Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 2121:7e8889bc95c6
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 07 Nov 2016 11:28:12 +0100 |
parents | 4b02ec79728a |
children | 2ecc95a239f7 |
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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" |
1747 | 41 #include "Search/LookupIdentifierQuery.h" |
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42 |
234 | 43 #include <cassert> |
44 | |
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45 namespace Orthanc |
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46 { |
2120 | 47 namespace ServerToolbox |
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48 { |
2121 | 49 static const DicomTag patientIdentifiers[] = |
50 { | |
51 DICOM_TAG_PATIENT_ID, | |
52 DICOM_TAG_PATIENT_NAME, | |
53 DICOM_TAG_PATIENT_BIRTH_DATE | |
54 }; | |
55 | |
56 static const DicomTag studyIdentifiers[] = | |
57 { | |
58 DICOM_TAG_PATIENT_ID, | |
59 DICOM_TAG_PATIENT_NAME, | |
60 DICOM_TAG_PATIENT_BIRTH_DATE, | |
61 DICOM_TAG_STUDY_INSTANCE_UID, | |
62 DICOM_TAG_ACCESSION_NUMBER, | |
63 DICOM_TAG_STUDY_DESCRIPTION, | |
64 DICOM_TAG_STUDY_DATE | |
65 }; | |
66 | |
67 static const DicomTag seriesIdentifiers[] = | |
68 { | |
69 DICOM_TAG_SERIES_INSTANCE_UID | |
70 }; | |
71 | |
72 static const DicomTag instanceIdentifiers[] = | |
73 { | |
74 DICOM_TAG_SOP_INSTANCE_UID | |
75 }; | |
76 | |
77 | |
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78 void SimplifyTags(Json::Value& target, |
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79 const Json::Value& source, |
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80 DicomToJsonFormat format) |
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81 { |
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82 assert(source.isObject()); |
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83 |
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84 target = Json::objectValue; |
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85 Json::Value::Members members = source.getMemberNames(); |
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86 |
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87 for (size_t i = 0; i < members.size(); i++) |
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88 { |
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89 const Json::Value& v = source[members[i]]; |
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90 const std::string& type = v["Type"].asString(); |
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91 |
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92 std::string name; |
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93 switch (format) |
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94 { |
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95 case DicomToJsonFormat_Human: |
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96 name = v["Name"].asString(); |
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97 break; |
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98 |
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99 case DicomToJsonFormat_Short: |
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100 name = members[i]; |
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101 break; |
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102 |
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103 default: |
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104 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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105 } |
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106 |
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107 if (type == "String") |
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108 { |
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109 target[name] = v["Value"].asString(); |
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110 } |
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111 else if (type == "TooLong" || |
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112 type == "Null") |
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113 { |
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114 target[name] = Json::nullValue; |
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115 } |
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116 else if (type == "Sequence") |
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117 { |
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118 const Json::Value& array = v["Value"]; |
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119 assert(array.isArray()); |
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120 |
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121 Json::Value children = Json::arrayValue; |
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122 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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123 { |
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124 Json::Value c; |
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125 SimplifyTags(c, array[i], format); |
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126 children.append(c); |
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127 } |
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128 |
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129 target[name] = children; |
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130 } |
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131 else |
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132 { |
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133 assert(0); |
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134 } |
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135 } |
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136 } |
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137 |
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138 |
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139 static std::string ValueAsString(const DicomMap& summary, |
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140 const DicomTag& tag) |
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141 { |
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142 const DicomValue& value = summary.GetValue(tag); |
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143 if (value.IsNull()) |
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144 { |
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145 return "(null)"; |
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146 } |
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147 else |
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148 { |
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149 return value.GetContent(); |
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150 } |
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151 } |
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152 |
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153 |
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154 void LogMissingRequiredTag(const DicomMap& summary) |
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155 { |
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156 std::string s, t; |
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157 |
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158 if (summary.HasTag(DICOM_TAG_PATIENT_ID)) |
213
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159 { |
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160 if (t.size() > 0) |
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161 t += ", "; |
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162 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID); |
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163 } |
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164 else |
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165 { |
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166 if (s.size() > 0) |
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167 s += ", "; |
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168 s += "PatientID"; |
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169 } |
213
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170 |
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171 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) |
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172 { |
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173 if (t.size() > 0) |
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174 t += ", "; |
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175 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID); |
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176 } |
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177 else |
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178 { |
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179 if (s.size() > 0) |
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180 s += ", "; |
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181 s += "StudyInstanceUID"; |
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182 } |
213
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183 |
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184 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) |
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185 { |
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186 if (t.size() > 0) |
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187 t += ", "; |
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188 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID); |
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189 } |
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190 else |
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191 { |
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192 if (s.size() > 0) |
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193 s += ", "; |
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194 s += "SeriesInstanceUID"; |
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195 } |
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196 |
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197 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) |
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198 { |
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199 if (t.size() > 0) |
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200 t += ", "; |
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201 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID); |
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202 } |
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203 else |
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204 { |
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205 if (s.size() > 0) |
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206 s += ", "; |
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207 s += "SOPInstanceUID"; |
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208 } |
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209 |
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210 if (t.size() == 0) |
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211 { |
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212 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; |
213
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213 } |
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214 else |
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215 { |
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216 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; |
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217 } |
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218 } |
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219 |
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220 |
2120 | 221 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database, |
222 int64_t resource, | |
223 const DicomMap& tags) | |
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224 { |
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225 DicomArray flattened(tags); |
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226 |
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227 for (size_t i = 0; i < flattened.GetSize(); i++) |
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228 { |
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229 const DicomElement& element = flattened.GetElement(i); |
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230 const DicomTag& tag = element.GetTag(); |
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231 const DicomValue& value = element.GetValue(); |
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232 if (!value.IsNull() && |
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233 !value.IsBinary()) |
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234 { |
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235 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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236 } |
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237 } |
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238 } |
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239 |
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240 |
2120 | 241 void StoreMainDicomTags(IDatabaseWrapper& database, |
242 int64_t resource, | |
243 ResourceType level, | |
244 const DicomMap& dicomSummary) | |
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245 { |
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246 // WARNING: The database should be locked with a transaction! |
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247 |
2121 | 248 StoreIdentifiers(database, resource, level, dicomSummary); |
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249 |
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250 DicomMap tags; |
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251 |
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252 switch (level) |
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253 { |
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254 case ResourceType_Patient: |
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255 dicomSummary.ExtractPatientInformation(tags); |
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256 break; |
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257 |
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258 case ResourceType_Study: |
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259 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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260 dicomSummary.ExtractPatientInformation(tags); |
2120 | 261 StoreMainDicomTagsInternal(database, resource, tags); |
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262 |
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263 dicomSummary.ExtractStudyInformation(tags); |
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264 break; |
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265 |
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266 case ResourceType_Series: |
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267 dicomSummary.ExtractSeriesInformation(tags); |
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268 break; |
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269 |
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270 case ResourceType_Instance: |
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271 dicomSummary.ExtractInstanceInformation(tags); |
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272 break; |
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273 |
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274 default: |
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275 throw OrthancException(ErrorCode_InternalError); |
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276 } |
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277 |
2120 | 278 StoreMainDicomTagsInternal(database, resource, tags); |
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279 } |
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280 |
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281 |
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282 bool FindOneChildInstance(int64_t& result, |
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283 IDatabaseWrapper& database, |
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284 int64_t resource, |
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285 ResourceType type) |
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286 { |
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287 for (;;) |
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288 { |
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289 if (type == ResourceType_Instance) |
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290 { |
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291 result = resource; |
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292 return true; |
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293 } |
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294 |
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295 std::list<int64_t> children; |
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296 database.GetChildrenInternalId(children, resource); |
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297 if (children.empty()) |
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298 { |
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299 return false; |
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300 } |
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301 |
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302 resource = children.front(); |
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303 type = GetChildResourceType(type); |
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304 } |
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305 } |
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306 |
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307 |
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308 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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309 IStorageArea& storageArea, |
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310 ResourceType level) |
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311 { |
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312 // WARNING: The database should be locked with a transaction! |
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313 |
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314 const char* plural = NULL; |
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315 |
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316 switch (level) |
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317 { |
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318 case ResourceType_Patient: |
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319 plural = "patients"; |
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320 break; |
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321 |
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322 case ResourceType_Study: |
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323 plural = "studies"; |
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324 break; |
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325 |
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326 case ResourceType_Series: |
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327 plural = "series"; |
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328 break; |
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329 |
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330 case ResourceType_Instance: |
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331 plural = "instances"; |
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332 break; |
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333 |
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334 default: |
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335 throw OrthancException(ErrorCode_InternalError); |
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336 } |
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337 |
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338 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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339 |
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340 std::list<std::string> resources; |
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341 database.GetAllPublicIds(resources, level); |
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342 |
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343 for (std::list<std::string>::const_iterator |
1847 | 344 it = resources.begin(); it != resources.end(); ++it) |
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345 { |
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346 // Locate the resource and one of its child instances |
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347 int64_t resource, instance; |
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348 ResourceType tmp; |
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349 |
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350 if (!database.LookupResource(resource, tmp, *it) || |
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351 tmp != level || |
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352 !FindOneChildInstance(instance, database, resource, level)) |
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353 { |
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354 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level) |
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355 << " with identifier " << *it; |
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356 throw OrthancException(ErrorCode_InternalError); |
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357 } |
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358 |
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359 // Get the DICOM file attached to some instances in the resource |
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360 FileInfo attachment; |
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361 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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362 { |
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363 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance); |
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364 throw OrthancException(ErrorCode_InternalError); |
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365 } |
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366 |
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367 try |
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368 { |
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369 // Read and parse the content of the DICOM file |
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370 StorageAccessor accessor(storageArea); |
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371 |
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372 std::string content; |
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373 accessor.Read(content, attachment); |
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374 |
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375 ParsedDicomFile dicom(content); |
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376 |
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377 // Update the tags of this resource |
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378 DicomMap dicomSummary; |
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379 dicom.Convert(dicomSummary); |
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380 |
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381 database.ClearMainDicomTags(resource); |
2120 | 382 StoreMainDicomTags(database, resource, level, dicomSummary); |
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383 } |
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384 catch (OrthancException&) |
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385 { |
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386 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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Improved logging information if upgrade fails
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387 << " associated with instance " << database.GetPublicId(instance); |
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Improved logging information if upgrade fails
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388 throw; |
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Improved logging information if upgrade fails
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389 } |
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access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
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390 } |
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access to tags, simplified-tags and file of an instance
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391 } |
2121 | 392 |
393 | |
394 void LoadIdentifiers(const DicomTag*& tags, | |
395 size_t& size, | |
396 ResourceType level) | |
397 { | |
398 switch (level) | |
399 { | |
400 case ResourceType_Patient: | |
401 tags = patientIdentifiers; | |
402 size = sizeof(patientIdentifiers) / sizeof(DicomTag); | |
403 break; | |
404 | |
405 case ResourceType_Study: | |
406 tags = studyIdentifiers; | |
407 size = sizeof(studyIdentifiers) / sizeof(DicomTag); | |
408 break; | |
409 | |
410 case ResourceType_Series: | |
411 tags = seriesIdentifiers; | |
412 size = sizeof(seriesIdentifiers) / sizeof(DicomTag); | |
413 break; | |
414 | |
415 case ResourceType_Instance: | |
416 tags = instanceIdentifiers; | |
417 size = sizeof(instanceIdentifiers) / sizeof(DicomTag); | |
418 break; | |
419 | |
420 default: | |
421 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
422 } | |
423 } | |
424 | |
425 | |
426 std::string NormalizeIdentifier(const std::string& value) | |
427 { | |
428 std::string t; | |
429 t.reserve(value.size()); | |
430 | |
431 for (size_t i = 0; i < value.size(); i++) | |
432 { | |
433 if (value[i] == '%' || | |
434 value[i] == '_') | |
435 { | |
436 t.push_back(' '); // These characters might break wildcard queries in SQL | |
437 } | |
438 else if (isascii(value[i]) && | |
439 !iscntrl(value[i]) && | |
440 (!isspace(value[i]) || value[i] == ' ')) | |
441 { | |
442 t.push_back(value[i]); | |
443 } | |
444 } | |
445 | |
446 Toolbox::ToUpperCase(t); | |
447 | |
448 return Toolbox::StripSpaces(t); | |
449 } | |
450 | |
451 | |
452 bool IsIdentifier(const DicomTag& tag, | |
453 ResourceType level) | |
454 { | |
455 const DicomTag* tags; | |
456 size_t size; | |
457 | |
458 LoadIdentifiers(tags, size, level); | |
459 | |
460 for (size_t i = 0; i < size; i++) | |
461 { | |
462 if (tag == tags[i]) | |
463 { | |
464 return true; | |
465 } | |
466 } | |
467 | |
468 return false; | |
469 } | |
470 | |
471 | |
472 void StoreIdentifiers(IDatabaseWrapper& database, | |
473 int64_t resource, | |
474 ResourceType level, | |
475 const DicomMap& map) | |
476 { | |
477 const DicomTag* tags; | |
478 size_t size; | |
479 | |
480 LoadIdentifiers(tags, size, level); | |
481 | |
482 for (size_t i = 0; i < size; i++) | |
483 { | |
484 const DicomValue* value = map.TestAndGetValue(tags[i]); | |
485 if (value != NULL && | |
486 !value->IsNull() && | |
487 !value->IsBinary()) | |
488 { | |
489 std::string s = NormalizeIdentifier(value->GetContent()); | |
490 database.SetIdentifierTag(resource, tags[i], s); | |
491 } | |
492 } | |
493 } | |
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access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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494 } |
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access to tags, simplified-tags and file of an instance
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parents:
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495 } |