Mercurial > hg > orthanc

annotate OrthancServer/ServerToolbox.cpp @ 2445:6e5bc5c6d1a4

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Fix to allow creating DICOM instances with empty Specific Character Set (0008,0005)
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 14 Dec 2017 13:02:06 +0100
parents e4045b3c9772
children 878b59270859
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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 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
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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 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 }
213
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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 void StoreMainDicomTagsInternal(IDatabaseWrapper& database,
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139 int64_t resource,
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140 const DicomMap& tags)
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141 {
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142 DicomArray flattened(tags);
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143
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144 for (size_t i = 0; i < flattened.GetSize(); i++)
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145 {
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146 const DicomElement& element = flattened.GetElement(i);
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147 const DicomTag& tag = element.GetTag();
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148 const DicomValue& value = element.GetValue();
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149 if (!value.IsNull() &&
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150 !value.IsBinary())
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151 {
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152 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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153 }
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154 }
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155 }
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156
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157
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158 static void StoreIdentifiers(IDatabaseWrapper& database,
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159 int64_t resource,
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160 ResourceType level,
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161 const DicomMap& map)
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162 {
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163 const DicomTag* tags;
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164 size_t size;
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165
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166 LoadIdentifiers(tags, size, level);
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167
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168 for (size_t i = 0; i < size; i++)
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169 {
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170 const DicomValue* value = map.TestAndGetValue(tags[i]);
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171 if (value != NULL &&
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172 !value->IsNull() &&
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173 !value->IsBinary())
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174 {
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175 std::string s = NormalizeIdentifier(value->GetContent());
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176 database.SetIdentifierTag(resource, tags[i], s);
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177 }
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178 }
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179 }
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180
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181
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182 void StoreMainDicomTags(IDatabaseWrapper& database,
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183 int64_t resource,
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184 ResourceType level,
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185 const DicomMap& dicomSummary)
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186 {
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187 // WARNING: The database should be locked with a transaction!
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188
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189 StoreIdentifiers(database, resource, level, dicomSummary);
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190
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191 DicomMap tags;
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192
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193 switch (level)
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194 {
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195 case ResourceType_Patient:
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196 dicomSummary.ExtractPatientInformation(tags);
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197 break;
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198
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199 case ResourceType_Study:
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200 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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201 dicomSummary.ExtractPatientInformation(tags);
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202 StoreMainDicomTagsInternal(database, resource, tags);
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203
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204 dicomSummary.ExtractStudyInformation(tags);
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205 break;
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206
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207 case ResourceType_Series:
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208 dicomSummary.ExtractSeriesInformation(tags);
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209 break;
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210
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211 case ResourceType_Instance:
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212 dicomSummary.ExtractInstanceInformation(tags);
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213 break;
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214
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215 default:
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216 throw OrthancException(ErrorCode_InternalError);
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217 }
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218
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219 StoreMainDicomTagsInternal(database, resource, tags);
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220 }
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221
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222
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223 bool FindOneChildInstance(int64_t& result,
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224 IDatabaseWrapper& database,
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225 int64_t resource,
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226 ResourceType type)
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227 {
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228 for (;;)
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229 {
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230 if (type == ResourceType_Instance)
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231 {
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232 result = resource;
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233 return true;
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234 }
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235
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236 std::list<int64_t> children;
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237 database.GetChildrenInternalId(children, resource);
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238 if (children.empty())
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239 {
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240 return false;
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241 }
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242
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243 resource = children.front();
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244 type = GetChildResourceType(type);
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245 }
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246 }
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247
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248
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249 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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250 IStorageArea& storageArea,
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251 ResourceType level)
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252 {
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253 // WARNING: The database should be locked with a transaction!
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254
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255 // TODO: This function might consume much memory if level ==
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256 // ResourceType_Instance. To improve this, first download the
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257 // list of studies, then remove the instances for each single
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258 // study (check out OrthancRestApi::InvalidateTags for an
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259 // example). Take this improvement into consideration for the
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260 // next upgrade of the database schema.
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261
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262 const char* plural = NULL;
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263
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264 switch (level)
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265 {
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266 case ResourceType_Patient:
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267 plural = "patients";
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268 break;
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269
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270 case ResourceType_Study:
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271 plural = "studies";
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272 break;
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273
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274 case ResourceType_Series:
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275 plural = "series";
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276 break;
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277
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278 case ResourceType_Instance:
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279 plural = "instances";
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280 break;
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281
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282 default:
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283 throw OrthancException(ErrorCode_InternalError);
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284 }
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285
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286 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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287
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288 std::list<std::string> resources;
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289 database.GetAllPublicIds(resources, level);
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290
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291 for (std::list<std::string>::const_iterator
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292 it = resources.begin(); it != resources.end(); ++it)
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293 {
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294 // Locate the resource and one of its child instances
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295 int64_t resource, instance;
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296 ResourceType tmp;
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297
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298 if (!database.LookupResource(resource, tmp, *it) ||
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299 tmp != level ||
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300 !FindOneChildInstance(instance, database, resource, level))
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301 {
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302 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level)
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303 << " with identifier " << *it;
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304 throw OrthancException(ErrorCode_InternalError);
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305 }
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306
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307 // Get the DICOM file attached to some instances in the resource
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308 FileInfo attachment;
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309 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
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310 {
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311 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance);
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312 throw OrthancException(ErrorCode_InternalError);
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313 }
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314
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315 try
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316 {
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317 // Read and parse the content of the DICOM file
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318 StorageAccessor accessor(storageArea);
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0bbcfd9695e5 UpgradeDatabase in the sample plugin
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319
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320 std::string content;
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321 accessor.Read(content, attachment);
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322
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323 ParsedDicomFile dicom(content);
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324
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325 // Update the tags of this resource
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326 DicomMap dicomSummary;
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e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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327 dicom.ExtractDicomSummary(dicomSummary);
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328
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329 database.ClearMainDicomTags(resource);
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330 StoreMainDicomTags(database, resource, level, dicomSummary);
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331 }
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332 catch (OrthancException&)
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333 {
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334 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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335 << " associated with instance " << database.GetPublicId(instance);
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336 throw;
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337 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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338 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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339 }
2121
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340
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341
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342 void LoadIdentifiers(const DicomTag*& tags,
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343 size_t& size,
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344 ResourceType level)
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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 tags = patientIdentifiers;
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350 size = sizeof(patientIdentifiers) / sizeof(DicomTag);
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351 break;
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352
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353 case ResourceType_Study:
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354 tags = studyIdentifiers;
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355 size = sizeof(studyIdentifiers) / sizeof(DicomTag);
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diff changeset
356 break;
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357
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358 case ResourceType_Series:
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359 tags = seriesIdentifiers;
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360 size = sizeof(seriesIdentifiers) / sizeof(DicomTag);
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parents: 2120
diff changeset
361 break;
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parents: 2120
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362
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diff changeset
363 case ResourceType_Instance:
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diff changeset
364 tags = instanceIdentifiers;
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diff changeset
365 size = sizeof(instanceIdentifiers) / sizeof(DicomTag);
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parents: 2120
diff changeset
366 break;
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parents: 2120
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367
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368 default:
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369 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 2120
diff changeset
370 }
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parents: 2120
diff changeset
371 }
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parents: 2120
diff changeset
372
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diff changeset
373
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diff changeset
374 std::string NormalizeIdentifier(const std::string& value)
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375 {
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parents: 2120
diff changeset
376 std::string t;
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diff changeset
377 t.reserve(value.size());
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378
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diff changeset
379 for (size_t i = 0; i < value.size(); i++)
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parents: 2120
diff changeset
380 {
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parents: 2120
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381 if (value[i] == '%' ||
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382 value[i] == '_')
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diff changeset
383 {
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parents: 2120
diff changeset
384 t.push_back(' '); // These characters might break wildcard queries in SQL
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diff changeset
385 }
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parents: 2120
diff changeset
386 else if (isascii(value[i]) &&
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387 !iscntrl(value[i]) &&
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diff changeset
388 (!isspace(value[i]) || value[i] == ' '))
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parents: 2120
diff changeset
389 {
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parents: 2120
diff changeset
390 t.push_back(value[i]);
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parents: 2120
diff changeset
391 }
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parents: 2120
diff changeset
392 }
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parents: 2120
diff changeset
393
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diff changeset
394 Toolbox::ToUpperCase(t);
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395
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396 return Toolbox::StripSpaces(t);
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parents: 2120
diff changeset
397 }
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parents: 2120
diff changeset
398
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parents: 2120
diff changeset
399
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
400 bool IsIdentifier(const DicomTag& tag,
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parents: 2120
diff changeset
401 ResourceType level)
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parents: 2120
diff changeset
402 {
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parents: 2120
diff changeset
403 const DicomTag* tags;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
404 size_t size;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
405
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
406 LoadIdentifiers(tags, size, level);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
407
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
408 for (size_t i = 0; i < size; i++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
409 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
410 if (tag == tags[i])
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
411 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
412 return true;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
413 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
414 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
415
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
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416 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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417 }
2209
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418
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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419
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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420 void ReconstructResource(ServerContext& context,
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421 const std::string& resource)
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parents: 2129
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422 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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423 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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424
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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425 std::list<std::string> instances;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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426 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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427
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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428 for (std::list<std::string>::const_iterator
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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429 it = instances.begin(); it != instances.end(); ++it)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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430 {
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parents: 2129
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431 ServerContext::DicomCacheLocker locker(context, *it);
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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 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2380
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434 locker.GetDicom().DatasetToJson(dicomAsJson);
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parents: 2129
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435
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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436 std::string s = dicomAsJson.toStyledString();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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437 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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438
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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439 context.GetIndex().ReconstructInstance(locker.GetDicom());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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440 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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441 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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442 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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443 }