Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/OrthancSeriesLoader.cpp @ 118:a4d0b6c82b29 wasm
using Orthanc::DicomMap instead of OrthancPlugins::DicomDatasetReader
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 02 Oct 2017 14:31:26 +0200 |
| parents | 2eca030792aa |
| children |
| rev | line source |
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| 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" |
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25 |
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26 #include <Core/Images/Image.h> |
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27 #include <Core/Images/ImageProcessing.h> |
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28 #include <Core/Logging.h> |
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29 #include <Core/OrthancException.h> |
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30 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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31 |
| 0 | 32 #include "DicomFrameConverter.h" |
| 33 | |
| 34 namespace OrthancStone | |
| 35 { | |
| 36 class OrthancSeriesLoader::Slice : public boost::noncopyable | |
| 37 { | |
| 38 private: | |
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39 std::string instanceId_; |
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40 CoordinateSystem3D geometry_; |
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41 double projectionAlongNormal_; |
| 0 | 42 |
| 43 public: | |
| 44 Slice(const std::string& instanceId, | |
| 45 const std::string& imagePositionPatient, | |
| 46 const std::string& imageOrientationPatient) : | |
| 47 instanceId_(instanceId), | |
| 48 geometry_(imagePositionPatient, imageOrientationPatient) | |
| 49 { | |
| 50 } | |
| 51 | |
| 52 const std::string GetInstanceId() const | |
| 53 { | |
| 54 return instanceId_; | |
| 55 } | |
| 56 | |
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57 const CoordinateSystem3D& GetGeometry() const |
| 0 | 58 { |
| 59 return geometry_; | |
| 60 } | |
| 61 | |
| 62 void SetNormal(const Vector& normal) | |
| 63 { | |
| 64 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); | |
| 65 } | |
| 66 | |
| 67 double GetProjectionAlongNormal() const | |
| 68 { | |
| 69 return projectionAlongNormal_; | |
| 70 } | |
| 71 }; | |
| 72 | |
| 73 | |
| 74 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable | |
| 75 { | |
| 76 private: | |
| 77 std::vector<Slice*> slices_; | |
| 78 | |
| 79 struct Comparator | |
| 80 { | |
| 81 bool operator() (const Slice* const a, | |
| 82 const Slice* const b) const | |
| 83 { | |
| 84 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal(); | |
| 85 } | |
| 86 }; | |
| 87 | |
| 88 public: | |
| 89 ~SetOfSlices() | |
| 90 { | |
| 91 for (size_t i = 0; i < slices_.size(); i++) | |
| 92 { | |
| 93 assert(slices_[i] != NULL); | |
| 94 delete slices_[i]; | |
| 95 } | |
| 96 } | |
| 97 | |
| 98 void Reserve(size_t size) | |
| 99 { | |
| 100 slices_.reserve(size); | |
| 101 } | |
| 102 | |
| 103 void AddSlice(const std::string& instanceId, | |
| 104 const std::string& imagePositionPatient, | |
| 105 const std::string& imageOrientationPatient) | |
| 106 { | |
| 107 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient)); | |
| 108 } | |
| 109 | |
| 110 size_t GetSliceCount() const | |
| 111 { | |
| 112 return slices_.size(); | |
| 113 } | |
| 114 | |
| 115 const Slice& GetSlice(size_t index) const | |
| 116 { | |
| 117 assert(slices_[index] != NULL); | |
| 118 return *slices_[index]; | |
| 119 } | |
| 120 | |
| 121 void Sort(const Vector& normal) | |
| 122 { | |
| 123 for (size_t i = 0; i < slices_.size(); i++) | |
| 124 { | |
| 125 slices_[i]->SetNormal(normal); | |
| 126 } | |
| 127 | |
| 128 Comparator comparator; | |
| 129 std::sort(slices_.begin(), slices_.end(), comparator); | |
| 130 } | |
| 131 | |
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132 void LoadSeriesFast(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 133 const std::string& series) |
| 134 { | |
| 135 // Retrieve the orientation of this series | |
| 136 Json::Value info; | |
| 137 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series); | |
| 138 | |
| 139 if (info.type() != Json::objectValue || | |
| 140 !info.isMember("MainDicomTags") || | |
| 141 info["MainDicomTags"].type() != Json::objectValue || | |
| 142 !info["MainDicomTags"].isMember("ImageOrientationPatient") || | |
| 143 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue) | |
| 144 { | |
| 145 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 146 } | |
| 147 | |
| 148 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString(); | |
| 149 | |
| 150 | |
| 151 // Retrieve the Orthanc ID of all the instances of this series | |
| 152 Json::Value instances; | |
| 153 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances"); | |
| 154 | |
| 155 if (instances.type() != Json::arrayValue) | |
| 156 { | |
| 157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 158 } | |
| 159 | |
| 160 if (instances.size() == 0) | |
| 161 { | |
| 162 LOG(ERROR) << "This series is empty"; | |
| 163 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 164 } | |
| 165 | |
| 166 | |
| 167 // Retrieve the DICOM tags of all the instances | |
| 168 std::vector<std::string> instancesId; | |
| 169 | |
| 170 instancesId.resize(instances.size()); | |
| 171 Reserve(instances.size()); | |
| 172 | |
| 173 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 174 { | |
| 175 if (instances[i].type() != Json::objectValue || | |
| 176 !instances[i].isMember("ID") || | |
| 177 !instances[i].isMember("MainDicomTags") || | |
| 178 instances[i]["ID"].type() != Json::stringValue || | |
| 179 instances[i]["MainDicomTags"].type() != Json::objectValue || | |
| 180 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") || | |
| 181 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue) | |
| 182 { | |
| 183 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 184 } | |
| 185 else | |
| 186 { | |
| 187 instancesId[i] = instances[i]["ID"].asString(); | |
| 188 AddSlice(instancesId[i], | |
| 189 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(), | |
| 190 imageOrientationPatient); | |
| 191 } | |
| 192 } | |
| 193 | |
| 194 assert(GetSliceCount() == instances.size()); | |
| 195 } | |
| 196 | |
| 197 | |
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198 void LoadSeriesSafe(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 199 const std::string& seriesId) |
| 200 { | |
| 201 Json::Value series; | |
| 202 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify"); | |
| 203 | |
| 204 if (series.type() != Json::objectValue) | |
| 205 { | |
| 206 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 207 } | |
| 208 | |
| 209 if (series.size() == 0) | |
| 210 { | |
| 211 LOG(ERROR) << "This series is empty"; | |
| 212 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 213 } | |
| 214 | |
| 215 Json::Value::Members instances = series.getMemberNames(); | |
| 216 | |
| 217 Reserve(instances.size()); | |
| 218 | |
| 219 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
| 220 { | |
| 221 const Json::Value& tags = series[instances[i]]; | |
| 222 | |
| 223 if (tags.type() != Json::objectValue || | |
| 224 !tags.isMember("ImagePositionPatient") || | |
| 225 !tags.isMember("ImageOrientationPatient") || | |
| 226 tags["ImagePositionPatient"].type() != Json::stringValue || | |
| 227 tags["ImageOrientationPatient"].type() != Json::stringValue) | |
| 228 { | |
| 229 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 230 } | |
| 231 else | |
| 232 { | |
| 233 AddSlice(instances[i], | |
| 234 tags["ImagePositionPatient"].asString(), | |
| 235 tags["ImageOrientationPatient"].asString()); | |
| 236 } | |
| 237 } | |
| 238 | |
| 239 assert(GetSliceCount() == instances.size()); | |
| 240 } | |
| 241 | |
| 242 | |
| 243 void SelectNormal(Vector& normal) const | |
| 244 { | |
| 245 std::vector<Vector> normalCandidates; | |
| 246 std::vector<unsigned int> normalCount; | |
| 247 | |
| 248 bool found = false; | |
| 249 | |
| 250 for (size_t i = 0; !found && i < GetSliceCount(); i++) | |
| 251 { | |
| 252 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
| 253 | |
| 254 bool add = true; | |
| 255 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
| 256 { | |
| 257 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
| 258 { | |
| 259 normalCount[j] += 1; | |
| 260 add = false; | |
| 261 } | |
| 262 } | |
| 263 | |
| 264 if (add) | |
| 265 { | |
| 266 if (normalCount.size() > 2) | |
| 267 { | |
| 268 // To get linear-time complexity in (*). This heuristics | |
| 269 // allows the series to have one single frame that is | |
| 270 // not parallel to the others (such a frame could be a | |
| 271 // generated preview) | |
| 272 found = false; | |
| 273 } | |
| 274 else | |
| 275 { | |
| 276 normalCandidates.push_back(normal); | |
| 277 normalCount.push_back(1); | |
| 278 } | |
| 279 } | |
| 280 } | |
| 281 | |
| 282 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
| 283 { | |
| 284 unsigned int count = normalCount[i]; | |
| 285 if (count == GetSliceCount() || | |
| 286 count + 1 == GetSliceCount()) | |
| 287 { | |
| 288 normal = normalCandidates[i]; | |
| 289 found = true; | |
| 290 } | |
| 291 } | |
| 292 | |
| 293 if (!found) | |
| 294 { | |
| 295 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series"; | |
| 296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 297 } | |
| 298 } | |
| 299 | |
| 300 | |
| 301 void FilterNormal(const Vector& normal) | |
| 302 { | |
| 303 size_t pos = 0; | |
| 304 | |
| 305 for (size_t i = 0; i < slices_.size(); i++) | |
| 306 { | |
| 307 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) | |
| 308 { | |
| 309 // This slice is compatible with the selected normal | |
| 310 slices_[pos] = slices_[i]; | |
| 311 pos += 1; | |
| 312 } | |
| 313 else | |
| 314 { | |
| 315 delete slices_[i]; | |
| 316 slices_[i] = NULL; | |
| 317 } | |
| 318 } | |
| 319 | |
| 320 slices_.resize(pos); | |
| 321 } | |
| 322 }; | |
| 323 | |
| 324 | |
| 325 | |
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326 OrthancSeriesLoader::OrthancSeriesLoader(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 327 const std::string& series) : |
| 328 orthanc_(orthanc), | |
| 329 slices_(new SetOfSlices) | |
| 330 { | |
| 331 /** | |
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332 * The function "LoadSeriesFast()" might not behave properly if |
| 0 | 333 * some slice has some outsider value for its normal, which |
| 334 * happens sometimes on reprojected series (e.g. coronal and | |
| 335 * sagittal of Delphine). Don't use it. | |
| 336 **/ | |
| 337 | |
| 338 slices_->LoadSeriesSafe(orthanc, series); | |
| 339 | |
| 340 Vector normal; | |
| 341 slices_->SelectNormal(normal); | |
| 342 slices_->FilterNormal(normal); | |
| 343 slices_->Sort(normal); | |
| 344 | |
| 345 if (slices_->GetSliceCount() == 0) // Sanity check | |
| 346 { | |
| 347 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 348 } | |
| 349 | |
| 350 for (size_t i = 0; i < slices_->GetSliceCount(); i++) | |
| 351 { | |
| 352 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal())); | |
| 353 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry()); | |
| 354 } | |
| 355 | |
| 32 | 356 std::string uri = "/instances/" + slices_->GetSlice(0).GetInstanceId() + "/tags"; |
| 357 | |
| 358 OrthancPlugins::FullOrthancDataset dataset(orthanc_, uri); | |
| 359 | |
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360 Orthanc::DicomMap dicom; |
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361 MessagingToolbox::ConvertDataset(dicom, dataset); |
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362 |
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363 if (!dicom.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) || |
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364 !dicom.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS)) |
| 0 | 365 { |
| 366 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
| 367 } | |
| 368 | |
| 369 DicomFrameConverter converter; | |
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370 converter.ReadParameters(dicom); |
| 0 | 371 format_ = converter.GetExpectedPixelFormat(); |
| 372 } | |
| 373 | |
| 374 | |
| 32 | 375 OrthancPlugins::IDicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index) |
| 0 | 376 { |
| 32 | 377 std::string uri = "/instances/" + slices_->GetSlice(index).GetInstanceId() + "/tags"; |
| 0 | 378 |
| 32 | 379 std::auto_ptr<OrthancPlugins::IDicomDataset> dataset(new OrthancPlugins::FullOrthancDataset(orthanc_, uri)); |
| 380 | |
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381 Orthanc::DicomMap dicom; |
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382 MessagingToolbox::ConvertDataset(dicom, *dataset); |
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383 |
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384 uint32_t frames; |
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385 if (dicom.ParseUnsignedInteger32(frames, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES) && |
| 32 | 386 frames != 1) |
| 0 | 387 { |
| 388 LOG(ERROR) << "One instance in this series has more than 1 frame"; | |
| 389 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 390 } | |
| 391 | |
| 392 return dataset.release(); | |
| 393 } | |
| 394 | |
| 395 | |
| 396 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const | |
| 397 { | |
| 398 if (frame.GetFormat() != format_ || | |
| 399 frame.GetWidth() != width_ || | |
| 400 frame.GetHeight() != height_) | |
| 401 { | |
| 402 LOG(ERROR) << "The parameters of this series vary accross its slices"; | |
| 403 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 404 } | |
| 405 } | |
| 406 | |
| 407 | |
| 408 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index) | |
| 409 { | |
| 410 const Slice& slice = slices_->GetSlice(index); | |
| 411 | |
| 412 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 413 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_)); | |
| 414 | |
| 415 if (frame.get() != NULL) | |
| 416 { | |
| 417 CheckFrame(*frame); | |
| 418 } | |
| 419 | |
| 420 return frame.release(); | |
| 421 } | |
| 422 | |
| 423 | |
| 424 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index, | |
| 425 unsigned int quality) | |
| 426 { | |
| 427 const Slice& slice = slices_->GetSlice(index); | |
| 428 | |
| 429 std::auto_ptr<Orthanc::ImageAccessor> frame | |
| 430 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_)); | |
| 431 | |
| 432 if (frame.get() != NULL) | |
| 433 { | |
| 434 CheckFrame(*frame); | |
| 435 } | |
| 436 | |
| 437 return frame.release(); | |
| 438 } | |
| 439 | |
| 440 | |
| 441 bool OrthancSeriesLoader::IsJpegAvailable() | |
| 442 { | |
| 443 return MessagingToolbox::HasWebViewerInstalled(orthanc_); | |
| 444 } | |
| 445 } |