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annotate OrthancServer/FromDcmtkBridge.cpp @ 1417:8e23f16a198d

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fix issues 35 and 37
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 10 Jun 2015 15:17:02 +0200
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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33
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34 #include "PrecompiledHeadersServer.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 "Internals/DicomImageDecoder.h"
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41
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42 #include "FromDcmtkBridge.h"
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43 #include "ToDcmtkBridge.h"
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44 #include "OrthancInitialization.h"
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45 #include "../Core/Toolbox.h"
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46 #include "../Core/OrthancException.h"
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47 #include "../Core/ImageFormats/PngWriter.h"
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48 #include "../Core/Uuid.h"
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49 #include "../Core/DicomFormat/DicomString.h"
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50 #include "../Core/DicomFormat/DicomNullValue.h"
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51 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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52
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53 #include <list>
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54 #include <limits>
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55
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56 #include <boost/lexical_cast.hpp>
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57
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58 #include <dcmtk/dcmdata/dcchrstr.h>
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59 #include <dcmtk/dcmdata/dcdicent.h>
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60 #include <dcmtk/dcmdata/dcdict.h>
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61 #include <dcmtk/dcmdata/dcfilefo.h>
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62 #include <dcmtk/dcmdata/dcistrmb.h>
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63 #include <dcmtk/dcmdata/dcuid.h>
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64 #include <dcmtk/dcmdata/dcmetinf.h>
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65 #include <dcmtk/dcmdata/dcdeftag.h>
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66
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67 #include <dcmtk/dcmdata/dcvrae.h>
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68 #include <dcmtk/dcmdata/dcvras.h>
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69 #include <dcmtk/dcmdata/dcvrcs.h>
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70 #include <dcmtk/dcmdata/dcvrda.h>
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71 #include <dcmtk/dcmdata/dcvrds.h>
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72 #include <dcmtk/dcmdata/dcvrdt.h>
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73 #include <dcmtk/dcmdata/dcvrfd.h>
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74 #include <dcmtk/dcmdata/dcvrfl.h>
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75 #include <dcmtk/dcmdata/dcvris.h>
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76 #include <dcmtk/dcmdata/dcvrlo.h>
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77 #include <dcmtk/dcmdata/dcvrlt.h>
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78 #include <dcmtk/dcmdata/dcvrpn.h>
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79 #include <dcmtk/dcmdata/dcvrsh.h>
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80 #include <dcmtk/dcmdata/dcvrsl.h>
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81 #include <dcmtk/dcmdata/dcvrss.h>
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82 #include <dcmtk/dcmdata/dcvrst.h>
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83 #include <dcmtk/dcmdata/dcvrtm.h>
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84 #include <dcmtk/dcmdata/dcvrui.h>
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85 #include <dcmtk/dcmdata/dcvrul.h>
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86 #include <dcmtk/dcmdata/dcvrus.h>
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87 #include <dcmtk/dcmdata/dcvrut.h>
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88 #include <dcmtk/dcmdata/dcpixel.h>
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89 #include <dcmtk/dcmdata/dcpixseq.h>
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90 #include <dcmtk/dcmdata/dcpxitem.h>
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91 #include <dcmtk/dcmdata/dcvrat.h>
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93
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94 #include <boost/math/special_functions/round.hpp>
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95 #include <glog/logging.h>
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96 #include <dcmtk/dcmdata/dcostrmb.h>
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98
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99 namespace Orthanc
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100 {
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101 static inline uint16_t GetCharValue(char c)
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102 {
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103 if (c >= '0' && c <= '9')
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104 return c - '0';
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105 else if (c >= 'a' && c <= 'f')
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106 return c - 'a' + 10;
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107 else if (c >= 'A' && c <= 'F')
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108 return c - 'A' + 10;
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109 else
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110 return 0;
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111 }
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112
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113 static inline uint16_t GetTagValue(const char* c)
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114 {
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115 return ((GetCharValue(c[0]) << 12) +
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116 (GetCharValue(c[1]) << 8) +
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117 (GetCharValue(c[2]) << 4) +
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118 GetCharValue(c[3]));
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119 }
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120
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121
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122 Encoding FromDcmtkBridge::DetectEncoding(DcmDataset& dataset)
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123 {
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124 // By default, Latin1 encoding is assumed
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125 std::string s = Configuration::GetGlobalStringParameter("DefaultEncoding", "");
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126 Encoding encoding = s.empty() ? Encoding_Latin1 : StringToEncoding(s.c_str());
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127
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128 OFString tmp;
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129 if (dataset.findAndGetOFString(DCM_SpecificCharacterSet, tmp).good())
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130 {
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131 std::string characterSet = Toolbox::StripSpaces(std::string(tmp.c_str()));
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132
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133 if (characterSet.empty())
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134 {
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135 // Empty specific character set tag: Use the default encoding
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136 }
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137 else if (GetDicomEncoding(encoding, characterSet.c_str()))
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138 {
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139 // The specific character set is supported by the Orthanc core
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140 }
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141 else
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142 {
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143 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet
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144 << ", fallback to ASCII (remove all special characters)";
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145 encoding = Encoding_Ascii;
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146 }
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147 }
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148 else
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149 {
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150 // No specific character set tag: Use the default encoding
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151 }
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152
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153 return encoding;
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154 }
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155
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156
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157 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset)
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158 {
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159 Encoding encoding = DetectEncoding(dataset);
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160
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161 target.Clear();
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162 for (unsigned long i = 0; i < dataset.card(); i++)
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163 {
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164 DcmElement* element = dataset.getElement(i);
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165 if (element && element->isLeaf())
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166 {
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167 target.SetValue(element->getTag().getGTag(),
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168 element->getTag().getETag(),
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169 ConvertLeafElement(*element, encoding));
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170 }
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171 }
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172 }
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173
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174
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175 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag)
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176 {
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177 return DicomTag(tag.getGTag(), tag.getETag());
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178 }
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179
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180
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181 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element)
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182 {
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183 return DicomTag(element.getGTag(), element.getETag());
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184 }
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185
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186
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187 bool FromDcmtkBridge::IsPrivateTag(DcmTag& tag)
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188 {
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189 #if 1
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190 DcmTagKey tmp(tag.getGTag(), tag.getETag());
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191 return tmp.isPrivate();
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192 #else
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193 // Implementation for Orthanc versions <= 0.8.5
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194 return (tag.getPrivateCreator() != NULL ||
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195 !strcmp("PrivateCreator", tag.getTagName())); // TODO - This may change with future versions of DCMTK
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196 #endif
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197 }
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198
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199
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200 bool FromDcmtkBridge::IsPrivateTag(const DicomTag& tag)
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201 {
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202 #if 1
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203 DcmTagKey tmp(tag.GetGroup(), tag.GetElement());
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204 return tmp.isPrivate();
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205 #else
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206 // Implementation for Orthanc versions <= 0.8.5
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207 DcmTag tmp(tag.GetGroup(), tag.GetElement());
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208 return IsPrivateTag(tmp);
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209 #endif
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210 }
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211
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212
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213 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element,
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214 Encoding encoding)
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215 {
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216 if (!element.isLeaf())
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217 {
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218 throw OrthancException("Only applicable to leaf elements");
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219 }
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220
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221 if (element.isaString())
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222 {
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223 char *c;
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224 if (element.getString(c).good() &&
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225 c != NULL)
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226 {
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227 std::string s(c);
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228 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding);
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229 return new DicomString(utf8);
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230 }
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231 else
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232 {
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233 return new DicomNullValue;
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234 }
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235 }
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236
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237 try
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238 {
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239 // http://support.dcmtk.org/docs/dcvr_8h-source.html
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240 switch (element.getVR())
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241 {
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242
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243 /**
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244 * TODO.
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245 **/
306
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246
302
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247 case EVR_OB: // other byte
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248 case EVR_OF: // other float
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249 case EVR_OW: // other word
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250 case EVR_UN: // unknown value representation
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251 return new DicomNullValue;
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252
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253 /**
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254 * String types, should never happen at this point because of
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255 * "element.isaString()".
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256 **/
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257
306
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258 case EVR_DS: // decimal string
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259 case EVR_IS: // integer string
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260 case EVR_AS: // age string
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261 case EVR_DA: // date string
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262 case EVR_DT: // date time string
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263 case EVR_TM: // time string
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264 case EVR_AE: // application entity title
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265 case EVR_CS: // code string
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266 case EVR_SH: // short string
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267 case EVR_LO: // long string
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268 case EVR_ST: // short text
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269 case EVR_LT: // long text
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270 case EVR_UT: // unlimited text
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271 case EVR_PN: // person name
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272 case EVR_UI: // unique identifier
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273 return new DicomNullValue;
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274
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275
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276 /**
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277 * Numberic types
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278 **/
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279
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280 case EVR_SL: // signed long
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281 {
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282 Sint32 f;
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283 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
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284 return new DicomString(boost::lexical_cast<std::string>(f));
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285 else
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286 return new DicomNullValue;
302
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287 }
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288
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289 case EVR_SS: // signed short
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290 {
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291 Sint16 f;
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292 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
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293 return new DicomString(boost::lexical_cast<std::string>(f));
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294 else
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295 return new DicomNullValue;
302
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296 }
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297
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298 case EVR_UL: // unsigned long
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299 {
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300 Uint32 f;
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301 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
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302 return new DicomString(boost::lexical_cast<std::string>(f));
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303 else
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304 return new DicomNullValue;
302
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305 }
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306
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307 case EVR_US: // unsigned short
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308 {
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309 Uint16 f;
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310 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
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311 return new DicomString(boost::lexical_cast<std::string>(f));
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312 else
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313 return new DicomNullValue;
302
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314 }
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315
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316 case EVR_FL: // float single-precision
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317 {
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318 Float32 f;
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319 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
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320 return new DicomString(boost::lexical_cast<std::string>(f));
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321 else
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322 return new DicomNullValue;
302
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323 }
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324
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325 case EVR_FD: // float double-precision
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326 {
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327 Float64 f;
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328 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
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329 return new DicomString(boost::lexical_cast<std::string>(f));
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330 else
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331 return new DicomNullValue;
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332 }
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333
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334
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335 /**
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336 * Attribute tag.
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337 **/
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338
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339 case EVR_AT:
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340 {
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341 DcmTagKey tag;
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342 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good())
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343 {
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344 DicomTag t(tag.getGroup(), tag.getElement());
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345 return new DicomString(t.Format());
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346 }
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347 else
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348 {
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349 return new DicomNullValue;
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350 }
302
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351 }
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352
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353
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354 /**
302
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355 * Sequence types, should never occur at this point because of
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356 * "element.isLeaf()".
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357 **/
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358
302
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359 case EVR_SQ: // sequence of items
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360 return new DicomNullValue;
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361
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362
302
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363 /**
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364 * Internal to DCMTK.
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365 **/
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366
302
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367 case EVR_ox: // OB or OW depending on context
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368 case EVR_xs: // SS or US depending on context
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369 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
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370 case EVR_na: // na="not applicable", for data which has no VR
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371 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
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372 case EVR_item: // used internally for items
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373 case EVR_metainfo: // used internally for meta info datasets
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374 case EVR_dataset: // used internally for datasets
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375 case EVR_fileFormat: // used internally for DICOM files
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376 case EVR_dicomDir: // used internally for DICOMDIR objects
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377 case EVR_dirRecord: // used internally for DICOMDIR records
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378 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
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379 case EVR_pixelItem: // used internally for pixel items in a compressed image
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380 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
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381 case EVR_PixelData: // used internally for uncompressed pixeld data
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382 case EVR_OverlayData: // used internally for overlay data
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383 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
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384 return new DicomNullValue;
0
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385
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386
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387 /**
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388 * Default case.
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389 **/
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390
302
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391 default:
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392 return new DicomNullValue;
0
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393 }
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394 }
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395 catch (boost::bad_lexical_cast)
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396 {
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397 return new DicomNullValue;
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398 }
306
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399 catch (std::bad_cast)
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400 {
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401 return new DicomNullValue;
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402 }
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403 }
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404
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405
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406 static void StoreElement(Json::Value& target,
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407 DcmElement& element,
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408 unsigned int maxStringLength,
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409 Encoding encoding);
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410
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411 static void StoreItem(Json::Value& target,
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412 DcmItem& item,
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413 unsigned int maxStringLength,
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414 Encoding encoding)
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415 {
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416 target = Json::Value(Json::objectValue);
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417
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418 for (unsigned long i = 0; i < item.card(); i++)
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419 {
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420 DcmElement* element = item.getElement(i);
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421 StoreElement(target, *element, maxStringLength, encoding);
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422 }
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423 }
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424
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425
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426 static void StoreElement(Json::Value& target,
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427 DcmElement& element,
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428 unsigned int maxStringLength,
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429 Encoding encoding)
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430 {
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431 assert(target.type() == Json::objectValue);
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432
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diff changeset
433 DicomTag tag(FromDcmtkBridge::GetTag(element));
305
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diff changeset
434 const std::string formattedTag = tag.Format();
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diff changeset
435
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diff changeset
436 #if 0
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437 const std::string tagName = FromDcmtkBridge::GetName(tag);
305
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diff changeset
438 #else
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diff changeset
439 // This version of the code gives access to the name of the private tags
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440 DcmTag tagbis(element.getTag());
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441 const std::string tagName(tagbis.getTagName());
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diff changeset
442 #endif
0
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443
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444 if (element.isLeaf())
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445 {
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diff changeset
446 Json::Value value(Json::objectValue);
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diff changeset
447 value["Name"] = tagName;
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448
306
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449 if (tagbis.getPrivateCreator() != NULL)
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450 {
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451 value["PrivateCreator"] = tagbis.getPrivateCreator();
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diff changeset
452 }
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diff changeset
453
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diff changeset
454 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element, encoding));
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455 if (v->IsNull())
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parents:
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456 {
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diff changeset
457 value["Type"] = "Null";
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diff changeset
458 value["Value"] = Json::nullValue;
0
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459 }
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460 else
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461 {
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462 std::string s = v->AsString();
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463 if (maxStringLength == 0 ||
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464 s.size() <= maxStringLength)
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465 {
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466 value["Type"] = "String";
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467 value["Value"] = s;
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468 }
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469 else
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470 {
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471 value["Type"] = "TooLong";
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472 value["Value"] = Json::nullValue;
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473 }
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474 }
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475
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476 target[formattedTag] = value;
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477 }
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478 else
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479 {
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480 Json::Value children(Json::arrayValue);
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481
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482 // "All subclasses of DcmElement except for DcmSequenceOfItems
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483 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
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484 // etc. are not." The following cast is thus OK.
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485 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
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486
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487 for (unsigned long i = 0; i < sequence.card(); i++)
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488 {
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489 DcmItem* child = sequence.getItem(i);
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490 Json::Value& v = children.append(Json::objectValue);
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491 StoreItem(v, *child, maxStringLength, encoding);
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492 }
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493
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494 target[formattedTag]["Name"] = tagName;
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495 target[formattedTag]["Type"] = "Sequence";
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496 target[formattedTag]["Value"] = children;
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497 }
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498 }
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parents:
diff changeset
499
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500
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501 void FromDcmtkBridge::ToJson(Json::Value& root,
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502 DcmDataset& dataset,
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503 unsigned int maxStringLength)
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parents:
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504 {
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diff changeset
505 StoreItem(root, dataset, maxStringLength, DetectEncoding(dataset));
0
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parents:
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506 }
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parents:
diff changeset
507
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parents:
diff changeset
508
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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509
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parents:
diff changeset
510 void FromDcmtkBridge::ToJson(Json::Value& target,
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511 const std::string& path,
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parents:
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512 unsigned int maxStringLength)
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parents:
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513 {
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514 DcmFileFormat dicom;
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515 if (!dicom.loadFile(path.c_str()).good())
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516 {
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517 throw OrthancException(ErrorCode_BadFileFormat);
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518 }
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parents:
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519 else
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520 {
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521 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength);
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522 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 }
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parents:
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524
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parents:
diff changeset
525
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526
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parents:
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527 std::string FromDcmtkBridge::GetName(const DicomTag& t)
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528 {
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529 // Some patches for important tags because of different DICOM
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530 // dictionaries between DCMTK versions
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diff changeset
531 std::string n = t.GetMainTagsName();
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diff changeset
532 if (n.size() != 0)
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diff changeset
533 {
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534 return n;
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diff changeset
535 }
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536 // End of patches
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parents: 80
diff changeset
537
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diff changeset
538 #if 0
0
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parents:
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539 DcmTagKey tag(t.GetGroup(), t.GetElement());
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parents:
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540 const DcmDataDictionary& dict = dcmDataDict.rdlock();
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parents:
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541 const DcmDictEntry* entry = dict.findEntry(tag, NULL);
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parents:
diff changeset
542
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diff changeset
543 std::string s(DcmTag_ERROR_TagName);
0
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parents:
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544 if (entry != NULL)
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parents:
diff changeset
545 {
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546 s = std::string(entry->getTagName());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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547 }
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parents:
diff changeset
548
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parents:
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549 dcmDataDict.unlock();
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parents:
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550 return s;
305
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diff changeset
551 #else
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diff changeset
552 DcmTag tag(t.GetGroup(), t.GetElement());
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diff changeset
553 const char* name = tag.getTagName();
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parents: 304
diff changeset
554 if (name == NULL)
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parents: 304
diff changeset
555 {
306
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diff changeset
556 return DcmTag_ERROR_TagName;
305
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diff changeset
557 }
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parents: 304
diff changeset
558 else
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parents: 304
diff changeset
559 {
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diff changeset
560 return std::string(name);
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parents: 304
diff changeset
561 }
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parents: 304
diff changeset
562 #endif
0
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parents:
diff changeset
563 }
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parents:
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564
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
565
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diff changeset
566 DicomTag FromDcmtkBridge::ParseTag(const char* name)
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parents:
diff changeset
567 {
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parents: 303
diff changeset
568 if (strlen(name) == 9 &&
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parents: 303
diff changeset
569 isxdigit(name[0]) &&
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parents: 303
diff changeset
570 isxdigit(name[1]) &&
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parents: 303
diff changeset
571 isxdigit(name[2]) &&
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parents: 303
diff changeset
572 isxdigit(name[3]) &&
991
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parents: 957
diff changeset
573 (name[4] == '-' || name[4] == ',') &&
304
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parents: 303
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574 isxdigit(name[5]) &&
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parents: 303
diff changeset
575 isxdigit(name[6]) &&
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parents: 303
diff changeset
576 isxdigit(name[7]) &&
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parents: 303
diff changeset
577 isxdigit(name[8]))
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diff changeset
578 {
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diff changeset
579 uint16_t group = GetTagValue(name);
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parents: 303
diff changeset
580 uint16_t element = GetTagValue(name + 5);
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parents: 303
diff changeset
581 return DicomTag(group, element);
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parents: 303
diff changeset
582 }
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parents: 303
diff changeset
583
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parents: 304
diff changeset
584 #if 0
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
585 const DcmDataDictionary& dict = dcmDataDict.rdlock();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
586 const DcmDictEntry* entry = dict.findEntry(name);
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
587
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
588 if (entry == NULL)
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
589 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
590 dcmDataDict.unlock();
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parents: 57
diff changeset
591 throw OrthancException("Unknown DICOM tag");
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
592 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
593 else
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
594 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
595 DcmTagKey key = entry->getKey();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
596 DicomTag tag(key.getGroup(), key.getElement());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
597 dcmDataDict.unlock();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
598 return tag;
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
599 }
305
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
600 #else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
601 DcmTag tag;
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parents: 304
diff changeset
602 if (DcmTag::findTagFromName(name, tag).good())
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
603 {
86bb79522f19 name of the private tags
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parents: 304
diff changeset
604 return DicomTag(tag.getGTag(), tag.getETag());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
605 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
606 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
607 {
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
608 throw OrthancException("Unknown DICOM tag");
86bb79522f19 name of the private tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
609 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 304
diff changeset
610 #endif
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
611 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
612
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
613
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
614 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
615 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
616 for (DicomMap::Map::const_iterator
656
08eca5d86aad fixes to cppcheck
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parents: 465
diff changeset
617 it = m.map_.begin(); it != m.map_.end(); ++it)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
618 {
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
619 DicomTag t = it->first;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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620 std::string s = it->second->AsString();
319
760d0f32cb34 PMSCT_RLE1
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parents: 318
diff changeset
621 fprintf(fp, "0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str());
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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622 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
623 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
624
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
625
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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626 void FromDcmtkBridge::ToJson(Json::Value& result,
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parents: 1360
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627 const DicomMap& values,
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parents: 1360
diff changeset
628 bool simplify)
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
629 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
630 if (result.type() != Json::objectValue)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
631 {
62
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parents: 57
diff changeset
632 throw OrthancException(ErrorCode_BadParameterType);
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
633 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
634
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
635 result.clear();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
636
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
637 for (DicomMap::Map::const_iterator
656
08eca5d86aad fixes to cppcheck
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parents: 465
diff changeset
638 it = values.map_.begin(); it != values.map_.end(); ++it)
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
639 {
1368
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parents: 1360
diff changeset
640 if (simplify)
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
641 {
b22ba8c5edbe query retrieve
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parents: 1360
diff changeset
642 result[GetName(it->first)] = it->second->AsString();
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
643 }
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
644 else
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
645 {
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
646 Json::Value value = Json::objectValue;
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
647
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
648 value["Name"] = GetName(it->first);
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
649
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
650 if (it->second->IsNull())
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
651 {
b22ba8c5edbe query retrieve
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parents: 1360
diff changeset
652 value["Type"] = "Null";
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
653 value["Value"] = Json::nullValue;
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
654 }
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
655 else
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
656 {
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
657 value["Type"] = "String";
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
658 value["Value"] = it->second->AsString();
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
659 }
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
660
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
661 result[it->first.Format()] = value;
b22ba8c5edbe query retrieve
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1360
diff changeset
662 }
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
663 }
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
664 }
176
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parents: 136
diff changeset
665
81f11fb357f2 uid generation
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parents: 136
diff changeset
666
788
7ebe4bf87196 refactoring
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parents: 784
diff changeset
667 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level)
176
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parents: 136
diff changeset
668 {
81f11fb357f2 uid generation
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parents: 136
diff changeset
669 char uid[100];
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
670
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
671 switch (level)
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
672 {
788
7ebe4bf87196 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 784
diff changeset
673 case ResourceType_Patient:
311
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parents: 308
diff changeset
674 // The "PatientID" field is of type LO (Long String), 64
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
675 // Bytes Maximum. An UUID is of length 36, thus it can be used
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
676 // as a random PatientID.
26efccdff583 anonymisation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 308
diff changeset
677 return Toolbox::GenerateUuid();
306
326d5a4a5af3 modification of instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 305
diff changeset
678
788
7ebe4bf87196 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 784
diff changeset
679 case ResourceType_Instance:
302
238134081136 modification of dicom files
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parents: 291
diff changeset
680 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
681
788
7ebe4bf87196 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 784
diff changeset
682 case ResourceType_Series:
302
238134081136 modification of dicom files
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parents: 291
diff changeset
683 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
684
788
7ebe4bf87196 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 784
diff changeset
685 case ResourceType_Study:
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
686 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
687
302
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
688 default:
238134081136 modification of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 291
diff changeset
689 throw OrthancException(ErrorCode_ParameterOutOfRange);
176
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
690 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
691 }
81f11fb357f2 uid generation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 136
diff changeset
692
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
693 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 991
diff changeset
694 DcmDataset& dataSet)
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
695 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
696 // Determine the transfer syntax which shall be used to write the
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
697 // information to the file. We always switch to the Little Endian
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
698 // syntax, with explicit length.
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
699
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
700 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
701
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
702
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
703 /**
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
704 * Note that up to Orthanc 0.7.1 (inclusive), the
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
705 * "EXS_LittleEndianExplicit" was always used to save the DICOM
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
706 * dataset into memory. We now keep the original transfer syntax
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
707 * (if available).
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
708 **/
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 991
diff changeset
709 E_TransferSyntax xfer = dataSet.getOriginalXfer();
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
710 if (xfer == EXS_Unknown)
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
711 {
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
712 // No information about the original transfer syntax: This is
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
713 // most probably a DICOM dataset that was read from memory.
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
714 xfer = EXS_LittleEndianExplicit;
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
715 }
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
716
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
717 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
718
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
719 // Create the meta-header information
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 991
diff changeset
720 DcmFileFormat ff(&dataSet);
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
721 ff.validateMetaInfo(xfer);
1316
1c8dfedefefe Fix anonymization generating non-portable DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1307
diff changeset
722 ff.removeInvalidGroups();
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
723
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
724 // Create a memory buffer with the proper size
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
725 uint32_t s = ff.calcElementLength(xfer, encodingType);
291
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
726 buffer.resize(s);
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
727 DcmOutputBufferStream ob(&buffer[0], s);
4d7469f72a0b embedding of dicom dictionaries
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diff changeset
728
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
729 // Fill the memory buffer with the meta-header and the dataset
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
730 ff.transferInit();
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
731 OFCondition c = ff.write(ob, xfer, encodingType, NULL,
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
732 /*opt_groupLength*/ EGL_recalcGL,
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
733 /*opt_paddingType*/ EPD_withoutPadding);
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
734 ff.transferEnd();
291
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diff changeset
735
661
d233b5090105 accept more transfer syntaxes for C-Store SCP, write meta-header when receiving files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 656
diff changeset
736 // Handle errors
291
4d7469f72a0b embedding of dicom dictionaries
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diff changeset
737 if (c.good())
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
738 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
739 return true;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
740 }
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
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741 else
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
742 {
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
743 buffer.clear();
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
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744 return false;
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
745 }
4d7469f72a0b embedding of dicom dictionaries
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 285
diff changeset
746 }
1360
0649c5aef34a DicomFindQuery
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1316
diff changeset
747
0649c5aef34a DicomFindQuery
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1316
diff changeset
748
1417
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
749 ValueRepresentation FromDcmtkBridge::GetValueRepresentation(const DicomTag& tag)
1360
0649c5aef34a DicomFindQuery
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1316
diff changeset
750 {
0649c5aef34a DicomFindQuery
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parents: 1316
diff changeset
751 DcmTag t(tag.GetGroup(), tag.GetElement());
1417
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
752 switch (t.getEVR())
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
753 {
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
754 case EVR_PN:
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
755 return ValueRepresentation_PatientName;
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
756
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
757 case EVR_DA:
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
758 return ValueRepresentation_Date;
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
759
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
760 case EVR_DT:
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
761 return ValueRepresentation_DateTime;
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
762
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
763 case EVR_TM:
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
764 return ValueRepresentation_Time;
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
765
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
766 default:
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
767 return ValueRepresentation_Other;
8e23f16a198d fix issues 35 and 37
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1368
diff changeset
768 }
1360
0649c5aef34a DicomFindQuery
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1316
diff changeset
769 }
0649c5aef34a DicomFindQuery
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1316
diff changeset
770
0
3959d33612cc initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
771 }