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 | // File I/O manager class for writing or reading calcuated dose |
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28 | // distribution and some event information |
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29 | // |
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30 | // |
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31 | // Mar. 31, 2009 : release for the gMocrenFile driver |
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32 | // |
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33 | // Akinori Kimura |
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34 | // |
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35 | // gMocren home page: |
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36 | // http://geant4.kek.jp/gMocren/ |
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37 | // |
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38 | #ifndef GMOCRENIO_HH |
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39 | #define GMOCRENIO_HH |
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40 | |
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41 | #include <vector> |
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42 | #include <string> |
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43 | #include <fstream> |
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44 | #include <map> |
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45 | |
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46 | // |
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47 | //----- GMocrenDataPrimitive class -----// |
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48 | // data primitive class for volume data |
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49 | // |
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50 | template <typename T> class GMocrenDataPrimitive { |
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51 | protected: |
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52 | int kSize[3]; |
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53 | double kScale; |
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54 | T kMinmax[2]; |
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55 | float kCenter[3]; |
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56 | std::vector<T *> kImage; |
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57 | std::string kDataName; |
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58 | //std::vector<std::vector<T>> image; |
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59 | |
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60 | public: |
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61 | GMocrenDataPrimitive(); |
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62 | //GMocrenDataPrimitive(GMocrenDataPrimitive<T> & _prim); |
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63 | ~GMocrenDataPrimitive(); |
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64 | |
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65 | GMocrenDataPrimitive<T> & operator = (const GMocrenDataPrimitive<T> & _right); |
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66 | GMocrenDataPrimitive<T> & operator + (const GMocrenDataPrimitive<T> & _right); |
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67 | GMocrenDataPrimitive<T> & operator += (const GMocrenDataPrimitive<T> & _right); |
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68 | |
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69 | void clear(); |
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70 | void clearImage(); |
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71 | void setSize(int _size[3]); |
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72 | void getSize(int _size[3]); |
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73 | void setScale(double & _scale); |
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74 | double getScale(); |
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75 | void setMinMax(T _minmax[2]); |
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76 | void getMinMax(T _minmax[2]); |
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77 | void setImage(std::vector<T *> & _image); |
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78 | void addImage(T * _image); |
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79 | std::vector<T *> & getImage(); |
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80 | T * getImage(int _z); // get image of each layer |
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81 | void setCenterPosition(float _center[3]); |
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82 | void getCenterPosition(float _center[3]); |
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83 | void setName(std::string & _name); |
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84 | std::string getName(); |
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85 | }; |
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86 | |
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87 | |
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88 | // |
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89 | //----- GMocrenTrack class -----// |
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90 | // |
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91 | class GMocrenTrack { |
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92 | public: |
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93 | struct Step { |
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94 | float startPoint[3]; |
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95 | float endPoint[3]; |
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96 | }; |
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97 | protected: |
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98 | std::vector<struct Step> kTrack; |
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99 | unsigned char kColor[3]; |
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100 | |
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101 | public: |
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102 | GMocrenTrack(); |
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103 | ~GMocrenTrack(){;} |
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104 | |
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105 | |
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106 | int getNumberOfSteps() {return (int)kTrack.size();} |
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107 | void addStep(float _startx, float _starty, float _startz, |
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108 | float _endx, float _endy, float _endz); |
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109 | void getStep(float & _startx, float & _starty, float & _startz, |
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110 | float & _endx, float & _endy, float & _endz, |
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111 | int _num); |
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112 | void setTrack(std::vector<struct Step> & _aTrack) {kTrack = _aTrack;} |
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113 | void setColor(unsigned char _color[3]) { |
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114 | for(int i = 0; i < 3; i++) kColor[i] = _color[i]; |
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115 | } |
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116 | void getColor(unsigned char _color[3]) { |
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117 | for(int i = 0; i < 3; i++) _color[i] = kColor[i]; |
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118 | } |
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119 | void translate(std::vector<float> & _tranlate); |
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120 | }; |
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121 | |
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122 | |
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123 | |
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124 | // |
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125 | //----- GMocrenDetector class -----// |
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126 | // |
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127 | class GMocrenDetector { |
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128 | public: |
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129 | struct Edge { |
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130 | float startPoint[3]; |
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131 | float endPoint[3]; |
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132 | }; |
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133 | protected: |
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134 | std::vector<struct Edge> kDetector; |
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135 | unsigned char kColor[3]; |
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136 | std::string kName; |
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137 | |
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138 | public: |
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139 | GMocrenDetector(); |
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140 | ~GMocrenDetector(){;} |
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141 | |
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142 | |
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143 | int getNumberOfEdges() {return (int)kDetector.size();} |
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144 | void addEdge(float _startx, float _starty, float _startz, |
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145 | float _endx, float _endy, float _endz); |
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146 | void getEdge(float & _startx, float & _starty, float & _startz, |
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147 | float & _endx, float & _endy, float & _endz, |
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148 | int _num); |
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149 | void setDetector(std::vector<struct Edge> & _aDetector) {kDetector = _aDetector;} |
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150 | void setColor(unsigned char _color[3]) { |
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151 | for(int i = 0; i < 3; i++) kColor[i] = _color[i]; |
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152 | } |
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153 | void getColor(unsigned char _color[3]) { |
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154 | for(int i = 0; i < 3; i++) _color[i] = kColor[i]; |
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155 | } |
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156 | void setName(std::string & _name) { kName = _name;} |
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157 | std::string getName() {return kName;} |
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158 | |
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159 | void translate(std::vector<float> & _tranlate); |
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160 | }; |
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161 | |
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162 | |
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163 | // |
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164 | //----- G4GMocrenIO class -----// |
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165 | // |
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166 | class G4GMocrenIO { |
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167 | public: |
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168 | // file id |
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169 | static std::string kId; |
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170 | |
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171 | // file version |
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172 | static std::string kVersion; |
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173 | |
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174 | // data file name |
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175 | static std::string kFileName; |
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176 | |
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177 | // file data endian: little or not |
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178 | static char kLittleEndianInput; |
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179 | static char kLittleEndianOutput; |
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180 | |
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181 | static std::string kComment; |
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182 | |
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183 | // number of events |
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184 | static int kNumberOfEvents; |
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185 | |
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186 | // pointer to the modality image data |
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187 | static unsigned int kPointerToModalityData; |
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188 | // pointer to the dose distribution image data |
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189 | static std::vector<unsigned int> kPointerToDoseDistData; |
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190 | // pointer to the ROI image data |
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191 | static unsigned int kPointerToROIData; |
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192 | // pointer to the track data |
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193 | static unsigned int kPointerToTrackData; |
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194 | // pointer to the detector data |
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195 | static unsigned int kPointerToDetectorData; |
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196 | |
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197 | // voxel spacing (universal size) |
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198 | static float kVoxelSpacing[3]; |
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199 | |
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200 | //----- modality image -----// |
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201 | static class GMocrenDataPrimitive<short> kModality; |
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202 | // density map to modality (CT) values |
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203 | static std::vector<float> kModalityImageDensityMap; |
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204 | static std::string kModalityUnit; |
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205 | |
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206 | //----- dose distribution -----// |
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207 | static std::vector<class GMocrenDataPrimitive<double> > kDose; |
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208 | //std::vector<short *> kShortDose; |
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209 | static std::string kDoseUnit; |
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210 | |
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211 | //----- RoI -----// |
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212 | static std::vector<class GMocrenDataPrimitive<short> > kRoi; |
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213 | |
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214 | //----- track information -----// |
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215 | static std::vector<float *> kSteps; // begin (x,y,z), end (x,y,z) |
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216 | static std::vector<unsigned char *> kStepColors; // r, g, b |
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217 | |
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218 | static std::vector<class GMocrenTrack> kTracks; |
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219 | bool kTracksWillBeStored; |
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220 | |
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221 | //----- detector information -----// |
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222 | static std::vector<class GMocrenDetector> kDetectors; |
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223 | |
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224 | //----- verbose information -----// |
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225 | static int kVerbose; // verbose level : 0 - 5 (none - overtalk) |
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226 | |
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227 | public: |
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228 | // constructor |
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229 | G4GMocrenIO(); |
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230 | // destructor |
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231 | ~G4GMocrenIO(); |
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232 | |
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233 | // initialize |
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234 | void initialize(); |
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235 | |
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236 | // set the gMocren data file name |
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237 | void setFileName(std::string & _filename) {kFileName = _filename;} |
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238 | void setFileName(char * _filename) {kFileName = _filename;} |
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239 | // get the gMocren data file name |
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240 | std::string & getFileName() {return kFileName;} |
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241 | // store all data in the gMocren data file |
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242 | bool storeData(char * _filename); // interface for version 4 |
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243 | bool storeData(); |
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244 | bool storeData2(char * _filename); // version 2 |
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245 | bool storeData2(); |
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246 | bool storeData3(char * _filename); // version 3 |
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247 | bool storeData3(); |
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248 | bool storeData4(char * _filename); // version 4 |
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249 | bool storeData4(); |
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250 | // retrieve all data from the gMocren data file |
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251 | bool retrieveData(char * _filename); // interface |
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252 | bool retrieveData(); |
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253 | bool retrieveData2(char * _filename); //version 2 |
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254 | bool retrieveData2(); |
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255 | bool retrieveData3(char * _filename); // version 3 |
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256 | bool retrieveData3(); |
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257 | bool retrieveData4(char * _filename); // version 4 |
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258 | bool retrieveData4(); |
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259 | |
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260 | // get & set the file id |
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261 | std::string & getID() {return kId;} |
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262 | void setID(); |
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263 | void setID(std::string & _id) {kId = _id;} |
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264 | |
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265 | // get & set the file version |
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266 | std::string & getVersion(); |
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267 | void setVersion(std::string & _version); |
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268 | |
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269 | // set endians of input/output data |
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270 | void setLittleEndianInput(bool _little); |
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271 | void setLittleEndianOutput(bool _little); |
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272 | |
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273 | // get & set comment |
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274 | std::string & getComment() {return kComment;} |
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275 | void setComment(std::string & _comment) {kComment = _comment;} |
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276 | |
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277 | |
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278 | // voxel spacing |
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279 | void setVoxelSpacing(float _spacing[3]); |
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280 | void getVoxelSpacing(float _spacing[3]); |
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281 | |
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282 | // get & set number of events |
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283 | int & getNumberOfEvents(); |
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284 | void setNumberOfEvents(int & _numberOfEvents); |
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285 | void addOneEvent(); |
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286 | |
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287 | // set pointer the modality image data |
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288 | void setPointerToModalityData(unsigned int & _pointer); |
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289 | unsigned int getPointerToModalityData(); |
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290 | // set pointer the dose distribution image data |
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291 | void addPointerToDoseDistData(unsigned int & _pointer); |
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292 | unsigned int getPointerToDoseDistData(int _elem = 0); |
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293 | // set pointer the ROI image data |
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294 | void setPointerToROIData(unsigned int & _pointer); |
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295 | unsigned int getPointerToROIData(); |
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296 | // set pointer the track data |
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297 | void setPointerToTrackData(unsigned int & _pointer); |
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298 | unsigned int getPointerToTrackData(); |
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299 | private: |
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300 | // calculate pointers |
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301 | void calcPointers4(); |
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302 | void calcPointers3(); |
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303 | void calcPointers2(); |
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304 | |
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305 | |
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306 | //----- Modality image -----// |
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307 | public: |
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308 | // get & set the modality image size |
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309 | void getModalityImageSize(int _size[3]); |
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310 | void setModalityImageSize(int _size[3]); |
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311 | // get & set the modality image spacing size |
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312 | void getModalityImageVoxelSpacing(float _size[3]); // un-usable |
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313 | void setModalityImageVoxelSpacing(float _size[3]); // un-usable |
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314 | // get & set the modality image size |
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315 | void setModalityImageScale(double & _scale); |
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316 | double getModalityImageScale(); |
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317 | // set the modality image in CT |
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318 | void setModalityImage(short * _image); |
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319 | short * getModalityImage(int _z); |
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320 | void clearModalityImage(); |
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321 | // set/get the modality image density map |
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322 | void setModalityImageDensityMap(std::vector<float> & _map); |
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323 | std::vector<float> & getModalityImageDensityMap(); |
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324 | // set the modality image min./max. |
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325 | void setModalityImageMinMax(short _minmax[2]); |
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326 | // get min. & max. of the modality image |
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327 | void getModalityImageMinMax(short _minmax[2]); |
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328 | short getModalityImageMax(); |
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329 | short getModalityImageMin(); |
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330 | // set center of the modality image position |
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331 | void setModalityCenterPosition(float _center[3]); |
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332 | void getModalityCenterPosition(float _center[3]); |
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333 | // get & set the modality image unit |
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334 | std::string getModalityImageUnit(); |
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335 | void setModalityImageUnit(std::string & _unit); |
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336 | |
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337 | short convertDensityToHU(float & _dens); |
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338 | |
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339 | //----- Dose distribution -----// |
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340 | |
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341 | // instanciate a dose distribution data object |
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342 | void newDoseDist(); |
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343 | // get number of dose distribion data |
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344 | int getNumDoseDist(); |
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345 | // get & set the dose distribution unit |
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346 | std::string getDoseDistUnit(int _num = 0); |
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347 | void setDoseDistUnit(std::string & _unit, int _num = 0); |
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348 | // get & set the dose distribution image size |
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349 | void getDoseDistSize(int _size[3], int _num = 0); |
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350 | void setDoseDistSize(int _size[3], int _num = 0); |
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351 | // get min. & max. of the dose distribution image |
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352 | void setDoseDistMinMax(short _minmax[2], int _num = 0); |
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353 | void getDoseDistMinMax(short _minmax[2], int _num = 0); |
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354 | // get min. & max. of the dose distribution |
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355 | void setDoseDistMinMax(double _minmax[2], int _num = 0); |
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356 | void getDoseDistMinMax(double _minmax[2], int _num = 0); |
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357 | // get & set scale value of the dose distribution for the image |
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358 | void setDoseDistScale(double & _scale, int _num = 0); |
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359 | double getDoseDistScale(int _num = 0); |
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360 | // set the dose distribution image |
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361 | void setShortDoseDist(short * _image, int _num = 0); |
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362 | void getShortDoseDist(short * _data, int _z, int _num = 0); |
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363 | void getShortDoseDistMinMax(short _minmax[2], int _num = 0); |
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364 | // set the dose distribution |
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365 | void setDoseDist(double * _image, int _num = 0); |
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366 | double * getDoseDist(int _z, int _num = 0); |
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367 | // add another dose ditribution map to this map |
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368 | bool addDoseDist(std::vector<double *> & _image, int _num = 0); |
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369 | |
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370 | // get & get center position of calculated dose region |
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371 | void getDoseDistCenterPosition(float _center[3], int _num = 0); |
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372 | void setDoseDistCenterPosition(float _center[3], int _num = 0); |
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373 | |
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374 | // get & get name of calculated dose distribution |
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375 | std::string getDoseDistName(int _num = 0); |
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376 | void setDoseDistName(std::string _name, int _num = 0); |
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377 | |
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378 | // copy dose distributions |
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379 | void copyDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose); |
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380 | // merge two dose distributions |
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381 | bool mergeDoseDist(std::vector<class GMocrenDataPrimitive<double> > & _dose); |
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382 | |
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383 | // clear all dose distributions |
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384 | void clearDoseDistAll(); |
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385 | protected: |
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386 | // check whether dose variable is empty or not |
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387 | bool isDoseEmpty(); |
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388 | // calcuated scale value to convert dose distribution into image |
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389 | void calcDoseDistScale(); |
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390 | |
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391 | public: |
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392 | //----- RoI -----// |
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393 | |
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394 | // instanciate an RoI data object |
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395 | void newROI(); |
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396 | // get number of RoI data |
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397 | int getNumROI(); |
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398 | // get & set the ROI image scale |
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399 | double getROIScale(int _num = 0); |
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400 | void setROIScale(double & _scale, int _num = 0); |
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401 | // get & set the ROI image |
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402 | short * getROI(int _z, int _num = 0); |
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403 | void setROI(short * _image, int _num = 0); |
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404 | // get & set the ROI image size |
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405 | void getROISize(int _size[3], int _num = 0); |
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406 | void setROISize(int _size[3], int _num = 0); |
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407 | // get & set position of the ROI region center |
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408 | void getROICenterPosition(float _center[3], int _num = 0); |
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409 | void setROICenterPosition(float _center[3], int _num = 0); |
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410 | // get & set the ROI image min. and max. |
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411 | void getROIMinMax(short _minmax[2], int _num = 0); |
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412 | void setROIMinMax(short _minmax[2], int _num = 0); |
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413 | void clearROIAll(); |
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414 | protected: |
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415 | // check whether RoI variable is empty or not |
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416 | bool isROIEmpty(); |
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417 | |
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418 | |
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419 | public: |
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420 | //----- Track -----// |
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421 | // get number of tracks |
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422 | int getNumTracks(); |
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423 | int getNumTracks4(); |
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424 | // get & set tracks |
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425 | std::vector<float *> & getTracks(); |
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426 | void getTrack(int _num, std::vector<float *> & _steps, |
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427 | std::vector<unsigned char * > & _color); |
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428 | void addTrack(float * _tracks); |
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429 | void setTracks(std::vector<float *> & _tracks); |
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430 | std::vector<unsigned char *> & getTrackColors(); |
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431 | void addTrackColor(unsigned char * _colors); |
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432 | void setTrackColors(std::vector<unsigned char *> & _trackColors); |
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433 | void copyTracks(std::vector<float *> & _tracks, std::vector<unsigned char *> & _colors); |
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434 | void mergeTracks(std::vector<float *> & _tracks, std::vector<unsigned char *> & _colors); |
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435 | void addTrack(std::vector<float *> & _steps, unsigned char _color[3]); |
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436 | |
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437 | void notStoredTracks() {kTracksWillBeStored = false;}; |
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438 | void translateTracks(std::vector<float> & _translateo); |
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439 | void clearTracks() {kTracks.clear();} |
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440 | |
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441 | |
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442 | //----- Detectors -----// |
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443 | // get number of detectors |
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444 | int getNumberOfDetectors(); |
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445 | // add one detector which consists of edges (float[6]) |
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446 | void addDetector(std::string & _name, std::vector<float *> & _det, unsigned char _color[3]); |
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447 | void getDetector(int _num, std::vector<float *> & _edges, |
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448 | std::vector<unsigned char *> & _color, |
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449 | std::string & _detectorName); |
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450 | void translateDetector(std::vector<float> & _translate); |
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451 | void clearDetector() {kDetectors.clear();} |
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452 | |
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453 | protected: |
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454 | // endian conversion |
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455 | template <typename Type> void convertEndian(char *, Type &); |
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456 | // byte order inversion |
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457 | template <typename T> void invertByteOrder(char * _val, T & _rval); |
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458 | |
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459 | |
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460 | public: |
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461 | //----- verbose information -----// |
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462 | void setVerboseLevel(int _level); |
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463 | |
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464 | }; |
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465 | |
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466 | #endif |
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467 | |
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