Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 331:cf828b381bc9
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 18 Oct 2024 13:16:02 +0200 |
| parents | c42083d50ddf |
| children |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
|
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 8 * |
| 9 * This program is free software: you can redistribute it and/or | |
| 10 * modify it under the terms of the GNU Affero General Public License | |
| 11 * as published by the Free Software Foundation, either version 3 of | |
| 12 * the License, or (at your option) any later version. | |
| 13 * | |
| 14 * This program is distributed in the hope that it will be useful, but | |
| 15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 17 * Affero General Public License for more details. | |
| 18 * | |
| 19 * You should have received a copy of the GNU Affero General Public License | |
| 20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 21 **/ | |
| 22 | |
| 23 | |
| 24 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 25 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
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26 #include "../Framework/ColorSpaces.h" |
| 0 | 27 #include "../Framework/DicomToolbox.h" |
| 28 #include "../Framework/DicomizerParameters.h" | |
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29 #include "../Framework/ImageToolbox.h" |
| 0 | 30 #include "../Framework/ImagedVolumeParameters.h" |
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31 #include "../Framework/Inputs/CytomineImage.h" |
| 0 | 32 #include "../Framework/Inputs/HierarchicalTiff.h" |
| 33 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
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34 #include "../Framework/Inputs/PlainTiff.h" |
| 0 | 35 #include "../Framework/Inputs/TiledJpegImage.h" |
| 36 #include "../Framework/Inputs/TiledPngImage.h" | |
| 37 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 38 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 39 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 40 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 41 | |
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42 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 43 #include <DicomParsing/FromDcmtkBridge.h> |
| 44 #include <Logging.h> | |
| 45 #include <OrthancException.h> | |
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46 #include <Toolbox.h> |
| 192 | 47 #include <SystemToolbox.h> |
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48 |
| 0 | 49 #include "ApplicationToolbox.h" |
| 50 | |
| 51 #include <EmbeddedResources.h> | |
| 52 | |
| 53 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 54 #include <dcmtk/dcmdata/dcuid.h> | |
| 55 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 56 #include <dcmtk/dcmdata/dcvrat.h> | |
| 57 | |
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58 #include <boost/math/special_functions/round.hpp> |
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59 |
| 0 | 60 |
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61 static const char* OPTION_COLOR = "color"; |
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62 static const char* OPTION_COMPRESSION = "compression"; |
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63 static const char* OPTION_DATASET = "dataset"; |
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64 static const char* OPTION_FOLDER = "folder"; |
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65 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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66 static const char* OPTION_HELP = "help"; |
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67 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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68 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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69 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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70 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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71 static const char* OPTION_INPUT = "input"; |
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72 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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73 static const char* OPTION_LEVELS = "levels"; |
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74 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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75 static const char* OPTION_MAX_SIZE = "max-size"; |
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76 static const char* OPTION_OFFSET_X = "offset-x"; |
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77 static const char* OPTION_OFFSET_Y = "offset-y"; |
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78 static const char* OPTION_OPENSLIDE = "openslide"; |
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79 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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80 static const char* OPTION_PYRAMID = "pyramid"; |
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81 static const char* OPTION_REENCODE = "reencode"; |
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82 static const char* OPTION_REPAINT = "repaint"; |
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83 static const char* OPTION_SAFETY = "safety"; |
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84 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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85 static const char* OPTION_SMOOTH = "smooth"; |
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86 static const char* OPTION_THREADS = "threads"; |
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87 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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88 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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89 static const char* OPTION_VERBOSE = "verbose"; |
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90 static const char* OPTION_VERSION = "version"; |
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91 |
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92 // New in release 1.1 |
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93 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
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94 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
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95 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
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96 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
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97 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
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98 |
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99 // New in release 2.1 |
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100 static const char* OPTION_FORCE_OPENSLIDE = "force-openslide"; |
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101 static const char* OPTION_PADDING = "padding"; |
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102 |
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103 |
| 226 | 104 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 105 | |
| 106 bool ReadJsonWithoutComments(Json::Value& target, | |
| 107 const std::string& source) | |
| 108 { | |
| 109 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 110 } | |
| 111 | |
| 112 #else | |
| 113 | |
| 114 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 115 #include <json/reader.h> | |
| 116 | |
| 117 bool ReadJsonWithoutComments(Json::Value& target, | |
| 118 const std::string& source) | |
| 119 { | |
| 120 Json::Reader reader; | |
| 121 return reader.parse(source, target, false); | |
| 122 } | |
| 123 #endif | |
| 124 | |
| 125 | |
| 0 | 126 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 127 OrthancWSI::ITiledPyramid& source, | |
| 128 const OrthancWSI::DicomizerParameters& parameters) | |
| 129 { | |
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130 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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131 |
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132 OrthancWSI::BagOfTasks tasks; |
| 0 | 133 |
| 134 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 135 { | |
| 136 LOG(WARNING) << "Creating level " << i << " of size " | |
| 137 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 138 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 139 } | |
| 140 | |
| 141 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 142 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 143 } | |
| 144 | |
| 145 | |
| 146 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 147 OrthancWSI::ITiledPyramid& source, | |
| 148 const OrthancWSI::DicomizerParameters& parameters) | |
| 149 { | |
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150 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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151 |
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152 OrthancWSI::BagOfTasks tasks; |
| 0 | 153 |
| 154 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 155 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 156 assert(levelsCount >= 1); | |
| 157 | |
| 158 for (unsigned int i = 0; i < levelsCount; i++) | |
| 159 { | |
| 160 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 161 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 162 | |
| 163 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 164 target.AddLevel(width, height); | |
| 165 } | |
| 166 | |
| 167 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 168 if (lowerLevelsCount > levelsCount) | |
| 169 { | |
| 170 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 171 << ") exceeds the number of levels (" << levelsCount | |
| 172 << "), cropping it"; | |
| 173 lowerLevelsCount = levelsCount; | |
| 174 } | |
| 175 | |
| 176 assert(lowerLevelsCount <= levelsCount); | |
| 177 if (lowerLevelsCount != levelsCount) | |
| 178 { | |
| 179 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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180 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 181 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 182 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 183 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 184 | |
| 185 assert(tasks.GetSize() == 0); | |
| 186 | |
| 187 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 188 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 189 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 190 (tasks, target, truncated.GetUpperLevel(), | |
| 191 upperLevelsCount, lowerLevelsCount, parameters); | |
| 192 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 193 } | |
| 194 else | |
| 195 { | |
| 196 LOG(WARNING) << "Constructing the pyramid"; | |
| 197 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 198 (tasks, target, source, levelsCount, 0, parameters); | |
| 199 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 200 } | |
| 201 } | |
| 202 | |
| 203 | |
| 204 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 205 OrthancWSI::ITiledPyramid& source, | |
| 206 const DcmDataset& dataset, | |
| 207 const OrthancWSI::DicomizerParameters& parameters, | |
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208 const OrthancWSI::ImagedVolumeParameters& volume, |
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209 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 210 { |
| 211 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 212 | |
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213 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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214 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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215 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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216 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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217 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 218 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 219 | |
| 220 if (parameters.IsRepaintBackground()) | |
| 221 { | |
| 222 LOG(WARNING) << "Repainting the background with color: (" | |
| 223 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 224 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 225 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 226 } | |
| 227 else | |
| 228 { | |
| 229 LOG(WARNING) << "No repainting of the background"; | |
| 230 } | |
| 231 | |
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232 Orthanc::PhotometricInterpretation targetPhotometric; |
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233 bool transcoding; |
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234 |
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235 if (parameters.IsForceReencode() || |
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236 parameters.IsReconstructPyramid() || |
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237 sourceCompression != parameters.GetTargetCompression()) |
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238 { |
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239 // The tiles of the source image will be re-encoded |
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240 transcoding = false; |
| 171 | 241 |
| 242 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 243 { | |
| 244 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 245 } | |
| 246 else | |
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247 { |
| 171 | 248 switch (parameters.GetTargetCompression()) |
| 249 { | |
| 250 case OrthancWSI::ImageCompression_Jpeg: | |
| 251 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 252 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 253 break; | |
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254 |
| 171 | 255 case OrthancWSI::ImageCompression_None: |
| 256 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 257 break; | |
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258 |
| 171 | 259 default: |
| 260 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 261 } | |
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262 } |
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263 } |
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264 else |
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265 { |
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266 // Transcoding: The tiles are copied (no re-encoding) |
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267 transcoding = true; |
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268 targetPhotometric = source.GetPhotometricInterpretation(); |
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269 } |
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270 |
| 0 | 271 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 272 source.GetPixelFormat(), | |
| 273 parameters.GetTargetCompression(), | |
| 274 parameters.GetTargetTileWidth(source), | |
| 275 parameters.GetTargetTileHeight(source), | |
| 276 parameters.GetDicomMaxFileSize(), | |
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277 volume, targetPhotometric); |
| 29 | 278 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 279 |
| 280 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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281 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 282 |
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283 if (!transcoding && |
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284 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 285 { |
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286 LOG(WARNING) << "Target compression: Jpeg with quality " |
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287 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 288 target.SetJpegQuality(target.GetJpegQuality()); |
| 289 } | |
| 290 else | |
| 291 { | |
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292 LOG(WARNING) << "Target compression: " |
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293 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 294 } |
| 295 | |
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296 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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297 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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298 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 299 { |
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300 LOG(ERROR) << "When resampling the tile size, " |
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301 << "it must be a integer divisor of the original tile size"; |
| 0 | 302 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 303 } | |
| 304 | |
| 305 if (target.GetTileWidth() <= 16 || | |
| 306 target.GetTileHeight() <= 16) | |
| 307 { | |
| 308 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 309 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 310 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 311 } | |
| 312 | |
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313 if (transcoding) |
| 0 | 314 { |
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315 TranscodePyramid(target, stats, parameters); |
| 0 | 316 } |
| 317 else | |
| 318 { | |
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319 ReconstructPyramid(target, stats, parameters); |
| 0 | 320 } |
| 321 | |
| 322 target.Flush(); | |
| 323 } | |
| 324 | |
| 325 | |
| 326 | |
| 327 static DcmDataset* ParseDataset(const std::string& path) | |
| 328 { | |
| 329 Json::Value json; | |
| 330 | |
| 331 if (path.empty()) | |
| 332 { | |
| 333 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 334 } | |
| 335 else | |
| 336 { | |
| 337 std::string content; | |
| 43 | 338 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 339 |
| 226 | 340 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 341 { |
| 342 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 343 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 344 } | |
| 345 } | |
| 346 | |
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347 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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348 "" /* no private tag, thus no private creator */)); |
| 0 | 349 if (dataset.get() == NULL) |
| 350 { | |
| 351 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 352 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 353 } | |
| 354 | |
| 355 // VL Whole Slide Microscopy Image IOD | |
|
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356 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
| 0 | 357 |
| 358 // Slide Microscopy | |
| 359 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 360 | |
| 361 // Patient orientation makes no sense in whole-slide images | |
| 362 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 363 | |
| 364 // Some basic coordinate information | |
| 365 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 366 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 367 | |
| 368 std::string date, time; | |
| 130 | 369 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 372 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 373 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 374 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 375 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 376 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 377 | |
| 378 return dataset.release(); | |
| 379 } | |
| 380 | |
| 381 | |
| 382 | |
| 383 static void SetupDimension(DcmDataset& dataset, | |
| 384 const std::string& opticalPathId, | |
| 385 const OrthancWSI::ITiledPyramid& source, | |
| 386 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 387 { | |
| 83 | 388 // Extract the identifier of the Dimension Organization, if provided |
| 389 std::string organization; | |
| 0 | 390 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 391 | |
| 83 | 392 if (previous != NULL && |
| 393 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 394 { | |
| 395 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 396 } | |
| 397 else | |
| 0 | 398 { |
| 83 | 399 // No Dimension Organization provided: Generate an unique identifier |
| 400 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 401 } | |
| 402 | |
| 403 | |
| 404 { | |
| 405 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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406 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 407 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 408 | |
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409 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 410 |
| 411 if (!sequence->insert(item.release(), false, false).good() || | |
| 412 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 413 { |
| 83 | 414 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 415 } |
| 416 } | |
| 417 | |
| 83 | 418 |
| 0 | 419 { |
| 83 | 420 // Construct tag "Dimension Index Sequence" (0020,9222) |
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421 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 422 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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423 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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424 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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425 |
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426 std::unique_ptr<DcmItem> item2(new DcmItem); |
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427 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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428 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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429 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 430 |
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431 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 432 |
| 83 | 433 if (!sequence->insert(item.release(), false, false).good() || |
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434 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 435 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 436 { | |
| 437 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 438 } | |
| 0 | 439 } |
| 440 | |
| 441 | |
| 83 | 442 { |
| 443 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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444 std::unique_ptr<DcmItem> item(new DcmItem); |
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445 |
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446 std::unique_ptr<DcmItem> item3(new DcmItem); |
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447 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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448 |
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449 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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450 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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451 |
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452 if (!sequence3->insert(item3.release(), false, false).good() || |
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453 !item->insert(sequence3.release(), false, false).good() || |
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454 !sequence->insert(item.release(), false, false).good() || |
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455 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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456 { |
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457 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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458 } |
| 0 | 459 } |
| 460 } | |
| 461 | |
| 462 | |
| 463 static void EnrichDataset(DcmDataset& dataset, | |
| 464 const OrthancWSI::ITiledPyramid& source, | |
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465 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 466 const OrthancWSI::DicomizerParameters& parameters, |
| 467 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 468 { | |
| 469 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 470 | |
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471 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 472 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 473 { | |
| 474 // Takes as estimation a 1:10 compression ratio | |
| 475 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 476 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 477 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 478 } | |
| 479 else | |
| 480 { | |
| 481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 482 } | |
| 483 | |
| 484 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 485 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 486 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 487 | |
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488 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 489 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 490 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 491 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 492 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 493 | |
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494 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 495 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 496 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 497 { | |
| 498 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 499 } | |
| 500 | |
| 501 | |
| 502 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 503 { | |
| 504 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 505 { | |
| 506 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 507 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 508 } | |
| 509 | |
| 510 std::string brightfield; | |
| 511 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 512 | |
| 513 Json::Value json; | |
| 226 | 514 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 515 { |
| 516 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 517 } | |
| 518 | |
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519 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 520 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 521 DCM_OpticalPathSequence.getElement()), | |
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522 json, false, encoding, |
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523 "" /* no private tag, thus no private creator */)); |
| 0 | 524 if (!dataset.insert(element.release()).good()) |
| 525 { | |
| 526 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 527 } | |
| 528 } | |
| 529 | |
| 530 | |
| 531 std::string profile; | |
| 532 if (parameters.GetIccProfilePath().empty()) | |
| 533 { | |
| 534 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 535 } | |
| 536 else | |
| 537 { | |
| 43 | 538 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 539 } |
| 540 | |
| 541 | |
| 542 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 543 if (opticalPath == NULL) | |
| 544 { | |
| 545 LOG(ERROR) << "No optical path specified"; | |
| 546 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 547 } | |
| 548 | |
| 549 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 550 { | |
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551 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 552 |
| 553 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 554 !opticalPath->insert(icc.release()).good()) | |
| 555 { | |
| 556 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 557 } | |
| 558 } | |
| 559 | |
| 560 const char* opticalPathId = NULL; | |
| 561 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 562 opticalPathId == NULL) | |
| 563 { | |
| 564 LOG(ERROR) << "No identifier in the optical path"; | |
| 565 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 566 } | |
| 567 | |
| 568 SetupDimension(dataset, opticalPathId, source, volume); | |
|
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569 |
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570 |
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571 // New in release 2.1 |
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572 if (!dataset.tagExists(DCM_RecommendedAbsentPixelCIELabValue)) |
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573 { |
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574 OrthancWSI::RGBColor rgb(parameters.GetBackgroundColorRed(), |
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575 parameters.GetBackgroundColorGreen(), |
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576 parameters.GetBackgroundColorBlue()); |
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577 OrthancWSI::sRGBColor srgb(rgb); |
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578 OrthancWSI::XYZColor xyz(srgb); |
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579 OrthancWSI::LABColor lab(xyz); |
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580 |
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581 uint16_t encoded[3]; |
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582 lab.EncodeDicomRecommendedAbsentPixelCIELab(encoded); |
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583 |
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584 if (!dataset.putAndInsertUint16Array(DCM_RecommendedAbsentPixelCIELabValue, encoded, 3).good()) |
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585 { |
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586 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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587 } |
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588 } |
| 0 | 589 } |
| 590 | |
| 591 | |
| 592 static bool ParseParameters(int& exitStatus, | |
| 593 OrthancWSI::DicomizerParameters& parameters, | |
| 594 OrthancWSI::ImagedVolumeParameters& volume, | |
| 595 int argc, | |
| 596 char* argv[]) | |
| 597 { | |
| 598 // Declare the supported parameters | |
| 599 boost::program_options::options_description generic("Generic options"); | |
| 600 generic.add_options() | |
|
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601 (OPTION_HELP, "Display this help and exit") |
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602 (OPTION_VERSION, "Output version information and exit") |
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603 (OPTION_VERBOSE, "Be verbose in logs") |
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604 (OPTION_THREADS, |
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605 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 606 "Number of processing threads to be used") |
|
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607 (OPTION_FORCE_OPENSLIDE, boost::program_options::value<bool>()->default_value(false), |
|
323
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608 "Whether to force the use of OpenSlide on input TIFF-like files (Boolean)") |
|
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609 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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610 "Path to the shared library of OpenSlide " |
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611 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 612 ; |
| 613 | |
| 614 boost::program_options::options_description source("Options for the source image"); | |
| 615 source.add_options() | |
|
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616 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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617 "Path to a JSON file containing the DICOM dataset") |
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618 (OPTION_SAMPLE_DATASET, |
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619 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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620 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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621 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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622 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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623 "Whether to repaint the background of the image (Boolean)") |
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624 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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625 "Color of the background (e.g. \"255,0,0\")") |
|
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626 (OPTION_PADDING, boost::program_options::value<int>()->default_value(1), |
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627 "Add padding to plain PNG/JPEG/TIFF images to align the width/height to multiples " |
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628 "of this value, which enables deep zoom with IIIF (1 means no padding)") |
| 0 | 629 ; |
| 630 | |
|
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631 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
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632 cytomine.add_options() |
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633 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
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634 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
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635 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
| 246 | 636 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
|
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637 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
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638 "Your personal private key in Cytomine (to be kept secret)") |
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639 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
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640 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
|
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641 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
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642 "Compression to be used for downloading the tiles from Cytomine, " |
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643 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
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644 ; |
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645 |
| 0 | 646 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
| 647 pyramid.add_options() | |
|
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648 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 649 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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650 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 651 "Apply smoothing when reconstructing the pyramid " |
| 652 "(slower, but higher quality) (Boolean)") | |
|
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653 (OPTION_LEVELS, boost::program_options::value<int>(), |
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654 "Number of levels in the target pyramid") |
| 0 | 655 ; |
| 656 | |
| 657 boost::program_options::options_description target("Options for the target image"); | |
| 658 target.add_options() | |
|
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659 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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660 "Width of the tiles in the target image") |
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661 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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662 "Height of the tiles in the target image") |
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663 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 664 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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665 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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666 "Set quality level for JPEG (0..100)") |
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667 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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668 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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669 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 670 "Folder where to store the output DICOM instances") |
|
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671 (OPTION_FOLDER_PATTERN, |
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672 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 673 "Pattern for the files in the output folder") |
| 674 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 675 "URL to the REST API of the target Orthanc server") | |
| 676 ; | |
| 677 | |
| 678 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 679 volumeOptions.add_options() | |
|
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680 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
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681 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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682 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
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683 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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684 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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685 "Depth of the specimen (in mm)") |
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686 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 687 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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688 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 689 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 690 ; | |
| 691 | |
|
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692 boost::program_options::options_description restOptions |
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693 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
125
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694 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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695 |
| 0 | 696 boost::program_options::options_description advancedOptions("Advanced options"); |
| 697 advancedOptions.add_options() | |
|
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698 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 699 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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700 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 701 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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702 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 703 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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704 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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705 "Number of pyramid levels up to which multithreading " |
| 0 | 706 "should be applied (only for performance/memory tuning)") |
| 707 ; | |
| 708 | |
| 709 boost::program_options::options_description hidden; | |
| 710 hidden.add_options() | |
|
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711 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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712 "Input file"); |
| 0 | 713 ; |
| 714 | |
| 715 boost::program_options::options_description allWithoutHidden; | |
|
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716 allWithoutHidden |
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717 .add(generic) |
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718 .add(source) |
|
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719 .add(cytomine) |
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720 .add(pyramid) |
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721 .add(target) |
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722 .add(volumeOptions) |
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723 .add(restOptions) |
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724 .add(advancedOptions); |
| 0 | 725 |
| 726 boost::program_options::options_description all = allWithoutHidden; | |
| 727 all.add(hidden); | |
| 728 | |
| 729 boost::program_options::positional_options_description positional; | |
|
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730 positional.add(OPTION_INPUT, 1); |
| 0 | 731 |
| 732 boost::program_options::variables_map options; | |
| 733 bool error = false; | |
| 734 | |
| 735 try | |
| 736 { | |
| 737 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 738 options(all).positional(positional).run(), options); | |
| 739 boost::program_options::notify(options); | |
| 740 } | |
| 741 catch (boost::program_options::error& e) | |
| 742 { | |
| 743 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 744 error = true; | |
| 745 } | |
| 746 | |
| 747 if (!error && | |
|
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748 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 749 { |
| 750 std::string sample; | |
| 751 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 752 | |
| 753 std::cout << std::endl << sample << std::endl; | |
| 754 | |
| 755 return false; | |
| 756 } | |
| 757 | |
|
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758 // New in release 1.1 |
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759 if (options.count(OPTION_CYTOMINE_URL) || |
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760 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
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761 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
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762 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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763 { |
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764 if (!options.count(OPTION_CYTOMINE_URL)) |
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765 { |
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766 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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767 "URL to the Cytomine server is missing"); |
|
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768 } |
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769 |
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770 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
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771 { |
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772 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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773 "Public key for the Cytomine server is missing"); |
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774 } |
|
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775 |
|
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776 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
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777 { |
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778 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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779 "Private key for the Cytomine server is missing"); |
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780 } |
|
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781 |
|
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782 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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783 { |
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784 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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785 "The Image Instance ID from the Cytomine server is missing"); |
|
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786 } |
|
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787 |
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788 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
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789 { |
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790 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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791 "The tile compression scheme for Cytomine is missing"); |
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792 } |
|
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793 |
|
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794 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
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795 |
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796 OrthancWSI::ImageCompression compression; |
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797 if (s == "jpeg") |
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798 { |
|
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799 compression = OrthancWSI::ImageCompression_Jpeg; |
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800 } |
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801 else if (s == "png") |
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802 { |
|
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803 compression = OrthancWSI::ImageCompression_Png; |
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804 } |
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805 else |
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806 { |
|
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807 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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808 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
|
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809 } |
|
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810 |
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811 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
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812 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
|
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813 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
|
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814 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
|
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815 } |
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816 |
| 0 | 817 if (!error && |
|
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818 options.count(OPTION_HELP) == 0 && |
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819 options.count(OPTION_VERSION) == 0 && |
|
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820 options.count(OPTION_INPUT) != 1 && |
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821 !parameters.IsCytomineSource()) |
| 0 | 822 { |
| 823 LOG(ERROR) << "No input file was specified"; | |
| 824 error = true; | |
| 825 } | |
| 826 | |
|
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827 if (error || options.count(OPTION_HELP)) |
| 0 | 828 { |
| 829 std::cout << std::endl | |
| 830 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 831 << std::endl | |
| 832 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 833 << std::endl << std::endl | |
| 834 << "Create a DICOM file from a digital pathology image." | |
| 835 << std::endl; | |
| 836 | |
| 837 std::cout << allWithoutHidden << "\n"; | |
| 838 | |
| 839 if (error) | |
| 840 { | |
| 841 exitStatus = -1; | |
| 842 } | |
| 843 | |
| 844 return false; | |
| 845 } | |
| 846 | |
|
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847 if (options.count(OPTION_VERSION)) |
|
8
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|
848 { |
|
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|
849 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
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|
850 return false; |
|
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|
851 } |
|
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|
852 |
|
129
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853 if (options.count(OPTION_VERBOSE)) |
| 0 | 854 { |
| 855 Orthanc::Logging::EnableInfoLevel(true); | |
| 856 } | |
| 857 | |
|
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858 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 859 { |
|
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860 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 861 } |
| 862 | |
|
323
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863 if (options.count(OPTION_FORCE_OPENSLIDE) && |
|
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864 options[OPTION_FORCE_OPENSLIDE].as<bool>()) |
|
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865 { |
|
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866 parameters.SetForceOpenSlide(true); |
|
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867 } |
|
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|
868 |
|
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869 if (options.count(OPTION_PYRAMID) && |
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870 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 871 { |
| 872 parameters.SetReconstructPyramid(true); | |
| 873 } | |
| 874 | |
|
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875 if (options.count(OPTION_SMOOTH) && |
|
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|
876 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 877 { |
| 878 parameters.SetSmoothEnabled(true); | |
| 879 } | |
| 880 | |
|
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881 if (options.count(OPTION_SAFETY) && |
|
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882 options[OPTION_SAFETY].as<bool>()) |
| 0 | 883 { |
| 884 parameters.SetSafetyCheck(true); | |
| 885 } | |
| 886 | |
|
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887 if (options.count(OPTION_REENCODE) && |
|
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888 options[OPTION_REENCODE].as<bool>()) |
| 0 | 889 { |
| 890 parameters.SetForceReencode(true); | |
| 891 } | |
| 892 | |
|
129
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893 if (options.count(OPTION_REPAINT) && |
|
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|
894 options[OPTION_REPAINT].as<bool>()) |
| 0 | 895 { |
| 896 parameters.SetRepaintBackground(true); | |
| 897 } | |
| 898 | |
|
129
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899 if (options.count(OPTION_TILE_WIDTH) || |
|
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900 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 901 { |
| 902 int w = 0; | |
|
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903 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 904 { |
|
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905 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 906 } |
| 907 | |
| 145 | 908 int h = 0; |
|
129
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|
909 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 910 { |
|
129
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911 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 912 } |
| 913 | |
| 914 if (w < 0 || h < 0) | |
| 915 { | |
| 916 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 917 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 918 } | |
| 919 | |
| 920 parameters.SetTargetTileSize(w, h); | |
| 921 } | |
| 922 | |
|
244
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923 if (!parameters.IsCytomineSource()) |
|
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|
924 { |
|
4273518c2009
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|
925 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
|
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|
926 } |
| 0 | 927 |
|
129
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|
928 if (options.count(OPTION_COLOR)) |
| 0 | 929 { |
| 930 uint8_t r, g, b; | |
|
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|
931 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 932 parameters.SetBackgroundColor(r, g, b); |
| 933 } | |
| 934 | |
|
129
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|
935 if (options.count(OPTION_COMPRESSION)) |
| 0 | 936 { |
|
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937 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 938 if (s == "none") |
| 939 { | |
| 940 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 941 } | |
| 942 else if (s == "jpeg") | |
| 943 { | |
| 944 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 945 } | |
| 946 else if (s == "jpeg2000") | |
| 947 { | |
| 948 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 949 } | |
| 950 else | |
| 951 { | |
| 952 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 953 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 954 } | |
| 955 } | |
| 956 | |
|
129
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|
957 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 958 { |
|
129
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959 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 960 } |
| 961 | |
|
129
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|
962 if (options.count(OPTION_LEVELS)) |
| 0 | 963 { |
|
129
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964 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 965 } |
| 966 | |
|
129
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|
967 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 968 { |
|
129
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969 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 970 } |
| 971 | |
|
129
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|
972 if (options.count(OPTION_THREADS)) |
| 0 | 973 { |
|
129
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974 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 975 } |
| 976 | |
|
129
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|
977 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 978 { |
|
129
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|
979 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 980 } |
| 981 | |
|
129
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|
982 if (options.count(OPTION_FOLDER)) |
| 0 | 983 { |
|
129
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|
984 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 985 } |
| 986 | |
|
129
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|
987 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 988 { |
|
129
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|
989 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 990 } |
| 991 | |
|
125
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|
992 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 993 |
|
129
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|
994 if (options.count(OPTION_DATASET)) |
| 0 | 995 { |
|
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996 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 997 } |
| 998 | |
|
129
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|
999 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 1000 { |
|
129
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|
1001 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 1002 } |
| 1003 | |
|
129
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1004 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 1005 { |
|
129
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1006 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 1007 } |
| 1008 | |
|
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1009 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 1010 { |
|
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1011 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 1012 } |
| 1013 | |
|
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1014 if (options.count(OPTION_OFFSET_X)) |
| 0 | 1015 { |
|
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1016 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 1017 } |
| 1018 | |
|
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1019 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 1020 { |
|
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1021 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 1022 } |
| 1023 | |
|
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1024 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 1025 { |
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1026 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 1027 if (s == "none") |
| 1028 { | |
| 1029 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 1030 } | |
| 1031 else if (s == "brightfield") | |
| 1032 { | |
| 1033 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 1034 } | |
| 1035 else | |
| 1036 { | |
| 1037 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 1038 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 1039 } | |
| 1040 } | |
| 1041 | |
|
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1042 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 1043 { |
|
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1044 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 1045 } |
| 1046 | |
|
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1047 if (options.count(OPTION_PADDING)) |
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1048 { |
|
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1049 int value = options[OPTION_PADDING].as<int>(); |
|
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1050 if (value <= 0) |
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1051 { |
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1052 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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1053 "Padding must be >= 1"); |
|
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1054 } |
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1055 else |
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1056 { |
|
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1057 parameters.SetPadding(static_cast<unsigned int>(value)); |
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1058 } |
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1059 } |
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1060 |
| 0 | 1061 return true; |
| 1062 } | |
| 1063 | |
| 1064 | |
|
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1065 |
|
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1066 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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1067 OrthancWSI::ImagedVolumeParameters& volume, |
|
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1068 const std::string& path, |
| 0 | 1069 const OrthancWSI::DicomizerParameters& parameters) |
| 1070 { | |
|
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1071 if (parameters.IsCytomineSource()) |
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1072 { |
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1073 // New in release 1.1 |
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1074 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
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1075 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
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1076 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1077 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
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1078 parameters.GetCytominePublicKey(), |
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1079 parameters.GetCytominePrivateKey(), |
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1080 parameters.GetCytomineImageInstanceId(), |
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1081 parameters.GetTargetTileWidth(512), |
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1082 parameters.GetTargetTileHeight(512)); |
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1083 } |
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1084 |
| 0 | 1085 LOG(WARNING) << "The input image is: " << path; |
| 1086 | |
| 1087 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 1088 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 1089 | |
|
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1090 std::unique_ptr<OrthancWSI::SingleLevelDecodedPyramid> plainImage; |
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1091 |
| 0 | 1092 switch (format) |
| 1093 { | |
| 1094 case OrthancWSI::ImageCompression_Png: | |
|
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1095 { |
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1096 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
|
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1097 plainImage.reset(new OrthancWSI::TiledPngImage(path, |
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1098 parameters.GetTargetTileWidth(512), |
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1099 parameters.GetTargetTileHeight(512))); |
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1100 break; |
|
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1101 } |
| 0 | 1102 |
| 1103 case OrthancWSI::ImageCompression_Jpeg: | |
|
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1104 { |
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1105 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
|
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1106 plainImage.reset(new OrthancWSI::TiledJpegImage(path, |
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1107 parameters.GetTargetTileWidth(512), |
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1108 parameters.GetTargetTileHeight(512))); |
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1109 break; |
|
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1110 } |
| 0 | 1111 |
| 1112 case OrthancWSI::ImageCompression_Tiff: | |
| 1113 { | |
|
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1114 if (parameters.IsForceOpenSlide()) |
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1115 { |
|
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1116 LOG(WARNING) << "Forcing the use of OpenSlide on a TIFF-like file"; |
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1117 break; |
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1118 } |
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1119 |
| 0 | 1120 try |
| 1121 { | |
|
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1122 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
|
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1123 sourceCompression = tiff->GetImageCompression(); |
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1124 return tiff.release(); |
| 0 | 1125 } |
| 1126 catch (Orthanc::OrthancException&) | |
| 1127 { | |
|
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1128 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
| 0 | 1129 } |
|
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1130 |
|
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1131 try |
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1132 { |
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1133 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
|
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1134 plainImage.reset(new OrthancWSI::PlainTiff(path, |
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1135 parameters.GetTargetTileWidth(512), |
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1136 parameters.GetTargetTileHeight(512))); |
|
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1137 } |
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1138 catch (Orthanc::OrthancException&) |
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1139 { |
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1140 LOG(WARNING) << "This is not a standard plain TIFF file, fallback to OpenSlide (if enabled)"; |
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1141 } |
| 0 | 1142 } |
| 1143 | |
| 1144 default: | |
| 1145 break; | |
| 1146 } | |
| 1147 | |
|
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1148 if (plainImage.get() != NULL) |
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1149 { |
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1150 if (parameters.GetPadding() > 1) |
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1151 { |
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1152 plainImage->SetPadding(parameters.GetPadding(), |
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1153 parameters.GetBackgroundColorRed(), |
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1154 parameters.GetBackgroundColorGreen(), |
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1155 parameters.GetBackgroundColorBlue()); |
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1156 } |
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1157 |
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1158 return plainImage.release(); |
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1159 } |
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1160 |
| 0 | 1161 try |
| 1162 { | |
| 1163 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
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1164 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1165 |
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1166 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
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1167 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
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1168 parameters.GetTargetTileHeight(512))); |
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1169 |
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1170 openslide->SetBackgroundColor(parameters.GetBackgroundColorRed(), |
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1171 parameters.GetBackgroundColorGreen(), |
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1172 parameters.GetBackgroundColorBlue()); |
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1173 |
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1174 float volumeWidth, volumeHeight; |
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1175 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
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1176 { |
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1177 if (!volume.HasWidth()) |
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1178 { |
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1179 volume.SetWidth(volumeWidth); |
| 281 | 1180 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
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1181 } |
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1182 |
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1183 if (!volume.HasHeight()) |
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1184 { |
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1185 volume.SetHeight(volumeHeight); |
| 281 | 1186 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
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1187 } |
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1188 } |
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1189 |
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1190 return openslide.release(); |
| 0 | 1191 } |
| 1192 catch (Orthanc::OrthancException&) | |
| 1193 { | |
| 1194 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 1195 return NULL; | |
| 1196 } | |
| 1197 } | |
| 1198 | |
| 1199 | |
|
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1200 #include "../Framework/ColorSpaces.h" |
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1201 |
| 0 | 1202 int main(int argc, char* argv[]) |
| 1203 { | |
| 1204 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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1205 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 1206 |
| 1207 int exitStatus = 0; | |
| 1208 | |
| 1209 try | |
| 1210 { | |
| 1211 OrthancWSI::DicomizerParameters parameters; | |
| 1212 OrthancWSI::ImagedVolumeParameters volume; | |
| 1213 | |
| 1214 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 1215 { | |
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1216 OrthancWSI::ImageCompression sourceCompression; |
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1217 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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1218 |
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1219 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
| 0 | 1220 if (source.get() == NULL) |
| 1221 { | |
| 1222 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1223 } | |
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1224 |
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1225 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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1226 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
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1227 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
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1228 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
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1229 { |
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1230 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
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1231 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
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1232 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
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1233 } |
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1234 |
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1235 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1236 |
| 1237 // Create the shared DICOM tags | |
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1238 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1239 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1240 |
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1241 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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1242 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1243 } |
| 1244 } | |
| 1245 catch (Orthanc::OrthancException& e) | |
| 1246 { | |
| 1247 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1248 exitStatus = -1; | |
| 1249 } | |
| 1250 | |
| 1251 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1252 | |
| 1253 return exitStatus; | |
| 1254 } |