Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 1709:2ad22b2970a2 db-changes
SearchableStudies
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 13 Oct 2015 17:48:30 +0200 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * |
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6 * This program is free software: you can redistribute it and/or |
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7 * modify it under the terms of the GNU General Public License as |
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8 * published by the Free Software Foundation, either version 3 of the |
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9 * License, or (at your option) any later version. |
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10 * |
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11 * In addition, as a special exception, the copyright holders of this |
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12 * program give permission to link the code of its release with the |
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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14 * that use the same license as the "OpenSSL" library), and distribute |
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15 * the linked executables. You must obey the GNU General Public License |
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16 * in all respects for all of the code used other than "OpenSSL". If you |
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17 * modify file(s) with this exception, you may extend this exception to |
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18 * your version of the file(s), but you are not obligated to do so. If |
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19 * you do not wish to do so, delete this exception statement from your |
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20 * version. If you delete this exception statement from all source files |
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21 * in the program, then also delete it here. |
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22 * |
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23 * This program is distributed in the hope that it will be useful, but |
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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26 * General Public License for more details. |
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27 * |
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28 * You should have received a copy of the GNU General Public License |
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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30 **/ |
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31 |
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32 |
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33 #include "PrecompiledHeadersServer.h" |
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34 #include "ServerToolbox.h" |
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35 |
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36 #include "../Core/DicomFormat/DicomArray.h" |
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37 #include "../Core/FileStorage/StorageAccessor.h" |
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38 #include "../Core/Logging.h" |
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39 #include "../Core/OrthancException.h" |
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40 #include "ParsedDicomFile.h" |
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41 |
234 | 42 #include <cassert> |
43 | |
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44 namespace Orthanc |
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45 { |
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46 namespace Toolbox |
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47 { |
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48 void SimplifyTags(Json::Value& target, |
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49 const Json::Value& source) |
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50 { |
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51 assert(source.isObject()); |
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52 |
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53 target = Json::objectValue; |
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54 Json::Value::Members members = source.getMemberNames(); |
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55 |
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56 for (size_t i = 0; i < members.size(); i++) |
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57 { |
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58 const Json::Value& v = source[members[i]]; |
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59 const std::string& name = v["Name"].asString(); |
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60 const std::string& type = v["Type"].asString(); |
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61 |
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62 if (type == "String") |
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63 { |
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64 target[name] = v["Value"].asString(); |
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65 } |
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66 else if (type == "TooLong" || |
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67 type == "Null") |
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68 { |
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69 target[name] = Json::nullValue; |
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70 } |
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71 else if (type == "Sequence") |
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72 { |
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73 const Json::Value& array = v["Value"]; |
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74 assert(array.isArray()); |
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75 |
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76 Json::Value children = Json::arrayValue; |
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77 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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78 { |
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79 Json::Value c; |
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80 SimplifyTags(c, array[i]); |
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81 children.append(c); |
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82 } |
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83 |
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84 target[name] = children; |
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85 } |
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86 else |
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87 { |
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88 assert(0); |
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89 } |
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90 } |
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91 } |
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92 |
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93 |
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94 void LogMissingRequiredTag(const DicomMap& summary) |
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95 { |
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96 std::string s, t; |
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97 |
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98 if (summary.HasTag(DICOM_TAG_PATIENT_ID)) |
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99 { |
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100 if (t.size() > 0) |
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101 t += ", "; |
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102 t += "PatientID=" + summary.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
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103 } |
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104 else |
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105 { |
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106 if (s.size() > 0) |
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107 s += ", "; |
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108 s += "PatientID"; |
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109 } |
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110 |
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111 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) |
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112 { |
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113 if (t.size() > 0) |
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114 t += ", "; |
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115 t += "StudyInstanceUID=" + summary.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString(); |
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116 } |
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117 else |
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118 { |
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119 if (s.size() > 0) |
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120 s += ", "; |
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121 s += "StudyInstanceUID"; |
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122 } |
213
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123 |
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124 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) |
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125 { |
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126 if (t.size() > 0) |
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127 t += ", "; |
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128 t += "SeriesInstanceUID=" + summary.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString(); |
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129 } |
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130 else |
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131 { |
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132 if (s.size() > 0) |
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133 s += ", "; |
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134 s += "SeriesInstanceUID"; |
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135 } |
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136 |
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137 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) |
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138 { |
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139 if (t.size() > 0) |
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140 t += ", "; |
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141 t += "SOPInstanceUID=" + summary.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString(); |
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142 } |
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143 else |
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144 { |
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145 if (s.size() > 0) |
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146 s += ", "; |
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147 s += "SOPInstanceUID"; |
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148 } |
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149 |
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150 if (t.size() == 0) |
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151 { |
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152 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; |
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153 } |
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154 else |
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155 { |
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156 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; |
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157 } |
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158 } |
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159 |
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160 |
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161 void SetMainDicomTags(IDatabaseWrapper& database, |
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162 int64_t resource, |
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163 ResourceType level, |
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164 const DicomMap& dicomSummary, |
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165 bool includeIdentifiers) |
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166 { |
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167 // WARNING: The database should be locked with a transaction! |
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168 |
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169 DicomMap tags; |
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170 |
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171 switch (level) |
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172 { |
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173 case ResourceType_Patient: |
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174 dicomSummary.ExtractPatientInformation(tags); |
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175 break; |
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176 |
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177 case ResourceType_Study: |
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178 dicomSummary.ExtractStudyInformation(tags); |
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179 break; |
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180 |
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181 case ResourceType_Series: |
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182 dicomSummary.ExtractSeriesInformation(tags); |
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183 break; |
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184 |
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185 case ResourceType_Instance: |
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186 dicomSummary.ExtractInstanceInformation(tags); |
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187 break; |
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188 |
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189 default: |
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190 throw OrthancException(ErrorCode_InternalError); |
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191 } |
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192 |
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193 DicomArray flattened(tags); |
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194 for (size_t i = 0; i < flattened.GetSize(); i++) |
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195 { |
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196 const DicomElement& element = flattened.GetElement(i); |
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197 |
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198 if (includeIdentifiers || |
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199 !element.GetTag().IsIdentifier()) |
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200 { |
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201 database.SetMainDicomTag(resource, element.GetTag(), element.GetValue().AsString()); |
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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 |
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207 bool FindOneChildInstance(int64_t& result, |
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208 IDatabaseWrapper& database, |
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209 int64_t resource, |
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210 ResourceType type) |
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211 { |
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212 for (;;) |
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213 { |
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214 if (type == ResourceType_Instance) |
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215 { |
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216 result = resource; |
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217 return true; |
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218 } |
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219 |
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220 std::list<int64_t> children; |
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221 database.GetChildrenInternalId(children, resource); |
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222 if (children.empty()) |
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223 { |
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224 return false; |
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225 } |
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226 |
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227 resource = children.front(); |
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228 type = GetChildResourceType(type); |
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229 } |
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230 } |
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231 |
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232 |
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233 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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234 IStorageArea& storageArea, |
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235 ResourceType level) |
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236 { |
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237 // WARNING: The database should be locked with a transaction! |
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238 |
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239 const char* plural = NULL; |
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240 |
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241 switch (level) |
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242 { |
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243 case ResourceType_Patient: |
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244 plural = "patients"; |
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245 break; |
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246 |
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247 case ResourceType_Study: |
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248 plural = "studies"; |
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249 break; |
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250 |
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251 case ResourceType_Series: |
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252 plural = "series"; |
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253 break; |
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254 |
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255 case ResourceType_Instance: |
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256 plural = "instances"; |
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257 break; |
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258 |
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259 default: |
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260 throw OrthancException(ErrorCode_InternalError); |
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261 } |
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262 |
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263 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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264 |
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265 std::list<std::string> resources; |
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266 database.GetAllPublicIds(resources, level); |
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267 |
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268 for (std::list<std::string>::const_iterator |
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269 it = resources.begin(); it != resources.end(); it++) |
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270 { |
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271 // Locate the resource and one of its child instances |
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272 int64_t resource, instance; |
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273 ResourceType tmp; |
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274 |
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275 if (!database.LookupResource(resource, tmp, *it) || |
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276 tmp != level || |
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277 !FindOneChildInstance(instance, database, resource, level)) |
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278 { |
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279 throw OrthancException(ErrorCode_InternalError); |
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280 } |
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281 |
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282 // Get the DICOM file attached to some instances in the resource |
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283 FileInfo attachment; |
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284 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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285 { |
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286 throw OrthancException(ErrorCode_InternalError); |
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287 } |
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288 |
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289 // Read and parse the content of the DICOM file |
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290 StorageAccessor accessor(storageArea); |
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291 |
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292 std::string content; |
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293 accessor.Read(content, attachment); |
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294 |
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295 ParsedDicomFile dicom(content); |
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296 |
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297 // Update the tags of this resource |
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298 DicomMap dicomSummary; |
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299 dicom.Convert(dicomSummary); |
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300 |
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301 database.ClearMainDicomTags(resource); |
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302 |
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303 switch (level) |
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304 { |
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305 case ResourceType_Patient: |
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306 Toolbox::SetMainDicomTags(database, resource, ResourceType_Patient, dicomSummary, true); |
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307 break; |
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308 |
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309 case ResourceType_Study: |
1709 | 310 { |
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311 Toolbox::SetMainDicomTags(database, resource, ResourceType_Study, dicomSummary, true); |
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312 |
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313 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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314 Toolbox::SetMainDicomTags(database, resource, ResourceType_Patient, dicomSummary, false); |
1709 | 315 |
316 DicomMap module; | |
317 Toolbox::ExtractModule(module, dicomSummary, DicomModule_Patient, true /* normalize */); | |
318 Toolbox::ExtractModule(module, dicomSummary, DicomModule_Study, true /* normalize */); | |
319 database.StoreStudyModule(resource, module); | |
320 | |
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321 break; |
1709 | 322 } |
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323 |
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324 case ResourceType_Series: |
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325 Toolbox::SetMainDicomTags(database, resource, ResourceType_Series, dicomSummary, true); |
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326 break; |
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327 |
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328 case ResourceType_Instance: |
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329 Toolbox::SetMainDicomTags(database, resource, ResourceType_Instance, dicomSummary, true); |
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330 break; |
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331 |
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332 default: |
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333 throw OrthancException(ErrorCode_InternalError); |
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334 } |
213
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335 } |
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336 } |
1709 | 337 |
338 | |
339 void ExtractModule(DicomMap& result, // WARNING: Will not be cleared! | |
340 const DicomMap& summary, | |
341 DicomModule module, | |
342 bool normalize) | |
343 { | |
344 typedef std::set<DicomTag> ModuleTags; | |
345 ModuleTags moduleTags; | |
346 DicomTag::AddTagsForModule(moduleTags, module); | |
347 | |
348 for (ModuleTags::const_iterator tag = moduleTags.begin(); tag != moduleTags.end(); ++tag) | |
349 { | |
350 const DicomValue* value = summary.TestAndGetValue(*tag); | |
351 if (value != NULL && | |
352 !value->IsNull()) | |
353 { | |
354 std::string t = value->AsString(); | |
355 | |
356 if (normalize) | |
357 { | |
358 t = StripSpaces(ConvertToAscii(t)); | |
359 ToUpperCase(t); | |
360 } | |
361 | |
362 result.SetValue(*tag, t); | |
363 } | |
364 } | |
365 } | |
213
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366 } |
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367 } |