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annotate OrthancServer/ServerToolbox.cpp @ 2084:20a001ea4aa2

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Image::Clone()
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 09 Sep 2016 12:09:04 +0200
parents b1291df2f780
children 4b02ec79728a
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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 *
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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 #include "Search/LookupIdentifierQuery.h"
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42
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43 #include <cassert>
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44
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45 namespace Orthanc
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46 {
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47 namespace Toolbox
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48 {
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49 void SimplifyTags(Json::Value& target,
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50 const Json::Value& source,
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51 DicomToJsonFormat format)
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52 {
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53 assert(source.isObject());
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54
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55 target = Json::objectValue;
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56 Json::Value::Members members = source.getMemberNames();
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57
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58 for (size_t i = 0; i < members.size(); i++)
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59 {
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60 const Json::Value& v = source[members[i]];
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61 const std::string& type = v["Type"].asString();
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62
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63 std::string name;
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64 switch (format)
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65 {
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66 case DicomToJsonFormat_Human:
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67 name = v["Name"].asString();
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68 break;
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69
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70 case DicomToJsonFormat_Short:
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71 name = members[i];
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72 break;
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73
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74 default:
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75 throw OrthancException(ErrorCode_ParameterOutOfRange);
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76 }
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77
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78 if (type == "String")
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79 {
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80 target[name] = v["Value"].asString();
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81 }
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82 else if (type == "TooLong" ||
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83 type == "Null")
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84 {
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85 target[name] = Json::nullValue;
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86 }
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87 else if (type == "Sequence")
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88 {
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89 const Json::Value& array = v["Value"];
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90 assert(array.isArray());
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91
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92 Json::Value children = Json::arrayValue;
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93 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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94 {
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95 Json::Value c;
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96 SimplifyTags(c, array[i], format);
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97 children.append(c);
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98 }
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99
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100 target[name] = children;
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101 }
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102 else
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103 {
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104 assert(0);
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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
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110 static std::string ValueAsString(const DicomMap& summary,
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111 const DicomTag& tag)
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112 {
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113 const DicomValue& value = summary.GetValue(tag);
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114 if (value.IsNull())
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115 {
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116 return "(null)";
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117 }
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118 else
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119 {
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120 return value.GetContent();
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121 }
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122 }
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123
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124
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125 void LogMissingRequiredTag(const DicomMap& summary)
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126 {
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127 std::string s, t;
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128
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129 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
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130 {
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131 if (t.size() > 0)
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132 t += ", ";
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133 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID);
213
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134 }
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135 else
213
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136 {
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137 if (s.size() > 0)
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138 s += ", ";
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139 s += "PatientID";
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140 }
213
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141
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142 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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143 {
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144 if (t.size() > 0)
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145 t += ", ";
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146 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID);
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147 }
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148 else
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149 {
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150 if (s.size() > 0)
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151 s += ", ";
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152 s += "StudyInstanceUID";
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153 }
213
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154
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155 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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156 {
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157 if (t.size() > 0)
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158 t += ", ";
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159 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID);
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160 }
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161 else
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162 {
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163 if (s.size() > 0)
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164 s += ", ";
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165 s += "SeriesInstanceUID";
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166 }
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167
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168 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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169 {
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170 if (t.size() > 0)
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171 t += ", ";
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172 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID);
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173 }
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174 else
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175 {
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176 if (s.size() > 0)
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177 s += ", ";
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178 s += "SOPInstanceUID";
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179 }
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180
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181 if (t.size() == 0)
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182 {
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183 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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184 }
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185 else
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186 {
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187 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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188 }
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189 }
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190
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191
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192 static void SetMainDicomTagsInternal(IDatabaseWrapper& database,
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193 int64_t resource,
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194 const DicomMap& tags)
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195 {
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196 DicomArray flattened(tags);
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197
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198 for (size_t i = 0; i < flattened.GetSize(); i++)
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199 {
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200 const DicomElement& element = flattened.GetElement(i);
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201 const DicomTag& tag = element.GetTag();
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202 const DicomValue& value = element.GetValue();
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203 if (!value.IsNull() &&
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204 !value.IsBinary())
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205 {
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206 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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207 }
1716
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208 }
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209 }
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210
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diff changeset
211
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212 void SetMainDicomTags(IDatabaseWrapper& database,
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213 int64_t resource,
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214 ResourceType level,
1716
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diff changeset
215 const DicomMap& dicomSummary)
1668
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216 {
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diff changeset
217 // WARNING: The database should be locked with a transaction!
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diff changeset
218
1745
38dda23c7d7d LookupIdentifierQuery
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diff changeset
219 LookupIdentifierQuery::StoreIdentifiers(database, resource, level, dicomSummary);
38dda23c7d7d LookupIdentifierQuery
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220
1668
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221 DicomMap tags;
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222
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223 switch (level)
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224 {
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225 case ResourceType_Patient:
1745
38dda23c7d7d LookupIdentifierQuery
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226 dicomSummary.ExtractPatientInformation(tags);
1668
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227 break;
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228
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229 case ResourceType_Study:
1717
3926e6317a43 SetIdentifierTagInternal
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diff changeset
230 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
1745
38dda23c7d7d LookupIdentifierQuery
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diff changeset
231 dicomSummary.ExtractPatientInformation(tags);
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diff changeset
232 SetMainDicomTagsInternal(database, resource, tags);
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diff changeset
233
1668
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234 dicomSummary.ExtractStudyInformation(tags);
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diff changeset
235 break;
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236
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diff changeset
237 case ResourceType_Series:
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238 dicomSummary.ExtractSeriesInformation(tags);
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diff changeset
239 break;
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240
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diff changeset
241 case ResourceType_Instance:
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242 dicomSummary.ExtractInstanceInformation(tags);
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diff changeset
243 break;
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diff changeset
244
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diff changeset
245 default:
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246 throw OrthancException(ErrorCode_InternalError);
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247 }
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diff changeset
248
1716
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diff changeset
249 SetMainDicomTagsInternal(database, resource, tags);
1668
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250 }
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251
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252
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diff changeset
253 bool FindOneChildInstance(int64_t& result,
de1413733c97 reconstructing main dicom tags
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diff changeset
254 IDatabaseWrapper& database,
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diff changeset
255 int64_t resource,
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diff changeset
256 ResourceType type)
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257 {
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diff changeset
258 for (;;)
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259 {
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diff changeset
260 if (type == ResourceType_Instance)
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diff changeset
261 {
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diff changeset
262 result = resource;
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263 return true;
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diff changeset
264 }
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265
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266 std::list<int64_t> children;
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diff changeset
267 database.GetChildrenInternalId(children, resource);
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268 if (children.empty())
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269 {
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270 return false;
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diff changeset
271 }
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272
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273 resource = children.front();
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274 type = GetChildResourceType(type);
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275 }
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276 }
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277
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278
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279 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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280 IStorageArea& storageArea,
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281 ResourceType level)
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282 {
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283 // WARNING: The database should be locked with a transaction!
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284
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285 const char* plural = NULL;
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286
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287 switch (level)
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288 {
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289 case ResourceType_Patient:
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290 plural = "patients";
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291 break;
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292
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293 case ResourceType_Study:
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294 plural = "studies";
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295 break;
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296
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297 case ResourceType_Series:
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298 plural = "series";
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299 break;
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300
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301 case ResourceType_Instance:
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302 plural = "instances";
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303 break;
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304
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305 default:
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306 throw OrthancException(ErrorCode_InternalError);
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307 }
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308
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309 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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310
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311 std::list<std::string> resources;
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312 database.GetAllPublicIds(resources, level);
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313
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314 for (std::list<std::string>::const_iterator
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315 it = resources.begin(); it != resources.end(); ++it)
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316 {
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317 // Locate the resource and one of its child instances
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318 int64_t resource, instance;
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319 ResourceType tmp;
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320
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321 if (!database.LookupResource(resource, tmp, *it) ||
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322 tmp != level ||
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323 !FindOneChildInstance(instance, database, resource, level))
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324 {
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325 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level)
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326 << " with identifier " << *it;
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327 throw OrthancException(ErrorCode_InternalError);
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328 }
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329
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330 // Get the DICOM file attached to some instances in the resource
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331 FileInfo attachment;
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332 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
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333 {
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334 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance);
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335 throw OrthancException(ErrorCode_InternalError);
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336 }
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337
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338 try
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339 {
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340 // Read and parse the content of the DICOM file
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341 StorageAccessor accessor(storageArea);
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342
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343 std::string content;
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344 accessor.Read(content, attachment);
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345
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346 ParsedDicomFile dicom(content);
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347
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348 // Update the tags of this resource
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349 DicomMap dicomSummary;
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350 dicom.Convert(dicomSummary);
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351
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352 database.ClearMainDicomTags(resource);
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353 Toolbox::SetMainDicomTags(database, resource, level, dicomSummary);
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354 }
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355 catch (OrthancException&)
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356 {
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357 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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358 << " associated with instance " << database.GetPublicId(instance);
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359 throw;
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360 }
213
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parents:
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361 }
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parents:
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362 }
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parents:
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363 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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364 }