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); |
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453 | } |
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454 | |
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455 | bool G4GMocrenIO::storeData4() { |
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456 | |
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457 | bool DEBUG = false;// |
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458 | |
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459 | if(DEBUG || kVerbose > 0) |
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460 | std::cout << ">>>>>>> store data (ver.4) <<<<<<<" << std::endl; |
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461 | if(DEBUG || kVerbose > 0) |
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462 | std::cout << " " << kFileName << std::endl; |
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463 | |
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464 | // output file open |
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465 | std::ofstream ofile(kFileName.c_str(), |
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466 | std::ios_base::out|std::ios_base::binary); |
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467 | if(DEBUG || kVerbose > 0) |
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468 | std::cout << " file open status: " << ofile << std::endl; |
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469 | |
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470 | // file identifier |
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471 | ofile.write("gMocren ", 8); |
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472 | |
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473 | // file version |
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474 | unsigned char ver = 0x04; |
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475 | ofile.write((char *)&ver, 1); |
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476 | |
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477 | // endian |
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478 | //ofile.write((char *)&kLittleEndianOutput, sizeof(char)); |
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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 | |
---|