Mercurial > hg > orthanc
annotate OrthancServer/Sources/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 5221:d0f7c742d397 db-protobuf
started implementation of labels
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 03 Apr 2023 20:53:14 +0200 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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7 * |
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8 * This program is free software: you can redistribute it and/or |
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9 * modify it under the terms of the GNU General Public License as |
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10 * published by the Free Software Foundation, either version 3 of the |
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11 * License, or (at your option) any later version. |
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12 * |
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13 * This program is distributed in the hope that it will be useful, but |
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU General Public License |
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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20 **/ |
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21 |
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22 |
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23 #include "../PrecompiledHeadersServer.h" |
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24 #include "OrthancRestApi.h" |
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25 |
4045 | 26 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" |
27 #include "../../../OrthancFramework/Sources/Logging.h" | |
28 #include "../../../OrthancFramework/Sources/SerializationToolbox.h" | |
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29 #include "../OrthancConfiguration.h" |
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30 #include "../ServerContext.h" |
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31 #include "../ServerJobs/MergeStudyJob.h" |
2642 | 32 #include "../ServerJobs/ResourceModificationJob.h" |
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33 #include "../ServerJobs/SplitStudyJob.h" |
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34 |
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35 #include <boost/lexical_cast.hpp> |
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36 #include <boost/algorithm/string/predicate.hpp> |
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37 |
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38 #define INFO_SUBSEQUENCES \ |
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39 "Starting with Orthanc 1.9.4, paths to subsequences can be provided using the "\ |
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40 "same syntax as the `dcmodify` command-line tool (wildcards are supported as well)." |
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41 |
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42 |
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43 static const char* const CONTENT = "Content"; |
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44 static const char* const FORCE = "Force"; |
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45 static const char* const INSTANCES = "Instances"; |
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46 static const char* const INTERPRET_BINARY_TAGS = "InterpretBinaryTags"; |
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47 static const char* const KEEP = "Keep"; |
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48 static const char* const KEEP_PRIVATE_TAGS = "KeepPrivateTags"; |
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49 static const char* const KEEP_SOURCE = "KeepSource"; |
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50 static const char* const LEVEL = "Level"; |
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51 static const char* const PARENT = "Parent"; |
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52 static const char* const PRIVATE_CREATOR = "PrivateCreator"; |
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53 static const char* const REMOVE = "Remove"; |
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54 static const char* const REPLACE = "Replace"; |
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55 static const char* const RESOURCES = "Resources"; |
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56 static const char* const SERIES = "Series"; |
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57 static const char* const TAGS = "Tags"; |
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58 static const char* const TRANSCODE = "Transcode"; |
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59 |
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60 |
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61 namespace Orthanc |
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62 { |
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63 // Modification of DICOM instances ------------------------------------------ |
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64 |
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65 |
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66 static std::string GeneratePatientName(ServerContext& context) |
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67 { |
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68 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence, true /* shared */); |
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69 return "Anonymized" + boost::lexical_cast<std::string>(seq); |
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70 } |
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71 |
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72 |
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73 static void DocumentKeepSource(RestApiPostCall& call) |
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74 { |
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75 call.GetDocumentation() |
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76 .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, |
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77 "If set to `false`, instructs Orthanc to the remove original resources. " |
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78 "By default, the original resources are kept in Orthanc.", false); |
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79 } |
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80 |
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81 |
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82 static void DocumentModifyOptions(RestApiPostCall& call) |
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83 { |
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84 // Check out "DicomModification::ParseModifyRequest()" |
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85 call.GetDocumentation() |
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86 .SetRequestField(TRANSCODE, RestApiCallDocumentation::Type_String, |
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87 "Transcode the DICOM instances to the provided DICOM transfer syntax: " |
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88 "https://book.orthanc-server.com/faq/transcoding.html", false) |
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89 .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, |
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90 "Allow the modification of tags related to DICOM identifiers, at the risk of " |
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91 "breaking the DICOM model of the real world", false) |
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92 .SetRequestField("RemovePrivateTags", RestApiCallDocumentation::Type_Boolean, |
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93 "Remove the private tags from the DICOM instances (defaults to `false`)", false) |
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94 .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, |
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95 "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) |
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96 .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, |
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97 "List of tags that must be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) |
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98 .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, |
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99 "Keep the original value of the specified tags, to be chosen among the `StudyInstanceUID`, " |
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100 "`SeriesInstanceUID` and `SOPInstanceUID` tags. Avoid this feature as much as possible, " |
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101 "as this breaks the DICOM model of the real world.", false) |
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102 .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, |
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103 "The private creator to be used for private tags in `Replace`", false); |
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104 |
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105 // This was existing, but undocumented in Orthanc <= 1.9.6 |
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106 DocumentKeepSource(call); |
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107 } |
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108 |
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109 |
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110 static void DocumentAnonymizationOptions(RestApiPostCall& call) |
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111 { |
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112 // Check out "DicomModification::ParseAnonymizationRequest()" |
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113 call.GetDocumentation() |
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114 .SetRequestField(TRANSCODE, RestApiCallDocumentation::Type_String, |
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115 "Transcode the DICOM instances to the provided DICOM transfer syntax: " |
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116 "https://book.orthanc-server.com/faq/transcoding.html", false) |
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117 .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, |
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118 "Allow the modification of tags related to DICOM identifiers, at the risk of " |
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119 "breaking the DICOM model of the real world", false) |
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120 .SetRequestField("DicomVersion", RestApiCallDocumentation::Type_String, |
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121 "Version of the DICOM standard to be used for anonymization. Check out " |
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122 "configuration option `DeidentifyLogsDicomVersion` for possible values.", false) |
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123 .SetRequestField(KEEP_PRIVATE_TAGS, RestApiCallDocumentation::Type_Boolean, |
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124 "Keep the private tags from the DICOM instances (defaults to `false`)", false) |
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125 .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, |
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126 "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) |
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127 .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, |
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128 "List of additional tags to be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) |
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129 .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, |
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130 "List of DICOM tags whose value must not be destroyed by the anonymization. " INFO_SUBSEQUENCES, false) |
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131 .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, |
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132 "The private creator to be used for private tags in `Replace`", false); |
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133 |
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134 // This was existing, but undocumented in Orthanc <= 1.9.6 |
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135 DocumentKeepSource(call); |
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136 } |
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137 |
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138 |
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139 static void ParseModifyRequest(Json::Value& request, |
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140 DicomModification& target, |
2517 | 141 const RestApiPostCall& call) |
142 { | |
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143 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"},"Priority":9}' |
2517 | 144 |
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145 { |
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146 OrthancConfiguration::ReaderLock lock; |
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147 target.SetPrivateCreator(lock.GetConfiguration().GetDefaultPrivateCreator()); |
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148 } |
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149 |
2517 | 150 if (call.ParseJsonRequest(request)) |
151 { | |
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152 target.ParseModifyRequest(request); |
2517 | 153 } |
154 else | |
155 { | |
156 throw OrthancException(ErrorCode_BadFileFormat); | |
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157 } |
2517 | 158 } |
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159 |
2517 | 160 |
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161 static void ParseAnonymizationRequest(Json::Value& request, |
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162 DicomModification& target, |
2517 | 163 RestApiPostCall& call) |
164 { | |
165 // curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"hello","0010-0020":"world"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": true,"Remove":["Modality"]}' > Anonymized.dcm | |
166 | |
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167 { |
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168 OrthancConfiguration::ReaderLock lock; |
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169 target.SetPrivateCreator(lock.GetConfiguration().GetDefaultPrivateCreator()); |
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170 } |
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171 |
2517 | 172 if (call.ParseJsonRequest(request) && |
173 request.isObject()) | |
174 { | |
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175 bool patientNameOverridden; |
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176 target.ParseAnonymizationRequest(patientNameOverridden, request); |
2518 | 177 |
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178 if (!patientNameOverridden) |
2518 | 179 { |
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180 // Override the random Patient's Name by one that is more |
2518 | 181 // user-friendly (provided none was specified by the user) |
182 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)), true); | |
183 } | |
2517 | 184 } |
185 else | |
186 { | |
187 throw OrthancException(ErrorCode_BadFileFormat); | |
188 } | |
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189 } |
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190 |
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191 |
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192 static void AnonymizeOrModifyInstance(DicomModification& modification, |
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193 RestApiPostCall& call, |
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194 bool transcode, |
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195 DicomTransferSyntax targetSyntax) |
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196 { |
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197 ServerContext& context = OrthancRestApi::GetContext(call); |
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198 std::string id = call.GetUriComponent("id", ""); |
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199 |
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200 std::unique_ptr<ParsedDicomFile> modified; |
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201 |
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202 { |
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203 ServerContext::DicomCacheLocker locker(context, id); |
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204 modified.reset(locker.GetDicom().Clone(true)); |
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205 } |
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206 |
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207 modification.Apply(*modified); |
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208 |
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209 if (transcode) |
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210 { |
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211 IDicomTranscoder::DicomImage source; |
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212 source.AcquireParsed(*modified); // "modified" is invalid below this point |
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213 |
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214 IDicomTranscoder::DicomImage transcoded; |
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215 |
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216 std::set<DicomTransferSyntax> s; |
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217 s.insert(targetSyntax); |
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218 |
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219 if (context.Transcode(transcoded, source, s, true)) |
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220 { |
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221 call.GetOutput().AnswerBuffer(transcoded.GetBufferData(), |
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222 transcoded.GetBufferSize(), MimeType_Dicom); |
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223 } |
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224 else |
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225 { |
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226 throw OrthancException(ErrorCode_InternalError, |
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227 "Cannot transcode to transfer syntax: " + |
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228 std::string(GetTransferSyntaxUid(targetSyntax))); |
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229 } |
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230 } |
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231 else |
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232 { |
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233 modified->Answer(call.GetOutput()); |
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234 } |
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235 } |
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236 |
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237 |
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238 static ResourceType DetectModifyLevel(const DicomModification& modification) |
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239 { |
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240 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID)) |
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241 { |
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242 return ResourceType_Patient; |
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243 } |
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244 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
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245 { |
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246 return ResourceType_Study; |
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247 } |
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248 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
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249 { |
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250 return ResourceType_Series; |
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251 } |
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252 else |
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253 { |
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254 return ResourceType_Instance; |
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255 } |
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256 } |
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257 |
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258 |
974 | 259 static void ModifyInstance(RestApiPostCall& call) |
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260 { |
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261 if (call.IsDocumentation()) |
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262 { |
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263 DocumentModifyOptions(call); |
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264 call.GetDocumentation() |
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265 .SetTag("Instances") |
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266 .SetSummary("Modify instance") |
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267 .SetDescription("Download a modified version of the DICOM instance whose Orthanc identifier is provided in the URL: " |
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268 "https://book.orthanc-server.com/users/anonymization.html#modification-of-a-single-instance") |
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269 .SetUriArgument("id", "Orthanc identifier of the instance of interest") |
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270 .AddAnswerType(MimeType_Dicom, "The modified DICOM instance"); |
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271 return; |
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272 } |
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273 |
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274 DicomModification modification; |
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275 modification.SetAllowManualIdentifiers(true); |
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276 |
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277 Json::Value request; |
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278 ParseModifyRequest(request, modification, call); |
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280 modification.SetLevel(DetectModifyLevel(modification)); |
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281 |
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282 if (request.isMember(TRANSCODE)) |
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283 { |
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284 std::string s = SerializationToolbox::ReadString(request, TRANSCODE); |
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285 |
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286 DicomTransferSyntax syntax; |
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287 if (LookupTransferSyntax(syntax, s)) |
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288 { |
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289 AnonymizeOrModifyInstance(modification, call, true, syntax); |
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290 } |
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291 else |
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292 { |
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293 throw OrthancException(ErrorCode_ParameterOutOfRange, "Unknown transfer syntax: " + s); |
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294 } |
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295 } |
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296 else |
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297 { |
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298 AnonymizeOrModifyInstance(modification, call, false /* no transcoding */, |
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299 DicomTransferSyntax_LittleEndianImplicit /* unused */); |
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300 } |
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301 } |
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302 |
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303 |
974 | 304 static void AnonymizeInstance(RestApiPostCall& call) |
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305 { |
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306 if (call.IsDocumentation()) |
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307 { |
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308 DocumentAnonymizationOptions(call); |
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309 call.GetDocumentation() |
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310 .SetTag("Instances") |
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311 .SetSummary("Anonymize instance") |
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312 .SetDescription("Download an anonymized version of the DICOM instance whose Orthanc identifier is provided in the URL: " |
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313 "https://book.orthanc-server.com/users/anonymization.html#anonymization-of-a-single-instance") |
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314 .SetUriArgument("id", "Orthanc identifier of the instance of interest") |
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315 .AddAnswerType(MimeType_Dicom, "The anonymized DICOM instance"); |
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316 return; |
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317 } |
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318 |
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319 DicomModification modification; |
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320 modification.SetAllowManualIdentifiers(true); |
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321 |
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322 Json::Value request; |
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323 ParseAnonymizationRequest(request, modification, call); |
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325 AnonymizeOrModifyInstance(modification, call, false /* no transcoding */, |
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326 DicomTransferSyntax_LittleEndianImplicit /* unused */); |
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327 } |
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328 |
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329 |
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330 static void SetKeepSource(CleaningInstancesJob& job, |
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331 const Json::Value& body) |
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332 { |
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333 if (body.isMember(KEEP_SOURCE)) |
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334 { |
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335 job.SetKeepSource(SerializationToolbox::ReadBoolean(body, KEEP_SOURCE)); |
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336 } |
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337 } |
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338 |
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339 static void SetKeepSource(ThreadedSetOfInstancesJob& job, |
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340 const Json::Value& body) |
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341 { |
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342 if (body.isMember(KEEP_SOURCE)) |
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343 { |
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344 job.SetKeepSource(SerializationToolbox::ReadBoolean(body, KEEP_SOURCE)); |
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345 } |
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346 } |
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347 |
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348 |
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349 static void SubmitModificationJob(std::unique_ptr<DicomModification>& modification, |
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350 bool isAnonymization, |
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351 RestApiPostCall& call, |
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352 const Json::Value& body, |
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353 ResourceType outputLevel /* unused for multiple resources */, |
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354 bool isSingleResource, |
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355 const std::set<std::string>& resources) |
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356 { |
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357 ServerContext& context = OrthancRestApi::GetContext(call); |
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358 unsigned int workersCount = 0; |
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359 |
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360 { |
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361 OrthancConfiguration::ReaderLock lock; |
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362 workersCount = lock.GetConfiguration().GetJobsEngineWorkersThread("ResourceModification"); |
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363 } |
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364 |
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365 std::unique_ptr<ResourceModificationJob> job(new ResourceModificationJob(context, workersCount)); |
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366 |
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367 if (isSingleResource) // This notably configures the output format |
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368 { |
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369 job->SetSingleResourceModification(modification.release(), outputLevel, isAnonymization); |
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370 } |
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371 else |
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372 { |
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373 job->SetMultipleResourcesModification(modification.release(), isAnonymization); |
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374 } |
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375 |
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376 job->SetOrigin(call); |
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377 SetKeepSource(*job, body); |
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378 |
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379 if (body.isMember(TRANSCODE)) |
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380 { |
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381 job->SetTranscode(SerializationToolbox::ReadString(body, TRANSCODE)); |
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382 } |
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383 |
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384 for (std::set<std::string>::const_iterator |
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385 it = resources.begin(); it != resources.end(); ++it) |
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386 { |
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387 std::list<std::string> instances; |
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388 context.GetIndex().GetChildInstances(instances, *it); |
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389 job->AddInstances(instances); |
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390 |
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391 job->AddParentResource(*it); |
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392 } |
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393 |
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394 job->PerformSanityChecks(); |
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395 |
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396 OrthancRestApi::GetApi(call).SubmitThreadedInstancesJob |
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397 (call, job.release(), true /* synchronous by default */, body); |
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398 } |
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399 |
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400 |
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401 static void SubmitModificationJob(std::unique_ptr<DicomModification>& modification, |
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402 bool isAnonymization, |
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403 RestApiPostCall& call, |
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404 const Json::Value& body, |
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405 ResourceType outputLevel) |
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406 { |
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407 // This was the only flavor in Orthanc <= 1.9.3 |
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408 std::set<std::string> resources; |
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409 resources.insert(call.GetUriComponent("id", "")); |
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410 |
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411 SubmitModificationJob(modification, isAnonymization, call, body, outputLevel, |
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412 true /* single resource */, resources); |
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413 } |
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414 |
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415 |
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416 static void SubmitBulkJob(std::unique_ptr<DicomModification>& modification, |
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417 bool isAnonymization, |
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418 RestApiPostCall& call, |
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419 const Json::Value& body) |
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420 { |
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421 std::set<std::string> resources; |
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422 SerializationToolbox::ReadSetOfStrings(resources, body, RESOURCES); |
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423 |
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424 SubmitModificationJob(modification, isAnonymization, |
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425 call, body, ResourceType_Instance /* arbitrary value, unused */, |
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426 false /* multiple resources */, resources); |
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427 } |
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428 |
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429 |
2639 | 430 template <enum ResourceType resourceType> |
974 | 431 static void ModifyResource(RestApiPostCall& call) |
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432 { |
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433 if (call.IsDocumentation()) |
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434 { |
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435 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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436 DocumentModifyOptions(call); |
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437 const std::string r = GetResourceTypeText(resourceType, false /* plural */, false /* lower case */); |
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438 call.GetDocumentation() |
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439 .SetTag(GetResourceTypeText(resourceType, true /* plural */, true /* upper case */)) |
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440 .SetSummary("Modify " + r) |
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441 .SetDescription("Start a job that will modify all the DICOM instances within the " + r + |
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442 " whose identifier is provided in the URL. The modified DICOM instances will be " |
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443 "stored into a brand new " + r + ", whose Orthanc identifiers will be returned by the job. " |
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444 "https://book.orthanc-server.com/users/anonymization.html#modification-of-studies-or-series") |
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445 .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest"); |
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446 return; |
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447 } |
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448 |
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449 std::unique_ptr<DicomModification> modification(new DicomModification); |
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450 |
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451 Json::Value body; |
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452 ParseModifyRequest(body, *modification, call); |
2517 | 453 |
2639 | 454 modification->SetLevel(resourceType); |
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455 |
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456 SubmitModificationJob(modification, false /* not an anonymization */, |
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457 call, body, resourceType); |
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458 } |
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459 |
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460 |
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461 // New in Orthanc 1.9.4 |
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462 static void BulkModify(RestApiPostCall& call) |
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463 { |
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464 if (call.IsDocumentation()) |
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465 { |
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466 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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467 DocumentModifyOptions(call); |
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468 call.GetDocumentation() |
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469 .SetTag("System") |
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470 .SetSummary("Modify a set of resources") |
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471 .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, |
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472 "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) |
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473 .SetRequestField(LEVEL, RestApiCallDocumentation::Type_String, |
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474 "Level of the modification (`Patient`, `Study`, `Series` or `Instance`). If absent, " |
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475 "the level defaults to `Instance`, but is set to `Patient` if `PatientID` is modified, " |
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476 "to `Study` if `StudyInstanceUID` is modified, or to `Series` if `SeriesInstancesUID` " |
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477 "is modified. (new in Orthanc 1.9.7)", false) |
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478 .SetDescription("Start a job that will modify all the DICOM patients, studies, series or instances " |
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479 "whose identifiers are provided in the `Resources` field.") |
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480 .AddAnswerType(MimeType_Json, "The list of all the resources that have been altered by this modification"); |
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481 return; |
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482 } |
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483 |
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484 std::unique_ptr<DicomModification> modification(new DicomModification); |
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485 |
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486 Json::Value body; |
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487 ParseModifyRequest(body, *modification, call); |
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488 |
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489 if (body.isMember(LEVEL)) |
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490 { |
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491 // This case was introduced in Orthanc 1.9.7 |
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492 modification->SetLevel(StringToResourceType(body[LEVEL].asCString())); |
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493 } |
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494 else |
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495 { |
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496 modification->SetLevel(DetectModifyLevel(*modification)); |
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497 } |
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498 |
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499 SubmitBulkJob(modification, false /* not an anonymization */, call, body); |
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500 } |
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501 |
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502 |
2639 | 503 template <enum ResourceType resourceType> |
974 | 504 static void AnonymizeResource(RestApiPostCall& call) |
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505 { |
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506 if (call.IsDocumentation()) |
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507 { |
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508 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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509 DocumentAnonymizationOptions(call); |
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510 const std::string r = GetResourceTypeText(resourceType, false /* plural */, false /* lower case */); |
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511 call.GetDocumentation() |
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512 .SetTag(GetResourceTypeText(resourceType, true /* plural */, true /* upper case */)) |
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513 .SetSummary("Anonymize " + r) |
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514 .SetDescription("Start a job that will anonymize all the DICOM instances within the " + r + |
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515 " whose identifier is provided in the URL. The modified DICOM instances will be " |
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516 "stored into a brand new " + r + ", whose Orthanc identifiers will be returned by the job. " |
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517 "https://book.orthanc-server.com/users/anonymization.html#anonymization-of-patients-studies-or-series") |
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518 .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest"); |
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519 return; |
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520 } |
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521 |
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522 std::unique_ptr<DicomModification> modification(new DicomModification); |
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523 |
2868
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524 Json::Value body; |
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525 ParseAnonymizationRequest(body, *modification, call); |
2640
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ResourceModificationJob
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526 |
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527 SubmitModificationJob(modification, true /* anonymization */, |
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528 call, body, resourceType); |
751
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529 } |
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530 |
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531 |
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532 // New in Orthanc 1.9.4 |
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533 static void BulkAnonymize(RestApiPostCall& call) |
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534 { |
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535 if (call.IsDocumentation()) |
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536 { |
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537 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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538 DocumentAnonymizationOptions(call); |
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539 call.GetDocumentation() |
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540 .SetTag("System") |
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541 .SetSummary("Anonymize a set of resources") |
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542 .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, |
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543 "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) |
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544 .SetDescription("Start a job that will anonymize all the DICOM patients, studies, series or instances " |
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545 "whose identifiers are provided in the `Resources` field.") |
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546 .AddAnswerType(MimeType_Json, "The list of all the resources that have been created by this anonymization"); |
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547 return; |
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548 } |
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549 |
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550 std::unique_ptr<DicomModification> modification(new DicomModification); |
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551 |
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552 Json::Value body; |
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553 ParseAnonymizationRequest(body, *modification, call); |
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554 |
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555 SubmitBulkJob(modification, true /* anonymization */, call, body); |
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556 } |
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557 |
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558 |
1569 | 559 static void StoreCreatedInstance(std::string& id /* out */, |
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560 RestApiPostCall& call, |
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561 ParsedDicomFile& dicom, |
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562 bool sendAnswer) |
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563 { |
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564 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(dicom)); |
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565 toStore->SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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566 |
1572
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567 ServerContext& context = OrthancRestApi::GetContext(call); |
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568 ServerContext::StoreResult result = context.Store(id, *toStore, StoreInstanceMode_Default); |
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569 |
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570 if (result.GetStatus() == StoreStatus_Failure) |
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571 { |
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572 throw OrthancException(ErrorCode_CannotStoreInstance); |
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573 } |
2899
5dd649de253d
POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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parents:
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diff
changeset
|
574 |
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POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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|
575 if (sendAnswer) |
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POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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|
576 { |
4796
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added ReceivedCStoreInstanceFilter lua callback + OrthancPluginRegisterIncomingCStoreInstanceFilter in sdk
Alain Mazy <am@osimis.io>
parents:
4766
diff
changeset
|
577 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, *toStore, result.GetStatus(), id); |
2899
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POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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|
578 } |
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|
579 } |
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580 |
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changeset
|
581 |
1569 | 582 static void CreateDicomV1(ParsedDicomFile& dicom, |
1572
904096e7367e
More information about the origin request in OnStoredInstance() callbacks
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
583 RestApiPostCall& call, |
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Creation of DICOM files with encapsulated PDF
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|
584 const Json::Value& request) |
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585 { |
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586 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}' |
800
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changeset
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587 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World","PixelData":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAAAAAA6mKC9AAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH3gUGDDcB53FulQAAAElJREFUGNNtj0sSAEEEQ1+U+185s1CtmRkblQ9CZldsKHJDk6DLGLJa6chjh0ooQmpjXMM86zPwydGEj6Ed/UGykkEM8X+p3u8/8LcOJIWLGeMAAAAASUVORK5CYII="}' |
796
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diff
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588 |
1555
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Creation of DICOM files with encapsulated PDF
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589 assert(request.isObject()); |
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changeset
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590 LOG(WARNING) << "Using a deprecated call to /tools/create-dicom"; |
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Creation of DICOM files with encapsulated PDF
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591 |
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Creation of DICOM files with encapsulated PDF
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592 Json::Value::Members members = request.getMemberNames(); |
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Creation of DICOM files with encapsulated PDF
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593 for (size_t i = 0; i < members.size(); i++) |
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Creation of DICOM files with encapsulated PDF
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594 { |
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Creation of DICOM files with encapsulated PDF
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595 const std::string& name = members[i]; |
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Creation of DICOM files with encapsulated PDF
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changeset
|
596 if (request[name].type() != Json::stringValue) |
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Creation of DICOM files with encapsulated PDF
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597 { |
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598 throw OrthancException(ErrorCode_CreateDicomNotString); |
1555
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Creation of DICOM files with encapsulated PDF
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|
599 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
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600 |
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Creation of DICOM files with encapsulated PDF
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changeset
|
601 std::string value = request[name].asString(); |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
602 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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603 DicomTag tag = FromDcmtkBridge::ParseTag(name); |
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Creation of DICOM files with encapsulated PDF
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|
604 if (tag == DICOM_TAG_PIXEL_DATA) |
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Creation of DICOM files with encapsulated PDF
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diff
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|
605 { |
1562 | 606 dicom.EmbedContent(value); |
1555
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Creation of DICOM files with encapsulated PDF
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607 } |
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Creation of DICOM files with encapsulated PDF
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608 else |
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Creation of DICOM files with encapsulated PDF
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609 { |
1982
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Modification of instances can now replace PixelData
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diff
changeset
|
610 // This is V1, don't try and decode data URI scheme |
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Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
611 dicom.ReplacePlainString(tag, value); |
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Creation of DICOM files with encapsulated PDF
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changeset
|
612 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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613 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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|
614 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
615 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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616 |
1569 | 617 static void InjectTags(ParsedDicomFile& dicom, |
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
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|
618 const Json::Value& tags, |
3691
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
619 bool decodeBinaryTags, |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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changeset
|
620 const std::string& privateCreator, |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
621 bool force) |
1565
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add tags per instances in a series
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diff
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|
622 { |
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623 if (tags.type() != Json::objectValue) |
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add tags per instances in a series
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diff
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|
624 { |
2955 | 625 throw OrthancException(ErrorCode_BadRequest, "Tags field is not an array"); |
1565
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|
626 } |
4b23310eb7e8
add tags per instances in a series
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diff
changeset
|
627 |
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diff
changeset
|
628 // Inject the user-specified tags |
4b23310eb7e8
add tags per instances in a series
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diff
changeset
|
629 Json::Value::Members members = tags.getMemberNames(); |
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add tags per instances in a series
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diff
changeset
|
630 for (size_t i = 0; i < members.size(); i++) |
4b23310eb7e8
add tags per instances in a series
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diff
changeset
|
631 { |
4b23310eb7e8
add tags per instances in a series
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changeset
|
632 const std::string& name = members[i]; |
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
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diff
changeset
|
633 DicomTag tag = FromDcmtkBridge::ParseTag(name); |
1565
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add tags per instances in a series
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|
634 |
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parents:
1564
diff
changeset
|
635 if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) |
4b23310eb7e8
add tags per instances in a series
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diff
changeset
|
636 { |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4437
diff
changeset
|
637 if (!force && |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
638 tag != DICOM_TAG_PATIENT_ID && |
1640
48224db51ee7
allow override date/time when creating DICOM files
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1616
diff
changeset
|
639 tag != DICOM_TAG_ACQUISITION_DATE && |
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allow override date/time when creating DICOM files
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1616
diff
changeset
|
640 tag != DICOM_TAG_ACQUISITION_TIME && |
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allow override date/time when creating DICOM files
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1616
diff
changeset
|
641 tag != DICOM_TAG_CONTENT_DATE && |
48224db51ee7
allow override date/time when creating DICOM files
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1616
diff
changeset
|
642 tag != DICOM_TAG_CONTENT_TIME && |
48224db51ee7
allow override date/time when creating DICOM files
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parents:
1616
diff
changeset
|
643 tag != DICOM_TAG_INSTANCE_CREATION_DATE && |
48224db51ee7
allow override date/time when creating DICOM files
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parents:
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diff
changeset
|
644 tag != DICOM_TAG_INSTANCE_CREATION_TIME && |
48224db51ee7
allow override date/time when creating DICOM files
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parents:
1616
diff
changeset
|
645 tag != DICOM_TAG_SERIES_DATE && |
48224db51ee7
allow override date/time when creating DICOM files
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parents:
1616
diff
changeset
|
646 tag != DICOM_TAG_SERIES_TIME && |
48224db51ee7
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diff
changeset
|
647 tag != DICOM_TAG_STUDY_DATE && |
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diff
changeset
|
648 tag != DICOM_TAG_STUDY_TIME && |
1565
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diff
changeset
|
649 dicom.HasTag(tag)) |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
650 { |
2952
4ceb9bf7b00c
added details string in OrthancException
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2936
diff
changeset
|
651 throw OrthancException(ErrorCode_CreateDicomOverrideTag, name); |
1565
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parents:
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diff
changeset
|
652 } |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
653 |
4b23310eb7e8
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diff
changeset
|
654 if (tag == DICOM_TAG_PIXEL_DATA) |
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add tags per instances in a series
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diff
changeset
|
655 { |
1582
bd1889029cbb
encoding of exceptions
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diff
changeset
|
656 throw OrthancException(ErrorCode_CreateDicomUseContent); |
1565
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diff
changeset
|
657 } |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
658 else |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
659 { |
3691
4922bdd046dd
Fix issue #140 (Modifying private tags with REST API changes VR from LO to UN) - DANGEROUS COMMIT
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3640
diff
changeset
|
660 dicom.Replace(tag, tags[name], decodeBinaryTags, DicomReplaceMode_InsertIfAbsent, privateCreator); |
1565
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add tags per instances in a series
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diff
changeset
|
661 } |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
662 } |
4b23310eb7e8
add tags per instances in a series
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parents:
1564
diff
changeset
|
663 } |
4b23310eb7e8
add tags per instances in a series
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parents:
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diff
changeset
|
664 } |
4b23310eb7e8
add tags per instances in a series
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parents:
1564
diff
changeset
|
665 |
4b23310eb7e8
add tags per instances in a series
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1564
diff
changeset
|
666 |
1564
1b7def486e62
creation of DICOM series
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1562
diff
changeset
|
667 static void CreateSeries(RestApiPostCall& call, |
1b7def486e62
creation of DICOM series
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1562
diff
changeset
|
668 ParsedDicomFile& base /* in */, |
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
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parents:
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diff
changeset
|
669 const Json::Value& content, |
3691
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Fix issue #140 (Modifying private tags with REST API changes VR from LO to UN) - DANGEROUS COMMIT
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3640
diff
changeset
|
670 bool decodeBinaryTags, |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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parents:
4437
diff
changeset
|
671 const std::string& privateCreator, |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
672 bool force) |
1564
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diff
changeset
|
673 { |
1b7def486e62
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diff
changeset
|
674 assert(content.isArray()); |
1b7def486e62
creation of DICOM series
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diff
changeset
|
675 assert(content.size() > 0); |
1b7def486e62
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1562
diff
changeset
|
676 ServerContext& context = OrthancRestApi::GetContext(call); |
1b7def486e62
creation of DICOM series
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diff
changeset
|
677 |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
678 base.ReplacePlainString(DICOM_TAG_IMAGES_IN_ACQUISITION, boost::lexical_cast<std::string>(content.size())); |
b5d4f9c156ad
Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
679 base.ReplacePlainString(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS, "1"); |
1564
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creation of DICOM series
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680 |
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681 std::string someInstance; |
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682 |
1566 | 683 try |
1564
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creation of DICOM series
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|
684 { |
1569 | 685 for (Json::ArrayIndex i = 0; i < content.size(); i++) |
1565
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686 { |
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687 std::unique_ptr<ParsedDicomFile> dicom(base.Clone(false)); |
1566 | 688 const Json::Value* payload = NULL; |
689 | |
690 if (content[i].type() == Json::stringValue) | |
691 { | |
692 payload = &content[i]; | |
693 } | |
694 else if (content[i].type() == Json::objectValue) | |
1565
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695 { |
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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696 if (!content[i].isMember(CONTENT)) |
1566 | 697 { |
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698 throw OrthancException(ErrorCode_CreateDicomNoPayload); |
1566 | 699 } |
700 | |
4712
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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701 payload = &content[i][CONTENT]; |
1566 | 702 |
4712
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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703 if (content[i].isMember(TAGS)) |
1570 | 704 { |
4712
bad8935cd5f2
"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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|
705 InjectTags(*dicom, content[i][TAGS], decodeBinaryTags, privateCreator, force); |
1570 | 706 } |
1565
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707 } |
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708 |
1566 | 709 if (payload == NULL || |
710 payload->type() != Json::stringValue) | |
711 { | |
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encoding of exceptions
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712 throw OrthancException(ErrorCode_CreateDicomUseDataUriScheme); |
1566 | 713 } |
1565
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714 |
1566 | 715 dicom->EmbedContent(payload->asString()); |
1982
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Modification of instances can now replace PixelData
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716 dicom->ReplacePlainString(DICOM_TAG_INSTANCE_NUMBER, boost::lexical_cast<std::string>(i + 1)); |
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717 dicom->ReplacePlainString(DICOM_TAG_IMAGE_INDEX, boost::lexical_cast<std::string>(i + 1)); |
1566 | 718 |
2899
5dd649de253d
POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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diff
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|
719 StoreCreatedInstance(someInstance, call, *dicom, false); |
1565
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add tags per instances in a series
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720 } |
1566 | 721 } |
1616 | 722 catch (OrthancException&) |
1566 | 723 { |
1569 | 724 // Error: Remove the newly-created series |
725 | |
726 std::string series; | |
727 if (context.GetIndex().LookupParent(series, someInstance)) | |
1570 | 728 { |
1569 | 729 Json::Value dummy; |
730 context.GetIndex().DeleteResource(dummy, series, ResourceType_Series); | |
1570 | 731 } |
1569 | 732 |
1616 | 733 throw; |
1564
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734 } |
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creation of DICOM series
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|
735 |
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changeset
|
736 std::string series; |
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creation of DICOM series
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|
737 if (context.GetIndex().LookupParent(series, someInstance)) |
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creation of DICOM series
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diff
changeset
|
738 { |
1569 | 739 OrthancRestApi::GetApi(call).AnswerStoredResource(call, series, ResourceType_Series, StoreStatus_Success); |
1564
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|
740 } |
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|
741 } |
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changeset
|
742 |
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changeset
|
743 |
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diff
changeset
|
744 static void CreateDicomV2(RestApiPostCall& call, |
1555
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Creation of DICOM files with encapsulated PDF
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745 const Json::Value& request) |
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Creation of DICOM files with encapsulated PDF
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746 { |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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747 static const char* const SPECIFIC_CHARACTER_SET_2 = "SpecificCharacterSet"; |
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"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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748 static const char* const TYPE = "Type"; |
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"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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749 static const char* const VALUE = "Value"; |
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"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
750 |
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Creation of DICOM files with encapsulated PDF
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751 assert(request.isObject()); |
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752 ServerContext& context = OrthancRestApi::GetContext(call); |
1555
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Creation of DICOM files with encapsulated PDF
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changeset
|
753 |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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754 if (!request.isMember(TAGS) || |
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"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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changeset
|
755 request[TAGS].type() != Json::objectValue) |
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Creation of DICOM files with encapsulated PDF
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changeset
|
756 { |
1569 | 757 throw OrthancException(ErrorCode_BadRequest); |
1555
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Creation of DICOM files with encapsulated PDF
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758 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
759 |
1805
f08978b1f45b
c-find scu for modality worklists
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parents:
1699
diff
changeset
|
760 ParsedDicomFile dicom(true); |
1558
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fix encodings of newly created dicom files
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diff
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|
761 |
1557 | 762 { |
1565
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add tags per instances in a series
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diff
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|
763 Encoding encoding; |
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diff
changeset
|
764 |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
765 if (request[TAGS].isMember(SPECIFIC_CHARACTER_SET_2)) |
1558
124de28b32ed
fix encodings of newly created dicom files
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diff
changeset
|
766 { |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
767 const char* tmp = request[TAGS][SPECIFIC_CHARACTER_SET_2].asCString(); |
1565
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add tags per instances in a series
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768 if (!GetDicomEncoding(encoding, tmp)) |
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diff
changeset
|
769 { |
2955 | 770 throw OrthancException(ErrorCode_ParameterOutOfRange, |
771 "Unknown specific character set: " + std::string(tmp)); | |
1565
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changeset
|
772 } |
1558
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fix encodings of newly created dicom files
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diff
changeset
|
773 } |
1565
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diff
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|
774 else |
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parents:
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diff
changeset
|
775 { |
2381
b8969010b534
uncoupling DCMTK primitives from Orthanc::Configuration
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2361
diff
changeset
|
776 encoding = GetDefaultDicomEncoding(); |
1565
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|
777 } |
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diff
changeset
|
778 |
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add tags per instances in a series
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parents:
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diff
changeset
|
779 dicom.SetEncoding(encoding); |
1557 | 780 } |
781 | |
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Creation of DICOM files with encapsulated PDF
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|
782 ResourceType parentType = ResourceType_Instance; |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
783 |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4437
diff
changeset
|
784 if (request.isMember(PARENT)) |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
785 { |
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Creation of DICOM files with encapsulated PDF
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changeset
|
786 // Locate the parent tags |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
787 std::string parent = request[PARENT].asString(); |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
788 if (!context.GetIndex().LookupResourceType(parentType, parent)) |
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Creation of DICOM files with encapsulated PDF
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|
789 { |
1582
bd1889029cbb
encoding of exceptions
Sebastien Jodogne <s.jodogne@gmail.com>
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1572
diff
changeset
|
790 throw OrthancException(ErrorCode_CreateDicomBadParent); |
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Creation of DICOM files with encapsulated PDF
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791 } |
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Creation of DICOM files with encapsulated PDF
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changeset
|
792 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
793 if (parentType == ResourceType_Instance) |
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Creation of DICOM files with encapsulated PDF
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794 { |
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parents:
1572
diff
changeset
|
795 throw OrthancException(ErrorCode_CreateDicomParentIsInstance); |
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Creation of DICOM files with encapsulated PDF
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796 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
797 |
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Creation of DICOM files with encapsulated PDF
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changeset
|
798 // Select one existing child instance of the parent resource, to |
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Creation of DICOM files with encapsulated PDF
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799 // retrieve all its tags |
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Creation of DICOM files with encapsulated PDF
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changeset
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800 Json::Value siblingTags; |
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diff
changeset
|
801 std::string siblingInstanceId; |
1555
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Creation of DICOM files with encapsulated PDF
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|
802 |
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
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803 { |
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Creation of DICOM files with encapsulated PDF
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|
804 // Retrieve all the instances of the parent resource |
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Creation of DICOM files with encapsulated PDF
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parents:
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805 std::list<std::string> siblingInstances; |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
806 context.GetIndex().GetChildInstances(siblingInstances, parent); |
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Creation of DICOM files with encapsulated PDF
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changeset
|
807 |
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Creation of DICOM files with encapsulated PDF
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|
808 if (siblingInstances.empty()) |
1569 | 809 { |
810 // Error: No instance (should never happen) | |
811 throw OrthancException(ErrorCode_InternalError); | |
1555
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Creation of DICOM files with encapsulated PDF
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changeset
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812 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
813 |
3009
750de70b3603
make "/tools/create-dicom" more tolerant to invalid specific character set
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parents:
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diff
changeset
|
814 siblingInstanceId = siblingInstances.front(); |
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diff
changeset
|
815 context.ReadDicomAsJson(siblingTags, siblingInstanceId); |
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
816 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
817 |
1565
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diff
changeset
|
818 |
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parents:
1564
diff
changeset
|
819 // Choose the same encoding as the parent resource |
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add tags per instances in a series
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changeset
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820 { |
4712
bad8935cd5f2
"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
821 static const char* const SPECIFIC_CHARACTER_SET = "0008,0005"; |
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diff
changeset
|
822 |
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diff
changeset
|
823 if (siblingTags.isMember(SPECIFIC_CHARACTER_SET)) |
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824 { |
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825 Encoding encoding; |
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826 |
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827 if (!siblingTags[SPECIFIC_CHARACTER_SET].isMember(VALUE) || |
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828 siblingTags[SPECIFIC_CHARACTER_SET][VALUE].type() != Json::stringValue || |
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829 !GetDicomEncoding(encoding, siblingTags[SPECIFIC_CHARACTER_SET][VALUE].asCString())) |
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830 { |
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831 LOG(WARNING) << "Instance with an incorrect Specific Character Set, " |
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832 << "using the default Orthanc encoding: " << siblingInstanceId; |
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833 encoding = GetDefaultDicomEncoding(); |
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834 } |
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835 |
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836 dicom.SetEncoding(encoding); |
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837 } |
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838 } |
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839 |
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840 |
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841 // Retrieve the tags for all the parent modules |
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842 typedef std::set<DicomTag> ModuleTags; |
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843 ModuleTags moduleTags; |
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844 |
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845 ResourceType type = parentType; |
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846 for (;;) |
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847 { |
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848 DicomTag::AddTagsForModule(moduleTags, GetModule(type)); |
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849 |
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850 if (type == ResourceType_Patient) |
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851 { |
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852 break; // We're done |
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853 } |
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854 |
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855 // Go up |
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856 std::string tmp; |
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857 if (!context.GetIndex().LookupParent(tmp, parent)) |
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858 { |
1569 | 859 throw OrthancException(ErrorCode_InternalError); |
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860 } |
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861 |
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862 parent = tmp; |
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863 type = GetParentResourceType(type); |
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864 } |
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865 |
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866 for (ModuleTags::const_iterator it = moduleTags.begin(); |
1616 | 867 it != moduleTags.end(); ++it) |
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868 { |
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869 std::string t = it->Format(); |
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870 if (siblingTags.isMember(t)) |
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871 { |
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872 const Json::Value& tag = siblingTags[t]; |
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873 if (tag[TYPE] == "Null") |
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874 { |
1982
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875 dicom.ReplacePlainString(*it, ""); |
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876 } |
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877 else if (tag[TYPE] == "String") |
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878 { |
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879 std::string value = tag[VALUE].asString(); // This is an UTF-8 value (as it comes from JSON) |
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880 dicom.ReplacePlainString(*it, value); |
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881 } |
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882 } |
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883 } |
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884 } |
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885 |
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886 |
1689 | 887 bool decodeBinaryTags = true; |
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888 if (request.isMember(INTERPRET_BINARY_TAGS)) |
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889 { |
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890 const Json::Value& v = request[INTERPRET_BINARY_TAGS]; |
1641
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891 if (v.type() != Json::booleanValue) |
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892 { |
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893 throw OrthancException(ErrorCode_BadRequest); |
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894 } |
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895 |
1689 | 896 decodeBinaryTags = v.asBool(); |
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897 } |
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898 |
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899 |
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900 // New argument in Orthanc 1.6.0 |
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901 std::string privateCreator; |
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902 if (request.isMember(PRIVATE_CREATOR)) |
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903 { |
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904 const Json::Value& v = request[PRIVATE_CREATOR]; |
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905 if (v.type() != Json::stringValue) |
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906 { |
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907 throw OrthancException(ErrorCode_BadRequest); |
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908 } |
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909 |
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910 privateCreator = v.asString(); |
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911 } |
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912 else |
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913 { |
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914 OrthancConfiguration::ReaderLock lock; |
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915 privateCreator = lock.GetConfiguration().GetDefaultPrivateCreator(); |
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916 } |
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917 |
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918 |
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919 // New in Orthanc 1.9.0 |
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920 bool force = false; |
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921 if (request.isMember(FORCE)) |
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922 { |
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923 const Json::Value& v = request[FORCE]; |
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924 if (v.type() != Json::booleanValue) |
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925 { |
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926 throw OrthancException(ErrorCode_BadRequest); |
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927 } |
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928 |
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929 force = v.asBool(); |
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930 } |
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diff
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|
931 |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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|
932 |
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Creation of DICOM files with encapsulated PDF
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|
933 // Inject time-related information |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
934 std::string date, time; |
2475
8cc3ca64a534
Orthanc now uses UTC (universal time) instead of local time in its database
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2447
diff
changeset
|
935 SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
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1934
diff
changeset
|
936 dicom.ReplacePlainString(DICOM_TAG_ACQUISITION_DATE, date); |
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Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
937 dicom.ReplacePlainString(DICOM_TAG_ACQUISITION_TIME, time); |
b5d4f9c156ad
Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
938 dicom.ReplacePlainString(DICOM_TAG_CONTENT_DATE, date); |
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Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
939 dicom.ReplacePlainString(DICOM_TAG_CONTENT_TIME, time); |
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Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
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1934
diff
changeset
|
940 dicom.ReplacePlainString(DICOM_TAG_INSTANCE_CREATION_DATE, date); |
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Modification of instances can now replace PixelData
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diff
changeset
|
941 dicom.ReplacePlainString(DICOM_TAG_INSTANCE_CREATION_TIME, time); |
1555
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|
942 |
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Creation of DICOM files with encapsulated PDF
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|
943 if (parentType == ResourceType_Patient || |
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944 parentType == ResourceType_Study || |
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|
945 parentType == ResourceType_Instance /* no parent */) |
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changeset
|
946 { |
1982
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Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
947 dicom.ReplacePlainString(DICOM_TAG_SERIES_DATE, date); |
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Modification of instances can now replace PixelData
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diff
changeset
|
948 dicom.ReplacePlainString(DICOM_TAG_SERIES_TIME, time); |
1555
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diff
changeset
|
949 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
950 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
951 if (parentType == ResourceType_Patient || |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
952 parentType == ResourceType_Instance /* no parent */) |
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Creation of DICOM files with encapsulated PDF
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953 { |
1982
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Modification of instances can now replace PixelData
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parents:
1934
diff
changeset
|
954 dicom.ReplacePlainString(DICOM_TAG_STUDY_DATE, date); |
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Modification of instances can now replace PixelData
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parents:
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diff
changeset
|
955 dicom.ReplacePlainString(DICOM_TAG_STUDY_TIME, time); |
1555
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Creation of DICOM files with encapsulated PDF
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changeset
|
956 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
957 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
958 |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
959 InjectTags(dicom, request[TAGS], decodeBinaryTags, privateCreator, force); |
1555
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changeset
|
960 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
961 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
962 // Inject the content (either an image, or a PDF file) |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
963 if (request.isMember(CONTENT)) |
1555
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
964 { |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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parents:
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diff
changeset
|
965 const Json::Value& content = request[CONTENT]; |
1564
1b7def486e62
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diff
changeset
|
966 |
1b7def486e62
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diff
changeset
|
967 if (content.type() == Json::stringValue) |
1b7def486e62
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diff
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|
968 { |
4479
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"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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|
969 dicom.EmbedContent(request[CONTENT].asString()); |
1564
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creation of DICOM series
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1562
diff
changeset
|
970 |
1b7def486e62
creation of DICOM series
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parents:
1562
diff
changeset
|
971 } |
1b7def486e62
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diff
changeset
|
972 else if (content.type() == Json::arrayValue) |
1b7def486e62
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1562
diff
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|
973 { |
1b7def486e62
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diff
changeset
|
974 if (content.size() > 0) |
1b7def486e62
creation of DICOM series
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diff
changeset
|
975 { |
1565
4b23310eb7e8
add tags per instances in a series
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parents:
1564
diff
changeset
|
976 // Let's create a series instead of a single instance |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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parents:
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diff
changeset
|
977 CreateSeries(call, dicom, content, decodeBinaryTags, privateCreator, force); |
1564
1b7def486e62
creation of DICOM series
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|
978 return; |
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diff
changeset
|
979 } |
1b7def486e62
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diff
changeset
|
980 } |
1b7def486e62
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diff
changeset
|
981 else |
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
982 { |
1582
bd1889029cbb
encoding of exceptions
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parents:
1572
diff
changeset
|
983 throw OrthancException(ErrorCode_CreateDicomUseDataUriScheme); |
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
984 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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|
985 } |
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Creation of DICOM files with encapsulated PDF
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changeset
|
986 |
1564
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diff
changeset
|
987 std::string id; |
2899
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POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
988 StoreCreatedInstance(id, call, dicom, true); |
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
989 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
990 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
991 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
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|
992 static void CreateDicom(RestApiPostCall& call) |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
993 { |
4422 | 994 if (call.IsDocumentation()) |
995 { | |
996 call.GetDocumentation() | |
997 .SetTag("System") | |
998 .SetSummary("Create one DICOM instance") | |
999 .SetDescription("Create one DICOM instance, and store it into Orthanc") | |
4712
bad8935cd5f2
"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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diff
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|
1000 .SetRequestField(TAGS, RestApiCallDocumentation::Type_JsonObject, |
4422 | 1001 "Associative array containing the tags of the new instance to be created", true) |
4712
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1002 .SetRequestField(CONTENT, RestApiCallDocumentation::Type_String, |
4422 | 1003 "This field can be used to embed an image (pixel data) or a PDF inside the created DICOM instance. " |
1004 "The PNG image, the JPEG image or the PDF file must be provided using their " | |
1005 "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme). " | |
1006 "This field can possibly contain a JSON array, in which case a DICOM series is created " | |
1007 "containing one DICOM instance for each item in the `Content` field.", false) | |
4712
bad8935cd5f2
"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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4699
diff
changeset
|
1008 .SetRequestField(PARENT, RestApiCallDocumentation::Type_String, |
4422 | 1009 "If present, the newly created instance will be attached to the parent DICOM resource " |
1010 "whose Orthanc identifier is contained in this field. The DICOM tags of the parent " | |
1011 "modules in the DICOM hierarchy will be automatically copied to the newly created instance.", false) | |
4712
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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diff
changeset
|
1012 .SetRequestField(INTERPRET_BINARY_TAGS, RestApiCallDocumentation::Type_Boolean, |
4422 | 1013 "If some value in the `Tags` associative array is formatted according to some " |
1014 "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme), " | |
1015 "whether this value is decoded to a binary value or kept as such (`true` by default)", false) | |
4712
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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diff
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|
1016 .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, |
4422 | 1017 "The private creator to be used for private tags in `Tags`", false) |
4712
bad8935cd5f2
"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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diff
changeset
|
1018 .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, |
4479
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
1019 "Avoid the consistency checks for the DICOM tags that enforce the DICOM model of the real-world. " |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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diff
changeset
|
1020 "You can notably use this flag if you need to manually set the tags `StudyInstanceUID`, " |
1619cffd1948
"/tools/create-dicom": New flag "Force" to bypass consistency checks for the DICOM tags
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changeset
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1021 "`SeriesInstanceUID`, or `SOPInstanceUID`. Be careful with this feature.", false) |
4422 | 1022 .SetAnswerField("ID", RestApiCallDocumentation::Type_String, "Orthanc identifier of the newly created instance") |
1023 .SetAnswerField("Path", RestApiCallDocumentation::Type_String, "Path to access the instance in the REST API"); | |
1024 return; | |
1025 } | |
1026 | |
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changeset
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1027 Json::Value request; |
1569 | 1028 if (!call.ParseJsonRequest(request) || |
1029 !request.isObject()) | |
1570 | 1030 { |
1031 throw OrthancException(ErrorCode_BadRequest); | |
1032 } | |
1569 | 1033 |
4712
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changeset
|
1034 if (request.isMember(TAGS)) |
1570 | 1035 { |
1036 CreateDicomV2(call, request); | |
1037 } | |
1569 | 1038 else |
1570 | 1039 { |
1040 // Compatibility with Orthanc <= 0.9.3 | |
1805
f08978b1f45b
c-find scu for modality worklists
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diff
changeset
|
1041 ParsedDicomFile dicom(true); |
1572
904096e7367e
More information about the origin request in OnStoredInstance() callbacks
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diff
changeset
|
1042 CreateDicomV1(dicom, call, request); |
1569 | 1043 |
1570 | 1044 std::string id; |
2899
5dd649de253d
POST-ing a DICOM file to "/instances" also answers the patient/study/series ID
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changeset
|
1045 StoreCreatedInstance(id, call, dicom, true); |
1570 | 1046 } |
796
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creation of dicom files
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diff
changeset
|
1047 } |
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diff
changeset
|
1048 |
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diff
changeset
|
1049 |
2844
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New URI: "/studies/.../split" to split a study
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diff
changeset
|
1050 static void SplitStudy(RestApiPostCall& call) |
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New URI: "/studies/.../split" to split a study
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changeset
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1051 { |
4424
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diff
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1052 if (call.IsDocumentation()) |
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diff
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|
1053 { |
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|
1054 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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diff
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|
1055 call.GetDocumentation() |
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diff
changeset
|
1056 .SetTag("Studies") |
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diff
changeset
|
1057 .SetSummary("Split study") |
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4422
diff
changeset
|
1058 .SetDescription("Start a new job so as to split the DICOM study whose Orthanc identifier is provided in the URL, " |
4712
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diff
changeset
|
1059 "by taking some of its children series or instances out of it and putting them into a brand new study " |
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"/studies/{id}/split" accepts "Instances" parameter to split instances instead of series
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diff
changeset
|
1060 "(this new study is created by setting the `StudyInstanceUID` tag to a random identifier): " |
4424
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4422
diff
changeset
|
1061 "https://book.orthanc-server.com/users/anonymization.html#splitting") |
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diff
changeset
|
1062 .SetUriArgument("id", "Orthanc identifier of the study of interest") |
4712
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diff
changeset
|
1063 .SetRequestField(SERIES, RestApiCallDocumentation::Type_JsonListOfStrings, |
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1064 "The list of series to be separated from the parent study. " |
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1065 "These series must all be children of the same source study, that is specified in the URI.", false) |
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1066 .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, |
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1067 "Associative array to change the value of some DICOM tags in the new study. " |
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1068 "These tags must be part of the \"Patient Module Attributes\" or the \"General Study " |
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1069 "Module Attributes\", as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3.", false) |
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1070 .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, |
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1071 "List of tags that must be removed in the new study (from the same modules as in the `Replace` option)", false) |
4712
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1072 .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, |
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1073 "If set to `true`, instructs Orthanc to keep a copy of the original series/instances in the source study. " |
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1074 "By default, the original series/instances are deleted from Orthanc.", false) |
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1075 .SetRequestField(INSTANCES, RestApiCallDocumentation::Type_JsonListOfStrings, |
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1076 "The list of instances to be separated from the parent study. " |
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1077 "These instances must all be children of the same source study, that is specified in the URI.", false); |
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1078 return; |
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1079 } |
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1080 |
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1081 ServerContext& context = OrthancRestApi::GetContext(call); |
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1082 |
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1083 Json::Value request; |
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1084 if (!call.ParseJsonRequest(request)) |
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1085 { |
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1086 // Bad JSON request |
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1087 throw OrthancException(ErrorCode_BadFileFormat); |
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1088 } |
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1089 |
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1090 const std::string study = call.GetUriComponent("id", ""); |
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1091 |
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1092 std::unique_ptr<SplitStudyJob> job(new SplitStudyJob(context, study)); |
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1093 job->SetOrigin(call); |
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1094 |
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1095 bool ok = false; |
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1096 if (request.isMember(SERIES)) |
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1097 { |
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1098 std::vector<std::string> series; |
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1099 SerializationToolbox::ReadArrayOfStrings(series, request, SERIES); |
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1100 |
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1101 for (size_t i = 0; i < series.size(); i++) |
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1102 { |
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1103 job->AddSourceSeries(series[i]); |
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1104 ok = true; |
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1105 } |
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1106 } |
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1107 |
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1108 if (request.isMember(INSTANCES)) |
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1109 { |
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1110 std::vector<std::string> instances; |
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1111 SerializationToolbox::ReadArrayOfStrings(instances, request, INSTANCES); |
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1112 |
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1113 for (size_t i = 0; i < instances.size(); i++) |
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1114 { |
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1115 job->AddSourceInstance(instances[i]); |
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1116 ok = true; |
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1117 } |
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1118 } |
4712
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1119 |
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1120 if (!ok) |
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1121 { |
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1122 throw OrthancException(ErrorCode_BadRequest, "Both the \"Series\" and the \"Instances\" fields are missing"); |
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1123 } |
3942
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1124 |
2860 | 1125 job->AddTrailingStep(); |
1126 | |
3942
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1127 SetKeepSource(*job, request); |
2844
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1128 |
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1129 if (request.isMember(REMOVE)) |
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1130 { |
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1131 if (request[REMOVE].type() != Json::arrayValue) |
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1132 { |
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1133 throw OrthancException(ErrorCode_BadFileFormat); |
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1134 } |
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1135 |
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1136 for (Json::Value::ArrayIndex i = 0; i < request[REMOVE].size(); i++) |
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1137 { |
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1138 if (request[REMOVE][i].type() != Json::stringValue) |
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1139 { |
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1140 throw OrthancException(ErrorCode_BadFileFormat); |
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1141 } |
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1142 else |
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1143 { |
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1144 job->Remove(FromDcmtkBridge::ParseTag(request[REMOVE][i].asCString())); |
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1145 } |
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1146 } |
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1147 } |
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1148 |
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1149 if (request.isMember(REPLACE)) |
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1150 { |
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1151 if (request[REPLACE].type() != Json::objectValue) |
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1152 { |
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1153 throw OrthancException(ErrorCode_BadFileFormat); |
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1154 } |
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1155 |
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1156 Json::Value::Members tags = request[REPLACE].getMemberNames(); |
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1157 |
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1158 for (size_t i = 0; i < tags.size(); i++) |
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1159 { |
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1160 const Json::Value& value = request[REPLACE][tags[i]]; |
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1161 |
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1162 if (value.type() != Json::stringValue) |
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1163 { |
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1164 throw OrthancException(ErrorCode_BadFileFormat); |
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1165 } |
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1166 else |
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1167 { |
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1168 job->Replace(FromDcmtkBridge::ParseTag(tags[i]), value.asString()); |
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1169 } |
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1170 } |
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1171 } |
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1172 |
2869 | 1173 OrthancRestApi::GetApi(call).SubmitCommandsJob |
1174 (call, job.release(), true /* synchronous by default */, request); | |
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1175 } |
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1176 |
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1177 |
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1178 static void MergeStudy(RestApiPostCall& call) |
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1179 { |
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1180 if (call.IsDocumentation()) |
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1181 { |
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1182 OrthancRestApi::DocumentSubmitCommandsJob(call); |
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1183 call.GetDocumentation() |
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1184 .SetTag("Studies") |
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1185 .SetSummary("Merge study") |
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1186 .SetDescription("Start a new job so as to move some DICOM resources into the DICOM study whose Orthanc identifier " |
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1187 "is provided in the URL: https://book.orthanc-server.com/users/anonymization.html#merging") |
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1188 .SetUriArgument("id", "Orthanc identifier of the study of interest") |
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1189 .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, |
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1190 "The list of DICOM resources (studies, series, and/or instances) to be merged " |
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1191 "into the study of interest (mandatory option)", true) |
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1192 .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, |
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1193 "If set to `true`, instructs Orthanc to keep a copy of the original resources in their source study. " |
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1194 "By default, the original resources are deleted from Orthanc.", false); |
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1195 return; |
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1196 } |
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1197 |
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1198 ServerContext& context = OrthancRestApi::GetContext(call); |
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1199 |
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1200 Json::Value request; |
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1201 if (!call.ParseJsonRequest(request)) |
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1202 { |
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1203 // Bad JSON request |
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1204 throw OrthancException(ErrorCode_BadFileFormat); |
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1205 } |
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1206 |
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1207 const std::string study = call.GetUriComponent("id", ""); |
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1208 |
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1209 std::unique_ptr<MergeStudyJob> job(new MergeStudyJob(context, study)); |
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1210 job->SetOrigin(call); |
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1211 |
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1212 std::vector<std::string> resources; |
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1213 SerializationToolbox::ReadArrayOfStrings(resources, request, RESOURCES); |
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1214 |
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1215 for (size_t i = 0; i < resources.size(); i++) |
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1216 { |
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1217 job->AddSource(resources[i]); |
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1218 } |
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1219 |
2860 | 1220 job->AddTrailingStep(); |
1221 | |
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1222 SetKeepSource(*job, request); |
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1223 |
2869 | 1224 OrthancRestApi::GetApi(call).SubmitCommandsJob |
1225 (call, job.release(), true /* synchronous by default */, request); | |
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1226 } |
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1227 |
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1228 |
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1229 void OrthancRestApi::RegisterAnonymizeModify() |
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1230 { |
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1231 Register("/instances/{id}/modify", ModifyInstance); |
2639 | 1232 Register("/series/{id}/modify", ModifyResource<ResourceType_Series>); |
1233 Register("/studies/{id}/modify", ModifyResource<ResourceType_Study>); | |
1234 Register("/patients/{id}/modify", ModifyResource<ResourceType_Patient>); | |
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1235 Register("/tools/bulk-modify", BulkModify); |
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1236 |
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1237 Register("/instances/{id}/anonymize", AnonymizeInstance); |
2639 | 1238 Register("/series/{id}/anonymize", AnonymizeResource<ResourceType_Series>); |
1239 Register("/studies/{id}/anonymize", AnonymizeResource<ResourceType_Study>); | |
1240 Register("/patients/{id}/anonymize", AnonymizeResource<ResourceType_Patient>); | |
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1241 Register("/tools/bulk-anonymize", BulkAnonymize); |
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1242 |
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1243 Register("/tools/create-dicom", CreateDicom); |
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1244 |
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1245 Register("/studies/{id}/split", SplitStudy); |
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1246 Register("/studies/{id}/merge", MergeStudy); |
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1247 } |
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1248 } |