Mercurial > hg > orthanc-wsi
annotate Framework/DicomizerParameters.cpp @ 244:4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 06 Dec 2021 21:18:18 +0100 |
| parents | 49f647ed1b4c |
| children | 793b8f9c9d52 |
| 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) 2017-2021 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2021 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 | |
|
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23 #include "PrecompiledHeadersWSI.h" |
| 0 | 24 #include "DicomizerParameters.h" |
| 25 | |
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26 #include "ImageToolbox.h" |
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27 #include "Targets/FolderTarget.h" |
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28 #include "Targets/OrthancTarget.h" |
| 0 | 29 |
| 192 | 30 #include <OrthancException.h> |
| 0 | 31 |
| 32 #include <boost/thread.hpp> | |
| 33 #include <boost/lexical_cast.hpp> | |
| 34 | |
| 35 namespace OrthancWSI | |
| 36 { | |
| 37 static unsigned int ChooseNumberOfThreads() | |
| 38 { | |
| 39 unsigned int nthreads = boost::thread::hardware_concurrency(); | |
| 40 | |
| 41 if (nthreads % 2 == 0) | |
| 42 { | |
| 43 nthreads = nthreads / 2; | |
| 44 } | |
| 45 else | |
| 46 { | |
| 47 nthreads = nthreads / 2 + 1; | |
| 48 } | |
| 49 | |
| 50 if (nthreads == 0) | |
| 51 { | |
| 52 nthreads = 1; | |
| 53 } | |
| 54 | |
| 55 return nthreads; | |
| 56 } | |
| 57 | |
| 58 | |
| 91 | 59 DicomizerParameters::DicomizerParameters() : |
| 60 safetyCheck_(false), | |
| 61 repaintBackground_(false), | |
| 62 targetCompression_(ImageCompression_Jpeg), | |
| 63 hasTargetTileSize_(false), | |
| 64 targetTileWidth_(512), | |
| 65 targetTileHeight_(512), | |
| 66 maxDicomFileSize_(10 * 1024 * 1024), // 10MB | |
| 67 reconstructPyramid_(false), | |
| 68 pyramidLevelsCount_(0), | |
| 69 pyramidLowerLevelsCount_(0), | |
| 70 smooth_(false), | |
| 71 jpegQuality_(90), | |
| 72 forceReencode_(false), | |
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73 opticalPath_(OpticalPath_Brightfield), |
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74 isCytomineSource_(false) |
| 0 | 75 { |
| 76 backgroundColor_[0] = 255; | |
| 77 backgroundColor_[1] = 255; | |
| 78 backgroundColor_[2] = 255; | |
| 79 threadsCount_ = ChooseNumberOfThreads(); | |
| 80 } | |
| 81 | |
| 82 | |
| 83 void DicomizerParameters::SetBackgroundColor(uint8_t red, | |
| 84 uint8_t green, | |
| 85 uint8_t blue) | |
| 86 { | |
| 87 repaintBackground_ = true; | |
| 88 backgroundColor_[0] = red; | |
| 89 backgroundColor_[1] = green; | |
| 90 backgroundColor_[2] = blue; | |
| 91 } | |
| 92 | |
| 93 | |
| 94 void DicomizerParameters::SetTargetTileSize(unsigned int width, | |
| 95 unsigned int height) | |
| 96 { | |
| 97 hasTargetTileSize_ = true; | |
| 98 targetTileWidth_ = width; | |
| 99 targetTileHeight_ = height; | |
| 100 } | |
| 101 | |
| 102 | |
| 103 unsigned int DicomizerParameters::GetTargetTileWidth(unsigned int defaultWidth) const | |
| 104 { | |
| 105 if (hasTargetTileSize_ && | |
| 106 targetTileWidth_ != 0) | |
| 107 { | |
| 108 return targetTileWidth_; | |
| 109 } | |
| 110 else | |
| 111 { | |
| 112 return defaultWidth; | |
| 113 } | |
| 114 } | |
| 115 | |
| 116 | |
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117 unsigned int DicomizerParameters::GetTargetTileWidth(const ITiledPyramid& source) const |
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118 { |
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119 ImageToolbox::CheckConstantTileSize(source); |
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120 return GetTargetTileWidth(source.GetTileWidth(0)); |
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121 } |
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122 |
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123 |
| 0 | 124 unsigned int DicomizerParameters::GetTargetTileHeight(unsigned int defaultHeight) const |
| 125 { | |
| 126 if (hasTargetTileSize_ && | |
| 127 targetTileHeight_ != 0) | |
| 128 { | |
| 129 return targetTileHeight_; | |
| 130 } | |
| 131 else | |
| 132 { | |
| 133 return defaultHeight; | |
| 134 } | |
| 135 } | |
| 136 | |
| 137 | |
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138 unsigned int DicomizerParameters::GetTargetTileHeight(const ITiledPyramid& source) const |
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139 { |
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140 ImageToolbox::CheckConstantTileSize(source); |
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141 return GetTargetTileHeight(source.GetTileHeight(0)); |
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142 } |
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143 |
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144 |
| 0 | 145 void DicomizerParameters::SetThreadsCount(unsigned int threads) |
| 146 { | |
| 147 if (threads == 0) | |
| 148 { | |
| 149 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 150 } | |
| 151 | |
| 152 threadsCount_ = threads; | |
| 153 } | |
| 154 | |
| 155 | |
| 156 void DicomizerParameters::SetDicomMaxFileSize(unsigned int size) | |
| 157 { | |
| 158 maxDicomFileSize_ = size; | |
| 159 } | |
| 160 | |
| 161 | |
| 162 void DicomizerParameters::SetPyramidLevelsCount(unsigned int count) | |
| 163 { | |
| 91 | 164 if (count == 0) |
| 0 | 165 { |
| 166 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 167 } | |
| 168 | |
| 169 pyramidLevelsCount_ = count; | |
| 170 } | |
| 171 | |
| 172 | |
| 173 unsigned int DicomizerParameters::GetPyramidLevelsCount(const IPyramidWriter& target, | |
| 174 const ITiledPyramid& source) const | |
| 175 { | |
| 176 if (pyramidLevelsCount_ != 0) | |
| 177 { | |
| 178 return pyramidLevelsCount_; | |
| 179 } | |
| 180 | |
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181 ImageToolbox::CheckConstantTileSize(source); |
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182 |
| 0 | 183 // By default, the number of levels for the pyramid is taken so that |
| 184 // the upper level is reduced either to 1 column of tiles, or to 1 | |
| 185 // row of tiles. | |
| 186 unsigned int totalWidth = source.GetLevelWidth(0); | |
| 187 unsigned int totalHeight = source.GetLevelHeight(0); | |
| 188 | |
| 189 unsigned int countLevels = 1; | |
| 190 for (;;) | |
| 191 { | |
| 192 unsigned int zoom = 1 << (countLevels - 1); | |
| 193 | |
| 194 if (CeilingDivision(totalWidth, zoom) <= target.GetTileWidth() || | |
| 195 CeilingDivision(totalHeight, zoom) <= target.GetTileHeight()) | |
| 196 { | |
| 197 break; | |
| 198 } | |
| 199 | |
| 200 countLevels += 1; | |
| 201 } | |
| 202 | |
| 203 return countLevels; | |
| 204 } | |
| 205 | |
| 206 | |
| 207 void DicomizerParameters::SetPyramidLowerLevelsCount(unsigned int count) | |
| 208 { | |
| 91 | 209 if (count == 0) |
| 0 | 210 { |
| 211 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 212 } | |
| 213 | |
| 214 pyramidLowerLevelsCount_ = count; | |
| 215 } | |
| 216 | |
| 217 | |
| 218 unsigned int DicomizerParameters::GetPyramidLowerLevelsCount(const IPyramidWriter& target, | |
| 219 const ITiledPyramid& source) const | |
| 220 { | |
| 221 if (pyramidLowerLevelsCount_ != 0) | |
| 222 { | |
| 223 return pyramidLowerLevelsCount_; | |
| 224 } | |
| 225 | |
| 226 unsigned int fullNumberOfTiles = ( | |
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227 CeilingDivision(source.GetLevelWidth(0), source.GetTileWidth(0)) * |
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228 CeilingDivision(source.GetLevelHeight(0), source.GetTileHeight(0))); |
| 0 | 229 |
| 230 // By default, the number of lower levels in the pyramid is chosen | |
| 231 // as a compromise between the number of tasks (there should not be | |
| 232 // too few tasks, otherwise multithreading would not be efficient) | |
| 233 // and memory consumption (maximum 64MB of RAM due to the decoding | |
| 234 // of the tiles of the source image per thread: cf. PyramidReader). | |
| 235 unsigned int result = 1; | |
| 236 for (;;) | |
| 237 { | |
| 238 unsigned int zoom = 1 << (result - 1); | |
| 239 unsigned int numberOfTiles = CeilingDivision(fullNumberOfTiles, zoom * zoom); | |
| 240 | |
| 241 if (result + 1 > target.GetLevelCount() || | |
| 242 numberOfTiles < 4 * GetThreadsCount() || | |
| 243 zoom * target.GetTileWidth() > 4096 || | |
| 244 zoom * target.GetTileHeight() > 4096) | |
| 245 { | |
| 246 break; | |
| 247 } | |
| 248 | |
| 249 result += 1; | |
| 250 } | |
| 251 | |
| 252 return result - 1; | |
| 253 } | |
| 254 | |
| 255 | |
| 256 void DicomizerParameters::SetJpegQuality(int quality) | |
| 257 { | |
| 258 if (quality <= 0 || | |
| 259 quality > 100) | |
| 260 { | |
| 261 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 262 } | |
| 263 | |
| 264 jpegQuality_ = quality; | |
| 265 } | |
| 266 | |
| 267 | |
| 268 IFileTarget* DicomizerParameters::CreateTarget() const | |
| 269 { | |
| 270 if (folder_.empty() || | |
| 271 folderPattern_.empty()) | |
| 272 { | |
| 273 return new OrthancTarget(orthanc_); | |
| 274 } | |
| 275 else | |
| 276 { | |
| 277 return new FolderTarget(folder_ + "/" + folderPattern_); | |
| 278 } | |
| 279 } | |
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280 |
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281 |
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282 void DicomizerParameters::SetCytomineSource(const std::string& url, |
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283 const std::string& publicKey, |
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284 const std::string& privateKey, |
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285 int imageInstanceId, |
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286 ImageCompression cytomineCompression) |
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287 { |
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288 isCytomineSource_ = true; |
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289 cytomineServer_.SetUrl(url); |
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290 cytominePublicKey_ = publicKey; |
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291 cytominePrivateKey_ = privateKey; |
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292 cytomineImageInstanceId_ = imageInstanceId; |
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293 cytomineCompression_ = cytomineCompression; |
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294 } |
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295 |
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296 |
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297 const Orthanc::WebServiceParameters& DicomizerParameters::GetCytomineServer() const |
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298 { |
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299 if (isCytomineSource_) |
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300 { |
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301 return cytomineServer_; |
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302 } |
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303 else |
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304 { |
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305 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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306 } |
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307 } |
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308 |
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309 |
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310 const std::string& DicomizerParameters::GetCytominePublicKey() const |
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311 { |
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312 if (isCytomineSource_) |
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313 { |
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314 return cytominePublicKey_; |
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315 } |
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316 else |
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317 { |
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318 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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319 } |
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320 } |
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321 |
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322 |
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323 const std::string& DicomizerParameters::GetCytominePrivateKey() const |
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324 { |
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325 if (isCytomineSource_) |
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326 { |
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327 return cytominePrivateKey_; |
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328 } |
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329 else |
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330 { |
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331 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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332 } |
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333 } |
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334 |
|
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335 |
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336 int DicomizerParameters::GetCytomineImageInstanceId() const |
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337 { |
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338 if (isCytomineSource_) |
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339 { |
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340 return cytomineImageInstanceId_; |
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341 } |
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342 else |
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343 { |
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344 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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345 } |
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346 } |
|
4273518c2009
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347 |
|
4273518c2009
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348 |
|
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349 ImageCompression DicomizerParameters::GetCytomineCompression() const |
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350 { |
|
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351 if (isCytomineSource_) |
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352 { |
|
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353 return cytomineCompression_; |
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354 } |
|
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
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355 else |
|
4273518c2009
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changeset
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356 { |
|
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357 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
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|
358 } |
|
4273518c2009
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359 } |
| 0 | 360 } |