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annotate Core/DicomParsing/ParsedDicomFile.h @ 3639:0c9a8f6d2349 storage-commitment

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better unserialization
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 31 Jan 2020 17:01:55 +0100
parents 33cfcc74d1b1
children 94f4a18a79cc
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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) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #pragma once
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35
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36 #if !defined(ORTHANC_ENABLE_JPEG)
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37 # error Macro ORTHANC_ENABLE_JPEG 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_PNG)
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41 # error Macro ORTHANC_ENABLE_PNG 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_ENABLE_CIVETWEB)
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45 # error Macro ORTHANC_ENABLE_CIVETWEB must be defined to use this file
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46 #endif
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47
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48 #if !defined(ORTHANC_ENABLE_MONGOOSE)
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49 # error Macro ORTHANC_ENABLE_MONGOOSE must be defined to use this file
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50 #endif
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51
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52 #if !defined(ORTHANC_SANDBOXED)
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53 # error The macro ORTHANC_SANDBOXED must be defined
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54 #endif
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55
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56 #if !defined(ORTHANC_ENABLE_DCMTK)
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57 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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58 #endif
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59
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60 #if ORTHANC_ENABLE_DCMTK != 1
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61 # error The macro ORTHANC_ENABLE_DCMTK must be set to 1 to use this file
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62 #endif
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63
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64 #include "ITagVisitor.h"
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65 #include "../DicomFormat/DicomInstanceHasher.h"
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66 #include "../Images/ImageAccessor.h"
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67 #include "../IDynamicObject.h"
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68 #include "../Toolbox.h"
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69
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70 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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71 # include "../RestApi/RestApiOutput.h"
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72 #endif
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73
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74 #include <boost/shared_ptr.hpp>
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75
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76
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77 class DcmDataset;
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78 class DcmFileFormat;
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79
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80 namespace Orthanc
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81 {
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82 class ParsedDicomFile : public IDynamicObject
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83 {
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84 private:
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85 struct PImpl;
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86 boost::shared_ptr<PImpl> pimpl_;
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88 ParsedDicomFile(ParsedDicomFile& other,
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89 bool keepSopInstanceUid);
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90
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91 void CreateFromDicomMap(const DicomMap& source,
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92 Encoding defaultEncoding,
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93 bool permissive);
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94
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95 void RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep);
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96
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97 void UpdateStorageUid(const DicomTag& tag,
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98 const std::string& value,
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99 bool decodeDataUriScheme);
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100
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101 void InvalidateCache();
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102
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103 bool EmbedContentInternal(const std::string& dataUriScheme);
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104
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105 public:
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106 ParsedDicomFile(bool createIdentifiers); // Create a minimal DICOM instance
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107
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108 ParsedDicomFile(const DicomMap& map,
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109 Encoding defaultEncoding,
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110 bool permissive);
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111
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112 ParsedDicomFile(const void* content,
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113 size_t size);
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114
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115 ParsedDicomFile(const std::string& content);
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116
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117 ParsedDicomFile(DcmDataset& dicom);
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118
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119 ParsedDicomFile(DcmFileFormat& dicom);
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120
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121 DcmFileFormat& GetDcmtkObject() const;
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122
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123 ParsedDicomFile* Clone(bool keepSopInstanceUid);
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124
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125 #if ORTHANC_ENABLE_CIVETWEB == 1 || ORTHANC_ENABLE_MONGOOSE == 1
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126 void SendPathValue(RestApiOutput& output,
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127 const UriComponents& uri);
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128
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129 void Answer(RestApiOutput& output);
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130 #endif
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131
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132 void Remove(const DicomTag& tag);
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133
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134 // Replace the DICOM tag as a NULL/empty value (e.g. for anonymization)
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135 void Clear(const DicomTag& tag,
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136 bool onlyIfExists);
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137
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138 void Replace(const DicomTag& tag,
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139 const std::string& utf8Value,
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140 bool decodeDataUriScheme,
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141 DicomReplaceMode mode);
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142
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143 void Replace(const DicomTag& tag,
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144 const Json::Value& value, // Assumed to be encoded with UTF-8
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145 bool decodeDataUriScheme,
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146 DicomReplaceMode mode);
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147
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148 void Insert(const DicomTag& tag,
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149 const Json::Value& value, // Assumed to be encoded with UTF-8
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150 bool decodeDataUriScheme);
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151
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152 void ReplacePlainString(const DicomTag& tag,
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153 const std::string& utf8Value)
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154 {
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155 Replace(tag, utf8Value, false, DicomReplaceMode_InsertIfAbsent);
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156 }
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157
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158 void SetIfAbsent(const DicomTag& tag,
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159 const std::string& utf8Value)
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160 {
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161 std::string currentValue;
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162 if (!GetTagValue(currentValue, tag))
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163 {
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164 ReplacePlainString(tag, utf8Value);
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165 }
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166 }
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167
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168 void RemovePrivateTags()
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169 {
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170 RemovePrivateTagsInternal(NULL);
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171 }
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172
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173 void RemovePrivateTags(const std::set<DicomTag>& toKeep)
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174 {
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175 RemovePrivateTagsInternal(&toKeep);
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176 }
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177
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178 // WARNING: This function handles the decoding of strings to UTF8
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179 bool GetTagValue(std::string& value,
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180 const DicomTag& tag);
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181
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182 DicomInstanceHasher GetHasher();
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183
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184 void SaveToMemoryBuffer(std::string& buffer);
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185
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186 #if ORTHANC_SANDBOXED == 0
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187 void SaveToFile(const std::string& path);
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188 #endif
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189
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190 void EmbedContent(const std::string& dataUriScheme);
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191
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192 void EmbedImage(const ImageAccessor& accessor);
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193
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194 void EmbedImage(MimeType mime,
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195 const std::string& content);
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196
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197 Encoding DetectEncoding(bool& hasCodeExtensions) const;
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198
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199 // WARNING: This function only sets the encoding, it will not
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200 // convert the encoding of the tags. Use "ChangeEncoding()" if need be.
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201 void SetEncoding(Encoding encoding);
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202
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203 void DatasetToJson(Json::Value& target,
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204 DicomToJsonFormat format,
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205 DicomToJsonFlags flags,
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diff changeset
206 unsigned int maxStringLength);
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207
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208 void DatasetToJson(Json::Value& target,
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209 DicomToJsonFormat format,
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210 DicomToJsonFlags flags,
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diff changeset
211 unsigned int maxStringLength,
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212 const std::set<DicomTag>& ignoreTagLength);
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213
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214 // This version uses the default parameters for
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215 // FileContentType_DicomAsJson
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216 void DatasetToJson(Json::Value& target,
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217 const std::set<DicomTag>& ignoreTagLength);
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218
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219 void DatasetToJson(Json::Value& target);
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220
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221 void HeaderToJson(Json::Value& target,
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222 DicomToJsonFormat format);
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223
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224 bool HasTag(const DicomTag& tag) const;
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225
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226 void EmbedPdf(const std::string& pdf);
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227
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228 bool ExtractPdf(std::string& pdf);
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229
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230 void GetRawFrame(std::string& target, // OUT
2908
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231 MimeType& mime, // OUT
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diff changeset
232 unsigned int frameId); // IN
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233
1950
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parents: 1935
diff changeset
234 unsigned int GetFramesCount() const;
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parents: 1935
diff changeset
235
1818
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236 static ParsedDicomFile* CreateFromJson(const Json::Value& value,
1065401501fb ParsedDicomFile::CreateFromJson
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237 DicomFromJsonFlags flags);
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238
6dc3bdb4088b Fix handling of encodings in C-FIND for worklists
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
239 void ChangeEncoding(Encoding target);
2209
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240
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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diff changeset
241 void ExtractDicomSummary(DicomMap& target) const;
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242
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diff changeset
243 void ExtractDicomSummary(DicomMap& target,
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244 const std::set<DicomTag>& ignoreTagLength) const;
33cfcc74d1b1 argument "ignoreTagLength" to ParsedDicomFile::ExtractDicomSummary()
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245
2209
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diff changeset
246 bool LookupTransferSyntax(std::string& result);
2281
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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parents: 2244
diff changeset
247
e002430baa41 Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2244
diff changeset
248 bool LookupPhotometricInterpretation(PhotometricInterpretation& result) const;
2499
83b8b6743531 ITagVisitor - for anonymization relationships
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diff changeset
249
83b8b6743531 ITagVisitor - for anonymization relationships
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diff changeset
250 void Apply(ITagVisitor& visitor);
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331eaf9d9d69 ParsedDicomFile
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251 };
331eaf9d9d69 ParsedDicomFile
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252 }