Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp @ 5136:e71b22a43c0b
Threaded modifications continued: call ReconstructInstance at the end of the modification to update the DB model
author | Alain Mazy <am@osimis.io> |
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date | Tue, 17 Jan 2023 17:54:38 +0100 |
parents | 6aa41d86b948 |
children | 15109c3f0f7d |
rev | line source |
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2642 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
2642 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU General Public License as | |
10 * published by the Free Software Foundation, either version 3 of the | |
11 * License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
23 #include "../PrecompiledHeadersServer.h" | |
24 #include "ResourceModificationJob.h" | |
25 | |
4045 | 26 #include "../../../OrthancFramework/Sources/Logging.h" |
27 #include "../../../OrthancFramework/Sources/SerializationToolbox.h" | |
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28 #include "../ServerContext.h" |
2642 | 29 |
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30 #include <dcmtk/dcmdata/dcfilefo.h> |
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31 #include <dcmtk/dcmdata/dcdeftag.h> |
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32 #include <cassert> |
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33 |
2642 | 34 namespace Orthanc |
35 { | |
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36 static void FormatResource(Json::Value& target, |
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37 ResourceType level, |
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38 const std::string& id) |
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39 { |
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40 target["Type"] = EnumerationToString(level); |
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41 target["ID"] = id; |
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42 target["Path"] = GetBasePath(level, id); |
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43 } |
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44 |
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45 class ResourceModificationJob::SingleOutput : public IOutput |
2642 | 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 explicit SingleOutput(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 virtual void Update(DicomInstanceHasher& hasher) ORTHANC_OVERRIDE |
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67 { |
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68 if (isFirst_) |
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69 { |
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70 switch (level_) |
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71 { |
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72 case ResourceType_Series: |
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73 id_ = hasher.HashSeries(); |
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74 break; |
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75 |
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76 case ResourceType_Study: |
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77 id_ = hasher.HashStudy(); |
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78 break; |
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79 |
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80 case ResourceType_Patient: |
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81 id_ = hasher.HashPatient(); |
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82 break; |
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83 |
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84 default: |
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85 throw OrthancException(ErrorCode_InternalError); |
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86 } |
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87 |
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88 patientId_ = hasher.HashPatient(); |
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89 isFirst_ = false; |
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90 } |
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91 } |
2642 | 92 |
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93 virtual void Format(Json::Value& target) const ORTHANC_OVERRIDE |
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94 { |
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95 assert(target.type() == Json::objectValue); |
2642 | 96 |
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97 if (!isFirst_) |
2642 | 98 { |
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99 FormatResource(target, level_, id_); |
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100 target["PatientID"] = patientId_; |
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101 } |
2642 | 102 } |
103 | |
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104 virtual bool IsSingleResource() const ORTHANC_OVERRIDE |
2642 | 105 { |
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106 return true; |
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107 } |
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108 |
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109 ResourceType GetLevel() const |
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110 { |
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111 return level_; |
2642 | 112 } |
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113 }; |
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114 |
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115 |
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116 class ResourceModificationJob::MultipleOutputs : public IOutput |
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117 { |
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118 private: |
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119 static void FormatResources(Json::Value& target, |
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120 ResourceType level, |
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121 const std::set<std::string>& resources) |
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122 { |
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123 assert(target.type() == Json::arrayValue); |
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124 |
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125 for (std::set<std::string>::const_iterator |
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126 it = resources.begin(); it != resources.end(); ++it) |
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127 { |
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128 Json::Value item = Json::objectValue; |
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129 FormatResource(item, level, *it); |
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130 target.append(item); |
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131 } |
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132 } |
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133 |
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134 std::set<std::string> instances_; |
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135 std::set<std::string> series_; |
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136 std::set<std::string> studies_; |
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137 std::set<std::string> patients_; |
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138 |
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139 public: |
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140 virtual void Update(DicomInstanceHasher& hasher) ORTHANC_OVERRIDE |
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141 { |
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142 instances_.insert(hasher.HashInstance()); |
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143 series_.insert(hasher.HashSeries()); |
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144 studies_.insert(hasher.HashStudy()); |
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145 patients_.insert(hasher.HashPatient()); |
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146 } |
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147 |
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148 virtual void Format(Json::Value& target) const ORTHANC_OVERRIDE |
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149 { |
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150 assert(target.type() == Json::objectValue); |
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151 Json::Value resources = Json::arrayValue; |
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152 FormatResources(resources, ResourceType_Instance, instances_); |
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153 FormatResources(resources, ResourceType_Series, series_); |
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154 FormatResources(resources, ResourceType_Study, studies_); |
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155 FormatResources(resources, ResourceType_Patient, patients_); |
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156 target["Resources"] = resources; |
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157 } |
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158 |
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159 virtual bool IsSingleResource() const ORTHANC_OVERRIDE |
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160 { |
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161 return false; |
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162 } |
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163 }; |
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164 |
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165 // Reset is called when resubmitting a failed job |
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166 void ResourceModificationJob::Reset() |
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167 { |
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168 boost::recursive_mutex::scoped_lock lock(mutex_); |
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169 |
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170 // TODO: cleanup the instances that have been generated during the previous run |
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171 modifiedInstances_.clear(); |
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172 |
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173 ThreadedSetOfInstancesJob::Reset(); |
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174 } |
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175 |
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176 void ResourceModificationJob::PostProcessInstances() |
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177 { |
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178 boost::recursive_mutex::scoped_lock lock(mutex_); |
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179 |
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180 // reconstruct the parents MainDicomTags in case one of them has changed |
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181 if (modifiedInstances_.size() > 0) |
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182 { |
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183 ServerContext::DicomCacheLocker locker(GetContext(), *(modifiedInstances_.begin())); |
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184 ParsedDicomFile& modifiedDicom = locker.GetDicom(); |
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185 |
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186 GetContext().GetIndex().ReconstructInstance(modifiedDicom); |
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187 } |
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188 |
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189 } |
2642 | 190 |
191 bool ResourceModificationJob::HandleInstance(const std::string& instance) | |
192 { | |
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193 if (modification_.get() == NULL || |
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194 output_.get() == NULL) |
2642 | 195 { |
2955 | 196 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
197 "No modification was provided for this job"); | |
2642 | 198 } |
199 | |
200 | |
201 LOG(INFO) << "Modifying instance in a job: " << instance; | |
202 | |
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203 /** |
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204 * Retrieve the original instance from the DICOM cache. |
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205 **/ |
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206 |
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207 std::unique_ptr<DicomInstanceHasher> originalHasher; |
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208 std::unique_ptr<ParsedDicomFile> modified; |
2642 | 209 |
210 try | |
211 { | |
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212 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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213 ParsedDicomFile& original = locker.GetDicom(); |
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214 |
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215 originalHasher.reset(new DicomInstanceHasher(original.GetHasher())); |
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216 modified.reset(original.Clone(true)); |
2642 | 217 } |
3430 | 218 catch (OrthancException& e) |
2642 | 219 { |
3430 | 220 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails(); |
2642 | 221 return false; |
222 } | |
223 | |
224 | |
225 /** | |
226 * Compute the resulting DICOM instance. | |
227 **/ | |
228 | |
229 modification_->Apply(*modified); | |
230 | |
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231 const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()); |
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232 |
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233 if (transcode_) |
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234 { |
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235 std::set<DicomTransferSyntax> syntaxes; |
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236 syntaxes.insert(transferSyntax_); |
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237 |
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238 IDicomTranscoder::DicomImage source; |
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239 source.AcquireParsed(*modified); // "modified" is invalid below this point |
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240 |
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241 IDicomTranscoder::DicomImage transcoded; |
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242 if (GetContext().Transcode(transcoded, source, syntaxes, true)) |
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243 { |
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244 modified.reset(transcoded.ReleaseAsParsedDicomFile()); |
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245 |
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246 // Fix the SOP instance UID in order the preserve the |
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247 // references between instance UIDs in the DICOM hierarchy |
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248 // (the UID might have changed in the case of lossy transcoding) |
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249 if (modified.get() == NULL || |
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250 modified->GetDcmtkObject().getDataset() == NULL || |
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251 !modified->GetDcmtkObject().getDataset()->putAndInsertString( |
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252 DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good()) |
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253 { |
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254 throw OrthancException(ErrorCode_InternalError); |
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255 } |
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256 } |
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257 else |
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258 { |
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259 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance; |
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260 modified.reset(source.ReleaseAsParsedDicomFile()); |
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261 } |
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262 } |
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263 |
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264 assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject())); |
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265 |
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266 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified)); |
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267 toStore->SetOrigin(origin_); |
2642 | 268 |
269 | |
270 /** | |
271 * Prepare the metadata information to associate with the | |
272 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). | |
273 **/ | |
274 | |
275 DicomInstanceHasher modifiedHasher = modified->GetHasher(); | |
276 | |
277 MetadataType metadataType = (isAnonymization_ ? | |
278 MetadataType_AnonymizedFrom : | |
279 MetadataType_ModifiedFrom); | |
280 | |
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281 if (originalHasher->HashSeries() != modifiedHasher.HashSeries()) |
2642 | 282 { |
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283 toStore->AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries()); |
2642 | 284 } |
285 | |
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286 if (originalHasher->HashStudy() != modifiedHasher.HashStudy()) |
2642 | 287 { |
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288 toStore->AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy()); |
2642 | 289 } |
290 | |
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291 if (originalHasher->HashPatient() != modifiedHasher.HashPatient()) |
2642 | 292 { |
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293 toStore->AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient()); |
2642 | 294 } |
295 | |
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296 assert(instance == originalHasher->HashInstance()); |
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297 toStore->AddMetadata(ResourceType_Instance, metadataType, instance); |
2642 | 298 |
299 | |
300 /** | |
301 * Store the resulting DICOM instance into the Orthanc store. | |
302 **/ | |
303 | |
304 std::string modifiedInstance; | |
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305 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default); |
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306 if (result.GetStatus() != StoreStatus_Success && result.GetStatus() != StoreStatus_AlreadyStored) // when retrying a job, we might save the same data again |
2642 | 307 { |
2955 | 308 throw OrthancException(ErrorCode_CannotStoreInstance, |
309 "Error while storing a modified instance " + instance); | |
2642 | 310 } |
311 | |
3938 | 312 /** |
313 * The assertion below will fail if automated transcoding to a | |
314 * lossy transfer syntax is enabled in the Orthanc core, and if | |
315 * the source instance is not in this transfer syntax. | |
316 **/ | |
317 // assert(modifiedInstance == modifiedHasher.HashInstance()); | |
2642 | 318 |
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319 { |
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320 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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321 |
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322 output_->Update(modifiedHasher); |
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323 modifiedInstances_.insert(modifiedInstance); |
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324 } |
2642 | 325 |
326 return true; | |
327 } | |
328 | |
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329 |
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330 ResourceModificationJob::ResourceModificationJob(ServerContext& context, unsigned int workersCount) : |
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331 ThreadedSetOfInstancesJob(context, true /* post processing step */, true /* by default, keep source */, workersCount), |
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332 isAnonymization_(false), |
4206 | 333 transcode_(false), |
334 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization | |
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335 { |
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336 } |
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337 |
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338 |
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339 void ResourceModificationJob::SetSingleResourceModification(DicomModification* modification, |
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340 ResourceType outputLevel, |
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341 bool isAnonymization) |
2642 | 342 { |
343 if (modification == NULL) | |
344 { | |
345 throw OrthancException(ErrorCode_NullPointer); | |
346 } | |
347 else if (IsStarted()) | |
348 { | |
349 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
350 } | |
351 else | |
352 { | |
353 modification_.reset(modification); | |
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354 output_.reset(new SingleOutput(outputLevel)); |
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355 isAnonymization_ = isAnonymization; |
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356 } |
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357 } |
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358 |
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359 |
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360 void ResourceModificationJob::SetMultipleResourcesModification(DicomModification* modification, |
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361 bool isAnonymization) |
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362 { |
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363 if (modification == NULL) |
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364 { |
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365 throw OrthancException(ErrorCode_NullPointer); |
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366 } |
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367 else if (IsStarted()) |
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368 { |
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369 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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370 } |
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371 else |
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372 { |
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373 modification_.reset(modification); |
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374 output_.reset(new MultipleOutputs); |
2642 | 375 isAnonymization_ = isAnonymization; |
376 } | |
377 } | |
378 | |
379 | |
380 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin) | |
381 { | |
382 if (IsStarted()) | |
383 { | |
384 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
385 } | |
386 else | |
387 { | |
388 origin_ = origin; | |
389 } | |
390 } | |
391 | |
392 | |
393 void ResourceModificationJob::SetOrigin(const RestApiCall& call) | |
394 { | |
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395 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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396 } |
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397 |
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398 |
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399 const DicomModification& ResourceModificationJob::GetModification() const |
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400 { |
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401 if (modification_.get() == NULL) |
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402 { |
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403 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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404 } |
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405 else |
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406 { |
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407 return *modification_; |
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408 } |
2642 | 409 } |
410 | |
411 | |
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412 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const |
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413 { |
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414 if (transcode_) |
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415 { |
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416 return transferSyntax_; |
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417 } |
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418 else |
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419 { |
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420 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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421 } |
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422 } |
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423 |
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424 |
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425 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax) |
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426 { |
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427 if (IsStarted()) |
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428 { |
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429 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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430 } |
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431 else |
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432 { |
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433 transcode_ = true; |
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434 transferSyntax_ = syntax; |
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435 } |
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436 } |
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437 |
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438 |
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439 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid) |
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440 { |
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441 DicomTransferSyntax s; |
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442 if (LookupTransferSyntax(s, transferSyntaxUid)) |
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443 { |
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444 SetTranscode(s); |
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445 } |
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446 else |
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447 { |
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448 throw OrthancException(ErrorCode_BadFileFormat, |
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449 "Unknown transfer syntax UID: " + transferSyntaxUid); |
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450 } |
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diff
changeset
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451 } |
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diff
changeset
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452 |
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453 |
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diff
changeset
|
454 void ResourceModificationJob::ClearTranscode() |
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changeset
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455 { |
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diff
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456 if (IsStarted()) |
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457 { |
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458 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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diff
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459 } |
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460 else |
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changeset
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461 { |
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462 transcode_ = false; |
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463 } |
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464 } |
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465 |
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466 |
4693
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467 bool ResourceModificationJob::IsSingleResourceModification() const |
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468 { |
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469 if (modification_.get() == NULL) |
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470 { |
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471 assert(output_.get() == NULL); |
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472 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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473 } |
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474 else |
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475 { |
5130
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|
476 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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477 |
4693
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478 assert(output_.get() != NULL); |
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479 return output_->IsSingleResource(); |
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480 } |
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481 } |
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|
482 |
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changeset
|
483 |
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changeset
|
484 ResourceType ResourceModificationJob::GetOutputLevel() const |
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485 { |
5130
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diff
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|
486 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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487 |
4693
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488 if (IsSingleResourceModification()) |
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489 { |
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|
490 assert(modification_.get() != NULL && |
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|
491 output_.get() != NULL); |
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492 return dynamic_cast<const SingleOutput&>(*output_).GetLevel(); |
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493 } |
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|
494 else |
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diff
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|
495 { |
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496 // Not applicable if multiple resources |
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497 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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|
498 } |
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|
499 } |
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diff
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|
500 |
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diff
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|
501 |
2642 | 502 void ResourceModificationJob::GetPublicContent(Json::Value& value) |
503 { | |
5130
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504 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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|
505 |
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|
506 ThreadedSetOfInstancesJob::GetPublicContent(value); |
2642 | 507 |
508 value["IsAnonymization"] = isAnonymization_; | |
2868
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sharing code within OrthancRestAnonymizeModify
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diff
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|
509 |
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changeset
|
510 if (output_.get() != NULL) |
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|
511 { |
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diff
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|
512 output_->Format(value); |
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|
513 } |
3943
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diff
changeset
|
514 |
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diff
changeset
|
515 if (transcode_) |
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|
516 { |
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diff
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|
517 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_); |
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|
518 } |
2642 | 519 } |
520 | |
2664
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serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff
changeset
|
521 |
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|
522 static const char* MODIFICATION = "Modification"; |
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|
523 static const char* ORIGIN = "Origin"; |
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|
524 static const char* IS_ANONYMIZATION = "IsAnonymization"; |
3943
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changeset
|
525 static const char* TRANSCODE = "Transcode"; |
4693
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|
526 static const char* OUTPUT_LEVEL = "OutputLevel"; |
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|
527 static const char* IS_SINGLE_RESOURCE = "IsSingleResource"; |
2664
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diff
changeset
|
528 |
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changeset
|
529 |
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changeset
|
530 ResourceModificationJob::ResourceModificationJob(ServerContext& context, |
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changeset
|
531 const Json::Value& serialized) : |
5130
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diff
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|
532 ThreadedSetOfInstancesJob(context, serialized, false /* no post processing step */, true /* by default, keep source */), |
4223 | 533 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization |
2664
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diff
changeset
|
534 { |
3943
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diff
changeset
|
535 assert(serialized.type() == Json::objectValue); |
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diff
changeset
|
536 |
2664
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diff
changeset
|
537 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
3943
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diff
changeset
|
538 |
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diff
changeset
|
539 if (serialized.isMember(TRANSCODE)) |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
540 { |
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diff
changeset
|
541 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE)); |
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changeset
|
542 } |
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changeset
|
543 else |
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changeset
|
544 { |
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changeset
|
545 transcode_ = false; |
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|
546 } |
4693
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diff
changeset
|
547 |
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diff
changeset
|
548 bool isSingleResource; |
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diff
changeset
|
549 if (serialized.isMember(IS_SINGLE_RESOURCE)) |
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diff
changeset
|
550 { |
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|
551 isSingleResource = SerializationToolbox::ReadBoolean(serialized, IS_SINGLE_RESOURCE); |
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|
552 } |
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added routes for bulk anonymization/modification
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|
553 else |
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diff
changeset
|
554 { |
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diff
changeset
|
555 isSingleResource = true; // Backward compatibility with Orthanc <= 1.9.3 |
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changeset
|
556 } |
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added routes for bulk anonymization/modification
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diff
changeset
|
557 |
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558 bool isAnonymization = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION); |
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559 std::unique_ptr<DicomModification> modification(new DicomModification(serialized[MODIFICATION])); |
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560 |
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561 if (isSingleResource) |
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562 { |
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563 ResourceType outputLevel; |
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564 |
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565 if (serialized.isMember(OUTPUT_LEVEL)) |
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566 { |
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567 // New in Orthanc 1.9.4. This fixes an *incorrect* behavior in |
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568 // Orthanc <= 1.9.3, in which "outputLevel" would be set to |
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569 // "modification->GetLevel()" |
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570 outputLevel = StringToResourceType(SerializationToolbox::ReadString(serialized, OUTPUT_LEVEL).c_str()); |
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571 } |
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572 else |
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573 { |
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574 // Use the buggy convention from Orthanc <= 1.9.3 (which is |
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575 // the only thing we have at hand) |
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576 outputLevel = modification->GetLevel(); |
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577 |
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578 if (outputLevel == ResourceType_Instance) |
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579 { |
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580 // This should never happen, but as "SingleOutput" doesn't |
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581 // support instance-level anonymization, don't take any risk |
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582 // and choose an arbitrary output level |
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583 outputLevel = ResourceType_Patient; |
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584 } |
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585 } |
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586 |
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587 SetSingleResourceModification(modification.release(), outputLevel, isAnonymization); |
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588 } |
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589 else |
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590 { |
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591 // New in Orthanc 1.9.4 |
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592 SetMultipleResourcesModification(modification.release(), isAnonymization); |
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593 } |
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594 } |
2642 | 595 |
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596 bool ResourceModificationJob::Serialize(Json::Value& value) |
2642 | 597 { |
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598 if (modification_.get() == NULL) |
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599 { |
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600 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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601 } |
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602 else if (!ThreadedSetOfInstancesJob::Serialize(value)) |
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603 { |
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604 return false; |
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605 } |
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606 else |
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607 { |
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608 assert(value.type() == Json::objectValue); |
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609 |
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610 value[IS_ANONYMIZATION] = isAnonymization_; |
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611 |
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612 if (transcode_) |
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613 { |
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614 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
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615 } |
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616 |
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617 origin_.Serialize(value[ORIGIN]); |
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618 |
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619 Json::Value tmp; |
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620 modification_->Serialize(tmp); |
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621 value[MODIFICATION] = tmp; |
2642 | 622 |
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623 // New in Orthanc 1.9.4 |
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624 value[IS_SINGLE_RESOURCE] = IsSingleResourceModification(); |
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625 if (IsSingleResourceModification()) |
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626 { |
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627 value[OUTPUT_LEVEL] = EnumerationToString(GetOutputLevel()); |
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628 } |
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629 |
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630 return true; |
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631 } |
2642 | 632 } |
633 } |