Mercurial > hg > orthanc-stone
annotate Framework/Loaders/OrthancMultiframeVolumeLoader.cpp @ 921:81d30cd93b65 toa2019072201
Ability to ask the loader for the geometry in PULL mode (when subscribing to the messages is not possible) + small changes (removed const/ref qualifiers for boost::shared_ptr param, added traces, doc change)
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Mon, 22 Jul 2019 11:21:09 +0200 |
| parents | 1f85e9c7d020 |
| children | 4639d0bf6390 |
| 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 | |
| 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium | |
| 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; | |
| 61 if (!dicom.CopyToString(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) | |
| 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 | |
| 116 | |
| 117 class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State | |
| 118 { | |
| 119 public: | |
| 120 LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) : | |
| 121 State(that) | |
| 122 { | |
| 123 } | |
| 124 | |
| 125 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 126 { | |
| 127 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer()); | |
| 128 } | |
| 129 }; | |
| 130 | |
| 131 | |
| 132 class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State | |
| 133 { | |
| 134 public: | |
| 135 LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) : | |
| 136 State(that) | |
| 137 { | |
| 138 } | |
| 139 | |
| 140 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 141 { | |
| 142 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer()); | |
| 143 } | |
| 144 }; | |
| 145 | |
| 146 | |
| 147 const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const | |
| 148 { | |
| 149 if (IsActive()) | |
| 150 { | |
| 151 return instanceId_; | |
| 152 } | |
| 153 else | |
| 154 { | |
| 155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
| 156 } | |
| 157 } | |
| 158 | |
| 159 | |
| 160 void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads() | |
| 161 { | |
| 162 if (transferSyntaxUid_.empty() || | |
| 163 !volume_->HasGeometry()) | |
| 164 { | |
| 165 return; | |
| 166 } | |
| 167 /* | |
| 168 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM | |
| 169 1.2.840.10008.1.2.1 Explicit VR Little Endian | |
| 170 1.2.840.10008.1.2.2 Explicit VR Big Endian | |
| 171 | |
| 172 See https://www.dicomlibrary.com/dicom/transfer-syntax/ | |
| 173 */ | |
| 174 if (transferSyntaxUid_ == "1.2.840.10008.1.2" || | |
| 175 transferSyntaxUid_ == "1.2.840.10008.1.2.1" || | |
| 176 transferSyntaxUid_ == "1.2.840.10008.1.2.2") | |
| 177 { | |
| 178 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 179 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
| 180 command->SetUri("/instances/" + instanceId_ + "/content/" + | |
| 181 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0"); | |
| 182 command->SetPayload(new LoadUncompressedPixelData(*this)); | |
| 183 Schedule(command.release()); | |
| 184 } | |
| 185 else | |
| 186 { | |
| 187 throw Orthanc::OrthancException( | |
| 188 Orthanc::ErrorCode_NotImplemented, | |
| 189 "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_); | |
| 190 } | |
| 191 } | |
| 192 | |
| 193 | |
| 194 void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax) | |
| 195 { | |
| 196 transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax); | |
| 197 ScheduleFrameDownloads(); | |
| 198 } | |
| 199 | |
| 200 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom) | |
| 201 { | |
| 202 DicomInstanceParameters parameters(dicom); | |
| 203 volume_->SetDicomParameters(parameters); | |
| 204 | |
| 205 Orthanc::PixelFormat format; | |
| 206 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true)) | |
| 207 { | |
| 208 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 209 } | |
| 210 | |
| 211 double spacingZ; | |
| 212 switch (parameters.GetSopClassUid()) | |
| 213 { | |
| 214 case SopClassUid_RTDose: | |
| 215 spacingZ = parameters.GetThickness(); | |
| 216 break; | |
| 217 | |
| 218 default: | |
| 219 throw Orthanc::OrthancException( | |
| 220 Orthanc::ErrorCode_NotImplemented, | |
| 221 "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom)); | |
| 222 } | |
| 223 | |
| 224 const unsigned int width = parameters.GetImageInformation().GetWidth(); | |
| 225 const unsigned int height = parameters.GetImageInformation().GetHeight(); | |
| 226 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames(); | |
| 227 | |
| 228 { | |
| 229 VolumeImageGeometry geometry; | |
| 230 geometry.SetSize(width, height, depth); | |
| 231 geometry.SetAxialGeometry(parameters.GetGeometry()); | |
| 232 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(), | |
| 233 parameters.GetPixelSpacingY(), spacingZ); | |
| 234 volume_->Initialize(geometry, format); | |
| 235 } | |
| 236 | |
| 237 volume_->GetPixelData().Clear(); | |
| 238 | |
| 239 ScheduleFrameDownloads(); | |
| 240 | |
| 241 BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_)); | |
| 242 } | |
| 243 | |
| 244 | |
| 245 ORTHANC_FORCE_INLINE | |
| 246 static void CopyPixel(uint32_t& target, | |
| 247 const void* source) | |
| 248 { | |
| 249 // TODO - check alignement? | |
| 250 target = le32toh(*reinterpret_cast<const uint32_t*>(source)); | |
| 251 } | |
| 252 | |
| 253 | |
| 254 template <typename T> | |
| 255 void OrthancMultiframeVolumeLoader::CopyPixelData(const std::string& pixelData) | |
| 256 { | |
| 257 ImageBuffer3D& target = volume_->GetPixelData(); | |
| 258 | |
| 259 const unsigned int bpp = target.GetBytesPerPixel(); | |
| 260 const unsigned int width = target.GetWidth(); | |
| 261 const unsigned int height = target.GetHeight(); | |
| 262 const unsigned int depth = target.GetDepth(); | |
| 263 | |
| 264 if (pixelData.size() != bpp * width * height * depth) | |
| 265 { | |
| 266 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, | |
| 267 "The pixel data has not the proper size"); | |
| 268 } | |
| 269 | |
| 270 if (pixelData.empty()) | |
| 271 { | |
| 272 return; | |
| 273 } | |
| 274 | |
| 275 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); | |
| 276 | |
| 277 for (unsigned int z = 0; z < depth; z++) | |
| 278 { | |
| 279 ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z); | |
| 280 | |
| 281 assert (writer.GetAccessor().GetWidth() == width && | |
| 282 writer.GetAccessor().GetHeight() == height); | |
| 283 | |
| 284 for (unsigned int y = 0; y < height; y++) | |
| 285 { | |
| 286 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat())); | |
| 287 | |
| 288 T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y)); | |
| 289 | |
| 290 for (unsigned int x = 0; x < width; x++) | |
| 291 { | |
| 292 CopyPixel(*target, source); | |
| 293 | |
| 294 target ++; | |
| 295 source += bpp; | |
| 296 } | |
| 297 } | |
| 298 } | |
| 299 } | |
| 300 | |
| 301 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData) | |
| 302 { | |
| 303 switch (volume_->GetPixelData().GetFormat()) | |
| 304 { | |
| 305 case Orthanc::PixelFormat_Grayscale32: | |
| 306 CopyPixelData<uint32_t>(pixelData); | |
| 307 break; | |
| 308 | |
| 309 default: | |
| 310 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 311 } | |
| 312 | |
| 313 volume_->IncrementRevision(); | |
| 314 | |
| 315 BroadcastMessage(DicomVolumeImage::ContentUpdatedMessage(*volume_)); | |
| 316 } | |
| 317 | |
| 318 | |
|
921
81d30cd93b65
Ability to ask the loader for the geometry in PULL mode (when subscribing to the messages is not possible) + small changes (removed const/ref qualifiers for boost::shared_ptr param, added traces, doc change)
Benjamin Golinvaux <bgo@osimis.io>
parents:
816
diff
changeset
|
319 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader(boost::shared_ptr<DicomVolumeImage> volume, |
| 815 | 320 IOracle& oracle, |
| 321 IObservable& oracleObservable) : | |
| 322 LoaderStateMachine(oracle, oracleObservable), | |
| 323 IObservable(oracleObservable.GetBroker()), | |
| 324 volume_(volume) | |
| 325 { | |
| 326 if (volume.get() == NULL) | |
| 327 { | |
| 328 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
| 329 } | |
| 330 } | |
| 331 | |
| 332 | |
| 333 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId) | |
| 334 { | |
| 335 Start(); | |
| 336 | |
| 337 instanceId_ = instanceId; | |
| 338 | |
| 339 { | |
| 340 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 341 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
| 342 command->SetUri("/instances/" + instanceId + "/tags"); | |
| 343 command->SetPayload(new LoadGeometry(*this)); | |
| 344 Schedule(command.release()); | |
| 345 } | |
| 346 | |
| 347 { | |
| 348 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 349 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax"); | |
| 350 command->SetPayload(new LoadTransferSyntax(*this)); | |
| 351 Schedule(command.release()); | |
| 352 } | |
| 353 } | |
| 354 } |