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annotate OrthancServer/ServerToolbox.cpp @ 3917:04fb907dfc85 transcoding

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NEWS: issue #169 was fixed by 8f7ad4989fec
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 11 May 2020 21:12:40 +0200
parents 94f4a18a79cc
children
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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) 2017-2020 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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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/DicomParsing/ParsedDicomFile.h"
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39 #include "../Core/FileStorage/StorageAccessor.h"
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40 #include "../Core/Logging.h"
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41 #include "../Core/OrthancException.h"
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42 #include "Database/IDatabaseWrapper.h"
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43 #include "Database/ResourcesContent.h"
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44 #include "ServerContext.h"
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45
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46 #include <cassert>
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47
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48 namespace Orthanc
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49 {
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50 static const DicomTag PATIENT_IDENTIFIERS[] =
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51 {
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52 DICOM_TAG_PATIENT_ID,
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53 DICOM_TAG_PATIENT_NAME,
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54 DICOM_TAG_PATIENT_BIRTH_DATE
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55 };
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56
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57 static const DicomTag STUDY_IDENTIFIERS[] =
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58 {
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59 DICOM_TAG_PATIENT_ID,
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60 DICOM_TAG_PATIENT_NAME,
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61 DICOM_TAG_PATIENT_BIRTH_DATE,
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62 DICOM_TAG_STUDY_INSTANCE_UID,
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63 DICOM_TAG_ACCESSION_NUMBER,
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64 DICOM_TAG_STUDY_DESCRIPTION,
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65 DICOM_TAG_STUDY_DATE
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66 };
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67
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68 static const DicomTag SERIES_IDENTIFIERS[] =
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69 {
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70 DICOM_TAG_SERIES_INSTANCE_UID
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71 };
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72
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73 static const DicomTag INSTANCE_IDENTIFIERS[] =
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74 {
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75 DICOM_TAG_SOP_INSTANCE_UID
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76 };
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77
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78
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79 static void StoreMainDicomTagsInternal(ResourcesContent& target,
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80 int64_t resource,
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81 const DicomMap& tags)
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82 {
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83 DicomArray flattened(tags);
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84
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85 for (size_t i = 0; i < flattened.GetSize(); i++)
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86 {
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87 const DicomElement& element = flattened.GetElement(i);
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88 const DicomTag& tag = element.GetTag();
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89 const DicomValue& value = element.GetValue();
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90 if (!value.IsNull() &&
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91 !value.IsBinary())
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92 {
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93 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent());
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94 }
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95 }
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96 }
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97
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98
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99 static void StoreIdentifiers(ResourcesContent& target,
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100 int64_t resource,
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101 ResourceType level,
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102 const DicomMap& map)
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103 {
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104 const DicomTag* tags;
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105 size_t size;
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106
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107 ServerToolbox::LoadIdentifiers(tags, size, level);
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108
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109 for (size_t i = 0; i < size; i++)
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110 {
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111 // The identifiers tags are a subset of the main DICOM tags
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112 assert(DicomMap::IsMainDicomTag(tags[i]));
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113
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114 const DicomValue* value = map.TestAndGetValue(tags[i]);
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115 if (value != NULL &&
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116 !value->IsNull() &&
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117 !value->IsBinary())
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118 {
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119 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent());
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120 target.AddIdentifierTag(resource, tags[i], s);
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121 }
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122 }
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123 }
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124
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125
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126 void ResourcesContent::AddResource(int64_t resource,
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127 ResourceType level,
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128 const DicomMap& dicomSummary)
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129 {
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130 StoreIdentifiers(*this, resource, level, dicomSummary);
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131
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132 DicomMap tags;
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133
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134 switch (level)
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135 {
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136 case ResourceType_Patient:
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137 dicomSummary.ExtractPatientInformation(tags);
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138 break;
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139
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140 case ResourceType_Study:
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141 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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142 dicomSummary.ExtractPatientInformation(tags);
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143 StoreMainDicomTagsInternal(*this, resource, tags);
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144
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145 dicomSummary.ExtractStudyInformation(tags);
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146 break;
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147
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148 case ResourceType_Series:
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149 dicomSummary.ExtractSeriesInformation(tags);
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150 break;
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151
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152 case ResourceType_Instance:
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153 dicomSummary.ExtractInstanceInformation(tags);
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154 break;
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155
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156 default:
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157 throw OrthancException(ErrorCode_InternalError);
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158 }
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159
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160 StoreMainDicomTagsInternal(*this, resource, tags);
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161 }
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162
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163
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164 namespace ServerToolbox
213
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165 {
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166 void SimplifyTags(Json::Value& target,
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167 const Json::Value& source,
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168 DicomToJsonFormat format)
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169 {
2951
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
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170 if (!source.isObject())
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171 {
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172 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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173 }
213
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174
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175 target = Json::objectValue;
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176 Json::Value::Members members = source.getMemberNames();
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177
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178 for (size_t i = 0; i < members.size(); i++)
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179 {
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180 const Json::Value& v = source[members[i]];
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181 const std::string& type = v["Type"].asString();
213
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182
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183 std::string name;
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184 switch (format)
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185 {
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c7d70f659190 DicomToJsonFormat_Simple -> DicomToJsonFormat_Human
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186 case DicomToJsonFormat_Human:
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187 name = v["Name"].asString();
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188 break;
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189
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190 case DicomToJsonFormat_Short:
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191 name = members[i];
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192 break;
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193
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194 default:
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195 throw OrthancException(ErrorCode_ParameterOutOfRange);
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196 }
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197
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198 if (type == "String")
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199 {
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200 target[name] = v["Value"].asString();
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201 }
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202 else if (type == "TooLong" ||
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203 type == "Null")
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204 {
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205 target[name] = Json::nullValue;
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206 }
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207 else if (type == "Sequence")
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208 {
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209 const Json::Value& array = v["Value"];
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210 assert(array.isArray());
213
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211
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212 Json::Value children = Json::arrayValue;
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213 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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214 {
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diff changeset
215 Json::Value c;
1859
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216 SimplifyTags(c, array[i], format);
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217 children.append(c);
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218 }
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219
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220 target[name] = children;
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221 }
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222 else
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223 {
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diff changeset
224 assert(0);
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225 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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226 }
1668
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227 }
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228
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229
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230 bool FindOneChildInstance(int64_t& result,
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231 IDatabaseWrapper& database,
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232 int64_t resource,
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233 ResourceType type)
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234 {
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diff changeset
235 for (;;)
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236 {
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237 if (type == ResourceType_Instance)
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238 {
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diff changeset
239 result = resource;
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240 return true;
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241 }
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242
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diff changeset
243 std::list<int64_t> children;
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244 database.GetChildrenInternalId(children, resource);
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245 if (children.empty())
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246 {
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247 return false;
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248 }
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249
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250 resource = children.front();
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251 type = GetChildResourceType(type);
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252 }
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253 }
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254
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255
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256 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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257 IStorageArea& storageArea,
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258 ResourceType level)
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259 {
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260 // WARNING: The database should be locked with a transaction!
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261
2129
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262 // TODO: This function might consume much memory if level ==
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263 // ResourceType_Instance. To improve this, first download the
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264 // list of studies, then remove the instances for each single
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265 // study (check out OrthancRestApi::InvalidateTags for an
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266 // example). Take this improvement into consideration for the
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267 // next upgrade of the database schema.
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268
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diff changeset
269 const char* plural = NULL;
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270
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
271 switch (level)
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diff changeset
272 {
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273 case ResourceType_Patient:
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274 plural = "patients";
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275 break;
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276
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277 case ResourceType_Study:
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278 plural = "studies";
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diff changeset
279 break;
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diff changeset
280
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diff changeset
281 case ResourceType_Series:
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282 plural = "series";
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diff changeset
283 break;
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diff changeset
284
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diff changeset
285 case ResourceType_Instance:
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286 plural = "instances";
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287 break;
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diff changeset
288
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289 default:
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290 throw OrthancException(ErrorCode_InternalError);
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291 }
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292
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293 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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294
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295 std::list<std::string> resources;
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296 database.GetAllPublicIds(resources, level);
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297
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298 for (std::list<std::string>::const_iterator
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299 it = resources.begin(); it != resources.end(); ++it)
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300 {
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301 // Locate the resource and one of its child instances
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302 int64_t resource, instance;
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303 ResourceType tmp;
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304
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305 if (!database.LookupResource(resource, tmp, *it) ||
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306 tmp != level ||
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307 !FindOneChildInstance(instance, database, resource, level))
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308 {
2955
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309 throw OrthancException(ErrorCode_InternalError,
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310 "Cannot find an instance for " +
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311 std::string(EnumerationToString(level)) +
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312 " with identifier " + *it);
1668
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313 }
de1413733c97 reconstructing main dicom tags
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314
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315 // Get the DICOM file attached to some instances in the resource
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316 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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317 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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318 {
2955
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319 throw OrthancException(ErrorCode_InternalError,
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320 "Cannot retrieve the DICOM file associated with instance " +
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321 database.GetPublicId(instance));
1668
de1413733c97 reconstructing main dicom tags
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322 }
de1413733c97 reconstructing main dicom tags
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323
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
324 try
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diff changeset
325 {
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diff changeset
326 // Read and parse the content of the DICOM file
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diff changeset
327 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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328
1870
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diff changeset
329 std::string content;
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diff changeset
330 accessor.Read(content, attachment);
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parents: 1860
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331
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diff changeset
332 ParsedDicomFile dicom(content);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
333
1870
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334 // Update the tags of this resource
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diff changeset
335 DicomMap dicomSummary;
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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parents: 2129
diff changeset
336 dicom.ExtractDicomSummary(dicomSummary);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
337
1870
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diff changeset
338 database.ClearMainDicomTags(resource);
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
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339
683d572424b6 IDatabaseWrapper::SetResourcesContent
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340 ResourcesContent tags;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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341 tags.AddResource(resource, level, dicomSummary);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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342 database.SetResourcesContent(tags);
1870
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diff changeset
343 }
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
344 catch (OrthancException&)
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
345 {
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
346 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
347 << " associated with instance " << database.GetPublicId(instance);
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
348 throw;
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
349 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
351 }
2121
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parents: 2120
diff changeset
352
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parents: 2120
diff changeset
353
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
354 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
355 size_t& size,
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
356 ResourceType level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
357 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
358 switch (level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
359 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
360 case ResourceType_Patient:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
361 tags = PATIENT_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
362 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
363 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
364
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
365 case ResourceType_Study:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
366 tags = STUDY_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
367 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
368 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
369
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
370 case ResourceType_Series:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
371 tags = SERIES_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
372 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
373 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
374
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
375 case ResourceType_Instance:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
376 tags = INSTANCE_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
377 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
378 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
379
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
380 default:
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
381 throw OrthancException(ErrorCode_ParameterOutOfRange);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
382 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
383 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
384
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
385
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
386 std::string NormalizeIdentifier(const std::string& value)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
387 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
388 std::string t;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
389 t.reserve(value.size());
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
390
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
391 for (size_t i = 0; i < value.size(); i++)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
392 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
393 if (value[i] == '%' ||
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
394 value[i] == '_')
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
395 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
396 t.push_back(' '); // These characters might break wildcard queries in SQL
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
397 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
398 else if (isascii(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
399 !iscntrl(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
400 (!isspace(value[i]) || value[i] == ' '))
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
401 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
402 t.push_back(value[i]);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
403 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
404 }
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 Toolbox::ToUpperCase(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
407
7e8889bc95c6 refactoring
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408 return Toolbox::StripSpaces(t);
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409 }
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410
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411
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412 bool IsIdentifier(const DicomTag& tag,
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413 ResourceType level)
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Sebastien Jodogne <s.jodogne@gmail.com>
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414 {
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Sebastien Jodogne <s.jodogne@gmail.com>
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415 const DicomTag* tags;
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416 size_t size;
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417
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Sebastien Jodogne <s.jodogne@gmail.com>
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418 LoadIdentifiers(tags, size, level);
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Sebastien Jodogne <s.jodogne@gmail.com>
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419
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420 for (size_t i = 0; i < size; i++)
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421 {
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422 if (tag == tags[i])
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parents: 2120
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423 {
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424 return true;
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425 }
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426 }
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427
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428 return false;
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429 }
2209
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430
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parents: 2129
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431
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432 void ReconstructResource(ServerContext& context,
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433 const std::string& resource)
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434 {
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435 LOG(WARNING) << "Reconstructing resource " << resource;
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parents: 2129
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436
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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437 std::list<std::string> instances;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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438 context.GetIndex().GetChildInstances(instances, resource);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
439
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parents: 2129
diff changeset
440 for (std::list<std::string>::const_iterator
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441 it = instances.begin(); it != instances.end(); ++it)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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442 {
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443 ServerContext::DicomCacheLocker locker(context, *it);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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444
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445 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
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446 locker.GetDicom().DatasetToJson(dicomAsJson);
2209
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447
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448 std::string s = dicomAsJson.toStyledString();
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Sebastien Jodogne <s.jodogne@gmail.com>
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449 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
450
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
451 context.GetIndex().ReconstructInstance(locker.GetDicom());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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452 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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453 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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454 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
455 }