Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 2980:63b724c7b046
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author | am@osimis.io |
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date | Thu, 06 Dec 2018 13:10:24 +0100 |
parents | bbfd95a0c429 |
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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 * Copyright (C) 2017-2018 Osimis S.A., Belgium |
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6 * |
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7 * This program is free software: you can redistribute it and/or |
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8 * modify it under the terms of the GNU General Public License as |
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9 * published by the Free Software Foundation, either version 3 of the |
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10 * License, or (at your option) any later version. |
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11 * |
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12 * In addition, as a special exception, the copyright holders of this |
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13 * program give permission to link the code of its release with the |
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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15 * that use the same license as the "OpenSSL" library), and distribute |
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16 * the linked executables. You must obey the GNU General Public License |
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17 * in all respects for all of the code used other than "OpenSSL". If you |
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18 * modify file(s) with this exception, you may extend this exception to |
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19 * your version of the file(s), but you are not obligated to do so. If |
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20 * you do not wish to do so, delete this exception statement from your |
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21 * version. If you delete this exception statement from all source files |
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22 * in the program, then also delete it here. |
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23 * |
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24 * This program is distributed in the hope that it will be useful, but |
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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27 * General Public License for more details. |
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28 * |
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29 * You should have received a copy of the GNU General Public License |
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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31 **/ |
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32 |
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33 |
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34 #include "PrecompiledHeadersServer.h" |
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35 #include "ServerToolbox.h" |
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36 |
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37 #include "../Core/DicomFormat/DicomArray.h" |
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38 #include "../Core/FileStorage/StorageAccessor.h" |
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39 #include "../Core/Logging.h" |
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40 #include "../Core/OrthancException.h" |
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41 |
234 | 42 #include <cassert> |
43 | |
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44 namespace Orthanc |
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45 { |
2120 | 46 namespace ServerToolbox |
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47 { |
2121 | 48 static const DicomTag patientIdentifiers[] = |
49 { | |
50 DICOM_TAG_PATIENT_ID, | |
51 DICOM_TAG_PATIENT_NAME, | |
52 DICOM_TAG_PATIENT_BIRTH_DATE | |
53 }; | |
54 | |
55 static const DicomTag studyIdentifiers[] = | |
56 { | |
57 DICOM_TAG_PATIENT_ID, | |
58 DICOM_TAG_PATIENT_NAME, | |
59 DICOM_TAG_PATIENT_BIRTH_DATE, | |
60 DICOM_TAG_STUDY_INSTANCE_UID, | |
61 DICOM_TAG_ACCESSION_NUMBER, | |
62 DICOM_TAG_STUDY_DESCRIPTION, | |
63 DICOM_TAG_STUDY_DATE | |
64 }; | |
65 | |
66 static const DicomTag seriesIdentifiers[] = | |
67 { | |
68 DICOM_TAG_SERIES_INSTANCE_UID | |
69 }; | |
70 | |
71 static const DicomTag instanceIdentifiers[] = | |
72 { | |
73 DICOM_TAG_SOP_INSTANCE_UID | |
74 }; | |
75 | |
76 | |
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77 void SimplifyTags(Json::Value& target, |
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78 const Json::Value& source, |
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79 DicomToJsonFormat format) |
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80 { |
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81 if (!source.isObject()) |
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82 { |
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83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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84 } |
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85 |
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86 target = Json::objectValue; |
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87 Json::Value::Members members = source.getMemberNames(); |
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88 |
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89 for (size_t i = 0; i < members.size(); i++) |
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90 { |
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91 const Json::Value& v = source[members[i]]; |
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92 const std::string& type = v["Type"].asString(); |
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93 |
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94 std::string name; |
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95 switch (format) |
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96 { |
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97 case DicomToJsonFormat_Human: |
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98 name = v["Name"].asString(); |
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99 break; |
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100 |
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101 case DicomToJsonFormat_Short: |
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102 name = members[i]; |
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103 break; |
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104 |
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105 default: |
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106 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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107 } |
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108 |
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109 if (type == "String") |
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110 { |
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111 target[name] = v["Value"].asString(); |
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112 } |
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113 else if (type == "TooLong" || |
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114 type == "Null") |
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115 { |
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116 target[name] = Json::nullValue; |
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117 } |
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118 else if (type == "Sequence") |
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119 { |
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120 const Json::Value& array = v["Value"]; |
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121 assert(array.isArray()); |
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122 |
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123 Json::Value children = Json::arrayValue; |
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124 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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125 { |
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126 Json::Value c; |
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127 SimplifyTags(c, array[i], format); |
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128 children.append(c); |
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129 } |
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130 |
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131 target[name] = children; |
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132 } |
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133 else |
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134 { |
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135 assert(0); |
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136 } |
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137 } |
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138 } |
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139 |
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140 |
2120 | 141 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database, |
142 int64_t resource, | |
143 const DicomMap& tags) | |
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144 { |
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145 DicomArray flattened(tags); |
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146 |
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147 for (size_t i = 0; i < flattened.GetSize(); i++) |
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148 { |
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149 const DicomElement& element = flattened.GetElement(i); |
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150 const DicomTag& tag = element.GetTag(); |
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151 const DicomValue& value = element.GetValue(); |
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152 if (!value.IsNull() && |
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153 !value.IsBinary()) |
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154 { |
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155 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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156 } |
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157 } |
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158 } |
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159 |
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160 |
2123 | 161 static void StoreIdentifiers(IDatabaseWrapper& database, |
162 int64_t resource, | |
163 ResourceType level, | |
164 const DicomMap& map) | |
165 { | |
166 const DicomTag* tags; | |
167 size_t size; | |
168 | |
169 LoadIdentifiers(tags, size, level); | |
170 | |
171 for (size_t i = 0; i < size; i++) | |
172 { | |
173 const DicomValue* value = map.TestAndGetValue(tags[i]); | |
174 if (value != NULL && | |
175 !value->IsNull() && | |
176 !value->IsBinary()) | |
177 { | |
178 std::string s = NormalizeIdentifier(value->GetContent()); | |
179 database.SetIdentifierTag(resource, tags[i], s); | |
180 } | |
181 } | |
182 } | |
183 | |
184 | |
2120 | 185 void StoreMainDicomTags(IDatabaseWrapper& database, |
186 int64_t resource, | |
187 ResourceType level, | |
188 const DicomMap& dicomSummary) | |
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189 { |
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190 // WARNING: The database should be locked with a transaction! |
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191 |
2121 | 192 StoreIdentifiers(database, resource, level, dicomSummary); |
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193 |
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194 DicomMap tags; |
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195 |
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196 switch (level) |
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197 { |
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198 case ResourceType_Patient: |
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199 dicomSummary.ExtractPatientInformation(tags); |
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200 break; |
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201 |
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202 case ResourceType_Study: |
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203 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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204 dicomSummary.ExtractPatientInformation(tags); |
2120 | 205 StoreMainDicomTagsInternal(database, resource, tags); |
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206 |
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207 dicomSummary.ExtractStudyInformation(tags); |
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208 break; |
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209 |
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210 case ResourceType_Series: |
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211 dicomSummary.ExtractSeriesInformation(tags); |
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212 break; |
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213 |
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214 case ResourceType_Instance: |
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215 dicomSummary.ExtractInstanceInformation(tags); |
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216 break; |
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217 |
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218 default: |
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219 throw OrthancException(ErrorCode_InternalError); |
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220 } |
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221 |
2120 | 222 StoreMainDicomTagsInternal(database, resource, tags); |
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223 } |
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224 |
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225 |
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226 bool FindOneChildInstance(int64_t& result, |
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227 IDatabaseWrapper& database, |
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228 int64_t resource, |
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229 ResourceType type) |
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230 { |
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231 for (;;) |
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232 { |
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233 if (type == ResourceType_Instance) |
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234 { |
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235 result = resource; |
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236 return true; |
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237 } |
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238 |
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239 std::list<int64_t> children; |
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240 database.GetChildrenInternalId(children, resource); |
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241 if (children.empty()) |
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242 { |
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243 return false; |
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244 } |
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245 |
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246 resource = children.front(); |
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247 type = GetChildResourceType(type); |
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248 } |
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249 } |
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250 |
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251 |
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252 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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253 IStorageArea& storageArea, |
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254 ResourceType level) |
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255 { |
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256 // WARNING: The database should be locked with a transaction! |
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257 |
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258 // TODO: This function might consume much memory if level == |
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259 // ResourceType_Instance. To improve this, first download the |
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260 // list of studies, then remove the instances for each single |
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261 // study (check out OrthancRestApi::InvalidateTags for an |
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262 // example). Take this improvement into consideration for the |
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263 // next upgrade of the database schema. |
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264 |
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265 const char* plural = NULL; |
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266 |
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267 switch (level) |
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268 { |
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269 case ResourceType_Patient: |
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270 plural = "patients"; |
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271 break; |
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272 |
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273 case ResourceType_Study: |
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274 plural = "studies"; |
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275 break; |
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276 |
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277 case ResourceType_Series: |
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278 plural = "series"; |
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279 break; |
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280 |
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281 case ResourceType_Instance: |
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282 plural = "instances"; |
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283 break; |
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284 |
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285 default: |
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286 throw OrthancException(ErrorCode_InternalError); |
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287 } |
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288 |
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289 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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290 |
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291 std::list<std::string> resources; |
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292 database.GetAllPublicIds(resources, level); |
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293 |
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294 for (std::list<std::string>::const_iterator |
1847 | 295 it = resources.begin(); it != resources.end(); ++it) |
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296 { |
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297 // Locate the resource and one of its child instances |
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298 int64_t resource, instance; |
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299 ResourceType tmp; |
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300 |
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301 if (!database.LookupResource(resource, tmp, *it) || |
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302 tmp != level || |
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303 !FindOneChildInstance(instance, database, resource, level)) |
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304 { |
2955 | 305 throw OrthancException(ErrorCode_InternalError, |
306 "Cannot find an instance for " + | |
307 std::string(EnumerationToString(level)) + | |
308 " with identifier " + *it); | |
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309 } |
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310 |
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311 // Get the DICOM file attached to some instances in the resource |
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312 FileInfo attachment; |
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313 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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314 { |
2955 | 315 throw OrthancException(ErrorCode_InternalError, |
316 "Cannot retrieve the DICOM file associated with instance " + | |
317 database.GetPublicId(instance)); | |
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318 } |
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319 |
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320 try |
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321 { |
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322 // Read and parse the content of the DICOM file |
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323 StorageAccessor accessor(storageArea); |
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324 |
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325 std::string content; |
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326 accessor.Read(content, attachment); |
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327 |
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328 ParsedDicomFile dicom(content); |
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329 |
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330 // Update the tags of this resource |
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331 DicomMap dicomSummary; |
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332 dicom.ExtractDicomSummary(dicomSummary); |
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333 |
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334 database.ClearMainDicomTags(resource); |
2120 | 335 StoreMainDicomTags(database, resource, level, dicomSummary); |
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336 } |
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337 catch (OrthancException&) |
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338 { |
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339 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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340 << " associated with instance " << database.GetPublicId(instance); |
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341 throw; |
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342 } |
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343 } |
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344 } |
2121 | 345 |
346 | |
347 void LoadIdentifiers(const DicomTag*& tags, | |
348 size_t& size, | |
349 ResourceType level) | |
350 { | |
351 switch (level) | |
352 { | |
353 case ResourceType_Patient: | |
354 tags = patientIdentifiers; | |
355 size = sizeof(patientIdentifiers) / sizeof(DicomTag); | |
356 break; | |
357 | |
358 case ResourceType_Study: | |
359 tags = studyIdentifiers; | |
360 size = sizeof(studyIdentifiers) / sizeof(DicomTag); | |
361 break; | |
362 | |
363 case ResourceType_Series: | |
364 tags = seriesIdentifiers; | |
365 size = sizeof(seriesIdentifiers) / sizeof(DicomTag); | |
366 break; | |
367 | |
368 case ResourceType_Instance: | |
369 tags = instanceIdentifiers; | |
370 size = sizeof(instanceIdentifiers) / sizeof(DicomTag); | |
371 break; | |
372 | |
373 default: | |
374 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
375 } | |
376 } | |
377 | |
378 | |
379 std::string NormalizeIdentifier(const std::string& value) | |
380 { | |
381 std::string t; | |
382 t.reserve(value.size()); | |
383 | |
384 for (size_t i = 0; i < value.size(); i++) | |
385 { | |
386 if (value[i] == '%' || | |
387 value[i] == '_') | |
388 { | |
389 t.push_back(' '); // These characters might break wildcard queries in SQL | |
390 } | |
391 else if (isascii(value[i]) && | |
392 !iscntrl(value[i]) && | |
393 (!isspace(value[i]) || value[i] == ' ')) | |
394 { | |
395 t.push_back(value[i]); | |
396 } | |
397 } | |
398 | |
399 Toolbox::ToUpperCase(t); | |
400 | |
401 return Toolbox::StripSpaces(t); | |
402 } | |
403 | |
404 | |
405 bool IsIdentifier(const DicomTag& tag, | |
406 ResourceType level) | |
407 { | |
408 const DicomTag* tags; | |
409 size_t size; | |
410 | |
411 LoadIdentifiers(tags, size, level); | |
412 | |
413 for (size_t i = 0; i < size; i++) | |
414 { | |
415 if (tag == tags[i]) | |
416 { | |
417 return true; | |
418 } | |
419 } | |
420 | |
421 return false; | |
422 } | |
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423 |
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424 |
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425 void ReconstructResource(ServerContext& context, |
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426 const std::string& resource) |
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427 { |
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428 LOG(WARNING) << "Reconstructing resource " << resource; |
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429 |
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430 std::list<std::string> instances; |
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431 context.GetIndex().GetChildInstances(instances, resource); |
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432 |
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433 for (std::list<std::string>::const_iterator |
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434 it = instances.begin(); it != instances.end(); ++it) |
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435 { |
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436 ServerContext::DicomCacheLocker locker(context, *it); |
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437 |
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438 Json::Value dicomAsJson; |
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439 locker.GetDicom().DatasetToJson(dicomAsJson); |
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440 |
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441 std::string s = dicomAsJson.toStyledString(); |
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442 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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443 |
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444 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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445 } |
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446 } |
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447 } |
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448 } |