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annotate OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h @ 4771:9f207131c7f4

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added ParsedDicomFile::LookupSubSequence()
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 25 Aug 2021 17:20:21 +0200
parents 248408d2b336
children 3b78ba359db3
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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) 2017-2021 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 Lesser General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Lesser General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Lesser General Public
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18 * License along with this program. If not, see
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19 * <http://www.gnu.org/licenses/>.
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20 **/
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23 #pragma once
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24
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25 #include "ITagVisitor.h"
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26 #include "../DicomFormat/DicomElement.h"
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27 #include "../DicomFormat/DicomMap.h"
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28 #include "../DicomFormat/DicomPath.h"
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30 #include <dcmtk/dcmdata/dcdatset.h>
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31 #include <dcmtk/dcmdata/dcmetinf.h>
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32 #include <dcmtk/dcmdata/dcpixseq.h>
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33 #include <dcmtk/dcmdata/dcfilefo.h>
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34 #include <json/value.h>
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36 #if ORTHANC_ENABLE_DCMTK != 1
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37 # error The macro ORTHANC_ENABLE_DCMTK must be set to 1
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38 #endif
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39
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40 #if ORTHANC_BUILD_UNIT_TESTS == 1
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41 # include <gtest/gtest_prod.h>
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42 #endif
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43
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44 #if !defined(ORTHANC_ENABLE_DCMTK_JPEG)
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45 # error The macro ORTHANC_ENABLE_DCMTK_JPEG must be defined
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46 #endif
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48 #if !defined(ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS)
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49 # error The macro ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS must be defined
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50 #endif
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51
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52
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53 namespace Orthanc
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54 {
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55 class ORTHANC_PUBLIC FromDcmtkBridge : public boost::noncopyable
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56 {
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57 #if ORTHANC_BUILD_UNIT_TESTS == 1
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58 FRIEND_TEST(FromDcmtkBridge, FromJson);
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59 #endif
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60
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61 friend class ParsedDicomFile;
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63 public:
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64 // New in Orthanc 1.9.4
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65 class ORTHANC_PUBLIC IDicomPathVisitor : public boost::noncopyable
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66 {
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67 private:
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68 static void ApplyInternal(FromDcmtkBridge::IDicomPathVisitor& visitor,
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69 DcmItem& item,
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70 const DicomPath& pattern,
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71 const DicomPath& actualPath);
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74 virtual ~IDicomPathVisitor()
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75 {
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76 }
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78 virtual void Visit(DcmItem& item,
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79 const DicomPath& path) = 0;
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81 static void Apply(IDicomPathVisitor& visitor,
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82 DcmDataset& dataset,
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83 const DicomPath& path);
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84 };
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87 private:
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88 FromDcmtkBridge(); // Pure static class
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89
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90 static void DatasetToJson(Json::Value& parent,
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91 DcmItem& item,
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92 DicomToJsonFormat format,
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93 DicomToJsonFlags flags,
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94 unsigned int maxStringLength,
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95 Encoding encoding,
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96 bool hasCodeExtensions,
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97 const std::set<DicomTag>& ignoreTagLength,
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98 unsigned int depth);
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99
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100 static void ElementToJson(Json::Value& parent,
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101 DcmElement& element,
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102 DicomToJsonFormat format,
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103 DicomToJsonFlags flags,
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104 unsigned int maxStringLength,
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105 Encoding dicomEncoding,
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106 bool hasCodeExtensions,
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107 const std::set<DicomTag>& ignoreTagLength,
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108 unsigned int depth);
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109
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110 static void ChangeStringEncoding(DcmItem& dataset,
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111 Encoding source,
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112 bool hasSourceCodeExtensions,
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113 Encoding target);
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114
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115 public:
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116 /**
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117 * Initialize DCMTK to use the default DICOM dictionaries (either
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118 * embedded into the binaries for official releases, or using the
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119 * environment variable "DCM_DICT_ENVIRONMENT_VARIABLE", or using
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120 * the system-wide path to the DCMTK library for developers)
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121 **/
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122 static void InitializeDictionary(bool loadPrivateDictionary);
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123
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124 /**
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125 * Replace the default DICOM dictionaries by the manually-provided
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126 * external dictionaries. This is needed to use DICONDE for
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127 * instance. Pay attention to the fact that the current dictionary
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128 * will be reinitialized (all its tags are cleared).
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129 **/
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130 static void LoadExternalDictionaries(const std::vector<std::string>& dictionaries);
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131
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132 static void RegisterDictionaryTag(const DicomTag& tag,
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133 ValueRepresentation vr,
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134 const std::string& name,
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135 unsigned int minMultiplicity,
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136 unsigned int maxMultiplicity,
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137 const std::string& privateCreator);
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138
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139 static Encoding DetectEncoding(bool& hasCodeExtensions,
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140 DcmItem& dataset,
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141 Encoding defaultEncoding);
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142
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143 // Compatibility wrapper for Orthanc <= 1.5.4
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144 static Encoding DetectEncoding(DcmItem& dataset,
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145 Encoding defaultEncoding);
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146
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147 static DicomTag Convert(const DcmTag& tag);
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148
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149 static DicomTag GetTag(const DcmElement& element);
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150
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151 static bool IsUnknownTag(const DicomTag& tag);
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152
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153 static DicomValue* ConvertLeafElement(DcmElement& element,
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154 DicomToJsonFlags flags,
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155 unsigned int maxStringLength,
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156 Encoding encoding,
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157 bool hasCodeExtensions,
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158 const std::set<DicomTag>& ignoreTagLength);
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159
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160 static void ExtractHeaderAsJson(Json::Value& target,
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161 DcmMetaInfo& header,
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162 DicomToJsonFormat format,
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163 DicomToJsonFlags flags,
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164 unsigned int maxStringLength);
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165
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166 static std::string GetTagName(const DicomTag& tag,
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167 const std::string& privateCreator);
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168
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169 static std::string GetTagName(const DcmElement& element);
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170
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171 static std::string GetTagName(const DicomElement& element);
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172
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173 static DicomTag ParseTag(const char* name);
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174
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175 static DicomTag ParseTag(const std::string& name);
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176
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177 static bool HasTag(const DicomMap& fields,
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178 const std::string& tagName);
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179
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180 static const DicomValue& GetValue(const DicomMap& fields,
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181 const std::string& tagName);
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182
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183 static void SetValue(DicomMap& target,
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184 const std::string& tagName,
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185 DicomValue* value);
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186
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187 static void ToJson(Json::Value& result,
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188 const DicomMap& values,
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189 DicomToJsonFormat format);
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190
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191 static std::string GenerateUniqueIdentifier(ResourceType level);
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192
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193 static bool SaveToMemoryBuffer(std::string& buffer,
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194 DcmDataset& dataSet);
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195
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196 static bool Transcode(DcmFileFormat& dicom,
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197 DicomTransferSyntax syntax,
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198 const DcmRepresentationParameter* representation);
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199
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200 static ValueRepresentation Convert(DcmEVR vr);
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201
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202 static ValueRepresentation LookupValueRepresentation(const DicomTag& tag);
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203
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204 static DcmElement* CreateElementForTag(const DicomTag& tag,
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205 const std::string& privateCreator);
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206
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207 static void FillElementWithString(DcmElement& element,
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208 const std::string& utf8alue, // Encoded using UTF-8
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209 bool decodeDataUriScheme,
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210 Encoding dicomEncoding);
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211
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212 static DcmElement* FromJson(const DicomTag& tag,
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213 const Json::Value& element, // Encoded using UTF-8
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214 bool decodeDataUriScheme,
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215 Encoding dicomEncoding,
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216 const std::string& privateCreator);
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217
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218 static DcmPixelSequence* GetPixelSequence(DcmDataset& dataset);
1934
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219
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220 static Encoding ExtractEncoding(const Json::Value& json,
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221 Encoding defaultEncoding);
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222
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223 static DcmDataset* FromJson(const Json::Value& json, // Encoded using UTF-8
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224 bool generateIdentifiers,
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225 bool decodeDataUriScheme,
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226 Encoding defaultEncoding,
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227 const std::string& privateCreator);
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228
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229 static DcmFileFormat* LoadFromMemoryBuffer(const void* buffer,
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230 size_t size);
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231
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232 static void FromJson(DicomMap& values,
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233 const Json::Value& result);
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234
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235 static void ExtractDicomSummary(DicomMap& target,
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236 DcmItem& dataset,
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237 unsigned int maxStringLength,
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238 const std::set<DicomTag>& ignoreTagLength);
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239
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240 static void ExtractDicomAsJson(Json::Value& target,
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241 DcmDataset& dataset,
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242 DicomToJsonFormat format,
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243 DicomToJsonFlags flags,
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244 unsigned int maxStringLength,
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245 const std::set<DicomTag>& ignoreTagLength);
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246
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247 static void InitializeCodecs();
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248
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249 static void FinalizeCodecs();
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250
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251 static void Apply(DcmItem& dataset,
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252 ITagVisitor& visitor,
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253 Encoding defaultEncoding);
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254
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255 static bool LookupDcmtkTransferSyntax(E_TransferSyntax& target,
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256 DicomTransferSyntax source);
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257
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258 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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259 E_TransferSyntax source);
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260
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261 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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262 DcmFileFormat& dicom);
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263
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264 static bool LookupOrthancTransferSyntax(DicomTransferSyntax& target,
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265 DcmDataset& dicom);
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266
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267 static void LogMissingTagsForStore(DcmDataset& dicom);
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268
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269 static void RemovePath(DcmDataset& dataset,
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270 const DicomPath& path);
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271
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272 static void ClearPath(DcmDataset& dataset,
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273 const DicomPath& path,
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274 bool onlyIfExists);
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275
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276 static void ReplacePath(DcmDataset& dataset,
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277 const DicomPath& path,
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278 const DcmElement& element,
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279 DicomReplaceMode mode);
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280
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281 static bool LookupSubSequence(DicomMap& target,
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282 DcmDataset& dataset,
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283 const DicomPath& path,
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284 size_t sequenceIndex);
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285 };
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286 }