Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/OrthancSeriesLoader.cpp @ 47:28956ed68280
agpl license
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 27 Apr 2017 11:00:15 +0200 |
| parents | 7207a407bcd8 |
| children | acb60cbb8301 4cff7b1ed31d |
| 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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5 * Copyright (C) 2017 Osimis, Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 47 | 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. | |
| 0 | 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 | |
| 47 | 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 | |
| 0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "OrthancSeriesLoader.h" | |
| 23 | |
| 35 | 24 #include "../Toolbox/MessagingToolbox.h" |
| 16 | 25 #include "../../Resources/Orthanc/Core/Images/Image.h" |
| 26 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h" | |
| 27 #include "../../Resources/Orthanc/Core/Logging.h" | |
| 28 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
| 32 | 29 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
| 0 | 30 #include "DicomFrameConverter.h" |
| 31 | |
| 32 namespace OrthancStone | |
| 33 { | |
| 34 class OrthancSeriesLoader::Slice : public boost::noncopyable | |
| 35 { | |
| 36 private: | |
| 37 std::string instanceId_; | |
| 38 SliceGeometry geometry_; | |
| 39 double projectionAlongNormal_; | |
| 40 | |
| 41 public: | |
| 42 Slice(const std::string& instanceId, | |
| 43 const std::string& imagePositionPatient, | |
| 44 const std::string& imageOrientationPatient) : | |
| 45 instanceId_(instanceId), | |
| 46 geometry_(imagePositionPatient, imageOrientationPatient) | |
| 47 { | |
| 48 } | |
| 49 | |
| 50 const std::string GetInstanceId() const | |
| 51 { | |
| 52 return instanceId_; | |
| 53 } | |
| 54 | |
| 55 const SliceGeometry& GetGeometry() const | |
| 56 { | |
| 57 return geometry_; | |
| 58 } | |
| 59 | |
| 60 void SetNormal(const Vector& normal) | |
| 61 { | |
| 62 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); | |
| 63 } | |
| 64 | |
| 65 double GetProjectionAlongNormal() const | |
| 66 { | |
| 67 return projectionAlongNormal_; | |
| 68 } | |
| 69 }; | |
| 70 | |
| 71 | |
| 72 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable | |
| 73 { | |
| 74 private: | |
| 75 std::vector<Slice*> slices_; | |
| 76 | |
| 77 struct Comparator | |
| 78 { | |
| 79 bool operator() (const Slice* const a, | |
| 80 const Slice* const b) const | |
| 81 { | |
| 82 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal(); | |
| 83 } | |
| 84 }; | |
| 85 | |
| 86 public: | |
| 87 ~SetOfSlices() | |
| 88 { | |
| 89 for (size_t i = 0; i < slices_.size(); i++) | |
| 90 { | |
| 91 assert(slices_[i] != NULL); | |
| 92 delete slices_[i]; | |
| 93 } | |
| 94 } | |
| 95 | |
| 96 void Reserve(size_t size) | |
| 97 { | |
| 98 slices_.reserve(size); | |
| 99 } | |
| 100 | |
| 101 void AddSlice(const std::string& instanceId, | |
| 102 const std::string& imagePositionPatient, | |
| 103 const std::string& imageOrientationPatient) | |
| 104 { | |
| 105 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient)); | |
| 106 } | |
| 107 | |
| 108 size_t GetSliceCount() const | |
| 109 { | |
| 110 return slices_.size(); | |
| 111 } | |
| 112 | |
| 113 const Slice& GetSlice(size_t index) const | |
| 114 { | |
| 115 assert(slices_[index] != NULL); | |
| 116 return *slices_[index]; | |
| 117 } | |
| 118 | |
| 119 void Sort(const Vector& normal) | |
| 120 { | |
| 121 for (size_t i = 0; i < slices_.size(); i++) | |
| 122 { | |
| 123 slices_[i]->SetNormal(normal); | |
| 124 } | |
| 125 | |
| 126 Comparator comparator; | |
| 127 std::sort(slices_.begin(), slices_.end(), comparator); | |
| 128 } | |
| 129 | |
|
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130 void LoadSeriesFast(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 131 const std::string& series) |
| 132 { | |
| 133 // Retrieve the orientation of this series | |
| 134 Json::Value info; | |
| 135 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series); | |
| 136 | |
| 137 if (info.type() != Json::objectValue || | |
| 138 !info.isMember("MainDicomTags") || | |
| 139 info["MainDicomTags"].type() != Json::objectValue || | |
| 140 !info["MainDicomTags"].isMember("ImageOrientationPatient") || | |
| 141 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue) | |
| 142 { | |
| 143 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 144 } | |
| 145 | |
| 146 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString(); | |
| 147 | |
| 148 | |
| 149 // Retrieve the Orthanc ID of all the instances of this series | |
| 150 Json::Value instances; | |
| 151 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances"); | |
| 152 | |
| 153 if (instances.type() != Json::arrayValue) | |
| 154 { | |
| 155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 156 } | |
| 157 | |
| 158 if (instances.size() == 0) | |
| 159 { | |
| 160 LOG(ERROR) << "This series is empty"; | |
| 161 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 162 } | |
| 163 | |
| 164 | |
| 165 // Retrieve the DICOM tags of all the instances | |
| 166 std::vector<std::string> instancesId; | |
| 167 | |
| 168 instancesId.resize(instances.size()); | |
| 169 Reserve(instances.size()); | |
| 170 | |
| 171 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 172 { | |
| 173 if (instances[i].type() != Json::objectValue || | |
| 174 !instances[i].isMember("ID") || | |
| 175 !instances[i].isMember("MainDicomTags") || | |
| 176 instances[i]["ID"].type() != Json::stringValue || | |
| 177 instances[i]["MainDicomTags"].type() != Json::objectValue || | |
| 178 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") || | |
| 179 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue) | |
| 180 { | |
| 181 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 182 } | |
| 183 else | |
| 184 { | |
| 185 instancesId[i] = instances[i]["ID"].asString(); | |
| 186 AddSlice(instancesId[i], | |
| 187 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(), | |
| 188 imageOrientationPatient); | |
| 189 } | |
| 190 } | |
| 191 | |
| 192 assert(GetSliceCount() == instances.size()); | |
| 193 } | |
| 194 | |
| 195 | |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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196 void LoadSeriesSafe(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 197 const std::string& seriesId) |
| 198 { | |
| 199 Json::Value series; | |
| 200 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify"); | |
| 201 | |
| 202 if (series.type() != Json::objectValue) | |
| 203 { | |
| 204 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 205 } | |
| 206 | |
| 207 if (series.size() == 0) | |
| 208 { | |
| 209 LOG(ERROR) << "This series is empty"; | |
| 210 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 211 } | |
| 212 | |
| 213 Json::Value::Members instances = series.getMemberNames(); | |
| 214 | |
| 215 Reserve(instances.size()); | |
| 216 | |
| 217 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 218 { | |
| 219 const Json::Value& tags = series[instances[i]]; | |
| 220 | |
| 221 if (tags.type() != Json::objectValue || | |
| 222 !tags.isMember("ImagePositionPatient") || | |
| 223 !tags.isMember("ImageOrientationPatient") || | |
| 224 tags["ImagePositionPatient"].type() != Json::stringValue || | |
| 225 tags["ImageOrientationPatient"].type() != Json::stringValue) | |
| 226 { | |
| 227 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 228 } | |
| 229 else | |
| 230 { | |
| 231 AddSlice(instances[i], | |
| 232 tags["ImagePositionPatient"].asString(), | |
| 233 tags["ImageOrientationPatient"].asString()); | |
| 234 } | |
| 235 } | |
| 236 | |
| 237 assert(GetSliceCount() == instances.size()); | |
| 238 } | |
| 239 | |
| 240 | |
| 241 void SelectNormal(Vector& normal) const | |
| 242 { | |
| 243 std::vector<Vector> normalCandidates; | |
| 244 std::vector<unsigned int> normalCount; | |
| 245 | |
| 246 bool found = false; | |
| 247 | |
| 248 for (size_t i = 0; !found && i < GetSliceCount(); i++) | |
| 249 { | |
| 250 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
| 251 | |
| 252 bool add = true; | |
| 253 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
| 254 { | |
| 255 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
| 256 { | |
| 257 normalCount[j] += 1; | |
| 258 add = false; | |
| 259 } | |
| 260 } | |
| 261 | |
| 262 if (add) | |
| 263 { | |
| 264 if (normalCount.size() > 2) | |
| 265 { | |
| 266 // To get linear-time complexity in (*). This heuristics | |
| 267 // allows the series to have one single frame that is | |
| 268 // not parallel to the others (such a frame could be a | |
| 269 // generated preview) | |
| 270 found = false; | |
| 271 } | |
| 272 else | |
| 273 { | |
| 274 normalCandidates.push_back(normal); | |
| 275 normalCount.push_back(1); | |
| 276 } | |
| 277 } | |
| 278 } | |
| 279 | |
| 280 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
| 281 { | |
| 282 unsigned int count = normalCount[i]; | |
| 283 if (count == GetSliceCount() || | |
| 284 count + 1 == GetSliceCount()) | |
| 285 { | |
| 286 normal = normalCandidates[i]; | |
| 287 found = true; | |
| 288 } | |
| 289 } | |
| 290 | |
| 291 if (!found) | |
| 292 { | |
| 293 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series"; | |
| 294 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 295 } | |
| 296 } | |
| 297 | |
| 298 | |
| 299 void FilterNormal(const Vector& normal) | |
| 300 { | |
| 301 size_t pos = 0; | |
| 302 | |
| 303 for (size_t i = 0; i < slices_.size(); i++) | |
| 304 { | |
| 305 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) | |
| 306 { | |
| 307 // This slice is compatible with the selected normal | |
| 308 slices_[pos] = slices_[i]; | |
| 309 pos += 1; | |
| 310 } | |
| 311 else | |
| 312 { | |
| 313 delete slices_[i]; | |
| 314 slices_[i] = NULL; | |
| 315 } | |
| 316 } | |
| 317 | |
| 318 slices_.resize(pos); | |
| 319 } | |
| 320 }; | |
| 321 | |
| 322 | |
| 323 | |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
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324 OrthancSeriesLoader::OrthancSeriesLoader(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 325 const std::string& series) : |
| 326 orthanc_(orthanc), | |
| 327 slices_(new SetOfSlices) | |
| 328 { | |
| 329 /** | |
| 330 * The function "LoadSeriesFast()" might now behave properly if | |
| 331 * some slice has some outsider value for its normal, which | |
| 332 * happens sometimes on reprojected series (e.g. coronal and | |
| 333 * sagittal of Delphine). Don't use it. | |
| 334 **/ | |
| 335 | |
| 336 slices_->LoadSeriesSafe(orthanc, series); | |
| 337 | |
| 338 Vector normal; | |
| 339 slices_->SelectNormal(normal); | |
| 340 slices_->FilterNormal(normal); | |
| 341 slices_->Sort(normal); | |
| 342 | |
| 343 if (slices_->GetSliceCount() == 0) // Sanity check | |
| 344 { | |
| 345 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 346 } | |
| 347 | |
| 348 for (size_t i = 0; i < slices_->GetSliceCount(); i++) | |
| 349 { | |
| 350 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal())); | |
| 351 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry()); | |
| 352 } | |
| 353 | |
| 32 | 354 std::string uri = "/instances/" + slices_->GetSlice(0).GetInstanceId() + "/tags"; |
| 355 | |
| 356 OrthancPlugins::FullOrthancDataset dataset(orthanc_, uri); | |
| 357 OrthancPlugins::DicomDatasetReader reader(dataset); | |
| 358 | |
| 359 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) || | |
| 360 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS)) | |
| 0 | 361 { |
| 362 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
| 363 } | |
| 364 | |
| 365 DicomFrameConverter converter; | |
| 32 | 366 converter.ReadParameters(dataset); |
| 0 | 367 format_ = converter.GetExpectedPixelFormat(); |
| 368 } | |
| 369 | |
| 370 | |
| 32 | 371 OrthancPlugins::IDicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index) |
| 0 | 372 { |
| 32 | 373 std::string uri = "/instances/" + slices_->GetSlice(index).GetInstanceId() + "/tags"; |
| 0 | 374 |
| 32 | 375 std::auto_ptr<OrthancPlugins::IDicomDataset> dataset(new OrthancPlugins::FullOrthancDataset(orthanc_, uri)); |
| 376 OrthancPlugins::DicomDatasetReader reader(*dataset); | |
| 377 | |
| 378 unsigned int frames; | |
| 379 if (reader.GetUnsignedIntegerValue(frames, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES) && | |
| 380 frames != 1) | |
| 0 | 381 { |
| 382 LOG(ERROR) << "One instance in this series has more than 1 frame"; | |
| 383 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 384 } | |
| 385 | |
| 386 return dataset.release(); | |
| 387 } | |
| 388 | |
| 389 | |
| 390 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const | |
| 391 { | |
| 392 if (frame.GetFormat() != format_ || | |
| 393 frame.GetWidth() != width_ || | |
| 394 frame.GetHeight() != height_) | |
| 395 { | |
| 396 LOG(ERROR) << "The parameters of this series vary accross its slices"; | |
| 397 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 398 } | |
| 399 } | |
| 400 | |
| 401 | |
| 402 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index) | |
| 403 { | |
| 404 const Slice& slice = slices_->GetSlice(index); | |
| 405 | |
| 406 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 407 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_)); | |
| 408 | |
| 409 if (frame.get() != NULL) | |
| 410 { | |
| 411 CheckFrame(*frame); | |
| 412 } | |
| 413 | |
| 414 return frame.release(); | |
| 415 } | |
| 416 | |
| 417 | |
| 418 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index, | |
| 419 unsigned int quality) | |
| 420 { | |
| 421 const Slice& slice = slices_->GetSlice(index); | |
| 422 | |
| 423 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 424 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_)); | |
| 425 | |
| 426 if (frame.get() != NULL) | |
| 427 { | |
| 428 CheckFrame(*frame); | |
| 429 } | |
| 430 | |
| 431 return frame.release(); | |
| 432 } | |
| 433 | |
| 434 | |
| 435 bool OrthancSeriesLoader::IsJpegAvailable() | |
| 436 { | |
| 437 return MessagingToolbox::HasWebViewerInstalled(orthanc_); | |
| 438 } | |
| 439 } |