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annotate OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h @ 5031:eec3e4a91663 delayed-deletion

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DelayedDeletion plugin: first version
author Alain Mazy <am@osimis.io>
date Tue, 21 Jun 2022 17:29:36 +0200
parents c014ab79fca5
children 0ea402b4d901
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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 "ITagVisitor.h"
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27 #include "../DicomFormat/DicomElement.h"
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28 #include "../DicomFormat/DicomMap.h"
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29 #include "../DicomFormat/DicomPath.h"
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31 #include <dcmtk/dcmdata/dcdatset.h>
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32 #include <dcmtk/dcmdata/dcmetinf.h>
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33 #include <dcmtk/dcmdata/dcpixseq.h>
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34 #include <dcmtk/dcmdata/dcfilefo.h>
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35 #include <json/value.h>
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36
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37 #if ORTHANC_ENABLE_DCMTK != 1
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38 # error The macro ORTHANC_ENABLE_DCMTK must be set to 1
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39 #endif
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40
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41 #if ORTHANC_BUILD_UNIT_TESTS == 1
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42 # include <gtest/gtest_prod.h>
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43 #endif
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44
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45 #if !defined(ORTHANC_ENABLE_DCMTK_JPEG)
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46 # error The macro ORTHANC_ENABLE_DCMTK_JPEG must be defined
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47 #endif
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48
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49 #if !defined(ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS)
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50 # error The macro ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS must be defined
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51 #endif
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52
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53
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54 namespace Orthanc
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55 {
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56 class ORTHANC_PUBLIC FromDcmtkBridge : public boost::noncopyable
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57 {
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58 #if ORTHANC_BUILD_UNIT_TESTS == 1
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59 FRIEND_TEST(FromDcmtkBridge, FromJson);
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60 #endif
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61
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62 friend class ParsedDicomFile;
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63
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64 public:
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65 // New in Orthanc 1.9.4
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66 class ORTHANC_PUBLIC IDicomPathVisitor : public boost::noncopyable
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67 {
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68 private:
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69 static void ApplyInternal(FromDcmtkBridge::IDicomPathVisitor& visitor,
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70 DcmItem& item,
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71 const DicomPath& pattern,
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72 const DicomPath& actualPath);
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74 public:
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75 virtual ~IDicomPathVisitor()
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76 {
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77 }
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78
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79 virtual void Visit(DcmItem& item,
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80 const DicomPath& path) = 0;
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82 static void Apply(IDicomPathVisitor& visitor,
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83 DcmDataset& dataset,
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84 const DicomPath& path);
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85 };
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86
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87
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88 private:
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89 FromDcmtkBridge(); // Pure static class
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90
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91 static void DatasetToJson(Json::Value& parent,
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92 DcmItem& item,
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93 DicomToJsonFormat format,
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94 DicomToJsonFlags flags,
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95 unsigned int maxStringLength,
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96 Encoding encoding,
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97 bool hasCodeExtensions,
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98 const std::set<DicomTag>& ignoreTagLength,
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99 unsigned int depth);
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100
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101 static void ElementToJson(Json::Value& parent,
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102 DcmElement& element,
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103 DicomToJsonFormat format,
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104 DicomToJsonFlags flags,
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105 unsigned int maxStringLength,
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106 Encoding dicomEncoding,
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107 bool hasCodeExtensions,
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108 const std::set<DicomTag>& ignoreTagLength,
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109 unsigned int depth);
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110
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111 static void ChangeStringEncoding(DcmItem& dataset,
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112 Encoding source,
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113 bool hasSourceCodeExtensions,
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114 Encoding target);
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115
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116 public:
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117 /**
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118 * Initialize DCMTK to use the default DICOM dictionaries (either
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119 * embedded into the binaries for official releases, or using the
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120 * environment variable "DCM_DICT_ENVIRONMENT_VARIABLE", or using
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121 * the system-wide path to the DCMTK library for developers)
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122 **/
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123 static void InitializeDictionary(bool loadPrivateDictionary);
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124
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125 /**
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126 * Replace the default DICOM dictionaries by the manually-provided
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127 * external dictionaries. This is needed to use DICONDE for
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128 * instance. Pay attention to the fact that the current dictionary
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129 * will be reinitialized (all its tags are cleared).
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130 **/
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131 static void LoadExternalDictionaries(const std::vector<std::string>& dictionaries);
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132
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133 static void RegisterDictionaryTag(const DicomTag& tag,
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134 ValueRepresentation vr,
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135 const std::string& name,
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136 unsigned int minMultiplicity,
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137 unsigned int maxMultiplicity,
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138 const std::string& privateCreator);
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139
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140 static Encoding DetectEncoding(bool& hasCodeExtensions,
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141 DcmItem& dataset,
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142 Encoding defaultEncoding);
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143
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144 // Compatibility wrapper for Orthanc <= 1.5.4
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145 static Encoding DetectEncoding(DcmItem& dataset,
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146 Encoding defaultEncoding);
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147
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148 static DicomTag Convert(const DcmTag& tag);
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149
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150 static DicomTag GetTag(const DcmElement& element);
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151
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152 static bool IsUnknownTag(const DicomTag& tag);
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153
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154 static DicomValue* ConvertLeafElement(DcmElement& element,
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155 DicomToJsonFlags flags,
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156 unsigned int maxStringLength,
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157 Encoding encoding,
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158 bool hasCodeExtensions,
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159 const std::set<DicomTag>& ignoreTagLength);
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160
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161 static void ExtractHeaderAsJson(Json::Value& target,
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162 DcmMetaInfo& header,
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163 DicomToJsonFormat format,
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164 DicomToJsonFlags flags,
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165 unsigned int maxStringLength);
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166
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167 static std::string GetTagName(const DicomTag& tag,
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168 const std::string& privateCreator);
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169
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170 static std::string GetTagName(const DcmElement& element);
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171
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172 static std::string GetTagName(const DicomElement& element);
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173
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174 static DicomTag ParseTag(const char* name);
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175
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176 static DicomTag ParseTag(const std::string& name);
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177
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178 // parses a list like "0010,0010;PatientBirthDate;0020,0020"
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179 static void ParseListOfTags(std::set<DicomTag>& result, const std::string& source);
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180
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181 static void ParseListOfTags(std::set<DicomTag>& result, const Json::Value& source);
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182
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183 static void FormatListOfTags(std::string& output, const std::set<DicomTag>& tags);
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184
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185 static void FormatListOfTags(Json::Value& output, const std::set<DicomTag>& tags);
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186
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187 static bool HasTag(const DicomMap& fields,
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188 const std::string& tagName);
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189
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190 static const DicomValue& GetValue(const DicomMap& fields,
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191 const std::string& tagName);
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192
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193 static void SetValue(DicomMap& target,
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194 const std::string& tagName,
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195 DicomValue* value);
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196
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197 static void ToJson(Json::Value& result,
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198 const DicomMap& values,
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199 DicomToJsonFormat format);
176
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200
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201 static std::string GenerateUniqueIdentifier(ResourceType level);
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202
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203 static bool SaveToMemoryBuffer(std::string& buffer,
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204 DcmDataset& dataSet);
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205
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206 static bool Transcode(DcmFileFormat& dicom,
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207 DicomTransferSyntax syntax,
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208 const DcmRepresentationParameter* representation);
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209
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diff changeset
210 static ValueRepresentation Convert(DcmEVR vr);
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211
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diff changeset
212 static ValueRepresentation LookupValueRepresentation(const DicomTag& tag);
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213
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214 static DcmElement* CreateElementForTag(const DicomTag& tag,
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215 const std::string& privateCreator);
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216
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217 static void FillElementWithString(DcmElement& element,
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218 const std::string& utf8alue, // Encoded using UTF-8
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219 bool decodeDataUriScheme,
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220 Encoding dicomEncoding);
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221
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222 static DcmElement* FromJson(const DicomTag& tag,
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223 const Json::Value& element, // Encoded using UTF-8
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224 bool decodeDataUriScheme,
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225 Encoding dicomEncoding,
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226 const std::string& privateCreator);
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227
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diff changeset
228 static DcmPixelSequence* GetPixelSequence(DcmDataset& dataset);
1934
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229
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230 static Encoding ExtractEncoding(const Json::Value& json,
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diff changeset
231 Encoding defaultEncoding);
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232
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233 static DcmDataset* FromJson(const Json::Value& json, // Encoded using UTF-8
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234 bool generateIdentifiers,
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235 bool decodeDataUriScheme,
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236 Encoding defaultEncoding,
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237 const std::string& privateCreator);
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238
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239 static DcmFileFormat* LoadFromMemoryBuffer(const void* buffer,
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240 size_t size);
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241
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diff changeset
242 static void FromJson(DicomMap& values,
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243 const Json::Value& result,
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244 const char* fieldName = NULL);
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245
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246 static void ExtractDicomSummary(DicomMap& target,
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247 DcmItem& dataset,
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248 unsigned int maxStringLength,
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249 const std::set<DicomTag>& ignoreTagLength);
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250
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diff changeset
251 static void ExtractDicomAsJson(Json::Value& target,
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252 DcmDataset& dataset,
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253 DicomToJsonFormat format,
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254 DicomToJsonFlags flags,
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255 unsigned int maxStringLength,
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256 const std::set<DicomTag>& ignoreTagLength);
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257
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258 static void InitializeCodecs();
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259
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260 static void FinalizeCodecs();
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261
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262 static void Apply(DcmItem& dataset,
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263 ITagVisitor& visitor,
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264 Encoding defaultEncoding);
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265
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266 static bool LookupDcmtkTransferSyntax(E_TransferSyntax& target,
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267 DicomTransferSyntax source);
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268
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269 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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270 E_TransferSyntax source);
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271
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272 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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273 DcmFileFormat& dicom);
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274
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275 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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276 DcmDataset& dicom);
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277
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278 static void LogMissingTagsForStore(DcmDataset& dicom);
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279
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280 static void RemovePath(DcmDataset& dataset,
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281 const DicomPath& path);
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282
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283 static void ClearPath(DcmDataset& dataset,
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284 const DicomPath& path,
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285 bool onlyIfExists);
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286
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287 static void ReplacePath(DcmDataset& dataset,
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288 const DicomPath& path,
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289 const DcmElement& element,
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290 DicomReplaceMode mode);
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291
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292 static bool LookupSequenceItem(DicomMap& target,
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293 DcmDataset& dataset,
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294 const DicomPath& path,
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295 size_t sequenceIndex);
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296
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297 static bool LookupStringValue(std::string& target,
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298 DcmDataset& dataset,
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299 const DicomTag& key);
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300 };
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301 }