Mercurial > hg > orthanc-wsi
annotate Applications/DicomToTiff.cpp @ 123:e8fe7c9a7d6c
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 05 Jan 2018 10:15:08 +0100 |
| parents | a51dee6a1515 |
| children | 7a3f4d580625 |
| 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 #include <boost/program_options.hpp> | |
| 35 | |
| 36 | |
| 37 static bool ParseParameters(int& exitStatus, | |
| 38 boost::program_options::variables_map& options, | |
| 39 int argc, | |
| 40 char* argv[]) | |
| 41 { | |
| 42 // Declare the supported parameters | |
| 43 boost::program_options::options_description generic("Generic options"); | |
| 44 generic.add_options() | |
| 45 ("help", "Display this help and exit") | |
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46 ("version", "Output version information and exit") |
| 0 | 47 ("verbose", "Be verbose in logs") |
| 48 ; | |
| 49 | |
| 50 boost::program_options::options_description source("Options for the source DICOM image"); | |
| 51 source.add_options() | |
| 52 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 53 "URL to the REST API of the target Orthanc server") | |
| 54 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
| 55 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
| 56 ; | |
| 57 | |
| 58 boost::program_options::options_description target("Options for the target TIFF image"); | |
| 59 target.add_options() | |
| 60 ("color", boost::program_options::value<std::string>(), "Color of the background for missing tiles (e.g. \"255,0,0\")") | |
| 61 ("reencode", boost::program_options::value<bool>(), | |
| 31 | 62 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
| 0 | 63 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") |
| 64 ; | |
| 65 | |
| 66 boost::program_options::options_description hidden; | |
| 67 hidden.add_options() | |
| 68 ("input", boost::program_options::value<std::string>(), "Orthanc identifier of the input series of interest") | |
| 69 ("output", boost::program_options::value<std::string>(), "Output TIFF file"); | |
| 70 ; | |
| 71 | |
| 72 boost::program_options::options_description allWithoutHidden; | |
| 73 allWithoutHidden.add(generic).add(source).add(target); | |
| 74 | |
| 75 boost::program_options::options_description all = allWithoutHidden; | |
| 76 all.add(hidden); | |
| 77 | |
| 78 boost::program_options::positional_options_description positional; | |
| 79 positional.add("input", 1); | |
| 80 positional.add("output", 1); | |
| 81 | |
| 82 bool error = false; | |
| 83 | |
| 84 try | |
| 85 { | |
| 86 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 87 options(all).positional(positional).run(), options); | |
| 88 boost::program_options::notify(options); | |
| 89 } | |
| 90 catch (boost::program_options::error& e) | |
| 91 { | |
| 92 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 93 error = true; | |
| 94 } | |
| 95 | |
| 96 if (!error && | |
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97 options.count("help") == 0 && |
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98 options.count("version") == 0) |
| 0 | 99 { |
| 100 if (options.count("input") != 1) | |
| 101 { | |
| 102 LOG(ERROR) << "No input series was specified"; | |
| 103 error = true; | |
| 104 } | |
| 105 | |
| 106 if (options.count("output") != 1) | |
| 107 { | |
| 108 LOG(ERROR) << "No output file was specified"; | |
| 109 error = true; | |
| 110 } | |
| 111 } | |
| 112 | |
| 113 if (error || options.count("help")) | |
| 114 { | |
| 115 std::cout << std::endl | |
| 116 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
| 117 << std::endl | |
| 118 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 119 << std::endl << std::endl | |
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120 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl |
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121 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)." |
| 0 | 122 << std::endl; |
| 123 | |
| 124 std::cout << allWithoutHidden << "\n"; | |
| 125 | |
| 126 if (error) | |
| 127 { | |
| 128 exitStatus = -1; | |
| 129 } | |
| 130 | |
| 131 return false; | |
| 132 } | |
| 133 | |
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134 if (options.count("version")) |
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135 { |
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136 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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137 return false; |
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138 } |
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139 |
| 0 | 140 if (options.count("verbose")) |
| 141 { | |
| 142 Orthanc::Logging::EnableInfoLevel(true); | |
| 143 } | |
| 144 | |
| 145 return true; | |
| 146 } | |
| 147 | |
| 148 | |
| 149 | |
| 150 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
| 151 const boost::program_options::variables_map& options) | |
| 152 { | |
| 153 std::auto_ptr<Orthanc::ImageAccessor> tile | |
| 154 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), | |
| 155 writer.GetTileWidth(), | |
| 156 writer.GetTileHeight())); | |
| 157 | |
| 158 uint8_t red = 255; | |
| 159 uint8_t green = 255; | |
| 160 uint8_t blue = 255; | |
| 161 | |
| 162 if (options.count("color")) | |
| 163 { | |
| 164 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options["color"].as<std::string>()); | |
| 165 } | |
| 166 | |
| 167 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
| 168 | |
| 169 return tile.release(); | |
| 170 } | |
| 171 | |
| 172 | |
| 173 | |
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174 static void Run(OrthancWSI::ITiledPyramid& source, |
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175 const boost::program_options::variables_map& options) |
| 0 | 176 { |
| 177 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(), | |
| 178 source.GetPixelFormat(), | |
| 179 OrthancWSI::ImageCompression_Jpeg, | |
| 180 source.GetTileWidth(), | |
| 181 source.GetTileHeight()); | |
| 182 | |
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183 bool reencode = (options.count("reencode") && |
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184 options["reencode"].as<bool>()); |
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185 |
| 0 | 186 if (options.count("jpeg-quality")) |
| 187 { | |
| 188 target.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
| 189 } | |
| 190 | |
| 191 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); | |
| 192 | |
| 193 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 194 { | |
| 195 LOG(WARNING) << "Creating level " << level << " of size " | |
| 196 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
| 197 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
| 198 } | |
| 199 | |
| 200 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 201 { | |
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202 LOG(WARNING) << std::string(reencode ? "Reencoding" : "Transcoding") << " level " << level; |
| 0 | 203 |
| 204 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth()); | |
| 205 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight()); | |
| 206 | |
| 207 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
| 208 { | |
| 209 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
| 210 { | |
| 211 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
| 212 | |
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213 bool missing = false; |
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214 bool success = true; |
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215 |
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216 // Give a first try to get the raw tile |
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217 std::string tile; |
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218 OrthancWSI::ImageCompression compression; |
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219 if (source.ReadRawTile(tile, compression, level, tileX, tileY)) |
| 0 | 220 { |
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221 if (reencode || |
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222 compression == OrthancWSI::ImageCompression_Jpeg) |
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223 { |
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224 target.WriteRawTile(tile, compression, level, tileX, tileY); |
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225 } |
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226 else |
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227 { |
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228 success = false; // Re-encoding is mandatory |
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229 } |
| 0 | 230 } |
| 231 else | |
| 232 { | |
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233 // Give a second try to get the decoded tile |
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234 compression = OrthancWSI::ImageCompression_Unknown; |
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235 |
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236 std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY)); |
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237 if (tile.get() == NULL) |
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238 { |
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239 // Unable to read the raw tile or to decode it: The tile is missing (sparse tiling) |
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240 missing = true; |
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241 } |
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242 else if (reencode) |
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243 { |
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244 target.EncodeTile(*empty, level, tileX, tileY); |
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245 } |
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246 else |
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247 { |
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248 success = false; // Re-encoding is mandatory |
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249 } |
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250 } |
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251 |
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252 if (!success) |
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253 { |
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254 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is " |
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255 << OrthancWSI::EnumerationToString(compression) |
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256 << "), please use the --reencode=1 option"; |
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257 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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258 } |
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259 |
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260 if (missing) |
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261 { |
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262 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile (" |
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263 << tileX << "," << tileY << ") at level " << level; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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264 target.EncodeTile(*empty, level, tileX, tileY); |
| 0 | 265 } |
| 266 } | |
| 267 } | |
| 268 | |
| 269 target.Flush(); | |
| 270 } | |
| 271 } | |
| 272 | |
| 273 | |
| 274 | |
| 275 int main(int argc, char* argv[]) | |
| 276 { | |
| 277 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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14146ecd1688
Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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278 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 279 |
| 280 int exitStatus = 0; | |
| 281 boost::program_options::variables_map options; | |
| 282 | |
| 283 try | |
| 284 { | |
| 285 if (ParseParameters(exitStatus, options, argc, argv)) | |
| 286 { | |
| 287 Orthanc::WebServiceParameters params; | |
| 288 | |
| 289 if (options.count("orthanc")) | |
| 290 { | |
| 291 params.SetUrl(options["orthanc"].as<std::string>()); | |
| 292 } | |
| 293 | |
| 294 if (options.count("username")) | |
| 295 { | |
| 296 params.SetUsername(options["username"].as<std::string>()); | |
| 297 } | |
| 298 | |
| 299 if (options.count("password")) | |
| 300 { | |
| 301 params.SetPassword(options["password"].as<std::string>()); | |
| 302 } | |
| 303 | |
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61
147bd6dc28db
refactoring using new items in the plugin toolbox of Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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304 OrthancPlugins::OrthancHttpConnection orthanc(params); |
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d529d9ce3c7e
cache for DicomPyramidInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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305 OrthancWSI::DicomPyramid source(orthanc, options["input"].as<std::string>(), |
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d529d9ce3c7e
cache for DicomPyramidInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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306 false /* don't use cached metadata */); |
| 0 | 307 |
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91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
31
diff
changeset
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308 OrthancWSI::TiledPyramidStatistics stats(source); |
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91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
31
diff
changeset
|
309 Run(stats, options); |
| 0 | 310 } |
| 311 } | |
| 312 catch (Orthanc::OrthancException& e) | |
| 313 { | |
| 314 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 315 | |
| 316 if (options.count("reencode") == 0) | |
| 317 { | |
| 318 LOG(ERROR) << "Consider using option \"--reencode\""; | |
| 319 } | |
| 320 | |
| 321 exitStatus = -1; | |
| 322 } | |
| 323 | |
| 324 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 325 | |
| 326 return exitStatus; | |
| 327 } |