Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 137:90b392cb1aba
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 11 Apr 2018 15:45:26 +0200 |
| parents | a51dee6a1515 |
| children | a0f9a3df1110 |
| 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) 2017-2018 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU Affero General Public License | |
| 9 * as published by the Free Software Foundation, either version 3 of | |
| 10 * the License, or (at your option) any later version. | |
| 11 * | |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 15 * Affero General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU Affero General Public License | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
|
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22 #include "../PrecompiledHeadersWSI.h" |
| 0 | 23 #include "HierarchicalTiffWriter.h" |
| 24 | |
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25 #include "../../Resources/Orthanc/Core/Logging.h" |
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26 #include "../../Resources/Orthanc/Core/OrthancException.h" |
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27 #include "../../Resources/Orthanc/Core/TemporaryFile.h" |
| 0 | 28 |
| 29 namespace OrthancWSI | |
| 30 { | |
| 31 class HierarchicalTiffWriter::PendingTile | |
| 32 { | |
| 33 private: | |
| 43 | 34 HierarchicalTiffWriter& that_; |
| 35 unsigned int level_; | |
| 36 unsigned int tileX_; | |
| 37 unsigned int tileY_; | |
| 38 Orthanc::TemporaryFile file_; | |
| 0 | 39 |
| 40 public: | |
| 41 PendingTile(HierarchicalTiffWriter& that, | |
| 42 unsigned int level, | |
| 43 unsigned int tileX, | |
| 44 unsigned int tileY, | |
| 45 const std::string& tile) : | |
| 46 that_(that), | |
| 47 level_(level), | |
| 48 tileX_(tileX), | |
| 49 tileY_(tileY) | |
| 50 { | |
| 51 file_.Write(tile); | |
| 52 } | |
| 53 | |
| 54 unsigned int GetLevel() const | |
| 55 { | |
| 56 return level_; | |
| 57 } | |
| 58 | |
| 59 unsigned int GetTileX() const | |
| 60 { | |
| 61 return tileX_; | |
| 62 } | |
| 63 | |
| 64 unsigned int GetTileY() const | |
| 65 { | |
| 66 return tileY_; | |
| 67 } | |
| 68 | |
| 69 void Store(TIFF* tiff) | |
| 70 { | |
| 71 std::string tile; | |
| 72 file_.Read(tile); | |
| 73 that_.StoreTile(tile, tileX_, tileY_); | |
| 74 } | |
| 75 }; | |
| 76 | |
| 77 | |
| 78 struct HierarchicalTiffWriter::Comparator | |
| 79 { | |
| 80 inline bool operator() (PendingTile* const& a, | |
| 81 PendingTile* const& b) | |
| 82 { | |
| 83 if (a->GetLevel() < b->GetLevel()) | |
| 84 { | |
| 85 return true; | |
| 86 } | |
| 87 | |
| 88 if (a->GetLevel() > b->GetLevel()) | |
| 89 { | |
| 90 return false; | |
| 91 } | |
| 92 | |
| 93 if (a->GetTileY() < b->GetTileY()) | |
| 94 { | |
| 95 return true; | |
| 96 } | |
| 97 | |
| 98 if (a->GetTileY() > b->GetTileY()) | |
| 99 { | |
| 100 return false; | |
| 101 } | |
| 102 | |
| 103 return a->GetTileX() < b->GetTileX(); | |
| 104 } | |
| 105 }; | |
| 106 | |
| 107 | |
| 108 static uint8_t GetUint8(const std::string& tile, | |
| 109 size_t index) | |
| 110 { | |
| 111 if (index >= tile.size()) | |
| 112 { | |
| 113 return 0; | |
| 114 } | |
| 115 else | |
| 116 { | |
| 117 return static_cast<uint8_t>(tile[index]); | |
| 118 } | |
| 119 } | |
| 120 | |
| 121 | |
| 122 #if 0 | |
| 123 static uint16_t GetUint16(const std::string& tile, | |
| 124 size_t index) | |
| 125 { | |
| 126 if (index + 1 >= tile.size()) | |
| 127 { | |
| 128 return 0; | |
| 129 } | |
| 130 else | |
| 131 { | |
| 132 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
| 133 } | |
| 134 } | |
| 135 #endif | |
| 136 | |
| 137 | |
| 138 static void CheckJpegTile(const std::string& tile, | |
| 139 Orthanc::PixelFormat pixelFormat) | |
| 140 { | |
| 141 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
| 142 | |
| 143 if (tile.size() < 3 || | |
| 144 static_cast<uint8_t>(tile[0]) != 0xff || | |
| 145 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
| 146 static_cast<uint8_t>(tile[2]) != 0xff) | |
| 147 { | |
| 148 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
| 149 return; | |
| 150 } | |
| 151 | |
| 152 // Look for the "Start of Frame" header (FF C0) | |
| 153 for (size_t i = 2; i + 1 < tile.size(); i++) | |
| 154 { | |
| 155 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
| 156 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
| 157 { | |
| 158 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
| 159 | |
| 160 switch (pixelFormat) | |
| 161 { | |
| 162 case Orthanc::PixelFormat_Grayscale8: | |
| 163 if (numberOfComponents != 3) | |
| 164 { | |
| 165 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
| 166 } | |
| 167 break; | |
| 168 | |
| 169 case Orthanc::PixelFormat_RGB24: | |
| 170 { | |
| 171 if (numberOfComponents != 3) | |
| 172 { | |
| 173 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
| 174 } | |
| 175 | |
| 176 // Read the header corresponding to the first component | |
| 177 const size_t component = 0; | |
| 178 const size_t offset = i + 10 + component * 3; | |
| 179 const uint8_t sampling = GetUint8(tile, offset + 1); | |
| 180 const int samplingH = sampling / 16; | |
| 181 const int samplingV = sampling % 16; | |
| 182 | |
| 183 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
| 184 | |
| 185 if (samplingH != 2 || | |
| 186 samplingV != 2) | |
| 187 { | |
| 188 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
| 189 << "you should consider using option \"--reencode\""; | |
| 190 } | |
| 191 | |
| 192 break; | |
| 193 } | |
| 194 | |
| 195 default: | |
| 196 break; | |
| 197 } | |
| 198 } | |
| 199 } | |
| 200 } | |
| 201 | |
| 202 | |
| 203 | |
| 204 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
| 205 unsigned int tileX, | |
| 206 unsigned int tileY) | |
| 207 { | |
| 208 // Get the index of the tile | |
| 209 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
| 210 | |
| 211 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
| 212 static_cast<tsize_t>(tile.size())) | |
| 213 { | |
| 214 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 215 } | |
| 216 | |
| 217 if (isFirst_ && | |
| 218 GetImageCompression() == ImageCompression_Jpeg) | |
| 219 { | |
| 220 CheckJpegTile(tile, GetPixelFormat()); | |
| 221 } | |
| 222 | |
| 223 isFirst_ = false; | |
| 224 } | |
| 225 | |
| 226 | |
| 227 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
| 228 bool createLevel) | |
| 229 { | |
| 230 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
| 231 { | |
| 232 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 233 } | |
| 234 | |
| 235 if (TIFFFlush(tiff_) != 1) | |
| 236 { | |
| 237 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 238 } | |
| 239 | |
| 240 currentLevel_ = level.z_; | |
| 241 nextX_ = 0; | |
| 242 nextY_ = 0; | |
| 243 | |
| 244 switch (GetImageCompression()) | |
| 245 { | |
| 246 case ImageCompression_Jpeg: | |
| 247 { | |
| 248 uint16_t c = COMPRESSION_JPEG; | |
| 249 | |
| 250 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
| 251 { | |
| 252 Close(); | |
| 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 254 } | |
| 255 | |
| 256 break; | |
| 257 } | |
| 258 | |
| 259 default: | |
| 260 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 261 } | |
| 262 | |
| 263 | |
| 264 switch (GetPixelFormat()) | |
| 265 { | |
| 266 case Orthanc::PixelFormat_RGB24: | |
| 267 { | |
| 268 uint16_t samplesPerPixel = 3; | |
| 269 uint16_t photometric = PHOTOMETRIC_YCBCR; | |
| 270 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB | |
| 271 uint16_t bpp = 8; | |
| 272 uint16_t subsampleHorizontal = 2; | |
| 273 uint16_t subsampleVertical = 2; | |
| 274 | |
| 275 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || | |
| 276 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
| 277 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
| 278 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
| 279 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
| 280 { | |
| 281 Close(); | |
| 282 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 283 } | |
| 284 | |
| 285 break; | |
| 286 } | |
| 287 | |
| 288 default: | |
| 289 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 290 } | |
| 291 | |
| 292 uint32_t w = level.width_; | |
| 293 uint32_t h = level.height_; | |
| 294 uint32_t tw = GetTileWidth(); | |
| 295 uint32_t th = GetTileHeight(); | |
| 296 | |
| 297 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
| 298 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
| 299 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
| 300 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
| 301 { | |
| 302 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 303 } | |
| 304 } | |
| 305 | |
| 306 | |
| 307 void HierarchicalTiffWriter::AdvanceToNextTile() | |
| 308 { | |
| 309 assert(currentLevel_ < levels_.size()); | |
| 310 | |
| 311 nextX_ += 1; | |
| 312 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
| 313 { | |
| 314 nextX_ = 0; | |
| 315 nextY_ += 1; | |
| 316 | |
| 317 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
| 318 { | |
| 319 currentLevel_ += 1; | |
| 320 | |
| 321 if (currentLevel_ < levels_.size()) | |
| 322 { | |
| 323 ConfigureLevel(levels_[currentLevel_], true); | |
| 324 } | |
| 325 } | |
| 326 } | |
| 327 } | |
| 328 | |
| 329 | |
| 330 void HierarchicalTiffWriter::ScanPending() | |
| 331 { | |
| 332 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
| 333 | |
| 334 while (currentLevel_ < levels_.size() && | |
| 335 !pending_.empty() && | |
| 336 pending_.front()->GetLevel() == currentLevel_ && | |
| 337 pending_.front()->GetTileX() == nextX_ && | |
| 338 pending_.front()->GetTileY() == nextY_) | |
| 339 { | |
| 340 pending_.front()->Store(tiff_); | |
| 341 delete pending_.front(); | |
| 342 pending_.pop_front(); | |
| 343 AdvanceToNextTile(); | |
| 344 } | |
| 345 } | |
| 346 | |
| 347 | |
| 348 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
| 349 const Level& level, | |
| 350 unsigned int tileX, | |
| 351 unsigned int tileY) | |
| 352 { | |
| 353 boost::mutex::scoped_lock lock(mutex_); | |
| 354 | |
| 355 if (level.z_ == currentLevel_ && | |
| 356 tileX == nextX_ && | |
| 357 tileY == nextY_) | |
| 358 { | |
| 359 StoreTile(tile, tileX, tileY); | |
| 360 AdvanceToNextTile(); | |
| 361 ScanPending(); | |
| 362 } | |
| 363 else | |
| 364 { | |
| 365 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
| 366 } | |
| 367 } | |
| 368 | |
| 369 | |
| 370 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
| 371 { | |
| 372 if (level.z_ == 0) | |
| 373 { | |
| 374 // Configure the finest level on initialization | |
| 375 ConfigureLevel(level, false); | |
| 376 } | |
| 377 | |
| 378 levels_.push_back(level); | |
| 379 } | |
| 380 | |
| 381 | |
| 382 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
| 383 Orthanc::PixelFormat pixelFormat, | |
| 384 ImageCompression compression, | |
| 385 unsigned int tileWidth, | |
| 386 unsigned int tileHeight) : | |
| 387 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), | |
| 388 currentLevel_(0), | |
| 389 isFirst_(true) | |
| 390 { | |
| 391 tiff_ = TIFFOpen(path.c_str(), "w"); | |
| 392 if (tiff_ == NULL) | |
| 393 { | |
| 394 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 395 } | |
| 396 } | |
| 397 | |
| 398 | |
| 399 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
| 400 { | |
| 401 if (pending_.size()) | |
| 402 { | |
| 403 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
| 404 } | |
| 405 | |
| 406 for (size_t i = 0; i < pending_.size(); i++) | |
| 407 { | |
| 408 if (pending_[i]) | |
| 409 { | |
| 410 delete pending_[i]; | |
| 411 } | |
| 412 } | |
| 413 | |
| 414 Close(); | |
| 415 } | |
| 416 | |
| 417 | |
| 418 void HierarchicalTiffWriter::Flush() | |
| 419 { | |
| 420 boost::mutex::scoped_lock lock(mutex_); | |
| 421 ScanPending(); | |
| 422 } | |
| 423 } |