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annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 935:9f32a3f8a347

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 24 Jun 2014 17:07:44 +0200
parents 84513f2ee1f3
children 83622b0f544c
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * 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 "../DicomModification.h"
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37 #include "../FromDcmtkBridge.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 static bool ParseModifyRequest(DicomModification& target,
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115 const RestApi::PostCall& call)
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116 {
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117 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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118
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119 Json::Value request;
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120 if (call.ParseJsonRequest(request) && request.isObject())
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121 {
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122 if (request.isMember("RemovePrivateTags"))
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123 {
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124 target.SetRemovePrivateTags(true);
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125 }
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126
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127 if (request.isMember("Remove"))
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128 {
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129 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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130 }
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131
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132 if (request.isMember("Replace"))
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133 {
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134 ParseReplacements(target, request["Replace"]);
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135 }
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136
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137 return true;
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138 }
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139 else
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140 {
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141 return false;
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142 }
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143 }
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144
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145
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146 static bool ParseAnonymizationRequest(DicomModification& target,
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147 RestApi::PostCall& call)
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148 {
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149 // 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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150
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151 target.SetupAnonymization();
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152 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME);
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153
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154 Json::Value request;
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155 if (call.ParseJsonRequest(request) && request.isObject())
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156 {
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157 if (request.isMember("KeepPrivateTags"))
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158 {
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159 target.SetRemovePrivateTags(false);
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160 }
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161
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162 if (request.isMember("Remove"))
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163 {
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164 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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165 }
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166
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167 if (request.isMember("Replace"))
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168 {
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169 ParseReplacements(target, request["Replace"]);
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170 }
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171
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172 if (request.isMember("Keep"))
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173 {
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174 ParseListOfTags(target, request["Keep"], TagOperation_Keep);
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175 }
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176
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177 if (target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName)
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178 {
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179 // Overwrite the random Patient's Name by one that is more
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180 // user-friendly (provided none was specified by the user)
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181 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)));
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182 }
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183
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184 return true;
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185 }
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186 else
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187 {
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188 return false;
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189 }
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190 }
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191
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192
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193 static void AnonymizeOrModifyInstance(DicomModification& modification,
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194 RestApi::PostCall& call)
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195 {
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196 std::string id = call.GetUriComponent("id", "");
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197
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198 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id);
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199
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200 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone());
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201 modification.Apply(*modified);
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202 modified->Answer(call.GetOutput());
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203 }
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204
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205
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206 static void AnonymizeOrModifyResource(DicomModification& modification,
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207 MetadataType metadataType,
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208 ChangeType changeType,
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209 ResourceType resourceType,
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210 RestApi::PostCall& call)
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211 {
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212 bool isFirst = true;
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213 Json::Value result(Json::objectValue);
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214
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215 ServerContext& context = OrthancRestApi::GetContext(call);
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216
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217 typedef std::list<std::string> Instances;
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218 Instances instances;
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219 std::string id = call.GetUriComponent("id", "");
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220 context.GetIndex().GetChildInstances(instances, id);
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221
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diff changeset
222 if (instances.empty())
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diff changeset
223 {
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224 return;
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225 }
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226
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227
751
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228 /**
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229 * Loop over all the instances of the resource.
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230 **/
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diff changeset
231
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232 for (Instances::const_iterator it = instances.begin();
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233 it != instances.end(); ++it)
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diff changeset
234 {
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235 LOG(INFO) << "Modifying instance " << *it;
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236
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diff changeset
237 std::auto_ptr<ServerContext::DicomCacheLocker> locker;
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238
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diff changeset
239 try
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240 {
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241 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it));
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242 }
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diff changeset
243 catch (OrthancException&)
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244 {
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245 // This child instance has been removed in between
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246 continue;
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247 }
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diff changeset
248
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diff changeset
249 ParsedDicomFile& original = locker->GetDicom();
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250 DicomInstanceHasher originalHasher = original.GetHasher();
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251
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252
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253 /**
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254 * Compute the resulting DICOM instance and store it into the Orthanc store.
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255 **/
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diff changeset
256
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257 std::auto_ptr<ParsedDicomFile> modified(original.Clone());
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diff changeset
258 modification.Apply(*modified);
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259
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diff changeset
260 std::string modifiedInstance;
791
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diff changeset
261 if (context.Store(modifiedInstance, *modified) != StoreStatus_Success)
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262 {
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263 LOG(ERROR) << "Error while storing a modified instance " << *it;
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264 return;
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diff changeset
265 }
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266
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267
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diff changeset
268 /**
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269 * Record metadata information (AnonymizedFrom/ModifiedFrom).
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diff changeset
270 **/
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271
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272 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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273
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diff changeset
274 if (originalHasher.HashSeries() != modifiedHasher.HashSeries())
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275 {
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276 context.GetIndex().SetMetadata(modifiedHasher.HashSeries(),
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277 metadataType, originalHasher.HashSeries());
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278 }
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279
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280 if (originalHasher.HashStudy() != modifiedHasher.HashStudy())
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281 {
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282 context.GetIndex().SetMetadata(modifiedHasher.HashStudy(),
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283 metadataType, originalHasher.HashStudy());
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284 }
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285
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286 if (originalHasher.HashPatient() != modifiedHasher.HashPatient())
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287 {
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288 context.GetIndex().SetMetadata(modifiedHasher.HashPatient(),
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289 metadataType, originalHasher.HashPatient());
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290 }
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291
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292 assert(*it == originalHasher.HashInstance());
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293 assert(modifiedInstance == modifiedHasher.HashInstance());
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294 context.GetIndex().SetMetadata(modifiedInstance, metadataType, *it);
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295
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296
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297 /**
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298 * Compute the JSON object that is returned by the REST call.
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299 **/
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300
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301 if (isFirst)
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302 {
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303 std::string newId;
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304
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305 switch (resourceType)
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306 {
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307 case ResourceType_Series:
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308 newId = modifiedHasher.HashSeries();
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309 break;
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310
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311 case ResourceType_Study:
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312 newId = modifiedHasher.HashStudy();
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313 break;
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314
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315 case ResourceType_Patient:
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316 newId = modifiedHasher.HashPatient();
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317 break;
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318
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319 default:
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320 throw OrthancException(ErrorCode_InternalError);
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321 }
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322
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323 result["Type"] = EnumerationToString(resourceType);
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324 result["ID"] = newId;
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325 result["Path"] = GetBasePath(resourceType, newId);
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326 result["PatientID"] = modifiedHasher.HashPatient();
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327 isFirst = false;
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328 }
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329 }
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330
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331 call.GetOutput().AnswerJson(result);
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332 }
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333
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334
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335
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336 static void ModifyInstance(RestApi::PostCall& call)
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337 {
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338 DicomModification modification;
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339
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340 if (ParseModifyRequest(modification, call))
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341 {
796
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342 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID))
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343 {
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344 modification.SetLevel(ResourceType_Patient);
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345 }
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346 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
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347 {
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348 modification.SetLevel(ResourceType_Study);
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349 }
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350 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
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351 {
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352 modification.SetLevel(ResourceType_Series);
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353 }
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354 else
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355 {
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356 modification.SetLevel(ResourceType_Instance);
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357 }
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358
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359 AnonymizeOrModifyInstance(modification, call);
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360 }
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361 }
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362
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diff changeset
363
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diff changeset
364 static void AnonymizeInstance(RestApi::PostCall& call)
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diff changeset
365 {
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366 DicomModification modification;
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367
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368 if (ParseAnonymizationRequest(modification, call))
751
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diff changeset
369 {
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370 AnonymizeOrModifyInstance(modification, call);
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diff changeset
371 }
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diff changeset
372 }
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373
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diff changeset
374
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diff changeset
375 template <enum ChangeType changeType,
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diff changeset
376 enum ResourceType resourceType>
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diff changeset
377 static void ModifyResource(RestApi::PostCall& call)
751
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diff changeset
378 {
787
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379 DicomModification modification;
751
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diff changeset
380
787
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diff changeset
381 if (ParseModifyRequest(modification, call))
751
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diff changeset
382 {
796
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diff changeset
383 modification.SetLevel(resourceType);
787
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diff changeset
384 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom,
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diff changeset
385 changeType, resourceType, call);
751
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diff changeset
386 }
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diff changeset
387 }
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diff changeset
388
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parents:
diff changeset
389
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diff changeset
390 template <enum ChangeType changeType,
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diff changeset
391 enum ResourceType resourceType>
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diff changeset
392 static void AnonymizeResource(RestApi::PostCall& call)
751
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diff changeset
393 {
787
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diff changeset
394 DicomModification modification;
751
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parents:
diff changeset
395
787
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diff changeset
396 if (ParseAnonymizationRequest(modification, call))
751
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diff changeset
397 {
787
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diff changeset
398 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom,
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diff changeset
399 changeType, resourceType, call);
751
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diff changeset
400 }
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parents:
diff changeset
401 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403
796
e7b1ca0f1e04 creation of dicom files
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diff changeset
404 static void Create(RestApi::PostCall& call)
e7b1ca0f1e04 creation of dicom files
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diff changeset
405 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
406 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}'
800
ecedd89055db generation of DICOM images from PNG files
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parents: 796
diff changeset
407 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World","PixelData":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAAAAAA6mKC9AAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH3gUGDDcB53FulQAAAElJREFUGNNtj0sSAEEEQ1+U+185s1CtmRkblQ9CZldsKHJDk6DLGLJa6chjh0ooQmpjXMM86zPwydGEj6Ed/UGykkEM8X+p3u8/8LcOJIWLGeMAAAAASUVORK5CYII="}'
796
e7b1ca0f1e04 creation of dicom files
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diff changeset
408
e7b1ca0f1e04 creation of dicom files
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diff changeset
409 Json::Value request;
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diff changeset
410 if (call.ParseJsonRequest(request) && request.isObject())
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diff changeset
411 {
e7b1ca0f1e04 creation of dicom files
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diff changeset
412 DicomModification modification;
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
413 ParseReplacements(modification, request);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
414
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
415 ParsedDicomFile dicom;
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
416
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
417 if (modification.IsReplaced(DICOM_TAG_PIXEL_DATA))
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
418 {
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
419 dicom.EmbedImage(modification.GetReplacement(DICOM_TAG_PIXEL_DATA));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
420 modification.Keep(DICOM_TAG_PIXEL_DATA);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
421 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
422
796
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
423 modification.Apply(dicom);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
424
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
425 std::string id;
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
426 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, dicom);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
427
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
428 if (status == StoreStatus_Failure)
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
429 {
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
430 LOG(ERROR) << "Error while storing a manually-created instance";
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
431 return;
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
432 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
433
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
434 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
435 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
436 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
437
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
438
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 void OrthancRestApi::RegisterAnonymizeModify()
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440 {
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 Register("/instances/{id}/modify", ModifyInstance);
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
442 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
443 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>);
796
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
444 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 Register("/instances/{id}/anonymize", AnonymizeInstance);
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
447 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
448 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
449 Register("/patients/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
796
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
450
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
451 Register("/tools/create-dicom", Create);
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
452 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
453 }