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116
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #include "../PrecompiledHeaders.h"
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35
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36 #ifndef NOMINMAX
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37 #define NOMINMAX
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38 #endif
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39
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40 #include "FromDcmtkBridge.h"
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41 #include "ToDcmtkBridge.h"
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42 #include "../Logging.h"
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43 #include "../SystemToolbox.h"
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44 #include "../Toolbox.h"
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45 #include "../TemporaryFile.h"
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46 #include "../OrthancException.h"
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47
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48 #include <list>
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49 #include <limits>
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50
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51 #include <boost/lexical_cast.hpp>
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52 #include <boost/filesystem.hpp>
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53 #include <boost/algorithm/string/predicate.hpp>
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54
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55 #include <dcmtk/dcmdata/dcdeftag.h>
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56 #include <dcmtk/dcmdata/dcdicent.h>
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57 #include <dcmtk/dcmdata/dcdict.h>
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58 #include <dcmtk/dcmdata/dcfilefo.h>
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59 #include <dcmtk/dcmdata/dcostrmb.h>
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60 #include <dcmtk/dcmdata/dcpixel.h>
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61 #include <dcmtk/dcmdata/dcuid.h>
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62 #include <dcmtk/dcmdata/dcistrmb.h>
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63
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64 #include <dcmtk/dcmdata/dcvrae.h>
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65 #include <dcmtk/dcmdata/dcvras.h>
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66 #include <dcmtk/dcmdata/dcvrat.h>
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67 #include <dcmtk/dcmdata/dcvrcs.h>
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68 #include <dcmtk/dcmdata/dcvrda.h>
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69 #include <dcmtk/dcmdata/dcvrds.h>
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70 #include <dcmtk/dcmdata/dcvrdt.h>
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71 #include <dcmtk/dcmdata/dcvrfd.h>
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72 #include <dcmtk/dcmdata/dcvrfl.h>
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73 #include <dcmtk/dcmdata/dcvris.h>
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74 #include <dcmtk/dcmdata/dcvrlo.h>
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75 #include <dcmtk/dcmdata/dcvrlt.h>
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76 #include <dcmtk/dcmdata/dcvrpn.h>
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77 #include <dcmtk/dcmdata/dcvrsh.h>
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78 #include <dcmtk/dcmdata/dcvrsl.h>
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79 #include <dcmtk/dcmdata/dcvrss.h>
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80 #include <dcmtk/dcmdata/dcvrst.h>
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81 #include <dcmtk/dcmdata/dcvrtm.h>
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82 #include <dcmtk/dcmdata/dcvrui.h>
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83 #include <dcmtk/dcmdata/dcvrul.h>
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84 #include <dcmtk/dcmdata/dcvrus.h>
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85 #include <dcmtk/dcmdata/dcvrut.h>
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86
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87 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1
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88 # include <EmbeddedResources.h>
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89 #endif
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90
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91 #if ORTHANC_ENABLE_DCMTK_JPEG == 1
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92 # include <dcmtk/dcmjpeg/djdecode.h>
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93 #endif
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94
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95 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
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96 # include <dcmtk/dcmjpls/djdecode.h>
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97 #endif
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98
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99
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100 namespace Orthanc
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101 {
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102 static inline uint16_t GetCharValue(char c)
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103 {
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104 if (c >= '0' && c <= '9')
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105 return c - '0';
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106 else if (c >= 'a' && c <= 'f')
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107 return c - 'a' + 10;
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108 else if (c >= 'A' && c <= 'F')
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109 return c - 'A' + 10;
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110 else
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111 return 0;
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112 }
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113
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114 static inline uint16_t GetTagValue(const char* c)
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115 {
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116 return ((GetCharValue(c[0]) << 12) +
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117 (GetCharValue(c[1]) << 8) +
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118 (GetCharValue(c[2]) << 4) +
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119 GetCharValue(c[3]));
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120 }
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121
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122
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123 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1
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124 static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary,
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125 EmbeddedResources::FileResourceId resource)
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126 {
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127 std::string content;
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128 EmbeddedResources::GetFileResource(content, resource);
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129
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130 TemporaryFile tmp;
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131 tmp.Write(content);
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132
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133 if (!dictionary.loadDictionary(tmp.GetPath().c_str()))
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134 {
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135 LOG(ERROR) << "Cannot read embedded dictionary. Under Windows, make sure that "
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136 << "your TEMP directory does not contain special characters.";
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137 throw OrthancException(ErrorCode_InternalError);
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138 }
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139 }
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140
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141 #else
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142 static void LoadExternalDictionary(DcmDataDictionary& dictionary,
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143 const std::string& directory,
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144 const std::string& filename)
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145 {
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146 boost::filesystem::path p = directory;
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147 p = p / filename;
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148
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149 LOG(WARNING) << "Loading the external DICOM dictionary " << p;
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150
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151 if (!dictionary.loadDictionary(p.string().c_str()))
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152 {
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153 throw OrthancException(ErrorCode_InternalError);
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154 }
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155 }
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156 #endif
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157
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158
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159 namespace
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160 {
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161 class DictionaryLocker
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162 {
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163 private:
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164 DcmDataDictionary& dictionary_;
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165
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166 public:
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167 DictionaryLocker() : dictionary_(dcmDataDict.wrlock())
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168 {
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169 }
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170
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171 ~DictionaryLocker()
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172 {
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173 dcmDataDict.unlock();
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174 }
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175
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176 DcmDataDictionary& operator*()
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177 {
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178 return dictionary_;
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179 }
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180
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181 DcmDataDictionary* operator->()
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182 {
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183 return &dictionary_;
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184 }
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185 };
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186 }
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187
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188
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189 void FromDcmtkBridge::InitializeDictionary(bool loadPrivateDictionary)
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190 {
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191 LOG(INFO) << "Using DCTMK version: " << DCMTK_VERSION_NUMBER;
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192
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193 {
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194 DictionaryLocker locker;
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195
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196 locker->clear();
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197
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198 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1
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199 LOG(WARNING) << "Loading the embedded dictionaries";
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200 /**
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201 * Do not load DICONDE dictionary, it breaks the other tags. The
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202 * command "strace storescu 2>&1 |grep dic" shows that DICONDE
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203 * dictionary is not loaded by storescu.
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204 **/
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205 //LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICONDE);
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206
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207 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_DICOM);
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208
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209 if (loadPrivateDictionary)
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210 {
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211 LOG(INFO) << "Loading the embedded dictionary of private tags";
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212 LoadEmbeddedDictionary(*locker, EmbeddedResources::DICTIONARY_PRIVATE);
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213 }
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214 else
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215 {
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216 LOG(INFO) << "The dictionary of private tags has not been loaded";
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217 }
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218
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219 #elif defined(__linux__) || defined(__FreeBSD_kernel__) || defined(__FreeBSD__) || defined(__OpenBSD__)
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220 std::string path = DCMTK_DICTIONARY_DIR;
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221
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222 const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE);
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223 if (env != NULL)
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224 {
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225 path = std::string(env);
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226 }
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227
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228 LoadExternalDictionary(*locker, path, "dicom.dic");
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229
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230 if (loadPrivateDictionary)
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231 {
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232 LoadExternalDictionary(*locker, path, "private.dic");
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233 }
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234 else
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235 {
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236 LOG(INFO) << "The dictionary of private tags has not been loaded";
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237 }
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238
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239 #else
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240 #error Support your platform here
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241 #endif
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242 }
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243
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244 /* make sure data dictionary is loaded */
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245 if (!dcmDataDict.isDictionaryLoaded())
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246 {
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247 LOG(ERROR) << "No DICOM dictionary loaded, check environment variable: " << DCM_DICT_ENVIRONMENT_VARIABLE;
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248 throw OrthancException(ErrorCode_InternalError);
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249 }
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250
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251 {
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252 // Test the dictionary with a simple DICOM tag
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253 DcmTag key(0x0010, 0x1030); // This is PatientWeight
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254 if (key.getEVR() != EVR_DS)
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255 {
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256 LOG(ERROR) << "The DICOM dictionary has not been correctly read";
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257 throw OrthancException(ErrorCode_InternalError);
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258 }
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259 }
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260 }
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261
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262
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263 void FromDcmtkBridge::RegisterDictionaryTag(const DicomTag& tag,
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264 ValueRepresentation vr,
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265 const std::string& name,
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266 unsigned int minMultiplicity,
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267 unsigned int maxMultiplicity,
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268 const std::string& privateCreator)
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269 {
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270 if (minMultiplicity < 1)
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271 {
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272 throw OrthancException(ErrorCode_ParameterOutOfRange);
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273 }
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274
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275 bool arbitrary = false;
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276 if (maxMultiplicity == 0)
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277 {
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278 maxMultiplicity = DcmVariableVM;
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279 arbitrary = true;
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280 }
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281 else if (maxMultiplicity < minMultiplicity)
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282 {
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283 throw OrthancException(ErrorCode_ParameterOutOfRange);
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284 }
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285
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286 DcmEVR evr = ToDcmtkBridge::Convert(vr);
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287
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288 LOG(INFO) << "Registering tag in dictionary: " << tag << " " << (DcmVR(evr).getValidVRName()) << " "
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289 << name << " (multiplicity: " << minMultiplicity << "-"
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290 << (arbitrary ? "n" : boost::lexical_cast<std::string>(maxMultiplicity)) << ")";
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291
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292 std::auto_ptr<DcmDictEntry> entry;
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293 if (privateCreator.empty())
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294 {
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295 if (tag.GetGroup() % 2 == 1)
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296 {
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297 char buf[128];
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298 sprintf(buf, "Warning: You are registering a private tag (%04x,%04x), "
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299 "but no private creator was associated with it",
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300 tag.GetGroup(), tag.GetElement());
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301 LOG(WARNING) << buf;
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302 }
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303
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304 entry.reset(new DcmDictEntry(tag.GetGroup(),
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305 tag.GetElement(),
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306 evr, name.c_str(),
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307 static_cast<int>(minMultiplicity),
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308 static_cast<int>(maxMultiplicity),
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309 NULL /* version */,
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310 OFTrue /* doCopyString */,
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311 NULL /* private creator */));
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312 }
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313 else
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314 {
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315 // "Private Data Elements have an odd Group Number that is not
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316 // (0001,eeee), (0003,eeee), (0005,eeee), (0007,eeee), or
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317 // (FFFF,eeee)."
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318 if (tag.GetGroup() % 2 == 0 /* even */ ||
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319 tag.GetGroup() == 0x0001 ||
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320 tag.GetGroup() == 0x0003 ||
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321 tag.GetGroup() == 0x0005 ||
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322 tag.GetGroup() == 0x0007 ||
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323 tag.GetGroup() == 0xffff)
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324 {
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325 char buf[128];
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326 sprintf(buf, "Trying to register private tag (%04x,%04x), but it must have an odd group >= 0x0009",
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327 tag.GetGroup(), tag.GetElement());
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328 LOG(ERROR) << buf;
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329 throw OrthancException(ErrorCode_ParameterOutOfRange);
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330 }
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331
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332 entry.reset(new DcmDictEntry(tag.GetGroup(),
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333 tag.GetElement(),
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334 evr, name.c_str(),
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335 static_cast<int>(minMultiplicity),
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336 static_cast<int>(maxMultiplicity),
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337 "private" /* version */,
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338 OFTrue /* doCopyString */,
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339 privateCreator.c_str()));
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340 }
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341
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342 entry->setGroupRangeRestriction(DcmDictRange_Unspecified);
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343 entry->setElementRangeRestriction(DcmDictRange_Unspecified);
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344
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345 {
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346 DictionaryLocker locker;
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347
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348 if (locker->findEntry(name.c_str()))
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349 {
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350 LOG(ERROR) << "Cannot register two tags with the same symbolic name \"" << name << "\"";
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351 throw OrthancException(ErrorCode_AlreadyExistingTag);
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352 }
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353
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354 locker->addEntry(entry.release());
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355 }
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356 }
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357
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358
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359 Encoding FromDcmtkBridge::DetectEncoding(DcmItem& dataset,
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360 Encoding defaultEncoding)
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361 {
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362 Encoding encoding = defaultEncoding;
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363
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364 OFString tmp;
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365 if (dataset.findAndGetOFString(DCM_SpecificCharacterSet, tmp).good())
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366 {
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367 std::string characterSet = Toolbox::StripSpaces(std::string(tmp.c_str()));
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368
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369 if (characterSet.empty())
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370 {
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371 // Empty specific character set tag: Use the default encoding
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372 }
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373 else if (GetDicomEncoding(encoding, characterSet.c_str()))
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374 {
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375 // The specific character set is supported by the Orthanc core
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376 }
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377 else
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378 {
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379 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet
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380 << ", fallback to ASCII (remove all special characters)";
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381 encoding = Encoding_Ascii;
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382 }
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383 }
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384 else
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385 {
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386 // No specific character set tag: Use the default encoding
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387 }
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388
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389 return encoding;
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390 }
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391
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392
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393 void FromDcmtkBridge::ExtractDicomSummary(DicomMap& target,
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394 DcmItem& dataset,
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395 unsigned int maxStringLength,
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396 Encoding defaultEncoding)
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397 {
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398 std::set<DicomTag> ignoreTagLength;
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399
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400 Encoding encoding = DetectEncoding(dataset, defaultEncoding);
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401
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402 target.Clear();
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403 for (unsigned long i = 0; i < dataset.card(); i++)
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404 {
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405 DcmElement* element = dataset.getElement(i);
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406 if (element && element->isLeaf())
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407 {
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408 target.SetValue(element->getTag().getGTag(),
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409 element->getTag().getETag(),
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410 ConvertLeafElement(*element, DicomToJsonFlags_Default,
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411 maxStringLength, encoding, ignoreTagLength));
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412 }
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413 }
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414 }
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415
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|
416
|
|
|
417 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag)
|
|
|
418 {
|
|
|
419 return DicomTag(tag.getGTag(), tag.getETag());
|
|
|
420 }
|
|
|
421
|
|
|
422
|
|
|
423 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element)
|
|
|
424 {
|
|
|
425 return DicomTag(element.getGTag(), element.getETag());
|
|
|
426 }
|
|
|
427
|
|
|
428
|
|
|
429 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element,
|
|
|
430 DicomToJsonFlags flags,
|
|
|
431 unsigned int maxStringLength,
|
|
|
432 Encoding encoding,
|
|
|
433 const std::set<DicomTag>& ignoreTagLength)
|
|
|
434 {
|
|
|
435 if (!element.isLeaf())
|
|
|
436 {
|
|
|
437 // This function is only applicable to leaf elements
|
|
|
438 throw OrthancException(ErrorCode_BadParameterType);
|
|
|
439 }
|
|
|
440
|
|
|
441 char *c = NULL;
|
|
|
442 if (element.isaString() &&
|
|
|
443 element.getString(c).good())
|
|
|
444 {
|
|
|
445 if (c == NULL) // This case corresponds to the empty string
|
|
|
446 {
|
|
|
447 return new DicomValue("", false);
|
|
|
448 }
|
|
|
449 else
|
|
|
450 {
|
|
|
451 std::string s(c);
|
|
|
452 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding);
|
|
|
453
|
|
|
454 if (maxStringLength != 0 &&
|
|
|
455 utf8.size() > maxStringLength &&
|
|
|
456 ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end())
|
|
|
457 {
|
|
|
458 return new DicomValue; // Too long, create a NULL value
|
|
|
459 }
|
|
|
460 else
|
|
|
461 {
|
|
|
462 return new DicomValue(utf8, false);
|
|
|
463 }
|
|
|
464 }
|
|
|
465 }
|
|
|
466
|
|
|
467
|
|
|
468 if (element.getVR() == EVR_UN)
|
|
|
469 {
|
|
|
470 // Unknown value representation: Lookup in the dictionary. This
|
|
|
471 // is notably the case for private tags registered with the
|
|
|
472 // "Dictionary" configuration option.
|
|
|
473 DictionaryLocker locker;
|
|
|
474
|
|
|
475 const DcmDictEntry* entry = locker->findEntry(element.getTag().getXTag(),
|
|
|
476 element.getTag().getPrivateCreator());
|
|
|
477 if (entry != NULL &&
|
|
|
478 entry->getVR().isaString())
|
|
|
479 {
|
|
|
480 Uint8* data = NULL;
|
|
|
481
|
|
|
482 // At (*), we do not try and convert to UTF-8, as nothing says
|
|
|
483 // the encoding of the private tag is the same as that of the
|
|
|
484 // remaining of the DICOM dataset. Only go for ASCII strings.
|
|
|
485
|
|
|
486 if (element.getUint8Array(data) == EC_Normal &&
|
|
|
487 Toolbox::IsAsciiString(data, element.getLength())) // (*)
|
|
|
488 {
|
|
|
489 if (data == NULL)
|
|
|
490 {
|
|
|
491 return new DicomValue("", false); // Empty string
|
|
|
492 }
|
|
|
493 else if (maxStringLength != 0 &&
|
|
|
494 element.getLength() > maxStringLength &&
|
|
|
495 ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end())
|
|
|
496 {
|
|
|
497 return new DicomValue; // Too long, create a NULL value
|
|
|
498 }
|
|
|
499 else
|
|
|
500 {
|
|
|
501 std::string s(reinterpret_cast<const char*>(data), element.getLength());
|
|
|
502 return new DicomValue(s, false);
|
|
|
503 }
|
|
|
504 }
|
|
|
505 }
|
|
|
506 }
|
|
|
507
|
|
|
508
|
|
|
509 try
|
|
|
510 {
|
|
|
511 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
512 switch (element.getVR())
|
|
|
513 {
|
|
|
514
|
|
|
515 /**
|
|
|
516 * Deal with binary data (including PixelData).
|
|
|
517 **/
|
|
|
518
|
|
|
519 case EVR_OB: // other byte
|
|
|
520 case EVR_OF: // other float
|
|
|
521 case EVR_OW: // other word
|
|
|
522 case EVR_UN: // unknown value representation
|
|
|
523 case EVR_ox: // OB or OW depending on context
|
|
|
524 case EVR_DS: // decimal string
|
|
|
525 case EVR_IS: // integer string
|
|
|
526 case EVR_AS: // age string
|
|
|
527 case EVR_DA: // date string
|
|
|
528 case EVR_DT: // date time string
|
|
|
529 case EVR_TM: // time string
|
|
|
530 case EVR_AE: // application entity title
|
|
|
531 case EVR_CS: // code string
|
|
|
532 case EVR_SH: // short string
|
|
|
533 case EVR_LO: // long string
|
|
|
534 case EVR_ST: // short text
|
|
|
535 case EVR_LT: // long text
|
|
|
536 case EVR_UT: // unlimited text
|
|
|
537 case EVR_PN: // person name
|
|
|
538 case EVR_UI: // unique identifier
|
|
|
539 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
540 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
541 {
|
|
|
542 if (!(flags & DicomToJsonFlags_ConvertBinaryToNull))
|
|
|
543 {
|
|
|
544 Uint8* data = NULL;
|
|
|
545 if (element.getUint8Array(data) == EC_Normal)
|
|
|
546 {
|
|
|
547 return new DicomValue(reinterpret_cast<const char*>(data), element.getLength(), true);
|
|
|
548 }
|
|
|
549 }
|
|
|
550
|
|
|
551 return new DicomValue;
|
|
|
552 }
|
|
|
553
|
|
|
554 /**
|
|
|
555 * Numeric types
|
|
|
556 **/
|
|
|
557
|
|
|
558 case EVR_SL: // signed long
|
|
|
559 {
|
|
|
560 Sint32 f;
|
|
|
561 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
|
|
|
562 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
563 else
|
|
|
564 return new DicomValue;
|
|
|
565 }
|
|
|
566
|
|
|
567 case EVR_SS: // signed short
|
|
|
568 {
|
|
|
569 Sint16 f;
|
|
|
570 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
|
|
|
571 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
572 else
|
|
|
573 return new DicomValue;
|
|
|
574 }
|
|
|
575
|
|
|
576 case EVR_UL: // unsigned long
|
|
|
577 {
|
|
|
578 Uint32 f;
|
|
|
579 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
|
|
|
580 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
581 else
|
|
|
582 return new DicomValue;
|
|
|
583 }
|
|
|
584
|
|
|
585 case EVR_US: // unsigned short
|
|
|
586 {
|
|
|
587 Uint16 f;
|
|
|
588 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
|
|
|
589 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
590 else
|
|
|
591 return new DicomValue;
|
|
|
592 }
|
|
|
593
|
|
|
594 case EVR_FL: // float single-precision
|
|
|
595 {
|
|
|
596 Float32 f;
|
|
|
597 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
|
|
|
598 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
599 else
|
|
|
600 return new DicomValue;
|
|
|
601 }
|
|
|
602
|
|
|
603 case EVR_FD: // float double-precision
|
|
|
604 {
|
|
|
605 Float64 f;
|
|
|
606 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
|
|
|
607 return new DicomValue(boost::lexical_cast<std::string>(f), false);
|
|
|
608 else
|
|
|
609 return new DicomValue;
|
|
|
610 }
|
|
|
611
|
|
|
612
|
|
|
613 /**
|
|
|
614 * Attribute tag.
|
|
|
615 **/
|
|
|
616
|
|
|
617 case EVR_AT:
|
|
|
618 {
|
|
|
619 DcmTagKey tag;
|
|
|
620 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good())
|
|
|
621 {
|
|
|
622 DicomTag t(tag.getGroup(), tag.getElement());
|
|
|
623 return new DicomValue(t.Format(), false);
|
|
|
624 }
|
|
|
625 else
|
|
|
626 {
|
|
|
627 return new DicomValue;
|
|
|
628 }
|
|
|
629 }
|
|
|
630
|
|
|
631
|
|
|
632 /**
|
|
|
633 * Sequence types, should never occur at this point because of
|
|
|
634 * "element.isLeaf()".
|
|
|
635 **/
|
|
|
636
|
|
|
637 case EVR_SQ: // sequence of items
|
|
|
638 return new DicomValue;
|
|
|
639
|
|
|
640
|
|
|
641 /**
|
|
|
642 * Internal to DCMTK.
|
|
|
643 **/
|
|
|
644
|
|
|
645 case EVR_xs: // SS or US depending on context
|
|
|
646 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
647 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
648 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
649 case EVR_item: // used internally for items
|
|
|
650 case EVR_metainfo: // used internally for meta info datasets
|
|
|
651 case EVR_dataset: // used internally for datasets
|
|
|
652 case EVR_fileFormat: // used internally for DICOM files
|
|
|
653 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
654 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
655 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
656 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
657 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
658 case EVR_OverlayData: // used internally for overlay data
|
|
|
659 return new DicomValue;
|
|
|
660
|
|
|
661
|
|
|
662 /**
|
|
|
663 * Default case.
|
|
|
664 **/
|
|
|
665
|
|
|
666 default:
|
|
|
667 return new DicomValue;
|
|
|
668 }
|
|
|
669 }
|
|
|
670 catch (boost::bad_lexical_cast)
|
|
|
671 {
|
|
|
672 return new DicomValue;
|
|
|
673 }
|
|
|
674 catch (std::bad_cast)
|
|
|
675 {
|
|
|
676 return new DicomValue;
|
|
|
677 }
|
|
|
678 }
|
|
|
679
|
|
|
680
|
|
|
681 static Json::Value& PrepareNode(Json::Value& parent,
|
|
|
682 DcmElement& element,
|
|
|
683 DicomToJsonFormat format)
|
|
|
684 {
|
|
|
685 assert(parent.type() == Json::objectValue);
|
|
|
686
|
|
|
687 DicomTag tag(FromDcmtkBridge::GetTag(element));
|
|
|
688 const std::string formattedTag = tag.Format();
|
|
|
689
|
|
|
690 if (format == DicomToJsonFormat_Short)
|
|
|
691 {
|
|
|
692 parent[formattedTag] = Json::nullValue;
|
|
|
693 return parent[formattedTag];
|
|
|
694 }
|
|
|
695
|
|
|
696 // This code gives access to the name of the private tags
|
|
|
697 std::string tagName = FromDcmtkBridge::GetTagName(element);
|
|
|
698
|
|
|
699 switch (format)
|
|
|
700 {
|
|
|
701 case DicomToJsonFormat_Human:
|
|
|
702 parent[tagName] = Json::nullValue;
|
|
|
703 return parent[tagName];
|
|
|
704
|
|
|
705 case DicomToJsonFormat_Full:
|
|
|
706 {
|
|
|
707 parent[formattedTag] = Json::objectValue;
|
|
|
708 Json::Value& node = parent[formattedTag];
|
|
|
709
|
|
|
710 if (element.isLeaf())
|
|
|
711 {
|
|
|
712 node["Name"] = tagName;
|
|
|
713
|
|
|
714 if (element.getTag().getPrivateCreator() != NULL)
|
|
|
715 {
|
|
|
716 node["PrivateCreator"] = element.getTag().getPrivateCreator();
|
|
|
717 }
|
|
|
718
|
|
|
719 return node;
|
|
|
720 }
|
|
|
721 else
|
|
|
722 {
|
|
|
723 node["Name"] = tagName;
|
|
|
724 node["Type"] = "Sequence";
|
|
|
725 node["Value"] = Json::nullValue;
|
|
|
726 return node["Value"];
|
|
|
727 }
|
|
|
728 }
|
|
|
729
|
|
|
730 default:
|
|
|
731 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
732 }
|
|
|
733 }
|
|
|
734
|
|
|
735
|
|
|
736 static void LeafValueToJson(Json::Value& target,
|
|
|
737 const DicomValue& value,
|
|
|
738 DicomToJsonFormat format,
|
|
|
739 DicomToJsonFlags flags,
|
|
|
740 unsigned int maxStringLength)
|
|
|
741 {
|
|
|
742 Json::Value* targetValue = NULL;
|
|
|
743 Json::Value* targetType = NULL;
|
|
|
744
|
|
|
745 switch (format)
|
|
|
746 {
|
|
|
747 case DicomToJsonFormat_Short:
|
|
|
748 case DicomToJsonFormat_Human:
|
|
|
749 {
|
|
|
750 assert(target.type() == Json::nullValue);
|
|
|
751 targetValue = ⌖
|
|
|
752 break;
|
|
|
753 }
|
|
|
754
|
|
|
755 case DicomToJsonFormat_Full:
|
|
|
756 {
|
|
|
757 assert(target.type() == Json::objectValue);
|
|
|
758 target["Value"] = Json::nullValue;
|
|
|
759 target["Type"] = Json::nullValue;
|
|
|
760 targetType = &target["Type"];
|
|
|
761 targetValue = &target["Value"];
|
|
|
762 break;
|
|
|
763 }
|
|
|
764
|
|
|
765 default:
|
|
|
766 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
767 }
|
|
|
768
|
|
|
769 assert(targetValue != NULL);
|
|
|
770 assert(targetValue->type() == Json::nullValue);
|
|
|
771 assert(targetType == NULL || targetType->type() == Json::nullValue);
|
|
|
772
|
|
|
773 if (value.IsNull())
|
|
|
774 {
|
|
|
775 if (targetType != NULL)
|
|
|
776 {
|
|
|
777 *targetType = "Null";
|
|
|
778 }
|
|
|
779 }
|
|
|
780 else if (value.IsBinary())
|
|
|
781 {
|
|
|
782 if (flags & DicomToJsonFlags_ConvertBinaryToAscii)
|
|
|
783 {
|
|
|
784 *targetValue = Toolbox::ConvertToAscii(value.GetContent());
|
|
|
785 }
|
|
|
786 else
|
|
|
787 {
|
|
|
788 std::string s;
|
|
|
789 value.FormatDataUriScheme(s);
|
|
|
790 *targetValue = s;
|
|
|
791 }
|
|
|
792
|
|
|
793 if (targetType != NULL)
|
|
|
794 {
|
|
|
795 *targetType = "Binary";
|
|
|
796 }
|
|
|
797 }
|
|
|
798 else if (maxStringLength == 0 ||
|
|
|
799 value.GetContent().size() <= maxStringLength)
|
|
|
800 {
|
|
|
801 *targetValue = value.GetContent();
|
|
|
802
|
|
|
803 if (targetType != NULL)
|
|
|
804 {
|
|
|
805 *targetType = "String";
|
|
|
806 }
|
|
|
807 }
|
|
|
808 else
|
|
|
809 {
|
|
|
810 if (targetType != NULL)
|
|
|
811 {
|
|
|
812 *targetType = "TooLong";
|
|
|
813 }
|
|
|
814 }
|
|
|
815 }
|
|
|
816
|
|
|
817
|
|
|
818 void FromDcmtkBridge::ElementToJson(Json::Value& parent,
|
|
|
819 DcmElement& element,
|
|
|
820 DicomToJsonFormat format,
|
|
|
821 DicomToJsonFlags flags,
|
|
|
822 unsigned int maxStringLength,
|
|
|
823 Encoding encoding,
|
|
|
824 const std::set<DicomTag>& ignoreTagLength)
|
|
|
825 {
|
|
|
826 if (parent.type() == Json::nullValue)
|
|
|
827 {
|
|
|
828 parent = Json::objectValue;
|
|
|
829 }
|
|
|
830
|
|
|
831 assert(parent.type() == Json::objectValue);
|
|
|
832 Json::Value& target = PrepareNode(parent, element, format);
|
|
|
833
|
|
|
834 if (element.isLeaf())
|
|
|
835 {
|
|
|
836 // The "0" below lets "LeafValueToJson()" take care of "TooLong" values
|
|
|
837 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement
|
|
|
838 (element, flags, 0, encoding, ignoreTagLength));
|
|
|
839
|
|
|
840 if (ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end())
|
|
|
841 {
|
|
|
842 LeafValueToJson(target, *v, format, flags, maxStringLength);
|
|
|
843 }
|
|
|
844 else
|
|
|
845 {
|
|
|
846 LeafValueToJson(target, *v, format, flags, 0);
|
|
|
847 }
|
|
|
848 }
|
|
|
849 else
|
|
|
850 {
|
|
|
851 assert(target.type() == Json::nullValue);
|
|
|
852 target = Json::arrayValue;
|
|
|
853
|
|
|
854 // "All subclasses of DcmElement except for DcmSequenceOfItems
|
|
|
855 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
|
|
|
856 // etc. are not." The following dynamic_cast is thus OK.
|
|
|
857 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
|
|
|
858
|
|
|
859 for (unsigned long i = 0; i < sequence.card(); i++)
|
|
|
860 {
|
|
|
861 DcmItem* child = sequence.getItem(i);
|
|
|
862 Json::Value& v = target.append(Json::objectValue);
|
|
|
863 DatasetToJson(v, *child, format, flags, maxStringLength, encoding, ignoreTagLength);
|
|
|
864 }
|
|
|
865 }
|
|
|
866 }
|
|
|
867
|
|
|
868
|
|
|
869 void FromDcmtkBridge::DatasetToJson(Json::Value& parent,
|
|
|
870 DcmItem& item,
|
|
|
871 DicomToJsonFormat format,
|
|
|
872 DicomToJsonFlags flags,
|
|
|
873 unsigned int maxStringLength,
|
|
|
874 Encoding encoding,
|
|
|
875 const std::set<DicomTag>& ignoreTagLength)
|
|
|
876 {
|
|
|
877 assert(parent.type() == Json::objectValue);
|
|
|
878
|
|
|
879 for (unsigned long i = 0; i < item.card(); i++)
|
|
|
880 {
|
|
|
881 DcmElement* element = item.getElement(i);
|
|
|
882 if (element == NULL)
|
|
|
883 {
|
|
|
884 throw OrthancException(ErrorCode_InternalError);
|
|
|
885 }
|
|
|
886
|
|
|
887 DicomTag tag(FromDcmtkBridge::Convert(element->getTag()));
|
|
|
888
|
|
|
889 /*element->getTag().isPrivate()*/
|
|
|
890 if (tag.IsPrivate() &&
|
|
|
891 !(flags & DicomToJsonFlags_IncludePrivateTags))
|
|
|
892 {
|
|
|
893 continue;
|
|
|
894 }
|
|
|
895
|
|
|
896 if (!(flags & DicomToJsonFlags_IncludeUnknownTags))
|
|
|
897 {
|
|
|
898 DictionaryLocker locker;
|
|
|
899 if (locker->findEntry(element->getTag(), NULL) == NULL)
|
|
|
900 {
|
|
|
901 continue;
|
|
|
902 }
|
|
|
903 }
|
|
|
904
|
|
|
905 DcmEVR evr = element->getTag().getEVR();
|
|
|
906 if (evr == EVR_OB ||
|
|
|
907 evr == EVR_OF ||
|
|
|
908 evr == EVR_OW ||
|
|
|
909 evr == EVR_UN ||
|
|
|
910 evr == EVR_ox)
|
|
|
911 {
|
|
|
912 // This is a binary tag
|
|
|
913 if ((tag == DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludePixelData)) ||
|
|
|
914 (tag != DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludeBinary)))
|
|
|
915 {
|
|
|
916 continue;
|
|
|
917 }
|
|
|
918 }
|
|
|
919
|
|
|
920 FromDcmtkBridge::ElementToJson(parent, *element, format, flags,
|
|
|
921 maxStringLength, encoding, ignoreTagLength);
|
|
|
922 }
|
|
|
923 }
|
|
|
924
|
|
|
925
|
|
|
926 void FromDcmtkBridge::ExtractDicomAsJson(Json::Value& target,
|
|
|
927 DcmDataset& dataset,
|
|
|
928 DicomToJsonFormat format,
|
|
|
929 DicomToJsonFlags flags,
|
|
|
930 unsigned int maxStringLength,
|
|
|
931 Encoding defaultEncoding,
|
|
|
932 const std::set<DicomTag>& ignoreTagLength)
|
|
|
933 {
|
|
|
934 Encoding encoding = DetectEncoding(dataset, defaultEncoding);
|
|
|
935
|
|
|
936 target = Json::objectValue;
|
|
|
937 DatasetToJson(target, dataset, format, flags, maxStringLength, encoding, ignoreTagLength);
|
|
|
938 }
|
|
|
939
|
|
|
940
|
|
|
941 void FromDcmtkBridge::ExtractHeaderAsJson(Json::Value& target,
|
|
|
942 DcmMetaInfo& dataset,
|
|
|
943 DicomToJsonFormat format,
|
|
|
944 DicomToJsonFlags flags,
|
|
|
945 unsigned int maxStringLength)
|
|
|
946 {
|
|
|
947 std::set<DicomTag> ignoreTagLength;
|
|
|
948 target = Json::objectValue;
|
|
|
949 DatasetToJson(target, dataset, format, flags, maxStringLength, Encoding_Ascii, ignoreTagLength);
|
|
|
950 }
|
|
|
951
|
|
|
952
|
|
|
953
|
|
|
954 static std::string GetTagNameInternal(DcmTag& tag)
|
|
|
955 {
|
|
|
956 {
|
|
|
957 // Some patches for important tags because of different DICOM
|
|
|
958 // dictionaries between DCMTK versions
|
|
|
959 DicomTag tmp(tag.getGroup(), tag.getElement());
|
|
|
960 std::string n = tmp.GetMainTagsName();
|
|
|
961 if (n.size() != 0)
|
|
|
962 {
|
|
|
963 return n;
|
|
|
964 }
|
|
|
965 // End of patches
|
|
|
966 }
|
|
|
967
|
|
|
968 #if 0
|
|
|
969 // This version explicitly calls the dictionary
|
|
|
970 const DcmDataDictionary& dict = dcmDataDict.rdlock();
|
|
|
971 const DcmDictEntry* entry = dict.findEntry(tag, NULL);
|
|
|
972
|
|
|
973 std::string s(DcmTag_ERROR_TagName);
|
|
|
974 if (entry != NULL)
|
|
|
975 {
|
|
|
976 s = std::string(entry->getTagName());
|
|
|
977 }
|
|
|
978
|
|
|
979 dcmDataDict.unlock();
|
|
|
980 return s;
|
|
|
981 #else
|
|
|
982 const char* name = tag.getTagName();
|
|
|
983 if (name == NULL)
|
|
|
984 {
|
|
|
985 return DcmTag_ERROR_TagName;
|
|
|
986 }
|
|
|
987 else
|
|
|
988 {
|
|
|
989 return std::string(name);
|
|
|
990 }
|
|
|
991 #endif
|
|
|
992 }
|
|
|
993
|
|
|
994
|
|
|
995 std::string FromDcmtkBridge::GetTagName(const DicomTag& t,
|
|
|
996 const std::string& privateCreator)
|
|
|
997 {
|
|
|
998 DcmTag tag(t.GetGroup(), t.GetElement());
|
|
|
999
|
|
|
1000 if (!privateCreator.empty())
|
|
|
1001 {
|
|
|
1002 tag.setPrivateCreator(privateCreator.c_str());
|
|
|
1003 }
|
|
|
1004
|
|
|
1005 return GetTagNameInternal(tag);
|
|
|
1006 }
|
|
|
1007
|
|
|
1008
|
|
|
1009 std::string FromDcmtkBridge::GetTagName(const DcmElement& element)
|
|
|
1010 {
|
|
|
1011 // Copy the tag to ensure const-correctness of DcmElement. Note
|
|
|
1012 // that the private creator information is also copied.
|
|
|
1013 DcmTag tag(element.getTag());
|
|
|
1014
|
|
|
1015 return GetTagNameInternal(tag);
|
|
|
1016 }
|
|
|
1017
|
|
|
1018
|
|
|
1019
|
|
|
1020 DicomTag FromDcmtkBridge::ParseTag(const char* name)
|
|
|
1021 {
|
|
|
1022 if (strlen(name) == 9 &&
|
|
|
1023 isxdigit(name[0]) &&
|
|
|
1024 isxdigit(name[1]) &&
|
|
|
1025 isxdigit(name[2]) &&
|
|
|
1026 isxdigit(name[3]) &&
|
|
|
1027 (name[4] == '-' || name[4] == ',') &&
|
|
|
1028 isxdigit(name[5]) &&
|
|
|
1029 isxdigit(name[6]) &&
|
|
|
1030 isxdigit(name[7]) &&
|
|
|
1031 isxdigit(name[8]))
|
|
|
1032 {
|
|
|
1033 uint16_t group = GetTagValue(name);
|
|
|
1034 uint16_t element = GetTagValue(name + 5);
|
|
|
1035 return DicomTag(group, element);
|
|
|
1036 }
|
|
|
1037
|
|
|
1038 if (strlen(name) == 8 &&
|
|
|
1039 isxdigit(name[0]) &&
|
|
|
1040 isxdigit(name[1]) &&
|
|
|
1041 isxdigit(name[2]) &&
|
|
|
1042 isxdigit(name[3]) &&
|
|
|
1043 isxdigit(name[4]) &&
|
|
|
1044 isxdigit(name[5]) &&
|
|
|
1045 isxdigit(name[6]) &&
|
|
|
1046 isxdigit(name[7]))
|
|
|
1047 {
|
|
|
1048 uint16_t group = GetTagValue(name);
|
|
|
1049 uint16_t element = GetTagValue(name + 4);
|
|
|
1050 return DicomTag(group, element);
|
|
|
1051 }
|
|
|
1052
|
|
|
1053 #if 0
|
|
|
1054 const DcmDataDictionary& dict = dcmDataDict.rdlock();
|
|
|
1055 const DcmDictEntry* entry = dict.findEntry(name);
|
|
|
1056
|
|
|
1057 if (entry == NULL)
|
|
|
1058 {
|
|
|
1059 dcmDataDict.unlock();
|
|
|
1060 throw OrthancException(ErrorCode_UnknownDicomTag);
|
|
|
1061 }
|
|
|
1062 else
|
|
|
1063 {
|
|
|
1064 DcmTagKey key = entry->getKey();
|
|
|
1065 DicomTag tag(key.getGroup(), key.getElement());
|
|
|
1066 dcmDataDict.unlock();
|
|
|
1067 return tag;
|
|
|
1068 }
|
|
|
1069 #else
|
|
|
1070 DcmTag tag;
|
|
|
1071 if (DcmTag::findTagFromName(name, tag).good())
|
|
|
1072 {
|
|
|
1073 return DicomTag(tag.getGTag(), tag.getETag());
|
|
|
1074 }
|
|
|
1075 else
|
|
|
1076 {
|
|
|
1077 throw OrthancException(ErrorCode_UnknownDicomTag);
|
|
|
1078 }
|
|
|
1079 #endif
|
|
|
1080 }
|
|
|
1081
|
|
|
1082
|
|
|
1083 bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag)
|
|
|
1084 {
|
|
|
1085 DcmTag tmp(tag.GetGroup(), tag.GetElement());
|
|
|
1086 return tmp.isUnknownVR();
|
|
|
1087 }
|
|
|
1088
|
|
|
1089
|
|
|
1090 void FromDcmtkBridge::ToJson(Json::Value& result,
|
|
|
1091 const DicomMap& values,
|
|
|
1092 bool simplify)
|
|
|
1093 {
|
|
|
1094 if (result.type() != Json::objectValue)
|
|
|
1095 {
|
|
|
1096 throw OrthancException(ErrorCode_BadParameterType);
|
|
|
1097 }
|
|
|
1098
|
|
|
1099 result.clear();
|
|
|
1100
|
|
|
1101 for (DicomMap::Map::const_iterator
|
|
|
1102 it = values.map_.begin(); it != values.map_.end(); ++it)
|
|
|
1103 {
|
|
|
1104 // TODO Inject PrivateCreator if some is available in the DicomMap?
|
|
|
1105 const std::string tagName = GetTagName(it->first, "");
|
|
|
1106
|
|
|
1107 if (simplify)
|
|
|
1108 {
|
|
|
1109 if (it->second->IsNull())
|
|
|
1110 {
|
|
|
1111 result[tagName] = Json::nullValue;
|
|
|
1112 }
|
|
|
1113 else
|
|
|
1114 {
|
|
|
1115 // TODO IsBinary
|
|
|
1116 result[tagName] = it->second->GetContent();
|
|
|
1117 }
|
|
|
1118 }
|
|
|
1119 else
|
|
|
1120 {
|
|
|
1121 Json::Value value = Json::objectValue;
|
|
|
1122
|
|
|
1123 value["Name"] = tagName;
|
|
|
1124
|
|
|
1125 if (it->second->IsNull())
|
|
|
1126 {
|
|
|
1127 value["Type"] = "Null";
|
|
|
1128 value["Value"] = Json::nullValue;
|
|
|
1129 }
|
|
|
1130 else
|
|
|
1131 {
|
|
|
1132 // TODO IsBinary
|
|
|
1133 value["Type"] = "String";
|
|
|
1134 value["Value"] = it->second->GetContent();
|
|
|
1135 }
|
|
|
1136
|
|
|
1137 result[it->first.Format()] = value;
|
|
|
1138 }
|
|
|
1139 }
|
|
|
1140 }
|
|
|
1141
|
|
|
1142
|
|
|
1143 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level)
|
|
|
1144 {
|
|
|
1145 char uid[100];
|
|
|
1146
|
|
|
1147 switch (level)
|
|
|
1148 {
|
|
|
1149 case ResourceType_Patient:
|
|
|
1150 // The "PatientID" field is of type LO (Long String), 64
|
|
|
1151 // Bytes Maximum. An UUID is of length 36, thus it can be used
|
|
|
1152 // as a random PatientID.
|
|
|
1153 return SystemToolbox::GenerateUuid();
|
|
|
1154
|
|
|
1155 case ResourceType_Instance:
|
|
|
1156 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
|
|
|
1157
|
|
|
1158 case ResourceType_Series:
|
|
|
1159 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT);
|
|
|
1160
|
|
|
1161 case ResourceType_Study:
|
|
|
1162 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT);
|
|
|
1163
|
|
|
1164 default:
|
|
|
1165 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
1166 }
|
|
|
1167 }
|
|
|
1168
|
|
|
1169 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
|
|
|
1170 DcmDataset& dataSet)
|
|
|
1171 {
|
|
|
1172 // Determine the transfer syntax which shall be used to write the
|
|
|
1173 // information to the file. We always switch to the Little Endian
|
|
|
1174 // syntax, with explicit length.
|
|
|
1175
|
|
|
1176 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
|
|
|
1177
|
|
|
1178
|
|
|
1179 /**
|
|
|
1180 * Note that up to Orthanc 0.7.1 (inclusive), the
|
|
|
1181 * "EXS_LittleEndianExplicit" was always used to save the DICOM
|
|
|
1182 * dataset into memory. We now keep the original transfer syntax
|
|
|
1183 * (if available).
|
|
|
1184 **/
|
|
|
1185 E_TransferSyntax xfer = dataSet.getOriginalXfer();
|
|
|
1186 if (xfer == EXS_Unknown)
|
|
|
1187 {
|
|
|
1188 // No information about the original transfer syntax: This is
|
|
|
1189 // most probably a DICOM dataset that was read from memory.
|
|
|
1190 xfer = EXS_LittleEndianExplicit;
|
|
|
1191 }
|
|
|
1192
|
|
|
1193 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
|
|
|
1194
|
|
|
1195 // Create the meta-header information
|
|
|
1196 DcmFileFormat ff(&dataSet);
|
|
|
1197 ff.validateMetaInfo(xfer);
|
|
|
1198 ff.removeInvalidGroups();
|
|
|
1199
|
|
|
1200 // Create a memory buffer with the proper size
|
|
|
1201 {
|
|
|
1202 const uint32_t estimatedSize = ff.calcElementLength(xfer, encodingType); // (*)
|
|
|
1203 buffer.resize(estimatedSize);
|
|
|
1204 }
|
|
|
1205
|
|
|
1206 DcmOutputBufferStream ob(&buffer[0], buffer.size());
|
|
|
1207
|
|
|
1208 // Fill the memory buffer with the meta-header and the dataset
|
|
|
1209 ff.transferInit();
|
|
|
1210 OFCondition c = ff.write(ob, xfer, encodingType, NULL,
|
|
|
1211 /*opt_groupLength*/ EGL_recalcGL,
|
|
|
1212 /*opt_paddingType*/ EPD_withoutPadding);
|
|
|
1213 ff.transferEnd();
|
|
|
1214
|
|
|
1215 if (c.good())
|
|
|
1216 {
|
|
|
1217 // The DICOM file is successfully written, truncate the target
|
|
|
1218 // buffer if its size was overestimated by (*)
|
|
|
1219 ob.flush();
|
|
|
1220
|
|
|
1221 size_t effectiveSize = static_cast<size_t>(ob.tell());
|
|
|
1222 if (effectiveSize < buffer.size())
|
|
|
1223 {
|
|
|
1224 buffer.resize(effectiveSize);
|
|
|
1225 }
|
|
|
1226
|
|
|
1227 return true;
|
|
|
1228 }
|
|
|
1229 else
|
|
|
1230 {
|
|
|
1231 // Error
|
|
|
1232 buffer.clear();
|
|
|
1233 return false;
|
|
|
1234 }
|
|
|
1235 }
|
|
|
1236
|
|
|
1237
|
|
|
1238 ValueRepresentation FromDcmtkBridge::LookupValueRepresentation(const DicomTag& tag)
|
|
|
1239 {
|
|
|
1240 DcmTag t(tag.GetGroup(), tag.GetElement());
|
|
|
1241 return Convert(t.getEVR());
|
|
|
1242 }
|
|
|
1243
|
|
|
1244 ValueRepresentation FromDcmtkBridge::Convert(const DcmEVR vr)
|
|
|
1245 {
|
|
|
1246 switch (vr)
|
|
|
1247 {
|
|
|
1248 case EVR_AE:
|
|
|
1249 return ValueRepresentation_ApplicationEntity;
|
|
|
1250
|
|
|
1251 case EVR_AS:
|
|
|
1252 return ValueRepresentation_AgeString;
|
|
|
1253
|
|
|
1254 case EVR_AT:
|
|
|
1255 return ValueRepresentation_AttributeTag;
|
|
|
1256
|
|
|
1257 case EVR_CS:
|
|
|
1258 return ValueRepresentation_CodeString;
|
|
|
1259
|
|
|
1260 case EVR_DA:
|
|
|
1261 return ValueRepresentation_Date;
|
|
|
1262
|
|
|
1263 case EVR_DS:
|
|
|
1264 return ValueRepresentation_DecimalString;
|
|
|
1265
|
|
|
1266 case EVR_DT:
|
|
|
1267 return ValueRepresentation_DateTime;
|
|
|
1268
|
|
|
1269 case EVR_FL:
|
|
|
1270 return ValueRepresentation_FloatingPointSingle;
|
|
|
1271
|
|
|
1272 case EVR_FD:
|
|
|
1273 return ValueRepresentation_FloatingPointDouble;
|
|
|
1274
|
|
|
1275 case EVR_IS:
|
|
|
1276 return ValueRepresentation_IntegerString;
|
|
|
1277
|
|
|
1278 case EVR_LO:
|
|
|
1279 return ValueRepresentation_LongString;
|
|
|
1280
|
|
|
1281 case EVR_LT:
|
|
|
1282 return ValueRepresentation_LongText;
|
|
|
1283
|
|
|
1284 case EVR_OB:
|
|
|
1285 return ValueRepresentation_OtherByte;
|
|
|
1286
|
|
|
1287 // Not supported as of DCMTK 3.6.0
|
|
|
1288 /*case EVR_OD:
|
|
|
1289 return ValueRepresentation_OtherDouble;*/
|
|
|
1290
|
|
|
1291 case EVR_OF:
|
|
|
1292 return ValueRepresentation_OtherFloat;
|
|
|
1293
|
|
|
1294 // Not supported as of DCMTK 3.6.0
|
|
|
1295 /*case EVR_OL:
|
|
|
1296 return ValueRepresentation_OtherLong;*/
|
|
|
1297
|
|
|
1298 case EVR_OW:
|
|
|
1299 return ValueRepresentation_OtherWord;
|
|
|
1300
|
|
|
1301 case EVR_PN:
|
|
|
1302 return ValueRepresentation_PersonName;
|
|
|
1303
|
|
|
1304 case EVR_SH:
|
|
|
1305 return ValueRepresentation_ShortString;
|
|
|
1306
|
|
|
1307 case EVR_SL:
|
|
|
1308 return ValueRepresentation_SignedLong;
|
|
|
1309
|
|
|
1310 case EVR_SQ:
|
|
|
1311 return ValueRepresentation_Sequence;
|
|
|
1312
|
|
|
1313 case EVR_SS:
|
|
|
1314 return ValueRepresentation_SignedShort;
|
|
|
1315
|
|
|
1316 case EVR_ST:
|
|
|
1317 return ValueRepresentation_ShortText;
|
|
|
1318
|
|
|
1319 case EVR_TM:
|
|
|
1320 return ValueRepresentation_Time;
|
|
|
1321
|
|
|
1322 // Not supported as of DCMTK 3.6.0
|
|
|
1323 /*case EVR_UC:
|
|
|
1324 return ValueRepresentation_UnlimitedCharacters;*/
|
|
|
1325
|
|
|
1326 case EVR_UI:
|
|
|
1327 return ValueRepresentation_UniqueIdentifier;
|
|
|
1328
|
|
|
1329 case EVR_UL:
|
|
|
1330 return ValueRepresentation_UnsignedLong;
|
|
|
1331
|
|
|
1332 case EVR_UN:
|
|
|
1333 return ValueRepresentation_Unknown;
|
|
|
1334
|
|
|
1335 // Not supported as of DCMTK 3.6.0
|
|
|
1336 /*case EVR_UR:
|
|
|
1337 return ValueRepresentation_UniversalResource;*/
|
|
|
1338
|
|
|
1339 case EVR_US:
|
|
|
1340 return ValueRepresentation_UnsignedShort;
|
|
|
1341
|
|
|
1342 case EVR_UT:
|
|
|
1343 return ValueRepresentation_UnlimitedText;
|
|
|
1344
|
|
|
1345 default:
|
|
|
1346 return ValueRepresentation_NotSupported;
|
|
|
1347 }
|
|
|
1348 }
|
|
|
1349
|
|
|
1350
|
|
|
1351 static bool IsBinaryTag(const DcmTag& key)
|
|
|
1352 {
|
|
|
1353 return (key.isUnknownVR() ||
|
|
|
1354 key.getEVR() == EVR_OB ||
|
|
|
1355 key.getEVR() == EVR_OF ||
|
|
|
1356 key.getEVR() == EVR_OW ||
|
|
|
1357 key.getEVR() == EVR_UN ||
|
|
|
1358 key.getEVR() == EVR_ox);
|
|
|
1359 }
|
|
|
1360
|
|
|
1361
|
|
|
1362 DcmElement* FromDcmtkBridge::CreateElementForTag(const DicomTag& tag)
|
|
|
1363 {
|
|
|
1364 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
1365
|
|
|
1366 if (tag.IsPrivate() ||
|
|
|
1367 IsBinaryTag(key))
|
|
|
1368 {
|
|
|
1369 return new DcmOtherByteOtherWord(key);
|
|
|
1370 }
|
|
|
1371
|
|
|
1372 switch (key.getEVR())
|
|
|
1373 {
|
|
|
1374 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
1375
|
|
|
1376 /**
|
|
|
1377 * Binary types, handled above
|
|
|
1378 **/
|
|
|
1379
|
|
|
1380 case EVR_OB: // other byte
|
|
|
1381 case EVR_OF: // other float
|
|
|
1382 case EVR_OW: // other word
|
|
|
1383 case EVR_UN: // unknown value representation
|
|
|
1384 case EVR_ox: // OB or OW depending on context
|
|
|
1385 throw OrthancException(ErrorCode_InternalError);
|
|
|
1386
|
|
|
1387
|
|
|
1388 /**
|
|
|
1389 * String types.
|
|
|
1390 * http://support.dcmtk.org/docs/classDcmByteString.html
|
|
|
1391 **/
|
|
|
1392
|
|
|
1393 case EVR_AS: // age string
|
|
|
1394 return new DcmAgeString(key);
|
|
|
1395
|
|
|
1396 case EVR_AE: // application entity title
|
|
|
1397 return new DcmApplicationEntity(key);
|
|
|
1398
|
|
|
1399 case EVR_CS: // code string
|
|
|
1400 return new DcmCodeString(key);
|
|
|
1401
|
|
|
1402 case EVR_DA: // date string
|
|
|
1403 return new DcmDate(key);
|
|
|
1404
|
|
|
1405 case EVR_DT: // date time string
|
|
|
1406 return new DcmDateTime(key);
|
|
|
1407
|
|
|
1408 case EVR_DS: // decimal string
|
|
|
1409 return new DcmDecimalString(key);
|
|
|
1410
|
|
|
1411 case EVR_IS: // integer string
|
|
|
1412 return new DcmIntegerString(key);
|
|
|
1413
|
|
|
1414 case EVR_TM: // time string
|
|
|
1415 return new DcmTime(key);
|
|
|
1416
|
|
|
1417 case EVR_UI: // unique identifier
|
|
|
1418 return new DcmUniqueIdentifier(key);
|
|
|
1419
|
|
|
1420 case EVR_ST: // short text
|
|
|
1421 return new DcmShortText(key);
|
|
|
1422
|
|
|
1423 case EVR_LO: // long string
|
|
|
1424 return new DcmLongString(key);
|
|
|
1425
|
|
|
1426 case EVR_LT: // long text
|
|
|
1427 return new DcmLongText(key);
|
|
|
1428
|
|
|
1429 case EVR_UT: // unlimited text
|
|
|
1430 return new DcmUnlimitedText(key);
|
|
|
1431
|
|
|
1432 case EVR_SH: // short string
|
|
|
1433 return new DcmShortString(key);
|
|
|
1434
|
|
|
1435 case EVR_PN: // person name
|
|
|
1436 return new DcmPersonName(key);
|
|
|
1437
|
|
|
1438
|
|
|
1439 /**
|
|
|
1440 * Numerical types
|
|
|
1441 **/
|
|
|
1442
|
|
|
1443 case EVR_SL: // signed long
|
|
|
1444 return new DcmSignedLong(key);
|
|
|
1445
|
|
|
1446 case EVR_SS: // signed short
|
|
|
1447 return new DcmSignedShort(key);
|
|
|
1448
|
|
|
1449 case EVR_UL: // unsigned long
|
|
|
1450 return new DcmUnsignedLong(key);
|
|
|
1451
|
|
|
1452 case EVR_US: // unsigned short
|
|
|
1453 return new DcmUnsignedShort(key);
|
|
|
1454
|
|
|
1455 case EVR_FL: // float single-precision
|
|
|
1456 return new DcmFloatingPointSingle(key);
|
|
|
1457
|
|
|
1458 case EVR_FD: // float double-precision
|
|
|
1459 return new DcmFloatingPointDouble(key);
|
|
|
1460
|
|
|
1461
|
|
|
1462 /**
|
|
|
1463 * Sequence types, should never occur at this point.
|
|
|
1464 **/
|
|
|
1465
|
|
|
1466 case EVR_SQ: // sequence of items
|
|
|
1467 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
1468
|
|
|
1469
|
|
|
1470 /**
|
|
|
1471 * TODO
|
|
|
1472 **/
|
|
|
1473
|
|
|
1474 case EVR_AT: // attribute tag
|
|
|
1475 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
1476
|
|
|
1477
|
|
|
1478 /**
|
|
|
1479 * Internal to DCMTK.
|
|
|
1480 **/
|
|
|
1481
|
|
|
1482 case EVR_xs: // SS or US depending on context
|
|
|
1483 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
1484 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
1485 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
1486 case EVR_item: // used internally for items
|
|
|
1487 case EVR_metainfo: // used internally for meta info datasets
|
|
|
1488 case EVR_dataset: // used internally for datasets
|
|
|
1489 case EVR_fileFormat: // used internally for DICOM files
|
|
|
1490 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
1491 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
1492 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
1493 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
1494 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
1495 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
1496 case EVR_OverlayData: // used internally for overlay data
|
|
|
1497 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
1498 default:
|
|
|
1499 break;
|
|
|
1500 }
|
|
|
1501
|
|
|
1502 throw OrthancException(ErrorCode_InternalError);
|
|
|
1503 }
|
|
|
1504
|
|
|
1505
|
|
|
1506
|
|
|
1507 void FromDcmtkBridge::FillElementWithString(DcmElement& element,
|
|
|
1508 const DicomTag& tag,
|
|
|
1509 const std::string& utf8Value,
|
|
|
1510 bool decodeDataUriScheme,
|
|
|
1511 Encoding dicomEncoding)
|
|
|
1512 {
|
|
|
1513 std::string binary;
|
|
|
1514 const std::string* decoded = &utf8Value;
|
|
|
1515
|
|
|
1516 if (decodeDataUriScheme &&
|
|
|
1517 boost::starts_with(utf8Value, "data:application/octet-stream;base64,"))
|
|
|
1518 {
|
|
|
1519 std::string mime;
|
|
|
1520 if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value))
|
|
|
1521 {
|
|
|
1522 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1523 }
|
|
|
1524
|
|
|
1525 decoded = &binary;
|
|
|
1526 }
|
|
|
1527 else if (dicomEncoding != Encoding_Utf8)
|
|
|
1528 {
|
|
|
1529 binary = Toolbox::ConvertFromUtf8(utf8Value, dicomEncoding);
|
|
|
1530 decoded = &binary;
|
|
|
1531 }
|
|
|
1532
|
|
|
1533 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
1534
|
|
|
1535 if (tag.IsPrivate() ||
|
|
|
1536 IsBinaryTag(key))
|
|
|
1537 {
|
|
|
1538 if (element.putUint8Array((const Uint8*) decoded->c_str(), decoded->size()).good())
|
|
|
1539 {
|
|
|
1540 return;
|
|
|
1541 }
|
|
|
1542 else
|
|
|
1543 {
|
|
|
1544 throw OrthancException(ErrorCode_InternalError);
|
|
|
1545 }
|
|
|
1546 }
|
|
|
1547
|
|
|
1548 bool ok = false;
|
|
|
1549
|
|
|
1550 try
|
|
|
1551 {
|
|
|
1552 switch (key.getEVR())
|
|
|
1553 {
|
|
|
1554 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
1555
|
|
|
1556 /**
|
|
|
1557 * TODO.
|
|
|
1558 **/
|
|
|
1559
|
|
|
1560 case EVR_OB: // other byte
|
|
|
1561 case EVR_OF: // other float
|
|
|
1562 case EVR_OW: // other word
|
|
|
1563 case EVR_AT: // attribute tag
|
|
|
1564 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
1565
|
|
|
1566 case EVR_UN: // unknown value representation
|
|
|
1567 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
1568
|
|
|
1569
|
|
|
1570 /**
|
|
|
1571 * String types.
|
|
|
1572 **/
|
|
|
1573
|
|
|
1574 case EVR_DS: // decimal string
|
|
|
1575 case EVR_IS: // integer string
|
|
|
1576 case EVR_AS: // age string
|
|
|
1577 case EVR_DA: // date string
|
|
|
1578 case EVR_DT: // date time string
|
|
|
1579 case EVR_TM: // time string
|
|
|
1580 case EVR_AE: // application entity title
|
|
|
1581 case EVR_CS: // code string
|
|
|
1582 case EVR_SH: // short string
|
|
|
1583 case EVR_LO: // long string
|
|
|
1584 case EVR_ST: // short text
|
|
|
1585 case EVR_LT: // long text
|
|
|
1586 case EVR_UT: // unlimited text
|
|
|
1587 case EVR_PN: // person name
|
|
|
1588 case EVR_UI: // unique identifier
|
|
|
1589 {
|
|
|
1590 ok = element.putString(decoded->c_str()).good();
|
|
|
1591 break;
|
|
|
1592 }
|
|
|
1593
|
|
|
1594
|
|
|
1595 /**
|
|
|
1596 * Numerical types
|
|
|
1597 **/
|
|
|
1598
|
|
|
1599 case EVR_SL: // signed long
|
|
|
1600 {
|
|
|
1601 ok = element.putSint32(boost::lexical_cast<Sint32>(*decoded)).good();
|
|
|
1602 break;
|
|
|
1603 }
|
|
|
1604
|
|
|
1605 case EVR_SS: // signed short
|
|
|
1606 {
|
|
|
1607 ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good();
|
|
|
1608 break;
|
|
|
1609 }
|
|
|
1610
|
|
|
1611 case EVR_UL: // unsigned long
|
|
|
1612 {
|
|
|
1613 ok = element.putUint32(boost::lexical_cast<Uint32>(*decoded)).good();
|
|
|
1614 break;
|
|
|
1615 }
|
|
|
1616
|
|
|
1617 case EVR_US: // unsigned short
|
|
|
1618 {
|
|
|
1619 ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good();
|
|
|
1620 break;
|
|
|
1621 }
|
|
|
1622
|
|
|
1623 case EVR_FL: // float single-precision
|
|
|
1624 {
|
|
|
1625 ok = element.putFloat32(boost::lexical_cast<float>(*decoded)).good();
|
|
|
1626 break;
|
|
|
1627 }
|
|
|
1628
|
|
|
1629 case EVR_FD: // float double-precision
|
|
|
1630 {
|
|
|
1631 ok = element.putFloat64(boost::lexical_cast<double>(*decoded)).good();
|
|
|
1632 break;
|
|
|
1633 }
|
|
|
1634
|
|
|
1635
|
|
|
1636 /**
|
|
|
1637 * Sequence types, should never occur at this point.
|
|
|
1638 **/
|
|
|
1639
|
|
|
1640 case EVR_SQ: // sequence of items
|
|
|
1641 {
|
|
|
1642 ok = false;
|
|
|
1643 break;
|
|
|
1644 }
|
|
|
1645
|
|
|
1646
|
|
|
1647 /**
|
|
|
1648 * Internal to DCMTK.
|
|
|
1649 **/
|
|
|
1650
|
|
|
1651 case EVR_ox: // OB or OW depending on context
|
|
|
1652 case EVR_xs: // SS or US depending on context
|
|
|
1653 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
1654 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
1655 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
1656 case EVR_item: // used internally for items
|
|
|
1657 case EVR_metainfo: // used internally for meta info datasets
|
|
|
1658 case EVR_dataset: // used internally for datasets
|
|
|
1659 case EVR_fileFormat: // used internally for DICOM files
|
|
|
1660 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
1661 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
1662 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
1663 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
1664 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
1665 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
1666 case EVR_OverlayData: // used internally for overlay data
|
|
|
1667 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
1668 default:
|
|
|
1669 break;
|
|
|
1670 }
|
|
|
1671 }
|
|
|
1672 catch (boost::bad_lexical_cast&)
|
|
|
1673 {
|
|
|
1674 ok = false;
|
|
|
1675 }
|
|
|
1676
|
|
|
1677 if (!ok)
|
|
|
1678 {
|
|
|
1679 LOG(ERROR) << "While creating a DICOM instance, tag (" << tag.Format()
|
|
|
1680 << ") has out-of-range value: \"" << *decoded << "\"";
|
|
|
1681 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1682 }
|
|
|
1683 }
|
|
|
1684
|
|
|
1685
|
|
|
1686 DcmElement* FromDcmtkBridge::FromJson(const DicomTag& tag,
|
|
|
1687 const Json::Value& value,
|
|
|
1688 bool decodeDataUriScheme,
|
|
|
1689 Encoding dicomEncoding)
|
|
|
1690 {
|
|
|
1691 std::auto_ptr<DcmElement> element;
|
|
|
1692
|
|
|
1693 switch (value.type())
|
|
|
1694 {
|
|
|
1695 case Json::stringValue:
|
|
|
1696 element.reset(CreateElementForTag(tag));
|
|
|
1697 FillElementWithString(*element, tag, value.asString(), decodeDataUriScheme, dicomEncoding);
|
|
|
1698 break;
|
|
|
1699
|
|
|
1700 case Json::nullValue:
|
|
|
1701 element.reset(CreateElementForTag(tag));
|
|
|
1702 FillElementWithString(*element, tag, "", decodeDataUriScheme, dicomEncoding);
|
|
|
1703 break;
|
|
|
1704
|
|
|
1705 case Json::arrayValue:
|
|
|
1706 {
|
|
|
1707 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
1708 if (key.getEVR() != EVR_SQ)
|
|
|
1709 {
|
|
|
1710 throw OrthancException(ErrorCode_BadParameterType);
|
|
|
1711 }
|
|
|
1712
|
|
|
1713 DcmSequenceOfItems* sequence = new DcmSequenceOfItems(key);
|
|
|
1714 element.reset(sequence);
|
|
|
1715
|
|
|
1716 for (Json::Value::ArrayIndex i = 0; i < value.size(); i++)
|
|
|
1717 {
|
|
|
1718 std::auto_ptr<DcmItem> item(new DcmItem);
|
|
|
1719
|
|
|
1720 Json::Value::Members members = value[i].getMemberNames();
|
|
|
1721 for (Json::Value::ArrayIndex j = 0; j < members.size(); j++)
|
|
|
1722 {
|
|
|
1723 item->insert(FromJson(ParseTag(members[j]), value[i][members[j]], decodeDataUriScheme, dicomEncoding));
|
|
|
1724 }
|
|
|
1725
|
|
|
1726 sequence->append(item.release());
|
|
|
1727 }
|
|
|
1728
|
|
|
1729 break;
|
|
|
1730 }
|
|
|
1731
|
|
|
1732 default:
|
|
|
1733 throw OrthancException(ErrorCode_BadParameterType);
|
|
|
1734 }
|
|
|
1735
|
|
|
1736 return element.release();
|
|
|
1737 }
|
|
|
1738
|
|
|
1739
|
|
|
1740 DcmPixelSequence* FromDcmtkBridge::GetPixelSequence(DcmDataset& dataset)
|
|
|
1741 {
|
|
|
1742 DcmElement *element = NULL;
|
|
|
1743 if (!dataset.findAndGetElement(DCM_PixelData, element).good())
|
|
|
1744 {
|
|
|
1745 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1746 }
|
|
|
1747
|
|
|
1748 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
|
|
|
1749 DcmPixelSequence* pixelSequence = NULL;
|
|
|
1750 if (!pixelData.getEncapsulatedRepresentation
|
|
|
1751 (dataset.getOriginalXfer(), NULL, pixelSequence).good())
|
|
|
1752 {
|
|
|
1753 return NULL;
|
|
|
1754 }
|
|
|
1755 else
|
|
|
1756 {
|
|
|
1757 return pixelSequence;
|
|
|
1758 }
|
|
|
1759 }
|
|
|
1760
|
|
|
1761
|
|
|
1762 Encoding FromDcmtkBridge::ExtractEncoding(const Json::Value& json,
|
|
|
1763 Encoding defaultEncoding)
|
|
|
1764 {
|
|
|
1765 if (json.type() != Json::objectValue)
|
|
|
1766 {
|
|
|
1767 throw OrthancException(ErrorCode_BadParameterType);
|
|
|
1768 }
|
|
|
1769
|
|
|
1770 Encoding encoding = defaultEncoding;
|
|
|
1771
|
|
|
1772 const Json::Value::Members tags = json.getMemberNames();
|
|
|
1773
|
|
|
1774 // Look for SpecificCharacterSet (0008,0005) in the JSON file
|
|
|
1775 for (size_t i = 0; i < tags.size(); i++)
|
|
|
1776 {
|
|
|
1777 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]);
|
|
|
1778 if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET)
|
|
|
1779 {
|
|
|
1780 const Json::Value& value = json[tags[i]];
|
|
|
1781 if (value.type() != Json::stringValue ||
|
|
|
1782 (value.asString().length() != 0 &&
|
|
|
1783 !GetDicomEncoding(encoding, value.asCString())))
|
|
|
1784 {
|
|
|
1785 LOG(ERROR) << "Unknown encoding while creating DICOM from JSON: " << value;
|
|
|
1786 throw OrthancException(ErrorCode_BadRequest);
|
|
|
1787 }
|
|
|
1788
|
|
|
1789 if (value.asString().length() == 0)
|
|
|
1790 {
|
|
|
1791 return defaultEncoding;
|
|
|
1792 }
|
|
|
1793 }
|
|
|
1794 }
|
|
|
1795
|
|
|
1796 return encoding;
|
|
|
1797 }
|
|
|
1798
|
|
|
1799
|
|
|
1800 static void SetString(DcmDataset& target,
|
|
|
1801 const DcmTag& tag,
|
|
|
1802 const std::string& value)
|
|
|
1803 {
|
|
|
1804 if (!target.putAndInsertString(tag, value.c_str()).good())
|
|
|
1805 {
|
|
|
1806 throw OrthancException(ErrorCode_InternalError);
|
|
|
1807 }
|
|
|
1808 }
|
|
|
1809
|
|
|
1810
|
|
|
1811 DcmDataset* FromDcmtkBridge::FromJson(const Json::Value& json, // Encoded using UTF-8
|
|
|
1812 bool generateIdentifiers,
|
|
|
1813 bool decodeDataUriScheme,
|
|
|
1814 Encoding defaultEncoding)
|
|
|
1815 {
|
|
|
1816 std::auto_ptr<DcmDataset> result(new DcmDataset);
|
|
|
1817 Encoding encoding = ExtractEncoding(json, defaultEncoding);
|
|
|
1818
|
|
|
1819 SetString(*result, DCM_SpecificCharacterSet, GetDicomSpecificCharacterSet(encoding));
|
|
|
1820
|
|
|
1821 const Json::Value::Members tags = json.getMemberNames();
|
|
|
1822
|
|
|
1823 bool hasPatientId = false;
|
|
|
1824 bool hasStudyInstanceUid = false;
|
|
|
1825 bool hasSeriesInstanceUid = false;
|
|
|
1826 bool hasSopInstanceUid = false;
|
|
|
1827
|
|
|
1828 for (size_t i = 0; i < tags.size(); i++)
|
|
|
1829 {
|
|
|
1830 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]);
|
|
|
1831 const Json::Value& value = json[tags[i]];
|
|
|
1832
|
|
|
1833 if (tag == DICOM_TAG_PATIENT_ID)
|
|
|
1834 {
|
|
|
1835 hasPatientId = true;
|
|
|
1836 }
|
|
|
1837 else if (tag == DICOM_TAG_STUDY_INSTANCE_UID)
|
|
|
1838 {
|
|
|
1839 hasStudyInstanceUid = true;
|
|
|
1840 }
|
|
|
1841 else if (tag == DICOM_TAG_SERIES_INSTANCE_UID)
|
|
|
1842 {
|
|
|
1843 hasSeriesInstanceUid = true;
|
|
|
1844 }
|
|
|
1845 else if (tag == DICOM_TAG_SOP_INSTANCE_UID)
|
|
|
1846 {
|
|
|
1847 hasSopInstanceUid = true;
|
|
|
1848 }
|
|
|
1849
|
|
|
1850 if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET)
|
|
|
1851 {
|
|
|
1852 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, encoding));
|
|
|
1853 const DcmTagKey& tag = element->getTag();
|
|
|
1854
|
|
|
1855 result->findAndDeleteElement(tag);
|
|
|
1856
|
|
|
1857 DcmElement* tmp = element.release();
|
|
|
1858 if (!result->insert(tmp, false, false).good())
|
|
|
1859 {
|
|
|
1860 delete tmp;
|
|
|
1861 throw OrthancException(ErrorCode_InternalError);
|
|
|
1862 }
|
|
|
1863 }
|
|
|
1864 }
|
|
|
1865
|
|
|
1866 if (!hasPatientId &&
|
|
|
1867 generateIdentifiers)
|
|
|
1868 {
|
|
|
1869 SetString(*result, DCM_PatientID, GenerateUniqueIdentifier(ResourceType_Patient));
|
|
|
1870 }
|
|
|
1871
|
|
|
1872 if (!hasStudyInstanceUid &&
|
|
|
1873 generateIdentifiers)
|
|
|
1874 {
|
|
|
1875 SetString(*result, DCM_StudyInstanceUID, GenerateUniqueIdentifier(ResourceType_Study));
|
|
|
1876 }
|
|
|
1877
|
|
|
1878 if (!hasSeriesInstanceUid &&
|
|
|
1879 generateIdentifiers)
|
|
|
1880 {
|
|
|
1881 SetString(*result, DCM_SeriesInstanceUID, GenerateUniqueIdentifier(ResourceType_Series));
|
|
|
1882 }
|
|
|
1883
|
|
|
1884 if (!hasSopInstanceUid &&
|
|
|
1885 generateIdentifiers)
|
|
|
1886 {
|
|
|
1887 SetString(*result, DCM_SOPInstanceUID, GenerateUniqueIdentifier(ResourceType_Instance));
|
|
|
1888 }
|
|
|
1889
|
|
|
1890 return result.release();
|
|
|
1891 }
|
|
|
1892
|
|
|
1893
|
|
|
1894 DcmFileFormat* FromDcmtkBridge::LoadFromMemoryBuffer(const void* buffer,
|
|
|
1895 size_t size)
|
|
|
1896 {
|
|
|
1897 DcmInputBufferStream is;
|
|
|
1898 if (size > 0)
|
|
|
1899 {
|
|
|
1900 is.setBuffer(buffer, size);
|
|
|
1901 }
|
|
|
1902 is.setEos();
|
|
|
1903
|
|
|
1904 std::auto_ptr<DcmFileFormat> result(new DcmFileFormat);
|
|
|
1905
|
|
|
1906 result->transferInit();
|
|
|
1907 if (!result->read(is).good())
|
|
|
1908 {
|
|
|
1909 LOG(ERROR) << "Cannot parse an invalid DICOM file (size: " << size << " bytes)";
|
|
|
1910 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1911 }
|
|
|
1912
|
|
|
1913 result->loadAllDataIntoMemory();
|
|
|
1914 result->transferEnd();
|
|
|
1915
|
|
|
1916 return result.release();
|
|
|
1917 }
|
|
|
1918
|
|
|
1919
|
|
|
1920 void FromDcmtkBridge::FromJson(DicomMap& target,
|
|
|
1921 const Json::Value& source)
|
|
|
1922 {
|
|
|
1923 if (source.type() != Json::objectValue)
|
|
|
1924 {
|
|
|
1925 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1926 }
|
|
|
1927
|
|
|
1928 target.Clear();
|
|
|
1929
|
|
|
1930 Json::Value::Members members = source.getMemberNames();
|
|
|
1931
|
|
|
1932 for (size_t i = 0; i < members.size(); i++)
|
|
|
1933 {
|
|
|
1934 const Json::Value& value = source[members[i]];
|
|
|
1935
|
|
|
1936 if (value.type() != Json::stringValue)
|
|
|
1937 {
|
|
|
1938 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
1939 }
|
|
|
1940
|
|
|
1941 target.SetValue(ParseTag(members[i]), value.asString(), false);
|
|
|
1942 }
|
|
|
1943 }
|
|
|
1944
|
|
|
1945
|
|
|
1946 void FromDcmtkBridge::ChangeStringEncoding(DcmItem& dataset,
|
|
|
1947 Encoding source,
|
|
|
1948 Encoding target)
|
|
|
1949 {
|
|
|
1950 // Recursive exploration of a dataset to change the encoding of
|
|
|
1951 // each string-like element
|
|
|
1952
|
|
|
1953 if (source == target)
|
|
|
1954 {
|
|
|
1955 return;
|
|
|
1956 }
|
|
|
1957
|
|
|
1958 for (unsigned long i = 0; i < dataset.card(); i++)
|
|
|
1959 {
|
|
|
1960 DcmElement* element = dataset.getElement(i);
|
|
|
1961 if (element)
|
|
|
1962 {
|
|
|
1963 if (element->isLeaf())
|
|
|
1964 {
|
|
|
1965 char *c = NULL;
|
|
|
1966 if (element->isaString() &&
|
|
|
1967 element->getString(c).good() &&
|
|
|
1968 c != NULL)
|
|
|
1969 {
|
|
|
1970 std::string a = Toolbox::ConvertToUtf8(c, source);
|
|
|
1971 std::string b = Toolbox::ConvertFromUtf8(a, target);
|
|
|
1972 element->putString(b.c_str());
|
|
|
1973 }
|
|
|
1974 }
|
|
|
1975 else
|
|
|
1976 {
|
|
|
1977 // "All subclasses of DcmElement except for DcmSequenceOfItems
|
|
|
1978 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
|
|
|
1979 // etc. are not." The following dynamic_cast is thus OK.
|
|
|
1980 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(*element);
|
|
|
1981
|
|
|
1982 for (unsigned long j = 0; j < sequence.card(); j++)
|
|
|
1983 {
|
|
|
1984 ChangeStringEncoding(*sequence.getItem(j), source, target);
|
|
|
1985 }
|
|
|
1986 }
|
|
|
1987 }
|
|
|
1988 }
|
|
|
1989 }
|
|
|
1990
|
|
|
1991
|
|
|
1992 bool FromDcmtkBridge::LookupTransferSyntax(std::string& result,
|
|
|
1993 DcmFileFormat& dicom)
|
|
|
1994 {
|
|
|
1995 const char* value = NULL;
|
|
|
1996
|
|
|
1997 if (dicom.getMetaInfo() != NULL &&
|
|
|
1998 dicom.getMetaInfo()->findAndGetString(DCM_TransferSyntaxUID, value).good() &&
|
|
|
1999 value != NULL)
|
|
|
2000 {
|
|
|
2001 result.assign(value);
|
|
|
2002 return true;
|
|
|
2003 }
|
|
|
2004 else
|
|
|
2005 {
|
|
|
2006 return false;
|
|
|
2007 }
|
|
|
2008 }
|
|
|
2009
|
|
|
2010
|
|
|
2011 #if ORTHANC_ENABLE_LUA == 1
|
|
|
2012 void FromDcmtkBridge::ExecuteToDicom(DicomMap& target,
|
|
|
2013 LuaFunctionCall& call)
|
|
|
2014 {
|
|
|
2015 Json::Value output;
|
|
|
2016 call.ExecuteToJson(output, true /* keep strings */);
|
|
|
2017
|
|
|
2018 target.Clear();
|
|
|
2019
|
|
|
2020 if (output.type() == Json::arrayValue &&
|
|
|
2021 output.size() == 0)
|
|
|
2022 {
|
|
|
2023 // This case happens for empty tables
|
|
|
2024 return;
|
|
|
2025 }
|
|
|
2026
|
|
|
2027 if (output.type() != Json::objectValue)
|
|
|
2028 {
|
|
|
2029 LOG(ERROR) << "Lua: IncomingFindRequestFilter must return a table";
|
|
|
2030 throw OrthancException(ErrorCode_LuaBadOutput);
|
|
|
2031 }
|
|
|
2032
|
|
|
2033 Json::Value::Members members = output.getMemberNames();
|
|
|
2034
|
|
|
2035 for (size_t i = 0; i < members.size(); i++)
|
|
|
2036 {
|
|
|
2037 if (output[members[i]].type() != Json::stringValue)
|
|
|
2038 {
|
|
|
2039 LOG(ERROR) << "Lua: IncomingFindRequestFilter must return a table mapping names of DICOM tags to strings";
|
|
|
2040 throw OrthancException(ErrorCode_LuaBadOutput);
|
|
|
2041 }
|
|
|
2042
|
|
|
2043 DicomTag tag(ParseTag(members[i]));
|
|
|
2044 target.SetValue(tag, output[members[i]].asString(), false);
|
|
|
2045 }
|
|
|
2046 }
|
|
|
2047 #endif
|
|
|
2048
|
|
|
2049
|
|
|
2050 void FromDcmtkBridge::ExtractDicomSummary(DicomMap& target,
|
|
|
2051 DcmItem& dataset)
|
|
|
2052 {
|
|
|
2053 ExtractDicomSummary(target, dataset,
|
|
|
2054 ORTHANC_MAXIMUM_TAG_LENGTH,
|
|
|
2055 GetDefaultDicomEncoding());
|
|
|
2056 }
|
|
|
2057
|
|
|
2058
|
|
|
2059 void FromDcmtkBridge::ExtractDicomAsJson(Json::Value& target,
|
|
|
2060 DcmDataset& dataset,
|
|
|
2061 const std::set<DicomTag>& ignoreTagLength)
|
|
|
2062 {
|
|
|
2063 ExtractDicomAsJson(target, dataset,
|
|
|
2064 DicomToJsonFormat_Full,
|
|
|
2065 DicomToJsonFlags_Default,
|
|
|
2066 ORTHANC_MAXIMUM_TAG_LENGTH,
|
|
|
2067 GetDefaultDicomEncoding(),
|
|
|
2068 ignoreTagLength);
|
|
|
2069 }
|
|
|
2070
|
|
|
2071
|
|
|
2072 void FromDcmtkBridge::InitializeCodecs()
|
|
|
2073 {
|
|
|
2074 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
|
|
|
2075 LOG(WARNING) << "Registering JPEG Lossless codecs in DCMTK";
|
|
|
2076 DJLSDecoderRegistration::registerCodecs();
|
|
|
2077 #endif
|
|
|
2078
|
|
|
2079 #if ORTHANC_ENABLE_DCMTK_JPEG == 1
|
|
|
2080 LOG(WARNING) << "Registering JPEG codecs in DCMTK";
|
|
|
2081 DJDecoderRegistration::registerCodecs();
|
|
|
2082 #endif
|
|
|
2083 }
|
|
|
2084
|
|
|
2085
|
|
|
2086 void FromDcmtkBridge::FinalizeCodecs()
|
|
|
2087 {
|
|
|
2088 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
|
|
|
2089 // Unregister JPEG-LS codecs
|
|
|
2090 DJLSDecoderRegistration::cleanup();
|
|
|
2091 #endif
|
|
|
2092
|
|
|
2093 #if ORTHANC_ENABLE_DCMTK_JPEG == 1
|
|
|
2094 // Unregister JPEG codecs
|
|
|
2095 DJDecoderRegistration::cleanup();
|
|
|
2096 #endif
|
|
|
2097 }
|
|
|
2098 }
|
