[1142] | 1 | // |
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| 2 | // ******************************************************************** |
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| 3 | // * License and Disclaimer * |
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| 4 | // * * |
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| 5 | // * The Geant4 software is copyright of the Copyright Holders of * |
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| 6 | // * the Geant4 Collaboration. It is provided under the terms and * |
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| 7 | // * conditions of the Geant4 Software License, included in the file * |
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| 8 | // * LICENSE and available at http://cern.ch/geant4/license . These * |
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| 9 | // * include a list of copyright holders. * |
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| 10 | // * * |
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| 11 | // * Neither the authors of this software system, nor their employing * |
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| 12 | // * institutes,nor the agencies providing financial support for this * |
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| 13 | // * work make any representation or warranty, express or implied, * |
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| 14 | // * regarding this software system or assume any liability for its * |
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| 15 | // * use. Please see the license in the file LICENSE and URL above * |
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| 16 | // * for the full disclaimer and the limitation of liability. * |
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| 17 | // * * |
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| 18 | // * This code implementation is the result of the scientific and * |
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| 19 | // * technical work of the GEANT4 collaboration. * |
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| 20 | // * By using, copying, modifying or distributing the software (or * |
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| 21 | // * any work based on the software) you agree to acknowledge its * |
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| 22 | // * use in resulting scientific publications, and indicate your * |
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| 23 | // * acceptance of all terms of the Geant4 Software license. * |
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| 24 | // ******************************************************************** |
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| 25 | // |
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| 26 | // |
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| 27 | // $Id: G4GMocrenIO.cc,v 1.3 2009/10/18 04:02:09 akimura Exp $ |
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| 28 | // GEANT4 tag $Name: $ |
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| 29 | // |
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| 30 | // |
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| 31 | // File I/O manager class for writing or reading calcuated dose |
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| 32 | // distribution and some event information |
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| 33 | // |
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| 34 | // Created: Mar. 31, 2009 Akinori Kimura : release for the gMocrenFile driver |
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| 35 | // |
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| 36 | // Akinori Kimura |
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| 37 | // gMocren home page: |
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| 38 | // http://geant4.kek.jp/gMocren/ |
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| 39 | // |
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| 40 | // |
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| 41 | #include "G4GMocrenIO.hh" |
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| 42 | |
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| 43 | #include <iostream> |
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| 44 | #include <ctime> |
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| 45 | #include <sstream> |
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| 46 | #include <iomanip> |
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| 47 | #include <cstdlib> |
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| 48 | #include <cstring> |
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| 49 | #if defined(_WIN32) |
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| 50 | #define LITTLE_ENDIAN 1234 |
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| 51 | #define BYTE_ORDER LITTLE_ENDIAN |
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| 52 | #endif |
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| 53 | |
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| 54 | const int DOSERANGE = 25000; |
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| 55 | |
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| 56 | //----- GMocrenDataPrimitive class in the GMocrenDataIO class-----// |
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| 57 | template <typename T> |
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| 58 | GMocrenDataPrimitive<T>::GMocrenDataPrimitive () { |
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| 59 | clear(); |
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| 60 | } |
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| 61 | template <typename T> |
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| 62 | GMocrenDataPrimitive<T>::~GMocrenDataPrimitive () { |
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| 63 | /* |
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| 64 | std::vector<short *>::iterator itr = image.begin(); |
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| 65 | for(; itr != image.end(); itr++) { |
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| 66 | delete [] *itr; |
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| 67 | } |
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| 68 | */ |
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| 69 | } |
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| 70 | |
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| 71 | template <typename T> GMocrenDataPrimitive<T> & |
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| 72 | GMocrenDataPrimitive<T>::operator = (const GMocrenDataPrimitive<T> & _right) { |
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| 73 | for(int i = 0; i < 3; i++) { |
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| 74 | kSize[i] = _right.kSize[i]; |
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| 75 | kCenter[i] = _right.kCenter[i]; |
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| 76 | } |
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| 77 | kScale = _right.kScale; |
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| 78 | for(int i = 0; i < 2; i++) kMinmax[i] = _right.kMinmax[i]; |
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| 79 | int num = kSize[0]*kSize[1]; |
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| 80 | kImage.clear(); |
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| 81 | for(int z = 0; z < kSize[2]; z++) { |
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| 82 | T * img = new T[num]; |
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| 83 | for(int i = 0; i < num; i++) img[i] =_right.kImage[z][i]; |
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| 84 | kImage.push_back(img); |
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| 85 | } |
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| 86 | return *this; |
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| 87 | } |
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| 88 | |
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| 89 | template <typename T> GMocrenDataPrimitive<T> & |
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| 90 | GMocrenDataPrimitive<T>::operator + (const GMocrenDataPrimitive<T> & _right) { |
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| 91 | |
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| 92 | GMocrenDataPrimitive<T> rprim; |
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| 93 | bool stat = true; |
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| 94 | for(int i = 0; i < 3; i++) { |
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| 95 | if(kSize[i] != _right.kSize[i]) stat = false; |
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| 96 | if(kCenter[i] != _right.kCenter[i]) stat = false; |
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| 97 | } |
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| 98 | if(!stat) { |
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| 99 | std::cerr << "Warning: operator + " |
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| 100 | << " Cannot do the operator +" |
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| 101 | << std::endl; |
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| 102 | return *this; |
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| 103 | } |
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| 104 | |
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| 105 | rprim.setSize(kSize); |
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| 106 | rprim.setCenterPosition(kCenter); |
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| 107 | |
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| 108 | T mm[2] = {9e100,-9e100}; |
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| 109 | //if(mm[0] > _right.minmax[0]) mm[0] = _right.minmax[0]; |
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| 110 | //if(mm[1] < _right.minmax[1]) mm[1] = _right.minmax[1]; |
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| 111 | |
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| 112 | int num = kSize[0]*kSize[1]; |
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| 113 | for(int z = 0; z < kSize[2]; z++) { |
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| 114 | T * img = new T[num]; |
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| 115 | for(int xy = 0; xy < num; xy++) { |
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| 116 | img[xy] = kImage[z][xy] + _right.kImage[z][xy]; |
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| 117 | if(mm[0] > img[xy]) mm[0] = img[xy]; |
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| 118 | if(mm[1] < img[xy]) mm[1] = img[xy]; |
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| 119 | } |
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| 120 | rprim.addImage(img); |
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| 121 | } |
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| 122 | rprim.setMinMax(mm); |
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| 123 | |
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| 124 | T scl = mm[1]/DOSERANGE; |
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| 125 | rprim.setScale(scl); |
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| 126 | |
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| 127 | return rprim; |
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| 128 | } |
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| 129 | |
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| 130 | template <typename T> GMocrenDataPrimitive<T> & |
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| 131 | GMocrenDataPrimitive<T>::operator += (const GMocrenDataPrimitive<T> & _right) { |
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| 132 | |
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| 133 | bool stat = true; |
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| 134 | for(int i = 0; i < 3; i++) { |
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| 135 | if(kSize[i] != _right.kSize[i]) stat = false; |
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| 136 | if(kCenter[i] != _right.kCenter[i]) stat = false; |
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| 137 | } |
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| 138 | if(!stat) { |
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| 139 | std::cerr << "Warning: operator += " << std::endl |
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| 140 | << " Cannot do the operator +=" |
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| 141 | << std::endl; |
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| 142 | return *this; |
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| 143 | } |
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| 144 | |
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| 145 | if(kMinmax[0] > _right.kMinmax[0]) kMinmax[0] = _right.kMinmax[0]; |
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| 146 | if(kMinmax[1] < _right.kMinmax[1]) kMinmax[1] = _right.kMinmax[1]; |
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| 147 | |
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| 148 | int num = kSize[0]*kSize[1]; |
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| 149 | for(int z = 0; z < kSize[2]; z++) { |
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| 150 | for(int xy = 0; xy < num; xy++) { |
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| 151 | kImage[z][xy] += _right.kImage[z][xy]; |
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| 152 | if(kMinmax[0] > kImage[z][xy]) kMinmax[0] = kImage[z][xy]; |
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| 153 | if(kMinmax[1] < kImage[z][xy]) kMinmax[1] = kImage[z][xy]; |
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| 154 | } |
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| 155 | } |
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| 156 | |
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| 157 | kScale = kMinmax[1]/DOSERANGE; |
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| 158 | |
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| 159 | return *this; |
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| 160 | } |
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| 161 | |
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| 162 | template <typename T> |
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| 163 | void GMocrenDataPrimitive<T>::clear() { |
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| 164 | for(int i = 0; i < 3; i++) { |
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| 165 | kSize[i] = 0; |
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| 166 | kCenter[i] = 0.; |
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| 167 | } |
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| 168 | kScale = 1.; |
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| 169 | kMinmax[0] = (T)32109; |
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| 170 | kMinmax[1] = (T)-32109; |
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| 171 | |
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| 172 | /* |
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| 173 | if(!image.empty()) { |
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| 174 | typename std::vector<T *>::iterator itr; |
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| 175 | for(itr = image.begin(); itr != image.end(); itr++) { |
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| 176 | delete [] *itr; |
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| 177 | } |
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| 178 | } |
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| 179 | */ |
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| 180 | kImage.clear(); |
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| 181 | } |
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| 182 | template <typename T> |
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| 183 | void GMocrenDataPrimitive<T>::setSize(int _size[3]) { |
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| 184 | for(int i = 0; i < 3; i++) kSize[i] = _size[i]; |
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| 185 | } |
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| 186 | template <typename T> |
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| 187 | void GMocrenDataPrimitive<T>::getSize(int _size[3]) { |
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| 188 | for(int i = 0; i < 3; i++) _size[i] = kSize[i]; |
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| 189 | } |
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| 190 | template <typename T> |
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| 191 | void GMocrenDataPrimitive<T>::setScale(double & _scale) { |
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| 192 | kScale = _scale; |
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| 193 | } |
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| 194 | template <typename T> |
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| 195 | double GMocrenDataPrimitive<T>::getScale() { |
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| 196 | return kScale; |
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| 197 | } |
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| 198 | template <typename T> |
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| 199 | void GMocrenDataPrimitive<T>::setMinMax(T _minmax[2]) { |
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| 200 | for(int i = 0; i < 2; i++) kMinmax[i] = _minmax[i]; |
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| 201 | } |
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| 202 | template <typename T> |
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| 203 | void GMocrenDataPrimitive<T>::getMinMax(T _minmax[2]) { |
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| 204 | for(int i = 0; i < 2; i++) _minmax[i] = kMinmax[i]; |
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| 205 | |
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| 206 | } |
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| 207 | template <typename T> |
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| 208 | void GMocrenDataPrimitive<T>::setImage(std::vector<T *> & _image) { |
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| 209 | kImage = _image; |
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| 210 | } |
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| 211 | template <typename T> |
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| 212 | void GMocrenDataPrimitive<T>::addImage(T * _image) { |
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| 213 | kImage.push_back(_image); |
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| 214 | } |
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| 215 | template <typename T> |
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| 216 | std::vector<T *> & GMocrenDataPrimitive<T>::getImage() { |
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| 217 | return kImage; |
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| 218 | } |
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| 219 | template <typename T> |
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| 220 | T * GMocrenDataPrimitive<T>::getImage(int _z) { |
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| 221 | if(_z >= (int)kImage.size()) return 0; |
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| 222 | return kImage[_z]; |
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| 223 | } |
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| 224 | template <typename T> |
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| 225 | void GMocrenDataPrimitive<T>::setCenterPosition(float _center[3]) { |
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| 226 | for(int i = 0; i < 3; i++) kCenter[i] = _center[i]; |
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| 227 | } |
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| 228 | template <typename T> |
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| 229 | void GMocrenDataPrimitive<T>::getCenterPosition(float _center[3]) { |
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| 230 | for(int i = 0; i < 3; i++) _center[i] = kCenter[i]; |
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| 231 | } |
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| 232 | template <typename T> |
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| 233 | void GMocrenDataPrimitive<T>::setName(std::string & _name) { |
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| 234 | kDataName = _name; |
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| 235 | } |
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| 236 | template <typename T> |
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| 237 | std::string GMocrenDataPrimitive<T>::getName() { |
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| 238 | return kDataName; |
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| 239 | } |
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| 240 | |
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| 241 | |
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| 242 | |
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| 243 | |
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| 244 | |
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| 245 | GMocrenTrack::GMocrenTrack() { |
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| 246 | kTrack.clear(); |
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| 247 | for(int i = 0; i < 3; i++) kColor[i] = 0; |
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| 248 | } |
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| 249 | |
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| 250 | void GMocrenTrack::addStep(float _startx, float _starty, float _startz, |
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| 251 | float _endx, float _endy, float _endz) { |
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| 252 | struct Step step; |
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| 253 | step.startPoint[0] = _startx; |
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| 254 | step.startPoint[1] = _starty; |
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| 255 | step.startPoint[2] = _startz; |
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| 256 | step.endPoint[0] = _endx; |
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| 257 | step.endPoint[1] = _endy; |
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| 258 | step.endPoint[2] = _endz; |
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| 259 | kTrack.push_back(step); |
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| 260 | } |
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| 261 | void GMocrenTrack::getStep(float & _startx, float & _starty, float & _startz, |
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| 262 | float & _endx, float & _endy, float & _endz, |
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| 263 | int _num) { |
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| 264 | if(_num >= (int)kTrack.size()) { |
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| 265 | std::cerr << "GMocrenTrack::getStep(...) Error: " |
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| 266 | << "invalid step # : " << _num << std::endl; |
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| 267 | return; |
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| 268 | } |
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| 269 | |
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| 270 | _startx = kTrack[_num].startPoint[0]; |
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| 271 | _starty = kTrack[_num].startPoint[1]; |
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| 272 | _startz = kTrack[_num].startPoint[2]; |
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| 273 | _endx = kTrack[_num].endPoint[0]; |
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| 274 | _endy = kTrack[_num].endPoint[1]; |
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| 275 | _endz = kTrack[_num].endPoint[2]; |
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| 276 | } |
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| 277 | void GMocrenTrack::translate(std::vector<float> & _translate) { |
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| 278 | std::vector<struct Step>::iterator itr = kTrack.begin(); |
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| 279 | for(; itr != kTrack.end(); itr++) { |
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| 280 | for(int i = 0; i < 3; i++ ) { |
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| 281 | itr->startPoint[i] += _translate[i]; |
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| 282 | itr->endPoint[i] += _translate[i]; |
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| 283 | } |
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| 284 | } |
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| 285 | } |
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| 286 | |
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| 287 | |
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| 288 | |
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| 289 | |
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| 290 | |
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| 291 | |
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| 292 | |
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| 293 | |
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| 294 | |
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| 295 | GMocrenDetector::GMocrenDetector() { |
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| 296 | kDetector.clear(); |
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| 297 | for(int i = 0; i < 3; i++) kColor[i] = 0; |
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| 298 | } |
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| 299 | |
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| 300 | void GMocrenDetector::addEdge(float _startx, float _starty, float _startz, |
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| 301 | float _endx, float _endy, float _endz) { |
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| 302 | struct Edge edge; |
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| 303 | edge.startPoint[0] = _startx; |
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| 304 | edge.startPoint[1] = _starty; |
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| 305 | edge.startPoint[2] = _startz; |
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| 306 | edge.endPoint[0] = _endx; |
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| 307 | edge.endPoint[1] = _endy; |
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| 308 | edge.endPoint[2] = _endz; |
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| 309 | kDetector.push_back(edge); |
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| 310 | } |
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| 311 | void GMocrenDetector::getEdge(float & _startx, float & _starty, float & _startz, |
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| 312 | float & _endx, float & _endy, float & _endz, |
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| 313 | int _num) { |
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| 314 | if(_num >= (int)kDetector.size()) { |
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| 315 | std::cerr << "GMocrenDetector::getEdge(...) Error: " |
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| 316 | << "invalid edge # : " << _num << std::endl; |
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| 317 | return; |
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| 318 | } |
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| 319 | |
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| 320 | _startx = kDetector[_num].startPoint[0]; |
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| 321 | _starty = kDetector[_num].startPoint[1]; |
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| 322 | _startz = kDetector[_num].startPoint[2]; |
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| 323 | _endx = kDetector[_num].endPoint[0]; |
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| 324 | _endy = kDetector[_num].endPoint[1]; |
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| 325 | _endz = kDetector[_num].endPoint[2]; |
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| 326 | } |
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| 327 | void GMocrenDetector::translate(std::vector<float> & _translate) { |
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| 328 | std::vector<struct Edge>::iterator itr = kDetector.begin(); |
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| 329 | for(; itr != kDetector.end(); itr++) { |
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| 330 | for(int i = 0; i < 3; i++) { |
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| 331 | itr->startPoint[i] += _translate[i]; |
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| 332 | itr->endPoint[i] += _translate[i]; |
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| 333 | } |
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| 334 | } |
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| 335 | } |
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| 336 | |
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| 337 | |
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| 338 | |
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| 339 | |
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| 340 | |
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| 341 | |
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| 342 | |
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| 343 | |
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| 344 | |
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| 345 | // file information |
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| 346 | std::string G4GMocrenIO::kId; |
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| 347 | std::string G4GMocrenIO::kVersion = "2.0.0"; |
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| 348 | int G4GMocrenIO::kNumberOfEvents = 0; |
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| 349 | char G4GMocrenIO::kLittleEndianInput = true; |
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| 350 | |
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| 351 | #if BYTE_ORDER == LITTLE_ENDIAN |
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| 352 | char G4GMocrenIO::kLittleEndianOutput = true; |
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| 353 | #else |
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| 354 | char G4GMocrenIO::kLittleEndianOutput = false; // Big endian |
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| 355 | #endif |
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| 356 | std::string G4GMocrenIO::kComment; |
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| 357 | // |
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| 358 | std::string G4GMocrenIO::kFileName = "dose.gdd"; |
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| 359 | |
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| 360 | // |
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| 361 | unsigned int G4GMocrenIO::kPointerToModalityData = 0; |
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| 362 | std::vector<unsigned int> G4GMocrenIO::kPointerToDoseDistData; |
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| 363 | unsigned int G4GMocrenIO::kPointerToROIData = 0; |
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| 364 | unsigned int G4GMocrenIO::kPointerToTrackData = 0; |
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| 365 | unsigned int G4GMocrenIO::kPointerToDetectorData = 0; |
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| 366 | |
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| 367 | // modality |
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| 368 | float G4GMocrenIO::kVoxelSpacing[3] = {0., 0., 0.}; |
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| 369 | class GMocrenDataPrimitive<short> G4GMocrenIO::kModality; |
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| 370 | std::vector<float> G4GMocrenIO::kModalityImageDensityMap; |
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| 371 | std::string G4GMocrenIO::kModalityUnit = "g/cm3 "; // 12 Bytes |
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| 372 | |
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| 373 | // dose |
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| 374 | std::vector<class GMocrenDataPrimitive<double> > G4GMocrenIO::kDose; |
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| 375 | std::string G4GMocrenIO::kDoseUnit = "keV "; // 12 Bytes |
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| 376 | |
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| 377 | // ROI |
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| 378 | std::vector<class GMocrenDataPrimitive<short> > G4GMocrenIO::kRoi; |
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| 379 | |
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| 380 | // track |
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| 381 | std::vector<float *> G4GMocrenIO::kSteps; |
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| 382 | std::vector<unsigned char *> G4GMocrenIO::kStepColors; |
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| 383 | std::vector<class GMocrenTrack> G4GMocrenIO::kTracks; |
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| 384 | |
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| 385 | // detector |
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| 386 | std::vector<class GMocrenDetector> G4GMocrenIO::kDetectors; |
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| 387 | |
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| 388 | // verbose |
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| 389 | int G4GMocrenIO::kVerbose = 0; |
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| 390 | |
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| 391 | const int IDLENGTH = 21; |
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| 392 | const int VERLENGTH = 6; |
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| 393 | |
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| 394 | // constructor |
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| 395 | G4GMocrenIO::G4GMocrenIO() |
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| 396 | : kTracksWillBeStored(true) { |
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| 397 | ; |
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| 398 | } |
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| 399 | |
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| 400 | // destructor |
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| 401 | G4GMocrenIO::~G4GMocrenIO() { |
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| 402 | ; |
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| 403 | } |
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| 404 | |
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| 405 | // initialize |
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| 406 | void G4GMocrenIO::initialize() { |
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| 407 | |
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| 408 | kId.clear(); |
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| 409 | kVersion = "2.0.0"; |
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| 410 | kNumberOfEvents = 0; |
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| 411 | kLittleEndianInput = true; |
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| 412 | #if BYTE_ORDER == LITTLE_ENDIAN |
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| 413 | kLittleEndianOutput = true; |
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| 414 | #else // Big endian |
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| 415 | kLittleEndianOutput = false; |
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| 416 | #endif |
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| 417 | kComment.clear(); |
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| 418 | kFileName = "dose.gdd"; |
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| 419 | kPointerToModalityData = 0; |
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| 420 | kPointerToDoseDistData.clear(); |
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| 421 | kPointerToROIData = 0; |
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| 422 | kPointerToTrackData = 0; |
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| 423 | // modality |
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| 424 | for(int i = 0; i < 3; i++) kVoxelSpacing[i] = 0.; |
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| 425 | kModality.clear(); |
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| 426 | kModalityImageDensityMap.clear(); |
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| 427 | kModalityUnit = "g/cm3 "; // 12 Bytes |
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| 428 | // dose |
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| 429 | kDose.clear(); |
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| 430 | kDoseUnit = "keV "; // 12 Bytes |
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| 431 | // ROI |
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| 432 | kRoi.clear(); |
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| 433 | // track |
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| 434 | std::vector<float *>::iterator itr; |
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| 435 | for(itr = kSteps.begin(); itr != kSteps.end(); itr++) delete [] *itr; |
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| 436 | kSteps.clear(); |
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| 437 | std::vector<unsigned char *>::iterator citr; |
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| 438 | for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++) |
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| 439 | delete [] *citr; |
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| 440 | kStepColors.clear(); |
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| 441 | kTracksWillBeStored = true; |
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| 442 | |
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| 443 | // verbose |
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| 444 | kVerbose = 0; |
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| 445 | } |
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| 446 | |
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| 447 | bool G4GMocrenIO::storeData() { |
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| 448 | return storeData4(); |
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| 449 | } |
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| 450 | // |
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| 451 | bool G4GMocrenIO::storeData(char * _filename) { |
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| 452 | return storeData4(_filename); |
---|
| 453 | } |
---|
| 454 | |
---|
| 455 | bool G4GMocrenIO::storeData4() { |
---|
| 456 | |
---|
| 457 | bool DEBUG = false;// |
---|
| 458 | |
---|
| 459 | if(DEBUG || kVerbose > 0) |
---|
| 460 | std::cout << ">>>>>>> store data (ver.4) <<<<<<<" << std::endl; |
---|
| 461 | if(DEBUG || kVerbose > 0) |
---|
| 462 | std::cout << " " << kFileName << std::endl; |
---|
| 463 | |
---|
| 464 | // output file open |
---|
| 465 | std::ofstream ofile(kFileName.c_str(), |
---|
| 466 | std::ios_base::out|std::ios_base::binary); |
---|
| 467 | if(DEBUG || kVerbose > 0) |
---|
| 468 | std::cout << " file open status: " << ofile << std::endl; |
---|
| 469 | |
---|
| 470 | // file identifier |
---|
| 471 | ofile.write("gMocren ", 8); |
---|
| 472 | |
---|
| 473 | // file version |
---|
| 474 | unsigned char ver = 0x04; |
---|
| 475 | ofile.write((char *)&ver, 1); |
---|
| 476 | |
---|
| 477 | // endian |
---|
| 478 | //ofile.write((char *)&kLittleEndianOutput, sizeof(char)); |
---|
| 479 | char littleEndian = 0x01; |
---|
| 480 | ofile.write((char *)&littleEndian, sizeof(char)); |
---|
| 481 | if(DEBUG || kVerbose > 0) { |
---|
| 482 | //std::cout << "Endian: " << (int)kLittleEndianOutput << std::endl; |
---|
| 483 | std::cout << "Endian: " << (int)littleEndian << std::endl; |
---|
| 484 | } |
---|
| 485 | |
---|
| 486 | // for inverting the byte order |
---|
| 487 | float ftmp[6]; |
---|
| 488 | int itmp[6]; |
---|
| 489 | short stmp[6]; |
---|
| 490 | |
---|
| 491 | // comment length (fixed size) |
---|
| 492 | int commentLength = 1024; |
---|
| 493 | if(kLittleEndianOutput) { |
---|
| 494 | ofile.write((char *)&commentLength, 4); |
---|
| 495 | } else { |
---|
| 496 | invertByteOrder((char *)&commentLength, itmp[0]); |
---|
| 497 | ofile.write((char *)itmp, 4); |
---|
| 498 | } |
---|
| 499 | |
---|
| 500 | // comment |
---|
| 501 | char cmt[1025]; |
---|
| 502 | for(int i = 0; i < 1025; i++) cmt[i] = '\0'; |
---|
| 503 | //std::strncpy(cmt, kComment.c_str(), 1024); |
---|
| 504 | std::strcpy(cmt, kComment.c_str()); |
---|
| 505 | ofile.write((char *)cmt, 1024); |
---|
| 506 | if(DEBUG || kVerbose > 0) { |
---|
| 507 | std::cout << "Data comment : " |
---|
| 508 | << kComment << std::endl; |
---|
| 509 | } |
---|
| 510 | |
---|
| 511 | // voxel spacings for all images |
---|
| 512 | if(kLittleEndianOutput) { |
---|
| 513 | ofile.write((char *)kVoxelSpacing, 12); |
---|
| 514 | } else { |
---|
| 515 | for(int j = 0; j < 3; j++) |
---|
| 516 | invertByteOrder((char *)&kVoxelSpacing[j], ftmp[j]); |
---|
| 517 | ofile.write((char *)ftmp, 12); |
---|
| 518 | } |
---|
| 519 | if(DEBUG || kVerbose > 0) { |
---|
| 520 | std::cout << "Voxel spacing : (" |
---|
| 521 | << kVoxelSpacing[0] << ", " |
---|
| 522 | << kVoxelSpacing[1] << ", " |
---|
| 523 | << kVoxelSpacing[2] |
---|
| 524 | << ") mm " << std::endl; |
---|
| 525 | } |
---|
| 526 | |
---|
| 527 | calcPointers4(); |
---|
| 528 | if(!kTracksWillBeStored) kPointerToTrackData = 0; |
---|
| 529 | |
---|
| 530 | // offset from file starting point to the modality image data |
---|
| 531 | if(kLittleEndianOutput) { |
---|
| 532 | ofile.write((char *)&kPointerToModalityData, 4); |
---|
| 533 | } else { |
---|
| 534 | invertByteOrder((char *)&kPointerToModalityData, itmp[0]); |
---|
| 535 | ofile.write((char *)itmp, 4); |
---|
| 536 | } |
---|
| 537 | |
---|
| 538 | // # of dose distributions |
---|
| 539 | //int nDoseDist = (int)pointerToDoseDistData.size(); |
---|
| 540 | int nDoseDist = getNumDoseDist(); |
---|
| 541 | if(kLittleEndianOutput) { |
---|
| 542 | ofile.write((char *)&nDoseDist, 4); |
---|
| 543 | } else { |
---|
| 544 | invertByteOrder((char *)&nDoseDist, itmp[0]); |
---|
| 545 | ofile.write((char *)itmp, 4); |
---|
| 546 | } |
---|
| 547 | |
---|
| 548 | // offset from file starting point to the dose image data |
---|
| 549 | if(kLittleEndianOutput) { |
---|
| 550 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 551 | ofile.write((char *)&kPointerToDoseDistData[i], 4); |
---|
| 552 | } |
---|
| 553 | } else { |
---|
| 554 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 555 | invertByteOrder((char *)&kPointerToDoseDistData[i], itmp[0]); |
---|
| 556 | ofile.write((char *)itmp, 4); |
---|
| 557 | } |
---|
| 558 | } |
---|
| 559 | |
---|
| 560 | // offset from file starting point to the ROI image data |
---|
| 561 | if(kLittleEndianOutput) { |
---|
| 562 | ofile.write((char *)&kPointerToROIData, 4); |
---|
| 563 | } else { |
---|
| 564 | invertByteOrder((char *)&kPointerToROIData, itmp[0]); |
---|
| 565 | ofile.write((char *)itmp, 4); |
---|
| 566 | } |
---|
| 567 | |
---|
| 568 | // offset from file starting point to the track data |
---|
| 569 | if(kLittleEndianOutput) { |
---|
| 570 | ofile.write((char *)&kPointerToTrackData, 4); |
---|
| 571 | } else { |
---|
| 572 | invertByteOrder((char *)&kPointerToTrackData, itmp[0]); |
---|
| 573 | ofile.write((char *)itmp, 4); |
---|
| 574 | } |
---|
| 575 | |
---|
| 576 | // offset from file starting point to the detector data |
---|
| 577 | if(kLittleEndianOutput) { |
---|
| 578 | ofile.write((char *)&kPointerToDetectorData, 4); |
---|
| 579 | } else { |
---|
| 580 | invertByteOrder((char *)&kPointerToDetectorData, itmp[0]); |
---|
| 581 | ofile.write((char *)itmp, 4); |
---|
| 582 | } |
---|
| 583 | |
---|
| 584 | if(DEBUG || kVerbose > 0) { |
---|
| 585 | std::cout << "Each pointer to data : " |
---|
| 586 | << kPointerToModalityData << ", "; |
---|
| 587 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 588 | std::cout << kPointerToDoseDistData[i] << ", "; |
---|
| 589 | } |
---|
| 590 | std::cout << kPointerToROIData << ", " |
---|
| 591 | << kPointerToTrackData << ", " |
---|
| 592 | << kPointerToDetectorData |
---|
| 593 | << std::endl; |
---|
| 594 | } |
---|
| 595 | |
---|
| 596 | //----- modality image -----// |
---|
| 597 | |
---|
| 598 | int size[3]; |
---|
| 599 | float scale; |
---|
| 600 | short minmax[2]; |
---|
| 601 | float fCenter[3]; |
---|
| 602 | int iCenter[3]; |
---|
| 603 | // modality image size |
---|
| 604 | kModality.getSize(size); |
---|
| 605 | |
---|
| 606 | if(kLittleEndianOutput) { |
---|
| 607 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 608 | } else { |
---|
| 609 | for(int j = 0; j < 3; j++) |
---|
| 610 | invertByteOrder((char *)&size[j], itmp[j]); |
---|
| 611 | ofile.write((char *)itmp, 12); |
---|
| 612 | } |
---|
| 613 | |
---|
| 614 | if(DEBUG || kVerbose > 0) { |
---|
| 615 | std::cout << "Modality image size : (" |
---|
| 616 | << size[0] << ", " |
---|
| 617 | << size[1] << ", " |
---|
| 618 | << size[2] << ")" |
---|
| 619 | << std::endl; |
---|
| 620 | } |
---|
| 621 | |
---|
| 622 | // modality image max. & min. |
---|
| 623 | kModality.getMinMax(minmax); |
---|
| 624 | if(kLittleEndianOutput) { |
---|
| 625 | ofile.write((char *)minmax, 4); |
---|
| 626 | } else { |
---|
| 627 | for(int j = 0; j < 2; j++) |
---|
| 628 | invertByteOrder((char *)&minmax[j], stmp[j]); |
---|
| 629 | ofile.write((char *)stmp, 4); |
---|
| 630 | } |
---|
| 631 | |
---|
| 632 | // modality image unit |
---|
| 633 | char munit[13] = "g/cm3\0"; |
---|
| 634 | ofile.write((char *)munit, 12); |
---|
| 635 | |
---|
| 636 | // modality image scale |
---|
| 637 | scale = (float)kModality.getScale(); |
---|
| 638 | if(kLittleEndianOutput) { |
---|
| 639 | ofile.write((char *)&scale, 4); |
---|
| 640 | } else { |
---|
| 641 | invertByteOrder((char *)&scale, ftmp[0]); |
---|
| 642 | ofile.write((char *)ftmp, 4); |
---|
| 643 | } |
---|
| 644 | if(DEBUG || kVerbose > 0) { |
---|
| 645 | std::cout << "Modality image min., max., scale : " |
---|
| 646 | << minmax[0] << ", " |
---|
| 647 | << minmax[1] << ", " |
---|
| 648 | << scale << std::endl; |
---|
| 649 | } |
---|
| 650 | |
---|
| 651 | // modality image |
---|
| 652 | int psize = size[0]*size[1]; |
---|
| 653 | if(DEBUG || kVerbose > 0) std::cout << "Modality image : "; |
---|
| 654 | for(int i = 0; i < size[2]; i++) { |
---|
| 655 | short * image = kModality.getImage(i); |
---|
| 656 | if(kLittleEndianOutput) { |
---|
| 657 | ofile.write((char *)image, psize*sizeof(short)); |
---|
| 658 | } else { |
---|
| 659 | for(int j = 0; j < psize; j++) { |
---|
| 660 | invertByteOrder((char *)&image[j], stmp[0]); |
---|
| 661 | ofile.write((char *)stmp, 2); |
---|
| 662 | } |
---|
| 663 | } |
---|
| 664 | |
---|
| 665 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", "; |
---|
| 666 | } |
---|
| 667 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 668 | |
---|
| 669 | // modality desity map for CT value |
---|
| 670 | size_t msize = minmax[1] - minmax[0]+1; |
---|
| 671 | if(DEBUG || kVerbose > 0) |
---|
| 672 | std::cout << "modality image : " << minmax[0] << ", " << minmax[1] << std::endl; |
---|
| 673 | float * pdmap = new float[msize]; |
---|
| 674 | for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i]; |
---|
| 675 | |
---|
| 676 | if(kLittleEndianOutput) { |
---|
| 677 | ofile.write((char *)pdmap, msize*sizeof(float)); |
---|
| 678 | } else { |
---|
| 679 | for(int j = 0; j < (int)msize; j++) { |
---|
| 680 | invertByteOrder((char *)&pdmap[j], ftmp[0]); |
---|
| 681 | ofile.write((char *)ftmp, 4); |
---|
| 682 | } |
---|
| 683 | } |
---|
| 684 | |
---|
| 685 | if(DEBUG || kVerbose > 0) { |
---|
| 686 | std::cout << "density map : " << std::ends; |
---|
| 687 | for(int i = 0; i < (int)msize; i+=50) |
---|
| 688 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 689 | std::cout << std::endl; |
---|
| 690 | } |
---|
| 691 | delete [] pdmap; |
---|
| 692 | |
---|
| 693 | |
---|
| 694 | //----- dose distribution image -----// |
---|
| 695 | |
---|
| 696 | if(!isDoseEmpty()) { |
---|
| 697 | |
---|
| 698 | calcDoseDistScale(); |
---|
| 699 | |
---|
| 700 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 701 | // dose distrbution image size |
---|
| 702 | kDose[ndose].getSize(size); |
---|
| 703 | if(kLittleEndianOutput) { |
---|
| 704 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 705 | } else { |
---|
| 706 | for(int j = 0; j < 3; j++) |
---|
| 707 | invertByteOrder((char *)&size[j], itmp[j]); |
---|
| 708 | ofile.write((char *)itmp, 12); |
---|
| 709 | } |
---|
| 710 | if(DEBUG || kVerbose > 0) { |
---|
| 711 | std::cout << "Dose dist. [" << ndose << "] image size : (" |
---|
| 712 | << size[0] << ", " |
---|
| 713 | << size[1] << ", " |
---|
| 714 | << size[2] << ")" |
---|
| 715 | << std::endl; |
---|
| 716 | } |
---|
| 717 | |
---|
| 718 | // dose distribution max. & min. |
---|
| 719 | getShortDoseDistMinMax(minmax, ndose); |
---|
| 720 | if(kLittleEndianOutput) { |
---|
| 721 | ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2 |
---|
| 722 | } else { |
---|
| 723 | for(int j = 0; j < 2; j++) |
---|
| 724 | invertByteOrder((char *)&minmax[j], stmp[j]); |
---|
| 725 | ofile.write((char *)stmp, 4); |
---|
| 726 | } |
---|
| 727 | |
---|
| 728 | // dose distribution unit |
---|
| 729 | char cdunit[13]; |
---|
| 730 | for(int i = 0; i < 13; i++) cdunit[i] = '\0'; |
---|
| 731 | std::strcpy(cdunit, kDoseUnit.c_str()); |
---|
| 732 | ofile.write((char *)cdunit, 12); |
---|
| 733 | if(DEBUG || kVerbose > 0) { |
---|
| 734 | std::cout << "Dose dist. unit : " << kDoseUnit << std::endl; |
---|
| 735 | } |
---|
| 736 | |
---|
| 737 | // dose distribution scaling |
---|
| 738 | double dscale; |
---|
| 739 | dscale = getDoseDistScale(ndose); |
---|
| 740 | scale = float(dscale); |
---|
| 741 | if(kLittleEndianOutput) { |
---|
| 742 | ofile.write((char *)&scale, 4); |
---|
| 743 | } else { |
---|
| 744 | invertByteOrder((char *)&scale, ftmp[0]); |
---|
| 745 | ofile.write((char *)ftmp, 4); |
---|
| 746 | } |
---|
| 747 | if(DEBUG || kVerbose > 0) { |
---|
| 748 | std::cout << "Dose dist. [" << ndose |
---|
| 749 | << "] image min., max., scale : " |
---|
| 750 | << minmax[0] << ", " |
---|
| 751 | << minmax[1] << ", " |
---|
| 752 | << scale << std::endl; |
---|
| 753 | } |
---|
| 754 | |
---|
| 755 | // dose distribution image |
---|
| 756 | int dsize = size[0]*size[1]; |
---|
| 757 | short * dimage = new short[dsize]; |
---|
| 758 | for(int z = 0; z < size[2]; z++) { |
---|
| 759 | getShortDoseDist(dimage, z, ndose); |
---|
| 760 | if(kLittleEndianOutput) { |
---|
| 761 | ofile.write((char *)dimage, dsize*2); //sizeof(short) |
---|
| 762 | } else { |
---|
| 763 | for(int j = 0; j < dsize; j++) { |
---|
| 764 | invertByteOrder((char *)&dimage[j], stmp[0]); |
---|
| 765 | ofile.write((char *)stmp, 2); |
---|
| 766 | } |
---|
| 767 | } |
---|
| 768 | |
---|
| 769 | if(DEBUG || kVerbose > 0) { |
---|
| 770 | for(int j = 0; j < dsize; j++) { |
---|
| 771 | if(dimage[j] < 0) |
---|
| 772 | std::cout << "[" << j << "," << z << "]" |
---|
| 773 | << dimage[j] << ", "; |
---|
| 774 | } |
---|
| 775 | } |
---|
| 776 | } |
---|
| 777 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 778 | delete [] dimage; |
---|
| 779 | |
---|
| 780 | // relative location of the dose distribution image for |
---|
| 781 | // the modality image |
---|
| 782 | getDoseDistCenterPosition(fCenter, ndose); |
---|
| 783 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 784 | if(kLittleEndianOutput) { |
---|
| 785 | ofile.write((char *)iCenter, 3*4); // 3*sizeof(int) |
---|
| 786 | } else { |
---|
| 787 | for(int j = 0; j < 3; j++) |
---|
| 788 | invertByteOrder((char *)&iCenter[j], itmp[j]); |
---|
| 789 | ofile.write((char *)itmp, 12); |
---|
| 790 | } |
---|
| 791 | if(DEBUG || kVerbose > 0) { |
---|
| 792 | std::cout << "Dose dist. [" << ndose |
---|
| 793 | << "]image relative location : (" |
---|
| 794 | << iCenter[0] << ", " |
---|
| 795 | << iCenter[1] << ", " |
---|
| 796 | << iCenter[2] << ")" << std::endl; |
---|
| 797 | } |
---|
| 798 | |
---|
| 799 | // dose distribution name |
---|
| 800 | std::string name = getDoseDistName(ndose); |
---|
| 801 | if(name.size() == 0) name = "dose"; |
---|
| 802 | name.resize(80); |
---|
| 803 | ofile.write((char *)name.c_str(), 80); |
---|
| 804 | if(DEBUG || kVerbose > 0) { |
---|
| 805 | std::cout << "Dose dist. name : " << name << std::endl; |
---|
| 806 | } |
---|
| 807 | |
---|
| 808 | } |
---|
| 809 | } |
---|
| 810 | |
---|
| 811 | //----- ROI image -----// |
---|
| 812 | if(!isROIEmpty()) { |
---|
| 813 | // ROI image size |
---|
| 814 | kRoi[0].getSize(size); |
---|
| 815 | if(kLittleEndianOutput) { |
---|
| 816 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 817 | } else { |
---|
| 818 | for(int j = 0; j < 3; j++) |
---|
| 819 | invertByteOrder((char *)&size[j], itmp[j]); |
---|
| 820 | ofile.write((char *)itmp, 12); |
---|
| 821 | } |
---|
| 822 | if(DEBUG || kVerbose > 0) { |
---|
| 823 | std::cout << "ROI image size : (" |
---|
| 824 | << size[0] << ", " |
---|
| 825 | << size[1] << ", " |
---|
| 826 | << size[2] << ")" |
---|
| 827 | << std::endl; |
---|
| 828 | } |
---|
| 829 | |
---|
| 830 | // ROI max. & min. |
---|
| 831 | kRoi[0].getMinMax(minmax); |
---|
| 832 | if(kLittleEndianOutput) { |
---|
| 833 | ofile.write((char *)minmax, sizeof(short)*2); |
---|
| 834 | } else { |
---|
| 835 | for(int j = 0; j < 2; j++) |
---|
| 836 | invertByteOrder((char *)&minmax[j], stmp[j]); |
---|
| 837 | ofile.write((char *)stmp, 4); |
---|
| 838 | } |
---|
| 839 | |
---|
| 840 | // ROI distribution scaling |
---|
| 841 | scale = (float)kRoi[0].getScale(); |
---|
| 842 | if(kLittleEndianOutput) { |
---|
| 843 | ofile.write((char *)&scale, sizeof(float)); |
---|
| 844 | } else { |
---|
| 845 | invertByteOrder((char *)&scale, ftmp[0]); |
---|
| 846 | ofile.write((char *)ftmp, 4); |
---|
| 847 | } |
---|
| 848 | if(DEBUG || kVerbose > 0) { |
---|
| 849 | std::cout << "ROI image min., max., scale : " |
---|
| 850 | << minmax[0] << ", " |
---|
| 851 | << minmax[1] << ", " |
---|
| 852 | << scale << std::endl; |
---|
| 853 | } |
---|
| 854 | |
---|
| 855 | // ROI image |
---|
| 856 | int rsize = size[0]*size[1]; |
---|
| 857 | for(int i = 0; i < size[2]; i++) { |
---|
| 858 | short * rimage = kRoi[0].getImage(i); |
---|
| 859 | if(kLittleEndianOutput) { |
---|
| 860 | ofile.write((char *)rimage, rsize*sizeof(short)); |
---|
| 861 | } else { |
---|
| 862 | for(int j = 0; j < rsize; j++) { |
---|
| 863 | invertByteOrder((char *)&rimage[j], stmp[0]); |
---|
| 864 | ofile.write((char *)stmp, 2); |
---|
| 865 | } |
---|
| 866 | } |
---|
| 867 | |
---|
| 868 | } |
---|
| 869 | |
---|
| 870 | // ROI relative location |
---|
| 871 | kRoi[0].getCenterPosition(fCenter); |
---|
| 872 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 873 | if(kLittleEndianOutput) { |
---|
| 874 | ofile.write((char *)iCenter, 3*sizeof(int)); |
---|
| 875 | } else { |
---|
| 876 | for(int j = 0; j < 3; j++) |
---|
| 877 | invertByteOrder((char *)&iCenter[j], itmp[j]); |
---|
| 878 | ofile.write((char *)itmp, 12); |
---|
| 879 | } |
---|
| 880 | if(DEBUG || kVerbose > 0) { |
---|
| 881 | std::cout << "ROI image relative location : (" |
---|
| 882 | << iCenter[0] << ", " |
---|
| 883 | << iCenter[1] << ", " |
---|
| 884 | << iCenter[2] << ")" << std::endl; |
---|
| 885 | } |
---|
| 886 | } |
---|
| 887 | |
---|
| 888 | //----- track information -----// |
---|
| 889 | // number of track |
---|
| 890 | if(kPointerToTrackData > 0) { |
---|
| 891 | |
---|
| 892 | int ntrk = kTracks.size(); |
---|
| 893 | if(kLittleEndianOutput) { |
---|
| 894 | ofile.write((char *)&ntrk, sizeof(int)); |
---|
| 895 | } else { |
---|
| 896 | invertByteOrder((char *)&ntrk, itmp[0]); |
---|
| 897 | ofile.write((char *)itmp, 4); |
---|
| 898 | } |
---|
| 899 | if(DEBUG || kVerbose > 0) { |
---|
| 900 | std::cout << "# of tracks : " |
---|
| 901 | << ntrk << std::endl; |
---|
| 902 | } |
---|
| 903 | |
---|
| 904 | for(int nt = 0; nt < ntrk; nt++) { |
---|
| 905 | |
---|
| 906 | // # of steps in a track |
---|
| 907 | int nsteps = kTracks[nt].getNumberOfSteps(); |
---|
| 908 | if(kLittleEndianOutput) { |
---|
| 909 | ofile.write((char *)&nsteps, sizeof(int)); |
---|
| 910 | } else { |
---|
| 911 | invertByteOrder((char *)&nsteps, itmp[0]); |
---|
| 912 | ofile.write((char *)itmp, 4); |
---|
| 913 | } |
---|
| 914 | if(DEBUG || kVerbose > 0) { |
---|
| 915 | std::cout << "# of steps : " << nsteps << std::endl; |
---|
| 916 | } |
---|
| 917 | |
---|
| 918 | // track color |
---|
| 919 | unsigned char tcolor[3]; |
---|
| 920 | kTracks[nt].getColor(tcolor); |
---|
| 921 | ofile.write((char *)tcolor, 3); |
---|
| 922 | |
---|
| 923 | // steps |
---|
| 924 | float stepPoints[6]; |
---|
| 925 | for(int ns = 0; ns < nsteps; ns++) { |
---|
| 926 | kTracks[nt].getStep(stepPoints[0], stepPoints[1], stepPoints[2], |
---|
| 927 | stepPoints[3], stepPoints[4], stepPoints[5], |
---|
| 928 | ns); |
---|
| 929 | |
---|
| 930 | if(kLittleEndianOutput) { |
---|
| 931 | ofile.write((char *)stepPoints, sizeof(float)*6); |
---|
| 932 | } else { |
---|
| 933 | for(int j = 0; j < 6; j++) |
---|
| 934 | invertByteOrder((char *)&stepPoints[j], ftmp[j]); |
---|
| 935 | ofile.write((char *)ftmp, 24); |
---|
| 936 | } |
---|
| 937 | } |
---|
| 938 | } |
---|
| 939 | } |
---|
| 940 | |
---|
| 941 | //----- detector information -----// |
---|
| 942 | // number of detectors |
---|
| 943 | if(kPointerToDetectorData > 0) { |
---|
| 944 | int ndet = kDetectors.size(); |
---|
| 945 | if(kLittleEndianOutput) { |
---|
| 946 | ofile.write((char *)&ndet, sizeof(int)); |
---|
| 947 | } else { |
---|
| 948 | invertByteOrder((char *)&ndet, itmp[0]); |
---|
| 949 | ofile.write((char *)itmp, 4); |
---|
| 950 | } |
---|
| 951 | if(DEBUG || kVerbose > 0) { |
---|
| 952 | std::cout << "# of detectors : " |
---|
| 953 | << ndet << std::endl; |
---|
| 954 | } |
---|
| 955 | |
---|
| 956 | for(int nd = 0; nd < ndet; nd++) { |
---|
| 957 | |
---|
| 958 | // # of edges of a detector |
---|
| 959 | int nedges = kDetectors[nd].getNumberOfEdges(); |
---|
| 960 | if(kLittleEndianOutput) { |
---|
| 961 | ofile.write((char *)&nedges, sizeof(int)); |
---|
| 962 | } else { |
---|
| 963 | invertByteOrder((char *)&nedges, itmp[0]); |
---|
| 964 | ofile.write((char *)itmp, 4); |
---|
| 965 | } |
---|
| 966 | if(DEBUG || kVerbose > 0) { |
---|
| 967 | std::cout << "# of edges in a detector : " << nedges << std::endl; |
---|
| 968 | } |
---|
| 969 | |
---|
| 970 | // edges |
---|
| 971 | float edgePoints[6]; |
---|
| 972 | for(int ne = 0; ne < nedges; ne++) { |
---|
| 973 | kDetectors[nd].getEdge(edgePoints[0], edgePoints[1], edgePoints[2], |
---|
| 974 | edgePoints[3], edgePoints[4], edgePoints[5], |
---|
| 975 | ne); |
---|
| 976 | |
---|
| 977 | if(kLittleEndianOutput) { |
---|
| 978 | ofile.write((char *)edgePoints, sizeof(float)*6); |
---|
| 979 | } else { |
---|
| 980 | for(int j = 0; j < 6; j++) |
---|
| 981 | invertByteOrder((char *)&edgePoints[j], ftmp[j]); |
---|
| 982 | ofile.write((char *)ftmp, 24); |
---|
| 983 | } |
---|
| 984 | |
---|
| 985 | if(DEBUG || kVerbose > 0) { |
---|
| 986 | if(ne < 1) { |
---|
| 987 | std::cout << " edge : (" << edgePoints[0] << ", " |
---|
| 988 | << edgePoints[1] << ", " |
---|
| 989 | << edgePoints[2] << ") - (" |
---|
| 990 | << edgePoints[3] << ", " |
---|
| 991 | << edgePoints[4] << ", " |
---|
| 992 | << edgePoints[5] << ")" << std::endl; |
---|
| 993 | } |
---|
| 994 | } |
---|
| 995 | } |
---|
| 996 | |
---|
| 997 | // detector color |
---|
| 998 | unsigned char dcolor[3]; |
---|
| 999 | kDetectors[nd].getColor(dcolor); |
---|
| 1000 | ofile.write((char *)dcolor, 3); |
---|
| 1001 | if(DEBUG || kVerbose > 0) { |
---|
| 1002 | std::cout << " rgb : (" << (int)dcolor[0] << ", " |
---|
| 1003 | << (int)dcolor[1] << ", " |
---|
| 1004 | << (int)dcolor[2] << ")" << std::endl; |
---|
| 1005 | } |
---|
| 1006 | |
---|
| 1007 | // detector name |
---|
| 1008 | std::string dname = kDetectors[nd].getName(); |
---|
| 1009 | dname.resize(80); |
---|
| 1010 | ofile.write((char *)dname.c_str(), 80); |
---|
| 1011 | if(DEBUG || kVerbose > 0) { |
---|
| 1012 | std::cout << " detector name : " << dname << std::endl; |
---|
| 1013 | |
---|
| 1014 | } |
---|
| 1015 | } |
---|
| 1016 | } |
---|
| 1017 | |
---|
| 1018 | // file end mark |
---|
| 1019 | ofile.write("END", 3); |
---|
| 1020 | |
---|
| 1021 | ofile.close(); |
---|
| 1022 | if(DEBUG || kVerbose > 0) |
---|
| 1023 | std::cout << ">>>> closed gdd file: " << kFileName << std::endl; |
---|
| 1024 | |
---|
| 1025 | return true; |
---|
| 1026 | } |
---|
| 1027 | bool G4GMocrenIO::storeData3() { |
---|
| 1028 | |
---|
| 1029 | if(kVerbose > 0) std::cout << ">>>>>>> store data (ver.3) <<<<<<<" << std::endl; |
---|
| 1030 | if(kVerbose > 0) std::cout << " " << kFileName << std::endl; |
---|
| 1031 | |
---|
| 1032 | bool DEBUG = false;// |
---|
| 1033 | |
---|
| 1034 | // output file open |
---|
| 1035 | std::ofstream ofile(kFileName.c_str(), |
---|
| 1036 | std::ios_base::out|std::ios_base::binary); |
---|
| 1037 | |
---|
| 1038 | // file identifier |
---|
| 1039 | ofile.write("gMocren ", 8); |
---|
| 1040 | |
---|
| 1041 | // file version |
---|
| 1042 | unsigned char ver = 0x03; |
---|
| 1043 | ofile.write((char *)&ver, 1); |
---|
| 1044 | |
---|
| 1045 | // endian |
---|
| 1046 | ofile.write((char *)&kLittleEndianOutput, sizeof(char)); |
---|
| 1047 | |
---|
| 1048 | // comment length (fixed size) |
---|
| 1049 | int commentLength = 1024; |
---|
| 1050 | ofile.write((char *)&commentLength, 4); |
---|
| 1051 | |
---|
| 1052 | // comment |
---|
| 1053 | char cmt[1025]; |
---|
| 1054 | std::strncpy(cmt, kComment.c_str(), 1024); |
---|
| 1055 | ofile.write((char *)cmt, 1024); |
---|
| 1056 | if(DEBUG || kVerbose > 0) { |
---|
| 1057 | std::cout << "Data comment : " |
---|
| 1058 | << kComment << std::endl; |
---|
| 1059 | } |
---|
| 1060 | |
---|
| 1061 | // voxel spacings for all images |
---|
| 1062 | ofile.write((char *)kVoxelSpacing, 12); |
---|
| 1063 | if(DEBUG || kVerbose > 0) { |
---|
| 1064 | std::cout << "Voxel spacing : (" |
---|
| 1065 | << kVoxelSpacing[0] << ", " |
---|
| 1066 | << kVoxelSpacing[1] << ", " |
---|
| 1067 | << kVoxelSpacing[2] |
---|
| 1068 | << ") mm " << std::endl; |
---|
| 1069 | } |
---|
| 1070 | |
---|
| 1071 | calcPointers3(); |
---|
| 1072 | |
---|
| 1073 | // offset from file starting point to the modality image data |
---|
| 1074 | ofile.write((char *)&kPointerToModalityData, 4); |
---|
| 1075 | |
---|
| 1076 | // # of dose distributions |
---|
| 1077 | //int nDoseDist = (int)pointerToDoseDistData.size(); |
---|
| 1078 | int nDoseDist = getNumDoseDist(); |
---|
| 1079 | ofile.write((char *)&nDoseDist, 4); |
---|
| 1080 | |
---|
| 1081 | // offset from file starting point to the dose image data |
---|
| 1082 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 1083 | ofile.write((char *)&kPointerToDoseDistData[i], 4); |
---|
| 1084 | } |
---|
| 1085 | |
---|
| 1086 | // offset from file starting point to the ROI image data |
---|
| 1087 | ofile.write((char *)&kPointerToROIData, 4); |
---|
| 1088 | |
---|
| 1089 | // offset from file starting point to the track data |
---|
| 1090 | ofile.write((char *)&kPointerToTrackData, 4); |
---|
| 1091 | if(DEBUG || kVerbose > 0) { |
---|
| 1092 | std::cout << "Each pointer to data : " |
---|
| 1093 | << kPointerToModalityData << ", "; |
---|
| 1094 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 1095 | std::cout << kPointerToDoseDistData[i] << ", "; |
---|
| 1096 | } |
---|
| 1097 | std::cout << kPointerToROIData << ", " |
---|
| 1098 | << kPointerToTrackData << std::endl; |
---|
| 1099 | } |
---|
| 1100 | |
---|
| 1101 | //----- modality image -----// |
---|
| 1102 | |
---|
| 1103 | int size[3]; |
---|
| 1104 | float scale; |
---|
| 1105 | short minmax[2]; |
---|
| 1106 | float fCenter[3]; |
---|
| 1107 | int iCenter[3]; |
---|
| 1108 | // modality image size |
---|
| 1109 | kModality.getSize(size); |
---|
| 1110 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1111 | if(DEBUG || kVerbose > 0) { |
---|
| 1112 | std::cout << "Modality image size : (" |
---|
| 1113 | << size[0] << ", " |
---|
| 1114 | << size[1] << ", " |
---|
| 1115 | << size[2] << ")" |
---|
| 1116 | << std::endl; |
---|
| 1117 | } |
---|
| 1118 | |
---|
| 1119 | // modality image max. & min. |
---|
| 1120 | kModality.getMinMax(minmax); |
---|
| 1121 | ofile.write((char *)minmax, 4); |
---|
| 1122 | |
---|
| 1123 | // modality image unit |
---|
| 1124 | char munit[13] = "g/cm3 "; |
---|
| 1125 | ofile.write((char *)munit, 12); |
---|
| 1126 | |
---|
| 1127 | // modality image scale |
---|
| 1128 | scale = (float)kModality.getScale(); |
---|
| 1129 | ofile.write((char *)&scale, 4); |
---|
| 1130 | if(DEBUG || kVerbose > 0) { |
---|
| 1131 | std::cout << "Modality image min., max., scale : " |
---|
| 1132 | << minmax[0] << ", " |
---|
| 1133 | << minmax[1] << ", " |
---|
| 1134 | << scale << std::endl; |
---|
| 1135 | } |
---|
| 1136 | |
---|
| 1137 | // modality image |
---|
| 1138 | int psize = size[0]*size[1]; |
---|
| 1139 | if(DEBUG || kVerbose > 0) std::cout << "Modality image : "; |
---|
| 1140 | for(int i = 0; i < size[2]; i++) { |
---|
| 1141 | short * image = kModality.getImage(i); |
---|
| 1142 | ofile.write((char *)image, psize*sizeof(short)); |
---|
| 1143 | |
---|
| 1144 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", "; |
---|
| 1145 | } |
---|
| 1146 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1147 | |
---|
| 1148 | // modality desity map for CT value |
---|
| 1149 | size_t msize = minmax[1] - minmax[0]+1; |
---|
| 1150 | float * pdmap = new float[msize]; |
---|
| 1151 | for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i]; |
---|
| 1152 | ofile.write((char *)pdmap, msize*sizeof(float)); |
---|
| 1153 | if(DEBUG || kVerbose > 0) { |
---|
| 1154 | std::cout << "density map : " << std::ends; |
---|
| 1155 | for(int i = 0; i < (int)msize; i+=50) |
---|
| 1156 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 1157 | std::cout << std::endl; |
---|
| 1158 | } |
---|
| 1159 | delete [] pdmap; |
---|
| 1160 | |
---|
| 1161 | |
---|
| 1162 | //----- dose distribution image -----// |
---|
| 1163 | |
---|
| 1164 | if(!isDoseEmpty()) { |
---|
| 1165 | |
---|
| 1166 | calcDoseDistScale(); |
---|
| 1167 | |
---|
| 1168 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 1169 | // dose distrbution image size |
---|
| 1170 | kDose[ndose].getSize(size); |
---|
| 1171 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1172 | if(DEBUG || kVerbose > 0) { |
---|
| 1173 | std::cout << "Dose dist. [" << ndose << "] image size : (" |
---|
| 1174 | << size[0] << ", " |
---|
| 1175 | << size[1] << ", " |
---|
| 1176 | << size[2] << ")" |
---|
| 1177 | << std::endl; |
---|
| 1178 | } |
---|
| 1179 | |
---|
| 1180 | // dose distribution max. & min. |
---|
| 1181 | getShortDoseDistMinMax(minmax, ndose); |
---|
| 1182 | ofile.write((char *)minmax, 2*2); // sizeof(shorft)*2 |
---|
| 1183 | |
---|
| 1184 | // dose distribution unit |
---|
| 1185 | ofile.write((char *)kDoseUnit.c_str(), 12); |
---|
| 1186 | if(DEBUG || kVerbose > 0) { |
---|
| 1187 | std::cout << "Dose dist. unit : " << kDoseUnit << std::endl; |
---|
| 1188 | } |
---|
| 1189 | |
---|
| 1190 | // dose distribution scaling |
---|
| 1191 | double dscale; |
---|
| 1192 | dscale = getDoseDistScale(ndose); |
---|
| 1193 | scale = float(dscale); |
---|
| 1194 | ofile.write((char *)&scale, 4); |
---|
| 1195 | if(DEBUG || kVerbose > 0) { |
---|
| 1196 | std::cout << "Dose dist. [" << ndose |
---|
| 1197 | << "] image min., max., scale : " |
---|
| 1198 | << minmax[0] << ", " |
---|
| 1199 | << minmax[1] << ", " |
---|
| 1200 | << scale << std::endl; |
---|
| 1201 | } |
---|
| 1202 | |
---|
| 1203 | // dose distribution image |
---|
| 1204 | int dsize = size[0]*size[1]; |
---|
| 1205 | short * dimage = new short[dsize]; |
---|
| 1206 | for(int z = 0; z < size[2]; z++) { |
---|
| 1207 | getShortDoseDist(dimage, z, ndose); |
---|
| 1208 | ofile.write((char *)dimage, dsize*2); //sizeof(short) |
---|
| 1209 | |
---|
| 1210 | if(DEBUG || kVerbose > 0) { |
---|
| 1211 | for(int j = 0; j < dsize; j++) { |
---|
| 1212 | if(dimage[j] < 0) |
---|
| 1213 | std::cout << "[" << j << "," << z << "]" |
---|
| 1214 | << dimage[j] << ", "; |
---|
| 1215 | } |
---|
| 1216 | } |
---|
| 1217 | } |
---|
| 1218 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1219 | delete [] dimage; |
---|
| 1220 | |
---|
| 1221 | // relative location of the dose distribution image for |
---|
| 1222 | // the modality image |
---|
| 1223 | getDoseDistCenterPosition(fCenter, ndose); |
---|
| 1224 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 1225 | ofile.write((char *)iCenter, 3*4); // 3*sizeof(int) |
---|
| 1226 | if(DEBUG || kVerbose > 0) { |
---|
| 1227 | std::cout << "Dose dist. [" << ndose |
---|
| 1228 | << "]image relative location : (" |
---|
| 1229 | << iCenter[0] << ", " |
---|
| 1230 | << iCenter[1] << ", " |
---|
| 1231 | << iCenter[2] << ")" << std::endl; |
---|
| 1232 | } |
---|
| 1233 | } |
---|
| 1234 | } |
---|
| 1235 | |
---|
| 1236 | //----- ROI image -----// |
---|
| 1237 | if(!isROIEmpty()) { |
---|
| 1238 | // ROI image size |
---|
| 1239 | kRoi[0].getSize(size); |
---|
| 1240 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1241 | if(DEBUG || kVerbose > 0) { |
---|
| 1242 | std::cout << "ROI image size : (" |
---|
| 1243 | << size[0] << ", " |
---|
| 1244 | << size[1] << ", " |
---|
| 1245 | << size[2] << ")" |
---|
| 1246 | << std::endl; |
---|
| 1247 | } |
---|
| 1248 | |
---|
| 1249 | // ROI max. & min. |
---|
| 1250 | kRoi[0].getMinMax(minmax); |
---|
| 1251 | ofile.write((char *)minmax, sizeof(short)*2); |
---|
| 1252 | |
---|
| 1253 | // ROI distribution scaling |
---|
| 1254 | scale = (float)kRoi[0].getScale(); |
---|
| 1255 | ofile.write((char *)&scale, sizeof(float)); |
---|
| 1256 | if(DEBUG || kVerbose > 0) { |
---|
| 1257 | std::cout << "ROI image min., max., scale : " |
---|
| 1258 | << minmax[0] << ", " |
---|
| 1259 | << minmax[1] << ", " |
---|
| 1260 | << scale << std::endl; |
---|
| 1261 | } |
---|
| 1262 | |
---|
| 1263 | // ROI image |
---|
| 1264 | int rsize = size[0]*size[1]; |
---|
| 1265 | for(int i = 0; i < size[2]; i++) { |
---|
| 1266 | short * rimage = kRoi[0].getImage(i); |
---|
| 1267 | ofile.write((char *)rimage, rsize*sizeof(short)); |
---|
| 1268 | |
---|
| 1269 | } |
---|
| 1270 | |
---|
| 1271 | // ROI relative location |
---|
| 1272 | kRoi[0].getCenterPosition(fCenter); |
---|
| 1273 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 1274 | ofile.write((char *)iCenter, 3*sizeof(int)); |
---|
| 1275 | if(DEBUG || kVerbose > 0) { |
---|
| 1276 | std::cout << "ROI image relative location : (" |
---|
| 1277 | << iCenter[0] << ", " |
---|
| 1278 | << iCenter[1] << ", " |
---|
| 1279 | << iCenter[2] << ")" << std::endl; |
---|
| 1280 | } |
---|
| 1281 | } |
---|
| 1282 | |
---|
| 1283 | //----- track information -----// |
---|
| 1284 | // number of track |
---|
| 1285 | int ntrk = kSteps.size(); |
---|
| 1286 | ofile.write((char *)&ntrk, sizeof(int)); |
---|
| 1287 | if(DEBUG || kVerbose > 0) { |
---|
| 1288 | std::cout << "# of tracks : " |
---|
| 1289 | << ntrk << std::endl; |
---|
| 1290 | } |
---|
| 1291 | // track position |
---|
| 1292 | for(int i = 0; i < ntrk; i++) { |
---|
| 1293 | float * tp = kSteps[i]; |
---|
| 1294 | ofile.write((char *)tp, sizeof(float)*6); |
---|
| 1295 | } |
---|
| 1296 | // track color |
---|
| 1297 | int ntcolor = int(kStepColors.size()); |
---|
| 1298 | if(ntrk != ntcolor) |
---|
| 1299 | std::cerr << "# of track color information must be the same as # of tracks." |
---|
| 1300 | << std::endl; |
---|
| 1301 | unsigned char white[3] = {255,255,255}; // default color |
---|
| 1302 | for(int i = 0; i < ntrk; i++) { |
---|
| 1303 | if(i < ntcolor) { |
---|
| 1304 | unsigned char * tcolor = kStepColors[i]; |
---|
| 1305 | ofile.write((char *)tcolor, 3); |
---|
| 1306 | } else { |
---|
| 1307 | ofile.write((char *)white, 3); |
---|
| 1308 | } |
---|
| 1309 | } |
---|
| 1310 | |
---|
| 1311 | // file end mark |
---|
| 1312 | ofile.write("END", 3); |
---|
| 1313 | |
---|
| 1314 | ofile.close(); |
---|
| 1315 | |
---|
| 1316 | return true; |
---|
| 1317 | } |
---|
| 1318 | // |
---|
| 1319 | bool G4GMocrenIO::storeData4(char * _filename) { |
---|
| 1320 | kFileName = _filename; |
---|
| 1321 | return storeData4(); |
---|
| 1322 | } |
---|
| 1323 | |
---|
| 1324 | // version 2 |
---|
| 1325 | bool G4GMocrenIO::storeData2() { |
---|
| 1326 | |
---|
| 1327 | if(kVerbose > 0) std::cout << ">>>>>>> store data (ver.2) <<<<<<<" << std::endl; |
---|
| 1328 | if(kVerbose > 0) std::cout << " " << kFileName << std::endl; |
---|
| 1329 | |
---|
| 1330 | bool DEBUG = false;// |
---|
| 1331 | |
---|
| 1332 | // output file open |
---|
| 1333 | std::ofstream ofile(kFileName.c_str(), |
---|
| 1334 | std::ios_base::out|std::ios_base::binary); |
---|
| 1335 | |
---|
| 1336 | // file identifier |
---|
| 1337 | ofile.write("GRAPE ", 8); |
---|
| 1338 | |
---|
| 1339 | // file version |
---|
| 1340 | unsigned char ver = 0x02; |
---|
| 1341 | ofile.write((char *)&ver, 1); |
---|
| 1342 | // file id for old file format support |
---|
| 1343 | ofile.write(kId.c_str(), IDLENGTH); |
---|
| 1344 | // file version for old file format support |
---|
| 1345 | ofile.write(kVersion.c_str(), VERLENGTH); |
---|
| 1346 | // endian |
---|
| 1347 | ofile.write((char *)&kLittleEndianOutput, sizeof(char)); |
---|
| 1348 | |
---|
| 1349 | /* |
---|
| 1350 | // event number |
---|
| 1351 | ofile.write((char *)&numberOfEvents, sizeof(int)); |
---|
| 1352 | float imageSpacing[3]; |
---|
| 1353 | imageSpacing[0] = modalityImageVoxelSpacing[0]; |
---|
| 1354 | imageSpacing[1] = modalityImageVoxelSpacing[1]; |
---|
| 1355 | imageSpacing[2] = modalityImageVoxelSpacing[2]; |
---|
| 1356 | ofile.write((char *)imageSpacing, 12); |
---|
| 1357 | */ |
---|
| 1358 | |
---|
| 1359 | |
---|
| 1360 | // voxel spacings for all images |
---|
| 1361 | ofile.write((char *)kVoxelSpacing, 12); |
---|
| 1362 | if(DEBUG || kVerbose > 0) { |
---|
| 1363 | std::cout << "Voxel spacing : (" |
---|
| 1364 | << kVoxelSpacing[0] << ", " |
---|
| 1365 | << kVoxelSpacing[1] << ", " |
---|
| 1366 | << kVoxelSpacing[2] |
---|
| 1367 | << ") mm " << std::endl; |
---|
| 1368 | } |
---|
| 1369 | |
---|
| 1370 | calcPointers2(); |
---|
| 1371 | // offset from file starting point to the modality image data |
---|
| 1372 | ofile.write((char *)&kPointerToModalityData, 4); |
---|
| 1373 | |
---|
| 1374 | // offset from file starting point to the dose image data |
---|
| 1375 | ofile.write((char *)&kPointerToDoseDistData[0], 4); |
---|
| 1376 | |
---|
| 1377 | // offset from file starting point to the ROI image data |
---|
| 1378 | ofile.write((char *)&kPointerToROIData, 4); |
---|
| 1379 | |
---|
| 1380 | // offset from file starting point to the track data |
---|
| 1381 | ofile.write((char *)&kPointerToTrackData, 4); |
---|
| 1382 | if(DEBUG || kVerbose > 0) { |
---|
| 1383 | std::cout << "Each pointer to data : " |
---|
| 1384 | << kPointerToModalityData << ", " |
---|
| 1385 | << kPointerToDoseDistData[0] << ", " |
---|
| 1386 | << kPointerToROIData << ", " |
---|
| 1387 | << kPointerToTrackData << std::endl; |
---|
| 1388 | } |
---|
| 1389 | |
---|
| 1390 | //----- modality image -----// |
---|
| 1391 | |
---|
| 1392 | int size[3]; |
---|
| 1393 | float scale; |
---|
| 1394 | short minmax[2]; |
---|
| 1395 | float fCenter[3]; |
---|
| 1396 | int iCenter[3]; |
---|
| 1397 | // modality image size |
---|
| 1398 | kModality.getSize(size); |
---|
| 1399 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1400 | if(DEBUG || kVerbose > 0) { |
---|
| 1401 | std::cout << "Modality image size : (" |
---|
| 1402 | << size[0] << ", " |
---|
| 1403 | << size[1] << ", " |
---|
| 1404 | << size[2] << ")" |
---|
| 1405 | << std::endl; |
---|
| 1406 | } |
---|
| 1407 | |
---|
| 1408 | // modality image max. & min. |
---|
| 1409 | kModality.getMinMax(minmax); |
---|
| 1410 | ofile.write((char *)minmax, 4); |
---|
| 1411 | |
---|
| 1412 | // modality image unit |
---|
| 1413 | //char munit[13] = "g/cm3 "; |
---|
| 1414 | //ofile.write((char *)&munit, 12); |
---|
| 1415 | |
---|
| 1416 | // modality image scale |
---|
| 1417 | scale = (float)kModality.getScale(); |
---|
| 1418 | ofile.write((char *)&scale, 4); |
---|
| 1419 | if(DEBUG || kVerbose > 0) { |
---|
| 1420 | std::cout << "Modality image min., max., scale : " |
---|
| 1421 | << minmax[0] << ", " |
---|
| 1422 | << minmax[1] << ", " |
---|
| 1423 | << scale << std::endl; |
---|
| 1424 | } |
---|
| 1425 | |
---|
| 1426 | // modality image |
---|
| 1427 | int psize = size[0]*size[1]; |
---|
| 1428 | if(DEBUG || kVerbose > 0) std::cout << "Modality image : "; |
---|
| 1429 | for(int i = 0; i < size[2]; i++) { |
---|
| 1430 | short * image =kModality.getImage(i); |
---|
| 1431 | ofile.write((char *)image, psize*sizeof(short)); |
---|
| 1432 | |
---|
| 1433 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << image[(size_t)(psize*0.55)] << ", "; |
---|
| 1434 | } |
---|
| 1435 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1436 | |
---|
| 1437 | // modality desity map for CT value |
---|
| 1438 | size_t msize = minmax[1] - minmax[0]+1; |
---|
| 1439 | float * pdmap = new float[msize]; |
---|
| 1440 | for(int i = 0; i < (int)msize; i++) pdmap[i] =kModalityImageDensityMap[i]; |
---|
| 1441 | ofile.write((char *)pdmap, msize*sizeof(float)); |
---|
| 1442 | if(DEBUG || kVerbose > 0) { |
---|
| 1443 | std::cout << "density map : " << std::ends; |
---|
| 1444 | for(int i = 0; i < (int)msize; i+=50) |
---|
| 1445 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 1446 | std::cout << std::endl; |
---|
| 1447 | } |
---|
| 1448 | delete [] pdmap; |
---|
| 1449 | |
---|
| 1450 | |
---|
| 1451 | //----- dose distribution image -----// |
---|
| 1452 | |
---|
| 1453 | if(!isDoseEmpty()) { |
---|
| 1454 | calcDoseDistScale(); |
---|
| 1455 | |
---|
| 1456 | // dose distrbution image size |
---|
| 1457 | kDose[0].getSize(size); |
---|
| 1458 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1459 | if(DEBUG || kVerbose > 0) { |
---|
| 1460 | std::cout << "Dose dist. image size : (" |
---|
| 1461 | << size[0] << ", " |
---|
| 1462 | << size[1] << ", " |
---|
| 1463 | << size[2] << ")" |
---|
| 1464 | << std::endl; |
---|
| 1465 | } |
---|
| 1466 | |
---|
| 1467 | // dose distribution max. & min. |
---|
| 1468 | getShortDoseDistMinMax(minmax); |
---|
| 1469 | ofile.write((char *)minmax, sizeof(short)*2); |
---|
| 1470 | |
---|
| 1471 | // dose distribution scaling |
---|
| 1472 | scale = (float)kDose[0].getScale(); |
---|
| 1473 | ofile.write((char *)&scale, sizeof(float)); |
---|
| 1474 | if(DEBUG || kVerbose > 0) { |
---|
| 1475 | std::cout << "Dose dist. image min., max., scale : " |
---|
| 1476 | << minmax[0] << ", " |
---|
| 1477 | << minmax[1] << ", " |
---|
| 1478 | << scale << std::endl; |
---|
| 1479 | } |
---|
| 1480 | |
---|
| 1481 | // dose distribution image |
---|
| 1482 | int dsize = size[0]*size[1]; |
---|
| 1483 | short * dimage = new short[dsize]; |
---|
| 1484 | for(int z = 0; z < size[2]; z++) { |
---|
| 1485 | getShortDoseDist(dimage, z); |
---|
| 1486 | ofile.write((char *)dimage, dsize*sizeof(short)); |
---|
| 1487 | |
---|
| 1488 | if(DEBUG || kVerbose > 0) { |
---|
| 1489 | for(int j = 0; j < dsize; j++) { |
---|
| 1490 | if(dimage[j] < 0) |
---|
| 1491 | std::cout << "[" << j << "," << z << "]" |
---|
| 1492 | << dimage[j] << ", "; |
---|
| 1493 | } |
---|
| 1494 | } |
---|
| 1495 | } |
---|
| 1496 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1497 | delete [] dimage; |
---|
| 1498 | |
---|
| 1499 | // relative location of the dose distribution image for |
---|
| 1500 | // the modality image |
---|
| 1501 | kDose[0].getCenterPosition(fCenter); |
---|
| 1502 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 1503 | ofile.write((char *)iCenter, 3*sizeof(int)); |
---|
| 1504 | if(DEBUG || kVerbose > 0) { |
---|
| 1505 | std::cout << "Dose dist. image relative location : (" |
---|
| 1506 | << iCenter[0] << ", " |
---|
| 1507 | << iCenter[1] << ", " |
---|
| 1508 | << iCenter[2] << ")" << std::endl; |
---|
| 1509 | } |
---|
| 1510 | |
---|
| 1511 | } |
---|
| 1512 | |
---|
| 1513 | //----- ROI image -----// |
---|
| 1514 | if(!isROIEmpty()) { |
---|
| 1515 | // ROI image size |
---|
| 1516 | kRoi[0].getSize(size); |
---|
| 1517 | ofile.write((char *)size, 3*sizeof(int)); |
---|
| 1518 | if(DEBUG || kVerbose > 0) { |
---|
| 1519 | std::cout << "ROI image size : (" |
---|
| 1520 | << size[0] << ", " |
---|
| 1521 | << size[1] << ", " |
---|
| 1522 | << size[2] << ")" |
---|
| 1523 | << std::endl; |
---|
| 1524 | } |
---|
| 1525 | |
---|
| 1526 | // ROI max. & min. |
---|
| 1527 | kRoi[0].getMinMax(minmax); |
---|
| 1528 | ofile.write((char *)minmax, sizeof(short)*2); |
---|
| 1529 | |
---|
| 1530 | // ROI distribution scaling |
---|
| 1531 | scale = (float)kRoi[0].getScale(); |
---|
| 1532 | ofile.write((char *)&scale, sizeof(float)); |
---|
| 1533 | if(DEBUG || kVerbose > 0) { |
---|
| 1534 | std::cout << "ROI image min., max., scale : " |
---|
| 1535 | << minmax[0] << ", " |
---|
| 1536 | << minmax[1] << ", " |
---|
| 1537 | << scale << std::endl; |
---|
| 1538 | } |
---|
| 1539 | |
---|
| 1540 | // ROI image |
---|
| 1541 | int rsize = size[0]*size[1]; |
---|
| 1542 | for(int i = 0; i < size[2]; i++) { |
---|
| 1543 | short * rimage = kRoi[0].getImage(i); |
---|
| 1544 | ofile.write((char *)rimage, rsize*sizeof(short)); |
---|
| 1545 | |
---|
| 1546 | } |
---|
| 1547 | |
---|
| 1548 | // ROI relative location |
---|
| 1549 | kRoi[0].getCenterPosition(fCenter); |
---|
| 1550 | for(int i = 0; i < 3; i++) iCenter[i] = (int)fCenter[i]; |
---|
| 1551 | ofile.write((char *)iCenter, 3*sizeof(int)); |
---|
| 1552 | if(DEBUG || kVerbose > 0) { |
---|
| 1553 | std::cout << "ROI image relative location : (" |
---|
| 1554 | << iCenter[0] << ", " |
---|
| 1555 | << iCenter[1] << ", " |
---|
| 1556 | << iCenter[2] << ")" << std::endl; |
---|
| 1557 | } |
---|
| 1558 | } |
---|
| 1559 | |
---|
| 1560 | |
---|
| 1561 | //----- track information -----// |
---|
| 1562 | // track |
---|
| 1563 | int ntrk = kSteps.size(); |
---|
| 1564 | ofile.write((char *)&ntrk, sizeof(int)); |
---|
| 1565 | if(DEBUG || kVerbose > 0) { |
---|
| 1566 | std::cout << "# of tracks : " |
---|
| 1567 | << ntrk << std::endl; |
---|
| 1568 | } |
---|
| 1569 | for(int i = 0; i < ntrk; i++) { |
---|
| 1570 | float * tp = kSteps[i]; |
---|
| 1571 | ofile.write((char *)tp, sizeof(float)*6); |
---|
| 1572 | } |
---|
| 1573 | |
---|
| 1574 | |
---|
| 1575 | // file end mark |
---|
| 1576 | ofile.write("END", 3); |
---|
| 1577 | |
---|
| 1578 | ofile.close(); |
---|
| 1579 | |
---|
| 1580 | return true; |
---|
| 1581 | } |
---|
| 1582 | // |
---|
| 1583 | bool G4GMocrenIO::storeData2(char * _filename) { |
---|
| 1584 | kFileName = _filename; |
---|
| 1585 | return storeData(); |
---|
| 1586 | } |
---|
| 1587 | |
---|
| 1588 | bool G4GMocrenIO::retrieveData() { |
---|
| 1589 | |
---|
| 1590 | // input file open |
---|
| 1591 | std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary); |
---|
| 1592 | if(!ifile) { |
---|
| 1593 | std::cerr << "Cannot open file: " << kFileName |
---|
| 1594 | << " in G4GMocrenIO::retrieveData()." << std::endl; |
---|
| 1595 | return false; |
---|
| 1596 | } |
---|
| 1597 | |
---|
| 1598 | // file identifier |
---|
| 1599 | char verid[9]; |
---|
| 1600 | ifile.read((char *)verid, 8); |
---|
| 1601 | // file version |
---|
| 1602 | unsigned char ver; |
---|
| 1603 | ifile.read((char *)&ver, 1); |
---|
| 1604 | ifile.close(); |
---|
| 1605 | |
---|
| 1606 | if(std::strncmp(verid, "gMocren", 7) == 0) { |
---|
| 1607 | if(ver == 0x03) { |
---|
| 1608 | std::cout << ">>>>>>> retrieve data (ver.3) <<<<<<<" << std::endl; |
---|
| 1609 | std::cout << " " << kFileName << std::endl; |
---|
| 1610 | retrieveData3(); |
---|
| 1611 | } else if (ver == 0x04) { |
---|
| 1612 | std::cout << ">>>>>>> retrieve data (ver.4) <<<<<<<" << std::endl; |
---|
| 1613 | std::cout << " " << kFileName << std::endl; |
---|
| 1614 | retrieveData4(); |
---|
| 1615 | } else { |
---|
| 1616 | std::cerr << "Error -- invalid file version : " << (int)ver |
---|
| 1617 | << std::endl; |
---|
| 1618 | std::cerr << " " << kFileName << std::endl; |
---|
| 1619 | std::exit(-1); |
---|
| 1620 | } |
---|
| 1621 | } else if(std::strncmp(verid, "GRAPE", 5) == 0) { |
---|
| 1622 | std::cout << ">>>>>>> retrieve data (ver.2) <<<<<<<" << std::endl; |
---|
| 1623 | std::cout << " " << kFileName << std::endl; |
---|
| 1624 | retrieveData2(); |
---|
| 1625 | } else { |
---|
| 1626 | std::cerr << kFileName << " was not gdd file." << std::endl; |
---|
| 1627 | return false; |
---|
| 1628 | } |
---|
| 1629 | |
---|
| 1630 | return true; |
---|
| 1631 | } |
---|
| 1632 | |
---|
| 1633 | bool G4GMocrenIO::retrieveData(char * _filename) { |
---|
| 1634 | kFileName = _filename; |
---|
| 1635 | return retrieveData(); |
---|
| 1636 | } |
---|
| 1637 | |
---|
| 1638 | // |
---|
| 1639 | bool G4GMocrenIO::retrieveData4() { |
---|
| 1640 | |
---|
| 1641 | bool DEBUG = false;// |
---|
| 1642 | |
---|
| 1643 | // input file open |
---|
| 1644 | std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary); |
---|
| 1645 | if(!ifile) { |
---|
| 1646 | std::cerr << "Cannot open file: " << kFileName |
---|
| 1647 | << " in G4GMocrenIO::retrieveData3()." << std::endl; |
---|
| 1648 | return false; |
---|
| 1649 | } |
---|
| 1650 | |
---|
| 1651 | // data buffer |
---|
| 1652 | char ctmp[12]; |
---|
| 1653 | |
---|
| 1654 | // file identifier |
---|
| 1655 | char verid[9]; |
---|
| 1656 | ifile.read((char *)verid, 8); |
---|
| 1657 | |
---|
| 1658 | // file version |
---|
| 1659 | unsigned char ver; |
---|
| 1660 | ifile.read((char *)&ver, 1); |
---|
| 1661 | std::stringstream ss; |
---|
| 1662 | ss << (int)ver; |
---|
| 1663 | kVersion = ss.str(); |
---|
| 1664 | if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl; |
---|
| 1665 | |
---|
| 1666 | // endian |
---|
| 1667 | ifile.read((char *)&kLittleEndianInput, sizeof(char)); |
---|
| 1668 | if(DEBUG || kVerbose > 0) { |
---|
| 1669 | std::cout << "Endian : "; |
---|
| 1670 | if(kLittleEndianInput == 1) |
---|
| 1671 | std::cout << " little" << std::endl; |
---|
| 1672 | else { |
---|
| 1673 | std::cout << " big" << std::endl; |
---|
| 1674 | } |
---|
| 1675 | } |
---|
| 1676 | |
---|
| 1677 | // comment length (fixed size) |
---|
| 1678 | int clength; |
---|
| 1679 | ifile.read((char *)ctmp, 4); |
---|
| 1680 | convertEndian(ctmp, clength); |
---|
| 1681 | // comment |
---|
| 1682 | char cmt[1025]; |
---|
| 1683 | ifile.read((char *)cmt, clength); |
---|
| 1684 | std::string scmt = cmt; |
---|
| 1685 | scmt += '\0'; |
---|
| 1686 | setComment(scmt); |
---|
| 1687 | if(DEBUG || kVerbose > 0) { |
---|
| 1688 | std::cout << "Data comment : " |
---|
| 1689 | << kComment << std::endl; |
---|
| 1690 | } |
---|
| 1691 | |
---|
| 1692 | // voxel spacings for all images |
---|
| 1693 | ifile.read((char *)ctmp, 12); |
---|
| 1694 | convertEndian(ctmp, kVoxelSpacing[0]); |
---|
| 1695 | convertEndian(ctmp+4, kVoxelSpacing[1]); |
---|
| 1696 | convertEndian(ctmp+8, kVoxelSpacing[2]); |
---|
| 1697 | if(DEBUG || kVerbose > 0) { |
---|
| 1698 | std::cout << "Voxel spacing : (" |
---|
| 1699 | << kVoxelSpacing[0] << ", " |
---|
| 1700 | << kVoxelSpacing[1] << ", " |
---|
| 1701 | << kVoxelSpacing[2] |
---|
| 1702 | << ") mm " << std::endl; |
---|
| 1703 | } |
---|
| 1704 | |
---|
| 1705 | |
---|
| 1706 | // offset from file starting point to the modality image data |
---|
| 1707 | ifile.read((char *)ctmp, 4); |
---|
| 1708 | convertEndian(ctmp, kPointerToModalityData); |
---|
| 1709 | |
---|
| 1710 | // # of dose distributions |
---|
| 1711 | ifile.read((char *)ctmp, 4); |
---|
| 1712 | int nDoseDist; |
---|
| 1713 | convertEndian(ctmp, nDoseDist); |
---|
| 1714 | |
---|
| 1715 | // offset from file starting point to the dose image data |
---|
| 1716 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 1717 | ifile.read((char *)ctmp, 4); |
---|
| 1718 | unsigned int dptr; |
---|
| 1719 | convertEndian(ctmp, dptr); |
---|
| 1720 | addPointerToDoseDistData(dptr); |
---|
| 1721 | } |
---|
| 1722 | |
---|
| 1723 | // offset from file starting point to the ROI image data |
---|
| 1724 | ifile.read((char *)ctmp, 4); |
---|
| 1725 | convertEndian(ctmp, kPointerToROIData); |
---|
| 1726 | |
---|
| 1727 | // offset from file starting point to the track data |
---|
| 1728 | ifile.read((char *)ctmp, 4); |
---|
| 1729 | convertEndian(ctmp, kPointerToTrackData); |
---|
| 1730 | |
---|
| 1731 | // offset from file starting point to the detector data |
---|
| 1732 | ifile.read((char *)ctmp, 4); |
---|
| 1733 | convertEndian(ctmp, kPointerToDetectorData); |
---|
| 1734 | |
---|
| 1735 | if(DEBUG || kVerbose > 0) { |
---|
| 1736 | std::cout << "Each pointer to data : " |
---|
| 1737 | << kPointerToModalityData << ", "; |
---|
| 1738 | for(int i = 0; i < nDoseDist; i++) |
---|
| 1739 | std::cout << kPointerToDoseDistData[i] << ", "; |
---|
| 1740 | std::cout << kPointerToROIData << ", " |
---|
| 1741 | << kPointerToTrackData << ", " |
---|
| 1742 | << kPointerToDetectorData |
---|
| 1743 | << std::endl; |
---|
| 1744 | } |
---|
| 1745 | |
---|
| 1746 | |
---|
| 1747 | |
---|
| 1748 | if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 && |
---|
| 1749 | kPointerToROIData == 0 && kPointerToTrackData == 0) { |
---|
| 1750 | if(DEBUG || kVerbose > 0) { |
---|
| 1751 | std::cout << "No data." << std::endl; |
---|
| 1752 | } |
---|
| 1753 | return false; |
---|
| 1754 | } |
---|
| 1755 | |
---|
| 1756 | // event number |
---|
| 1757 | /* ver 1 |
---|
| 1758 | ifile.read(ctmp, sizeof(int)); |
---|
| 1759 | convertEndian(ctmp, numberOfEvents); |
---|
| 1760 | */ |
---|
| 1761 | |
---|
| 1762 | int size[3]; |
---|
| 1763 | float scale; |
---|
| 1764 | double dscale; |
---|
| 1765 | short minmax[2]; |
---|
| 1766 | float fCenter[3]; |
---|
| 1767 | int iCenter[3]; |
---|
| 1768 | |
---|
| 1769 | //----- Modality image -----// |
---|
| 1770 | // modality image size |
---|
| 1771 | ifile.read(ctmp, 3*sizeof(int)); |
---|
| 1772 | convertEndian(ctmp, size[0]); |
---|
| 1773 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 1774 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 1775 | if(DEBUG || kVerbose > 0) { |
---|
| 1776 | std::cout << "Modality image size : (" |
---|
| 1777 | << size[0] << ", " |
---|
| 1778 | << size[1] << ", " |
---|
| 1779 | << size[2] << ")" |
---|
| 1780 | << std::endl; |
---|
| 1781 | } |
---|
| 1782 | kModality.setSize(size); |
---|
| 1783 | |
---|
| 1784 | // modality image voxel spacing |
---|
| 1785 | /* |
---|
| 1786 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 1787 | convertEndian(ctmp, modalityImageVoxelSpacing[0]); |
---|
| 1788 | convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]); |
---|
| 1789 | convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]); |
---|
| 1790 | */ |
---|
| 1791 | |
---|
| 1792 | if(kPointerToModalityData != 0) { |
---|
| 1793 | |
---|
| 1794 | // modality density max. & min. |
---|
| 1795 | ifile.read((char *)ctmp, 4); |
---|
| 1796 | convertEndian(ctmp, minmax[0]); |
---|
| 1797 | convertEndian(ctmp+2, minmax[1]); |
---|
| 1798 | kModality.setMinMax(minmax); |
---|
| 1799 | |
---|
| 1800 | // modality image unit |
---|
| 1801 | char munit[13]; |
---|
| 1802 | munit[12] = '\0'; |
---|
| 1803 | ifile.read((char *)munit, 12); |
---|
| 1804 | std::string smunit = munit; |
---|
| 1805 | setModalityImageUnit(smunit); |
---|
| 1806 | |
---|
| 1807 | // modality density scale |
---|
| 1808 | ifile.read((char *)ctmp, 4); |
---|
| 1809 | convertEndian(ctmp, scale); |
---|
| 1810 | kModality.setScale(dscale = scale); |
---|
| 1811 | if(DEBUG || kVerbose > 0) { |
---|
| 1812 | std::cout << "Modality image min., max., scale : " |
---|
| 1813 | << minmax[0] << ", " |
---|
| 1814 | << minmax[1] << ", " |
---|
| 1815 | << scale << std::endl; |
---|
| 1816 | } |
---|
| 1817 | |
---|
| 1818 | // modality density |
---|
| 1819 | int psize = size[0]*size[1]; |
---|
| 1820 | if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): "; |
---|
| 1821 | char * cimage = new char[psize*sizeof(short)]; |
---|
| 1822 | for(int i = 0; i < size[2]; i++) { |
---|
| 1823 | ifile.read((char *)cimage, psize*sizeof(short)); |
---|
| 1824 | short * mimage = new short[psize]; |
---|
| 1825 | for(int j = 0; j < psize; j++) { |
---|
| 1826 | convertEndian(cimage+j*sizeof(short), mimage[j]); |
---|
| 1827 | } |
---|
| 1828 | kModality.addImage(mimage); |
---|
| 1829 | |
---|
| 1830 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", "; |
---|
| 1831 | } |
---|
| 1832 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1833 | delete [] cimage; |
---|
| 1834 | |
---|
| 1835 | // modality desity map for CT value |
---|
| 1836 | size_t msize = minmax[1]-minmax[0]+1; |
---|
| 1837 | if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl; |
---|
| 1838 | char * pdmap = new char[msize*sizeof(float)]; |
---|
| 1839 | ifile.read((char *)pdmap, msize*sizeof(float)); |
---|
| 1840 | float ftmp; |
---|
| 1841 | for(int i = 0; i < (int)msize; i++) { |
---|
| 1842 | convertEndian(pdmap+i*sizeof(float), ftmp); |
---|
| 1843 | kModalityImageDensityMap.push_back(ftmp); |
---|
| 1844 | } |
---|
| 1845 | if(DEBUG || kVerbose > 0) { |
---|
| 1846 | std::cout << "density map : " << std::ends; |
---|
| 1847 | for(int i = 0; i < 10; i++) |
---|
| 1848 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 1849 | std::cout << std::endl; |
---|
| 1850 | for(int i = 0; i < 10; i++) std::cout << ".."; |
---|
| 1851 | std::cout << std::endl; |
---|
| 1852 | for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++) |
---|
| 1853 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 1854 | std::cout << std::endl; |
---|
| 1855 | } |
---|
| 1856 | |
---|
| 1857 | } |
---|
| 1858 | |
---|
| 1859 | |
---|
| 1860 | //----- dose distribution image -----// |
---|
| 1861 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 1862 | |
---|
| 1863 | newDoseDist(); |
---|
| 1864 | |
---|
| 1865 | // dose distrbution image size |
---|
| 1866 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 1867 | convertEndian(ctmp, size[0]); |
---|
| 1868 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 1869 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 1870 | if(DEBUG || kVerbose > 0) { |
---|
| 1871 | std::cout << "Dose dist. image size : (" |
---|
| 1872 | << size[0] << ", " |
---|
| 1873 | << size[1] << ", " |
---|
| 1874 | << size[2] << ")" |
---|
| 1875 | << std::endl; |
---|
| 1876 | } |
---|
| 1877 | kDose[ndose].setSize(size); |
---|
| 1878 | |
---|
| 1879 | // dose distribution max. & min. |
---|
| 1880 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 1881 | convertEndian(ctmp, minmax[0]); |
---|
| 1882 | convertEndian(ctmp+2, minmax[1]); |
---|
| 1883 | |
---|
| 1884 | // dose distribution unit |
---|
| 1885 | char dunit[13]; |
---|
| 1886 | dunit[12] = '\0'; |
---|
| 1887 | ifile.read((char *)dunit, 12); |
---|
| 1888 | std::string sdunit = dunit; |
---|
| 1889 | setDoseDistUnit(sdunit, ndose); |
---|
| 1890 | if(DEBUG || kVerbose > 0) { |
---|
| 1891 | std::cout << "Dose dist. unit : " << kDoseUnit << std::endl; |
---|
| 1892 | } |
---|
| 1893 | |
---|
| 1894 | // dose distribution scaling |
---|
| 1895 | ifile.read((char *)ctmp, 4); // sizeof(float) |
---|
| 1896 | convertEndian(ctmp, scale); |
---|
| 1897 | kDose[ndose].setScale(dscale = scale); |
---|
| 1898 | |
---|
| 1899 | double dminmax[2]; |
---|
| 1900 | for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale; |
---|
| 1901 | kDose[ndose].setMinMax(dminmax); |
---|
| 1902 | |
---|
| 1903 | if(DEBUG || kVerbose > 0) { |
---|
| 1904 | std::cout << "Dose dist. image min., max., scale : " |
---|
| 1905 | << dminmax[0] << ", " |
---|
| 1906 | << dminmax[1] << ", " |
---|
| 1907 | << scale << std::endl; |
---|
| 1908 | } |
---|
| 1909 | |
---|
| 1910 | // dose distribution image |
---|
| 1911 | int dsize = size[0]*size[1]; |
---|
| 1912 | if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): "; |
---|
| 1913 | char * di = new char[dsize*sizeof(short)]; |
---|
| 1914 | short * shimage = new short[dsize]; |
---|
| 1915 | for(int z = 0; z < size[2]; z++) { |
---|
| 1916 | ifile.read((char *)di, dsize*sizeof(short)); |
---|
| 1917 | double * dimage = new double[dsize]; |
---|
| 1918 | for(int xy = 0; xy < dsize; xy++) { |
---|
| 1919 | convertEndian(di+xy*sizeof(short), shimage[xy]); |
---|
| 1920 | dimage[xy] = shimage[xy]*dscale; |
---|
| 1921 | } |
---|
| 1922 | kDose[ndose].addImage(dimage); |
---|
| 1923 | |
---|
| 1924 | if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", "; |
---|
| 1925 | |
---|
| 1926 | if(DEBUG || kVerbose > 0) { |
---|
| 1927 | for(int j = 0; j < dsize; j++) { |
---|
| 1928 | if(dimage[j] < 0) |
---|
| 1929 | std::cout << "[" << j << "," << z << "]" |
---|
| 1930 | << dimage[j] << ", "; |
---|
| 1931 | } |
---|
| 1932 | } |
---|
| 1933 | } |
---|
| 1934 | delete [] shimage; |
---|
| 1935 | delete [] di; |
---|
| 1936 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 1937 | |
---|
| 1938 | ifile.read((char *)ctmp, 3*4); // 3*sizeof(int) |
---|
| 1939 | convertEndian(ctmp, iCenter[0]); |
---|
| 1940 | convertEndian(ctmp+4, iCenter[1]); |
---|
| 1941 | convertEndian(ctmp+8, iCenter[2]); |
---|
| 1942 | for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i]; |
---|
| 1943 | kDose[ndose].setCenterPosition(fCenter); |
---|
| 1944 | |
---|
| 1945 | if(DEBUG || kVerbose > 0) { |
---|
| 1946 | std::cout << "Dose dist. image relative location : (" |
---|
| 1947 | << fCenter[0] << ", " |
---|
| 1948 | << fCenter[1] << ", " |
---|
| 1949 | << fCenter[2] << ")" << std::endl; |
---|
| 1950 | } |
---|
| 1951 | |
---|
| 1952 | |
---|
| 1953 | // dose distribution name |
---|
| 1954 | char cname[81]; |
---|
| 1955 | ifile.read((char *)cname, 80); |
---|
| 1956 | std::string dosename = cname; |
---|
| 1957 | setDoseDistName(dosename, ndose); |
---|
| 1958 | if(DEBUG || kVerbose > 0) { |
---|
| 1959 | std::cout << "Dose dist. name : " << dosename << std::endl; |
---|
| 1960 | } |
---|
| 1961 | |
---|
| 1962 | } |
---|
| 1963 | |
---|
| 1964 | //----- ROI image -----// |
---|
| 1965 | if(kPointerToROIData != 0) { |
---|
| 1966 | |
---|
| 1967 | newROI(); |
---|
| 1968 | |
---|
| 1969 | // ROI image size |
---|
| 1970 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 1971 | convertEndian(ctmp, size[0]); |
---|
| 1972 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 1973 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 1974 | kRoi[0].setSize(size); |
---|
| 1975 | if(DEBUG || kVerbose > 0) { |
---|
| 1976 | std::cout << "ROI image size : (" |
---|
| 1977 | << size[0] << ", " |
---|
| 1978 | << size[1] << ", " |
---|
| 1979 | << size[2] << ")" |
---|
| 1980 | << std::endl; |
---|
| 1981 | } |
---|
| 1982 | |
---|
| 1983 | // ROI max. & min. |
---|
| 1984 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 1985 | convertEndian(ctmp, minmax[0]); |
---|
| 1986 | convertEndian(ctmp+sizeof(short), minmax[1]); |
---|
| 1987 | kRoi[0].setMinMax(minmax); |
---|
| 1988 | |
---|
| 1989 | // ROI distribution scaling |
---|
| 1990 | ifile.read((char *)ctmp, sizeof(float)); |
---|
| 1991 | convertEndian(ctmp, scale); |
---|
| 1992 | kRoi[0].setScale(dscale = scale); |
---|
| 1993 | if(DEBUG || kVerbose > 0) { |
---|
| 1994 | std::cout << "ROI image min., max., scale : " |
---|
| 1995 | << minmax[0] << ", " |
---|
| 1996 | << minmax[1] << ", " |
---|
| 1997 | << scale << std::endl; |
---|
| 1998 | } |
---|
| 1999 | |
---|
| 2000 | // ROI image |
---|
| 2001 | int rsize = size[0]*size[1]; |
---|
| 2002 | char * ri = new char[rsize*sizeof(short)]; |
---|
| 2003 | for(int i = 0; i < size[2]; i++) { |
---|
| 2004 | ifile.read((char *)ri, rsize*sizeof(short)); |
---|
| 2005 | short * rimage = new short[rsize]; |
---|
| 2006 | for(int j = 0; j < rsize; j++) { |
---|
| 2007 | convertEndian(ri+j*sizeof(short), rimage[j]); |
---|
| 2008 | } |
---|
| 2009 | kRoi[0].addImage(rimage); |
---|
| 2010 | |
---|
| 2011 | } |
---|
| 2012 | delete [] ri; |
---|
| 2013 | |
---|
| 2014 | // ROI relative location |
---|
| 2015 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2016 | convertEndian(ctmp, iCenter[0]); |
---|
| 2017 | convertEndian(ctmp+sizeof(int), iCenter[1]); |
---|
| 2018 | convertEndian(ctmp+2*sizeof(int), iCenter[2]); |
---|
| 2019 | for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i]; |
---|
| 2020 | kRoi[0].setCenterPosition(fCenter); |
---|
| 2021 | if(DEBUG || kVerbose > 0) { |
---|
| 2022 | std::cout << "ROI image relative location : (" |
---|
| 2023 | << fCenter[0] << ", " |
---|
| 2024 | << fCenter[1] << ", " |
---|
| 2025 | << fCenter[2] << ")" << std::endl; |
---|
| 2026 | } |
---|
| 2027 | |
---|
| 2028 | } |
---|
| 2029 | |
---|
| 2030 | //----- track information -----// |
---|
| 2031 | if(kPointerToTrackData != 0) { |
---|
| 2032 | |
---|
| 2033 | // track |
---|
| 2034 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2035 | int ntrk; |
---|
| 2036 | convertEndian(ctmp, ntrk); |
---|
| 2037 | if(DEBUG || kVerbose > 0) { |
---|
| 2038 | std::cout << "# of tracks: " << ntrk << std::endl; |
---|
| 2039 | } |
---|
| 2040 | |
---|
| 2041 | // track position |
---|
| 2042 | unsigned char rgb[3]; |
---|
| 2043 | for(int i = 0; i < ntrk; i++) { |
---|
| 2044 | |
---|
| 2045 | |
---|
| 2046 | // # of steps in a track |
---|
| 2047 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2048 | int nsteps; |
---|
| 2049 | convertEndian(ctmp, nsteps); |
---|
| 2050 | |
---|
| 2051 | // track color |
---|
| 2052 | ifile.read((char *)rgb, 3); |
---|
| 2053 | |
---|
| 2054 | std::vector<float *> steps; |
---|
| 2055 | // steps |
---|
| 2056 | for(int j = 0; j < nsteps; j++) { |
---|
| 2057 | |
---|
| 2058 | float * steppoint = new float[6]; |
---|
| 2059 | ifile.read((char *)ctmp, sizeof(float)*6); |
---|
| 2060 | |
---|
| 2061 | for(int k = 0; k < 6; k++) { |
---|
| 2062 | convertEndian(ctmp+k*sizeof(float), steppoint[k]); |
---|
| 2063 | } |
---|
| 2064 | |
---|
| 2065 | steps.push_back(steppoint); |
---|
| 2066 | } |
---|
| 2067 | |
---|
| 2068 | // add a track to the track container |
---|
| 2069 | addTrack(steps, rgb); |
---|
| 2070 | |
---|
| 2071 | if(DEBUG || kVerbose > 0) { |
---|
| 2072 | if(i < 5) { |
---|
| 2073 | std::cout << i << ": " ; |
---|
| 2074 | for(int j = 0; j < 3; j++) std::cout << steps[0][j] << " "; |
---|
| 2075 | int nstp = steps.size(); |
---|
| 2076 | std::cout << "<-> "; |
---|
| 2077 | for(int j = 3; j < 6; j++) std::cout << steps[nstp-1][j] << " "; |
---|
| 2078 | std::cout << " rgb( "; |
---|
| 2079 | for(int j = 0; j < 3; j++) std::cout << (int)rgb[j] << " "; |
---|
| 2080 | std::cout << ")" << std::endl; |
---|
| 2081 | } |
---|
| 2082 | } |
---|
| 2083 | } |
---|
| 2084 | |
---|
| 2085 | |
---|
| 2086 | } |
---|
| 2087 | |
---|
| 2088 | |
---|
| 2089 | //----- detector information -----// |
---|
| 2090 | if(kPointerToDetectorData != 0) { |
---|
| 2091 | |
---|
| 2092 | // number of detectors |
---|
| 2093 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2094 | int ndet; |
---|
| 2095 | convertEndian(ctmp, ndet); |
---|
| 2096 | |
---|
| 2097 | if(DEBUG || kVerbose > 0) { |
---|
| 2098 | std::cout << "# of detectors : " |
---|
| 2099 | << ndet << std::endl; |
---|
| 2100 | } |
---|
| 2101 | |
---|
| 2102 | for(int nd = 0; nd < ndet; nd++) { |
---|
| 2103 | |
---|
| 2104 | // # of edges of a detector |
---|
| 2105 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2106 | int nedges; |
---|
| 2107 | convertEndian(ctmp, nedges); |
---|
| 2108 | if(DEBUG || kVerbose > 0) { |
---|
| 2109 | std::cout << "# of edges in a detector : " << nedges << std::endl; |
---|
| 2110 | } |
---|
| 2111 | |
---|
| 2112 | // edges |
---|
| 2113 | std::vector<float *> detector; |
---|
| 2114 | char cftmp[24]; |
---|
| 2115 | for(int ne = 0; ne < nedges; ne++) { |
---|
| 2116 | |
---|
| 2117 | ifile.read((char *)cftmp, sizeof(float)*6); |
---|
| 2118 | float * edgePoints = new float[6]; |
---|
| 2119 | for(int j = 0; j < 6; j++) convertEndian(&cftmp[sizeof(float)*j], edgePoints[j]); |
---|
| 2120 | detector.push_back(edgePoints); |
---|
| 2121 | |
---|
| 2122 | } |
---|
| 2123 | |
---|
| 2124 | if(DEBUG || kVerbose > 0) { |
---|
| 2125 | std::cout << " first edge : (" << detector[0][0] << ", " |
---|
| 2126 | << detector[0][1] << ", " |
---|
| 2127 | << detector[0][2] << ") - (" |
---|
| 2128 | << detector[0][3] << ", " |
---|
| 2129 | << detector[0][4] << ", " |
---|
| 2130 | << detector[0][5] << ")" << std::endl; |
---|
| 2131 | } |
---|
| 2132 | |
---|
| 2133 | // detector color |
---|
| 2134 | unsigned char dcolor[3]; |
---|
| 2135 | ifile.read((char *)dcolor, 3); |
---|
| 2136 | if(DEBUG || kVerbose > 0) { |
---|
| 2137 | std::cout << " detector color : rgb(" |
---|
| 2138 | << (int)dcolor[0] << ", " |
---|
| 2139 | << (int)dcolor[1] << ", " |
---|
| 2140 | << (int)dcolor[2] << std::endl; |
---|
| 2141 | } |
---|
| 2142 | |
---|
| 2143 | |
---|
| 2144 | // detector name |
---|
| 2145 | char cname[80]; |
---|
| 2146 | ifile.read((char *)cname, 80); |
---|
| 2147 | std::string dname = cname; |
---|
| 2148 | if(DEBUG || kVerbose > 0) { |
---|
| 2149 | std::cout << " detector name : " << dname << std::endl; |
---|
| 2150 | } |
---|
| 2151 | |
---|
| 2152 | |
---|
| 2153 | addDetector(dname, detector, dcolor); |
---|
| 2154 | |
---|
| 2155 | } |
---|
| 2156 | } |
---|
| 2157 | |
---|
| 2158 | |
---|
| 2159 | ifile.close(); |
---|
| 2160 | |
---|
| 2161 | return true; |
---|
| 2162 | } |
---|
| 2163 | bool G4GMocrenIO::retrieveData4(char * _filename) { |
---|
| 2164 | kFileName = _filename; |
---|
| 2165 | return retrieveData(); |
---|
| 2166 | } |
---|
| 2167 | |
---|
| 2168 | // |
---|
| 2169 | bool G4GMocrenIO::retrieveData3() { |
---|
| 2170 | |
---|
| 2171 | bool DEBUG = false;// |
---|
| 2172 | |
---|
| 2173 | // input file open |
---|
| 2174 | std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary); |
---|
| 2175 | if(!ifile) { |
---|
| 2176 | std::cerr << "Cannot open file: " << kFileName |
---|
| 2177 | << " in G4GMocrenIO::retrieveData3()." << std::endl; |
---|
| 2178 | return false; |
---|
| 2179 | } |
---|
| 2180 | |
---|
| 2181 | // data buffer |
---|
| 2182 | char ctmp[12]; |
---|
| 2183 | |
---|
| 2184 | // file identifier |
---|
| 2185 | char verid[9]; |
---|
| 2186 | ifile.read((char *)verid, 8); |
---|
| 2187 | |
---|
| 2188 | // file version |
---|
| 2189 | unsigned char ver; |
---|
| 2190 | ifile.read((char *)&ver, 1); |
---|
| 2191 | std::stringstream ss; |
---|
| 2192 | ss << (int)ver; |
---|
| 2193 | kVersion = ss.str(); |
---|
| 2194 | if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl; |
---|
| 2195 | |
---|
| 2196 | // endian |
---|
| 2197 | ifile.read((char *)&kLittleEndianInput, sizeof(char)); |
---|
| 2198 | if(DEBUG || kVerbose > 0) { |
---|
| 2199 | std::cout << "Endian : "; |
---|
| 2200 | if(kLittleEndianInput == 1) |
---|
| 2201 | std::cout << " little" << std::endl; |
---|
| 2202 | else { |
---|
| 2203 | std::cout << " big" << std::endl; |
---|
| 2204 | } |
---|
| 2205 | } |
---|
| 2206 | |
---|
| 2207 | // comment length (fixed size) |
---|
| 2208 | int clength; |
---|
| 2209 | ifile.read((char *)ctmp, 4); |
---|
| 2210 | convertEndian(ctmp, clength); |
---|
| 2211 | // comment |
---|
| 2212 | char cmt[1025]; |
---|
| 2213 | ifile.read((char *)cmt, clength); |
---|
| 2214 | std::string scmt = cmt; |
---|
| 2215 | setComment(scmt); |
---|
| 2216 | if(DEBUG || kVerbose > 0) { |
---|
| 2217 | std::cout << "Data comment : " |
---|
| 2218 | << kComment << std::endl; |
---|
| 2219 | } |
---|
| 2220 | |
---|
| 2221 | // voxel spacings for all images |
---|
| 2222 | ifile.read((char *)ctmp, 12); |
---|
| 2223 | convertEndian(ctmp, kVoxelSpacing[0]); |
---|
| 2224 | convertEndian(ctmp+4, kVoxelSpacing[1]); |
---|
| 2225 | convertEndian(ctmp+8, kVoxelSpacing[2]); |
---|
| 2226 | if(DEBUG || kVerbose > 0) { |
---|
| 2227 | std::cout << "Voxel spacing : (" |
---|
| 2228 | << kVoxelSpacing[0] << ", " |
---|
| 2229 | << kVoxelSpacing[1] << ", " |
---|
| 2230 | << kVoxelSpacing[2] |
---|
| 2231 | << ") mm " << std::endl; |
---|
| 2232 | } |
---|
| 2233 | |
---|
| 2234 | |
---|
| 2235 | // offset from file starting point to the modality image data |
---|
| 2236 | ifile.read((char *)ctmp, 4); |
---|
| 2237 | convertEndian(ctmp, kPointerToModalityData); |
---|
| 2238 | |
---|
| 2239 | // # of dose distributions |
---|
| 2240 | ifile.read((char *)ctmp, 4); |
---|
| 2241 | int nDoseDist; |
---|
| 2242 | convertEndian(ctmp, nDoseDist); |
---|
| 2243 | |
---|
| 2244 | // offset from file starting point to the dose image data |
---|
| 2245 | for(int i = 0; i < nDoseDist; i++) { |
---|
| 2246 | ifile.read((char *)ctmp, 4); |
---|
| 2247 | unsigned int dptr; |
---|
| 2248 | convertEndian(ctmp, dptr); |
---|
| 2249 | addPointerToDoseDistData(dptr); |
---|
| 2250 | } |
---|
| 2251 | |
---|
| 2252 | // offset from file starting point to the ROI image data |
---|
| 2253 | ifile.read((char *)ctmp, 4); |
---|
| 2254 | convertEndian(ctmp, kPointerToROIData); |
---|
| 2255 | |
---|
| 2256 | // offset from file starting point to the track data |
---|
| 2257 | ifile.read((char *)ctmp, 4); |
---|
| 2258 | convertEndian(ctmp, kPointerToTrackData); |
---|
| 2259 | if(DEBUG || kVerbose > 0) { |
---|
| 2260 | std::cout << "Each pointer to data : " |
---|
| 2261 | << kPointerToModalityData << ", "; |
---|
| 2262 | for(int i = 0; i < nDoseDist; i++) |
---|
| 2263 | std::cout << kPointerToDoseDistData[0] << ", "; |
---|
| 2264 | std::cout << kPointerToROIData << ", " |
---|
| 2265 | << kPointerToTrackData << std::endl; |
---|
| 2266 | } |
---|
| 2267 | |
---|
| 2268 | if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 && |
---|
| 2269 | kPointerToROIData == 0 && kPointerToTrackData == 0) { |
---|
| 2270 | if(DEBUG || kVerbose > 0) { |
---|
| 2271 | std::cout << "No data." << std::endl; |
---|
| 2272 | } |
---|
| 2273 | return false; |
---|
| 2274 | } |
---|
| 2275 | |
---|
| 2276 | // event number |
---|
| 2277 | /* ver 1 |
---|
| 2278 | ifile.read(ctmp, sizeof(int)); |
---|
| 2279 | convertEndian(ctmp, numberOfEvents); |
---|
| 2280 | */ |
---|
| 2281 | |
---|
| 2282 | int size[3]; |
---|
| 2283 | float scale; |
---|
| 2284 | double dscale; |
---|
| 2285 | short minmax[2]; |
---|
| 2286 | float fCenter[3]; |
---|
| 2287 | int iCenter[3]; |
---|
| 2288 | |
---|
| 2289 | //----- Modality image -----// |
---|
| 2290 | // modality image size |
---|
| 2291 | ifile.read(ctmp, 3*sizeof(int)); |
---|
| 2292 | convertEndian(ctmp, size[0]); |
---|
| 2293 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2294 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2295 | if(DEBUG || kVerbose > 0) { |
---|
| 2296 | std::cout << "Modality image size : (" |
---|
| 2297 | << size[0] << ", " |
---|
| 2298 | << size[1] << ", " |
---|
| 2299 | << size[2] << ")" |
---|
| 2300 | << std::endl; |
---|
| 2301 | } |
---|
| 2302 | kModality.setSize(size); |
---|
| 2303 | |
---|
| 2304 | // modality image voxel spacing |
---|
| 2305 | /* |
---|
| 2306 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 2307 | convertEndian(ctmp, modalityImageVoxelSpacing[0]); |
---|
| 2308 | convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]); |
---|
| 2309 | convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]); |
---|
| 2310 | */ |
---|
| 2311 | |
---|
| 2312 | if(kPointerToModalityData != 0) { |
---|
| 2313 | |
---|
| 2314 | // modality density max. & min. |
---|
| 2315 | ifile.read((char *)ctmp, 4); |
---|
| 2316 | convertEndian(ctmp, minmax[0]); |
---|
| 2317 | convertEndian(ctmp+2, minmax[1]); |
---|
| 2318 | kModality.setMinMax(minmax); |
---|
| 2319 | |
---|
| 2320 | // modality image unit |
---|
| 2321 | char munit[13]; |
---|
| 2322 | ifile.read((char *)munit, 12); |
---|
| 2323 | std::string smunit = munit; |
---|
| 2324 | setModalityImageUnit(smunit); |
---|
| 2325 | |
---|
| 2326 | // modality density scale |
---|
| 2327 | ifile.read((char *)ctmp, 4); |
---|
| 2328 | convertEndian(ctmp, scale); |
---|
| 2329 | kModality.setScale(dscale = scale); |
---|
| 2330 | if(DEBUG || kVerbose > 0) { |
---|
| 2331 | std::cout << "Modality image min., max., scale : " |
---|
| 2332 | << minmax[0] << ", " |
---|
| 2333 | << minmax[1] << ", " |
---|
| 2334 | << scale << std::endl; |
---|
| 2335 | } |
---|
| 2336 | |
---|
| 2337 | // modality density |
---|
| 2338 | int psize = size[0]*size[1]; |
---|
| 2339 | if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): "; |
---|
| 2340 | char * cimage = new char[psize*sizeof(short)]; |
---|
| 2341 | for(int i = 0; i < size[2]; i++) { |
---|
| 2342 | ifile.read((char *)cimage, psize*sizeof(short)); |
---|
| 2343 | short * mimage = new short[psize]; |
---|
| 2344 | for(int j = 0; j < psize; j++) { |
---|
| 2345 | convertEndian(cimage+j*sizeof(short), mimage[j]); |
---|
| 2346 | } |
---|
| 2347 | kModality.addImage(mimage); |
---|
| 2348 | |
---|
| 2349 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", "; |
---|
| 2350 | } |
---|
| 2351 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 2352 | delete [] cimage; |
---|
| 2353 | |
---|
| 2354 | // modality desity map for CT value |
---|
| 2355 | size_t msize = minmax[1]-minmax[0]+1; |
---|
| 2356 | if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl; |
---|
| 2357 | char * pdmap = new char[msize*sizeof(float)]; |
---|
| 2358 | ifile.read((char *)pdmap, msize*sizeof(float)); |
---|
| 2359 | float ftmp; |
---|
| 2360 | for(int i = 0; i < (int)msize; i++) { |
---|
| 2361 | convertEndian(pdmap+i*sizeof(float), ftmp); |
---|
| 2362 | kModalityImageDensityMap.push_back(ftmp); |
---|
| 2363 | } |
---|
| 2364 | if(DEBUG || kVerbose > 0) { |
---|
| 2365 | std::cout << "density map : " << std::ends; |
---|
| 2366 | for(int i = 0; i < 10; i++) |
---|
| 2367 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 2368 | std::cout << std::endl; |
---|
| 2369 | for(int i = 0; i < 10; i++) std::cout << ".."; |
---|
| 2370 | std::cout << std::endl; |
---|
| 2371 | for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++) |
---|
| 2372 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 2373 | std::cout << std::endl; |
---|
| 2374 | } |
---|
| 2375 | |
---|
| 2376 | } |
---|
| 2377 | |
---|
| 2378 | |
---|
| 2379 | //----- dose distribution image -----// |
---|
| 2380 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 2381 | |
---|
| 2382 | newDoseDist(); |
---|
| 2383 | |
---|
| 2384 | // dose distrbution image size |
---|
| 2385 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2386 | convertEndian(ctmp, size[0]); |
---|
| 2387 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2388 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2389 | if(DEBUG || kVerbose > 0) { |
---|
| 2390 | std::cout << "Dose dist. image size : (" |
---|
| 2391 | << size[0] << ", " |
---|
| 2392 | << size[1] << ", " |
---|
| 2393 | << size[2] << ")" |
---|
| 2394 | << std::endl; |
---|
| 2395 | } |
---|
| 2396 | kDose[ndose].setSize(size); |
---|
| 2397 | |
---|
| 2398 | // dose distribution max. & min. |
---|
| 2399 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 2400 | convertEndian(ctmp, minmax[0]); |
---|
| 2401 | convertEndian(ctmp+2, minmax[1]); |
---|
| 2402 | |
---|
| 2403 | // dose distribution unit |
---|
| 2404 | char dunit[13]; |
---|
| 2405 | ifile.read((char *)dunit, 12); |
---|
| 2406 | std::string sdunit = dunit; |
---|
| 2407 | setDoseDistUnit(sdunit, ndose); |
---|
| 2408 | if(DEBUG || kVerbose > 0) { |
---|
| 2409 | std::cout << "Dose dist. unit : " << kDoseUnit << std::endl; |
---|
| 2410 | } |
---|
| 2411 | |
---|
| 2412 | // dose distribution scaling |
---|
| 2413 | ifile.read((char *)ctmp, 4); // sizeof(float) |
---|
| 2414 | convertEndian(ctmp, scale); |
---|
| 2415 | kDose[ndose].setScale(dscale = scale); |
---|
| 2416 | |
---|
| 2417 | double dminmax[2]; |
---|
| 2418 | for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale; |
---|
| 2419 | kDose[ndose].setMinMax(dminmax); |
---|
| 2420 | |
---|
| 2421 | if(DEBUG || kVerbose > 0) { |
---|
| 2422 | std::cout << "Dose dist. image min., max., scale : " |
---|
| 2423 | << dminmax[0] << ", " |
---|
| 2424 | << dminmax[1] << ", " |
---|
| 2425 | << scale << std::endl; |
---|
| 2426 | } |
---|
| 2427 | |
---|
| 2428 | // dose distribution image |
---|
| 2429 | int dsize = size[0]*size[1]; |
---|
| 2430 | if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): "; |
---|
| 2431 | char * di = new char[dsize*sizeof(short)]; |
---|
| 2432 | short * shimage = new short[dsize]; |
---|
| 2433 | for(int z = 0; z < size[2]; z++) { |
---|
| 2434 | ifile.read((char *)di, dsize*sizeof(short)); |
---|
| 2435 | double * dimage = new double[dsize]; |
---|
| 2436 | for(int xy = 0; xy < dsize; xy++) { |
---|
| 2437 | convertEndian(di+xy*sizeof(short), shimage[xy]); |
---|
| 2438 | dimage[xy] = shimage[xy]*dscale; |
---|
| 2439 | } |
---|
| 2440 | kDose[ndose].addImage(dimage); |
---|
| 2441 | |
---|
| 2442 | if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", "; |
---|
| 2443 | |
---|
| 2444 | if(DEBUG || kVerbose > 0) { |
---|
| 2445 | for(int j = 0; j < dsize; j++) { |
---|
| 2446 | if(dimage[j] < 0) |
---|
| 2447 | std::cout << "[" << j << "," << z << "]" |
---|
| 2448 | << dimage[j] << ", "; |
---|
| 2449 | } |
---|
| 2450 | } |
---|
| 2451 | } |
---|
| 2452 | delete [] shimage; |
---|
| 2453 | delete [] di; |
---|
| 2454 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 2455 | |
---|
| 2456 | ifile.read((char *)ctmp, 3*4); // 3*sizeof(int) |
---|
| 2457 | convertEndian(ctmp, iCenter[0]); |
---|
| 2458 | convertEndian(ctmp+4, iCenter[1]); |
---|
| 2459 | convertEndian(ctmp+8, iCenter[2]); |
---|
| 2460 | for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i]; |
---|
| 2461 | kDose[ndose].setCenterPosition(fCenter); |
---|
| 2462 | |
---|
| 2463 | if(DEBUG || kVerbose > 0) { |
---|
| 2464 | std::cout << "Dose dist. image relative location : (" |
---|
| 2465 | << fCenter[0] << ", " |
---|
| 2466 | << fCenter[1] << ", " |
---|
| 2467 | << fCenter[2] << ")" << std::endl; |
---|
| 2468 | } |
---|
| 2469 | |
---|
| 2470 | |
---|
| 2471 | } |
---|
| 2472 | |
---|
| 2473 | //----- ROI image -----// |
---|
| 2474 | if(kPointerToROIData != 0) { |
---|
| 2475 | |
---|
| 2476 | newROI(); |
---|
| 2477 | |
---|
| 2478 | // ROI image size |
---|
| 2479 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2480 | convertEndian(ctmp, size[0]); |
---|
| 2481 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2482 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2483 | kRoi[0].setSize(size); |
---|
| 2484 | if(DEBUG || kVerbose > 0) { |
---|
| 2485 | std::cout << "ROI image size : (" |
---|
| 2486 | << size[0] << ", " |
---|
| 2487 | << size[1] << ", " |
---|
| 2488 | << size[2] << ")" |
---|
| 2489 | << std::endl; |
---|
| 2490 | } |
---|
| 2491 | |
---|
| 2492 | // ROI max. & min. |
---|
| 2493 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 2494 | convertEndian(ctmp, minmax[0]); |
---|
| 2495 | convertEndian(ctmp+sizeof(short), minmax[1]); |
---|
| 2496 | kRoi[0].setMinMax(minmax); |
---|
| 2497 | |
---|
| 2498 | // ROI distribution scaling |
---|
| 2499 | ifile.read((char *)ctmp, sizeof(float)); |
---|
| 2500 | convertEndian(ctmp, scale); |
---|
| 2501 | kRoi[0].setScale(dscale = scale); |
---|
| 2502 | if(DEBUG || kVerbose > 0) { |
---|
| 2503 | std::cout << "ROI image min., max., scale : " |
---|
| 2504 | << minmax[0] << ", " |
---|
| 2505 | << minmax[1] << ", " |
---|
| 2506 | << scale << std::endl; |
---|
| 2507 | } |
---|
| 2508 | |
---|
| 2509 | // ROI image |
---|
| 2510 | int rsize = size[0]*size[1]; |
---|
| 2511 | char * ri = new char[rsize*sizeof(short)]; |
---|
| 2512 | for(int i = 0; i < size[2]; i++) { |
---|
| 2513 | ifile.read((char *)ri, rsize*sizeof(short)); |
---|
| 2514 | short * rimage = new short[rsize]; |
---|
| 2515 | for(int j = 0; j < rsize; j++) { |
---|
| 2516 | convertEndian(ri+j*sizeof(short), rimage[j]); |
---|
| 2517 | } |
---|
| 2518 | kRoi[0].addImage(rimage); |
---|
| 2519 | |
---|
| 2520 | } |
---|
| 2521 | delete [] ri; |
---|
| 2522 | |
---|
| 2523 | // ROI relative location |
---|
| 2524 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2525 | convertEndian(ctmp, iCenter[0]); |
---|
| 2526 | convertEndian(ctmp+sizeof(int), iCenter[1]); |
---|
| 2527 | convertEndian(ctmp+2*sizeof(int), iCenter[2]); |
---|
| 2528 | for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i]; |
---|
| 2529 | kRoi[0].setCenterPosition(fCenter); |
---|
| 2530 | if(DEBUG || kVerbose > 0) { |
---|
| 2531 | std::cout << "ROI image relative location : (" |
---|
| 2532 | << fCenter[0] << ", " |
---|
| 2533 | << fCenter[1] << ", " |
---|
| 2534 | << fCenter[2] << ")" << std::endl; |
---|
| 2535 | } |
---|
| 2536 | |
---|
| 2537 | } |
---|
| 2538 | |
---|
| 2539 | //----- track information -----// |
---|
| 2540 | if(kPointerToTrackData != 0) { |
---|
| 2541 | |
---|
| 2542 | // track |
---|
| 2543 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2544 | int ntrk; |
---|
| 2545 | convertEndian(ctmp, ntrk); |
---|
| 2546 | if(DEBUG || kVerbose > 0) { |
---|
| 2547 | std::cout << "# of tracks: " << ntrk << std::endl; |
---|
| 2548 | } |
---|
| 2549 | |
---|
| 2550 | // v4 |
---|
| 2551 | std::vector<float *> trkv4; |
---|
| 2552 | |
---|
| 2553 | // track position |
---|
| 2554 | for(int i = 0; i < ntrk; i++) { |
---|
| 2555 | float * tp = new float[6]; |
---|
| 2556 | |
---|
| 2557 | ifile.read((char *)ctmp, sizeof(float)*3); |
---|
| 2558 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << i << ": " ; |
---|
| 2559 | for(int j = 0; j < 3; j++) { |
---|
| 2560 | convertEndian(ctmp+j*sizeof(float), tp[j]); |
---|
| 2561 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j] << ", "; |
---|
| 2562 | } |
---|
| 2563 | |
---|
| 2564 | ifile.read((char *)ctmp, sizeof(float)*3); |
---|
| 2565 | for(int j = 0; j < 3; j++) { |
---|
| 2566 | convertEndian(ctmp+j*sizeof(float), tp[j+3]); |
---|
| 2567 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j+3] << ", "; |
---|
| 2568 | } |
---|
| 2569 | addTrack(tp); |
---|
| 2570 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << std::endl; |
---|
| 2571 | |
---|
| 2572 | // v4 |
---|
| 2573 | trkv4.push_back(tp); |
---|
| 2574 | } |
---|
| 2575 | |
---|
| 2576 | //v4 |
---|
| 2577 | unsigned char trkcolorv4[3]; |
---|
| 2578 | |
---|
| 2579 | // track color |
---|
| 2580 | for(int i = 0; i < ntrk; i++) { |
---|
| 2581 | unsigned char * rgb = new unsigned char[3]; |
---|
| 2582 | ifile.read((char *)rgb, 3); |
---|
| 2583 | addTrackColor(rgb); |
---|
| 2584 | |
---|
| 2585 | // v4 |
---|
| 2586 | for(int j = 0; j < 3; j++) trkcolorv4[j] = rgb[j]; |
---|
| 2587 | std::vector<float *> trk; |
---|
| 2588 | trk.push_back(trkv4[i]); |
---|
| 2589 | addTrack(trk, trkcolorv4); |
---|
| 2590 | |
---|
| 2591 | } |
---|
| 2592 | |
---|
| 2593 | } |
---|
| 2594 | |
---|
| 2595 | ifile.close(); |
---|
| 2596 | |
---|
| 2597 | return true; |
---|
| 2598 | } |
---|
| 2599 | bool G4GMocrenIO::retrieveData3(char * _filename) { |
---|
| 2600 | kFileName = _filename; |
---|
| 2601 | return retrieveData(); |
---|
| 2602 | } |
---|
| 2603 | |
---|
| 2604 | // |
---|
| 2605 | bool G4GMocrenIO::retrieveData2() { |
---|
| 2606 | |
---|
| 2607 | bool DEBUG = false;// |
---|
| 2608 | |
---|
| 2609 | // input file open |
---|
| 2610 | std::ifstream ifile(kFileName.c_str(), std::ios_base::in|std::ios_base::binary); |
---|
| 2611 | if(!ifile) { |
---|
| 2612 | std::cerr << "Cannot open file: " << kFileName |
---|
| 2613 | << " in G4GMocrenIO::retrieveData2()." << std::endl; |
---|
| 2614 | return false; |
---|
| 2615 | } |
---|
| 2616 | |
---|
| 2617 | // data buffer |
---|
| 2618 | char ctmp[12]; |
---|
| 2619 | |
---|
| 2620 | // file identifier |
---|
| 2621 | char verid[9]; |
---|
| 2622 | ifile.read((char *)verid, 8); |
---|
| 2623 | |
---|
| 2624 | // file version |
---|
| 2625 | unsigned char ver; |
---|
| 2626 | ifile.read((char *)&ver, 1); |
---|
| 2627 | std::stringstream ss; |
---|
| 2628 | ss << (int)ver; |
---|
| 2629 | kVersion = ss.str(); |
---|
| 2630 | if(DEBUG || kVerbose > 0) std::cout << "File version : " << kVersion << std::endl; |
---|
| 2631 | |
---|
| 2632 | // id of version 1 |
---|
| 2633 | char idtmp[IDLENGTH]; |
---|
| 2634 | ifile.read((char *)idtmp, IDLENGTH); |
---|
| 2635 | kId = idtmp; |
---|
| 2636 | // version of version 1 |
---|
| 2637 | char vertmp[VERLENGTH]; |
---|
| 2638 | ifile.read((char *)vertmp, VERLENGTH); |
---|
| 2639 | |
---|
| 2640 | // endian |
---|
| 2641 | ifile.read((char *)&kLittleEndianInput, sizeof(char)); |
---|
| 2642 | if(DEBUG || kVerbose > 0) { |
---|
| 2643 | std::cout << "Endian : "; |
---|
| 2644 | if(kLittleEndianInput == 1) |
---|
| 2645 | std::cout << " little" << std::endl; |
---|
| 2646 | else { |
---|
| 2647 | std::cout << " big" << std::endl; |
---|
| 2648 | } |
---|
| 2649 | } |
---|
| 2650 | |
---|
| 2651 | // voxel spacings for all images |
---|
| 2652 | ifile.read((char *)ctmp, 12); |
---|
| 2653 | convertEndian(ctmp, kVoxelSpacing[0]); |
---|
| 2654 | convertEndian(ctmp+4, kVoxelSpacing[1]); |
---|
| 2655 | convertEndian(ctmp+8, kVoxelSpacing[2]); |
---|
| 2656 | if(DEBUG || kVerbose > 0) { |
---|
| 2657 | std::cout << "Voxel spacing : (" |
---|
| 2658 | << kVoxelSpacing[0] << ", " |
---|
| 2659 | << kVoxelSpacing[1] << ", " |
---|
| 2660 | << kVoxelSpacing[2] |
---|
| 2661 | << ") mm " << std::endl; |
---|
| 2662 | } |
---|
| 2663 | |
---|
| 2664 | |
---|
| 2665 | // offset from file starting point to the modality image data |
---|
| 2666 | ifile.read((char *)ctmp, 4); |
---|
| 2667 | convertEndian(ctmp, kPointerToModalityData); |
---|
| 2668 | |
---|
| 2669 | // offset from file starting point to the dose image data |
---|
| 2670 | unsigned int ptddd; |
---|
| 2671 | ifile.read((char *)ctmp, 4); |
---|
| 2672 | convertEndian(ctmp, ptddd); |
---|
| 2673 | kPointerToDoseDistData.push_back(ptddd); |
---|
| 2674 | |
---|
| 2675 | // offset from file starting point to the ROI image data |
---|
| 2676 | ifile.read((char *)ctmp, 4); |
---|
| 2677 | convertEndian(ctmp, kPointerToROIData); |
---|
| 2678 | |
---|
| 2679 | // offset from file starting point to the track data |
---|
| 2680 | ifile.read((char *)ctmp, 4); |
---|
| 2681 | convertEndian(ctmp, kPointerToTrackData); |
---|
| 2682 | if(DEBUG || kVerbose > 0) { |
---|
| 2683 | std::cout << "Each pointer to data : " |
---|
| 2684 | << kPointerToModalityData << ", " |
---|
| 2685 | << kPointerToDoseDistData[0] << ", " |
---|
| 2686 | << kPointerToROIData << ", " |
---|
| 2687 | << kPointerToTrackData << std::endl; |
---|
| 2688 | } |
---|
| 2689 | |
---|
| 2690 | if(kPointerToModalityData == 0 && kPointerToDoseDistData.size() == 0 && |
---|
| 2691 | kPointerToROIData == 0 && kPointerToTrackData == 0) { |
---|
| 2692 | if(DEBUG || kVerbose > 0) { |
---|
| 2693 | std::cout << "No data." << std::endl; |
---|
| 2694 | } |
---|
| 2695 | return false; |
---|
| 2696 | } |
---|
| 2697 | |
---|
| 2698 | // event number |
---|
| 2699 | /* ver 1 |
---|
| 2700 | ifile.read(ctmp, sizeof(int)); |
---|
| 2701 | convertEndian(ctmp, numberOfEvents); |
---|
| 2702 | */ |
---|
| 2703 | |
---|
| 2704 | int size[3]; |
---|
| 2705 | float scale; |
---|
| 2706 | double dscale; |
---|
| 2707 | short minmax[2]; |
---|
| 2708 | float fCenter[3]; |
---|
| 2709 | int iCenter[3]; |
---|
| 2710 | |
---|
| 2711 | //----- Modality image -----// |
---|
| 2712 | // modality image size |
---|
| 2713 | ifile.read(ctmp, 3*sizeof(int)); |
---|
| 2714 | convertEndian(ctmp, size[0]); |
---|
| 2715 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2716 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2717 | if(DEBUG || kVerbose > 0) { |
---|
| 2718 | std::cout << "Modality image size : (" |
---|
| 2719 | << size[0] << ", " |
---|
| 2720 | << size[1] << ", " |
---|
| 2721 | << size[2] << ")" |
---|
| 2722 | << std::endl; |
---|
| 2723 | } |
---|
| 2724 | kModality.setSize(size); |
---|
| 2725 | |
---|
| 2726 | // modality image voxel spacing |
---|
| 2727 | /* |
---|
| 2728 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 2729 | convertEndian(ctmp, modalityImageVoxelSpacing[0]); |
---|
| 2730 | convertEndian(ctmp+sizeof(float), modalityImageVoxelSpacing[1]); |
---|
| 2731 | convertEndian(ctmp+2*sizeof(float), modalityImageVoxelSpacing[2]); |
---|
| 2732 | */ |
---|
| 2733 | |
---|
| 2734 | if(kPointerToModalityData != 0) { |
---|
| 2735 | |
---|
| 2736 | // modality density max. & min. |
---|
| 2737 | ifile.read((char *)ctmp, 4); |
---|
| 2738 | convertEndian(ctmp, minmax[0]); |
---|
| 2739 | convertEndian(ctmp+2, minmax[1]); |
---|
| 2740 | kModality.setMinMax(minmax); |
---|
| 2741 | |
---|
| 2742 | // modality density scale |
---|
| 2743 | ifile.read((char *)ctmp, 4); |
---|
| 2744 | convertEndian(ctmp, scale); |
---|
| 2745 | kModality.setScale(dscale = scale); |
---|
| 2746 | if(DEBUG || kVerbose > 0) { |
---|
| 2747 | std::cout << "Modality image min., max., scale : " |
---|
| 2748 | << minmax[0] << ", " |
---|
| 2749 | << minmax[1] << ", " |
---|
| 2750 | << scale << std::endl; |
---|
| 2751 | } |
---|
| 2752 | |
---|
| 2753 | // modality density |
---|
| 2754 | int psize = size[0]*size[1]; |
---|
| 2755 | if(DEBUG || kVerbose > 0) std::cout << "Modality image (" << psize << "): "; |
---|
| 2756 | char * cimage = new char[psize*sizeof(short)]; |
---|
| 2757 | for(int i = 0; i < size[2]; i++) { |
---|
| 2758 | ifile.read((char *)cimage, psize*sizeof(short)); |
---|
| 2759 | short * mimage = new short[psize]; |
---|
| 2760 | for(int j = 0; j < psize; j++) { |
---|
| 2761 | convertEndian(cimage+j*sizeof(short), mimage[j]); |
---|
| 2762 | } |
---|
| 2763 | kModality.addImage(mimage); |
---|
| 2764 | |
---|
| 2765 | if(DEBUG || kVerbose > 0) std::cout << "[" << i << "]" << mimage[(size_t)(psize*0.55)] << ", "; |
---|
| 2766 | } |
---|
| 2767 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 2768 | delete [] cimage; |
---|
| 2769 | |
---|
| 2770 | // modality desity map for CT value |
---|
| 2771 | size_t msize = minmax[1]-minmax[0]+1; |
---|
| 2772 | if(DEBUG || kVerbose > 0) std::cout << "msize: " << msize << std::endl; |
---|
| 2773 | char * pdmap = new char[msize*sizeof(float)]; |
---|
| 2774 | ifile.read((char *)pdmap, msize*sizeof(float)); |
---|
| 2775 | float ftmp; |
---|
| 2776 | for(int i = 0; i < (int)msize; i++) { |
---|
| 2777 | convertEndian(pdmap+i*sizeof(float), ftmp); |
---|
| 2778 | kModalityImageDensityMap.push_back(ftmp); |
---|
| 2779 | } |
---|
| 2780 | if(DEBUG || kVerbose > 0) { |
---|
| 2781 | std::cout << "density map : " << std::ends; |
---|
| 2782 | for(int i = 0; i < 10; i++) |
---|
| 2783 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 2784 | std::cout << std::endl; |
---|
| 2785 | for(int i = 0; i < 10; i++) std::cout << ".."; |
---|
| 2786 | std::cout << std::endl; |
---|
| 2787 | for(size_t i =kModalityImageDensityMap.size() - 10; i <kModalityImageDensityMap.size(); i++) |
---|
| 2788 | std::cout <<kModalityImageDensityMap[i] << ", "; |
---|
| 2789 | std::cout << std::endl; |
---|
| 2790 | } |
---|
| 2791 | |
---|
| 2792 | } |
---|
| 2793 | |
---|
| 2794 | |
---|
| 2795 | //----- dose distribution image -----// |
---|
| 2796 | if(kPointerToDoseDistData[0] != 0) { |
---|
| 2797 | |
---|
| 2798 | newDoseDist(); |
---|
| 2799 | |
---|
| 2800 | // dose distrbution image size |
---|
| 2801 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2802 | convertEndian(ctmp, size[0]); |
---|
| 2803 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2804 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2805 | if(DEBUG || kVerbose > 0) { |
---|
| 2806 | std::cout << "Dose dist. image size : (" |
---|
| 2807 | << size[0] << ", " |
---|
| 2808 | << size[1] << ", " |
---|
| 2809 | << size[2] << ")" |
---|
| 2810 | << std::endl; |
---|
| 2811 | } |
---|
| 2812 | kDose[0].setSize(size); |
---|
| 2813 | |
---|
| 2814 | // dose distribution max. & min. |
---|
| 2815 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 2816 | convertEndian(ctmp, minmax[0]); |
---|
| 2817 | convertEndian(ctmp+2, minmax[1]); |
---|
| 2818 | // dose distribution scaling |
---|
| 2819 | ifile.read((char *)ctmp, sizeof(float)); |
---|
| 2820 | convertEndian(ctmp, scale); |
---|
| 2821 | kDose[0].setScale(dscale = scale); |
---|
| 2822 | |
---|
| 2823 | double dminmax[2]; |
---|
| 2824 | for(int i = 0; i < 2; i++) dminmax[i] = minmax[i]*dscale; |
---|
| 2825 | kDose[0].setMinMax(dminmax); |
---|
| 2826 | |
---|
| 2827 | if(DEBUG || kVerbose > 0) { |
---|
| 2828 | std::cout << "Dose dist. image min., max., scale : " |
---|
| 2829 | << dminmax[0] << ", " |
---|
| 2830 | << dminmax[1] << ", " |
---|
| 2831 | << scale << std::endl; |
---|
| 2832 | } |
---|
| 2833 | |
---|
| 2834 | // dose distribution image |
---|
| 2835 | int dsize = size[0]*size[1]; |
---|
| 2836 | if(DEBUG || kVerbose > 0) std::cout << "Dose dist. (" << dsize << "): "; |
---|
| 2837 | char * di = new char[dsize*sizeof(short)]; |
---|
| 2838 | short * shimage = new short[dsize]; |
---|
| 2839 | for(int z = 0; z < size[2]; z++) { |
---|
| 2840 | ifile.read((char *)di, dsize*sizeof(short)); |
---|
| 2841 | double * dimage = new double[dsize]; |
---|
| 2842 | for(int xy = 0; xy < dsize; xy++) { |
---|
| 2843 | convertEndian(di+xy*sizeof(short), shimage[xy]); |
---|
| 2844 | dimage[xy] = shimage[xy]*dscale; |
---|
| 2845 | } |
---|
| 2846 | kDose[0].addImage(dimage); |
---|
| 2847 | |
---|
| 2848 | if(DEBUG || kVerbose > 0) std::cout << "[" << z << "]" << dimage[(size_t)(dsize*0.55)] << ", "; |
---|
| 2849 | |
---|
| 2850 | if(DEBUG || kVerbose > 0) { |
---|
| 2851 | for(int j = 0; j < dsize; j++) { |
---|
| 2852 | if(dimage[j] < 0) |
---|
| 2853 | std::cout << "[" << j << "," << z << "]" |
---|
| 2854 | << dimage[j] << ", "; |
---|
| 2855 | } |
---|
| 2856 | } |
---|
| 2857 | } |
---|
| 2858 | delete [] shimage; |
---|
| 2859 | delete [] di; |
---|
| 2860 | if(DEBUG || kVerbose > 0) std::cout << std::endl; |
---|
| 2861 | |
---|
| 2862 | /* ver 1 |
---|
| 2863 | float doseDist; |
---|
| 2864 | int dosePid; |
---|
| 2865 | double * doseData = new double[numDoseImageVoxels]; |
---|
| 2866 | for(int i = 0; i < numDose; i++) { |
---|
| 2867 | ifile.read(ctmp, sizeof(int)); |
---|
| 2868 | convertEndian(ctmp, dosePid); |
---|
| 2869 | for(int j = 0; j < numDoseImageVoxels; j++) { |
---|
| 2870 | ifile.read(ctmp, sizeof(float)); |
---|
| 2871 | convertEndian(ctmp, doseDist); |
---|
| 2872 | doseData[j] = doseDist; |
---|
| 2873 | } |
---|
| 2874 | setDose(dosePid, doseData); |
---|
| 2875 | } |
---|
| 2876 | delete [] doseData; |
---|
| 2877 | if(totalDose == NULL) totalDose = new double[numDoseImageVoxels]; |
---|
| 2878 | for(int i = 0; i < numDoseImageVoxels; i++) { |
---|
| 2879 | ifile.read(ctmp, sizeof(float)); |
---|
| 2880 | convertEndian(ctmp, doseDist); |
---|
| 2881 | totalDose[i] = doseDist; |
---|
| 2882 | } |
---|
| 2883 | */ |
---|
| 2884 | |
---|
| 2885 | /* ver 1 |
---|
| 2886 | // relative location between the two images |
---|
| 2887 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 2888 | convertEndian(ctmp, relativeLocation[0]); |
---|
| 2889 | convertEndian(ctmp+sizeof(float), relativeLocation[1]); |
---|
| 2890 | convertEndian(ctmp+2*sizeof(float), relativeLocation[2]); |
---|
| 2891 | */ |
---|
| 2892 | |
---|
| 2893 | // relative location of the dose distribution image for |
---|
| 2894 | // the modality image |
---|
| 2895 | //ofile.write((char *)relativeLocation, 3*sizeof(float)); |
---|
| 2896 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2897 | convertEndian(ctmp, iCenter[0]); |
---|
| 2898 | convertEndian(ctmp+sizeof(int), iCenter[1]); |
---|
| 2899 | convertEndian(ctmp+2*sizeof(int), iCenter[2]); |
---|
| 2900 | for(int i = 0; i < 3; i++) fCenter[i] = (float)iCenter[i]; |
---|
| 2901 | kDose[0].setCenterPosition(fCenter); |
---|
| 2902 | |
---|
| 2903 | if(DEBUG || kVerbose > 0) { |
---|
| 2904 | std::cout << "Dose dist. image relative location : (" |
---|
| 2905 | << fCenter[0] << ", " |
---|
| 2906 | << fCenter[1] << ", " |
---|
| 2907 | << fCenter[2] << ")" << std::endl; |
---|
| 2908 | } |
---|
| 2909 | |
---|
| 2910 | |
---|
| 2911 | } |
---|
| 2912 | |
---|
| 2913 | //----- ROI image -----// |
---|
| 2914 | if(kPointerToROIData != 0) { |
---|
| 2915 | |
---|
| 2916 | newROI(); |
---|
| 2917 | |
---|
| 2918 | // ROI image size |
---|
| 2919 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2920 | convertEndian(ctmp, size[0]); |
---|
| 2921 | convertEndian(ctmp+sizeof(int), size[1]); |
---|
| 2922 | convertEndian(ctmp+2*sizeof(int), size[2]); |
---|
| 2923 | kRoi[0].setSize(size); |
---|
| 2924 | if(DEBUG || kVerbose > 0) { |
---|
| 2925 | std::cout << "ROI image size : (" |
---|
| 2926 | << size[0] << ", " |
---|
| 2927 | << size[1] << ", " |
---|
| 2928 | << size[2] << ")" |
---|
| 2929 | << std::endl; |
---|
| 2930 | } |
---|
| 2931 | |
---|
| 2932 | // ROI max. & min. |
---|
| 2933 | ifile.read((char *)ctmp, sizeof(short)*2); |
---|
| 2934 | convertEndian(ctmp, minmax[0]); |
---|
| 2935 | convertEndian(ctmp+sizeof(short), minmax[1]); |
---|
| 2936 | kRoi[0].setMinMax(minmax); |
---|
| 2937 | |
---|
| 2938 | // ROI distribution scaling |
---|
| 2939 | ifile.read((char *)ctmp, sizeof(float)); |
---|
| 2940 | convertEndian(ctmp, scale); |
---|
| 2941 | kRoi[0].setScale(dscale = scale); |
---|
| 2942 | if(DEBUG || kVerbose > 0) { |
---|
| 2943 | std::cout << "ROI image min., max., scale : " |
---|
| 2944 | << minmax[0] << ", " |
---|
| 2945 | << minmax[1] << ", " |
---|
| 2946 | << scale << std::endl; |
---|
| 2947 | } |
---|
| 2948 | |
---|
| 2949 | // ROI image |
---|
| 2950 | int rsize = size[0]*size[1]; |
---|
| 2951 | char * ri = new char[rsize*sizeof(short)]; |
---|
| 2952 | for(int i = 0; i < size[2]; i++) { |
---|
| 2953 | ifile.read((char *)ri, rsize*sizeof(short)); |
---|
| 2954 | short * rimage = new short[rsize]; |
---|
| 2955 | for(int j = 0; j < rsize; j++) { |
---|
| 2956 | convertEndian(ri+j*sizeof(short), rimage[j]); |
---|
| 2957 | } |
---|
| 2958 | kRoi[0].addImage(rimage); |
---|
| 2959 | |
---|
| 2960 | } |
---|
| 2961 | delete [] ri; |
---|
| 2962 | |
---|
| 2963 | // ROI relative location |
---|
| 2964 | ifile.read((char *)ctmp, 3*sizeof(int)); |
---|
| 2965 | convertEndian(ctmp, iCenter[0]); |
---|
| 2966 | convertEndian(ctmp+sizeof(int), iCenter[1]); |
---|
| 2967 | convertEndian(ctmp+2*sizeof(int), iCenter[2]); |
---|
| 2968 | for(int i = 0; i < 3; i++) fCenter[i] = iCenter[i]; |
---|
| 2969 | kRoi[0].setCenterPosition(fCenter); |
---|
| 2970 | if(DEBUG || kVerbose > 0) { |
---|
| 2971 | std::cout << "ROI image relative location : (" |
---|
| 2972 | << fCenter[0] << ", " |
---|
| 2973 | << fCenter[1] << ", " |
---|
| 2974 | << fCenter[2] << ")" << std::endl; |
---|
| 2975 | } |
---|
| 2976 | |
---|
| 2977 | } |
---|
| 2978 | |
---|
| 2979 | //----- track information -----// |
---|
| 2980 | if(kPointerToTrackData != 0) { |
---|
| 2981 | |
---|
| 2982 | // track |
---|
| 2983 | ifile.read((char *)ctmp, sizeof(int)); |
---|
| 2984 | int ntrk; |
---|
| 2985 | convertEndian(ctmp, ntrk); |
---|
| 2986 | if(DEBUG || kVerbose > 0) { |
---|
| 2987 | std::cout << "# of tracks: " << ntrk << std::endl; |
---|
| 2988 | } |
---|
| 2989 | |
---|
| 2990 | //v4 |
---|
| 2991 | unsigned char trkcolorv4[3] = {255, 0, 0}; |
---|
| 2992 | |
---|
| 2993 | for(int i = 0; i < ntrk; i++) { |
---|
| 2994 | float * tp = new float[6]; |
---|
| 2995 | // v4 |
---|
| 2996 | std::vector<float *> trkv4; |
---|
| 2997 | |
---|
| 2998 | ifile.read((char *)ctmp, sizeof(float)*3); |
---|
| 2999 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << i << ": " ; |
---|
| 3000 | for(int j = 0; j < 3; j++) { |
---|
| 3001 | convertEndian(ctmp+j*sizeof(float), tp[j]); |
---|
| 3002 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j] << ", "; |
---|
| 3003 | } |
---|
| 3004 | |
---|
| 3005 | ifile.read((char *)ctmp, sizeof(float)*3); |
---|
| 3006 | for(int j = 0; j < 3; j++) { |
---|
| 3007 | convertEndian(ctmp+j*sizeof(float), tp[j+3]); |
---|
| 3008 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << tp[j+3] << ", "; |
---|
| 3009 | } |
---|
| 3010 | |
---|
| 3011 | kSteps.push_back(tp); |
---|
| 3012 | // v4 |
---|
| 3013 | trkv4.push_back(tp); |
---|
| 3014 | addTrack(trkv4, trkcolorv4); |
---|
| 3015 | |
---|
| 3016 | if(DEBUG || kVerbose > 0) if(i < 10) std::cout << std::endl; |
---|
| 3017 | } |
---|
| 3018 | |
---|
| 3019 | } |
---|
| 3020 | |
---|
| 3021 | /* ver 1 |
---|
| 3022 | // track |
---|
| 3023 | int ntracks; |
---|
| 3024 | ifile.read(ctmp, sizeof(int)); |
---|
| 3025 | convertEndian(ctmp, ntracks); |
---|
| 3026 | // track displacement |
---|
| 3027 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 3028 | convertEndian(ctmp, trackDisplacement[0]); |
---|
| 3029 | convertEndian(ctmp+sizeof(float), trackDisplacement[2]); // exchanged with [1] |
---|
| 3030 | convertEndian(ctmp+2*sizeof(float), trackDisplacement[1]); |
---|
| 3031 | // |
---|
| 3032 | //for(int i = 0; i < ntracks && i < 100; i++) { |
---|
| 3033 | for(int i = 0; i < ntracks; i++) { |
---|
| 3034 | DicomDoseTrack trk; |
---|
| 3035 | short trackid, parentid, pid; |
---|
| 3036 | int npoints; |
---|
| 3037 | ifile.read(ctmp, sizeof(short)); |
---|
| 3038 | convertEndian(ctmp, trackid); |
---|
| 3039 | trk.setID(trackid); |
---|
| 3040 | ifile.read(ctmp, sizeof(short)); |
---|
| 3041 | convertEndian(ctmp, parentid); |
---|
| 3042 | trk.setParentID(parentid); |
---|
| 3043 | ifile.read(ctmp, sizeof(short)); |
---|
| 3044 | convertEndian(ctmp, pid); |
---|
| 3045 | trk.setPID(pid); |
---|
| 3046 | ifile.read(ctmp, sizeof(int)); |
---|
| 3047 | convertEndian(ctmp, npoints); |
---|
| 3048 | for(int i = 0; i < npoints; i++) { |
---|
| 3049 | ifile.read(ctmp, 3*sizeof(float)); |
---|
| 3050 | // storing only start and end points |
---|
| 3051 | //if(i == 0 || i == npoints - 1) { |
---|
| 3052 | float * point = new float[3]; |
---|
| 3053 | convertEndian(ctmp, point[0]); |
---|
| 3054 | convertEndian(ctmp+sizeof(float), point[1]); |
---|
| 3055 | convertEndian(ctmp+2*sizeof(float), point[2]); |
---|
| 3056 | trk.addPoint(point); |
---|
| 3057 | //} |
---|
| 3058 | } |
---|
| 3059 | track.push_back(trk); |
---|
| 3060 | } |
---|
| 3061 | */ |
---|
| 3062 | |
---|
| 3063 | ifile.close(); |
---|
| 3064 | |
---|
| 3065 | return true; |
---|
| 3066 | } |
---|
| 3067 | |
---|
| 3068 | bool G4GMocrenIO::retrieveData2(char * _filename) { |
---|
| 3069 | kFileName = _filename; |
---|
| 3070 | return retrieveData(); |
---|
| 3071 | } |
---|
| 3072 | |
---|
| 3073 | void G4GMocrenIO::setID() { |
---|
| 3074 | time_t t; |
---|
| 3075 | time(&t); |
---|
| 3076 | |
---|
| 3077 | tm * ti; |
---|
| 3078 | ti = localtime(&t); |
---|
| 3079 | |
---|
| 3080 | char cmonth[12][4] = {"Jan", "Feb", "Mar", "Apr", |
---|
| 3081 | "May", "Jun", "Jul", "Aug", |
---|
| 3082 | "Sep", "Oct", "Nov", "Dec"}; |
---|
| 3083 | std::stringstream ss; |
---|
| 3084 | ss << std::setfill('0') |
---|
| 3085 | << std::setw(2) |
---|
| 3086 | << ti->tm_hour << ":" |
---|
| 3087 | << std::setw(2) |
---|
| 3088 | << ti->tm_min << ":" |
---|
| 3089 | << std::setw(2) |
---|
| 3090 | << ti->tm_sec << "," |
---|
| 3091 | << cmonth[ti->tm_mon] << "." |
---|
| 3092 | << std::setw(2) |
---|
| 3093 | << ti->tm_mday << "," |
---|
| 3094 | << ti->tm_year+1900; |
---|
| 3095 | |
---|
| 3096 | kId = ss.str(); |
---|
| 3097 | } |
---|
| 3098 | |
---|
| 3099 | // get & set the file version |
---|
| 3100 | std::string & G4GMocrenIO::getVersion() {return kVersion;} |
---|
| 3101 | void G4GMocrenIO::setVersion(std::string & _version) {kVersion = _version;} |
---|
| 3102 | |
---|
| 3103 | // set endians of input/output data |
---|
| 3104 | void G4GMocrenIO::setLittleEndianInput(bool _little) {kLittleEndianInput = _little;} |
---|
| 3105 | void G4GMocrenIO::setLittleEndianOutput(bool _little) {kLittleEndianOutput = _little;} |
---|
| 3106 | |
---|
| 3107 | // voxel spacing |
---|
| 3108 | void G4GMocrenIO::setVoxelSpacing(float _spacing[3]) { |
---|
| 3109 | for(int i = 0; i < 3; i++) kVoxelSpacing[i] = _spacing[i]; |
---|
| 3110 | } |
---|
| 3111 | void G4GMocrenIO::getVoxelSpacing(float _spacing[3]) { |
---|
| 3112 | for(int i = 0; i < 3; i++) _spacing[i] = kVoxelSpacing[i]; |
---|
| 3113 | } |
---|
| 3114 | |
---|
| 3115 | // get & set number of events |
---|
| 3116 | int & G4GMocrenIO::getNumberOfEvents() { |
---|
| 3117 | return kNumberOfEvents; |
---|
| 3118 | } |
---|
| 3119 | void G4GMocrenIO::setNumberOfEvents(int & _numberOfEvents) { |
---|
| 3120 | kNumberOfEvents = _numberOfEvents; |
---|
| 3121 | } |
---|
| 3122 | void G4GMocrenIO::addOneEvent() { |
---|
| 3123 | kNumberOfEvents++; |
---|
| 3124 | } |
---|
| 3125 | |
---|
| 3126 | // set/get pointer the modality image data |
---|
| 3127 | void G4GMocrenIO::setPointerToModalityData(unsigned int & _pointer) { |
---|
| 3128 | kPointerToModalityData = _pointer; |
---|
| 3129 | } |
---|
| 3130 | unsigned int G4GMocrenIO::getPointerToModalityData() { |
---|
| 3131 | return kPointerToModalityData; |
---|
| 3132 | } |
---|
| 3133 | // set/get pointer the dose distribution image data |
---|
| 3134 | void G4GMocrenIO::addPointerToDoseDistData(unsigned int & _pointer) { |
---|
| 3135 | kPointerToDoseDistData.push_back(_pointer); |
---|
| 3136 | } |
---|
| 3137 | unsigned int G4GMocrenIO::getPointerToDoseDistData(int _elem) { |
---|
| 3138 | if(kPointerToDoseDistData.size() == 0 || |
---|
| 3139 | kPointerToDoseDistData.size() < (size_t)_elem) |
---|
| 3140 | return 0; |
---|
| 3141 | else |
---|
| 3142 | return kPointerToDoseDistData[_elem]; |
---|
| 3143 | } |
---|
| 3144 | |
---|
| 3145 | // set/get pointer the ROI image data |
---|
| 3146 | void G4GMocrenIO::setPointerToROIData(unsigned int & _pointer) { |
---|
| 3147 | kPointerToROIData = _pointer; |
---|
| 3148 | } |
---|
| 3149 | unsigned int G4GMocrenIO::getPointerToROIData() { |
---|
| 3150 | return kPointerToROIData; |
---|
| 3151 | } |
---|
| 3152 | // set/get pointer the track data |
---|
| 3153 | void G4GMocrenIO::setPointerToTrackData(unsigned int & _pointer) { |
---|
| 3154 | kPointerToTrackData = _pointer; |
---|
| 3155 | } |
---|
| 3156 | unsigned int G4GMocrenIO::getPointerToTrackData() { |
---|
| 3157 | return kPointerToTrackData; |
---|
| 3158 | } |
---|
| 3159 | |
---|
| 3160 | // calculate pointers for version 4 |
---|
| 3161 | void G4GMocrenIO::calcPointers4() { |
---|
| 3162 | |
---|
| 3163 | // pointer to modality data |
---|
| 3164 | unsigned int pointer = 1070; // up to "pointer to the detector data" except for "pointer to the dose dist data" |
---|
| 3165 | int nDoseDist = getNumDoseDist(); |
---|
| 3166 | pointer += nDoseDist*4; |
---|
| 3167 | |
---|
| 3168 | setPointerToModalityData(pointer); |
---|
| 3169 | |
---|
| 3170 | // pointer to dose data |
---|
| 3171 | // ct-density map for modality data |
---|
| 3172 | int msize[3]; |
---|
| 3173 | getModalityImageSize(msize); |
---|
| 3174 | short mminmax[2]; |
---|
| 3175 | getModalityImageMinMax(mminmax); |
---|
| 3176 | int pmsize = 2*msize[0]*msize[1]*msize[2]; |
---|
| 3177 | int pmmap = 4*(mminmax[1] - mminmax[0] + 1); |
---|
| 3178 | pointer += 32 + pmsize + pmmap; |
---|
| 3179 | // |
---|
| 3180 | kPointerToDoseDistData.clear(); |
---|
| 3181 | if(nDoseDist == 0) { |
---|
| 3182 | unsigned int pointer0 = 0; |
---|
| 3183 | addPointerToDoseDistData(pointer0); |
---|
| 3184 | } |
---|
| 3185 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 3186 | addPointerToDoseDistData(pointer); |
---|
| 3187 | int dsize[3]; |
---|
| 3188 | getDoseDistSize(dsize); |
---|
| 3189 | pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2 + 80; |
---|
| 3190 | } |
---|
| 3191 | |
---|
| 3192 | // pointer to roi data |
---|
| 3193 | if(!isROIEmpty()) { |
---|
| 3194 | setPointerToROIData(pointer); |
---|
| 3195 | |
---|
| 3196 | int rsize[3]; |
---|
| 3197 | getROISize(rsize); |
---|
| 3198 | int prsize = 2*rsize[0]*rsize[1]*rsize[2]; |
---|
| 3199 | pointer += 20 + prsize + 12; |
---|
| 3200 | } else { |
---|
| 3201 | unsigned int pointer0 = 0; |
---|
| 3202 | setPointerToROIData(pointer0); |
---|
| 3203 | } |
---|
| 3204 | |
---|
| 3205 | // pointer to track data |
---|
| 3206 | int ntrk = kTracks.size(); |
---|
| 3207 | if(ntrk != 0) { |
---|
| 3208 | setPointerToTrackData(pointer); |
---|
| 3209 | |
---|
| 3210 | pointer += 4; // # of tracks |
---|
| 3211 | for(int nt = 0; nt < ntrk; nt++) { |
---|
| 3212 | int nsteps = kTracks[nt].getNumberOfSteps(); |
---|
| 3213 | pointer += 4 + 3 + nsteps*(4*6); // # of steps + color + steps(float*6) |
---|
| 3214 | } |
---|
| 3215 | } else { |
---|
| 3216 | unsigned int pointer0 = 0; |
---|
| 3217 | setPointerToTrackData(pointer0); |
---|
| 3218 | } |
---|
| 3219 | if(kVerbose > 0) std::cout << " pointer to the track data :" |
---|
| 3220 | << kPointerToTrackData << std::endl; |
---|
| 3221 | |
---|
| 3222 | // pointer to detector data |
---|
| 3223 | int ndet = kDetectors.size(); |
---|
| 3224 | if(ndet != 0) { |
---|
| 3225 | kPointerToDetectorData = pointer; |
---|
| 3226 | } else { |
---|
| 3227 | kPointerToDetectorData = 0; |
---|
| 3228 | } |
---|
| 3229 | if(kVerbose > 0) std::cout << " pointer to the detector data :" |
---|
| 3230 | << kPointerToDetectorData << std::endl; |
---|
| 3231 | |
---|
| 3232 | } |
---|
| 3233 | |
---|
| 3234 | // calculate pointers for ver.3 |
---|
| 3235 | void G4GMocrenIO::calcPointers3() { |
---|
| 3236 | |
---|
| 3237 | // pointer to modality data |
---|
| 3238 | unsigned int pointer = 1066; // up to "pointer to the track data" except for "pointer to the dose dist data" |
---|
| 3239 | int nDoseDist = getNumDoseDist(); |
---|
| 3240 | pointer += nDoseDist*4; |
---|
| 3241 | |
---|
| 3242 | setPointerToModalityData(pointer); |
---|
| 3243 | |
---|
| 3244 | // pointer to dose data |
---|
| 3245 | // ct-density map for modality data |
---|
| 3246 | int msize[3]; |
---|
| 3247 | getModalityImageSize(msize); |
---|
| 3248 | short mminmax[2]; |
---|
| 3249 | getModalityImageMinMax(mminmax); |
---|
| 3250 | int pmsize = 2*msize[0]*msize[1]*msize[2]; |
---|
| 3251 | int pmmap = 4*(mminmax[1] - mminmax[0] + 1); |
---|
| 3252 | pointer += 32 + pmsize + pmmap; |
---|
| 3253 | // |
---|
| 3254 | kPointerToDoseDistData.clear(); |
---|
| 3255 | if(nDoseDist == 0) { |
---|
| 3256 | unsigned int pointer0 = 0; |
---|
| 3257 | addPointerToDoseDistData(pointer0); |
---|
| 3258 | } |
---|
| 3259 | for(int ndose = 0; ndose < nDoseDist; ndose++) { |
---|
| 3260 | addPointerToDoseDistData(pointer); |
---|
| 3261 | int dsize[3]; |
---|
| 3262 | getDoseDistSize(dsize); |
---|
| 3263 | pointer += 44 + dsize[0]*dsize[1]*dsize[2]*2; |
---|
| 3264 | } |
---|
| 3265 | |
---|
| 3266 | // pointer to roi data |
---|
| 3267 | if(!isROIEmpty()) { |
---|
| 3268 | setPointerToROIData(pointer); |
---|
| 3269 | |
---|
| 3270 | int rsize[3]; |
---|
| 3271 | getROISize(rsize); |
---|
| 3272 | int prsize = 2*rsize[0]*rsize[1]*rsize[2]; |
---|
| 3273 | pointer += 20 + prsize + 12; |
---|
| 3274 | } else { |
---|
| 3275 | unsigned int pointer0 = 0; |
---|
| 3276 | setPointerToROIData(pointer0); |
---|
| 3277 | } |
---|
| 3278 | |
---|
| 3279 | // |
---|
| 3280 | if(getNumTracks() != 0) |
---|
| 3281 | setPointerToTrackData(pointer); |
---|
| 3282 | else { |
---|
| 3283 | unsigned int pointer0 = 0; |
---|
| 3284 | setPointerToTrackData(pointer0); |
---|
| 3285 | } |
---|
| 3286 | |
---|
| 3287 | } |
---|
| 3288 | |
---|
| 3289 | // calculate pointers for ver.2 |
---|
| 3290 | void G4GMocrenIO::calcPointers2() { |
---|
| 3291 | |
---|
| 3292 | // pointer to modality data |
---|
| 3293 | unsigned int pointer = 65; |
---|
| 3294 | setPointerToModalityData(pointer); |
---|
| 3295 | |
---|
| 3296 | // pointer to dose data |
---|
| 3297 | int msize[3]; |
---|
| 3298 | getModalityImageSize(msize); |
---|
| 3299 | short mminmax[2]; |
---|
| 3300 | getModalityImageMinMax(mminmax); |
---|
| 3301 | int pmsize = 2*msize[0]*msize[1]*msize[2]; |
---|
| 3302 | int pmmap = 4*(mminmax[1] - mminmax[0] + 1); |
---|
| 3303 | pointer += 20 + pmsize + pmmap; |
---|
| 3304 | int dsize[3]; |
---|
| 3305 | getDoseDistSize(dsize); |
---|
| 3306 | kPointerToDoseDistData.clear(); |
---|
| 3307 | if(dsize[0] != 0) { |
---|
| 3308 | kPointerToDoseDistData.push_back(pointer); |
---|
| 3309 | |
---|
| 3310 | int pdsize = 2*dsize[0]*dsize[1]*dsize[2]; |
---|
| 3311 | pointer += 20 + pdsize + 12; |
---|
| 3312 | } else { |
---|
| 3313 | unsigned int pointer0 = 0; |
---|
| 3314 | kPointerToDoseDistData.push_back(pointer0); |
---|
| 3315 | } |
---|
| 3316 | |
---|
| 3317 | // pointer to roi data |
---|
| 3318 | if(!isROIEmpty()) { |
---|
| 3319 | int rsize[3]; |
---|
| 3320 | getROISize(rsize); |
---|
| 3321 | setPointerToROIData(pointer); |
---|
| 3322 | int prsize = 2*rsize[0]*rsize[1]*rsize[2]; |
---|
| 3323 | pointer += 20 + prsize + 12; |
---|
| 3324 | |
---|
| 3325 | } else { |
---|
| 3326 | unsigned int pointer0 = 0; |
---|
| 3327 | setPointerToROIData(pointer0); |
---|
| 3328 | } |
---|
| 3329 | |
---|
| 3330 | // |
---|
| 3331 | if(getNumTracks() != 0) |
---|
| 3332 | setPointerToTrackData(pointer); |
---|
| 3333 | else { |
---|
| 3334 | unsigned int pointer0 = 0; |
---|
| 3335 | setPointerToTrackData(pointer0); |
---|
| 3336 | } |
---|
| 3337 | |
---|
| 3338 | } |
---|
| 3339 | |
---|
| 3340 | |
---|
| 3341 | //----- Modality image -----// |
---|
| 3342 | void G4GMocrenIO::getModalityImageSize(int _size[3]) { |
---|
| 3343 | |
---|
| 3344 | kModality.getSize(_size); |
---|
| 3345 | } |
---|
| 3346 | void G4GMocrenIO::setModalityImageSize(int _size[3]) { |
---|
| 3347 | |
---|
| 3348 | kModality.setSize(_size); |
---|
| 3349 | } |
---|
| 3350 | |
---|
| 3351 | // get & set the modality image size |
---|
| 3352 | void G4GMocrenIO::setModalityImageScale(double & _scale) { |
---|
| 3353 | |
---|
| 3354 | kModality.setScale(_scale); |
---|
| 3355 | } |
---|
| 3356 | double G4GMocrenIO::getModalityImageScale() { |
---|
| 3357 | |
---|
| 3358 | return kModality.getScale(); |
---|
| 3359 | } |
---|
| 3360 | |
---|
| 3361 | // set the modality image in CT |
---|
| 3362 | void G4GMocrenIO::setModalityImage(short * _image) { |
---|
| 3363 | |
---|
| 3364 | kModality.addImage(_image); |
---|
| 3365 | } |
---|
| 3366 | short * G4GMocrenIO::getModalityImage(int _z) { |
---|
| 3367 | |
---|
| 3368 | return kModality.getImage(_z); |
---|
| 3369 | } |
---|
| 3370 | // set/get the modality image density map |
---|
| 3371 | void G4GMocrenIO::setModalityImageDensityMap(std::vector<float> & _map) { |
---|
| 3372 | kModalityImageDensityMap = _map; |
---|
| 3373 | } |
---|
| 3374 | std::vector<float> & G4GMocrenIO::getModalityImageDensityMap() { |
---|
| 3375 | return kModalityImageDensityMap; |
---|
| 3376 | } |
---|
| 3377 | // set the modality image min./max. |
---|
| 3378 | void G4GMocrenIO::setModalityImageMinMax(short _minmax[2]) { |
---|
| 3379 | |
---|
| 3380 | kModality.setMinMax(_minmax); |
---|
| 3381 | } |
---|
| 3382 | // get the modality image min./max. |
---|
| 3383 | void G4GMocrenIO::getModalityImageMinMax(short _minmax[2]) { |
---|
| 3384 | |
---|
| 3385 | short minmax[2]; |
---|
| 3386 | kModality.getMinMax(minmax); |
---|
| 3387 | for(int i = 0; i < 2; i++) _minmax[i] = minmax[i]; |
---|
| 3388 | } |
---|
| 3389 | short G4GMocrenIO::getModalityImageMax() { |
---|
| 3390 | |
---|
| 3391 | short minmax[2]; |
---|
| 3392 | kModality.getMinMax(minmax); |
---|
| 3393 | return minmax[1]; |
---|
| 3394 | } |
---|
| 3395 | short G4GMocrenIO::getModalityImageMin() { |
---|
| 3396 | |
---|
| 3397 | short minmax[2]; |
---|
| 3398 | kModality.getMinMax(minmax); |
---|
| 3399 | return minmax[0]; |
---|
| 3400 | } |
---|
| 3401 | // set/get position of the modality image center |
---|
| 3402 | void G4GMocrenIO::setModalityCenterPosition(float _center[3]) { |
---|
| 3403 | |
---|
| 3404 | kModality.setCenterPosition(_center); |
---|
| 3405 | } |
---|
| 3406 | void G4GMocrenIO::getModalityCenterPosition(float _center[3]) { |
---|
| 3407 | |
---|
| 3408 | if(isROIEmpty()) |
---|
| 3409 | for(int i = 0; i < 3; i++) _center[i] = 0; |
---|
| 3410 | else |
---|
| 3411 | kModality.getCenterPosition(_center); |
---|
| 3412 | } |
---|
| 3413 | // get & set the modality image unit |
---|
| 3414 | std::string G4GMocrenIO::getModalityImageUnit() { |
---|
| 3415 | return kModalityUnit; |
---|
| 3416 | } |
---|
| 3417 | void G4GMocrenIO::setModalityImageUnit(std::string & _unit) { |
---|
| 3418 | kModalityUnit = _unit; |
---|
| 3419 | } |
---|
| 3420 | // |
---|
| 3421 | short G4GMocrenIO::convertDensityToHU(float & _dens) { |
---|
| 3422 | short rval = -1024; // default: air |
---|
| 3423 | int nmap = (int)kModalityImageDensityMap.size(); |
---|
| 3424 | if(nmap != 0) { |
---|
| 3425 | short minmax[2]; |
---|
| 3426 | kModality.getMinMax(minmax); |
---|
| 3427 | rval = minmax[1]; |
---|
| 3428 | for(int i = 0; i < nmap; i++) { |
---|
| 3429 | //std::cout << kModalityImageDensityMap[i] << std::endl; |
---|
| 3430 | if(_dens <= kModalityImageDensityMap[i]) { |
---|
| 3431 | rval = i + minmax[0]; |
---|
| 3432 | break; |
---|
| 3433 | } |
---|
| 3434 | } |
---|
| 3435 | } |
---|
| 3436 | return rval; |
---|
| 3437 | } |
---|
| 3438 | |
---|
| 3439 | |
---|
| 3440 | //----- Dose distribution -----// |
---|
| 3441 | // |
---|
| 3442 | void G4GMocrenIO::newDoseDist() { |
---|
| 3443 | GMocrenDataPrimitive<double> doseData; |
---|
| 3444 | kDose.push_back(doseData); |
---|
| 3445 | } |
---|
| 3446 | int G4GMocrenIO::getNumDoseDist() { |
---|
| 3447 | return (int)kDose.size(); |
---|
| 3448 | } |
---|
| 3449 | |
---|
| 3450 | // get & set the dose distribution unit |
---|
| 3451 | std::string G4GMocrenIO::getDoseDistUnit(int _num) { |
---|
| 3452 | // to avoid a warning in the compile process |
---|
| 3453 | int dummynum; |
---|
| 3454 | dummynum = _num; |
---|
| 3455 | |
---|
| 3456 | return kDoseUnit; |
---|
| 3457 | } |
---|
| 3458 | void G4GMocrenIO::setDoseDistUnit(std::string & _unit, int _num) { |
---|
| 3459 | // to avoid a warning in the compile process |
---|
| 3460 | int dummynum; |
---|
| 3461 | dummynum = _num; |
---|
| 3462 | |
---|
| 3463 | //char unit[13]; |
---|
| 3464 | //std::strncpy(unit, _unit.c_str(), 12); |
---|
| 3465 | //doseUnit = unit; |
---|
| 3466 | kDoseUnit = _unit; |
---|
| 3467 | } |
---|
| 3468 | // |
---|
| 3469 | void G4GMocrenIO::getDoseDistSize(int _size[3], int _num) { |
---|
| 3470 | if(isDoseEmpty()) |
---|
| 3471 | for(int i = 0; i < 3; i++) _size[i] = 0; |
---|
| 3472 | else |
---|
| 3473 | kDose[_num].getSize(_size); |
---|
| 3474 | } |
---|
| 3475 | void G4GMocrenIO::setDoseDistSize(int _size[3], int _num) { |
---|
| 3476 | |
---|
| 3477 | kDose[_num].setSize(_size); |
---|
| 3478 | |
---|
| 3479 | //resetDose(); |
---|
| 3480 | } |
---|
| 3481 | |
---|
| 3482 | void G4GMocrenIO::setDoseDistMinMax(short _minmax[2], int _num) { |
---|
| 3483 | |
---|
| 3484 | double minmax[2]; |
---|
| 3485 | double scale = kDose[_num].getScale(); |
---|
| 3486 | for(int i = 0; i < 2; i++) minmax[i] = (double)_minmax[i]*scale; |
---|
| 3487 | kDose[_num].setMinMax(minmax); |
---|
| 3488 | } |
---|
| 3489 | void G4GMocrenIO::getDoseDistMinMax(short _minmax[2], int _num) { |
---|
| 3490 | |
---|
| 3491 | if(isDoseEmpty()) |
---|
| 3492 | for(int i = 0; i < 2; i++) _minmax[i] = 0; |
---|
| 3493 | else { |
---|
| 3494 | double minmax[2]; |
---|
| 3495 | kDose[_num].getMinMax(minmax); |
---|
| 3496 | double scale = kDose[_num].getScale(); |
---|
| 3497 | for(int i = 0; i < 2; i++) _minmax[i] = (short)(minmax[i]/scale+0.5); |
---|
| 3498 | } |
---|
| 3499 | } |
---|
| 3500 | void G4GMocrenIO::setDoseDistMinMax(double _minmax[2], int _num) { |
---|
| 3501 | |
---|
| 3502 | kDose[_num].setMinMax(_minmax); |
---|
| 3503 | } |
---|
| 3504 | void G4GMocrenIO::getDoseDistMinMax(double _minmax[2], int _num) { |
---|
| 3505 | |
---|
| 3506 | if(isDoseEmpty()) |
---|
| 3507 | for(int i = 0; i < 2; i++) _minmax[i] = 0.; |
---|
| 3508 | else |
---|
| 3509 | kDose[_num].getMinMax(_minmax); |
---|
| 3510 | } |
---|
| 3511 | |
---|
| 3512 | // get & set the dose distribution image scale |
---|
| 3513 | void G4GMocrenIO::setDoseDistScale(double & _scale, int _num) { |
---|
| 3514 | |
---|
| 3515 | kDose[_num].setScale(_scale); |
---|
| 3516 | } |
---|
| 3517 | double G4GMocrenIO::getDoseDistScale(int _num) { |
---|
| 3518 | |
---|
| 3519 | if(isDoseEmpty()) |
---|
| 3520 | return 0.; |
---|
| 3521 | else |
---|
| 3522 | return kDose[_num].getScale(); |
---|
| 3523 | } |
---|
| 3524 | |
---|
| 3525 | /* |
---|
| 3526 | void G4GMocrenIO::initializeShortDoseDist() { |
---|
| 3527 | ; |
---|
| 3528 | } |
---|
| 3529 | void G4GMocrenIO::finalizeShortDoseDist() { |
---|
| 3530 | ; |
---|
| 3531 | } |
---|
| 3532 | */ |
---|
| 3533 | // set the dose distribution image |
---|
| 3534 | void G4GMocrenIO::setShortDoseDist(short * _image, int _num) { |
---|
| 3535 | |
---|
| 3536 | int size[3]; |
---|
| 3537 | kDose[_num].getSize(size); |
---|
| 3538 | int dsize = size[0]*size[1]; |
---|
| 3539 | double * ddata = new double[dsize]; |
---|
| 3540 | double scale = kDose[_num].getScale(); |
---|
| 3541 | double minmax[2]; |
---|
| 3542 | kDose[_num].getMinMax(minmax); |
---|
| 3543 | for(int xy = 0; xy < dsize; xy++) { |
---|
| 3544 | ddata[xy] = _image[xy]*scale; |
---|
| 3545 | if(ddata[xy] < minmax[0]) minmax[0] = ddata[xy]; |
---|
| 3546 | if(ddata[xy] > minmax[1]) minmax[1] = ddata[xy]; |
---|
| 3547 | } |
---|
| 3548 | kDose[_num].addImage(ddata); |
---|
| 3549 | |
---|
| 3550 | // set min./max. |
---|
| 3551 | kDose[_num].setMinMax(minmax); |
---|
| 3552 | } |
---|
| 3553 | void G4GMocrenIO::getShortDoseDist(short * _data, int _z, int _num) { |
---|
| 3554 | |
---|
| 3555 | if(_data == NULL) { |
---|
| 3556 | std::cerr << "In G4GMocrenIO::getShortDoseDist(), " |
---|
| 3557 | << "first argument is NULL pointer. " |
---|
| 3558 | << "The argument must be allocated array." |
---|
| 3559 | << std::endl; |
---|
| 3560 | std::exit(-1); |
---|
| 3561 | } |
---|
| 3562 | |
---|
| 3563 | int size[3]; |
---|
| 3564 | kDose[_num].getSize(size); |
---|
| 3565 | //short * shdata = new short[size[0]*size[1]]; |
---|
| 3566 | double * ddata = kDose[_num].getImage(_z); |
---|
| 3567 | double scale = kDose[_num].getScale(); |
---|
| 3568 | for(int xy = 0; xy < size[0]*size[1]; xy++) { |
---|
| 3569 | _data[xy] = (short)(ddata[xy]/scale+0.5); //there is never negative value |
---|
| 3570 | } |
---|
| 3571 | } |
---|
| 3572 | void G4GMocrenIO::getShortDoseDistMinMax(short _minmax[2], int _num) { |
---|
| 3573 | double scale = kDose[_num].getScale(); |
---|
| 3574 | double minmax[2]; |
---|
| 3575 | kDose[_num].getMinMax(minmax); |
---|
| 3576 | for(int i = 0; i < 2; i++) |
---|
| 3577 | _minmax[i] = (short)(minmax[i]/scale+0.5); |
---|
| 3578 | } |
---|
| 3579 | // |
---|
| 3580 | void G4GMocrenIO::setDoseDist(double * _image, int _num) { |
---|
| 3581 | |
---|
| 3582 | kDose[_num].addImage(_image); |
---|
| 3583 | } |
---|
| 3584 | double * G4GMocrenIO::getDoseDist(int _z, int _num) { |
---|
| 3585 | |
---|
| 3586 | double * image; |
---|
| 3587 | if(isDoseEmpty()) { |
---|
| 3588 | image = 0; |
---|
| 3589 | } else { |
---|
| 3590 | image = kDose[_num].getImage(_z); |
---|
| 3591 | } |
---|
| 3592 | return image; |
---|
| 3593 | } |
---|
| 3594 | /* |
---|
| 3595 | void G4GMocrenIO::getDoseDist(double * & _image, int _z, int _num) { |
---|
| 3596 | |
---|
| 3597 | std::cout << " <" << (void*)_image << "> "; |
---|
| 3598 | if(isDoseEmpty()) { |
---|
| 3599 | _image = 0; |
---|
| 3600 | } else { |
---|
| 3601 | _image = kDose[_num].getImage(_z); |
---|
| 3602 | std::cout << " <" << (void*)_image << "> "; |
---|
| 3603 | std::cout << _image[100] << " "; |
---|
| 3604 | } |
---|
| 3605 | } |
---|
| 3606 | */ |
---|
| 3607 | bool G4GMocrenIO::addDoseDist(std::vector<double *> & _image, int _num) { |
---|
| 3608 | |
---|
| 3609 | int size[3]; |
---|
| 3610 | getDoseDistSize(size, _num); |
---|
| 3611 | std::vector<double *> dosedist = kDose[_num].getImage(); |
---|
| 3612 | |
---|
| 3613 | int nimg = size[0]*size[1]; |
---|
| 3614 | for(int z = 0; z < size[2]; z++) { |
---|
| 3615 | for(int xy = 0; xy < nimg; xy++) { |
---|
| 3616 | dosedist[z][xy] += _image[z][xy]; |
---|
| 3617 | } |
---|
| 3618 | } |
---|
| 3619 | |
---|
| 3620 | return true; |
---|
| 3621 | } |
---|
| 3622 | //void setDoseDistDensityMap(float * _map) {doseImageDensityMap = _map;}; |
---|
| 3623 | // set the dose distribution image displacement |
---|
| 3624 | void G4GMocrenIO::setDoseDistCenterPosition(float _center[3], int _num) { |
---|
| 3625 | |
---|
| 3626 | kDose[_num].setCenterPosition(_center); |
---|
| 3627 | } |
---|
| 3628 | void G4GMocrenIO::getDoseDistCenterPosition(float _center[3], int _num) { |
---|
| 3629 | |
---|
| 3630 | if(isDoseEmpty()) |
---|
| 3631 | for(int i = 0; i < 3; i++) _center[i] = 0; |
---|
| 3632 | else |
---|
| 3633 | kDose[_num].getCenterPosition(_center); |
---|
| 3634 | } |
---|
| 3635 | // set & get name of dose distribution |
---|
| 3636 | void G4GMocrenIO::setDoseDistName(std::string _name, int _num) { |
---|
| 3637 | |
---|
| 3638 | kDose[_num].setName(_name); |
---|
| 3639 | } |
---|
| 3640 | std::string G4GMocrenIO::getDoseDistName(int _num) { |
---|
| 3641 | |
---|
| 3642 | std::string name; |
---|
| 3643 | if(isDoseEmpty()) |
---|
| 3644 | return name; |
---|
| 3645 | else |
---|
| 3646 | return kDose[_num].getName(); |
---|
| 3647 | } |
---|
| 3648 | // copy dose distributions |
---|
| 3649 | void G4GMocrenIO::copyDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) { |
---|
| 3650 | std::vector<class GMocrenDataPrimitive<double> >::iterator itr; |
---|
| 3651 | for(itr = kDose.begin(); itr != kDose.end(); itr++) { |
---|
| 3652 | _dose.push_back(*itr); |
---|
| 3653 | } |
---|
| 3654 | } |
---|
| 3655 | // merge two dose distributions |
---|
| 3656 | bool G4GMocrenIO::mergeDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose) { |
---|
| 3657 | if(kDose.size() != _dose.size()) { |
---|
| 3658 | std::cerr << "G4GMocrenIO::mergeDoseDist() : Error" << std::endl; |
---|
| 3659 | std::cerr << " Unable to merge the dose distributions,"<< std::endl; |
---|
| 3660 | std::cerr << " because of different size of dose maps."<< std::endl; |
---|
| 3661 | return false; |
---|
| 3662 | } |
---|
| 3663 | |
---|
| 3664 | int num = kDose.size(); |
---|
| 3665 | std::vector<class GMocrenDataPrimitive<double> >::iterator itr1 = kDose.begin(); |
---|
| 3666 | std::vector<class GMocrenDataPrimitive<double> >::iterator itr2 = _dose.begin(); |
---|
| 3667 | for(int i = 0; i < num; i++, itr1++, itr2++) { |
---|
| 3668 | if(kVerbose > 0) std::cerr << "merged dose distribution [" << i << "]" << std::endl; |
---|
| 3669 | *itr1 += *itr2; |
---|
| 3670 | } |
---|
| 3671 | |
---|
| 3672 | return true; |
---|
| 3673 | } |
---|
| 3674 | // |
---|
| 3675 | void G4GMocrenIO::clearDoseDistAll() { |
---|
| 3676 | |
---|
| 3677 | if(!isDoseEmpty()) { |
---|
| 3678 | for(int i = 0; i < getNumDoseDist(); i++) { |
---|
| 3679 | kDose[i].clear(); |
---|
| 3680 | } |
---|
| 3681 | kDose.clear(); |
---|
| 3682 | } |
---|
| 3683 | } |
---|
| 3684 | // |
---|
| 3685 | bool G4GMocrenIO::isDoseEmpty() { |
---|
| 3686 | if(kDose.empty()) { |
---|
| 3687 | std::cerr << "!!! dose distribution data is empty." << std::endl; |
---|
| 3688 | return true; |
---|
| 3689 | } else { |
---|
| 3690 | return false; |
---|
| 3691 | } |
---|
| 3692 | } |
---|
| 3693 | |
---|
| 3694 | // |
---|
| 3695 | void G4GMocrenIO::calcDoseDistScale() { |
---|
| 3696 | |
---|
| 3697 | double scale; |
---|
| 3698 | double minmax[2]; |
---|
| 3699 | |
---|
| 3700 | for(int i = 0; i < (int)kDose.size(); i++) { |
---|
| 3701 | kDose[i].getMinMax(minmax); |
---|
| 3702 | scale = minmax[1]/DOSERANGE; |
---|
| 3703 | kDose[i].setScale(scale); |
---|
| 3704 | } |
---|
| 3705 | } |
---|
| 3706 | |
---|
| 3707 | |
---|
| 3708 | //----- RoI -----// |
---|
| 3709 | |
---|
| 3710 | // add one RoI data |
---|
| 3711 | void G4GMocrenIO::newROI() { |
---|
| 3712 | GMocrenDataPrimitive<short> roiData; |
---|
| 3713 | kRoi.push_back(roiData); |
---|
| 3714 | } |
---|
| 3715 | int G4GMocrenIO::getNumROI() { |
---|
| 3716 | return (int)kRoi.size(); |
---|
| 3717 | } |
---|
| 3718 | |
---|
| 3719 | // set/get the ROI image scale |
---|
| 3720 | void G4GMocrenIO::setROIScale(double & _scale, int _num) { |
---|
| 3721 | |
---|
| 3722 | kRoi[_num].setScale(_scale); |
---|
| 3723 | } |
---|
| 3724 | double G4GMocrenIO::getROIScale(int _num) { |
---|
| 3725 | |
---|
| 3726 | if(isROIEmpty()) |
---|
| 3727 | return 0.; |
---|
| 3728 | else |
---|
| 3729 | return kRoi[_num].getScale(); |
---|
| 3730 | } |
---|
| 3731 | // set the ROI image |
---|
| 3732 | void G4GMocrenIO::setROI(short * _image, int _num) { |
---|
| 3733 | |
---|
| 3734 | kRoi[_num].addImage(_image); |
---|
| 3735 | } |
---|
| 3736 | short * G4GMocrenIO::getROI(int _z, int _num) { |
---|
| 3737 | |
---|
| 3738 | if(isROIEmpty()) |
---|
| 3739 | return 0; |
---|
| 3740 | else |
---|
| 3741 | return kRoi[_num].getImage(_z); |
---|
| 3742 | } |
---|
| 3743 | // set/get the ROI image size |
---|
| 3744 | void G4GMocrenIO::setROISize(int _size[3], int _num) { |
---|
| 3745 | |
---|
| 3746 | return kRoi[_num].setSize(_size); |
---|
| 3747 | } |
---|
| 3748 | void G4GMocrenIO::getROISize(int _size[3], int _num) { |
---|
| 3749 | |
---|
| 3750 | if(isROIEmpty()) |
---|
| 3751 | for(int i = 0; i < 3; i++) _size[i] = 0; |
---|
| 3752 | else |
---|
| 3753 | return kRoi[_num].getSize(_size); |
---|
| 3754 | } |
---|
| 3755 | // set/get the ROI image min. and max. |
---|
| 3756 | void G4GMocrenIO::setROIMinMax(short _minmax[2], int _num) { |
---|
| 3757 | |
---|
| 3758 | kRoi[_num].setMinMax(_minmax); |
---|
| 3759 | } |
---|
| 3760 | void G4GMocrenIO::getROIMinMax(short _minmax[2], int _num) { |
---|
| 3761 | |
---|
| 3762 | if(isROIEmpty()) |
---|
| 3763 | for(int i = 0; i < 2; i++) _minmax[i] = 0; |
---|
| 3764 | else |
---|
| 3765 | kRoi[_num].getMinMax(_minmax); |
---|
| 3766 | } |
---|
| 3767 | // set/get the ROI image displacement |
---|
| 3768 | void G4GMocrenIO::setROICenterPosition(float _center[3], int _num) { |
---|
| 3769 | |
---|
| 3770 | kRoi[_num].setCenterPosition(_center); |
---|
| 3771 | } |
---|
| 3772 | void G4GMocrenIO::getROICenterPosition(float _center[3], int _num) { |
---|
| 3773 | |
---|
| 3774 | if(isROIEmpty()) |
---|
| 3775 | for(int i = 0; i < 3; i++) _center[i] = 0; |
---|
| 3776 | else |
---|
| 3777 | kRoi[_num].getCenterPosition(_center); |
---|
| 3778 | } |
---|
| 3779 | // |
---|
| 3780 | void G4GMocrenIO::clearROIAll() { |
---|
| 3781 | |
---|
| 3782 | if(!isROIEmpty()) { |
---|
| 3783 | for(int i = 0; i < getNumROI(); i++) { |
---|
| 3784 | kRoi[i].clear(); |
---|
| 3785 | } |
---|
| 3786 | kRoi.clear(); |
---|
| 3787 | } |
---|
| 3788 | } |
---|
| 3789 | // |
---|
| 3790 | bool G4GMocrenIO::isROIEmpty() { |
---|
| 3791 | if(kRoi.empty()) { |
---|
| 3792 | //std::cerr << "!!! ROI data is empty." << std::endl; |
---|
| 3793 | return true; |
---|
| 3794 | } else { |
---|
| 3795 | return false; |
---|
| 3796 | } |
---|
| 3797 | } |
---|
| 3798 | |
---|
| 3799 | |
---|
| 3800 | |
---|
| 3801 | //----- Track information -----// |
---|
| 3802 | |
---|
| 3803 | int G4GMocrenIO::getNumTracks() { |
---|
| 3804 | return (int)kSteps.size(); |
---|
| 3805 | } |
---|
| 3806 | int G4GMocrenIO::getNumTracks4() { |
---|
| 3807 | return (int)kTracks.size(); |
---|
| 3808 | } |
---|
| 3809 | void G4GMocrenIO::addTrack(float * _tracks) { |
---|
| 3810 | kSteps.push_back(_tracks); |
---|
| 3811 | } |
---|
| 3812 | void G4GMocrenIO::setTracks(std::vector<float *> & _tracks) { |
---|
| 3813 | kSteps = _tracks; |
---|
| 3814 | } |
---|
| 3815 | std::vector<float *> & G4GMocrenIO::getTracks() { |
---|
| 3816 | return kSteps; |
---|
| 3817 | } |
---|
| 3818 | void G4GMocrenIO::addTrackColor(unsigned char * _colors) { |
---|
| 3819 | kStepColors.push_back(_colors); |
---|
| 3820 | } |
---|
| 3821 | void G4GMocrenIO::setTrackColors(std::vector<unsigned char *> & _trackColors) { |
---|
| 3822 | kStepColors = _trackColors; |
---|
| 3823 | } |
---|
| 3824 | std::vector<unsigned char *> & G4GMocrenIO::getTrackColors() { |
---|
| 3825 | return kStepColors; |
---|
| 3826 | } |
---|
| 3827 | void G4GMocrenIO::copyTracks(std::vector<float *> & _tracks, |
---|
| 3828 | std::vector<unsigned char *> & _colors) { |
---|
| 3829 | std::vector<float *>::iterator titr; |
---|
| 3830 | for(titr = kSteps.begin(); titr != kSteps.end(); titr++) { |
---|
| 3831 | float * pts = new float[6]; |
---|
| 3832 | for(int i = 0; i < 6; i++) { |
---|
| 3833 | pts[i] = (*titr)[i]; |
---|
| 3834 | } |
---|
| 3835 | _tracks.push_back(pts); |
---|
| 3836 | } |
---|
| 3837 | |
---|
| 3838 | std::vector<unsigned char *>::iterator citr; |
---|
| 3839 | for(citr = kStepColors.begin(); citr != kStepColors.end(); citr++) { |
---|
| 3840 | unsigned char * pts = new unsigned char[3]; |
---|
| 3841 | for(int i = 0; i < 3; i++) { |
---|
| 3842 | pts[i] = (*citr)[i]; |
---|
| 3843 | } |
---|
| 3844 | _colors.push_back(pts); |
---|
| 3845 | } |
---|
| 3846 | } |
---|
| 3847 | void G4GMocrenIO::mergeTracks(std::vector<float *> & _tracks, |
---|
| 3848 | std::vector<unsigned char *> & _colors) { |
---|
| 3849 | std::vector<float *>::iterator titr; |
---|
| 3850 | for(titr = _tracks.begin(); titr != _tracks.end(); titr++) { |
---|
| 3851 | addTrack(*titr); |
---|
| 3852 | } |
---|
| 3853 | |
---|
| 3854 | std::vector<unsigned char *>::iterator citr; |
---|
| 3855 | for(citr = _colors.begin(); citr != _colors.end(); citr++) { |
---|
| 3856 | addTrackColor(*citr); |
---|
| 3857 | } |
---|
| 3858 | } |
---|
| 3859 | void G4GMocrenIO::addTrack(std::vector<float *> & _steps, unsigned char _color[3]) { |
---|
| 3860 | |
---|
| 3861 | std::vector<float *>::iterator itr = _steps.begin(); |
---|
| 3862 | std::vector<struct GMocrenTrack::Step> steps; |
---|
| 3863 | for(; itr != _steps.end(); itr++) { |
---|
| 3864 | struct GMocrenTrack::Step step; |
---|
| 3865 | for(int i = 0; i < 3; i++) { |
---|
| 3866 | step.startPoint[i] = (*itr)[i]; |
---|
| 3867 | step.endPoint[i] = (*itr)[i+3]; |
---|
| 3868 | } |
---|
| 3869 | steps.push_back(step); |
---|
| 3870 | } |
---|
| 3871 | GMocrenTrack track; |
---|
| 3872 | track.setTrack(steps); |
---|
| 3873 | track.setColor(_color); |
---|
| 3874 | kTracks.push_back(track); |
---|
| 3875 | |
---|
| 3876 | } |
---|
| 3877 | void G4GMocrenIO::getTrack(int _num, std::vector<float *> & _steps, |
---|
| 3878 | std::vector<unsigned char *> & _color) { |
---|
| 3879 | |
---|
| 3880 | if(_num > (int)kTracks.size()) { |
---|
| 3881 | std::cerr << "ERROR in getTrack() : " << std::endl; |
---|
| 3882 | std::exit(-1); |
---|
| 3883 | } |
---|
| 3884 | unsigned char * color = new unsigned char[3]; |
---|
| 3885 | kTracks[_num].getColor(color); |
---|
| 3886 | _color.push_back(color); |
---|
| 3887 | |
---|
| 3888 | // steps |
---|
| 3889 | int nsteps = kTracks[_num].getNumberOfSteps(); |
---|
| 3890 | for(int ns = 0; ns < nsteps; ns++) { |
---|
| 3891 | float * stepPoints = new float[6]; |
---|
| 3892 | kTracks[_num].getStep(stepPoints[0], stepPoints[1], stepPoints[2], |
---|
| 3893 | stepPoints[3], stepPoints[4], stepPoints[5], |
---|
| 3894 | ns); |
---|
| 3895 | _steps.push_back(stepPoints); |
---|
| 3896 | } |
---|
| 3897 | } |
---|
| 3898 | |
---|
| 3899 | void G4GMocrenIO::translateTracks(std::vector<float> & _translate) { |
---|
| 3900 | std::vector<class GMocrenTrack>::iterator itr = kTracks.begin(); |
---|
| 3901 | for(; itr != kTracks.end(); itr++) { |
---|
| 3902 | itr->translate(_translate); |
---|
| 3903 | } |
---|
| 3904 | } |
---|
| 3905 | |
---|
| 3906 | |
---|
| 3907 | |
---|
| 3908 | |
---|
| 3909 | //----- Detector information -----// |
---|
| 3910 | int G4GMocrenIO::getNumberOfDetectors() { |
---|
| 3911 | return (int)kDetectors.size(); |
---|
| 3912 | } |
---|
| 3913 | void G4GMocrenIO::addDetector(std::string & _name, |
---|
| 3914 | std::vector<float *> & _det, |
---|
| 3915 | unsigned char _color[3]) { |
---|
| 3916 | |
---|
| 3917 | std::vector<float *>::iterator itr = _det.begin(); |
---|
| 3918 | std::vector<struct GMocrenDetector::Edge> edges; |
---|
| 3919 | for(; itr != _det.end(); itr++) { |
---|
| 3920 | struct GMocrenDetector::Edge edge; |
---|
| 3921 | for(int i = 0; i < 3; i++) { |
---|
| 3922 | edge.startPoint[i] = (*itr)[i]; |
---|
| 3923 | edge.endPoint[i] = (*itr)[i+3]; |
---|
| 3924 | } |
---|
| 3925 | edges.push_back(edge); |
---|
| 3926 | } |
---|
| 3927 | GMocrenDetector detector; |
---|
| 3928 | detector.setDetector(edges); |
---|
| 3929 | detector.setColor(_color); |
---|
| 3930 | detector.setName(_name); |
---|
| 3931 | kDetectors.push_back(detector); |
---|
| 3932 | |
---|
| 3933 | } |
---|
| 3934 | |
---|
| 3935 | void G4GMocrenIO::getDetector(int _num, std::vector<float *> & _edges, |
---|
| 3936 | std::vector<unsigned char *> & _color, |
---|
| 3937 | std::string & _detName) { |
---|
| 3938 | |
---|
| 3939 | if(_num > (int)kDetectors.size()) { |
---|
| 3940 | std::cerr << "ERROR in getDetector() : " << std::endl; |
---|
| 3941 | std::exit(-1); |
---|
| 3942 | } |
---|
| 3943 | |
---|
| 3944 | _detName = kDetectors[_num].getName(); |
---|
| 3945 | |
---|
| 3946 | unsigned char * color = new unsigned char[3]; |
---|
| 3947 | kDetectors[_num].getColor(color); |
---|
| 3948 | _color.push_back(color); |
---|
| 3949 | |
---|
| 3950 | // edges |
---|
| 3951 | int nedges = kDetectors[_num].getNumberOfEdges(); |
---|
| 3952 | for(int ne = 0; ne < nedges; ne++) { |
---|
| 3953 | float * edgePoints = new float[6]; |
---|
| 3954 | kDetectors[_num].getEdge(edgePoints[0], edgePoints[1], edgePoints[2], |
---|
| 3955 | edgePoints[3], edgePoints[4], edgePoints[5], |
---|
| 3956 | ne); |
---|
| 3957 | _edges.push_back(edgePoints); |
---|
| 3958 | } |
---|
| 3959 | } |
---|
| 3960 | |
---|
| 3961 | void G4GMocrenIO::translateDetector(std::vector<float> & _translate) { |
---|
| 3962 | std::vector<class GMocrenDetector>::iterator itr = kDetectors.begin(); |
---|
| 3963 | for(; itr != kDetectors.end(); itr++) { |
---|
| 3964 | itr->translate(_translate); |
---|
| 3965 | } |
---|
| 3966 | } |
---|
| 3967 | |
---|
| 3968 | // endian conversion |
---|
| 3969 | template <typename T> |
---|
| 3970 | void G4GMocrenIO::convertEndian(char * _val, T & _rval) { |
---|
| 3971 | |
---|
| 3972 | if((kLittleEndianOutput && !kLittleEndianInput) || // big endian |
---|
| 3973 | (!kLittleEndianOutput && kLittleEndianInput)) { // little endian |
---|
| 3974 | |
---|
| 3975 | const int SIZE = sizeof(_rval); |
---|
| 3976 | char ctemp; |
---|
| 3977 | for(int i = 0; i < SIZE/2; i++) { |
---|
| 3978 | ctemp = _val[i]; |
---|
| 3979 | _val[i] = _val[SIZE - 1 - i]; |
---|
| 3980 | _val[SIZE - 1 - i] = ctemp; |
---|
| 3981 | } |
---|
| 3982 | } |
---|
| 3983 | _rval = *(T *)_val; |
---|
| 3984 | } |
---|
| 3985 | |
---|
| 3986 | // inversion of byte order |
---|
| 3987 | template <typename T> |
---|
| 3988 | void G4GMocrenIO::invertByteOrder(char * _val, T & _rval) { |
---|
| 3989 | |
---|
| 3990 | const int SIZE = sizeof(_rval); |
---|
| 3991 | //char * cval = new char[SIZE]; |
---|
| 3992 | union { |
---|
| 3993 | char cu[16]; |
---|
| 3994 | T tu; |
---|
| 3995 | } uni; |
---|
| 3996 | for(int i = 0; i < SIZE; i++) { |
---|
| 3997 | uni.cu[i] = _val[SIZE-1-i]; |
---|
| 3998 | //cval[i] = _val[SIZE-i-1]; |
---|
| 3999 | } |
---|
| 4000 | //_rval = *(T *)cval; |
---|
| 4001 | _rval = uni.tu; |
---|
| 4002 | //delete [] cval; |
---|
| 4003 | } |
---|
| 4004 | |
---|
| 4005 | //----- kVerbose information -----// |
---|
| 4006 | void G4GMocrenIO::setVerboseLevel(int _level) { |
---|
| 4007 | kVerbose = _level; |
---|
| 4008 | } |
---|
| 4009 | |
---|