Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerToolbox.cpp @ 4533:409cba9c1dba Orthanc-1.9.1
Orthanc-1.9.1
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 25 Feb 2021 16:59:24 +0100 |
parents | 7b99e8bb8246 |
children | ff8170d17d90 |
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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) 2017-2021 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 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 |
4045 | 37 #include "../../OrthancFramework/Sources/DicomFormat/DicomArray.h" |
38 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h" | |
39 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h" | |
40 #include "../../OrthancFramework/Sources/Logging.h" | |
41 #include "../../OrthancFramework/Sources/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 "OrthancConfiguration.h" |
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45 #include "ServerContext.h" |
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46 |
234 | 47 #include <cassert> |
48 | |
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49 namespace Orthanc |
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50 { |
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51 static const DicomTag PATIENT_IDENTIFIERS[] = |
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52 { |
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53 DICOM_TAG_PATIENT_ID, |
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54 DICOM_TAG_PATIENT_NAME, |
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55 DICOM_TAG_PATIENT_BIRTH_DATE |
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56 }; |
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57 |
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58 static const DicomTag STUDY_IDENTIFIERS[] = |
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59 { |
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60 DICOM_TAG_PATIENT_ID, |
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61 DICOM_TAG_PATIENT_NAME, |
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62 DICOM_TAG_PATIENT_BIRTH_DATE, |
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63 DICOM_TAG_STUDY_INSTANCE_UID, |
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64 DICOM_TAG_ACCESSION_NUMBER, |
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65 DICOM_TAG_STUDY_DESCRIPTION, |
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66 DICOM_TAG_STUDY_DATE |
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67 }; |
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68 |
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69 static const DicomTag SERIES_IDENTIFIERS[] = |
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70 { |
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71 DICOM_TAG_SERIES_INSTANCE_UID |
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72 }; |
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73 |
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74 static const DicomTag INSTANCE_IDENTIFIERS[] = |
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75 { |
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76 DICOM_TAG_SOP_INSTANCE_UID |
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77 }; |
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78 |
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79 |
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80 static void StoreMainDicomTagsInternal(ResourcesContent& target, |
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81 int64_t resource, |
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82 const DicomMap& tags) |
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83 { |
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84 DicomArray flattened(tags); |
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85 |
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86 for (size_t i = 0; i < flattened.GetSize(); i++) |
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87 { |
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88 const DicomElement& element = flattened.GetElement(i); |
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89 const DicomTag& tag = element.GetTag(); |
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90 const DicomValue& value = element.GetValue(); |
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91 if (!value.IsNull() && |
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92 !value.IsBinary()) |
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93 { |
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94 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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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 |
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100 static void StoreIdentifiers(ResourcesContent& target, |
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101 int64_t resource, |
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102 ResourceType level, |
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103 const DicomMap& map) |
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104 { |
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105 const DicomTag* tags; |
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106 size_t size; |
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107 |
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108 ServerToolbox::LoadIdentifiers(tags, size, level); |
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109 |
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110 for (size_t i = 0; i < size; i++) |
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111 { |
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112 // The identifiers tags are a subset of the main DICOM tags |
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113 assert(DicomMap::IsMainDicomTag(tags[i])); |
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114 |
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115 const DicomValue* value = map.TestAndGetValue(tags[i]); |
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116 if (value != NULL && |
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117 !value->IsNull() && |
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118 !value->IsBinary()) |
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119 { |
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120 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent()); |
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121 target.AddIdentifierTag(resource, tags[i], s); |
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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 |
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127 void ResourcesContent::AddResource(int64_t resource, |
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128 ResourceType level, |
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129 const DicomMap& dicomSummary) |
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130 { |
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131 StoreIdentifiers(*this, resource, level, dicomSummary); |
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132 |
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133 DicomMap tags; |
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134 |
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135 switch (level) |
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136 { |
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137 case ResourceType_Patient: |
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138 dicomSummary.ExtractPatientInformation(tags); |
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139 break; |
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140 |
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141 case ResourceType_Study: |
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142 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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143 dicomSummary.ExtractPatientInformation(tags); |
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144 StoreMainDicomTagsInternal(*this, resource, tags); |
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145 |
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146 dicomSummary.ExtractStudyInformation(tags); |
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147 break; |
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148 |
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149 case ResourceType_Series: |
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150 dicomSummary.ExtractSeriesInformation(tags); |
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151 break; |
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152 |
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153 case ResourceType_Instance: |
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154 dicomSummary.ExtractInstanceInformation(tags); |
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155 break; |
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156 |
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157 default: |
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158 throw OrthancException(ErrorCode_InternalError); |
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159 } |
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160 |
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161 StoreMainDicomTagsInternal(*this, resource, tags); |
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162 } |
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163 |
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164 |
2120 | 165 namespace ServerToolbox |
213
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166 { |
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167 bool FindOneChildInstance(int64_t& result, |
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168 IDatabaseWrapper& database, |
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169 int64_t resource, |
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170 ResourceType type) |
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171 { |
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172 for (;;) |
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173 { |
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174 if (type == ResourceType_Instance) |
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175 { |
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176 result = resource; |
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177 return true; |
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178 } |
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179 |
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180 std::list<int64_t> children; |
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181 database.GetChildrenInternalId(children, resource); |
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182 if (children.empty()) |
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183 { |
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184 return false; |
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185 } |
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186 |
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187 resource = children.front(); |
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188 type = GetChildResourceType(type); |
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189 } |
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190 } |
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191 |
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192 |
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193 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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194 IStorageArea& storageArea, |
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195 ResourceType level) |
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196 { |
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197 // WARNING: The database should be locked with a transaction! |
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198 |
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199 // TODO: This function might consume much memory if level == |
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200 // ResourceType_Instance. To improve this, first download the |
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201 // list of studies, then remove the instances for each single |
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202 // study (check out OrthancRestApi::InvalidateTags for an |
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203 // example). Take this improvement into consideration for the |
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204 // next upgrade of the database schema. |
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205 |
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206 const char* plural = NULL; |
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207 |
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208 switch (level) |
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209 { |
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210 case ResourceType_Patient: |
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211 plural = "patients"; |
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212 break; |
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213 |
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214 case ResourceType_Study: |
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215 plural = "studies"; |
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216 break; |
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217 |
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218 case ResourceType_Series: |
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219 plural = "series"; |
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220 break; |
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221 |
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222 case ResourceType_Instance: |
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223 plural = "instances"; |
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224 break; |
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225 |
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226 default: |
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227 throw OrthancException(ErrorCode_InternalError); |
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228 } |
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229 |
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230 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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231 |
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232 std::list<std::string> resources; |
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233 database.GetAllPublicIds(resources, level); |
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234 |
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235 for (std::list<std::string>::const_iterator |
1847 | 236 it = resources.begin(); it != resources.end(); ++it) |
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237 { |
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238 // Locate the resource and one of its child instances |
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239 int64_t resource, instance; |
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240 ResourceType tmp; |
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241 |
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242 if (!database.LookupResource(resource, tmp, *it) || |
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243 tmp != level || |
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244 !FindOneChildInstance(instance, database, resource, level)) |
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245 { |
2955 | 246 throw OrthancException(ErrorCode_InternalError, |
247 "Cannot find an instance for " + | |
248 std::string(EnumerationToString(level)) + | |
249 " with identifier " + *it); | |
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250 } |
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251 |
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252 // Get the DICOM file attached to some instances in the resource |
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253 FileInfo attachment; |
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254 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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255 { |
2955 | 256 throw OrthancException(ErrorCode_InternalError, |
257 "Cannot retrieve the DICOM file associated with instance " + | |
258 database.GetPublicId(instance)); | |
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259 } |
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260 |
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261 try |
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262 { |
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263 // Read and parse the content of the DICOM file |
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264 StorageAccessor accessor(storageArea); |
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265 |
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266 std::string content; |
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267 accessor.Read(content, attachment); |
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268 |
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269 ParsedDicomFile dicom(content); |
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270 |
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271 // Update the tags of this resource |
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272 DicomMap dicomSummary; |
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273 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom); |
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274 |
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275 database.ClearMainDicomTags(resource); |
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276 |
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277 ResourcesContent tags; |
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278 tags.AddResource(resource, level, dicomSummary); |
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279 database.SetResourcesContent(tags); |
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280 } |
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281 catch (OrthancException&) |
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282 { |
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283 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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284 << " associated with instance " << database.GetPublicId(instance); |
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285 throw; |
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286 } |
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287 } |
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288 } |
2121 | 289 |
290 | |
291 void LoadIdentifiers(const DicomTag*& tags, | |
292 size_t& size, | |
293 ResourceType level) | |
294 { | |
295 switch (level) | |
296 { | |
297 case ResourceType_Patient: | |
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298 tags = PATIENT_IDENTIFIERS; |
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299 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 300 break; |
301 | |
302 case ResourceType_Study: | |
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303 tags = STUDY_IDENTIFIERS; |
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304 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 305 break; |
306 | |
307 case ResourceType_Series: | |
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308 tags = SERIES_IDENTIFIERS; |
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309 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 310 break; |
311 | |
312 case ResourceType_Instance: | |
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313 tags = INSTANCE_IDENTIFIERS; |
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314 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 315 break; |
316 | |
317 default: | |
318 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
319 } | |
320 } | |
321 | |
322 | |
323 std::string NormalizeIdentifier(const std::string& value) | |
324 { | |
325 std::string t; | |
326 t.reserve(value.size()); | |
327 | |
328 for (size_t i = 0; i < value.size(); i++) | |
329 { | |
330 if (value[i] == '%' || | |
331 value[i] == '_') | |
332 { | |
333 t.push_back(' '); // These characters might break wildcard queries in SQL | |
334 } | |
335 else if (isascii(value[i]) && | |
336 !iscntrl(value[i]) && | |
337 (!isspace(value[i]) || value[i] == ' ')) | |
338 { | |
339 t.push_back(value[i]); | |
340 } | |
341 } | |
342 | |
343 Toolbox::ToUpperCase(t); | |
344 | |
345 return Toolbox::StripSpaces(t); | |
346 } | |
347 | |
348 | |
349 bool IsIdentifier(const DicomTag& tag, | |
350 ResourceType level) | |
351 { | |
352 const DicomTag* tags; | |
353 size_t size; | |
354 | |
355 LoadIdentifiers(tags, size, level); | |
356 | |
357 for (size_t i = 0; i < size; i++) | |
358 { | |
359 if (tag == tags[i]) | |
360 { | |
361 return true; | |
362 } | |
363 } | |
364 | |
365 return false; | |
366 } | |
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367 |
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368 |
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369 void ReconstructResource(ServerContext& context, |
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370 const std::string& resource) |
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371 { |
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372 LOG(WARNING) << "Reconstructing resource " << resource; |
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373 |
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374 std::list<std::string> instances; |
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375 context.GetIndex().GetChildInstances(instances, resource); |
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376 |
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377 for (std::list<std::string>::const_iterator |
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378 it = instances.begin(); it != instances.end(); ++it) |
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379 { |
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380 ServerContext::DicomCacheLocker locker(context, *it); |
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381 |
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382 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext" |
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383 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson); |
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384 |
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385 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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386 } |
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387 } |
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388 } |
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389 } |