Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 2252:002b94046c69
colorspace conversion from BGRA32 to RGB24
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 20 Jan 2017 13:14:30 +0100 |
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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 Osimis, 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 assert(source.isObject()); |
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82 |
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83 target = Json::objectValue; |
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84 Json::Value::Members members = source.getMemberNames(); |
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85 |
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86 for (size_t i = 0; i < members.size(); i++) |
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87 { |
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88 const Json::Value& v = source[members[i]]; |
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89 const std::string& type = v["Type"].asString(); |
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90 |
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91 std::string name; |
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92 switch (format) |
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93 { |
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94 case DicomToJsonFormat_Human: |
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95 name = v["Name"].asString(); |
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96 break; |
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97 |
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98 case DicomToJsonFormat_Short: |
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99 name = members[i]; |
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100 break; |
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101 |
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102 default: |
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103 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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104 } |
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105 |
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106 if (type == "String") |
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107 { |
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108 target[name] = v["Value"].asString(); |
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109 } |
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110 else if (type == "TooLong" || |
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111 type == "Null") |
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112 { |
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113 target[name] = Json::nullValue; |
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114 } |
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115 else if (type == "Sequence") |
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116 { |
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117 const Json::Value& array = v["Value"]; |
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118 assert(array.isArray()); |
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119 |
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120 Json::Value children = Json::arrayValue; |
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121 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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122 { |
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123 Json::Value c; |
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124 SimplifyTags(c, array[i], format); |
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125 children.append(c); |
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126 } |
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127 |
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128 target[name] = children; |
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129 } |
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130 else |
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131 { |
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132 assert(0); |
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133 } |
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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 static std::string ValueAsString(const DicomMap& summary, |
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139 const DicomTag& tag) |
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140 { |
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141 const DicomValue& value = summary.GetValue(tag); |
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142 if (value.IsNull()) |
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143 { |
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144 return "(null)"; |
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145 } |
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146 else |
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147 { |
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148 return value.GetContent(); |
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149 } |
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150 } |
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151 |
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152 |
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153 void LogMissingRequiredTag(const DicomMap& summary) |
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154 { |
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155 std::string s, t; |
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156 |
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157 if (summary.HasTag(DICOM_TAG_PATIENT_ID)) |
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158 { |
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159 if (t.size() > 0) |
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160 t += ", "; |
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161 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID); |
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162 } |
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163 else |
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164 { |
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165 if (s.size() > 0) |
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166 s += ", "; |
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167 s += "PatientID"; |
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168 } |
213
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169 |
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170 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) |
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171 { |
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172 if (t.size() > 0) |
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173 t += ", "; |
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174 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID); |
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175 } |
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176 else |
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177 { |
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178 if (s.size() > 0) |
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179 s += ", "; |
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180 s += "StudyInstanceUID"; |
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181 } |
213
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182 |
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183 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) |
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184 { |
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185 if (t.size() > 0) |
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186 t += ", "; |
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187 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID); |
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188 } |
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189 else |
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190 { |
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191 if (s.size() > 0) |
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192 s += ", "; |
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193 s += "SeriesInstanceUID"; |
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194 } |
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195 |
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196 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) |
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197 { |
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198 if (t.size() > 0) |
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199 t += ", "; |
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200 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID); |
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201 } |
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202 else |
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203 { |
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204 if (s.size() > 0) |
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205 s += ", "; |
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206 s += "SOPInstanceUID"; |
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207 } |
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208 |
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209 if (t.size() == 0) |
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210 { |
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211 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; |
213
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212 } |
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213 else |
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214 { |
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215 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; |
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216 } |
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217 } |
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218 |
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219 |
2120 | 220 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database, |
221 int64_t resource, | |
222 const DicomMap& tags) | |
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223 { |
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224 DicomArray flattened(tags); |
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225 |
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226 for (size_t i = 0; i < flattened.GetSize(); i++) |
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227 { |
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228 const DicomElement& element = flattened.GetElement(i); |
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229 const DicomTag& tag = element.GetTag(); |
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230 const DicomValue& value = element.GetValue(); |
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231 if (!value.IsNull() && |
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232 !value.IsBinary()) |
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233 { |
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234 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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235 } |
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236 } |
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237 } |
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238 |
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239 |
2123 | 240 static void StoreIdentifiers(IDatabaseWrapper& database, |
241 int64_t resource, | |
242 ResourceType level, | |
243 const DicomMap& map) | |
244 { | |
245 const DicomTag* tags; | |
246 size_t size; | |
247 | |
248 LoadIdentifiers(tags, size, level); | |
249 | |
250 for (size_t i = 0; i < size; i++) | |
251 { | |
252 const DicomValue* value = map.TestAndGetValue(tags[i]); | |
253 if (value != NULL && | |
254 !value->IsNull() && | |
255 !value->IsBinary()) | |
256 { | |
257 std::string s = NormalizeIdentifier(value->GetContent()); | |
258 database.SetIdentifierTag(resource, tags[i], s); | |
259 } | |
260 } | |
261 } | |
262 | |
263 | |
2120 | 264 void StoreMainDicomTags(IDatabaseWrapper& database, |
265 int64_t resource, | |
266 ResourceType level, | |
267 const DicomMap& dicomSummary) | |
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268 { |
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269 // WARNING: The database should be locked with a transaction! |
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270 |
2121 | 271 StoreIdentifiers(database, resource, level, dicomSummary); |
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272 |
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273 DicomMap tags; |
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274 |
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275 switch (level) |
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276 { |
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277 case ResourceType_Patient: |
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278 dicomSummary.ExtractPatientInformation(tags); |
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279 break; |
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280 |
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281 case ResourceType_Study: |
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282 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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283 dicomSummary.ExtractPatientInformation(tags); |
2120 | 284 StoreMainDicomTagsInternal(database, resource, tags); |
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285 |
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286 dicomSummary.ExtractStudyInformation(tags); |
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287 break; |
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288 |
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289 case ResourceType_Series: |
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290 dicomSummary.ExtractSeriesInformation(tags); |
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291 break; |
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292 |
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293 case ResourceType_Instance: |
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294 dicomSummary.ExtractInstanceInformation(tags); |
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295 break; |
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296 |
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297 default: |
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298 throw OrthancException(ErrorCode_InternalError); |
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299 } |
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300 |
2120 | 301 StoreMainDicomTagsInternal(database, resource, tags); |
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302 } |
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303 |
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304 |
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305 bool FindOneChildInstance(int64_t& result, |
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306 IDatabaseWrapper& database, |
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307 int64_t resource, |
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308 ResourceType type) |
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309 { |
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310 for (;;) |
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311 { |
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312 if (type == ResourceType_Instance) |
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313 { |
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314 result = resource; |
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315 return true; |
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316 } |
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317 |
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318 std::list<int64_t> children; |
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319 database.GetChildrenInternalId(children, resource); |
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320 if (children.empty()) |
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321 { |
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322 return false; |
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323 } |
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324 |
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325 resource = children.front(); |
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326 type = GetChildResourceType(type); |
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327 } |
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328 } |
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329 |
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330 |
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331 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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332 IStorageArea& storageArea, |
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333 ResourceType level) |
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334 { |
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335 // WARNING: The database should be locked with a transaction! |
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336 |
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337 // TODO: This function might consume much memory if level == |
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338 // ResourceType_Instance. To improve this, first download the |
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339 // list of studies, then remove the instances for each single |
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340 // study (check out OrthancRestApi::InvalidateTags for an |
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341 // example). Take this improvement into consideration for the |
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342 // next upgrade of the database schema. |
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343 |
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344 const char* plural = NULL; |
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345 |
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346 switch (level) |
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347 { |
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348 case ResourceType_Patient: |
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349 plural = "patients"; |
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350 break; |
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351 |
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352 case ResourceType_Study: |
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353 plural = "studies"; |
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354 break; |
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355 |
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356 case ResourceType_Series: |
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357 plural = "series"; |
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358 break; |
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359 |
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360 case ResourceType_Instance: |
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361 plural = "instances"; |
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362 break; |
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363 |
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364 default: |
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365 throw OrthancException(ErrorCode_InternalError); |
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366 } |
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367 |
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368 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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369 |
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370 std::list<std::string> resources; |
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371 database.GetAllPublicIds(resources, level); |
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372 |
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373 for (std::list<std::string>::const_iterator |
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375 { |
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376 // Locate the resource and one of its child instances |
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377 int64_t resource, instance; |
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378 ResourceType tmp; |
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379 |
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380 if (!database.LookupResource(resource, tmp, *it) || |
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381 tmp != level || |
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382 !FindOneChildInstance(instance, database, resource, level)) |
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383 { |
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384 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level) |
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385 << " with identifier " << *it; |
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386 throw OrthancException(ErrorCode_InternalError); |
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387 } |
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388 |
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389 // Get the DICOM file attached to some instances in the resource |
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390 FileInfo attachment; |
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391 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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392 { |
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393 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance); |
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394 throw OrthancException(ErrorCode_InternalError); |
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395 } |
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396 |
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397 try |
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398 { |
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399 // Read and parse the content of the DICOM file |
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400 StorageAccessor accessor(storageArea); |
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401 |
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402 std::string content; |
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403 accessor.Read(content, attachment); |
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404 |
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405 ParsedDicomFile dicom(content); |
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406 |
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407 // Update the tags of this resource |
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408 DicomMap dicomSummary; |
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409 dicom.ExtractDicomSummary(dicomSummary); |
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410 |
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411 database.ClearMainDicomTags(resource); |
2120 | 412 StoreMainDicomTags(database, resource, level, dicomSummary); |
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413 } |
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414 catch (OrthancException&) |
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415 { |
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416 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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417 << " associated with instance " << database.GetPublicId(instance); |
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418 throw; |
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419 } |
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420 } |
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421 } |
2121 | 422 |
423 | |
424 void LoadIdentifiers(const DicomTag*& tags, | |
425 size_t& size, | |
426 ResourceType level) | |
427 { | |
428 switch (level) | |
429 { | |
430 case ResourceType_Patient: | |
431 tags = patientIdentifiers; | |
432 size = sizeof(patientIdentifiers) / sizeof(DicomTag); | |
433 break; | |
434 | |
435 case ResourceType_Study: | |
436 tags = studyIdentifiers; | |
437 size = sizeof(studyIdentifiers) / sizeof(DicomTag); | |
438 break; | |
439 | |
440 case ResourceType_Series: | |
441 tags = seriesIdentifiers; | |
442 size = sizeof(seriesIdentifiers) / sizeof(DicomTag); | |
443 break; | |
444 | |
445 case ResourceType_Instance: | |
446 tags = instanceIdentifiers; | |
447 size = sizeof(instanceIdentifiers) / sizeof(DicomTag); | |
448 break; | |
449 | |
450 default: | |
451 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
452 } | |
453 } | |
454 | |
455 | |
456 std::string NormalizeIdentifier(const std::string& value) | |
457 { | |
458 std::string t; | |
459 t.reserve(value.size()); | |
460 | |
461 for (size_t i = 0; i < value.size(); i++) | |
462 { | |
463 if (value[i] == '%' || | |
464 value[i] == '_') | |
465 { | |
466 t.push_back(' '); // These characters might break wildcard queries in SQL | |
467 } | |
468 else if (isascii(value[i]) && | |
469 !iscntrl(value[i]) && | |
470 (!isspace(value[i]) || value[i] == ' ')) | |
471 { | |
472 t.push_back(value[i]); | |
473 } | |
474 } | |
475 | |
476 Toolbox::ToUpperCase(t); | |
477 | |
478 return Toolbox::StripSpaces(t); | |
479 } | |
480 | |
481 | |
482 bool IsIdentifier(const DicomTag& tag, | |
483 ResourceType level) | |
484 { | |
485 const DicomTag* tags; | |
486 size_t size; | |
487 | |
488 LoadIdentifiers(tags, size, level); | |
489 | |
490 for (size_t i = 0; i < size; i++) | |
491 { | |
492 if (tag == tags[i]) | |
493 { | |
494 return true; | |
495 } | |
496 } | |
497 | |
498 return false; | |
499 } | |
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500 |
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501 |
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502 void ReconstructResource(ServerContext& context, |
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503 const std::string& resource) |
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504 { |
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505 LOG(WARNING) << "Reconstructing resource " << resource; |
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506 |
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507 std::list<std::string> instances; |
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508 context.GetIndex().GetChildInstances(instances, resource); |
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509 |
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510 for (std::list<std::string>::const_iterator |
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511 it = instances.begin(); it != instances.end(); ++it) |
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512 { |
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513 ServerContext::DicomCacheLocker locker(context, *it); |
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514 |
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515 Json::Value dicomAsJson; |
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516 locker.GetDicom().ExtractDicomAsJson(dicomAsJson); |
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517 |
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518 std::string s = dicomAsJson.toStyledString(); |
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519 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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520 |
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521 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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522 } |
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523 } |
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524 } |
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525 } |