Mercurial > hg > orthanc

annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 1010:160dfe770618 lua-scripting

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 09 Jul 2014 17:05:00 +0200
parents 84b6d7bca6db
children 009dce4ea2f6
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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 "../FromDcmtkBridge.h"
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37
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38 #include <glog/logging.h>
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39
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40 namespace Orthanc
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41 {
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42 // Modification of DICOM instances ------------------------------------------
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43
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44 enum TagOperation
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45 {
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46 TagOperation_Keep,
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47 TagOperation_Remove
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48 };
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49
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50 static void ParseListOfTags(DicomModification& target,
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51 const Json::Value& query,
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52 TagOperation operation)
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53 {
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54 if (!query.isArray())
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55 {
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56 throw OrthancException(ErrorCode_BadRequest);
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57 }
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58
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59 for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
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60 {
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61 std::string name = query[i].asString();
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62
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63 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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64
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65 switch (operation)
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66 {
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67 case TagOperation_Keep:
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68 target.Keep(tag);
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69 VLOG(1) << "Keep: " << name << " " << tag << std::endl;
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70 break;
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71
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72 case TagOperation_Remove:
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73 target.Remove(tag);
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74 VLOG(1) << "Remove: " << name << " " << tag << std::endl;
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75 break;
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76
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77 default:
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78 throw OrthancException(ErrorCode_InternalError);
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79 }
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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 static void ParseReplacements(DicomModification& target,
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85 const Json::Value& replacements)
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86 {
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87 if (!replacements.isObject())
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88 {
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89 throw OrthancException(ErrorCode_BadRequest);
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90 }
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91
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92 Json::Value::Members members = replacements.getMemberNames();
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93 for (size_t i = 0; i < members.size(); i++)
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94 {
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95 const std::string& name = members[i];
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96 std::string value = replacements[name].asString();
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97
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98 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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99 target.Replace(tag, value);
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100
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101 VLOG(1) << "Replace: " << name << " " << tag << " == " << value << std::endl;
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102 }
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103 }
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104
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105
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106 static std::string GeneratePatientName(ServerContext& context)
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107 {
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108 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence);
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109 return "Anonymized" + boost::lexical_cast<std::string>(seq);
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110 }
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111
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112
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113
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114 bool OrthancRestApi::ParseModifyRequest(DicomModification& target,
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115 const Json::Value& request)
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116 {
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117 if (request.isObject())
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118 {
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119 if (request.isMember("RemovePrivateTags"))
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120 {
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121 target.SetRemovePrivateTags(true);
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122 }
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123
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124 if (request.isMember("Remove"))
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125 {
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126 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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127 }
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128
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129 if (request.isMember("Replace"))
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130 {
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131 ParseReplacements(target, request["Replace"]);
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132 }
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133
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134 return true;
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135 }
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136 else
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137 {
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138 return false;
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139 }
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140 }
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141
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142
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143 static bool ParseModifyRequest(DicomModification& target,
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144 const RestApiPostCall& call)
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145 {
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146 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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147
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148 Json::Value request;
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149 if (call.ParseJsonRequest(request))
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150 {
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151 return OrthancRestApi::ParseModifyRequest(target, request);
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152 }
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153 else
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154 {
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155 return false;
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156 }
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157 }
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158
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159
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160 static bool ParseAnonymizationRequest(DicomModification& target,
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161 RestApiPostCall& call)
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162 {
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163 // 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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164
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165 target.SetupAnonymization();
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166 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME);
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167
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168 Json::Value request;
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169 if (call.ParseJsonRequest(request) && request.isObject())
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170 {
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171 if (request.isMember("KeepPrivateTags"))
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172 {
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173 target.SetRemovePrivateTags(false);
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174 }
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175
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176 if (request.isMember("Remove"))
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177 {
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178 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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179 }
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180
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181 if (request.isMember("Replace"))
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182 {
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183 ParseReplacements(target, request["Replace"]);
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184 }
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185
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186 if (request.isMember("Keep"))
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187 {
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188 ParseListOfTags(target, request["Keep"], TagOperation_Keep);
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189 }
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190
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191 if (target.IsReplaced(DICOM_TAG_PATIENT_NAME) &&
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192 target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName)
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193 {
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194 // Overwrite the random Patient's Name by one that is more
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195 // user-friendly (provided none was specified by the user)
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196 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)));
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197 }
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198
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199 return true;
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200 }
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201 else
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202 {
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203 return false;
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204 }
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205 }
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206
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207
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208 static void AnonymizeOrModifyInstance(DicomModification& modification,
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209 RestApiPostCall& call)
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210 {
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211 std::string id = call.GetUriComponent("id", "");
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212
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213 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id);
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214
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215 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone());
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216 modification.Apply(*modified);
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217 modified->Answer(call.GetOutput());
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218 }
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219
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220
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221 static void AnonymizeOrModifyResource(DicomModification& modification,
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222 MetadataType metadataType,
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223 ChangeType changeType,
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224 ResourceType resourceType,
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225 RestApiPostCall& call)
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226 {
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227 bool isFirst = true;
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228 Json::Value result(Json::objectValue);
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229
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230 ServerContext& context = OrthancRestApi::GetContext(call);
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231
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232 typedef std::list<std::string> Instances;
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233 Instances instances;
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234 std::string id = call.GetUriComponent("id", "");
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235 context.GetIndex().GetChildInstances(instances, id);
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236
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237 if (instances.empty())
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238 {
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239 return;
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240 }
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241
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242
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243 /**
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244 * Loop over all the instances of the resource.
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245 **/
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246
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247 for (Instances::const_iterator it = instances.begin();
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248 it != instances.end(); ++it)
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249 {
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250 LOG(INFO) << "Modifying instance " << *it;
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251
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252 std::auto_ptr<ServerContext::DicomCacheLocker> locker;
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253
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254 try
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255 {
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256 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it));
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257 }
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258 catch (OrthancException&)
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259 {
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260 // This child instance has been removed in between
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261 continue;
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262 }
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263
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264 ParsedDicomFile& original = locker->GetDicom();
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265 DicomInstanceHasher originalHasher = original.GetHasher();
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266
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267
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268 /**
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269 * Compute the resulting DICOM instance.
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270 **/
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271
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272 std::auto_ptr<ParsedDicomFile> modified(original.Clone());
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diff changeset
273 modification.Apply(*modified);
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274
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275 DicomInstanceToStore toStore;
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276 toStore.SetParsedDicomFile(*modified);
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277
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278
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279 /**
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280 * Prepare the metadata information to associate with the
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281 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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282 **/
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283
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284 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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285
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286 if (originalHasher.HashSeries() != modifiedHasher.HashSeries())
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287 {
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288 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher.HashSeries());
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289 }
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290
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291 if (originalHasher.HashStudy() != modifiedHasher.HashStudy())
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292 {
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293 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher.HashStudy());
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294 }
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295
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296 if (originalHasher.HashPatient() != modifiedHasher.HashPatient())
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297 {
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298 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher.HashPatient());
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299 }
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300
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301 assert(*it == originalHasher.HashInstance());
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302 toStore.AddMetadata(ResourceType_Instance, metadataType, *it);
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303
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304
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305 /**
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306 * Store the resulting DICOM instance into the Orthanc store.
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307 **/
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308
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309 std::string modifiedInstance;
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310 if (context.Store(modifiedInstance, toStore) != StoreStatus_Success)
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311 {
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312 LOG(ERROR) << "Error while storing a modified instance " << *it;
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313 return;
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314 }
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315
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316 // Sanity checks in debug mode
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317 assert(modifiedInstance == modifiedHasher.HashInstance());
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318
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319
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320 /**
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321 * Compute the JSON object that is returned by the REST call.
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322 **/
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323
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324 if (isFirst)
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325 {
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326 std::string newId;
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327
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328 switch (resourceType)
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329 {
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330 case ResourceType_Series:
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331 newId = modifiedHasher.HashSeries();
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332 break;
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333
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334 case ResourceType_Study:
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335 newId = modifiedHasher.HashStudy();
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336 break;
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337
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338 case ResourceType_Patient:
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339 newId = modifiedHasher.HashPatient();
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340 break;
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341
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342 default:
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343 throw OrthancException(ErrorCode_InternalError);
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344 }
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345
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346 result["Type"] = EnumerationToString(resourceType);
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347 result["ID"] = newId;
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348 result["Path"] = GetBasePath(resourceType, newId);
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349 result["PatientID"] = modifiedHasher.HashPatient();
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350 isFirst = false;
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351 }
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352 }
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353
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354 call.GetOutput().AnswerJson(result);
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355 }
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356
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357
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358
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359 static void ModifyInstance(RestApiPostCall& call)
751
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360 {
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361 DicomModification modification;
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362
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363 if (ParseModifyRequest(modification, call))
751
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364 {
796
e7b1ca0f1e04 creation of dicom files
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diff changeset
365 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID))
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366 {
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367 modification.SetLevel(ResourceType_Patient);
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368 }
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369 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
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370 {
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371 modification.SetLevel(ResourceType_Study);
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372 }
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373 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
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374 {
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375 modification.SetLevel(ResourceType_Series);
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376 }
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diff changeset
377 else
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diff changeset
378 {
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379 modification.SetLevel(ResourceType_Instance);
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380 }
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381
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382 AnonymizeOrModifyInstance(modification, call);
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383 }
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parents:
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384 }
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385
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diff changeset
386
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diff changeset
387 static void AnonymizeInstance(RestApiPostCall& call)
751
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388 {
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389 DicomModification modification;
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diff changeset
390
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391 if (ParseAnonymizationRequest(modification, call))
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392 {
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diff changeset
393 AnonymizeOrModifyInstance(modification, call);
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diff changeset
394 }
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parents:
diff changeset
395 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
396
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
397
787
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diff changeset
398 template <enum ChangeType changeType,
ac18946afa74 refactoring of anonymization/modification
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diff changeset
399 enum ResourceType resourceType>
974
83622b0f544c refactoring
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diff changeset
400 static void ModifyResource(RestApiPostCall& call)
751
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diff changeset
401 {
787
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diff changeset
402 DicomModification modification;
751
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diff changeset
403
787
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diff changeset
404 if (ParseModifyRequest(modification, call))
751
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parents:
diff changeset
405 {
796
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diff changeset
406 modification.SetLevel(resourceType);
787
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diff changeset
407 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom,
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
408 changeType, resourceType, call);
751
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diff changeset
409 }
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parents:
diff changeset
410 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
412
787
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diff changeset
413 template <enum ChangeType changeType,
ac18946afa74 refactoring of anonymization/modification
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diff changeset
414 enum ResourceType resourceType>
974
83622b0f544c refactoring
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diff changeset
415 static void AnonymizeResource(RestApiPostCall& call)
751
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diff changeset
416 {
787
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diff changeset
417 DicomModification modification;
751
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diff changeset
418
787
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419 if (ParseAnonymizationRequest(modification, call))
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5197fd35333c refactoring of OrthancRestApi
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420 {
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421 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom,
ac18946afa74 refactoring of anonymization/modification
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diff changeset
422 changeType, resourceType, call);
751
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Sebastien Jodogne <s.jodogne@gmail.com>
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423 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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424 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
426
974
83622b0f544c refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
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427 static void Create(RestApiPostCall& call)
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
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428 {
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parents: 795
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429 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}'
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ecedd89055db generation of DICOM images from PNG files
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parents: 796
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430 // 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
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
431
e7b1ca0f1e04 creation of dicom files
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432 Json::Value request;
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parents: 795
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433 if (call.ParseJsonRequest(request) && request.isObject())
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434 {
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435 DicomModification modification;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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436 ParseReplacements(modification, request);
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parents: 795
diff changeset
437
e7b1ca0f1e04 creation of dicom files
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438 ParsedDicomFile dicom;
800
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
439
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
440 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
441 {
ecedd89055db generation of DICOM images from PNG files
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diff changeset
442 dicom.EmbedImage(modification.GetReplacement(DICOM_TAG_PIXEL_DATA));
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
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443 modification.Keep(DICOM_TAG_PIXEL_DATA);
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
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444 }
ecedd89055db generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 796
diff changeset
445
796
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parents: 795
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446 modification.Apply(dicom);
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parents: 795
diff changeset
447
1005
84b6d7bca6db refactoring of ServerContext::Store
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diff changeset
448 DicomInstanceToStore toStore;
84b6d7bca6db refactoring of ServerContext::Store
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449 toStore.SetParsedDicomFile(dicom);
84b6d7bca6db refactoring of ServerContext::Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
450
796
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451 std::string id;
1005
84b6d7bca6db refactoring of ServerContext::Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
452 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, toStore);
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
453
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
454 if (status == StoreStatus_Failure)
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
455 {
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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456 LOG(ERROR) << "Error while storing a manually-created instance";
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
457 return;
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
458 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
459
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
460 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status);
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
461 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
462 }
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
463
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
464
751
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parents:
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465 void OrthancRestApi::RegisterAnonymizeModify()
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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466 {
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
467 Register("/instances/{id}/modify", ModifyInstance);
787
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
468 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
469 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>);
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
470 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
751
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
471
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
472 Register("/instances/{id}/anonymize", AnonymizeInstance);
787
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
473 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
474 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
diff changeset
475 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
476
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
477 Register("/tools/create-dicom", Create);
751
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
478 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
479 }