Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/HierarchicalTiff.cpp @ 166:f0dac1e8f736
access to photometric interpretation of source pyramids
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 12 Jul 2019 09:06:54 +0200 |
| parents | 6b8ccfc02051 |
| children | 11413cc2b9d6 |
| 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 | |
| 157 | 5 * Copyright (C) 2017-2019 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 "HierarchicalTiff.h" |
| 24 | |
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25 #include <Core/Logging.h> |
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26 #include <Core/OrthancException.h> |
| 0 | 27 |
| 28 #include <iostream> | |
| 29 #include <algorithm> | |
| 30 #include <cassert> | |
| 31 #include <string.h> | |
| 32 | |
| 33 namespace OrthancWSI | |
| 34 { | |
| 35 HierarchicalTiff::Level::Level(TIFF* tiff, | |
| 36 tdir_t directory, | |
| 37 unsigned int width, | |
| 38 unsigned int height) : | |
| 39 directory_(directory), | |
| 40 width_(width), | |
| 41 height_(height) | |
| 42 { | |
| 43 // Read the JPEG headers shared at that level, if any | |
| 44 uint8_t *tables = NULL; | |
| 45 uint32_t size; | |
| 46 if (TIFFGetField(tiff, TIFFTAG_JPEGTABLES, &size, &tables) && | |
| 47 size > 0 && | |
| 48 tables != NULL) | |
| 49 { | |
| 50 // Look for the EOI (end-of-image) tag == FF D9 | |
| 51 // https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format | |
| 52 | |
| 53 bool found = false; | |
| 54 | |
| 55 for (size_t i = 0; i + 1 < size; i++) | |
| 56 { | |
| 57 if (tables[i] == 0xff && | |
| 58 tables[i + 1] == 0xd9) | |
| 59 { | |
| 60 headers_.assign(reinterpret_cast<const char*>(tables), i); | |
| 61 found = true; | |
| 62 } | |
| 63 } | |
| 64 | |
| 65 if (!found) | |
| 66 { | |
| 67 headers_.assign(reinterpret_cast<const char*>(tables), size); | |
| 68 } | |
| 69 } | |
| 70 } | |
| 71 | |
| 72 struct HierarchicalTiff::Comparator | |
| 73 { | |
| 74 bool operator() (const HierarchicalTiff::Level& a, | |
| 75 const HierarchicalTiff::Level& b) const | |
| 76 { | |
| 77 return a.width_ > b.width_; | |
| 78 } | |
| 79 }; | |
| 80 | |
| 81 | |
| 82 void HierarchicalTiff::Finalize() | |
| 83 { | |
| 84 if (tiff_) | |
| 85 { | |
| 86 TIFFClose(tiff_); | |
| 87 tiff_ = NULL; | |
| 88 } | |
| 89 } | |
| 90 | |
| 91 | |
| 92 void HierarchicalTiff::CheckLevel(unsigned int level) const | |
| 93 { | |
| 94 if (level >= levels_.size()) | |
| 95 { | |
| 96 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 97 } | |
| 98 } | |
| 99 | |
| 100 | |
| 101 bool HierarchicalTiff::GetCurrentCompression(ImageCompression& compression) | |
| 102 { | |
| 103 uint16_t c; | |
| 104 if (!TIFFGetField(tiff_, TIFFTAG_COMPRESSION, &c)) | |
| 105 { | |
| 106 return false; | |
| 107 } | |
| 108 | |
| 109 switch (c) | |
| 110 { | |
| 111 case COMPRESSION_NONE: | |
| 112 compression = ImageCompression_None; | |
| 113 return true; | |
| 114 | |
| 115 case COMPRESSION_JPEG: | |
| 116 compression = ImageCompression_Jpeg; | |
| 117 return true; | |
| 118 | |
| 119 default: | |
| 120 return false; | |
| 121 } | |
| 122 } | |
| 123 | |
| 124 | |
| 125 bool HierarchicalTiff::GetCurrentPixelFormat(Orthanc::PixelFormat& pixelFormat, | |
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126 Orthanc::PhotometricInterpretation& photometric, |
| 0 | 127 ImageCompression compression) |
| 128 { | |
| 129 // http://www.awaresystems.be/imaging/tiff/tifftags/baseline.html | |
| 130 | |
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131 uint16_t channels, photometricTiff, bpp, planar; |
| 0 | 132 if (!TIFFGetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, &channels) || |
| 133 channels == 0 || | |
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134 !TIFFGetField(tiff_, TIFFTAG_PHOTOMETRIC, &photometricTiff) || |
| 0 | 135 !TIFFGetField(tiff_, TIFFTAG_BITSPERSAMPLE, &bpp) || |
| 136 !TIFFGetField(tiff_, TIFFTAG_PLANARCONFIG, &planar)) | |
| 137 { | |
| 138 return false; | |
| 139 } | |
| 140 | |
| 141 if (compression == ImageCompression_Jpeg && | |
| 142 channels == 3 && // This is a color image | |
| 143 bpp == 8 && | |
| 144 planar == PLANARCONFIG_CONTIG) // This is interleaved RGB | |
| 145 { | |
| 146 pixelFormat = Orthanc::PixelFormat_RGB24; | |
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147 |
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148 switch (photometricTiff) |
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149 { |
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150 case PHOTOMETRIC_YCBCR: |
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151 photometric = Orthanc::PhotometricInterpretation_YBRFull422; |
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152 return true; |
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153 |
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154 case PHOTOMETRIC_RGB: |
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155 photometric = Orthanc::PhotometricInterpretation_RGB; |
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156 return true; |
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157 |
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158 default: |
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159 LOG(ERROR) << "Unknown photometric interpretation in TIFF: " << photometricTiff; |
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160 return false; |
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161 } |
| 0 | 162 } |
| 163 else | |
| 164 { | |
| 165 return false; | |
| 166 } | |
| 167 | |
| 168 return true; | |
| 169 } | |
| 170 | |
| 171 | |
| 172 bool HierarchicalTiff::Initialize() | |
| 173 { | |
| 174 bool first = true; | |
| 175 tdir_t pos = 0; | |
| 176 | |
| 177 do | |
| 178 { | |
| 179 uint32_t w, h, tw, th; | |
| 180 ImageCompression compression; | |
| 181 Orthanc::PixelFormat pixelFormat; | |
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182 Orthanc::PhotometricInterpretation photometric; |
| 0 | 183 |
| 184 if (TIFFSetDirectory(tiff_, pos) && | |
| 185 TIFFGetField(tiff_, TIFFTAG_IMAGEWIDTH, &w) && | |
| 186 TIFFGetField(tiff_, TIFFTAG_IMAGELENGTH, &h) && | |
| 187 TIFFGetField(tiff_, TIFFTAG_TILEWIDTH, &tw) && | |
| 188 TIFFGetField(tiff_, TIFFTAG_TILELENGTH, &th) && | |
| 189 w > 0 && | |
| 190 h > 0 && | |
| 191 tw > 0 && | |
| 192 th > 0 && | |
| 193 GetCurrentCompression(compression) && | |
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194 GetCurrentPixelFormat(pixelFormat, photometric, compression)) |
| 0 | 195 { |
| 196 if (first) | |
| 197 { | |
| 198 tileWidth_ = tw; | |
| 199 tileHeight_ = th; | |
| 200 compression_ = compression; | |
| 201 pixelFormat_ = pixelFormat; | |
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202 photometric_ = photometric; |
| 0 | 203 first = false; |
| 204 } | |
| 205 else if (tw != tileWidth_ || | |
| 206 th != tileHeight_ || | |
| 207 compression_ != compression || | |
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208 pixelFormat_ != pixelFormat || |
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209 photometric_ != photometric) |
| 0 | 210 { |
| 211 LOG(ERROR) << "The tile size or compression of the TIFF file varies along levels, this is not supported"; | |
| 212 return false; | |
| 213 } | |
| 214 | |
| 215 levels_.push_back(Level(tiff_, pos, w, h)); | |
| 216 } | |
| 217 | |
| 218 pos++; | |
| 219 } | |
| 220 while (TIFFReadDirectory(tiff_)); | |
| 221 | |
| 222 if (levels_.size() == 0) | |
| 223 { | |
| 224 LOG(ERROR) << "This is not a tiled TIFF image"; | |
| 225 return false; | |
| 226 } | |
| 227 | |
| 228 std::sort(levels_.begin(), levels_.end(), Comparator()); | |
| 229 return true; | |
| 230 } | |
| 231 | |
| 232 | |
| 233 HierarchicalTiff::HierarchicalTiff(const std::string& path) : | |
| 234 tileWidth_(0), | |
| 235 tileHeight_(0) | |
| 236 { | |
| 237 tiff_ = TIFFOpen(path.c_str(), "r"); | |
| 238 if (tiff_ == NULL) | |
| 239 { | |
| 240 LOG(ERROR) << "libtiff cannot open: " << path; | |
| 241 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentFile); | |
| 242 } | |
| 243 | |
| 244 if (!Initialize()) | |
| 245 { | |
| 246 Finalize(); | |
| 247 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 248 } | |
| 249 } | |
| 250 | |
| 251 | |
| 252 unsigned int HierarchicalTiff::GetLevelWidth(unsigned int level) const | |
| 253 { | |
| 254 CheckLevel(level); | |
| 255 return levels_[level].width_; | |
| 256 } | |
| 257 | |
| 258 | |
| 259 unsigned int HierarchicalTiff::GetLevelHeight(unsigned int level) const | |
| 260 { | |
| 261 CheckLevel(level); | |
| 262 return levels_[level].height_; | |
| 263 } | |
| 264 | |
| 265 | |
| 266 bool HierarchicalTiff::ReadRawTile(std::string& tile, | |
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267 ImageCompression& compression, |
| 0 | 268 unsigned int level, |
| 269 unsigned int tileX, | |
| 270 unsigned int tileY) | |
| 271 { | |
| 272 boost::mutex::scoped_lock lock(mutex_); | |
| 273 | |
| 274 CheckLevel(level); | |
| 275 | |
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276 compression = compression_; |
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277 |
| 0 | 278 // Make the TIFF context point to the level of interest |
| 279 if (!TIFFSetDirectory(tiff_, levels_[level].directory_)) | |
| 280 { | |
| 281 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 282 } | |
| 283 | |
| 284 // Get the index of the tile | |
| 285 ttile_t index = TIFFComputeTile(tiff_, tileX * tileWidth_, tileY * tileHeight_, 0 /*z*/, 0 /*sample*/); | |
| 286 | |
| 287 // Read the raw tile | |
| 288 toff_t *sizes; | |
| 289 if (!TIFFGetField(tiff_, TIFFTAG_TILEBYTECOUNTS, &sizes)) | |
| 290 { | |
| 291 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 292 } | |
| 293 | |
| 294 std::string raw; | |
| 295 raw.resize(sizes[index]); | |
| 296 | |
| 297 tsize_t read = TIFFReadRawTile(tiff_, index, &raw[0], raw.size()); | |
| 298 if (read != static_cast<tsize_t>(sizes[index])) | |
| 299 { | |
| 300 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 301 } | |
| 302 | |
| 303 const std::string& headers = levels_[level].headers_; | |
| 304 | |
| 305 // Possibly prepend the raw tile with the shared JPEG headers | |
| 306 if (headers.empty() || | |
| 307 compression_ != ImageCompression_Jpeg) | |
| 308 { | |
| 309 tile.swap(raw); // Same as "tile.assign(raw)", but optimizes memory | |
| 310 } | |
| 311 else | |
| 312 { | |
| 313 assert(compression_ == ImageCompression_Jpeg); | |
| 314 | |
| 315 // Check that the raw JPEG tile starts with the SOI (start-of-image) tag == FF D8 | |
| 316 if (raw.size() < 2 || | |
| 317 static_cast<uint8_t>(raw[0]) != 0xff || | |
| 318 static_cast<uint8_t>(raw[1]) != 0xd8) | |
| 319 { | |
| 320 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 321 } | |
| 322 | |
| 323 tile.resize(headers.size() + raw.size() - 2); | |
| 324 memcpy(&tile[0], &headers[0], headers.size()); | |
| 325 memcpy(&tile[0] + headers.size(), &raw[2], raw.size() - 2); | |
| 326 } | |
| 327 | |
| 328 return true; | |
| 329 } | |
| 330 } |