Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 1811:67466dcd23b1
integration worklists->mainline
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 23 Nov 2015 17:10:11 +0100 |
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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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42 |
234 | 43 #include <cassert> |
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 { |
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52 assert(source.isObject()); |
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53 |
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54 target = Json::objectValue; |
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55 Json::Value::Members members = source.getMemberNames(); |
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56 |
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57 for (size_t i = 0; i < members.size(); i++) |
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58 { |
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59 const Json::Value& v = source[members[i]]; |
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60 const std::string& name = v["Name"].asString(); |
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61 const std::string& type = v["Type"].asString(); |
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62 |
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63 if (type == "String") |
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64 { |
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65 target[name] = v["Value"].asString(); |
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66 } |
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67 else if (type == "TooLong" || |
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68 type == "Null") |
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69 { |
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70 target[name] = Json::nullValue; |
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71 } |
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72 else if (type == "Sequence") |
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73 { |
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74 const Json::Value& array = v["Value"]; |
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75 assert(array.isArray()); |
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76 |
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77 Json::Value children = Json::arrayValue; |
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78 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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79 { |
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80 Json::Value c; |
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81 SimplifyTags(c, array[i]); |
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82 children.append(c); |
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83 } |
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84 |
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85 target[name] = children; |
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86 } |
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87 else |
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88 { |
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89 assert(0); |
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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 |
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95 static std::string ValueAsString(const DicomMap& summary, |
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96 const DicomTag& tag) |
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97 { |
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98 const DicomValue& value = summary.GetValue(tag); |
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99 if (value.IsNull()) |
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100 { |
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101 return "(null)"; |
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102 } |
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103 else |
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104 { |
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105 return value.GetContent(); |
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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 void LogMissingRequiredTag(const DicomMap& summary) |
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111 { |
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112 std::string s, t; |
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113 |
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114 if (summary.HasTag(DICOM_TAG_PATIENT_ID)) |
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115 { |
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116 if (t.size() > 0) |
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117 t += ", "; |
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118 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID); |
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119 } |
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120 else |
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121 { |
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122 if (s.size() > 0) |
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123 s += ", "; |
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124 s += "PatientID"; |
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125 } |
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126 |
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127 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) |
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128 { |
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129 if (t.size() > 0) |
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130 t += ", "; |
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131 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID); |
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132 } |
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133 else |
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134 { |
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135 if (s.size() > 0) |
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136 s += ", "; |
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137 s += "StudyInstanceUID"; |
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138 } |
213
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139 |
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140 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) |
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141 { |
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142 if (t.size() > 0) |
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143 t += ", "; |
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144 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID); |
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145 } |
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146 else |
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147 { |
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148 if (s.size() > 0) |
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149 s += ", "; |
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150 s += "SeriesInstanceUID"; |
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151 } |
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152 |
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153 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) |
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154 { |
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155 if (t.size() > 0) |
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156 t += ", "; |
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157 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID); |
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158 } |
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159 else |
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160 { |
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161 if (s.size() > 0) |
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162 s += ", "; |
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163 s += "SOPInstanceUID"; |
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164 } |
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165 |
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166 if (t.size() == 0) |
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167 { |
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168 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; |
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169 } |
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170 else |
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171 { |
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172 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; |
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173 } |
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174 } |
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175 |
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176 |
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177 static void SetMainDicomTagsInternal(IDatabaseWrapper& database, |
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178 int64_t resource, |
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179 const DicomMap& tags) |
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180 { |
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181 DicomArray flattened(tags); |
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182 |
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183 for (size_t i = 0; i < flattened.GetSize(); i++) |
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184 { |
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185 const DicomElement& element = flattened.GetElement(i); |
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186 const DicomTag& tag = element.GetTag(); |
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187 const DicomValue& value = element.GetValue(); |
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188 if (!value.IsNull() && |
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189 !value.IsBinary()) |
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190 { |
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191 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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192 } |
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193 } |
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194 } |
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195 |
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196 |
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197 void SetMainDicomTags(IDatabaseWrapper& database, |
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198 int64_t resource, |
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199 ResourceType level, |
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200 const DicomMap& dicomSummary) |
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201 { |
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202 // WARNING: The database should be locked with a transaction! |
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203 |
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204 LookupIdentifierQuery::StoreIdentifiers(database, resource, level, dicomSummary); |
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205 |
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206 DicomMap tags; |
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207 |
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208 switch (level) |
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209 { |
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210 case ResourceType_Patient: |
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211 dicomSummary.ExtractPatientInformation(tags); |
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212 break; |
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213 |
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214 case ResourceType_Study: |
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215 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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216 dicomSummary.ExtractPatientInformation(tags); |
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217 SetMainDicomTagsInternal(database, resource, tags); |
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218 |
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219 dicomSummary.ExtractStudyInformation(tags); |
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220 break; |
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221 |
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222 case ResourceType_Series: |
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223 dicomSummary.ExtractSeriesInformation(tags); |
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224 break; |
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225 |
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226 case ResourceType_Instance: |
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227 dicomSummary.ExtractInstanceInformation(tags); |
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228 break; |
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229 |
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230 default: |
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231 throw OrthancException(ErrorCode_InternalError); |
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232 } |
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233 |
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234 SetMainDicomTagsInternal(database, resource, tags); |
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235 } |
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236 |
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237 |
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238 bool FindOneChildInstance(int64_t& result, |
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239 IDatabaseWrapper& database, |
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240 int64_t resource, |
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241 ResourceType type) |
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242 { |
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243 for (;;) |
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244 { |
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245 if (type == ResourceType_Instance) |
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246 { |
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247 result = resource; |
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248 return true; |
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249 } |
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250 |
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251 std::list<int64_t> children; |
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252 database.GetChildrenInternalId(children, resource); |
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253 if (children.empty()) |
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254 { |
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255 return false; |
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256 } |
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257 |
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258 resource = children.front(); |
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259 type = GetChildResourceType(type); |
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260 } |
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261 } |
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262 |
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263 |
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264 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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265 IStorageArea& storageArea, |
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266 ResourceType level) |
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267 { |
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268 // WARNING: The database should be locked with a transaction! |
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269 |
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270 const char* plural = NULL; |
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271 |
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272 switch (level) |
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273 { |
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274 case ResourceType_Patient: |
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275 plural = "patients"; |
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276 break; |
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277 |
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278 case ResourceType_Study: |
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279 plural = "studies"; |
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280 break; |
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281 |
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282 case ResourceType_Series: |
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283 plural = "series"; |
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284 break; |
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285 |
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286 case ResourceType_Instance: |
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287 plural = "instances"; |
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288 break; |
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289 |
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290 default: |
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291 throw OrthancException(ErrorCode_InternalError); |
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292 } |
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293 |
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294 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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295 |
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296 std::list<std::string> resources; |
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297 database.GetAllPublicIds(resources, level); |
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298 |
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299 for (std::list<std::string>::const_iterator |
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300 it = resources.begin(); it != resources.end(); it++) |
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301 { |
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302 // Locate the resource and one of its child instances |
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303 int64_t resource, instance; |
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304 ResourceType tmp; |
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305 |
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306 if (!database.LookupResource(resource, tmp, *it) || |
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307 tmp != level || |
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308 !FindOneChildInstance(instance, database, resource, level)) |
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309 { |
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310 throw OrthancException(ErrorCode_InternalError); |
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311 } |
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312 |
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313 // Get the DICOM file attached to some instances in the resource |
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314 FileInfo attachment; |
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315 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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316 { |
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317 throw OrthancException(ErrorCode_InternalError); |
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318 } |
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319 |
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320 // Read and parse the content of the DICOM file |
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321 StorageAccessor accessor(storageArea); |
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322 |
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323 std::string content; |
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324 accessor.Read(content, attachment); |
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325 |
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326 ParsedDicomFile dicom(content); |
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327 |
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328 // Update the tags of this resource |
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329 DicomMap dicomSummary; |
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330 dicom.Convert(dicomSummary); |
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331 |
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332 database.ClearMainDicomTags(resource); |
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333 Toolbox::SetMainDicomTags(database, resource, level, dicomSummary); |
213
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334 } |
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335 } |
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336 } |
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337 } |