Mercurial > hg > orthanc-wsi
annotate Applications/DicomToTiff.cpp @ 254:20a730889ae2
upgrade to 2023
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 07 Jul 2023 17:38:07 +0200 |
parents | 49f647ed1b4c |
children | 7020852a8fa9 |
rev | line source |
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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 | |
254 | 5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium | |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU Affero General Public License | |
10 * as published by the Free Software Foundation, either version 3 of | |
11 * the License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * Affero General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU Affero General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
23 #include "../Framework/DicomToolbox.h" | |
24 #include "../Framework/ImageToolbox.h" | |
25 #include "../Framework/Inputs/DicomPyramid.h" | |
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26 #include "../Framework/Inputs/TiledPyramidStatistics.h" |
0 | 27 #include "../Framework/Outputs/HierarchicalTiffWriter.h" |
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28 #include "../Resources/Orthanc/Stone/OrthancHttpConnection.h" |
0 | 29 |
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30 #include <Compatibility.h> // For std::unique_ptr |
192 | 31 #include <Logging.h> |
32 #include <OrthancException.h> | |
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33 |
0 | 34 #include "ApplicationToolbox.h" |
35 | |
36 | |
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37 static const char* OPTION_COLOR = "color"; |
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38 static const char* OPTION_HELP = "help"; |
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39 static const char* OPTION_INPUT = "input"; |
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40 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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41 static const char* OPTION_OUTPUT = "output"; |
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42 static const char* OPTION_REENCODE = "reencode"; |
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43 static const char* OPTION_VERBOSE = "verbose"; |
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44 static const char* OPTION_VERSION = "version"; |
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45 |
0 | 46 static bool ParseParameters(int& exitStatus, |
47 boost::program_options::variables_map& options, | |
48 int argc, | |
49 char* argv[]) | |
50 { | |
51 // Declare the supported parameters | |
52 boost::program_options::options_description generic("Generic options"); | |
53 generic.add_options() | |
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54 (OPTION_HELP, "Display this help and exit") |
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55 (OPTION_VERSION, "Output version information and exit") |
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56 (OPTION_VERBOSE, "Be verbose in logs") |
0 | 57 ; |
58 | |
59 boost::program_options::options_description source("Options for the source DICOM image"); | |
60 source.add_options() | |
61 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
62 "URL to the REST API of the target Orthanc server") | |
63 ; | |
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64 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source); |
0 | 65 |
66 boost::program_options::options_description target("Options for the target TIFF image"); | |
67 target.add_options() | |
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68 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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69 "Color of the background for missing tiles (e.g. \"255,0,0\")") |
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70 (OPTION_REENCODE, boost::program_options::value<bool>(), |
31 | 71 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
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72 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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73 "Set quality level for JPEG (0..100)") |
0 | 74 ; |
75 | |
76 boost::program_options::options_description hidden; | |
77 hidden.add_options() | |
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78 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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79 "Orthanc identifier of the input series of interest") |
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80 (OPTION_OUTPUT, boost::program_options::value<std::string>(), |
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81 "Output TIFF file"); |
0 | 82 |
83 boost::program_options::options_description allWithoutHidden; | |
84 allWithoutHidden.add(generic).add(source).add(target); | |
85 | |
86 boost::program_options::options_description all = allWithoutHidden; | |
87 all.add(hidden); | |
88 | |
89 boost::program_options::positional_options_description positional; | |
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90 positional.add(OPTION_INPUT, 1); |
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91 positional.add(OPTION_OUTPUT, 1); |
0 | 92 |
93 bool error = false; | |
94 | |
95 try | |
96 { | |
97 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
98 options(all).positional(positional).run(), options); | |
99 boost::program_options::notify(options); | |
100 } | |
101 catch (boost::program_options::error& e) | |
102 { | |
103 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
104 error = true; | |
105 } | |
106 | |
107 if (!error && | |
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108 options.count(OPTION_HELP) == 0 && |
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109 options.count(OPTION_VERSION) == 0) |
0 | 110 { |
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111 if (options.count(OPTION_INPUT) != 1) |
0 | 112 { |
113 LOG(ERROR) << "No input series was specified"; | |
114 error = true; | |
115 } | |
116 | |
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117 if (options.count(OPTION_OUTPUT) != 1) |
0 | 118 { |
119 LOG(ERROR) << "No output file was specified"; | |
120 error = true; | |
121 } | |
122 } | |
123 | |
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124 if (error || options.count(OPTION_HELP)) |
0 | 125 { |
126 std::cout << std::endl | |
127 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
128 << std::endl | |
129 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
130 << std::endl << std::endl | |
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131 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl |
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132 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)." |
0 | 133 << std::endl; |
134 | |
135 std::cout << allWithoutHidden << "\n"; | |
136 | |
137 if (error) | |
138 { | |
139 exitStatus = -1; | |
140 } | |
141 | |
142 return false; | |
143 } | |
144 | |
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145 if (options.count(OPTION_VERSION)) |
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146 { |
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147 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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148 return false; |
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149 } |
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150 |
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151 if (options.count(OPTION_VERBOSE)) |
0 | 152 { |
153 Orthanc::Logging::EnableInfoLevel(true); | |
154 } | |
155 | |
156 return true; | |
157 } | |
158 | |
159 | |
160 | |
161 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
162 const boost::program_options::variables_map& options) | |
163 { | |
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164 std::unique_ptr<Orthanc::ImageAccessor> tile |
0 | 165 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), |
166 writer.GetTileWidth(), | |
167 writer.GetTileHeight())); | |
168 | |
169 uint8_t red = 255; | |
170 uint8_t green = 255; | |
171 uint8_t blue = 255; | |
172 | |
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173 if (options.count(OPTION_COLOR)) |
0 | 174 { |
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175 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>()); |
0 | 176 } |
177 | |
178 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
179 | |
180 return tile.release(); | |
181 } | |
182 | |
183 | |
184 | |
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185 static void Run(OrthancWSI::ITiledPyramid& source, |
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186 const boost::program_options::variables_map& options) |
0 | 187 { |
167
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188 bool reencode = (options.count(OPTION_REENCODE) && |
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189 options[OPTION_REENCODE].as<bool>()); |
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190 |
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191 Orthanc::PhotometricInterpretation targetPhotometric; |
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192 |
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193 if (reencode) |
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194 { |
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195 // The DicomToTiff tool only creates TIFF images with JPEG tiles (*) |
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196 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; |
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197 } |
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198 else |
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199 { |
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200 targetPhotometric = source.GetPhotometricInterpretation(); |
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201 } |
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202 |
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203 OrthancWSI::ImageToolbox::CheckConstantTileSize(source); // (**) |
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204 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(), |
0 | 205 source.GetPixelFormat(), |
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206 OrthancWSI::ImageCompression_Jpeg, // (*) |
217
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207 source.GetTileWidth(0), // (**) |
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208 source.GetTileHeight(0), // (**) |
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209 targetPhotometric); |
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210 |
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211 if (options.count(OPTION_JPEG_QUALITY)) |
0 | 212 { |
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213 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
0 | 214 } |
215 | |
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216 LOG(WARNING) << "Source photometric interpretation: " << EnumerationToString(source.GetPhotometricInterpretation()); |
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217 LOG(WARNING) << "Target photometric interpretation: " << EnumerationToString(targetPhotometric); |
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218 |
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219 std::unique_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); |
0 | 220 |
221 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
222 { | |
223 LOG(WARNING) << "Creating level " << level << " of size " | |
224 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
225 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
226 } | |
227 | |
228 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
229 { | |
163 | 230 LOG(WARNING) << std::string(reencode ? "Re-encoding" : "Transcoding") |
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231 << " level " << level; |
0 | 232 |
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233 unsigned int countX = OrthancWSI::CeilingDivision |
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234 (source.GetLevelWidth(level), source.GetTileWidth(level)); |
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235 |
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236 unsigned int countY = OrthancWSI::CeilingDivision |
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237 (source.GetLevelHeight(level), source.GetTileHeight(level)); |
0 | 238 |
239 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
240 { | |
241 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
242 { | |
243 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
244 | |
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245 bool missing = false; |
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246 bool success = true; |
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247 |
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248 std::string tile; |
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249 OrthancWSI::ImageCompression compression; |
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250 |
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251 if (source.ReadRawTile(tile, compression, level, tileX, tileY)) |
0 | 252 { |
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253 if (compression == OrthancWSI::ImageCompression_Jpeg) |
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254 { |
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255 // Transcoding of JPEG tiles |
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256 target.WriteRawTile(tile, compression, level, tileX, tileY); |
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257 } |
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258 else if (reencode) |
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259 { |
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260 std::unique_ptr<Orthanc::ImageAccessor> decoded; |
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261 |
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262 if (compression == OrthancWSI::ImageCompression_None) |
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263 { |
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264 decoded.reset(OrthancWSI::ImageToolbox::DecodeRawTile( |
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265 tile, source.GetPixelFormat(), |
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266 source.GetTileWidth(level), source.GetTileHeight(level))); |
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267 } |
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268 else |
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269 { |
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270 decoded.reset(OrthancWSI::ImageToolbox::DecodeTile(tile, compression)); |
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271 } |
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272 |
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273 target.EncodeTile(*decoded, level, tileX, tileY); |
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274 } |
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275 else |
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276 { |
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277 success = false; // Re-encoding is mandatory |
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278 } |
0 | 279 } |
280 else | |
281 { | |
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282 // Unable to read the raw tile: The tile is missing (sparse tiling) |
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283 missing = true; |
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284 } |
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285 |
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286 if (!success) |
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287 { |
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288 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is " |
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289 << OrthancWSI::EnumerationToString(compression) |
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290 << "), please use the --" << OPTION_REENCODE << "=1 option"; |
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291 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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292 } |
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293 |
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294 if (missing) |
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295 { |
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296 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile (" |
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297 << tileX << "," << tileY << ") at level " << level; |
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298 target.EncodeTile(*empty, level, tileX, tileY); |
0 | 299 } |
300 } | |
301 } | |
302 | |
303 target.Flush(); | |
304 } | |
305 } | |
306 | |
307 | |
308 | |
309 int main(int argc, char* argv[]) | |
310 { | |
311 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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312 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
0 | 313 |
314 int exitStatus = 0; | |
315 boost::program_options::variables_map options; | |
316 | |
317 try | |
318 { | |
319 if (ParseParameters(exitStatus, options, argc, argv)) | |
320 { | |
321 Orthanc::WebServiceParameters params; | |
322 | |
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323 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options); |
0 | 324 |
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325 OrthancStone::OrthancHttpConnection orthanc(params); |
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326 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(), |
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327 false /* don't use cached metadata */); |
0 | 328 |
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329 OrthancWSI::TiledPyramidStatistics stats(source); |
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330 Run(stats, options); |
0 | 331 } |
332 } | |
333 catch (Orthanc::OrthancException& e) | |
334 { | |
335 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
336 | |
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337 if (options.count(OPTION_REENCODE) == 0) |
0 | 338 { |
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339 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\""; |
0 | 340 } |
341 | |
342 exitStatus = -1; | |
343 } | |
344 | |
345 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
346 | |
347 return exitStatus; | |
348 } |