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annotate OrthancServer/ServerToolbox.cpp @ 1669:a412ad57f0f9 db-changes

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refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 01 Oct 2015 11:55:25 +0200
parents de1413733c97
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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/Logging.h"
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37 #include "../Core/OrthancException.h"
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38 #include "../Core/DicomFormat/DicomArray.h"
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39 #include "ParsedDicomFile.h"
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40
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41 #include <cassert>
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42
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43 namespace Orthanc
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44 {
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45 namespace Toolbox
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46 {
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47 void SimplifyTags(Json::Value& target,
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48 const Json::Value& source)
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49 {
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50 assert(source.isObject());
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51
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52 target = Json::objectValue;
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53 Json::Value::Members members = source.getMemberNames();
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54
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55 for (size_t i = 0; i < members.size(); i++)
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56 {
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57 const Json::Value& v = source[members[i]];
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58 const std::string& name = v["Name"].asString();
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59 const std::string& type = v["Type"].asString();
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60
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61 if (type == "String")
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62 {
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63 target[name] = v["Value"].asString();
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64 }
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65 else if (type == "TooLong" ||
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66 type == "Null")
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67 {
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68 target[name] = Json::nullValue;
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69 }
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70 else if (type == "Sequence")
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71 {
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72 const Json::Value& array = v["Value"];
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73 assert(array.isArray());
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74
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75 Json::Value children = Json::arrayValue;
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76 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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77 {
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78 Json::Value c;
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79 SimplifyTags(c, array[i]);
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80 children.append(c);
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81 }
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82
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83 target[name] = children;
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84 }
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85 else
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86 {
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87 assert(0);
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88 }
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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 void LogMissingRequiredTag(const DicomMap& summary)
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94 {
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95 std::string s, t;
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96
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97 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
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98 {
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99 if (t.size() > 0)
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100 t += ", ";
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101 t += "PatientID=" + summary.GetValue(DICOM_TAG_PATIENT_ID).AsString();
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102 }
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103 else
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104 {
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105 if (s.size() > 0)
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106 s += ", ";
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107 s += "PatientID";
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108 }
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109
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110 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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111 {
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112 if (t.size() > 0)
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113 t += ", ";
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114 t += "StudyInstanceUID=" + summary.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString();
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115 }
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116 else
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117 {
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118 if (s.size() > 0)
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119 s += ", ";
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120 s += "StudyInstanceUID";
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121 }
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122
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123 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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124 {
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125 if (t.size() > 0)
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126 t += ", ";
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127 t += "SeriesInstanceUID=" + summary.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString();
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128 }
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129 else
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130 {
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131 if (s.size() > 0)
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132 s += ", ";
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133 s += "SeriesInstanceUID";
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134 }
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135
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136 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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137 {
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138 if (t.size() > 0)
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139 t += ", ";
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140 t += "SOPInstanceUID=" + summary.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString();
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141 }
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142 else
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143 {
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144 if (s.size() > 0)
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145 s += ", ";
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146 s += "SOPInstanceUID";
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147 }
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148
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149 if (t.size() == 0)
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150 {
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151 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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152 }
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153 else
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154 {
1668
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155 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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156 }
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157 }
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158
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159
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160 void SetMainDicomTags(IDatabaseWrapper& database,
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161 int64_t resource,
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162 ResourceType level,
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163 const DicomMap& dicomSummary,
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164 bool includeIdentifiers)
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165 {
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166 // WARNING: The database should be locked with a transaction!
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167
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168 DicomMap tags;
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169
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170 switch (level)
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171 {
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172 case ResourceType_Patient:
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173 dicomSummary.ExtractPatientInformation(tags);
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174 break;
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175
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176 case ResourceType_Study:
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177 dicomSummary.ExtractStudyInformation(tags);
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178 break;
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179
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180 case ResourceType_Series:
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181 dicomSummary.ExtractSeriesInformation(tags);
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182 break;
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183
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184 case ResourceType_Instance:
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185 dicomSummary.ExtractInstanceInformation(tags);
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186 break;
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187
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188 default:
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189 throw OrthancException(ErrorCode_InternalError);
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190 }
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191
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192 DicomArray flattened(tags);
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193 for (size_t i = 0; i < flattened.GetSize(); i++)
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194 {
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195 const DicomElement& element = flattened.GetElement(i);
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196
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197 if (includeIdentifiers ||
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198 !element.GetTag().IsIdentifier())
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199 {
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200 database.SetMainDicomTag(resource, element.GetTag(), element.GetValue().AsString());
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201 }
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202 }
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203 }
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204
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205
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206 bool FindOneChildInstance(int64_t& result,
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207 IDatabaseWrapper& database,
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208 int64_t resource,
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209 ResourceType type)
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210 {
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211 for (;;)
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212 {
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213 if (type == ResourceType_Instance)
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214 {
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215 result = resource;
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216 return true;
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217 }
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218
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219 std::list<int64_t> children;
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220 database.GetChildrenInternalId(children, resource);
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221 if (children.empty())
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222 {
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223 return false;
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224 }
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225
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226 resource = children.front();
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227 type = GetChildResourceType(type);
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228 }
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229 }
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230
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231
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232 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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233 IStorageArea& storageArea,
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234 ResourceType level)
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235 {
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236 // WARNING: The database should be locked with a transaction!
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237
1669
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238 const char* plural = NULL;
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239
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240 switch (level)
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241 {
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242 case ResourceType_Patient:
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243 plural = "patients";
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244 break;
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245
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246 case ResourceType_Study:
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247 plural = "studies";
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248 break;
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249
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250 case ResourceType_Series:
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251 plural = "series";
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252 break;
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253
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254 case ResourceType_Instance:
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255 plural = "instances";
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256 break;
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diff changeset
257
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diff changeset
258 default:
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259 throw OrthancException(ErrorCode_InternalError);
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260 }
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diff changeset
261
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diff changeset
262 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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diff changeset
263
1668
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diff changeset
264 std::list<std::string> resources;
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265 database.GetAllPublicIds(resources, level);
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266
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267 for (std::list<std::string>::const_iterator
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268 it = resources.begin(); it != resources.end(); it++)
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269 {
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270 // Locate the resource and one of its child instances
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271 int64_t resource, instance;
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272 ResourceType tmp;
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273
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diff changeset
274 if (!database.LookupResource(resource, tmp, *it) ||
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275 tmp != level ||
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276 !FindOneChildInstance(instance, database, resource, level))
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277 {
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278 throw OrthancException(ErrorCode_InternalError);
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279 }
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280
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281 // Get the DICOM file attached to some instances in the resource
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282 FileInfo attachment;
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283 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
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284 {
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285 throw OrthancException(ErrorCode_InternalError);
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286 }
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287
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288 // Read and parse the content of the DICOM file
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289 std::string content;
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290 storageArea.Read(content, attachment.GetUuid(), FileContentType_Dicom);
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291
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292 ParsedDicomFile dicom(content);
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293
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294 // Update the tags of this resource
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295 DicomMap dicomSummary;
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296 dicom.Convert(dicomSummary);
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297
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298 database.ClearMainDicomTags(resource);
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299
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300 switch (level)
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301 {
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302 case ResourceType_Patient:
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303 Toolbox::SetMainDicomTags(database, resource, ResourceType_Patient, dicomSummary, true);
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304 break;
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305
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306 case ResourceType_Study:
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307 Toolbox::SetMainDicomTags(database, resource, ResourceType_Study, dicomSummary, true);
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308
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309 // Duplicate the patient tags at the study level
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310 Toolbox::SetMainDicomTags(database, resource, ResourceType_Patient, dicomSummary, false);
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311 break;
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312
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313 case ResourceType_Series:
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314 Toolbox::SetMainDicomTags(database, resource, ResourceType_Series, dicomSummary, true);
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315 break;
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316
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317 case ResourceType_Instance:
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318 Toolbox::SetMainDicomTags(database, resource, ResourceType_Instance, dicomSummary, true);
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319 break;
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320
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321 default:
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322 throw OrthancException(ErrorCode_InternalError);
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323 }
213
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324 }
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325 }
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326 }
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327 }