Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 242:49f647ed1b4c
added copyright UCLouvain
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 06 Dec 2021 16:05:42 +0100 |
parents | 1e864138f0da |
children | 20a730889ae2 |
rev | line source |
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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) 2017-2021 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2021 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 "HierarchicalTiffWriter.h" |
25 | |
192 | 26 #include <Logging.h> |
27 #include <OrthancException.h> | |
28 #include <TemporaryFile.h> | |
0 | 29 |
30 namespace OrthancWSI | |
31 { | |
32 class HierarchicalTiffWriter::PendingTile | |
33 { | |
34 private: | |
43 | 35 HierarchicalTiffWriter& that_; |
36 unsigned int level_; | |
37 unsigned int tileX_; | |
38 unsigned int tileY_; | |
39 Orthanc::TemporaryFile file_; | |
0 | 40 |
41 public: | |
42 PendingTile(HierarchicalTiffWriter& that, | |
43 unsigned int level, | |
44 unsigned int tileX, | |
45 unsigned int tileY, | |
46 const std::string& tile) : | |
47 that_(that), | |
48 level_(level), | |
49 tileX_(tileX), | |
50 tileY_(tileY) | |
51 { | |
52 file_.Write(tile); | |
53 } | |
54 | |
55 unsigned int GetLevel() const | |
56 { | |
57 return level_; | |
58 } | |
59 | |
60 unsigned int GetTileX() const | |
61 { | |
62 return tileX_; | |
63 } | |
64 | |
65 unsigned int GetTileY() const | |
66 { | |
67 return tileY_; | |
68 } | |
69 | |
70 void Store(TIFF* tiff) | |
71 { | |
72 std::string tile; | |
73 file_.Read(tile); | |
74 that_.StoreTile(tile, tileX_, tileY_); | |
75 } | |
76 }; | |
77 | |
78 | |
79 struct HierarchicalTiffWriter::Comparator | |
80 { | |
81 inline bool operator() (PendingTile* const& a, | |
82 PendingTile* const& b) | |
83 { | |
84 if (a->GetLevel() < b->GetLevel()) | |
85 { | |
86 return true; | |
87 } | |
88 | |
89 if (a->GetLevel() > b->GetLevel()) | |
90 { | |
91 return false; | |
92 } | |
93 | |
94 if (a->GetTileY() < b->GetTileY()) | |
95 { | |
96 return true; | |
97 } | |
98 | |
99 if (a->GetTileY() > b->GetTileY()) | |
100 { | |
101 return false; | |
102 } | |
103 | |
104 return a->GetTileX() < b->GetTileX(); | |
105 } | |
106 }; | |
107 | |
108 | |
109 static uint8_t GetUint8(const std::string& tile, | |
110 size_t index) | |
111 { | |
112 if (index >= tile.size()) | |
113 { | |
114 return 0; | |
115 } | |
116 else | |
117 { | |
118 return static_cast<uint8_t>(tile[index]); | |
119 } | |
120 } | |
121 | |
122 | |
123 #if 0 | |
124 static uint16_t GetUint16(const std::string& tile, | |
125 size_t index) | |
126 { | |
127 if (index + 1 >= tile.size()) | |
128 { | |
129 return 0; | |
130 } | |
131 else | |
132 { | |
133 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
134 } | |
135 } | |
136 #endif | |
137 | |
138 | |
139 static void CheckJpegTile(const std::string& tile, | |
140 Orthanc::PixelFormat pixelFormat) | |
141 { | |
142 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
143 | |
144 if (tile.size() < 3 || | |
145 static_cast<uint8_t>(tile[0]) != 0xff || | |
146 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
147 static_cast<uint8_t>(tile[2]) != 0xff) | |
148 { | |
149 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
150 return; | |
151 } | |
152 | |
153 // Look for the "Start of Frame" header (FF C0) | |
154 for (size_t i = 2; i + 1 < tile.size(); i++) | |
155 { | |
156 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
157 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
158 { | |
159 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
160 | |
161 switch (pixelFormat) | |
162 { | |
163 case Orthanc::PixelFormat_Grayscale8: | |
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164 if (numberOfComponents != 1) |
0 | 165 { |
166 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
167 } | |
168 break; | |
169 | |
170 case Orthanc::PixelFormat_RGB24: | |
171 { | |
172 if (numberOfComponents != 3) | |
173 { | |
174 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
175 } | |
176 | |
177 // Read the header corresponding to the first component | |
178 const size_t component = 0; | |
179 const size_t offset = i + 10 + component * 3; | |
180 const uint8_t sampling = GetUint8(tile, offset + 1); | |
181 const int samplingH = sampling / 16; | |
182 const int samplingV = sampling % 16; | |
183 | |
184 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
185 | |
186 if (samplingH != 2 || | |
187 samplingV != 2) | |
188 { | |
189 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
190 << "you should consider using option \"--reencode\""; | |
191 } | |
192 | |
193 break; | |
194 } | |
195 | |
196 default: | |
197 break; | |
198 } | |
199 } | |
200 } | |
201 } | |
202 | |
203 | |
204 | |
205 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
206 unsigned int tileX, | |
207 unsigned int tileY) | |
208 { | |
209 // Get the index of the tile | |
210 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
211 | |
212 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
213 static_cast<tsize_t>(tile.size())) | |
214 { | |
215 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
216 } | |
217 | |
218 if (isFirst_ && | |
219 GetImageCompression() == ImageCompression_Jpeg) | |
220 { | |
221 CheckJpegTile(tile, GetPixelFormat()); | |
222 } | |
223 | |
224 isFirst_ = false; | |
225 } | |
226 | |
227 | |
228 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
229 bool createLevel) | |
230 { | |
231 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
232 { | |
233 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
234 } | |
235 | |
236 if (TIFFFlush(tiff_) != 1) | |
237 { | |
238 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
239 } | |
240 | |
241 currentLevel_ = level.z_; | |
242 nextX_ = 0; | |
243 nextY_ = 0; | |
244 | |
245 switch (GetImageCompression()) | |
246 { | |
247 case ImageCompression_Jpeg: | |
248 { | |
249 uint16_t c = COMPRESSION_JPEG; | |
250 | |
251 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
252 { | |
253 Close(); | |
254 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
255 } | |
256 | |
257 break; | |
258 } | |
259 | |
260 default: | |
261 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
262 } | |
263 | |
264 | |
265 switch (GetPixelFormat()) | |
266 { | |
267 case Orthanc::PixelFormat_RGB24: | |
268 { | |
269 uint16_t samplesPerPixel = 3; | |
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270 uint16_t photometric; |
0 | 271 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB |
272 uint16_t bpp = 8; | |
273 uint16_t subsampleHorizontal = 2; | |
274 uint16_t subsampleVertical = 2; | |
275 | |
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276 switch (photometric_) |
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277 { |
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278 case Orthanc::PhotometricInterpretation_YBRFull422: |
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279 photometric = PHOTOMETRIC_YCBCR; |
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280 break; |
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281 |
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282 case Orthanc::PhotometricInterpretation_RGB: |
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283 photometric = PHOTOMETRIC_RGB; |
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284 break; |
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285 |
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286 default: |
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287 throw Orthanc::OrthancException( |
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288 Orthanc::ErrorCode_ParameterOutOfRange, |
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289 "Unsupported photometric interpreation: " + |
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290 std::string(Orthanc::EnumerationToString(photometric_))); |
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291 } |
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292 |
0 | 293 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
294 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
295 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
296 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
297 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
298 { | |
299 Close(); | |
300 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
301 } | |
302 | |
303 break; | |
304 } | |
305 | |
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306 case Orthanc::PixelFormat_Grayscale8: |
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307 { |
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308 uint16_t samplesPerPixel = 1; |
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309 uint16_t bpp = 8; |
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310 uint16_t photometric = PHOTOMETRIC_MINISBLACK; |
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311 |
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312 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
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313 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || |
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314 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1) |
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315 { |
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316 Close(); |
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317 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); |
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318 } |
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319 |
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320 break; |
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321 } |
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322 |
0 | 323 default: |
324 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
325 } | |
326 | |
327 uint32_t w = level.width_; | |
328 uint32_t h = level.height_; | |
329 uint32_t tw = GetTileWidth(); | |
330 uint32_t th = GetTileHeight(); | |
331 | |
332 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
333 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
334 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
335 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
336 { | |
337 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
338 } | |
339 } | |
340 | |
341 | |
342 void HierarchicalTiffWriter::AdvanceToNextTile() | |
343 { | |
344 assert(currentLevel_ < levels_.size()); | |
345 | |
346 nextX_ += 1; | |
347 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
348 { | |
349 nextX_ = 0; | |
350 nextY_ += 1; | |
351 | |
352 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
353 { | |
354 currentLevel_ += 1; | |
355 | |
356 if (currentLevel_ < levels_.size()) | |
357 { | |
358 ConfigureLevel(levels_[currentLevel_], true); | |
359 } | |
360 } | |
361 } | |
362 } | |
363 | |
364 | |
365 void HierarchicalTiffWriter::ScanPending() | |
366 { | |
367 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
368 | |
369 while (currentLevel_ < levels_.size() && | |
370 !pending_.empty() && | |
371 pending_.front()->GetLevel() == currentLevel_ && | |
372 pending_.front()->GetTileX() == nextX_ && | |
373 pending_.front()->GetTileY() == nextY_) | |
374 { | |
375 pending_.front()->Store(tiff_); | |
376 delete pending_.front(); | |
377 pending_.pop_front(); | |
378 AdvanceToNextTile(); | |
379 } | |
380 } | |
381 | |
382 | |
383 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
384 const Level& level, | |
385 unsigned int tileX, | |
386 unsigned int tileY) | |
387 { | |
388 boost::mutex::scoped_lock lock(mutex_); | |
389 | |
390 if (level.z_ == currentLevel_ && | |
391 tileX == nextX_ && | |
392 tileY == nextY_) | |
393 { | |
394 StoreTile(tile, tileX, tileY); | |
395 AdvanceToNextTile(); | |
396 ScanPending(); | |
397 } | |
398 else | |
399 { | |
400 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
401 } | |
402 } | |
403 | |
404 | |
405 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
406 { | |
407 if (level.z_ == 0) | |
408 { | |
409 // Configure the finest level on initialization | |
410 ConfigureLevel(level, false); | |
411 } | |
412 | |
413 levels_.push_back(level); | |
414 } | |
415 | |
416 | |
417 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
418 Orthanc::PixelFormat pixelFormat, | |
419 ImageCompression compression, | |
420 unsigned int tileWidth, | |
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421 unsigned int tileHeight, |
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422 Orthanc::PhotometricInterpretation photometric) : |
0 | 423 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
424 currentLevel_(0), | |
145 | 425 nextX_(0), |
426 nextY_(0), | |
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427 isFirst_(true), |
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428 photometric_(photometric) |
0 | 429 { |
430 tiff_ = TIFFOpen(path.c_str(), "w"); | |
431 if (tiff_ == NULL) | |
432 { | |
433 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
434 } | |
435 } | |
436 | |
437 | |
438 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
439 { | |
440 if (pending_.size()) | |
441 { | |
442 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
443 } | |
444 | |
445 for (size_t i = 0; i < pending_.size(); i++) | |
446 { | |
447 if (pending_[i]) | |
448 { | |
449 delete pending_[i]; | |
450 } | |
451 } | |
452 | |
453 Close(); | |
454 } | |
455 | |
456 | |
457 void HierarchicalTiffWriter::Flush() | |
458 { | |
459 boost::mutex::scoped_lock lock(mutex_); | |
460 ScanPending(); | |
461 } | |
462 } |