Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 221:dbcf9ad44a70
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 12 Jan 2021 18:42:04 +0100 |
| parents | 20bc074ec19a |
| children | 443f219a68fd |
| 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 |
| 0 | 86 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 87 OrthancWSI::ITiledPyramid& source, | |
| 88 const OrthancWSI::DicomizerParameters& parameters) | |
| 89 { | |
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90 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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91 |
| 0 | 92 Orthanc::BagOfTasks tasks; |
| 93 | |
| 94 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 95 { | |
| 96 LOG(WARNING) << "Creating level " << i << " of size " | |
| 97 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 98 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 99 } | |
| 100 | |
| 101 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 102 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 103 } | |
| 104 | |
| 105 | |
| 106 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 107 OrthancWSI::ITiledPyramid& source, | |
| 108 const OrthancWSI::DicomizerParameters& parameters) | |
| 109 { | |
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110 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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111 |
| 0 | 112 Orthanc::BagOfTasks tasks; |
| 113 | |
| 114 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 115 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 116 assert(levelsCount >= 1); | |
| 117 | |
| 118 for (unsigned int i = 0; i < levelsCount; i++) | |
| 119 { | |
| 120 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 121 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 122 | |
| 123 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 124 target.AddLevel(width, height); | |
| 125 } | |
| 126 | |
| 127 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 128 if (lowerLevelsCount > levelsCount) | |
| 129 { | |
| 130 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 131 << ") exceeds the number of levels (" << levelsCount | |
| 132 << "), cropping it"; | |
| 133 lowerLevelsCount = levelsCount; | |
| 134 } | |
| 135 | |
| 136 assert(lowerLevelsCount <= levelsCount); | |
| 137 if (lowerLevelsCount != levelsCount) | |
| 138 { | |
| 139 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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140 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 141 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 142 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 143 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 144 | |
| 145 assert(tasks.GetSize() == 0); | |
| 146 | |
| 147 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 148 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 149 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 150 (tasks, target, truncated.GetUpperLevel(), | |
| 151 upperLevelsCount, lowerLevelsCount, parameters); | |
| 152 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 153 } | |
| 154 else | |
| 155 { | |
| 156 LOG(WARNING) << "Constructing the pyramid"; | |
| 157 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 158 (tasks, target, source, levelsCount, 0, parameters); | |
| 159 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 160 } | |
| 161 } | |
| 162 | |
| 163 | |
| 164 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 165 OrthancWSI::ITiledPyramid& source, | |
| 166 const DcmDataset& dataset, | |
| 167 const OrthancWSI::DicomizerParameters& parameters, | |
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168 const OrthancWSI::ImagedVolumeParameters& volume, |
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169 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 170 { |
| 171 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 172 | |
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173 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
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174 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
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175 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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176 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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177 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 178 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 179 | |
| 180 if (parameters.IsRepaintBackground()) | |
| 181 { | |
| 182 LOG(WARNING) << "Repainting the background with color: (" | |
| 183 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 184 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 185 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 186 } | |
| 187 else | |
| 188 { | |
| 189 LOG(WARNING) << "No repainting of the background"; | |
| 190 } | |
| 191 | |
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192 Orthanc::PhotometricInterpretation targetPhotometric; |
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193 bool transcoding; |
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194 |
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195 if (parameters.IsForceReencode() || |
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196 parameters.IsReconstructPyramid() || |
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197 sourceCompression != parameters.GetTargetCompression()) |
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198 { |
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199 // The tiles of the source image will be re-encoded |
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200 transcoding = false; |
| 171 | 201 |
| 202 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 203 { | |
| 204 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 205 } | |
| 206 else | |
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207 { |
| 171 | 208 switch (parameters.GetTargetCompression()) |
| 209 { | |
| 210 case OrthancWSI::ImageCompression_Jpeg: | |
| 211 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 212 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 213 break; | |
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214 |
| 171 | 215 case OrthancWSI::ImageCompression_None: |
| 216 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 217 break; | |
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218 |
| 171 | 219 default: |
| 220 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 221 } | |
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222 } |
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223 } |
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224 else |
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225 { |
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226 // Transcoding: The tiles are copied (no re-encoding) |
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227 transcoding = true; |
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228 targetPhotometric = source.GetPhotometricInterpretation(); |
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229 } |
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230 |
| 0 | 231 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 232 source.GetPixelFormat(), | |
| 233 parameters.GetTargetCompression(), | |
| 234 parameters.GetTargetTileWidth(source), | |
| 235 parameters.GetTargetTileHeight(source), | |
| 236 parameters.GetDicomMaxFileSize(), | |
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237 volume, targetPhotometric); |
| 29 | 238 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 239 |
| 240 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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241 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 242 |
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243 if (!transcoding && |
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244 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 245 { |
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246 LOG(WARNING) << "Target compression: Jpeg with quality " |
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247 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 248 target.SetJpegQuality(target.GetJpegQuality()); |
| 249 } | |
| 250 else | |
| 251 { | |
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252 LOG(WARNING) << "Target compression: " |
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253 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 254 } |
| 255 | |
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256 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
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257 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
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258 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
| 0 | 259 { |
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260 LOG(ERROR) << "When resampling the tile size, " |
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261 << "it must be a integer divisor of the original tile size"; |
| 0 | 262 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 263 } | |
| 264 | |
| 265 if (target.GetTileWidth() <= 16 || | |
| 266 target.GetTileHeight() <= 16) | |
| 267 { | |
| 268 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 269 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 270 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 271 } | |
| 272 | |
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273 if (transcoding) |
| 0 | 274 { |
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275 TranscodePyramid(target, stats, parameters); |
| 0 | 276 } |
| 277 else | |
| 278 { | |
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279 ReconstructPyramid(target, stats, parameters); |
| 0 | 280 } |
| 281 | |
| 282 target.Flush(); | |
| 283 } | |
| 284 | |
| 285 | |
| 286 | |
| 287 static DcmDataset* ParseDataset(const std::string& path) | |
| 288 { | |
| 289 Json::Value json; | |
| 290 | |
| 291 if (path.empty()) | |
| 292 { | |
| 293 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 294 } | |
| 295 else | |
| 296 { | |
| 297 std::string content; | |
| 43 | 298 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 299 |
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300 if (!Orthanc::Toolbox::ReadJsonWithoutComments(json, content)) |
| 0 | 301 { |
| 302 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 303 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 304 } | |
| 305 } | |
| 306 | |
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307 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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308 "" /* no private tag, thus no private creator */)); |
| 0 | 309 if (dataset.get() == NULL) |
| 310 { | |
| 311 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 312 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 313 } | |
| 314 | |
| 315 // VL Whole Slide Microscopy Image IOD | |
| 316 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 317 | |
| 318 // Slide Microscopy | |
| 319 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 320 | |
| 321 // Patient orientation makes no sense in whole-slide images | |
| 322 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 323 | |
| 324 // Some basic coordinate information | |
| 325 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 326 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 327 | |
| 328 std::string date, time; | |
| 130 | 329 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 330 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 331 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 332 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 333 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 334 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 335 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 336 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 337 | |
| 338 return dataset.release(); | |
| 339 } | |
| 340 | |
| 341 | |
| 342 | |
| 343 static void SetupDimension(DcmDataset& dataset, | |
| 344 const std::string& opticalPathId, | |
| 345 const OrthancWSI::ITiledPyramid& source, | |
| 346 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 347 { | |
| 83 | 348 // Extract the identifier of the Dimension Organization, if provided |
| 349 std::string organization; | |
| 0 | 350 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 351 | |
| 83 | 352 if (previous != NULL && |
| 353 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 354 { | |
| 355 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 356 } | |
| 357 else | |
| 0 | 358 { |
| 83 | 359 // No Dimension Organization provided: Generate an unique identifier |
| 360 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 361 } | |
| 362 | |
| 363 | |
| 364 { | |
| 365 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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366 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 367 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
| 368 | |
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369 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
| 83 | 370 |
| 371 if (!sequence->insert(item.release(), false, false).good() || | |
| 372 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 373 { |
| 83 | 374 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 375 } |
| 376 } | |
| 377 | |
| 83 | 378 |
| 0 | 379 { |
| 83 | 380 // Construct tag "Dimension Index Sequence" (0020,9222) |
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381 std::unique_ptr<DcmItem> item(new DcmItem); |
| 83 | 382 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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383 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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384 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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385 |
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386 std::unique_ptr<DcmItem> item2(new DcmItem); |
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387 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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388 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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389 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 390 |
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391 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 392 |
| 83 | 393 if (!sequence->insert(item.release(), false, false).good() || |
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394 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 395 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 396 { | |
| 397 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 398 } | |
| 0 | 399 } |
| 400 | |
| 401 | |
| 83 | 402 { |
| 403 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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404 std::unique_ptr<DcmItem> item(new DcmItem); |
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405 |
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406 std::unique_ptr<DcmItem> item3(new DcmItem); |
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407 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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408 |
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409 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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410 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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411 |
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412 if (!sequence3->insert(item3.release(), false, false).good() || |
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413 !item->insert(sequence3.release(), false, false).good() || |
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414 !sequence->insert(item.release(), false, false).good() || |
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415 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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416 { |
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417 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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418 } |
| 0 | 419 } |
| 420 } | |
| 421 | |
| 422 | |
| 423 static void EnrichDataset(DcmDataset& dataset, | |
| 424 const OrthancWSI::ITiledPyramid& source, | |
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425 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 426 const OrthancWSI::DicomizerParameters& parameters, |
| 427 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 428 { | |
| 429 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 430 | |
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431 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 432 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 433 { | |
| 434 // Takes as estimation a 1:10 compression ratio | |
| 435 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 436 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 437 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 438 } | |
| 439 else | |
| 440 { | |
| 441 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 442 } | |
| 443 | |
| 444 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 445 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 446 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 447 | |
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448 std::unique_ptr<DcmItem> origin(new DcmItem); |
| 0 | 449 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
| 450 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 451 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 452 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 453 | |
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454 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
| 0 | 455 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
| 456 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 457 { | |
| 458 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 459 } | |
| 460 | |
| 461 | |
| 462 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 463 { | |
| 464 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 465 { | |
| 466 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 467 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 468 } | |
| 469 | |
| 470 std::string brightfield; | |
| 471 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 472 | |
| 473 Json::Value json; | |
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474 if (!Orthanc::Toolbox::ReadJsonWithoutComments(json, brightfield)) |
| 0 | 475 { |
| 476 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 477 } | |
| 478 | |
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479 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
| 0 | 480 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
| 481 DCM_OpticalPathSequence.getElement()), | |
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482 json, false, encoding, |
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483 "" /* no private tag, thus no private creator */)); |
| 0 | 484 if (!dataset.insert(element.release()).good()) |
| 485 { | |
| 486 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 487 } | |
| 488 } | |
| 489 | |
| 490 | |
| 491 std::string profile; | |
| 492 if (parameters.GetIccProfilePath().empty()) | |
| 493 { | |
| 494 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 495 } | |
| 496 else | |
| 497 { | |
| 43 | 498 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 499 } |
| 500 | |
| 501 | |
| 502 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 503 if (opticalPath == NULL) | |
| 504 { | |
| 505 LOG(ERROR) << "No optical path specified"; | |
| 506 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 507 } | |
| 508 | |
| 509 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 510 { | |
|
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511 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
| 0 | 512 |
| 513 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 514 !opticalPath->insert(icc.release()).good()) | |
| 515 { | |
| 516 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 517 } | |
| 518 } | |
| 519 | |
| 520 const char* opticalPathId = NULL; | |
| 521 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 522 opticalPathId == NULL) | |
| 523 { | |
| 524 LOG(ERROR) << "No identifier in the optical path"; | |
| 525 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 526 } | |
| 527 | |
| 528 SetupDimension(dataset, opticalPathId, source, volume); | |
| 529 } | |
| 530 | |
| 531 | |
| 532 static bool ParseParameters(int& exitStatus, | |
| 533 OrthancWSI::DicomizerParameters& parameters, | |
| 534 OrthancWSI::ImagedVolumeParameters& volume, | |
| 535 int argc, | |
| 536 char* argv[]) | |
| 537 { | |
| 538 // Declare the supported parameters | |
| 539 boost::program_options::options_description generic("Generic options"); | |
| 540 generic.add_options() | |
|
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541 (OPTION_HELP, "Display this help and exit") |
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542 (OPTION_VERSION, "Output version information and exit") |
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543 (OPTION_VERBOSE, "Be verbose in logs") |
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544 (OPTION_THREADS, |
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545 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 546 "Number of processing threads to be used") |
|
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547 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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548 "Path to the shared library of OpenSlide " |
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549 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 550 ; |
| 551 | |
| 552 boost::program_options::options_description source("Options for the source image"); | |
| 553 source.add_options() | |
|
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554 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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555 "Path to a JSON file containing the DICOM dataset") |
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556 (OPTION_SAMPLE_DATASET, |
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557 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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558 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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559 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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560 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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561 "Whether to repaint the background of the image (Boolean)") |
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562 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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563 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 564 ; |
| 565 | |
| 566 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 567 pyramid.add_options() | |
|
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568 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 569 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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570 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 571 "Apply smoothing when reconstructing the pyramid " |
| 572 "(slower, but higher quality) (Boolean)") | |
|
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573 (OPTION_LEVELS, boost::program_options::value<int>(), |
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574 "Number of levels in the target pyramid") |
| 0 | 575 ; |
| 576 | |
| 577 boost::program_options::options_description target("Options for the target image"); | |
| 578 target.add_options() | |
|
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579 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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580 "Width of the tiles in the target image") |
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581 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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582 "Height of the tiles in the target image") |
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583 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 584 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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585 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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586 "Set quality level for JPEG (0..100)") |
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587 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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588 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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589 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 590 "Folder where to store the output DICOM instances") |
|
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591 (OPTION_FOLDER_PATTERN, |
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592 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 593 "Pattern for the files in the output folder") |
| 594 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 595 "URL to the REST API of the target Orthanc server") | |
| 596 ; | |
| 597 | |
| 598 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 599 volumeOptions.add_options() | |
|
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600 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
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601 "Width of the specimen (in mm)") |
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602 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
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603 "Height of the specimen (in mm)") |
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604 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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605 "Depth of the specimen (in mm)") |
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606 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 607 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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608 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 609 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 610 ; | |
| 611 | |
|
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612 boost::program_options::options_description restOptions |
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613 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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614 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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615 |
| 0 | 616 boost::program_options::options_description advancedOptions("Advanced options"); |
| 617 advancedOptions.add_options() | |
|
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618 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 619 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
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620 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 621 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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622 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 623 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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624 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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625 "Number of pyramid levels up to which multithreading " |
| 0 | 626 "should be applied (only for performance/memory tuning)") |
| 627 ; | |
| 628 | |
| 629 boost::program_options::options_description hidden; | |
| 630 hidden.add_options() | |
|
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631 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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632 "Input file"); |
| 0 | 633 ; |
| 634 | |
| 635 boost::program_options::options_description allWithoutHidden; | |
|
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636 allWithoutHidden |
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637 .add(generic) |
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638 .add(source) |
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639 .add(pyramid) |
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640 .add(target) |
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641 .add(volumeOptions) |
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642 .add(restOptions) |
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643 .add(advancedOptions); |
| 0 | 644 |
| 645 boost::program_options::options_description all = allWithoutHidden; | |
| 646 all.add(hidden); | |
| 647 | |
| 648 boost::program_options::positional_options_description positional; | |
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649 positional.add(OPTION_INPUT, 1); |
| 0 | 650 |
| 651 boost::program_options::variables_map options; | |
| 652 bool error = false; | |
| 653 | |
| 654 try | |
| 655 { | |
| 656 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 657 options(all).positional(positional).run(), options); | |
| 658 boost::program_options::notify(options); | |
| 659 } | |
| 660 catch (boost::program_options::error& e) | |
| 661 { | |
| 662 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 663 error = true; | |
| 664 } | |
| 665 | |
| 666 if (!error && | |
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667 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 668 { |
| 669 std::string sample; | |
| 670 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 671 | |
| 672 std::cout << std::endl << sample << std::endl; | |
| 673 | |
| 674 return false; | |
| 675 } | |
| 676 | |
| 677 if (!error && | |
|
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678 options.count(OPTION_HELP) == 0 && |
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679 options.count(OPTION_VERSION) == 0 && |
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680 options.count(OPTION_INPUT) != 1) |
| 0 | 681 { |
| 682 LOG(ERROR) << "No input file was specified"; | |
| 683 error = true; | |
| 684 } | |
| 685 | |
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686 if (error || options.count(OPTION_HELP)) |
| 0 | 687 { |
| 688 std::cout << std::endl | |
| 689 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 690 << std::endl | |
| 691 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 692 << std::endl << std::endl | |
| 693 << "Create a DICOM file from a digital pathology image." | |
| 694 << std::endl; | |
| 695 | |
| 696 std::cout << allWithoutHidden << "\n"; | |
| 697 | |
| 698 if (error) | |
| 699 { | |
| 700 exitStatus = -1; | |
| 701 } | |
| 702 | |
| 703 return false; | |
| 704 } | |
| 705 | |
|
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706 if (options.count(OPTION_VERSION)) |
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707 { |
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708 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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709 return false; |
|
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710 } |
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711 |
|
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712 if (options.count(OPTION_VERBOSE)) |
| 0 | 713 { |
| 714 Orthanc::Logging::EnableInfoLevel(true); | |
| 715 } | |
| 716 | |
|
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717 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 718 { |
|
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719 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 720 } |
| 721 | |
|
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722 if (options.count(OPTION_PYRAMID) && |
|
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723 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 724 { |
| 725 parameters.SetReconstructPyramid(true); | |
| 726 } | |
| 727 | |
|
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728 if (options.count(OPTION_SMOOTH) && |
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729 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 730 { |
| 731 parameters.SetSmoothEnabled(true); | |
| 732 } | |
| 733 | |
|
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734 if (options.count(OPTION_SAFETY) && |
|
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735 options[OPTION_SAFETY].as<bool>()) |
| 0 | 736 { |
| 737 parameters.SetSafetyCheck(true); | |
| 738 } | |
| 739 | |
|
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740 if (options.count(OPTION_REENCODE) && |
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741 options[OPTION_REENCODE].as<bool>()) |
| 0 | 742 { |
| 743 parameters.SetForceReencode(true); | |
| 744 } | |
| 745 | |
|
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746 if (options.count(OPTION_REPAINT) && |
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747 options[OPTION_REPAINT].as<bool>()) |
| 0 | 748 { |
| 749 parameters.SetRepaintBackground(true); | |
| 750 } | |
| 751 | |
|
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752 if (options.count(OPTION_TILE_WIDTH) || |
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753 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 754 { |
| 755 int w = 0; | |
|
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756 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 757 { |
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758 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 759 } |
| 760 | |
| 145 | 761 int h = 0; |
|
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762 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 763 { |
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764 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 765 } |
| 766 | |
| 767 if (w < 0 || h < 0) | |
| 768 { | |
| 769 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 770 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 771 } | |
| 772 | |
| 773 parameters.SetTargetTileSize(w, h); | |
| 774 } | |
| 775 | |
|
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776 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
| 0 | 777 |
|
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778 if (options.count(OPTION_COLOR)) |
| 0 | 779 { |
| 780 uint8_t r, g, b; | |
|
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781 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 782 parameters.SetBackgroundColor(r, g, b); |
| 783 } | |
| 784 | |
|
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785 if (options.count(OPTION_COMPRESSION)) |
| 0 | 786 { |
|
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787 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 788 if (s == "none") |
| 789 { | |
| 790 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 791 } | |
| 792 else if (s == "jpeg") | |
| 793 { | |
| 794 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 795 } | |
| 796 else if (s == "jpeg2000") | |
| 797 { | |
| 798 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 799 } | |
| 800 else | |
| 801 { | |
| 802 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 803 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 804 } | |
| 805 } | |
| 806 | |
|
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807 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 808 { |
|
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809 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 810 } |
| 811 | |
|
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812 if (options.count(OPTION_LEVELS)) |
| 0 | 813 { |
|
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814 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 815 } |
| 816 | |
|
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817 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 818 { |
|
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819 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 820 } |
| 821 | |
|
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822 if (options.count(OPTION_THREADS)) |
| 0 | 823 { |
|
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824 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 825 } |
| 826 | |
|
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827 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 828 { |
|
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829 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 830 } |
| 831 | |
|
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832 if (options.count(OPTION_FOLDER)) |
| 0 | 833 { |
|
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834 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 835 } |
| 836 | |
|
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837 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 838 { |
|
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839 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 840 } |
| 841 | |
|
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842 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 843 |
|
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844 if (options.count(OPTION_DATASET)) |
| 0 | 845 { |
|
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846 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 847 } |
| 848 | |
|
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849 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 850 { |
|
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851 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 852 } |
| 853 | |
|
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854 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 855 { |
|
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856 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 857 } |
| 858 | |
|
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859 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 860 { |
|
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861 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 862 } |
| 863 | |
|
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864 if (options.count(OPTION_OFFSET_X)) |
| 0 | 865 { |
|
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866 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 867 } |
| 868 | |
|
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869 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 870 { |
|
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871 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 872 } |
| 873 | |
|
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874 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 875 { |
|
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876 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 877 if (s == "none") |
| 878 { | |
| 879 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 880 } | |
| 881 else if (s == "brightfield") | |
| 882 { | |
| 883 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 884 } | |
| 885 else | |
| 886 { | |
| 887 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 888 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 889 } | |
| 890 } | |
| 891 | |
|
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892 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 893 { |
|
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894 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 895 } |
| 896 | |
| 897 return true; | |
| 898 } | |
| 899 | |
| 900 | |
|
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901 |
|
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902 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
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903 const std::string& path, |
| 0 | 904 const OrthancWSI::DicomizerParameters& parameters) |
| 905 { | |
| 906 LOG(WARNING) << "The input image is: " << path; | |
| 907 | |
| 908 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 909 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 910 | |
| 911 switch (format) | |
| 912 { | |
| 913 case OrthancWSI::ImageCompression_Png: | |
|
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914 { |
|
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915 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 916 return new OrthancWSI::TiledPngImage(path, |
| 917 parameters.GetTargetTileWidth(512), | |
| 918 parameters.GetTargetTileHeight(512)); | |
|
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919 } |
| 0 | 920 |
| 921 case OrthancWSI::ImageCompression_Jpeg: | |
|
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922 { |
|
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923 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 924 return new OrthancWSI::TiledJpegImage(path, |
| 925 parameters.GetTargetTileWidth(512), | |
| 926 parameters.GetTargetTileHeight(512)); | |
|
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927 } |
| 0 | 928 |
| 929 case OrthancWSI::ImageCompression_Tiff: | |
| 930 { | |
| 931 try | |
| 932 { | |
|
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933 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
|
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934 sourceCompression = tiff->GetImageCompression(); |
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935 return tiff.release(); |
| 0 | 936 } |
| 937 catch (Orthanc::OrthancException&) | |
| 938 { | |
| 939 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 940 } | |
| 941 } | |
| 942 | |
| 943 default: | |
| 944 break; | |
| 945 } | |
| 946 | |
| 947 try | |
| 948 { | |
| 949 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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950 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 951 return new OrthancWSI::OpenSlidePyramid(path, |
| 952 parameters.GetTargetTileWidth(512), | |
| 953 parameters.GetTargetTileHeight(512)); | |
| 954 } | |
| 955 catch (Orthanc::OrthancException&) | |
| 956 { | |
| 957 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 958 return NULL; | |
| 959 } | |
| 960 } | |
| 961 | |
| 962 | |
| 963 int main(int argc, char* argv[]) | |
| 964 { | |
| 965 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
93
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966 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 967 |
| 968 int exitStatus = 0; | |
| 969 | |
| 970 try | |
| 971 { | |
| 972 OrthancWSI::DicomizerParameters parameters; | |
| 973 OrthancWSI::ImagedVolumeParameters volume; | |
| 974 | |
| 975 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 976 { | |
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977 OrthancWSI::ImageCompression sourceCompression; |
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978 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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979 |
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980 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 981 if (source.get() == NULL) |
| 982 { | |
| 983 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 984 } | |
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985 |
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986 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 987 |
| 988 // Create the shared DICOM tags | |
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989 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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990 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 991 |
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992 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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993 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 994 } |
| 995 } | |
| 996 catch (Orthanc::OrthancException& e) | |
| 997 { | |
| 998 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 999 exitStatus = -1; | |
| 1000 } | |
| 1001 | |
| 1002 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1003 | |
| 1004 return exitStatus; | |
| 1005 } |