Mercurial > hg > orthanc-wsi
annotate Applications/DicomToTiff.cpp @ 89:61e629ce7c94
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 16 Dec 2016 21:13:29 +0100 |
| parents | d529d9ce3c7e |
| children | 14146ecd1688 |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
| 21 #include "../Framework/DicomToolbox.h" | |
| 22 #include "../Framework/ImageToolbox.h" | |
| 23 #include "../Framework/Inputs/DicomPyramid.h" | |
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24 #include "../Framework/Inputs/TiledPyramidStatistics.h" |
| 0 | 25 #include "../Framework/Outputs/HierarchicalTiffWriter.h" |
| 26 | |
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27 #include "../Resources/Orthanc/Core/Logging.h" |
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28 #include "../Resources/Orthanc/Core/OrthancException.h" |
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29 #include "../Resources/Orthanc/Plugins/Samples/Common/OrthancHttpConnection.h" |
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30 |
| 0 | 31 #include "ApplicationToolbox.h" |
| 32 | |
| 33 #include <boost/program_options.hpp> | |
| 34 | |
| 35 | |
| 36 static bool ParseParameters(int& exitStatus, | |
| 37 boost::program_options::variables_map& options, | |
| 38 int argc, | |
| 39 char* argv[]) | |
| 40 { | |
| 41 // Declare the supported parameters | |
| 42 boost::program_options::options_description generic("Generic options"); | |
| 43 generic.add_options() | |
| 44 ("help", "Display this help and exit") | |
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45 ("version", "Output version information and exit") |
| 0 | 46 ("verbose", "Be verbose in logs") |
| 47 ; | |
| 48 | |
| 49 boost::program_options::options_description source("Options for the source DICOM image"); | |
| 50 source.add_options() | |
| 51 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 52 "URL to the REST API of the target Orthanc server") | |
| 53 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
| 54 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
| 55 ; | |
| 56 | |
| 57 boost::program_options::options_description target("Options for the target TIFF image"); | |
| 58 target.add_options() | |
| 59 ("color", boost::program_options::value<std::string>(), "Color of the background for missing tiles (e.g. \"255,0,0\")") | |
| 60 ("reencode", boost::program_options::value<bool>(), | |
| 31 | 61 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
| 0 | 62 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") |
| 63 ; | |
| 64 | |
| 65 boost::program_options::options_description hidden; | |
| 66 hidden.add_options() | |
| 67 ("input", boost::program_options::value<std::string>(), "Orthanc identifier of the input series of interest") | |
| 68 ("output", boost::program_options::value<std::string>(), "Output TIFF file"); | |
| 69 ; | |
| 70 | |
| 71 boost::program_options::options_description allWithoutHidden; | |
| 72 allWithoutHidden.add(generic).add(source).add(target); | |
| 73 | |
| 74 boost::program_options::options_description all = allWithoutHidden; | |
| 75 all.add(hidden); | |
| 76 | |
| 77 boost::program_options::positional_options_description positional; | |
| 78 positional.add("input", 1); | |
| 79 positional.add("output", 1); | |
| 80 | |
| 81 bool error = false; | |
| 82 | |
| 83 try | |
| 84 { | |
| 85 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 86 options(all).positional(positional).run(), options); | |
| 87 boost::program_options::notify(options); | |
| 88 } | |
| 89 catch (boost::program_options::error& e) | |
| 90 { | |
| 91 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 92 error = true; | |
| 93 } | |
| 94 | |
| 95 if (!error && | |
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96 options.count("help") == 0 && |
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97 options.count("version") == 0) |
| 0 | 98 { |
| 99 if (options.count("input") != 1) | |
| 100 { | |
| 101 LOG(ERROR) << "No input series was specified"; | |
| 102 error = true; | |
| 103 } | |
| 104 | |
| 105 if (options.count("output") != 1) | |
| 106 { | |
| 107 LOG(ERROR) << "No output file was specified"; | |
| 108 error = true; | |
| 109 } | |
| 110 } | |
| 111 | |
| 112 if (error || options.count("help")) | |
| 113 { | |
| 114 std::cout << std::endl | |
| 115 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
| 116 << std::endl | |
| 117 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 118 << std::endl << std::endl | |
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119 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl |
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120 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)." |
| 0 | 121 << std::endl; |
| 122 | |
| 123 std::cout << allWithoutHidden << "\n"; | |
| 124 | |
| 125 if (error) | |
| 126 { | |
| 127 exitStatus = -1; | |
| 128 } | |
| 129 | |
| 130 return false; | |
| 131 } | |
| 132 | |
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133 if (options.count("version")) |
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134 { |
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135 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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136 return false; |
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137 } |
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138 |
| 0 | 139 if (options.count("verbose")) |
| 140 { | |
| 141 Orthanc::Logging::EnableInfoLevel(true); | |
| 142 } | |
| 143 | |
| 144 return true; | |
| 145 } | |
| 146 | |
| 147 | |
| 148 | |
| 149 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
| 150 const boost::program_options::variables_map& options) | |
| 151 { | |
| 152 std::auto_ptr<Orthanc::ImageAccessor> tile | |
| 153 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), | |
| 154 writer.GetTileWidth(), | |
| 155 writer.GetTileHeight())); | |
| 156 | |
| 157 uint8_t red = 255; | |
| 158 uint8_t green = 255; | |
| 159 uint8_t blue = 255; | |
| 160 | |
| 161 if (options.count("color")) | |
| 162 { | |
| 163 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options["color"].as<std::string>()); | |
| 164 } | |
| 165 | |
| 166 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
| 167 | |
| 168 return tile.release(); | |
| 169 } | |
| 170 | |
| 171 | |
| 172 | |
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173 static void Run(OrthancWSI::ITiledPyramid& source, |
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174 const boost::program_options::variables_map& options) |
| 0 | 175 { |
| 176 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(), | |
| 177 source.GetPixelFormat(), | |
| 178 OrthancWSI::ImageCompression_Jpeg, | |
| 179 source.GetTileWidth(), | |
| 180 source.GetTileHeight()); | |
| 181 | |
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182 bool reencode = (options.count("reencode") && |
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183 options["reencode"].as<bool>()); |
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184 |
| 0 | 185 if (options.count("jpeg-quality")) |
| 186 { | |
| 187 target.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
| 188 } | |
| 189 | |
| 190 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); | |
| 191 | |
| 192 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 193 { | |
| 194 LOG(WARNING) << "Creating level " << level << " of size " | |
| 195 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
| 196 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
| 197 } | |
| 198 | |
| 199 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 200 { | |
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201 LOG(WARNING) << std::string(reencode ? "Reencoding" : "Transcoding") << " level " << level; |
| 0 | 202 |
| 203 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth()); | |
| 204 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight()); | |
| 205 | |
| 206 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
| 207 { | |
| 208 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
| 209 { | |
| 210 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
| 211 | |
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212 bool missing = false; |
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213 bool success = true; |
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214 |
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215 // Give a first try to get the raw tile |
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216 std::string tile; |
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217 OrthancWSI::ImageCompression compression; |
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218 if (source.ReadRawTile(tile, compression, level, tileX, tileY)) |
| 0 | 219 { |
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220 if (reencode || |
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221 compression == OrthancWSI::ImageCompression_Jpeg) |
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222 { |
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223 target.WriteRawTile(tile, compression, level, tileX, tileY); |
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224 } |
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225 else |
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226 { |
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227 success = false; // Re-encoding is mandatory |
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228 } |
| 0 | 229 } |
| 230 else | |
| 231 { | |
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232 // Give a second try to get the decoded tile |
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233 compression = OrthancWSI::ImageCompression_Unknown; |
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234 |
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235 std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY)); |
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236 if (tile.get() == NULL) |
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237 { |
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238 // Unable to read the raw tile or to decode it: The tile is missing (sparse tiling) |
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239 missing = true; |
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240 } |
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241 else if (reencode) |
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242 { |
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243 target.EncodeTile(*empty, level, tileX, tileY); |
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244 } |
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245 else |
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246 { |
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247 success = false; // Re-encoding is mandatory |
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248 } |
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249 } |
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250 |
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251 if (!success) |
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252 { |
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253 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is " |
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254 << OrthancWSI::EnumerationToString(compression) |
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255 << "), please use the --reencode=1 option"; |
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256 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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257 } |
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258 |
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259 if (missing) |
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260 { |
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261 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile (" |
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262 << tileX << "," << tileY << ") at level " << level; |
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263 target.EncodeTile(*empty, level, tileX, tileY); |
| 0 | 264 } |
| 265 } | |
| 266 } | |
| 267 | |
| 268 target.Flush(); | |
| 269 } | |
| 270 } | |
| 271 | |
| 272 | |
| 273 | |
| 274 int main(int argc, char* argv[]) | |
| 275 { | |
| 276 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
| 277 | |
| 278 int exitStatus = 0; | |
| 279 boost::program_options::variables_map options; | |
| 280 | |
| 281 try | |
| 282 { | |
| 283 if (ParseParameters(exitStatus, options, argc, argv)) | |
| 284 { | |
| 285 Orthanc::WebServiceParameters params; | |
| 286 | |
| 287 if (options.count("orthanc")) | |
| 288 { | |
| 289 params.SetUrl(options["orthanc"].as<std::string>()); | |
| 290 } | |
| 291 | |
| 292 if (options.count("username")) | |
| 293 { | |
| 294 params.SetUsername(options["username"].as<std::string>()); | |
| 295 } | |
| 296 | |
| 297 if (options.count("password")) | |
| 298 { | |
| 299 params.SetPassword(options["password"].as<std::string>()); | |
| 300 } | |
| 301 | |
|
61
147bd6dc28db
refactoring using new items in the plugin toolbox of Orthanc
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parents:
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changeset
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302 OrthancPlugins::OrthancHttpConnection orthanc(params); |
|
69
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cache for DicomPyramidInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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303 OrthancWSI::DicomPyramid source(orthanc, options["input"].as<std::string>(), |
|
d529d9ce3c7e
cache for DicomPyramidInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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304 false /* don't use cached metadata */); |
| 0 | 305 |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
31
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changeset
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306 OrthancWSI::TiledPyramidStatistics stats(source); |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
307 Run(stats, options); |
| 0 | 308 } |
| 309 } | |
| 310 catch (Orthanc::OrthancException& e) | |
| 311 { | |
| 312 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 313 | |
| 314 if (options.count("reencode") == 0) | |
| 315 { | |
| 316 LOG(ERROR) << "Consider using option \"--reencode\""; | |
| 317 } | |
| 318 | |
| 319 exitStatus = -1; | |
| 320 } | |
| 321 | |
| 322 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 323 | |
| 324 return exitStatus; | |
| 325 } |