Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 229:d9bd12e3747a
use Orthanc::ImageProcessing::Halve() instead of ImageToolbox::Halve()
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 13 Jan 2021 17:40:56 +0100 |
| parents | 4eefa34657f0 |
| children | b0ee417b667a |
| 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) 2017-2021 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU Affero General Public License | |
| 9 * as published by the Free Software Foundation, either version 3 of | |
| 10 * the License, or (at your option) any later version. | |
| 11 * | |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 15 * Affero General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU Affero General Public License | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 23 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
| 24 #include "../Framework/DicomToolbox.h" | |
| 25 #include "../Framework/DicomizerParameters.h" | |
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26 #include "../Framework/ImageToolbox.h" |
| 0 | 27 #include "../Framework/ImagedVolumeParameters.h" |
| 28 #include "../Framework/Inputs/HierarchicalTiff.h" | |
| 29 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 30 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 31 #include "../Framework/Inputs/TiledPngImage.h" | |
| 32 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 33 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 34 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 35 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 36 | |
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37 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 38 #include <DicomParsing/FromDcmtkBridge.h> |
| 39 #include <Logging.h> | |
| 40 #include <OrthancException.h> | |
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41 #include <Toolbox.h> |
| 192 | 42 #include <SystemToolbox.h> |
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43 |
| 0 | 44 #include "ApplicationToolbox.h" |
| 45 | |
| 46 #include <EmbeddedResources.h> | |
| 47 | |
| 48 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 49 #include <dcmtk/dcmdata/dcuid.h> | |
| 50 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 51 #include <dcmtk/dcmdata/dcvrat.h> | |
| 52 | |
| 53 | |
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54 static const char* OPTION_COLOR = "color"; |
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55 static const char* OPTION_COMPRESSION = "compression"; |
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56 static const char* OPTION_DATASET = "dataset"; |
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57 static const char* OPTION_FOLDER = "folder"; |
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58 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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59 static const char* OPTION_HELP = "help"; |
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60 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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61 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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62 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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63 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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64 static const char* OPTION_INPUT = "input"; |
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65 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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66 static const char* OPTION_LEVELS = "levels"; |
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67 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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68 static const char* OPTION_MAX_SIZE = "max-size"; |
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69 static const char* OPTION_OFFSET_X = "offset-x"; |
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70 static const char* OPTION_OFFSET_Y = "offset-y"; |
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71 static const char* OPTION_OPENSLIDE = "openslide"; |
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72 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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73 static const char* OPTION_PYRAMID = "pyramid"; |
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74 static const char* OPTION_REENCODE = "reencode"; |
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75 static const char* OPTION_REPAINT = "repaint"; |
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76 static const char* OPTION_SAFETY = "safety"; |
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77 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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78 static const char* OPTION_SMOOTH = "smooth"; |
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79 static const char* OPTION_THREADS = "threads"; |
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80 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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81 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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82 static const char* OPTION_VERBOSE = "verbose"; |
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83 static const char* OPTION_VERSION = "version"; |
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84 |
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85 |
| 226 | 86 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
| 87 | |
| 88 bool ReadJsonWithoutComments(Json::Value& target, | |
| 89 const std::string& source) | |
| 90 { | |
| 91 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
| 92 } | |
| 93 | |
| 94 #else | |
| 95 | |
| 96 // Backward compatibility with Orthanc framework <= 1.8.2 | |
| 97 #include <json/reader.h> | |
| 98 | |
| 99 bool ReadJsonWithoutComments(Json::Value& target, | |
| 100 const std::string& source) | |
| 101 { | |
| 102 Json::Reader reader; | |
| 103 return reader.parse(source, target, false); | |
| 104 } | |
| 105 #endif | |
| 106 | |
| 107 | |
| 0 | 108 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 109 OrthancWSI::ITiledPyramid& source, | |
| 110 const OrthancWSI::DicomizerParameters& parameters) | |
| 111 { | |
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112 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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113 |
| 0 | 114 Orthanc::BagOfTasks tasks; |
| 115 | |
| 116 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 117 { | |
| 118 LOG(WARNING) << "Creating level " << i << " of size " | |
| 119 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 120 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 121 } | |
| 122 | |
| 123 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 124 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 125 } | |
| 126 | |
| 127 | |
| 128 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 129 OrthancWSI::ITiledPyramid& source, | |
| 130 const OrthancWSI::DicomizerParameters& parameters) | |
| 131 { | |
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132 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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133 |
| 0 | 134 Orthanc::BagOfTasks tasks; |
| 135 | |
| 136 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 137 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 138 assert(levelsCount >= 1); | |
| 139 | |
| 140 for (unsigned int i = 0; i < levelsCount; i++) | |
| 141 { | |
| 142 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 143 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 144 | |
| 145 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 146 target.AddLevel(width, height); | |
| 147 } | |
| 148 | |
| 149 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 150 if (lowerLevelsCount > levelsCount) | |
| 151 { | |
| 152 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 153 << ") exceeds the number of levels (" << levelsCount | |
| 154 << "), cropping it"; | |
| 155 lowerLevelsCount = levelsCount; | |
| 156 } | |
| 157 | |
| 158 assert(lowerLevelsCount <= levelsCount); | |
| 159 if (lowerLevelsCount != levelsCount) | |
| 160 { | |
| 161 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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162 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 163 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 164 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 165 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 166 | |
| 167 assert(tasks.GetSize() == 0); | |
| 168 | |
| 169 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 170 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 171 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 172 (tasks, target, truncated.GetUpperLevel(), | |
| 173 upperLevelsCount, lowerLevelsCount, parameters); | |
| 174 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 175 } | |
| 176 else | |
| 177 { | |
| 178 LOG(WARNING) << "Constructing the pyramid"; | |
| 179 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 180 (tasks, target, source, levelsCount, 0, parameters); | |
| 181 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 182 } | |
| 183 } | |
| 184 | |
| 185 | |
| 186 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 187 OrthancWSI::ITiledPyramid& source, | |
| 188 const DcmDataset& dataset, | |
| 189 const OrthancWSI::DicomizerParameters& parameters, | |
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190 const OrthancWSI::ImagedVolumeParameters& volume, |
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191 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 192 { |
| 193 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 194 | |
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195 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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196 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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197 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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198 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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199 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 200 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 201 | |
| 202 if (parameters.IsRepaintBackground()) | |
| 203 { | |
| 204 LOG(WARNING) << "Repainting the background with color: (" | |
| 205 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 206 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 207 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 208 } | |
| 209 else | |
| 210 { | |
| 211 LOG(WARNING) << "No repainting of the background"; | |
| 212 } | |
| 213 | |
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214 Orthanc::PhotometricInterpretation targetPhotometric; |
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215 bool transcoding; |
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216 |
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217 if (parameters.IsForceReencode() || |
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218 parameters.IsReconstructPyramid() || |
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219 sourceCompression != parameters.GetTargetCompression()) |
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220 { |
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221 // The tiles of the source image will be re-encoded |
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222 transcoding = false; |
| 171 | 223 |
| 224 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 225 { | |
| 226 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 227 } | |
| 228 else | |
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229 { |
| 171 | 230 switch (parameters.GetTargetCompression()) |
| 231 { | |
| 232 case OrthancWSI::ImageCompression_Jpeg: | |
| 233 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 234 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 235 break; | |
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236 |
| 171 | 237 case OrthancWSI::ImageCompression_None: |
| 238 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 239 break; | |
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240 |
| 171 | 241 default: |
| 242 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 243 } | |
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244 } |
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245 } |
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246 else |
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247 { |
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248 // Transcoding: The tiles are copied (no re-encoding) |
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249 transcoding = true; |
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250 targetPhotometric = source.GetPhotometricInterpretation(); |
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251 } |
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252 |
| 0 | 253 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 254 source.GetPixelFormat(), | |
| 255 parameters.GetTargetCompression(), | |
| 256 parameters.GetTargetTileWidth(source), | |
| 257 parameters.GetTargetTileHeight(source), | |
| 258 parameters.GetDicomMaxFileSize(), | |
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259 volume, targetPhotometric); |
| 29 | 260 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 261 |
| 262 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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263 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 264 |
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265 if (!transcoding && |
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266 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 267 { |
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268 LOG(WARNING) << "Target compression: Jpeg with quality " |
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269 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 270 target.SetJpegQuality(target.GetJpegQuality()); |
| 271 } | |
| 272 else | |
| 273 { | |
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274 LOG(WARNING) << "Target compression: " |
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275 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 276 } |
| 277 | |
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278 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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279 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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280 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 281 { |
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282 LOG(ERROR) << "When resampling the tile size, " |
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283 << "it must be a integer divisor of the original tile size"; |
| 0 | 284 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 285 } | |
| 286 | |
| 287 if (target.GetTileWidth() <= 16 || | |
| 288 target.GetTileHeight() <= 16) | |
| 289 { | |
| 290 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 291 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 292 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 293 } | |
| 294 | |
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295 if (transcoding) |
| 0 | 296 { |
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297 TranscodePyramid(target, stats, parameters); |
| 0 | 298 } |
| 299 else | |
| 300 { | |
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301 ReconstructPyramid(target, stats, parameters); |
| 0 | 302 } |
| 303 | |
| 304 target.Flush(); | |
| 305 } | |
| 306 | |
| 307 | |
| 308 | |
| 309 static DcmDataset* ParseDataset(const std::string& path) | |
| 310 { | |
| 311 Json::Value json; | |
| 312 | |
| 313 if (path.empty()) | |
| 314 { | |
| 315 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 316 } | |
| 317 else | |
| 318 { | |
| 319 std::string content; | |
| 43 | 320 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 321 |
| 226 | 322 if (!ReadJsonWithoutComments(json, content)) |
| 0 | 323 { |
| 324 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 325 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 326 } | |
| 327 } | |
| 328 | |
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329 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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330 "" /* no private tag, thus no private creator */)); |
| 0 | 331 if (dataset.get() == NULL) |
| 332 { | |
| 333 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 335 } | |
| 336 | |
| 337 // VL Whole Slide Microscopy Image IOD | |
| 338 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 339 | |
| 340 // Slide Microscopy | |
| 341 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 342 | |
| 343 // Patient orientation makes no sense in whole-slide images | |
| 344 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 345 | |
| 346 // Some basic coordinate information | |
| 347 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 348 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 349 | |
| 350 std::string date, time; | |
| 130 | 351 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 352 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 353 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 354 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 355 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 356 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 357 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 358 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 359 | |
| 360 return dataset.release(); | |
| 361 } | |
| 362 | |
| 363 | |
| 364 | |
| 365 static void SetupDimension(DcmDataset& dataset, | |
| 366 const std::string& opticalPathId, | |
| 367 const OrthancWSI::ITiledPyramid& source, | |
| 368 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 369 { | |
| 83 | 370 // Extract the identifier of the Dimension Organization, if provided |
| 371 std::string organization; | |
| 0 | 372 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 373 | |
| 83 | 374 if (previous != NULL && |
| 375 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 376 { | |
| 377 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 378 } | |
| 379 else | |
| 0 | 380 { |
| 83 | 381 // No Dimension Organization provided: Generate an unique identifier |
| 382 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 383 } | |
| 384 | |
| 385 | |
| 386 { | |
| 387 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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388 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 389 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 390 | |
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391 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 392 |
| 393 if (!sequence->insert(item.release(), false, false).good() || | |
| 394 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 395 { |
| 83 | 396 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 397 } |
| 398 } | |
| 399 | |
| 83 | 400 |
| 0 | 401 { |
| 83 | 402 // Construct tag "Dimension Index Sequence" (0020,9222) |
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403 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 404 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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405 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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406 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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407 |
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408 std::unique_ptr<DcmItem> item2(new DcmItem); |
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409 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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410 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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411 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 412 |
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413 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 414 |
| 83 | 415 if (!sequence->insert(item.release(), false, false).good() || |
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416 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 417 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 418 { | |
| 419 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 420 } | |
| 0 | 421 } |
| 422 | |
| 423 | |
| 83 | 424 { |
| 425 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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426 std::unique_ptr<DcmItem> item(new DcmItem); |
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427 |
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428 std::unique_ptr<DcmItem> item3(new DcmItem); |
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429 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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430 |
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431 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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432 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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433 |
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434 if (!sequence3->insert(item3.release(), false, false).good() || |
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435 !item->insert(sequence3.release(), false, false).good() || |
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436 !sequence->insert(item.release(), false, false).good() || |
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437 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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438 { |
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439 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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440 } |
| 0 | 441 } |
| 442 } | |
| 443 | |
| 444 | |
| 445 static void EnrichDataset(DcmDataset& dataset, | |
| 446 const OrthancWSI::ITiledPyramid& source, | |
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447 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 448 const OrthancWSI::DicomizerParameters& parameters, |
| 449 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 450 { | |
| 451 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 452 | |
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453 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 454 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 455 { | |
| 456 // Takes as estimation a 1:10 compression ratio | |
| 457 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 458 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 459 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 460 } | |
| 461 else | |
| 462 { | |
| 463 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 464 } | |
| 465 | |
| 466 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 467 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 468 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 469 | |
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470 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 471 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 472 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 473 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 474 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 475 | |
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476 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 477 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 478 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 479 { | |
| 480 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 481 } | |
| 482 | |
| 483 | |
| 484 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 485 { | |
| 486 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 487 { | |
| 488 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 489 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 490 } | |
| 491 | |
| 492 std::string brightfield; | |
| 493 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 494 | |
| 495 Json::Value json; | |
| 226 | 496 if (!ReadJsonWithoutComments(json, brightfield)) |
| 0 | 497 { |
| 498 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 499 } | |
| 500 | |
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501 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 502 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 503 DCM_OpticalPathSequence.getElement()), | |
|
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504 json, false, encoding, |
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505 "" /* no private tag, thus no private creator */)); |
| 0 | 506 if (!dataset.insert(element.release()).good()) |
| 507 { | |
| 508 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 509 } | |
| 510 } | |
| 511 | |
| 512 | |
| 513 std::string profile; | |
| 514 if (parameters.GetIccProfilePath().empty()) | |
| 515 { | |
| 516 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 517 } | |
| 518 else | |
| 519 { | |
| 43 | 520 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 521 } |
| 522 | |
| 523 | |
| 524 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 525 if (opticalPath == NULL) | |
| 526 { | |
| 527 LOG(ERROR) << "No optical path specified"; | |
| 528 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 529 } | |
| 530 | |
| 531 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 532 { | |
|
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533 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 534 |
| 535 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 536 !opticalPath->insert(icc.release()).good()) | |
| 537 { | |
| 538 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 539 } | |
| 540 } | |
| 541 | |
| 542 const char* opticalPathId = NULL; | |
| 543 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 544 opticalPathId == NULL) | |
| 545 { | |
| 546 LOG(ERROR) << "No identifier in the optical path"; | |
| 547 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 548 } | |
| 549 | |
| 550 SetupDimension(dataset, opticalPathId, source, volume); | |
| 551 } | |
| 552 | |
| 553 | |
| 554 static bool ParseParameters(int& exitStatus, | |
| 555 OrthancWSI::DicomizerParameters& parameters, | |
| 556 OrthancWSI::ImagedVolumeParameters& volume, | |
| 557 int argc, | |
| 558 char* argv[]) | |
| 559 { | |
| 560 // Declare the supported parameters | |
| 561 boost::program_options::options_description generic("Generic options"); | |
| 562 generic.add_options() | |
|
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563 (OPTION_HELP, "Display this help and exit") |
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564 (OPTION_VERSION, "Output version information and exit") |
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565 (OPTION_VERBOSE, "Be verbose in logs") |
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566 (OPTION_THREADS, |
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567 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 568 "Number of processing threads to be used") |
|
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569 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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570 "Path to the shared library of OpenSlide " |
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571 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 572 ; |
| 573 | |
| 574 boost::program_options::options_description source("Options for the source image"); | |
| 575 source.add_options() | |
|
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576 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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577 "Path to a JSON file containing the DICOM dataset") |
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578 (OPTION_SAMPLE_DATASET, |
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579 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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580 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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581 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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582 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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583 "Whether to repaint the background of the image (Boolean)") |
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584 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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585 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 586 ; |
| 587 | |
| 588 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 589 pyramid.add_options() | |
|
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590 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 591 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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592 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 593 "Apply smoothing when reconstructing the pyramid " |
| 594 "(slower, but higher quality) (Boolean)") | |
|
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595 (OPTION_LEVELS, boost::program_options::value<int>(), |
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596 "Number of levels in the target pyramid") |
| 0 | 597 ; |
| 598 | |
| 599 boost::program_options::options_description target("Options for the target image"); | |
| 600 target.add_options() | |
|
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601 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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602 "Width of the tiles in the target image") |
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603 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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604 "Height of the tiles in the target image") |
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605 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 606 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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607 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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608 "Set quality level for JPEG (0..100)") |
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609 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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610 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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611 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 612 "Folder where to store the output DICOM instances") |
|
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613 (OPTION_FOLDER_PATTERN, |
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614 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 615 "Pattern for the files in the output folder") |
| 616 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 617 "URL to the REST API of the target Orthanc server") | |
| 618 ; | |
| 619 | |
| 620 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 621 volumeOptions.add_options() | |
|
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622 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
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623 "Width of the specimen (in mm)") |
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624 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
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625 "Height of the specimen (in mm)") |
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626 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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627 "Depth of the specimen (in mm)") |
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628 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 629 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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630 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 631 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 632 ; | |
| 633 | |
|
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634 boost::program_options::options_description restOptions |
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635 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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636 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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637 |
| 0 | 638 boost::program_options::options_description advancedOptions("Advanced options"); |
| 639 advancedOptions.add_options() | |
|
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640 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 641 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
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642 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 643 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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644 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 645 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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646 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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647 "Number of pyramid levels up to which multithreading " |
| 0 | 648 "should be applied (only for performance/memory tuning)") |
| 649 ; | |
| 650 | |
| 651 boost::program_options::options_description hidden; | |
| 652 hidden.add_options() | |
|
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653 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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654 "Input file"); |
| 0 | 655 ; |
| 656 | |
| 657 boost::program_options::options_description allWithoutHidden; | |
|
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658 allWithoutHidden |
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659 .add(generic) |
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660 .add(source) |
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661 .add(pyramid) |
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662 .add(target) |
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663 .add(volumeOptions) |
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664 .add(restOptions) |
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665 .add(advancedOptions); |
| 0 | 666 |
| 667 boost::program_options::options_description all = allWithoutHidden; | |
| 668 all.add(hidden); | |
| 669 | |
| 670 boost::program_options::positional_options_description positional; | |
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671 positional.add(OPTION_INPUT, 1); |
| 0 | 672 |
| 673 boost::program_options::variables_map options; | |
| 674 bool error = false; | |
| 675 | |
| 676 try | |
| 677 { | |
| 678 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 679 options(all).positional(positional).run(), options); | |
| 680 boost::program_options::notify(options); | |
| 681 } | |
| 682 catch (boost::program_options::error& e) | |
| 683 { | |
| 684 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 685 error = true; | |
| 686 } | |
| 687 | |
| 688 if (!error && | |
|
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689 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 690 { |
| 691 std::string sample; | |
| 692 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 693 | |
| 694 std::cout << std::endl << sample << std::endl; | |
| 695 | |
| 696 return false; | |
| 697 } | |
| 698 | |
| 699 if (!error && | |
|
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700 options.count(OPTION_HELP) == 0 && |
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701 options.count(OPTION_VERSION) == 0 && |
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702 options.count(OPTION_INPUT) != 1) |
| 0 | 703 { |
| 704 LOG(ERROR) << "No input file was specified"; | |
| 705 error = true; | |
| 706 } | |
| 707 | |
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708 if (error || options.count(OPTION_HELP)) |
| 0 | 709 { |
| 710 std::cout << std::endl | |
| 711 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 712 << std::endl | |
| 713 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 714 << std::endl << std::endl | |
| 715 << "Create a DICOM file from a digital pathology image." | |
| 716 << std::endl; | |
| 717 | |
| 718 std::cout << allWithoutHidden << "\n"; | |
| 719 | |
| 720 if (error) | |
| 721 { | |
| 722 exitStatus = -1; | |
| 723 } | |
| 724 | |
| 725 return false; | |
| 726 } | |
| 727 | |
|
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728 if (options.count(OPTION_VERSION)) |
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729 { |
|
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730 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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731 return false; |
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732 } |
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733 |
|
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734 if (options.count(OPTION_VERBOSE)) |
| 0 | 735 { |
| 736 Orthanc::Logging::EnableInfoLevel(true); | |
| 737 } | |
| 738 | |
|
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739 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 740 { |
|
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741 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 742 } |
| 743 | |
|
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744 if (options.count(OPTION_PYRAMID) && |
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745 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 746 { |
| 747 parameters.SetReconstructPyramid(true); | |
| 748 } | |
| 749 | |
|
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750 if (options.count(OPTION_SMOOTH) && |
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751 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 752 { |
| 753 parameters.SetSmoothEnabled(true); | |
| 754 } | |
| 755 | |
|
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756 if (options.count(OPTION_SAFETY) && |
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757 options[OPTION_SAFETY].as<bool>()) |
| 0 | 758 { |
| 759 parameters.SetSafetyCheck(true); | |
| 760 } | |
| 761 | |
|
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762 if (options.count(OPTION_REENCODE) && |
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763 options[OPTION_REENCODE].as<bool>()) |
| 0 | 764 { |
| 765 parameters.SetForceReencode(true); | |
| 766 } | |
| 767 | |
|
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768 if (options.count(OPTION_REPAINT) && |
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769 options[OPTION_REPAINT].as<bool>()) |
| 0 | 770 { |
| 771 parameters.SetRepaintBackground(true); | |
| 772 } | |
| 773 | |
|
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774 if (options.count(OPTION_TILE_WIDTH) || |
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775 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 776 { |
| 777 int w = 0; | |
|
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778 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 779 { |
|
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780 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 781 } |
| 782 | |
| 145 | 783 int h = 0; |
|
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784 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 785 { |
|
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786 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 787 } |
| 788 | |
| 789 if (w < 0 || h < 0) | |
| 790 { | |
| 791 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 792 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 793 } | |
| 794 | |
| 795 parameters.SetTargetTileSize(w, h); | |
| 796 } | |
| 797 | |
|
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798 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
| 0 | 799 |
|
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800 if (options.count(OPTION_COLOR)) |
| 0 | 801 { |
| 802 uint8_t r, g, b; | |
|
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803 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 804 parameters.SetBackgroundColor(r, g, b); |
| 805 } | |
| 806 | |
|
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807 if (options.count(OPTION_COMPRESSION)) |
| 0 | 808 { |
|
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809 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 810 if (s == "none") |
| 811 { | |
| 812 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 813 } | |
| 814 else if (s == "jpeg") | |
| 815 { | |
| 816 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 817 } | |
| 818 else if (s == "jpeg2000") | |
| 819 { | |
| 820 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 821 } | |
| 822 else | |
| 823 { | |
| 824 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 825 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 826 } | |
| 827 } | |
| 828 | |
|
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829 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 830 { |
|
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831 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 832 } |
| 833 | |
|
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834 if (options.count(OPTION_LEVELS)) |
| 0 | 835 { |
|
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836 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 837 } |
| 838 | |
|
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839 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 840 { |
|
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841 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 842 } |
| 843 | |
|
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844 if (options.count(OPTION_THREADS)) |
| 0 | 845 { |
|
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846 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 847 } |
| 848 | |
|
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849 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 850 { |
|
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851 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 852 } |
| 853 | |
|
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854 if (options.count(OPTION_FOLDER)) |
| 0 | 855 { |
|
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856 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 857 } |
| 858 | |
|
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859 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 860 { |
|
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861 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 862 } |
| 863 | |
|
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864 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 865 |
|
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866 if (options.count(OPTION_DATASET)) |
| 0 | 867 { |
|
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868 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 869 } |
| 870 | |
|
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871 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 872 { |
|
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873 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 874 } |
| 875 | |
|
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876 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 877 { |
|
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878 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 879 } |
| 880 | |
|
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881 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 882 { |
|
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883 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 884 } |
| 885 | |
|
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886 if (options.count(OPTION_OFFSET_X)) |
| 0 | 887 { |
|
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888 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 889 } |
| 890 | |
|
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891 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 892 { |
|
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893 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 894 } |
| 895 | |
|
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896 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 897 { |
|
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898 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 899 if (s == "none") |
| 900 { | |
| 901 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 902 } | |
| 903 else if (s == "brightfield") | |
| 904 { | |
| 905 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 906 } | |
| 907 else | |
| 908 { | |
| 909 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 910 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 911 } | |
| 912 } | |
| 913 | |
|
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914 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 915 { |
|
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916 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 917 } |
| 918 | |
| 919 return true; | |
| 920 } | |
| 921 | |
| 922 | |
|
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923 |
|
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924 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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925 const std::string& path, |
| 0 | 926 const OrthancWSI::DicomizerParameters& parameters) |
| 927 { | |
| 928 LOG(WARNING) << "The input image is: " << path; | |
| 929 | |
| 930 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 931 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 932 | |
| 933 switch (format) | |
| 934 { | |
| 935 case OrthancWSI::ImageCompression_Png: | |
|
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936 { |
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937 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 938 return new OrthancWSI::TiledPngImage(path, |
| 939 parameters.GetTargetTileWidth(512), | |
| 940 parameters.GetTargetTileHeight(512)); | |
|
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941 } |
| 0 | 942 |
| 943 case OrthancWSI::ImageCompression_Jpeg: | |
|
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944 { |
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|
945 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 946 return new OrthancWSI::TiledJpegImage(path, |
| 947 parameters.GetTargetTileWidth(512), | |
| 948 parameters.GetTargetTileHeight(512)); | |
|
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949 } |
| 0 | 950 |
| 951 case OrthancWSI::ImageCompression_Tiff: | |
| 952 { | |
| 953 try | |
| 954 { | |
|
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955 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
|
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956 sourceCompression = tiff->GetImageCompression(); |
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957 return tiff.release(); |
| 0 | 958 } |
| 959 catch (Orthanc::OrthancException&) | |
| 960 { | |
| 961 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 962 } | |
| 963 } | |
| 964 | |
| 965 default: | |
| 966 break; | |
| 967 } | |
| 968 | |
| 969 try | |
| 970 { | |
| 971 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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972 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 973 return new OrthancWSI::OpenSlidePyramid(path, |
| 974 parameters.GetTargetTileWidth(512), | |
| 975 parameters.GetTargetTileHeight(512)); | |
| 976 } | |
| 977 catch (Orthanc::OrthancException&) | |
| 978 { | |
| 979 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 980 return NULL; | |
| 981 } | |
| 982 } | |
| 983 | |
| 984 | |
| 985 int main(int argc, char* argv[]) | |
| 986 { | |
| 987 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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988 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 989 |
| 990 int exitStatus = 0; | |
| 991 | |
| 992 try | |
| 993 { | |
| 994 OrthancWSI::DicomizerParameters parameters; | |
| 995 OrthancWSI::ImagedVolumeParameters volume; | |
| 996 | |
| 997 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 998 { | |
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999 OrthancWSI::ImageCompression sourceCompression; |
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1000 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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1001 |
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1002 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 1003 if (source.get() == NULL) |
| 1004 { | |
| 1005 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 1006 } | |
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1007 |
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1008 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 1009 |
| 1010 // Create the shared DICOM tags | |
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1011 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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1012 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 1013 |
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1014 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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1015 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 1016 } |
| 1017 } | |
| 1018 catch (Orthanc::OrthancException& e) | |
| 1019 { | |
| 1020 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 1021 exitStatus = -1; | |
| 1022 } | |
| 1023 | |
| 1024 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1025 | |
| 1026 return exitStatus; | |
| 1027 } |