Mercurial > hg > orthanc

annotate OrthancServer/ServerJobs/ResourceModificationJob.cpp @ 3945:0b3256c3ee14 transcoding

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simplified IDicomTranscoder
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 19 May 2020 11:24:00 +0200
parents b26d25d3c1c7
children 3d2fc1b5cc8c
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #include "../PrecompiledHeadersServer.h"
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35 #include "ResourceModificationJob.h"
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36
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37 #include "../../Core/Logging.h"
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38 #include "../../Core/SerializationToolbox.h"
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39 #include "../ServerContext.h"
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40
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41 #include <dcmtk/dcmdata/dcfilefo.h>
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42
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43 namespace Orthanc
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44 {
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45 class ResourceModificationJob::Output : public boost::noncopyable
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46 {
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47 private:
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48 ResourceType level_;
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49 bool isFirst_;
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50 std::string id_;
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51 std::string patientId_;
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52
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53 public:
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54 Output(ResourceType level) :
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55 level_(level),
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56 isFirst_(true)
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57 {
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58 if (level_ != ResourceType_Patient &&
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59 level_ != ResourceType_Study &&
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60 level_ != ResourceType_Series)
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61 {
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62 throw OrthancException(ErrorCode_ParameterOutOfRange);
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63 }
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64 }
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65
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66 ResourceType GetLevel() const
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67 {
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68 return level_;
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69 }
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70
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71
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72 void Update(DicomInstanceHasher& hasher)
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73 {
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74 if (isFirst_)
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75 {
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76 switch (level_)
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77 {
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78 case ResourceType_Series:
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79 id_ = hasher.HashSeries();
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80 break;
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81
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82 case ResourceType_Study:
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83 id_ = hasher.HashStudy();
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84 break;
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85
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86 case ResourceType_Patient:
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87 id_ = hasher.HashPatient();
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88 break;
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89
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90 default:
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91 throw OrthancException(ErrorCode_InternalError);
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92 }
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93
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94 patientId_ = hasher.HashPatient();
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95 isFirst_ = false;
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96 }
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97 }
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98
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99
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100 bool Format(Json::Value& target)
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101 {
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102 if (isFirst_)
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103 {
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104 return false;
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105 }
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106 else
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107 {
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108 target = Json::objectValue;
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109 target["Type"] = EnumerationToString(level_);
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110 target["ID"] = id_;
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111 target["Path"] = GetBasePath(level_, id_);
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112 target["PatientID"] = patientId_;
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113 return true;
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114 }
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115 }
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116
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117
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118 bool GetIdentifier(std::string& id)
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119 {
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120 if (isFirst_)
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121 {
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122 return false;
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123 }
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124 else
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125 {
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126 id = id_;
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127 return true;
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128 }
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129 }
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130 };
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131
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132
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133
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134
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135 bool ResourceModificationJob::HandleInstance(const std::string& instance)
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136 {
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137 if (modification_.get() == NULL ||
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138 output_.get() == NULL)
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139 {
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140 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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141 "No modification was provided for this job");
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142 }
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143
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144
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145 LOG(INFO) << "Modifying instance in a job: " << instance;
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146
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147
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148 /**
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149 * Retrieve the original instance from the DICOM cache.
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150 **/
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151
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152 std::unique_ptr<DicomInstanceHasher> originalHasher;
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153 std::unique_ptr<ParsedDicomFile> modified;
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154
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155 try
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156 {
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157 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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158 ParsedDicomFile& original = locker.GetDicom();
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159
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160 originalHasher.reset(new DicomInstanceHasher(original.GetHasher()));
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161 modified.reset(original.Clone(true));
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162 }
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163 catch (OrthancException& e)
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164 {
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165 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails();
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166 return false;
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167 }
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168
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169
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170 /**
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171 * Compute the resulting DICOM instance.
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172 **/
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173
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174 modification_->Apply(*modified);
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175
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176 if (transcode_)
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177 {
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178 std::set<DicomTransferSyntax> syntaxes;
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179 syntaxes.insert(transferSyntax_);
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180
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181 IDicomTranscoder::DicomImage source;
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182 source.AcquireParsed(*modified); // "modified" is invalid below this point
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183
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184 IDicomTranscoder::DicomImage transcoded;
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185 bool hasSopInstanceUidChanged;
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186 if (GetContext().Transcode(transcoded, hasSopInstanceUidChanged, source, syntaxes, true))
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187 {
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188 modified.reset(transcoded.ReleaseAsParsedDicomFile());
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189 }
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190 else
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191 {
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192 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance;
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193 modified.reset(source.ReleaseAsParsedDicomFile());
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194 }
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195 }
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196
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197 DicomInstanceToStore toStore;
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198 toStore.SetOrigin(origin_);
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199 toStore.SetParsedDicomFile(*modified);
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200
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201
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202 /**
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203 * Prepare the metadata information to associate with the
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204 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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205 **/
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206
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207 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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208
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209 MetadataType metadataType = (isAnonymization_ ?
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210 MetadataType_AnonymizedFrom :
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211 MetadataType_ModifiedFrom);
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212
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213 if (originalHasher->HashSeries() != modifiedHasher.HashSeries())
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214 {
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215 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries());
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216 }
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217
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diff changeset
218 if (originalHasher->HashStudy() != modifiedHasher.HashStudy())
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219 {
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diff changeset
220 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy());
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221 }
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222
2825
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diff changeset
223 if (originalHasher->HashPatient() != modifiedHasher.HashPatient())
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224 {
2825
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diff changeset
225 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient());
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226 }
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227
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diff changeset
228 assert(instance == originalHasher->HashInstance());
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229 toStore.AddMetadata(ResourceType_Instance, metadataType, instance);
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230
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231
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232 /**
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233 * Store the resulting DICOM instance into the Orthanc store.
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parents:
diff changeset
234 **/
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235
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diff changeset
236 std::string modifiedInstance;
3942
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diff changeset
237 if (GetContext().Store(modifiedInstance, toStore,
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diff changeset
238 StoreInstanceMode_Default) != StoreStatus_Success)
2642
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239 {
2955
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diff changeset
240 throw OrthancException(ErrorCode_CannotStoreInstance,
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241 "Error while storing a modified instance " + instance);
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Sebastien Jodogne <s.jodogne@gmail.com>
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242 }
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parents:
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243
3938
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parents: 3814
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244 /**
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245 * The assertion below will fail if automated transcoding to a
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parents: 3814
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246 * lossy transfer syntax is enabled in the Orthanc core, and if
Sebastien Jodogne <s.jodogne@gmail.com>
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247 * the source instance is not in this transfer syntax.
Sebastien Jodogne <s.jodogne@gmail.com>
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248 **/
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diff changeset
249 // assert(modifiedInstance == modifiedHasher.HashInstance());
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250
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251 output_->Update(modifiedHasher);
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252
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253 return true;
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parents:
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254 }
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255
2842
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diff changeset
256
3943
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diff changeset
257 ResourceModificationJob::ResourceModificationJob(ServerContext& context) :
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diff changeset
258 CleaningInstancesJob(context, true /* by default, keep source */),
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diff changeset
259 modification_(new DicomModification),
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diff changeset
260 isAnonymization_(false),
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diff changeset
261 transcode_(false)
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diff changeset
262 {
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diff changeset
263 }
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parents: 3942
diff changeset
264
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diff changeset
265
2642
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266 void ResourceModificationJob::SetModification(DicomModification* modification,
2868
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diff changeset
267 ResourceType level,
2642
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diff changeset
268 bool isAnonymization)
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269 {
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diff changeset
270 if (modification == NULL)
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parents:
diff changeset
271 {
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272 throw OrthancException(ErrorCode_NullPointer);
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273 }
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diff changeset
274 else if (IsStarted())
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parents:
diff changeset
275 {
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276 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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277 }
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diff changeset
278 else
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parents:
diff changeset
279 {
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diff changeset
280 modification_.reset(modification);
2868
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diff changeset
281 output_.reset(new Output(level));
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282 isAnonymization_ = isAnonymization;
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283 }
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284 }
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285
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286
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287 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin)
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288 {
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289 if (IsStarted())
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290 {
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291 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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292 }
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293 else
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294 {
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295 origin_ = origin;
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296 }
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297 }
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298
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299
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300 void ResourceModificationJob::SetOrigin(const RestApiCall& call)
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301 {
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302 SetOrigin(DicomInstanceOrigin::FromRest(call));
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303 }
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304
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305
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306 const DicomModification& ResourceModificationJob::GetModification() const
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307 {
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308 if (modification_.get() == NULL)
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309 {
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310 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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311 }
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312 else
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313 {
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314 return *modification_;
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315 }
2642
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316 }
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317
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318
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319 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const
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320 {
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321 if (transcode_)
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322 {
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323 return transferSyntax_;
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324 }
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325 else
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326 {
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diff changeset
327 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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328 }
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329 }
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330
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331
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diff changeset
332 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax)
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333 {
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diff changeset
334 if (IsStarted())
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diff changeset
335 {
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336 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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337 }
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diff changeset
338 else
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diff changeset
339 {
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diff changeset
340 transcode_ = true;
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diff changeset
341 transferSyntax_ = syntax;
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diff changeset
342 }
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diff changeset
343 }
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344
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345
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346 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid)
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347 {
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348 DicomTransferSyntax s;
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349 if (LookupTransferSyntax(s, transferSyntaxUid))
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diff changeset
350 {
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diff changeset
351 SetTranscode(s);
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352 }
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diff changeset
353 else
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diff changeset
354 {
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diff changeset
355 throw OrthancException(ErrorCode_BadFileFormat,
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diff changeset
356 "Unknown transfer syntax UID: " + transferSyntaxUid);
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diff changeset
357 }
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diff changeset
358 }
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diff changeset
359
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diff changeset
360
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diff changeset
361 void ResourceModificationJob::ClearTranscode()
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diff changeset
362 {
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diff changeset
363 if (IsStarted())
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diff changeset
364 {
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diff changeset
365 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
366 }
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diff changeset
367 else
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parents: 3942
diff changeset
368 {
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diff changeset
369 transcode_ = false;
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diff changeset
370 }
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diff changeset
371 }
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diff changeset
372
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diff changeset
373
2642
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diff changeset
374 void ResourceModificationJob::GetPublicContent(Json::Value& value)
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375 {
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diff changeset
376 CleaningInstancesJob::GetPublicContent(value);
2642
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diff changeset
377
ccc470091ea6 reorganization
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diff changeset
378 value["IsAnonymization"] = isAnonymization_;
2868
abce036683cd sharing code within OrthancRestAnonymizeModify
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diff changeset
379
abce036683cd sharing code within OrthancRestAnonymizeModify
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diff changeset
380 if (output_.get() != NULL)
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diff changeset
381 {
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diff changeset
382 output_->Format(value);
abce036683cd sharing code within OrthancRestAnonymizeModify
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diff changeset
383 }
3943
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diff changeset
384
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diff changeset
385 if (transcode_)
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diff changeset
386 {
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diff changeset
387 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_);
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
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diff changeset
388 }
2642
ccc470091ea6 reorganization
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parents:
diff changeset
389 }
ccc470091ea6 reorganization
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parents:
diff changeset
390
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
391
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
392 static const char* MODIFICATION = "Modification";
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
393 static const char* ORIGIN = "Origin";
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
394 static const char* IS_ANONYMIZATION = "IsAnonymization";
3943
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
395 static const char* TRANSCODE = "Transcode";
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
396
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
397
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
398 ResourceModificationJob::ResourceModificationJob(ServerContext& context,
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
399 const Json::Value& serialized) :
3942
5b882ad2ffd0 "/{patients|studies|series}/.../modify": New option "KeepSource"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3938
diff changeset
400 CleaningInstancesJob(context, serialized, true /* by default, keep source */)
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
401 {
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
402 assert(serialized.type() == Json::objectValue);
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
403
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
404 isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
405 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
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406 modification_.reset(new DicomModification(serialized[MODIFICATION]));
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
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407
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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408 if (serialized.isMember(TRANSCODE))
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parents: 3942
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409 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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410 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE));
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parents: 3942
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411 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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412 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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413 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
414 transcode_ = false;
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parents: 3942
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415 }
2664
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
416 }
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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417
2663
228e2783ce83 some jobs might not be serializable
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2648
diff changeset
418 bool ResourceModificationJob::Serialize(Json::Value& value)
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419 {
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diff changeset
420 if (!CleaningInstancesJob::Serialize(value))
2664
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
421 {
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
422 return false;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
423 }
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
424 else
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
425 {
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
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426 assert(value.type() == Json::objectValue);
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parents: 3942
diff changeset
427
2664
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
428 value[IS_ANONYMIZATION] = isAnonymization_;
3943
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parents: 3942
diff changeset
429
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
430 if (transcode_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
431 {
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parents: 3942
diff changeset
432 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_);
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parents: 3942
diff changeset
433 }
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parents: 3942
diff changeset
434
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
435 origin_.Serialize(value[ORIGIN]);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
436
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
437 Json::Value tmp;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
438 modification_->Serialize(tmp);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
439 value[MODIFICATION] = tmp;
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
441 return true;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
442 }
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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443 }
ccc470091ea6 reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 }