Mercurial > hg > orthanc-wsi
annotate Applications/DicomToTiff.cpp @ 43:9621fd6f17c9
sync
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 09 Nov 2016 17:34:20 +0100 |
| parents | 8e1dfd531335 |
| children | 91fc9583b2de |
| 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" | |
| 24 #include "../Framework/Messaging/CurlOrthancConnection.h" | |
| 25 #include "../Framework/Orthanc/Core/Logging.h" | |
| 26 #include "../Framework/Orthanc/Core/OrthancException.h" | |
| 27 #include "../Framework/Outputs/HierarchicalTiffWriter.h" | |
| 28 | |
| 29 #include "ApplicationToolbox.h" | |
| 30 | |
| 31 #include <boost/program_options.hpp> | |
| 32 | |
| 33 | |
| 34 static bool ParseParameters(int& exitStatus, | |
| 35 boost::program_options::variables_map& options, | |
| 36 int argc, | |
| 37 char* argv[]) | |
| 38 { | |
| 39 // Declare the supported parameters | |
| 40 boost::program_options::options_description generic("Generic options"); | |
| 41 generic.add_options() | |
| 42 ("help", "Display this help and exit") | |
|
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43 ("version", "Output version information and exit") |
| 0 | 44 ("verbose", "Be verbose in logs") |
| 45 ; | |
| 46 | |
| 47 boost::program_options::options_description source("Options for the source DICOM image"); | |
| 48 source.add_options() | |
| 49 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 50 "URL to the REST API of the target Orthanc server") | |
| 51 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
| 52 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
| 53 ; | |
| 54 | |
| 55 boost::program_options::options_description target("Options for the target TIFF image"); | |
| 56 target.add_options() | |
| 57 ("color", boost::program_options::value<std::string>(), "Color of the background for missing tiles (e.g. \"255,0,0\")") | |
| 58 ("reencode", boost::program_options::value<bool>(), | |
| 31 | 59 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
| 0 | 60 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") |
| 61 ; | |
| 62 | |
| 63 boost::program_options::options_description hidden; | |
| 64 hidden.add_options() | |
| 65 ("input", boost::program_options::value<std::string>(), "Orthanc identifier of the input series of interest") | |
| 66 ("output", boost::program_options::value<std::string>(), "Output TIFF file"); | |
| 67 ; | |
| 68 | |
| 69 boost::program_options::options_description allWithoutHidden; | |
| 70 allWithoutHidden.add(generic).add(source).add(target); | |
| 71 | |
| 72 boost::program_options::options_description all = allWithoutHidden; | |
| 73 all.add(hidden); | |
| 74 | |
| 75 boost::program_options::positional_options_description positional; | |
| 76 positional.add("input", 1); | |
| 77 positional.add("output", 1); | |
| 78 | |
| 79 bool error = false; | |
| 80 | |
| 81 try | |
| 82 { | |
| 83 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 84 options(all).positional(positional).run(), options); | |
| 85 boost::program_options::notify(options); | |
| 86 } | |
| 87 catch (boost::program_options::error& e) | |
| 88 { | |
| 89 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 90 error = true; | |
| 91 } | |
| 92 | |
| 93 if (!error && | |
|
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parents:
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diff
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94 options.count("help") == 0 && |
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parents:
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diff
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95 options.count("version") == 0) |
| 0 | 96 { |
| 97 if (options.count("input") != 1) | |
| 98 { | |
| 99 LOG(ERROR) << "No input series was specified"; | |
| 100 error = true; | |
| 101 } | |
| 102 | |
| 103 if (options.count("output") != 1) | |
| 104 { | |
| 105 LOG(ERROR) << "No output file was specified"; | |
| 106 error = true; | |
| 107 } | |
| 108 } | |
| 109 | |
| 110 if (error || options.count("help")) | |
| 111 { | |
| 112 std::cout << std::endl | |
| 113 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
| 114 << std::endl | |
| 115 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 116 << std::endl << std::endl | |
| 117 << "Convert a DICOM for digital pathology stored in some Orthanc server as a standard hierarchical TIFF." | |
| 118 << std::endl; | |
| 119 | |
| 120 std::cout << allWithoutHidden << "\n"; | |
| 121 | |
| 122 if (error) | |
| 123 { | |
| 124 exitStatus = -1; | |
| 125 } | |
| 126 | |
| 127 return false; | |
| 128 } | |
| 129 | |
|
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62adabb8c122
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parents:
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diff
changeset
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130 if (options.count("version")) |
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62adabb8c122
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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131 { |
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62adabb8c122
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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132 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
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133 return false; |
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62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
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134 } |
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62adabb8c122
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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135 |
| 0 | 136 if (options.count("verbose")) |
| 137 { | |
| 138 Orthanc::Logging::EnableInfoLevel(true); | |
| 139 } | |
| 140 | |
| 141 return true; | |
| 142 } | |
| 143 | |
| 144 | |
| 145 | |
| 146 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
| 147 const boost::program_options::variables_map& options) | |
| 148 { | |
| 149 std::auto_ptr<Orthanc::ImageAccessor> tile | |
| 150 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), | |
| 151 writer.GetTileWidth(), | |
| 152 writer.GetTileHeight())); | |
| 153 | |
| 154 uint8_t red = 255; | |
| 155 uint8_t green = 255; | |
| 156 uint8_t blue = 255; | |
| 157 | |
| 158 if (options.count("color")) | |
| 159 { | |
| 160 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options["color"].as<std::string>()); | |
| 161 } | |
| 162 | |
| 163 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
| 164 | |
| 165 return tile.release(); | |
| 166 } | |
| 167 | |
| 168 | |
| 169 | |
| 170 static void RunTranscode(OrthancWSI::ITiledPyramid& source, | |
| 171 const boost::program_options::variables_map& options) | |
| 172 { | |
| 173 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(), | |
| 174 source.GetPixelFormat(), | |
| 175 source.GetImageCompression(), | |
| 176 source.GetTileWidth(), | |
| 177 source.GetTileHeight()); | |
| 178 | |
| 179 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); | |
| 180 | |
| 181 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 182 { | |
| 183 LOG(WARNING) << "Creating level " << level << " of size " | |
| 184 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
| 185 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
| 186 } | |
| 187 | |
| 188 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 189 { | |
| 190 LOG(WARNING) << "Transcoding level " << level; | |
| 191 | |
| 192 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth()); | |
| 193 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight()); | |
| 194 | |
| 195 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
| 196 { | |
| 197 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
| 198 { | |
| 199 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
| 200 std::string tile; | |
| 201 | |
| 202 if (source.ReadRawTile(tile, level, tileX, tileY)) | |
| 203 { | |
| 204 target.WriteRawTile(tile, source.GetImageCompression(), level, tileX, tileY); | |
| 205 } | |
| 206 else | |
| 207 { | |
| 208 target.EncodeTile(*empty, level, tileX, tileY); | |
| 209 } | |
| 210 } | |
| 211 } | |
| 212 | |
| 213 target.Flush(); | |
| 214 } | |
| 215 } | |
| 216 | |
| 217 | |
| 218 static void RunReencode(OrthancWSI::ITiledPyramid& source, | |
| 219 const boost::program_options::variables_map& options) | |
| 220 { | |
| 221 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(), | |
| 222 source.GetPixelFormat(), | |
| 223 OrthancWSI::ImageCompression_Jpeg, | |
| 224 source.GetTileWidth(), | |
| 225 source.GetTileHeight()); | |
| 226 | |
| 227 if (options.count("jpeg-quality")) | |
| 228 { | |
| 229 target.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
| 230 } | |
| 231 | |
| 232 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); | |
| 233 | |
| 234 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 235 { | |
| 236 LOG(WARNING) << "Creating level " << level << " of size " | |
| 237 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
| 238 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
| 239 } | |
| 240 | |
| 241 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
| 242 { | |
| 243 LOG(WARNING) << "Reencoding level " << level; | |
| 244 | |
| 245 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth()); | |
| 246 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight()); | |
| 247 | |
| 248 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
| 249 { | |
| 250 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
| 251 { | |
| 252 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
| 253 | |
| 254 std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY)); | |
| 255 if (tile.get() == NULL) | |
| 256 { | |
| 257 target.EncodeTile(*empty, level, tileX, tileY); | |
| 258 } | |
| 259 else | |
| 260 { | |
| 261 target.EncodeTile(*tile, level, tileX, tileY); | |
| 262 } | |
| 263 } | |
| 264 } | |
| 265 | |
| 266 target.Flush(); | |
| 267 } | |
| 268 } | |
| 269 | |
| 270 | |
| 271 | |
| 272 int main(int argc, char* argv[]) | |
| 273 { | |
| 274 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
| 275 | |
| 276 int exitStatus = 0; | |
| 277 boost::program_options::variables_map options; | |
| 278 | |
| 279 try | |
| 280 { | |
| 281 if (ParseParameters(exitStatus, options, argc, argv)) | |
| 282 { | |
| 283 Orthanc::WebServiceParameters params; | |
| 284 | |
| 285 if (options.count("orthanc")) | |
| 286 { | |
| 287 params.SetUrl(options["orthanc"].as<std::string>()); | |
| 288 } | |
| 289 | |
| 290 if (options.count("username")) | |
| 291 { | |
| 292 params.SetUsername(options["username"].as<std::string>()); | |
| 293 } | |
| 294 | |
| 295 if (options.count("password")) | |
| 296 { | |
| 297 params.SetPassword(options["password"].as<std::string>()); | |
| 298 } | |
| 299 | |
| 300 OrthancWSI::CurlOrthancConnection orthanc(params); | |
| 301 OrthancWSI::DicomPyramid source(orthanc, options["input"].as<std::string>()); | |
| 302 | |
| 303 if (options.count("reencode") && | |
| 304 options["reencode"].as<bool>()) | |
| 305 { | |
| 306 RunReencode(source, options); | |
| 307 } | |
| 308 else | |
| 309 { | |
| 310 RunTranscode(source, options); | |
| 311 } | |
| 312 } | |
| 313 } | |
| 314 catch (Orthanc::OrthancException& e) | |
| 315 { | |
| 316 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 317 | |
| 318 if (options.count("reencode") == 0) | |
| 319 { | |
| 320 LOG(ERROR) << "Consider using option \"--reencode\""; | |
| 321 } | |
| 322 | |
| 323 exitStatus = -1; | |
| 324 } | |
| 325 | |
| 326 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 327 | |
| 328 return exitStatus; | |
| 329 } |