Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 169:de783db2a7c3
making fix for issue #139 permanent
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 12 Jul 2019 12:53:26 +0200 |
| parents | d3aea0af03e1 |
| children | 1390d5c87603 |
| 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 | |
| 157 | 5 * Copyright (C) 2017-2019 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" | |
| 26 #include "../Framework/ImagedVolumeParameters.h" | |
| 27 #include "../Framework/Inputs/HierarchicalTiff.h" | |
| 28 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 29 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 30 #include "../Framework/Inputs/TiledPngImage.h" | |
| 31 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 32 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 33 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 34 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 35 | |
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36 #include <Core/DicomParsing/FromDcmtkBridge.h> |
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37 #include <Core/Logging.h> |
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38 #include <Core/OrthancException.h> |
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39 #include <Core/SystemToolbox.h> |
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40 |
| 0 | 41 #include "ApplicationToolbox.h" |
| 42 | |
| 43 #include <EmbeddedResources.h> | |
| 44 | |
| 45 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 46 #include <dcmtk/dcmdata/dcuid.h> | |
| 47 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 48 #include <dcmtk/dcmdata/dcvrat.h> | |
| 49 | |
| 50 | |
|
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51 static const char* OPTION_COLOR = "color"; |
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52 static const char* OPTION_COMPRESSION = "compression"; |
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53 static const char* OPTION_DATASET = "dataset"; |
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54 static const char* OPTION_FOLDER = "folder"; |
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55 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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56 static const char* OPTION_HELP = "help"; |
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57 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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58 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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59 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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60 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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61 static const char* OPTION_INPUT = "input"; |
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62 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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63 static const char* OPTION_LEVELS = "levels"; |
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64 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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65 static const char* OPTION_MAX_SIZE = "max-size"; |
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66 static const char* OPTION_OFFSET_X = "offset-x"; |
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67 static const char* OPTION_OFFSET_Y = "offset-y"; |
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68 static const char* OPTION_OPENSLIDE = "openslide"; |
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69 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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70 static const char* OPTION_PYRAMID = "pyramid"; |
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71 static const char* OPTION_REENCODE = "reencode"; |
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72 static const char* OPTION_REPAINT = "repaint"; |
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73 static const char* OPTION_SAFETY = "safety"; |
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74 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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75 static const char* OPTION_SMOOTH = "smooth"; |
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76 static const char* OPTION_THREADS = "threads"; |
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77 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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78 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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79 static const char* OPTION_VERBOSE = "verbose"; |
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80 static const char* OPTION_VERSION = "version"; |
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81 |
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82 |
| 0 | 83 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 84 OrthancWSI::ITiledPyramid& source, | |
| 85 const OrthancWSI::DicomizerParameters& parameters) | |
| 86 { | |
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87 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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88 |
| 0 | 89 Orthanc::BagOfTasks tasks; |
| 90 | |
| 91 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 92 { | |
| 93 LOG(WARNING) << "Creating level " << i << " of size " | |
| 94 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 95 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 96 } | |
| 97 | |
| 98 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 99 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 100 } | |
| 101 | |
| 102 | |
| 103 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 104 OrthancWSI::ITiledPyramid& source, | |
| 105 const OrthancWSI::DicomizerParameters& parameters) | |
| 106 { | |
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107 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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108 |
| 0 | 109 Orthanc::BagOfTasks tasks; |
| 110 | |
| 111 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 112 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 113 assert(levelsCount >= 1); | |
| 114 | |
| 115 for (unsigned int i = 0; i < levelsCount; i++) | |
| 116 { | |
| 117 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 118 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 119 | |
| 120 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 121 target.AddLevel(width, height); | |
| 122 } | |
| 123 | |
| 124 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 125 if (lowerLevelsCount > levelsCount) | |
| 126 { | |
| 127 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 128 << ") exceeds the number of levels (" << levelsCount | |
| 129 << "), cropping it"; | |
| 130 lowerLevelsCount = levelsCount; | |
| 131 } | |
| 132 | |
| 133 assert(lowerLevelsCount <= levelsCount); | |
| 134 if (lowerLevelsCount != levelsCount) | |
| 135 { | |
| 136 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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137 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 138 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 139 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 140 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 141 | |
| 142 assert(tasks.GetSize() == 0); | |
| 143 | |
| 144 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 145 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 146 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 147 (tasks, target, truncated.GetUpperLevel(), | |
| 148 upperLevelsCount, lowerLevelsCount, parameters); | |
| 149 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 150 } | |
| 151 else | |
| 152 { | |
| 153 LOG(WARNING) << "Constructing the pyramid"; | |
| 154 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 155 (tasks, target, source, levelsCount, 0, parameters); | |
| 156 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 157 } | |
| 158 } | |
| 159 | |
| 160 | |
| 161 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 162 OrthancWSI::ITiledPyramid& source, | |
| 163 const DcmDataset& dataset, | |
| 164 const OrthancWSI::DicomizerParameters& parameters, | |
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165 const OrthancWSI::ImagedVolumeParameters& volume, |
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166 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 167 { |
| 168 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 169 | |
| 170 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
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171 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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172 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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173 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 174 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 175 | |
| 176 if (parameters.IsRepaintBackground()) | |
| 177 { | |
| 178 LOG(WARNING) << "Repainting the background with color: (" | |
| 179 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 180 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 181 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 182 } | |
| 183 else | |
| 184 { | |
| 185 LOG(WARNING) << "No repainting of the background"; | |
| 186 } | |
| 187 | |
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188 Orthanc::PhotometricInterpretation targetPhotometric; |
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189 bool transcoding; |
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190 |
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191 if (parameters.IsForceReencode() || |
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192 parameters.IsReconstructPyramid() || |
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193 sourceCompression != parameters.GetTargetCompression()) |
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194 { |
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195 // The tiles of the source image will be re-encoded |
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196 transcoding = false; |
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197 |
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198 switch (parameters.GetTargetCompression()) |
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199 { |
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200 case OrthancWSI::ImageCompression_Jpeg: |
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201 case OrthancWSI::ImageCompression_Jpeg2000: |
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202 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; |
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203 break; |
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204 |
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205 case OrthancWSI::ImageCompression_None: |
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206 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; |
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207 break; |
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208 |
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209 default: |
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210 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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211 } |
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212 } |
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213 else |
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214 { |
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215 // Transcoding: The tiles are copied (no re-encoding) |
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216 transcoding = true; |
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217 targetPhotometric = source.GetPhotometricInterpretation(); |
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218 } |
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219 |
| 0 | 220 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 221 source.GetPixelFormat(), | |
| 222 parameters.GetTargetCompression(), | |
| 223 parameters.GetTargetTileWidth(source), | |
| 224 parameters.GetTargetTileHeight(source), | |
| 225 parameters.GetDicomMaxFileSize(), | |
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226 volume, targetPhotometric); |
| 29 | 227 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 228 |
| 229 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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230 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 231 |
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232 if (!transcoding && |
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233 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 234 { |
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235 LOG(WARNING) << "Target compression: Jpeg with quality " |
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236 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 237 target.SetJpegQuality(target.GetJpegQuality()); |
| 238 } | |
| 239 else | |
| 240 { | |
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241 LOG(WARNING) << "Target compression: " |
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242 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 243 } |
| 244 | |
| 245 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
| 246 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
| 247 { | |
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248 LOG(ERROR) << "When resampling the tile size, " |
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249 << "it must be a integer divisor of the original tile size"; |
| 0 | 250 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 251 } | |
| 252 | |
| 253 if (target.GetTileWidth() <= 16 || | |
| 254 target.GetTileHeight() <= 16) | |
| 255 { | |
| 256 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 257 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 258 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 259 } | |
| 260 | |
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261 if (transcoding) |
| 0 | 262 { |
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263 TranscodePyramid(target, stats, parameters); |
| 0 | 264 } |
| 265 else | |
| 266 { | |
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267 ReconstructPyramid(target, stats, parameters); |
| 0 | 268 } |
| 269 | |
| 270 target.Flush(); | |
| 271 } | |
| 272 | |
| 273 | |
| 274 | |
| 275 static DcmDataset* ParseDataset(const std::string& path) | |
| 276 { | |
| 277 Json::Value json; | |
| 278 | |
| 279 if (path.empty()) | |
| 280 { | |
| 281 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 282 } | |
| 283 else | |
| 284 { | |
| 285 std::string content; | |
| 43 | 286 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 287 |
| 288 Json::Reader reader; | |
| 289 if (!reader.parse(content, json, false)) | |
| 290 { | |
| 291 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 292 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 293 } | |
| 294 } | |
| 295 | |
| 296 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1)); | |
| 297 if (dataset.get() == NULL) | |
| 298 { | |
| 299 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 300 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 301 } | |
| 302 | |
| 303 // VL Whole Slide Microscopy Image IOD | |
| 304 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 305 | |
| 306 // Slide Microscopy | |
| 307 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 308 | |
| 309 // Patient orientation makes no sense in whole-slide images | |
| 310 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 311 | |
| 312 // Some basic coordinate information | |
| 313 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 314 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 315 | |
| 316 std::string date, time; | |
| 130 | 317 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 318 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 319 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 320 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 321 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 322 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 323 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 324 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 325 | |
| 326 return dataset.release(); | |
| 327 } | |
| 328 | |
| 329 | |
| 330 | |
| 331 static void SetupDimension(DcmDataset& dataset, | |
| 332 const std::string& opticalPathId, | |
| 333 const OrthancWSI::ITiledPyramid& source, | |
| 334 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 335 { | |
| 83 | 336 // Extract the identifier of the Dimension Organization, if provided |
| 337 std::string organization; | |
| 0 | 338 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 339 | |
| 83 | 340 if (previous != NULL && |
| 341 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 342 { | |
| 343 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 344 } | |
| 345 else | |
| 0 | 346 { |
| 83 | 347 // No Dimension Organization provided: Generate an unique identifier |
| 348 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 349 } | |
| 350 | |
| 351 | |
| 352 { | |
| 353 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
| 354 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 355 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
| 356 | |
| 357 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
| 358 | |
| 359 if (!sequence->insert(item.release(), false, false).good() || | |
| 360 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 361 { |
| 83 | 362 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 363 } |
| 364 } | |
| 365 | |
| 83 | 366 |
| 0 | 367 { |
| 83 | 368 // Construct tag "Dimension Index Sequence" (0020,9222) |
| 369 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 370 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
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371 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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372 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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373 |
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374 std::auto_ptr<DcmItem> item2(new DcmItem); |
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375 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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376 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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377 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 378 |
| 83 | 379 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 380 |
| 83 | 381 if (!sequence->insert(item.release(), false, false).good() || |
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382 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 383 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 384 { | |
| 385 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 386 } | |
| 0 | 387 } |
| 388 | |
| 389 | |
| 83 | 390 { |
| 391 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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392 std::auto_ptr<DcmItem> item(new DcmItem); |
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393 |
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394 std::auto_ptr<DcmItem> item3(new DcmItem); |
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395 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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396 |
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397 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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398 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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399 |
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400 if (!sequence3->insert(item3.release(), false, false).good() || |
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401 !item->insert(sequence3.release(), false, false).good() || |
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402 !sequence->insert(item.release(), false, false).good() || |
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403 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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404 { |
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405 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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406 } |
| 0 | 407 } |
| 408 } | |
| 409 | |
| 410 | |
| 411 static void EnrichDataset(DcmDataset& dataset, | |
| 412 const OrthancWSI::ITiledPyramid& source, | |
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413 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 414 const OrthancWSI::DicomizerParameters& parameters, |
| 415 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 416 { | |
| 417 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 418 | |
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419 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 420 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 421 { | |
| 422 // Takes as estimation a 1:10 compression ratio | |
| 423 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 424 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 425 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 426 } | |
| 427 else | |
| 428 { | |
| 429 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 430 } | |
| 431 | |
| 432 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 433 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 434 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 435 | |
| 436 std::auto_ptr<DcmItem> origin(new DcmItem); | |
| 437 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
| 438 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 439 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 440 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 441 | |
| 442 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
| 443 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
| 444 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 445 { | |
| 446 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 447 } | |
| 448 | |
| 449 | |
| 450 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 451 { | |
| 452 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 453 { | |
| 454 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 455 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 456 } | |
| 457 | |
| 458 std::string brightfield; | |
| 459 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 460 | |
| 461 Json::Value json; | |
| 462 Json::Reader reader; | |
| 463 if (!reader.parse(brightfield, json, false)) | |
| 464 { | |
| 465 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 466 } | |
| 467 | |
| 468 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
| 469 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
| 470 DCM_OpticalPathSequence.getElement()), | |
| 471 json, false, encoding)); | |
| 472 if (!dataset.insert(element.release()).good()) | |
| 473 { | |
| 474 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 475 } | |
| 476 } | |
| 477 | |
| 478 | |
| 479 std::string profile; | |
| 480 if (parameters.GetIccProfilePath().empty()) | |
| 481 { | |
| 482 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 483 } | |
| 484 else | |
| 485 { | |
| 43 | 486 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 487 } |
| 488 | |
| 489 | |
| 490 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 491 if (opticalPath == NULL) | |
| 492 { | |
| 493 LOG(ERROR) << "No optical path specified"; | |
| 494 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 495 } | |
| 496 | |
| 497 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 498 { | |
| 499 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
| 500 | |
| 501 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 502 !opticalPath->insert(icc.release()).good()) | |
| 503 { | |
| 504 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 505 } | |
| 506 } | |
| 507 | |
| 508 const char* opticalPathId = NULL; | |
| 509 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 510 opticalPathId == NULL) | |
| 511 { | |
| 512 LOG(ERROR) << "No identifier in the optical path"; | |
| 513 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 514 } | |
| 515 | |
| 516 SetupDimension(dataset, opticalPathId, source, volume); | |
| 517 } | |
| 518 | |
| 519 | |
| 520 static bool ParseParameters(int& exitStatus, | |
| 521 OrthancWSI::DicomizerParameters& parameters, | |
| 522 OrthancWSI::ImagedVolumeParameters& volume, | |
| 523 int argc, | |
| 524 char* argv[]) | |
| 525 { | |
| 526 // Declare the supported parameters | |
| 527 boost::program_options::options_description generic("Generic options"); | |
| 528 generic.add_options() | |
|
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529 (OPTION_HELP, "Display this help and exit") |
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530 (OPTION_VERSION, "Output version information and exit") |
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531 (OPTION_VERBOSE, "Be verbose in logs") |
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532 (OPTION_THREADS, |
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533 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 534 "Number of processing threads to be used") |
|
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535 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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536 "Path to the shared library of OpenSlide " |
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537 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 538 ; |
| 539 | |
| 540 boost::program_options::options_description source("Options for the source image"); | |
| 541 source.add_options() | |
|
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542 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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543 "Path to a JSON file containing the DICOM dataset") |
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544 (OPTION_SAMPLE_DATASET, |
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545 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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546 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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547 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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548 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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549 "Whether to repaint the background of the image (Boolean)") |
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550 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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551 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 552 ; |
| 553 | |
| 554 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 555 pyramid.add_options() | |
|
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556 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 557 "Reconstruct the full pyramid (slow) (Boolean)") |
|
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558 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 559 "Apply smoothing when reconstructing the pyramid " |
| 560 "(slower, but higher quality) (Boolean)") | |
|
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561 (OPTION_LEVELS, boost::program_options::value<int>(), |
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562 "Number of levels in the target pyramid") |
| 0 | 563 ; |
| 564 | |
| 565 boost::program_options::options_description target("Options for the target image"); | |
| 566 target.add_options() | |
|
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567 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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568 "Width of the tiles in the target image") |
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569 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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570 "Height of the tiles in the target image") |
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571 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 572 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
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573 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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574 "Set quality level for JPEG (0..100)") |
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575 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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576 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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577 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 578 "Folder where to store the output DICOM instances") |
|
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579 (OPTION_FOLDER_PATTERN, |
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580 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 581 "Pattern for the files in the output folder") |
| 582 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 583 "URL to the REST API of the target Orthanc server") | |
| 584 ; | |
| 585 | |
| 586 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 587 volumeOptions.add_options() | |
|
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588 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
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589 "Width of the specimen (in mm)") |
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590 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
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591 "Height of the specimen (in mm)") |
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592 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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593 "Depth of the specimen (in mm)") |
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594 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 595 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
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596 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 597 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 598 ; | |
| 599 | |
|
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600 boost::program_options::options_description restOptions |
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601 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
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602 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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603 |
| 0 | 604 boost::program_options::options_description advancedOptions("Advanced options"); |
| 605 advancedOptions.add_options() | |
|
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606 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 607 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
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608 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 609 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
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610 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 611 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
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612 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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613 "Number of pyramid levels up to which multithreading " |
| 0 | 614 "should be applied (only for performance/memory tuning)") |
| 615 ; | |
| 616 | |
| 617 boost::program_options::options_description hidden; | |
| 618 hidden.add_options() | |
|
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619 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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620 "Input file"); |
| 0 | 621 ; |
| 622 | |
| 623 boost::program_options::options_description allWithoutHidden; | |
|
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624 allWithoutHidden |
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625 .add(generic) |
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626 .add(source) |
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627 .add(pyramid) |
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628 .add(target) |
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629 .add(volumeOptions) |
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630 .add(restOptions) |
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631 .add(advancedOptions); |
| 0 | 632 |
| 633 boost::program_options::options_description all = allWithoutHidden; | |
| 634 all.add(hidden); | |
| 635 | |
| 636 boost::program_options::positional_options_description positional; | |
|
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637 positional.add(OPTION_INPUT, 1); |
| 0 | 638 |
| 639 boost::program_options::variables_map options; | |
| 640 bool error = false; | |
| 641 | |
| 642 try | |
| 643 { | |
| 644 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 645 options(all).positional(positional).run(), options); | |
| 646 boost::program_options::notify(options); | |
| 647 } | |
| 648 catch (boost::program_options::error& e) | |
| 649 { | |
| 650 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 651 error = true; | |
| 652 } | |
| 653 | |
| 654 if (!error && | |
|
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655 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 656 { |
| 657 std::string sample; | |
| 658 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 659 | |
| 660 std::cout << std::endl << sample << std::endl; | |
| 661 | |
| 662 return false; | |
| 663 } | |
| 664 | |
| 665 if (!error && | |
|
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666 options.count(OPTION_HELP) == 0 && |
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667 options.count(OPTION_VERSION) == 0 && |
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668 options.count(OPTION_INPUT) != 1) |
| 0 | 669 { |
| 670 LOG(ERROR) << "No input file was specified"; | |
| 671 error = true; | |
| 672 } | |
| 673 | |
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674 if (error || options.count(OPTION_HELP)) |
| 0 | 675 { |
| 676 std::cout << std::endl | |
| 677 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 678 << std::endl | |
| 679 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 680 << std::endl << std::endl | |
| 681 << "Create a DICOM file from a digital pathology image." | |
| 682 << std::endl; | |
| 683 | |
| 684 std::cout << allWithoutHidden << "\n"; | |
| 685 | |
| 686 if (error) | |
| 687 { | |
| 688 exitStatus = -1; | |
| 689 } | |
| 690 | |
| 691 return false; | |
| 692 } | |
| 693 | |
|
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694 if (options.count(OPTION_VERSION)) |
|
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695 { |
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696 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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697 return false; |
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698 } |
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699 |
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700 if (options.count(OPTION_VERBOSE)) |
| 0 | 701 { |
| 702 Orthanc::Logging::EnableInfoLevel(true); | |
| 703 } | |
| 704 | |
|
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705 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 706 { |
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707 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 708 } |
| 709 | |
|
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710 if (options.count(OPTION_PYRAMID) && |
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711 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 712 { |
| 713 parameters.SetReconstructPyramid(true); | |
| 714 } | |
| 715 | |
|
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716 if (options.count(OPTION_SMOOTH) && |
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717 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 718 { |
| 719 parameters.SetSmoothEnabled(true); | |
| 720 } | |
| 721 | |
|
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722 if (options.count(OPTION_SAFETY) && |
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723 options[OPTION_SAFETY].as<bool>()) |
| 0 | 724 { |
| 725 parameters.SetSafetyCheck(true); | |
| 726 } | |
| 727 | |
|
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728 if (options.count(OPTION_REENCODE) && |
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729 options[OPTION_REENCODE].as<bool>()) |
| 0 | 730 { |
| 731 parameters.SetForceReencode(true); | |
| 732 } | |
| 733 | |
|
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734 if (options.count(OPTION_REPAINT) && |
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735 options[OPTION_REPAINT].as<bool>()) |
| 0 | 736 { |
| 737 parameters.SetRepaintBackground(true); | |
| 738 } | |
| 739 | |
|
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740 if (options.count(OPTION_TILE_WIDTH) || |
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741 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 742 { |
| 743 int w = 0; | |
|
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744 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 745 { |
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746 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 747 } |
| 748 | |
| 145 | 749 int h = 0; |
|
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750 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 751 { |
|
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752 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 753 } |
| 754 | |
| 755 if (w < 0 || h < 0) | |
| 756 { | |
| 757 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 758 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 759 } | |
| 760 | |
| 761 parameters.SetTargetTileSize(w, h); | |
| 762 } | |
| 763 | |
|
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764 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
| 0 | 765 |
|
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766 if (options.count(OPTION_COLOR)) |
| 0 | 767 { |
| 768 uint8_t r, g, b; | |
|
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769 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 770 parameters.SetBackgroundColor(r, g, b); |
| 771 } | |
| 772 | |
|
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773 if (options.count(OPTION_COMPRESSION)) |
| 0 | 774 { |
|
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775 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 776 if (s == "none") |
| 777 { | |
| 778 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 779 } | |
| 780 else if (s == "jpeg") | |
| 781 { | |
| 782 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 783 } | |
| 784 else if (s == "jpeg2000") | |
| 785 { | |
| 786 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 787 } | |
| 788 else | |
| 789 { | |
| 790 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 791 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 792 } | |
| 793 } | |
| 794 | |
|
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795 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 796 { |
|
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797 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 798 } |
| 799 | |
|
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800 if (options.count(OPTION_LEVELS)) |
| 0 | 801 { |
|
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802 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 803 } |
| 804 | |
|
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805 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 806 { |
|
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807 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 808 } |
| 809 | |
|
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810 if (options.count(OPTION_THREADS)) |
| 0 | 811 { |
|
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812 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 813 } |
| 814 | |
|
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815 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 816 { |
|
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817 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 818 } |
| 819 | |
|
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820 if (options.count(OPTION_FOLDER)) |
| 0 | 821 { |
|
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822 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 823 } |
| 824 | |
|
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825 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 826 { |
|
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827 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 828 } |
| 829 | |
|
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830 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 831 |
|
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832 if (options.count(OPTION_DATASET)) |
| 0 | 833 { |
|
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834 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 835 } |
| 836 | |
|
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837 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 838 { |
|
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839 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 840 } |
| 841 | |
|
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842 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 843 { |
|
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844 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 845 } |
| 846 | |
|
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847 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 848 { |
|
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849 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 850 } |
| 851 | |
|
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852 if (options.count(OPTION_OFFSET_X)) |
| 0 | 853 { |
|
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854 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 855 } |
| 856 | |
|
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857 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 858 { |
|
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859 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 860 } |
| 861 | |
|
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862 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 863 { |
|
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864 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 865 if (s == "none") |
| 866 { | |
| 867 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 868 } | |
| 869 else if (s == "brightfield") | |
| 870 { | |
| 871 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 872 } | |
| 873 else | |
| 874 { | |
| 875 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 876 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 877 } | |
| 878 } | |
| 879 | |
|
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880 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 881 { |
|
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882 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 883 } |
| 884 | |
| 885 return true; | |
| 886 } | |
| 887 | |
| 888 | |
|
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889 |
|
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890 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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891 const std::string& path, |
| 0 | 892 const OrthancWSI::DicomizerParameters& parameters) |
| 893 { | |
| 894 LOG(WARNING) << "The input image is: " << path; | |
| 895 | |
| 896 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 897 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 898 | |
| 899 switch (format) | |
| 900 { | |
| 901 case OrthancWSI::ImageCompression_Png: | |
|
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902 { |
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903 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 904 return new OrthancWSI::TiledPngImage(path, |
| 905 parameters.GetTargetTileWidth(512), | |
| 906 parameters.GetTargetTileHeight(512)); | |
|
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907 } |
| 0 | 908 |
| 909 case OrthancWSI::ImageCompression_Jpeg: | |
|
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910 { |
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911 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 912 return new OrthancWSI::TiledJpegImage(path, |
| 913 parameters.GetTargetTileWidth(512), | |
| 914 parameters.GetTargetTileHeight(512)); | |
|
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915 } |
| 0 | 916 |
| 917 case OrthancWSI::ImageCompression_Tiff: | |
| 918 { | |
| 919 try | |
| 920 { | |
|
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921 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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922 sourceCompression = tiff->GetImageCompression(); |
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923 return tiff.release(); |
| 0 | 924 } |
| 925 catch (Orthanc::OrthancException&) | |
| 926 { | |
| 927 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 928 } | |
| 929 } | |
| 930 | |
| 931 default: | |
| 932 break; | |
| 933 } | |
| 934 | |
| 935 try | |
| 936 { | |
| 937 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
|
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938 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 939 return new OrthancWSI::OpenSlidePyramid(path, |
| 940 parameters.GetTargetTileWidth(512), | |
| 941 parameters.GetTargetTileHeight(512)); | |
| 942 } | |
| 943 catch (Orthanc::OrthancException&) | |
| 944 { | |
| 945 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 946 return NULL; | |
| 947 } | |
| 948 } | |
| 949 | |
| 950 | |
| 951 int main(int argc, char* argv[]) | |
| 952 { | |
| 953 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
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954 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 955 |
| 956 int exitStatus = 0; | |
| 957 | |
| 958 try | |
| 959 { | |
| 960 OrthancWSI::DicomizerParameters parameters; | |
| 961 OrthancWSI::ImagedVolumeParameters volume; | |
| 962 | |
| 963 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 964 { | |
|
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965 OrthancWSI::ImageCompression sourceCompression; |
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966 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
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967 |
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968 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 969 if (source.get() == NULL) |
| 970 { | |
| 971 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 972 } | |
|
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973 |
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974 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 975 |
| 976 // Create the shared DICOM tags | |
| 977 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
|
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978 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 979 |
| 980 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
|
167
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Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
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981 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 982 } |
| 983 } | |
| 984 catch (Orthanc::OrthancException& e) | |
| 985 { | |
| 986 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 987 exitStatus = -1; | |
| 988 } | |
| 989 | |
| 990 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 991 | |
| 992 return exitStatus; | |
| 993 } |