Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/OrthancSeriesLoader.cpp @ 40:7207a407bcd8
shared copyright with osimis
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 04 Jan 2017 16:37:42 +0100 |
| parents | 6465fbd23bce |
| 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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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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 "OrthancSeriesLoader.h" | |
| 35 | |
| 35 | 36 #include "../Toolbox/MessagingToolbox.h" |
| 16 | 37 #include "../../Resources/Orthanc/Core/Images/Image.h" |
| 38 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h" | |
| 39 #include "../../Resources/Orthanc/Core/Logging.h" | |
| 40 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
| 32 | 41 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
| 0 | 42 #include "DicomFrameConverter.h" |
| 43 | |
| 44 namespace OrthancStone | |
| 45 { | |
| 46 class OrthancSeriesLoader::Slice : public boost::noncopyable | |
| 47 { | |
| 48 private: | |
| 49 std::string instanceId_; | |
| 50 SliceGeometry geometry_; | |
| 51 double projectionAlongNormal_; | |
| 52 | |
| 53 public: | |
| 54 Slice(const std::string& instanceId, | |
| 55 const std::string& imagePositionPatient, | |
| 56 const std::string& imageOrientationPatient) : | |
| 57 instanceId_(instanceId), | |
| 58 geometry_(imagePositionPatient, imageOrientationPatient) | |
| 59 { | |
| 60 } | |
| 61 | |
| 62 const std::string GetInstanceId() const | |
| 63 { | |
| 64 return instanceId_; | |
| 65 } | |
| 66 | |
| 67 const SliceGeometry& GetGeometry() const | |
| 68 { | |
| 69 return geometry_; | |
| 70 } | |
| 71 | |
| 72 void SetNormal(const Vector& normal) | |
| 73 { | |
| 74 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); | |
| 75 } | |
| 76 | |
| 77 double GetProjectionAlongNormal() const | |
| 78 { | |
| 79 return projectionAlongNormal_; | |
| 80 } | |
| 81 }; | |
| 82 | |
| 83 | |
| 84 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable | |
| 85 { | |
| 86 private: | |
| 87 std::vector<Slice*> slices_; | |
| 88 | |
| 89 struct Comparator | |
| 90 { | |
| 91 bool operator() (const Slice* const a, | |
| 92 const Slice* const b) const | |
| 93 { | |
| 94 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal(); | |
| 95 } | |
| 96 }; | |
| 97 | |
| 98 public: | |
| 99 ~SetOfSlices() | |
| 100 { | |
| 101 for (size_t i = 0; i < slices_.size(); i++) | |
| 102 { | |
| 103 assert(slices_[i] != NULL); | |
| 104 delete slices_[i]; | |
| 105 } | |
| 106 } | |
| 107 | |
| 108 void Reserve(size_t size) | |
| 109 { | |
| 110 slices_.reserve(size); | |
| 111 } | |
| 112 | |
| 113 void AddSlice(const std::string& instanceId, | |
| 114 const std::string& imagePositionPatient, | |
| 115 const std::string& imageOrientationPatient) | |
| 116 { | |
| 117 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient)); | |
| 118 } | |
| 119 | |
| 120 size_t GetSliceCount() const | |
| 121 { | |
| 122 return slices_.size(); | |
| 123 } | |
| 124 | |
| 125 const Slice& GetSlice(size_t index) const | |
| 126 { | |
| 127 assert(slices_[index] != NULL); | |
| 128 return *slices_[index]; | |
| 129 } | |
| 130 | |
| 131 void Sort(const Vector& normal) | |
| 132 { | |
| 133 for (size_t i = 0; i < slices_.size(); i++) | |
| 134 { | |
| 135 slices_[i]->SetNormal(normal); | |
| 136 } | |
| 137 | |
| 138 Comparator comparator; | |
| 139 std::sort(slices_.begin(), slices_.end(), comparator); | |
| 140 } | |
| 141 | |
|
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142 void LoadSeriesFast(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 143 const std::string& series) |
| 144 { | |
| 145 // Retrieve the orientation of this series | |
| 146 Json::Value info; | |
| 147 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series); | |
| 148 | |
| 149 if (info.type() != Json::objectValue || | |
| 150 !info.isMember("MainDicomTags") || | |
| 151 info["MainDicomTags"].type() != Json::objectValue || | |
| 152 !info["MainDicomTags"].isMember("ImageOrientationPatient") || | |
| 153 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue) | |
| 154 { | |
| 155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 156 } | |
| 157 | |
| 158 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString(); | |
| 159 | |
| 160 | |
| 161 // Retrieve the Orthanc ID of all the instances of this series | |
| 162 Json::Value instances; | |
| 163 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances"); | |
| 164 | |
| 165 if (instances.type() != Json::arrayValue) | |
| 166 { | |
| 167 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 168 } | |
| 169 | |
| 170 if (instances.size() == 0) | |
| 171 { | |
| 172 LOG(ERROR) << "This series is empty"; | |
| 173 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 174 } | |
| 175 | |
| 176 | |
| 177 // Retrieve the DICOM tags of all the instances | |
| 178 std::vector<std::string> instancesId; | |
| 179 | |
| 180 instancesId.resize(instances.size()); | |
| 181 Reserve(instances.size()); | |
| 182 | |
| 183 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 184 { | |
| 185 if (instances[i].type() != Json::objectValue || | |
| 186 !instances[i].isMember("ID") || | |
| 187 !instances[i].isMember("MainDicomTags") || | |
| 188 instances[i]["ID"].type() != Json::stringValue || | |
| 189 instances[i]["MainDicomTags"].type() != Json::objectValue || | |
| 190 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") || | |
| 191 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue) | |
| 192 { | |
| 193 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 194 } | |
| 195 else | |
| 196 { | |
| 197 instancesId[i] = instances[i]["ID"].asString(); | |
| 198 AddSlice(instancesId[i], | |
| 199 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(), | |
| 200 imageOrientationPatient); | |
| 201 } | |
| 202 } | |
| 203 | |
| 204 assert(GetSliceCount() == instances.size()); | |
| 205 } | |
| 206 | |
| 207 | |
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208 void LoadSeriesSafe(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 209 const std::string& seriesId) |
| 210 { | |
| 211 Json::Value series; | |
| 212 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify"); | |
| 213 | |
| 214 if (series.type() != Json::objectValue) | |
| 215 { | |
| 216 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 217 } | |
| 218 | |
| 219 if (series.size() == 0) | |
| 220 { | |
| 221 LOG(ERROR) << "This series is empty"; | |
| 222 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 223 } | |
| 224 | |
| 225 Json::Value::Members instances = series.getMemberNames(); | |
| 226 | |
| 227 Reserve(instances.size()); | |
| 228 | |
| 229 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 230 { | |
| 231 const Json::Value& tags = series[instances[i]]; | |
| 232 | |
| 233 if (tags.type() != Json::objectValue || | |
| 234 !tags.isMember("ImagePositionPatient") || | |
| 235 !tags.isMember("ImageOrientationPatient") || | |
| 236 tags["ImagePositionPatient"].type() != Json::stringValue || | |
| 237 tags["ImageOrientationPatient"].type() != Json::stringValue) | |
| 238 { | |
| 239 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 240 } | |
| 241 else | |
| 242 { | |
| 243 AddSlice(instances[i], | |
| 244 tags["ImagePositionPatient"].asString(), | |
| 245 tags["ImageOrientationPatient"].asString()); | |
| 246 } | |
| 247 } | |
| 248 | |
| 249 assert(GetSliceCount() == instances.size()); | |
| 250 } | |
| 251 | |
| 252 | |
| 253 void SelectNormal(Vector& normal) const | |
| 254 { | |
| 255 std::vector<Vector> normalCandidates; | |
| 256 std::vector<unsigned int> normalCount; | |
| 257 | |
| 258 bool found = false; | |
| 259 | |
| 260 for (size_t i = 0; !found && i < GetSliceCount(); i++) | |
| 261 { | |
| 262 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
| 263 | |
| 264 bool add = true; | |
| 265 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
| 266 { | |
| 267 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
| 268 { | |
| 269 normalCount[j] += 1; | |
| 270 add = false; | |
| 271 } | |
| 272 } | |
| 273 | |
| 274 if (add) | |
| 275 { | |
| 276 if (normalCount.size() > 2) | |
| 277 { | |
| 278 // To get linear-time complexity in (*). This heuristics | |
| 279 // allows the series to have one single frame that is | |
| 280 // not parallel to the others (such a frame could be a | |
| 281 // generated preview) | |
| 282 found = false; | |
| 283 } | |
| 284 else | |
| 285 { | |
| 286 normalCandidates.push_back(normal); | |
| 287 normalCount.push_back(1); | |
| 288 } | |
| 289 } | |
| 290 } | |
| 291 | |
| 292 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
| 293 { | |
| 294 unsigned int count = normalCount[i]; | |
| 295 if (count == GetSliceCount() || | |
| 296 count + 1 == GetSliceCount()) | |
| 297 { | |
| 298 normal = normalCandidates[i]; | |
| 299 found = true; | |
| 300 } | |
| 301 } | |
| 302 | |
| 303 if (!found) | |
| 304 { | |
| 305 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series"; | |
| 306 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 307 } | |
| 308 } | |
| 309 | |
| 310 | |
| 311 void FilterNormal(const Vector& normal) | |
| 312 { | |
| 313 size_t pos = 0; | |
| 314 | |
| 315 for (size_t i = 0; i < slices_.size(); i++) | |
| 316 { | |
| 317 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) | |
| 318 { | |
| 319 // This slice is compatible with the selected normal | |
| 320 slices_[pos] = slices_[i]; | |
| 321 pos += 1; | |
| 322 } | |
| 323 else | |
| 324 { | |
| 325 delete slices_[i]; | |
| 326 slices_[i] = NULL; | |
| 327 } | |
| 328 } | |
| 329 | |
| 330 slices_.resize(pos); | |
| 331 } | |
| 332 }; | |
| 333 | |
| 334 | |
| 335 | |
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parents:
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diff
changeset
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336 OrthancSeriesLoader::OrthancSeriesLoader(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 337 const std::string& series) : |
| 338 orthanc_(orthanc), | |
| 339 slices_(new SetOfSlices) | |
| 340 { | |
| 341 /** | |
| 342 * The function "LoadSeriesFast()" might now behave properly if | |
| 343 * some slice has some outsider value for its normal, which | |
| 344 * happens sometimes on reprojected series (e.g. coronal and | |
| 345 * sagittal of Delphine). Don't use it. | |
| 346 **/ | |
| 347 | |
| 348 slices_->LoadSeriesSafe(orthanc, series); | |
| 349 | |
| 350 Vector normal; | |
| 351 slices_->SelectNormal(normal); | |
| 352 slices_->FilterNormal(normal); | |
| 353 slices_->Sort(normal); | |
| 354 | |
| 355 if (slices_->GetSliceCount() == 0) // Sanity check | |
| 356 { | |
| 357 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 358 } | |
| 359 | |
| 360 for (size_t i = 0; i < slices_->GetSliceCount(); i++) | |
| 361 { | |
| 362 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal())); | |
| 363 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry()); | |
| 364 } | |
| 365 | |
| 32 | 366 std::string uri = "/instances/" + slices_->GetSlice(0).GetInstanceId() + "/tags"; |
| 367 | |
| 368 OrthancPlugins::FullOrthancDataset dataset(orthanc_, uri); | |
| 369 OrthancPlugins::DicomDatasetReader reader(dataset); | |
| 370 | |
| 371 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) || | |
| 372 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS)) | |
| 0 | 373 { |
| 374 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
| 375 } | |
| 376 | |
| 377 DicomFrameConverter converter; | |
| 32 | 378 converter.ReadParameters(dataset); |
| 0 | 379 format_ = converter.GetExpectedPixelFormat(); |
| 380 } | |
| 381 | |
| 382 | |
| 32 | 383 OrthancPlugins::IDicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index) |
| 0 | 384 { |
| 32 | 385 std::string uri = "/instances/" + slices_->GetSlice(index).GetInstanceId() + "/tags"; |
| 0 | 386 |
| 32 | 387 std::auto_ptr<OrthancPlugins::IDicomDataset> dataset(new OrthancPlugins::FullOrthancDataset(orthanc_, uri)); |
| 388 OrthancPlugins::DicomDatasetReader reader(*dataset); | |
| 389 | |
| 390 unsigned int frames; | |
| 391 if (reader.GetUnsignedIntegerValue(frames, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES) && | |
| 392 frames != 1) | |
| 0 | 393 { |
| 394 LOG(ERROR) << "One instance in this series has more than 1 frame"; | |
| 395 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 396 } | |
| 397 | |
| 398 return dataset.release(); | |
| 399 } | |
| 400 | |
| 401 | |
| 402 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const | |
| 403 { | |
| 404 if (frame.GetFormat() != format_ || | |
| 405 frame.GetWidth() != width_ || | |
| 406 frame.GetHeight() != height_) | |
| 407 { | |
| 408 LOG(ERROR) << "The parameters of this series vary accross its slices"; | |
| 409 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 410 } | |
| 411 } | |
| 412 | |
| 413 | |
| 414 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index) | |
| 415 { | |
| 416 const Slice& slice = slices_->GetSlice(index); | |
| 417 | |
| 418 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 419 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_)); | |
| 420 | |
| 421 if (frame.get() != NULL) | |
| 422 { | |
| 423 CheckFrame(*frame); | |
| 424 } | |
| 425 | |
| 426 return frame.release(); | |
| 427 } | |
| 428 | |
| 429 | |
| 430 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index, | |
| 431 unsigned int quality) | |
| 432 { | |
| 433 const Slice& slice = slices_->GetSlice(index); | |
| 434 | |
| 435 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 436 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_)); | |
| 437 | |
| 438 if (frame.get() != NULL) | |
| 439 { | |
| 440 CheckFrame(*frame); | |
| 441 } | |
| 442 | |
| 443 return frame.release(); | |
| 444 } | |
| 445 | |
| 446 | |
| 447 bool OrthancSeriesLoader::IsJpegAvailable() | |
| 448 { | |
| 449 return MessagingToolbox::HasWebViewerInstalled(orthanc_); | |
| 450 } | |
| 451 } |