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annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 1368:b22ba8c5edbe query-retrieve

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 26 May 2015 17:54:34 +0200
parents 6e7e5ed91c2d
children 02f5a3f5c0a0
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2015 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 "OrthancRestApi.h"
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35
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36 #include "../FromDcmtkBridge.h"
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37 #include "../../Core/Uuid.h"
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38
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39 #include <glog/logging.h>
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40
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41 namespace Orthanc
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42 {
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43 // Modification of DICOM instances ------------------------------------------
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44
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45 enum TagOperation
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46 {
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47 TagOperation_Keep,
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48 TagOperation_Remove
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49 };
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50
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51 static void ParseListOfTags(DicomModification& target,
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52 const Json::Value& query,
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53 TagOperation operation)
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54 {
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55 if (!query.isArray())
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56 {
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57 throw OrthancException(ErrorCode_BadRequest);
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58 }
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59
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60 for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
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61 {
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62 std::string name = query[i].asString();
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63
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64 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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65
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66 switch (operation)
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67 {
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68 case TagOperation_Keep:
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69 target.Keep(tag);
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70 VLOG(1) << "Keep: " << name << " " << tag << std::endl;
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71 break;
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72
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73 case TagOperation_Remove:
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74 target.Remove(tag);
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75 VLOG(1) << "Remove: " << name << " " << tag << std::endl;
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76 break;
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77
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78 default:
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79 throw OrthancException(ErrorCode_InternalError);
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80 }
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81 }
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82 }
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83
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84
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85 static void ParseReplacements(DicomModification& target,
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86 const Json::Value& replacements)
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87 {
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88 if (!replacements.isObject())
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89 {
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90 throw OrthancException(ErrorCode_BadRequest);
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91 }
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92
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93 Json::Value::Members members = replacements.getMemberNames();
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94 for (size_t i = 0; i < members.size(); i++)
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95 {
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96 const std::string& name = members[i];
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97 std::string value = replacements[name].asString();
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98
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99 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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100 target.Replace(tag, value);
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101
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102 VLOG(1) << "Replace: " << name << " " << tag << " == " << value << std::endl;
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103 }
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104 }
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105
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106
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107 static std::string GeneratePatientName(ServerContext& context)
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108 {
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109 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence);
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110 return "Anonymized" + boost::lexical_cast<std::string>(seq);
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111 }
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112
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113
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114
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115 bool OrthancRestApi::ParseModifyRequest(DicomModification& target,
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116 const Json::Value& request)
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117 {
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118 if (request.isObject())
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119 {
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120 if (request.isMember("RemovePrivateTags"))
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121 {
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122 target.SetRemovePrivateTags(true);
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123 }
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124
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125 if (request.isMember("Remove"))
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126 {
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127 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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128 }
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129
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130 if (request.isMember("Replace"))
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131 {
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132 ParseReplacements(target, request["Replace"]);
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133 }
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134
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135 return true;
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136 }
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137 else
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138 {
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139 return false;
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140 }
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141 }
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142
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143
1010
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144 static bool ParseModifyRequest(DicomModification& target,
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145 const RestApiPostCall& call)
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146 {
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147 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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148
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149 Json::Value request;
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150 if (call.ParseJsonRequest(request))
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151 {
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152 return OrthancRestApi::ParseModifyRequest(target, request);
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153 }
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154 else
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155 {
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156 return false;
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157 }
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158 }
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159
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160
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161 static bool ParseAnonymizationRequest(DicomModification& target,
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162 RestApiPostCall& call)
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163 {
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164 // curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"hello","0010-0020":"world"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": null,"Remove":["Modality"]}' > Anonymized.dcm
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165
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166 target.SetupAnonymization();
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167 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME);
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168
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169 Json::Value request;
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170 if (call.ParseJsonRequest(request) && request.isObject())
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171 {
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172 if (request.isMember("KeepPrivateTags"))
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173 {
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174 target.SetRemovePrivateTags(false);
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175 }
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176
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177 if (request.isMember("Remove"))
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178 {
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179 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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180 }
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181
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182 if (request.isMember("Replace"))
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183 {
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184 ParseReplacements(target, request["Replace"]);
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185 }
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186
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187 if (request.isMember("Keep"))
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188 {
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189 ParseListOfTags(target, request["Keep"], TagOperation_Keep);
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190 }
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191
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192 if (target.IsReplaced(DICOM_TAG_PATIENT_NAME) &&
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193 target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName)
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194 {
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195 // Overwrite the random Patient's Name by one that is more
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196 // user-friendly (provided none was specified by the user)
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197 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)), true);
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198 }
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199
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200 return true;
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201 }
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202 else
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203 {
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204 return false;
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205 }
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206 }
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207
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208
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209 static void AnonymizeOrModifyInstance(DicomModification& modification,
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210 RestApiPostCall& call)
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211 {
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212 std::string id = call.GetUriComponent("id", "");
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213
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214 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id);
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215
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216 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone());
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217 modification.Apply(*modified);
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218 modified->Answer(call.GetOutput());
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219 }
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220
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221
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diff changeset
222 static void AnonymizeOrModifyResource(DicomModification& modification,
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223 MetadataType metadataType,
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224 ChangeType changeType,
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225 ResourceType resourceType,
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226 RestApiPostCall& call)
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227 {
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228 bool isFirst = true;
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229 Json::Value result(Json::objectValue);
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230
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diff changeset
231 ServerContext& context = OrthancRestApi::GetContext(call);
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232
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233 typedef std::list<std::string> Instances;
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234 Instances instances;
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235 std::string id = call.GetUriComponent("id", "");
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diff changeset
236 context.GetIndex().GetChildInstances(instances, id);
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237
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diff changeset
238 if (instances.empty())
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diff changeset
239 {
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diff changeset
240 return;
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diff changeset
241 }
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242
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diff changeset
243
751
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244 /**
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245 * Loop over all the instances of the resource.
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246 **/
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247
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248 for (Instances::const_iterator it = instances.begin();
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diff changeset
249 it != instances.end(); ++it)
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250 {
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diff changeset
251 LOG(INFO) << "Modifying instance " << *it;
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diff changeset
252
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diff changeset
253 std::auto_ptr<ServerContext::DicomCacheLocker> locker;
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diff changeset
254
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diff changeset
255 try
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diff changeset
256 {
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diff changeset
257 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it));
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258 }
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diff changeset
259 catch (OrthancException&)
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diff changeset
260 {
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diff changeset
261 // This child instance has been removed in between
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262 continue;
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diff changeset
263 }
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diff changeset
264
1129
8dabdc0d3007 fix possible deadlock
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diff changeset
265
778
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diff changeset
266 ParsedDicomFile& original = locker->GetDicom();
751
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267 DicomInstanceHasher originalHasher = original.GetHasher();
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268
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269
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diff changeset
270 /**
1002
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diff changeset
271 * Compute the resulting DICOM instance.
751
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diff changeset
272 **/
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273
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diff changeset
274 std::auto_ptr<ParsedDicomFile> modified(original.Clone());
787
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diff changeset
275 modification.Apply(*modified);
751
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276
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277 DicomInstanceToStore toStore;
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278 toStore.SetParsedDicomFile(*modified);
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279
1002
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280
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281 /**
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282 * Prepare the metadata information to associate with the
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283 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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284 **/
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285
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286 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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287
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288 if (originalHasher.HashSeries() != modifiedHasher.HashSeries())
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289 {
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290 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher.HashSeries());
1002
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291 }
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292
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293 if (originalHasher.HashStudy() != modifiedHasher.HashStudy())
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294 {
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295 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher.HashStudy());
1002
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296 }
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297
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298 if (originalHasher.HashPatient() != modifiedHasher.HashPatient())
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299 {
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300 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher.HashPatient());
1002
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301 }
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302
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303 assert(*it == originalHasher.HashInstance());
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304 toStore.AddMetadata(ResourceType_Instance, metadataType, *it);
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305
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306
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307 /**
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308 * Store the resulting DICOM instance into the Orthanc store.
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309 **/
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310
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311 std::string modifiedInstance;
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312 if (context.Store(modifiedInstance, toStore) != StoreStatus_Success)
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313 {
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314 LOG(ERROR) << "Error while storing a modified instance " << *it;
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315 return;
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316 }
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317
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318 // Sanity checks in debug mode
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319 assert(modifiedInstance == modifiedHasher.HashInstance());
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320
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321
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322 /**
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323 * Compute the JSON object that is returned by the REST call.
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324 **/
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325
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326 if (isFirst)
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327 {
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328 std::string newId;
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329
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330 switch (resourceType)
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331 {
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332 case ResourceType_Series:
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333 newId = modifiedHasher.HashSeries();
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334 break;
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335
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336 case ResourceType_Study:
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337 newId = modifiedHasher.HashStudy();
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338 break;
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339
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diff changeset
340 case ResourceType_Patient:
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341 newId = modifiedHasher.HashPatient();
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342 break;
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343
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344 default:
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345 throw OrthancException(ErrorCode_InternalError);
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346 }
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diff changeset
347
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348 result["Type"] = EnumerationToString(resourceType);
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349 result["ID"] = newId;
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350 result["Path"] = GetBasePath(resourceType, newId);
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351 result["PatientID"] = modifiedHasher.HashPatient();
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352 isFirst = false;
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353 }
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diff changeset
354 }
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diff changeset
355
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356 call.GetOutput().AnswerJson(result);
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parents:
diff changeset
357 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
358
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
359
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diff changeset
360
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diff changeset
361 static void ModifyInstance(RestApiPostCall& call)
751
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362 {
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diff changeset
363 DicomModification modification;
1279
7f3a65e84d4b More flexible /modify and /anonymize for single instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1160
diff changeset
364 modification.SetAllowManualIdentifiers(true);
787
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parents: 782
diff changeset
365
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diff changeset
366 if (ParseModifyRequest(modification, call))
751
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diff changeset
367 {
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
368 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
369 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
370 modification.SetLevel(ResourceType_Patient);
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
371 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
372 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
373 {
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parents: 795
diff changeset
374 modification.SetLevel(ResourceType_Study);
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parents: 795
diff changeset
375 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
376 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
377 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
378 modification.SetLevel(ResourceType_Series);
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
379 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
380 else
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
381 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
382 modification.SetLevel(ResourceType_Instance);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
383 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
384
787
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parents: 782
diff changeset
385 AnonymizeOrModifyInstance(modification, call);
751
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parents:
diff changeset
386 }
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parents:
diff changeset
387 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
388
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
389
974
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diff changeset
390 static void AnonymizeInstance(RestApiPostCall& call)
751
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diff changeset
391 {
787
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diff changeset
392 DicomModification modification;
1279
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parents: 1160
diff changeset
393 modification.SetAllowManualIdentifiers(true);
751
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parents:
diff changeset
394
787
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diff changeset
395 if (ParseAnonymizationRequest(modification, call))
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
396 {
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
397 AnonymizeOrModifyInstance(modification, call);
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
398 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
402 template <enum ChangeType changeType,
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
403 enum ResourceType resourceType>
974
83622b0f544c refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 831
diff changeset
404 static void ModifyResource(RestApiPostCall& call)
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 {
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
406 DicomModification modification;
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
408 if (ParseModifyRequest(modification, call))
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 {
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
410 modification.SetLevel(resourceType);
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
411 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom,
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
412 changeType, resourceType, call);
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
414 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
415
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
417 template <enum ChangeType changeType,
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418 enum ResourceType resourceType>
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419 static void AnonymizeResource(RestApiPostCall& call)
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420 {
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421 DicomModification modification;
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422
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423 if (ParseAnonymizationRequest(modification, call))
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424 {
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425 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom,
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426 changeType, resourceType, call);
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427 }
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428 }
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429
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430
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431 static void CreateDicom(RestApiPostCall& call)
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432 {
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433 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}'
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434 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World","PixelData":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAAAAAA6mKC9AAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH3gUGDDcB53FulQAAAElJREFUGNNtj0sSAEEEQ1+U+185s1CtmRkblQ9CZldsKHJDk6DLGLJa6chjh0ooQmpjXMM86zPwydGEj6Ed/UGykkEM8X+p3u8/8LcOJIWLGeMAAAAASUVORK5CYII="}'
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435
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436 Json::Value replacements;
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437 if (call.ParseJsonRequest(replacements) && replacements.isObject())
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438 {
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439 ParsedDicomFile dicom;
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440
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441 Json::Value::Members members = replacements.getMemberNames();
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442 for (size_t i = 0; i < members.size(); i++)
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443 {
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444 const std::string& name = members[i];
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445 std::string value = replacements[name].asString();
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446
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447 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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448 if (tag == DICOM_TAG_PIXEL_DATA)
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449 {
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450 dicom.EmbedImage(value);
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451 }
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452 else
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453 {
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454 dicom.Replace(tag, value);
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455 }
800
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456 }
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457
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458 DicomInstanceToStore toStore;
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459 toStore.SetParsedDicomFile(dicom);
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460
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461 std::string id;
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462 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, toStore);
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463
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464 if (status == StoreStatus_Failure)
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465 {
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466 LOG(ERROR) << "Error while storing a manually-created instance";
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467 return;
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468 }
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diff changeset
469
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470 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status);
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471 }
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diff changeset
472 }
e7b1ca0f1e04 creation of dicom files
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diff changeset
473
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474
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475 void OrthancRestApi::RegisterAnonymizeModify()
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476 {
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477 Register("/instances/{id}/modify", ModifyInstance);
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478 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>);
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479 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>);
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480 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
751
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481
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482 Register("/instances/{id}/anonymize", AnonymizeInstance);
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483 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>);
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484 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>);
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485 Register("/patients/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
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diff changeset
486
1120
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487 Register("/tools/create-dicom", CreateDicom);
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488 }
5197fd35333c refactoring of OrthancRestApi
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489 }