Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 292:053af6d76f2a
fix shared library linking
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 13 Jul 2023 17:20:14 +0200 |
| parents | 5f783bf882fe |
| children | fa734a851551 |
| 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 | |
| 254 | 5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
| 6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium | |
| 0 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
| 9 * modify it under the terms of the GNU Affero General Public License | |
| 10 * as published by the Free Software Foundation, either version 3 of | |
| 11 * the License, or (at your option) any later version. | |
| 12 * | |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 16 * Affero General Public License for more details. | |
| 17 * | |
| 18 * You should have received a copy of the GNU Affero General Public License | |
| 19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 20 **/ | |
| 21 | |
| 22 | |
| 23 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 24 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
| 25 #include "../Framework/DicomToolbox.h" | |
| 26 #include "../Framework/DicomizerParameters.h" | |
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27 #include "../Framework/ImageToolbox.h" |
| 0 | 28 #include "../Framework/ImagedVolumeParameters.h" |
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29 #include "../Framework/Inputs/CytomineImage.h" |
| 0 | 30 #include "../Framework/Inputs/HierarchicalTiff.h" |
| 31 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 32 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 33 #include "../Framework/Inputs/TiledPngImage.h" | |
| 34 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 35 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 36 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 37 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 38 | |
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39 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 40 #include <DicomParsing/FromDcmtkBridge.h> |
| 41 #include <Logging.h> | |
| 42 #include <OrthancException.h> | |
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43 #include <Toolbox.h> |
| 192 | 44 #include <SystemToolbox.h> |
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45 |
| 0 | 46 #include "ApplicationToolbox.h" |
| 47 | |
| 48 #include <EmbeddedResources.h> | |
| 49 | |
| 50 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 51 #include <dcmtk/dcmdata/dcuid.h> | |
| 52 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 53 #include <dcmtk/dcmdata/dcvrat.h> | |
| 54 | |
| 55 | |
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56 static const char* OPTION_COLOR = "color"; |
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57 static const char* OPTION_COMPRESSION = "compression"; |
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58 static const char* OPTION_DATASET = "dataset"; |
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59 static const char* OPTION_FOLDER = "folder"; |
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60 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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61 static const char* OPTION_HELP = "help"; |
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62 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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63 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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64 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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65 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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66 static const char* OPTION_INPUT = "input"; |
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67 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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68 static const char* OPTION_LEVELS = "levels"; |
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69 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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70 static const char* OPTION_MAX_SIZE = "max-size"; |
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71 static const char* OPTION_OFFSET_X = "offset-x"; |
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72 static const char* OPTION_OFFSET_Y = "offset-y"; |
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73 static const char* OPTION_OPENSLIDE = "openslide"; |
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74 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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75 static const char* OPTION_PYRAMID = "pyramid"; |
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76 static const char* OPTION_REENCODE = "reencode"; |
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77 static const char* OPTION_REPAINT = "repaint"; |
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78 static const char* OPTION_SAFETY = "safety"; |
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79 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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80 static const char* OPTION_SMOOTH = "smooth"; |
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81 static const char* OPTION_THREADS = "threads"; |
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82 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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83 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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84 static const char* OPTION_VERBOSE = "verbose"; |
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85 static const char* OPTION_VERSION = "version"; |
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86 |
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87 // New in release 1.1 |
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88 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
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89 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
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90 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
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91 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
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92 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
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93 |
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94 |
| 226 | 95 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 96 | |
| 97 bool ReadJsonWithoutComments(Json::Value& target, | |
| 98 const std::string& source) | |
| 99 { | |
| 100 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 101 } | |
| 102 | |
| 103 #else | |
| 104 | |
| 105 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 106 #include <json/reader.h> | |
| 107 | |
| 108 bool ReadJsonWithoutComments(Json::Value& target, | |
| 109 const std::string& source) | |
| 110 { | |
| 111 Json::Reader reader; | |
| 112 return reader.parse(source, target, false); | |
| 113 } | |
| 114 #endif | |
| 115 | |
| 116 | |
| 0 | 117 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 118 OrthancWSI::ITiledPyramid& source, | |
| 119 const OrthancWSI::DicomizerParameters& parameters) | |
| 120 { | |
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121 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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122 |
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123 OrthancWSI::BagOfTasks tasks; |
| 0 | 124 |
| 125 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 126 { | |
| 127 LOG(WARNING) << "Creating level " << i << " of size " | |
| 128 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 129 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 130 } | |
| 131 | |
| 132 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 133 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 134 } | |
| 135 | |
| 136 | |
| 137 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 138 OrthancWSI::ITiledPyramid& source, | |
| 139 const OrthancWSI::DicomizerParameters& parameters) | |
| 140 { | |
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141 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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142 |
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143 OrthancWSI::BagOfTasks tasks; |
| 0 | 144 |
| 145 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 146 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 147 assert(levelsCount >= 1); | |
| 148 | |
| 149 for (unsigned int i = 0; i < levelsCount; i++) | |
| 150 { | |
| 151 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 152 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 153 | |
| 154 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 155 target.AddLevel(width, height); | |
| 156 } | |
| 157 | |
| 158 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 159 if (lowerLevelsCount > levelsCount) | |
| 160 { | |
| 161 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 162 << ") exceeds the number of levels (" << levelsCount | |
| 163 << "), cropping it"; | |
| 164 lowerLevelsCount = levelsCount; | |
| 165 } | |
| 166 | |
| 167 assert(lowerLevelsCount <= levelsCount); | |
| 168 if (lowerLevelsCount != levelsCount) | |
| 169 { | |
| 170 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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171 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 172 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 173 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 174 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 175 | |
| 176 assert(tasks.GetSize() == 0); | |
| 177 | |
| 178 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 179 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 180 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 181 (tasks, target, truncated.GetUpperLevel(), | |
| 182 upperLevelsCount, lowerLevelsCount, parameters); | |
| 183 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 184 } | |
| 185 else | |
| 186 { | |
| 187 LOG(WARNING) << "Constructing the pyramid"; | |
| 188 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 189 (tasks, target, source, levelsCount, 0, parameters); | |
| 190 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 191 } | |
| 192 } | |
| 193 | |
| 194 | |
| 195 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 196 OrthancWSI::ITiledPyramid& source, | |
| 197 const DcmDataset& dataset, | |
| 198 const OrthancWSI::DicomizerParameters& parameters, | |
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199 const OrthancWSI::ImagedVolumeParameters& volume, |
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200 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 201 { |
| 202 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 203 | |
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204 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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205 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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206 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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207 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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208 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 209 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 210 | |
| 211 if (parameters.IsRepaintBackground()) | |
| 212 { | |
| 213 LOG(WARNING) << "Repainting the background with color: (" | |
| 214 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 215 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 216 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 217 } | |
| 218 else | |
| 219 { | |
| 220 LOG(WARNING) << "No repainting of the background"; | |
| 221 } | |
| 222 | |
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223 Orthanc::PhotometricInterpretation targetPhotometric; |
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224 bool transcoding; |
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225 |
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226 if (parameters.IsForceReencode() || |
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227 parameters.IsReconstructPyramid() || |
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228 sourceCompression != parameters.GetTargetCompression()) |
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229 { |
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230 // The tiles of the source image will be re-encoded |
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231 transcoding = false; |
| 171 | 232 |
| 233 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 234 { | |
| 235 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 236 } | |
| 237 else | |
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238 { |
| 171 | 239 switch (parameters.GetTargetCompression()) |
| 240 { | |
| 241 case OrthancWSI::ImageCompression_Jpeg: | |
| 242 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 243 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 244 break; | |
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245 |
| 171 | 246 case OrthancWSI::ImageCompression_None: |
| 247 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 248 break; | |
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249 |
| 171 | 250 default: |
| 251 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 252 } | |
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253 } |
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254 } |
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255 else |
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256 { |
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257 // Transcoding: The tiles are copied (no re-encoding) |
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258 transcoding = true; |
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259 targetPhotometric = source.GetPhotometricInterpretation(); |
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260 } |
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261 |
| 0 | 262 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 263 source.GetPixelFormat(), | |
| 264 parameters.GetTargetCompression(), | |
| 265 parameters.GetTargetTileWidth(source), | |
| 266 parameters.GetTargetTileHeight(source), | |
| 267 parameters.GetDicomMaxFileSize(), | |
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268 volume, targetPhotometric); |
| 29 | 269 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 270 |
| 271 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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272 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 273 |
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274 if (!transcoding && |
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275 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 276 { |
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277 LOG(WARNING) << "Target compression: Jpeg with quality " |
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278 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 279 target.SetJpegQuality(target.GetJpegQuality()); |
| 280 } | |
| 281 else | |
| 282 { | |
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283 LOG(WARNING) << "Target compression: " |
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284 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 285 } |
| 286 | |
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287 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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288 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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289 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 290 { |
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291 LOG(ERROR) << "When resampling the tile size, " |
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292 << "it must be a integer divisor of the original tile size"; |
| 0 | 293 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 294 } | |
| 295 | |
| 296 if (target.GetTileWidth() <= 16 || | |
| 297 target.GetTileHeight() <= 16) | |
| 298 { | |
| 299 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 300 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 301 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 302 } | |
| 303 | |
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304 if (transcoding) |
| 0 | 305 { |
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306 TranscodePyramid(target, stats, parameters); |
| 0 | 307 } |
| 308 else | |
| 309 { | |
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310 ReconstructPyramid(target, stats, parameters); |
| 0 | 311 } |
| 312 | |
| 313 target.Flush(); | |
| 314 } | |
| 315 | |
| 316 | |
| 317 | |
| 318 static DcmDataset* ParseDataset(const std::string& path) | |
| 319 { | |
| 320 Json::Value json; | |
| 321 | |
| 322 if (path.empty()) | |
| 323 { | |
| 324 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 325 } | |
| 326 else | |
| 327 { | |
| 328 std::string content; | |
| 43 | 329 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 330 |
| 226 | 331 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 332 { |
| 333 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 335 } | |
| 336 } | |
| 337 | |
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338 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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339 "" /* no private tag, thus no private creator */)); |
| 0 | 340 if (dataset.get() == NULL) |
| 341 { | |
| 342 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 343 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 344 } | |
| 345 | |
| 346 // VL Whole Slide Microscopy Image IOD | |
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347 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
| 0 | 348 |
| 349 // Slide Microscopy | |
| 350 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 351 | |
| 352 // Patient orientation makes no sense in whole-slide images | |
| 353 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 354 | |
| 355 // Some basic coordinate information | |
| 356 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 357 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 358 | |
| 359 std::string date, time; | |
| 130 | 360 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 361 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 362 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 363 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 364 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 365 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 366 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 368 | |
| 369 return dataset.release(); | |
| 370 } | |
| 371 | |
| 372 | |
| 373 | |
| 374 static void SetupDimension(DcmDataset& dataset, | |
| 375 const std::string& opticalPathId, | |
| 376 const OrthancWSI::ITiledPyramid& source, | |
| 377 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 378 { | |
| 83 | 379 // Extract the identifier of the Dimension Organization, if provided |
| 380 std::string organization; | |
| 0 | 381 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 382 | |
| 83 | 383 if (previous != NULL && |
| 384 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 385 { | |
| 386 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 387 } | |
| 388 else | |
| 0 | 389 { |
| 83 | 390 // No Dimension Organization provided: Generate an unique identifier |
| 391 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 392 } | |
| 393 | |
| 394 | |
| 395 { | |
| 396 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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397 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 398 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 399 | |
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400 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 401 |
| 402 if (!sequence->insert(item.release(), false, false).good() || | |
| 403 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 404 { |
| 83 | 405 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 406 } |
| 407 } | |
| 408 | |
| 83 | 409 |
| 0 | 410 { |
| 83 | 411 // Construct tag "Dimension Index Sequence" (0020,9222) |
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412 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 413 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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414 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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415 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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416 |
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417 std::unique_ptr<DcmItem> item2(new DcmItem); |
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418 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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419 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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420 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 421 |
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422 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 423 |
| 83 | 424 if (!sequence->insert(item.release(), false, false).good() || |
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425 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 426 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 427 { | |
| 428 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 429 } | |
| 0 | 430 } |
| 431 | |
| 432 | |
| 83 | 433 { |
| 434 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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435 std::unique_ptr<DcmItem> item(new DcmItem); |
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436 |
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437 std::unique_ptr<DcmItem> item3(new DcmItem); |
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438 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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439 |
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440 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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441 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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442 |
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443 if (!sequence3->insert(item3.release(), false, false).good() || |
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444 !item->insert(sequence3.release(), false, false).good() || |
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445 !sequence->insert(item.release(), false, false).good() || |
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446 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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447 { |
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448 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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449 } |
| 0 | 450 } |
| 451 } | |
| 452 | |
| 453 | |
| 454 static void EnrichDataset(DcmDataset& dataset, | |
| 455 const OrthancWSI::ITiledPyramid& source, | |
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456 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 457 const OrthancWSI::DicomizerParameters& parameters, |
| 458 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 459 { | |
| 460 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 461 | |
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462 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 463 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 464 { | |
| 465 // Takes as estimation a 1:10 compression ratio | |
| 466 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 467 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 468 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 469 } | |
| 470 else | |
| 471 { | |
| 472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 473 } | |
| 474 | |
| 475 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 476 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 477 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 478 | |
|
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479 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 480 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 481 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 482 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 483 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 484 | |
|
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485 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 486 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 487 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 488 { | |
| 489 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 490 } | |
| 491 | |
| 492 | |
| 493 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 494 { | |
| 495 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 496 { | |
| 497 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 498 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 499 } | |
| 500 | |
| 501 std::string brightfield; | |
| 502 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 503 | |
| 504 Json::Value json; | |
| 226 | 505 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 506 { |
| 507 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 508 } | |
| 509 | |
|
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510 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 511 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 512 DCM_OpticalPathSequence.getElement()), | |
|
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513 json, false, encoding, |
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514 "" /* no private tag, thus no private creator */)); |
| 0 | 515 if (!dataset.insert(element.release()).good()) |
| 516 { | |
| 517 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 518 } | |
| 519 } | |
| 520 | |
| 521 | |
| 522 std::string profile; | |
| 523 if (parameters.GetIccProfilePath().empty()) | |
| 524 { | |
| 525 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 526 } | |
| 527 else | |
| 528 { | |
| 43 | 529 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 530 } |
| 531 | |
| 532 | |
| 533 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 534 if (opticalPath == NULL) | |
| 535 { | |
| 536 LOG(ERROR) << "No optical path specified"; | |
| 537 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 538 } | |
| 539 | |
| 540 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 541 { | |
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542 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 543 |
| 544 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 545 !opticalPath->insert(icc.release()).good()) | |
| 546 { | |
| 547 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 548 } | |
| 549 } | |
| 550 | |
| 551 const char* opticalPathId = NULL; | |
| 552 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 553 opticalPathId == NULL) | |
| 554 { | |
| 555 LOG(ERROR) << "No identifier in the optical path"; | |
| 556 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 557 } | |
| 558 | |
| 559 SetupDimension(dataset, opticalPathId, source, volume); | |
| 560 } | |
| 561 | |
| 562 | |
| 563 static bool ParseParameters(int& exitStatus, | |
| 564 OrthancWSI::DicomizerParameters& parameters, | |
| 565 OrthancWSI::ImagedVolumeParameters& volume, | |
| 566 int argc, | |
| 567 char* argv[]) | |
| 568 { | |
| 569 // Declare the supported parameters | |
| 570 boost::program_options::options_description generic("Generic options"); | |
| 571 generic.add_options() | |
|
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572 (OPTION_HELP, "Display this help and exit") |
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573 (OPTION_VERSION, "Output version information and exit") |
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574 (OPTION_VERBOSE, "Be verbose in logs") |
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575 (OPTION_THREADS, |
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576 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 577 "Number of processing threads to be used") |
|
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578 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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579 "Path to the shared library of OpenSlide " |
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580 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 581 ; |
| 582 | |
| 583 boost::program_options::options_description source("Options for the source image"); | |
| 584 source.add_options() | |
|
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585 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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586 "Path to a JSON file containing the DICOM dataset") |
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587 (OPTION_SAMPLE_DATASET, |
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588 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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589 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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590 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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591 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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592 "Whether to repaint the background of the image (Boolean)") |
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593 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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594 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 595 ; |
| 596 | |
|
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597 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
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598 cytomine.add_options() |
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599 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
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600 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
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601 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
| 246 | 602 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
|
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603 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
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604 "Your personal private key in Cytomine (to be kept secret)") |
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605 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
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606 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
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607 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
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608 "Compression to be used for downloading the tiles from Cytomine, " |
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609 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
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610 ; |
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611 |
| 0 | 612 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
| 613 pyramid.add_options() | |
|
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614 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 615 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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616 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 617 "Apply smoothing when reconstructing the pyramid " |
| 618 "(slower, but higher quality) (Boolean)") | |
|
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619 (OPTION_LEVELS, boost::program_options::value<int>(), |
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620 "Number of levels in the target pyramid") |
| 0 | 621 ; |
| 622 | |
| 623 boost::program_options::options_description target("Options for the target image"); | |
| 624 target.add_options() | |
|
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625 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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626 "Width of the tiles in the target image") |
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627 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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628 "Height of the tiles in the target image") |
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629 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 630 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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631 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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632 "Set quality level for JPEG (0..100)") |
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633 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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634 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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635 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 636 "Folder where to store the output DICOM instances") |
|
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637 (OPTION_FOLDER_PATTERN, |
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638 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 639 "Pattern for the files in the output folder") |
| 640 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 641 "URL to the REST API of the target Orthanc server") | |
| 642 ; | |
| 643 | |
| 644 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 645 volumeOptions.add_options() | |
|
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646 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
|
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647 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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648 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
|
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649 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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650 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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651 "Depth of the specimen (in mm)") |
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652 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 653 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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654 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 655 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 656 ; | |
| 657 | |
|
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658 boost::program_options::options_description restOptions |
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659 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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660 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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661 |
| 0 | 662 boost::program_options::options_description advancedOptions("Advanced options"); |
| 663 advancedOptions.add_options() | |
|
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664 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 665 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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666 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 667 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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668 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 669 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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670 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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671 "Number of pyramid levels up to which multithreading " |
| 0 | 672 "should be applied (only for performance/memory tuning)") |
| 673 ; | |
| 674 | |
| 675 boost::program_options::options_description hidden; | |
| 676 hidden.add_options() | |
|
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677 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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678 "Input file"); |
| 0 | 679 ; |
| 680 | |
| 681 boost::program_options::options_description allWithoutHidden; | |
|
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682 allWithoutHidden |
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683 .add(generic) |
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684 .add(source) |
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685 .add(cytomine) |
|
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686 .add(pyramid) |
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687 .add(target) |
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688 .add(volumeOptions) |
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689 .add(restOptions) |
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690 .add(advancedOptions); |
| 0 | 691 |
| 692 boost::program_options::options_description all = allWithoutHidden; | |
| 693 all.add(hidden); | |
| 694 | |
| 695 boost::program_options::positional_options_description positional; | |
|
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696 positional.add(OPTION_INPUT, 1); |
| 0 | 697 |
| 698 boost::program_options::variables_map options; | |
| 699 bool error = false; | |
| 700 | |
| 701 try | |
| 702 { | |
| 703 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 704 options(all).positional(positional).run(), options); | |
| 705 boost::program_options::notify(options); | |
| 706 } | |
| 707 catch (boost::program_options::error& e) | |
| 708 { | |
| 709 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 710 error = true; | |
| 711 } | |
| 712 | |
| 713 if (!error && | |
|
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714 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 715 { |
| 716 std::string sample; | |
| 717 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 718 | |
| 719 std::cout << std::endl << sample << std::endl; | |
| 720 | |
| 721 return false; | |
| 722 } | |
| 723 | |
|
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724 // New in release 1.1 |
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725 if (options.count(OPTION_CYTOMINE_URL) || |
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726 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
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727 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
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728 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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729 { |
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730 if (!options.count(OPTION_CYTOMINE_URL)) |
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731 { |
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732 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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733 "URL to the Cytomine server is missing"); |
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734 } |
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735 |
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736 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
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737 { |
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738 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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739 "Public key for the Cytomine server is missing"); |
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740 } |
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741 |
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742 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
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743 { |
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744 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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745 "Private key for the Cytomine server is missing"); |
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746 } |
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747 |
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748 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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749 { |
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750 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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751 "The Image Instance ID from the Cytomine server is missing"); |
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752 } |
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753 |
|
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754 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
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755 { |
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756 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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757 "The tile compression scheme for Cytomine is missing"); |
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758 } |
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|
759 |
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760 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
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761 |
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762 OrthancWSI::ImageCompression compression; |
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763 if (s == "jpeg") |
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764 { |
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765 compression = OrthancWSI::ImageCompression_Jpeg; |
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766 } |
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767 else if (s == "png") |
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768 { |
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769 compression = OrthancWSI::ImageCompression_Png; |
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770 } |
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771 else |
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772 { |
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773 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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774 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
|
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775 } |
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776 |
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777 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
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778 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
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779 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
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780 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
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781 } |
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782 |
| 0 | 783 if (!error && |
|
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784 options.count(OPTION_HELP) == 0 && |
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785 options.count(OPTION_VERSION) == 0 && |
|
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786 options.count(OPTION_INPUT) != 1 && |
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787 !parameters.IsCytomineSource()) |
| 0 | 788 { |
| 789 LOG(ERROR) << "No input file was specified"; | |
| 790 error = true; | |
| 791 } | |
| 792 | |
|
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793 if (error || options.count(OPTION_HELP)) |
| 0 | 794 { |
| 795 std::cout << std::endl | |
| 796 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 797 << std::endl | |
| 798 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 799 << std::endl << std::endl | |
| 800 << "Create a DICOM file from a digital pathology image." | |
| 801 << std::endl; | |
| 802 | |
| 803 std::cout << allWithoutHidden << "\n"; | |
| 804 | |
| 805 if (error) | |
| 806 { | |
| 807 exitStatus = -1; | |
| 808 } | |
| 809 | |
| 810 return false; | |
| 811 } | |
| 812 | |
|
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813 if (options.count(OPTION_VERSION)) |
|
8
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|
814 { |
|
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|
815 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
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|
816 return false; |
|
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|
817 } |
|
62adabb8c122
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|
818 |
|
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819 if (options.count(OPTION_VERBOSE)) |
| 0 | 820 { |
| 821 Orthanc::Logging::EnableInfoLevel(true); | |
| 822 } | |
| 823 | |
|
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824 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 825 { |
|
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826 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 827 } |
| 828 | |
|
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829 if (options.count(OPTION_PYRAMID) && |
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830 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 831 { |
| 832 parameters.SetReconstructPyramid(true); | |
| 833 } | |
| 834 | |
|
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835 if (options.count(OPTION_SMOOTH) && |
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836 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 837 { |
| 838 parameters.SetSmoothEnabled(true); | |
| 839 } | |
| 840 | |
|
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841 if (options.count(OPTION_SAFETY) && |
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842 options[OPTION_SAFETY].as<bool>()) |
| 0 | 843 { |
| 844 parameters.SetSafetyCheck(true); | |
| 845 } | |
| 846 | |
|
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847 if (options.count(OPTION_REENCODE) && |
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848 options[OPTION_REENCODE].as<bool>()) |
| 0 | 849 { |
| 850 parameters.SetForceReencode(true); | |
| 851 } | |
| 852 | |
|
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853 if (options.count(OPTION_REPAINT) && |
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854 options[OPTION_REPAINT].as<bool>()) |
| 0 | 855 { |
| 856 parameters.SetRepaintBackground(true); | |
| 857 } | |
| 858 | |
|
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859 if (options.count(OPTION_TILE_WIDTH) || |
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860 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 861 { |
| 862 int w = 0; | |
|
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863 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 864 { |
|
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865 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 866 } |
| 867 | |
| 145 | 868 int h = 0; |
|
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869 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 870 { |
|
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871 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 872 } |
| 873 | |
| 874 if (w < 0 || h < 0) | |
| 875 { | |
| 876 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 877 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 878 } | |
| 879 | |
| 880 parameters.SetTargetTileSize(w, h); | |
| 881 } | |
| 882 | |
|
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883 if (!parameters.IsCytomineSource()) |
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884 { |
|
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885 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
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886 } |
| 0 | 887 |
|
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888 if (options.count(OPTION_COLOR)) |
| 0 | 889 { |
| 890 uint8_t r, g, b; | |
|
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891 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 892 parameters.SetBackgroundColor(r, g, b); |
| 893 } | |
| 894 | |
|
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895 if (options.count(OPTION_COMPRESSION)) |
| 0 | 896 { |
|
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897 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 898 if (s == "none") |
| 899 { | |
| 900 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 901 } | |
| 902 else if (s == "jpeg") | |
| 903 { | |
| 904 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 905 } | |
| 906 else if (s == "jpeg2000") | |
| 907 { | |
| 908 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 909 } | |
| 910 else | |
| 911 { | |
| 912 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 913 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 914 } | |
| 915 } | |
| 916 | |
|
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917 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 918 { |
|
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919 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 920 } |
| 921 | |
|
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922 if (options.count(OPTION_LEVELS)) |
| 0 | 923 { |
|
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924 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 925 } |
| 926 | |
|
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927 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 928 { |
|
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929 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 930 } |
| 931 | |
|
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932 if (options.count(OPTION_THREADS)) |
| 0 | 933 { |
|
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934 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 935 } |
| 936 | |
|
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937 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 938 { |
|
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939 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 940 } |
| 941 | |
|
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942 if (options.count(OPTION_FOLDER)) |
| 0 | 943 { |
|
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944 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 945 } |
| 946 | |
|
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947 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 948 { |
|
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949 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 950 } |
| 951 | |
|
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952 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 953 |
|
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954 if (options.count(OPTION_DATASET)) |
| 0 | 955 { |
|
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956 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 957 } |
| 958 | |
|
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959 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 960 { |
|
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961 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 962 } |
| 963 | |
|
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964 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 965 { |
|
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966 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 967 } |
| 968 | |
|
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969 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 970 { |
|
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971 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 972 } |
| 973 | |
|
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974 if (options.count(OPTION_OFFSET_X)) |
| 0 | 975 { |
|
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976 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 977 } |
| 978 | |
|
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979 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 980 { |
|
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981 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 982 } |
| 983 | |
|
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984 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 985 { |
|
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986 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 987 if (s == "none") |
| 988 { | |
| 989 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 990 } | |
| 991 else if (s == "brightfield") | |
| 992 { | |
| 993 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 994 } | |
| 995 else | |
| 996 { | |
| 997 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 998 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 999 } | |
| 1000 } | |
| 1001 | |
|
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1002 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 1003 { |
|
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1004 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 1005 } |
| 1006 | |
| 1007 return true; | |
| 1008 } | |
| 1009 | |
| 1010 | |
|
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1011 |
|
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1012 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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1013 OrthancWSI::ImagedVolumeParameters& volume, |
|
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1014 const std::string& path, |
| 0 | 1015 const OrthancWSI::DicomizerParameters& parameters) |
| 1016 { | |
|
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1017 if (parameters.IsCytomineSource()) |
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1018 { |
|
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1019 // New in release 1.1 |
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1020 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
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1021 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
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1022 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1023 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
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1024 parameters.GetCytominePublicKey(), |
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1025 parameters.GetCytominePrivateKey(), |
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1026 parameters.GetCytomineImageInstanceId(), |
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1027 parameters.GetTargetTileWidth(512), |
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1028 parameters.GetTargetTileHeight(512)); |
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1029 } |
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1030 |
| 0 | 1031 LOG(WARNING) << "The input image is: " << path; |
| 1032 | |
| 1033 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 1034 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 1035 | |
| 1036 switch (format) | |
| 1037 { | |
| 1038 case OrthancWSI::ImageCompression_Png: | |
|
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1039 { |
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1040 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1041 return new OrthancWSI::TiledPngImage(path, |
| 1042 parameters.GetTargetTileWidth(512), | |
| 1043 parameters.GetTargetTileHeight(512)); | |
|
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1044 } |
| 0 | 1045 |
| 1046 case OrthancWSI::ImageCompression_Jpeg: | |
|
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1047 { |
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1048 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1049 return new OrthancWSI::TiledJpegImage(path, |
| 1050 parameters.GetTargetTileWidth(512), | |
| 1051 parameters.GetTargetTileHeight(512)); | |
|
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1052 } |
| 0 | 1053 |
| 1054 case OrthancWSI::ImageCompression_Tiff: | |
| 1055 { | |
| 1056 try | |
| 1057 { | |
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1058 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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1059 sourceCompression = tiff->GetImageCompression(); |
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1060 return tiff.release(); |
| 0 | 1061 } |
| 1062 catch (Orthanc::OrthancException&) | |
| 1063 { | |
| 1064 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 1065 } | |
| 1066 } | |
| 1067 | |
| 1068 default: | |
| 1069 break; | |
| 1070 } | |
| 1071 | |
| 1072 try | |
| 1073 { | |
| 1074 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
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1075 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1076 |
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1077 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
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1078 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
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1079 parameters.GetTargetTileHeight(512))); |
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1080 |
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1081 float volumeWidth, volumeHeight; |
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1082 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
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1083 { |
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1084 if (!volume.HasWidth()) |
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1085 { |
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1086 volume.SetWidth(volumeWidth); |
| 281 | 1087 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
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1088 } |
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1089 |
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1090 if (!volume.HasHeight()) |
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1091 { |
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1092 volume.SetHeight(volumeHeight); |
| 281 | 1093 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
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1094 } |
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1095 } |
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1096 |
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1097 return openslide.release(); |
| 0 | 1098 } |
| 1099 catch (Orthanc::OrthancException&) | |
| 1100 { | |
| 1101 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 1102 return NULL; | |
| 1103 } | |
| 1104 } | |
| 1105 | |
| 1106 | |
| 1107 int main(int argc, char* argv[]) | |
| 1108 { | |
| 1109 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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1110 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 1111 |
| 1112 int exitStatus = 0; | |
| 1113 | |
| 1114 try | |
| 1115 { | |
| 1116 OrthancWSI::DicomizerParameters parameters; | |
| 1117 OrthancWSI::ImagedVolumeParameters volume; | |
| 1118 | |
| 1119 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 1120 { | |
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1121 OrthancWSI::ImageCompression sourceCompression; |
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1122 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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1123 |
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1124 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
| 0 | 1125 if (source.get() == NULL) |
| 1126 { | |
| 1127 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1128 } | |
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1129 |
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1130 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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1131 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
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1132 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
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1133 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
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1134 { |
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1135 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
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1136 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
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1137 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
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1138 } |
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1139 |
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1140 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1141 |
| 1142 // Create the shared DICOM tags | |
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1143 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1144 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1145 |
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1146 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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1147 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1148 } |
| 1149 } | |
| 1150 catch (Orthanc::OrthancException& e) | |
| 1151 { | |
| 1152 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1153 exitStatus = -1; | |
| 1154 } | |
| 1155 | |
| 1156 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1157 | |
| 1158 return exitStatus; | |
| 1159 } |