Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 145:0b7e7be7d655
cppcheck
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 23 Apr 2018 16:21:58 +0200 |
| parents | a0f9a3df1110 |
| children | fb8d4cd2f618 |
| 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 | |
|
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 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. | |
| 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 | |
| 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 | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 23 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
| 24 #include "../Framework/DicomToolbox.h" | |
| 25 #include "../Framework/DicomizerParameters.h" | |
| 26 #include "../Framework/ImagedVolumeParameters.h" | |
| 27 #include "../Framework/Inputs/HierarchicalTiff.h" | |
| 28 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 29 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 30 #include "../Framework/Inputs/TiledPngImage.h" | |
| 31 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 32 #include "../Framework/Outputs/DicomPyramidWriter.h" | |
| 33 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 34 | |
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35 #include <Core/DicomParsing/FromDcmtkBridge.h> |
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36 #include <Core/Logging.h> |
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37 #include <Core/MultiThreading/BagOfTasksProcessor.h> |
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38 #include <Core/OrthancException.h> |
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39 #include <Core/SystemToolbox.h> |
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40 |
| 0 | 41 #include "ApplicationToolbox.h" |
| 42 | |
| 43 #include <EmbeddedResources.h> | |
| 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 | |
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51 static const char* OPTION_COLOR = "color"; |
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52 static const char* OPTION_COMPRESSION = "compression"; |
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53 static const char* OPTION_DATASET = "dataset"; |
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54 static const char* OPTION_FOLDER = "folder"; |
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55 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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56 static const char* OPTION_HELP = "help"; |
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57 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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58 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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59 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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60 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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61 static const char* OPTION_INPUT = "input"; |
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62 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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63 static const char* OPTION_LEVELS = "levels"; |
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64 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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65 static const char* OPTION_MAX_SIZE = "max-size"; |
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66 static const char* OPTION_OFFSET_X = "offset-x"; |
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67 static const char* OPTION_OFFSET_Y = "offset-y"; |
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68 static const char* OPTION_OPENSLIDE = "openslide"; |
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69 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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70 static const char* OPTION_PYRAMID = "pyramid"; |
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71 static const char* OPTION_REENCODE = "reencode"; |
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72 static const char* OPTION_REPAINT = "repaint"; |
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73 static const char* OPTION_SAFETY = "safety"; |
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74 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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75 static const char* OPTION_SMOOTH = "smooth"; |
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76 static const char* OPTION_THREADS = "threads"; |
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77 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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78 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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79 static const char* OPTION_VERBOSE = "verbose"; |
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80 static const char* OPTION_VERSION = "version"; |
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81 |
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82 |
| 0 | 83 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 84 OrthancWSI::ITiledPyramid& source, | |
| 85 const OrthancWSI::DicomizerParameters& parameters) | |
| 86 { | |
| 87 Orthanc::BagOfTasks tasks; | |
| 88 | |
| 89 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 90 { | |
| 91 LOG(WARNING) << "Creating level " << i << " of size " | |
| 92 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 93 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 94 } | |
| 95 | |
| 96 LOG(WARNING) << "Transcoding the source pyramid"; | |
| 97 | |
| 98 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 99 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 100 } | |
| 101 | |
| 102 | |
| 103 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 104 OrthancWSI::ITiledPyramid& source, | |
| 105 const OrthancWSI::DicomizerParameters& parameters) | |
| 106 { | |
| 107 Orthanc::BagOfTasks tasks; | |
| 108 | |
| 109 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 110 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 111 assert(levelsCount >= 1); | |
| 112 | |
| 113 for (unsigned int i = 0; i < levelsCount; i++) | |
| 114 { | |
| 115 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 116 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 117 | |
| 118 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 119 target.AddLevel(width, height); | |
| 120 } | |
| 121 | |
| 122 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 123 if (lowerLevelsCount > levelsCount) | |
| 124 { | |
| 125 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 126 << ") exceeds the number of levels (" << levelsCount | |
| 127 << "), cropping it"; | |
| 128 lowerLevelsCount = levelsCount; | |
| 129 } | |
| 130 | |
| 131 assert(lowerLevelsCount <= levelsCount); | |
| 132 if (lowerLevelsCount != levelsCount) | |
| 133 { | |
| 134 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
| 135 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount); | |
| 136 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 137 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 138 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 139 | |
| 140 assert(tasks.GetSize() == 0); | |
| 141 | |
| 142 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 143 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 144 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 145 (tasks, target, truncated.GetUpperLevel(), | |
| 146 upperLevelsCount, lowerLevelsCount, parameters); | |
| 147 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 148 } | |
| 149 else | |
| 150 { | |
| 151 LOG(WARNING) << "Constructing the pyramid"; | |
| 152 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 153 (tasks, target, source, levelsCount, 0, parameters); | |
| 154 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 155 } | |
| 156 } | |
| 157 | |
| 158 | |
| 159 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 160 OrthancWSI::ITiledPyramid& source, | |
| 161 const DcmDataset& dataset, | |
| 162 const OrthancWSI::DicomizerParameters& parameters, | |
| 163 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 164 { | |
| 165 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 166 | |
| 167 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
| 168 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(stats.GetPixelFormat()); | |
| 169 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); | |
| 170 | |
| 171 if (parameters.IsRepaintBackground()) | |
| 172 { | |
| 173 LOG(WARNING) << "Repainting the background with color: (" | |
| 174 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 175 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 176 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 177 } | |
| 178 else | |
| 179 { | |
| 180 LOG(WARNING) << "No repainting of the background"; | |
| 181 } | |
| 182 | |
| 183 OrthancWSI::DicomPyramidWriter target(output, dataset, | |
| 184 source.GetPixelFormat(), | |
| 185 parameters.GetTargetCompression(), | |
| 186 parameters.GetTargetTileWidth(source), | |
| 187 parameters.GetTargetTileHeight(source), | |
| 188 parameters.GetDicomMaxFileSize(), | |
| 189 volume); | |
| 29 | 190 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 191 |
| 192 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 193 | |
| 194 if (target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) | |
| 195 { | |
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196 LOG(WARNING) << "Target image compression: Jpeg with quality " |
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197 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 198 target.SetJpegQuality(target.GetJpegQuality()); |
| 199 } | |
| 200 else | |
| 201 { | |
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202 LOG(WARNING) << "Target image compression: " |
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203 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 204 } |
| 205 | |
| 206 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
| 207 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
| 208 { | |
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209 LOG(ERROR) << "When resampling the tile size, " |
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210 << "it must be a integer divisor of the original tile size"; |
| 0 | 211 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 212 } | |
| 213 | |
| 214 if (target.GetTileWidth() <= 16 || | |
| 215 target.GetTileHeight() <= 16) | |
| 216 { | |
| 217 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 218 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 219 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 220 } | |
| 221 | |
| 222 if (parameters.IsReconstructPyramid()) | |
| 223 { | |
| 224 ReconstructPyramid(target, stats, parameters); | |
| 225 } | |
| 226 else | |
| 227 { | |
| 228 TranscodePyramid(target, stats, parameters); | |
| 229 } | |
| 230 | |
| 231 target.Flush(); | |
| 232 } | |
| 233 | |
| 234 | |
| 235 | |
| 236 static DcmDataset* ParseDataset(const std::string& path) | |
| 237 { | |
| 238 Json::Value json; | |
| 239 | |
| 240 if (path.empty()) | |
| 241 { | |
| 242 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 243 } | |
| 244 else | |
| 245 { | |
| 246 std::string content; | |
| 43 | 247 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 248 |
| 249 Json::Reader reader; | |
| 250 if (!reader.parse(content, json, false)) | |
| 251 { | |
| 252 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 254 } | |
| 255 } | |
| 256 | |
| 257 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1)); | |
| 258 if (dataset.get() == NULL) | |
| 259 { | |
| 260 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 261 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 262 } | |
| 263 | |
| 264 // VL Whole Slide Microscopy Image IOD | |
| 265 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 266 | |
| 267 // Slide Microscopy | |
| 268 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 269 | |
| 270 // Patient orientation makes no sense in whole-slide images | |
| 271 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 272 | |
| 273 // Some basic coordinate information | |
| 274 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 275 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 276 | |
| 277 std::string date, time; | |
| 130 | 278 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 279 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 280 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 281 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 282 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 283 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 284 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 285 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 286 | |
| 287 return dataset.release(); | |
| 288 } | |
| 289 | |
| 290 | |
| 291 | |
| 292 static void SetupDimension(DcmDataset& dataset, | |
| 293 const std::string& opticalPathId, | |
| 294 const OrthancWSI::ITiledPyramid& source, | |
| 295 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 296 { | |
| 83 | 297 // Extract the identifier of the Dimension Organization, if provided |
| 298 std::string organization; | |
| 0 | 299 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 300 | |
| 83 | 301 if (previous != NULL && |
| 302 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 303 { | |
| 304 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 305 } | |
| 306 else | |
| 0 | 307 { |
| 83 | 308 // No Dimension Organization provided: Generate an unique identifier |
| 309 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 310 } | |
| 311 | |
| 312 | |
| 313 { | |
| 314 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
| 315 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 316 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
| 317 | |
| 318 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
| 319 | |
| 320 if (!sequence->insert(item.release(), false, false).good() || | |
| 321 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 322 { |
| 83 | 323 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 324 } |
| 325 } | |
| 326 | |
| 83 | 327 |
| 0 | 328 { |
| 83 | 329 // Construct tag "Dimension Index Sequence" (0020,9222) |
| 330 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 331 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
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332 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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333 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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334 |
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335 std::auto_ptr<DcmItem> item2(new DcmItem); |
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336 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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337 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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338 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 339 |
| 83 | 340 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 341 |
| 83 | 342 if (!sequence->insert(item.release(), false, false).good() || |
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343 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 344 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 345 { | |
| 346 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 347 } | |
| 0 | 348 } |
| 349 | |
| 350 | |
| 83 | 351 { |
| 352 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
| 0 | 353 |
| 83 | 354 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
| 355 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); | |
| 356 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); | |
| 357 | |
| 358 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
| 359 boost::lexical_cast<std::string>(spacingY)); | |
| 360 | |
| 361 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 0 | 362 |
| 83 | 363 std::auto_ptr<DcmItem> item2(new DcmItem); |
| 364 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, | |
| 365 boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 366 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
| 0 | 367 |
| 83 | 368 std::auto_ptr<DcmItem> item3(new DcmItem); |
| 369 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
| 0 | 370 |
| 83 | 371 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
| 372 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
| 373 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
| 0 | 374 |
| 83 | 375 if (!sequence2->insert(item2.release(), false, false).good() || |
| 376 !sequence3->insert(item3.release(), false, false).good() || | |
| 377 !item->insert(sequence2.release(), false, false).good() || | |
| 378 !item->insert(sequence3.release(), false, false).good() || | |
| 379 !sequence->insert(item.release(), false, false).good() || | |
| 380 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 381 { | |
| 382 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 383 } | |
| 0 | 384 } |
| 385 } | |
| 386 | |
| 387 | |
| 388 static void EnrichDataset(DcmDataset& dataset, | |
| 389 const OrthancWSI::ITiledPyramid& source, | |
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390 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 391 const OrthancWSI::DicomizerParameters& parameters, |
| 392 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 393 { | |
| 394 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 395 | |
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396 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 397 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 398 { | |
| 399 // Takes as estimation a 1:10 compression ratio | |
| 400 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 401 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 402 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 403 } | |
| 404 else | |
| 405 { | |
| 406 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 407 } | |
| 408 | |
| 409 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 410 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 411 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 412 | |
| 413 std::auto_ptr<DcmItem> origin(new DcmItem); | |
| 414 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
| 415 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 416 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 417 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 418 | |
| 419 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
| 420 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
| 421 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 422 { | |
| 423 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 424 } | |
| 425 | |
| 426 | |
| 427 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 428 { | |
| 429 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 430 { | |
| 431 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 432 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 433 } | |
| 434 | |
| 435 std::string brightfield; | |
| 436 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 437 | |
| 438 Json::Value json; | |
| 439 Json::Reader reader; | |
| 440 if (!reader.parse(brightfield, json, false)) | |
| 441 { | |
| 442 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 443 } | |
| 444 | |
| 445 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
| 446 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
| 447 DCM_OpticalPathSequence.getElement()), | |
| 448 json, false, encoding)); | |
| 449 if (!dataset.insert(element.release()).good()) | |
| 450 { | |
| 451 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 452 } | |
| 453 } | |
| 454 | |
| 455 | |
| 456 std::string profile; | |
| 457 if (parameters.GetIccProfilePath().empty()) | |
| 458 { | |
| 459 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 460 } | |
| 461 else | |
| 462 { | |
| 43 | 463 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 464 } |
| 465 | |
| 466 | |
| 467 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 468 if (opticalPath == NULL) | |
| 469 { | |
| 470 LOG(ERROR) << "No optical path specified"; | |
| 471 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 472 } | |
| 473 | |
| 474 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 475 { | |
| 476 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
| 477 | |
| 478 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 479 !opticalPath->insert(icc.release()).good()) | |
| 480 { | |
| 481 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 482 } | |
| 483 } | |
| 484 | |
| 485 const char* opticalPathId = NULL; | |
| 486 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 487 opticalPathId == NULL) | |
| 488 { | |
| 489 LOG(ERROR) << "No identifier in the optical path"; | |
| 490 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 491 } | |
| 492 | |
| 493 SetupDimension(dataset, opticalPathId, source, volume); | |
| 494 } | |
| 495 | |
| 496 | |
| 497 static bool ParseParameters(int& exitStatus, | |
| 498 OrthancWSI::DicomizerParameters& parameters, | |
| 499 OrthancWSI::ImagedVolumeParameters& volume, | |
| 500 int argc, | |
| 501 char* argv[]) | |
| 502 { | |
| 503 // Declare the supported parameters | |
| 504 boost::program_options::options_description generic("Generic options"); | |
| 505 generic.add_options() | |
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506 (OPTION_HELP, "Display this help and exit") |
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507 (OPTION_VERSION, "Output version information and exit") |
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508 (OPTION_VERBOSE, "Be verbose in logs") |
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509 (OPTION_THREADS, |
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510 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 511 "Number of processing threads to be used") |
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512 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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513 "Path to the shared library of OpenSlide " |
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514 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 515 ; |
| 516 | |
| 517 boost::program_options::options_description source("Options for the source image"); | |
| 518 source.add_options() | |
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519 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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520 "Path to a JSON file containing the DICOM dataset") |
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521 (OPTION_SAMPLE_DATASET, |
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522 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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523 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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524 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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525 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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526 "Whether to repaint the background of the image (Boolean)") |
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527 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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528 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 529 ; |
| 530 | |
| 531 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 532 pyramid.add_options() | |
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533 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 534 "Reconstruct the full pyramid (slow) (Boolean)") |
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535 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 536 "Apply smoothing when reconstructing the pyramid " |
| 537 "(slower, but higher quality) (Boolean)") | |
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538 (OPTION_LEVELS, boost::program_options::value<int>(), |
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539 "Number of levels in the target pyramid") |
| 0 | 540 ; |
| 541 | |
| 542 boost::program_options::options_description target("Options for the target image"); | |
| 543 target.add_options() | |
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544 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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545 "Width of the tiles in the target image") |
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546 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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547 "Height of the tiles in the target image") |
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548 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 549 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
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550 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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551 "Set quality level for JPEG (0..100)") |
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552 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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553 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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554 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 555 "Folder where to store the output DICOM instances") |
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556 (OPTION_FOLDER_PATTERN, |
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557 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 558 "Pattern for the files in the output folder") |
| 559 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 560 "URL to the REST API of the target Orthanc server") | |
| 561 ; | |
| 562 | |
| 563 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 564 volumeOptions.add_options() | |
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565 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
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566 "Width of the specimen (in mm)") |
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567 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
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568 "Height of the specimen (in mm)") |
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569 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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570 "Depth of the specimen (in mm)") |
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571 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 572 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
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573 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 574 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 575 ; | |
| 576 | |
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577 boost::program_options::options_description restOptions |
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578 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
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579 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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580 |
| 0 | 581 boost::program_options::options_description advancedOptions("Advanced options"); |
| 582 advancedOptions.add_options() | |
|
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583 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 584 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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585 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 586 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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587 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 588 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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589 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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590 "Number of pyramid levels up to which multithreading " |
| 0 | 591 "should be applied (only for performance/memory tuning)") |
| 592 ; | |
| 593 | |
| 594 boost::program_options::options_description hidden; | |
| 595 hidden.add_options() | |
|
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596 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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597 "Input file"); |
| 0 | 598 ; |
| 599 | |
| 600 boost::program_options::options_description allWithoutHidden; | |
|
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601 allWithoutHidden |
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602 .add(generic) |
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603 .add(source) |
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604 .add(pyramid) |
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605 .add(target) |
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606 .add(volumeOptions) |
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607 .add(restOptions) |
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608 .add(advancedOptions); |
| 0 | 609 |
| 610 boost::program_options::options_description all = allWithoutHidden; | |
| 611 all.add(hidden); | |
| 612 | |
| 613 boost::program_options::positional_options_description positional; | |
|
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614 positional.add(OPTION_INPUT, 1); |
| 0 | 615 |
| 616 boost::program_options::variables_map options; | |
| 617 bool error = false; | |
| 618 | |
| 619 try | |
| 620 { | |
| 621 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 622 options(all).positional(positional).run(), options); | |
| 623 boost::program_options::notify(options); | |
| 624 } | |
| 625 catch (boost::program_options::error& e) | |
| 626 { | |
| 627 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 628 error = true; | |
| 629 } | |
| 630 | |
| 631 if (!error && | |
|
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632 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 633 { |
| 634 std::string sample; | |
| 635 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 636 | |
| 637 std::cout << std::endl << sample << std::endl; | |
| 638 | |
| 639 return false; | |
| 640 } | |
| 641 | |
| 642 if (!error && | |
|
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643 options.count(OPTION_HELP) == 0 && |
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644 options.count(OPTION_VERSION) == 0 && |
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645 options.count(OPTION_INPUT) != 1) |
| 0 | 646 { |
| 647 LOG(ERROR) << "No input file was specified"; | |
| 648 error = true; | |
| 649 } | |
| 650 | |
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651 if (error || options.count(OPTION_HELP)) |
| 0 | 652 { |
| 653 std::cout << std::endl | |
| 654 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 655 << std::endl | |
| 656 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 657 << std::endl << std::endl | |
| 658 << "Create a DICOM file from a digital pathology image." | |
| 659 << std::endl; | |
| 660 | |
| 661 std::cout << allWithoutHidden << "\n"; | |
| 662 | |
| 663 if (error) | |
| 664 { | |
| 665 exitStatus = -1; | |
| 666 } | |
| 667 | |
| 668 return false; | |
| 669 } | |
| 670 | |
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671 if (options.count(OPTION_VERSION)) |
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672 { |
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673 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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674 return false; |
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675 } |
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676 |
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677 if (options.count(OPTION_VERBOSE)) |
| 0 | 678 { |
| 679 Orthanc::Logging::EnableInfoLevel(true); | |
| 680 } | |
| 681 | |
|
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682 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 683 { |
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684 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 685 } |
| 686 | |
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687 if (options.count(OPTION_PYRAMID) && |
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688 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 689 { |
| 690 parameters.SetReconstructPyramid(true); | |
| 691 } | |
| 692 | |
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693 if (options.count(OPTION_SMOOTH) && |
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694 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 695 { |
| 696 parameters.SetSmoothEnabled(true); | |
| 697 } | |
| 698 | |
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699 if (options.count(OPTION_SAFETY) && |
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700 options[OPTION_SAFETY].as<bool>()) |
| 0 | 701 { |
| 702 parameters.SetSafetyCheck(true); | |
| 703 } | |
| 704 | |
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705 if (options.count(OPTION_REENCODE) && |
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706 options[OPTION_REENCODE].as<bool>()) |
| 0 | 707 { |
| 708 parameters.SetForceReencode(true); | |
| 709 } | |
| 710 | |
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711 if (options.count(OPTION_REPAINT) && |
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712 options[OPTION_REPAINT].as<bool>()) |
| 0 | 713 { |
| 714 parameters.SetRepaintBackground(true); | |
| 715 } | |
| 716 | |
|
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717 if (options.count(OPTION_TILE_WIDTH) || |
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718 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 719 { |
| 720 int w = 0; | |
|
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721 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 722 { |
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723 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 724 } |
| 725 | |
| 145 | 726 int h = 0; |
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727 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 728 { |
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729 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 730 } |
| 731 | |
| 732 if (w < 0 || h < 0) | |
| 733 { | |
| 734 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 735 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 736 } | |
| 737 | |
| 738 parameters.SetTargetTileSize(w, h); | |
| 739 } | |
| 740 | |
|
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741 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
| 0 | 742 |
|
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743 if (options.count(OPTION_COLOR)) |
| 0 | 744 { |
| 745 uint8_t r, g, b; | |
|
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746 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 747 parameters.SetBackgroundColor(r, g, b); |
| 748 } | |
| 749 | |
|
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750 if (options.count(OPTION_COMPRESSION)) |
| 0 | 751 { |
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752 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 753 if (s == "none") |
| 754 { | |
| 755 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 756 } | |
| 757 else if (s == "jpeg") | |
| 758 { | |
| 759 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 760 } | |
| 761 else if (s == "jpeg2000") | |
| 762 { | |
| 763 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 764 } | |
| 765 else | |
| 766 { | |
| 767 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 768 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 769 } | |
| 770 } | |
| 771 | |
|
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772 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 773 { |
|
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774 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 775 } |
| 776 | |
|
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777 if (options.count(OPTION_LEVELS)) |
| 0 | 778 { |
|
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779 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 780 } |
| 781 | |
|
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782 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 783 { |
|
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784 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 785 } |
| 786 | |
|
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787 if (options.count(OPTION_THREADS)) |
| 0 | 788 { |
|
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789 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 790 } |
| 791 | |
|
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792 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 793 { |
|
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794 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 795 } |
| 796 | |
|
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797 if (options.count(OPTION_FOLDER)) |
| 0 | 798 { |
|
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799 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 800 } |
| 801 | |
|
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802 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 803 { |
|
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804 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 805 } |
| 806 | |
|
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807 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 808 |
|
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809 if (options.count(OPTION_DATASET)) |
| 0 | 810 { |
|
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811 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 812 } |
| 813 | |
|
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814 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 815 { |
|
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816 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 817 } |
| 818 | |
|
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819 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 820 { |
|
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821 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 822 } |
| 823 | |
|
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824 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 825 { |
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826 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 827 } |
| 828 | |
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829 if (options.count(OPTION_OFFSET_X)) |
| 0 | 830 { |
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831 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 832 } |
| 833 | |
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834 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 835 { |
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836 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 837 } |
| 838 | |
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839 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 840 { |
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841 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 842 if (s == "none") |
| 843 { | |
| 844 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 845 } | |
| 846 else if (s == "brightfield") | |
| 847 { | |
| 848 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 849 } | |
| 850 else | |
| 851 { | |
| 852 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 853 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 854 } | |
| 855 } | |
| 856 | |
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857 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 858 { |
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859 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 860 } |
| 861 | |
| 862 return true; | |
| 863 } | |
| 864 | |
| 865 | |
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866 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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867 const std::string& path, |
| 0 | 868 const OrthancWSI::DicomizerParameters& parameters) |
| 869 { | |
| 870 LOG(WARNING) << "The input image is: " << path; | |
| 871 | |
| 872 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 873 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 874 | |
| 875 switch (format) | |
| 876 { | |
| 877 case OrthancWSI::ImageCompression_Png: | |
|
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878 { |
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879 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 880 return new OrthancWSI::TiledPngImage(path, |
| 881 parameters.GetTargetTileWidth(512), | |
| 882 parameters.GetTargetTileHeight(512)); | |
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883 } |
| 0 | 884 |
| 885 case OrthancWSI::ImageCompression_Jpeg: | |
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886 { |
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887 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 888 return new OrthancWSI::TiledJpegImage(path, |
| 889 parameters.GetTargetTileWidth(512), | |
| 890 parameters.GetTargetTileHeight(512)); | |
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891 } |
| 0 | 892 |
| 893 case OrthancWSI::ImageCompression_Tiff: | |
| 894 { | |
| 895 try | |
| 896 { | |
|
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897 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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898 sourceCompression = tiff->GetImageCompression(); |
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899 return tiff.release(); |
| 0 | 900 } |
| 901 catch (Orthanc::OrthancException&) | |
| 902 { | |
| 903 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 904 } | |
| 905 } | |
| 906 | |
| 907 default: | |
| 908 break; | |
| 909 } | |
| 910 | |
| 911 try | |
| 912 { | |
| 913 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
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914 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 915 return new OrthancWSI::OpenSlidePyramid(path, |
| 916 parameters.GetTargetTileWidth(512), | |
| 917 parameters.GetTargetTileHeight(512)); | |
| 918 } | |
| 919 catch (Orthanc::OrthancException&) | |
| 920 { | |
| 921 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 922 return NULL; | |
| 923 } | |
| 924 } | |
| 925 | |
| 926 | |
| 927 int main(int argc, char* argv[]) | |
| 928 { | |
| 929 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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930 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 931 |
| 932 int exitStatus = 0; | |
| 933 | |
| 934 try | |
| 935 { | |
| 936 OrthancWSI::DicomizerParameters parameters; | |
| 937 OrthancWSI::ImagedVolumeParameters volume; | |
| 938 | |
| 939 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 940 { | |
|
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941 OrthancWSI::ImageCompression sourceCompression; |
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942 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
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943 |
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944 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 945 if (source.get() == NULL) |
| 946 { | |
| 947 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 948 } | |
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949 |
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950 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 951 |
| 952 // Create the shared DICOM tags | |
| 953 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
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954 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 955 |
| 956 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
| 957 Recompress(*output, *source, *dataset, parameters, volume); | |
| 958 } | |
| 959 } | |
| 960 catch (Orthanc::OrthancException& e) | |
| 961 { | |
| 962 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 963 exitStatus = -1; | |
| 964 } | |
| 965 | |
| 966 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 967 | |
| 968 return exitStatus; | |
| 969 } |