Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 314:9dc7f1e8716d
reverse the order of the "sizes" field in the IIIF manifest
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 14 Aug 2024 15:52:13 +0200 |
| parents | 0683312e21ba |
| children | 072968f00d26 |
| 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_HELP = "help"; |
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64 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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65 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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66 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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67 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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68 static const char* OPTION_INPUT = "input"; |
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69 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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70 static const char* OPTION_LEVELS = "levels"; |
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71 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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72 static const char* OPTION_MAX_SIZE = "max-size"; |
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73 static const char* OPTION_OFFSET_X = "offset-x"; |
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74 static const char* OPTION_OFFSET_Y = "offset-y"; |
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75 static const char* OPTION_OPENSLIDE = "openslide"; |
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76 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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77 static const char* OPTION_PYRAMID = "pyramid"; |
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78 static const char* OPTION_REENCODE = "reencode"; |
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79 static const char* OPTION_REPAINT = "repaint"; |
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80 static const char* OPTION_SAFETY = "safety"; |
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81 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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82 static const char* OPTION_SMOOTH = "smooth"; |
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83 static const char* OPTION_THREADS = "threads"; |
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84 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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85 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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86 static const char* OPTION_VERBOSE = "verbose"; |
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87 static const char* OPTION_VERSION = "version"; |
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88 |
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89 // New in release 1.1 |
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90 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
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91 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
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92 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
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93 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
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94 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
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95 |
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96 // New in release 2.1 |
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97 static const char* OPTION_TIFF_ALIGNMENT = "tiff-alignment"; |
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98 |
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99 |
| 226 | 100 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 101 | |
| 102 bool ReadJsonWithoutComments(Json::Value& target, | |
| 103 const std::string& source) | |
| 104 { | |
| 105 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 106 } | |
| 107 | |
| 108 #else | |
| 109 | |
| 110 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 111 #include <json/reader.h> | |
| 112 | |
| 113 bool ReadJsonWithoutComments(Json::Value& target, | |
| 114 const std::string& source) | |
| 115 { | |
| 116 Json::Reader reader; | |
| 117 return reader.parse(source, target, false); | |
| 118 } | |
| 119 #endif | |
| 120 | |
| 121 | |
| 0 | 122 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 123 OrthancWSI::ITiledPyramid& source, | |
| 124 const OrthancWSI::DicomizerParameters& parameters) | |
| 125 { | |
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126 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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127 |
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128 OrthancWSI::BagOfTasks tasks; |
| 0 | 129 |
| 130 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 131 { | |
| 132 LOG(WARNING) << "Creating level " << i << " of size " | |
| 133 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 134 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 135 } | |
| 136 | |
| 137 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 138 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 139 } | |
| 140 | |
| 141 | |
| 142 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 143 OrthancWSI::ITiledPyramid& source, | |
| 144 const OrthancWSI::DicomizerParameters& parameters) | |
| 145 { | |
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146 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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147 |
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148 OrthancWSI::BagOfTasks tasks; |
| 0 | 149 |
| 150 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 151 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 152 assert(levelsCount >= 1); | |
| 153 | |
| 154 for (unsigned int i = 0; i < levelsCount; i++) | |
| 155 { | |
| 156 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 157 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 158 | |
| 159 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 160 target.AddLevel(width, height); | |
| 161 } | |
| 162 | |
| 163 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 164 if (lowerLevelsCount > levelsCount) | |
| 165 { | |
| 166 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 167 << ") exceeds the number of levels (" << levelsCount | |
| 168 << "), cropping it"; | |
| 169 lowerLevelsCount = levelsCount; | |
| 170 } | |
| 171 | |
| 172 assert(lowerLevelsCount <= levelsCount); | |
| 173 if (lowerLevelsCount != levelsCount) | |
| 174 { | |
| 175 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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176 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 177 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 178 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 179 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 180 | |
| 181 assert(tasks.GetSize() == 0); | |
| 182 | |
| 183 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 184 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 185 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 186 (tasks, target, truncated.GetUpperLevel(), | |
| 187 upperLevelsCount, lowerLevelsCount, parameters); | |
| 188 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 189 } | |
| 190 else | |
| 191 { | |
| 192 LOG(WARNING) << "Constructing the pyramid"; | |
| 193 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 194 (tasks, target, source, levelsCount, 0, parameters); | |
| 195 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 196 } | |
| 197 } | |
| 198 | |
| 199 | |
| 200 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 201 OrthancWSI::ITiledPyramid& source, | |
| 202 const DcmDataset& dataset, | |
| 203 const OrthancWSI::DicomizerParameters& parameters, | |
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204 const OrthancWSI::ImagedVolumeParameters& volume, |
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205 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 206 { |
| 207 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 208 | |
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209 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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210 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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211 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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212 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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213 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 214 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 215 | |
| 216 if (parameters.IsRepaintBackground()) | |
| 217 { | |
| 218 LOG(WARNING) << "Repainting the background with color: (" | |
| 219 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 220 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 221 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 222 } | |
| 223 else | |
| 224 { | |
| 225 LOG(WARNING) << "No repainting of the background"; | |
| 226 } | |
| 227 | |
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228 Orthanc::PhotometricInterpretation targetPhotometric; |
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229 bool transcoding; |
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230 |
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231 if (parameters.IsForceReencode() || |
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232 parameters.IsReconstructPyramid() || |
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233 sourceCompression != parameters.GetTargetCompression()) |
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234 { |
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235 // The tiles of the source image will be re-encoded |
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236 transcoding = false; |
| 171 | 237 |
| 238 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 239 { | |
| 240 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 241 } | |
| 242 else | |
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243 { |
| 171 | 244 switch (parameters.GetTargetCompression()) |
| 245 { | |
| 246 case OrthancWSI::ImageCompression_Jpeg: | |
| 247 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 248 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 249 break; | |
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250 |
| 171 | 251 case OrthancWSI::ImageCompression_None: |
| 252 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 253 break; | |
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254 |
| 171 | 255 default: |
| 256 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 257 } | |
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258 } |
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259 } |
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260 else |
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261 { |
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262 // Transcoding: The tiles are copied (no re-encoding) |
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263 transcoding = true; |
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264 targetPhotometric = source.GetPhotometricInterpretation(); |
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265 } |
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266 |
| 0 | 267 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 268 source.GetPixelFormat(), | |
| 269 parameters.GetTargetCompression(), | |
| 270 parameters.GetTargetTileWidth(source), | |
| 271 parameters.GetTargetTileHeight(source), | |
| 272 parameters.GetDicomMaxFileSize(), | |
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273 volume, targetPhotometric); |
| 29 | 274 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 275 |
| 276 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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277 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 278 |
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279 if (!transcoding && |
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280 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 281 { |
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282 LOG(WARNING) << "Target compression: Jpeg with quality " |
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283 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 284 target.SetJpegQuality(target.GetJpegQuality()); |
| 285 } | |
| 286 else | |
| 287 { | |
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288 LOG(WARNING) << "Target compression: " |
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289 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 290 } |
| 291 | |
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292 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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293 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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294 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 295 { |
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296 LOG(ERROR) << "When resampling the tile size, " |
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297 << "it must be a integer divisor of the original tile size"; |
| 0 | 298 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 299 } | |
| 300 | |
| 301 if (target.GetTileWidth() <= 16 || | |
| 302 target.GetTileHeight() <= 16) | |
| 303 { | |
| 304 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 305 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 306 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 307 } | |
| 308 | |
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309 if (transcoding) |
| 0 | 310 { |
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311 TranscodePyramid(target, stats, parameters); |
| 0 | 312 } |
| 313 else | |
| 314 { | |
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315 ReconstructPyramid(target, stats, parameters); |
| 0 | 316 } |
| 317 | |
| 318 target.Flush(); | |
| 319 } | |
| 320 | |
| 321 | |
| 322 | |
| 323 static DcmDataset* ParseDataset(const std::string& path) | |
| 324 { | |
| 325 Json::Value json; | |
| 326 | |
| 327 if (path.empty()) | |
| 328 { | |
| 329 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 330 } | |
| 331 else | |
| 332 { | |
| 333 std::string content; | |
| 43 | 334 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 335 |
| 226 | 336 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 337 { |
| 338 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 339 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 340 } | |
| 341 } | |
| 342 | |
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343 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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344 "" /* no private tag, thus no private creator */)); |
| 0 | 345 if (dataset.get() == NULL) |
| 346 { | |
| 347 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 348 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 349 } | |
| 350 | |
| 351 // VL Whole Slide Microscopy Image IOD | |
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352 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
| 0 | 353 |
| 354 // Slide Microscopy | |
| 355 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 356 | |
| 357 // Patient orientation makes no sense in whole-slide images | |
| 358 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 359 | |
| 360 // Some basic coordinate information | |
| 361 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 362 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 363 | |
| 364 std::string date, time; | |
| 130 | 365 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 366 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 368 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 369 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 372 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 373 | |
| 374 return dataset.release(); | |
| 375 } | |
| 376 | |
| 377 | |
| 378 | |
| 379 static void SetupDimension(DcmDataset& dataset, | |
| 380 const std::string& opticalPathId, | |
| 381 const OrthancWSI::ITiledPyramid& source, | |
| 382 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 383 { | |
| 83 | 384 // Extract the identifier of the Dimension Organization, if provided |
| 385 std::string organization; | |
| 0 | 386 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 387 | |
| 83 | 388 if (previous != NULL && |
| 389 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 390 { | |
| 391 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 392 } | |
| 393 else | |
| 0 | 394 { |
| 83 | 395 // No Dimension Organization provided: Generate an unique identifier |
| 396 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 397 } | |
| 398 | |
| 399 | |
| 400 { | |
| 401 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
|
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402 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 403 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 404 | |
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405 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 406 |
| 407 if (!sequence->insert(item.release(), false, false).good() || | |
| 408 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 409 { |
| 83 | 410 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 411 } |
| 412 } | |
| 413 | |
| 83 | 414 |
| 0 | 415 { |
| 83 | 416 // Construct tag "Dimension Index Sequence" (0020,9222) |
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417 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 418 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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419 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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420 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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421 |
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422 std::unique_ptr<DcmItem> item2(new DcmItem); |
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423 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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424 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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425 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 426 |
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427 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 428 |
| 83 | 429 if (!sequence->insert(item.release(), false, false).good() || |
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430 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 431 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 432 { | |
| 433 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 434 } | |
| 0 | 435 } |
| 436 | |
| 437 | |
| 83 | 438 { |
| 439 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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440 std::unique_ptr<DcmItem> item(new DcmItem); |
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441 |
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442 std::unique_ptr<DcmItem> item3(new DcmItem); |
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443 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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444 |
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445 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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446 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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447 |
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448 if (!sequence3->insert(item3.release(), false, false).good() || |
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449 !item->insert(sequence3.release(), false, false).good() || |
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450 !sequence->insert(item.release(), false, false).good() || |
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451 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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452 { |
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453 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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454 } |
| 0 | 455 } |
| 456 } | |
| 457 | |
| 458 | |
| 459 static void EnrichDataset(DcmDataset& dataset, | |
| 460 const OrthancWSI::ITiledPyramid& source, | |
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461 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 462 const OrthancWSI::DicomizerParameters& parameters, |
| 463 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 464 { | |
| 465 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 466 | |
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467 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 468 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 469 { | |
| 470 // Takes as estimation a 1:10 compression ratio | |
| 471 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 473 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 474 } | |
| 475 else | |
| 476 { | |
| 477 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 478 } | |
| 479 | |
| 480 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 482 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 483 | |
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484 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 485 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 486 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 487 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 488 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 489 | |
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490 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 491 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 492 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 493 { | |
| 494 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 495 } | |
| 496 | |
| 497 | |
| 498 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 499 { | |
| 500 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 501 { | |
| 502 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 503 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 504 } | |
| 505 | |
| 506 std::string brightfield; | |
| 507 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 508 | |
| 509 Json::Value json; | |
| 226 | 510 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 511 { |
| 512 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 513 } | |
| 514 | |
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515 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 516 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 517 DCM_OpticalPathSequence.getElement()), | |
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518 json, false, encoding, |
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519 "" /* no private tag, thus no private creator */)); |
| 0 | 520 if (!dataset.insert(element.release()).good()) |
| 521 { | |
| 522 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 523 } | |
| 524 } | |
| 525 | |
| 526 | |
| 527 std::string profile; | |
| 528 if (parameters.GetIccProfilePath().empty()) | |
| 529 { | |
| 530 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 531 } | |
| 532 else | |
| 533 { | |
| 43 | 534 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 535 } |
| 536 | |
| 537 | |
| 538 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 539 if (opticalPath == NULL) | |
| 540 { | |
| 541 LOG(ERROR) << "No optical path specified"; | |
| 542 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 543 } | |
| 544 | |
| 545 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 546 { | |
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547 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 548 |
| 549 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 550 !opticalPath->insert(icc.release()).good()) | |
| 551 { | |
| 552 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 553 } | |
| 554 } | |
| 555 | |
| 556 const char* opticalPathId = NULL; | |
| 557 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 558 opticalPathId == NULL) | |
| 559 { | |
| 560 LOG(ERROR) << "No identifier in the optical path"; | |
| 561 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 562 } | |
| 563 | |
| 564 SetupDimension(dataset, opticalPathId, source, volume); | |
| 565 } | |
| 566 | |
| 567 | |
| 568 static bool ParseParameters(int& exitStatus, | |
| 569 OrthancWSI::DicomizerParameters& parameters, | |
| 570 OrthancWSI::ImagedVolumeParameters& volume, | |
| 571 int argc, | |
| 572 char* argv[]) | |
| 573 { | |
| 574 // Declare the supported parameters | |
| 575 boost::program_options::options_description generic("Generic options"); | |
| 576 generic.add_options() | |
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577 (OPTION_HELP, "Display this help and exit") |
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578 (OPTION_VERSION, "Output version information and exit") |
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579 (OPTION_VERBOSE, "Be verbose in logs") |
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580 (OPTION_THREADS, |
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581 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 582 "Number of processing threads to be used") |
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583 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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584 "Path to the shared library of OpenSlide " |
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585 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 586 ; |
| 587 | |
| 588 boost::program_options::options_description source("Options for the source image"); | |
| 589 source.add_options() | |
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590 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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591 "Path to a JSON file containing the DICOM dataset") |
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592 (OPTION_SAMPLE_DATASET, |
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593 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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594 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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595 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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596 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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597 "Whether to repaint the background of the image (Boolean)") |
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598 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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599 "Color of the background (e.g. \"255,0,0\")") |
|
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600 (OPTION_TIFF_ALIGNMENT, boost::program_options::value<int>()->default_value(64), |
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601 "Add padding to plain TIFF images to align the width/height to multiples " |
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602 "of this value, very useful to enable deep zoom with IIIF (1 means no padding)") |
| 0 | 603 ; |
| 604 | |
|
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605 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
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606 cytomine.add_options() |
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607 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
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608 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
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609 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
| 246 | 610 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
|
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611 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
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612 "Your personal private key in Cytomine (to be kept secret)") |
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613 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
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614 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
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615 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
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616 "Compression to be used for downloading the tiles from Cytomine, " |
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617 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
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618 ; |
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619 |
| 0 | 620 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
| 621 pyramid.add_options() | |
|
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622 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 623 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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624 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 625 "Apply smoothing when reconstructing the pyramid " |
| 626 "(slower, but higher quality) (Boolean)") | |
|
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627 (OPTION_LEVELS, boost::program_options::value<int>(), |
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628 "Number of levels in the target pyramid") |
| 0 | 629 ; |
| 630 | |
| 631 boost::program_options::options_description target("Options for the target image"); | |
| 632 target.add_options() | |
|
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633 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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634 "Width of the tiles in the target image") |
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635 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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636 "Height of the tiles in the target image") |
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637 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 638 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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639 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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640 "Set quality level for JPEG (0..100)") |
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641 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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642 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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643 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 644 "Folder where to store the output DICOM instances") |
|
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645 (OPTION_FOLDER_PATTERN, |
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646 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 647 "Pattern for the files in the output folder") |
| 648 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 649 "URL to the REST API of the target Orthanc server") | |
| 650 ; | |
| 651 | |
| 652 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 653 volumeOptions.add_options() | |
|
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654 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
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655 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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656 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
|
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657 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
|
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658 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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659 "Depth of the specimen (in mm)") |
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660 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 661 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
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662 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 663 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 664 ; | |
| 665 | |
|
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666 boost::program_options::options_description restOptions |
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667 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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668 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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669 |
| 0 | 670 boost::program_options::options_description advancedOptions("Advanced options"); |
| 671 advancedOptions.add_options() | |
|
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672 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 673 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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674 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 675 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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676 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 677 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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678 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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679 "Number of pyramid levels up to which multithreading " |
| 0 | 680 "should be applied (only for performance/memory tuning)") |
| 681 ; | |
| 682 | |
| 683 boost::program_options::options_description hidden; | |
| 684 hidden.add_options() | |
|
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685 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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686 "Input file"); |
| 0 | 687 ; |
| 688 | |
| 689 boost::program_options::options_description allWithoutHidden; | |
|
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690 allWithoutHidden |
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691 .add(generic) |
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692 .add(source) |
|
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693 .add(cytomine) |
|
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694 .add(pyramid) |
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695 .add(target) |
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696 .add(volumeOptions) |
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697 .add(restOptions) |
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698 .add(advancedOptions); |
| 0 | 699 |
| 700 boost::program_options::options_description all = allWithoutHidden; | |
| 701 all.add(hidden); | |
| 702 | |
| 703 boost::program_options::positional_options_description positional; | |
|
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704 positional.add(OPTION_INPUT, 1); |
| 0 | 705 |
| 706 boost::program_options::variables_map options; | |
| 707 bool error = false; | |
| 708 | |
| 709 try | |
| 710 { | |
| 711 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 712 options(all).positional(positional).run(), options); | |
| 713 boost::program_options::notify(options); | |
| 714 } | |
| 715 catch (boost::program_options::error& e) | |
| 716 { | |
| 717 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 718 error = true; | |
| 719 } | |
| 720 | |
| 721 if (!error && | |
|
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722 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 723 { |
| 724 std::string sample; | |
| 725 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 726 | |
| 727 std::cout << std::endl << sample << std::endl; | |
| 728 | |
| 729 return false; | |
| 730 } | |
| 731 | |
|
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732 // New in release 1.1 |
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733 if (options.count(OPTION_CYTOMINE_URL) || |
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734 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
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735 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
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736 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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737 { |
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738 if (!options.count(OPTION_CYTOMINE_URL)) |
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739 { |
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740 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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741 "URL to the Cytomine server is missing"); |
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742 } |
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743 |
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744 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
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745 { |
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746 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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747 "Public key for the Cytomine server is missing"); |
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748 } |
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749 |
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750 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
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751 { |
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752 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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753 "Private key for the Cytomine server is missing"); |
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754 } |
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755 |
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756 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
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757 { |
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758 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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759 "The Image Instance ID from the Cytomine server is missing"); |
|
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760 } |
|
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761 |
|
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762 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
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763 { |
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764 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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765 "The tile compression scheme for Cytomine is missing"); |
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766 } |
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767 |
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768 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
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769 |
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770 OrthancWSI::ImageCompression compression; |
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771 if (s == "jpeg") |
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772 { |
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773 compression = OrthancWSI::ImageCompression_Jpeg; |
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774 } |
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775 else if (s == "png") |
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776 { |
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777 compression = OrthancWSI::ImageCompression_Png; |
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778 } |
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779 else |
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780 { |
|
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781 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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782 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
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783 } |
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784 |
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785 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
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786 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
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787 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
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788 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
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789 } |
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790 |
| 0 | 791 if (!error && |
|
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792 options.count(OPTION_HELP) == 0 && |
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793 options.count(OPTION_VERSION) == 0 && |
|
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794 options.count(OPTION_INPUT) != 1 && |
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795 !parameters.IsCytomineSource()) |
| 0 | 796 { |
| 797 LOG(ERROR) << "No input file was specified"; | |
| 798 error = true; | |
| 799 } | |
| 800 | |
|
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801 if (error || options.count(OPTION_HELP)) |
| 0 | 802 { |
| 803 std::cout << std::endl | |
| 804 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 805 << std::endl | |
| 806 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 807 << std::endl << std::endl | |
| 808 << "Create a DICOM file from a digital pathology image." | |
| 809 << std::endl; | |
| 810 | |
| 811 std::cout << allWithoutHidden << "\n"; | |
| 812 | |
| 813 if (error) | |
| 814 { | |
| 815 exitStatus = -1; | |
| 816 } | |
| 817 | |
| 818 return false; | |
| 819 } | |
| 820 | |
|
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821 if (options.count(OPTION_VERSION)) |
|
8
62adabb8c122
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|
822 { |
|
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Provide "--version" in command-line tools
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823 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
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|
824 return false; |
|
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825 } |
|
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826 |
|
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|
827 if (options.count(OPTION_VERBOSE)) |
| 0 | 828 { |
| 829 Orthanc::Logging::EnableInfoLevel(true); | |
| 830 } | |
| 831 | |
|
129
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832 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 833 { |
|
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834 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 835 } |
| 836 | |
|
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837 if (options.count(OPTION_PYRAMID) && |
|
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838 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 839 { |
| 840 parameters.SetReconstructPyramid(true); | |
| 841 } | |
| 842 | |
|
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843 if (options.count(OPTION_SMOOTH) && |
|
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|
844 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 845 { |
| 846 parameters.SetSmoothEnabled(true); | |
| 847 } | |
| 848 | |
|
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849 if (options.count(OPTION_SAFETY) && |
|
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850 options[OPTION_SAFETY].as<bool>()) |
| 0 | 851 { |
| 852 parameters.SetSafetyCheck(true); | |
| 853 } | |
| 854 | |
|
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855 if (options.count(OPTION_REENCODE) && |
|
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|
856 options[OPTION_REENCODE].as<bool>()) |
| 0 | 857 { |
| 858 parameters.SetForceReencode(true); | |
| 859 } | |
| 860 | |
|
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861 if (options.count(OPTION_REPAINT) && |
|
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862 options[OPTION_REPAINT].as<bool>()) |
| 0 | 863 { |
| 864 parameters.SetRepaintBackground(true); | |
| 865 } | |
| 866 | |
|
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867 if (options.count(OPTION_TILE_WIDTH) || |
|
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868 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 869 { |
| 870 int w = 0; | |
|
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871 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 872 { |
|
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873 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 874 } |
| 875 | |
| 145 | 876 int h = 0; |
|
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|
877 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 878 { |
|
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879 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 880 } |
| 881 | |
| 882 if (w < 0 || h < 0) | |
| 883 { | |
| 884 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 885 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 886 } | |
| 887 | |
| 888 parameters.SetTargetTileSize(w, h); | |
| 889 } | |
| 890 | |
|
244
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891 if (!parameters.IsCytomineSource()) |
|
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892 { |
|
4273518c2009
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893 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
|
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894 } |
| 0 | 895 |
|
129
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896 if (options.count(OPTION_COLOR)) |
| 0 | 897 { |
| 898 uint8_t r, g, b; | |
|
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899 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 900 parameters.SetBackgroundColor(r, g, b); |
| 901 } | |
| 902 | |
|
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903 if (options.count(OPTION_COMPRESSION)) |
| 0 | 904 { |
|
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905 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 906 if (s == "none") |
| 907 { | |
| 908 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 909 } | |
| 910 else if (s == "jpeg") | |
| 911 { | |
| 912 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 913 } | |
| 914 else if (s == "jpeg2000") | |
| 915 { | |
| 916 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 917 } | |
| 918 else | |
| 919 { | |
| 920 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 921 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 922 } | |
| 923 } | |
| 924 | |
|
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925 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 926 { |
|
129
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927 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 928 } |
| 929 | |
|
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930 if (options.count(OPTION_LEVELS)) |
| 0 | 931 { |
|
129
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932 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 933 } |
| 934 | |
|
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935 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 936 { |
|
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937 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 938 } |
| 939 | |
|
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940 if (options.count(OPTION_THREADS)) |
| 0 | 941 { |
|
129
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942 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 943 } |
| 944 | |
|
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945 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 946 { |
|
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947 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 948 } |
| 949 | |
|
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950 if (options.count(OPTION_FOLDER)) |
| 0 | 951 { |
|
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952 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 953 } |
| 954 | |
|
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955 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 956 { |
|
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957 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 958 } |
| 959 | |
|
125
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960 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 961 |
|
129
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962 if (options.count(OPTION_DATASET)) |
| 0 | 963 { |
|
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964 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 965 } |
| 966 | |
|
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967 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 968 { |
|
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969 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 970 } |
| 971 | |
|
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972 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 973 { |
|
129
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974 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 975 } |
| 976 | |
|
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977 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 978 { |
|
129
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979 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 980 } |
| 981 | |
|
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982 if (options.count(OPTION_OFFSET_X)) |
| 0 | 983 { |
|
129
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984 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 985 } |
| 986 | |
|
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987 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 988 { |
|
129
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989 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 990 } |
| 991 | |
|
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992 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 993 { |
|
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994 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 995 if (s == "none") |
| 996 { | |
| 997 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 998 } | |
| 999 else if (s == "brightfield") | |
| 1000 { | |
| 1001 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 1002 } | |
| 1003 else | |
| 1004 { | |
| 1005 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 1006 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 1007 } | |
| 1008 } | |
| 1009 | |
|
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1010 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 1011 { |
|
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1012 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 1013 } |
| 1014 | |
|
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1015 if (options.count(OPTION_TIFF_ALIGNMENT)) |
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|
1016 { |
|
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|
1017 int value = options[OPTION_TIFF_ALIGNMENT].as<int>(); |
|
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1018 if (value <= 0) |
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1019 { |
|
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1020 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
|
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1021 "TIFF alignment must be >= 1"); |
|
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1022 } |
|
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1023 else |
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1024 { |
|
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1025 parameters.SetTiffAlignment(static_cast<unsigned int>(value)); |
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1026 } |
|
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1027 } |
|
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1028 |
| 0 | 1029 return true; |
| 1030 } | |
| 1031 | |
| 1032 | |
|
167
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Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
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1033 |
|
57
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|
1034 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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1035 OrthancWSI::ImagedVolumeParameters& volume, |
|
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1036 const std::string& path, |
| 0 | 1037 const OrthancWSI::DicomizerParameters& parameters) |
| 1038 { | |
|
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1039 if (parameters.IsCytomineSource()) |
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1040 { |
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1041 // New in release 1.1 |
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1042 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
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1043 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
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1044 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1045 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
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1046 parameters.GetCytominePublicKey(), |
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1047 parameters.GetCytominePrivateKey(), |
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1048 parameters.GetCytomineImageInstanceId(), |
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1049 parameters.GetTargetTileWidth(512), |
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1050 parameters.GetTargetTileHeight(512)); |
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1051 } |
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1052 |
| 0 | 1053 LOG(WARNING) << "The input image is: " << path; |
| 1054 | |
| 1055 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 1056 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 1057 | |
| 1058 switch (format) | |
| 1059 { | |
| 1060 case OrthancWSI::ImageCompression_Png: | |
|
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1061 { |
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1062 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1063 return new OrthancWSI::TiledPngImage(path, |
| 1064 parameters.GetTargetTileWidth(512), | |
| 1065 parameters.GetTargetTileHeight(512)); | |
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1066 } |
| 0 | 1067 |
| 1068 case OrthancWSI::ImageCompression_Jpeg: | |
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1069 { |
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1070 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 1071 return new OrthancWSI::TiledJpegImage(path, |
| 1072 parameters.GetTargetTileWidth(512), | |
| 1073 parameters.GetTargetTileHeight(512)); | |
|
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1074 } |
| 0 | 1075 |
| 1076 case OrthancWSI::ImageCompression_Tiff: | |
| 1077 { | |
| 1078 try | |
| 1079 { | |
|
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1080 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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1081 sourceCompression = tiff->GetImageCompression(); |
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1082 return tiff.release(); |
| 0 | 1083 } |
| 1084 catch (Orthanc::OrthancException&) | |
| 1085 { | |
|
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1086 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
| 0 | 1087 } |
|
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1088 |
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1089 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1090 return new OrthancWSI::PlainTiff(path, |
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1091 parameters.GetTargetTileWidth(512), |
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1092 parameters.GetTargetTileHeight(512), |
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1093 parameters.GetTiffAlignment(), |
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1094 parameters.GetBackgroundColorRed(), |
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1095 parameters.GetBackgroundColorGreen(), |
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1096 parameters.GetBackgroundColorBlue()); |
| 0 | 1097 } |
| 1098 | |
| 1099 default: | |
| 1100 break; | |
| 1101 } | |
| 1102 | |
| 1103 try | |
| 1104 { | |
| 1105 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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1106 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
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1107 |
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1108 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
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1109 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
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1110 parameters.GetTargetTileHeight(512))); |
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1111 |
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1112 float volumeWidth, volumeHeight; |
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1113 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
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1114 { |
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1115 if (!volume.HasWidth()) |
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1116 { |
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1117 volume.SetWidth(volumeWidth); |
| 281 | 1118 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
|
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1119 } |
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1120 |
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1121 if (!volume.HasHeight()) |
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1122 { |
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1123 volume.SetHeight(volumeHeight); |
| 281 | 1124 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
|
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1125 } |
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1126 } |
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1127 |
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1128 return openslide.release(); |
| 0 | 1129 } |
| 1130 catch (Orthanc::OrthancException&) | |
| 1131 { | |
| 1132 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 1133 return NULL; | |
| 1134 } | |
| 1135 } | |
| 1136 | |
| 1137 | |
| 1138 int main(int argc, char* argv[]) | |
| 1139 { | |
| 1140 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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1141 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 1142 |
| 1143 int exitStatus = 0; | |
| 1144 | |
| 1145 try | |
| 1146 { | |
| 1147 OrthancWSI::DicomizerParameters parameters; | |
| 1148 OrthancWSI::ImagedVolumeParameters volume; | |
| 1149 | |
| 1150 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 1151 { | |
|
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1152 OrthancWSI::ImageCompression sourceCompression; |
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1153 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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1154 |
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1155 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
| 0 | 1156 if (source.get() == NULL) |
| 1157 { | |
| 1158 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1159 } | |
|
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1160 |
|
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1161 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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1162 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
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1163 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
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1164 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
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1165 { |
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1166 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
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1167 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
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1168 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
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1169 } |
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1170 |
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1171 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1172 |
| 1173 // Create the shared DICOM tags | |
|
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1174 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1175 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1176 |
|
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1177 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
|
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1178 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1179 } |
| 1180 } | |
| 1181 catch (Orthanc::OrthancException& e) | |
| 1182 { | |
| 1183 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1184 exitStatus = -1; | |
| 1185 } | |
| 1186 | |
| 1187 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1188 | |
| 1189 return exitStatus; | |
| 1190 } |