Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 308:13721d3da291
cont
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sat, 27 Jan 2024 14:40:32 +0100 |
| parents | fa734a851551 |
| children | 7020852a8fa9 |
| 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" | |
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32 #include "../Framework/Inputs/PlainTiff.h" |
| 0 | 33 #include "../Framework/Inputs/TiledJpegImage.h" |
| 34 #include "../Framework/Inputs/TiledPngImage.h" | |
| 35 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 36 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 37 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 38 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 39 | |
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40 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 41 #include <DicomParsing/FromDcmtkBridge.h> |
| 42 #include <Logging.h> | |
| 43 #include <OrthancException.h> | |
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44 #include <Toolbox.h> |
| 192 | 45 #include <SystemToolbox.h> |
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46 |
| 0 | 47 #include "ApplicationToolbox.h" |
| 48 | |
| 49 #include <EmbeddedResources.h> | |
| 50 | |
| 51 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 52 #include <dcmtk/dcmdata/dcuid.h> | |
| 53 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 54 #include <dcmtk/dcmdata/dcvrat.h> | |
| 55 | |
| 56 | |
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57 static const char* OPTION_COLOR = "color"; |
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58 static const char* OPTION_COMPRESSION = "compression"; |
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59 static const char* OPTION_DATASET = "dataset"; |
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60 static const char* OPTION_FOLDER = "folder"; |
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61 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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62 static const char* OPTION_HELP = "help"; |
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63 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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64 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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65 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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66 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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67 static const char* OPTION_INPUT = "input"; |
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68 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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69 static const char* OPTION_LEVELS = "levels"; |
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70 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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71 static const char* OPTION_MAX_SIZE = "max-size"; |
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72 static const char* OPTION_OFFSET_X = "offset-x"; |
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73 static const char* OPTION_OFFSET_Y = "offset-y"; |
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74 static const char* OPTION_OPENSLIDE = "openslide"; |
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75 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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76 static const char* OPTION_PYRAMID = "pyramid"; |
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77 static const char* OPTION_REENCODE = "reencode"; |
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78 static const char* OPTION_REPAINT = "repaint"; |
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79 static const char* OPTION_SAFETY = "safety"; |
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80 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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81 static const char* OPTION_SMOOTH = "smooth"; |
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82 static const char* OPTION_THREADS = "threads"; |
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83 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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84 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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85 static const char* OPTION_VERBOSE = "verbose"; |
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86 static const char* OPTION_VERSION = "version"; |
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87 |
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88 // New in release 1.1 |
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89 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
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90 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
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91 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
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92 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
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93 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
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94 |
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95 // New in release 2.1 |
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96 static const char* OPTION_TIFF_ALIGNMENT = "tiff-alignment"; |
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97 |
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98 |
| 226 | 99 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 100 | |
| 101 bool ReadJsonWithoutComments(Json::Value& target, | |
| 102 const std::string& source) | |
| 103 { | |
| 104 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 105 } | |
| 106 | |
| 107 #else | |
| 108 | |
| 109 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 110 #include <json/reader.h> | |
| 111 | |
| 112 bool ReadJsonWithoutComments(Json::Value& target, | |
| 113 const std::string& source) | |
| 114 { | |
| 115 Json::Reader reader; | |
| 116 return reader.parse(source, target, false); | |
| 117 } | |
| 118 #endif | |
| 119 | |
| 120 | |
| 0 | 121 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 122 OrthancWSI::ITiledPyramid& source, | |
| 123 const OrthancWSI::DicomizerParameters& parameters) | |
| 124 { | |
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125 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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126 |
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127 OrthancWSI::BagOfTasks tasks; |
| 0 | 128 |
| 129 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 130 { | |
| 131 LOG(WARNING) << "Creating level " << i << " of size " | |
| 132 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 133 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 134 } | |
| 135 | |
| 136 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 137 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 138 } | |
| 139 | |
| 140 | |
| 141 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 142 OrthancWSI::ITiledPyramid& source, | |
| 143 const OrthancWSI::DicomizerParameters& parameters) | |
| 144 { | |
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145 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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146 |
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147 OrthancWSI::BagOfTasks tasks; |
| 0 | 148 |
| 149 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 150 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 151 assert(levelsCount >= 1); | |
| 152 | |
| 153 for (unsigned int i = 0; i < levelsCount; i++) | |
| 154 { | |
| 155 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 156 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 157 | |
| 158 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 159 target.AddLevel(width, height); | |
| 160 } | |
| 161 | |
| 162 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 163 if (lowerLevelsCount > levelsCount) | |
| 164 { | |
| 165 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 166 << ") exceeds the number of levels (" << levelsCount | |
| 167 << "), cropping it"; | |
| 168 lowerLevelsCount = levelsCount; | |
| 169 } | |
| 170 | |
| 171 assert(lowerLevelsCount <= levelsCount); | |
| 172 if (lowerLevelsCount != levelsCount) | |
| 173 { | |
| 174 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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175 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 176 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 177 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 178 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 179 | |
| 180 assert(tasks.GetSize() == 0); | |
| 181 | |
| 182 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 183 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 184 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 185 (tasks, target, truncated.GetUpperLevel(), | |
| 186 upperLevelsCount, lowerLevelsCount, parameters); | |
| 187 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 188 } | |
| 189 else | |
| 190 { | |
| 191 LOG(WARNING) << "Constructing the pyramid"; | |
| 192 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 193 (tasks, target, source, levelsCount, 0, parameters); | |
| 194 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 195 } | |
| 196 } | |
| 197 | |
| 198 | |
| 199 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 200 OrthancWSI::ITiledPyramid& source, | |
| 201 const DcmDataset& dataset, | |
| 202 const OrthancWSI::DicomizerParameters& parameters, | |
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203 const OrthancWSI::ImagedVolumeParameters& volume, |
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204 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 205 { |
| 206 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 207 | |
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208 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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209 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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210 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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211 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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212 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 213 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 214 | |
| 215 if (parameters.IsRepaintBackground()) | |
| 216 { | |
| 217 LOG(WARNING) << "Repainting the background with color: (" | |
| 218 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 219 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 220 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 221 } | |
| 222 else | |
| 223 { | |
| 224 LOG(WARNING) << "No repainting of the background"; | |
| 225 } | |
| 226 | |
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227 Orthanc::PhotometricInterpretation targetPhotometric; |
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228 bool transcoding; |
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229 |
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230 if (parameters.IsForceReencode() || |
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231 parameters.IsReconstructPyramid() || |
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232 sourceCompression != parameters.GetTargetCompression()) |
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233 { |
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234 // The tiles of the source image will be re-encoded |
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235 transcoding = false; |
| 171 | 236 |
| 237 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 238 { | |
| 239 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 240 } | |
| 241 else | |
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242 { |
| 171 | 243 switch (parameters.GetTargetCompression()) |
| 244 { | |
| 245 case OrthancWSI::ImageCompression_Jpeg: | |
| 246 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 247 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 248 break; | |
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249 |
| 171 | 250 case OrthancWSI::ImageCompression_None: |
| 251 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 252 break; | |
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253 |
| 171 | 254 default: |
| 255 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 256 } | |
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257 } |
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258 } |
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259 else |
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260 { |
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261 // Transcoding: The tiles are copied (no re-encoding) |
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262 transcoding = true; |
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263 targetPhotometric = source.GetPhotometricInterpretation(); |
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264 } |
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265 |
| 0 | 266 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 267 source.GetPixelFormat(), | |
| 268 parameters.GetTargetCompression(), | |
| 269 parameters.GetTargetTileWidth(source), | |
| 270 parameters.GetTargetTileHeight(source), | |
| 271 parameters.GetDicomMaxFileSize(), | |
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272 volume, targetPhotometric); |
| 29 | 273 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 274 |
| 275 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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276 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 277 |
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278 if (!transcoding && |
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279 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 280 { |
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281 LOG(WARNING) << "Target compression: Jpeg with quality " |
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282 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 283 target.SetJpegQuality(target.GetJpegQuality()); |
| 284 } | |
| 285 else | |
| 286 { | |
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287 LOG(WARNING) << "Target compression: " |
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288 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 289 } |
| 290 | |
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291 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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292 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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293 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 294 { |
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295 LOG(ERROR) << "When resampling the tile size, " |
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296 << "it must be a integer divisor of the original tile size"; |
| 0 | 297 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 298 } | |
| 299 | |
| 300 if (target.GetTileWidth() <= 16 || | |
| 301 target.GetTileHeight() <= 16) | |
| 302 { | |
| 303 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 304 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 305 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 306 } | |
| 307 | |
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308 if (transcoding) |
| 0 | 309 { |
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310 TranscodePyramid(target, stats, parameters); |
| 0 | 311 } |
| 312 else | |
| 313 { | |
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314 ReconstructPyramid(target, stats, parameters); |
| 0 | 315 } |
| 316 | |
| 317 target.Flush(); | |
| 318 } | |
| 319 | |
| 320 | |
| 321 | |
| 322 static DcmDataset* ParseDataset(const std::string& path) | |
| 323 { | |
| 324 Json::Value json; | |
| 325 | |
| 326 if (path.empty()) | |
| 327 { | |
| 328 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 329 } | |
| 330 else | |
| 331 { | |
| 332 std::string content; | |
| 43 | 333 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 334 |
| 226 | 335 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 336 { |
| 337 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 338 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 339 } | |
| 340 } | |
| 341 | |
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342 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
|
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343 "" /* no private tag, thus no private creator */)); |
| 0 | 344 if (dataset.get() == NULL) |
| 345 { | |
| 346 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 347 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 348 } | |
| 349 | |
| 350 // VL Whole Slide Microscopy Image IOD | |
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351 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
| 0 | 352 |
| 353 // Slide Microscopy | |
| 354 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 355 | |
| 356 // Patient orientation makes no sense in whole-slide images | |
| 357 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 358 | |
| 359 // Some basic coordinate information | |
| 360 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 361 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 362 | |
| 363 std::string date, time; | |
| 130 | 364 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 365 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 366 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 368 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 369 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 372 | |
| 373 return dataset.release(); | |
| 374 } | |
| 375 | |
| 376 | |
| 377 | |
| 378 static void SetupDimension(DcmDataset& dataset, | |
| 379 const std::string& opticalPathId, | |
| 380 const OrthancWSI::ITiledPyramid& source, | |
| 381 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 382 { | |
| 83 | 383 // Extract the identifier of the Dimension Organization, if provided |
| 384 std::string organization; | |
| 0 | 385 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 386 | |
| 83 | 387 if (previous != NULL && |
| 388 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 389 { | |
| 390 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 391 } | |
| 392 else | |
| 0 | 393 { |
| 83 | 394 // No Dimension Organization provided: Generate an unique identifier |
| 395 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 396 } | |
| 397 | |
| 398 | |
| 399 { | |
| 400 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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401 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 402 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 403 | |
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404 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 405 |
| 406 if (!sequence->insert(item.release(), false, false).good() || | |
| 407 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 408 { |
| 83 | 409 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 410 } |
| 411 } | |
| 412 | |
| 83 | 413 |
| 0 | 414 { |
| 83 | 415 // Construct tag "Dimension Index Sequence" (0020,9222) |
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416 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 417 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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418 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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419 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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420 |
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421 std::unique_ptr<DcmItem> item2(new DcmItem); |
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422 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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423 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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424 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 425 |
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426 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 427 |
| 83 | 428 if (!sequence->insert(item.release(), false, false).good() || |
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429 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 430 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 431 { | |
| 432 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 433 } | |
| 0 | 434 } |
| 435 | |
| 436 | |
| 83 | 437 { |
| 438 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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439 std::unique_ptr<DcmItem> item(new DcmItem); |
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440 |
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441 std::unique_ptr<DcmItem> item3(new DcmItem); |
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442 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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443 |
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444 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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445 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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446 |
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447 if (!sequence3->insert(item3.release(), false, false).good() || |
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448 !item->insert(sequence3.release(), false, false).good() || |
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449 !sequence->insert(item.release(), false, false).good() || |
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450 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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451 { |
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452 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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453 } |
| 0 | 454 } |
| 455 } | |
| 456 | |
| 457 | |
| 458 static void EnrichDataset(DcmDataset& dataset, | |
| 459 const OrthancWSI::ITiledPyramid& source, | |
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460 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 461 const OrthancWSI::DicomizerParameters& parameters, |
| 462 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 463 { | |
| 464 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 465 | |
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466 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 467 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 468 { | |
| 469 // Takes as estimation a 1:10 compression ratio | |
| 470 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 471 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 473 } | |
| 474 else | |
| 475 { | |
| 476 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 477 } | |
| 478 | |
| 479 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 480 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 482 | |
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483 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 484 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 485 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 486 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 487 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 488 | |
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489 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 490 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 491 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 492 { | |
| 493 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 494 } | |
| 495 | |
| 496 | |
| 497 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 498 { | |
| 499 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 500 { | |
| 501 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 502 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 503 } | |
| 504 | |
| 505 std::string brightfield; | |
| 506 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 507 | |
| 508 Json::Value json; | |
| 226 | 509 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 510 { |
| 511 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 512 } | |
| 513 | |
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514 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 515 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 516 DCM_OpticalPathSequence.getElement()), | |
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517 json, false, encoding, |
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518 "" /* no private tag, thus no private creator */)); |
| 0 | 519 if (!dataset.insert(element.release()).good()) |
| 520 { | |
| 521 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 522 } | |
| 523 } | |
| 524 | |
| 525 | |
| 526 std::string profile; | |
| 527 if (parameters.GetIccProfilePath().empty()) | |
| 528 { | |
| 529 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 530 } | |
| 531 else | |
| 532 { | |
| 43 | 533 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 534 } |
| 535 | |
| 536 | |
| 537 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 538 if (opticalPath == NULL) | |
| 539 { | |
| 540 LOG(ERROR) << "No optical path specified"; | |
| 541 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 542 } | |
| 543 | |
| 544 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 545 { | |
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546 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 547 |
| 548 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 549 !opticalPath->insert(icc.release()).good()) | |
| 550 { | |
| 551 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 552 } | |
| 553 } | |
| 554 | |
| 555 const char* opticalPathId = NULL; | |
| 556 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 557 opticalPathId == NULL) | |
| 558 { | |
| 559 LOG(ERROR) << "No identifier in the optical path"; | |
| 560 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 561 } | |
| 562 | |
| 563 SetupDimension(dataset, opticalPathId, source, volume); | |
| 564 } | |
| 565 | |
| 566 | |
| 567 static bool ParseParameters(int& exitStatus, | |
| 568 OrthancWSI::DicomizerParameters& parameters, | |
| 569 OrthancWSI::ImagedVolumeParameters& volume, | |
| 570 int argc, | |
| 571 char* argv[]) | |
| 572 { | |
| 573 // Declare the supported parameters | |
| 574 boost::program_options::options_description generic("Generic options"); | |
| 575 generic.add_options() | |
|
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576 (OPTION_HELP, "Display this help and exit") |
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577 (OPTION_VERSION, "Output version information and exit") |
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578 (OPTION_VERBOSE, "Be verbose in logs") |
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579 (OPTION_THREADS, |
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580 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 581 "Number of processing threads to be used") |
|
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582 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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583 "Path to the shared library of OpenSlide " |
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584 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 585 ; |
| 586 | |
| 587 boost::program_options::options_description source("Options for the source image"); | |
| 588 source.add_options() | |
|
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589 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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590 "Path to a JSON file containing the DICOM dataset") |
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591 (OPTION_SAMPLE_DATASET, |
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592 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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593 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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594 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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595 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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596 "Whether to repaint the background of the image (Boolean)") |
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597 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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598 "Color of the background (e.g. \"255,0,0\")") |
|
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599 (OPTION_TIFF_ALIGNMENT, boost::program_options::value<int>()->default_value(64), |
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600 "Add padding to plain TIFF images to align the width/height to multiples " |
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601 "of this value, very useful to enable deep zoom with IIIF (1 means no padding)") |
| 0 | 602 ; |
| 603 | |
|
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604 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
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605 cytomine.add_options() |
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606 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
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607 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
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608 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
| 246 | 609 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
|
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610 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
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611 "Your personal private key in Cytomine (to be kept secret)") |
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612 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
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613 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
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614 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
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615 "Compression to be used for downloading the tiles from Cytomine, " |
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616 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
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617 ; |
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618 |
| 0 | 619 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
| 620 pyramid.add_options() | |
|
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621 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 622 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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623 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 624 "Apply smoothing when reconstructing the pyramid " |
| 625 "(slower, but higher quality) (Boolean)") | |
|
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626 (OPTION_LEVELS, boost::program_options::value<int>(), |
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627 "Number of levels in the target pyramid") |
| 0 | 628 ; |
| 629 | |
| 630 boost::program_options::options_description target("Options for the target image"); | |
| 631 target.add_options() | |
|
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632 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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633 "Width of the tiles in the target image") |
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634 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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635 "Height of the tiles in the target image") |
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636 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 637 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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638 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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639 "Set quality level for JPEG (0..100)") |
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640 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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641 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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642 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 643 "Folder where to store the output DICOM instances") |
|
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644 (OPTION_FOLDER_PATTERN, |
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645 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 646 "Pattern for the files in the output folder") |
| 647 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 648 "URL to the REST API of the target Orthanc server") | |
| 649 ; | |
| 650 | |
| 651 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 652 volumeOptions.add_options() | |
|
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653 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
|
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654 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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655 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
|
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656 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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657 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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658 "Depth of the specimen (in mm)") |
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659 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 660 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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661 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 662 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 663 ; | |
| 664 | |
|
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665 boost::program_options::options_description restOptions |
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666 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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667 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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668 |
| 0 | 669 boost::program_options::options_description advancedOptions("Advanced options"); |
| 670 advancedOptions.add_options() | |
|
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671 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 672 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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673 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 674 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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675 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 676 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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677 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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678 "Number of pyramid levels up to which multithreading " |
| 0 | 679 "should be applied (only for performance/memory tuning)") |
| 680 ; | |
| 681 | |
| 682 boost::program_options::options_description hidden; | |
| 683 hidden.add_options() | |
|
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684 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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685 "Input file"); |
| 0 | 686 ; |
| 687 | |
| 688 boost::program_options::options_description allWithoutHidden; | |
|
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689 allWithoutHidden |
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690 .add(generic) |
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691 .add(source) |
|
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692 .add(cytomine) |
|
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693 .add(pyramid) |
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694 .add(target) |
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695 .add(volumeOptions) |
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696 .add(restOptions) |
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697 .add(advancedOptions); |
| 0 | 698 |
| 699 boost::program_options::options_description all = allWithoutHidden; | |
| 700 all.add(hidden); | |
| 701 | |
| 702 boost::program_options::positional_options_description positional; | |
|
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703 positional.add(OPTION_INPUT, 1); |
| 0 | 704 |
| 705 boost::program_options::variables_map options; | |
| 706 bool error = false; | |
| 707 | |
| 708 try | |
| 709 { | |
| 710 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 711 options(all).positional(positional).run(), options); | |
| 712 boost::program_options::notify(options); | |
| 713 } | |
| 714 catch (boost::program_options::error& e) | |
| 715 { | |
| 716 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 717 error = true; | |
| 718 } | |
| 719 | |
| 720 if (!error && | |
|
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721 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 722 { |
| 723 std::string sample; | |
| 724 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 725 | |
| 726 std::cout << std::endl << sample << std::endl; | |
| 727 | |
| 728 return false; | |
| 729 } | |
| 730 | |
|
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731 // New in release 1.1 |
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732 if (options.count(OPTION_CYTOMINE_URL) || |
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733 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
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734 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
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735 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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736 { |
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737 if (!options.count(OPTION_CYTOMINE_URL)) |
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738 { |
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739 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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740 "URL to the Cytomine server is missing"); |
|
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741 } |
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742 |
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743 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
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744 { |
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745 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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746 "Public key for the Cytomine server is missing"); |
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747 } |
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748 |
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749 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
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750 { |
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751 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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752 "Private key for the Cytomine server is missing"); |
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753 } |
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754 |
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755 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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756 { |
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757 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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758 "The Image Instance ID from the Cytomine server is missing"); |
|
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759 } |
|
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|
760 |
|
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761 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
|
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762 { |
|
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763 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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764 "The tile compression scheme for Cytomine is missing"); |
|
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765 } |
|
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766 |
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767 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
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768 |
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769 OrthancWSI::ImageCompression compression; |
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770 if (s == "jpeg") |
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771 { |
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772 compression = OrthancWSI::ImageCompression_Jpeg; |
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773 } |
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774 else if (s == "png") |
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775 { |
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776 compression = OrthancWSI::ImageCompression_Png; |
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777 } |
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778 else |
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779 { |
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780 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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781 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
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782 } |
|
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783 |
|
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784 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
|
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785 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
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786 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
|
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787 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
|
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788 } |
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789 |
| 0 | 790 if (!error && |
|
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791 options.count(OPTION_HELP) == 0 && |
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792 options.count(OPTION_VERSION) == 0 && |
|
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793 options.count(OPTION_INPUT) != 1 && |
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794 !parameters.IsCytomineSource()) |
| 0 | 795 { |
| 796 LOG(ERROR) << "No input file was specified"; | |
| 797 error = true; | |
| 798 } | |
| 799 | |
|
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800 if (error || options.count(OPTION_HELP)) |
| 0 | 801 { |
| 802 std::cout << std::endl | |
| 803 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 804 << std::endl | |
| 805 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 806 << std::endl << std::endl | |
| 807 << "Create a DICOM file from a digital pathology image." | |
| 808 << std::endl; | |
| 809 | |
| 810 std::cout << allWithoutHidden << "\n"; | |
| 811 | |
| 812 if (error) | |
| 813 { | |
| 814 exitStatus = -1; | |
| 815 } | |
| 816 | |
| 817 return false; | |
| 818 } | |
| 819 | |
|
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820 if (options.count(OPTION_VERSION)) |
|
8
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|
821 { |
|
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|
822 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
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|
823 return false; |
|
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diff
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|
824 } |
|
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825 |
|
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826 if (options.count(OPTION_VERBOSE)) |
| 0 | 827 { |
| 828 Orthanc::Logging::EnableInfoLevel(true); | |
| 829 } | |
| 830 | |
|
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831 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 832 { |
|
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833 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 834 } |
| 835 | |
|
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836 if (options.count(OPTION_PYRAMID) && |
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837 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 838 { |
| 839 parameters.SetReconstructPyramid(true); | |
| 840 } | |
| 841 | |
|
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842 if (options.count(OPTION_SMOOTH) && |
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843 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 844 { |
| 845 parameters.SetSmoothEnabled(true); | |
| 846 } | |
| 847 | |
|
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848 if (options.count(OPTION_SAFETY) && |
|
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849 options[OPTION_SAFETY].as<bool>()) |
| 0 | 850 { |
| 851 parameters.SetSafetyCheck(true); | |
| 852 } | |
| 853 | |
|
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854 if (options.count(OPTION_REENCODE) && |
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855 options[OPTION_REENCODE].as<bool>()) |
| 0 | 856 { |
| 857 parameters.SetForceReencode(true); | |
| 858 } | |
| 859 | |
|
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860 if (options.count(OPTION_REPAINT) && |
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861 options[OPTION_REPAINT].as<bool>()) |
| 0 | 862 { |
| 863 parameters.SetRepaintBackground(true); | |
| 864 } | |
| 865 | |
|
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866 if (options.count(OPTION_TILE_WIDTH) || |
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867 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 868 { |
| 869 int w = 0; | |
|
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870 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 871 { |
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872 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 873 } |
| 874 | |
| 145 | 875 int h = 0; |
|
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876 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 877 { |
|
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878 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 879 } |
| 880 | |
| 881 if (w < 0 || h < 0) | |
| 882 { | |
| 883 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 884 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 885 } | |
| 886 | |
| 887 parameters.SetTargetTileSize(w, h); | |
| 888 } | |
| 889 | |
|
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890 if (!parameters.IsCytomineSource()) |
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891 { |
|
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892 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
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893 } |
| 0 | 894 |
|
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895 if (options.count(OPTION_COLOR)) |
| 0 | 896 { |
| 897 uint8_t r, g, b; | |
|
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898 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 899 parameters.SetBackgroundColor(r, g, b); |
| 900 } | |
| 901 | |
|
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902 if (options.count(OPTION_COMPRESSION)) |
| 0 | 903 { |
|
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904 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 905 if (s == "none") |
| 906 { | |
| 907 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 908 } | |
| 909 else if (s == "jpeg") | |
| 910 { | |
| 911 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 912 } | |
| 913 else if (s == "jpeg2000") | |
| 914 { | |
| 915 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 916 } | |
| 917 else | |
| 918 { | |
| 919 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 920 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 921 } | |
| 922 } | |
| 923 | |
|
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924 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 925 { |
|
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926 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 927 } |
| 928 | |
|
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929 if (options.count(OPTION_LEVELS)) |
| 0 | 930 { |
|
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931 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 932 } |
| 933 | |
|
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934 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 935 { |
|
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936 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 937 } |
| 938 | |
|
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939 if (options.count(OPTION_THREADS)) |
| 0 | 940 { |
|
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941 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 942 } |
| 943 | |
|
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944 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 945 { |
|
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946 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 947 } |
| 948 | |
|
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949 if (options.count(OPTION_FOLDER)) |
| 0 | 950 { |
|
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951 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 952 } |
| 953 | |
|
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954 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 955 { |
|
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956 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 957 } |
| 958 | |
|
125
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959 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 960 |
|
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961 if (options.count(OPTION_DATASET)) |
| 0 | 962 { |
|
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963 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 964 } |
| 965 | |
|
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966 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 967 { |
|
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968 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 969 } |
| 970 | |
|
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971 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 972 { |
|
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973 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 974 } |
| 975 | |
|
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976 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 977 { |
|
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978 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 979 } |
| 980 | |
|
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981 if (options.count(OPTION_OFFSET_X)) |
| 0 | 982 { |
|
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983 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 984 } |
| 985 | |
|
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986 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 987 { |
|
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988 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 989 } |
| 990 | |
|
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991 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 992 { |
|
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993 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 994 if (s == "none") |
| 995 { | |
| 996 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 997 } | |
| 998 else if (s == "brightfield") | |
| 999 { | |
| 1000 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 1001 } | |
| 1002 else | |
| 1003 { | |
| 1004 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 1005 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 1006 } | |
| 1007 } | |
| 1008 | |
|
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1009 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 1010 { |
|
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1011 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 1012 } |
| 1013 | |
|
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1014 if (options.count(OPTION_TIFF_ALIGNMENT)) |
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1015 { |
|
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1016 int value = options[OPTION_TIFF_ALIGNMENT].as<int>(); |
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1017 if (value <= 0) |
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1018 { |
|
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1019 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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1020 "TIFF alignment must be >= 1"); |
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1021 } |
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1022 else |
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1023 { |
|
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1024 parameters.SetTiffAlignment(static_cast<unsigned int>(value)); |
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1025 } |
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1026 } |
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1027 |
| 0 | 1028 return true; |
| 1029 } | |
| 1030 | |
| 1031 | |
|
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1032 |
|
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1033 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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1034 OrthancWSI::ImagedVolumeParameters& volume, |
|
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1035 const std::string& path, |
| 0 | 1036 const OrthancWSI::DicomizerParameters& parameters) |
| 1037 { | |
|
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1038 if (parameters.IsCytomineSource()) |
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1039 { |
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1040 // New in release 1.1 |
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1041 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
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1042 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
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1043 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1044 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
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1045 parameters.GetCytominePublicKey(), |
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1046 parameters.GetCytominePrivateKey(), |
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1047 parameters.GetCytomineImageInstanceId(), |
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1048 parameters.GetTargetTileWidth(512), |
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1049 parameters.GetTargetTileHeight(512)); |
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1050 } |
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1051 |
| 0 | 1052 LOG(WARNING) << "The input image is: " << path; |
| 1053 | |
| 1054 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 1055 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 1056 | |
| 1057 switch (format) | |
| 1058 { | |
| 1059 case OrthancWSI::ImageCompression_Png: | |
|
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1060 { |
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1061 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1062 return new OrthancWSI::TiledPngImage(path, |
| 1063 parameters.GetTargetTileWidth(512), | |
| 1064 parameters.GetTargetTileHeight(512)); | |
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1065 } |
| 0 | 1066 |
| 1067 case OrthancWSI::ImageCompression_Jpeg: | |
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1068 { |
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1069 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1070 return new OrthancWSI::TiledJpegImage(path, |
| 1071 parameters.GetTargetTileWidth(512), | |
| 1072 parameters.GetTargetTileHeight(512)); | |
|
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1073 } |
| 0 | 1074 |
| 1075 case OrthancWSI::ImageCompression_Tiff: | |
| 1076 { | |
| 1077 try | |
| 1078 { | |
|
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1079 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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1080 sourceCompression = tiff->GetImageCompression(); |
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1081 return tiff.release(); |
| 0 | 1082 } |
| 1083 catch (Orthanc::OrthancException&) | |
| 1084 { | |
|
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1085 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
| 0 | 1086 } |
|
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1087 |
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1088 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1089 return new OrthancWSI::PlainTiff(path, |
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1090 parameters.GetTargetTileWidth(512), |
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1091 parameters.GetTargetTileHeight(512), |
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1092 parameters.GetTiffAlignment(), |
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1093 parameters.GetBackgroundColorRed(), |
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1094 parameters.GetBackgroundColorGreen(), |
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1095 parameters.GetBackgroundColorBlue()); |
| 0 | 1096 } |
| 1097 | |
| 1098 default: | |
| 1099 break; | |
| 1100 } | |
| 1101 | |
| 1102 try | |
| 1103 { | |
| 1104 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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1105 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1106 |
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1107 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
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1108 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
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1109 parameters.GetTargetTileHeight(512))); |
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1110 |
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1111 float volumeWidth, volumeHeight; |
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1112 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
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1113 { |
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1114 if (!volume.HasWidth()) |
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1115 { |
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1116 volume.SetWidth(volumeWidth); |
| 281 | 1117 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
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1118 } |
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1119 |
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1120 if (!volume.HasHeight()) |
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1121 { |
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1122 volume.SetHeight(volumeHeight); |
| 281 | 1123 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
|
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1124 } |
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1125 } |
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1126 |
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1127 return openslide.release(); |
| 0 | 1128 } |
| 1129 catch (Orthanc::OrthancException&) | |
| 1130 { | |
| 1131 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 1132 return NULL; | |
| 1133 } | |
| 1134 } | |
| 1135 | |
| 1136 | |
| 1137 int main(int argc, char* argv[]) | |
| 1138 { | |
| 1139 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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1140 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 1141 |
| 1142 int exitStatus = 0; | |
| 1143 | |
| 1144 try | |
| 1145 { | |
| 1146 OrthancWSI::DicomizerParameters parameters; | |
| 1147 OrthancWSI::ImagedVolumeParameters volume; | |
| 1148 | |
| 1149 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 1150 { | |
|
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1151 OrthancWSI::ImageCompression sourceCompression; |
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1152 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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1153 |
|
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1154 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
| 0 | 1155 if (source.get() == NULL) |
| 1156 { | |
| 1157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1158 } | |
|
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1159 |
|
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1160 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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1161 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
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1162 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
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1163 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
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1164 { |
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1165 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
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1166 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
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1167 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
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1168 } |
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1169 |
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1170 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1171 |
| 1172 // Create the shared DICOM tags | |
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1173 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1174 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1175 |
|
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1176 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
|
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1177 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1178 } |
| 1179 } | |
| 1180 catch (Orthanc::OrthancException& e) | |
| 1181 { | |
| 1182 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1183 exitStatus = -1; | |
| 1184 } | |
| 1185 | |
| 1186 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1187 | |
| 1188 return exitStatus; | |
| 1189 } |