Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 3434:6503ab9489ba
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 18 Jun 2019 11:37:18 +0200 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 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 #include "PrecompiledHeadersServer.h" |
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35 #include "ServerToolbox.h" |
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36 |
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37 #include "../Core/DicomFormat/DicomArray.h" |
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38 #include "../Core/DicomParsing/ParsedDicomFile.h" |
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39 #include "../Core/FileStorage/StorageAccessor.h" |
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40 #include "../Core/Logging.h" |
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41 #include "../Core/OrthancException.h" |
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42 #include "Database/IDatabaseWrapper.h" |
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43 #include "Database/ResourcesContent.h" |
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44 #include "ServerContext.h" |
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45 |
234 | 46 #include <cassert> |
47 | |
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48 namespace Orthanc |
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49 { |
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50 static const DicomTag PATIENT_IDENTIFIERS[] = |
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51 { |
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52 DICOM_TAG_PATIENT_ID, |
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53 DICOM_TAG_PATIENT_NAME, |
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54 DICOM_TAG_PATIENT_BIRTH_DATE |
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55 }; |
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56 |
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57 static const DicomTag STUDY_IDENTIFIERS[] = |
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58 { |
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59 DICOM_TAG_PATIENT_ID, |
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60 DICOM_TAG_PATIENT_NAME, |
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61 DICOM_TAG_PATIENT_BIRTH_DATE, |
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62 DICOM_TAG_STUDY_INSTANCE_UID, |
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63 DICOM_TAG_ACCESSION_NUMBER, |
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64 DICOM_TAG_STUDY_DESCRIPTION, |
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65 DICOM_TAG_STUDY_DATE |
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66 }; |
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67 |
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68 static const DicomTag SERIES_IDENTIFIERS[] = |
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69 { |
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70 DICOM_TAG_SERIES_INSTANCE_UID |
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71 }; |
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72 |
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73 static const DicomTag INSTANCE_IDENTIFIERS[] = |
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74 { |
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75 DICOM_TAG_SOP_INSTANCE_UID |
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76 }; |
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77 |
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78 |
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79 static void StoreMainDicomTagsInternal(ResourcesContent& target, |
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80 int64_t resource, |
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81 const DicomMap& tags) |
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82 { |
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83 DicomArray flattened(tags); |
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84 |
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85 for (size_t i = 0; i < flattened.GetSize(); i++) |
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86 { |
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87 const DicomElement& element = flattened.GetElement(i); |
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88 const DicomTag& tag = element.GetTag(); |
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89 const DicomValue& value = element.GetValue(); |
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90 if (!value.IsNull() && |
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91 !value.IsBinary()) |
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92 { |
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93 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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94 } |
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95 } |
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96 } |
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97 |
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98 |
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99 static void StoreIdentifiers(ResourcesContent& target, |
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100 int64_t resource, |
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101 ResourceType level, |
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102 const DicomMap& map) |
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103 { |
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104 const DicomTag* tags; |
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105 size_t size; |
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106 |
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107 ServerToolbox::LoadIdentifiers(tags, size, level); |
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108 |
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109 for (size_t i = 0; i < size; i++) |
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110 { |
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111 // The identifiers tags are a subset of the main DICOM tags |
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112 assert(DicomMap::IsMainDicomTag(tags[i])); |
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113 |
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114 const DicomValue* value = map.TestAndGetValue(tags[i]); |
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115 if (value != NULL && |
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116 !value->IsNull() && |
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117 !value->IsBinary()) |
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118 { |
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119 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent()); |
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120 target.AddIdentifierTag(resource, tags[i], s); |
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121 } |
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122 } |
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123 } |
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124 |
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125 |
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126 void ResourcesContent::AddResource(int64_t resource, |
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127 ResourceType level, |
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128 const DicomMap& dicomSummary) |
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129 { |
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130 StoreIdentifiers(*this, resource, level, dicomSummary); |
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131 |
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132 DicomMap tags; |
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133 |
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134 switch (level) |
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135 { |
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136 case ResourceType_Patient: |
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137 dicomSummary.ExtractPatientInformation(tags); |
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138 break; |
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139 |
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140 case ResourceType_Study: |
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141 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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142 dicomSummary.ExtractPatientInformation(tags); |
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143 StoreMainDicomTagsInternal(*this, resource, tags); |
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144 |
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145 dicomSummary.ExtractStudyInformation(tags); |
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146 break; |
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147 |
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148 case ResourceType_Series: |
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149 dicomSummary.ExtractSeriesInformation(tags); |
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150 break; |
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151 |
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152 case ResourceType_Instance: |
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153 dicomSummary.ExtractInstanceInformation(tags); |
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154 break; |
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155 |
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156 default: |
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157 throw OrthancException(ErrorCode_InternalError); |
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158 } |
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159 |
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160 StoreMainDicomTagsInternal(*this, resource, tags); |
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161 } |
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162 |
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163 |
2120 | 164 namespace ServerToolbox |
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165 { |
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166 void SimplifyTags(Json::Value& target, |
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167 const Json::Value& source, |
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168 DicomToJsonFormat format) |
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169 { |
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170 if (!source.isObject()) |
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171 { |
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172 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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173 } |
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174 |
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175 target = Json::objectValue; |
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176 Json::Value::Members members = source.getMemberNames(); |
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177 |
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178 for (size_t i = 0; i < members.size(); i++) |
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179 { |
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180 const Json::Value& v = source[members[i]]; |
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181 const std::string& type = v["Type"].asString(); |
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182 |
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183 std::string name; |
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184 switch (format) |
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185 { |
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186 case DicomToJsonFormat_Human: |
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187 name = v["Name"].asString(); |
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188 break; |
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189 |
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190 case DicomToJsonFormat_Short: |
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191 name = members[i]; |
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192 break; |
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193 |
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194 default: |
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195 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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196 } |
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197 |
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198 if (type == "String") |
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199 { |
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200 target[name] = v["Value"].asString(); |
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201 } |
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202 else if (type == "TooLong" || |
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203 type == "Null") |
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204 { |
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205 target[name] = Json::nullValue; |
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206 } |
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207 else if (type == "Sequence") |
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208 { |
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209 const Json::Value& array = v["Value"]; |
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210 assert(array.isArray()); |
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211 |
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212 Json::Value children = Json::arrayValue; |
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213 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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214 { |
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215 Json::Value c; |
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216 SimplifyTags(c, array[i], format); |
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217 children.append(c); |
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218 } |
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219 |
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220 target[name] = children; |
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221 } |
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222 else |
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223 { |
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224 assert(0); |
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225 } |
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226 } |
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227 } |
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228 |
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229 |
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230 bool FindOneChildInstance(int64_t& result, |
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231 IDatabaseWrapper& database, |
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232 int64_t resource, |
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233 ResourceType type) |
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234 { |
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235 for (;;) |
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236 { |
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237 if (type == ResourceType_Instance) |
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238 { |
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239 result = resource; |
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240 return true; |
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241 } |
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242 |
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243 std::list<int64_t> children; |
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244 database.GetChildrenInternalId(children, resource); |
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245 if (children.empty()) |
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246 { |
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247 return false; |
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248 } |
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249 |
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250 resource = children.front(); |
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251 type = GetChildResourceType(type); |
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252 } |
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253 } |
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254 |
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255 |
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256 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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257 IStorageArea& storageArea, |
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258 ResourceType level) |
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259 { |
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260 // WARNING: The database should be locked with a transaction! |
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261 |
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262 // TODO: This function might consume much memory if level == |
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263 // ResourceType_Instance. To improve this, first download the |
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264 // list of studies, then remove the instances for each single |
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265 // study (check out OrthancRestApi::InvalidateTags for an |
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266 // example). Take this improvement into consideration for the |
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267 // next upgrade of the database schema. |
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268 |
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269 const char* plural = NULL; |
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270 |
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271 switch (level) |
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272 { |
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273 case ResourceType_Patient: |
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274 plural = "patients"; |
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275 break; |
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276 |
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277 case ResourceType_Study: |
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278 plural = "studies"; |
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279 break; |
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280 |
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281 case ResourceType_Series: |
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282 plural = "series"; |
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283 break; |
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284 |
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285 case ResourceType_Instance: |
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286 plural = "instances"; |
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287 break; |
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288 |
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289 default: |
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290 throw OrthancException(ErrorCode_InternalError); |
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291 } |
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292 |
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293 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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294 |
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295 std::list<std::string> resources; |
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296 database.GetAllPublicIds(resources, level); |
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297 |
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298 for (std::list<std::string>::const_iterator |
1847 | 299 it = resources.begin(); it != resources.end(); ++it) |
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300 { |
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301 // Locate the resource and one of its child instances |
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302 int64_t resource, instance; |
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303 ResourceType tmp; |
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304 |
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305 if (!database.LookupResource(resource, tmp, *it) || |
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306 tmp != level || |
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307 !FindOneChildInstance(instance, database, resource, level)) |
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308 { |
2955 | 309 throw OrthancException(ErrorCode_InternalError, |
310 "Cannot find an instance for " + | |
311 std::string(EnumerationToString(level)) + | |
312 " with identifier " + *it); | |
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313 } |
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314 |
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315 // Get the DICOM file attached to some instances in the resource |
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316 FileInfo attachment; |
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317 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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318 { |
2955 | 319 throw OrthancException(ErrorCode_InternalError, |
320 "Cannot retrieve the DICOM file associated with instance " + | |
321 database.GetPublicId(instance)); | |
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322 } |
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323 |
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324 try |
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325 { |
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326 // Read and parse the content of the DICOM file |
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327 StorageAccessor accessor(storageArea); |
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328 |
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329 std::string content; |
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330 accessor.Read(content, attachment); |
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331 |
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332 ParsedDicomFile dicom(content); |
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333 |
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334 // Update the tags of this resource |
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335 DicomMap dicomSummary; |
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336 dicom.ExtractDicomSummary(dicomSummary); |
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337 |
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338 database.ClearMainDicomTags(resource); |
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339 |
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340 ResourcesContent tags; |
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341 tags.AddResource(resource, level, dicomSummary); |
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342 database.SetResourcesContent(tags); |
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343 } |
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344 catch (OrthancException&) |
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345 { |
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346 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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347 << " associated with instance " << database.GetPublicId(instance); |
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348 throw; |
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349 } |
213
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350 } |
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351 } |
2121 | 352 |
353 | |
354 void LoadIdentifiers(const DicomTag*& tags, | |
355 size_t& size, | |
356 ResourceType level) | |
357 { | |
358 switch (level) | |
359 { | |
360 case ResourceType_Patient: | |
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361 tags = PATIENT_IDENTIFIERS; |
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362 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 363 break; |
364 | |
365 case ResourceType_Study: | |
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366 tags = STUDY_IDENTIFIERS; |
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367 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 368 break; |
369 | |
370 case ResourceType_Series: | |
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371 tags = SERIES_IDENTIFIERS; |
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372 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 373 break; |
374 | |
375 case ResourceType_Instance: | |
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376 tags = INSTANCE_IDENTIFIERS; |
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377 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 378 break; |
379 | |
380 default: | |
381 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
382 } | |
383 } | |
384 | |
385 | |
386 std::string NormalizeIdentifier(const std::string& value) | |
387 { | |
388 std::string t; | |
389 t.reserve(value.size()); | |
390 | |
391 for (size_t i = 0; i < value.size(); i++) | |
392 { | |
393 if (value[i] == '%' || | |
394 value[i] == '_') | |
395 { | |
396 t.push_back(' '); // These characters might break wildcard queries in SQL | |
397 } | |
398 else if (isascii(value[i]) && | |
399 !iscntrl(value[i]) && | |
400 (!isspace(value[i]) || value[i] == ' ')) | |
401 { | |
402 t.push_back(value[i]); | |
403 } | |
404 } | |
405 | |
406 Toolbox::ToUpperCase(t); | |
407 | |
408 return Toolbox::StripSpaces(t); | |
409 } | |
410 | |
411 | |
412 bool IsIdentifier(const DicomTag& tag, | |
413 ResourceType level) | |
414 { | |
415 const DicomTag* tags; | |
416 size_t size; | |
417 | |
418 LoadIdentifiers(tags, size, level); | |
419 | |
420 for (size_t i = 0; i < size; i++) | |
421 { | |
422 if (tag == tags[i]) | |
423 { | |
424 return true; | |
425 } | |
426 } | |
427 | |
428 return false; | |
429 } | |
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430 |
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431 |
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432 void ReconstructResource(ServerContext& context, |
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433 const std::string& resource) |
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434 { |
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435 LOG(WARNING) << "Reconstructing resource " << resource; |
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436 |
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437 std::list<std::string> instances; |
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438 context.GetIndex().GetChildInstances(instances, resource); |
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439 |
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440 for (std::list<std::string>::const_iterator |
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441 it = instances.begin(); it != instances.end(); ++it) |
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442 { |
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443 ServerContext::DicomCacheLocker locker(context, *it); |
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444 |
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445 Json::Value dicomAsJson; |
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446 locker.GetDicom().DatasetToJson(dicomAsJson); |
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447 |
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448 std::string s = dicomAsJson.toStyledString(); |
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449 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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450 |
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451 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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452 } |
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453 } |
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454 } |
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455 } |