annotate OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h @ 5122:8638522eeda1

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 19 Dec 2022 15:46:33 +0100
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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) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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24 #pragma once
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25
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26 #include "../OrthancFramework.h"
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27
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28 #if !defined(ORTHANC_ENABLE_JPEG)
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29 # error Macro ORTHANC_ENABLE_JPEG must be defined to use this file
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30 #endif
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31
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32 #if !defined(ORTHANC_ENABLE_PNG)
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33 # error Macro ORTHANC_ENABLE_PNG must be defined to use this file
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34 #endif
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35
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36 #if !defined(ORTHANC_ENABLE_CIVETWEB)
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37 # error Macro ORTHANC_ENABLE_CIVETWEB must be defined to use this file
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38 #endif
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39
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40 #if !defined(ORTHANC_ENABLE_MONGOOSE)
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41 # error Macro ORTHANC_ENABLE_MONGOOSE must be defined to use this file
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42 #endif
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43
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44 #if !defined(ORTHANC_SANDBOXED)
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45 # error The macro ORTHANC_SANDBOXED must be defined
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46 #endif
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47
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48 #if !defined(ORTHANC_ENABLE_DCMTK)
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49 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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50 #endif
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51
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52 #if ORTHANC_ENABLE_DCMTK != 1
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53 # error The macro ORTHANC_ENABLE_DCMTK must be set to 1 to use this file
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54 #endif
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55
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56 #include "ITagVisitor.h"
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57 #include "../DicomFormat/DicomInstanceHasher.h"
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58 #include "../DicomFormat/DicomPath.h"
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59 #include "../Images/ImageAccessor.h"
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60 #include "../IDynamicObject.h"
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61 #include "../Toolbox.h"
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62
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63 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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64 # include "../RestApi/RestApiOutput.h"
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65 #endif
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66
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67 #include <boost/shared_ptr.hpp>
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69
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70 class DcmDataset;
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71 class DcmFileFormat;
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72
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73 namespace Orthanc
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74 {
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75 class ORTHANC_PUBLIC ParsedDicomFile : public IDynamicObject
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76 {
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77 private:
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78 struct PImpl;
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79 boost::shared_ptr<PImpl> pimpl_;
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80
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81 ParsedDicomFile(const ParsedDicomFile& other,
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82 bool keepSopInstanceUid);
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83
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84 void CreateFromDicomMap(const DicomMap& source,
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85 Encoding defaultEncoding,
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86 bool permissive,
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87 const std::string& defaultPrivateCreator,
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88 const std::map<uint16_t, std::string>& privateCreators);
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89
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90 void RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep);
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91
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92 void UpdateStorageUid(const DicomTag& tag,
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93 const std::string& value,
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94 bool decodeDataUriScheme);
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95
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96 void InvalidateCache();
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97
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98 bool EmbedContentInternal(const std::string& dataUriScheme);
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99
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100 // For internal use only, in order to provide const-correctness on
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101 // the top of DCMTK API
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102 DcmFileFormat& GetDcmtkObjectConst() const;
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103
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104 explicit ParsedDicomFile(DcmFileFormat* dicom); // This takes ownership (no clone)
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105
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106 #if ORTHANC_BUILDING_FRAMEWORK_LIBRARY == 1
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107 // Alias for binary compatibility with Orthanc Framework 1.7.2 => don't use it anymore
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108 void DatasetToJson(Json::Value& target,
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109 DicomToJsonFormat format,
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110 DicomToJsonFlags flags,
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111 unsigned int maxStringLength);
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112 DcmFileFormat& GetDcmtkObject() const;
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113 void Apply(ITagVisitor& visitor);
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114 ParsedDicomFile* Clone(bool keepSopInstanceUid);
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115 bool LookupTransferSyntax(std::string& result);
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116 bool LookupTransferSyntax(std::string& result) const;
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117 bool GetTagValue(std::string& value,
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118 const DicomTag& tag);
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119 #endif
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120
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121 public:
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122 explicit ParsedDicomFile(bool createIdentifiers); // Create a minimal DICOM instance
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123
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124 ParsedDicomFile(const DicomMap& map,
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125 Encoding defaultEncoding,
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126 bool permissive);
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127
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128 ParsedDicomFile(const DicomMap& map,
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129 Encoding defaultEncoding,
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130 bool permissive,
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131 const std::string& defaultPrivateCreator,
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132 const std::map<uint16_t, std::string>& privateCreators);
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133
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134 ParsedDicomFile(const void* content,
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135 size_t size);
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136
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137 explicit ParsedDicomFile(const std::string& content);
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138
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139 explicit ParsedDicomFile(DcmDataset& dicom); // This clones the DCMTK object
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140
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141 explicit ParsedDicomFile(DcmFileFormat& dicom); // This clones the DCMTK object
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142
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143 static ParsedDicomFile* AcquireDcmtkObject(DcmFileFormat* dicom);
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144
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145 DcmFileFormat& GetDcmtkObject();
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146
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147 // The "ParsedDicomFile" object cannot be used after calling this method
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148 DcmFileFormat* ReleaseDcmtkObject();
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149
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150 ParsedDicomFile* Clone(bool keepSopInstanceUid) const;
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151
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152 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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153 void SendPathValue(RestApiOutput& output,
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154 const UriComponents& uri) const;
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155
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156 void Answer(RestApiOutput& output) const;
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157 #endif
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158
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159 void Remove(const DicomTag& tag);
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160
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161 // Replace the DICOM tag as a NULL/empty value (e.g. for anonymization)
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162 void Clear(const DicomTag& tag,
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163 bool onlyIfExists);
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164
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165 void Replace(const DicomTag& tag,
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166 const std::string& utf8Value,
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167 bool decodeDataUriScheme,
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168 DicomReplaceMode mode,
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169 const std::string& privateCreator /* used only for private tags */);
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170
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171 void Replace(const DicomTag& tag,
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172 const Json::Value& value, // Assumed to be encoded with UTF-8
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173 bool decodeDataUriScheme,
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174 DicomReplaceMode mode,
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175 const std::string& privateCreator /* used only for private tags */);
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176
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177 void Insert(const DicomTag& tag,
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178 const Json::Value& value, // Assumed to be encoded with UTF-8
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179 bool decodeDataUriScheme,
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180 const std::string& privateCreator /* used only for private tags */);
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181
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182 // Cannot be applied to private tags
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183 void ReplacePlainString(const DicomTag& tag,
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184 const std::string& utf8Value);
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185
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186 // Cannot be applied to private tags
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amazy
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187 void SetIfAbsent(const DicomTag& tag,
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188 const std::string& utf8Value);
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189
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190 void RemovePrivateTags();
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191
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192 void RemovePrivateTags(const std::set<DicomTag>& toKeep);
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193
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194 // WARNING: This function handles the decoding of strings to UTF8
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195 bool GetTagValue(std::string& value,
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196 const DicomTag& tag) const;
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197
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198 DicomInstanceHasher GetHasher() const;
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199
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200 // The "Save" methods are not tagged as "const", as the internal
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201 // representation might be changed after serialization
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202 void SaveToMemoryBuffer(std::string& buffer);
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203
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204 #if ORTHANC_SANDBOXED == 0
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205 void SaveToFile(const std::string& path);
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206 #endif
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207
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208 void EmbedContent(const std::string& dataUriScheme);
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209
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diff changeset
210 void EmbedImage(const ImageAccessor& accessor);
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diff changeset
211
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diff changeset
212 void EmbedImage(MimeType mime,
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213 const std::string& content);
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214
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Alain Mazy <am@osimis.io>
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diff changeset
215 void EmbedRawPixelData(const std::string& content);
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diff changeset
216
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parents: 3060
diff changeset
217 Encoding DetectEncoding(bool& hasCodeExtensions) const;
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218
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219 // WARNING: This function only sets the encoding, it will not
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220 // convert the encoding of the tags. Use "ChangeEncoding()" if need be.
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221 void SetEncoding(Encoding encoding);
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222
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parents: 1982
diff changeset
223 void DatasetToJson(Json::Value& target,
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224 DicomToJsonFormat format,
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225 DicomToJsonFlags flags,
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diff changeset
226 unsigned int maxStringLength) const;
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227
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diff changeset
228 void DatasetToJson(Json::Value& target,
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229 DicomToJsonFormat format,
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230 DicomToJsonFlags flags,
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diff changeset
231 unsigned int maxStringLength,
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232 const std::set<DicomTag>& ignoreTagLength) const;
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233
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234 void HeaderToJson(Json::Value& target,
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diff changeset
235 DicomToJsonFormat format) const;
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236
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diff changeset
237 bool HasTag(const DicomTag& tag) const;
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238
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diff changeset
239 void EmbedPdf(const std::string& pdf);
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240
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diff changeset
241 bool ExtractPdf(std::string& pdf) const;
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242
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parents: 1902
diff changeset
243 void GetRawFrame(std::string& target, // OUT
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244 MimeType& mime, // OUT
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245 unsigned int frameId) const; // IN
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246
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247 unsigned int GetFramesCount() const;
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248
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249 static ParsedDicomFile* CreateFromJson(const Json::Value& value,
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250 DicomFromJsonFlags flags,
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251 const std::string& privateCreator);
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252
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253 void ChangeEncoding(Encoding target);
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254
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255 /**
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256 * The DICOM tags with a string whose size is greater than
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257 * "maxTagLength", are replaced by a DicomValue whose type is
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258 * "DicomValue_Null". If "maxTagLength" is zero, all the leaf tags
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259 * are included, independently of their length.
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260 **/
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261 void ExtractDicomSummary(DicomMap& target,
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262 unsigned int maxTagLength) const;
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263
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264 /**
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265 * This flavor can be used to bypass the "maxTagLength" limitation
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266 * on a selected set of DICOM tags.
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267 **/
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268 void ExtractDicomSummary(DicomMap& target,
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269 unsigned int maxTagLength,
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270 const std::set<DicomTag>& ignoreTagLength) const;
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271
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272 bool LookupTransferSyntax(DicomTransferSyntax& result) const;
2281
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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273
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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274 bool LookupPhotometricInterpretation(PhotometricInterpretation& result) const;
2499
83b8b6743531 ITagVisitor - for anonymization relationships
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275
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276 void Apply(ITagVisitor& visitor) const;
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277
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278 // Decode the given frame, using the built-in DICOM decoder of Orthanc
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279 ImageAccessor* DecodeFrame(unsigned int frame) const;
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280
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281 void ReplacePath(const DicomPath& path,
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282 const Json::Value& value, // Assumed to be encoded with UTF-8
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283 bool decodeDataUriScheme,
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284 DicomReplaceMode mode,
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285 const std::string& privateCreator /* used only for private tags */);
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286
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287 void RemovePath(const DicomPath& path);
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288
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289 void ClearPath(const DicomPath& path,
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290 bool onlyIfExists);
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291
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292 bool LookupSequenceItem(DicomMap& target,
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293 const DicomPath& path,
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294 size_t sequenceIndex) const;
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295
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296 void GetDefaultWindowing(double& windowCenter,
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297 double& windowWidth,
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298 unsigned int frame) const;
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299
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300 void GetRescale(double& rescaleIntercept,
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301 double& rescaleSlope,
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302 unsigned int frame) const;
4945
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303
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304 void ListOverlays(std::set<uint16_t>& groups) const;
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305
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306 ImageAccessor* DecodeOverlay(int& originX,
6a59dc426f93 added ParsedDicomFile::DecodeOverlay()
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307 int& originY,
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308 uint16_t group) const;
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309
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310 ImageAccessor* DecodeAllOverlays(int& originX,
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311 int& originY) const;
790
331eaf9d9d69 ParsedDicomFile
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312 };
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313 }