Mercurial > hg > orthanc-stone
annotate Framework/Volumes/VolumeImage.cpp @ 43:e4acd5f331f3
fix
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 14 Apr 2017 12:24:01 +0200 |
| parents | 7207a407bcd8 |
| children | 28956ed68280 |
| rev | line source |
|---|---|
| 0 | 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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7207a407bcd8
shared copyright with osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
5 * Copyright (C) 2017 Osimis, Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * In addition, as a special exception, the copyright holders of this | |
| 13 * program give permission to link the code of its release with the | |
| 14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 15 * that use the same license as the "OpenSSL" library), and distribute | |
| 16 * the linked executables. You must obey the GNU General Public License | |
| 17 * in all respects for all of the code used other than "OpenSSL". If you | |
| 18 * modify file(s) with this exception, you may extend this exception to | |
| 19 * your version of the file(s), but you are not obligated to do so. If | |
| 20 * you do not wish to do so, delete this exception statement from your | |
| 21 * version. If you delete this exception statement from all source files | |
| 22 * in the program, then also delete it here. | |
| 23 * | |
| 24 * This program is distributed in the hope that it will be useful, but | |
| 25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 27 * General Public License for more details. | |
| 28 * | |
| 29 * You should have received a copy of the GNU General Public License | |
| 30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 31 **/ | |
| 32 | |
| 33 | |
| 34 #include "VolumeImage.h" | |
| 35 | |
| 16 | 36 #include "../../Resources/Orthanc/Core/Logging.h" |
| 0 | 37 #include "../Layers/FrameRenderer.h" |
| 38 | |
| 39 namespace OrthancStone | |
| 40 { | |
| 41 void VolumeImage::StoreUpdateTime() | |
| 42 { | |
| 43 lastUpdate_ = MessagingToolbox::Timestamp(); | |
| 44 } | |
| 45 | |
| 46 | |
| 47 void VolumeImage::NotifyChange(bool force) | |
| 48 { | |
| 49 bool go = false; | |
| 50 | |
| 51 if (force) | |
| 52 { | |
| 53 go = true; | |
| 54 } | |
| 55 else | |
| 56 { | |
| 57 // Don't notify the observers more than 5 times per second | |
| 58 MessagingToolbox::Timestamp now; | |
| 59 go = (now.GetMillisecondsSince(lastUpdate_) > 200); | |
| 60 } | |
| 61 | |
| 62 if (go) | |
| 63 { | |
| 64 StoreUpdateTime(); | |
| 65 observers_.NotifyChange(this); | |
| 66 } | |
| 67 } | |
| 68 | |
| 69 | |
| 70 void VolumeImage::LoadThread(VolumeImage* that) | |
| 71 { | |
| 72 while (that->continue_) | |
| 73 { | |
| 74 bool complete = false; | |
| 75 bool done = that->policy_->DownloadStep(complete); | |
| 76 | |
| 77 if (complete) | |
| 78 { | |
| 79 that->loadingComplete_ = true; | |
| 80 } | |
| 81 | |
| 82 if (done) | |
| 83 { | |
| 84 break; | |
| 85 } | |
| 86 else | |
| 87 { | |
| 88 that->NotifyChange(false); | |
| 89 } | |
| 90 } | |
| 91 | |
| 92 that->NotifyChange(true); | |
| 93 } | |
| 94 | |
| 95 | |
| 96 VolumeImage::VolumeImage(ISeriesLoader* loader) : // Takes ownership | |
| 97 loader_(loader), | |
| 98 threads_(1), | |
| 99 started_(false), | |
| 100 continue_(false), | |
| 101 loadingComplete_(false) | |
| 102 { | |
| 103 if (loader == NULL) | |
| 104 { | |
| 105 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 106 } | |
| 107 | |
| 108 const size_t depth = loader_->GetGeometry().GetSliceCount(); | |
| 109 | |
| 110 if (depth < 2) | |
| 111 { | |
| 112 // Empty or flat series | |
| 113 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 114 } | |
| 115 | |
| 116 // TODO Check pixel spacing, slice thickness, and windowing are | |
| 117 // constant across slices | |
| 118 referenceDataset_.reset(loader->DownloadDicom(0)); | |
| 119 | |
| 120 double spacingZ; | |
| 121 | |
| 122 { | |
| 123 // Project the origin of the first and last slices onto the normal | |
| 124 const SliceGeometry& s1 = loader_->GetGeometry().GetSlice(0); | |
| 125 const SliceGeometry& s2 = loader_->GetGeometry().GetSlice(depth - 1); | |
| 126 const Vector& normal = loader_->GetGeometry().GetNormal(); | |
| 127 | |
| 128 double p1 = boost::numeric::ublas::inner_prod(s1.GetOrigin(), normal); | |
| 129 double p2 = boost::numeric::ublas::inner_prod(s2.GetOrigin(), normal); | |
| 130 | |
| 131 spacingZ = fabs(p2 - p1) / static_cast<double>(depth); | |
| 132 | |
| 133 // TODO Check that all slices are evenly distributed | |
| 134 } | |
| 135 | |
| 136 buffer_.reset(new ImageBuffer3D(loader_->GetPixelFormat(), | |
| 137 loader_->GetWidth(), | |
| 138 loader_->GetHeight(), | |
| 139 depth)); | |
| 140 buffer_->Clear(); | |
| 141 buffer_->SetAxialGeometry(loader_->GetGeometry().GetSlice(0)); | |
| 142 | |
| 143 double spacingX, spacingY; | |
| 32 | 144 GeometryToolbox::GetPixelSpacing(spacingX, spacingY, *referenceDataset_); |
| 0 | 145 buffer_->SetVoxelDimensions(spacingX, spacingY, spacingZ); |
| 146 | |
| 147 // These 3 values are only used to speed up the LayerFactory | |
| 148 axialGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Axial)); | |
| 149 coronalGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Coronal)); | |
| 150 sagittalGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Sagittal)); | |
| 151 } | |
| 152 | |
| 153 | |
| 154 VolumeImage::~VolumeImage() | |
| 155 { | |
| 156 Stop(); | |
| 157 | |
| 158 for (size_t i = 0; i < threads_.size(); i++) | |
| 159 { | |
| 160 if (threads_[i] != NULL) | |
| 161 { | |
| 162 delete threads_[i]; | |
| 163 } | |
| 164 } | |
| 165 } | |
| 166 | |
| 167 | |
| 168 void VolumeImage::SetDownloadPolicy(IDownloadPolicy* policy) // Takes ownership | |
| 169 { | |
| 170 if (started_) | |
| 171 { | |
| 172 LOG(ERROR) << "Cannot change the number of threads after a call to Start()"; | |
| 173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
| 174 } | |
| 175 | |
| 176 policy_.reset(policy); | |
| 177 } | |
| 178 | |
| 179 | |
| 180 void VolumeImage::SetThreadCount(size_t count) | |
| 181 { | |
| 182 if (started_) | |
| 183 { | |
| 184 LOG(ERROR) << "Cannot change the number of threads after a call to Start()"; | |
| 185 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
| 186 } | |
| 187 | |
| 188 if (count <= 0) | |
| 189 { | |
| 190 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 191 } | |
| 192 | |
| 193 threads_.resize(count); | |
| 194 } | |
| 195 | |
| 196 | |
| 197 void VolumeImage::Register(IChangeObserver& observer) | |
| 198 { | |
| 199 observers_.Register(observer); | |
| 200 } | |
| 201 | |
| 202 | |
| 203 void VolumeImage::Unregister(IChangeObserver& observer) | |
| 204 { | |
| 205 observers_.Unregister(observer); | |
| 206 } | |
| 207 | |
| 208 | |
| 209 void VolumeImage::Start() | |
| 210 { | |
| 211 if (started_) | |
| 212 { | |
| 213 LOG(ERROR) << "Cannot call Start() twice"; | |
| 214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
| 215 } | |
| 216 | |
| 217 started_ = true; | |
| 218 StoreUpdateTime(); | |
| 219 | |
| 220 if (policy_.get() != NULL && | |
| 221 threads_.size() > 0) | |
| 222 { | |
| 223 continue_ = true; | |
| 224 policy_->Initialize(*buffer_, *loader_); | |
| 225 | |
| 226 for (size_t i = 0; i < threads_.size(); i++) | |
| 227 { | |
| 228 assert(threads_[i] == NULL); | |
| 229 threads_[i] = new boost::thread(LoadThread, this); | |
| 230 } | |
| 231 } | |
| 232 } | |
| 233 | |
| 234 | |
| 235 void VolumeImage::Stop() | |
| 236 { | |
| 237 if (!started_) | |
| 238 { | |
| 239 LOG(ERROR) << "Cannot call Stop() without calling Start() beforehand"; | |
| 240 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
| 241 } | |
| 242 | |
| 243 if (continue_) | |
| 244 { | |
| 245 continue_ = false; | |
| 246 | |
| 247 for (size_t i = 0; i < threads_.size(); i++) | |
| 248 { | |
| 249 if (threads_[i]->joinable()) | |
| 250 { | |
| 251 threads_[i]->join(); | |
| 252 } | |
| 253 } | |
| 254 | |
| 255 assert(policy_.get() != NULL); | |
| 256 policy_->Finalize(); | |
| 257 } | |
| 258 } | |
| 259 | |
| 260 | |
| 261 ParallelSlices* VolumeImage::GetGeometry(VolumeProjection projection, | |
| 262 bool reverse) | |
| 263 { | |
| 264 std::auto_ptr<ParallelSlices> slices(buffer_->GetGeometry(projection)); | |
| 265 | |
| 266 if (reverse) | |
| 267 { | |
| 268 return slices->Reverse(); | |
| 269 } | |
| 270 else | |
| 271 { | |
| 272 return slices.release(); | |
| 273 } | |
| 274 } | |
| 275 | |
| 276 | |
| 277 bool VolumeImage::DetectProjection(VolumeProjection& projection, | |
| 278 bool& reverse, | |
| 279 const SliceGeometry& viewportSlice) | |
| 280 { | |
| 281 if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), axialGeometry_->GetNormal())) | |
| 282 { | |
| 283 projection = VolumeProjection_Axial; | |
| 284 return true; | |
| 285 } | |
| 286 else if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), sagittalGeometry_->GetNormal())) | |
| 287 { | |
| 288 projection = VolumeProjection_Sagittal; | |
| 289 return true; | |
| 290 } | |
| 291 else if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), coronalGeometry_->GetNormal())) | |
| 292 { | |
| 293 projection = VolumeProjection_Coronal; | |
| 294 return true; | |
| 295 } | |
| 296 else | |
| 297 { | |
| 298 return false; | |
| 299 } | |
| 300 } | |
| 301 | |
| 302 | |
| 303 const ParallelSlices& VolumeImage::GetGeometryInternal(VolumeProjection projection) | |
| 304 { | |
| 305 switch (projection) | |
| 306 { | |
| 307 case VolumeProjection_Axial: | |
| 308 return *axialGeometry_; | |
| 309 | |
| 310 case VolumeProjection_Sagittal: | |
| 311 return *sagittalGeometry_; | |
| 312 | |
| 313 case VolumeProjection_Coronal: | |
| 314 return *coronalGeometry_; | |
| 315 | |
| 316 default: | |
| 317 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 318 } | |
| 319 } | |
| 320 | |
| 321 | |
| 322 bool VolumeImage::LayerFactory::GetExtent(double& x1, | |
| 323 double& y1, | |
| 324 double& x2, | |
| 325 double& y2, | |
| 326 const SliceGeometry& viewportSlice) | |
| 327 { | |
| 328 VolumeProjection projection; | |
| 329 bool reverse; | |
| 330 | |
| 331 if (that_.buffer_->GetWidth() == 0 || | |
| 332 that_.buffer_->GetHeight() == 0 || | |
| 333 that_.buffer_->GetDepth() == 0 || | |
| 334 !that_.DetectProjection(projection, reverse, viewportSlice)) | |
| 335 { | |
| 336 return false; | |
| 337 } | |
| 338 else | |
| 339 { | |
| 340 Vector spacing = that_.GetVoxelDimensions(projection); | |
| 341 | |
| 342 unsigned int width, height; | |
| 343 that_.buffer_->GetSliceSize(width, height, projection); | |
| 344 | |
| 345 // As the slices of the volumic image are arranged in a box, | |
| 346 // we only consider one single reference slice (the one with index 0). | |
| 347 const SliceGeometry& volumeSlice = that_.GetGeometryInternal(projection).GetSlice(0); | |
| 348 | |
| 349 return FrameRenderer::ComputeFrameExtent(x1, y1, x2, y2, | |
| 350 viewportSlice, volumeSlice, | |
| 351 width, height, | |
| 352 spacing[0], spacing[1]); | |
| 353 } | |
| 354 } | |
| 355 | |
| 356 | |
| 357 ILayerRenderer* VolumeImage::LayerFactory::CreateLayerRenderer(const SliceGeometry& viewportSlice) | |
| 358 { | |
| 359 VolumeProjection projection; | |
| 360 bool reverse; | |
| 361 | |
| 362 if (that_.buffer_->GetWidth() == 0 || | |
| 363 that_.buffer_->GetHeight() == 0 || | |
| 364 that_.buffer_->GetDepth() == 0 || | |
| 365 !that_.DetectProjection(projection, reverse, viewportSlice)) | |
| 366 { | |
| 367 return NULL; | |
| 368 } | |
| 369 | |
| 370 const ParallelSlices& geometry = that_.GetGeometryInternal(projection); | |
| 371 | |
| 372 size_t closest; | |
| 373 double distance; | |
| 374 | |
| 375 const Vector spacing = that_.GetVoxelDimensions(projection); | |
| 376 const double sliceThickness = spacing[2]; | |
| 377 | |
| 378 if (geometry.ComputeClosestSlice(closest, distance, viewportSlice.GetOrigin()) && | |
| 379 distance <= sliceThickness / 2.0) | |
| 380 { | |
| 381 bool isFullQuality; | |
| 382 | |
| 383 if (projection == VolumeProjection_Axial && | |
| 384 that_.policy_.get() != NULL) | |
| 385 { | |
| 386 isFullQuality = that_.policy_->IsFullQualityAxial(closest); | |
| 387 } | |
| 388 else | |
| 389 { | |
| 390 isFullQuality = that_.IsLoadingComplete(); | |
| 391 } | |
| 392 | |
| 393 std::auto_ptr<Orthanc::Image> frame; | |
| 394 SliceGeometry frameSlice = geometry.GetSlice(closest); | |
| 395 | |
| 396 { | |
| 397 ImageBuffer3D::SliceReader reader(*that_.buffer_, projection, closest); | |
| 398 frame.reset(Orthanc::Image::Clone(reader.GetAccessor())); | |
| 399 } | |
| 400 | |
| 401 return FrameRenderer::CreateRenderer(frame.release(), | |
| 402 viewportSlice, | |
| 403 frameSlice, | |
| 404 *that_.referenceDataset_, | |
| 405 spacing[0], spacing[1], | |
| 406 isFullQuality); | |
| 407 } | |
| 408 else | |
| 409 { | |
| 410 return NULL; | |
| 411 } | |
| 412 } | |
| 413 } |