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annotate OrthancFramework/Sources/DicomParsing/DicomModification.h @ 5137:15109c3f0f7d

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added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
author Alain Mazy <am@osimis.io>
date Wed, 18 Jan 2023 17:58:51 +0100
parents f2dcdbe05884
children 023569e7155b
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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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22
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23
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24 #pragma once
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25
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26 #include "ParsedDicomFile.h"
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27 #include <boost/thread/recursive_mutex.hpp>
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28
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29 #include <list>
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30
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31
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32 namespace Orthanc
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33 {
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34 class ORTHANC_PUBLIC DicomModification : public boost::noncopyable
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35 {
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36 /**
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37 * Process:
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38 * (1) Remove private tags
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39 * (2) Remove tags specified by the user
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40 * (3) Replace tags
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41 **/
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42
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43 public:
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44 class IDicomIdentifierGenerator : public boost::noncopyable
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45 {
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46 public:
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47 virtual ~IDicomIdentifierGenerator()
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48 {
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49 }
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50
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51 virtual bool Apply(std::string& target,
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52 const std::string& sourceIdentifier,
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53 ResourceType level,
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54 const DicomMap& sourceDicom) = 0;
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55 };
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56
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57 private:
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58 class RelationshipsVisitor;
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59
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60 class DicomTagRange
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61 {
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62 private:
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63 uint16_t groupFrom_;
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64 uint16_t groupTo_;
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65 uint16_t elementFrom_;
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66 uint16_t elementTo_;
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67
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68 public:
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69 DicomTagRange(uint16_t groupFrom,
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70 uint16_t groupTo,
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71 uint16_t elementFrom,
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72 uint16_t elementTo);
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73
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74 uint16_t GetGroupFrom() const
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75 {
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76 return groupFrom_;
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77 }
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78
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79 uint16_t GetGroupTo() const
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80 {
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81 return groupTo_;
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82 }
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83
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84 uint16_t GetElementFrom() const
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85 {
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86 return elementFrom_;
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87 }
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88
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89 uint16_t GetElementTo() const
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90 {
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91 return elementTo_;
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92 }
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93
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94 bool Contains(const DicomTag& tag) const;
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95 };
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97 class SequenceReplacement : public boost::noncopyable
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98 {
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99 private:
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100 DicomPath path_;
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101 Json::Value value_;
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102
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103 public:
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104 SequenceReplacement(const DicomPath& path,
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105 const Json::Value& value) :
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106 path_(path),
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107 value_(value)
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108 {
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109 }
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111 const DicomPath& GetPath() const
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112 {
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113 return path_;
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114 }
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116 const Json::Value& GetValue() const
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117 {
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118 return value_;
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119 }
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120 };
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121
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122 typedef std::set<DicomTag> SetOfTags;
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123 typedef std::map<DicomTag, Json::Value*> Replacements;
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124 typedef std::list<DicomTagRange> RemovedRanges;
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125 typedef std::list<DicomPath> ListOfPaths;
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126 typedef std::list<SequenceReplacement*> SequenceReplacements;
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127
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128 typedef std::map< std::pair<ResourceType, std::string>, std::string> UidMap;
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129
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130 mutable boost::recursive_mutex uidMapMutex_;
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131 SetOfTags removals_;
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132 SetOfTags clearings_;
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133 SetOfTags keep_;
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134 Replacements replacements_;
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135 bool removePrivateTags_;
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136 ResourceType level_;
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137 UidMap uidMap_;
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138 SetOfTags privateTagsToKeep_;
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139 bool allowManualIdentifiers_;
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140 bool keepStudyInstanceUid_;
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141 bool keepSeriesInstanceUid_;
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142 bool keepSopInstanceUid_;
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143 bool updateReferencedRelationships_;
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144 bool isAnonymization_;
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145 DicomMap currentSource_;
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146 std::string privateCreator_;
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147
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148 IDicomIdentifierGenerator* identifierGenerator_;
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149
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150 // New in Orthanc 1.9.4
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151 SetOfTags uids_;
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152 RemovedRanges removedRanges_;
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153 ListOfPaths keepSequences_; // Can *possibly* be a path whose prefix is empty
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154 ListOfPaths removeSequences_; // Must *never* be a path whose prefix is empty
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155 SequenceReplacements sequenceReplacements_; // Must *never* be a path whose prefix is empty
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156
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157 std::string MapDicomIdentifier(const std::string& original,
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158 ResourceType level);
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159
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160 void RegisterMappedDicomIdentifier(const std::string& original,
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161 const std::string& mapped,
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162 ResourceType level);
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163
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164 void MapDicomTags(ParsedDicomFile& dicom,
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165 ResourceType level);
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166
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167 void MarkNotOrthancAnonymization();
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168
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169 void ClearReplacements();
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170
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171 void CancelReplacement(const DicomTag& tag);
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172
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173 void ReplaceInternal(const DicomTag& tag,
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174 const Json::Value& value);
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175
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176 void SetupUidsFromOrthanc_1_9_3();
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177
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178 void SetupAnonymization2008();
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179
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180 void SetupAnonymization2017c();
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181
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182 void SetupAnonymization2021b();
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183
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184 void UnserializeUidMap(ResourceType level,
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185 const Json::Value& serialized,
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186 const char* field);
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187
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188 public:
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189 DicomModification();
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190
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191 explicit DicomModification(const Json::Value& serialized);
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192
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193 ~DicomModification();
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194
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195 void Keep(const DicomTag& tag);
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196
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197 void Remove(const DicomTag& tag);
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198
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199 // Replace the DICOM tag as a NULL/empty value (e.g. for anonymization)
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200 void Clear(const DicomTag& tag);
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201
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202 bool IsRemoved(const DicomTag& tag) const;
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203
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204 bool IsCleared(const DicomTag& tag) const;
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205
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206 // "safeForAnonymization" tells Orthanc that this replacement does
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207 // not break the anonymization process it implements (for internal use only)
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208 void Replace(const DicomTag& tag,
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209 const Json::Value& value, // Encoded using UTF-8
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210 bool safeForAnonymization);
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211
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212 bool IsReplaced(const DicomTag& tag) const;
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213
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214 void GetReplacedTags(std::set<DicomTag>& target) const;
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215
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216 const Json::Value& GetReplacement(const DicomTag& tag) const;
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217
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218 std::string GetReplacementAsString(const DicomTag& tag) const;
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219
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220 bool IsKept(const DicomTag& tag) const;
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221
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222 void SetRemovePrivateTags(bool removed);
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223
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224 bool ArePrivateTagsRemoved() const;
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225
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226 void SetLevel(ResourceType level);
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227
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228 ResourceType GetLevel() const;
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229
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230 void SetupAnonymization(DicomVersion version);
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231
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232 void Apply(ParsedDicomFile& toModify);
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233
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234 void SetAllowManualIdentifiers(bool check);
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235
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236 bool AreAllowManualIdentifiers() const;
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237
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238 void ParseModifyRequest(const Json::Value& request);
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239
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240 // "patientNameOverridden" is set to "true" iff. the PatientName
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241 // (0010,0010) tag is manually replaced, removed, cleared or kept
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242 void ParseAnonymizationRequest(bool& patientNameOverridden /* out */,
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243 const Json::Value& request);
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244
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245 void SetDicomIdentifierGenerator(IDicomIdentifierGenerator& generator);
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246
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247 void Serialize(Json::Value& value) const;
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248
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249 void SetPrivateCreator(const std::string& privateCreator);
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250
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251 const std::string& GetPrivateCreator() const;
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252
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253 // New in Orthanc 1.9.4
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254 void Keep(const DicomPath& path);
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255
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256 // New in Orthanc 1.9.4
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257 void Remove(const DicomPath& path);
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258
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259 // New in Orthanc 1.9.4
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260 void Replace(const DicomPath& path,
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261 const Json::Value& value, // Encoded using UTF-8
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262 bool safeForAnonymization);
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263
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264 bool IsAlteredTag(const DicomTag& tag) const;
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265 };
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266 }