Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp @ 4793:fc2ba1ce6538
new configuration 'DicomThreadsCount'
author | Alain Mazy <am@osimis.io> |
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date | Thu, 30 Sep 2021 15:03:35 +0200 |
parents | 45bce660ce3a |
children | f0038043fb97 94616af363ec |
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) 2017-2021 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 | |
4045 | 37 #include "../../../OrthancFramework/Sources/Logging.h" |
38 #include "../../../OrthancFramework/Sources/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 static void FormatResource(Json::Value& target, |
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48 ResourceType level, |
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49 const std::string& id) |
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50 { |
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51 target["Type"] = EnumerationToString(level); |
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52 target["ID"] = id; |
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53 target["Path"] = GetBasePath(level, id); |
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54 } |
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55 |
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56 class ResourceModificationJob::SingleOutput : public IOutput |
2642 | 57 { |
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58 private: |
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59 ResourceType level_; |
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60 bool isFirst_; |
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61 std::string id_; |
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62 std::string patientId_; |
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63 |
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64 public: |
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65 explicit SingleOutput(ResourceType level) : |
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66 level_(level), |
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67 isFirst_(true) |
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68 { |
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69 if (level_ != ResourceType_Patient && |
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70 level_ != ResourceType_Study && |
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71 level_ != ResourceType_Series) |
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72 { |
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73 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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74 } |
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75 } |
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76 |
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77 virtual void Update(DicomInstanceHasher& hasher) ORTHANC_OVERRIDE |
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78 { |
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79 if (isFirst_) |
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80 { |
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81 switch (level_) |
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82 { |
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83 case ResourceType_Series: |
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84 id_ = hasher.HashSeries(); |
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85 break; |
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86 |
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87 case ResourceType_Study: |
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88 id_ = hasher.HashStudy(); |
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89 break; |
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90 |
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91 case ResourceType_Patient: |
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92 id_ = hasher.HashPatient(); |
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93 break; |
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94 |
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95 default: |
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96 throw OrthancException(ErrorCode_InternalError); |
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97 } |
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98 |
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99 patientId_ = hasher.HashPatient(); |
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100 isFirst_ = false; |
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101 } |
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102 } |
2642 | 103 |
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104 virtual void Format(Json::Value& target) const ORTHANC_OVERRIDE |
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105 { |
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106 assert(target.type() == Json::objectValue); |
2642 | 107 |
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108 if (!isFirst_) |
2642 | 109 { |
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110 FormatResource(target, level_, id_); |
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111 target["PatientID"] = patientId_; |
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112 } |
2642 | 113 } |
114 | |
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115 virtual bool IsSingleResource() const ORTHANC_OVERRIDE |
2642 | 116 { |
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117 return true; |
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118 } |
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119 |
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120 ResourceType GetLevel() const |
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121 { |
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122 return level_; |
2642 | 123 } |
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124 }; |
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125 |
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126 |
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127 class ResourceModificationJob::MultipleOutputs : public IOutput |
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128 { |
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129 private: |
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130 static void FormatResources(Json::Value& target, |
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131 ResourceType level, |
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132 const std::set<std::string>& resources) |
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133 { |
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134 assert(target.type() == Json::arrayValue); |
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135 |
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136 for (std::set<std::string>::const_iterator |
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137 it = resources.begin(); it != resources.end(); ++it) |
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138 { |
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139 Json::Value item = Json::objectValue; |
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140 FormatResource(item, level, *it); |
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141 target.append(item); |
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142 } |
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143 } |
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144 |
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145 std::set<std::string> instances_; |
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146 std::set<std::string> series_; |
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147 std::set<std::string> studies_; |
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148 std::set<std::string> patients_; |
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149 |
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150 public: |
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151 virtual void Update(DicomInstanceHasher& hasher) ORTHANC_OVERRIDE |
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152 { |
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153 instances_.insert(hasher.HashInstance()); |
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154 series_.insert(hasher.HashSeries()); |
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155 studies_.insert(hasher.HashStudy()); |
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156 patients_.insert(hasher.HashPatient()); |
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157 } |
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158 |
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159 virtual void Format(Json::Value& target) const ORTHANC_OVERRIDE |
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160 { |
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161 assert(target.type() == Json::objectValue); |
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162 Json::Value resources = Json::arrayValue; |
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163 FormatResources(resources, ResourceType_Instance, instances_); |
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164 FormatResources(resources, ResourceType_Series, series_); |
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165 FormatResources(resources, ResourceType_Study, studies_); |
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166 FormatResources(resources, ResourceType_Patient, patients_); |
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167 target["Resources"] = resources; |
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168 } |
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169 |
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170 virtual bool IsSingleResource() const ORTHANC_OVERRIDE |
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171 { |
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172 return false; |
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173 } |
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174 }; |
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175 |
2642 | 176 |
177 | |
178 bool ResourceModificationJob::HandleInstance(const std::string& instance) | |
179 { | |
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180 if (modification_.get() == NULL || |
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181 output_.get() == NULL) |
2642 | 182 { |
2955 | 183 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
184 "No modification was provided for this job"); | |
2642 | 185 } |
186 | |
187 | |
188 LOG(INFO) << "Modifying instance in a job: " << instance; | |
189 | |
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190 |
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191 /** |
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192 * Retrieve the original instance from the DICOM cache. |
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193 **/ |
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194 |
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195 std::unique_ptr<DicomInstanceHasher> originalHasher; |
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196 std::unique_ptr<ParsedDicomFile> modified; |
2642 | 197 |
198 try | |
199 { | |
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200 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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201 ParsedDicomFile& original = locker.GetDicom(); |
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202 |
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203 originalHasher.reset(new DicomInstanceHasher(original.GetHasher())); |
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204 modified.reset(original.Clone(true)); |
2642 | 205 } |
3430 | 206 catch (OrthancException& e) |
2642 | 207 { |
3430 | 208 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails(); |
2642 | 209 return false; |
210 } | |
211 | |
212 | |
213 /** | |
214 * Compute the resulting DICOM instance. | |
215 **/ | |
216 | |
217 modification_->Apply(*modified); | |
218 | |
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219 const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()); |
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220 |
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221 if (transcode_) |
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222 { |
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223 std::set<DicomTransferSyntax> syntaxes; |
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224 syntaxes.insert(transferSyntax_); |
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225 |
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226 IDicomTranscoder::DicomImage source; |
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227 source.AcquireParsed(*modified); // "modified" is invalid below this point |
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228 |
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229 IDicomTranscoder::DicomImage transcoded; |
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230 if (GetContext().Transcode(transcoded, source, syntaxes, true)) |
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231 { |
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232 modified.reset(transcoded.ReleaseAsParsedDicomFile()); |
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233 |
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234 // Fix the SOP instance UID in order the preserve the |
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235 // references between instance UIDs in the DICOM hierarchy |
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236 // (the UID might have changed in the case of lossy transcoding) |
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237 if (modified.get() == NULL || |
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238 modified->GetDcmtkObject().getDataset() == NULL || |
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239 !modified->GetDcmtkObject().getDataset()->putAndInsertString( |
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240 DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good()) |
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241 { |
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242 throw OrthancException(ErrorCode_InternalError); |
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243 } |
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244 } |
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245 else |
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246 { |
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247 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance; |
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248 modified.reset(source.ReleaseAsParsedDicomFile()); |
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249 } |
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250 } |
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251 |
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252 assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject())); |
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253 |
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254 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified)); |
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255 toStore->SetOrigin(origin_); |
2642 | 256 |
257 | |
258 /** | |
259 * Prepare the metadata information to associate with the | |
260 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). | |
261 **/ | |
262 | |
263 DicomInstanceHasher modifiedHasher = modified->GetHasher(); | |
264 | |
265 MetadataType metadataType = (isAnonymization_ ? | |
266 MetadataType_AnonymizedFrom : | |
267 MetadataType_ModifiedFrom); | |
268 | |
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269 if (originalHasher->HashSeries() != modifiedHasher.HashSeries()) |
2642 | 270 { |
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271 toStore->AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries()); |
2642 | 272 } |
273 | |
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274 if (originalHasher->HashStudy() != modifiedHasher.HashStudy()) |
2642 | 275 { |
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276 toStore->AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy()); |
2642 | 277 } |
278 | |
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279 if (originalHasher->HashPatient() != modifiedHasher.HashPatient()) |
2642 | 280 { |
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281 toStore->AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient()); |
2642 | 282 } |
283 | |
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284 assert(instance == originalHasher->HashInstance()); |
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285 toStore->AddMetadata(ResourceType_Instance, metadataType, instance); |
2642 | 286 |
287 | |
288 /** | |
289 * Store the resulting DICOM instance into the Orthanc store. | |
290 **/ | |
291 | |
292 std::string modifiedInstance; | |
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293 if (GetContext().Store(modifiedInstance, *toStore, |
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294 StoreInstanceMode_Default) != StoreStatus_Success) |
2642 | 295 { |
2955 | 296 throw OrthancException(ErrorCode_CannotStoreInstance, |
297 "Error while storing a modified instance " + instance); | |
2642 | 298 } |
299 | |
3938 | 300 /** |
301 * The assertion below will fail if automated transcoding to a | |
302 * lossy transfer syntax is enabled in the Orthanc core, and if | |
303 * the source instance is not in this transfer syntax. | |
304 **/ | |
305 // assert(modifiedInstance == modifiedHasher.HashInstance()); | |
2642 | 306 |
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307 output_->Update(modifiedHasher); |
2642 | 308 |
309 return true; | |
310 } | |
311 | |
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312 |
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313 ResourceModificationJob::ResourceModificationJob(ServerContext& context) : |
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314 CleaningInstancesJob(context, true /* by default, keep source */), |
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315 isAnonymization_(false), |
4206 | 316 transcode_(false), |
317 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization | |
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318 { |
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319 } |
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320 |
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321 |
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322 void ResourceModificationJob::SetSingleResourceModification(DicomModification* modification, |
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323 ResourceType outputLevel, |
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324 bool isAnonymization) |
2642 | 325 { |
326 if (modification == NULL) | |
327 { | |
328 throw OrthancException(ErrorCode_NullPointer); | |
329 } | |
330 else if (IsStarted()) | |
331 { | |
332 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
333 } | |
334 else | |
335 { | |
336 modification_.reset(modification); | |
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337 output_.reset(new SingleOutput(outputLevel)); |
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338 isAnonymization_ = isAnonymization; |
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339 } |
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340 } |
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341 |
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342 |
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343 void ResourceModificationJob::SetMultipleResourcesModification(DicomModification* modification, |
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344 bool isAnonymization) |
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345 { |
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346 if (modification == NULL) |
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347 { |
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348 throw OrthancException(ErrorCode_NullPointer); |
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349 } |
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350 else 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 modification_.reset(modification); |
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357 output_.reset(new MultipleOutputs); |
2642 | 358 isAnonymization_ = isAnonymization; |
359 } | |
360 } | |
361 | |
362 | |
363 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin) | |
364 { | |
365 if (IsStarted()) | |
366 { | |
367 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
368 } | |
369 else | |
370 { | |
371 origin_ = origin; | |
372 } | |
373 } | |
374 | |
375 | |
376 void ResourceModificationJob::SetOrigin(const RestApiCall& call) | |
377 { | |
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378 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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379 } |
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380 |
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381 |
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382 const DicomModification& ResourceModificationJob::GetModification() const |
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383 { |
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384 if (modification_.get() == NULL) |
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385 { |
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386 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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387 } |
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388 else |
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389 { |
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390 return *modification_; |
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391 } |
2642 | 392 } |
393 | |
394 | |
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395 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const |
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396 { |
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397 if (transcode_) |
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398 { |
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399 return transferSyntax_; |
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400 } |
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401 else |
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402 { |
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403 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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404 } |
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405 } |
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406 |
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407 |
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408 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax) |
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409 { |
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410 if (IsStarted()) |
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411 { |
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412 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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413 } |
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414 else |
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415 { |
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416 transcode_ = true; |
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417 transferSyntax_ = syntax; |
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418 } |
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419 } |
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420 |
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421 |
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422 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid) |
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423 { |
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424 DicomTransferSyntax s; |
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425 if (LookupTransferSyntax(s, transferSyntaxUid)) |
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426 { |
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427 SetTranscode(s); |
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428 } |
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429 else |
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430 { |
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431 throw OrthancException(ErrorCode_BadFileFormat, |
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432 "Unknown transfer syntax UID: " + transferSyntaxUid); |
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433 } |
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434 } |
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435 |
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436 |
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437 void ResourceModificationJob::ClearTranscode() |
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438 { |
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439 if (IsStarted()) |
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440 { |
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441 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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442 } |
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443 else |
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444 { |
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445 transcode_ = false; |
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446 } |
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447 } |
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448 |
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449 |
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450 bool ResourceModificationJob::IsSingleResourceModification() const |
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451 { |
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452 if (modification_.get() == NULL) |
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453 { |
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454 assert(output_.get() == NULL); |
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455 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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456 } |
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457 else |
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458 { |
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459 assert(output_.get() != NULL); |
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460 return output_->IsSingleResource(); |
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461 } |
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462 } |
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463 |
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464 |
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465 ResourceType ResourceModificationJob::GetOutputLevel() const |
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466 { |
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467 if (IsSingleResourceModification()) |
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468 { |
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469 assert(modification_.get() != NULL && |
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470 output_.get() != NULL); |
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471 return dynamic_cast<const SingleOutput&>(*output_).GetLevel(); |
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472 } |
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473 else |
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474 { |
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475 // Not applicable if multiple resources |
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476 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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477 } |
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478 } |
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479 |
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480 |
2642 | 481 void ResourceModificationJob::GetPublicContent(Json::Value& value) |
482 { | |
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483 CleaningInstancesJob::GetPublicContent(value); |
2642 | 484 |
485 value["IsAnonymization"] = isAnonymization_; | |
2868
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486 |
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487 if (output_.get() != NULL) |
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488 { |
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489 output_->Format(value); |
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490 } |
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491 |
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492 if (transcode_) |
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493 { |
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494 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_); |
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495 } |
2642 | 496 } |
497 | |
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498 |
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499 static const char* MODIFICATION = "Modification"; |
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500 static const char* ORIGIN = "Origin"; |
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501 static const char* IS_ANONYMIZATION = "IsAnonymization"; |
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502 static const char* TRANSCODE = "Transcode"; |
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503 static const char* OUTPUT_LEVEL = "OutputLevel"; |
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504 static const char* IS_SINGLE_RESOURCE = "IsSingleResource"; |
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505 |
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506 |
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507 ResourceModificationJob::ResourceModificationJob(ServerContext& context, |
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508 const Json::Value& serialized) : |
4223 | 509 CleaningInstancesJob(context, serialized, true /* by default, keep source */), |
510 transferSyntax_(DicomTransferSyntax_LittleEndianExplicit) // dummy initialization | |
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511 { |
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512 assert(serialized.type() == Json::objectValue); |
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513 |
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514 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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515 |
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516 if (serialized.isMember(TRANSCODE)) |
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517 { |
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518 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE)); |
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519 } |
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520 else |
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521 { |
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522 transcode_ = false; |
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523 } |
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524 |
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525 bool isSingleResource; |
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526 if (serialized.isMember(IS_SINGLE_RESOURCE)) |
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527 { |
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528 isSingleResource = SerializationToolbox::ReadBoolean(serialized, IS_SINGLE_RESOURCE); |
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529 } |
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530 else |
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531 { |
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532 isSingleResource = true; // Backward compatibility with Orthanc <= 1.9.3 |
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533 } |
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534 |
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535 bool isAnonymization = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION); |
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536 std::unique_ptr<DicomModification> modification(new DicomModification(serialized[MODIFICATION])); |
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537 |
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538 if (isSingleResource) |
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539 { |
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540 ResourceType outputLevel; |
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541 |
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542 if (serialized.isMember(OUTPUT_LEVEL)) |
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543 { |
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544 // New in Orthanc 1.9.4. This fixes an *incorrect* behavior in |
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545 // Orthanc <= 1.9.3, in which "outputLevel" would be set to |
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546 // "modification->GetLevel()" |
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547 outputLevel = StringToResourceType(SerializationToolbox::ReadString(serialized, OUTPUT_LEVEL).c_str()); |
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548 } |
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549 else |
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550 { |
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551 // Use the buggy convention from Orthanc <= 1.9.3 (which is |
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552 // the only thing we have at hand) |
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553 outputLevel = modification->GetLevel(); |
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554 |
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555 if (outputLevel == ResourceType_Instance) |
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556 { |
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557 // This should never happen, but as "SingleOutput" doesn't |
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558 // support instance-level anonymization, don't take any risk |
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559 // and choose an arbitrary output level |
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560 outputLevel = ResourceType_Patient; |
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561 } |
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562 } |
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563 |
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564 SetSingleResourceModification(modification.release(), outputLevel, isAnonymization); |
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565 } |
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566 else |
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567 { |
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568 // New in Orthanc 1.9.4 |
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569 SetMultipleResourcesModification(modification.release(), isAnonymization); |
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570 } |
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571 } |
2642 | 572 |
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573 bool ResourceModificationJob::Serialize(Json::Value& value) |
2642 | 574 { |
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575 if (modification_.get() == NULL) |
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576 { |
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577 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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578 } |
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579 else if (!CleaningInstancesJob::Serialize(value)) |
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580 { |
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581 return false; |
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582 } |
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583 else |
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584 { |
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585 assert(value.type() == Json::objectValue); |
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586 |
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587 value[IS_ANONYMIZATION] = isAnonymization_; |
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588 |
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589 if (transcode_) |
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590 { |
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591 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
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592 } |
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593 |
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594 origin_.Serialize(value[ORIGIN]); |
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595 |
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596 Json::Value tmp; |
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597 modification_->Serialize(tmp); |
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598 value[MODIFICATION] = tmp; |
2642 | 599 |
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600 // New in Orthanc 1.9.4 |
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601 value[IS_SINGLE_RESOURCE] = IsSingleResourceModification(); |
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602 if (IsSingleResourceModification()) |
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603 { |
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604 value[OUTPUT_LEVEL] = EnumerationToString(GetOutputLevel()); |
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605 } |
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606 |
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607 return true; |
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608 } |
2642 | 609 } |
610 } |