Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 2099:bcbc9137a535
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 07 Oct 2016 11:13:41 +0200 |
parents | b1291df2f780 |
children | 4b02ec79728a |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * |
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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 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); |
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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?)"; |
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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 } |
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208 } |
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209 } |
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210 |
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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, |
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215 const DicomMap& dicomSummary) |
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216 { |
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217 // WARNING: The database should be locked with a transaction! |
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218 |
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219 LookupIdentifierQuery::StoreIdentifiers(database, resource, level, dicomSummary); |
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220 |
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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: |
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226 dicomSummary.ExtractPatientInformation(tags); |
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227 break; |
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228 |
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229 case ResourceType_Study: |
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230 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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231 dicomSummary.ExtractPatientInformation(tags); |
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232 SetMainDicomTagsInternal(database, resource, tags); |
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233 |
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234 dicomSummary.ExtractStudyInformation(tags); |
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235 break; |
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236 |
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237 case ResourceType_Series: |
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238 dicomSummary.ExtractSeriesInformation(tags); |
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239 break; |
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240 |
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241 case ResourceType_Instance: |
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242 dicomSummary.ExtractInstanceInformation(tags); |
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243 break; |
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244 |
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245 default: |
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246 throw OrthancException(ErrorCode_InternalError); |
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247 } |
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248 |
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249 SetMainDicomTagsInternal(database, resource, tags); |
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250 } |
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251 |
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252 |
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253 bool FindOneChildInstance(int64_t& result, |
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254 IDatabaseWrapper& database, |
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255 int64_t resource, |
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256 ResourceType type) |
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257 { |
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258 for (;;) |
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259 { |
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260 if (type == ResourceType_Instance) |
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261 { |
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262 result = resource; |
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263 return true; |
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264 } |
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265 |
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266 std::list<int64_t> children; |
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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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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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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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361 } |
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362 } |
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363 } |
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364 } |