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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4945:6a59dc426f93

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added ParsedDicomFile::DecodeOverlay()
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 20 Mar 2022 11:35:17 +0100
parents 6eff25f70121
children b7ce2bb6b881
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation, either version 3 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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21
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22
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23 #include "PrecompiledHeadersServer.h"
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24 #include "ServerToolbox.h"
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25
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26 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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27 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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28 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h"
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29 #include "../../OrthancFramework/Sources/Logging.h"
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30 #include "../../OrthancFramework/Sources/OrthancException.h"
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31 #include "Database/IDatabaseWrapper.h"
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32 #include "Database/ResourcesContent.h"
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33 #include "OrthancConfiguration.h"
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34 #include "ServerContext.h"
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35
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36 #include <cassert>
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37
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38 namespace Orthanc
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39 {
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40 static const DicomTag PATIENT_IDENTIFIERS[] =
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41 {
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42 DICOM_TAG_PATIENT_ID,
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43 DICOM_TAG_PATIENT_NAME,
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44 DICOM_TAG_PATIENT_BIRTH_DATE
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45 };
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46
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47 static const DicomTag STUDY_IDENTIFIERS[] =
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48 {
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49 DICOM_TAG_PATIENT_ID,
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50 DICOM_TAG_PATIENT_NAME,
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51 DICOM_TAG_PATIENT_BIRTH_DATE,
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52 DICOM_TAG_STUDY_INSTANCE_UID,
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53 DICOM_TAG_ACCESSION_NUMBER,
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54 DICOM_TAG_STUDY_DESCRIPTION,
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55 DICOM_TAG_STUDY_DATE
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56 };
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57
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58 static const DicomTag SERIES_IDENTIFIERS[] =
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59 {
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60 DICOM_TAG_SERIES_INSTANCE_UID
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61 };
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62
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63 static const DicomTag INSTANCE_IDENTIFIERS[] =
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64 {
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65 DICOM_TAG_SOP_INSTANCE_UID
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66 };
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67
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68
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69 namespace ServerToolbox
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70 {
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71 bool FindOneChildInstance(int64_t& result,
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72 IDatabaseWrapper::ITransaction& transaction,
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73 int64_t resource,
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74 ResourceType type)
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75 {
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76 for (;;)
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77 {
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78 if (type == ResourceType_Instance)
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79 {
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80 result = resource;
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81 return true;
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82 }
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83
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84 std::list<int64_t> children;
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85 transaction.GetChildrenInternalId(children, resource);
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86 if (children.empty())
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87 {
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88 return false;
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89 }
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90
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91 resource = children.front();
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92 type = GetChildResourceType(type);
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93 }
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94 }
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95
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96
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97 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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98 IStorageArea& storageArea,
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99 ResourceType level)
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100 {
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101 // WARNING: The database should be locked with a transaction!
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102
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103 // TODO: This function might consume much memory if level ==
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104 // ResourceType_Instance. To improve this, first download the
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105 // list of studies, then remove the instances for each single
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106 // study (check out OrthancRestApi::InvalidateTags for an
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107 // example). Take this improvement into consideration for the
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108 // next upgrade of the database schema.
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109
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110 const char* plural = NULL;
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111
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112 switch (level)
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113 {
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114 case ResourceType_Patient:
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115 plural = "patients";
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116 break;
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117
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118 case ResourceType_Study:
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119 plural = "studies";
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120 break;
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121
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122 case ResourceType_Series:
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123 plural = "series";
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124 break;
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125
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126 case ResourceType_Instance:
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127 plural = "instances";
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128 break;
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129
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130 default:
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131 throw OrthancException(ErrorCode_InternalError);
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132 }
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133
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134 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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135
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136 std::list<std::string> resources;
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137 transaction.GetAllPublicIds(resources, level);
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138
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139 for (std::list<std::string>::const_iterator
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140 it = resources.begin(); it != resources.end(); ++it)
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141 {
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142 // Locate the resource and one of its child instances
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143 int64_t resource, instance;
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144 ResourceType tmp;
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145
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146 if (!transaction.LookupResource(resource, tmp, *it) ||
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147 tmp != level ||
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148 !FindOneChildInstance(instance, transaction, resource, level))
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149 {
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150 throw OrthancException(ErrorCode_InternalError,
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151 "Cannot find an instance for " +
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152 std::string(EnumerationToString(level)) +
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153 " with identifier " + *it);
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154 }
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155
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156 // Get the DICOM file attached to some instances in the resource
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157 FileInfo attachment;
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158 int64_t revision;
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159 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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160 {
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161 throw OrthancException(ErrorCode_InternalError,
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162 "Cannot retrieve the DICOM file associated with instance " +
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163 transaction.GetPublicId(instance));
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164 }
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165
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166 try
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167 {
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168 // Read and parse the content of the DICOM file
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169 StorageCache cache; // we create a temporary cache for this operation (required by the StorageAccessor)
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170 StorageAccessor accessor(storageArea, cache);
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171
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172 std::string content;
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173 accessor.Read(content, attachment);
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174
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175 ParsedDicomFile dicom(content);
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176
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177 // Update the tags of this resource
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178 DicomMap dicomSummary;
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179 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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180
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181 transaction.ClearMainDicomTags(resource);
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182
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183 ResourcesContent tags(false /* prevent the setting of metadata */);
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184 tags.AddResource(resource, level, dicomSummary);
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185 transaction.SetResourcesContent(tags);
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186 }
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187 catch (OrthancException&)
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188 {
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189 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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190 << " associated with instance " << transaction.GetPublicId(instance);
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191 throw;
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192 }
213
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193 }
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194 }
2121
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195
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196
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197 void LoadIdentifiers(const DicomTag*& tags,
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198 size_t& size,
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199 ResourceType level)
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200 {
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201 switch (level)
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202 {
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203 case ResourceType_Patient:
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204 tags = PATIENT_IDENTIFIERS;
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205 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
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206 break;
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207
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208 case ResourceType_Study:
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209 tags = STUDY_IDENTIFIERS;
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210 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
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211 break;
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212
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213 case ResourceType_Series:
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214 tags = SERIES_IDENTIFIERS;
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215 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
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216 break;
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217
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218 case ResourceType_Instance:
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219 tags = INSTANCE_IDENTIFIERS;
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220 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
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221 break;
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222
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223 default:
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224 throw OrthancException(ErrorCode_ParameterOutOfRange);
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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 std::string NormalizeIdentifier(const std::string& value)
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230 {
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231 std::string t;
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232 t.reserve(value.size());
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233
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234 for (size_t i = 0; i < value.size(); i++)
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235 {
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236 if (value[i] == '%' ||
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237 value[i] == '_')
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238 {
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239 t.push_back(' '); // These characters might break wildcard queries in SQL
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240 }
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241 else if (isascii(value[i]) &&
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242 !iscntrl(value[i]) &&
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243 (!isspace(value[i]) || value[i] == ' '))
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244 {
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245 t.push_back(value[i]);
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246 }
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247 }
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248
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249 Toolbox::ToUpperCase(t);
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250
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251 return Toolbox::StripSpaces(t);
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252 }
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253
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254
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255 bool IsIdentifier(const DicomTag& tag,
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256 ResourceType level)
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257 {
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258 const DicomTag* tags;
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259 size_t size;
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260
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261 LoadIdentifiers(tags, size, level);
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262
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263 for (size_t i = 0; i < size; i++)
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264 {
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265 if (tag == tags[i])
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266 {
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267 return true;
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268 }
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269 }
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270
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271 return false;
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272 }
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273
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274
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275 void ReconstructResource(ServerContext& context,
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276 const std::string& resource)
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277 {
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278 LOG(WARNING) << "Reconstructing resource " << resource;
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279
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280 std::list<std::string> instances;
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281 context.GetIndex().GetChildInstances(instances, resource);
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282
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283 for (std::list<std::string>::const_iterator
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284 it = instances.begin(); it != instances.end(); ++it)
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285 {
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286 ServerContext::DicomCacheLocker locker(context, *it);
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287
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288 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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289 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
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290 -1 /* dummy revision */, "" /* dummy MD5 */);
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291
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292 context.GetIndex().ReconstructInstance(locker.GetDicom());
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293 }
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294 }
213
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295 }
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296 }