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annotate OrthancServer/ServerToolbox.cpp @ 2121:7e8889bc95c6

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 07 Nov 2016 11:28:12 +0100
parents 4b02ec79728a
children 2ecc95a239f7
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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "PrecompiledHeadersServer.h"
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34 #include "ServerToolbox.h"
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35
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36 #include "../Core/DicomFormat/DicomArray.h"
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37 #include "../Core/FileStorage/StorageAccessor.h"
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38 #include "../Core/Logging.h"
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39 #include "../Core/OrthancException.h"
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40 #include "ParsedDicomFile.h"
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41 #include "Search/LookupIdentifierQuery.h"
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42
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43 #include <cassert>
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44
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45 namespace Orthanc
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46 {
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47 namespace ServerToolbox
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48 {
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49 static const DicomTag patientIdentifiers[] =
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50 {
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51 DICOM_TAG_PATIENT_ID,
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52 DICOM_TAG_PATIENT_NAME,
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53 DICOM_TAG_PATIENT_BIRTH_DATE
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54 };
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55
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56 static const DicomTag studyIdentifiers[] =
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57 {
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58 DICOM_TAG_PATIENT_ID,
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59 DICOM_TAG_PATIENT_NAME,
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60 DICOM_TAG_PATIENT_BIRTH_DATE,
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61 DICOM_TAG_STUDY_INSTANCE_UID,
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62 DICOM_TAG_ACCESSION_NUMBER,
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63 DICOM_TAG_STUDY_DESCRIPTION,
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64 DICOM_TAG_STUDY_DATE
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65 };
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66
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67 static const DicomTag seriesIdentifiers[] =
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68 {
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69 DICOM_TAG_SERIES_INSTANCE_UID
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70 };
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71
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72 static const DicomTag instanceIdentifiers[] =
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73 {
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74 DICOM_TAG_SOP_INSTANCE_UID
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75 };
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76
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77
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78 void SimplifyTags(Json::Value& target,
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79 const Json::Value& source,
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80 DicomToJsonFormat format)
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81 {
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82 assert(source.isObject());
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83
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84 target = Json::objectValue;
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85 Json::Value::Members members = source.getMemberNames();
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86
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87 for (size_t i = 0; i < members.size(); i++)
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88 {
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89 const Json::Value& v = source[members[i]];
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90 const std::string& type = v["Type"].asString();
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91
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92 std::string name;
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93 switch (format)
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94 {
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95 case DicomToJsonFormat_Human:
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96 name = v["Name"].asString();
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97 break;
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98
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99 case DicomToJsonFormat_Short:
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100 name = members[i];
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101 break;
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102
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103 default:
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104 throw OrthancException(ErrorCode_ParameterOutOfRange);
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105 }
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106
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107 if (type == "String")
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108 {
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109 target[name] = v["Value"].asString();
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110 }
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111 else if (type == "TooLong" ||
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112 type == "Null")
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113 {
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114 target[name] = Json::nullValue;
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115 }
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116 else if (type == "Sequence")
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117 {
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118 const Json::Value& array = v["Value"];
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119 assert(array.isArray());
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120
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121 Json::Value children = Json::arrayValue;
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122 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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123 {
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124 Json::Value c;
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125 SimplifyTags(c, array[i], format);
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126 children.append(c);
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127 }
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128
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129 target[name] = children;
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130 }
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131 else
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132 {
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133 assert(0);
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134 }
213
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135 }
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136 }
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137
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138
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139 static std::string ValueAsString(const DicomMap& summary,
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140 const DicomTag& tag)
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141 {
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142 const DicomValue& value = summary.GetValue(tag);
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143 if (value.IsNull())
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144 {
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145 return "(null)";
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146 }
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147 else
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148 {
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149 return value.GetContent();
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150 }
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151 }
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152
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153
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154 void LogMissingRequiredTag(const DicomMap& summary)
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155 {
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156 std::string s, t;
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157
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158 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
213
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159 {
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160 if (t.size() > 0)
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161 t += ", ";
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162 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID);
213
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163 }
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164 else
213
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165 {
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166 if (s.size() > 0)
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167 s += ", ";
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168 s += "PatientID";
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169 }
213
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170
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171 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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172 {
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173 if (t.size() > 0)
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174 t += ", ";
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175 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID);
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176 }
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177 else
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178 {
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179 if (s.size() > 0)
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180 s += ", ";
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181 s += "StudyInstanceUID";
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182 }
213
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183
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184 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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185 {
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186 if (t.size() > 0)
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187 t += ", ";
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188 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID);
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189 }
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190 else
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191 {
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192 if (s.size() > 0)
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193 s += ", ";
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194 s += "SeriesInstanceUID";
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195 }
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196
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197 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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198 {
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199 if (t.size() > 0)
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200 t += ", ";
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201 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID);
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202 }
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203 else
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204 {
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205 if (s.size() > 0)
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206 s += ", ";
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207 s += "SOPInstanceUID";
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208 }
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diff changeset
209
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210 if (t.size() == 0)
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211 {
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212 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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213 }
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214 else
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215 {
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216 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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217 }
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218 }
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219
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220
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221 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database,
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222 int64_t resource,
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223 const DicomMap& tags)
1716
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224 {
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225 DicomArray flattened(tags);
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226
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227 for (size_t i = 0; i < flattened.GetSize(); i++)
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228 {
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229 const DicomElement& element = flattened.GetElement(i);
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230 const DicomTag& tag = element.GetTag();
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231 const DicomValue& value = element.GetValue();
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232 if (!value.IsNull() &&
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233 !value.IsBinary())
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234 {
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235 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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236 }
1716
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237 }
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238 }
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239
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240
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diff changeset
241 void StoreMainDicomTags(IDatabaseWrapper& database,
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242 int64_t resource,
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243 ResourceType level,
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244 const DicomMap& dicomSummary)
1668
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245 {
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246 // WARNING: The database should be locked with a transaction!
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diff changeset
247
2121
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diff changeset
248 StoreIdentifiers(database, resource, level, dicomSummary);
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249
1668
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250 DicomMap tags;
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251
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diff changeset
252 switch (level)
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253 {
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254 case ResourceType_Patient:
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255 dicomSummary.ExtractPatientInformation(tags);
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256 break;
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257
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diff changeset
258 case ResourceType_Study:
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3926e6317a43 SetIdentifierTagInternal
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diff changeset
259 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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diff changeset
260 dicomSummary.ExtractPatientInformation(tags);
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diff changeset
261 StoreMainDicomTagsInternal(database, resource, tags);
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diff changeset
262
1668
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263 dicomSummary.ExtractStudyInformation(tags);
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264 break;
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265
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266 case ResourceType_Series:
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267 dicomSummary.ExtractSeriesInformation(tags);
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268 break;
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269
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diff changeset
270 case ResourceType_Instance:
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diff changeset
271 dicomSummary.ExtractInstanceInformation(tags);
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272 break;
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273
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274 default:
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275 throw OrthancException(ErrorCode_InternalError);
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276 }
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277
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diff changeset
278 StoreMainDicomTagsInternal(database, resource, tags);
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279 }
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280
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281
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282 bool FindOneChildInstance(int64_t& result,
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283 IDatabaseWrapper& database,
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284 int64_t resource,
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285 ResourceType type)
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286 {
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287 for (;;)
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288 {
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289 if (type == ResourceType_Instance)
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290 {
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291 result = resource;
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292 return true;
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293 }
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294
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295 std::list<int64_t> children;
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296 database.GetChildrenInternalId(children, resource);
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297 if (children.empty())
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298 {
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299 return false;
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300 }
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301
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302 resource = children.front();
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303 type = GetChildResourceType(type);
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304 }
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305 }
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306
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307
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308 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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309 IStorageArea& storageArea,
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310 ResourceType level)
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311 {
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312 // WARNING: The database should be locked with a transaction!
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313
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314 const char* plural = NULL;
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315
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316 switch (level)
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317 {
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318 case ResourceType_Patient:
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319 plural = "patients";
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320 break;
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321
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322 case ResourceType_Study:
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323 plural = "studies";
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324 break;
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325
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326 case ResourceType_Series:
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327 plural = "series";
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diff changeset
328 break;
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329
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330 case ResourceType_Instance:
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331 plural = "instances";
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332 break;
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333
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334 default:
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335 throw OrthancException(ErrorCode_InternalError);
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336 }
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diff changeset
337
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338 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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339
1668
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340 std::list<std::string> resources;
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341 database.GetAllPublicIds(resources, level);
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342
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343 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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diff changeset
344 it = resources.begin(); it != resources.end(); ++it)
1668
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345 {
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346 // Locate the resource and one of its child instances
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347 int64_t resource, instance;
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348 ResourceType tmp;
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349
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350 if (!database.LookupResource(resource, tmp, *it) ||
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351 tmp != level ||
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352 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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353 {
1870
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diff changeset
354 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level)
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parents: 1860
diff changeset
355 << " with identifier " << *it;
1668
de1413733c97 reconstructing main dicom tags
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356 throw OrthancException(ErrorCode_InternalError);
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357 }
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diff changeset
358
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diff changeset
359 // Get the DICOM file attached to some instances in the resource
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diff changeset
360 FileInfo attachment;
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diff changeset
361 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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diff changeset
362 {
1870
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diff changeset
363 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
364 throw OrthancException(ErrorCode_InternalError);
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
365 }
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
366
1870
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diff changeset
367 try
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diff changeset
368 {
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diff changeset
369 // Read and parse the content of the DICOM file
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diff changeset
370 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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parents: 1669
diff changeset
371
1870
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diff changeset
372 std::string content;
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parents: 1860
diff changeset
373 accessor.Read(content, attachment);
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parents: 1860
diff changeset
374
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diff changeset
375 ParsedDicomFile dicom(content);
1668
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diff changeset
376
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parents: 1860
diff changeset
377 // Update the tags of this resource
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diff changeset
378 DicomMap dicomSummary;
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diff changeset
379 dicom.Convert(dicomSummary);
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diff changeset
380
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diff changeset
381 database.ClearMainDicomTags(resource);
2120
4b02ec79728a refactoring
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diff changeset
382 StoreMainDicomTags(database, resource, level, dicomSummary);
1870
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parents: 1860
diff changeset
383 }
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parents: 1860
diff changeset
384 catch (OrthancException&)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
385 {
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parents: 1860
diff changeset
386 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
387 << " associated with instance " << database.GetPublicId(instance);
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parents: 1860
diff changeset
388 throw;
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parents: 1860
diff changeset
389 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
391 }
2121
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
392
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
393
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
394 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
395 size_t& size,
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
396 ResourceType level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
397 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
398 switch (level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
399 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
400 case ResourceType_Patient:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
401 tags = patientIdentifiers;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
402 size = sizeof(patientIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
403 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
404
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
405 case ResourceType_Study:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
406 tags = studyIdentifiers;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
407 size = sizeof(studyIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
408 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
409
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
410 case ResourceType_Series:
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411 tags = seriesIdentifiers;
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412 size = sizeof(seriesIdentifiers) / sizeof(DicomTag);
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413 break;
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414
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415 case ResourceType_Instance:
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416 tags = instanceIdentifiers;
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417 size = sizeof(instanceIdentifiers) / sizeof(DicomTag);
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418 break;
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419
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420 default:
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421 throw OrthancException(ErrorCode_ParameterOutOfRange);
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422 }
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423 }
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424
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425
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426 std::string NormalizeIdentifier(const std::string& value)
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427 {
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428 std::string t;
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429 t.reserve(value.size());
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430
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431 for (size_t i = 0; i < value.size(); i++)
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432 {
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433 if (value[i] == '%' ||
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434 value[i] == '_')
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435 {
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436 t.push_back(' '); // These characters might break wildcard queries in SQL
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437 }
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438 else if (isascii(value[i]) &&
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439 !iscntrl(value[i]) &&
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440 (!isspace(value[i]) || value[i] == ' '))
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441 {
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442 t.push_back(value[i]);
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443 }
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444 }
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445
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446 Toolbox::ToUpperCase(t);
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447
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448 return Toolbox::StripSpaces(t);
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449 }
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diff changeset
450
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451
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452 bool IsIdentifier(const DicomTag& tag,
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453 ResourceType level)
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454 {
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455 const DicomTag* tags;
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456 size_t size;
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diff changeset
457
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458 LoadIdentifiers(tags, size, level);
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diff changeset
459
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diff changeset
460 for (size_t i = 0; i < size; i++)
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diff changeset
461 {
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diff changeset
462 if (tag == tags[i])
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diff changeset
463 {
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diff changeset
464 return true;
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diff changeset
465 }
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diff changeset
466 }
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diff changeset
467
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diff changeset
468 return false;
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parents: 2120
diff changeset
469 }
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parents: 2120
diff changeset
470
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diff changeset
471
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
472 void StoreIdentifiers(IDatabaseWrapper& database,
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diff changeset
473 int64_t resource,
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474 ResourceType level,
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diff changeset
475 const DicomMap& map)
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diff changeset
476 {
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diff changeset
477 const DicomTag* tags;
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diff changeset
478 size_t size;
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diff changeset
479
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diff changeset
480 LoadIdentifiers(tags, size, level);
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diff changeset
481
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diff changeset
482 for (size_t i = 0; i < size; i++)
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
483 {
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
484 const DicomValue* value = map.TestAndGetValue(tags[i]);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
485 if (value != NULL &&
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
486 !value->IsNull() &&
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
487 !value->IsBinary())
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
488 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
489 std::string s = NormalizeIdentifier(value->GetContent());
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
490 database.SetIdentifierTag(resource, tags[i], s);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
491 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
492 }
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parents: 2120
diff changeset
493 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
494 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 }