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annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 1449:164a381abb2b

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 02 Jul 2015 09:14:53 +0200
parents 02f5a3f5c0a0
children f967bdf8534e
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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 #include "../ServerContext.h"
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39
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40 #include <glog/logging.h>
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41
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42 namespace Orthanc
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43 {
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44 // Modification of DICOM instances ------------------------------------------
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45
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46 enum TagOperation
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47 {
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48 TagOperation_Keep,
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49 TagOperation_Remove
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50 };
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51
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52 static void ParseListOfTags(DicomModification& target,
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53 const Json::Value& query,
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54 TagOperation operation)
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55 {
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56 if (!query.isArray())
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57 {
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58 throw OrthancException(ErrorCode_BadRequest);
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59 }
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60
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61 for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
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62 {
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63 std::string name = query[i].asString();
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64
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65 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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66
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67 switch (operation)
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68 {
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69 case TagOperation_Keep:
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70 target.Keep(tag);
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71 VLOG(1) << "Keep: " << name << " " << tag << std::endl;
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72 break;
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73
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74 case TagOperation_Remove:
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75 target.Remove(tag);
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76 VLOG(1) << "Remove: " << name << " " << tag << std::endl;
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77 break;
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78
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79 default:
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80 throw OrthancException(ErrorCode_InternalError);
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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
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86 static void ParseReplacements(DicomModification& target,
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87 const Json::Value& replacements)
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88 {
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89 if (!replacements.isObject())
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90 {
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91 throw OrthancException(ErrorCode_BadRequest);
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92 }
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93
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94 Json::Value::Members members = replacements.getMemberNames();
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95 for (size_t i = 0; i < members.size(); i++)
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96 {
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97 const std::string& name = members[i];
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98 std::string value = replacements[name].asString();
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99
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100 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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101 target.Replace(tag, value);
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102
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103 VLOG(1) << "Replace: " << name << " " << tag << " == " << value << std::endl;
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104 }
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105 }
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106
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107
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108 static std::string GeneratePatientName(ServerContext& context)
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109 {
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110 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence);
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111 return "Anonymized" + boost::lexical_cast<std::string>(seq);
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112 }
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113
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114
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115
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116 bool OrthancRestApi::ParseModifyRequest(DicomModification& target,
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117 const Json::Value& request)
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118 {
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119 if (request.isObject())
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120 {
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121 if (request.isMember("RemovePrivateTags"))
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122 {
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123 target.SetRemovePrivateTags(true);
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124 }
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125
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126 if (request.isMember("Remove"))
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127 {
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128 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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129 }
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130
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131 if (request.isMember("Replace"))
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132 {
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133 ParseReplacements(target, request["Replace"]);
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134 }
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135
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136 return true;
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137 }
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138 else
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139 {
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140 return false;
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141 }
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142 }
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143
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144
1010
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145 static bool ParseModifyRequest(DicomModification& target,
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146 const RestApiPostCall& call)
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147 {
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148 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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149
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150 Json::Value request;
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151 if (call.ParseJsonRequest(request))
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152 {
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153 return OrthancRestApi::ParseModifyRequest(target, request);
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154 }
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155 else
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156 {
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157 return false;
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158 }
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159 }
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160
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161
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162 static bool ParseAnonymizationRequest(DicomModification& target,
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163 RestApiPostCall& call)
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164 {
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165 // 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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166
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167 target.SetupAnonymization();
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168 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME);
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169
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170 Json::Value request;
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171 if (call.ParseJsonRequest(request) && request.isObject())
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172 {
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173 if (request.isMember("KeepPrivateTags"))
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174 {
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175 target.SetRemovePrivateTags(false);
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176 }
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177
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178 if (request.isMember("Remove"))
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179 {
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180 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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181 }
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182
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183 if (request.isMember("Replace"))
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184 {
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185 ParseReplacements(target, request["Replace"]);
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186 }
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187
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188 if (request.isMember("Keep"))
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189 {
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190 ParseListOfTags(target, request["Keep"], TagOperation_Keep);
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191 }
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192
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193 if (target.IsReplaced(DICOM_TAG_PATIENT_NAME) &&
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194 target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName)
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195 {
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196 // Overwrite the random Patient's Name by one that is more
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197 // user-friendly (provided none was specified by the user)
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198 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)), true);
787
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199 }
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200
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201 return true;
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202 }
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203 else
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204 {
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205 return false;
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206 }
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207 }
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208
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209
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210 static void AnonymizeOrModifyInstance(DicomModification& modification,
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211 RestApiPostCall& call)
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212 {
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213 std::string id = call.GetUriComponent("id", "");
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214
778
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215 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id);
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216
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217 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone());
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218 modification.Apply(*modified);
751
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diff changeset
219 modified->Answer(call.GetOutput());
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220 }
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diff changeset
221
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diff changeset
222
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diff changeset
223 static void AnonymizeOrModifyResource(DicomModification& modification,
751
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diff changeset
224 MetadataType metadataType,
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225 ChangeType changeType,
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226 ResourceType resourceType,
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diff changeset
227 RestApiPostCall& call)
751
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diff changeset
228 {
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229 bool isFirst = true;
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230 Json::Value result(Json::objectValue);
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diff changeset
231
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diff changeset
232 ServerContext& context = OrthancRestApi::GetContext(call);
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233
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diff changeset
234 typedef std::list<std::string> Instances;
751
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235 Instances instances;
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diff changeset
236 std::string id = call.GetUriComponent("id", "");
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diff changeset
237 context.GetIndex().GetChildInstances(instances, id);
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diff changeset
238
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diff changeset
239 if (instances.empty())
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diff changeset
240 {
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parents:
diff changeset
241 return;
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parents:
diff changeset
242 }
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diff changeset
243
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diff changeset
244
751
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245 /**
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246 * Loop over all the instances of the resource.
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247 **/
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diff changeset
248
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diff changeset
249 for (Instances::const_iterator it = instances.begin();
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diff changeset
250 it != instances.end(); ++it)
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diff changeset
251 {
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diff changeset
252 LOG(INFO) << "Modifying instance " << *it;
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diff changeset
253
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diff changeset
254 std::auto_ptr<ServerContext::DicomCacheLocker> locker;
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diff changeset
255
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diff changeset
256 try
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diff changeset
257 {
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diff changeset
258 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it));
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diff changeset
259 }
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diff changeset
260 catch (OrthancException&)
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diff changeset
261 {
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diff changeset
262 // This child instance has been removed in between
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diff changeset
263 continue;
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diff changeset
264 }
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diff changeset
265
1129
8dabdc0d3007 fix possible deadlock
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diff changeset
266
778
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diff changeset
267 ParsedDicomFile& original = locker->GetDicom();
751
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268 DicomInstanceHasher originalHasher = original.GetHasher();
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269
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diff changeset
270
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diff changeset
271 /**
1002
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diff changeset
272 * Compute the resulting DICOM instance.
751
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diff changeset
273 **/
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diff changeset
274
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diff changeset
275 std::auto_ptr<ParsedDicomFile> modified(original.Clone());
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diff changeset
276 modification.Apply(*modified);
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277
1005
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diff changeset
278 DicomInstanceToStore toStore;
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279 toStore.SetParsedDicomFile(*modified);
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280
1002
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diff changeset
281
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282 /**
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283 * Prepare the metadata information to associate with the
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284 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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285 **/
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286
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287 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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288
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289 if (originalHasher.HashSeries() != modifiedHasher.HashSeries())
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290 {
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291 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher.HashSeries());
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292 }
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293
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294 if (originalHasher.HashStudy() != modifiedHasher.HashStudy())
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295 {
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diff changeset
296 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher.HashStudy());
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297 }
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298
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299 if (originalHasher.HashPatient() != modifiedHasher.HashPatient())
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300 {
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301 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher.HashPatient());
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302 }
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303
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304 assert(*it == originalHasher.HashInstance());
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305 toStore.AddMetadata(ResourceType_Instance, metadataType, *it);
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306
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307
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308 /**
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309 * Store the resulting DICOM instance into the Orthanc store.
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310 **/
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311
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312 std::string modifiedInstance;
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313 if (context.Store(modifiedInstance, toStore) != StoreStatus_Success)
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314 {
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315 LOG(ERROR) << "Error while storing a modified instance " << *it;
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316 return;
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317 }
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318
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319 // Sanity checks in debug mode
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320 assert(modifiedInstance == modifiedHasher.HashInstance());
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321
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322
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323 /**
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324 * Compute the JSON object that is returned by the REST call.
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325 **/
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326
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327 if (isFirst)
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328 {
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329 std::string newId;
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330
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331 switch (resourceType)
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332 {
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333 case ResourceType_Series:
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334 newId = modifiedHasher.HashSeries();
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335 break;
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336
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337 case ResourceType_Study:
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338 newId = modifiedHasher.HashStudy();
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339 break;
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340
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341 case ResourceType_Patient:
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342 newId = modifiedHasher.HashPatient();
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343 break;
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344
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345 default:
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346 throw OrthancException(ErrorCode_InternalError);
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347 }
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348
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349 result["Type"] = EnumerationToString(resourceType);
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350 result["ID"] = newId;
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351 result["Path"] = GetBasePath(resourceType, newId);
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352 result["PatientID"] = modifiedHasher.HashPatient();
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353 isFirst = false;
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354 }
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diff changeset
355 }
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parents:
diff changeset
356
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diff changeset
357 call.GetOutput().AnswerJson(result);
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parents:
diff changeset
358 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
359
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
360
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
361
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diff changeset
362 static void ModifyInstance(RestApiPostCall& call)
751
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diff changeset
363 {
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diff changeset
364 DicomModification modification;
1279
7f3a65e84d4b More flexible /modify and /anonymize for single instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1160
diff changeset
365 modification.SetAllowManualIdentifiers(true);
787
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diff changeset
366
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diff changeset
367 if (ParseModifyRequest(modification, call))
751
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diff changeset
368 {
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
369 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
370 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
371 modification.SetLevel(ResourceType_Patient);
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
372 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
373 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
374 {
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diff changeset
375 modification.SetLevel(ResourceType_Study);
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diff changeset
376 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
377 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
378 {
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
379 modification.SetLevel(ResourceType_Series);
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
380 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
381 else
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
382 {
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
383 modification.SetLevel(ResourceType_Instance);
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
384 }
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
385
787
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parents: 782
diff changeset
386 AnonymizeOrModifyInstance(modification, call);
751
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parents:
diff changeset
387 }
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parents:
diff changeset
388 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
390
974
83622b0f544c refactoring
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diff changeset
391 static void AnonymizeInstance(RestApiPostCall& call)
751
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diff changeset
392 {
787
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diff changeset
393 DicomModification modification;
1279
7f3a65e84d4b More flexible /modify and /anonymize for single instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1160
diff changeset
394 modification.SetAllowManualIdentifiers(true);
751
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parents:
diff changeset
395
787
ac18946afa74 refactoring of anonymization/modification
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diff changeset
396 if (ParseAnonymizationRequest(modification, call))
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
397 {
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
398 AnonymizeOrModifyInstance(modification, call);
751
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
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
403 template <enum ChangeType changeType,
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
404 enum ResourceType resourceType>
974
83622b0f544c refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 831
diff changeset
405 static void ModifyResource(RestApiPostCall& call)
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 {
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
407 DicomModification modification;
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
409 if (ParseModifyRequest(modification, call))
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 {
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
411 modification.SetLevel(resourceType);
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
412 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom,
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
413 changeType, resourceType, call);
751
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
5197fd35333c refactoring of OrthancRestApi
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417
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418 template <enum ChangeType changeType,
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419 enum ResourceType resourceType>
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420 static void AnonymizeResource(RestApiPostCall& call)
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421 {
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422 DicomModification modification;
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423
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424 if (ParseAnonymizationRequest(modification, call))
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425 {
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426 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom,
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427 changeType, resourceType, call);
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428 }
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429 }
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430
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431
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432 static void CreateDicom(RestApiPostCall& call)
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433 {
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434 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}'
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435 // 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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436
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437 Json::Value replacements;
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438 if (call.ParseJsonRequest(replacements) && replacements.isObject())
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439 {
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440 ParsedDicomFile dicom;
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441
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442 Json::Value::Members members = replacements.getMemberNames();
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443 for (size_t i = 0; i < members.size(); i++)
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444 {
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445 const std::string& name = members[i];
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446 std::string value = replacements[name].asString();
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447
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448 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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449 if (tag == DICOM_TAG_PIXEL_DATA)
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450 {
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451 dicom.EmbedImage(value);
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452 }
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453 else
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454 {
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455 dicom.Replace(tag, value);
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456 }
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457 }
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458
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459 DicomInstanceToStore toStore;
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460 toStore.SetParsedDicomFile(dicom);
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461
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462 std::string id;
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463 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, toStore);
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464
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465 if (status == StoreStatus_Failure)
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466 {
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467 LOG(ERROR) << "Error while storing a manually-created instance";
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468 return;
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469 }
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470
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471 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status);
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472 }
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473 }
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474
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475
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476 void OrthancRestApi::RegisterAnonymizeModify()
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477 {
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478 Register("/instances/{id}/modify", ModifyInstance);
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479 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>);
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480 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>);
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481 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
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482
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483 Register("/instances/{id}/anonymize", AnonymizeInstance);
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484 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>);
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485 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>);
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486 Register("/patients/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
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487
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488 Register("/tools/create-dicom", CreateDicom);
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489 }
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490 }