Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 93:14146ecd1688
Display version of the framework in the logs
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 23 Dec 2016 16:49:23 +0100 |
| parents | 727670c5c125 |
| children | ff0ef01c332c |
| 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/Outputs/DicomPyramidWriter.h" | |
| 32 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 33 | |
|
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34 #include "../Resources/Orthanc/Core/HttpClient.h" |
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35 #include "../Resources/Orthanc/Core/Logging.h" |
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36 #include "../Resources/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h" |
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37 #include "../Resources/Orthanc/Core/SystemToolbox.h" |
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38 #include "../Resources/Orthanc/OrthancServer/FromDcmtkBridge.h" |
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39 |
| 0 | 40 #include "ApplicationToolbox.h" |
| 41 | |
| 42 #include <EmbeddedResources.h> | |
| 43 | |
| 44 #include <boost/program_options.hpp> | |
| 45 | |
| 46 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 47 #include <dcmtk/dcmdata/dcuid.h> | |
| 48 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 49 #include <dcmtk/dcmdata/dcvrat.h> | |
| 50 | |
| 51 | |
| 52 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, | |
| 53 OrthancWSI::ITiledPyramid& source, | |
| 54 const OrthancWSI::DicomizerParameters& parameters) | |
| 55 { | |
| 56 Orthanc::BagOfTasks tasks; | |
| 57 | |
| 58 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 59 { | |
| 60 LOG(WARNING) << "Creating level " << i << " of size " | |
| 61 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 62 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 63 } | |
| 64 | |
| 65 LOG(WARNING) << "Transcoding the source pyramid"; | |
| 66 | |
| 67 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 68 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 69 } | |
| 70 | |
| 71 | |
| 72 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 73 OrthancWSI::ITiledPyramid& source, | |
| 74 const OrthancWSI::DicomizerParameters& parameters) | |
| 75 { | |
| 76 Orthanc::BagOfTasks tasks; | |
| 77 | |
| 78 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 79 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 80 assert(levelsCount >= 1); | |
| 81 | |
| 82 for (unsigned int i = 0; i < levelsCount; i++) | |
| 83 { | |
| 84 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 85 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 86 | |
| 87 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 88 target.AddLevel(width, height); | |
| 89 } | |
| 90 | |
| 91 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 92 if (lowerLevelsCount > levelsCount) | |
| 93 { | |
| 94 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 95 << ") exceeds the number of levels (" << levelsCount | |
| 96 << "), cropping it"; | |
| 97 lowerLevelsCount = levelsCount; | |
| 98 } | |
| 99 | |
| 100 assert(lowerLevelsCount <= levelsCount); | |
| 101 if (lowerLevelsCount != levelsCount) | |
| 102 { | |
| 103 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
| 104 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount); | |
| 105 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 106 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 107 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 108 | |
| 109 assert(tasks.GetSize() == 0); | |
| 110 | |
| 111 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 112 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 113 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 114 (tasks, target, truncated.GetUpperLevel(), | |
| 115 upperLevelsCount, lowerLevelsCount, parameters); | |
| 116 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 117 } | |
| 118 else | |
| 119 { | |
| 120 LOG(WARNING) << "Constructing the pyramid"; | |
| 121 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 122 (tasks, target, source, levelsCount, 0, parameters); | |
| 123 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 124 } | |
| 125 } | |
| 126 | |
| 127 | |
| 128 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 129 OrthancWSI::ITiledPyramid& source, | |
| 130 const DcmDataset& dataset, | |
| 131 const OrthancWSI::DicomizerParameters& parameters, | |
| 132 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 133 { | |
| 134 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 135 | |
| 136 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
| 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 { | |
| 83 | 263 // Extract the identifier of the Dimension Organization, if provided |
| 264 std::string organization; | |
| 0 | 265 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 266 | |
| 83 | 267 if (previous != NULL && |
| 268 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 269 { | |
| 270 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 271 } | |
| 272 else | |
| 0 | 273 { |
| 83 | 274 // No Dimension Organization provided: Generate an unique identifier |
| 275 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 276 } | |
| 277 | |
| 278 | |
| 279 { | |
| 280 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
| 281 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 282 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
| 283 | |
| 284 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
| 285 | |
| 286 if (!sequence->insert(item.release(), false, false).good() || | |
| 287 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 288 { |
| 83 | 289 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 290 } |
| 291 } | |
| 292 | |
| 83 | 293 |
| 0 | 294 { |
| 83 | 295 // Construct tag "Dimension Index Sequence" (0020,9222) |
| 296 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 297 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
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298 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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299 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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300 |
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301 std::auto_ptr<DcmItem> item2(new DcmItem); |
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302 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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303 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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304 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 305 |
| 83 | 306 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 307 |
| 83 | 308 if (!sequence->insert(item.release(), false, false).good() || |
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309 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 310 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 311 { | |
| 312 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 313 } | |
| 0 | 314 } |
| 315 | |
| 316 | |
| 83 | 317 { |
| 318 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
| 0 | 319 |
| 83 | 320 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
| 321 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); | |
| 322 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); | |
| 323 | |
| 324 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
| 325 boost::lexical_cast<std::string>(spacingY)); | |
| 326 | |
| 327 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 0 | 328 |
| 83 | 329 std::auto_ptr<DcmItem> item2(new DcmItem); |
| 330 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, | |
| 331 boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 332 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
| 0 | 333 |
| 83 | 334 std::auto_ptr<DcmItem> item3(new DcmItem); |
| 335 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
| 0 | 336 |
| 83 | 337 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
| 338 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
| 339 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
| 0 | 340 |
| 83 | 341 if (!sequence2->insert(item2.release(), false, false).good() || |
| 342 !sequence3->insert(item3.release(), false, false).good() || | |
| 343 !item->insert(sequence2.release(), false, false).good() || | |
| 344 !item->insert(sequence3.release(), false, false).good() || | |
| 345 !sequence->insert(item.release(), false, false).good() || | |
| 346 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 347 { | |
| 348 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 349 } | |
| 0 | 350 } |
| 351 } | |
| 352 | |
| 353 | |
| 354 static void EnrichDataset(DcmDataset& dataset, | |
| 355 const OrthancWSI::ITiledPyramid& source, | |
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356 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 357 const OrthancWSI::DicomizerParameters& parameters, |
| 358 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 359 { | |
| 360 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 361 | |
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362 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 363 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 364 { | |
| 365 // Takes as estimation a 1:10 compression ratio | |
| 366 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 367 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 368 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 369 } | |
| 370 else | |
| 371 { | |
| 372 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 373 } | |
| 374 | |
| 375 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 376 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 377 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 378 | |
| 379 std::auto_ptr<DcmItem> origin(new DcmItem); | |
| 380 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
| 381 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 382 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 383 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 384 | |
| 385 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
| 386 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
| 387 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 388 { | |
| 389 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 390 } | |
| 391 | |
| 392 | |
| 393 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 394 { | |
| 395 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 396 { | |
| 397 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 398 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 399 } | |
| 400 | |
| 401 std::string brightfield; | |
| 402 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 403 | |
| 404 Json::Value json; | |
| 405 Json::Reader reader; | |
| 406 if (!reader.parse(brightfield, json, false)) | |
| 407 { | |
| 408 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 409 } | |
| 410 | |
| 411 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
| 412 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
| 413 DCM_OpticalPathSequence.getElement()), | |
| 414 json, false, encoding)); | |
| 415 if (!dataset.insert(element.release()).good()) | |
| 416 { | |
| 417 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 418 } | |
| 419 } | |
| 420 | |
| 421 | |
| 422 std::string profile; | |
| 423 if (parameters.GetIccProfilePath().empty()) | |
| 424 { | |
| 425 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 426 } | |
| 427 else | |
| 428 { | |
| 43 | 429 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 430 } |
| 431 | |
| 432 | |
| 433 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 434 if (opticalPath == NULL) | |
| 435 { | |
| 436 LOG(ERROR) << "No optical path specified"; | |
| 437 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 438 } | |
| 439 | |
| 440 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 441 { | |
| 442 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
| 443 | |
| 444 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 445 !opticalPath->insert(icc.release()).good()) | |
| 446 { | |
| 447 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 448 } | |
| 449 } | |
| 450 | |
| 451 const char* opticalPathId = NULL; | |
| 452 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 453 opticalPathId == NULL) | |
| 454 { | |
| 455 LOG(ERROR) << "No identifier in the optical path"; | |
| 456 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 457 } | |
| 458 | |
| 459 SetupDimension(dataset, opticalPathId, source, volume); | |
| 460 } | |
| 461 | |
| 462 | |
| 463 static bool ParseParameters(int& exitStatus, | |
| 464 OrthancWSI::DicomizerParameters& parameters, | |
| 465 OrthancWSI::ImagedVolumeParameters& volume, | |
| 466 int argc, | |
| 467 char* argv[]) | |
| 468 { | |
| 469 // Declare the supported parameters | |
| 470 boost::program_options::options_description generic("Generic options"); | |
| 471 generic.add_options() | |
| 472 ("help", "Display this help and exit") | |
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473 ("version", "Output version information and exit") |
| 0 | 474 ("verbose", "Be verbose in logs") |
| 475 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
| 476 "Number of processing threads to be used") | |
| 477 ("openslide", boost::program_options::value<std::string>(), | |
| 478 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
| 479 ; | |
| 480 | |
| 481 boost::program_options::options_description source("Options for the source image"); | |
| 482 source.add_options() | |
| 483 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
| 484 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
| 31 | 485 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
| 0 | 486 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") |
| 487 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
| 488 ; | |
| 489 | |
| 490 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 491 pyramid.add_options() | |
| 492 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
| 493 "Reconstruct the full pyramid (slow) (Boolean)") | |
| 494 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
| 495 "Apply smoothing when reconstructing the pyramid " | |
| 496 "(slower, but higher quality) (Boolean)") | |
| 497 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
| 498 ; | |
| 499 | |
| 500 boost::program_options::options_description target("Options for the target image"); | |
| 501 target.add_options() | |
| 502 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
| 503 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
| 504 ("compression", boost::program_options::value<std::string>(), | |
| 505 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
| 506 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
| 507 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
| 508 ("folder", boost::program_options::value<std::string>(), | |
| 509 "Folder where to store the output DICOM instances") | |
| 510 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
| 511 "Pattern for the files in the output folder") | |
| 512 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 513 "URL to the REST API of the target Orthanc server") | |
| 514 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
| 515 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
| 516 ; | |
| 517 | |
| 518 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 519 volumeOptions.add_options() | |
| 520 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
| 521 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
| 522 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
| 523 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
| 524 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
| 525 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
| 526 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
| 527 ; | |
| 528 | |
| 529 boost::program_options::options_description advancedOptions("Advanced options"); | |
| 530 advancedOptions.add_options() | |
| 531 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
| 532 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
| 533 ("icc-profile", boost::program_options::value<std::string>(), | |
| 534 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
| 535 ("safety", boost::program_options::value<bool>()->default_value(true), | |
| 536 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
| 537 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
| 538 "should be applied (only for performance/memory tuning)") | |
| 539 ; | |
| 540 | |
| 541 boost::program_options::options_description hidden; | |
| 542 hidden.add_options() | |
| 543 ("input", boost::program_options::value<std::string>(), "Input file"); | |
| 544 ; | |
| 545 | |
| 546 boost::program_options::options_description allWithoutHidden; | |
| 547 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
| 548 | |
| 549 boost::program_options::options_description all = allWithoutHidden; | |
| 550 all.add(hidden); | |
| 551 | |
| 552 boost::program_options::positional_options_description positional; | |
| 553 positional.add("input", 1); | |
| 554 | |
| 555 boost::program_options::variables_map options; | |
| 556 bool error = false; | |
| 557 | |
| 558 try | |
| 559 { | |
| 560 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 561 options(all).positional(positional).run(), options); | |
| 562 boost::program_options::notify(options); | |
| 563 } | |
| 564 catch (boost::program_options::error& e) | |
| 565 { | |
| 566 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 567 error = true; | |
| 568 } | |
| 569 | |
| 570 if (!error && | |
| 571 options.count("sample-dataset")) | |
| 572 { | |
| 573 std::string sample; | |
| 574 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 575 | |
| 576 std::cout << std::endl << sample << std::endl; | |
| 577 | |
| 578 return false; | |
| 579 } | |
| 580 | |
| 581 if (!error && | |
| 582 options.count("help") == 0 && | |
|
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583 options.count("version") == 0 && |
| 0 | 584 options.count("input") != 1) |
| 585 { | |
| 586 LOG(ERROR) << "No input file was specified"; | |
| 587 error = true; | |
| 588 } | |
| 589 | |
| 590 if (error || options.count("help")) | |
| 591 { | |
| 592 std::cout << std::endl | |
| 593 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 594 << std::endl | |
| 595 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 596 << std::endl << std::endl | |
| 597 << "Create a DICOM file from a digital pathology image." | |
| 598 << std::endl; | |
| 599 | |
| 600 std::cout << allWithoutHidden << "\n"; | |
| 601 | |
| 602 if (error) | |
| 603 { | |
| 604 exitStatus = -1; | |
| 605 } | |
| 606 | |
| 607 return false; | |
| 608 } | |
| 609 | |
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610 if (options.count("version")) |
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611 { |
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612 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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613 return false; |
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614 } |
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615 |
| 0 | 616 if (options.count("verbose")) |
| 617 { | |
| 618 Orthanc::Logging::EnableInfoLevel(true); | |
| 619 } | |
| 620 | |
| 621 if (options.count("openslide")) | |
| 622 { | |
| 623 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
| 624 } | |
| 625 | |
| 626 if (options.count("pyramid") && | |
| 627 options["pyramid"].as<bool>()) | |
| 628 { | |
| 629 parameters.SetReconstructPyramid(true); | |
| 630 } | |
| 631 | |
| 632 if (options.count("smooth") && | |
| 633 options["smooth"].as<bool>()) | |
| 634 { | |
| 635 parameters.SetSmoothEnabled(true); | |
| 636 } | |
| 637 | |
| 638 if (options.count("safety") && | |
| 639 options["safety"].as<bool>()) | |
| 640 { | |
| 641 parameters.SetSafetyCheck(true); | |
| 642 } | |
| 643 | |
| 644 if (options.count("reencode") && | |
| 645 options["reencode"].as<bool>()) | |
| 646 { | |
| 647 parameters.SetForceReencode(true); | |
| 648 } | |
| 649 | |
| 650 if (options.count("repaint") && | |
| 651 options["repaint"].as<bool>()) | |
| 652 { | |
| 653 parameters.SetRepaintBackground(true); | |
| 654 } | |
| 655 | |
| 656 if (options.count("tile-width") || | |
| 657 options.count("tile-height")) | |
| 658 { | |
| 659 int w = 0; | |
| 660 if (options.count("tile-width")) | |
| 661 { | |
| 662 w = options["tile-width"].as<int>(); | |
| 663 } | |
| 664 | |
| 665 unsigned int h = 0; | |
| 666 if (options.count("tile-height")) | |
| 667 { | |
| 668 h = options["tile-height"].as<int>(); | |
| 669 } | |
| 670 | |
| 671 if (w < 0 || h < 0) | |
| 672 { | |
| 673 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 674 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 675 } | |
| 676 | |
| 677 parameters.SetTargetTileSize(w, h); | |
| 678 } | |
| 679 | |
| 680 parameters.SetInputFile(options["input"].as<std::string>()); | |
| 681 | |
| 682 if (options.count("color")) | |
| 683 { | |
| 684 uint8_t r, g, b; | |
| 685 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
| 686 parameters.SetBackgroundColor(r, g, b); | |
| 687 } | |
| 688 | |
| 689 if (options.count("compression")) | |
| 690 { | |
| 691 std::string s = options["compression"].as<std::string>(); | |
| 692 if (s == "none") | |
| 693 { | |
| 694 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 695 } | |
| 696 else if (s == "jpeg") | |
| 697 { | |
| 698 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 699 } | |
| 700 else if (s == "jpeg2000") | |
| 701 { | |
| 702 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 703 } | |
| 704 else | |
| 705 { | |
| 706 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 707 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 708 } | |
| 709 } | |
| 710 | |
| 711 if (options.count("jpeg-quality")) | |
| 712 { | |
| 713 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
| 714 } | |
| 715 | |
| 716 if (options.count("levels")) | |
| 717 { | |
| 718 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
| 719 } | |
| 720 | |
| 721 if (options.count("lower-levels")) | |
| 722 { | |
| 723 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
| 724 } | |
| 725 | |
| 726 if (options.count("threads")) | |
| 727 { | |
| 728 parameters.SetThreadsCount(options["threads"].as<int>()); | |
| 729 } | |
| 730 | |
| 731 if (options.count("max-size")) | |
| 732 { | |
| 733 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
| 734 } | |
| 735 | |
| 736 if (options.count("folder")) | |
| 737 { | |
| 738 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
| 739 } | |
| 740 | |
| 741 if (options.count("folder-pattern")) | |
| 742 { | |
| 743 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
| 744 } | |
| 745 | |
| 746 if (options.count("orthanc")) | |
| 747 { | |
| 748 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
| 749 | |
| 750 if (options.count("username") && | |
| 751 options.count("password")) | |
| 752 { | |
| 753 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
| 754 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
| 755 } | |
| 756 } | |
| 757 | |
| 758 if (options.count("dataset")) | |
| 759 { | |
| 760 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
| 761 } | |
| 762 | |
| 763 if (options.count("imaged-width")) | |
| 764 { | |
| 765 volume.SetWidth(options["imaged-width"].as<float>()); | |
| 766 } | |
| 767 | |
| 768 if (options.count("imaged-height")) | |
| 769 { | |
| 770 volume.SetHeight(options["imaged-height"].as<float>()); | |
| 771 } | |
| 772 | |
| 773 if (options.count("imaged-depth")) | |
| 774 { | |
| 775 volume.SetDepth(options["imaged-depth"].as<float>()); | |
| 776 } | |
| 777 | |
| 778 if (options.count("offset-x")) | |
| 779 { | |
| 780 volume.SetOffsetX(options["offset-x"].as<float>()); | |
| 781 } | |
| 782 | |
| 783 if (options.count("offset-y")) | |
| 784 { | |
| 785 volume.SetOffsetY(options["offset-y"].as<float>()); | |
| 786 } | |
| 787 | |
| 788 if (options.count("optical-path")) | |
| 789 { | |
| 790 std::string s = options["optical-path"].as<std::string>(); | |
| 791 if (s == "none") | |
| 792 { | |
| 793 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 794 } | |
| 795 else if (s == "brightfield") | |
| 796 { | |
| 797 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 798 } | |
| 799 else | |
| 800 { | |
| 801 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 802 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 803 } | |
| 804 } | |
| 805 | |
| 806 if (options.count("icc-profile")) | |
| 807 { | |
| 808 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
| 809 } | |
| 810 | |
| 811 return true; | |
| 812 } | |
| 813 | |
| 814 | |
|
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815 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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816 const std::string& path, |
| 0 | 817 const OrthancWSI::DicomizerParameters& parameters) |
| 818 { | |
| 819 LOG(WARNING) << "The input image is: " << path; | |
| 820 | |
| 821 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 822 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 823 | |
| 824 switch (format) | |
| 825 { | |
| 826 case OrthancWSI::ImageCompression_Png: | |
|
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827 { |
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828 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 829 return new OrthancWSI::TiledPngImage(path, |
| 830 parameters.GetTargetTileWidth(512), | |
| 831 parameters.GetTargetTileHeight(512)); | |
|
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832 } |
| 0 | 833 |
| 834 case OrthancWSI::ImageCompression_Jpeg: | |
|
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835 { |
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836 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 837 return new OrthancWSI::TiledJpegImage(path, |
| 838 parameters.GetTargetTileWidth(512), | |
| 839 parameters.GetTargetTileHeight(512)); | |
|
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840 } |
| 0 | 841 |
| 842 case OrthancWSI::ImageCompression_Tiff: | |
| 843 { | |
| 844 try | |
| 845 { | |
|
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846 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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847 sourceCompression = tiff->GetImageCompression(); |
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848 return tiff.release(); |
| 0 | 849 } |
| 850 catch (Orthanc::OrthancException&) | |
| 851 { | |
| 852 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 853 } | |
| 854 } | |
| 855 | |
| 856 default: | |
| 857 break; | |
| 858 } | |
| 859 | |
| 860 try | |
| 861 { | |
| 862 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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863 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 864 return new OrthancWSI::OpenSlidePyramid(path, |
| 865 parameters.GetTargetTileWidth(512), | |
| 866 parameters.GetTargetTileHeight(512)); | |
| 867 } | |
| 868 catch (Orthanc::OrthancException&) | |
| 869 { | |
| 870 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 871 return NULL; | |
| 872 } | |
| 873 } | |
| 874 | |
| 875 | |
| 876 int main(int argc, char* argv[]) | |
| 877 { | |
| 878 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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879 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 880 |
| 881 int exitStatus = 0; | |
| 882 | |
| 883 try | |
| 884 { | |
| 885 OrthancWSI::DicomizerParameters parameters; | |
| 886 OrthancWSI::ImagedVolumeParameters volume; | |
| 887 | |
| 888 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 889 { | |
|
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890 OrthancWSI::ImageCompression sourceCompression; |
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891 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
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892 |
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893 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 894 if (source.get() == NULL) |
| 895 { | |
| 896 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 897 } | |
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898 |
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899 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 900 |
| 901 // Create the shared DICOM tags | |
| 902 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
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903 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 904 |
| 905 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
| 906 Recompress(*output, *source, *dataset, parameters, volume); | |
| 907 } | |
| 908 } | |
| 909 catch (Orthanc::OrthancException& e) | |
| 910 { | |
| 911 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 912 exitStatus = -1; | |
| 913 } | |
| 914 | |
| 915 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 916 | |
| 917 return exitStatus; | |
| 918 } |