Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/ResourceModificationJob.cpp @ 4019:bf35c4628777
macro ORTHANC_FRAMEWORK_VERSION_IS_ABOVE
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 09 Jun 2020 09:20:09 +0200 |
parents | 5fe8c6d3212e |
children |
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) 2017-2020 Osimis S.A., Belgium |
2642 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU General Public License as | |
9 * published by the Free Software Foundation, either version 3 of the | |
10 * License, or (at your option) any later version. | |
11 * | |
12 * In addition, as a special exception, the copyright holders of this | |
13 * program give permission to link the code of its release with the | |
14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
15 * that use the same license as the "OpenSSL" library), and distribute | |
16 * the linked executables. You must obey the GNU General Public License | |
17 * in all respects for all of the code used other than "OpenSSL". If you | |
18 * modify file(s) with this exception, you may extend this exception to | |
19 * your version of the file(s), but you are not obligated to do so. If | |
20 * you do not wish to do so, delete this exception statement from your | |
21 * version. If you delete this exception statement from all source files | |
22 * in the program, then also delete it here. | |
23 * | |
24 * This program is distributed in the hope that it will be useful, but | |
25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
27 * General Public License for more details. | |
28 * | |
29 * You should have received a copy of the GNU General Public License | |
30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
31 **/ | |
32 | |
33 | |
34 #include "../PrecompiledHeadersServer.h" | |
35 #include "ResourceModificationJob.h" | |
36 | |
37 #include "../../Core/Logging.h" | |
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38 #include "../../Core/SerializationToolbox.h" |
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39 #include "../ServerContext.h" |
2642 | 40 |
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41 #include <dcmtk/dcmdata/dcfilefo.h> |
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42 #include <dcmtk/dcmdata/dcdeftag.h> |
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43 #include <cassert> |
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44 |
2642 | 45 namespace Orthanc |
46 { | |
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47 class ResourceModificationJob::Output : public boost::noncopyable |
2642 | 48 { |
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49 private: |
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50 ResourceType level_; |
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51 bool isFirst_; |
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52 std::string id_; |
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53 std::string patientId_; |
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54 |
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55 public: |
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56 Output(ResourceType level) : |
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57 level_(level), |
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58 isFirst_(true) |
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59 { |
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60 if (level_ != ResourceType_Patient && |
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61 level_ != ResourceType_Study && |
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62 level_ != ResourceType_Series) |
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63 { |
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64 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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65 } |
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66 } |
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67 |
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68 ResourceType GetLevel() const |
2642 | 69 { |
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70 return level_; |
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71 } |
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72 |
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73 |
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74 void Update(DicomInstanceHasher& hasher) |
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75 { |
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76 if (isFirst_) |
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77 { |
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78 switch (level_) |
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79 { |
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80 case ResourceType_Series: |
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81 id_ = hasher.HashSeries(); |
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82 break; |
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83 |
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84 case ResourceType_Study: |
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85 id_ = hasher.HashStudy(); |
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86 break; |
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87 |
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88 case ResourceType_Patient: |
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89 id_ = hasher.HashPatient(); |
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90 break; |
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91 |
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92 default: |
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93 throw OrthancException(ErrorCode_InternalError); |
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94 } |
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95 |
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96 patientId_ = hasher.HashPatient(); |
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97 isFirst_ = false; |
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98 } |
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99 } |
2642 | 100 |
101 | |
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102 bool Format(Json::Value& target) |
2642 | 103 { |
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104 if (isFirst_) |
2642 | 105 { |
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106 return false; |
2642 | 107 } |
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108 else |
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109 { |
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110 target = Json::objectValue; |
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111 target["Type"] = EnumerationToString(level_); |
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112 target["ID"] = id_; |
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113 target["Path"] = GetBasePath(level_, id_); |
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114 target["PatientID"] = patientId_; |
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115 return true; |
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116 } |
2642 | 117 } |
118 | |
119 | |
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120 bool GetIdentifier(std::string& id) |
2642 | 121 { |
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122 if (isFirst_) |
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123 { |
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124 return false; |
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125 } |
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126 else |
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127 { |
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128 id = id_; |
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129 return true; |
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130 } |
2642 | 131 } |
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132 }; |
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133 |
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134 |
2642 | 135 |
136 | |
137 bool ResourceModificationJob::HandleInstance(const std::string& instance) | |
138 { | |
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139 if (modification_.get() == NULL || |
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140 output_.get() == NULL) |
2642 | 141 { |
2955 | 142 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
143 "No modification was provided for this job"); | |
2642 | 144 } |
145 | |
146 | |
147 LOG(INFO) << "Modifying instance in a job: " << instance; | |
148 | |
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149 |
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150 /** |
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151 * Retrieve the original instance from the DICOM cache. |
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152 **/ |
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153 |
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154 std::unique_ptr<DicomInstanceHasher> originalHasher; |
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155 std::unique_ptr<ParsedDicomFile> modified; |
2642 | 156 |
157 try | |
158 { | |
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159 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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160 ParsedDicomFile& original = locker.GetDicom(); |
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161 |
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162 originalHasher.reset(new DicomInstanceHasher(original.GetHasher())); |
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163 modified.reset(original.Clone(true)); |
2642 | 164 } |
3430 | 165 catch (OrthancException& e) |
2642 | 166 { |
3430 | 167 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails(); |
2642 | 168 return false; |
169 } | |
170 | |
171 | |
172 /** | |
173 * Compute the resulting DICOM instance. | |
174 **/ | |
175 | |
176 modification_->Apply(*modified); | |
177 | |
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178 const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()); |
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179 |
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180 if (transcode_) |
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181 { |
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182 std::set<DicomTransferSyntax> syntaxes; |
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183 syntaxes.insert(transferSyntax_); |
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184 |
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185 IDicomTranscoder::DicomImage source; |
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186 source.AcquireParsed(*modified); // "modified" is invalid below this point |
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187 |
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188 IDicomTranscoder::DicomImage transcoded; |
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189 if (GetContext().Transcode(transcoded, source, syntaxes, true)) |
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190 { |
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191 modified.reset(transcoded.ReleaseAsParsedDicomFile()); |
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192 |
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193 // Fix the SOP instance UID in order the preserve the |
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194 // references between instance UIDs in the DICOM hierarchy |
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195 // (the UID might have changed in the case of lossy transcoding) |
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196 if (modified.get() == NULL || |
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197 modified->GetDcmtkObject().getDataset() == NULL || |
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198 !modified->GetDcmtkObject().getDataset()->putAndInsertString( |
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199 DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good()) |
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200 { |
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201 throw OrthancException(ErrorCode_InternalError); |
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202 } |
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203 } |
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204 else |
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205 { |
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206 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance; |
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207 modified.reset(source.ReleaseAsParsedDicomFile()); |
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208 } |
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209 } |
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210 |
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211 assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject())); |
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212 |
2642 | 213 DicomInstanceToStore toStore; |
214 toStore.SetOrigin(origin_); | |
215 toStore.SetParsedDicomFile(*modified); | |
216 | |
217 | |
218 /** | |
219 * Prepare the metadata information to associate with the | |
220 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). | |
221 **/ | |
222 | |
223 DicomInstanceHasher modifiedHasher = modified->GetHasher(); | |
224 | |
225 MetadataType metadataType = (isAnonymization_ ? | |
226 MetadataType_AnonymizedFrom : | |
227 MetadataType_ModifiedFrom); | |
228 | |
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229 if (originalHasher->HashSeries() != modifiedHasher.HashSeries()) |
2642 | 230 { |
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231 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries()); |
2642 | 232 } |
233 | |
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234 if (originalHasher->HashStudy() != modifiedHasher.HashStudy()) |
2642 | 235 { |
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236 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy()); |
2642 | 237 } |
238 | |
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239 if (originalHasher->HashPatient() != modifiedHasher.HashPatient()) |
2642 | 240 { |
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241 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient()); |
2642 | 242 } |
243 | |
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244 assert(instance == originalHasher->HashInstance()); |
2642 | 245 toStore.AddMetadata(ResourceType_Instance, metadataType, instance); |
246 | |
247 | |
248 /** | |
249 * Store the resulting DICOM instance into the Orthanc store. | |
250 **/ | |
251 | |
252 std::string modifiedInstance; | |
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253 if (GetContext().Store(modifiedInstance, toStore, |
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254 StoreInstanceMode_Default) != StoreStatus_Success) |
2642 | 255 { |
2955 | 256 throw OrthancException(ErrorCode_CannotStoreInstance, |
257 "Error while storing a modified instance " + instance); | |
2642 | 258 } |
259 | |
3938 | 260 /** |
261 * The assertion below will fail if automated transcoding to a | |
262 * lossy transfer syntax is enabled in the Orthanc core, and if | |
263 * the source instance is not in this transfer syntax. | |
264 **/ | |
265 // assert(modifiedInstance == modifiedHasher.HashInstance()); | |
2642 | 266 |
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267 output_->Update(modifiedHasher); |
2642 | 268 |
269 return true; | |
270 } | |
271 | |
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272 |
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273 ResourceModificationJob::ResourceModificationJob(ServerContext& context) : |
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274 CleaningInstancesJob(context, true /* by default, keep source */), |
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275 modification_(new DicomModification), |
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276 isAnonymization_(false), |
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277 transcode_(false) |
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278 { |
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279 } |
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280 |
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281 |
2642 | 282 void ResourceModificationJob::SetModification(DicomModification* modification, |
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283 ResourceType level, |
2642 | 284 bool isAnonymization) |
285 { | |
286 if (modification == NULL) | |
287 { | |
288 throw OrthancException(ErrorCode_NullPointer); | |
289 } | |
290 else if (IsStarted()) | |
291 { | |
292 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
293 } | |
294 else | |
295 { | |
296 modification_.reset(modification); | |
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297 output_.reset(new Output(level)); |
2642 | 298 isAnonymization_ = isAnonymization; |
299 } | |
300 } | |
301 | |
302 | |
303 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin) | |
304 { | |
305 if (IsStarted()) | |
306 { | |
307 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
308 } | |
309 else | |
310 { | |
311 origin_ = origin; | |
312 } | |
313 } | |
314 | |
315 | |
316 void ResourceModificationJob::SetOrigin(const RestApiCall& call) | |
317 { | |
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318 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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319 } |
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320 |
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321 |
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322 const DicomModification& ResourceModificationJob::GetModification() const |
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323 { |
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324 if (modification_.get() == NULL) |
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325 { |
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326 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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327 } |
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328 else |
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329 { |
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330 return *modification_; |
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331 } |
2642 | 332 } |
333 | |
334 | |
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335 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const |
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336 { |
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337 if (transcode_) |
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338 { |
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339 return transferSyntax_; |
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340 } |
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341 else |
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342 { |
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343 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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344 } |
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345 } |
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346 |
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347 |
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348 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax) |
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349 { |
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350 if (IsStarted()) |
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351 { |
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352 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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353 } |
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354 else |
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355 { |
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356 transcode_ = true; |
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357 transferSyntax_ = syntax; |
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358 } |
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359 } |
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360 |
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361 |
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362 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid) |
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363 { |
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364 DicomTransferSyntax s; |
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365 if (LookupTransferSyntax(s, transferSyntaxUid)) |
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366 { |
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367 SetTranscode(s); |
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368 } |
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369 else |
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370 { |
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371 throw OrthancException(ErrorCode_BadFileFormat, |
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372 "Unknown transfer syntax UID: " + transferSyntaxUid); |
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373 } |
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374 } |
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375 |
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376 |
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377 void ResourceModificationJob::ClearTranscode() |
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378 { |
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379 if (IsStarted()) |
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380 { |
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381 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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382 } |
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383 else |
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384 { |
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385 transcode_ = false; |
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386 } |
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387 } |
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388 |
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389 |
2642 | 390 void ResourceModificationJob::GetPublicContent(Json::Value& value) |
391 { | |
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392 CleaningInstancesJob::GetPublicContent(value); |
2642 | 393 |
394 value["IsAnonymization"] = isAnonymization_; | |
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395 |
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396 if (output_.get() != NULL) |
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397 { |
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398 output_->Format(value); |
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399 } |
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400 |
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401 if (transcode_) |
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402 { |
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403 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_); |
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404 } |
2642 | 405 } |
406 | |
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407 |
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408 static const char* MODIFICATION = "Modification"; |
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409 static const char* ORIGIN = "Origin"; |
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410 static const char* IS_ANONYMIZATION = "IsAnonymization"; |
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411 static const char* TRANSCODE = "Transcode"; |
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412 |
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413 |
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414 ResourceModificationJob::ResourceModificationJob(ServerContext& context, |
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415 const Json::Value& serialized) : |
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416 CleaningInstancesJob(context, serialized, true /* by default, keep source */) |
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417 { |
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418 assert(serialized.type() == Json::objectValue); |
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419 |
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420 isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION); |
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421 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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422 modification_.reset(new DicomModification(serialized[MODIFICATION])); |
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423 |
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424 if (serialized.isMember(TRANSCODE)) |
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425 { |
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426 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE)); |
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427 } |
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428 else |
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429 { |
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430 transcode_ = false; |
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431 } |
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432 } |
2642 | 433 |
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434 bool ResourceModificationJob::Serialize(Json::Value& value) |
2642 | 435 { |
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436 if (!CleaningInstancesJob::Serialize(value)) |
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437 { |
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438 return false; |
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439 } |
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440 else |
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441 { |
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442 assert(value.type() == Json::objectValue); |
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443 |
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444 value[IS_ANONYMIZATION] = isAnonymization_; |
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445 |
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446 if (transcode_) |
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447 { |
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448 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
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449 } |
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450 |
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451 origin_.Serialize(value[ORIGIN]); |
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452 |
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453 Json::Value tmp; |
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454 modification_->Serialize(tmp); |
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455 value[MODIFICATION] = tmp; |
2642 | 456 |
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457 return true; |
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2663
diff
changeset
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458 } |
2642 | 459 } |
460 } |