Mercurial > hg > orthanc
annotate OrthancServer/DicomModification.cpp @ 1762:2b91363cc1d1 db-changes
fix
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 29 Oct 2015 11:25:45 +0100 |
| parents | d78b87f93bcf |
| children | 1065401501fb |
| rev | line source |
|---|---|
| 786 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
| 786 | 5 * |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
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33 #include "PrecompiledHeadersServer.h" |
| 786 | 34 #include "DicomModification.h" |
| 35 | |
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36 #include "../Core/Logging.h" |
| 786 | 37 #include "../Core/OrthancException.h" |
| 790 | 38 #include "FromDcmtkBridge.h" |
| 786 | 39 |
| 795 | 40 #include <memory> // For std::auto_ptr |
| 41 | |
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42 |
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43 static const std::string ORTHANC_DEIDENTIFICATION_METHOD = "Orthanc " ORTHANC_VERSION " - PS 3.15-2008 Table E.1-1"; |
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44 |
| 786 | 45 namespace Orthanc |
| 46 { | |
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47 void DicomModification::RemoveInternal(const DicomTag& tag) |
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48 { |
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49 Replacements::iterator it = replacements_.find(tag); |
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50 |
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51 if (it != replacements_.end()) |
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52 { |
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53 delete it->second; |
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54 replacements_.erase(it); |
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55 } |
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56 } |
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57 |
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58 |
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59 void DicomModification::ReplaceInternal(const DicomTag& tag, |
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60 const Json::Value& value) |
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61 { |
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62 Replacements::iterator it = replacements_.find(tag); |
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63 |
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64 if (it != replacements_.end()) |
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65 { |
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66 delete it->second; |
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67 it->second = NULL; // In the case of an exception during the clone |
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68 it->second = new Json::Value(value); // Clone |
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69 } |
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70 else |
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71 { |
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72 replacements_[tag] = new Json::Value(value); // Clone |
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73 } |
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74 } |
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75 |
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76 |
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77 void DicomModification::ClearReplacements() |
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78 { |
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79 for (Replacements::iterator it = replacements_.begin(); |
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80 it != replacements_.end(); ++it) |
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81 { |
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82 delete it->second; |
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83 } |
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84 |
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85 replacements_.clear(); |
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86 } |
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87 |
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88 |
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89 void DicomModification::MarkNotOrthancAnonymization() |
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90 { |
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91 Replacements::iterator it = replacements_.find(DICOM_TAG_DEIDENTIFICATION_METHOD); |
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92 |
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93 if (it != replacements_.end() && |
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94 it->second->asString() == ORTHANC_DEIDENTIFICATION_METHOD) |
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95 { |
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96 delete it->second; |
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97 replacements_.erase(it); |
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98 } |
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99 } |
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100 |
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101 |
| 786 | 102 void DicomModification::MapDicomIdentifier(ParsedDicomFile& dicom, |
| 788 | 103 ResourceType level) |
| 786 | 104 { |
| 105 std::auto_ptr<DicomTag> tag; | |
| 106 | |
| 107 switch (level) | |
| 108 { | |
| 788 | 109 case ResourceType_Study: |
| 786 | 110 tag.reset(new DicomTag(DICOM_TAG_STUDY_INSTANCE_UID)); |
| 111 break; | |
| 112 | |
| 788 | 113 case ResourceType_Series: |
| 786 | 114 tag.reset(new DicomTag(DICOM_TAG_SERIES_INSTANCE_UID)); |
| 115 break; | |
| 116 | |
| 788 | 117 case ResourceType_Instance: |
| 786 | 118 tag.reset(new DicomTag(DICOM_TAG_SOP_INSTANCE_UID)); |
| 119 break; | |
| 120 | |
| 121 default: | |
| 122 throw OrthancException(ErrorCode_InternalError); | |
| 123 } | |
| 124 | |
| 125 std::string original; | |
| 126 if (!dicom.GetTagValue(original, *tag)) | |
| 127 { | |
| 128 original = ""; | |
| 129 } | |
| 130 | |
| 131 std::string mapped; | |
| 132 | |
| 133 UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original)); | |
| 134 if (previous == uidMap_.end()) | |
| 135 { | |
| 136 mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level); | |
| 137 uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped)); | |
| 138 } | |
| 139 else | |
| 140 { | |
| 141 mapped = previous->second; | |
| 142 } | |
| 143 | |
| 144 dicom.Replace(*tag, mapped); | |
| 145 } | |
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146 |
| 786 | 147 DicomModification::DicomModification() |
| 148 { | |
| 149 removePrivateTags_ = false; | |
| 788 | 150 level_ = ResourceType_Instance; |
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151 allowManualIdentifiers_ = true; |
| 786 | 152 } |
| 153 | |
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154 DicomModification::~DicomModification() |
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155 { |
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156 ClearReplacements(); |
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157 } |
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158 |
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159 void DicomModification::Keep(const DicomTag& tag) |
| 786 | 160 { |
| 161 removals_.erase(tag); | |
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162 RemoveInternal(tag); |
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163 |
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164 if (FromDcmtkBridge::IsPrivateTag(tag)) |
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165 { |
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166 privateTagsToKeep_.insert(tag); |
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167 } |
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168 |
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169 MarkNotOrthancAnonymization(); |
| 786 | 170 } |
| 171 | |
| 172 void DicomModification::Remove(const DicomTag& tag) | |
| 173 { | |
| 174 removals_.insert(tag); | |
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175 RemoveInternal(tag); |
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176 privateTagsToKeep_.erase(tag); |
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177 |
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178 MarkNotOrthancAnonymization(); |
| 786 | 179 } |
| 180 | |
| 181 bool DicomModification::IsRemoved(const DicomTag& tag) const | |
| 182 { | |
| 183 return removals_.find(tag) != removals_.end(); | |
| 184 } | |
| 185 | |
| 186 void DicomModification::Replace(const DicomTag& tag, | |
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187 const Json::Value& value, |
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188 bool safeForAnonymization) |
| 786 | 189 { |
| 190 removals_.erase(tag); | |
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191 privateTagsToKeep_.erase(tag); |
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192 ReplaceInternal(tag, value); |
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193 |
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194 if (!safeForAnonymization) |
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195 { |
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196 MarkNotOrthancAnonymization(); |
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197 } |
| 786 | 198 } |
| 199 | |
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200 |
| 786 | 201 bool DicomModification::IsReplaced(const DicomTag& tag) const |
| 202 { | |
| 203 return replacements_.find(tag) != replacements_.end(); | |
| 204 } | |
| 205 | |
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206 const Json::Value& DicomModification::GetReplacement(const DicomTag& tag) const |
| 786 | 207 { |
| 208 Replacements::const_iterator it = replacements_.find(tag); | |
| 209 | |
| 210 if (it == replacements_.end()) | |
| 211 { | |
| 212 throw OrthancException(ErrorCode_InexistentItem); | |
| 213 } | |
| 214 else | |
| 215 { | |
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216 return *it->second; |
| 786 | 217 } |
| 218 } | |
| 219 | |
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220 |
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221 std::string DicomModification::GetReplacementAsString(const DicomTag& tag) const |
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222 { |
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223 const Json::Value& json = GetReplacement(tag); |
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224 |
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225 if (json.type() != Json::stringValue) |
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226 { |
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227 throw OrthancException(ErrorCode_BadParameterType); |
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228 } |
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229 else |
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230 { |
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231 return json.asString(); |
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232 } |
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233 } |
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234 |
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235 |
| 786 | 236 void DicomModification::SetRemovePrivateTags(bool removed) |
| 237 { | |
| 238 removePrivateTags_ = removed; | |
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239 |
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240 if (!removed) |
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241 { |
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242 MarkNotOrthancAnonymization(); |
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243 } |
| 786 | 244 } |
| 245 | |
| 788 | 246 void DicomModification::SetLevel(ResourceType level) |
| 786 | 247 { |
| 248 uidMap_.clear(); | |
| 249 level_ = level; | |
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250 |
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251 if (level != ResourceType_Patient) |
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252 { |
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253 MarkNotOrthancAnonymization(); |
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254 } |
| 786 | 255 } |
| 256 | |
| 257 void DicomModification::SetupAnonymization() | |
| 258 { | |
| 259 removals_.clear(); | |
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260 ClearReplacements(); |
| 786 | 261 removePrivateTags_ = true; |
| 788 | 262 level_ = ResourceType_Patient; |
| 786 | 263 uidMap_.clear(); |
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264 privateTagsToKeep_.clear(); |
| 786 | 265 |
| 266 // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles | |
| 267 removals_.insert(DicomTag(0x0008, 0x0014)); // Instance Creator UID | |
| 268 //removals_.insert(DicomTag(0x0008, 0x0018)); // SOP Instance UID => set in Apply() | |
| 269 removals_.insert(DicomTag(0x0008, 0x0050)); // Accession Number | |
| 270 removals_.insert(DicomTag(0x0008, 0x0080)); // Institution Name | |
| 271 removals_.insert(DicomTag(0x0008, 0x0081)); // Institution Address | |
| 272 removals_.insert(DicomTag(0x0008, 0x0090)); // Referring Physician's Name | |
| 273 removals_.insert(DicomTag(0x0008, 0x0092)); // Referring Physician's Address | |
| 274 removals_.insert(DicomTag(0x0008, 0x0094)); // Referring Physician's Telephone Numbers | |
| 275 removals_.insert(DicomTag(0x0008, 0x1010)); // Station Name | |
| 276 removals_.insert(DicomTag(0x0008, 0x1030)); // Study Description | |
| 277 removals_.insert(DicomTag(0x0008, 0x103e)); // Series Description | |
| 278 removals_.insert(DicomTag(0x0008, 0x1040)); // Institutional Department Name | |
| 279 removals_.insert(DicomTag(0x0008, 0x1048)); // Physician(s) of Record | |
| 280 removals_.insert(DicomTag(0x0008, 0x1050)); // Performing Physicians' Name | |
| 281 removals_.insert(DicomTag(0x0008, 0x1060)); // Name of Physician(s) Reading Study | |
| 282 removals_.insert(DicomTag(0x0008, 0x1070)); // Operators' Name | |
| 283 removals_.insert(DicomTag(0x0008, 0x1080)); // Admitting Diagnoses Description | |
| 284 removals_.insert(DicomTag(0x0008, 0x1155)); // Referenced SOP Instance UID | |
| 285 removals_.insert(DicomTag(0x0008, 0x2111)); // Derivation Description | |
| 286 //removals_.insert(DicomTag(0x0010, 0x0010)); // Patient's Name => cf. below (*) | |
| 287 //removals_.insert(DicomTag(0x0010, 0x0020)); // Patient ID => cf. below (*) | |
| 288 removals_.insert(DicomTag(0x0010, 0x0030)); // Patient's Birth Date | |
| 289 removals_.insert(DicomTag(0x0010, 0x0032)); // Patient's Birth Time | |
| 290 removals_.insert(DicomTag(0x0010, 0x0040)); // Patient's Sex | |
| 291 removals_.insert(DicomTag(0x0010, 0x1000)); // Other Patient Ids | |
| 292 removals_.insert(DicomTag(0x0010, 0x1001)); // Other Patient Names | |
| 293 removals_.insert(DicomTag(0x0010, 0x1010)); // Patient's Age | |
| 294 removals_.insert(DicomTag(0x0010, 0x1020)); // Patient's Size | |
| 295 removals_.insert(DicomTag(0x0010, 0x1030)); // Patient's Weight | |
| 296 removals_.insert(DicomTag(0x0010, 0x1090)); // Medical Record Locator | |
| 297 removals_.insert(DicomTag(0x0010, 0x2160)); // Ethnic Group | |
| 298 removals_.insert(DicomTag(0x0010, 0x2180)); // Occupation | |
| 299 removals_.insert(DicomTag(0x0010, 0x21b0)); // Additional Patient's History | |
| 300 removals_.insert(DicomTag(0x0010, 0x4000)); // Patient Comments | |
| 301 removals_.insert(DicomTag(0x0018, 0x1000)); // Device Serial Number | |
| 302 removals_.insert(DicomTag(0x0018, 0x1030)); // Protocol Name | |
| 303 //removals_.insert(DicomTag(0x0020, 0x000d)); // Study Instance UID => set in Apply() | |
| 304 //removals_.insert(DicomTag(0x0020, 0x000e)); // Series Instance UID => set in Apply() | |
| 305 removals_.insert(DicomTag(0x0020, 0x0010)); // Study ID | |
| 306 removals_.insert(DicomTag(0x0020, 0x0052)); // Frame of Reference UID | |
| 307 removals_.insert(DicomTag(0x0020, 0x0200)); // Synchronization Frame of Reference UID | |
| 308 removals_.insert(DicomTag(0x0020, 0x4000)); // Image Comments | |
| 309 removals_.insert(DicomTag(0x0040, 0x0275)); // Request Attributes Sequence | |
| 310 removals_.insert(DicomTag(0x0040, 0xa124)); // UID | |
| 311 removals_.insert(DicomTag(0x0040, 0xa730)); // Content Sequence | |
| 312 removals_.insert(DicomTag(0x0088, 0x0140)); // Storage Media File-set UID | |
| 313 removals_.insert(DicomTag(0x3006, 0x0024)); // Referenced Frame of Reference UID | |
| 314 removals_.insert(DicomTag(0x3006, 0x00c2)); // Related Frame of Reference UID | |
| 315 | |
| 316 // Some more removals (from the experience of DICOM files at the CHU of Liege) | |
| 317 removals_.insert(DicomTag(0x0010, 0x1040)); // Patient's Address | |
| 318 removals_.insert(DicomTag(0x0032, 0x1032)); // Requesting Physician | |
| 319 removals_.insert(DicomTag(0x0010, 0x2154)); // PatientTelephoneNumbers | |
| 320 removals_.insert(DicomTag(0x0010, 0x2000)); // Medical Alerts | |
| 321 | |
| 322 // Set the DeidentificationMethod tag | |
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323 ReplaceInternal(DICOM_TAG_DEIDENTIFICATION_METHOD, ORTHANC_DEIDENTIFICATION_METHOD); |
| 786 | 324 |
| 325 // Set the PatientIdentityRemoved tag | |
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326 ReplaceInternal(DicomTag(0x0012, 0x0062), "YES"); |
| 786 | 327 |
| 328 // (*) Choose a random patient name and ID | |
| 788 | 329 std::string patientId = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient); |
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330 ReplaceInternal(DICOM_TAG_PATIENT_ID, patientId); |
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331 ReplaceInternal(DICOM_TAG_PATIENT_NAME, patientId); |
| 786 | 332 } |
| 333 | |
| 334 void DicomModification::Apply(ParsedDicomFile& toModify) | |
| 335 { | |
| 336 // Check the request | |
| 788 | 337 assert(ResourceType_Patient + 1 == ResourceType_Study && |
| 338 ResourceType_Study + 1 == ResourceType_Series && | |
| 339 ResourceType_Series + 1 == ResourceType_Instance); | |
| 786 | 340 |
| 341 if (IsRemoved(DICOM_TAG_PATIENT_ID) || | |
| 342 IsRemoved(DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 343 IsRemoved(DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 344 IsRemoved(DICOM_TAG_SOP_INSTANCE_UID)) | |
| 345 { | |
| 346 throw OrthancException(ErrorCode_BadRequest); | |
| 347 } | |
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348 |
| 786 | 349 |
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350 // Sanity checks at the patient level |
| 788 | 351 if (level_ == ResourceType_Patient && !IsReplaced(DICOM_TAG_PATIENT_ID)) |
| 786 | 352 { |
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353 LOG(ERROR) << "When modifying a patient, her PatientID is required to be modified"; |
| 786 | 354 throw OrthancException(ErrorCode_BadRequest); |
| 355 } | |
| 356 | |
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357 if (!allowManualIdentifiers_) |
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358 { |
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359 if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
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360 { |
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361 LOG(ERROR) << "When modifying a patient, the StudyInstanceUID cannot be manually modified"; |
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362 throw OrthancException(ErrorCode_BadRequest); |
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363 } |
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364 |
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365 if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
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366 { |
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367 LOG(ERROR) << "When modifying a patient, the SeriesInstanceUID cannot be manually modified"; |
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368 throw OrthancException(ErrorCode_BadRequest); |
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369 } |
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370 |
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371 if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID)) |
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372 { |
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373 LOG(ERROR) << "When modifying a patient, the SopInstanceUID cannot be manually modified"; |
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374 throw OrthancException(ErrorCode_BadRequest); |
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375 } |
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376 } |
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377 |
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378 |
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379 // Sanity checks at the study level |
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380 if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_PATIENT_ID)) |
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381 { |
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382 LOG(ERROR) << "When modifying a study, the parent PatientID cannot be manually modified"; |
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383 throw OrthancException(ErrorCode_BadRequest); |
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384 } |
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385 |
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386 if (!allowManualIdentifiers_) |
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387 { |
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388 if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
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389 { |
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390 LOG(ERROR) << "When modifying a study, the SeriesInstanceUID cannot be manually modified"; |
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391 throw OrthancException(ErrorCode_BadRequest); |
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392 } |
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393 |
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394 if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID)) |
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395 { |
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396 LOG(ERROR) << "When modifying a study, the SopInstanceUID cannot be manually modified"; |
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397 throw OrthancException(ErrorCode_BadRequest); |
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398 } |
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399 } |
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400 |
| 786 | 401 |
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402 // Sanity checks at the series level |
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403 if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_PATIENT_ID)) |
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404 { |
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405 LOG(ERROR) << "When modifying a series, the parent PatientID cannot be manually modified"; |
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406 throw OrthancException(ErrorCode_BadRequest); |
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407 } |
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408 |
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409 if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
| 786 | 410 { |
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411 LOG(ERROR) << "When modifying a series, the parent StudyInstanceUID cannot be manually modified"; |
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412 throw OrthancException(ErrorCode_BadRequest); |
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413 } |
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414 |
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415 if (!allowManualIdentifiers_) |
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416 { |
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417 if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID)) |
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418 { |
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419 LOG(ERROR) << "When modifying a series, the SopInstanceUID cannot be manually modified"; |
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420 throw OrthancException(ErrorCode_BadRequest); |
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421 } |
| 786 | 422 } |
| 423 | |
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424 |
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425 // Sanity checks at the instance level |
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426 if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_PATIENT_ID)) |
| 786 | 427 { |
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428 LOG(ERROR) << "When modifying an instance, the parent PatientID cannot be manually modified"; |
| 786 | 429 throw OrthancException(ErrorCode_BadRequest); |
| 430 } | |
| 431 | |
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432 if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
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433 { |
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434 LOG(ERROR) << "When modifying an instance, the parent StudyInstanceUID cannot be manually modified"; |
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435 throw OrthancException(ErrorCode_BadRequest); |
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436 } |
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437 |
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438 if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
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439 { |
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440 LOG(ERROR) << "When modifying an instance, the parent SeriesInstanceUID cannot be manually modified"; |
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441 throw OrthancException(ErrorCode_BadRequest); |
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442 } |
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443 |
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444 |
| 786 | 445 // (1) Remove the private tags, if need be |
| 446 if (removePrivateTags_) | |
| 447 { | |
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448 toModify.RemovePrivateTags(privateTagsToKeep_); |
| 786 | 449 } |
| 450 | |
| 451 // (2) Remove the tags specified by the user | |
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452 for (SetOfTags::const_iterator it = removals_.begin(); |
| 786 | 453 it != removals_.end(); ++it) |
| 454 { | |
| 455 toModify.Remove(*it); | |
| 456 } | |
| 457 | |
| 458 // (3) Replace the tags | |
| 459 for (Replacements::const_iterator it = replacements_.begin(); | |
| 460 it != replacements_.end(); ++it) | |
| 461 { | |
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462 toModify.Replace(it->first, *it->second, DicomReplaceMode_InsertIfAbsent); |
| 786 | 463 } |
| 464 | |
| 465 // (4) Update the DICOM identifiers | |
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466 if (level_ <= ResourceType_Study && |
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467 !IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
| 786 | 468 { |
| 788 | 469 MapDicomIdentifier(toModify, ResourceType_Study); |
| 786 | 470 } |
| 471 | |
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472 if (level_ <= ResourceType_Series && |
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473 !IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
| 786 | 474 { |
| 788 | 475 MapDicomIdentifier(toModify, ResourceType_Series); |
| 786 | 476 } |
| 477 | |
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478 if (level_ <= ResourceType_Instance && // Always true |
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479 !IsReplaced(DICOM_TAG_SOP_INSTANCE_UID)) |
| 786 | 480 { |
| 788 | 481 MapDicomIdentifier(toModify, ResourceType_Instance); |
| 786 | 482 } |
| 483 } | |
| 484 } |