Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/OrthancSeriesLoader.cpp @ 32:517c46f527cd
sync
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 19 Dec 2016 11:00:23 +0100 |
| parents | 9aace933cb64 |
| children | 6465fbd23bce |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 #include "OrthancSeriesLoader.h" | |
| 34 | |
| 35 #include "../Messaging/MessagingToolbox.h" | |
| 16 | 36 #include "../../Resources/Orthanc/Core/Images/Image.h" |
| 37 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h" | |
| 38 #include "../../Resources/Orthanc/Core/Logging.h" | |
| 39 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
| 32 | 40 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
| 0 | 41 #include "DicomFrameConverter.h" |
| 42 | |
| 43 namespace OrthancStone | |
| 44 { | |
| 45 class OrthancSeriesLoader::Slice : public boost::noncopyable | |
| 46 { | |
| 47 private: | |
| 48 std::string instanceId_; | |
| 49 SliceGeometry geometry_; | |
| 50 double projectionAlongNormal_; | |
| 51 | |
| 52 public: | |
| 53 Slice(const std::string& instanceId, | |
| 54 const std::string& imagePositionPatient, | |
| 55 const std::string& imageOrientationPatient) : | |
| 56 instanceId_(instanceId), | |
| 57 geometry_(imagePositionPatient, imageOrientationPatient) | |
| 58 { | |
| 59 } | |
| 60 | |
| 61 const std::string GetInstanceId() const | |
| 62 { | |
| 63 return instanceId_; | |
| 64 } | |
| 65 | |
| 66 const SliceGeometry& GetGeometry() const | |
| 67 { | |
| 68 return geometry_; | |
| 69 } | |
| 70 | |
| 71 void SetNormal(const Vector& normal) | |
| 72 { | |
| 73 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); | |
| 74 } | |
| 75 | |
| 76 double GetProjectionAlongNormal() const | |
| 77 { | |
| 78 return projectionAlongNormal_; | |
| 79 } | |
| 80 }; | |
| 81 | |
| 82 | |
| 83 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable | |
| 84 { | |
| 85 private: | |
| 86 std::vector<Slice*> slices_; | |
| 87 | |
| 88 struct Comparator | |
| 89 { | |
| 90 bool operator() (const Slice* const a, | |
| 91 const Slice* const b) const | |
| 92 { | |
| 93 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal(); | |
| 94 } | |
| 95 }; | |
| 96 | |
| 97 public: | |
| 98 ~SetOfSlices() | |
| 99 { | |
| 100 for (size_t i = 0; i < slices_.size(); i++) | |
| 101 { | |
| 102 assert(slices_[i] != NULL); | |
| 103 delete slices_[i]; | |
| 104 } | |
| 105 } | |
| 106 | |
| 107 void Reserve(size_t size) | |
| 108 { | |
| 109 slices_.reserve(size); | |
| 110 } | |
| 111 | |
| 112 void AddSlice(const std::string& instanceId, | |
| 113 const std::string& imagePositionPatient, | |
| 114 const std::string& imageOrientationPatient) | |
| 115 { | |
| 116 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient)); | |
| 117 } | |
| 118 | |
| 119 size_t GetSliceCount() const | |
| 120 { | |
| 121 return slices_.size(); | |
| 122 } | |
| 123 | |
| 124 const Slice& GetSlice(size_t index) const | |
| 125 { | |
| 126 assert(slices_[index] != NULL); | |
| 127 return *slices_[index]; | |
| 128 } | |
| 129 | |
| 130 void Sort(const Vector& normal) | |
| 131 { | |
| 132 for (size_t i = 0; i < slices_.size(); i++) | |
| 133 { | |
| 134 slices_[i]->SetNormal(normal); | |
| 135 } | |
| 136 | |
| 137 Comparator comparator; | |
| 138 std::sort(slices_.begin(), slices_.end(), comparator); | |
| 139 } | |
| 140 | |
|
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
141 void LoadSeriesFast(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 142 const std::string& series) |
| 143 { | |
| 144 // Retrieve the orientation of this series | |
| 145 Json::Value info; | |
| 146 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series); | |
| 147 | |
| 148 if (info.type() != Json::objectValue || | |
| 149 !info.isMember("MainDicomTags") || | |
| 150 info["MainDicomTags"].type() != Json::objectValue || | |
| 151 !info["MainDicomTags"].isMember("ImageOrientationPatient") || | |
| 152 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue) | |
| 153 { | |
| 154 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 155 } | |
| 156 | |
| 157 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString(); | |
| 158 | |
| 159 | |
| 160 // Retrieve the Orthanc ID of all the instances of this series | |
| 161 Json::Value instances; | |
| 162 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances"); | |
| 163 | |
| 164 if (instances.type() != Json::arrayValue) | |
| 165 { | |
| 166 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 167 } | |
| 168 | |
| 169 if (instances.size() == 0) | |
| 170 { | |
| 171 LOG(ERROR) << "This series is empty"; | |
| 172 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 173 } | |
| 174 | |
| 175 | |
| 176 // Retrieve the DICOM tags of all the instances | |
| 177 std::vector<std::string> instancesId; | |
| 178 | |
| 179 instancesId.resize(instances.size()); | |
| 180 Reserve(instances.size()); | |
| 181 | |
| 182 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 183 { | |
| 184 if (instances[i].type() != Json::objectValue || | |
| 185 !instances[i].isMember("ID") || | |
| 186 !instances[i].isMember("MainDicomTags") || | |
| 187 instances[i]["ID"].type() != Json::stringValue || | |
| 188 instances[i]["MainDicomTags"].type() != Json::objectValue || | |
| 189 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") || | |
| 190 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue) | |
| 191 { | |
| 192 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 193 } | |
| 194 else | |
| 195 { | |
| 196 instancesId[i] = instances[i]["ID"].asString(); | |
| 197 AddSlice(instancesId[i], | |
| 198 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(), | |
| 199 imageOrientationPatient); | |
| 200 } | |
| 201 } | |
| 202 | |
| 203 assert(GetSliceCount() == instances.size()); | |
| 204 } | |
| 205 | |
| 206 | |
|
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
207 void LoadSeriesSafe(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 208 const std::string& seriesId) |
| 209 { | |
| 210 Json::Value series; | |
| 211 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify"); | |
| 212 | |
| 213 if (series.type() != Json::objectValue) | |
| 214 { | |
| 215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 216 } | |
| 217 | |
| 218 if (series.size() == 0) | |
| 219 { | |
| 220 LOG(ERROR) << "This series is empty"; | |
| 221 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 222 } | |
| 223 | |
| 224 Json::Value::Members instances = series.getMemberNames(); | |
| 225 | |
| 226 Reserve(instances.size()); | |
| 227 | |
| 228 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 229 { | |
| 230 const Json::Value& tags = series[instances[i]]; | |
| 231 | |
| 232 if (tags.type() != Json::objectValue || | |
| 233 !tags.isMember("ImagePositionPatient") || | |
| 234 !tags.isMember("ImageOrientationPatient") || | |
| 235 tags["ImagePositionPatient"].type() != Json::stringValue || | |
| 236 tags["ImageOrientationPatient"].type() != Json::stringValue) | |
| 237 { | |
| 238 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 239 } | |
| 240 else | |
| 241 { | |
| 242 AddSlice(instances[i], | |
| 243 tags["ImagePositionPatient"].asString(), | |
| 244 tags["ImageOrientationPatient"].asString()); | |
| 245 } | |
| 246 } | |
| 247 | |
| 248 assert(GetSliceCount() == instances.size()); | |
| 249 } | |
| 250 | |
| 251 | |
| 252 void SelectNormal(Vector& normal) const | |
| 253 { | |
| 254 std::vector<Vector> normalCandidates; | |
| 255 std::vector<unsigned int> normalCount; | |
| 256 | |
| 257 bool found = false; | |
| 258 | |
| 259 for (size_t i = 0; !found && i < GetSliceCount(); i++) | |
| 260 { | |
| 261 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
| 262 | |
| 263 bool add = true; | |
| 264 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
| 265 { | |
| 266 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
| 267 { | |
| 268 normalCount[j] += 1; | |
| 269 add = false; | |
| 270 } | |
| 271 } | |
| 272 | |
| 273 if (add) | |
| 274 { | |
| 275 if (normalCount.size() > 2) | |
| 276 { | |
| 277 // To get linear-time complexity in (*). This heuristics | |
| 278 // allows the series to have one single frame that is | |
| 279 // not parallel to the others (such a frame could be a | |
| 280 // generated preview) | |
| 281 found = false; | |
| 282 } | |
| 283 else | |
| 284 { | |
| 285 normalCandidates.push_back(normal); | |
| 286 normalCount.push_back(1); | |
| 287 } | |
| 288 } | |
| 289 } | |
| 290 | |
| 291 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
| 292 { | |
| 293 unsigned int count = normalCount[i]; | |
| 294 if (count == GetSliceCount() || | |
| 295 count + 1 == GetSliceCount()) | |
| 296 { | |
| 297 normal = normalCandidates[i]; | |
| 298 found = true; | |
| 299 } | |
| 300 } | |
| 301 | |
| 302 if (!found) | |
| 303 { | |
| 304 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series"; | |
| 305 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 306 } | |
| 307 } | |
| 308 | |
| 309 | |
| 310 void FilterNormal(const Vector& normal) | |
| 311 { | |
| 312 size_t pos = 0; | |
| 313 | |
| 314 for (size_t i = 0; i < slices_.size(); i++) | |
| 315 { | |
| 316 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) | |
| 317 { | |
| 318 // This slice is compatible with the selected normal | |
| 319 slices_[pos] = slices_[i]; | |
| 320 pos += 1; | |
| 321 } | |
| 322 else | |
| 323 { | |
| 324 delete slices_[i]; | |
| 325 slices_[i] = NULL; | |
| 326 } | |
| 327 } | |
| 328 | |
| 329 slices_.resize(pos); | |
| 330 } | |
| 331 }; | |
| 332 | |
| 333 | |
| 334 | |
|
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
335 OrthancSeriesLoader::OrthancSeriesLoader(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 336 const std::string& series) : |
| 337 orthanc_(orthanc), | |
| 338 slices_(new SetOfSlices) | |
| 339 { | |
| 340 /** | |
| 341 * The function "LoadSeriesFast()" might now behave properly if | |
| 342 * some slice has some outsider value for its normal, which | |
| 343 * happens sometimes on reprojected series (e.g. coronal and | |
| 344 * sagittal of Delphine). Don't use it. | |
| 345 **/ | |
| 346 | |
| 347 slices_->LoadSeriesSafe(orthanc, series); | |
| 348 | |
| 349 Vector normal; | |
| 350 slices_->SelectNormal(normal); | |
| 351 slices_->FilterNormal(normal); | |
| 352 slices_->Sort(normal); | |
| 353 | |
| 354 if (slices_->GetSliceCount() == 0) // Sanity check | |
| 355 { | |
| 356 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 357 } | |
| 358 | |
| 359 for (size_t i = 0; i < slices_->GetSliceCount(); i++) | |
| 360 { | |
| 361 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal())); | |
| 362 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry()); | |
| 363 } | |
| 364 | |
| 32 | 365 std::string uri = "/instances/" + slices_->GetSlice(0).GetInstanceId() + "/tags"; |
| 366 | |
| 367 OrthancPlugins::FullOrthancDataset dataset(orthanc_, uri); | |
| 368 OrthancPlugins::DicomDatasetReader reader(dataset); | |
| 369 | |
| 370 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) || | |
| 371 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS)) | |
| 0 | 372 { |
| 373 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
| 374 } | |
| 375 | |
| 376 DicomFrameConverter converter; | |
| 32 | 377 converter.ReadParameters(dataset); |
| 0 | 378 format_ = converter.GetExpectedPixelFormat(); |
| 379 } | |
| 380 | |
| 381 | |
| 32 | 382 OrthancPlugins::IDicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index) |
| 0 | 383 { |
| 32 | 384 std::string uri = "/instances/" + slices_->GetSlice(index).GetInstanceId() + "/tags"; |
| 0 | 385 |
| 32 | 386 std::auto_ptr<OrthancPlugins::IDicomDataset> dataset(new OrthancPlugins::FullOrthancDataset(orthanc_, uri)); |
| 387 OrthancPlugins::DicomDatasetReader reader(*dataset); | |
| 388 | |
| 389 unsigned int frames; | |
| 390 if (reader.GetUnsignedIntegerValue(frames, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES) && | |
| 391 frames != 1) | |
| 0 | 392 { |
| 393 LOG(ERROR) << "One instance in this series has more than 1 frame"; | |
| 394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 395 } | |
| 396 | |
| 397 return dataset.release(); | |
| 398 } | |
| 399 | |
| 400 | |
| 401 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const | |
| 402 { | |
| 403 if (frame.GetFormat() != format_ || | |
| 404 frame.GetWidth() != width_ || | |
| 405 frame.GetHeight() != height_) | |
| 406 { | |
| 407 LOG(ERROR) << "The parameters of this series vary accross its slices"; | |
| 408 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 409 } | |
| 410 } | |
| 411 | |
| 412 | |
| 413 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index) | |
| 414 { | |
| 415 const Slice& slice = slices_->GetSlice(index); | |
| 416 | |
| 417 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 418 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_)); | |
| 419 | |
| 420 if (frame.get() != NULL) | |
| 421 { | |
| 422 CheckFrame(*frame); | |
| 423 } | |
| 424 | |
| 425 return frame.release(); | |
| 426 } | |
| 427 | |
| 428 | |
| 429 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index, | |
| 430 unsigned int quality) | |
| 431 { | |
| 432 const Slice& slice = slices_->GetSlice(index); | |
| 433 | |
| 434 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 435 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_)); | |
| 436 | |
| 437 if (frame.get() != NULL) | |
| 438 { | |
| 439 CheckFrame(*frame); | |
| 440 } | |
| 441 | |
| 442 return frame.release(); | |
| 443 } | |
| 444 | |
| 445 | |
| 446 bool OrthancSeriesLoader::IsJpegAvailable() | |
| 447 { | |
| 448 return MessagingToolbox::HasWebViewerInstalled(orthanc_); | |
| 449 } | |
| 450 } |