Mercurial > hg > orthanc-stone
annotate Framework/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1270:2d8ab34c8c91
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 31 Jan 2020 17:34:29 +0100 |
parents | 5a2d5380148d |
children | 86400fa16091 |
rev | line source |
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815 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
815 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "OrthancMultiframeVolumeLoader.h" | |
23 | |
816 | 24 #include <Core/Endianness.h> |
815 | 25 #include <Core/Toolbox.h> |
26 | |
27 namespace OrthancStone | |
28 { | |
29 class OrthancMultiframeVolumeLoader::LoadRTDoseGeometry : public LoaderStateMachine::State | |
30 { | |
31 private: | |
32 std::auto_ptr<Orthanc::DicomMap> dicom_; | |
33 | |
34 public: | |
35 LoadRTDoseGeometry(OrthancMultiframeVolumeLoader& that, | |
36 Orthanc::DicomMap* dicom) : | |
37 State(that), | |
38 dicom_(dicom) | |
39 { | |
40 if (dicom == NULL) | |
41 { | |
42 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
43 } | |
44 | |
45 } | |
46 | |
47 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
48 { | |
49 // Complete the DICOM tags with just-received "Grid Frame Offset Vector" | |
50 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer()); | |
51 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false); | |
52 | |
53 GetLoader<OrthancMultiframeVolumeLoader>().SetGeometry(*dicom_); | |
54 } | |
55 }; | |
56 | |
57 | |
58 static std::string GetSopClassUid(const Orthanc::DicomMap& dicom) | |
59 { | |
60 std::string s; | |
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61 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
815 | 62 { |
63 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, | |
64 "DICOM file without SOP class UID"); | |
65 } | |
66 else | |
67 { | |
68 return s; | |
69 } | |
70 } | |
71 | |
72 | |
73 class OrthancMultiframeVolumeLoader::LoadGeometry : public State | |
74 { | |
75 public: | |
76 LoadGeometry(OrthancMultiframeVolumeLoader& that) : | |
77 State(that) | |
78 { | |
79 } | |
80 | |
81 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
82 { | |
83 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>(); | |
84 | |
85 Json::Value body; | |
86 message.ParseJsonBody(body); | |
87 | |
88 if (body.type() != Json::objectValue) | |
89 { | |
90 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
91 } | |
92 | |
93 std::auto_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap); | |
94 dicom->FromDicomAsJson(body); | |
95 | |
96 if (StringToSopClassUid(GetSopClassUid(*dicom)) == SopClassUid_RTDose) | |
97 { | |
98 // Download the "Grid Frame Offset Vector" DICOM tag, that is | |
99 // mandatory for RT-DOSE, but is too long to be returned by default | |
100 | |
101 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
102 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" + | |
103 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format()); | |
104 command->SetPayload(new LoadRTDoseGeometry(loader, dicom.release())); | |
105 | |
106 Schedule(command.release()); | |
107 } | |
108 else | |
109 { | |
110 loader.SetGeometry(*dicom); | |
111 } | |
112 } | |
113 }; | |
114 | |
115 class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State | |
116 { | |
117 public: | |
118 LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) : | |
119 State(that) | |
120 { | |
121 } | |
122 | |
123 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
124 { | |
125 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer()); | |
126 } | |
127 }; | |
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128 |
815 | 129 class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State |
130 { | |
131 public: | |
132 LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) : | |
133 State(that) | |
134 { | |
135 } | |
136 | |
137 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
138 { | |
139 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer()); | |
140 } | |
141 }; | |
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142 |
815 | 143 const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const |
144 { | |
145 if (IsActive()) | |
146 { | |
147 return instanceId_; | |
148 } | |
149 else | |
150 { | |
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151 LOG(ERROR) << "OrthancMultiframeVolumeLoader::GetInstanceId(): (!IsActive())"; |
815 | 152 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
153 } | |
154 } | |
155 | |
156 void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads() | |
157 { | |
158 if (transferSyntaxUid_.empty() || | |
159 !volume_->HasGeometry()) | |
160 { | |
161 return; | |
162 } | |
163 /* | |
164 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM | |
165 1.2.840.10008.1.2.1 Explicit VR Little Endian | |
166 1.2.840.10008.1.2.2 Explicit VR Big Endian | |
167 | |
168 See https://www.dicomlibrary.com/dicom/transfer-syntax/ | |
169 */ | |
170 if (transferSyntaxUid_ == "1.2.840.10008.1.2" || | |
171 transferSyntaxUid_ == "1.2.840.10008.1.2.1" || | |
172 transferSyntaxUid_ == "1.2.840.10008.1.2.2") | |
173 { | |
174 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
175 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
176 command->SetUri("/instances/" + instanceId_ + "/content/" + | |
177 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0"); | |
178 command->SetPayload(new LoadUncompressedPixelData(*this)); | |
179 Schedule(command.release()); | |
180 } | |
181 else | |
182 { | |
183 throw Orthanc::OrthancException( | |
184 Orthanc::ErrorCode_NotImplemented, | |
185 "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_); | |
186 } | |
187 } | |
188 | |
189 void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax) | |
190 { | |
191 transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax); | |
192 ScheduleFrameDownloads(); | |
193 } | |
194 | |
195 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom) | |
196 { | |
197 DicomInstanceParameters parameters(dicom); | |
198 volume_->SetDicomParameters(parameters); | |
199 | |
200 Orthanc::PixelFormat format; | |
201 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true)) | |
202 { | |
203 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
204 } | |
205 | |
206 double spacingZ; | |
207 switch (parameters.GetSopClassUid()) | |
208 { | |
209 case SopClassUid_RTDose: | |
210 spacingZ = parameters.GetThickness(); | |
211 break; | |
212 | |
213 default: | |
214 throw Orthanc::OrthancException( | |
215 Orthanc::ErrorCode_NotImplemented, | |
216 "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom)); | |
217 } | |
218 | |
219 const unsigned int width = parameters.GetImageInformation().GetWidth(); | |
220 const unsigned int height = parameters.GetImageInformation().GetHeight(); | |
221 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames(); | |
222 | |
223 { | |
224 VolumeImageGeometry geometry; | |
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225 geometry.SetSizeInVoxels(width, height, depth); |
815 | 226 geometry.SetAxialGeometry(parameters.GetGeometry()); |
227 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(), | |
228 parameters.GetPixelSpacingY(), spacingZ); | |
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229 volume_->Initialize(geometry, format, true /* Do compute range */); |
815 | 230 } |
231 | |
232 volume_->GetPixelData().Clear(); | |
233 | |
234 ScheduleFrameDownloads(); | |
235 | |
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236 |
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237 |
815 | 238 BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_)); |
239 } | |
240 | |
241 | |
242 ORTHANC_FORCE_INLINE | |
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243 static void CopyPixel(uint32_t& target, const void* source) |
815 | 244 { |
245 // TODO - check alignement? | |
246 target = le32toh(*reinterpret_cast<const uint32_t*>(source)); | |
247 } | |
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248 |
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249 ORTHANC_FORCE_INLINE |
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250 static void CopyPixel(uint16_t& target, const void* source) |
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251 { |
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252 // TODO - check alignement? |
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253 target = le16toh(*reinterpret_cast<const uint16_t*>(source)); |
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254 } |
815 | 255 |
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256 ORTHANC_FORCE_INLINE |
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257 static void CopyPixel(int16_t& target, const void* source) |
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258 { |
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259 // byte swapping is the same for unsigned and signed integers |
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260 // (the sign bit is always stored with the MSByte) |
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261 uint16_t* targetUp = reinterpret_cast<uint16_t*>(&target); |
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262 CopyPixel(*targetUp, source); |
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263 } |
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264 |
815 | 265 template <typename T> |
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266 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution( |
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267 const std::string& pixelData, std::map<T,uint64_t>& distribution) |
815 | 268 { |
269 ImageBuffer3D& target = volume_->GetPixelData(); | |
270 | |
271 const unsigned int bpp = target.GetBytesPerPixel(); | |
272 const unsigned int width = target.GetWidth(); | |
273 const unsigned int height = target.GetHeight(); | |
274 const unsigned int depth = target.GetDepth(); | |
275 | |
276 if (pixelData.size() != bpp * width * height * depth) | |
277 { | |
278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, | |
279 "The pixel data has not the proper size"); | |
280 } | |
281 | |
282 if (pixelData.empty()) | |
283 { | |
284 return; | |
285 } | |
286 | |
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287 // first pass to initialize map |
815 | 288 { |
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289 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); |
815 | 290 |
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291 for (unsigned int z = 0; z < depth; z++) |
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292 { |
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293 for (unsigned int y = 0; y < height; y++) |
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294 { |
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295 for (unsigned int x = 0; x < width; x++) |
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296 { |
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297 T value; |
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298 CopyPixel(value, source); |
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299 distribution[value] = 0; |
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300 source += bpp; |
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301 } |
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302 } |
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303 } |
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304 } |
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305 |
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306 { |
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307 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); |
815 | 308 |
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309 for (unsigned int z = 0; z < depth; z++) |
815 | 310 { |
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311 ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z); |
815 | 312 |
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313 assert(writer.GetAccessor().GetWidth() == width && |
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314 writer.GetAccessor().GetHeight() == height); |
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315 |
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316 for (unsigned int y = 0; y < height; y++) |
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317 { |
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318 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat())); |
815 | 319 |
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320 T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y)); |
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321 |
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322 for (unsigned int x = 0; x < width; x++) |
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323 { |
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324 CopyPixel(*target, source); |
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325 |
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326 distribution[*target] += 1; |
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327 |
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328 target++; |
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329 source += bpp; |
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330 } |
815 | 331 } |
332 } | |
333 } | |
334 } | |
335 | |
1260
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336 template <typename T> |
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337 void OrthancMultiframeVolumeLoader::ComputeMinMaxWithOutlierRejection( |
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338 const std::map<T, uint64_t>& distribution) |
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339 { |
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340 if (distribution.size() == 0) |
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341 { |
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342 LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty."; |
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343 } |
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344 else |
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345 { |
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346 ImageBuffer3D& target = volume_->GetPixelData(); |
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347 |
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348 const uint64_t bpp = target.GetBytesPerPixel(); |
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349 const uint64_t width = target.GetWidth(); |
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350 const uint64_t height = target.GetHeight(); |
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351 const uint64_t depth = target.GetDepth(); |
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352 const uint64_t voxelCount = width * height * depth; |
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353 |
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354 // now that we have distribution[pixelValue] == numberOfPixelsWithValue |
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355 // compute number of values and check (assertion) that it is equal to |
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356 // width * height * depth |
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357 { |
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358 typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); |
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359 uint64_t totalCount = 0; |
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360 distributionRawMin_ = static_cast<float>(it->first); |
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361 |
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362 while (it != distribution.end()) |
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363 { |
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364 T pixelValue = it->first; |
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365 uint64_t count = it->second; |
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366 totalCount += count; |
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367 it++; |
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368 if (it == distribution.end()) |
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369 distributionRawMax_ = static_cast<float>(pixelValue); |
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370 } |
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371 LOG(INFO) << "Volume image. First distribution value = " |
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372 << static_cast<float>(distributionRawMin_) |
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373 << " | Last distribution value = " |
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374 << static_cast<float>(distributionRawMax_); |
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375 |
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376 if (totalCount != voxelCount) |
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377 { |
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378 LOG(ERROR) << "Internal error in dose distribution computation. TC (" |
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379 << totalCount << ") != VoxC (" << voxelCount; |
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380 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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381 } |
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382 } |
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383 |
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384 // compute the number of voxels to reject at each end of the distribution |
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385 uint64_t endRejectionCount = static_cast<uint64_t>( |
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386 outliersHalfRejectionRate_ * voxelCount); |
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387 |
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388 if (endRejectionCount > voxelCount) |
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389 { |
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390 LOG(ERROR) << "Internal error in dose distribution computation." |
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391 << " endRejectionCount = " << endRejectionCount |
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392 << " | voxelCount = " << voxelCount; |
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393 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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394 } |
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395 |
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396 // this will contain the actual distribution minimum after outlier |
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397 // rejection |
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398 T resultMin = 0; |
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399 |
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400 // then start from start and remove pixel values up to |
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401 // endRejectionCount voxels rejected |
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402 { |
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403 typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); |
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404 |
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405 uint64_t currentCount = 0; |
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406 |
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407 while (it != distribution.end()) |
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408 { |
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409 T pixelValue = it->first; |
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410 uint64_t count = it->second; |
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411 |
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412 // if this pixelValue crosses the rejection threshold, let's set it |
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413 // and exit the loop |
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414 if ((currentCount <= endRejectionCount) && |
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415 (currentCount + count > endRejectionCount)) |
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416 { |
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417 resultMin = pixelValue; |
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418 break; |
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419 } |
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420 else |
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421 { |
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422 currentCount += count; |
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423 } |
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424 // and continue walking along the distribution |
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425 it++; |
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426 } |
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427 } |
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428 |
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429 // this will contain the actual distribution maximum after outlier |
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430 // rejection |
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431 T resultMax = 0; |
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432 // now start from END and remove pixel values up to |
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433 // endRejectionCount voxels rejected |
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434 { |
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435 typename std::map<T, uint64_t>::const_reverse_iterator it = distribution.rbegin(); |
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436 |
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437 uint64_t currentCount = 0; |
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438 |
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439 while (it != distribution.rend()) |
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440 { |
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441 T pixelValue = it->first; |
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442 uint64_t count = it->second; |
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443 |
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444 if ((currentCount <= endRejectionCount) && |
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445 (currentCount + count > endRejectionCount)) |
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446 { |
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447 resultMax = pixelValue; |
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448 break; |
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449 } |
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450 else |
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451 { |
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452 currentCount += count; |
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453 } |
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454 // and continue walking along the distribution |
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455 it++; |
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456 } |
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457 } |
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458 if (resultMin > resultMax) |
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459 { |
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460 LOG(ERROR) << "Internal error in dose distribution computation! " << |
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461 "resultMin (" << resultMin << ") > resultMax (" << resultMax << ")"; |
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462 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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463 } |
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464 computedDistributionMin_ = static_cast<float>(resultMin); |
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465 computedDistributionMax_ = static_cast<float>(resultMax); |
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466 } |
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467 } |
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468 |
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469 template <typename T> |
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470 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeMinMax( |
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471 const std::string& pixelData) |
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472 { |
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473 std::map<T, uint64_t> distribution; |
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474 CopyPixelDataAndComputeDistribution(pixelData, distribution); |
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475 ComputeMinMaxWithOutlierRejection(distribution); |
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476 } |
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477 |
815 | 478 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData) |
479 { | |
480 switch (volume_->GetPixelData().GetFormat()) | |
481 { | |
482 case Orthanc::PixelFormat_Grayscale32: | |
1260
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483 CopyPixelDataAndComputeMinMax<uint32_t>(pixelData); |
815 | 484 break; |
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485 case Orthanc::PixelFormat_Grayscale16: |
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486 CopyPixelDataAndComputeMinMax<uint16_t>(pixelData); |
925
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487 break; |
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488 case Orthanc::PixelFormat_SignedGrayscale16: |
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489 CopyPixelDataAndComputeMinMax<int16_t>(pixelData); |
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490 break; |
815 | 491 default: |
492 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
493 } | |
494 | |
495 volume_->IncrementRevision(); | |
496 | |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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497 pixelDataLoaded_ = true; |
815 | 498 BroadcastMessage(DicomVolumeImage::ContentUpdatedMessage(*volume_)); |
499 } | |
949
32eaf4929b08
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500 |
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501 bool OrthancMultiframeVolumeLoader::HasGeometry() const |
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502 { |
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503 return volume_->HasGeometry(); |
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504 } |
815 | 505 |
949
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506 const OrthancStone::VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const |
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507 { |
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508 return volume_->GetGeometry(); |
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509 } |
815 | 510 |
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511 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader( |
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512 boost::shared_ptr<DicomVolumeImage> volume, |
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513 IOracle& oracle, |
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514 IObservable& oracleObservable, |
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515 float outliersHalfRejectionRate) : |
815 | 516 LoaderStateMachine(oracle, oracleObservable), |
517 IObservable(oracleObservable.GetBroker()), | |
937
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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518 volume_(volume), |
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519 pixelDataLoaded_(false), |
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520 outliersHalfRejectionRate_(outliersHalfRejectionRate), |
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521 distributionRawMin_(0), |
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522 distributionRawMax_(0), |
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523 computedDistributionMin_(0), |
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524 computedDistributionMax_(0) |
815 | 525 { |
526 if (volume.get() == NULL) | |
527 { | |
528 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
529 } | |
530 } | |
531 | |
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532 OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader() |
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533 { |
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534 LOG(TRACE) << "OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()"; |
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535 } |
815 | 536 |
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537 |
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538 void OrthancMultiframeVolumeLoader::GetDistributionMinMax |
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539 (float& minValue, float& maxValue) const |
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540 { |
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541 if (distributionRawMin_ == 0 && distributionRawMax_ == 0) |
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542 { |
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543 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; |
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544 } |
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545 minValue = distributionRawMin_; |
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546 maxValue = distributionRawMax_; |
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547 } |
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548 |
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549 void OrthancMultiframeVolumeLoader::GetDistributionMinMaxWithOutliersRejection |
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550 (float& minValue, float& maxValue) const |
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551 { |
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552 if (computedDistributionMin_ == 0 && computedDistributionMax_ == 0) |
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553 { |
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554 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; |
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555 } |
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556 minValue = computedDistributionMin_; |
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557 maxValue = computedDistributionMax_; |
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558 } |
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559 |
815 | 560 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId) |
561 { | |
562 Start(); | |
563 | |
564 instanceId_ = instanceId; | |
565 | |
566 { | |
567 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
568 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
569 command->SetUri("/instances/" + instanceId + "/tags"); | |
570 command->SetPayload(new LoadGeometry(*this)); | |
571 Schedule(command.release()); | |
572 } | |
573 | |
574 { | |
575 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
576 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax"); | |
577 command->SetPayload(new LoadTransferSyntax(*this)); | |
578 Schedule(command.release()); | |
579 } | |
580 } | |
581 } |