Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 43:9621fd6f17c9
sync
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 09 Nov 2016 17:34:20 +0100 |
| parents | 8e1dfd531335 |
| children | 91fc9583b2de |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 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 Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
| 21 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 22 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
| 23 #include "../Framework/DicomToolbox.h" | |
| 24 #include "../Framework/DicomizerParameters.h" | |
| 25 #include "../Framework/ImagedVolumeParameters.h" | |
| 26 #include "../Framework/Inputs/HierarchicalTiff.h" | |
| 27 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 28 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 29 #include "../Framework/Inputs/TiledPngImage.h" | |
| 30 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 31 #include "../Framework/Orthanc/Core/HttpClient.h" | |
| 32 #include "../Framework/Orthanc/Core/Logging.h" | |
| 33 #include "../Framework/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h" | |
| 43 | 34 #include "../Framework/Orthanc/Core/SystemToolbox.h" |
| 0 | 35 #include "../Framework/Orthanc/OrthancServer/FromDcmtkBridge.h" |
| 36 #include "../Framework/Outputs/DicomPyramidWriter.h" | |
| 37 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 38 | |
| 39 #include "ApplicationToolbox.h" | |
| 40 | |
| 41 #include <EmbeddedResources.h> | |
| 42 | |
| 43 #include <boost/program_options.hpp> | |
| 44 | |
| 45 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 46 #include <dcmtk/dcmdata/dcuid.h> | |
| 47 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 48 #include <dcmtk/dcmdata/dcvrat.h> | |
| 49 | |
| 50 | |
| 51 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, | |
| 52 OrthancWSI::ITiledPyramid& source, | |
| 53 const OrthancWSI::DicomizerParameters& parameters) | |
| 54 { | |
| 55 Orthanc::BagOfTasks tasks; | |
| 56 | |
| 57 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 58 { | |
| 59 LOG(WARNING) << "Creating level " << i << " of size " | |
| 60 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 61 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 62 } | |
| 63 | |
| 64 LOG(WARNING) << "Transcoding the source pyramid"; | |
| 65 | |
| 66 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 67 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 68 } | |
| 69 | |
| 70 | |
| 71 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 72 OrthancWSI::ITiledPyramid& source, | |
| 73 const OrthancWSI::DicomizerParameters& parameters) | |
| 74 { | |
| 75 Orthanc::BagOfTasks tasks; | |
| 76 | |
| 77 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 78 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 79 assert(levelsCount >= 1); | |
| 80 | |
| 81 for (unsigned int i = 0; i < levelsCount; i++) | |
| 82 { | |
| 83 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 84 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 85 | |
| 86 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 87 target.AddLevel(width, height); | |
| 88 } | |
| 89 | |
| 90 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 91 if (lowerLevelsCount > levelsCount) | |
| 92 { | |
| 93 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 94 << ") exceeds the number of levels (" << levelsCount | |
| 95 << "), cropping it"; | |
| 96 lowerLevelsCount = levelsCount; | |
| 97 } | |
| 98 | |
| 99 assert(lowerLevelsCount <= levelsCount); | |
| 100 if (lowerLevelsCount != levelsCount) | |
| 101 { | |
| 102 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
| 103 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount); | |
| 104 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 105 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 106 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 107 | |
| 108 assert(tasks.GetSize() == 0); | |
| 109 | |
| 110 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 111 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 112 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 113 (tasks, target, truncated.GetUpperLevel(), | |
| 114 upperLevelsCount, lowerLevelsCount, parameters); | |
| 115 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 116 } | |
| 117 else | |
| 118 { | |
| 119 LOG(WARNING) << "Constructing the pyramid"; | |
| 120 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 121 (tasks, target, source, levelsCount, 0, parameters); | |
| 122 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 123 } | |
| 124 } | |
| 125 | |
| 126 | |
| 127 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 128 OrthancWSI::ITiledPyramid& source, | |
| 129 const DcmDataset& dataset, | |
| 130 const OrthancWSI::DicomizerParameters& parameters, | |
| 131 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 132 { | |
| 133 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 134 | |
| 135 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
| 136 LOG(WARNING) << "Source image compression: " << OrthancWSI::EnumerationToString(stats.GetImageCompression()); | |
| 137 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(stats.GetPixelFormat()); | |
| 138 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); | |
| 139 | |
| 140 if (parameters.IsRepaintBackground()) | |
| 141 { | |
| 142 LOG(WARNING) << "Repainting the background with color: (" | |
| 143 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 144 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 145 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 146 } | |
| 147 else | |
| 148 { | |
| 149 LOG(WARNING) << "No repainting of the background"; | |
| 150 } | |
| 151 | |
| 152 OrthancWSI::DicomPyramidWriter target(output, dataset, | |
| 153 source.GetPixelFormat(), | |
| 154 parameters.GetTargetCompression(), | |
| 155 parameters.GetTargetTileWidth(source), | |
| 156 parameters.GetTargetTileHeight(source), | |
| 157 parameters.GetDicomMaxFileSize(), | |
| 158 volume); | |
| 29 | 159 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 160 |
| 161 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 162 | |
| 163 if (target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) | |
| 164 { | |
| 165 LOG(WARNING) << "Target image compression: Jpeg with quality " << static_cast<int>(target.GetJpegQuality()); | |
| 166 target.SetJpegQuality(target.GetJpegQuality()); | |
| 167 } | |
| 168 else | |
| 169 { | |
| 170 LOG(WARNING) << "Target image compression: " << OrthancWSI::EnumerationToString(target.GetImageCompression()); | |
| 171 } | |
| 172 | |
| 173 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
| 174 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
| 175 { | |
| 176 LOG(ERROR) << "When resampling the tile size, it must be a integer divisor of the original tile size"; | |
| 177 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 178 } | |
| 179 | |
| 180 if (target.GetTileWidth() <= 16 || | |
| 181 target.GetTileHeight() <= 16) | |
| 182 { | |
| 183 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 184 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 185 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 186 } | |
| 187 | |
| 188 if (parameters.IsReconstructPyramid()) | |
| 189 { | |
| 190 ReconstructPyramid(target, stats, parameters); | |
| 191 } | |
| 192 else | |
| 193 { | |
| 194 TranscodePyramid(target, stats, parameters); | |
| 195 } | |
| 196 | |
| 197 target.Flush(); | |
| 198 } | |
| 199 | |
| 200 | |
| 201 | |
| 202 static DcmDataset* ParseDataset(const std::string& path) | |
| 203 { | |
| 204 Json::Value json; | |
| 205 | |
| 206 if (path.empty()) | |
| 207 { | |
| 208 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 209 } | |
| 210 else | |
| 211 { | |
| 212 std::string content; | |
| 43 | 213 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 214 |
| 215 Json::Reader reader; | |
| 216 if (!reader.parse(content, json, false)) | |
| 217 { | |
| 218 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 220 } | |
| 221 } | |
| 222 | |
| 223 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1)); | |
| 224 if (dataset.get() == NULL) | |
| 225 { | |
| 226 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 227 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 228 } | |
| 229 | |
| 230 // VL Whole Slide Microscopy Image IOD | |
| 231 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 232 | |
| 233 // Slide Microscopy | |
| 234 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 235 | |
| 236 // Patient orientation makes no sense in whole-slide images | |
| 237 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 238 | |
| 239 // Some basic coordinate information | |
| 240 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 241 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 242 | |
| 243 std::string date, time; | |
| 43 | 244 Orthanc::SystemToolbox::GetNowDicom(date, time); |
| 0 | 245 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 246 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 247 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 248 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 249 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 250 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 251 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 252 | |
| 253 return dataset.release(); | |
| 254 } | |
| 255 | |
| 256 | |
| 257 | |
| 258 static void SetupDimension(DcmDataset& dataset, | |
| 259 const std::string& opticalPathId, | |
| 260 const OrthancWSI::ITiledPyramid& source, | |
| 261 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 262 { | |
| 263 std::string uid; | |
| 264 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); | |
| 265 | |
| 266 if (previous != NULL) | |
| 267 { | |
| 268 const char* tmp = NULL; | |
| 269 if (previous->findAndGetString(DCM_DimensionOrganizationUID, tmp).good() && | |
| 270 tmp != NULL) | |
| 271 { | |
| 272 uid.assign(tmp); | |
| 273 } | |
| 274 } | |
| 275 | |
| 276 if (uid.empty()) | |
| 277 { | |
| 278 // Generate an unique identifier for the Dimension Organization | |
| 279 uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 280 } | |
| 281 | |
| 282 dataset.remove(DCM_DimensionIndexSequence); | |
| 283 | |
| 284 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 285 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
| 286 | |
| 287 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
| 288 !sequence->insert(item.release(), false, false).good() || | |
| 289 !dataset.insert(sequence.release(), true, false).good()) | |
| 290 { | |
| 291 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 292 } | |
| 293 | |
| 294 item.reset(new DcmItem); | |
| 295 sequence.reset(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); | |
| 296 | |
| 297 std::auto_ptr<DcmAttributeTag> a1(new DcmAttributeTag(DCM_FunctionalGroupPointer)); | |
| 298 std::auto_ptr<DcmAttributeTag> a2(new DcmAttributeTag(DCM_DimensionIndexPointer)); | |
| 299 | |
| 300 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
| 301 !a1->putTagVal(DCM_FrameContentSequence).good() || | |
| 302 !a2->putTagVal(DCM_DimensionIndexValues).good() || | |
| 26 | 303 !item->insert(a1.release()).good() || |
| 304 !item->insert(a2.release()).good() || | |
| 0 | 305 !sequence->insert(item.release(), false, false).good() || |
| 306 !dataset.insert(sequence.release(), true, false).good()) | |
| 307 { | |
| 308 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 309 } | |
| 310 | |
| 311 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); // Remember to switch X/Y! | |
| 312 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); // Remember to switch X/Y! | |
| 313 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
| 314 boost::lexical_cast<std::string>(spacingY)); | |
| 315 | |
| 316 item.reset(new DcmItem); | |
| 317 sequence.reset(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); | |
| 318 std::auto_ptr<DcmItem> item2(new DcmItem); | |
| 319 std::auto_ptr<DcmItem> item3(new DcmItem); | |
| 320 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
| 321 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
| 322 | |
| 323 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 324 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
| 325 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
| 326 | |
| 327 if (!sequence2->insert(item2.release(), false, false).good() || | |
| 328 !sequence3->insert(item3.release(), false, false).good() || | |
| 329 !item->insert(sequence2.release(), false, false).good() || | |
| 330 !item->insert(sequence3.release(), false, false).good() || | |
| 331 !sequence->insert(item.release(), false, false).good() || | |
| 332 !dataset.insert(sequence.release(), true, false).good()) | |
| 333 { | |
| 334 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 335 } | |
| 336 } | |
| 337 | |
| 338 | |
| 339 static void EnrichDataset(DcmDataset& dataset, | |
| 340 const OrthancWSI::ITiledPyramid& source, | |
| 341 const OrthancWSI::DicomizerParameters& parameters, | |
| 342 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 343 { | |
| 344 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 345 | |
| 346 if (source.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg || | |
| 347 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) | |
| 348 { | |
| 349 // Takes as estimation a 1:10 compression ratio | |
| 350 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 351 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 352 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 353 } | |
| 354 else | |
| 355 { | |
| 356 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 357 } | |
| 358 | |
| 359 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 360 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 361 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 362 | |
| 363 std::auto_ptr<DcmItem> origin(new DcmItem); | |
| 364 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
| 365 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 366 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 367 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 368 | |
| 369 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
| 370 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
| 371 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 372 { | |
| 373 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 374 } | |
| 375 | |
| 376 | |
| 377 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 378 { | |
| 379 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 380 { | |
| 381 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 382 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 383 } | |
| 384 | |
| 385 std::string brightfield; | |
| 386 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 387 | |
| 388 Json::Value json; | |
| 389 Json::Reader reader; | |
| 390 if (!reader.parse(brightfield, json, false)) | |
| 391 { | |
| 392 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 393 } | |
| 394 | |
| 395 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
| 396 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
| 397 DCM_OpticalPathSequence.getElement()), | |
| 398 json, false, encoding)); | |
| 399 if (!dataset.insert(element.release()).good()) | |
| 400 { | |
| 401 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 402 } | |
| 403 } | |
| 404 | |
| 405 | |
| 406 std::string profile; | |
| 407 if (parameters.GetIccProfilePath().empty()) | |
| 408 { | |
| 409 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 410 } | |
| 411 else | |
| 412 { | |
| 43 | 413 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 414 } |
| 415 | |
| 416 | |
| 417 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 418 if (opticalPath == NULL) | |
| 419 { | |
| 420 LOG(ERROR) << "No optical path specified"; | |
| 421 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 422 } | |
| 423 | |
| 424 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 425 { | |
| 426 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
| 427 | |
| 428 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 429 !opticalPath->insert(icc.release()).good()) | |
| 430 { | |
| 431 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 432 } | |
| 433 } | |
| 434 | |
| 435 const char* opticalPathId = NULL; | |
| 436 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 437 opticalPathId == NULL) | |
| 438 { | |
| 439 LOG(ERROR) << "No identifier in the optical path"; | |
| 440 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 441 } | |
| 442 | |
| 443 SetupDimension(dataset, opticalPathId, source, volume); | |
| 444 } | |
| 445 | |
| 446 | |
| 447 static bool ParseParameters(int& exitStatus, | |
| 448 OrthancWSI::DicomizerParameters& parameters, | |
| 449 OrthancWSI::ImagedVolumeParameters& volume, | |
| 450 int argc, | |
| 451 char* argv[]) | |
| 452 { | |
| 453 // Declare the supported parameters | |
| 454 boost::program_options::options_description generic("Generic options"); | |
| 455 generic.add_options() | |
| 456 ("help", "Display this help and exit") | |
|
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
457 ("version", "Output version information and exit") |
| 0 | 458 ("verbose", "Be verbose in logs") |
| 459 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
| 460 "Number of processing threads to be used") | |
| 461 ("openslide", boost::program_options::value<std::string>(), | |
| 462 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
| 463 ; | |
| 464 | |
| 465 boost::program_options::options_description source("Options for the source image"); | |
| 466 source.add_options() | |
| 467 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
| 468 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
| 31 | 469 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
| 0 | 470 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") |
| 471 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
| 472 ; | |
| 473 | |
| 474 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 475 pyramid.add_options() | |
| 476 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
| 477 "Reconstruct the full pyramid (slow) (Boolean)") | |
| 478 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
| 479 "Apply smoothing when reconstructing the pyramid " | |
| 480 "(slower, but higher quality) (Boolean)") | |
| 481 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
| 482 ; | |
| 483 | |
| 484 boost::program_options::options_description target("Options for the target image"); | |
| 485 target.add_options() | |
| 486 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
| 487 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
| 488 ("compression", boost::program_options::value<std::string>(), | |
| 489 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
| 490 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
| 491 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
| 492 ("folder", boost::program_options::value<std::string>(), | |
| 493 "Folder where to store the output DICOM instances") | |
| 494 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
| 495 "Pattern for the files in the output folder") | |
| 496 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 497 "URL to the REST API of the target Orthanc server") | |
| 498 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
| 499 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
| 500 ; | |
| 501 | |
| 502 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 503 volumeOptions.add_options() | |
| 504 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
| 505 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
| 506 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
| 507 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
| 508 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
| 509 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
| 510 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
| 511 ; | |
| 512 | |
| 513 boost::program_options::options_description advancedOptions("Advanced options"); | |
| 514 advancedOptions.add_options() | |
| 515 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
| 516 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
| 517 ("icc-profile", boost::program_options::value<std::string>(), | |
| 518 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
| 519 ("safety", boost::program_options::value<bool>()->default_value(true), | |
| 520 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
| 521 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
| 522 "should be applied (only for performance/memory tuning)") | |
| 523 ; | |
| 524 | |
| 525 boost::program_options::options_description hidden; | |
| 526 hidden.add_options() | |
| 527 ("input", boost::program_options::value<std::string>(), "Input file"); | |
| 528 ; | |
| 529 | |
| 530 boost::program_options::options_description allWithoutHidden; | |
| 531 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
| 532 | |
| 533 boost::program_options::options_description all = allWithoutHidden; | |
| 534 all.add(hidden); | |
| 535 | |
| 536 boost::program_options::positional_options_description positional; | |
| 537 positional.add("input", 1); | |
| 538 | |
| 539 boost::program_options::variables_map options; | |
| 540 bool error = false; | |
| 541 | |
| 542 try | |
| 543 { | |
| 544 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 545 options(all).positional(positional).run(), options); | |
| 546 boost::program_options::notify(options); | |
| 547 } | |
| 548 catch (boost::program_options::error& e) | |
| 549 { | |
| 550 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 551 error = true; | |
| 552 } | |
| 553 | |
| 554 if (!error && | |
| 555 options.count("sample-dataset")) | |
| 556 { | |
| 557 std::string sample; | |
| 558 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 559 | |
| 560 std::cout << std::endl << sample << std::endl; | |
| 561 | |
| 562 return false; | |
| 563 } | |
| 564 | |
| 565 if (!error && | |
| 566 options.count("help") == 0 && | |
|
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567 options.count("version") == 0 && |
| 0 | 568 options.count("input") != 1) |
| 569 { | |
| 570 LOG(ERROR) << "No input file was specified"; | |
| 571 error = true; | |
| 572 } | |
| 573 | |
| 574 if (error || options.count("help")) | |
| 575 { | |
| 576 std::cout << std::endl | |
| 577 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 578 << std::endl | |
| 579 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 580 << std::endl << std::endl | |
| 581 << "Create a DICOM file from a digital pathology image." | |
| 582 << std::endl; | |
| 583 | |
| 584 std::cout << allWithoutHidden << "\n"; | |
| 585 | |
| 586 if (error) | |
| 587 { | |
| 588 exitStatus = -1; | |
| 589 } | |
| 590 | |
| 591 return false; | |
| 592 } | |
| 593 | |
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594 if (options.count("version")) |
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595 { |
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596 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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597 return false; |
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598 } |
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599 |
| 0 | 600 if (options.count("verbose")) |
| 601 { | |
| 602 Orthanc::Logging::EnableInfoLevel(true); | |
| 603 } | |
| 604 | |
| 605 if (options.count("openslide")) | |
| 606 { | |
| 607 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
| 608 } | |
| 609 | |
| 610 if (options.count("pyramid") && | |
| 611 options["pyramid"].as<bool>()) | |
| 612 { | |
| 613 parameters.SetReconstructPyramid(true); | |
| 614 } | |
| 615 | |
| 616 if (options.count("smooth") && | |
| 617 options["smooth"].as<bool>()) | |
| 618 { | |
| 619 parameters.SetSmoothEnabled(true); | |
| 620 } | |
| 621 | |
| 622 if (options.count("safety") && | |
| 623 options["safety"].as<bool>()) | |
| 624 { | |
| 625 parameters.SetSafetyCheck(true); | |
| 626 } | |
| 627 | |
| 628 if (options.count("reencode") && | |
| 629 options["reencode"].as<bool>()) | |
| 630 { | |
| 631 parameters.SetForceReencode(true); | |
| 632 } | |
| 633 | |
| 634 if (options.count("repaint") && | |
| 635 options["repaint"].as<bool>()) | |
| 636 { | |
| 637 parameters.SetRepaintBackground(true); | |
| 638 } | |
| 639 | |
| 640 if (options.count("tile-width") || | |
| 641 options.count("tile-height")) | |
| 642 { | |
| 643 int w = 0; | |
| 644 if (options.count("tile-width")) | |
| 645 { | |
| 646 w = options["tile-width"].as<int>(); | |
| 647 } | |
| 648 | |
| 649 unsigned int h = 0; | |
| 650 if (options.count("tile-height")) | |
| 651 { | |
| 652 h = options["tile-height"].as<int>(); | |
| 653 } | |
| 654 | |
| 655 if (w < 0 || h < 0) | |
| 656 { | |
| 657 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 658 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 659 } | |
| 660 | |
| 661 parameters.SetTargetTileSize(w, h); | |
| 662 } | |
| 663 | |
| 664 parameters.SetInputFile(options["input"].as<std::string>()); | |
| 665 | |
| 666 if (options.count("color")) | |
| 667 { | |
| 668 uint8_t r, g, b; | |
| 669 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
| 670 parameters.SetBackgroundColor(r, g, b); | |
| 671 } | |
| 672 | |
| 673 if (options.count("compression")) | |
| 674 { | |
| 675 std::string s = options["compression"].as<std::string>(); | |
| 676 if (s == "none") | |
| 677 { | |
| 678 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 679 } | |
| 680 else if (s == "jpeg") | |
| 681 { | |
| 682 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 683 } | |
| 684 else if (s == "jpeg2000") | |
| 685 { | |
| 686 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 687 } | |
| 688 else | |
| 689 { | |
| 690 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 691 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 692 } | |
| 693 } | |
| 694 | |
| 695 if (options.count("jpeg-quality")) | |
| 696 { | |
| 697 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
| 698 } | |
| 699 | |
| 700 if (options.count("levels")) | |
| 701 { | |
| 702 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
| 703 } | |
| 704 | |
| 705 if (options.count("lower-levels")) | |
| 706 { | |
| 707 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
| 708 } | |
| 709 | |
| 710 if (options.count("threads")) | |
| 711 { | |
| 712 parameters.SetThreadsCount(options["threads"].as<int>()); | |
| 713 } | |
| 714 | |
| 715 if (options.count("max-size")) | |
| 716 { | |
| 717 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
| 718 } | |
| 719 | |
| 720 if (options.count("folder")) | |
| 721 { | |
| 722 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
| 723 } | |
| 724 | |
| 725 if (options.count("folder-pattern")) | |
| 726 { | |
| 727 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
| 728 } | |
| 729 | |
| 730 if (options.count("orthanc")) | |
| 731 { | |
| 732 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
| 733 | |
| 734 if (options.count("username") && | |
| 735 options.count("password")) | |
| 736 { | |
| 737 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
| 738 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
| 739 } | |
| 740 } | |
| 741 | |
| 742 if (options.count("dataset")) | |
| 743 { | |
| 744 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
| 745 } | |
| 746 | |
| 747 if (options.count("imaged-width")) | |
| 748 { | |
| 749 volume.SetWidth(options["imaged-width"].as<float>()); | |
| 750 } | |
| 751 | |
| 752 if (options.count("imaged-height")) | |
| 753 { | |
| 754 volume.SetHeight(options["imaged-height"].as<float>()); | |
| 755 } | |
| 756 | |
| 757 if (options.count("imaged-depth")) | |
| 758 { | |
| 759 volume.SetDepth(options["imaged-depth"].as<float>()); | |
| 760 } | |
| 761 | |
| 762 if (options.count("offset-x")) | |
| 763 { | |
| 764 volume.SetOffsetX(options["offset-x"].as<float>()); | |
| 765 } | |
| 766 | |
| 767 if (options.count("offset-y")) | |
| 768 { | |
| 769 volume.SetOffsetY(options["offset-y"].as<float>()); | |
| 770 } | |
| 771 | |
| 772 if (options.count("optical-path")) | |
| 773 { | |
| 774 std::string s = options["optical-path"].as<std::string>(); | |
| 775 if (s == "none") | |
| 776 { | |
| 777 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 778 } | |
| 779 else if (s == "brightfield") | |
| 780 { | |
| 781 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 782 } | |
| 783 else | |
| 784 { | |
| 785 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 786 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 787 } | |
| 788 } | |
| 789 | |
| 790 if (options.count("icc-profile")) | |
| 791 { | |
| 792 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
| 793 } | |
| 794 | |
| 795 return true; | |
| 796 } | |
| 797 | |
| 798 | |
| 799 OrthancWSI::ITiledPyramid* OpenInputPyramid(const std::string& path, | |
| 800 const OrthancWSI::DicomizerParameters& parameters) | |
| 801 { | |
| 802 LOG(WARNING) << "The input image is: " << path; | |
| 803 | |
| 804 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 805 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 806 | |
| 807 switch (format) | |
| 808 { | |
| 809 case OrthancWSI::ImageCompression_Png: | |
| 810 return new OrthancWSI::TiledPngImage(path, | |
| 811 parameters.GetTargetTileWidth(512), | |
| 812 parameters.GetTargetTileHeight(512)); | |
| 813 | |
| 814 case OrthancWSI::ImageCompression_Jpeg: | |
| 815 return new OrthancWSI::TiledJpegImage(path, | |
| 816 parameters.GetTargetTileWidth(512), | |
| 817 parameters.GetTargetTileHeight(512)); | |
| 818 | |
| 819 case OrthancWSI::ImageCompression_Tiff: | |
| 820 { | |
| 821 try | |
| 822 { | |
| 823 return new OrthancWSI::HierarchicalTiff(path); | |
| 824 } | |
| 825 catch (Orthanc::OrthancException&) | |
| 826 { | |
| 827 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 828 } | |
| 829 } | |
| 830 | |
| 831 default: | |
| 832 break; | |
| 833 } | |
| 834 | |
| 835 try | |
| 836 { | |
| 837 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
| 838 return new OrthancWSI::OpenSlidePyramid(path, | |
| 839 parameters.GetTargetTileWidth(512), | |
| 840 parameters.GetTargetTileHeight(512)); | |
| 841 } | |
| 842 catch (Orthanc::OrthancException&) | |
| 843 { | |
| 844 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 845 return NULL; | |
| 846 } | |
| 847 } | |
| 848 | |
| 849 | |
| 850 int main(int argc, char* argv[]) | |
| 851 { | |
| 852 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
| 853 | |
| 854 int exitStatus = 0; | |
| 855 | |
| 856 try | |
| 857 { | |
| 858 OrthancWSI::DicomizerParameters parameters; | |
| 859 OrthancWSI::ImagedVolumeParameters volume; | |
| 860 | |
| 861 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 862 { | |
| 863 std::auto_ptr<OrthancWSI::ITiledPyramid> source(OpenInputPyramid(parameters.GetInputFile(), parameters)); | |
| 864 if (source.get() == NULL) | |
| 865 { | |
| 866 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 867 } | |
| 868 | |
| 869 // Create the shared DICOM tags | |
| 870 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
| 871 EnrichDataset(*dataset, *source, parameters, volume); | |
| 872 | |
| 873 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
| 874 Recompress(*output, *source, *dataset, parameters, volume); | |
| 875 } | |
| 876 } | |
| 877 catch (Orthanc::OrthancException& e) | |
| 878 { | |
| 879 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 880 exitStatus = -1; | |
| 881 } | |
| 882 | |
| 883 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 884 | |
| 885 return exitStatus; | |
| 886 } |