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annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 334:f011fc199b6a default tip
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 18 Oct 2024 15:44:18 +0200 |
| parents | 0683312e21ba |
| children |
| 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) 2017-2023 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 | |
|
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24 #include "../PrecompiledHeadersWSI.h" |
| 0 | 25 #include "HierarchicalTiffWriter.h" |
| 26 | |
| 192 | 27 #include <Logging.h> |
| 28 #include <OrthancException.h> | |
| 29 #include <TemporaryFile.h> | |
| 0 | 30 |
| 31 namespace OrthancWSI | |
| 32 { | |
| 33 class HierarchicalTiffWriter::PendingTile | |
| 34 { | |
| 35 private: | |
| 43 | 36 HierarchicalTiffWriter& that_; |
| 37 unsigned int level_; | |
| 38 unsigned int tileX_; | |
| 39 unsigned int tileY_; | |
| 40 Orthanc::TemporaryFile file_; | |
| 0 | 41 |
| 42 public: | |
| 43 PendingTile(HierarchicalTiffWriter& that, | |
| 44 unsigned int level, | |
| 45 unsigned int tileX, | |
| 46 unsigned int tileY, | |
| 47 const std::string& tile) : | |
| 48 that_(that), | |
| 49 level_(level), | |
| 50 tileX_(tileX), | |
| 51 tileY_(tileY) | |
| 52 { | |
| 53 file_.Write(tile); | |
| 54 } | |
| 55 | |
| 56 unsigned int GetLevel() const | |
| 57 { | |
| 58 return level_; | |
| 59 } | |
| 60 | |
| 61 unsigned int GetTileX() const | |
| 62 { | |
| 63 return tileX_; | |
| 64 } | |
| 65 | |
| 66 unsigned int GetTileY() const | |
| 67 { | |
| 68 return tileY_; | |
| 69 } | |
| 70 | |
| 71 void Store(TIFF* tiff) | |
| 72 { | |
| 73 std::string tile; | |
| 74 file_.Read(tile); | |
| 75 that_.StoreTile(tile, tileX_, tileY_); | |
| 76 } | |
| 77 }; | |
| 78 | |
| 79 | |
| 80 struct HierarchicalTiffWriter::Comparator | |
| 81 { | |
| 82 inline bool operator() (PendingTile* const& a, | |
| 83 PendingTile* const& b) | |
| 84 { | |
| 85 if (a->GetLevel() < b->GetLevel()) | |
| 86 { | |
| 87 return true; | |
| 88 } | |
| 89 | |
| 90 if (a->GetLevel() > b->GetLevel()) | |
| 91 { | |
| 92 return false; | |
| 93 } | |
| 94 | |
| 95 if (a->GetTileY() < b->GetTileY()) | |
| 96 { | |
| 97 return true; | |
| 98 } | |
| 99 | |
| 100 if (a->GetTileY() > b->GetTileY()) | |
| 101 { | |
| 102 return false; | |
| 103 } | |
| 104 | |
| 105 return a->GetTileX() < b->GetTileX(); | |
| 106 } | |
| 107 }; | |
| 108 | |
| 109 | |
| 110 static uint8_t GetUint8(const std::string& tile, | |
| 111 size_t index) | |
| 112 { | |
| 113 if (index >= tile.size()) | |
| 114 { | |
| 115 return 0; | |
| 116 } | |
| 117 else | |
| 118 { | |
| 119 return static_cast<uint8_t>(tile[index]); | |
| 120 } | |
| 121 } | |
| 122 | |
| 123 | |
| 124 #if 0 | |
| 125 static uint16_t GetUint16(const std::string& tile, | |
| 126 size_t index) | |
| 127 { | |
| 128 if (index + 1 >= tile.size()) | |
| 129 { | |
| 130 return 0; | |
| 131 } | |
| 132 else | |
| 133 { | |
| 134 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
| 135 } | |
| 136 } | |
| 137 #endif | |
| 138 | |
| 139 | |
| 140 static void CheckJpegTile(const std::string& tile, | |
| 141 Orthanc::PixelFormat pixelFormat) | |
| 142 { | |
| 143 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
| 144 | |
| 145 if (tile.size() < 3 || | |
| 146 static_cast<uint8_t>(tile[0]) != 0xff || | |
| 147 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
| 148 static_cast<uint8_t>(tile[2]) != 0xff) | |
| 149 { | |
| 150 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
| 151 return; | |
| 152 } | |
| 153 | |
| 154 // Look for the "Start of Frame" header (FF C0) | |
| 155 for (size_t i = 2; i + 1 < tile.size(); i++) | |
| 156 { | |
| 157 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
| 158 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
| 159 { | |
| 160 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
| 161 | |
| 162 switch (pixelFormat) | |
| 163 { | |
| 164 case Orthanc::PixelFormat_Grayscale8: | |
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165 if (numberOfComponents != 1) |
| 0 | 166 { |
| 167 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
| 168 } | |
| 169 break; | |
| 170 | |
| 171 case Orthanc::PixelFormat_RGB24: | |
| 172 { | |
| 173 if (numberOfComponents != 3) | |
| 174 { | |
| 175 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
| 176 } | |
| 177 | |
| 178 // Read the header corresponding to the first component | |
| 179 const size_t component = 0; | |
| 180 const size_t offset = i + 10 + component * 3; | |
| 181 const uint8_t sampling = GetUint8(tile, offset + 1); | |
| 182 const int samplingH = sampling / 16; | |
| 183 const int samplingV = sampling % 16; | |
| 184 | |
| 185 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
| 186 | |
| 187 if (samplingH != 2 || | |
| 188 samplingV != 2) | |
| 189 { | |
| 190 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
| 191 << "you should consider using option \"--reencode\""; | |
| 192 } | |
| 193 | |
| 194 break; | |
| 195 } | |
| 196 | |
| 197 default: | |
| 198 break; | |
| 199 } | |
| 200 } | |
| 201 } | |
| 202 } | |
| 203 | |
| 204 | |
| 205 | |
| 206 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
| 207 unsigned int tileX, | |
| 208 unsigned int tileY) | |
| 209 { | |
| 210 // Get the index of the tile | |
| 211 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
| 212 | |
| 213 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
| 214 static_cast<tsize_t>(tile.size())) | |
| 215 { | |
| 216 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 217 } | |
| 218 | |
| 219 if (isFirst_ && | |
| 220 GetImageCompression() == ImageCompression_Jpeg) | |
| 221 { | |
| 222 CheckJpegTile(tile, GetPixelFormat()); | |
| 223 } | |
| 224 | |
| 225 isFirst_ = false; | |
| 226 } | |
| 227 | |
| 228 | |
| 229 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
| 230 bool createLevel) | |
| 231 { | |
| 232 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
| 233 { | |
| 234 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 235 } | |
| 236 | |
| 237 if (TIFFFlush(tiff_) != 1) | |
| 238 { | |
| 239 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 240 } | |
| 241 | |
| 242 currentLevel_ = level.z_; | |
| 243 nextX_ = 0; | |
| 244 nextY_ = 0; | |
| 245 | |
| 246 switch (GetImageCompression()) | |
| 247 { | |
| 248 case ImageCompression_Jpeg: | |
| 249 { | |
| 250 uint16_t c = COMPRESSION_JPEG; | |
| 251 | |
| 252 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
| 253 { | |
| 254 Close(); | |
| 255 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 256 } | |
| 257 | |
| 258 break; | |
| 259 } | |
| 260 | |
| 261 default: | |
| 262 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 263 } | |
| 264 | |
| 265 | |
| 266 switch (GetPixelFormat()) | |
| 267 { | |
| 268 case Orthanc::PixelFormat_RGB24: | |
| 269 { | |
| 270 uint16_t samplesPerPixel = 3; | |
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271 uint16_t photometric; |
| 0 | 272 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB |
| 273 uint16_t bpp = 8; | |
| 274 uint16_t subsampleHorizontal = 2; | |
| 275 uint16_t subsampleVertical = 2; | |
| 276 | |
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277 switch (photometric_) |
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278 { |
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279 case Orthanc::PhotometricInterpretation_YBRFull422: |
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280 photometric = PHOTOMETRIC_YCBCR; |
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281 break; |
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282 |
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283 case Orthanc::PhotometricInterpretation_RGB: |
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284 photometric = PHOTOMETRIC_RGB; |
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285 break; |
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286 |
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287 default: |
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288 throw Orthanc::OrthancException( |
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289 Orthanc::ErrorCode_ParameterOutOfRange, |
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290 "Unsupported photometric interpreation: " + |
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291 std::string(Orthanc::EnumerationToString(photometric_))); |
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292 } |
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293 |
| 0 | 294 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
| 295 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
| 296 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
| 297 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
| 298 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
| 299 { | |
| 300 Close(); | |
| 301 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 302 } | |
| 303 | |
| 304 break; | |
| 305 } | |
| 306 | |
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307 case Orthanc::PixelFormat_Grayscale8: |
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308 { |
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309 uint16_t samplesPerPixel = 1; |
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310 uint16_t bpp = 8; |
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311 uint16_t photometric = PHOTOMETRIC_MINISBLACK; |
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312 |
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313 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
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314 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || |
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315 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1) |
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316 { |
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317 Close(); |
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318 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); |
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319 } |
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320 |
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321 break; |
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322 } |
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323 |
| 0 | 324 default: |
| 325 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 326 } | |
| 327 | |
| 328 uint32_t w = level.width_; | |
| 329 uint32_t h = level.height_; | |
| 330 uint32_t tw = GetTileWidth(); | |
| 331 uint32_t th = GetTileHeight(); | |
| 332 | |
| 333 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
| 334 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
| 335 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
| 336 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
| 337 { | |
| 338 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 339 } | |
| 340 } | |
| 341 | |
| 342 | |
| 343 void HierarchicalTiffWriter::AdvanceToNextTile() | |
| 344 { | |
| 345 assert(currentLevel_ < levels_.size()); | |
| 346 | |
| 347 nextX_ += 1; | |
| 348 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
| 349 { | |
| 350 nextX_ = 0; | |
| 351 nextY_ += 1; | |
| 352 | |
| 353 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
| 354 { | |
| 355 currentLevel_ += 1; | |
| 356 | |
| 357 if (currentLevel_ < levels_.size()) | |
| 358 { | |
| 359 ConfigureLevel(levels_[currentLevel_], true); | |
| 360 } | |
| 361 } | |
| 362 } | |
| 363 } | |
| 364 | |
| 365 | |
| 366 void HierarchicalTiffWriter::ScanPending() | |
| 367 { | |
| 368 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
| 369 | |
| 370 while (currentLevel_ < levels_.size() && | |
| 371 !pending_.empty() && | |
| 372 pending_.front()->GetLevel() == currentLevel_ && | |
| 373 pending_.front()->GetTileX() == nextX_ && | |
| 374 pending_.front()->GetTileY() == nextY_) | |
| 375 { | |
| 376 pending_.front()->Store(tiff_); | |
| 377 delete pending_.front(); | |
| 378 pending_.pop_front(); | |
| 379 AdvanceToNextTile(); | |
| 380 } | |
| 381 } | |
| 382 | |
| 383 | |
| 384 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
| 385 const Level& level, | |
| 386 unsigned int tileX, | |
| 387 unsigned int tileY) | |
| 388 { | |
| 389 boost::mutex::scoped_lock lock(mutex_); | |
| 390 | |
| 391 if (level.z_ == currentLevel_ && | |
| 392 tileX == nextX_ && | |
| 393 tileY == nextY_) | |
| 394 { | |
| 395 StoreTile(tile, tileX, tileY); | |
| 396 AdvanceToNextTile(); | |
| 397 ScanPending(); | |
| 398 } | |
| 399 else | |
| 400 { | |
| 401 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
| 402 } | |
| 403 } | |
| 404 | |
| 405 | |
| 406 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
| 407 { | |
| 408 if (level.z_ == 0) | |
| 409 { | |
| 410 // Configure the finest level on initialization | |
| 411 ConfigureLevel(level, false); | |
| 412 } | |
| 413 | |
| 414 levels_.push_back(level); | |
| 415 } | |
| 416 | |
| 417 | |
| 418 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
| 419 Orthanc::PixelFormat pixelFormat, | |
| 420 ImageCompression compression, | |
| 421 unsigned int tileWidth, | |
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422 unsigned int tileHeight, |
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423 Orthanc::PhotometricInterpretation photometric) : |
| 0 | 424 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
| 425 currentLevel_(0), | |
| 145 | 426 nextX_(0), |
| 427 nextY_(0), | |
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Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
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428 isFirst_(true), |
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605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
429 photometric_(photometric) |
| 0 | 430 { |
| 431 tiff_ = TIFFOpen(path.c_str(), "w"); | |
| 432 if (tiff_ == NULL) | |
| 433 { | |
| 434 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 435 } | |
| 436 } | |
| 437 | |
| 438 | |
| 439 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
| 440 { | |
| 441 if (pending_.size()) | |
| 442 { | |
| 443 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
| 444 } | |
| 445 | |
| 446 for (size_t i = 0; i < pending_.size(); i++) | |
| 447 { | |
| 448 if (pending_[i]) | |
| 449 { | |
| 450 delete pending_[i]; | |
| 451 } | |
| 452 } | |
| 453 | |
| 454 Close(); | |
| 455 } | |
| 456 | |
| 457 | |
| 458 void HierarchicalTiffWriter::Flush() | |
| 459 { | |
| 460 boost::mutex::scoped_lock lock(mutex_); | |
| 461 ScanPending(); | |
| 462 } | |
| 463 } |