Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/HierarchicalTiff.cpp @ 296:559499b80da8
refactoring
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 18 Jul 2023 06:45:44 +0200 |
| parents | 20a730889ae2 |
| children | c1687b8fc800 |
| 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 | |
| 254 | 5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
| 6 * Copyright (C) 2021-2023 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 "HierarchicalTiff.h" |
| 25 | |
| 192 | 26 #include <Logging.h> |
| 27 #include <OrthancException.h> | |
| 0 | 28 |
| 29 #include <iostream> | |
| 30 #include <algorithm> | |
| 31 #include <cassert> | |
| 32 #include <string.h> | |
| 33 | |
| 34 namespace OrthancWSI | |
| 35 { | |
| 36 HierarchicalTiff::Level::Level(TIFF* tiff, | |
| 37 tdir_t directory, | |
| 38 unsigned int width, | |
| 39 unsigned int height) : | |
| 40 directory_(directory), | |
| 41 width_(width), | |
| 42 height_(height) | |
| 43 { | |
| 44 // Read the JPEG headers shared at that level, if any | |
| 45 uint8_t *tables = NULL; | |
| 46 uint32_t size; | |
| 47 if (TIFFGetField(tiff, TIFFTAG_JPEGTABLES, &size, &tables) && | |
| 48 size > 0 && | |
| 49 tables != NULL) | |
| 50 { | |
| 51 // Look for the EOI (end-of-image) tag == FF D9 | |
| 52 // https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format | |
| 53 | |
| 54 bool found = false; | |
| 55 | |
| 56 for (size_t i = 0; i + 1 < size; i++) | |
| 57 { | |
| 58 if (tables[i] == 0xff && | |
| 59 tables[i + 1] == 0xd9) | |
| 60 { | |
| 61 headers_.assign(reinterpret_cast<const char*>(tables), i); | |
| 62 found = true; | |
| 63 } | |
| 64 } | |
| 65 | |
| 66 if (!found) | |
| 67 { | |
| 68 headers_.assign(reinterpret_cast<const char*>(tables), size); | |
| 69 } | |
| 70 } | |
| 71 } | |
| 72 | |
| 73 struct HierarchicalTiff::Comparator | |
| 74 { | |
| 75 bool operator() (const HierarchicalTiff::Level& a, | |
| 76 const HierarchicalTiff::Level& b) const | |
| 77 { | |
| 78 return a.width_ > b.width_; | |
| 79 } | |
| 80 }; | |
| 81 | |
| 82 | |
| 83 void HierarchicalTiff::Finalize() | |
| 84 { | |
| 85 if (tiff_) | |
| 86 { | |
| 87 TIFFClose(tiff_); | |
| 88 tiff_ = NULL; | |
| 89 } | |
| 90 } | |
| 91 | |
| 92 | |
| 93 void HierarchicalTiff::CheckLevel(unsigned int level) const | |
| 94 { | |
| 95 if (level >= levels_.size()) | |
| 96 { | |
| 97 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 98 } | |
| 99 } | |
| 100 | |
| 101 | |
| 296 | 102 bool HierarchicalTiff::GetCurrentDirectoryInformation(TIFF* tiff, |
| 103 ImageCompression& compression, | |
| 104 Orthanc::PixelFormat& pixelFormat, | |
| 105 Orthanc::PhotometricInterpretation& photometric) | |
| 0 | 106 { |
| 107 uint16_t c; | |
| 296 | 108 if (!TIFFGetField(tiff, TIFFTAG_COMPRESSION, &c)) |
| 0 | 109 { |
| 110 return false; | |
| 111 } | |
| 112 | |
| 113 switch (c) | |
| 114 { | |
| 115 case COMPRESSION_NONE: | |
| 116 compression = ImageCompression_None; | |
| 296 | 117 break; |
| 0 | 118 |
| 119 case COMPRESSION_JPEG: | |
| 120 compression = ImageCompression_Jpeg; | |
| 296 | 121 break; |
| 0 | 122 |
| 123 default: | |
| 124 return false; | |
| 125 } | |
| 126 | |
| 127 // http://www.awaresystems.be/imaging/tiff/tifftags/baseline.html | |
| 128 | |
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129 uint16_t channels, photometricTiff, bpp, planar; |
| 296 | 130 if (!TIFFGetField(tiff, TIFFTAG_SAMPLESPERPIXEL, &channels) || |
| 0 | 131 channels == 0 || |
| 296 | 132 !TIFFGetField(tiff, TIFFTAG_PHOTOMETRIC, &photometricTiff) || |
| 133 !TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &bpp) || | |
| 134 !TIFFGetField(tiff, TIFFTAG_PLANARCONFIG, &planar)) | |
| 0 | 135 { |
| 136 return false; | |
| 137 } | |
| 138 | |
| 139 if (compression == ImageCompression_Jpeg && | |
| 140 channels == 3 && // This is a color image | |
| 141 bpp == 8 && | |
| 142 planar == PLANARCONFIG_CONTIG) // This is interleaved RGB | |
| 143 { | |
| 144 pixelFormat = Orthanc::PixelFormat_RGB24; | |
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145 |
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146 switch (photometricTiff) |
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147 { |
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148 case PHOTOMETRIC_YCBCR: |
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149 photometric = Orthanc::PhotometricInterpretation_YBRFull422; |
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150 return true; |
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151 |
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152 case PHOTOMETRIC_RGB: |
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153 photometric = Orthanc::PhotometricInterpretation_RGB; |
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154 return true; |
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155 |
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156 default: |
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157 LOG(ERROR) << "Unknown photometric interpretation in TIFF: " << photometricTiff; |
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158 return false; |
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159 } |
| 0 | 160 } |
| 296 | 161 else if (compression == ImageCompression_None && |
| 162 channels == 3 && // This is a color image | |
| 163 bpp == 8 && | |
| 164 planar == PLANARCONFIG_CONTIG) // This is interleaved RGB | |
| 165 { | |
| 166 pixelFormat = Orthanc::PixelFormat_RGB24; | |
| 167 photometric = Orthanc::PhotometricInterpretation_RGB; | |
| 168 return true; | |
| 169 } | |
|
172
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170 else if (compression == ImageCompression_Jpeg && |
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171 channels == 1 && // This is a grayscale image |
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172 bpp == 8) |
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173 { |
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174 pixelFormat = Orthanc::PixelFormat_Grayscale8; |
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175 photometric = Orthanc::PhotometricInterpretation_Monochrome2; |
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176 } |
| 0 | 177 else |
| 178 { | |
| 179 return false; | |
| 180 } | |
| 181 | |
| 182 return true; | |
| 183 } | |
| 184 | |
| 185 | |
| 186 bool HierarchicalTiff::Initialize() | |
| 187 { | |
| 188 bool first = true; | |
| 189 tdir_t pos = 0; | |
| 190 | |
| 191 do | |
| 192 { | |
| 193 uint32_t w, h, tw, th; | |
| 194 ImageCompression compression; | |
| 195 Orthanc::PixelFormat pixelFormat; | |
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196 Orthanc::PhotometricInterpretation photometric; |
| 0 | 197 |
| 198 if (TIFFSetDirectory(tiff_, pos) && | |
| 199 TIFFGetField(tiff_, TIFFTAG_IMAGEWIDTH, &w) && | |
| 200 TIFFGetField(tiff_, TIFFTAG_IMAGELENGTH, &h) && | |
| 201 TIFFGetField(tiff_, TIFFTAG_TILEWIDTH, &tw) && | |
| 202 TIFFGetField(tiff_, TIFFTAG_TILELENGTH, &th) && | |
| 203 w > 0 && | |
| 204 h > 0 && | |
| 205 tw > 0 && | |
| 206 th > 0 && | |
| 296 | 207 GetCurrentDirectoryInformation(tiff_, compression, pixelFormat, photometric)) |
| 0 | 208 { |
| 209 if (first) | |
| 210 { | |
| 211 tileWidth_ = tw; | |
| 212 tileHeight_ = th; | |
| 213 compression_ = compression; | |
| 214 pixelFormat_ = pixelFormat; | |
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215 photometric_ = photometric; |
| 0 | 216 first = false; |
| 217 } | |
| 218 else if (tw != tileWidth_ || | |
| 219 th != tileHeight_ || | |
| 220 compression_ != compression || | |
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221 pixelFormat_ != pixelFormat || |
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222 photometric_ != photometric) |
| 0 | 223 { |
| 224 LOG(ERROR) << "The tile size or compression of the TIFF file varies along levels, this is not supported"; | |
| 225 return false; | |
| 226 } | |
| 227 | |
| 228 levels_.push_back(Level(tiff_, pos, w, h)); | |
| 229 } | |
| 230 | |
| 231 pos++; | |
| 232 } | |
| 233 while (TIFFReadDirectory(tiff_)); | |
| 234 | |
| 235 if (levels_.size() == 0) | |
| 236 { | |
| 237 LOG(ERROR) << "This is not a tiled TIFF image"; | |
| 238 return false; | |
| 239 } | |
| 240 | |
| 241 std::sort(levels_.begin(), levels_.end(), Comparator()); | |
| 242 return true; | |
| 243 } | |
| 244 | |
| 245 | |
| 246 HierarchicalTiff::HierarchicalTiff(const std::string& path) : | |
| 247 tileWidth_(0), | |
| 248 tileHeight_(0) | |
| 249 { | |
| 250 tiff_ = TIFFOpen(path.c_str(), "r"); | |
| 251 if (tiff_ == NULL) | |
| 252 { | |
| 253 LOG(ERROR) << "libtiff cannot open: " << path; | |
| 254 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentFile); | |
| 255 } | |
| 256 | |
| 257 if (!Initialize()) | |
| 258 { | |
| 259 Finalize(); | |
| 260 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 261 } | |
| 262 } | |
| 263 | |
| 264 | |
| 265 unsigned int HierarchicalTiff::GetLevelWidth(unsigned int level) const | |
| 266 { | |
| 267 CheckLevel(level); | |
| 268 return levels_[level].width_; | |
| 269 } | |
| 270 | |
| 271 | |
| 272 unsigned int HierarchicalTiff::GetLevelHeight(unsigned int level) const | |
| 273 { | |
| 274 CheckLevel(level); | |
| 275 return levels_[level].height_; | |
| 276 } | |
| 277 | |
| 278 | |
| 279 bool HierarchicalTiff::ReadRawTile(std::string& tile, | |
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280 ImageCompression& compression, |
| 0 | 281 unsigned int level, |
| 282 unsigned int tileX, | |
| 283 unsigned int tileY) | |
| 284 { | |
| 285 boost::mutex::scoped_lock lock(mutex_); | |
| 286 | |
| 287 CheckLevel(level); | |
| 288 | |
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289 compression = compression_; |
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290 |
| 0 | 291 // Make the TIFF context point to the level of interest |
| 292 if (!TIFFSetDirectory(tiff_, levels_[level].directory_)) | |
| 293 { | |
| 294 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 295 } | |
| 296 | |
| 297 // Get the index of the tile | |
| 298 ttile_t index = TIFFComputeTile(tiff_, tileX * tileWidth_, tileY * tileHeight_, 0 /*z*/, 0 /*sample*/); | |
| 299 | |
| 300 // Read the raw tile | |
| 301 toff_t *sizes; | |
| 302 if (!TIFFGetField(tiff_, TIFFTAG_TILEBYTECOUNTS, &sizes)) | |
| 303 { | |
| 304 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 305 } | |
| 306 | |
| 307 std::string raw; | |
| 308 raw.resize(sizes[index]); | |
| 309 | |
| 310 tsize_t read = TIFFReadRawTile(tiff_, index, &raw[0], raw.size()); | |
| 311 if (read != static_cast<tsize_t>(sizes[index])) | |
| 312 { | |
| 313 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 314 } | |
| 315 | |
| 316 const std::string& headers = levels_[level].headers_; | |
| 317 | |
| 318 // Possibly prepend the raw tile with the shared JPEG headers | |
| 319 if (headers.empty() || | |
| 320 compression_ != ImageCompression_Jpeg) | |
| 321 { | |
| 322 tile.swap(raw); // Same as "tile.assign(raw)", but optimizes memory | |
| 323 } | |
| 324 else | |
| 325 { | |
| 326 assert(compression_ == ImageCompression_Jpeg); | |
| 327 | |
| 328 // Check that the raw JPEG tile starts with the SOI (start-of-image) tag == FF D8 | |
| 329 if (raw.size() < 2 || | |
| 330 static_cast<uint8_t>(raw[0]) != 0xff || | |
| 331 static_cast<uint8_t>(raw[1]) != 0xd8) | |
| 332 { | |
| 333 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 334 } | |
| 335 | |
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336 if (photometric_ == Orthanc::PhotometricInterpretation_RGB && |
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337 pixelFormat_ == Orthanc::PixelFormat_RGB24) |
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338 { |
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339 /** |
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340 * Insert an Adobe APP14 marker with the "transform" flag set |
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341 * to value 0, which indicates to the JPEG decoder that |
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342 * "3-channel images are assumed to be RGB". Section 18 of |
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343 * "Supporting the DCT Filters in PostScript Level 2 - |
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344 * Technical Note #5116": |
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345 * https://stackoverflow.com/a/9658206/881731 |
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346 * https://docs.oracle.com/javase/6/docs/api/javax/imageio/metadata/doc-files/jpeg_metadata.html |
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347 * https://www.pdfa.org/wp-content/uploads/2020/07/5116.DCT_Filter.pdf |
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348 **/ |
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349 static const uint8_t APP14[] = { |
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350 0xff, 0xee, /* JPEG Marker for Adobe segment: http://www.ozhiker.com/electronics/pjmt/jpeg_info/app_segments.html */ |
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351 0x00, 0x0e, /* Length (without the JPEG marker) == 0x0e == 14 bytes */ |
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352 0x41, 0x64, 0x6f, 0x62, 0x65, /* "Adobe" string in ASCII */ |
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353 0x00, 0x64, /* Version == Two-byte DCTEncode/DCTDecode version number == 0x64 */ |
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354 0x80, 0x00, /* Two-byte "flags0" 0x8000 bit: Encoder used Blend=1 downsampling */ |
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355 0x00, 0x00, /* Two-byte "flags1": Set to zero */ |
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356 0x00 /* One-byte color transform code == 0 <== This is the important one */ |
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357 }; |
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358 assert(sizeof(APP14) == 16); |
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359 |
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360 tile.resize(headers.size() + sizeof(APP14) + raw.size() - 2); |
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361 memcpy(&tile[0], &headers[0], headers.size()); |
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362 memcpy(&tile[0] + headers.size(), APP14, sizeof(APP14)); |
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363 memcpy(&tile[0] + headers.size() + sizeof(APP14), &raw[2], raw.size() - 2); |
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364 } |
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365 else |
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366 { |
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367 tile.resize(headers.size() + raw.size() - 2); |
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368 memcpy(&tile[0], &headers[0], headers.size()); |
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369 memcpy(&tile[0] + headers.size(), &raw[2], raw.size() - 2); |
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370 } |
| 0 | 371 } |
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372 |
| 0 | 373 return true; |
| 374 } | |
| 375 } |