Mercurial > hg > orthanc

annotate OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h @ 4046:7ff1e6c80627 framework

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moving ImageTests.cpp to framework
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 10 Jun 2020 21:43:31 +0200
parents d25f4c0fa160
children e00f3d089991
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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) 2017-2020 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 #pragma once
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35
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36 #include "../OrthancFramework.h"
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37
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38 #if !defined(ORTHANC_ENABLE_JPEG)
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39 # error Macro ORTHANC_ENABLE_JPEG must be defined to use this file
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40 #endif
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41
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42 #if !defined(ORTHANC_ENABLE_PNG)
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43 # error Macro ORTHANC_ENABLE_PNG must be defined to use this file
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44 #endif
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45
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46 #if !defined(ORTHANC_ENABLE_CIVETWEB)
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47 # error Macro ORTHANC_ENABLE_CIVETWEB must be defined to use this file
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48 #endif
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49
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50 #if !defined(ORTHANC_ENABLE_MONGOOSE)
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51 # error Macro ORTHANC_ENABLE_MONGOOSE must be defined to use this file
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52 #endif
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53
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54 #if !defined(ORTHANC_SANDBOXED)
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55 # error The macro ORTHANC_SANDBOXED must be defined
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56 #endif
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57
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58 #if !defined(ORTHANC_ENABLE_DCMTK)
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59 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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60 #endif
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61
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62 #if ORTHANC_ENABLE_DCMTK != 1
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63 # error The macro ORTHANC_ENABLE_DCMTK must be set to 1 to use this file
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64 #endif
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65
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66 #include "ITagVisitor.h"
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67 #include "../DicomFormat/DicomInstanceHasher.h"
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68 #include "../Images/ImageAccessor.h"
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69 #include "../IDynamicObject.h"
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70 #include "../Toolbox.h"
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71
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72 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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73 # include "../RestApi/RestApiOutput.h"
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74 #endif
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75
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76 #include <boost/shared_ptr.hpp>
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77
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78
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79 class DcmDataset;
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80 class DcmFileFormat;
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81
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82 namespace Orthanc
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83 {
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84 class ORTHANC_PUBLIC ParsedDicomFile : public IDynamicObject
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85 {
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86 private:
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87 struct PImpl;
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88 boost::shared_ptr<PImpl> pimpl_;
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89
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90 ParsedDicomFile(ParsedDicomFile& other,
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91 bool keepSopInstanceUid);
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92
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93 void CreateFromDicomMap(const DicomMap& source,
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94 Encoding defaultEncoding,
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95 bool permissive,
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96 const std::string& defaultPrivateCreator,
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97 const std::map<uint16_t, std::string>& privateCreators);
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98
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99 void RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep);
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100
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101 void UpdateStorageUid(const DicomTag& tag,
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102 const std::string& value,
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103 bool decodeDataUriScheme);
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104
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105 void InvalidateCache();
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106
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107 bool EmbedContentInternal(const std::string& dataUriScheme);
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108
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109 ParsedDicomFile(DcmFileFormat* dicom); // This takes ownership (no clone)
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110
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111 public:
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112 ParsedDicomFile(bool createIdentifiers); // Create a minimal DICOM instance
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114 ParsedDicomFile(const DicomMap& map,
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115 Encoding defaultEncoding,
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116 bool permissive
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117 );
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118
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119 ParsedDicomFile(const DicomMap& map,
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120 Encoding defaultEncoding,
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121 bool permissive,
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122 const std::string& defaultPrivateCreator,
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123 const std::map<uint16_t, std::string>& privateCreators
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124 );
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125
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126 ParsedDicomFile(const void* content,
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127 size_t size);
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128
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129 ParsedDicomFile(const std::string& content);
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130
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131 ParsedDicomFile(DcmDataset& dicom); // This clones the DCMTK object
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132
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133 ParsedDicomFile(DcmFileFormat& dicom); // This clones the DCMTK object
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134
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135 static ParsedDicomFile* AcquireDcmtkObject(DcmFileFormat* dicom) // No clone here
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136 {
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137 return new ParsedDicomFile(dicom);
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138 }
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139
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140 DcmFileFormat& GetDcmtkObject() const;
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141
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142 // The "ParsedDicomFile" object cannot be used after calling this method
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143 DcmFileFormat* ReleaseDcmtkObject();
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144
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145 ParsedDicomFile* Clone(bool keepSopInstanceUid);
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146
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147 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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148 void SendPathValue(RestApiOutput& output,
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149 const UriComponents& uri);
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150
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151 void Answer(RestApiOutput& output);
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152 #endif
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153
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154 void Remove(const DicomTag& tag);
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155
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156 // Replace the DICOM tag as a NULL/empty value (e.g. for anonymization)
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157 void Clear(const DicomTag& tag,
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158 bool onlyIfExists);
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159
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160 void Replace(const DicomTag& tag,
8ca0e89798b2 "/modify" can insert/modify sequences
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161 const std::string& utf8Value,
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162 bool decodeDataUriScheme,
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Sebastien Jodogne <s.jodogne@gmail.com>
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163 DicomReplaceMode mode,
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164 const std::string& privateCreator /* used only for private tags */);
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165
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166 void Replace(const DicomTag& tag,
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167 const Json::Value& value, // Assumed to be encoded with UTF-8
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168 bool decodeDataUriScheme,
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169 DicomReplaceMode mode,
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Sebastien Jodogne <s.jodogne@gmail.com>
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170 const std::string& privateCreator /* used only for private tags */);
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171
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172 void Insert(const DicomTag& tag,
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173 const Json::Value& value, // Assumed to be encoded with UTF-8
3691
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3640
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174 bool decodeDataUriScheme,
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Sebastien Jodogne <s.jodogne@gmail.com>
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175 const std::string& privateCreator /* used only for private tags */);
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176
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177 // Cannot be applied to private tags
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178 void ReplacePlainString(const DicomTag& tag,
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Sebastien Jodogne <s.jodogne@gmail.com>
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179 const std::string& utf8Value);
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180
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181 // Cannot be applied to private tags
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amazy
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182 void SetIfAbsent(const DicomTag& tag,
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183 const std::string& utf8Value);
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184
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185 void RemovePrivateTags()
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186 {
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187 RemovePrivateTagsInternal(NULL);
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188 }
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189
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190 void RemovePrivateTags(const std::set<DicomTag>& toKeep)
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191 {
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192 RemovePrivateTagsInternal(&toKeep);
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193 }
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194
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195 // WARNING: This function handles the decoding of strings to UTF8
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196 bool GetTagValue(std::string& value,
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197 const DicomTag& tag);
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198
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199 DicomInstanceHasher GetHasher();
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200
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201 void SaveToMemoryBuffer(std::string& buffer);
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Sebastien Jodogne <s.jodogne@gmail.com>
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202
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Sebastien Jodogne <s.jodogne@gmail.com>
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203 #if ORTHANC_SANDBOXED == 0
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204 void SaveToFile(const std::string& path);
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Sebastien Jodogne <s.jodogne@gmail.com>
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205 #endif
800
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206
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diff changeset
207 void EmbedContent(const std::string& dataUriScheme);
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208
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diff changeset
209 void EmbedImage(const ImageAccessor& accessor);
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diff changeset
210
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diff changeset
211 void EmbedImage(MimeType mime,
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diff changeset
212 const std::string& content);
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diff changeset
213
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diff changeset
214 Encoding DetectEncoding(bool& hasCodeExtensions) const;
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215
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Sebastien Jodogne <s.jodogne@gmail.com>
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216 // WARNING: This function only sets the encoding, it will not
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217 // convert the encoding of the tags. Use "ChangeEncoding()" if need be.
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diff changeset
218 void SetEncoding(Encoding encoding);
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219
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parents: 1982
diff changeset
220 void DatasetToJson(Json::Value& target,
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parents: 1982
diff changeset
221 DicomToJsonFormat format,
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parents: 1982
diff changeset
222 DicomToJsonFlags flags,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1982
diff changeset
223 unsigned int maxStringLength);
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parents: 1982
diff changeset
224
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diff changeset
225 void DatasetToJson(Json::Value& target,
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226 DicomToJsonFormat format,
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
227 DicomToJsonFlags flags,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2394
diff changeset
228 unsigned int maxStringLength,
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
229 const std::set<DicomTag>& ignoreTagLength);
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230
2128
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parents: 1982
diff changeset
231 // This version uses the default parameters for
9329ba17a069 Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1982
diff changeset
232 // FileContentType_DicomAsJson
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diff changeset
233 void DatasetToJson(Json::Value& target,
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parents: 2394
diff changeset
234 const std::set<DicomTag>& ignoreTagLength);
e4045b3c9772 ignore-length argument if retrieving DICOM tags
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235
2128
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1982
diff changeset
236 void DatasetToJson(Json::Value& target);
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
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diff changeset
237
1831
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1826
diff changeset
238 void HeaderToJson(Json::Value& target,
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
239 DicomToJsonFormat format);
3ae2ff249675 "/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
240
1555
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
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diff changeset
241 bool HasTag(const DicomTag& tag) const;
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
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242
d6a93e12b1c1 Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
243 void EmbedPdf(const std::string& pdf);
1556
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
244
b8dc2f855a83 Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1555
diff changeset
245 bool ExtractPdf(std::string& pdf);
1662
09be34b2f30e ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1612
diff changeset
246
1924
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1902
diff changeset
247 void GetRawFrame(std::string& target, // OUT
2908
9d277f8ad698 new enumeration: MimeType
Sebastien Jodogne <s.jodogne@gmail.com>
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248 MimeType& mime, // OUT
1924
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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249 unsigned int frameId); // IN
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250
1950
533ff46e944b return a single raw frame from DICOM videos
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251 unsigned int GetFramesCount() const;
533ff46e944b return a single raw frame from DICOM videos
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1935
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252
1818
1065401501fb ParsedDicomFile::CreateFromJson
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253 static ParsedDicomFile* CreateFromJson(const Json::Value& value,
3691
4922bdd046dd Fix issue #140 (Modifying private tags with REST API changes VR from LO to UN) - DANGEROUS COMMIT
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3640
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254 DicomFromJsonFlags flags,
4922bdd046dd Fix issue #140 (Modifying private tags with REST API changes VR from LO to UN) - DANGEROUS COMMIT
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3640
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255 const std::string& privateCreator);
2207
6dc3bdb4088b Fix handling of encodings in C-FIND for worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2202
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256
6dc3bdb4088b Fix handling of encodings in C-FIND for worklists
Sebastien Jodogne <s.jodogne@gmail.com>
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257 void ChangeEncoding(Encoding target);
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2207
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258
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2207
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259 void ExtractDicomSummary(DicomMap& target) const;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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parents: 2207
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260
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33cfcc74d1b1 argument "ignoreTagLength" to ParsedDicomFile::ExtractDicomSummary()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3558
diff changeset
261 void ExtractDicomSummary(DicomMap& target,
33cfcc74d1b1 argument "ignoreTagLength" to ParsedDicomFile::ExtractDicomSummary()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3558
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262 const std::set<DicomTag>& ignoreTagLength) const;
33cfcc74d1b1 argument "ignoreTagLength" to ParsedDicomFile::ExtractDicomSummary()
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parents: 3558
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263
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2207
diff changeset
264 bool LookupTransferSyntax(std::string& result);
2281
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2244
diff changeset
265
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2244
diff changeset
266 bool LookupPhotometricInterpretation(PhotometricInterpretation& result) const;
2499
83b8b6743531 ITagVisitor - for anonymization relationships
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2447
diff changeset
267
83b8b6743531 ITagVisitor - for anonymization relationships
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2447
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268 void Apply(ITagVisitor& visitor);
790
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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269 };
331eaf9d9d69 ParsedDicomFile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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270 }