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 | // The code was written by : |
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27 | // *Louis Archambault louis.archambault@phy.ulaval.ca, |
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28 | // *Luc Beaulieu beaulieu@phy.ulaval.ca |
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29 | // +Vincent Hubert-Tremblay at tigre.2@sympatico.ca |
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30 | // |
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31 | // |
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32 | // *Centre Hospitalier Universitaire de Quebec (CHUQ), |
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33 | // Hotel-Dieu de Quebec, departement de Radio-oncologie |
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34 | // 11 cote du palais. Quebec, QC, Canada, G1R 2J6 |
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35 | // tel (418) 525-4444 #6720 |
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36 | // fax (418) 691 5268 |
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37 | // |
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38 | // + Universit.Aé Laval, Québec (QC) Canada |
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39 | //******************************************************* |
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40 | // |
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41 | //******************************************************* |
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42 | // |
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43 | //******************************************************* |
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44 | // |
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45 | // DicomHandler.cc : |
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46 | // - Handling of DICM images |
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47 | // - Reading headers and pixels |
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48 | // - Transforming pixel to density and creating *.g4dcm |
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49 | // files |
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50 | // - Definitions are in DicomHandler.hh |
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51 | //******************************************************* |
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52 | |
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53 | #include "DicomHandler.hh" |
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54 | #include "globals.hh" |
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55 | #include "G4ios.hh" |
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56 | #include <fstream> |
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57 | |
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58 | #include <cctype> |
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59 | #include <cstring> |
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60 | |
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61 | |
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62 | DicomHandler::DicomHandler() |
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63 | : DATABUFFSIZE(8192), LINEBUFFSIZE(128), FILENAMESIZE(512), |
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64 | compression(0), nFiles(0), rows(0), columns(0), |
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65 | bitAllocated(0), maxPixelValue(0), minPixelValue(0), |
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66 | pixelSpacingX(0.), pixelSpacingY(0.), |
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67 | sliceThickness(0.), sliceLocation(0.), |
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68 | rescaleIntercept(0), rescaleSlope(0), |
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69 | littleEndian(true), implicitEndian(false), |
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70 | pixelRepresentation(0) { |
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71 | ; |
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72 | } |
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73 | |
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74 | DicomHandler::~DicomHandler() { |
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75 | ; |
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76 | } |
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77 | |
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78 | G4int DicomHandler::ReadFile(FILE *dicom, char * filename2) |
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79 | { |
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80 | G4cout << " ReadFile " << filename2 << G4endl; |
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81 | G4int returnvalue = 0; |
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82 | char * buffer = new char[LINEBUFFSIZE]; |
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83 | |
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84 | implicitEndian = false; |
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85 | littleEndian = true; |
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86 | |
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87 | std::fread( buffer, 1, 128, dicom ); // The first 128 bytes |
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88 | //are not important |
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89 | // Reads the "DICOM" letters |
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90 | std::fread( buffer, 1, 4, dicom ); |
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91 | // if there is no preamble, the FILE pointer is rewinded. |
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92 | if(std::strncmp("DICM", buffer, 4) != 0) { |
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93 | std::fseek(dicom, 0, SEEK_SET); |
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94 | implicitEndian = true; |
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95 | } |
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96 | |
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97 | short readGroupId; // identify the kind of input data |
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98 | short readElementId; // identify a particular type information |
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99 | short elementLength2; // deal with element length in 2 bytes |
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100 | G4int elementLength4; // deal with element length in 4 bytes |
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101 | |
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102 | char * data = new char[DATABUFFSIZE]; |
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103 | |
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104 | // Read information up to the pixel data |
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105 | while(true) { |
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106 | |
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107 | //Reading groups and elements : |
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108 | readGroupId = 0; |
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109 | readElementId = 0; |
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110 | // group ID |
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111 | std::fread(buffer, 2, 1, dicom); |
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112 | GetValue(buffer, readGroupId); |
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113 | // element ID |
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114 | std::fread(buffer, 2, 1, dicom); |
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115 | GetValue(buffer, readElementId); |
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116 | |
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117 | // Creating a tag to be identified afterward |
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118 | G4int tagDictionary = readGroupId*0x10000 + readElementId; |
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119 | |
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120 | |
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121 | // VR or element length |
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122 | std::fread(buffer,2,1,dicom); |
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123 | GetValue(buffer, elementLength2); |
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124 | |
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125 | // If value representation (VR) is OB, OW, SQ, UN, |
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126 | //the next length is 32 bits |
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127 | if((elementLength2 == 0x424f || // "OB" |
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128 | elementLength2 == 0x574f || // "OW" |
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129 | elementLength2 == 0x5153 || // "SQ" |
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130 | elementLength2 == 0x4e55) && // "UN" |
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131 | !implicitEndian ) { // explicit VR |
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132 | |
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133 | std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes |
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134 | |
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135 | // element length |
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136 | std::fread(buffer, 4, 1, dicom); |
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137 | GetValue(buffer, elementLength4); |
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138 | |
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139 | // beginning of the pixels |
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140 | if(tagDictionary == 0x7FE00010) break; |
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141 | |
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142 | // Reading the information with data |
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143 | std::fread(data, elementLength4,1,dicom); |
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144 | |
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145 | |
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146 | } else { // length is 16 bits : |
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147 | |
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148 | if(!implicitEndian || readGroupId == 2) { |
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149 | // element length (2 bytes) |
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150 | std::fread(buffer, 2, 1, dicom); |
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151 | GetValue(buffer, elementLength2); |
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152 | elementLength4 = elementLength2; |
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153 | |
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154 | } else { |
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155 | // element length (4 bytes) |
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156 | if(std::fseek(dicom, -2, SEEK_CUR) != 0) { |
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157 | G4cerr << "[DicomHandler] fseek failed" << G4endl; |
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158 | exit(-10); |
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159 | } |
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160 | std::fread(buffer, 4, 1, dicom); |
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161 | GetValue(buffer, elementLength4); |
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162 | } |
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163 | |
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164 | // beginning of the pixels |
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165 | if(tagDictionary == 0x7FE00010) break; |
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166 | |
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167 | std::fread(data, elementLength4, 1, dicom); |
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168 | } |
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169 | |
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170 | // NULL termination |
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171 | data[elementLength4] = '\0'; |
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172 | |
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173 | // analyzing information |
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174 | GetInformation(tagDictionary, data); |
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175 | } |
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176 | |
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177 | // Creating files to store information |
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178 | std::ofstream foutG4DCM; |
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179 | G4String fnameG4DCM = G4String(filename2) + ".g4dcm"; |
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180 | foutG4DCM.open(fnameG4DCM); |
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181 | G4cout << " opened fnameG4DCM file " << fnameG4DCM << G4endl; |
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182 | |
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183 | foutG4DCM << fMaterialIndices.size() << G4endl; |
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184 | //--- Write materials |
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185 | size_t ii = 0; |
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186 | std::map<G4double,G4String>::const_iterator ite; |
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187 | for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++, ii++ ){ |
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188 | foutG4DCM << ii << " " << (*ite).second << G4endl; |
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189 | } |
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190 | //--- Write number of voxels (assume only one voxel in Z) |
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191 | foutG4DCM << rows/compression << " " << columns/compression << " 1 " << G4endl; |
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192 | //--- Write minimum and maximum extensions |
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193 | foutG4DCM << -pixelSpacingX*rows/2 << " " << pixelSpacingX*rows/2 << G4endl; |
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194 | foutG4DCM << -pixelSpacingY*columns/2 << " " << pixelSpacingY*columns/2 << G4endl; |
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195 | foutG4DCM << sliceLocation-sliceThickness/2. << " " << sliceLocation+sliceThickness/2. << G4endl; |
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196 | |
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197 | ReadData( dicom, filename2 ); |
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198 | |
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199 | StoreData( foutG4DCM ); |
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200 | |
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201 | foutG4DCM.close(); |
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202 | |
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203 | // |
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204 | delete [] buffer; |
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205 | delete [] data; |
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206 | |
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207 | return returnvalue; |
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208 | } |
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209 | |
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210 | // |
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211 | void DicomHandler::GetInformation(G4int & tagDictionary, char * data) { |
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212 | if(tagDictionary == 0x00280010 ) { // Number of Rows |
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213 | GetValue(data, rows); |
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214 | std::printf("[0x00280010] Rows -> %i\n",rows); |
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215 | |
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216 | } else if(tagDictionary == 0x00280011 ) { // Number of columns |
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217 | GetValue(data, columns); |
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218 | std::printf("[0x00280011] Columns -> %i\n",columns); |
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219 | |
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220 | } else if(tagDictionary == 0x00280102 ) { // High bits ( not used ) |
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221 | short highBits; |
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222 | GetValue(data, highBits); |
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223 | std::printf("[0x00280102] High bits -> %i\n",highBits); |
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224 | |
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225 | } else if(tagDictionary == 0x00280100 ) { // Bits allocated |
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226 | GetValue(data, bitAllocated); |
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227 | std::printf("[0x00280100] Bits allocated -> %i\n", bitAllocated); |
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228 | |
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229 | } else if(tagDictionary == 0x00280101 ) { // Bits stored ( not used ) |
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230 | short bitStored; |
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231 | GetValue(data, bitStored); |
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232 | std::printf("[0x00280101] Bits stored -> %i\n",bitStored); |
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233 | |
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234 | } else if(tagDictionary == 0x00280106 ) { // Min. pixel value |
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235 | GetValue(data, minPixelValue); |
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236 | std::printf("[0x00280106] Min. pixel value -> %i\n", minPixelValue); |
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237 | |
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238 | } else if(tagDictionary == 0x00280107 ) { // Max. pixel value |
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239 | GetValue(data, maxPixelValue); |
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240 | std::printf("[0x00280107] Max. pixel value -> %i\n", maxPixelValue); |
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241 | |
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242 | } else if(tagDictionary == 0x00281053) { // Rescale slope |
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243 | rescaleSlope = atoi(data); |
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244 | std::printf("[0x00281053] Rescale Slope -> %d\n", rescaleSlope); |
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245 | |
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246 | } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept |
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247 | rescaleIntercept = atoi(data); |
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248 | std::printf("[0x00281052] Rescale Intercept -> %d\n", rescaleIntercept ); |
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249 | |
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250 | } else if(tagDictionary == 0x00280103 ) { |
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251 | // Pixel representation ( functions not design to read signed bits ) |
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252 | pixelRepresentation = atoi(data); // 0: unsigned 1: signed |
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253 | std::printf("[0x00280103] Pixel Representation -> %i\n", pixelRepresentation); |
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254 | if(pixelRepresentation == 1 ) { |
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255 | std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, "); |
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256 | std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE "); |
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257 | std::printf("ERROR !!!!!! -> \n"); |
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258 | } |
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259 | |
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260 | } else if(tagDictionary == 0x00080006 ) { // Modality |
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261 | std::printf("[0x00080006] Modality -> %s\n", data); |
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262 | |
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263 | } else if(tagDictionary == 0x00080070 ) { // Manufacturer |
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264 | std::printf("[0x00080070] Manufacturer -> %s\n", data); |
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265 | |
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266 | } else if(tagDictionary == 0x00080080 ) { // Institution Name |
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267 | std::printf("[0x00080080] Institution Name -> %s\n", data); |
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268 | |
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269 | } else if(tagDictionary == 0x00080081 ) { // Institution Address |
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270 | std::printf("[0x00080081] Institution Address -> %s\n", data); |
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271 | |
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272 | } else if(tagDictionary == 0x00081040 ) { // Institution Department Name |
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273 | std::printf("[0x00081040] Institution Department Name -> %s\n", data); |
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274 | |
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275 | } else if(tagDictionary == 0x00081090 ) { // Manufacturer's Model Name |
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276 | std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data); |
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277 | |
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278 | } else if(tagDictionary == 0x00181000 ) { // Device Serial Number |
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279 | std::printf("[0x00181000] Device Serial Number -> %s\n", data); |
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280 | |
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281 | } else if(tagDictionary == 0x00080008 ) { // Image type ( not used ) |
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282 | std::printf("[0x00080008] Image Types -> %s\n", data); |
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283 | |
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284 | } else if(tagDictionary == 0x00283000 ) { // Modality LUT Sequence ( not used ) |
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285 | std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data); |
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286 | |
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287 | } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used ) |
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288 | std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data); |
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289 | |
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290 | } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used ) |
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291 | std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data); |
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292 | |
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293 | } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used ) |
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294 | std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data); |
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295 | |
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296 | } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used ) |
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297 | std::printf("[0x00283006] LUT Data US or SS -> %s\n", data); |
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298 | |
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299 | } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used ) |
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300 | std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data); |
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301 | |
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302 | } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value ( not used ) |
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303 | std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data); |
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304 | |
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305 | } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing |
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306 | G4String datas(data); |
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307 | int iss = datas.find('\\'); |
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308 | pixelSpacingX = atof( datas.substr(0,iss).c_str() ); |
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309 | pixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() ); |
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310 | |
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311 | } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used ) |
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312 | std::printf("[0x00200037] Image Orientation (Patient) -> %s\n", data); |
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313 | |
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314 | } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used ) |
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315 | std::printf("[0x00200032] Image Position (Patient,mm) -> %s\n", data); |
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316 | |
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317 | } else if(tagDictionary == 0x00180050 ) { // Slice Thickness |
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318 | sliceThickness = atof(data); |
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319 | std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", sliceThickness); |
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320 | |
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321 | } else if(tagDictionary == 0x00201041 ) { // Slice Location |
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322 | sliceLocation = atof(data); |
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323 | std::printf("[0x00201041] Slice Location -> %f\n", sliceLocation); |
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324 | |
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325 | } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation ( not used ) |
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326 | std::printf("[0x00280004] Photometric Interpretation -> %s\n", data); |
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327 | |
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328 | } else if(tagDictionary == 0x00020010) { // Endian |
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329 | if(strcmp(data, "1.2.840.10008.1.2") == 0) |
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330 | implicitEndian = true; |
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331 | else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0) |
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332 | littleEndian = false; |
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333 | //else 1.2.840..10008.1.2.1 (explicit little endian) |
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334 | |
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335 | std::printf("[0x00020010] Endian -> %s\n", data); |
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336 | } |
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337 | |
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338 | // others |
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339 | else { |
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340 | std::printf("[0x%x] -> %s\n", tagDictionary, data); |
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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 | |
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346 | void DicomHandler::StoreData(std::ofstream& foutG4DCM) |
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347 | { |
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348 | G4int mean; |
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349 | G4double density; |
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350 | G4bool overflow = false; |
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351 | G4int cpt=1; |
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352 | |
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353 | //----- Print indices of material |
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354 | if(compression == 1) { // no compression: each pixel has a density value) |
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355 | for( G4int ww = 0; ww < rows; ww++) { |
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356 | for( G4int xx = 0; xx < columns; xx++) { |
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357 | mean = tab[ww][xx]; |
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358 | density = Pixel2density(mean); |
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359 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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360 | } |
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361 | foutG4DCM << G4endl; |
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362 | } |
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363 | |
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364 | } else { |
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365 | // density value is the average of a square region of |
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366 | // compression*compression pixels |
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367 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
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368 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
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369 | overflow = false; |
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370 | mean = 0; |
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371 | for(int sumx = 0; sumx < compression; sumx++) { |
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372 | for(int sumy = 0; sumy < compression; sumy++) { |
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373 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
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374 | mean += tab[ww+sumy][xx+sumx]; |
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375 | } |
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376 | if(overflow) break; |
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377 | } |
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378 | mean /= compression*compression; |
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379 | cpt = 1; |
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380 | |
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381 | if(!overflow) { |
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382 | G4double density = Pixel2density(mean); |
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383 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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384 | } |
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385 | } |
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386 | foutG4DCM << G4endl; |
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387 | } |
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388 | |
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389 | } |
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390 | |
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391 | //----- Print densities |
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392 | if(compression == 1) { // no compression: each pixel has a density value) |
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393 | for( G4int ww = 0; ww < rows; ww++) { |
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394 | for( G4int xx = 0; xx < columns; xx++) { |
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395 | mean = tab[ww][xx]; |
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396 | density = Pixel2density(mean); |
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397 | foutG4DCM << density << " "; |
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398 | if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
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399 | } |
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400 | } |
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401 | |
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402 | } else { |
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403 | // density value is the average of a square region of |
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404 | // compression*compression pixels |
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405 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
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406 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
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407 | overflow = false; |
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408 | mean = 0; |
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409 | for(int sumx = 0; sumx < compression; sumx++) { |
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410 | for(int sumy = 0; sumy < compression; sumy++) { |
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411 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
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412 | mean += tab[ww+sumy][xx+sumx]; |
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413 | } |
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414 | if(overflow) break; |
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415 | } |
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416 | mean /= compression*compression; |
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417 | cpt = 1; |
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418 | |
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419 | if(!overflow) { |
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420 | G4double density = Pixel2density(mean); |
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421 | foutG4DCM << density << " "; |
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422 | if( xx/compression%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
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423 | } |
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424 | } |
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425 | } |
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426 | |
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427 | } |
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428 | |
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429 | } |
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430 | |
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431 | void DicomHandler::ReadMaterialIndices( std::ifstream& finData) |
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432 | { |
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433 | size_t nMate; |
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434 | G4String mateName; |
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435 | G4double densityMax; |
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436 | finData >> nMate; |
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437 | if( finData.eof() ) return; |
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438 | |
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439 | G4cout << " ReadMaterialIndices " << nMate << G4endl; |
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440 | for( size_t ii = 0; ii < nMate; ii++ ){ |
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441 | finData >> mateName >> densityMax; |
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442 | fMaterialIndices[densityMax] = mateName; |
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443 | G4cout << ii << " ReadMaterialIndices " << mateName << " " << densityMax << G4endl; |
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444 | } |
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445 | |
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446 | } |
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447 | |
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448 | size_t DicomHandler::GetMaterialIndex( G4double density ) |
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449 | { |
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450 | size_t mateID; |
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451 | std::map<G4double,G4String>::reverse_iterator ite; |
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452 | G4int ii = fMaterialIndices.size(); |
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453 | for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend(); ite++, ii-- ) { |
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454 | if( density >= (*ite).first ) { |
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455 | break; |
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456 | } |
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457 | } |
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458 | //- G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl; |
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459 | return ii; |
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460 | |
---|
461 | } |
---|
462 | |
---|
463 | // |
---|
464 | G4int DicomHandler::ReadData(FILE *dicom,char * filename2) |
---|
465 | { |
---|
466 | G4int returnvalue = 0; |
---|
467 | |
---|
468 | // READING THE PIXELS : |
---|
469 | G4int w = 0; |
---|
470 | G4int len = 0; |
---|
471 | |
---|
472 | tab = new G4int*[rows]; |
---|
473 | for ( G4int i = 0; i < rows; i ++ ) { |
---|
474 | tab[i] = new G4int[columns]; |
---|
475 | } |
---|
476 | |
---|
477 | if(bitAllocated == 8) { // Case 8 bits : |
---|
478 | |
---|
479 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
480 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
481 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
482 | |
---|
483 | unsigned char ch = 0; |
---|
484 | |
---|
485 | len = rows*columns; |
---|
486 | for(G4int j = 0; j < rows; j++) { |
---|
487 | for(G4int i = 0; i < columns; i++) { |
---|
488 | w++; |
---|
489 | std::fread( &ch, 1, 1, dicom); |
---|
490 | tab[j][i] = ch*rescaleSlope + rescaleIntercept; |
---|
491 | } |
---|
492 | } |
---|
493 | returnvalue = 1; |
---|
494 | |
---|
495 | } else { // from 12 to 16 bits : |
---|
496 | char sbuff[2]; |
---|
497 | short pixel; |
---|
498 | len = rows*columns; |
---|
499 | for( G4int j = 0; j < rows; j++) { |
---|
500 | for( G4int i = 0; i < columns; i++) { |
---|
501 | w++; |
---|
502 | std::fread(sbuff, 2, 1, dicom); |
---|
503 | GetValue(sbuff, pixel); |
---|
504 | tab[j][i] = pixel*rescaleSlope + rescaleIntercept; |
---|
505 | } |
---|
506 | } |
---|
507 | } |
---|
508 | |
---|
509 | // Creation of .g4 files wich contains averaged density data |
---|
510 | |
---|
511 | char * nameProcessed = new char[FILENAMESIZE]; |
---|
512 | FILE* processed; |
---|
513 | |
---|
514 | std::sprintf(nameProcessed,"%s.g4",filename2); |
---|
515 | processed = std::fopen(nameProcessed,"w+b"); |
---|
516 | std::printf("### Writing of %s ###\n",nameProcessed); |
---|
517 | |
---|
518 | std::fwrite(&rows, 2, 1, processed); |
---|
519 | std::fwrite(&columns, 2, 1, processed); |
---|
520 | std::fwrite(&pixelSpacingX, 8, 1, processed); |
---|
521 | std::fwrite(&pixelSpacingY, 8, 1, processed); |
---|
522 | std::fwrite(&sliceThickness, 8, 1, processed); |
---|
523 | std::fwrite(&sliceLocation, 8, 1, processed); |
---|
524 | std::fwrite(&compression, 2, 1, processed); |
---|
525 | |
---|
526 | std::printf("%8i %8i\n",rows,columns); |
---|
527 | std::printf("%8f %8f\n",pixelSpacingX,pixelSpacingY); |
---|
528 | std::printf("%8f\n", sliceThickness); |
---|
529 | std::printf("%8f\n", sliceLocation); |
---|
530 | std::printf("%8i\n", compression); |
---|
531 | |
---|
532 | G4int compSize = compression; |
---|
533 | G4int mean; |
---|
534 | G4double density; |
---|
535 | G4bool overflow = false; |
---|
536 | G4int cpt=1; |
---|
537 | |
---|
538 | if(compSize == 1) { // no compression: each pixel has a density value) |
---|
539 | for( G4int ww = 0; ww < rows; ww++) { |
---|
540 | for( G4int xx = 0; xx < columns; xx++) { |
---|
541 | mean = tab[ww][xx]; |
---|
542 | density = Pixel2density(mean); |
---|
543 | std::fwrite(&density, sizeof(G4double), 1, processed); |
---|
544 | } |
---|
545 | } |
---|
546 | |
---|
547 | } else { |
---|
548 | // density value is the average of a square region of |
---|
549 | // compression*compression pixels |
---|
550 | for(G4int ww = 0; ww < rows ;ww += compSize ) { |
---|
551 | for(G4int xx = 0; xx < columns ;xx +=compSize ) { |
---|
552 | overflow = false; |
---|
553 | mean = 0; |
---|
554 | for(int sumx = 0; sumx < compSize; sumx++) { |
---|
555 | for(int sumy = 0; sumy < compSize; sumy++) { |
---|
556 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
---|
557 | mean += tab[ww+sumy][xx+sumx]; |
---|
558 | } |
---|
559 | if(overflow) break; |
---|
560 | } |
---|
561 | mean /= compSize*compSize; |
---|
562 | cpt = 1; |
---|
563 | |
---|
564 | if(!overflow) { |
---|
565 | G4double density = Pixel2density(mean); |
---|
566 | std::fwrite(&density, sizeof(G4double), 1, processed); |
---|
567 | } |
---|
568 | } |
---|
569 | |
---|
570 | } |
---|
571 | } |
---|
572 | std::fclose(processed); |
---|
573 | |
---|
574 | delete [] nameProcessed; |
---|
575 | |
---|
576 | /* for ( G4int i = 0; i < rows; i ++ ) { |
---|
577 | delete [] tab[i]; |
---|
578 | } |
---|
579 | delete [] tab; |
---|
580 | */ |
---|
581 | |
---|
582 | return returnvalue; |
---|
583 | } |
---|
584 | |
---|
585 | /* |
---|
586 | G4int DicomHandler::displayImage(char command[300]) |
---|
587 | { |
---|
588 | // Display DICOM images using ImageMagick |
---|
589 | char commandName[500]; |
---|
590 | std::sprintf(commandName,"display %s",command); |
---|
591 | std::printf(commandName); |
---|
592 | G4int i = system(commandName); |
---|
593 | return (G4int )i; |
---|
594 | } |
---|
595 | */ |
---|
596 | |
---|
597 | G4double DicomHandler::Pixel2density(G4int pixel) |
---|
598 | { |
---|
599 | G4double density = -1.; |
---|
600 | G4int nbrequali = 0; |
---|
601 | G4double deltaCT = 0; |
---|
602 | G4double deltaDensity = 0; |
---|
603 | |
---|
604 | // CT2Density.dat contains the calibration curve to convert CT (Hounsfield) |
---|
605 | // number to physical density |
---|
606 | std::ifstream calibration("CT2Density.dat"); |
---|
607 | calibration >> nbrequali; |
---|
608 | |
---|
609 | G4double * valuedensity = new G4double[nbrequali]; |
---|
610 | G4double * valueCT = new G4double[nbrequali]; |
---|
611 | |
---|
612 | if(!calibration) { |
---|
613 | G4cerr << "@@@ No value to transform pixels in density!" << G4endl; |
---|
614 | exit(1); |
---|
615 | |
---|
616 | } else { // calibration was successfully opened |
---|
617 | for(G4int i = 0; i < nbrequali; i++) { // Loop to store all the pts in CT2Density.dat |
---|
618 | calibration >> valueCT[i] >> valuedensity[i]; |
---|
619 | } |
---|
620 | } |
---|
621 | calibration.close(); |
---|
622 | |
---|
623 | for(G4int j = 1; j < nbrequali; j++) { |
---|
624 | if( pixel >= valueCT[j-1] && pixel < valueCT[j]) { |
---|
625 | |
---|
626 | deltaCT = valueCT[j] - valueCT[j-1]; |
---|
627 | deltaDensity = valuedensity[j] - valuedensity[j-1]; |
---|
628 | |
---|
629 | // interpolating linearly |
---|
630 | density = valuedensity[j] - ((valueCT[j] - pixel)*deltaDensity/deltaCT ); |
---|
631 | break; |
---|
632 | } |
---|
633 | } |
---|
634 | |
---|
635 | if(density < 0.) { |
---|
636 | std::printf("@@@ Error density = %f && Pixel = %i (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel, deltaDensity/deltaCT); |
---|
637 | } |
---|
638 | |
---|
639 | delete [] valuedensity; |
---|
640 | delete [] valueCT; |
---|
641 | |
---|
642 | return density; |
---|
643 | } |
---|
644 | |
---|
645 | |
---|
646 | void DicomHandler::CheckFileFormat() |
---|
647 | { |
---|
648 | std::ifstream checkData("Data.dat"); |
---|
649 | char * oneLine = new char[128]; |
---|
650 | |
---|
651 | if(!(checkData.is_open())) { //Check existance of Data.dat |
---|
652 | |
---|
653 | G4cout << "\nDicomG4 needs Data.dat :\n\tFirst line: number of image pixel for a " |
---|
654 | << "voxel (G4Box)\n\tSecond line: number of images (CT slices) to " |
---|
655 | << "read\n\tEach following line contains the name of a Dicom image except " |
---|
656 | << "for the .dcm extension\n"; |
---|
657 | exit(0); |
---|
658 | } |
---|
659 | |
---|
660 | checkData >> compression; |
---|
661 | checkData >> nFiles; |
---|
662 | G4String oneName; |
---|
663 | checkData.getline(oneLine,100); |
---|
664 | std::ifstream testExistence; |
---|
665 | G4bool existAlready = true; |
---|
666 | for(G4int rep = 0; rep < nFiles; rep++) { |
---|
667 | checkData.getline(oneLine,100); |
---|
668 | oneName = oneLine; |
---|
669 | oneName += ".g4dcm"; // create dicomFile.g4dcm |
---|
670 | G4cout << nFiles << " test file " << oneName << G4endl; |
---|
671 | testExistence.open(oneName.data()); |
---|
672 | if(!(testExistence.is_open())) { |
---|
673 | existAlready = false; |
---|
674 | testExistence.clear(); |
---|
675 | testExistence.close(); |
---|
676 | } |
---|
677 | testExistence.clear(); |
---|
678 | testExistence.close(); |
---|
679 | } |
---|
680 | |
---|
681 | ReadMaterialIndices( checkData ); |
---|
682 | |
---|
683 | checkData.close(); |
---|
684 | delete [] oneLine; |
---|
685 | |
---|
686 | if( existAlready == false ) { // The files *.g4dcm have to be created |
---|
687 | |
---|
688 | G4cout << "\nAll the necessary images were not found in processed form, starting " |
---|
689 | << "with .dcm images\n"; |
---|
690 | |
---|
691 | FILE * dicom; |
---|
692 | FILE * lecturePref; |
---|
693 | char * compressionc = new char[LINEBUFFSIZE]; |
---|
694 | char * maxc = new char[LINEBUFFSIZE]; |
---|
695 | //char name[300], inputFile[300]; |
---|
696 | char * name = new char[FILENAMESIZE]; |
---|
697 | char * inputFile = new char[FILENAMESIZE]; |
---|
698 | |
---|
699 | lecturePref = std::fopen("Data.dat","r"); |
---|
700 | std::fscanf(lecturePref,"%s",compressionc); |
---|
701 | compression = atoi(compressionc); |
---|
702 | std::fscanf(lecturePref,"%s",maxc); |
---|
703 | nFiles = atoi(maxc); |
---|
704 | G4cout << " nFiles " << nFiles << G4endl; |
---|
705 | |
---|
706 | for( G4int i = 1; i <= nFiles; i++ ) { // Begin loop on filenames |
---|
707 | |
---|
708 | std::fscanf(lecturePref,"%s",inputFile); |
---|
709 | std::sprintf(name,"%s.dcm",inputFile); |
---|
710 | std::cout << "check 1: " << name << std::endl; |
---|
711 | // Open input file and give it to gestion_dicom : |
---|
712 | std::printf("### Opening %s and reading :\n",name); |
---|
713 | dicom = std::fopen(name,"rb"); |
---|
714 | // Reading the .dcm in two steps: |
---|
715 | // 1. reading the header |
---|
716 | // 2. reading the pixel data and store the density in Moyenne.dat |
---|
717 | if( dicom != 0 ) { |
---|
718 | ReadFile(dicom,inputFile); |
---|
719 | } else { |
---|
720 | G4cout << "\nError opening file : " << name << G4endl; |
---|
721 | } |
---|
722 | std::fclose(dicom); |
---|
723 | } |
---|
724 | std::fclose(lecturePref); |
---|
725 | |
---|
726 | delete [] compressionc; |
---|
727 | delete [] maxc; |
---|
728 | delete [] name; |
---|
729 | delete [] inputFile; |
---|
730 | |
---|
731 | } |
---|
732 | |
---|
733 | } |
---|
734 | |
---|
735 | |
---|
736 | template <class Type> |
---|
737 | void DicomHandler::GetValue(char * _val, Type & _rval) { |
---|
738 | |
---|
739 | #if BYTE_ORDER == BIG_ENDIAN |
---|
740 | if(littleEndian) { // little endian |
---|
741 | #else // BYTE_ORDER == LITTLE_ENDIAN |
---|
742 | if(!littleEndian) { // big endian |
---|
743 | #endif |
---|
744 | const int SIZE = sizeof(_rval); |
---|
745 | char ctemp; |
---|
746 | for(int i = 0; i < SIZE/2; i++) { |
---|
747 | ctemp = _val[i]; |
---|
748 | _val[i] = _val[SIZE - 1 - i]; |
---|
749 | _val[SIZE - 1 - i] = ctemp; |
---|
750 | } |
---|
751 | } |
---|
752 | _rval = *(Type *)_val; |
---|
753 | } |
---|