Mercurial > hg > orthanc

annotate OrthancServer/ServerToolbox.cpp @ 1716:2ca7888f8600 db-changes

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refactoring DicomIdentifiers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 17 Oct 2015 12:16:27 +0200
parents 4db9200c7f46
children 3926e6317a43
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "PrecompiledHeadersServer.h"
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34 #include "ServerToolbox.h"
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35
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36 #include "../Core/DicomFormat/DicomArray.h"
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37 #include "../Core/FileStorage/StorageAccessor.h"
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38 #include "../Core/Logging.h"
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39 #include "../Core/OrthancException.h"
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40 #include "ParsedDicomFile.h"
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41
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42 #include <cassert>
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43
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44 namespace Orthanc
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45 {
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46 namespace Toolbox
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47 {
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48 void SimplifyTags(Json::Value& target,
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49 const Json::Value& source)
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50 {
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51 assert(source.isObject());
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52
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53 target = Json::objectValue;
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54 Json::Value::Members members = source.getMemberNames();
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55
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56 for (size_t i = 0; i < members.size(); i++)
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57 {
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58 const Json::Value& v = source[members[i]];
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59 const std::string& name = v["Name"].asString();
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60 const std::string& type = v["Type"].asString();
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61
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62 if (type == "String")
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63 {
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64 target[name] = v["Value"].asString();
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65 }
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66 else if (type == "TooLong" ||
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67 type == "Null")
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68 {
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69 target[name] = Json::nullValue;
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70 }
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71 else if (type == "Sequence")
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72 {
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73 const Json::Value& array = v["Value"];
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74 assert(array.isArray());
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75
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76 Json::Value children = Json::arrayValue;
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77 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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78 {
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79 Json::Value c;
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80 SimplifyTags(c, array[i]);
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81 children.append(c);
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82 }
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83
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84 target[name] = children;
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85 }
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86 else
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87 {
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88 assert(0);
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89 }
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90 }
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91 }
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92
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93
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94 void LogMissingRequiredTag(const DicomMap& summary)
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95 {
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96 std::string s, t;
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97
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98 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
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99 {
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100 if (t.size() > 0)
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101 t += ", ";
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102 t += "PatientID=" + summary.GetValue(DICOM_TAG_PATIENT_ID).AsString();
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103 }
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104 else
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105 {
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106 if (s.size() > 0)
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107 s += ", ";
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108 s += "PatientID";
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109 }
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110
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111 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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112 {
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113 if (t.size() > 0)
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114 t += ", ";
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115 t += "StudyInstanceUID=" + summary.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString();
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116 }
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117 else
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118 {
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119 if (s.size() > 0)
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120 s += ", ";
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121 s += "StudyInstanceUID";
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122 }
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123
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124 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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125 {
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126 if (t.size() > 0)
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127 t += ", ";
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128 t += "SeriesInstanceUID=" + summary.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString();
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129 }
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130 else
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131 {
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132 if (s.size() > 0)
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133 s += ", ";
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134 s += "SeriesInstanceUID";
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135 }
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136
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137 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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138 {
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139 if (t.size() > 0)
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140 t += ", ";
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141 t += "SOPInstanceUID=" + summary.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString();
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142 }
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143 else
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144 {
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145 if (s.size() > 0)
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146 s += ", ";
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147 s += "SOPInstanceUID";
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148 }
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149
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150 if (t.size() == 0)
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151 {
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152 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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153 }
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154 else
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155 {
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156 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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157 }
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158 }
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159
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160
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161 static void SetMainDicomTagsInternal(IDatabaseWrapper& database,
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162 int64_t resource,
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163 const DicomMap& tags)
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164 {
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165 DicomArray flattened(tags);
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166
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167 for (size_t i = 0; i < flattened.GetSize(); i++)
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168 {
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169 const DicomElement& element = flattened.GetElement(i);
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170 const DicomTag& tag = element.GetTag();
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171 database.SetMainDicomTag(resource, tag, element.GetValue().AsString());
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172 }
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173 }
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174
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175
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176 static void SetIdentifierTagInternal(IDatabaseWrapper& database,
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177 int64_t resource,
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178 const DicomMap& tags,
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179 const DicomTag& tag)
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180 {
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181 const DicomValue* value = tags.TestAndGetValue(tag);
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182 if (value != NULL &&
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183 !value->IsNull())
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184 {
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185 database.SetIdentifierTag(resource, tag, value->AsString());
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186 }
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187 }
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188
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189
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190 void SetMainDicomTags(IDatabaseWrapper& database,
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191 int64_t resource,
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192 ResourceType level,
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193 const DicomMap& dicomSummary)
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194 {
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195 // WARNING: The database should be locked with a transaction!
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196
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197 DicomMap tags;
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198
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199 switch (level)
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200 {
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201 case ResourceType_Patient:
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202 dicomSummary.ExtractPatientInformation(tags);
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203 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_ID);
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204 break;
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205
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206 case ResourceType_Study:
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207 dicomSummary.ExtractStudyInformation(tags);
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208 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_INSTANCE_UID);
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209 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_DESCRIPTION); // ???
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210 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_DATE); // ???
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211 break;
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212
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213 case ResourceType_Series:
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214 dicomSummary.ExtractSeriesInformation(tags);
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215 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_SERIES_INSTANCE_UID);
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216 break;
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217
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218 case ResourceType_Instance:
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219 dicomSummary.ExtractInstanceInformation(tags);
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220 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_SOP_INSTANCE_UID);
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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_InternalError);
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225 }
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226
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227 SetMainDicomTagsInternal(database, resource, tags);
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228
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229 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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230 if (level == ResourceType_Study)
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231 {
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232 dicomSummary.ExtractPatientInformation(tags);
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233 SetMainDicomTagsInternal(database, resource, tags);
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234 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_NAME); // ???
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235 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_BIRTH_DATE); // ???
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236 }
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237 }
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238
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239
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240 bool FindOneChildInstance(int64_t& result,
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241 IDatabaseWrapper& database,
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242 int64_t resource,
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243 ResourceType type)
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244 {
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245 for (;;)
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246 {
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247 if (type == ResourceType_Instance)
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248 {
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249 result = resource;
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250 return true;
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251 }
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252
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253 std::list<int64_t> children;
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254 database.GetChildrenInternalId(children, resource);
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255 if (children.empty())
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256 {
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257 return false;
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258 }
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259
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260 resource = children.front();
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261 type = GetChildResourceType(type);
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262 }
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263 }
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264
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265
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266 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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267 IStorageArea& storageArea,
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268 ResourceType level)
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269 {
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270 // WARNING: The database should be locked with a transaction!
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271
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272 const char* plural = NULL;
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273
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274 switch (level)
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275 {
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276 case ResourceType_Patient:
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277 plural = "patients";
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278 break;
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279
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280 case ResourceType_Study:
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281 plural = "studies";
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282 break;
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283
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284 case ResourceType_Series:
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285 plural = "series";
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286 break;
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287
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288 case ResourceType_Instance:
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289 plural = "instances";
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290 break;
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291
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292 default:
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293 throw OrthancException(ErrorCode_InternalError);
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294 }
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295
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296 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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297
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298 std::list<std::string> resources;
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299 database.GetAllPublicIds(resources, level);
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300
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301 for (std::list<std::string>::const_iterator
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302 it = resources.begin(); it != resources.end(); it++)
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303 {
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304 // Locate the resource and one of its child instances
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305 int64_t resource, instance;
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306 ResourceType tmp;
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307
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308 if (!database.LookupResource(resource, tmp, *it) ||
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309 tmp != level ||
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310 !FindOneChildInstance(instance, database, resource, level))
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311 {
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312 throw OrthancException(ErrorCode_InternalError);
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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 {
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319 throw OrthancException(ErrorCode_InternalError);
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320 }
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321
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322 // Read and parse the content of the DICOM file
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323 StorageAccessor accessor(storageArea);
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324
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325 std::string content;
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326 accessor.Read(content, attachment);
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327
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328 ParsedDicomFile dicom(content);
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329
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330 // Update the tags of this resource
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331 DicomMap dicomSummary;
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332 dicom.Convert(dicomSummary);
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333
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334 database.ClearMainDicomTags(resource);
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335 Toolbox::SetMainDicomTags(database, resource, level, dicomSummary);
213
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336 }
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337 }
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338 }
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339 }