Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerToolbox.cpp @ 4872:b1556cefa5c6
reimplementation from scratch of ImageProcessing::FillPolygon()
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 17 Jan 2022 21:11:40 +0100 |
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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) 2017-2022 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 * In addition, as a special exception, the copyright holders of this |
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14 * program give permission to link the code of its release with the |
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15 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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16 * that use the same license as the "OpenSSL" library), and distribute |
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17 * the linked executables. You must obey the GNU General Public License |
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18 * in all respects for all of the code used other than "OpenSSL". If you |
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19 * modify file(s) with this exception, you may extend this exception to |
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20 * your version of the file(s), but you are not obligated to do so. If |
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21 * you do not wish to do so, delete this exception statement from your |
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22 * version. If you delete this exception statement from all source files |
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23 * in the program, then also delete it here. |
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24 * |
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25 * This program is distributed in the hope that it will be useful, but |
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26 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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27 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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28 * General Public License for more details. |
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29 * |
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30 * You should have received a copy of the GNU General Public License |
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31 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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32 **/ |
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33 |
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34 |
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35 #include "PrecompiledHeadersServer.h" |
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36 #include "ServerToolbox.h" |
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37 |
4045 | 38 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h" |
39 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h" | |
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40 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h" |
4045 | 41 #include "../../OrthancFramework/Sources/Logging.h" |
42 #include "../../OrthancFramework/Sources/OrthancException.h" | |
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43 #include "Database/IDatabaseWrapper.h" |
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44 #include "Database/ResourcesContent.h" |
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45 #include "OrthancConfiguration.h" |
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46 #include "ServerContext.h" |
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47 |
234 | 48 #include <cassert> |
49 | |
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50 namespace Orthanc |
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51 { |
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52 static const DicomTag PATIENT_IDENTIFIERS[] = |
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53 { |
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54 DICOM_TAG_PATIENT_ID, |
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55 DICOM_TAG_PATIENT_NAME, |
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56 DICOM_TAG_PATIENT_BIRTH_DATE |
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57 }; |
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58 |
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59 static const DicomTag STUDY_IDENTIFIERS[] = |
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60 { |
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61 DICOM_TAG_PATIENT_ID, |
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62 DICOM_TAG_PATIENT_NAME, |
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63 DICOM_TAG_PATIENT_BIRTH_DATE, |
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64 DICOM_TAG_STUDY_INSTANCE_UID, |
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65 DICOM_TAG_ACCESSION_NUMBER, |
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66 DICOM_TAG_STUDY_DESCRIPTION, |
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67 DICOM_TAG_STUDY_DATE |
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68 }; |
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69 |
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70 static const DicomTag SERIES_IDENTIFIERS[] = |
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71 { |
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72 DICOM_TAG_SERIES_INSTANCE_UID |
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73 }; |
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74 |
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75 static const DicomTag INSTANCE_IDENTIFIERS[] = |
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76 { |
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77 DICOM_TAG_SOP_INSTANCE_UID |
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78 }; |
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79 |
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80 |
2120 | 81 namespace ServerToolbox |
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82 { |
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83 bool FindOneChildInstance(int64_t& result, |
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84 IDatabaseWrapper::ITransaction& transaction, |
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85 int64_t resource, |
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86 ResourceType type) |
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87 { |
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88 for (;;) |
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89 { |
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90 if (type == ResourceType_Instance) |
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91 { |
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92 result = resource; |
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93 return true; |
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94 } |
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95 |
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96 std::list<int64_t> children; |
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97 transaction.GetChildrenInternalId(children, resource); |
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98 if (children.empty()) |
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99 { |
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100 return false; |
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101 } |
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102 |
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103 resource = children.front(); |
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104 type = GetChildResourceType(type); |
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105 } |
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106 } |
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107 |
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108 |
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109 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction, |
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110 IStorageArea& storageArea, |
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111 ResourceType level) |
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112 { |
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113 // WARNING: The database should be locked with a transaction! |
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114 |
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115 // TODO: This function might consume much memory if level == |
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116 // ResourceType_Instance. To improve this, first download the |
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117 // list of studies, then remove the instances for each single |
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118 // study (check out OrthancRestApi::InvalidateTags for an |
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119 // example). Take this improvement into consideration for the |
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120 // next upgrade of the database schema. |
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121 |
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122 const char* plural = NULL; |
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123 |
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124 switch (level) |
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125 { |
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126 case ResourceType_Patient: |
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127 plural = "patients"; |
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128 break; |
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129 |
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130 case ResourceType_Study: |
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131 plural = "studies"; |
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132 break; |
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133 |
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134 case ResourceType_Series: |
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135 plural = "series"; |
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136 break; |
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137 |
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138 case ResourceType_Instance: |
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139 plural = "instances"; |
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140 break; |
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141 |
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142 default: |
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143 throw OrthancException(ErrorCode_InternalError); |
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144 } |
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145 |
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146 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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147 |
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148 std::list<std::string> resources; |
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149 transaction.GetAllPublicIds(resources, level); |
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150 |
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151 for (std::list<std::string>::const_iterator |
1847 | 152 it = resources.begin(); it != resources.end(); ++it) |
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153 { |
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154 // Locate the resource and one of its child instances |
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155 int64_t resource, instance; |
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156 ResourceType tmp; |
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157 |
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158 if (!transaction.LookupResource(resource, tmp, *it) || |
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159 tmp != level || |
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160 !FindOneChildInstance(instance, transaction, resource, level)) |
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161 { |
2955 | 162 throw OrthancException(ErrorCode_InternalError, |
163 "Cannot find an instance for " + | |
164 std::string(EnumerationToString(level)) + | |
165 " with identifier " + *it); | |
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166 } |
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167 |
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168 // Get the DICOM file attached to some instances in the resource |
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169 FileInfo attachment; |
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170 int64_t revision; |
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171 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom)) |
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172 { |
2955 | 173 throw OrthancException(ErrorCode_InternalError, |
174 "Cannot retrieve the DICOM file associated with instance " + | |
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175 transaction.GetPublicId(instance)); |
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176 } |
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177 |
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178 try |
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179 { |
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180 // Read and parse the content of the DICOM file |
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181 StorageCache cache; // we create a temporary cache for this operation (required by the StorageAccessor) |
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182 StorageAccessor accessor(storageArea, cache); |
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183 |
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184 std::string content; |
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185 accessor.Read(content, attachment); |
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186 |
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187 ParsedDicomFile dicom(content); |
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188 |
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189 // Update the tags of this resource |
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190 DicomMap dicomSummary; |
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191 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom); |
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192 |
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193 transaction.ClearMainDicomTags(resource); |
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194 |
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195 ResourcesContent tags(false /* prevent the setting of metadata */); |
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196 tags.AddResource(resource, level, dicomSummary); |
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197 transaction.SetResourcesContent(tags); |
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198 } |
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199 catch (OrthancException&) |
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200 { |
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201 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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202 << " associated with instance " << transaction.GetPublicId(instance); |
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203 throw; |
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204 } |
213
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205 } |
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206 } |
2121 | 207 |
208 | |
209 void LoadIdentifiers(const DicomTag*& tags, | |
210 size_t& size, | |
211 ResourceType level) | |
212 { | |
213 switch (level) | |
214 { | |
215 case ResourceType_Patient: | |
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216 tags = PATIENT_IDENTIFIERS; |
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217 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 218 break; |
219 | |
220 case ResourceType_Study: | |
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221 tags = STUDY_IDENTIFIERS; |
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222 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 223 break; |
224 | |
225 case ResourceType_Series: | |
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226 tags = SERIES_IDENTIFIERS; |
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227 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 228 break; |
229 | |
230 case ResourceType_Instance: | |
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231 tags = INSTANCE_IDENTIFIERS; |
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232 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 233 break; |
234 | |
235 default: | |
236 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
237 } | |
238 } | |
239 | |
240 | |
241 std::string NormalizeIdentifier(const std::string& value) | |
242 { | |
243 std::string t; | |
244 t.reserve(value.size()); | |
245 | |
246 for (size_t i = 0; i < value.size(); i++) | |
247 { | |
248 if (value[i] == '%' || | |
249 value[i] == '_') | |
250 { | |
251 t.push_back(' '); // These characters might break wildcard queries in SQL | |
252 } | |
253 else if (isascii(value[i]) && | |
254 !iscntrl(value[i]) && | |
255 (!isspace(value[i]) || value[i] == ' ')) | |
256 { | |
257 t.push_back(value[i]); | |
258 } | |
259 } | |
260 | |
261 Toolbox::ToUpperCase(t); | |
262 | |
263 return Toolbox::StripSpaces(t); | |
264 } | |
265 | |
266 | |
267 bool IsIdentifier(const DicomTag& tag, | |
268 ResourceType level) | |
269 { | |
270 const DicomTag* tags; | |
271 size_t size; | |
272 | |
273 LoadIdentifiers(tags, size, level); | |
274 | |
275 for (size_t i = 0; i < size; i++) | |
276 { | |
277 if (tag == tags[i]) | |
278 { | |
279 return true; | |
280 } | |
281 } | |
282 | |
283 return false; | |
284 } | |
2209
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285 |
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286 |
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287 void ReconstructResource(ServerContext& context, |
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288 const std::string& resource) |
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289 { |
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290 LOG(WARNING) << "Reconstructing resource " << resource; |
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291 |
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292 std::list<std::string> instances; |
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293 context.GetIndex().GetChildInstances(instances, resource); |
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294 |
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295 for (std::list<std::string>::const_iterator |
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296 it = instances.begin(); it != instances.end(); ++it) |
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297 { |
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298 ServerContext::DicomCacheLocker locker(context, *it); |
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299 |
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300 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext" |
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301 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */, |
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302 -1 /* dummy revision */, "" /* dummy MD5 */); |
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303 |
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304 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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305 } |
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306 } |
213
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307 } |
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308 } |