Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/MergeStudyJob.cpp @ 3841:be7df7fe3d80
avoid one memcpy of the DICOM buffer on "POST /instances"
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 16 Apr 2020 16:58:37 +0200 |
parents | 2a170a8f1faf |
children | 023b2a9f3aa1 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
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6 * |
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7 * This program is free software: you can redistribute it and/or |
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8 * modify it under the terms of the GNU General Public License as |
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9 * published by the Free Software Foundation, either version 3 of the |
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10 * License, or (at your option) any later version. |
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11 * |
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12 * In addition, as a special exception, the copyright holders of this |
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13 * program give permission to link the code of its release with the |
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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15 * that use the same license as the "OpenSSL" library), and distribute |
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16 * the linked executables. You must obey the GNU General Public License |
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17 * in all respects for all of the code used other than "OpenSSL". If you |
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18 * modify file(s) with this exception, you may extend this exception to |
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19 * your version of the file(s), but you are not obligated to do so. If |
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20 * you do not wish to do so, delete this exception statement from your |
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21 * version. If you delete this exception statement from all source files |
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22 * in the program, then also delete it here. |
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23 * |
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24 * This program is distributed in the hope that it will be useful, but |
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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27 * General Public License for more details. |
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28 * |
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29 * You should have received a copy of the GNU General Public License |
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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31 **/ |
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32 |
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33 |
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34 #include "MergeStudyJob.h" |
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35 |
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36 #include "../../Core/DicomParsing/FromDcmtkBridge.h" |
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37 #include "../../Core/Logging.h" |
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38 #include "../../Core/SerializationToolbox.h" |
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39 #include "../ServerContext.h" |
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40 |
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41 |
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42 namespace Orthanc |
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43 { |
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44 void MergeStudyJob::AddSourceSeriesInternal(const std::string& series) |
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45 { |
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46 // Generate a target SeriesInstanceUID for this series |
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47 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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48 |
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49 // Add all the instances of the series as to be processed |
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50 std::list<std::string> instances; |
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51 context_.GetIndex().GetChildren(instances, series); |
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52 |
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53 for (std::list<std::string>::const_iterator |
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54 it = instances.begin(); it != instances.end(); ++it) |
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55 { |
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56 AddInstance(*it); |
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57 } |
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58 } |
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59 |
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60 |
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61 void MergeStudyJob::AddSourceStudyInternal(const std::string& study) |
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62 { |
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63 if (study == targetStudy_) |
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64 { |
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66 "Cannot merge a study into the same study: " + study); | |
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67 } |
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68 else |
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69 { |
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70 std::list<std::string> series; |
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71 context_.GetIndex().GetChildren(series, study); |
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72 |
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73 for (std::list<std::string>::const_iterator |
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74 it = series.begin(); it != series.end(); ++it) |
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75 { |
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76 AddSourceSeriesInternal(*it); |
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77 } |
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78 } |
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79 } |
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80 |
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81 |
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82 bool MergeStudyJob::HandleInstance(const std::string& instance) |
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83 { |
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84 /** |
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85 * Retrieve the DICOM instance to be modified |
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86 **/ |
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87 |
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88 std::unique_ptr<ParsedDicomFile> modified; |
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89 |
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90 try |
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91 { |
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92 ServerContext::DicomCacheLocker locker(context_, instance); |
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93 modified.reset(locker.GetDicom().Clone(true)); |
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94 } |
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95 catch (OrthancException&) |
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96 { |
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97 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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98 return false; |
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99 } |
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100 |
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101 |
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102 /** |
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103 * Chose the target UIDs |
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104 **/ |
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105 |
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106 std::string series = modified->GetHasher().HashSeries(); |
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107 |
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108 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series); |
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109 |
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110 if (targetSeriesUid == seriesUidMap_.end()) |
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111 { |
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112 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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113 } |
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114 |
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115 |
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116 /** |
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117 * Copy the tags from the "Patient Module Attributes" and "General |
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118 * Study Module Attributes" modules of the target study |
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119 **/ |
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120 |
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121 for (std::set<DicomTag>::const_iterator it = removals_.begin(); |
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122 it != removals_.end(); ++it) |
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123 { |
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124 modified->Remove(*it); |
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125 } |
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126 |
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127 for (Replacements::const_iterator it = replacements_.begin(); |
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128 it != replacements_.end(); ++it) |
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129 { |
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130 modified->ReplacePlainString(it->first, it->second); |
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131 } |
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132 |
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133 |
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134 /** |
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135 * Store the new instance into Orthanc |
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136 **/ |
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137 |
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138 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second); |
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139 |
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140 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified |
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141 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
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142 |
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143 DicomInstanceToStore toStore; |
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144 toStore.SetOrigin(origin_); |
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145 toStore.SetParsedDicomFile(*modified); |
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146 |
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147 std::string modifiedInstance; |
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148 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success) |
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149 { |
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150 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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151 return false; |
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152 } |
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153 |
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154 return true; |
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155 } |
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156 |
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157 |
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158 bool MergeStudyJob::HandleTrailingStep() |
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159 { |
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160 if (!keepSource_) |
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161 { |
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162 const size_t n = GetInstancesCount(); |
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163 |
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164 for (size_t i = 0; i < n; i++) |
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165 { |
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166 Json::Value tmp; |
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167 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance); |
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168 } |
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169 } |
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170 |
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171 return true; |
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172 } |
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173 |
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174 |
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175 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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176 const std::string& targetStudy) : |
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177 context_(context), |
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178 keepSource_(false), |
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179 targetStudy_(targetStudy) |
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180 { |
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181 /** |
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182 * Check the validity of the input ID |
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183 **/ |
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184 |
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185 ResourceType type; |
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186 |
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187 if (!context_.GetIndex().LookupResourceType(type, targetStudy) || |
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188 type != ResourceType_Study) |
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189 { |
2955 | 190 throw OrthancException(ErrorCode_UnknownResource, |
191 "Cannot merge into an unknown study: " + targetStudy); | |
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192 } |
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193 |
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194 |
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195 /** |
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196 * Detect the tags to be removed/replaced by parsing one child |
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197 * instance of the study |
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198 **/ |
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199 |
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200 DicomTag::AddTagsForModule(removals_, DicomModule_Patient); |
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201 DicomTag::AddTagsForModule(removals_, DicomModule_Study); |
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202 |
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203 std::list<std::string> instances; |
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204 context_.GetIndex().GetChildInstances(instances, targetStudy); |
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205 |
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206 if (instances.empty()) |
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207 { |
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208 throw OrthancException(ErrorCode_UnknownResource); |
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209 } |
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210 |
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211 DicomMap dicom; |
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212 |
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213 { |
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214 ServerContext::DicomCacheLocker locker(context_, instances.front()); |
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215 locker.GetDicom().ExtractDicomSummary(dicom); |
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216 } |
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217 |
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218 const std::set<DicomTag> moduleTags = removals_; |
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219 for (std::set<DicomTag>::const_iterator it = moduleTags.begin(); |
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220 it != moduleTags.end(); ++it) |
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221 { |
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222 const DicomValue* value = dicom.TestAndGetValue(*it); |
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223 std::string str; |
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224 |
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225 if (value != NULL && |
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226 value->CopyToString(str, false)) |
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227 { |
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228 removals_.erase(*it); |
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229 replacements_.insert(std::make_pair(*it, str)); |
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230 } |
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231 } |
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232 } |
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233 |
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234 |
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235 void MergeStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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236 { |
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237 if (IsStarted()) |
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238 { |
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239 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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240 } |
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241 else |
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242 { |
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243 origin_ = origin; |
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244 } |
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245 } |
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246 |
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247 |
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248 void MergeStudyJob::SetOrigin(const RestApiCall& call) |
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249 { |
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250 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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251 } |
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252 |
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253 |
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254 void MergeStudyJob::AddSource(const std::string& studyOrSeries) |
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255 { |
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256 ResourceType level; |
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257 |
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258 if (IsStarted()) |
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259 { |
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260 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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261 } |
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262 else if (!context_.GetIndex().LookupResourceType(level, studyOrSeries)) |
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263 { |
2955 | 264 throw OrthancException(ErrorCode_UnknownResource, |
265 "Cannot find this resource: " + studyOrSeries); | |
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266 } |
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267 else |
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268 { |
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269 switch (level) |
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270 { |
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271 case ResourceType_Study: |
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272 AddSourceStudyInternal(studyOrSeries); |
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273 break; |
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274 |
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275 case ResourceType_Series: |
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276 AddSourceSeries(studyOrSeries); |
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277 break; |
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278 |
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279 default: |
2955 | 280 throw OrthancException(ErrorCode_UnknownResource, |
281 "This resource is neither a study, nor a series: " + | |
282 studyOrSeries + " is a " + | |
283 std::string(EnumerationToString(level))); | |
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284 } |
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285 } |
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286 } |
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287 |
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288 |
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289 void MergeStudyJob::AddSourceSeries(const std::string& series) |
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290 { |
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291 std::string parent; |
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292 |
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293 if (IsStarted()) |
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294 { |
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295 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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296 } |
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297 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study)) |
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298 { |
2955 | 299 throw OrthancException(ErrorCode_UnknownResource, |
300 "This resource is not a series: " + series); | |
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301 } |
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302 else if (parent == targetStudy_) |
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303 { |
2955 | 304 throw OrthancException(ErrorCode_UnknownResource, |
305 "Cannot merge series " + series + | |
306 " into its parent study " + targetStudy_); | |
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307 } |
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308 else |
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309 { |
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310 AddSourceSeriesInternal(series); |
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311 } |
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312 } |
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313 |
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314 |
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315 void MergeStudyJob::AddSourceStudy(const std::string& study) |
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316 { |
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317 ResourceType actualLevel; |
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318 |
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319 if (IsStarted()) |
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320 { |
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321 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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322 } |
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323 else if (!context_.GetIndex().LookupResourceType(actualLevel, study) || |
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324 actualLevel != ResourceType_Study) |
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325 { |
2955 | 326 throw OrthancException(ErrorCode_UnknownResource, |
327 "This resource is not a study: " + study); | |
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328 } |
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329 else |
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330 { |
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331 AddSourceStudyInternal(study); |
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332 } |
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333 } |
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334 |
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335 |
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336 void MergeStudyJob::SetKeepSource(bool keep) |
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337 { |
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338 if (IsStarted()) |
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339 { |
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340 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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341 } |
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342 |
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343 keepSource_ = keep; |
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344 } |
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345 |
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346 |
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347 void MergeStudyJob::GetPublicContent(Json::Value& value) |
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348 { |
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349 SetOfInstancesJob::GetPublicContent(value); |
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350 value["TargetStudy"] = targetStudy_; |
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351 } |
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352 |
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353 |
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354 static const char* KEEP_SOURCE = "KeepSource"; |
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355 static const char* TARGET_STUDY = "TargetStudy"; |
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356 static const char* REPLACEMENTS = "Replacements"; |
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357 static const char* REMOVALS = "Removals"; |
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358 static const char* SERIES_UID_MAP = "SeriesUIDMap"; |
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359 static const char* ORIGIN = "Origin"; |
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360 |
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361 |
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362 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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363 const Json::Value& serialized) : |
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364 SetOfInstancesJob(serialized), // (*) |
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365 context_(context) |
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366 { |
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367 if (!HasTrailingStep()) |
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368 { |
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369 // Should have been set by (*) |
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370 throw OrthancException(ErrorCode_InternalError); |
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371 } |
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372 |
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373 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE); |
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374 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); |
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375 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); |
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376 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); |
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377 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP); |
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378 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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379 } |
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380 |
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381 |
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382 bool MergeStudyJob::Serialize(Json::Value& target) |
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383 { |
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384 if (!SetOfInstancesJob::Serialize(target)) |
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385 { |
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386 return false; |
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387 } |
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388 else |
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389 { |
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390 target[KEEP_SOURCE] = keepSource_; |
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391 target[TARGET_STUDY] = targetStudy_; |
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392 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); |
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393 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); |
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394 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP); |
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395 origin_.Serialize(target[ORIGIN]); |
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396 |
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397 return true; |
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398 } |
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399 } |
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400 } |