Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 323:429c4efa1fde
added option --force-openslide
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 16 Oct 2024 19:36:01 +0200 |
| parents | 778e08291d52 |
| children | a92bb720f90b |
| 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" | |
| 26 #include "../Framework/DicomToolbox.h" | |
| 27 #include "../Framework/DicomizerParameters.h" | |
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28 #include "../Framework/ImageToolbox.h" |
| 0 | 29 #include "../Framework/ImagedVolumeParameters.h" |
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30 #include "../Framework/Inputs/CytomineImage.h" |
| 0 | 31 #include "../Framework/Inputs/HierarchicalTiff.h" |
| 32 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
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33 #include "../Framework/Inputs/PlainTiff.h" |
| 0 | 34 #include "../Framework/Inputs/TiledJpegImage.h" |
| 35 #include "../Framework/Inputs/TiledPngImage.h" | |
| 36 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 37 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 38 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 39 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 40 | |
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41 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 42 #include <DicomParsing/FromDcmtkBridge.h> |
| 43 #include <Logging.h> | |
| 44 #include <OrthancException.h> | |
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45 #include <Toolbox.h> |
| 192 | 46 #include <SystemToolbox.h> |
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47 |
| 0 | 48 #include "ApplicationToolbox.h" |
| 49 | |
| 50 #include <EmbeddedResources.h> | |
| 51 | |
| 52 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 53 #include <dcmtk/dcmdata/dcuid.h> | |
| 54 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 55 #include <dcmtk/dcmdata/dcvrat.h> | |
| 56 | |
| 57 | |
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58 static const char* OPTION_COLOR = "color"; |
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59 static const char* OPTION_COMPRESSION = "compression"; |
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60 static const char* OPTION_DATASET = "dataset"; |
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61 static const char* OPTION_FOLDER = "folder"; |
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62 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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63 static const char* OPTION_FORCE_OPENSLIDE = "force-openslide"; |
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64 static const char* OPTION_HELP = "help"; |
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65 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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66 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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67 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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68 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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69 static const char* OPTION_INPUT = "input"; |
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70 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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71 static const char* OPTION_LEVELS = "levels"; |
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72 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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73 static const char* OPTION_MAX_SIZE = "max-size"; |
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74 static const char* OPTION_OFFSET_X = "offset-x"; |
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75 static const char* OPTION_OFFSET_Y = "offset-y"; |
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76 static const char* OPTION_OPENSLIDE = "openslide"; |
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77 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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78 static const char* OPTION_PYRAMID = "pyramid"; |
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79 static const char* OPTION_REENCODE = "reencode"; |
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80 static const char* OPTION_REPAINT = "repaint"; |
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81 static const char* OPTION_SAFETY = "safety"; |
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82 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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83 static const char* OPTION_SMOOTH = "smooth"; |
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84 static const char* OPTION_THREADS = "threads"; |
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85 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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86 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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87 static const char* OPTION_VERBOSE = "verbose"; |
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88 static const char* OPTION_VERSION = "version"; |
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89 |
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90 // New in release 1.1 |
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91 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
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92 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
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93 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
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94 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
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95 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
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96 |
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97 // New in release 2.1 |
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98 static const char* OPTION_TIFF_ALIGNMENT = "tiff-alignment"; |
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99 |
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100 |
| 226 | 101 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 102 | |
| 103 bool ReadJsonWithoutComments(Json::Value& target, | |
| 104 const std::string& source) | |
| 105 { | |
| 106 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 107 } | |
| 108 | |
| 109 #else | |
| 110 | |
| 111 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 112 #include <json/reader.h> | |
| 113 | |
| 114 bool ReadJsonWithoutComments(Json::Value& target, | |
| 115 const std::string& source) | |
| 116 { | |
| 117 Json::Reader reader; | |
| 118 return reader.parse(source, target, false); | |
| 119 } | |
| 120 #endif | |
| 121 | |
| 122 | |
| 0 | 123 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 124 OrthancWSI::ITiledPyramid& source, | |
| 125 const OrthancWSI::DicomizerParameters& parameters) | |
| 126 { | |
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127 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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128 |
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129 OrthancWSI::BagOfTasks tasks; |
| 0 | 130 |
| 131 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 132 { | |
| 133 LOG(WARNING) << "Creating level " << i << " of size " | |
| 134 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 135 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 136 } | |
| 137 | |
| 138 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 139 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 140 } | |
| 141 | |
| 142 | |
| 143 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 144 OrthancWSI::ITiledPyramid& source, | |
| 145 const OrthancWSI::DicomizerParameters& parameters) | |
| 146 { | |
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147 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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148 |
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149 OrthancWSI::BagOfTasks tasks; |
| 0 | 150 |
| 151 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 152 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 153 assert(levelsCount >= 1); | |
| 154 | |
| 155 for (unsigned int i = 0; i < levelsCount; i++) | |
| 156 { | |
| 157 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 158 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 159 | |
| 160 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 161 target.AddLevel(width, height); | |
| 162 } | |
| 163 | |
| 164 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 165 if (lowerLevelsCount > levelsCount) | |
| 166 { | |
| 167 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 168 << ") exceeds the number of levels (" << levelsCount | |
| 169 << "), cropping it"; | |
| 170 lowerLevelsCount = levelsCount; | |
| 171 } | |
| 172 | |
| 173 assert(lowerLevelsCount <= levelsCount); | |
| 174 if (lowerLevelsCount != levelsCount) | |
| 175 { | |
| 176 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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177 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 178 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 179 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 180 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 181 | |
| 182 assert(tasks.GetSize() == 0); | |
| 183 | |
| 184 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 185 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 186 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 187 (tasks, target, truncated.GetUpperLevel(), | |
| 188 upperLevelsCount, lowerLevelsCount, parameters); | |
| 189 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 190 } | |
| 191 else | |
| 192 { | |
| 193 LOG(WARNING) << "Constructing the pyramid"; | |
| 194 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 195 (tasks, target, source, levelsCount, 0, parameters); | |
| 196 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 197 } | |
| 198 } | |
| 199 | |
| 200 | |
| 201 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 202 OrthancWSI::ITiledPyramid& source, | |
| 203 const DcmDataset& dataset, | |
| 204 const OrthancWSI::DicomizerParameters& parameters, | |
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205 const OrthancWSI::ImagedVolumeParameters& volume, |
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206 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 207 { |
| 208 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 209 | |
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210 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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211 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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212 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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213 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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214 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 215 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 216 | |
| 217 if (parameters.IsRepaintBackground()) | |
| 218 { | |
| 219 LOG(WARNING) << "Repainting the background with color: (" | |
| 220 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 221 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 222 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 223 } | |
| 224 else | |
| 225 { | |
| 226 LOG(WARNING) << "No repainting of the background"; | |
| 227 } | |
| 228 | |
|
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229 Orthanc::PhotometricInterpretation targetPhotometric; |
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230 bool transcoding; |
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231 |
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232 if (parameters.IsForceReencode() || |
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233 parameters.IsReconstructPyramid() || |
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234 sourceCompression != parameters.GetTargetCompression()) |
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235 { |
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236 // The tiles of the source image will be re-encoded |
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237 transcoding = false; |
| 171 | 238 |
| 239 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 240 { | |
| 241 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 242 } | |
| 243 else | |
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244 { |
| 171 | 245 switch (parameters.GetTargetCompression()) |
| 246 { | |
| 247 case OrthancWSI::ImageCompression_Jpeg: | |
| 248 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 249 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 250 break; | |
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251 |
| 171 | 252 case OrthancWSI::ImageCompression_None: |
| 253 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 254 break; | |
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255 |
| 171 | 256 default: |
| 257 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 258 } | |
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259 } |
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260 } |
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261 else |
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262 { |
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263 // Transcoding: The tiles are copied (no re-encoding) |
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264 transcoding = true; |
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265 targetPhotometric = source.GetPhotometricInterpretation(); |
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266 } |
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267 |
| 0 | 268 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 269 source.GetPixelFormat(), | |
| 270 parameters.GetTargetCompression(), | |
| 271 parameters.GetTargetTileWidth(source), | |
| 272 parameters.GetTargetTileHeight(source), | |
| 273 parameters.GetDicomMaxFileSize(), | |
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274 volume, targetPhotometric); |
| 29 | 275 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 276 |
| 277 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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278 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 279 |
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280 if (!transcoding && |
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281 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 282 { |
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283 LOG(WARNING) << "Target compression: Jpeg with quality " |
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284 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 285 target.SetJpegQuality(target.GetJpegQuality()); |
| 286 } | |
| 287 else | |
| 288 { | |
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289 LOG(WARNING) << "Target compression: " |
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290 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 291 } |
| 292 | |
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293 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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294 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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295 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 296 { |
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297 LOG(ERROR) << "When resampling the tile size, " |
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298 << "it must be a integer divisor of the original tile size"; |
| 0 | 299 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 300 } | |
| 301 | |
| 302 if (target.GetTileWidth() <= 16 || | |
| 303 target.GetTileHeight() <= 16) | |
| 304 { | |
| 305 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 306 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 307 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 308 } | |
| 309 | |
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310 if (transcoding) |
| 0 | 311 { |
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312 TranscodePyramid(target, stats, parameters); |
| 0 | 313 } |
| 314 else | |
| 315 { | |
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316 ReconstructPyramid(target, stats, parameters); |
| 0 | 317 } |
| 318 | |
| 319 target.Flush(); | |
| 320 } | |
| 321 | |
| 322 | |
| 323 | |
| 324 static DcmDataset* ParseDataset(const std::string& path) | |
| 325 { | |
| 326 Json::Value json; | |
| 327 | |
| 328 if (path.empty()) | |
| 329 { | |
| 330 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 331 } | |
| 332 else | |
| 333 { | |
| 334 std::string content; | |
| 43 | 335 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 336 |
| 226 | 337 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 338 { |
| 339 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 340 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 341 } | |
| 342 } | |
| 343 | |
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344 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
|
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345 "" /* no private tag, thus no private creator */)); |
| 0 | 346 if (dataset.get() == NULL) |
| 347 { | |
| 348 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 349 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 350 } | |
| 351 | |
| 352 // VL Whole Slide Microscopy Image IOD | |
|
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353 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
| 0 | 354 |
| 355 // Slide Microscopy | |
| 356 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 357 | |
| 358 // Patient orientation makes no sense in whole-slide images | |
| 359 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 360 | |
| 361 // Some basic coordinate information | |
| 362 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 363 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 364 | |
| 365 std::string date, time; | |
| 130 | 366 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 368 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 369 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 372 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 373 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 374 | |
| 375 return dataset.release(); | |
| 376 } | |
| 377 | |
| 378 | |
| 379 | |
| 380 static void SetupDimension(DcmDataset& dataset, | |
| 381 const std::string& opticalPathId, | |
| 382 const OrthancWSI::ITiledPyramid& source, | |
| 383 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 384 { | |
| 83 | 385 // Extract the identifier of the Dimension Organization, if provided |
| 386 std::string organization; | |
| 0 | 387 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 388 | |
| 83 | 389 if (previous != NULL && |
| 390 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 391 { | |
| 392 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 393 } | |
| 394 else | |
| 0 | 395 { |
| 83 | 396 // No Dimension Organization provided: Generate an unique identifier |
| 397 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 398 } | |
| 399 | |
| 400 | |
| 401 { | |
| 402 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
|
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403 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 404 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 405 | |
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406 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 407 |
| 408 if (!sequence->insert(item.release(), false, false).good() || | |
| 409 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 410 { |
| 83 | 411 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 412 } |
| 413 } | |
| 414 | |
| 83 | 415 |
| 0 | 416 { |
| 83 | 417 // Construct tag "Dimension Index Sequence" (0020,9222) |
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418 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 419 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
|
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420 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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421 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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422 |
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423 std::unique_ptr<DcmItem> item2(new DcmItem); |
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424 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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425 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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426 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 427 |
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428 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 429 |
| 83 | 430 if (!sequence->insert(item.release(), false, false).good() || |
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431 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 432 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 433 { | |
| 434 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 435 } | |
| 0 | 436 } |
| 437 | |
| 438 | |
| 83 | 439 { |
| 440 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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441 std::unique_ptr<DcmItem> item(new DcmItem); |
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442 |
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443 std::unique_ptr<DcmItem> item3(new DcmItem); |
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444 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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445 |
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446 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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447 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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448 |
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449 if (!sequence3->insert(item3.release(), false, false).good() || |
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450 !item->insert(sequence3.release(), false, false).good() || |
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451 !sequence->insert(item.release(), false, false).good() || |
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452 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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453 { |
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454 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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455 } |
| 0 | 456 } |
| 457 } | |
| 458 | |
| 459 | |
| 460 static void EnrichDataset(DcmDataset& dataset, | |
| 461 const OrthancWSI::ITiledPyramid& source, | |
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462 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 463 const OrthancWSI::DicomizerParameters& parameters, |
| 464 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 465 { | |
| 466 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 467 | |
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468 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 469 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 470 { | |
| 471 // Takes as estimation a 1:10 compression ratio | |
| 472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 473 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 474 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 475 } | |
| 476 else | |
| 477 { | |
| 478 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 479 } | |
| 480 | |
| 481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 482 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 483 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 484 | |
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485 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 486 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 487 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 488 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 489 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 490 | |
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491 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 492 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 493 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 494 { | |
| 495 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 496 } | |
| 497 | |
| 498 | |
| 499 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 500 { | |
| 501 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 502 { | |
| 503 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 504 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 505 } | |
| 506 | |
| 507 std::string brightfield; | |
| 508 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 509 | |
| 510 Json::Value json; | |
| 226 | 511 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 512 { |
| 513 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 514 } | |
| 515 | |
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516 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 517 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 518 DCM_OpticalPathSequence.getElement()), | |
|
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519 json, false, encoding, |
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520 "" /* no private tag, thus no private creator */)); |
| 0 | 521 if (!dataset.insert(element.release()).good()) |
| 522 { | |
| 523 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 524 } | |
| 525 } | |
| 526 | |
| 527 | |
| 528 std::string profile; | |
| 529 if (parameters.GetIccProfilePath().empty()) | |
| 530 { | |
| 531 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 532 } | |
| 533 else | |
| 534 { | |
| 43 | 535 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 536 } |
| 537 | |
| 538 | |
| 539 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 540 if (opticalPath == NULL) | |
| 541 { | |
| 542 LOG(ERROR) << "No optical path specified"; | |
| 543 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 544 } | |
| 545 | |
| 546 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 547 { | |
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548 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 549 |
| 550 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 551 !opticalPath->insert(icc.release()).good()) | |
| 552 { | |
| 553 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 554 } | |
| 555 } | |
| 556 | |
| 557 const char* opticalPathId = NULL; | |
| 558 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 559 opticalPathId == NULL) | |
| 560 { | |
| 561 LOG(ERROR) << "No identifier in the optical path"; | |
| 562 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 563 } | |
| 564 | |
| 565 SetupDimension(dataset, opticalPathId, source, volume); | |
| 566 } | |
| 567 | |
| 568 | |
| 569 static bool ParseParameters(int& exitStatus, | |
| 570 OrthancWSI::DicomizerParameters& parameters, | |
| 571 OrthancWSI::ImagedVolumeParameters& volume, | |
| 572 int argc, | |
| 573 char* argv[]) | |
| 574 { | |
| 575 // Declare the supported parameters | |
| 576 boost::program_options::options_description generic("Generic options"); | |
| 577 generic.add_options() | |
|
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578 (OPTION_HELP, "Display this help and exit") |
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579 (OPTION_VERSION, "Output version information and exit") |
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580 (OPTION_VERBOSE, "Be verbose in logs") |
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581 (OPTION_THREADS, |
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582 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 583 "Number of processing threads to be used") |
|
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584 (OPTION_FORCE_OPENSLIDE, boost::program_options::value<bool>(), |
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585 "Whether to force the use of OpenSlide on input TIFF-like files (Boolean)") |
|
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586 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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587 "Path to the shared library of OpenSlide " |
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588 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 589 ; |
| 590 | |
| 591 boost::program_options::options_description source("Options for the source image"); | |
| 592 source.add_options() | |
|
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593 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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594 "Path to a JSON file containing the DICOM dataset") |
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595 (OPTION_SAMPLE_DATASET, |
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596 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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597 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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598 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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599 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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600 "Whether to repaint the background of the image (Boolean)") |
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601 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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602 "Color of the background (e.g. \"255,0,0\")") |
|
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603 (OPTION_TIFF_ALIGNMENT, boost::program_options::value<int>()->default_value(64), |
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604 "Add padding to plain TIFF images to align the width/height to multiples " |
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605 "of this value, very useful to enable deep zoom with IIIF (1 means no padding)") |
| 0 | 606 ; |
| 607 | |
|
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608 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
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609 cytomine.add_options() |
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610 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
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611 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
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612 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
| 246 | 613 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
|
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614 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
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615 "Your personal private key in Cytomine (to be kept secret)") |
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616 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
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617 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
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618 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
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619 "Compression to be used for downloading the tiles from Cytomine, " |
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620 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
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621 ; |
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622 |
| 0 | 623 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
| 624 pyramid.add_options() | |
|
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625 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 626 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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627 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 628 "Apply smoothing when reconstructing the pyramid " |
| 629 "(slower, but higher quality) (Boolean)") | |
|
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630 (OPTION_LEVELS, boost::program_options::value<int>(), |
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631 "Number of levels in the target pyramid") |
| 0 | 632 ; |
| 633 | |
| 634 boost::program_options::options_description target("Options for the target image"); | |
| 635 target.add_options() | |
|
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636 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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637 "Width of the tiles in the target image") |
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638 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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639 "Height of the tiles in the target image") |
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640 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 641 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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642 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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643 "Set quality level for JPEG (0..100)") |
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644 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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645 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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646 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 647 "Folder where to store the output DICOM instances") |
|
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648 (OPTION_FOLDER_PATTERN, |
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649 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 650 "Pattern for the files in the output folder") |
| 651 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 652 "URL to the REST API of the target Orthanc server") | |
| 653 ; | |
| 654 | |
| 655 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 656 volumeOptions.add_options() | |
|
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657 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
|
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658 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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659 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
|
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660 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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661 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
|
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662 "Depth of the specimen (in mm)") |
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663 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 664 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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665 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 666 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 667 ; | |
| 668 | |
|
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669 boost::program_options::options_description restOptions |
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670 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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671 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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672 |
| 0 | 673 boost::program_options::options_description advancedOptions("Advanced options"); |
| 674 advancedOptions.add_options() | |
|
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675 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 676 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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677 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 678 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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679 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 680 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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681 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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682 "Number of pyramid levels up to which multithreading " |
| 0 | 683 "should be applied (only for performance/memory tuning)") |
| 684 ; | |
| 685 | |
| 686 boost::program_options::options_description hidden; | |
| 687 hidden.add_options() | |
|
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688 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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689 "Input file"); |
| 0 | 690 ; |
| 691 | |
| 692 boost::program_options::options_description allWithoutHidden; | |
|
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693 allWithoutHidden |
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694 .add(generic) |
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695 .add(source) |
|
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696 .add(cytomine) |
|
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697 .add(pyramid) |
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698 .add(target) |
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699 .add(volumeOptions) |
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700 .add(restOptions) |
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701 .add(advancedOptions); |
| 0 | 702 |
| 703 boost::program_options::options_description all = allWithoutHidden; | |
| 704 all.add(hidden); | |
| 705 | |
| 706 boost::program_options::positional_options_description positional; | |
|
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707 positional.add(OPTION_INPUT, 1); |
| 0 | 708 |
| 709 boost::program_options::variables_map options; | |
| 710 bool error = false; | |
| 711 | |
| 712 try | |
| 713 { | |
| 714 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 715 options(all).positional(positional).run(), options); | |
| 716 boost::program_options::notify(options); | |
| 717 } | |
| 718 catch (boost::program_options::error& e) | |
| 719 { | |
| 720 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 721 error = true; | |
| 722 } | |
| 723 | |
| 724 if (!error && | |
|
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725 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 726 { |
| 727 std::string sample; | |
| 728 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 729 | |
| 730 std::cout << std::endl << sample << std::endl; | |
| 731 | |
| 732 return false; | |
| 733 } | |
| 734 | |
|
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735 // New in release 1.1 |
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736 if (options.count(OPTION_CYTOMINE_URL) || |
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737 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
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738 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
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739 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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740 { |
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741 if (!options.count(OPTION_CYTOMINE_URL)) |
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742 { |
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743 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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744 "URL to the Cytomine server is missing"); |
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745 } |
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746 |
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747 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
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748 { |
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749 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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750 "Public key for the Cytomine server is missing"); |
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751 } |
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752 |
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753 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
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754 { |
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755 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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756 "Private key for the Cytomine server is missing"); |
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757 } |
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758 |
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759 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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760 { |
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761 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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762 "The Image Instance ID from the Cytomine server is missing"); |
|
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763 } |
|
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764 |
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765 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
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766 { |
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767 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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768 "The tile compression scheme for Cytomine is missing"); |
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769 } |
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770 |
|
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771 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
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772 |
|
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773 OrthancWSI::ImageCompression compression; |
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774 if (s == "jpeg") |
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775 { |
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776 compression = OrthancWSI::ImageCompression_Jpeg; |
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777 } |
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778 else if (s == "png") |
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779 { |
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780 compression = OrthancWSI::ImageCompression_Png; |
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781 } |
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782 else |
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783 { |
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784 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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785 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
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786 } |
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787 |
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788 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
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789 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
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790 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
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791 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
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792 } |
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793 |
| 0 | 794 if (!error && |
|
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795 options.count(OPTION_HELP) == 0 && |
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796 options.count(OPTION_VERSION) == 0 && |
|
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797 options.count(OPTION_INPUT) != 1 && |
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798 !parameters.IsCytomineSource()) |
| 0 | 799 { |
| 800 LOG(ERROR) << "No input file was specified"; | |
| 801 error = true; | |
| 802 } | |
| 803 | |
|
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804 if (error || options.count(OPTION_HELP)) |
| 0 | 805 { |
| 806 std::cout << std::endl | |
| 807 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 808 << std::endl | |
| 809 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 810 << std::endl << std::endl | |
| 811 << "Create a DICOM file from a digital pathology image." | |
| 812 << std::endl; | |
| 813 | |
| 814 std::cout << allWithoutHidden << "\n"; | |
| 815 | |
| 816 if (error) | |
| 817 { | |
| 818 exitStatus = -1; | |
| 819 } | |
| 820 | |
| 821 return false; | |
| 822 } | |
| 823 | |
|
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824 if (options.count(OPTION_VERSION)) |
|
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825 { |
|
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|
826 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
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827 return false; |
|
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|
828 } |
|
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829 |
|
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830 if (options.count(OPTION_VERBOSE)) |
| 0 | 831 { |
| 832 Orthanc::Logging::EnableInfoLevel(true); | |
| 833 } | |
| 834 | |
|
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835 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 836 { |
|
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837 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 838 } |
| 839 | |
|
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840 if (options.count(OPTION_FORCE_OPENSLIDE) && |
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841 options[OPTION_FORCE_OPENSLIDE].as<bool>()) |
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842 { |
|
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843 parameters.SetForceOpenSlide(true); |
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844 } |
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845 |
|
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846 if (options.count(OPTION_PYRAMID) && |
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847 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 848 { |
| 849 parameters.SetReconstructPyramid(true); | |
| 850 } | |
| 851 | |
|
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852 if (options.count(OPTION_SMOOTH) && |
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853 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 854 { |
| 855 parameters.SetSmoothEnabled(true); | |
| 856 } | |
| 857 | |
|
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858 if (options.count(OPTION_SAFETY) && |
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859 options[OPTION_SAFETY].as<bool>()) |
| 0 | 860 { |
| 861 parameters.SetSafetyCheck(true); | |
| 862 } | |
| 863 | |
|
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864 if (options.count(OPTION_REENCODE) && |
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865 options[OPTION_REENCODE].as<bool>()) |
| 0 | 866 { |
| 867 parameters.SetForceReencode(true); | |
| 868 } | |
| 869 | |
|
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870 if (options.count(OPTION_REPAINT) && |
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871 options[OPTION_REPAINT].as<bool>()) |
| 0 | 872 { |
| 873 parameters.SetRepaintBackground(true); | |
| 874 } | |
| 875 | |
|
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876 if (options.count(OPTION_TILE_WIDTH) || |
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877 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 878 { |
| 879 int w = 0; | |
|
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880 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 881 { |
|
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882 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 883 } |
| 884 | |
| 145 | 885 int h = 0; |
|
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886 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 887 { |
|
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888 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 889 } |
| 890 | |
| 891 if (w < 0 || h < 0) | |
| 892 { | |
| 893 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 894 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 895 } | |
| 896 | |
| 897 parameters.SetTargetTileSize(w, h); | |
| 898 } | |
| 899 | |
|
244
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900 if (!parameters.IsCytomineSource()) |
|
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901 { |
|
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902 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
|
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903 } |
| 0 | 904 |
|
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905 if (options.count(OPTION_COLOR)) |
| 0 | 906 { |
| 907 uint8_t r, g, b; | |
|
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908 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 909 parameters.SetBackgroundColor(r, g, b); |
| 910 } | |
| 911 | |
|
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912 if (options.count(OPTION_COMPRESSION)) |
| 0 | 913 { |
|
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914 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 915 if (s == "none") |
| 916 { | |
| 917 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 918 } | |
| 919 else if (s == "jpeg") | |
| 920 { | |
| 921 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 922 } | |
| 923 else if (s == "jpeg2000") | |
| 924 { | |
| 925 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 926 } | |
| 927 else | |
| 928 { | |
| 929 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 930 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 931 } | |
| 932 } | |
| 933 | |
|
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934 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 935 { |
|
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936 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 937 } |
| 938 | |
|
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939 if (options.count(OPTION_LEVELS)) |
| 0 | 940 { |
|
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941 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 942 } |
| 943 | |
|
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944 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 945 { |
|
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946 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 947 } |
| 948 | |
|
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949 if (options.count(OPTION_THREADS)) |
| 0 | 950 { |
|
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951 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 952 } |
| 953 | |
|
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954 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 955 { |
|
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956 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 957 } |
| 958 | |
|
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|
959 if (options.count(OPTION_FOLDER)) |
| 0 | 960 { |
|
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961 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 962 } |
| 963 | |
|
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964 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 965 { |
|
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966 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 967 } |
| 968 | |
|
125
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969 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 970 |
|
129
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971 if (options.count(OPTION_DATASET)) |
| 0 | 972 { |
|
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973 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 974 } |
| 975 | |
|
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976 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 977 { |
|
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978 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 979 } |
| 980 | |
|
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981 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 982 { |
|
129
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983 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 984 } |
| 985 | |
|
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986 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 987 { |
|
129
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988 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 989 } |
| 990 | |
|
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991 if (options.count(OPTION_OFFSET_X)) |
| 0 | 992 { |
|
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993 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 994 } |
| 995 | |
|
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996 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 997 { |
|
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998 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 999 } |
| 1000 | |
|
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1001 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 1002 { |
|
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1003 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 1004 if (s == "none") |
| 1005 { | |
| 1006 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 1007 } | |
| 1008 else if (s == "brightfield") | |
| 1009 { | |
| 1010 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 1011 } | |
| 1012 else | |
| 1013 { | |
| 1014 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 1015 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 1016 } | |
| 1017 } | |
| 1018 | |
|
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1019 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 1020 { |
|
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1021 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 1022 } |
| 1023 | |
|
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1024 if (options.count(OPTION_TIFF_ALIGNMENT)) |
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1025 { |
|
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|
1026 int value = options[OPTION_TIFF_ALIGNMENT].as<int>(); |
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1027 if (value <= 0) |
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1028 { |
|
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1029 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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|
1030 "TIFF alignment must be >= 1"); |
|
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1031 } |
|
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1032 else |
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1033 { |
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1034 parameters.SetTiffAlignment(static_cast<unsigned int>(value)); |
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1035 } |
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1036 } |
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1037 |
| 0 | 1038 return true; |
| 1039 } | |
| 1040 | |
| 1041 | |
|
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1042 |
|
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1043 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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1044 OrthancWSI::ImagedVolumeParameters& volume, |
|
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1045 const std::string& path, |
| 0 | 1046 const OrthancWSI::DicomizerParameters& parameters) |
| 1047 { | |
|
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1048 if (parameters.IsCytomineSource()) |
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1049 { |
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1050 // New in release 1.1 |
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1051 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
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1052 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
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1053 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1054 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
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1055 parameters.GetCytominePublicKey(), |
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1056 parameters.GetCytominePrivateKey(), |
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1057 parameters.GetCytomineImageInstanceId(), |
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1058 parameters.GetTargetTileWidth(512), |
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1059 parameters.GetTargetTileHeight(512)); |
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1060 } |
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1061 |
| 0 | 1062 LOG(WARNING) << "The input image is: " << path; |
| 1063 | |
| 1064 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 1065 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 1066 | |
| 1067 switch (format) | |
| 1068 { | |
| 1069 case OrthancWSI::ImageCompression_Png: | |
|
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1070 { |
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1071 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1072 return new OrthancWSI::TiledPngImage(path, |
| 1073 parameters.GetTargetTileWidth(512), | |
| 1074 parameters.GetTargetTileHeight(512)); | |
|
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1075 } |
| 0 | 1076 |
| 1077 case OrthancWSI::ImageCompression_Jpeg: | |
|
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1078 { |
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1079 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1080 return new OrthancWSI::TiledJpegImage(path, |
| 1081 parameters.GetTargetTileWidth(512), | |
| 1082 parameters.GetTargetTileHeight(512)); | |
|
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1083 } |
| 0 | 1084 |
| 1085 case OrthancWSI::ImageCompression_Tiff: | |
| 1086 { | |
|
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1087 if (parameters.IsForceOpenSlide()) |
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1088 { |
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1089 LOG(WARNING) << "Forcing the use of OpenSlide on a TIFF-like file"; |
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1090 break; |
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1091 } |
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1092 |
| 0 | 1093 try |
| 1094 { | |
|
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1095 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
|
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1096 sourceCompression = tiff->GetImageCompression(); |
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1097 return tiff.release(); |
| 0 | 1098 } |
| 1099 catch (Orthanc::OrthancException&) | |
| 1100 { | |
|
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1101 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
| 0 | 1102 } |
|
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1103 |
|
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1104 try |
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1105 { |
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1106 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1107 return new OrthancWSI::PlainTiff(path, |
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1108 parameters.GetTargetTileWidth(512), |
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1109 parameters.GetTargetTileHeight(512), |
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1110 parameters.GetTiffAlignment(), |
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1111 parameters.GetBackgroundColorRed(), |
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1112 parameters.GetBackgroundColorGreen(), |
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1113 parameters.GetBackgroundColorBlue()); |
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1114 } |
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1115 catch (Orthanc::OrthancException&) |
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1116 { |
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1117 LOG(WARNING) << "This is not a standard plain TIFF file, fallback to OpenSlide (if enabled)"; |
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1118 } |
| 0 | 1119 } |
| 1120 | |
| 1121 default: | |
| 1122 break; | |
| 1123 } | |
| 1124 | |
| 1125 try | |
| 1126 { | |
| 1127 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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1128 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
|
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1129 |
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1130 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
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1131 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
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1132 parameters.GetTargetTileHeight(512))); |
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1133 |
|
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1134 openslide->SetBackgroundColor(parameters.GetBackgroundColorRed(), |
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1135 parameters.GetBackgroundColorGreen(), |
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1136 parameters.GetBackgroundColorBlue()); |
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1137 |
|
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1138 float volumeWidth, volumeHeight; |
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1139 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
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1140 { |
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1141 if (!volume.HasWidth()) |
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1142 { |
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1143 volume.SetWidth(volumeWidth); |
| 281 | 1144 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
|
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1145 } |
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1146 |
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1147 if (!volume.HasHeight()) |
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1148 { |
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1149 volume.SetHeight(volumeHeight); |
| 281 | 1150 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
|
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1151 } |
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1152 } |
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1153 |
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1154 return openslide.release(); |
| 0 | 1155 } |
| 1156 catch (Orthanc::OrthancException&) | |
| 1157 { | |
| 1158 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 1159 return NULL; | |
| 1160 } | |
| 1161 } | |
| 1162 | |
| 1163 | |
| 1164 int main(int argc, char* argv[]) | |
| 1165 { | |
| 1166 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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1167 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 1168 |
| 1169 int exitStatus = 0; | |
| 1170 | |
| 1171 try | |
| 1172 { | |
| 1173 OrthancWSI::DicomizerParameters parameters; | |
| 1174 OrthancWSI::ImagedVolumeParameters volume; | |
| 1175 | |
| 1176 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 1177 { | |
|
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1178 OrthancWSI::ImageCompression sourceCompression; |
|
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1179 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
|
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1180 |
|
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1181 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
| 0 | 1182 if (source.get() == NULL) |
| 1183 { | |
| 1184 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1185 } | |
|
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1186 |
|
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1187 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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1188 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
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1189 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
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1190 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
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1191 { |
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1192 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
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1193 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
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1194 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
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1195 } |
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1196 |
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1197 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1198 |
| 1199 // Create the shared DICOM tags | |
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1200 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1201 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1202 |
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1203 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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1204 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1205 } |
| 1206 } | |
| 1207 catch (Orthanc::OrthancException& e) | |
| 1208 { | |
| 1209 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1210 exitStatus = -1; | |
| 1211 } | |
| 1212 | |
| 1213 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1214 | |
| 1215 return exitStatus; | |
| 1216 } |