Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/HierarchicalTiff.cpp @ 40:371243c270cc
fix
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 09 Nov 2016 14:17:55 +0100 |
| parents | 7a88c614be04 |
| children | 91fc9583b2de |
| 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 | |
|
16
7a88c614be04
preparing for precompiled headers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
21 #include "../PrecompiledHeadersWSI.h" |
| 0 | 22 #include "HierarchicalTiff.h" |
| 23 | |
| 24 #include "../Orthanc/Core/Logging.h" | |
| 25 #include "../Orthanc/Core/OrthancException.h" | |
| 26 | |
| 27 #include <iostream> | |
| 28 #include <algorithm> | |
| 29 #include <cassert> | |
| 30 #include <string.h> | |
| 31 | |
| 32 namespace OrthancWSI | |
| 33 { | |
| 34 HierarchicalTiff::Level::Level(TIFF* tiff, | |
| 35 tdir_t directory, | |
| 36 unsigned int width, | |
| 37 unsigned int height) : | |
| 38 directory_(directory), | |
| 39 width_(width), | |
| 40 height_(height) | |
| 41 { | |
| 42 // Read the JPEG headers shared at that level, if any | |
| 43 uint8_t *tables = NULL; | |
| 44 uint32_t size; | |
| 45 if (TIFFGetField(tiff, TIFFTAG_JPEGTABLES, &size, &tables) && | |
| 46 size > 0 && | |
| 47 tables != NULL) | |
| 48 { | |
| 49 // Look for the EOI (end-of-image) tag == FF D9 | |
| 50 // https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format | |
| 51 | |
| 52 bool found = false; | |
| 53 | |
| 54 for (size_t i = 0; i + 1 < size; i++) | |
| 55 { | |
| 56 if (tables[i] == 0xff && | |
| 57 tables[i + 1] == 0xd9) | |
| 58 { | |
| 59 headers_.assign(reinterpret_cast<const char*>(tables), i); | |
| 60 found = true; | |
| 61 } | |
| 62 } | |
| 63 | |
| 64 if (!found) | |
| 65 { | |
| 66 headers_.assign(reinterpret_cast<const char*>(tables), size); | |
| 67 } | |
| 68 } | |
| 69 } | |
| 70 | |
| 71 struct HierarchicalTiff::Comparator | |
| 72 { | |
| 73 bool operator() (const HierarchicalTiff::Level& a, | |
| 74 const HierarchicalTiff::Level& b) const | |
| 75 { | |
| 76 return a.width_ > b.width_; | |
| 77 } | |
| 78 }; | |
| 79 | |
| 80 | |
| 81 void HierarchicalTiff::Finalize() | |
| 82 { | |
| 83 if (tiff_) | |
| 84 { | |
| 85 TIFFClose(tiff_); | |
| 86 tiff_ = NULL; | |
| 87 } | |
| 88 } | |
| 89 | |
| 90 | |
| 91 void HierarchicalTiff::CheckLevel(unsigned int level) const | |
| 92 { | |
| 93 if (level >= levels_.size()) | |
| 94 { | |
| 95 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 96 } | |
| 97 } | |
| 98 | |
| 99 | |
| 100 bool HierarchicalTiff::GetCurrentCompression(ImageCompression& compression) | |
| 101 { | |
| 102 uint16_t c; | |
| 103 if (!TIFFGetField(tiff_, TIFFTAG_COMPRESSION, &c)) | |
| 104 { | |
| 105 return false; | |
| 106 } | |
| 107 | |
| 108 switch (c) | |
| 109 { | |
| 110 case COMPRESSION_NONE: | |
| 111 compression = ImageCompression_None; | |
| 112 return true; | |
| 113 | |
| 114 case COMPRESSION_JPEG: | |
| 115 compression = ImageCompression_Jpeg; | |
| 116 return true; | |
| 117 | |
| 118 default: | |
| 119 return false; | |
| 120 } | |
| 121 } | |
| 122 | |
| 123 | |
| 124 bool HierarchicalTiff::GetCurrentPixelFormat(Orthanc::PixelFormat& pixelFormat, | |
| 125 ImageCompression compression) | |
| 126 { | |
| 127 // http://www.awaresystems.be/imaging/tiff/tifftags/baseline.html | |
| 128 | |
| 129 uint16_t channels, photometric, bpp, planar; | |
| 130 if (!TIFFGetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, &channels) || | |
| 131 channels == 0 || | |
| 132 !TIFFGetField(tiff_, TIFFTAG_PHOTOMETRIC, &photometric) || | |
| 133 !TIFFGetField(tiff_, TIFFTAG_BITSPERSAMPLE, &bpp) || | |
| 134 !TIFFGetField(tiff_, TIFFTAG_PLANARCONFIG, &planar)) | |
| 135 { | |
| 136 return false; | |
| 137 } | |
| 138 | |
| 139 if (compression == ImageCompression_Jpeg && | |
| 140 channels == 3 && // This is a color image | |
| 141 bpp == 8 && | |
| 142 photometric == PHOTOMETRIC_YCBCR && | |
| 143 planar == PLANARCONFIG_CONTIG) // This is interleaved RGB | |
| 144 { | |
| 145 pixelFormat = Orthanc::PixelFormat_RGB24; | |
| 146 } | |
| 147 else | |
| 148 { | |
| 149 return false; | |
| 150 } | |
| 151 | |
| 152 return true; | |
| 153 } | |
| 154 | |
| 155 | |
| 156 bool HierarchicalTiff::Initialize() | |
| 157 { | |
| 158 bool first = true; | |
| 159 tdir_t pos = 0; | |
| 160 | |
| 161 do | |
| 162 { | |
| 163 uint32_t w, h, tw, th; | |
| 164 ImageCompression compression; | |
| 165 Orthanc::PixelFormat pixelFormat; | |
| 166 | |
| 167 if (TIFFSetDirectory(tiff_, pos) && | |
| 168 TIFFGetField(tiff_, TIFFTAG_IMAGEWIDTH, &w) && | |
| 169 TIFFGetField(tiff_, TIFFTAG_IMAGELENGTH, &h) && | |
| 170 TIFFGetField(tiff_, TIFFTAG_TILEWIDTH, &tw) && | |
| 171 TIFFGetField(tiff_, TIFFTAG_TILELENGTH, &th) && | |
| 172 w > 0 && | |
| 173 h > 0 && | |
| 174 tw > 0 && | |
| 175 th > 0 && | |
| 176 GetCurrentCompression(compression) && | |
| 177 GetCurrentPixelFormat(pixelFormat, compression)) | |
| 178 { | |
| 179 if (first) | |
| 180 { | |
| 181 tileWidth_ = tw; | |
| 182 tileHeight_ = th; | |
| 183 compression_ = compression; | |
| 184 pixelFormat_ = pixelFormat; | |
| 185 first = false; | |
| 186 } | |
| 187 else if (tw != tileWidth_ || | |
| 188 th != tileHeight_ || | |
| 189 compression_ != compression || | |
| 190 pixelFormat_ != pixelFormat) | |
| 191 { | |
| 192 LOG(ERROR) << "The tile size or compression of the TIFF file varies along levels, this is not supported"; | |
| 193 return false; | |
| 194 } | |
| 195 | |
| 196 levels_.push_back(Level(tiff_, pos, w, h)); | |
| 197 } | |
| 198 | |
| 199 pos++; | |
| 200 } | |
| 201 while (TIFFReadDirectory(tiff_)); | |
| 202 | |
| 203 if (levels_.size() == 0) | |
| 204 { | |
| 205 LOG(ERROR) << "This is not a tiled TIFF image"; | |
| 206 return false; | |
| 207 } | |
| 208 | |
| 209 std::sort(levels_.begin(), levels_.end(), Comparator()); | |
| 210 return true; | |
| 211 } | |
| 212 | |
| 213 | |
| 214 HierarchicalTiff::HierarchicalTiff(const std::string& path) : | |
| 215 tileWidth_(0), | |
| 216 tileHeight_(0) | |
| 217 { | |
| 218 tiff_ = TIFFOpen(path.c_str(), "r"); | |
| 219 if (tiff_ == NULL) | |
| 220 { | |
| 221 LOG(ERROR) << "libtiff cannot open: " << path; | |
| 222 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentFile); | |
| 223 } | |
| 224 | |
| 225 if (!Initialize()) | |
| 226 { | |
| 227 Finalize(); | |
| 228 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 229 } | |
| 230 } | |
| 231 | |
| 232 | |
| 233 unsigned int HierarchicalTiff::GetLevelWidth(unsigned int level) const | |
| 234 { | |
| 235 CheckLevel(level); | |
| 236 return levels_[level].width_; | |
| 237 } | |
| 238 | |
| 239 | |
| 240 unsigned int HierarchicalTiff::GetLevelHeight(unsigned int level) const | |
| 241 { | |
| 242 CheckLevel(level); | |
| 243 return levels_[level].height_; | |
| 244 } | |
| 245 | |
| 246 | |
| 247 bool HierarchicalTiff::ReadRawTile(std::string& tile, | |
| 248 unsigned int level, | |
| 249 unsigned int tileX, | |
| 250 unsigned int tileY) | |
| 251 { | |
| 252 boost::mutex::scoped_lock lock(mutex_); | |
| 253 | |
| 254 CheckLevel(level); | |
| 255 | |
| 256 // Make the TIFF context point to the level of interest | |
| 257 if (!TIFFSetDirectory(tiff_, levels_[level].directory_)) | |
| 258 { | |
| 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 260 } | |
| 261 | |
| 262 // Get the index of the tile | |
| 263 ttile_t index = TIFFComputeTile(tiff_, tileX * tileWidth_, tileY * tileHeight_, 0 /*z*/, 0 /*sample*/); | |
| 264 | |
| 265 // Read the raw tile | |
| 266 toff_t *sizes; | |
| 267 if (!TIFFGetField(tiff_, TIFFTAG_TILEBYTECOUNTS, &sizes)) | |
| 268 { | |
| 269 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 270 } | |
| 271 | |
| 272 std::string raw; | |
| 273 raw.resize(sizes[index]); | |
| 274 | |
| 275 tsize_t read = TIFFReadRawTile(tiff_, index, &raw[0], raw.size()); | |
| 276 if (read != static_cast<tsize_t>(sizes[index])) | |
| 277 { | |
| 278 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 279 } | |
| 280 | |
| 281 const std::string& headers = levels_[level].headers_; | |
| 282 | |
| 283 // Possibly prepend the raw tile with the shared JPEG headers | |
| 284 if (headers.empty() || | |
| 285 compression_ != ImageCompression_Jpeg) | |
| 286 { | |
| 287 tile.swap(raw); // Same as "tile.assign(raw)", but optimizes memory | |
| 288 } | |
| 289 else | |
| 290 { | |
| 291 assert(compression_ == ImageCompression_Jpeg); | |
| 292 | |
| 293 // Check that the raw JPEG tile starts with the SOI (start-of-image) tag == FF D8 | |
| 294 if (raw.size() < 2 || | |
| 295 static_cast<uint8_t>(raw[0]) != 0xff || | |
| 296 static_cast<uint8_t>(raw[1]) != 0xd8) | |
| 297 { | |
| 298 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
| 299 } | |
| 300 | |
| 301 tile.resize(headers.size() + raw.size() - 2); | |
| 302 memcpy(&tile[0], &headers[0], headers.size()); | |
| 303 memcpy(&tile[0] + headers.size(), &raw[2], raw.size() - 2); | |
| 304 } | |
| 305 | |
| 306 return true; | |
| 307 } | |
| 308 } |