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annotate OrthancServer/ServerToolbox.cpp @ 3005:8265a6b56100

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DicomMap::FromDicomAsJson
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 12 Dec 2018 15:42:33 +0100
parents bbfd95a0c429
children 5da6d1063d8f 4e43e67f8ecf
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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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
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42 #include <cassert>
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43
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44 namespace Orthanc
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45 {
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46 namespace ServerToolbox
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47 {
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48 static const DicomTag patientIdentifiers[] =
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49 {
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50 DICOM_TAG_PATIENT_ID,
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51 DICOM_TAG_PATIENT_NAME,
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52 DICOM_TAG_PATIENT_BIRTH_DATE
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53 };
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54
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55 static const DicomTag studyIdentifiers[] =
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56 {
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57 DICOM_TAG_PATIENT_ID,
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58 DICOM_TAG_PATIENT_NAME,
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59 DICOM_TAG_PATIENT_BIRTH_DATE,
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60 DICOM_TAG_STUDY_INSTANCE_UID,
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61 DICOM_TAG_ACCESSION_NUMBER,
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62 DICOM_TAG_STUDY_DESCRIPTION,
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63 DICOM_TAG_STUDY_DATE
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64 };
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65
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66 static const DicomTag seriesIdentifiers[] =
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67 {
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68 DICOM_TAG_SERIES_INSTANCE_UID
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69 };
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70
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71 static const DicomTag instanceIdentifiers[] =
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72 {
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73 DICOM_TAG_SOP_INSTANCE_UID
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74 };
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75
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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 }
213
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137 }
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138 }
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139
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140
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141 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database,
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142 int64_t resource,
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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
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161 static void StoreIdentifiers(IDatabaseWrapper& database,
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162 int64_t resource,
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163 ResourceType level,
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164 const DicomMap& map)
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165 {
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166 const DicomTag* tags;
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167 size_t size;
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168
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169 LoadIdentifiers(tags, size, level);
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170
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171 for (size_t i = 0; i < size; i++)
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172 {
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173 const DicomValue* value = map.TestAndGetValue(tags[i]);
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174 if (value != NULL &&
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175 !value->IsNull() &&
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176 !value->IsBinary())
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177 {
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178 std::string s = NormalizeIdentifier(value->GetContent());
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179 database.SetIdentifierTag(resource, tags[i], s);
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180 }
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181 }
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182 }
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183
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184
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185 void StoreMainDicomTags(IDatabaseWrapper& database,
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186 int64_t resource,
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187 ResourceType level,
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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
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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);
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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
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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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diff changeset
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
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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 {
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305 throw OrthancException(ErrorCode_InternalError,
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306 "Cannot find an instance for " +
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307 std::string(EnumerationToString(level)) +
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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 {
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315 throw OrthancException(ErrorCode_InternalError,
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316 "Cannot retrieve the DICOM file associated with instance " +
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317 database.GetPublicId(instance));
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318 }
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319
1870
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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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0bbcfd9695e5 UpgradeDatabase in the sample plugin
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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;
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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332 dicom.ExtractDicomSummary(dicomSummary);
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333
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334 database.ClearMainDicomTags(resource);
2120
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335 StoreMainDicomTags(database, resource, level, dicomSummary);
1870
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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 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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343 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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344 }
2121
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345
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346
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347 void LoadIdentifiers(const DicomTag*& tags,
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348 size_t& size,
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349 ResourceType level)
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350 {
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351 switch (level)
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352 {
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353 case ResourceType_Patient:
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354 tags = patientIdentifiers;
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355 size = sizeof(patientIdentifiers) / sizeof(DicomTag);
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356 break;
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357
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358 case ResourceType_Study:
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359 tags = studyIdentifiers;
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360 size = sizeof(studyIdentifiers) / sizeof(DicomTag);
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361 break;
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362
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diff changeset
363 case ResourceType_Series:
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364 tags = seriesIdentifiers;
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diff changeset
365 size = sizeof(seriesIdentifiers) / sizeof(DicomTag);
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diff changeset
366 break;
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367
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diff changeset
368 case ResourceType_Instance:
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369 tags = instanceIdentifiers;
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diff changeset
370 size = sizeof(instanceIdentifiers) / sizeof(DicomTag);
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diff changeset
371 break;
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diff changeset
372
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diff changeset
373 default:
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374 throw OrthancException(ErrorCode_ParameterOutOfRange);
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375 }
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parents: 2120
diff changeset
376 }
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parents: 2120
diff changeset
377
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378
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diff changeset
379 std::string NormalizeIdentifier(const std::string& value)
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380 {
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diff changeset
381 std::string t;
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382 t.reserve(value.size());
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383
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diff changeset
384 for (size_t i = 0; i < value.size(); i++)
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diff changeset
385 {
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parents: 2120
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386 if (value[i] == '%' ||
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387 value[i] == '_')
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diff changeset
388 {
7e8889bc95c6 refactoring
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diff changeset
389 t.push_back(' '); // These characters might break wildcard queries in SQL
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390 }
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391 else if (isascii(value[i]) &&
7e8889bc95c6 refactoring
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392 !iscntrl(value[i]) &&
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parents: 2120
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393 (!isspace(value[i]) || value[i] == ' '))
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parents: 2120
diff changeset
394 {
7e8889bc95c6 refactoring
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diff changeset
395 t.push_back(value[i]);
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diff changeset
396 }
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parents: 2120
diff changeset
397 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
398
7e8889bc95c6 refactoring
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399 Toolbox::ToUpperCase(t);
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400
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401 return Toolbox::StripSpaces(t);
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diff changeset
402 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
403
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
404
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
405 bool IsIdentifier(const DicomTag& tag,
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diff changeset
406 ResourceType level)
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diff changeset
407 {
7e8889bc95c6 refactoring
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diff changeset
408 const DicomTag* tags;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
409 size_t size;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
410
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
411 LoadIdentifiers(tags, size, level);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
412
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
413 for (size_t i = 0; i < size; i++)
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parents: 2120
diff changeset
414 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
415 if (tag == tags[i])
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
416 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
417 return true;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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418 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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419 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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420
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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421 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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422 }
2209
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parents: 2129
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423
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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424
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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425 void ReconstructResource(ServerContext& context,
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
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426 const std::string& resource)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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427 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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428 LOG(WARNING) << "Reconstructing resource " << resource;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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429
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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430 std::list<std::string> instances;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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431 context.GetIndex().GetChildInstances(instances, resource);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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432
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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433 for (std::list<std::string>::const_iterator
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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434 it = instances.begin(); it != instances.end(); ++it)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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435 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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436 ServerContext::DicomCacheLocker locker(context, *it);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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437
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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438 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2380
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439 locker.GetDicom().DatasetToJson(dicomAsJson);
2209
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440
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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441 std::string s = dicomAsJson.toStyledString();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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442 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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443
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
444 context.GetIndex().ReconstructInstance(locker.GetDicom());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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445 }
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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446 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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447 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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448 }