Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 242:49f647ed1b4c
added copyright UCLouvain
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 06 Dec 2021 16:05:42 +0100 |
| parents | 1e864138f0da |
| children | 20a730889ae2 |
| 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 "HierarchicalTiffWriter.h" |
| 25 | |
| 192 | 26 #include <Logging.h> |
| 27 #include <OrthancException.h> | |
| 28 #include <TemporaryFile.h> | |
| 0 | 29 |
| 30 namespace OrthancWSI | |
| 31 { | |
| 32 class HierarchicalTiffWriter::PendingTile | |
| 33 { | |
| 34 private: | |
| 43 | 35 HierarchicalTiffWriter& that_; |
| 36 unsigned int level_; | |
| 37 unsigned int tileX_; | |
| 38 unsigned int tileY_; | |
| 39 Orthanc::TemporaryFile file_; | |
| 0 | 40 |
| 41 public: | |
| 42 PendingTile(HierarchicalTiffWriter& that, | |
| 43 unsigned int level, | |
| 44 unsigned int tileX, | |
| 45 unsigned int tileY, | |
| 46 const std::string& tile) : | |
| 47 that_(that), | |
| 48 level_(level), | |
| 49 tileX_(tileX), | |
| 50 tileY_(tileY) | |
| 51 { | |
| 52 file_.Write(tile); | |
| 53 } | |
| 54 | |
| 55 unsigned int GetLevel() const | |
| 56 { | |
| 57 return level_; | |
| 58 } | |
| 59 | |
| 60 unsigned int GetTileX() const | |
| 61 { | |
| 62 return tileX_; | |
| 63 } | |
| 64 | |
| 65 unsigned int GetTileY() const | |
| 66 { | |
| 67 return tileY_; | |
| 68 } | |
| 69 | |
| 70 void Store(TIFF* tiff) | |
| 71 { | |
| 72 std::string tile; | |
| 73 file_.Read(tile); | |
| 74 that_.StoreTile(tile, tileX_, tileY_); | |
| 75 } | |
| 76 }; | |
| 77 | |
| 78 | |
| 79 struct HierarchicalTiffWriter::Comparator | |
| 80 { | |
| 81 inline bool operator() (PendingTile* const& a, | |
| 82 PendingTile* const& b) | |
| 83 { | |
| 84 if (a->GetLevel() < b->GetLevel()) | |
| 85 { | |
| 86 return true; | |
| 87 } | |
| 88 | |
| 89 if (a->GetLevel() > b->GetLevel()) | |
| 90 { | |
| 91 return false; | |
| 92 } | |
| 93 | |
| 94 if (a->GetTileY() < b->GetTileY()) | |
| 95 { | |
| 96 return true; | |
| 97 } | |
| 98 | |
| 99 if (a->GetTileY() > b->GetTileY()) | |
| 100 { | |
| 101 return false; | |
| 102 } | |
| 103 | |
| 104 return a->GetTileX() < b->GetTileX(); | |
| 105 } | |
| 106 }; | |
| 107 | |
| 108 | |
| 109 static uint8_t GetUint8(const std::string& tile, | |
| 110 size_t index) | |
| 111 { | |
| 112 if (index >= tile.size()) | |
| 113 { | |
| 114 return 0; | |
| 115 } | |
| 116 else | |
| 117 { | |
| 118 return static_cast<uint8_t>(tile[index]); | |
| 119 } | |
| 120 } | |
| 121 | |
| 122 | |
| 123 #if 0 | |
| 124 static uint16_t GetUint16(const std::string& tile, | |
| 125 size_t index) | |
| 126 { | |
| 127 if (index + 1 >= tile.size()) | |
| 128 { | |
| 129 return 0; | |
| 130 } | |
| 131 else | |
| 132 { | |
| 133 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
| 134 } | |
| 135 } | |
| 136 #endif | |
| 137 | |
| 138 | |
| 139 static void CheckJpegTile(const std::string& tile, | |
| 140 Orthanc::PixelFormat pixelFormat) | |
| 141 { | |
| 142 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
| 143 | |
| 144 if (tile.size() < 3 || | |
| 145 static_cast<uint8_t>(tile[0]) != 0xff || | |
| 146 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
| 147 static_cast<uint8_t>(tile[2]) != 0xff) | |
| 148 { | |
| 149 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
| 150 return; | |
| 151 } | |
| 152 | |
| 153 // Look for the "Start of Frame" header (FF C0) | |
| 154 for (size_t i = 2; i + 1 < tile.size(); i++) | |
| 155 { | |
| 156 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
| 157 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
| 158 { | |
| 159 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
| 160 | |
| 161 switch (pixelFormat) | |
| 162 { | |
| 163 case Orthanc::PixelFormat_Grayscale8: | |
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164 if (numberOfComponents != 1) |
| 0 | 165 { |
| 166 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
| 167 } | |
| 168 break; | |
| 169 | |
| 170 case Orthanc::PixelFormat_RGB24: | |
| 171 { | |
| 172 if (numberOfComponents != 3) | |
| 173 { | |
| 174 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
| 175 } | |
| 176 | |
| 177 // Read the header corresponding to the first component | |
| 178 const size_t component = 0; | |
| 179 const size_t offset = i + 10 + component * 3; | |
| 180 const uint8_t sampling = GetUint8(tile, offset + 1); | |
| 181 const int samplingH = sampling / 16; | |
| 182 const int samplingV = sampling % 16; | |
| 183 | |
| 184 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
| 185 | |
| 186 if (samplingH != 2 || | |
| 187 samplingV != 2) | |
| 188 { | |
| 189 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
| 190 << "you should consider using option \"--reencode\""; | |
| 191 } | |
| 192 | |
| 193 break; | |
| 194 } | |
| 195 | |
| 196 default: | |
| 197 break; | |
| 198 } | |
| 199 } | |
| 200 } | |
| 201 } | |
| 202 | |
| 203 | |
| 204 | |
| 205 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
| 206 unsigned int tileX, | |
| 207 unsigned int tileY) | |
| 208 { | |
| 209 // Get the index of the tile | |
| 210 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
| 211 | |
| 212 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
| 213 static_cast<tsize_t>(tile.size())) | |
| 214 { | |
| 215 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 216 } | |
| 217 | |
| 218 if (isFirst_ && | |
| 219 GetImageCompression() == ImageCompression_Jpeg) | |
| 220 { | |
| 221 CheckJpegTile(tile, GetPixelFormat()); | |
| 222 } | |
| 223 | |
| 224 isFirst_ = false; | |
| 225 } | |
| 226 | |
| 227 | |
| 228 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
| 229 bool createLevel) | |
| 230 { | |
| 231 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
| 232 { | |
| 233 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 234 } | |
| 235 | |
| 236 if (TIFFFlush(tiff_) != 1) | |
| 237 { | |
| 238 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 239 } | |
| 240 | |
| 241 currentLevel_ = level.z_; | |
| 242 nextX_ = 0; | |
| 243 nextY_ = 0; | |
| 244 | |
| 245 switch (GetImageCompression()) | |
| 246 { | |
| 247 case ImageCompression_Jpeg: | |
| 248 { | |
| 249 uint16_t c = COMPRESSION_JPEG; | |
| 250 | |
| 251 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
| 252 { | |
| 253 Close(); | |
| 254 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 255 } | |
| 256 | |
| 257 break; | |
| 258 } | |
| 259 | |
| 260 default: | |
| 261 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 262 } | |
| 263 | |
| 264 | |
| 265 switch (GetPixelFormat()) | |
| 266 { | |
| 267 case Orthanc::PixelFormat_RGB24: | |
| 268 { | |
| 269 uint16_t samplesPerPixel = 3; | |
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270 uint16_t photometric; |
| 0 | 271 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB |
| 272 uint16_t bpp = 8; | |
| 273 uint16_t subsampleHorizontal = 2; | |
| 274 uint16_t subsampleVertical = 2; | |
| 275 | |
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276 switch (photometric_) |
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277 { |
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278 case Orthanc::PhotometricInterpretation_YBRFull422: |
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279 photometric = PHOTOMETRIC_YCBCR; |
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280 break; |
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281 |
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282 case Orthanc::PhotometricInterpretation_RGB: |
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283 photometric = PHOTOMETRIC_RGB; |
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284 break; |
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285 |
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286 default: |
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287 throw Orthanc::OrthancException( |
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288 Orthanc::ErrorCode_ParameterOutOfRange, |
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289 "Unsupported photometric interpreation: " + |
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290 std::string(Orthanc::EnumerationToString(photometric_))); |
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291 } |
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292 |
| 0 | 293 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
| 294 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
| 295 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
| 296 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
| 297 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
| 298 { | |
| 299 Close(); | |
| 300 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 301 } | |
| 302 | |
| 303 break; | |
| 304 } | |
| 305 | |
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306 case Orthanc::PixelFormat_Grayscale8: |
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307 { |
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308 uint16_t samplesPerPixel = 1; |
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309 uint16_t bpp = 8; |
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310 uint16_t photometric = PHOTOMETRIC_MINISBLACK; |
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311 |
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312 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
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313 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || |
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314 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1) |
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315 { |
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316 Close(); |
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317 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); |
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318 } |
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319 |
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320 break; |
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321 } |
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322 |
| 0 | 323 default: |
| 324 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 325 } | |
| 326 | |
| 327 uint32_t w = level.width_; | |
| 328 uint32_t h = level.height_; | |
| 329 uint32_t tw = GetTileWidth(); | |
| 330 uint32_t th = GetTileHeight(); | |
| 331 | |
| 332 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
| 333 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
| 334 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
| 335 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
| 336 { | |
| 337 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 338 } | |
| 339 } | |
| 340 | |
| 341 | |
| 342 void HierarchicalTiffWriter::AdvanceToNextTile() | |
| 343 { | |
| 344 assert(currentLevel_ < levels_.size()); | |
| 345 | |
| 346 nextX_ += 1; | |
| 347 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
| 348 { | |
| 349 nextX_ = 0; | |
| 350 nextY_ += 1; | |
| 351 | |
| 352 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
| 353 { | |
| 354 currentLevel_ += 1; | |
| 355 | |
| 356 if (currentLevel_ < levels_.size()) | |
| 357 { | |
| 358 ConfigureLevel(levels_[currentLevel_], true); | |
| 359 } | |
| 360 } | |
| 361 } | |
| 362 } | |
| 363 | |
| 364 | |
| 365 void HierarchicalTiffWriter::ScanPending() | |
| 366 { | |
| 367 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
| 368 | |
| 369 while (currentLevel_ < levels_.size() && | |
| 370 !pending_.empty() && | |
| 371 pending_.front()->GetLevel() == currentLevel_ && | |
| 372 pending_.front()->GetTileX() == nextX_ && | |
| 373 pending_.front()->GetTileY() == nextY_) | |
| 374 { | |
| 375 pending_.front()->Store(tiff_); | |
| 376 delete pending_.front(); | |
| 377 pending_.pop_front(); | |
| 378 AdvanceToNextTile(); | |
| 379 } | |
| 380 } | |
| 381 | |
| 382 | |
| 383 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
| 384 const Level& level, | |
| 385 unsigned int tileX, | |
| 386 unsigned int tileY) | |
| 387 { | |
| 388 boost::mutex::scoped_lock lock(mutex_); | |
| 389 | |
| 390 if (level.z_ == currentLevel_ && | |
| 391 tileX == nextX_ && | |
| 392 tileY == nextY_) | |
| 393 { | |
| 394 StoreTile(tile, tileX, tileY); | |
| 395 AdvanceToNextTile(); | |
| 396 ScanPending(); | |
| 397 } | |
| 398 else | |
| 399 { | |
| 400 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
| 401 } | |
| 402 } | |
| 403 | |
| 404 | |
| 405 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
| 406 { | |
| 407 if (level.z_ == 0) | |
| 408 { | |
| 409 // Configure the finest level on initialization | |
| 410 ConfigureLevel(level, false); | |
| 411 } | |
| 412 | |
| 413 levels_.push_back(level); | |
| 414 } | |
| 415 | |
| 416 | |
| 417 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
| 418 Orthanc::PixelFormat pixelFormat, | |
| 419 ImageCompression compression, | |
| 420 unsigned int tileWidth, | |
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421 unsigned int tileHeight, |
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422 Orthanc::PhotometricInterpretation photometric) : |
| 0 | 423 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
| 424 currentLevel_(0), | |
| 145 | 425 nextX_(0), |
| 426 nextY_(0), | |
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427 isFirst_(true), |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
428 photometric_(photometric) |
| 0 | 429 { |
| 430 tiff_ = TIFFOpen(path.c_str(), "w"); | |
| 431 if (tiff_ == NULL) | |
| 432 { | |
| 433 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 434 } | |
| 435 } | |
| 436 | |
| 437 | |
| 438 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
| 439 { | |
| 440 if (pending_.size()) | |
| 441 { | |
| 442 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
| 443 } | |
| 444 | |
| 445 for (size_t i = 0; i < pending_.size(); i++) | |
| 446 { | |
| 447 if (pending_[i]) | |
| 448 { | |
| 449 delete pending_[i]; | |
| 450 } | |
| 451 } | |
| 452 | |
| 453 Close(); | |
| 454 } | |
| 455 | |
| 456 | |
| 457 void HierarchicalTiffWriter::Flush() | |
| 458 { | |
| 459 boost::mutex::scoped_lock lock(mutex_); | |
| 460 ScanPending(); | |
| 461 } | |
| 462 } |