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comparison OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1640:52b8b96cb55f

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cleaning namespaces
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 10 Nov 2020 16:55:22 +0100
parents a4418a489e86
children 9ac2a65d4172
comparison
equal deleted inserted replaced
1639:5cdc5b98f14d 1640:52b8b96cb55f
43 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); 43 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
44 } 44 }
45 45
46 } 46 }
47 47
48 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE 48 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE
49 { 49 {
50 // Complete the DICOM tags with just-received "Grid Frame Offset Vector" 50 // Complete the DICOM tags with just-received "Grid Frame Offset Vector"
51 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer()); 51 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer());
52 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false); 52 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false);
53 53
77 explicit LoadGeometry(OrthancMultiframeVolumeLoader& that) : 77 explicit LoadGeometry(OrthancMultiframeVolumeLoader& that) :
78 State(that) 78 State(that)
79 { 79 {
80 } 80 }
81 81
82 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) 82 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
83 { 83 {
84 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>(); 84 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>();
85 85
86 Json::Value body; 86 Json::Value body;
87 message.ParseJsonBody(body); 87 message.ParseJsonBody(body);
92 } 92 }
93 93
94 std::unique_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap); 94 std::unique_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap);
95 dicom->FromDicomAsJson(body); 95 dicom->FromDicomAsJson(body);
96 96
97 if (OrthancStone::StringToSopClassUid(GetSopClassUid(*dicom)) == OrthancStone::SopClassUid_RTDose) 97 if (StringToSopClassUid(GetSopClassUid(*dicom)) == SopClassUid_RTDose)
98 { 98 {
99 // Download the "Grid Frame Offset Vector" DICOM tag, that is 99 // Download the "Grid Frame Offset Vector" DICOM tag, that is
100 // mandatory for RT-DOSE, but is too long to be returned by default 100 // mandatory for RT-DOSE, but is too long to be returned by default
101 101
102 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); 102 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
103 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" + 103 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" +
104 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format()); 104 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format());
105 command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release())); 105 command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release()));
106 106
107 Schedule(command.release()); 107 Schedule(command.release());
119 explicit LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) : 119 explicit LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) :
120 State(that) 120 State(that)
121 { 121 {
122 } 122 }
123 123
124 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) 124 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
125 { 125 {
126 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer()); 126 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer());
127 } 127 }
128 }; 128 };
129 129
133 explicit LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) : 133 explicit LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) :
134 State(that) 134 State(that)
135 { 135 {
136 } 136 }
137 137
138 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) 138 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
139 { 139 {
140 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer()); 140 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer());
141 } 141 }
142 }; 142 };
143 143
170 */ 170 */
171 if (transferSyntaxUid_ == "1.2.840.10008.1.2" || 171 if (transferSyntaxUid_ == "1.2.840.10008.1.2" ||
172 transferSyntaxUid_ == "1.2.840.10008.1.2.1" || 172 transferSyntaxUid_ == "1.2.840.10008.1.2.1" ||
173 transferSyntaxUid_ == "1.2.840.10008.1.2.2") 173 transferSyntaxUid_ == "1.2.840.10008.1.2.2")
174 { 174 {
175 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); 175 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
176 command->SetHttpHeader("Accept-Encoding", "gzip"); 176 command->SetHttpHeader("Accept-Encoding", "gzip");
177 command->SetUri("/instances/" + instanceId_ + "/content/" + 177 command->SetUri("/instances/" + instanceId_ + "/content/" +
178 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0"); 178 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0");
179 command->AcquirePayload(new LoadUncompressedPixelData(*this)); 179 command->AcquirePayload(new LoadUncompressedPixelData(*this));
180 Schedule(command.release()); 180 Schedule(command.release());
193 ScheduleFrameDownloads(); 193 ScheduleFrameDownloads();
194 } 194 }
195 195
196 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom) 196 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom)
197 { 197 {
198 OrthancStone::DicomInstanceParameters parameters(dicom); 198 DicomInstanceParameters parameters(dicom);
199 volume_->SetDicomParameters(parameters); 199 volume_->SetDicomParameters(parameters);
200 200
201 Orthanc::PixelFormat format; 201 Orthanc::PixelFormat format;
202 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true)) 202 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true))
203 { 203 {
205 } 205 }
206 206
207 double spacingZ; 207 double spacingZ;
208 switch (parameters.GetSopClassUid()) 208 switch (parameters.GetSopClassUid())
209 { 209 {
210 case OrthancStone::SopClassUid_RTDose: 210 case SopClassUid_RTDose:
211 spacingZ = parameters.GetSliceThickness(); 211 spacingZ = parameters.GetSliceThickness();
212 break; 212 break;
213 213
214 default: 214 default:
215 throw Orthanc::OrthancException( 215 throw Orthanc::OrthancException(
220 const unsigned int width = parameters.GetImageInformation().GetWidth(); 220 const unsigned int width = parameters.GetImageInformation().GetWidth();
221 const unsigned int height = parameters.GetImageInformation().GetHeight(); 221 const unsigned int height = parameters.GetImageInformation().GetHeight();
222 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames(); 222 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames();
223 223
224 { 224 {
225 OrthancStone::VolumeImageGeometry geometry; 225 VolumeImageGeometry geometry;
226 geometry.SetSizeInVoxels(width, height, depth); 226 geometry.SetSizeInVoxels(width, height, depth);
227 geometry.SetAxialGeometry(parameters.GetGeometry()); 227 geometry.SetAxialGeometry(parameters.GetGeometry());
228 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(), 228 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(),
229 parameters.GetPixelSpacingY(), spacingZ); 229 parameters.GetPixelSpacingY(), spacingZ);
230 volume_->Initialize(geometry, format, true /* Do compute range */); 230 volume_->Initialize(geometry, format, true /* Do compute range */);
234 234
235 ScheduleFrameDownloads(); 235 ScheduleFrameDownloads();
236 236
237 237
238 238
239 BroadcastMessage(OrthancStone::DicomVolumeImage::GeometryReadyMessage(*volume_)); 239 BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_));
240 } 240 }
241 241
242 242
243 ORTHANC_FORCE_INLINE 243 ORTHANC_FORCE_INLINE
244 static void CopyPixel(uint32_t& target, const void* source) 244 static void CopyPixel(uint32_t& target, const void* source)
265 265
266 template <typename T> 266 template <typename T>
267 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution( 267 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution(
268 const std::string& pixelData, std::map<T,uint64_t>& distribution) 268 const std::string& pixelData, std::map<T,uint64_t>& distribution)
269 { 269 {
270 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); 270 ImageBuffer3D& target = volume_->GetPixelData();
271 271
272 const unsigned int bpp = target.GetBytesPerPixel(); 272 const unsigned int bpp = target.GetBytesPerPixel();
273 const unsigned int width = target.GetWidth(); 273 const unsigned int width = target.GetWidth();
274 const unsigned int height = target.GetHeight(); 274 const unsigned int height = target.GetHeight();
275 const unsigned int depth = target.GetDepth(); 275 const unsigned int depth = target.GetDepth();
307 { 307 {
308 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); 308 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
309 309
310 for (unsigned int z = 0; z < depth; z++) 310 for (unsigned int z = 0; z < depth; z++)
311 { 311 {
312 OrthancStone::ImageBuffer3D::SliceWriter writer(target, OrthancStone::VolumeProjection_Axial, z); 312 ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z);
313 313
314 assert(writer.GetAccessor().GetWidth() == width && 314 assert(writer.GetAccessor().GetWidth() == width &&
315 writer.GetAccessor().GetHeight() == height); 315 writer.GetAccessor().GetHeight() == height);
316 #if 0 316 #if 0
317 for (unsigned int y = 0; y < height; y++) 317 for (unsigned int y = 0; y < height; y++)
364 { 364 {
365 LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty."; 365 LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty.";
366 } 366 }
367 else 367 else
368 { 368 {
369 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); 369 ImageBuffer3D& target = volume_->GetPixelData();
370 370
371 const uint64_t width = target.GetWidth(); 371 const uint64_t width = target.GetWidth();
372 const uint64_t height = target.GetHeight(); 372 const uint64_t height = target.GetHeight();
373 const uint64_t depth = target.GetDepth(); 373 const uint64_t depth = target.GetDepth();
374 const uint64_t voxelCount = width * height * depth; 374 const uint64_t voxelCount = width * height * depth;
515 } 515 }
516 516
517 volume_->IncrementRevision(); 517 volume_->IncrementRevision();
518 518
519 pixelDataLoaded_ = true; 519 pixelDataLoaded_ = true;
520 BroadcastMessage(OrthancStone::DicomVolumeImage::ContentUpdatedMessage(*volume_)); 520 BroadcastMessage(DicomVolumeImage::ContentUpdatedMessage(*volume_));
521 } 521 }
522 522
523 bool OrthancMultiframeVolumeLoader::HasGeometry() const 523 bool OrthancMultiframeVolumeLoader::HasGeometry() const
524 { 524 {
525 return volume_->HasGeometry(); 525 return volume_->HasGeometry();
526 } 526 }
527 527
528 const OrthancStone::VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const 528 const VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const
529 { 529 {
530 return volume_->GetGeometry(); 530 return volume_->GetGeometry();
531 } 531 }
532 532
533 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader( 533 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader(
534 OrthancStone::ILoadersContext& loadersContext, 534 ILoadersContext& loadersContext,
535 boost::shared_ptr<OrthancStone::DicomVolumeImage> volume, 535 boost::shared_ptr<DicomVolumeImage> volume,
536 float outliersHalfRejectionRate) 536 float outliersHalfRejectionRate)
537 : LoaderStateMachine(loadersContext) 537 : LoaderStateMachine(loadersContext)
538 , volume_(volume) 538 , volume_(volume)
539 , pixelDataLoaded_(false) 539 , pixelDataLoaded_(false)
540 , outliersHalfRejectionRate_(outliersHalfRejectionRate) 540 , outliersHalfRejectionRate_(outliersHalfRejectionRate)
550 } 550 }
551 551
552 552
553 boost::shared_ptr<OrthancMultiframeVolumeLoader> 553 boost::shared_ptr<OrthancMultiframeVolumeLoader>
554 OrthancMultiframeVolumeLoader::Create( 554 OrthancMultiframeVolumeLoader::Create(
555 OrthancStone::ILoadersContext& loadersContext, 555 ILoadersContext& loadersContext,
556 boost::shared_ptr<OrthancStone::DicomVolumeImage> volume, 556 boost::shared_ptr<DicomVolumeImage> volume,
557 float outliersHalfRejectionRate /*= 0.0005*/) 557 float outliersHalfRejectionRate /*= 0.0005*/)
558 { 558 {
559 boost::shared_ptr<OrthancMultiframeVolumeLoader> obj( 559 boost::shared_ptr<OrthancMultiframeVolumeLoader> obj(
560 new OrthancMultiframeVolumeLoader( 560 new OrthancMultiframeVolumeLoader(
561 loadersContext, 561 loadersContext,
597 Start(); 597 Start();
598 598
599 instanceId_ = instanceId; 599 instanceId_ = instanceId;
600 600
601 { 601 {
602 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); 602 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
603 command->SetHttpHeader("Accept-Encoding", "gzip"); 603 command->SetHttpHeader("Accept-Encoding", "gzip");
604 command->SetUri("/instances/" + instanceId + "/tags"); 604 command->SetUri("/instances/" + instanceId + "/tags");
605 command->AcquirePayload(new LoadGeometry(*this)); 605 command->AcquirePayload(new LoadGeometry(*this));
606 Schedule(command.release()); 606 Schedule(command.release());
607 } 607 }
608 608
609 { 609 {
610 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); 610 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
611 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax"); 611 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax");
612 command->AcquirePayload(new LoadTransferSyntax(*this)); 612 command->AcquirePayload(new LoadTransferSyntax(*this));
613 Schedule(command.release()); 613 Schedule(command.release());
614 } 614 }
615 } 615 }