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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 18 Oct 2024 15:44:18 +0200 |
parents | 0683312e21ba |
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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 | |
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
10 * modify it under the terms of the GNU Affero General Public License | |
11 * as published by the Free Software Foundation, either version 3 of | |
12 * the License, or (at your option) any later version. | |
13 * | |
14 * This program is distributed in the hope that it will be useful, but | |
15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
17 * Affero General Public License for more details. | |
18 * | |
19 * You should have received a copy of the GNU Affero General Public License | |
20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
21 **/ | |
22 | |
23 | |
24 #include "../Framework/DicomToolbox.h" | |
25 #include "../Framework/ImageToolbox.h" | |
26 #include "../Framework/Inputs/DicomPyramid.h" | |
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27 #include "../Framework/Inputs/TiledPyramidStatistics.h" |
0 | 28 #include "../Framework/Outputs/HierarchicalTiffWriter.h" |
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29 #include "../Resources/Orthanc/Stone/OrthancHttpConnection.h" |
0 | 30 |
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31 #include <Compatibility.h> // For std::unique_ptr |
192 | 32 #include <Logging.h> |
33 #include <OrthancException.h> | |
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34 |
0 | 35 #include "ApplicationToolbox.h" |
36 | |
37 | |
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38 static const char* OPTION_COLOR = "color"; |
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39 static const char* OPTION_HELP = "help"; |
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40 static const char* OPTION_INPUT = "input"; |
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41 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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42 static const char* OPTION_OUTPUT = "output"; |
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43 static const char* OPTION_REENCODE = "reencode"; |
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44 static const char* OPTION_VERBOSE = "verbose"; |
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45 static const char* OPTION_VERSION = "version"; |
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46 |
0 | 47 static bool ParseParameters(int& exitStatus, |
48 boost::program_options::variables_map& options, | |
49 int argc, | |
50 char* argv[]) | |
51 { | |
52 // Declare the supported parameters | |
53 boost::program_options::options_description generic("Generic options"); | |
54 generic.add_options() | |
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55 (OPTION_HELP, "Display this help and exit") |
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56 (OPTION_VERSION, "Output version information and exit") |
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57 (OPTION_VERBOSE, "Be verbose in logs") |
0 | 58 ; |
59 | |
60 boost::program_options::options_description source("Options for the source DICOM image"); | |
61 source.add_options() | |
62 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
63 "URL to the REST API of the target Orthanc server") | |
64 ; | |
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65 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source); |
0 | 66 |
67 boost::program_options::options_description target("Options for the target TIFF image"); | |
68 target.add_options() | |
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69 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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70 "Color of the background for missing tiles (e.g. \"255,0,0\")") |
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71 (OPTION_REENCODE, boost::program_options::value<bool>(), |
31 | 72 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)") |
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73 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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74 "Set quality level for JPEG (0..100)") |
0 | 75 ; |
76 | |
77 boost::program_options::options_description hidden; | |
78 hidden.add_options() | |
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79 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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80 "Orthanc identifier of the input series of interest") |
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81 (OPTION_OUTPUT, boost::program_options::value<std::string>(), |
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82 "Output TIFF file"); |
0 | 83 |
84 boost::program_options::options_description allWithoutHidden; | |
85 allWithoutHidden.add(generic).add(source).add(target); | |
86 | |
87 boost::program_options::options_description all = allWithoutHidden; | |
88 all.add(hidden); | |
89 | |
90 boost::program_options::positional_options_description positional; | |
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91 positional.add(OPTION_INPUT, 1); |
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92 positional.add(OPTION_OUTPUT, 1); |
0 | 93 |
94 bool error = false; | |
95 | |
96 try | |
97 { | |
98 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
99 options(all).positional(positional).run(), options); | |
100 boost::program_options::notify(options); | |
101 } | |
102 catch (boost::program_options::error& e) | |
103 { | |
104 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
105 error = true; | |
106 } | |
107 | |
108 if (!error && | |
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109 options.count(OPTION_HELP) == 0 && |
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110 options.count(OPTION_VERSION) == 0) |
0 | 111 { |
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112 if (options.count(OPTION_INPUT) != 1) |
0 | 113 { |
114 LOG(ERROR) << "No input series was specified"; | |
115 error = true; | |
116 } | |
117 | |
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118 if (options.count(OPTION_OUTPUT) != 1) |
0 | 119 { |
120 LOG(ERROR) << "No output file was specified"; | |
121 error = true; | |
122 } | |
123 } | |
124 | |
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125 if (error || options.count(OPTION_HELP)) |
0 | 126 { |
127 std::cout << std::endl | |
128 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]" | |
129 << std::endl | |
130 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
131 << std::endl << std::endl | |
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132 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl |
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133 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)." |
0 | 134 << std::endl; |
135 | |
136 std::cout << allWithoutHidden << "\n"; | |
137 | |
138 if (error) | |
139 { | |
140 exitStatus = -1; | |
141 } | |
142 | |
143 return false; | |
144 } | |
145 | |
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146 if (options.count(OPTION_VERSION)) |
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147 { |
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148 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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149 return false; |
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150 } |
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151 |
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152 if (options.count(OPTION_VERBOSE)) |
0 | 153 { |
154 Orthanc::Logging::EnableInfoLevel(true); | |
155 } | |
156 | |
157 return true; | |
158 } | |
159 | |
160 | |
161 | |
162 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer, | |
163 const boost::program_options::variables_map& options) | |
164 { | |
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165 std::unique_ptr<Orthanc::ImageAccessor> tile |
0 | 166 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), |
167 writer.GetTileWidth(), | |
168 writer.GetTileHeight())); | |
169 | |
170 uint8_t red = 255; | |
171 uint8_t green = 255; | |
172 uint8_t blue = 255; | |
173 | |
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174 if (options.count(OPTION_COLOR)) |
0 | 175 { |
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176 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>()); |
0 | 177 } |
178 | |
179 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue); | |
180 | |
181 return tile.release(); | |
182 } | |
183 | |
184 | |
185 | |
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186 static void Run(OrthancWSI::ITiledPyramid& source, |
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187 const boost::program_options::variables_map& options) |
0 | 188 { |
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189 bool reencode = (options.count(OPTION_REENCODE) && |
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190 options[OPTION_REENCODE].as<bool>()); |
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191 |
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192 Orthanc::PhotometricInterpretation targetPhotometric; |
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193 |
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194 if (reencode) |
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195 { |
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196 // The DicomToTiff tool only creates TIFF images with JPEG tiles (*) |
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197 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; |
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198 } |
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199 else |
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200 { |
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201 targetPhotometric = source.GetPhotometricInterpretation(); |
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202 } |
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203 |
217
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204 OrthancWSI::ImageToolbox::CheckConstantTileSize(source); // (**) |
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205 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(), |
0 | 206 source.GetPixelFormat(), |
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207 OrthancWSI::ImageCompression_Jpeg, // (*) |
217
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208 source.GetTileWidth(0), // (**) |
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209 source.GetTileHeight(0), // (**) |
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210 targetPhotometric); |
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211 |
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212 if (options.count(OPTION_JPEG_QUALITY)) |
0 | 213 { |
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214 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
0 | 215 } |
216 | |
167
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217 LOG(WARNING) << "Source photometric interpretation: " << EnumerationToString(source.GetPhotometricInterpretation()); |
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218 LOG(WARNING) << "Target photometric interpretation: " << EnumerationToString(targetPhotometric); |
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219 |
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220 std::unique_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options)); |
0 | 221 |
222 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
223 { | |
224 LOG(WARNING) << "Creating level " << level << " of size " | |
225 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level); | |
226 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level)); | |
227 } | |
228 | |
229 for (unsigned int level = 0; level < source.GetLevelCount(); level++) | |
230 { | |
163 | 231 LOG(WARNING) << std::string(reencode ? "Re-encoding" : "Transcoding") |
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232 << " level " << level; |
0 | 233 |
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234 unsigned int countX = OrthancWSI::CeilingDivision |
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235 (source.GetLevelWidth(level), source.GetTileWidth(level)); |
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236 |
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237 unsigned int countY = OrthancWSI::CeilingDivision |
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238 (source.GetLevelHeight(level), source.GetTileHeight(level)); |
0 | 239 |
240 for (unsigned int tileY = 0; tileY < countY; tileY++) | |
241 { | |
242 for (unsigned int tileX = 0; tileX < countX; tileX++) | |
243 { | |
244 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level; | |
245 | |
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246 bool missing = false; |
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247 bool success = true; |
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248 |
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249 std::string tile; |
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250 OrthancWSI::ImageCompression compression; |
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251 |
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252 if (source.ReadRawTile(tile, compression, level, tileX, tileY)) |
0 | 253 { |
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254 if (compression == OrthancWSI::ImageCompression_Jpeg) |
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255 { |
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256 // Transcoding of JPEG tiles |
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257 target.WriteRawTile(tile, compression, level, tileX, tileY); |
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258 } |
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259 else if (reencode) |
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260 { |
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261 std::unique_ptr<Orthanc::ImageAccessor> decoded; |
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262 |
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263 if (compression == OrthancWSI::ImageCompression_None) |
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264 { |
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265 decoded.reset(OrthancWSI::ImageToolbox::DecodeRawTile( |
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266 tile, source.GetPixelFormat(), |
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267 source.GetTileWidth(level), source.GetTileHeight(level))); |
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268 } |
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269 else |
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270 { |
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271 decoded.reset(OrthancWSI::ImageToolbox::DecodeTile(tile, compression)); |
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272 } |
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273 |
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274 target.EncodeTile(*decoded, level, tileX, tileY); |
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275 } |
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276 else |
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277 { |
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278 success = false; // Re-encoding is mandatory |
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279 } |
0 | 280 } |
281 else | |
282 { | |
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283 // Unable to read the raw tile: The tile is missing (sparse tiling) |
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284 missing = true; |
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285 } |
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286 |
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287 if (!success) |
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288 { |
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289 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is " |
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290 << OrthancWSI::EnumerationToString(compression) |
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291 << "), please use the --" << OPTION_REENCODE << "=1 option"; |
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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293 } |
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294 |
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295 if (missing) |
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296 { |
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297 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile (" |
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298 << tileX << "," << tileY << ") at level " << level; |
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299 target.EncodeTile(*empty, level, tileX, tileY); |
0 | 300 } |
301 } | |
302 } | |
303 | |
304 target.Flush(); | |
305 } | |
306 } | |
307 | |
308 | |
309 | |
310 int main(int argc, char* argv[]) | |
311 { | |
312 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
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313 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
0 | 314 |
315 int exitStatus = 0; | |
316 boost::program_options::variables_map options; | |
317 | |
318 try | |
319 { | |
320 if (ParseParameters(exitStatus, options, argc, argv)) | |
321 { | |
322 Orthanc::WebServiceParameters params; | |
323 | |
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324 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options); |
0 | 325 |
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326 OrthancStone::OrthancHttpConnection orthanc(params); |
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327 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(), |
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328 false /* don't use cached metadata */); |
0 | 329 |
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330 OrthancWSI::TiledPyramidStatistics stats(source); |
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331 Run(stats, options); |
0 | 332 } |
333 } | |
334 catch (Orthanc::OrthancException& e) | |
335 { | |
336 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
337 | |
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338 if (options.count(OPTION_REENCODE) == 0) |
0 | 339 { |
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340 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\""; |
0 | 341 } |
342 | |
343 exitStatus = -1; | |
344 } | |
345 | |
346 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
347 | |
348 return exitStatus; | |
349 } |