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annotate OrthancServer/ServerToolbox.cpp @ 2122:2ecc95a239f7

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cleaning up
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 07 Nov 2016 11:33:18 +0100
parents 7e8889bc95c6
children 1cf093cbdad8
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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
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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 std::string ValueAsString(const DicomMap& summary,
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139 const DicomTag& tag)
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140 {
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141 const DicomValue& value = summary.GetValue(tag);
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142 if (value.IsNull())
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143 {
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144 return "(null)";
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145 }
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146 else
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147 {
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148 return value.GetContent();
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149 }
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150 }
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151
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152
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153 void LogMissingRequiredTag(const DicomMap& summary)
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154 {
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155 std::string s, t;
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156
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157 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
213
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158 {
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159 if (t.size() > 0)
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160 t += ", ";
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161 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID);
213
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162 }
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163 else
213
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164 {
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165 if (s.size() > 0)
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166 s += ", ";
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167 s += "PatientID";
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168 }
213
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169
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170 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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171 {
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172 if (t.size() > 0)
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173 t += ", ";
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174 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID);
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175 }
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176 else
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177 {
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178 if (s.size() > 0)
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179 s += ", ";
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180 s += "StudyInstanceUID";
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181 }
213
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182
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183 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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184 {
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185 if (t.size() > 0)
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186 t += ", ";
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187 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID);
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188 }
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189 else
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190 {
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191 if (s.size() > 0)
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192 s += ", ";
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193 s += "SeriesInstanceUID";
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194 }
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195
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196 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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197 {
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198 if (t.size() > 0)
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199 t += ", ";
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200 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID);
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201 }
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202 else
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203 {
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204 if (s.size() > 0)
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205 s += ", ";
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206 s += "SOPInstanceUID";
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207 }
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diff changeset
208
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209 if (t.size() == 0)
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210 {
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diff changeset
211 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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212 }
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213 else
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214 {
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215 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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216 }
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217 }
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218
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219
2120
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220 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database,
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221 int64_t resource,
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222 const DicomMap& tags)
1716
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223 {
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224 DicomArray flattened(tags);
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225
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226 for (size_t i = 0; i < flattened.GetSize(); i++)
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227 {
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228 const DicomElement& element = flattened.GetElement(i);
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diff changeset
229 const DicomTag& tag = element.GetTag();
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230 const DicomValue& value = element.GetValue();
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diff changeset
231 if (!value.IsNull() &&
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diff changeset
232 !value.IsBinary())
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233 {
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diff changeset
234 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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235 }
1716
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236 }
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237 }
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238
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239
2120
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diff changeset
240 void StoreMainDicomTags(IDatabaseWrapper& database,
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241 int64_t resource,
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242 ResourceType level,
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diff changeset
243 const DicomMap& dicomSummary)
1668
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244 {
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245 // WARNING: The database should be locked with a transaction!
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diff changeset
246
2121
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diff changeset
247 StoreIdentifiers(database, resource, level, dicomSummary);
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diff changeset
248
1668
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249 DicomMap tags;
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diff changeset
250
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diff changeset
251 switch (level)
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252 {
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253 case ResourceType_Patient:
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diff changeset
254 dicomSummary.ExtractPatientInformation(tags);
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255 break;
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256
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diff changeset
257 case ResourceType_Study:
1717
3926e6317a43 SetIdentifierTagInternal
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diff changeset
258 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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diff changeset
259 dicomSummary.ExtractPatientInformation(tags);
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diff changeset
260 StoreMainDicomTagsInternal(database, resource, tags);
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diff changeset
261
1668
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262 dicomSummary.ExtractStudyInformation(tags);
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263 break;
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diff changeset
264
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diff changeset
265 case ResourceType_Series:
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266 dicomSummary.ExtractSeriesInformation(tags);
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267 break;
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268
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diff changeset
269 case ResourceType_Instance:
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diff changeset
270 dicomSummary.ExtractInstanceInformation(tags);
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diff changeset
271 break;
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272
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273 default:
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274 throw OrthancException(ErrorCode_InternalError);
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275 }
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276
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277 StoreMainDicomTagsInternal(database, resource, tags);
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278 }
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279
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280
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281 bool FindOneChildInstance(int64_t& result,
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282 IDatabaseWrapper& database,
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283 int64_t resource,
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284 ResourceType type)
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285 {
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286 for (;;)
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287 {
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288 if (type == ResourceType_Instance)
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289 {
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290 result = resource;
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291 return true;
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292 }
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293
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294 std::list<int64_t> children;
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295 database.GetChildrenInternalId(children, resource);
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296 if (children.empty())
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297 {
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298 return false;
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299 }
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300
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301 resource = children.front();
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302 type = GetChildResourceType(type);
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303 }
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304 }
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305
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306
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307 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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308 IStorageArea& storageArea,
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309 ResourceType level)
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310 {
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311 // WARNING: The database should be locked with a transaction!
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312
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313 const char* plural = NULL;
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314
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315 switch (level)
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316 {
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317 case ResourceType_Patient:
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318 plural = "patients";
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319 break;
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320
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321 case ResourceType_Study:
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322 plural = "studies";
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323 break;
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324
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325 case ResourceType_Series:
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326 plural = "series";
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diff changeset
327 break;
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328
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329 case ResourceType_Instance:
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330 plural = "instances";
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331 break;
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332
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333 default:
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334 throw OrthancException(ErrorCode_InternalError);
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335 }
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diff changeset
336
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337 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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diff changeset
338
1668
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339 std::list<std::string> resources;
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340 database.GetAllPublicIds(resources, level);
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341
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342 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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parents: 1747
diff changeset
343 it = resources.begin(); it != resources.end(); ++it)
1668
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344 {
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345 // Locate the resource and one of its child instances
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346 int64_t resource, instance;
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347 ResourceType tmp;
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348
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diff changeset
349 if (!database.LookupResource(resource, tmp, *it) ||
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350 tmp != level ||
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351 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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352 {
1870
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parents: 1860
diff changeset
353 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level)
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parents: 1860
diff changeset
354 << " with identifier " << *it;
1668
de1413733c97 reconstructing main dicom tags
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355 throw OrthancException(ErrorCode_InternalError);
de1413733c97 reconstructing main dicom tags
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356 }
de1413733c97 reconstructing main dicom tags
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diff changeset
357
de1413733c97 reconstructing main dicom tags
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diff changeset
358 // Get the DICOM file attached to some instances in the resource
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diff changeset
359 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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diff changeset
360 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
361 {
1870
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parents: 1860
diff changeset
362 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
363 throw OrthancException(ErrorCode_InternalError);
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
364 }
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
365
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
366 try
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parents: 1860
diff changeset
367 {
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parents: 1860
diff changeset
368 // Read and parse the content of the DICOM file
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parents: 1860
diff changeset
369 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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parents: 1669
diff changeset
370
1870
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diff changeset
371 std::string content;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
372 accessor.Read(content, attachment);
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parents: 1860
diff changeset
373
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
374 ParsedDicomFile dicom(content);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
375
1870
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
376 // Update the tags of this resource
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
377 DicomMap dicomSummary;
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parents: 1860
diff changeset
378 dicom.Convert(dicomSummary);
1668
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
379
1870
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parents: 1860
diff changeset
380 database.ClearMainDicomTags(resource);
2120
4b02ec79728a refactoring
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diff changeset
381 StoreMainDicomTags(database, resource, level, dicomSummary);
1870
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parents: 1860
diff changeset
382 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
383 catch (OrthancException&)
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
384 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
385 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
386 << " associated with instance " << database.GetPublicId(instance);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
387 throw;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
388 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 }
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
391
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
392
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
393 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
394 size_t& size,
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
395 ResourceType level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
396 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
397 switch (level)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
398 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
399 case ResourceType_Patient:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
400 tags = patientIdentifiers;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
401 size = sizeof(patientIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
402 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
403
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
404 case ResourceType_Study:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
405 tags = studyIdentifiers;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
406 size = sizeof(studyIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
407 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
408
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
409 case ResourceType_Series:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
410 tags = seriesIdentifiers;
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411 size = sizeof(seriesIdentifiers) / sizeof(DicomTag);
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412 break;
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413
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414 case ResourceType_Instance:
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415 tags = instanceIdentifiers;
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416 size = sizeof(instanceIdentifiers) / sizeof(DicomTag);
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417 break;
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418
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419 default:
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420 throw OrthancException(ErrorCode_ParameterOutOfRange);
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421 }
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422 }
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423
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424
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425 std::string NormalizeIdentifier(const std::string& value)
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426 {
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427 std::string t;
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428 t.reserve(value.size());
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429
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430 for (size_t i = 0; i < value.size(); i++)
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431 {
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432 if (value[i] == '%' ||
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433 value[i] == '_')
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434 {
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435 t.push_back(' '); // These characters might break wildcard queries in SQL
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436 }
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437 else if (isascii(value[i]) &&
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438 !iscntrl(value[i]) &&
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439 (!isspace(value[i]) || value[i] == ' '))
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440 {
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441 t.push_back(value[i]);
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442 }
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443 }
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444
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445 Toolbox::ToUpperCase(t);
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446
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447 return Toolbox::StripSpaces(t);
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448 }
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449
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450
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451 bool IsIdentifier(const DicomTag& tag,
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452 ResourceType level)
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453 {
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454 const DicomTag* tags;
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455 size_t size;
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456
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457 LoadIdentifiers(tags, size, level);
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458
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459 for (size_t i = 0; i < size; i++)
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460 {
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461 if (tag == tags[i])
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462 {
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463 return true;
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464 }
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465 }
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466
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467 return false;
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468 }
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diff changeset
469
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470
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471 void StoreIdentifiers(IDatabaseWrapper& database,
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472 int64_t resource,
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473 ResourceType level,
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474 const DicomMap& map)
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475 {
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476 const DicomTag* tags;
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477 size_t size;
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478
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479 LoadIdentifiers(tags, size, level);
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diff changeset
480
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481 for (size_t i = 0; i < size; i++)
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482 {
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483 const DicomValue* value = map.TestAndGetValue(tags[i]);
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484 if (value != NULL &&
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Sebastien Jodogne <s.jodogne@gmail.com>
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485 !value->IsNull() &&
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486 !value->IsBinary())
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487 {
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diff changeset
488 std::string s = NormalizeIdentifier(value->GetContent());
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
489 database.SetIdentifierTag(resource, tags[i], s);
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490 }
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diff changeset
491 }
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diff changeset
492 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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493 }
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parents:
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494 }