Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp @ 5141:023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
author | Alain Mazy <am@osimis.io> |
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date | Fri, 20 Jan 2023 18:10:42 +0100 |
parents | 021d7fdcb659 |
children | 45ce9dfa42e0 |
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 modifiedSeries_.clear(); |
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172 instancesToReconstruct_.clear(); |
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173 |
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174 ThreadedSetOfInstancesJob::Reset(); |
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175 } |
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176 |
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177 void ResourceModificationJob::PostProcessInstances() |
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178 { |
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179 boost::recursive_mutex::scoped_lock lock(mutex_); |
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180 |
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181 // reconstruct the parents MainDicomTags in case one of them has changed |
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182 if (instancesToReconstruct_.size() > 0) |
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183 { |
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184 for (std::set<std::string>::const_iterator it = instancesToReconstruct_.begin(); it != instancesToReconstruct_.end(); ++it) |
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185 { |
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186 ServerContext::DicomCacheLocker locker(GetContext(), *it); |
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187 ParsedDicomFile& modifiedDicom = locker.GetDicom(); |
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188 |
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189 GetContext().GetIndex().ReconstructInstance(modifiedDicom); |
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190 } |
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191 } |
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192 |
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193 } |
2642 | 194 |
195 bool ResourceModificationJob::HandleInstance(const std::string& instance) | |
196 { | |
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197 if (modification_.get() == NULL || |
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198 output_.get() == NULL) |
2642 | 199 { |
2955 | 200 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
201 "No modification was provided for this job"); | |
2642 | 202 } |
203 | |
204 | |
205 LOG(INFO) << "Modifying instance in a job: " << instance; | |
206 | |
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207 /** |
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208 * Retrieve the original instance from the DICOM cache. |
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209 **/ |
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210 |
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211 std::unique_ptr<DicomInstanceHasher> originalHasher; |
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212 std::unique_ptr<ParsedDicomFile> modified; |
2642 | 213 |
214 try | |
215 { | |
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216 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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217 ParsedDicomFile& original = locker.GetDicom(); |
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218 |
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219 originalHasher.reset(new DicomInstanceHasher(original.GetHasher())); |
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220 modified.reset(original.Clone(true)); |
2642 | 221 } |
3430 | 222 catch (OrthancException& e) |
2642 | 223 { |
3430 | 224 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails(); |
2642 | 225 return false; |
226 } | |
227 | |
228 | |
229 /** | |
230 * Compute the resulting DICOM instance. | |
231 **/ | |
232 | |
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233 { |
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234 boost::recursive_mutex::scoped_lock lock(mutex_); // DicomModification object is not thread safe, we must protect it from here |
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235 |
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236 modification_->Apply(*modified); |
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237 } |
2642 | 238 |
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239 const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()); |
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240 |
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241 if (transcode_) |
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242 { |
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243 std::set<DicomTransferSyntax> syntaxes; |
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244 syntaxes.insert(transferSyntax_); |
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245 |
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246 IDicomTranscoder::DicomImage source; |
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247 source.AcquireParsed(*modified); // "modified" is invalid below this point |
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248 |
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249 IDicomTranscoder::DicomImage transcoded; |
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250 if (GetContext().Transcode(transcoded, source, syntaxes, true)) |
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251 { |
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252 modified.reset(transcoded.ReleaseAsParsedDicomFile()); |
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253 |
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254 // Fix the SOP instance UID in order the preserve the |
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255 // references between instance UIDs in the DICOM hierarchy |
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256 // (the UID might have changed in the case of lossy transcoding) |
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257 if (modified.get() == NULL || |
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258 modified->GetDcmtkObject().getDataset() == NULL || |
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259 !modified->GetDcmtkObject().getDataset()->putAndInsertString( |
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260 DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good()) |
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261 { |
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262 throw OrthancException(ErrorCode_InternalError); |
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263 } |
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264 } |
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265 else |
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266 { |
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267 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance; |
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268 modified.reset(source.ReleaseAsParsedDicomFile()); |
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269 } |
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270 } |
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271 |
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272 assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject())); |
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273 |
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274 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified)); |
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275 toStore->SetOrigin(origin_); |
2642 | 276 |
277 | |
278 /** | |
279 * Prepare the metadata information to associate with the | |
280 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). | |
281 **/ | |
282 | |
283 DicomInstanceHasher modifiedHasher = modified->GetHasher(); | |
284 | |
285 MetadataType metadataType = (isAnonymization_ ? | |
286 MetadataType_AnonymizedFrom : | |
287 MetadataType_ModifiedFrom); | |
288 | |
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289 if (originalHasher->HashSeries() != modifiedHasher.HashSeries()) |
2642 | 290 { |
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291 toStore->AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries()); |
2642 | 292 } |
293 | |
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294 if (originalHasher->HashStudy() != modifiedHasher.HashStudy()) |
2642 | 295 { |
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296 toStore->AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy()); |
2642 | 297 } |
298 | |
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299 if (originalHasher->HashPatient() != modifiedHasher.HashPatient()) |
2642 | 300 { |
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301 toStore->AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient()); |
2642 | 302 } |
303 | |
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304 assert(instance == originalHasher->HashInstance()); |
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305 toStore->AddMetadata(ResourceType_Instance, metadataType, instance); |
2642 | 306 |
307 | |
308 /** | |
309 * Store the resulting DICOM instance into the Orthanc store. | |
310 **/ | |
311 | |
312 std::string modifiedInstance; | |
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313 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default); |
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314 if (result.GetStatus() != StoreStatus_Success && result.GetStatus() != StoreStatus_AlreadyStored) // when retrying a job, we might save the same data again |
2642 | 315 { |
2955 | 316 throw OrthancException(ErrorCode_CannotStoreInstance, |
317 "Error while storing a modified instance " + instance); | |
2642 | 318 } |
319 | |
3938 | 320 /** |
321 * The assertion below will fail if automated transcoding to a | |
322 * lossy transfer syntax is enabled in the Orthanc core, and if | |
323 * the source instance is not in this transfer syntax. | |
324 **/ | |
325 // assert(modifiedInstance == modifiedHasher.HashInstance()); | |
2642 | 326 |
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327 { |
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328 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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329 |
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330 output_->Update(modifiedHasher); |
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331 if (modifiedSeries_.find(modifiedHasher.HashSeries()) == modifiedSeries_.end()) |
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332 { |
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333 modifiedSeries_.insert(modifiedHasher.HashSeries()); |
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334 // add an instance to reconstruct for each series |
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335 instancesToReconstruct_.insert(modifiedHasher.HashInstance()); |
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336 } |
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337 |
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338 } |
2642 | 339 |
340 return true; | |
341 } | |
342 | |
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343 |
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344 ResourceModificationJob::ResourceModificationJob(ServerContext& context, unsigned int workersCount) : |
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345 ThreadedSetOfInstancesJob(context, true /* post processing step */, true /* by default, keep source */, workersCount), |
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346 isAnonymization_(false), |
4206 | 347 transcode_(false), |
348 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization | |
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349 { |
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350 } |
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351 |
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352 |
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353 void ResourceModificationJob::SetSingleResourceModification(DicomModification* modification, |
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354 ResourceType outputLevel, |
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355 bool isAnonymization) |
2642 | 356 { |
357 if (modification == NULL) | |
358 { | |
359 throw OrthancException(ErrorCode_NullPointer); | |
360 } | |
361 else if (IsStarted()) | |
362 { | |
363 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
364 } | |
365 else | |
366 { | |
367 modification_.reset(modification); | |
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368 output_.reset(new SingleOutput(outputLevel)); |
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369 isAnonymization_ = isAnonymization; |
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370 } |
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371 } |
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372 |
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373 |
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374 void ResourceModificationJob::SetMultipleResourcesModification(DicomModification* modification, |
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375 bool isAnonymization) |
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376 { |
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377 if (modification == NULL) |
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378 { |
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379 throw OrthancException(ErrorCode_NullPointer); |
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380 } |
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381 else if (IsStarted()) |
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382 { |
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383 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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384 } |
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385 else |
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386 { |
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387 modification_.reset(modification); |
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388 output_.reset(new MultipleOutputs); |
2642 | 389 isAnonymization_ = isAnonymization; |
390 } | |
391 } | |
392 | |
393 | |
394 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin) | |
395 { | |
396 if (IsStarted()) | |
397 { | |
398 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
399 } | |
400 else | |
401 { | |
402 origin_ = origin; | |
403 } | |
404 } | |
405 | |
406 | |
407 void ResourceModificationJob::SetOrigin(const RestApiCall& call) | |
408 { | |
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409 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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410 } |
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411 |
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412 |
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413 #if ORTHANC_BUILD_UNIT_TESTS == 1 |
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414 const DicomModification& ResourceModificationJob::GetModification() const |
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415 { |
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416 if (modification_.get() == NULL) |
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417 { |
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418 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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419 } |
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420 else |
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421 { |
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422 return *modification_; |
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423 } |
2642 | 424 } |
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425 #endif |
2642 | 426 |
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427 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const |
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428 { |
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429 if (transcode_) |
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430 { |
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431 return transferSyntax_; |
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432 } |
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433 else |
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434 { |
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435 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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436 } |
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437 } |
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438 |
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439 |
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440 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax) |
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441 { |
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442 if (IsStarted()) |
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443 { |
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444 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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445 } |
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446 else |
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447 { |
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448 transcode_ = true; |
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449 transferSyntax_ = syntax; |
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450 } |
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451 } |
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452 |
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453 |
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454 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid) |
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455 { |
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456 DicomTransferSyntax s; |
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457 if (LookupTransferSyntax(s, transferSyntaxUid)) |
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458 { |
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459 SetTranscode(s); |
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460 } |
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461 else |
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462 { |
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463 throw OrthancException(ErrorCode_BadFileFormat, |
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464 "Unknown transfer syntax UID: " + transferSyntaxUid); |
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465 } |
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466 } |
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467 |
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468 |
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469 void ResourceModificationJob::ClearTranscode() |
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470 { |
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471 if (IsStarted()) |
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472 { |
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473 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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474 } |
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475 else |
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476 { |
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477 transcode_ = false; |
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478 } |
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479 } |
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480 |
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481 |
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482 bool ResourceModificationJob::IsSingleResourceModification() const |
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483 { |
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484 if (modification_.get() == NULL) |
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485 { |
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486 assert(output_.get() == NULL); |
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487 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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488 } |
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489 else |
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490 { |
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491 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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492 |
4693
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493 assert(output_.get() != NULL); |
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494 return output_->IsSingleResource(); |
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495 } |
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496 } |
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|
497 |
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|
498 |
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|
499 ResourceType ResourceModificationJob::GetOutputLevel() const |
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500 { |
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501 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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502 |
4693
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503 if (IsSingleResourceModification()) |
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504 { |
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505 assert(modification_.get() != NULL && |
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|
506 output_.get() != NULL); |
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507 return dynamic_cast<const SingleOutput&>(*output_).GetLevel(); |
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508 } |
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509 else |
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|
510 { |
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|
511 // Not applicable if multiple resources |
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512 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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513 } |
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514 } |
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changeset
|
515 |
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|
516 |
2642 | 517 void ResourceModificationJob::GetPublicContent(Json::Value& value) |
518 { | |
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519 boost::recursive_mutex::scoped_lock lock(outputMutex_); |
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|
520 |
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|
521 ThreadedSetOfInstancesJob::GetPublicContent(value); |
2642 | 522 |
523 value["IsAnonymization"] = isAnonymization_; | |
2868
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|
524 |
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|
525 if (output_.get() != NULL) |
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|
526 { |
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|
527 output_->Format(value); |
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|
528 } |
3943
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|
529 |
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|
530 if (transcode_) |
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|
531 { |
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532 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_); |
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533 } |
2642 | 534 } |
535 | |
2664
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|
536 |
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|
537 static const char* MODIFICATION = "Modification"; |
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|
538 static const char* ORIGIN = "Origin"; |
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|
539 static const char* IS_ANONYMIZATION = "IsAnonymization"; |
3943
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|
540 static const char* TRANSCODE = "Transcode"; |
4693
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|
541 static const char* OUTPUT_LEVEL = "OutputLevel"; |
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|
542 static const char* IS_SINGLE_RESOURCE = "IsSingleResource"; |
2664
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diff
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|
543 |
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|
544 |
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|
545 ResourceModificationJob::ResourceModificationJob(ServerContext& context, |
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|
546 const Json::Value& serialized) : |
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|
547 ThreadedSetOfInstancesJob(context, serialized, false /* no post processing step */, true /* by default, keep source */), |
4223 | 548 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization |
2664
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|
549 { |
3943
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changeset
|
550 assert(serialized.type() == Json::objectValue); |
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|
551 |
2664
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changeset
|
552 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
3943
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553 |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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554 if (serialized.isMember(TRANSCODE)) |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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|
555 { |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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556 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE)); |
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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557 } |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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|
558 else |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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parents:
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|
559 { |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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560 transcode_ = false; |
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"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
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561 } |
4693
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|
562 |
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changeset
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563 bool isSingleResource; |
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564 if (serialized.isMember(IS_SINGLE_RESOURCE)) |
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565 { |
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|
566 isSingleResource = SerializationToolbox::ReadBoolean(serialized, IS_SINGLE_RESOURCE); |
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567 } |
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|
568 else |
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569 { |
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|
570 isSingleResource = true; // Backward compatibility with Orthanc <= 1.9.3 |
45bce660ce3a
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|
571 } |
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572 |
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|
573 bool isAnonymization = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION); |
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574 std::unique_ptr<DicomModification> modification(new DicomModification(serialized[MODIFICATION])); |
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575 |
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diff
changeset
|
576 if (isSingleResource) |
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577 { |
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578 ResourceType outputLevel; |
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579 |
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|
580 if (serialized.isMember(OUTPUT_LEVEL)) |
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581 { |
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582 // New in Orthanc 1.9.4. This fixes an *incorrect* behavior in |
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583 // Orthanc <= 1.9.3, in which "outputLevel" would be set to |
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584 // "modification->GetLevel()" |
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585 outputLevel = StringToResourceType(SerializationToolbox::ReadString(serialized, OUTPUT_LEVEL).c_str()); |
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|
586 } |
45bce660ce3a
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diff
changeset
|
587 else |
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diff
changeset
|
588 { |
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589 // Use the buggy convention from Orthanc <= 1.9.3 (which is |
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|
590 // the only thing we have at hand) |
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|
591 outputLevel = modification->GetLevel(); |
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diff
changeset
|
592 |
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parents:
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diff
changeset
|
593 if (outputLevel == ResourceType_Instance) |
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|
594 { |
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changeset
|
595 // This should never happen, but as "SingleOutput" doesn't |
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added routes for bulk anonymization/modification
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changeset
|
596 // support instance-level anonymization, don't take any risk |
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diff
changeset
|
597 // and choose an arbitrary output level |
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598 outputLevel = ResourceType_Patient; |
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changeset
|
599 } |
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diff
changeset
|
600 } |
45bce660ce3a
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diff
changeset
|
601 |
45bce660ce3a
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diff
changeset
|
602 SetSingleResourceModification(modification.release(), outputLevel, isAnonymization); |
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diff
changeset
|
603 } |
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added routes for bulk anonymization/modification
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diff
changeset
|
604 else |
45bce660ce3a
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diff
changeset
|
605 { |
45bce660ce3a
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diff
changeset
|
606 // New in Orthanc 1.9.4 |
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changeset
|
607 SetMultipleResourcesModification(modification.release(), isAnonymization); |
45bce660ce3a
added routes for bulk anonymization/modification
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diff
changeset
|
608 } |
2664
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2663
diff
changeset
|
609 } |
2642 | 610 |
2663
228e2783ce83
some jobs might not be serializable
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
611 bool ResourceModificationJob::Serialize(Json::Value& value) |
2642 | 612 { |
4693
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|
613 if (modification_.get() == NULL) |
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diff
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|
614 { |
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changeset
|
615 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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diff
changeset
|
616 } |
5130
f2dcdbe05884
ResourceModification jobs can now use multiple threads
Alain Mazy <am@osimis.io>
parents:
4892
diff
changeset
|
617 else if (!ThreadedSetOfInstancesJob::Serialize(value)) |
2664
a21b244efb37
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diff
changeset
|
618 { |
a21b244efb37
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diff
changeset
|
619 return false; |
a21b244efb37
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diff
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|
620 } |
a21b244efb37
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diff
changeset
|
621 else |
a21b244efb37
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diff
changeset
|
622 { |
3943
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
623 assert(value.type() == Json::objectValue); |
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
624 |
2664
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff
changeset
|
625 value[IS_ANONYMIZATION] = isAnonymization_; |
3943
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
626 |
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
627 if (transcode_) |
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
628 { |
b26d25d3c1c7
"/{patients|studies|series}/.../modify": New option "Transcode"
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diff
changeset
|
629 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
b26d25d3c1c7
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diff
changeset
|
630 } |
5137
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
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5136
diff
changeset
|
631 |
2664
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diff
changeset
|
632 origin_.Serialize(value[ORIGIN]); |
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff
changeset
|
633 |
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff
changeset
|
634 Json::Value tmp; |
5141
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
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5139
diff
changeset
|
635 |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
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5139
diff
changeset
|
636 { |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
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5139
diff
changeset
|
637 boost::recursive_mutex::scoped_lock lock(mutex_); // DicomModification object is not thread safe, we must protect it from here |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
parents:
5139
diff
changeset
|
638 |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
parents:
5139
diff
changeset
|
639 modification_->Serialize(tmp); |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
parents:
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diff
changeset
|
640 } |
023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
Alain Mazy <am@osimis.io>
parents:
5139
diff
changeset
|
641 |
2664
a21b244efb37
serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
642 value[MODIFICATION] = tmp; |
2642 | 643 |
4693
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diff
changeset
|
644 // New in Orthanc 1.9.4 |
45bce660ce3a
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diff
changeset
|
645 value[IS_SINGLE_RESOURCE] = IsSingleResourceModification(); |
45bce660ce3a
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changeset
|
646 if (IsSingleResourceModification()) |
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|
647 { |
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diff
changeset
|
648 value[OUTPUT_LEVEL] = EnumerationToString(GetOutputLevel()); |
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diff
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|
649 } |
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added routes for bulk anonymization/modification
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diff
changeset
|
650 |
2664
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diff
changeset
|
651 return true; |
a21b244efb37
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diff
changeset
|
652 } |
2642 | 653 } |
5137
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
654 |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
655 void ResourceModificationJob::PerformSanityChecks() |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
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5136
diff
changeset
|
656 { |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
657 boost::recursive_mutex::scoped_lock lock(mutex_); // because we access the parentResources_ |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
658 |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
659 std::set<DicomTag> emptyRequestedTags; |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
660 |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
661 if (modification_.get() == NULL) |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
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diff
changeset
|
662 { |
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663 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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664 } |
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665 |
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666 bool replacePatientMainDicomTags = false; |
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667 bool replaceStudyMainDicomTags = false; |
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668 bool replaceSeriesMainDicomTags = false; |
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669 bool replaceInstanceMainDicomTags = false; |
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670 |
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671 ResourceType modificationLevel = modification_->GetLevel(); |
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672 std::set<DicomTag> replacedTags; |
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673 modification_->GetReplacedTags(replacedTags); |
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674 |
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675 for (std::set<DicomTag>::const_iterator it = replacedTags.begin(); it != replacedTags.end(); it++) |
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676 { |
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677 replacePatientMainDicomTags |= DicomMap::IsMainDicomTag(*it, ResourceType_Patient); |
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678 replaceStudyMainDicomTags |= DicomMap::IsMainDicomTag(*it, ResourceType_Study); |
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679 replaceSeriesMainDicomTags |= DicomMap::IsMainDicomTag(*it, ResourceType_Series); |
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680 replaceInstanceMainDicomTags |= DicomMap::IsMainDicomTag(*it, ResourceType_Instance); |
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681 } |
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682 |
5139
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683 if (modification_->IsKept(DICOM_TAG_SOP_INSTANCE_UID) |
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684 && (modificationLevel == ResourceType_Series || modificationLevel == ResourceType_Study || modificationLevel == ResourceType_Patient)) |
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685 { |
5139
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686 // if we keep the SOPInstanceUID, it very likely means that we are modifying existing resources 'in place' |
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687 |
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688 // we must make sure we do not delete them at the end of the job |
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689 if (!IsKeepSource()) // note: we can refine this criteria -> this is valid only if all DicomUIDs are kept identical (but this can happen through Keep or Replace options) |
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690 { |
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691 throw OrthancException(ErrorCode_BadRequest, |
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692 "When keeping SOPInstanceUID tag, you must set KeepSource to true to avoid deleting the modified files at the end of the process"); |
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693 } |
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694 |
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695 // and we must make sure that we overwite them with the modified resources |
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696 if (IsKeepSource() && !GetContext().IsOverwriteInstances()) |
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697 { |
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698 throw OrthancException(ErrorCode_BadRequest, |
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699 "When keeping SOPInstanceUID tag, you must have the 'OverwriteInstances' Orthanc configuration set to true in order to replace the modified resources"); |
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700 } |
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701 } |
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702 |
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703 if (modificationLevel == ResourceType_Study && replacePatientMainDicomTags) |
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704 { |
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705 for (std::set<std::string>::const_iterator studyId = parentResources_.begin(); studyId != parentResources_.end(); ++studyId) |
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706 { |
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707 // When modifying a study, you may not modify patient tags as you wish. |
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708 // - If this is the patient's only study, you may modify all patient tags. This could be performed in 2 steps (modify the patient and then, the study) but, |
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709 // for many use cases, it's helpful to be able to do it one step (e.g, to modify a name in a study that has just been acquired) |
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710 // - If the patient already has other studies, you may only 'attach' the study to an existing patient by modifying |
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711 // all patient tags from the study to match those of the target patient. |
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712 // - Otherwise, you can't modify the patient tags |
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713 |
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714 std::string targetPatientId; |
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715 if (modification_->IsReplaced(DICOM_TAG_PATIENT_ID)) |
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716 { |
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717 targetPatientId = modification_->GetReplacementAsString(DICOM_TAG_PATIENT_ID); |
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718 } |
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719 else |
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720 { |
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721 ExpandedResource originalStudy; |
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722 if (GetContext().GetIndex().ExpandResource(originalStudy, *studyId, ResourceType_Study, emptyRequestedTags, ExpandResourceDbFlags_IncludeMainDicomTags)) |
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723 { |
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724 targetPatientId = originalStudy.tags_.GetStringValue(DICOM_TAG_PATIENT_ID, "", false); |
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725 } |
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726 else |
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727 { |
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728 throw OrthancException(ErrorCode_UnknownResource, "Study not found"); |
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729 } |
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730 } |
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731 |
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732 // try to find the targetPatient |
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733 std::vector<std::string> lookupPatientResult; |
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734 GetContext().GetIndex().LookupIdentifierExact(lookupPatientResult, ResourceType_Patient, DICOM_TAG_PATIENT_ID, targetPatientId); |
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735 |
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736 // if the patient exists, check how many child studies it has. |
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737 if (lookupPatientResult.size() >= 1) |
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738 { |
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739 ExpandedResource targetPatient; |
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740 |
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741 if (GetContext().GetIndex().ExpandResource(targetPatient, lookupPatientResult[0], ResourceType_Patient, emptyRequestedTags, static_cast<ExpandResourceDbFlags>(ExpandResourceDbFlags_IncludeMainDicomTags | ExpandResourceDbFlags_IncludeChildren))) |
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742 { |
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743 const std::list<std::string> childrenIds = targetPatient.childrenIds_; |
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744 bool targetPatientHasOtherStudies = childrenIds.size() > 1; |
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745 if (childrenIds.size() == 1) |
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746 { |
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747 targetPatientHasOtherStudies = std::find(childrenIds.begin(), childrenIds.end(), *studyId) == childrenIds.end(); // if the patient has one study that is not the one being modified |
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748 } |
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749 |
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750 if (targetPatientHasOtherStudies) |
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751 { |
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752 // this is allowed if all patient replacedTags do match the target patient tags |
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753 DicomMap targetPatientTags; |
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754 targetPatient.tags_.ExtractPatientInformation(targetPatientTags); |
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755 |
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756 for (std::set<DicomTag>::const_iterator mainPatientTag = DicomMap::GetMainDicomTags(ResourceType_Patient).begin(); |
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757 mainPatientTag != DicomMap::GetMainDicomTags(ResourceType_Patient).end(); ++mainPatientTag) |
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758 { |
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759 if (targetPatientTags.HasTag(*mainPatientTag) |
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changeset
|
760 && (!modification_->IsReplaced(*mainPatientTag) |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
761 || modification_->GetReplacementAsString(*mainPatientTag) != targetPatientTags.GetStringValue(*mainPatientTag, "", false))) |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
762 { |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
763 throw OrthancException(ErrorCode_BadRequest, std::string("Trying to change patient tags in a study. The Patient already exists and has other studies. All the 'Replace' tags should match the existing patient main dicom tags. Try using /patients/../modify instead to modify the patient. Failing tag: ") + mainPatientTag->Format()); |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
764 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
765 else if (!targetPatientTags.HasTag(*mainPatientTag) && modification_->IsReplaced(*mainPatientTag) ) |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
766 { |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
767 throw OrthancException(ErrorCode_BadRequest, std::string("Trying to change patient tags in a study. The Patient already exists and has other studies. You are trying to replace a tag that is not defined yet in this patient. Try using /patients/../modify instead to modify the patient. Failing tag: ") + mainPatientTag->Format()); |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
768 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
769 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
770 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
771 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
772 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
773 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
774 |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
775 } |
15109c3f0f7d
added sanity checks in DicomModificationJob + automatically reconstruct resources at the end of a DicomModificationJob
Alain Mazy <am@osimis.io>
parents:
5136
diff
changeset
|
776 } |
2642 | 777 } |