Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 77:9220f61997e2
fix mainline version
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 28 Nov 2016 17:44:48 +0100 |
| parents | 7a3853d51c45 |
| children | ff0ef01c332c |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
|
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preparing for precompiled headers
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21 #include "../PrecompiledHeadersWSI.h" |
| 0 | 22 #include "HierarchicalTiffWriter.h" |
| 23 | |
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24 #include "../../Resources/Orthanc/Core/Logging.h" |
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25 #include "../../Resources/Orthanc/Core/OrthancException.h" |
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26 #include "../../Resources/Orthanc/Core/TemporaryFile.h" |
| 0 | 27 |
| 28 namespace OrthancWSI | |
| 29 { | |
| 30 class HierarchicalTiffWriter::PendingTile | |
| 31 { | |
| 32 private: | |
| 43 | 33 HierarchicalTiffWriter& that_; |
| 34 unsigned int level_; | |
| 35 unsigned int tileX_; | |
| 36 unsigned int tileY_; | |
| 37 Orthanc::TemporaryFile file_; | |
| 0 | 38 |
| 39 public: | |
| 40 PendingTile(HierarchicalTiffWriter& that, | |
| 41 unsigned int level, | |
| 42 unsigned int tileX, | |
| 43 unsigned int tileY, | |
| 44 const std::string& tile) : | |
| 45 that_(that), | |
| 46 level_(level), | |
| 47 tileX_(tileX), | |
| 48 tileY_(tileY) | |
| 49 { | |
| 50 file_.Write(tile); | |
| 51 } | |
| 52 | |
| 53 unsigned int GetLevel() const | |
| 54 { | |
| 55 return level_; | |
| 56 } | |
| 57 | |
| 58 unsigned int GetTileX() const | |
| 59 { | |
| 60 return tileX_; | |
| 61 } | |
| 62 | |
| 63 unsigned int GetTileY() const | |
| 64 { | |
| 65 return tileY_; | |
| 66 } | |
| 67 | |
| 68 void Store(TIFF* tiff) | |
| 69 { | |
| 70 std::string tile; | |
| 71 file_.Read(tile); | |
| 72 that_.StoreTile(tile, tileX_, tileY_); | |
| 73 } | |
| 74 }; | |
| 75 | |
| 76 | |
| 77 struct HierarchicalTiffWriter::Comparator | |
| 78 { | |
| 79 inline bool operator() (PendingTile* const& a, | |
| 80 PendingTile* const& b) | |
| 81 { | |
| 82 if (a->GetLevel() < b->GetLevel()) | |
| 83 { | |
| 84 return true; | |
| 85 } | |
| 86 | |
| 87 if (a->GetLevel() > b->GetLevel()) | |
| 88 { | |
| 89 return false; | |
| 90 } | |
| 91 | |
| 92 if (a->GetTileY() < b->GetTileY()) | |
| 93 { | |
| 94 return true; | |
| 95 } | |
| 96 | |
| 97 if (a->GetTileY() > b->GetTileY()) | |
| 98 { | |
| 99 return false; | |
| 100 } | |
| 101 | |
| 102 return a->GetTileX() < b->GetTileX(); | |
| 103 } | |
| 104 }; | |
| 105 | |
| 106 | |
| 107 static uint8_t GetUint8(const std::string& tile, | |
| 108 size_t index) | |
| 109 { | |
| 110 if (index >= tile.size()) | |
| 111 { | |
| 112 return 0; | |
| 113 } | |
| 114 else | |
| 115 { | |
| 116 return static_cast<uint8_t>(tile[index]); | |
| 117 } | |
| 118 } | |
| 119 | |
| 120 | |
| 121 #if 0 | |
| 122 static uint16_t GetUint16(const std::string& tile, | |
| 123 size_t index) | |
| 124 { | |
| 125 if (index + 1 >= tile.size()) | |
| 126 { | |
| 127 return 0; | |
| 128 } | |
| 129 else | |
| 130 { | |
| 131 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
| 132 } | |
| 133 } | |
| 134 #endif | |
| 135 | |
| 136 | |
| 137 static void CheckJpegTile(const std::string& tile, | |
| 138 Orthanc::PixelFormat pixelFormat) | |
| 139 { | |
| 140 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
| 141 | |
| 142 if (tile.size() < 3 || | |
| 143 static_cast<uint8_t>(tile[0]) != 0xff || | |
| 144 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
| 145 static_cast<uint8_t>(tile[2]) != 0xff) | |
| 146 { | |
| 147 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
| 148 return; | |
| 149 } | |
| 150 | |
| 151 // Look for the "Start of Frame" header (FF C0) | |
| 152 for (size_t i = 2; i + 1 < tile.size(); i++) | |
| 153 { | |
| 154 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
| 155 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
| 156 { | |
| 157 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
| 158 | |
| 159 switch (pixelFormat) | |
| 160 { | |
| 161 case Orthanc::PixelFormat_Grayscale8: | |
| 162 if (numberOfComponents != 3) | |
| 163 { | |
| 164 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
| 165 } | |
| 166 break; | |
| 167 | |
| 168 case Orthanc::PixelFormat_RGB24: | |
| 169 { | |
| 170 if (numberOfComponents != 3) | |
| 171 { | |
| 172 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
| 173 } | |
| 174 | |
| 175 // Read the header corresponding to the first component | |
| 176 const size_t component = 0; | |
| 177 const size_t offset = i + 10 + component * 3; | |
| 178 const uint8_t sampling = GetUint8(tile, offset + 1); | |
| 179 const int samplingH = sampling / 16; | |
| 180 const int samplingV = sampling % 16; | |
| 181 | |
| 182 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
| 183 | |
| 184 if (samplingH != 2 || | |
| 185 samplingV != 2) | |
| 186 { | |
| 187 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
| 188 << "you should consider using option \"--reencode\""; | |
| 189 } | |
| 190 | |
| 191 break; | |
| 192 } | |
| 193 | |
| 194 default: | |
| 195 break; | |
| 196 } | |
| 197 } | |
| 198 } | |
| 199 } | |
| 200 | |
| 201 | |
| 202 | |
| 203 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
| 204 unsigned int tileX, | |
| 205 unsigned int tileY) | |
| 206 { | |
| 207 // Get the index of the tile | |
| 208 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
| 209 | |
| 210 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
| 211 static_cast<tsize_t>(tile.size())) | |
| 212 { | |
| 213 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 214 } | |
| 215 | |
| 216 if (isFirst_ && | |
| 217 GetImageCompression() == ImageCompression_Jpeg) | |
| 218 { | |
| 219 CheckJpegTile(tile, GetPixelFormat()); | |
| 220 } | |
| 221 | |
| 222 isFirst_ = false; | |
| 223 } | |
| 224 | |
| 225 | |
| 226 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
| 227 bool createLevel) | |
| 228 { | |
| 229 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
| 230 { | |
| 231 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 232 } | |
| 233 | |
| 234 if (TIFFFlush(tiff_) != 1) | |
| 235 { | |
| 236 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 237 } | |
| 238 | |
| 239 currentLevel_ = level.z_; | |
| 240 nextX_ = 0; | |
| 241 nextY_ = 0; | |
| 242 | |
| 243 switch (GetImageCompression()) | |
| 244 { | |
| 245 case ImageCompression_Jpeg: | |
| 246 { | |
| 247 uint16_t c = COMPRESSION_JPEG; | |
| 248 | |
| 249 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
| 250 { | |
| 251 Close(); | |
| 252 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 253 } | |
| 254 | |
| 255 break; | |
| 256 } | |
| 257 | |
| 258 default: | |
| 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 260 } | |
| 261 | |
| 262 | |
| 263 switch (GetPixelFormat()) | |
| 264 { | |
| 265 case Orthanc::PixelFormat_RGB24: | |
| 266 { | |
| 267 uint16_t samplesPerPixel = 3; | |
| 268 uint16_t photometric = PHOTOMETRIC_YCBCR; | |
| 269 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB | |
| 270 uint16_t bpp = 8; | |
| 271 uint16_t subsampleHorizontal = 2; | |
| 272 uint16_t subsampleVertical = 2; | |
| 273 | |
| 274 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || | |
| 275 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
| 276 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
| 277 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
| 278 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
| 279 { | |
| 280 Close(); | |
| 281 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 282 } | |
| 283 | |
| 284 break; | |
| 285 } | |
| 286 | |
| 287 default: | |
| 288 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 289 } | |
| 290 | |
| 291 uint32_t w = level.width_; | |
| 292 uint32_t h = level.height_; | |
| 293 uint32_t tw = GetTileWidth(); | |
| 294 uint32_t th = GetTileHeight(); | |
| 295 | |
| 296 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
| 297 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
| 298 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
| 299 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
| 300 { | |
| 301 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 302 } | |
| 303 } | |
| 304 | |
| 305 | |
| 306 void HierarchicalTiffWriter::AdvanceToNextTile() | |
| 307 { | |
| 308 assert(currentLevel_ < levels_.size()); | |
| 309 | |
| 310 nextX_ += 1; | |
| 311 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
| 312 { | |
| 313 nextX_ = 0; | |
| 314 nextY_ += 1; | |
| 315 | |
| 316 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
| 317 { | |
| 318 currentLevel_ += 1; | |
| 319 | |
| 320 if (currentLevel_ < levels_.size()) | |
| 321 { | |
| 322 ConfigureLevel(levels_[currentLevel_], true); | |
| 323 } | |
| 324 } | |
| 325 } | |
| 326 } | |
| 327 | |
| 328 | |
| 329 void HierarchicalTiffWriter::ScanPending() | |
| 330 { | |
| 331 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
| 332 | |
| 333 while (currentLevel_ < levels_.size() && | |
| 334 !pending_.empty() && | |
| 335 pending_.front()->GetLevel() == currentLevel_ && | |
| 336 pending_.front()->GetTileX() == nextX_ && | |
| 337 pending_.front()->GetTileY() == nextY_) | |
| 338 { | |
| 339 pending_.front()->Store(tiff_); | |
| 340 delete pending_.front(); | |
| 341 pending_.pop_front(); | |
| 342 AdvanceToNextTile(); | |
| 343 } | |
| 344 } | |
| 345 | |
| 346 | |
| 347 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
| 348 const Level& level, | |
| 349 unsigned int tileX, | |
| 350 unsigned int tileY) | |
| 351 { | |
| 352 boost::mutex::scoped_lock lock(mutex_); | |
| 353 | |
| 354 if (level.z_ == currentLevel_ && | |
| 355 tileX == nextX_ && | |
| 356 tileY == nextY_) | |
| 357 { | |
| 358 StoreTile(tile, tileX, tileY); | |
| 359 AdvanceToNextTile(); | |
| 360 ScanPending(); | |
| 361 } | |
| 362 else | |
| 363 { | |
| 364 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
| 365 } | |
| 366 } | |
| 367 | |
| 368 | |
| 369 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
| 370 { | |
| 371 if (level.z_ == 0) | |
| 372 { | |
| 373 // Configure the finest level on initialization | |
| 374 ConfigureLevel(level, false); | |
| 375 } | |
| 376 | |
| 377 levels_.push_back(level); | |
| 378 } | |
| 379 | |
| 380 | |
| 381 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
| 382 Orthanc::PixelFormat pixelFormat, | |
| 383 ImageCompression compression, | |
| 384 unsigned int tileWidth, | |
| 385 unsigned int tileHeight) : | |
| 386 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), | |
| 387 currentLevel_(0), | |
| 388 isFirst_(true) | |
| 389 { | |
| 390 tiff_ = TIFFOpen(path.c_str(), "w"); | |
| 391 if (tiff_ == NULL) | |
| 392 { | |
| 393 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
| 394 } | |
| 395 } | |
| 396 | |
| 397 | |
| 398 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
| 399 { | |
| 400 if (pending_.size()) | |
| 401 { | |
| 402 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
| 403 } | |
| 404 | |
| 405 for (size_t i = 0; i < pending_.size(); i++) | |
| 406 { | |
| 407 if (pending_[i]) | |
| 408 { | |
| 409 delete pending_[i]; | |
| 410 } | |
| 411 } | |
| 412 | |
| 413 Close(); | |
| 414 } | |
| 415 | |
| 416 | |
| 417 void HierarchicalTiffWriter::Flush() | |
| 418 { | |
| 419 boost::mutex::scoped_lock lock(mutex_); | |
| 420 ScanPending(); | |
| 421 } | |
| 422 } |