Geant4 Cross Reference

Cross-Referencing   Geant4
Geant4/visualization/gMocren/src/G4GMocrenIO.cc

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