Mercurial > hg > orthanc-stone
annotate Framework/Deprecated/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1297:6ab03e429f06 broker
integration mainline->broker
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sun, 23 Feb 2020 15:32:24 +0100 |
| parents | Framework/Loaders/OrthancMultiframeVolumeLoader.cpp@86400fa16091 Framework/Loaders/OrthancMultiframeVolumeLoader.cpp@7ec8fea061b9 |
| children | c38c89684d83 |
| rev | line source |
|---|---|
| 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 | |
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27 namespace Deprecated |
| 815 | 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 | |
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47 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) |
| 815 | 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 | |
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81 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) |
| 815 | 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 | |
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96 if (OrthancStone::StringToSopClassUid(GetSopClassUid(*dicom)) == OrthancStone::SopClassUid_RTDose) |
| 815 | 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 | |
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101 std::auto_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); |
| 815 | 102 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" + |
| 103 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format()); | |
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104 command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release())); |
| 815 | 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 | |
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123 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) |
| 815 | 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 | |
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137 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) |
| 815 | 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 { | |
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174 std::auto_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); |
| 815 | 175 command->SetHttpHeader("Accept-Encoding", "gzip"); |
| 176 command->SetUri("/instances/" + instanceId_ + "/content/" + | |
| 177 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0"); | |
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178 command->AcquirePayload(new LoadUncompressedPixelData(*this)); |
| 815 | 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 { | |
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197 OrthancStone::DicomInstanceParameters parameters(dicom); |
| 815 | 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 { | |
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209 case OrthancStone::SopClassUid_RTDose: |
| 815 | 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 { | |
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224 OrthancStone::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 |
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238 BroadcastMessage(OrthancStone::DicomVolumeImage::GeometryReadyMessage(*volume_)); |
| 815 | 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 { |
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269 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); |
| 815 | 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 { |
| 1279 | 311 OrthancStone::ImageBuffer3D::SliceWriter writer(target, OrthancStone::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 | |
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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 { |
| 1279 | 346 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); |
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347 |
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348 const uint64_t width = target.GetWidth(); |
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349 const uint64_t height = target.GetHeight(); |
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350 const uint64_t depth = target.GetDepth(); |
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351 const uint64_t voxelCount = width * height * depth; |
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352 |
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353 // now that we have distribution[pixelValue] == numberOfPixelsWithValue |
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354 // compute number of values and check (assertion) that it is equal to |
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355 // width * height * depth |
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356 { |
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357 typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); |
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358 uint64_t totalCount = 0; |
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359 distributionRawMin_ = static_cast<float>(it->first); |
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360 |
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361 while (it != distribution.end()) |
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362 { |
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363 T pixelValue = it->first; |
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364 uint64_t count = it->second; |
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365 totalCount += count; |
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366 it++; |
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367 if (it == distribution.end()) |
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368 distributionRawMax_ = static_cast<float>(pixelValue); |
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369 } |
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370 LOG(INFO) << "Volume image. First distribution value = " |
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371 << static_cast<float>(distributionRawMin_) |
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372 << " | Last distribution value = " |
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373 << static_cast<float>(distributionRawMax_); |
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374 |
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375 if (totalCount != voxelCount) |
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376 { |
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377 LOG(ERROR) << "Internal error in dose distribution computation. TC (" |
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378 << totalCount << ") != VoxC (" << voxelCount; |
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379 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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380 } |
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381 } |
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382 |
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383 // compute the number of voxels to reject at each end of the distribution |
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384 uint64_t endRejectionCount = static_cast<uint64_t>( |
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385 outliersHalfRejectionRate_ * voxelCount); |
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386 |
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387 if (endRejectionCount > voxelCount) |
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388 { |
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389 LOG(ERROR) << "Internal error in dose distribution computation." |
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390 << " endRejectionCount = " << endRejectionCount |
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391 << " | voxelCount = " << voxelCount; |
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392 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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393 } |
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394 |
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395 // this will contain the actual distribution minimum after outlier |
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396 // rejection |
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397 T resultMin = 0; |
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398 |
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399 // then start from start and remove pixel values up to |
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400 // endRejectionCount voxels rejected |
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401 { |
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402 typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); |
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403 |
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404 uint64_t currentCount = 0; |
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405 |
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406 while (it != distribution.end()) |
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407 { |
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408 T pixelValue = it->first; |
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409 uint64_t count = it->second; |
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410 |
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411 // if this pixelValue crosses the rejection threshold, let's set it |
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412 // and exit the loop |
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413 if ((currentCount <= endRejectionCount) && |
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414 (currentCount + count > endRejectionCount)) |
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415 { |
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416 resultMin = pixelValue; |
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417 break; |
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418 } |
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419 else |
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420 { |
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421 currentCount += count; |
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422 } |
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423 // and continue walking along the distribution |
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424 it++; |
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425 } |
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426 } |
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427 |
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428 // this will contain the actual distribution maximum after outlier |
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429 // rejection |
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430 T resultMax = 0; |
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431 // now start from END and remove pixel values up to |
|
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432 // endRejectionCount voxels rejected |
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433 { |
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434 typename std::map<T, uint64_t>::const_reverse_iterator it = distribution.rbegin(); |
|
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435 |
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436 uint64_t currentCount = 0; |
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437 |
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438 while (it != distribution.rend()) |
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439 { |
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440 T pixelValue = it->first; |
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441 uint64_t count = it->second; |
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442 |
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443 if ((currentCount <= endRejectionCount) && |
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444 (currentCount + count > endRejectionCount)) |
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445 { |
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446 resultMax = pixelValue; |
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447 break; |
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448 } |
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449 else |
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450 { |
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451 currentCount += count; |
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452 } |
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453 // and continue walking along the distribution |
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454 it++; |
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455 } |
|
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456 } |
|
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457 if (resultMin > resultMax) |
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458 { |
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459 LOG(ERROR) << "Internal error in dose distribution computation! " << |
|
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460 "resultMin (" << resultMin << ") > resultMax (" << resultMax << ")"; |
|
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461 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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462 } |
|
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Added outlier rejection for min max computation in multiframe volume loader
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463 computedDistributionMin_ = static_cast<float>(resultMin); |
|
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464 computedDistributionMax_ = static_cast<float>(resultMax); |
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465 } |
|
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466 } |
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467 |
|
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Added outlier rejection for min max computation in multiframe volume loader
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|
468 template <typename T> |
|
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469 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeMinMax( |
|
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Added outlier rejection for min max computation in multiframe volume loader
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470 const std::string& pixelData) |
|
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471 { |
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472 std::map<T, uint64_t> distribution; |
|
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473 CopyPixelDataAndComputeDistribution(pixelData, distribution); |
|
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Added outlier rejection for min max computation in multiframe volume loader
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474 ComputeMinMaxWithOutlierRejection(distribution); |
|
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Added outlier rejection for min max computation in multiframe volume loader
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|
475 } |
|
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Added outlier rejection for min max computation in multiframe volume loader
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|
476 |
| 815 | 477 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData) |
| 478 { | |
| 479 switch (volume_->GetPixelData().GetFormat()) | |
| 480 { | |
| 481 case Orthanc::PixelFormat_Grayscale32: | |
|
1260
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|
482 CopyPixelDataAndComputeMinMax<uint32_t>(pixelData); |
| 815 | 483 break; |
|
925
4639d0bf6390
Added support for Grayscale16 in the multiframe loader (Victor)
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
484 case Orthanc::PixelFormat_Grayscale16: |
|
1260
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485 CopyPixelDataAndComputeMinMax<uint16_t>(pixelData); |
|
925
4639d0bf6390
Added support for Grayscale16 in the multiframe loader (Victor)
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parents:
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diff
changeset
|
486 break; |
|
1114
33b0a762e98a
Added support for signed 16-bit pixels/voxels in multiframe loader
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
487 case Orthanc::PixelFormat_SignedGrayscale16: |
|
1260
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Added outlier rejection for min max computation in multiframe volume loader
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diff
changeset
|
488 CopyPixelDataAndComputeMinMax<int16_t>(pixelData); |
|
1114
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Added support for signed 16-bit pixels/voxels in multiframe loader
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
489 break; |
| 815 | 490 default: |
| 491 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 492 } | |
| 493 | |
| 494 volume_->IncrementRevision(); | |
| 495 | |
|
937
86ac61a040c9
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)
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
496 pixelDataLoaded_ = true; |
|
1225
16738485e457
deprecating DicomStructureSetLoader, OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1128
diff
changeset
|
497 BroadcastMessage(OrthancStone::DicomVolumeImage::ContentUpdatedMessage(*volume_)); |
| 815 | 498 } |
|
949
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
499 |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
500 bool OrthancMultiframeVolumeLoader::HasGeometry() const |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
501 { |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
502 return volume_->HasGeometry(); |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
503 } |
| 815 | 504 |
|
949
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
505 const OrthancStone::VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
506 { |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
507 return volume_->GetGeometry(); |
|
32eaf4929b08
OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
Benjamin Golinvaux <bgo@osimis.io>
parents:
937
diff
changeset
|
508 } |
| 815 | 509 |
|
1260
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
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1114
diff
changeset
|
510 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader( |
| 1279 | 511 boost::shared_ptr<OrthancStone::DicomVolumeImage> volume, |
| 512 OrthancStone::IOracle& oracle, | |
| 513 OrthancStone::IObservable& oracleObservable, | |
|
1260
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Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
514 float outliersHalfRejectionRate) : |
| 815 | 515 LoaderStateMachine(oracle, oracleObservable), |
|
937
86ac61a040c9
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)
Benjamin Golinvaux <bgo@osimis.io>
parents:
935
diff
changeset
|
516 volume_(volume), |
|
1260
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diff
changeset
|
517 pixelDataLoaded_(false), |
|
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changeset
|
518 outliersHalfRejectionRate_(outliersHalfRejectionRate), |
|
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Added outlier rejection for min max computation in multiframe volume loader
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changeset
|
519 distributionRawMin_(0), |
|
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Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
520 distributionRawMax_(0), |
|
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Added outlier rejection for min max computation in multiframe volume loader
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1114
diff
changeset
|
521 computedDistributionMin_(0), |
|
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Added outlier rejection for min max computation in multiframe volume loader
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diff
changeset
|
522 computedDistributionMax_(0) |
| 815 | 523 { |
| 524 if (volume.get() == NULL) | |
| 525 { | |
| 526 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
| 527 } | |
| 528 } | |
| 529 | |
|
935
401808e7ff2e
Added traces in LoaderCache objects dtors + fuse to prevent dead weak ptrs to be calleds in VisitWdigets (in GuiAdapter.h)
Benjamin Golinvaux <bgo@osimis.io>
parents:
925
diff
changeset
|
530 OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader() |
|
401808e7ff2e
Added traces in LoaderCache objects dtors + fuse to prevent dead weak ptrs to be calleds in VisitWdigets (in GuiAdapter.h)
Benjamin Golinvaux <bgo@osimis.io>
parents:
925
diff
changeset
|
531 { |
|
401808e7ff2e
Added traces in LoaderCache objects dtors + fuse to prevent dead weak ptrs to be calleds in VisitWdigets (in GuiAdapter.h)
Benjamin Golinvaux <bgo@osimis.io>
parents:
925
diff
changeset
|
532 LOG(TRACE) << "OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()"; |
|
401808e7ff2e
Added traces in LoaderCache objects dtors + fuse to prevent dead weak ptrs to be calleds in VisitWdigets (in GuiAdapter.h)
Benjamin Golinvaux <bgo@osimis.io>
parents:
925
diff
changeset
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533 } |
| 815 | 534 |
|
1260
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
535 |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
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536 void OrthancMultiframeVolumeLoader::GetDistributionMinMax |
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5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
537 (float& minValue, float& maxValue) const |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
538 { |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
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539 if (distributionRawMin_ == 0 && distributionRawMax_ == 0) |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
540 { |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
541 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
542 } |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
543 minValue = distributionRawMin_; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
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544 maxValue = distributionRawMax_; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
545 } |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
546 |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
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547 void OrthancMultiframeVolumeLoader::GetDistributionMinMaxWithOutliersRejection |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
548 (float& minValue, float& maxValue) const |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
549 { |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
550 if (computedDistributionMin_ == 0 && computedDistributionMax_ == 0) |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
551 { |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
552 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
553 } |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
554 minValue = computedDistributionMin_; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
555 maxValue = computedDistributionMax_; |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
556 } |
|
5a2d5380148d
Added outlier rejection for min max computation in multiframe volume loader
Benjamin Golinvaux <bgo@osimis.io>
parents:
1114
diff
changeset
|
557 |
| 815 | 558 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId) |
| 559 { | |
| 560 Start(); | |
| 561 | |
| 562 instanceId_ = instanceId; | |
| 563 | |
| 564 { | |
|
1225
16738485e457
deprecating DicomStructureSetLoader, OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1128
diff
changeset
|
565 std::auto_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); |
| 815 | 566 command->SetHttpHeader("Accept-Encoding", "gzip"); |
| 567 command->SetUri("/instances/" + instanceId + "/tags"); | |
|
1128
8e3763d1736a
removing CustomOracleCommand
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1117
diff
changeset
|
568 command->AcquirePayload(new LoadGeometry(*this)); |
| 815 | 569 Schedule(command.release()); |
| 570 } | |
| 571 | |
| 572 { | |
|
1225
16738485e457
deprecating DicomStructureSetLoader, OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1128
diff
changeset
|
573 std::auto_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); |
| 815 | 574 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax"); |
|
1128
8e3763d1736a
removing CustomOracleCommand
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1117
diff
changeset
|
575 command->AcquirePayload(new LoadTransferSyntax(*this)); |
| 815 | 576 Schedule(command.release()); |
| 577 } | |
| 578 } | |
| 579 } |