _color) {
3911 3911
3912 if(_num > (int)kTracks.size()) { 3912 if(_num > (int)kTracks.size()) {
3913 if (G4VisManager::GetVerbosity() >= G4Vis 3913 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3914 G4cout << "ERROR in getTrack() : " << G 3914 G4cout << "ERROR in getTrack() : " << G4endl;
3915 G4Exception("G4GMocrenIO::getTrack()", 3915 G4Exception("G4GMocrenIO::getTrack()",
3916 "gMocren2003", FatalException 3916 "gMocren2003", FatalException,
3917 "Error."); 3917 "Error.");
3918 } 3918 }
3919 unsigned char * color = new unsigned char[3 3919 unsigned char * color = new unsigned char[3];
3920 kTracks[_num].getColor(color); 3920 kTracks[_num].getColor(color);
3921 _color.push_back(color); 3921 _color.push_back(color);
3922 3922
3923 // steps 3923 // steps
3924 int nsteps = kTracks[_num].getNumberOfSteps 3924 int nsteps = kTracks[_num].getNumberOfSteps();
3925 for(int isteps = 0; isteps < nsteps; isteps 3925 for(int isteps = 0; isteps < nsteps; isteps++) {
3926 float * stepPoints = new float[6]; 3926 float * stepPoints = new float[6];
3927 kTracks[_num].getStep(stepPoints[0], step 3927 kTracks[_num].getStep(stepPoints[0], stepPoints[1], stepPoints[2],
3928 stepPoints[3], stepPoints[4], stepPoi 3928 stepPoints[3], stepPoints[4], stepPoints[5],
3929 isteps); 3929 isteps);
3930 _steps.push_back(stepPoints); 3930 _steps.push_back(stepPoints);
3931 } 3931 }
3932 } 3932 }
3933 3933
3934 void G4GMocrenIO::translateTracks(std::vector 3934 void G4GMocrenIO::translateTracks(std::vector<float> & _translate) {
3935 std::vector<class GMocrenTrack>::iterator i 3935 std::vector<class GMocrenTrack>::iterator itr = kTracks.begin();
3936 for(; itr != kTracks.end(); itr++) { 3936 for(; itr != kTracks.end(); itr++) {
3937 itr->translate(_translate); 3937 itr->translate(_translate);
3938 } 3938 }
3939 } 3939 }
3940 3940
3941 3941
3942 3942
3943 3943
3944 //----- Detector information -----// 3944 //----- Detector information -----//
3945 int G4GMocrenIO::getNumberOfDetectors() { 3945 int G4GMocrenIO::getNumberOfDetectors() {
3946 return (int)kDetectors.size(); 3946 return (int)kDetectors.size();
3947 } 3947 }
3948 void G4GMocrenIO::addDetector(std::string & _ 3948 void G4GMocrenIO::addDetector(std::string & _name,
3949 std::vector<float *> & _det, 3949 std::vector<float *> & _det,
3950 unsigned char _color[3]) { 3950 unsigned char _color[3]) {
3951 3951
3952 std::vector<float *>::iterator itr = _det 3952 std::vector<float *>::iterator itr = _det.begin();
3953 std::vector<struct GMocrenDetector::Edge> 3953 std::vector<struct GMocrenDetector::Edge> edges;
3954 for(; itr != _det.end(); itr++) { 3954 for(; itr != _det.end(); itr++) {
3955 struct GMocrenDetector::Edge edge; 3955 struct GMocrenDetector::Edge edge;
3956 for(int i = 0; i < 3; i++) { 3956 for(int i = 0; i < 3; i++) {
3957 edge.startPoint[i] = (*itr)[i]; 3957 edge.startPoint[i] = (*itr)[i];
3958 edge.endPoint[i] = (*itr)[i+3]; 3958 edge.endPoint[i] = (*itr)[i+3];
3959 } 3959 }
3960 edges.push_back(edge); 3960 edges.push_back(edge);
3961 } 3961 }
3962 GMocrenDetector detector; 3962 GMocrenDetector detector;
3963 detector.setDetector(edges); 3963 detector.setDetector(edges);
3964 detector.setColor(_color); 3964 detector.setColor(_color);
3965 detector.setName(_name); 3965 detector.setName(_name);
3966 kDetectors.push_back(detector); 3966 kDetectors.push_back(detector);
3967 3967
3968 } 3968 }
3969 3969
3970 void G4GMocrenIO::getDetector(int _num, std:: 3970 void G4GMocrenIO::getDetector(int _num, std::vector<float *> & _edges,
3971 std::vector<unsigned char *> & _color 3971 std::vector<unsigned char *> & _color,
3972 std::string & _detName) { 3972 std::string & _detName) {
3973 3973
3974 if(_num > (int)kDetectors.size()) { 3974 if(_num > (int)kDetectors.size()) {
3975 if (G4VisManager::GetVerbosity() >= G4Vis 3975 if (G4VisManager::GetVerbosity() >= G4VisManager::errors)
3976 G4cout << "ERROR in getDetector() : " < 3976 G4cout << "ERROR in getDetector() : " << G4endl;
3977 3977
3978 G4Exception("G4GMocrenIO::getDetector()", 3978 G4Exception("G4GMocrenIO::getDetector()",
3979 "gMocren2004", FatalException 3979 "gMocren2004", FatalException,
3980 "Error."); 3980 "Error.");
3981 } 3981 }
3982 3982
3983 _detName = kDetectors[_num].getName(); 3983 _detName = kDetectors[_num].getName();
3984 3984
3985 unsigned char * color = new unsigned char[3 3985 unsigned char * color = new unsigned char[3];
3986 kDetectors[_num].getColor(color); 3986 kDetectors[_num].getColor(color);
3987 _color.push_back(color); 3987 _color.push_back(color);
3988 3988
3989 // edges 3989 // edges
3990 int nedges = kDetectors[_num].getNumberOfEd 3990 int nedges = kDetectors[_num].getNumberOfEdges();
3991 for(int ne = 0; ne < nedges; ne++) { 3991 for(int ne = 0; ne < nedges; ne++) {
3992 float * edgePoints = new float[6]; 3992 float * edgePoints = new float[6];
3993 kDetectors[_num].getEdge(edgePoints[0], e 3993 kDetectors[_num].getEdge(edgePoints[0], edgePoints[1], edgePoints[2],
3994 edgePoints[3], edgePoints[4], edge 3994 edgePoints[3], edgePoints[4], edgePoints[5],
3995 ne); 3995 ne);
3996 _edges.push_back(edgePoints); 3996 _edges.push_back(edgePoints);
3997 } 3997 }
3998 } 3998 }
3999 3999
4000 void G4GMocrenIO::translateDetector(std::vect 4000 void G4GMocrenIO::translateDetector(std::vector<float> & _translate) {
4001 std::vector<class GMocrenDetector>::iterato 4001 std::vector<class GMocrenDetector>::iterator itr = kDetectors.begin();
4002 for(; itr != kDetectors.end(); itr++) { 4002 for(; itr != kDetectors.end(); itr++) {
4003 itr->translate(_translate); 4003 itr->translate(_translate);
4004 } 4004 }
4005 } 4005 }
4006 4006
4007 // endian conversion 4007 // endian conversion
4008 template <typename T> 4008 template <typename T>
4009 void G4GMocrenIO::convertEndian(char * _val, 4009 void G4GMocrenIO::convertEndian(char * _val, T & _rval) {
4010 4010
4011 if((kLittleEndianOutput && !kLittleEndianIn 4011 if((kLittleEndianOutput && !kLittleEndianInput) || // big endian
4012 (!kLittleEndianOutput && kLittleEndianIn 4012 (!kLittleEndianOutput && kLittleEndianInput)) { // little endian
4013 4013
4014 const int SIZE = sizeof(_rval); 4014 const int SIZE = sizeof(_rval);
4015 char ctemp; 4015 char ctemp;
4016 for(int i = 0; i < SIZE/2; i++) { 4016 for(int i = 0; i < SIZE/2; i++) {
4017 ctemp = _val[i]; 4017 ctemp = _val[i];
4018 _val[i] = _val[SIZE - 1 - i]; 4018 _val[i] = _val[SIZE - 1 - i];
4019 _val[SIZE - 1 - i] = ctemp; 4019 _val[SIZE - 1 - i] = ctemp;
4020 } 4020 }
4021 } 4021 }
4022 _rval = *(T *)_val; 4022 _rval = *(T *)_val;
4023 } 4023 }
4024 4024
4025 // inversion of byte order 4025 // inversion of byte order
4026 template <typename T> 4026 template <typename T>
4027 void G4GMocrenIO::invertByteOrder(char * _val 4027 void G4GMocrenIO::invertByteOrder(char * _val, T & _rval) {
4028 4028
4029 const int SIZE = sizeof(_rval); 4029 const int SIZE = sizeof(_rval);
4030 //char * cval = new char[SIZE]; 4030 //char * cval = new char[SIZE];
4031 union { 4031 union {
4032 char cu[16]; 4032 char cu[16];
4033 T tu; 4033 T tu;
4034 } uni; 4034 } uni;
4035 for(int i = 0; i < SIZE; i++) { 4035 for(int i = 0; i < SIZE; i++) {
4036 uni.cu[i] = _val[SIZE-1-i]; 4036 uni.cu[i] = _val[SIZE-1-i];
4037 //cval[i] = _val[SIZE-i-1]; 4037 //cval[i] = _val[SIZE-i-1];
4038 } 4038 }
4039 //_rval = *(T *)cval; 4039 //_rval = *(T *)cval;
4040 _rval = uni.tu; 4040 _rval = uni.tu;
4041 //delete [] cval; 4041 //delete [] cval;
4042 } 4042 }
4043 4043
4044 //----- kVerbose information -----// 4044 //----- kVerbose information -----//
4045 void G4GMocrenIO::setVerboseLevel(int _level) 4045 void G4GMocrenIO::setVerboseLevel(int _level) {
4046 kVerbose = _level; 4046 kVerbose = _level;
4047 } 4047 }
4048 4048
4049 4049