Mercurial > hg > orthanc-wsi
annotate Applications/DicomToTiff.cpp @ 128:788dd04b87f5
cleaning up options in DicomToTiff
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 02 Feb 2018 17:56:48 +0100 |
| parents | 7a3f4d580625 |
| children | a0f9a3df1110 |
| 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) 2017-2018 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/DicomToolbox.h" | |
| 23 #include "../Framework/ImageToolbox.h" | |
| 24 #include "../Framework/Inputs/DicomPyramid.h" | |
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25 #include "../Framework/Inputs/TiledPyramidStatistics.h" |
| 0 | 26 #include "../Framework/Outputs/HierarchicalTiffWriter.h" |
| 27 | |
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28 #include "../Resources/Orthanc/Core/Logging.h" |
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29 #include "../Resources/Orthanc/Core/OrthancException.h" |
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30 #include "../Resources/Orthanc/Plugins/Samples/Common/OrthancHttpConnection.h" |
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31 |
| 0 | 32 #include "ApplicationToolbox.h" |
| 33 | |
| 34 | |
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35 static const char* OPTION_COLOR = "color"; |
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36 static const char* OPTION_HELP = "help"; |
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37 static const char* OPTION_INPUT = "input"; |
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38 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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39 static const char* OPTION_OUTPUT = "output"; |
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40 static const char* OPTION_REENCODE = "reencode"; |
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41 static const char* OPTION_VERBOSE = "verbose"; |
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42 static const char* OPTION_VERSION = "version"; |
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43 |
| 0 | 44 static bool ParseParameters(int& exitStatus, |
| 45 boost::program_options::variables_map& options, | |
| 46 int argc, | |
| 47 char* argv[]) | |
| 48 { | |
| 49 // Declare the supported parameters | |
| 50 boost::program_options::options_description generic("Generic options"); | |
| 51 generic.add_options() | |
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52 (OPTION_HELP, "Display this help and exit") |
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53 (OPTION_VERSION, "Output version information and exit") |
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54 (OPTION_VERBOSE, "Be verbose in logs") |
| 0 | 55 ; |
| 56 | |
| 57 boost::program_options::options_description source("Options for the source DICOM image"); | |
| 58 source.add_options() | |
| 59 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 60 "URL to the REST API of the target Orthanc server") | |
| 61 ; | |
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62 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source); |
| 0 | 63 |
| 64 boost::program_options::options_description target("Options for the target TIFF image"); | |
| 65 target.add_options() | |
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66 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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67 "Color of the background for missing tiles (e.g. \"255,0,0\")") |
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68 (OPTION_REENCODE, boost::program_options::value<bool>(), |
| 31 | 69 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
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70 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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71 "Set quality level for JPEG (0..100)") |
| 0 | 72 ; |
| 73 | |
| 74 boost::program_options::options_description hidden; | |
| 75 hidden.add_options() | |
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76 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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77 "Orthanc identifier of the input series of interest") |
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78 (OPTION_OUTPUT, boost::program_options::value<std::string>(), |
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79 "Output TIFF file"); |
| 0 | 80 |
| 81 boost::program_options::options_description allWithoutHidden; | |
| 82 allWithoutHidden.add(generic).add(source).add(target); | |
| 83 | |
| 84 boost::program_options::options_description all = allWithoutHidden; | |
| 85 all.add(hidden); | |
| 86 | |
| 87 boost::program_options::positional_options_description positional; | |
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88 positional.add(OPTION_INPUT, 1); |
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89 positional.add(OPTION_OUTPUT, 1); |
| 0 | 90 |
| 91 bool error = false; | |
| 92 | |
| 93 try | |
| 94 { | |
| 95 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 96 options(all).positional(positional).run(), options); | |
| 97 boost::program_options::notify(options); | |
| 98 } | |
| 99 catch (boost::program_options::error& e) | |
| 100 { | |
| 101 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 102 error = true; | |
| 103 } | |
| 104 | |
| 105 if (!error && | |
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106 options.count(OPTION_HELP) == 0 && |
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107 options.count(OPTION_VERSION) == 0) |
| 0 | 108 { |
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109 if (options.count(OPTION_INPUT) != 1) |
| 0 | 110 { |
| 111 LOG(ERROR) << "No input series was specified"; | |
| 112 error = true; | |
| 113 } | |
| 114 | |
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115 if (options.count(OPTION_OUTPUT) != 1) |
| 0 | 116 { |
| 117 LOG(ERROR) << "No output file was specified"; | |
| 118 error = true; | |
| 119 } | |
| 120 } | |
| 121 | |
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122 if (error || options.count(OPTION_HELP)) |
| 0 | 123 { |
| 124 std::cout << std::endl | |
| 125 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
| 126 << std::endl | |
| 127 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 128 << std::endl << std::endl | |
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129 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl |
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130 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)." |
| 0 | 131 << std::endl; |
| 132 | |
| 133 std::cout << allWithoutHidden << "\n"; | |
| 134 | |
| 135 if (error) | |
| 136 { | |
| 137 exitStatus = -1; | |
| 138 } | |
| 139 | |
| 140 return false; | |
| 141 } | |
| 142 | |
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143 if (options.count(OPTION_VERSION)) |
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144 { |
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145 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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146 return false; |
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147 } |
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148 |
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149 if (options.count(OPTION_VERBOSE)) |
| 0 | 150 { |
| 151 Orthanc::Logging::EnableInfoLevel(true); | |
| 152 } | |
| 153 | |
| 154 return true; | |
| 155 } | |
| 156 | |
| 157 | |
| 158 | |
| 159 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
| 160 const boost::program_options::variables_map& options) | |
| 161 { | |
| 162 std::auto_ptr<Orthanc::ImageAccessor> tile | |
| 163 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), | |
| 164 writer.GetTileWidth(), | |
| 165 writer.GetTileHeight())); | |
| 166 | |
| 167 uint8_t red = 255; | |
| 168 uint8_t green = 255; | |
| 169 uint8_t blue = 255; | |
| 170 | |
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171 if (options.count(OPTION_COLOR)) |
| 0 | 172 { |
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173 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>()); |
| 0 | 174 } |
| 175 | |
| 176 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
| 177 | |
| 178 return tile.release(); | |
| 179 } | |
| 180 | |
| 181 | |
| 182 | |
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183 static void Run(OrthancWSI::ITiledPyramid& source, |
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184 const boost::program_options::variables_map& options) |
| 0 | 185 { |
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186 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(), |
| 0 | 187 source.GetPixelFormat(), |
| 188 OrthancWSI::ImageCompression_Jpeg, | |
| 189 source.GetTileWidth(), | |
| 190 source.GetTileHeight()); | |
| 191 | |
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192 bool reencode = (options.count(OPTION_REENCODE) && |
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193 options[OPTION_REENCODE].as<bool>()); |
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194 |
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195 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 196 { |
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197 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 198 } |
| 199 | |
| 200 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); | |
| 201 | |
| 202 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 203 { | |
| 204 LOG(WARNING) << "Creating level " << level << " of size " | |
| 205 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
| 206 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
| 207 } | |
| 208 | |
| 209 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 210 { | |
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211 LOG(WARNING) << std::string(reencode ? "Reencoding" : "Transcoding") |
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212 << " level " << level; |
| 0 | 213 |
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214 unsigned int countX = OrthancWSI::CeilingDivision |
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215 (source.GetLevelWidth(level), source.GetTileWidth()); |
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216 |
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217 unsigned int countY = OrthancWSI::CeilingDivision |
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218 (source.GetLevelHeight(level), source.GetTileHeight()); |
| 0 | 219 |
| 220 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
| 221 { | |
| 222 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
| 223 { | |
| 224 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
| 225 | |
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226 bool missing = false; |
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227 bool success = true; |
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228 |
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229 // Give a first try to get the raw tile |
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230 std::string tile; |
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231 OrthancWSI::ImageCompression compression; |
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232 if (source.ReadRawTile(tile, compression, level, tileX, tileY)) |
| 0 | 233 { |
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234 if (reencode || |
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235 compression == OrthancWSI::ImageCompression_Jpeg) |
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236 { |
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237 target.WriteRawTile(tile, compression, level, tileX, tileY); |
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238 } |
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239 else |
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240 { |
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241 success = false; // Re-encoding is mandatory |
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242 } |
| 0 | 243 } |
| 244 else | |
| 245 { | |
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246 // Give a second try to get the decoded tile |
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247 compression = OrthancWSI::ImageCompression_Unknown; |
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248 |
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249 std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY)); |
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250 if (tile.get() == NULL) |
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251 { |
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252 // Unable to read the raw tile or to decode it: The tile is missing (sparse tiling) |
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253 missing = true; |
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254 } |
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255 else if (reencode) |
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256 { |
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257 target.EncodeTile(*empty, level, tileX, tileY); |
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258 } |
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259 else |
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260 { |
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261 success = false; // Re-encoding is mandatory |
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262 } |
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263 } |
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264 |
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265 if (!success) |
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266 { |
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267 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is " |
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268 << OrthancWSI::EnumerationToString(compression) |
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269 << "), please use the --" << OPTION_REENCODE << "=1 option"; |
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270 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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271 } |
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272 |
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273 if (missing) |
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274 { |
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275 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile (" |
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276 << tileX << "," << tileY << ") at level " << level; |
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277 target.EncodeTile(*empty, level, tileX, tileY); |
| 0 | 278 } |
| 279 } | |
| 280 } | |
| 281 | |
| 282 target.Flush(); | |
| 283 } | |
| 284 } | |
| 285 | |
| 286 | |
| 287 | |
| 288 int main(int argc, char* argv[]) | |
| 289 { | |
| 290 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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291 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 292 |
| 293 int exitStatus = 0; | |
| 294 boost::program_options::variables_map options; | |
| 295 | |
| 296 try | |
| 297 { | |
| 298 if (ParseParameters(exitStatus, options, argc, argv)) | |
| 299 { | |
| 300 Orthanc::WebServiceParameters params; | |
| 301 | |
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302 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options); |
| 0 | 303 |
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304 OrthancPlugins::OrthancHttpConnection orthanc(params); |
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305 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(), |
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306 false /* don't use cached metadata */); |
| 0 | 307 |
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308 OrthancWSI::TiledPyramidStatistics stats(source); |
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309 Run(stats, options); |
| 0 | 310 } |
| 311 } | |
| 312 catch (Orthanc::OrthancException& e) | |
| 313 { | |
| 314 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 315 | |
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316 if (options.count(OPTION_REENCODE) == 0) |
| 0 | 317 { |
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318 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\""; |
| 0 | 319 } |
| 320 | |
| 321 exitStatus = -1; | |
| 322 } | |
| 323 | |
| 324 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 325 | |
| 326 return exitStatus; | |
| 327 } |